OPEP is a suite of FORTRAN programs targeted at the optimal partitioning of molecular electric properties. It includes an interactive module for the construction of Cartesian grids of points, on which either the molecular electrostatic potential or the induction energy is mapped. The generation of distributed multipoles and polarizabilities is achieved using either the formalism of the normal equations of the least-squares problem, which restates the fitting procedure in terms of simple matrix operations, or a statistical approach, which provides a pictorial description of the distributed models of multipoles and polarizabilities, thereby allowing the pinpointing of pathological cases. Molecular symmetry is accounted for by means of local atomic frames, which are generated in an automated fashion. A Tcl/Tk graphical user interface wraps the suite of programs, thereby making OPEP a user-friendly package for building models of distributed multipoles and polarizabilities. OPEP is an open-source suite of programs distributed free of charge under the GNU general public license (GPL) at http://www.lctn.uhp-nancy.fr/Opep.
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http://dx.doi.org/10.1002/jcc.10236 | DOI Listing |
J Chem Theory Comput
January 2025
Chemical and Materials Physics Graduate Program, Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
Molecular dynamics (MD) simulations are essential for understanding molecular phenomena at the atomic level, with their accuracy largely dependent on both the employed force field and sampling. Polarizable force fields, which incorporate atomic polarization effects, represent a significant advancement in simulation technology. The polarizable Gaussian multipole (pGM) model has been noted for its accurate reproduction of ab initio electrostatic interactions.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, U.K.
Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 Cl channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. Here, we implement the fully polarizable force field AMOEBA in MD simulations on different conformations of hBest1.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Aix Marseille Univ, CNRS, ICR, 13397 Marseille, France.
Electronic polarization and dispersion are decisive actors in determining interaction energies between molecules. These interactions have a particularly profound effect on excitation energies of molecules in complex environments, especially when the excitation involves a significant degree of charge reorganization. The direct reaction field (DRF) approach, which has seen a recent revival of interest, provides a powerful framework for describing these interactions in quantum mechanics/molecular mechanics (QM/MM) models of systems, where a small subsystem of interest is described using quantum chemical methods and the remainder is treated with a simple MM force field.
View Article and Find Full Text PDFIn this paper, we study the optical properties of a planar array consisting of nanodisks using the coupled multipole model (CMM). As we demonstrate, this model shows its advantages in uncovering the complex inter-particle mutual interaction mechanisms, which are usually obscured by direct numerical simulations. We first propose a method to compute the polarizabilities of the individual non-spherical particles up to the magnetic quadrupole.
View Article and Find Full Text PDFPhys Chem Chem Phys
September 2024
Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an City 710119, People's Republic of China.
For planar and rigid π-conjugated molecular systems, electrostatic and inductive interactions are pivotal in governing molecular packing structures and electron polarization energies. These electrostatic interactions typically exhibit an anisotropic nature within π-conjugated systems. In this study, we utilize the atoms in molecules (AIM) theory in conjunction with linear response theory to decompose molecular polarizability into distributed atomic polarizability tensors.
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