Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/ct600350s | DOI Listing |
JACS Au
December 2024
Freie Universität Berlin, Physics Department, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany.
Vibrational Stark effect (VSE) spectroscopy has become one of the most important experimental approaches to determine the strength of noncovalent, electrostatic interactions in chemistry and biology and to quantify their influence on structure and reactivity. Nitriles (C≡N) have been widely used as VSE probes, but their application has been complicated by an anomalous hydrogen bond (HB) blueshift which is not encompassed within the VSE framework. We present an empirical model describing the anomalous HB blueshift in terms of H-bonding geometry, i.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy.
We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
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 PDFPolymers (Basel)
November 2024
"Petru Poni" Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania.
Optical filters are essential components for a variety of applicative fields, such as communications, chemical analysis and optical signal processing. This article describes the preparation and characterization of a new optical filter made of polyvinyl alcohol and incremental amounts of crystal violet. By using distinct solvents (HO, dimethyl sulfoxide (DMSO) and HO) to obtain the dyed polymer films, new insights were gained into the pathway that underlies the possibility of tailoring the material's optical performance.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, USA.
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!