The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.
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http://dx.doi.org/10.1021/acs.jpca.0c05461 | DOI Listing |
Transfus Clin Biol
November 2024
Johns Hopkins University School of Medicine, Department of Pathology, Baltimore, MD, United States. Electronic address:
J Chem Theory Comput
November 2024
Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
The computational complexity of quantum chemistry methods has prompted the development of reactive force fields, facilitating practical applications of molecular dynamics simulations for large-scale reactive systems. Current reactive force fields typically employ intricate corrections based on prior chemical knowledge, which severely impedes their further advancement. This study presents a new atomic multipole-based reactive model with bond free (OPERATOR).
View Article and Find Full Text PDFRSC Adv
October 2024
Chemical & Materials Engineering, New Mexico State University Las Cruces NM 88001 USA
This article derives theoretical foundations of force field functional theory (FFFT). FFFT studies topics related to the functional representation of nonreactive forcefields to achieve various desirable properties such as: (a) formal exactness of the forcefield's energy functional under certain conditions, (b) a formally exact ansatz separating the bonded potential energy from the nonbonded potential energy within a bonded cluster in a way that enables bonded parameters to be optimized using linear regression instead of requiring nonlinear regression, (c) the potential energy's continuous differentiability to various orders with respect to energetically accessible internal coordinate displacements within a subdomain defined by one electronic ground state, (d) forcefield design that guarantees the reference ground-state geometry is exactly reproduced as an equilibrium structure on the forcefield's potential energy landscape, (e) reasonably accurate and broadly applicable frugal model potentials, (f) computationally efficient embedded feature selection that identifies and removes unimportant forcefield terms, (g) well-designed methods to parameterize the forcefield from quantum-mechanically-computed and (optionally) experimental reference data, and (h) forcefields that approximately reproduce experimentally-measured properties. This article also introduces: (1) an angle-bending model potential that more accurately describes physical dynamics and is continuously differentiable to all orders with respect to internal coordinate displacements even when the bond angle is linear (, = π (180°)) and (2) a first-principles-derived stretch potential that accurately describes short-range Pauli repulsion and the long-range bond dissociation energy.
View Article and Find Full Text PDFJ Viral Hepat
October 2024
Health Research Union, Tbilisi, Georgia.
Exposure to healthcare procedures might be a source of hepatitis C virus (HCV) transmission in Georgia, one of the few countries currently on track to eliminate hepatitis C. While there has been a history of iatrogenic transmission of HCV, the risk of HCV transmission related to endoscopic procedures has not been previously assessed in Georgia. The goal of this study was to assess HCV seroconversion among individuals undergoing endoscopic procedures to estimate the relative role and incidence of HCV infection attributable to endoscopic procedures.
View Article and Find Full Text PDFEnviron Sci Technol
October 2024
Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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