Molecular dynamics with electronic transitions
15 Jul 1990-Journal of Chemical Physics (American Institute of Physics)-Vol. 93, Iss: 2, pp 1061-1071
TL;DR: In this article, a method for carrying out molecular dynamics simulations of processes that involve electronic transitions is proposed, where the time dependent electronic Schrodinger equation is solved self-consistently with the classical mechanical equations of motion of the atoms.
Abstract: A method is proposed for carrying out molecular dynamics simulations of processes that involve electronic transitions. The time dependent electronic Schrodinger equation is solved self‐consistently with the classical mechanical equations of motion of the atoms. At each integration time step a decision is made whether to switch electronic states, according to probabilistic ‘‘fewest switches’’ algorithm. If a switch occurs, the component of velocity in the direction of the nonadiabatic coupling vector is adjusted to conserve energy. The procedure allows electronic transitions to occur anywhere among any number of coupled states, governed by the quantum mechanical probabilities. The method is tested against accurate quantal calculations for three one‐dimensional, two‐state models, two of which have been specifically designed to challenge any such mixed classical–quantal dynamical theory. Although there are some discrepancies, initial indications are encouraging. The model should be applicable to a wide variety of gas‐phase and condensed‐phase phenomena occurring even down to thermal energies.
Citations
More filters
TL;DR: In this paper, a qualitative discussion of electron transfer, its time and distance scales, energy curves, and basic parabolic energy models are introduced to define the electron transfer process, and some of the important, challenging, and problematic issues in contemporary electron transfer research are discussed.
Abstract: This is an overview of some of the important, challenging, and problematic issues in contemporary electron transfer research. After a qualitative discussion of electron transfer, its time and distance scales, energy curves, and basic parabolic energy models are introduced to define the electron transfer process. Application of transition state theory leads to the standard Marcus formulation of electron transfer rate constants. Electron transfer in solution is coupled to solvent polarization effects, and relaxation processes can contribute to and even control electron transfer. The inverted region, in which electron transfer rate constants decrease with increasing exoergicity, is one of the most striking phenomena in electron transfer chemistry. It is predicted by both semiclassical and quantum mechanical models, with the latter appropriate if there are coupled high- or medium-frequency vibrations. The intramolecular reorganizational energy has different contributions from different vibrational modes, whic...
1,413 citations
TL;DR: The report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm.
Abstract: In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
1,258 citations
TL;DR: In this article, the authors apply the surface-hopping method to proton transfer in solution, where the quantum particle is an atom, using full classical mechanical molecular dynamics for the heavy atom degrees of freedom, including the solvent molecules.
Abstract: We apply ‘‘molecular dynamics with quantum transitions’’ (MDQT), a surface‐hopping method previously used only for electronic transitions, to proton transfer in solution, where the quantum particle is an atom. We use full classical mechanical molecular dynamics for the heavy atom degrees of freedom, including the solvent molecules, and treat the hydrogen motion quantum mechanically. We identify new obstacles that arise in this application of MDQT and present methods for overcoming them. We implement these new methods to demonstrate that application of MDQT to proton transfer in solution is computationally feasible and appears capable of accurately incorporating quantum mechanical phenomena such as tunneling and isotope effects. As an initial application of the method, we employ a model used previously by Azzouz and Borgis to represent the proton transfer reaction AH–B■A−–H+B in liquid methyl chloride, where the AH–B complex corresponds to a typical phenol–amine complex. We have chosen this model, in part, because it exhibits both adiabatic and diabatic behavior, thereby offering a stringent test of the theory. MDQT proves capable of treating both limits, as well as the intermediate regime. Up to four quantum states were included in this simulation, and the method can easily be extended to include additional excited states, so it can be applied to a wide range of processes, such as photoassisted tunneling. In addition, this method is not perturbative, so trajectories can be continued after the barrier is crossed to follow the subsequent dynamics.
1,150 citations
TL;DR: This paper presents a meta-analyses of the proton-probes of Na6(CO3)(SO4)2, Na2SO4, and Na2CO3 of the response of the H2O/O2 “spatially aggregating substance,” which has the potential to alter the structure of the molecule and provide clues to the “building blocks” of DNA.
Abstract: Lung Wa Chung,† W. M. C. Sameera,‡ Romain Ramozzi,‡ Alister J. Page, Miho Hatanaka,‡ Galina P. Petrova, Travis V. Harris,‡,⊥ Xin Li, Zhuofeng Ke, Fengyi Liu, Hai-Bei Li, Lina Ding, and Keiji Morokuma*,‡ †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710119, China School of Ocean, Shandong University, Weihai 264209, China School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
833 citations
TL;DR: Several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
Abstract: In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
775 citations
References
More filters
TL;DR: In this article, an extension of the classical trajectory approach is proposed that may be useful in treating many types of nonadiabatic molecular collisions, where nuclei are assumed to move classically on a single potential energy surface until an avoided surface crossing or other region of large NDE coupling is reached.
Abstract: An extension of the classical trajectory approach is proposed that may be useful in treating many types of nonadiabatic molecular collisions. Nuclei are assumed to move classically on a single potential energy surface until an avoided surface crossing or other region of large nonadiabatic coupling is reached. At such points the trajectory is split into two branches, each of which follows a different potential surface. The validity of this model as applied to the HD2+ system is assessed by numerical integration of the appropriate semiclassical equations. A 3d “trajectory surface hopping” treatment of the reaction of H+ with D2 at a collision energy of 4 eV is reported. The excellent agreement with experiment is an encouraging indication of the potential usefulness of this approach.
1,416 citations
TL;DR: In this paper, a new method is presented for the solution of the time dependent SchrBdinger equation in its application to physical and chemical molecular phenomena, which is based on discretizing space and time on a grid, and using the Fourier method to produce both spatial derivatives, and second order differencing for time derivatives.
1,138 citations
Book•
01 Jan 1960
TL;DR: This is the book that many people in the world waiting for to publish, mathematical methods for digital computers, and the book lovers are really curious to see how this book is actually.
Abstract: Now welcome, the most inspiring book today from a very professional writer in the world, mathematical methods for digital computers. This is the book that many people in the world waiting for to publish. After the announced of this book, the book lovers are really curious to see how this book is actually. Are you one of them? That's very proper. You may not be regret now to seek for this book to read.
1,056 citations
01 Jan 1976
TL;DR: In this paper, the potential energy surfaces and their effect on collision processes are discussed. But the authors focus on the nonadiabatic processes in collision theory and not on the classical trajectories of trajectories.
Abstract: 1. Classical Trajectory Methods in Molecular Collisions.- 2. Features of Potential Energy Surfaces and Their Effect on Collisions.- 3. Dynamics of Unimolecular Reactions.- 4. Semiclassical Methods in Molecular Collision Theory.- 5. Nonadiabatic Processes in Molecular Collisions.- 6. Statistical Approximations in Collision Theory.- 7. Thermodynamic Approach to Collision Processes.- Author Index.
1,002 citations