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Ab initio and force field molecular dynamics study of bulk organophosphorus and organochlorine liquid structures

Journal Article · · Journal of Chemical Physics
DOI:https://doi.org/10.1063/5.0033426· OSTI ID:1782576

Here, we performed ab initio molecular dynamics (AIMD) simulations to benchmark bulk liquid structures and to evaluate results from all-atom force field molecular dynamics (FFMD) simulations with the generalized Amber force field (GAFF) for organophosphorus (OP) and organochlorine (OC) compounds. Our work also addresses the current and important topic of force field validation, applied here to a set of nonaqueous organic liquids. Our approach differs from standard treatments, which validate force fields based on thermodynamic data. Utilizing radial distribution functions (RDFs), our results show that GAFF reproduces the AIMD-predicted asymmetric liquid structures moderately well for OP compounds that contain bulky alkyl groups. Among the OCs, RDFs obtained from FFMD overlap well with AIMD results, with some offsets in position and peak structuring. However, re-parameterization of GAFF for some OCs is needed to reproduce fully the liquid structures predicted by AIMD. The offsets between AIMD and FFMD peak positions suggest inconsistencies in the developed force fields, but, in general, GAFF is able to capture short-ranged and long-ranged interactions of OPs and OCs observed in AIMD. Along with the local coordination structure, we also compared enthalpies of vaporization. Overall, calculated bulk properties from FFMD compared reasonably well with experimental values, suggesting that small improvements within the FF should focus on parameters that adjust the bulk liquid structures of these compounds.

Research Organization:
Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA); Defense Threat Reduction Agency (DTRA)
Grant/Contract Number:
AC04-94AL85000; NA0003525
OSTI ID:
1782576
Report Number(s):
SAND--2021-1286J; 693859
Journal Information:
Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 8 Vol. 154; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English

References (55)

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? journal January 2000
Langevin dynamics of peptides: The frictional dependence of isomerization rates ofN-acetylalanyl-N?-methylamide journal May 1992
Effect of Dispersion on the Structure and Dynamics of the Ionic Liquid 1-Ethyl-3-methylimidazolium Thiocyanate journal March 2012
Development and testing of a general amber force field journal January 2004
The Amber biomolecular simulation programs journal January 2005
Effect of the damping function in dispersion corrected density functional theory journal March 2011
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes journal March 1977
Structural Models and Molecular Thermodynamics of Hydration of Ions and Small Molecules book September 2012
Molecular dynamics simulation of the interface between sulfur mustard and graphene journal September 2018
Detection of chemical warfare agents using nanostructured metal oxide sensors journal July 2005
Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes journal November 2020
Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies journal November 2020
Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration journal June 2015
Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion journal November 2016
The General AMBER Force Field (GAFF) Can Accurately Predict Thermodynamic and Transport Properties of Many Ionic Liquids journal April 2015
Machine Learning Force Fields: Construction, Validation, and Outlook journal December 2016
Nerve agent stereoisomers: analysis, isolation and toxicology journal October 1988
Destruction and Detection of Chemical Warfare Agents journal September 2011
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant journal December 2011
Optimizing Protein–Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field journal November 2013
Lipid14: The Amber Lipid Force Field journal January 2014
Theoretical Study of Aqueous Solvation of K + Comparing ab Initio, Polarizable, and Fixed-Charge Models journal October 2007
A new force field for molecular mechanical simulation of nucleic acids and proteins journal February 1984
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids journal January 1996
Molecular Model of Dimethylmethylphosphonate and Its Interactions with Water journal February 2004
Studies of the Thermodynamic Properties of Hydrogen Gas in Bulk Water journal January 2008
Molecular Modeling of Organophosphorous Agents and Their Aqueous Solutions journal May 2011
Interactions of Phosphororganic Agents with Water and Components of Polyelectrolyte Membranes journal November 2011
Interactions of Sarin with Polyelectrolyte Membranes: A Molecular Dynamics Simulation Study journal December 2012
How Is Acetylcholinesterase Phosphonylated by Soman? An Ab Initio QM/MM Molecular Dynamics Study journal May 2014
Hydration of Kr(aq) in Dilute and Concentrated Solutions journal September 2014
Extension of the Transferable Potentials for Phase Equilibria Force Field to Dimethylmethyl Phosphonate, Sarin, and Soman journal July 2009
Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes March 1998
Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes journal May 1999
Transferable Potentials for Phase Equilibria. 3. Explicit-Hydrogen Description of Normal Alkanes journal June 1999
Some physical properties of aliphatic diphosphonates. Part I. Ethyl esters journal January 1955
On “the complete basis set limit” and plane-wave methods in first-principles simulations of water journal January 2008
Performance of dispersion-corrected density functional theory for the interactions in ionic liquids journal January 2012
Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase journal January 2013
Case study of Rb+(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule journal January 2013
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu journal April 2010
A unified formulation of the constant temperature molecular dynamics methods journal July 1984
Molecular dynamics with coupling to an external bath journal October 1984
Perspective: How good is DFT for water? journal April 2016
Predicting vapor liquid equilibria using density functional theory: A case study of argon journal June 2018
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems journal May 2005
Ab initio theory and modeling of water journal September 2017
An analysis of the accuracy of Langevin and molecular dynamics algorithms journal December 1988
Canonical dynamics: Equilibrium phase-space distributions journal March 1985
Ab initiomolecular dynamics for liquid metals journal January 1993
Projector augmented-wave method journal December 1994
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set journal October 1996
From ultrasoft pseudopotentials to the projector augmented-wave method journal January 1999
Generalized Gradient Approximation Made Simple journal October 1996
Hydration Mimicry by Membrane Ion Channels journal April 2020

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