Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

J Chem Theory Comput

Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892.

Published: May 2007

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/ct600350sDOI Listing

Publication Analysis

Top Keywords

polarizable force
12
force fields
12
parameters
10
additive classical
8
classical drude
8
linear cyclic
8
cyclic ethers
8
force field
8
aliphatic parameters
8
satisfactory agreement
8

Similar Publications

Hydrogen Bond Blueshifts in Nitrile Vibrational Spectra Are Dictated by Hydrogen Bond Geometry and Dynamics.

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 PDF

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 PDF

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 PDF

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 PDF
Article Synopsis
  • Molecular dynamics simulations are essential for understanding the behavior of biomolecules but often face challenges due to discrepancies in time scales compared to real-world experiments, prompting the development of enhanced methods.
  • This study utilizes advanced techniques like oscillating chemical potential grand canonical Monte Carlo and machine learning to investigate how electronic polarizability and Mg2+ distribution influence the stability of the twister ribozyme.
  • The findings highlight that incorporating electronic polarizability significantly improves simulation stability compared to traditional methods, revealing critical interactions between Mg2+ ions and RNA components that contribute to this stabilization.
View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!