On the Interplay between Electronic Structure and Polarizable Force Fields When Calculating Solution-Phase Charge-Transfer Rates

2020 ◽  
Vol 16 (10) ◽  
pp. 6481-6490
Author(s):  
Jaebeom Han ◽  
Pengzhi Zhang ◽  
Huseyin Aksu ◽  
Buddhadev Maiti ◽  
Xiang Sun ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Charge Transfer ◽  
Force Fields ◽  
Solution Phase ◽  
Transfer Rates ◽  
Polarizable Force Fields

Photoinduced Charge Transfer Dynamics in Carotenoid-Porphyrin-C60 Triad via the Linearized Semiclassical Nonequilibrium Fermi's Golden Rule

2020 ◽  
Author(s):  
Zhengqing Tong ◽  
Margaret S. Cheung ◽  
Barry D. Dunietz ◽  
Eitan Geva ◽  
Xiang Sun
Keyword(s):  
Charge Transfer ◽  
Golden Rule ◽  
Time Dependent ◽  
Rate Coefficients ◽  
Initial State ◽  
Photoinduced Charge Transfer ◽  
Transfer Rates ◽  
Fermi's Golden Rule ◽  
Photoinduced Charge ◽  
Fermi’S Golden Rule

The nonequilibrium Fermi’s golden rule (NE-FGR) describes the time-dependent rate coefficient for electronic transitions, when the nuclear degrees of freedom start out in a <i>nonequilibrium</i> state. In this letter, the linearized semiclassical (LSC) approximation of the NE-FGR is used to calculate the photoinduced charge transfer rates in the carotenoid-porphyrin-C<sub>60</sub> molecular triad dissolved in explicit tetrahydrofuran. The initial nonequilibrium state corresponds to impulsive photoexcitation from the equilibrated ground-state to the ππ* state, and the porphyrin-to-C<sub>60</sub> and the carotenoid-to-C<sub>60</sub> charge transfer rates are calculated. Our results show that accounting for the nonequilibrium nature of the initial state significantly enhances the transition rate of the porphyrin-to-C<sub>60</sub> CT process. We also derive the instantaneous Marcus theory (IMT) from LSC NE-FGR, which casts the CT rate coefficients in terms of a Marcus-like expression, with explicitly time-dependent reorganization energy and reaction free energy. IMT is found to reproduce the CT rates in the system under consideration remarkably well.

Molecular Dynamics Using Non-Variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model

2019 ◽  
Author(s):  
Pier Paolo Poier ◽  
Louis Lagardere ◽  
Jean-Philip Piquemal ◽  
Frank Jensen
Keyword(s):  
Boundary Conditions ◽  
Periodic Boundary ◽  
Force Fields ◽  
Periodic Boundary Conditions ◽  
Computational Effort ◽  
Polarizable Force Fields ◽  
Energy Models ◽  
Capacity Model ◽  
Energy Gradient ◽  
Polarization Models

<div> <div> <div> <p>We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations. </p><div> <div> <div> <p>By making use of a Lagrange formalism, however, this computational demanding task can be re- placed by solving a single equation similar to that for determining the electrostatic variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p><div><div><div> </div> </div> </div> <p> </p><div> <div> <div> <p>variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p> </div> </div> </div> </div> </div> </div> </div> </div> </div>

scholarly journals Quantum Calculations on Ion Channels: Why Are They More Useful Than Classical Calculations, and for Which Processes Are They Essential?

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 655
Author(s):  
Alisher M. Kariev ◽  
Michael E. Green
Keyword(s):  
Charge Transfer ◽  
Ion Channels ◽  
Correlation Energy ◽  
Force Fields ◽  
Critical Role ◽  
Atomic Scale ◽  
Quantum Calculations ◽  
Interatomic Distances ◽  
Classical Analogue ◽  
Exchange And Correlation

There are reasons to consider quantum calculations to be necessary for ion channels, for two types of reasons. The calculations must account for charge transfer, and the possible switching of hydrogen bonds, which are very difficult with classical force fields. Without understanding charge transfer and hydrogen bonding in detail, the channel cannot be understood. Thus, although classical approximations to the correct force fields are possible, they are unable to reproduce at least some details of the behavior of a system that has atomic scale. However, there is a second class of effects that is essentially quantum mechanical. There are two types of such phenomena: exchange and correlation energies, which have no classical analogues, and tunneling. Tunneling, an intrinsically quantum phenomenon, may well play a critical role in initiating a proton cascade critical to gating. As there is no classical analogue of tunneling, this cannot be approximated classically. Finally, there are energy terms, exchange and correlation energy, whose values can be approximated classically, but these approximations must be subsumed within classical terms, and as a result, will not have the correct dependence on interatomic distances. Charge transfer, and tunneling, require quantum calculations for ion channels. Some results of quantum calculations are shown.

scholarly journals Exploring the Franck-Condon region of a photoexcited charge transfer complex in solution to interpret femtosecond stimulated Raman spectroscopy: excited state electronic structure methods to unveil non-radiative pathways

2021 ◽  
Author(s):  
Federico Coppola ◽  
Paola Cimino ◽  
Umberto Raucci ◽  
Maria Gabriella Chiariello ◽  
Alessio Petrone ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Electronic Structure ◽  
Excited State ◽  
Charge Transfer ◽  
Charge Transfer Complex ◽  
Main Role ◽  
Photoinduced Charge Transfer ◽  
Electronic Structure Methods ◽  
Franck Condon ◽  
Photoinduced Charge

We present electronic structure methods to unveil non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A prototypical π-stacked molecular...

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

Molecular Dynamics Study Of Si/Si3N4 Interface

1996 ◽  
Vol 446 ◽  
Author(s):  
Martina E. Bachlechner ◽  
Ingvar Ebbsjö ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Md Simulations ◽  
Electronic Structure Calculations ◽  
Interface Structure ◽  
Bond Bending ◽  
Three Body ◽  
Structure Calculations ◽  
Weber Potential

AbstractStructural correlations at the Si(111)/Si3N4(0001) interface are studied using the molecular dynamics (MD) method. In the bulk, Si is described by the Stillinger-Weber potential and Si3N4 by an interaction potential which contains two-body (steric, Coulomb, electronic polarizabilities) and three-body (bond bending and stretching) terms. At the interface, the charge transfer from silicon to nitrogen is taken from LCAO electronic structure calculations. Using these Si, Si3N4 and interface interactions in MD simulations, the interface structure (atomic positions, bond lengths, and bond angles) is determined. Results for fracture in silicon are also presented.

Correction to Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes

2012 ◽  
Vol 134 (31) ◽  
pp. 13141-13141 ◽  
Author(s):  
Emil Wierzbinski ◽  
Arnie de Leon ◽  
Xing Yin ◽  
Alexander Balaeff ◽  
Kathryn L. Davis ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Backbone Flexibility ◽  
Transfer Rates
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