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

In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel

The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 ± 0.7 kJ mol-1 and 10.8 ± 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.

Multilayer Model of Gold Nanoparticles (AuNPs) and Its Application in the Classical Molecular Dynamics Simulation of Citrate-Capped AuNPs

Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au13 and Au55 models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na+ and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size.

Role of Dielectric Screening in Calculating Excited States of Solvated Azobenzene: A Benchmark Study Comparing Quantum Embedding and Polarizable Continuum Model for Representing the Solvent

The low energy excited states of the conformational isomers of solvated azobenzene are calculated with several DFT methods accounting for the solute-solvent interaction implicitly with the polarizable continuum model or explicitly with subsystem DFT. For the latter, embedding potentials are calculated for 21 sampled snapshots of the solvent molecules. First, we find that accounting for the solvent implicitly or explicitly has little effect on the predicted cis-trans S₁ excitation energy gap. Second, we find that azobenzene's S₁ cis and trans energies are accurate as long as a screened range-separated hybrid exchange-correlation functional is employed. Finally, we also tested a simplified workflow whereby a single, averaged, embedding potential is used. Unfortunately, we find larger deviations against the experiment for the simplified workflow. This highlights a basic flaw in the approach, where the time scale of solvent averaging is much longer than that of the solute's electronic polarization.

An Accurate Linearized Semiclassical Approach for Calculating Cavity-Modified Charge Transfer Rate Constants

We show that combining the linearized semiclasscial approximation with Fermi's golden rule (FGR) rate theory gives rise to a general-purpose cost-effective and scalable computational framework that can accurately capture the cavity-induced rate enhancement of charge transfer reactions that occurs when the molecular system is placed inside a microcavity. Both partial linearization with respect to the nuclear and photonic degrees of freedom and full linerization with respect to nuclear, photonic, and electronic degrees of freedom (the latter within the mapping Hamiltonian approach) are shown to be highly accurate, provided that the Wigner transforms of the product (WoP) of operators at the initial time is not replaced by the product of their Wigner transforms. We also show that the partial linearization method yields the quantum-mechanically exact cavity-modified FGR rate constant for a model system in which the donor and acceptor potential energy surfaces are harmonic and identical except for a shift in the equilibrium energy and geometry, if WoP is applied.

Charge-Separation and Charge-Recombination Rate Constants in a Donor-Acceptor Buckybowl-Based Supramolecular Complex: Multistate and Solvent Effects

The kinetics of the nonradiative photoinduced processes (charge-separation and charge-recombination) experimented in solution by a supramolecular complex formed by an electron-donating bowl-shaped truxene-tetrathiafulvalene (truxTTF) derivative and an electron-accepting fullerene fragment (hemifullerene, C30H12) has been theoretically investigated. The truxTTF·C30H12 heterodimer shows a complex decay mechanism after photoexcitation with the participation of several low-lying excited states of different nature (local and charge-transfer excitations) all close in energy. In this scenario, the absolute rate constants for all of the plausible charge-separation (CS) and charge-recombination (CR) channels have been successfully estimated using the Marcus-Levich-Jortner (MLJ) rate expression, electronic structure calculations, and a multistate diabatization method. The outcomes suggest that for a reasonable estimate of the CS and CR rate constants, it is necessary to include the following: (i) optimally tuned long-range (LC) corrected density functionals, to predict a correct energy ordering of the low-lying excited states; (ii) multistate effects, to account for the electronic couplings; and (iii) environmental solvent effects, to provide a proper stabilization of the charge-transfer excited states and accurate external reorganization energies. The predicted rate constants have been incorporated in a simple but insightful kinetic model that allows estimating global CS and CR rate constants in line with the most generalized three-state model used for the CS and CR processes. The values computed for the global CS and CR rates of the donor-acceptor truxTTF·C30H12 supramolecular complex are found to be in good agreement with the experimental values.

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)-an open-source software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi's golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.