Experience

Publications

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective

  J. Phys. Soc. Jpn., 84, 094002

  We analyze the applicability of the seminal fewest switches surface hopping (FSSH) method of Tully to modeling quantum transitions between electronic states that are not coupled directly, in the processes such as Auger recombination. We address the known deficiency of the method to describe such transitions by introducing an alternative definition for the surface hopping probabilities, as derived from the Markov state model perspective. We show that the resulting transition probabilities simplify to the quantum state populations derived from the time-dependent Schrödinger equation, reducing to the rapidly switching surface hopping approach of Tully and Preston. The resulting surface hopping scheme is simple and appeals to the fundamentals of quantum mechanics. The computational approach is similar to the FSSH method of Tully, yet it leads to a notably different performance. We demonstrate that the method is particularly accurate when applied to superexchange modeling. We further show improved accuracy of the method, when applied to one of the standard test problems, Finally, we adapt the derived scheme to atomistic simulation, combine it with the time-domain density functional theory, and show that it provides the Auger energy transfer timescales which are in good agreement with experiment, significantly improving upon other considered techniques.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective

  J. Phys. Soc. Jpn., 84, 094002

  We analyze the applicability of the seminal fewest switches surface hopping (FSSH) method of Tully to modeling quantum transitions between electronic states that are not coupled directly, in the processes such as Auger recombination. We address the known deficiency of the method to describe such transitions by introducing an alternative definition for the surface hopping probabilities, as derived from the Markov state model perspective. We show that the resulting transition probabilities simplify to the quantum state populations derived from the time-dependent Schrödinger equation, reducing to the rapidly switching surface hopping approach of Tully and Preston. The resulting surface hopping scheme is simple and appeals to the fundamentals of quantum mechanics. The computational approach is similar to the FSSH method of Tully, yet it leads to a notably different performance. We demonstrate that the method is particularly accurate when applied to superexchange modeling. We further show improved accuracy of the method, when applied to one of the standard test problems, Finally, we adapt the derived scheme to atomistic simulation, combine it with the time-domain density functional theory, and show that it provides the Auger energy transfer timescales which are in good agreement with experiment, significantly improving upon other considered techniques.

• Theoretical insights into photoinduced charge transfer and catalysis at metal oxide surfaces

  Chem. Rev., 2013, 113 (6), pp 4496–4565

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective

  J. Phys. Soc. Jpn., 84, 094002

  We analyze the applicability of the seminal fewest switches surface hopping (FSSH) method of Tully to modeling quantum transitions between electronic states that are not coupled directly, in the processes such as Auger recombination. We address the known deficiency of the method to describe such transitions by introducing an alternative definition for the surface hopping probabilities, as derived from the Markov state model perspective. We show that the resulting transition probabilities simplify to the quantum state populations derived from the time-dependent Schrödinger equation, reducing to the rapidly switching surface hopping approach of Tully and Preston. The resulting surface hopping scheme is simple and appeals to the fundamentals of quantum mechanics. The computational approach is similar to the FSSH method of Tully, yet it leads to a notably different performance. We demonstrate that the method is particularly accurate when applied to superexchange modeling. We further show improved accuracy of the method, when applied to one of the standard test problems, Finally, we adapt the derived scheme to atomistic simulation, combine it with the time-domain density functional theory, and show that it provides the Auger energy transfer timescales which are in good agreement with experiment, significantly improving upon other considered techniques.

• Theoretical insights into photoinduced charge transfer and catalysis at metal oxide surfaces

  Chem. Rev., 2013, 113 (6), pp 4496–4565

• Second-Quantized Surface Hopping

  Phys. Rev. Lett. 2014, 113, 153003

  The trajectory surface hopping method for quantum dynamics is reformulated in the space of many-particle states to include entanglement and correlation of trajectories. Used to describe many-body correlation effects in electronic structure theories, second quantization is applied to semiclassical trajectories. The new method allows coupling between individual trajectories via energy flow and common phase evolution. It captures the properties of a wave packet, such as branching, Heisenberg uncertainty, and decoherence. Applied to a superexchange process, the method shows very accurate results, comparable to exact quantum data and improving greatly on the standard approach.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective

  J. Phys. Soc. Jpn., 84, 094002

  We analyze the applicability of the seminal fewest switches surface hopping (FSSH) method of Tully to modeling quantum transitions between electronic states that are not coupled directly, in the processes such as Auger recombination. We address the known deficiency of the method to describe such transitions by introducing an alternative definition for the surface hopping probabilities, as derived from the Markov state model perspective. We show that the resulting transition probabilities simplify to the quantum state populations derived from the time-dependent Schrödinger equation, reducing to the rapidly switching surface hopping approach of Tully and Preston. The resulting surface hopping scheme is simple and appeals to the fundamentals of quantum mechanics. The computational approach is similar to the FSSH method of Tully, yet it leads to a notably different performance. We demonstrate that the method is particularly accurate when applied to superexchange modeling. We further show improved accuracy of the method, when applied to one of the standard test problems, Finally, we adapt the derived scheme to atomistic simulation, combine it with the time-domain density functional theory, and show that it provides the Auger energy transfer timescales which are in good agreement with experiment, significantly improving upon other considered techniques.

• Theoretical insights into photoinduced charge transfer and catalysis at metal oxide surfaces

  Chem. Rev., 2013, 113 (6), pp 4496–4565

• Second-Quantized Surface Hopping

  Phys. Rev. Lett. 2014, 113, 153003

  The trajectory surface hopping method for quantum dynamics is reformulated in the space of many-particle states to include entanglement and correlation of trajectories. Used to describe many-body correlation effects in electronic structure theories, second quantization is applied to semiclassical trajectories. The new method allows coupling between individual trajectories via energy flow and common phase evolution. It captures the properties of a wave packet, such as branching, Heisenberg uncertainty, and decoherence. Applied to a superexchange process, the method shows very accurate results, comparable to exact quantum data and improving greatly on the standard approach.

• Persistent electronic coherence despite rapid loss of electron-nuclear correlation

  J. Phys. Chem. Lett., 2013, 4 (22), pp 3857–3864

  Long-lived coherences of excited states are notable for their positive effect on energy conversion mechanisms and efficiencies in photosynthetic complexes. Rational engineering of such persistent coherences could open a new way to increase energy conversion rates in man-made photovoltaic and photocatalytic materials. Therefore, a comprehensive understanding of the fundamental principles behind the long-lived coherences is necessary. In this work we show that the main factor determining the decoherence rates is the magnitude of the nuclear-induced fluctuation of the energy gap between the electronic states of interest, rather than the electron–nuclear correlation on its own. Utilizing combined atomistic and electronic structure calculations, we demonstrate an inverse relationship between decoherence times and magnitude of the energy gap fluctuation. We also show that the energy gap fluctuation can often correlate with the gap itself. For sufficiently small energy gaps, the coherence time can be nearly an order of magnitude larger than the electron–nuclear correlation time.

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective

  J. Phys. Soc. Jpn., 84, 094002

  We analyze the applicability of the seminal fewest switches surface hopping (FSSH) method of Tully to modeling quantum transitions between electronic states that are not coupled directly, in the processes such as Auger recombination. We address the known deficiency of the method to describe such transitions by introducing an alternative definition for the surface hopping probabilities, as derived from the Markov state model perspective. We show that the resulting transition probabilities simplify to the quantum state populations derived from the time-dependent Schrödinger equation, reducing to the rapidly switching surface hopping approach of Tully and Preston. The resulting surface hopping scheme is simple and appeals to the fundamentals of quantum mechanics. The computational approach is similar to the FSSH method of Tully, yet it leads to a notably different performance. We demonstrate that the method is particularly accurate when applied to superexchange modeling. We further show improved accuracy of the method, when applied to one of the standard test problems, Finally, we adapt the derived scheme to atomistic simulation, combine it with the time-domain density functional theory, and show that it provides the Auger energy transfer timescales which are in good agreement with experiment, significantly improving upon other considered techniques.

• Theoretical insights into photoinduced charge transfer and catalysis at metal oxide surfaces

  Chem. Rev., 2013, 113 (6), pp 4496–4565

• Second-Quantized Surface Hopping

  Phys. Rev. Lett. 2014, 113, 153003

  The trajectory surface hopping method for quantum dynamics is reformulated in the space of many-particle states to include entanglement and correlation of trajectories. Used to describe many-body correlation effects in electronic structure theories, second quantization is applied to semiclassical trajectories. The new method allows coupling between individual trajectories via energy flow and common phase evolution. It captures the properties of a wave packet, such as branching, Heisenberg uncertainty, and decoherence. Applied to a superexchange process, the method shows very accurate results, comparable to exact quantum data and improving greatly on the standard approach.

• Persistent electronic coherence despite rapid loss of electron-nuclear correlation

  J. Phys. Chem. Lett., 2013, 4 (22), pp 3857–3864

  Long-lived coherences of excited states are notable for their positive effect on energy conversion mechanisms and efficiencies in photosynthetic complexes. Rational engineering of such persistent coherences could open a new way to increase energy conversion rates in man-made photovoltaic and photocatalytic materials. Therefore, a comprehensive understanding of the fundamental principles behind the long-lived coherences is necessary. In this work we show that the main factor determining the decoherence rates is the magnitude of the nuclear-induced fluctuation of the energy gap between the electronic states of interest, rather than the electron–nuclear correlation on its own. Utilizing combined atomistic and electronic structure calculations, we demonstrate an inverse relationship between decoherence times and magnitude of the energy gap fluctuation. We also show that the energy gap fluctuation can often correlate with the gap itself. For sufficiently small energy gaps, the coherence time can be nearly an order of magnitude larger than the electron–nuclear correlation time.

• Theory of solar energy materials

  J. Phys.: Condens. Matter 2015, 27, 130301

  Editorial for the special issue

• Dynamics of Single-Molecule on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

  J. Phys. Chem. C, 2011, 115 (1), pp 125–131

  Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well-understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

• Analysis of self-consistent Extended Hückel theory (SC-EHT): A new look at the old method

  J. Math. Chem. 2015, 53, 528

  We present an extensive analysis of the self-consistent extended Hückel theory (SC-EHT) and discuss the possibilities of constructing accurate and efficient semiempirical methods on its basis. We describe the mapping approach to derive a self-consistency correction to the effective 1-electron Hamiltonian (Fock) operator that is utilized in electronic structure calculations and that variationally minimizes the total energy in the SC-EHT method. We show that the SC-EHT Hamiltonian can play the role of the 1-electron operator by definition, in which case no self-consistency correction is needed. Then, the SC-EHT method can be derived from the Hartree–Fock theory by approximation of the Fock matrix. Therefore, the SC-EHT based methods have rigorous foundations that may be utilized to develop a family of successively accurate model Hamiltonians. We analyze the underlying approximation and discuss it in the light of existing formulations of the EHT method. We indicate two major deficiencies of the existing formulations of the EHT method—neglect of exchange integrals and incorrect asymptotic behavior of the Coulomb integrals. The SC-EHT is compared to the charge equilibration scheme and to the DFTB family of approximations. We show that an improved version of the SC-EHT method can be connected to both of them, indicating relation of the SC-EHT derived approximations to the fundamental DFT origins and their potential for efficient computations on large-scale systems.

• The PYXAID program for non-adiabatic molecular dynamics in condensed matter systems

  J. Chem. Theory Comput., 2013, 9 (11), pp 4959–4972

  This work introduces the PYXAID program, developed for non-adiabatic molecular dynamics simulations in condensed matter systems. By applying the classical path approximation to the fewest switches surface hopping approach, we have developed an efficient computational tool that can be applied to study photoinduced dynamics at the ab initio level in systems composed of hundreds of atoms and involving thousands of electronic states. The technique is used to study in detail the ultrafast relaxation of hot electrons in crystalline pentacene. The simulated relaxation occurs on a 500 fs time scale, in excellent agreement with experiment, and is driven by molecular lattice vibrations in the 200–250 cm–1 frequency range. The PYXAID program is organized as a Python extension module and can be easily combined with other Python-driven modules, enhancing user-friendliness and flexibility of the software. The source code and additional information are available on the Web at the address http://gdriv.es/pyxaid. The program is released under the GNU General Public License.

• Formulation of quantized Hamiltonian dynamics in terms of natural variables

  J. Chem. Phys. 137, 224115 (2012)

  We present a formulation of quantized Hamiltonian dynamics (QHD) using variables that arise naturally from the Heisenberg equation of motion. The QHD equations are obtained and solved either directly in terms of these generalized variables, or by employing a wavefunction ansatz. The approach avoids a Taylor expansion and other approximations to the potential, leading to more stable dynamics and a higher precision of the calculated quantities. The proposed formulation is also amenable to for analytic and numerical implementations, thus facilitating its use in molecular dynamics simulation.

• Molecular Dynamics Study of Cristalline Molecular Gyroscopes

  J. Phys. Chem. C, 2011, 115 (28), pp 13584–13591

  In recent years molecular rotors have attracted the attention of many research groups for possible applications as new nanoscale devices and materials with controlled chemical, physical, and mechanical properties. One of the most unique systems with molecular rotations is amphidynamic molecular crystals, also known as crystalline molecular gyroscopes. This system can be viewed as a solid-state assembly of molecules that cannot move translationally but show internal rotations. Recent experiments on amphidynamic crystals indicate importance of rotational symmetry for describing their dynamics. However, mechanisms and rotational dynamic properties of molecular gyroscopes are still not well understood. We present here a theoretical investigation of amphidynamic crystals by utilizing extensive rigid-body molecular dynamics simulations and simple phenomenological arguments. Theoretical analysis suggests that intramolecular interactions within stator and rotator segments of molecular rotors as well as their flexibility strongly affect their crystal packing, energies and rotational behavior. Our quantitative predictions for dynamic properties agree well with available experimental results.

• Directed motion of periodically driven molecular motors: A graph-theoretical approach

  J. Chem. Phys. 138, 024109 (2013)

  We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 106 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

• Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics

  J. Chem. Phys. 140, 194107 (2014)

  We present a new semiclassical approach for description of decoherence in electronically non-adiabatic molecular dynamics. The method is formulated on the grounds of the Ehrenfest dynamics and the Meyer-Miller-Thoss-Stock mapping of the time-dependent Schrödinger equation onto a fully classical Hamiltonian representation. We introduce a coherence penalty functional (CPF) that accounts for decoherence effects by randomizing the wavefunction phase and penalizing development of coherences in regions of strong non-adiabatic coupling. The performance of the method is demonstrated with several model and realistic systems. Compared to other semiclassical methods tested, the CPF method eliminates artificial interference and improves agreement with the fully quantum calculations on the models. When applied to study electron transfer dynamics in the nanoscale systems, the method shows an improved accuracy of the predicted time scales. The simplicity and high computational efficiency of the CPF approach make it a perfect practical candidate for applications in realistic systems.

• Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

  J. Am. Chem. Soc., 2013, 135 (23), pp 8682–8691

  Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N–H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

• Analysis of depolarization ratios of ClNO2 dissolved in methanol

  J. Chem. Phys. 140, 014301 (2014)

  A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N–O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (21A1 and 31B1), which are taken as linearly dissociative along the Cl–N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 21A1 is greater than for 31B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett.383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 31B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

• Theoretical insights into the impact of Ru catalyst anchors on the efficiency of photocatalytic CO2 reduction on Ta2O5

  J. Phys. Chem. B, 2014, Article ASAP

  We present a computational study of the dynamical and electronic structure origins of the impact of anchoring groups, PO3H2, COOH, and OH, on the efficiency of photochemical CO2 reduction in Ru(di-X-bpy)(CO)2Cl2/Ta2O5 systems. Recent experimental studies indicate that the efficiency may not directly correlate with the driving force for electron transfer (ET) in these systems, prompting the need for further investigation of the role of anchor groups. Our analysis shows that there are at least two key roles of the anchor in determining the efficiency of CO2 reduction by the Ru complex. First, depending on local steric interactions, different tilting angles and their fluctuations may emerge for different anchors, affecting the magnitude of the donor–acceptor coupling. Second, depending on localization of acceptor states on the anchor, determined by the anchor’s tendency to form conjugate subsystems, the yields of ET to the catalytic center may vary, directly affecting the photocatalytic efficiency. Finally, our calculations indicate that surface modeling with N-doping and many-body effects are needed to describe the ET process in the systems properly. N-doping imparts the Ta2O5 surface with a dipole moment, while Coulomb and exchange contributions to the electron–hole interaction can produce excitons that should be taken into account.

• Unidirectional Rolling Motion of Nanocars Induced by Electric Field

  J. Phys. Chem. C, 2012, 116 (42), pp 22595–22601

  Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

• Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars

  J. Phys. Chem. C, 2012, 116 (25), pp 13816–13826

  It is widely believed that the dynamics of surface-bound fullerene molecules is not fully understood because current theoretical analyses do not include charge-transfer phenomena. A new theoretical approach to describe charge transfer and chemisorption processes for fullerenes on gold surfaces has been developed. The method is based on extensive semiempirical calculations that provide a consistent description of charge transfer and adsorption phenomena. Our theoretical approach is applied for analyzing complex dynamics of fullerene-based molecular machines, known as nanocars. It is found that the charge transfer makes the rolling of nanocars' wheels a preferable mode for translational motion because of the complex interactions with the metal surfaces. The physical-chemical aspects of the rolling mechanism are discussed.

• Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals

  J. Chem. Phys. 139, 174109 (2013)

  The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

• Advanced capabilities of the PYXAID program: Integration schemes, decoherence effects, multiexcitonic states, and field-matter interaction

  J. Chem. Theory Comput., 2014, 10 (2), pp 789–804

  In our previous work [J. Chem. Theory Comput. 2013, 9, 4959], we introduced the PYXAID program, developed for the purpose of performing nonadiabatic molecular dynamics simulations in large-scale condensed matter systems. The methodological aspects and the basic capabilities of the program have been extensively discussed. In the present work, we perform a thorough investigation of advanced capabilities of the program, namely, the advanced integration techniques for the time-dependent Schrodinger equation (TD-SE), the decoherence corrections via decoherence-induced surface hopping, the use of multiexciton basis configurations, and the direct simulation of photoexcitation via explicit light–matter interaction. We demonstrate the importance of the mentioned features by studying the electronic dynamics in a variety of systems. In particular, we demonstrate that the advanced integration techniques for solving TD-SE may lead to a significant speedup of the calculations and provide more stable solutions. We show that decoherence is necessary for accurate description of slow relaxation processes such as electron–hole recombination in solid C60. By using multiexciton configurations and direct, nonperturbative treatment of field–matter interactions, we found nontrivial optimality conditions for the multiple exciton generation in a small silicon cluster.

• Analysis of the Trajectory Surface Hopping Method from the Markov State Model Perspective

  J. Phys. Soc. Jpn., 84, 094002

  We analyze the applicability of the seminal fewest switches surface hopping (FSSH) method of Tully to modeling quantum transitions between electronic states that are not coupled directly, in the processes such as Auger recombination. We address the known deficiency of the method to describe such transitions by introducing an alternative definition for the surface hopping probabilities, as derived from the Markov state model perspective. We show that the resulting transition probabilities simplify to the quantum state populations derived from the time-dependent Schrödinger equation, reducing to the rapidly switching surface hopping approach of Tully and Preston. The resulting surface hopping scheme is simple and appeals to the fundamentals of quantum mechanics. The computational approach is similar to the FSSH method of Tully, yet it leads to a notably different performance. We demonstrate that the method is particularly accurate when applied to superexchange modeling. We further show improved accuracy of the method, when applied to one of the standard test problems, Finally, we adapt the derived scheme to atomistic simulation, combine it with the time-domain density functional theory, and show that it provides the Auger energy transfer timescales which are in good agreement with experiment, significantly improving upon other considered techniques.

• Theoretical insights into photoinduced charge transfer and catalysis at metal oxide surfaces

  Chem. Rev., 2013, 113 (6), pp 4496–4565

• Second-Quantized Surface Hopping

  Phys. Rev. Lett. 2014, 113, 153003

  The trajectory surface hopping method for quantum dynamics is reformulated in the space of many-particle states to include entanglement and correlation of trajectories. Used to describe many-body correlation effects in electronic structure theories, second quantization is applied to semiclassical trajectories. The new method allows coupling between individual trajectories via energy flow and common phase evolution. It captures the properties of a wave packet, such as branching, Heisenberg uncertainty, and decoherence. Applied to a superexchange process, the method shows very accurate results, comparable to exact quantum data and improving greatly on the standard approach.

• Persistent electronic coherence despite rapid loss of electron-nuclear correlation

  J. Phys. Chem. Lett., 2013, 4 (22), pp 3857–3864

  Long-lived coherences of excited states are notable for their positive effect on energy conversion mechanisms and efficiencies in photosynthetic complexes. Rational engineering of such persistent coherences could open a new way to increase energy conversion rates in man-made photovoltaic and photocatalytic materials. Therefore, a comprehensive understanding of the fundamental principles behind the long-lived coherences is necessary. In this work we show that the main factor determining the decoherence rates is the magnitude of the nuclear-induced fluctuation of the energy gap between the electronic states of interest, rather than the electron–nuclear correlation on its own. Utilizing combined atomistic and electronic structure calculations, we demonstrate an inverse relationship between decoherence times and magnitude of the energy gap fluctuation. We also show that the energy gap fluctuation can often correlate with the gap itself. For sufficiently small energy gaps, the coherence time can be nearly an order of magnitude larger than the electron–nuclear correlation time.

• Theory of solar energy materials

  J. Phys.: Condens. Matter 2015, 27, 130301

  Editorial for the special issue

• Nonadiabatic dynamics of charge transfer and singlet fission at the pentacene/C60 interface

  J. Am. Chem. Soc., 2014, 136 (4), pp 1599–1608

  Charge carrier multiplication in organic heterojunction systems, a process known as singlet fission (SF), holds promise for development of solar cells with enhanced photon-to-electron yields, and therefore it is of substantial fundamental interest. The efficiency of photovoltaic devices based on this principle is determined by complex dynamics involving key electronic states coupled to particular nuclear motions. Extensive experimental and theoretical studies are dedicated to this topic, generating multiple opinions on the nature of such states and motions, their properties, and mechanisms of the competing processes, including electron–phonon relaxation, SF, and charge separation. Using nonadiabatic molecular dynamics, we identify the key steps and mechanisms involved in the SF and subsequent charge separation, and build a comprehensive kinetic scheme that is consistent with the existing experimental and theoretical results. The ensuing model provides time scales that are in excellent agreement with the experimental observations. We demonstrate that SF competes with the traditional photoinduced electron transfer between pentacene and C60. Efficient SF relies on the presence of intermediate dark states within the pentacene subsystem. Having multiexciton and charge transfer character, these states play critical roles in the dynamics, and should be considered explicitly when explaining the entire process from the photoexcitation to the final charge separation.