arXiv subjects

Vojtech Kostal

Publications and source records attributed to Vojtech Kostal.

6 recordsLinked to original sources

arXiv2025

Bayesian learning for accurate and robust biomolecular force fields

Molecular dynamics is a valuable tool to probe biological processes at the atomistic level - a resolution often elusive to experiments. However, the credibility of molecular models is limited by the accuracy of the underlying force field, which is often parametrized relying on ad hoc assumptions. To address this gap, we present a Bayesian framework for learning physically grounded parameters directly from ab initio molecular dynamics data. By representing both model parameters and data probabilistically, the framework yields interpretable, statistically rigorous models in which uncertainty and transferability emerge naturally from the learning process. This approach provides a transparent, data-driven foundation for developing predictive molecular models and enhances confidence in computational descriptions of biophysical systems. We demonstrate the method using 18 biologically relevant molecular fragments that capture key motifs in proteins, nucleic acids, and lipids, and, as a proof of concept, apply it to calcium binding to troponin - a central event in cardiac regulation.

physics.chem-ph↗

arXiv2023

Common Cations are not Polarizable: Effects of Dispersion Correction on Hydration Structures from Ab Initio Molecular Dynamics

We employed density functional theory-based ab initio molecular dynamics simulations to examine the hydration structure of several common alkali and alkali earth metal cations. We found that the commonly used atom pairwise dispersion correction scheme D3, which assigns dispersion coefficients based on the neutral form of the atom rather than its actual oxidation state, leads to inaccuracies in the hydration structures of these cations. We evaluated this effect for lithium, sodium, potassium, and calcium and found that the inaccuracies are particularly pronounced for sodium and potassium compared to the experiment. To remedy this issue, we propose disabling the D3 correction specifically for all cation-including pairs, which leads to a much better agreement with experimental data.

physics.chem-ph↗

arXiv2023

Non-Aqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations

The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge-charge interactions in solution may become severely overestimated leading to unrealistically strong bindings of ions to biomolecules. The electronic continuum correction introduces electronic polarization in a mean-field way via scaling of charges by the reciprocal of the square root of the high-frequency dielectric constant of the solvent environment. Here, we use ab initio molecular dynamics simulations to quantify the effect of electronic polarization on pairs of like-charged ions in a model non-aqueous environment where electronic polarization is the only dielectric response. Our findings confirm the conceptual validity of the present approach, underlining its applicability to complex aqueous biomolecular systems. Simultaneously, the present results justify the potential employment of weaker charge scaling factors in force field development.

physics.chem-ph↗

arXiv2022

Bridging Electrochemistry and Photoelectron Spectroscopy in the Context of Birch Reduction: Detachment Energies and Redox Potentials of Electron, Dielectron, and Benzene Radical Anion in Liquid Ammonia

Birch reduction is a time-proven way to hydrogenate aromatic hydrocarbons (such as benzene), which relies on the reducing power of electrons released from alkali metals into liquid ammonia. We have succeeded to characterize the key intermediates of the Birch reduction process - the solvated electron and dielectron and the benzene radical anion - using cyclic voltammetry and photoelectron spectroscopy, aided by electronic structure calculations. In this way, we not only quantify the electron binding energies of these species, which are decisive for the mechanism of the reaction but also use Birch reduction as a case study to directly connect the two seemingly unrelated experimental techniques.

physics.chem-ph↗

arXiv2021

Electronic Structure of the Solvated Benzene Radical Anion

The benzene radical anion is a molecular ion pertinent to several organic reactions, including the Birch reduction of benzene in liquid ammonia. The species exhibits a dynamic Jahn-Teller effect due to its open-shell nature and undergoes pseudorotation of its geometry. Here we characterize the complex electronic structure of this condensed-phase system based on ab initio molecular dynamics simulations and GW calculations of the benzene radical anion solvated in liquid ammonia. Using detailed analysis of molecular and electronic structure, we find that the spatial character of the excess electron of the solvated radical anion follows the underlying Jahn-Teller distortions of the molecular geometry. We decompose the electronic density of states to isolate the contribution of the solute and to examine the response of the solvent to its presence. Our findings show the correspondence between instantaneous molecular structure and spin density, provide important insights into the electronic stability of the species, revealing that it is indeed a bound state in the condensed phase, and offer electronic densities of states that aid in the interpretation of experimental photoelectron spectra.

physics.chem-ph↗

arXiv2021

Benzene Radical Anion Microsolvated in Ammonia Clusters: Modelling the Transition from an Unbound Resonance to a Bound Species

The benzene radical anion, well-known in organic chemistry as the first intermediate in the Birch reduction of benzene in liquid ammonia, exhibits intriguing properties from the point of view of quantum chemistry. Notably, it has the character of a metastable shape resonance in the gas phase, while measurements in solution find it to be experimentally detectable and stable. In this light, our previous calculations performed in bulk liquid ammonia explicitly reveal that solvation leads to stabilization. Here, we focus on the transition of the benzene radical anion from an unstable gas-phase ion to a fully solvated bound species by explicit ionization calculations of the radical anion solvated in molecular clusters of increasing size. The computational cost of the largest systems is mitigated by combining density functional theory with auxiliary methods including effective fragment potentials or approximating the bulk by polarizable continuum models. Using this methodology, we obtain the cluster size dependence of the vertical binding energy of the benzene radical anion converging to the value of $-$2.3 eV at a modest computational cost.

physics.chem-ph↗