AMOEBA+ Classical Potential for Modeling Molecular Interactions

2019 ◽  
Author(s):  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren
Keyword(s):  
Organic Molecules ◽  
Intermolecular Forces ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
General Applicability ◽  
The Past ◽  
Physical Environments ◽  
Classical Potential ◽  
Dynamics Simulations

<p>Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to the Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model developed based on the AMOEBA+ framework captures various liquid phase properties in molecular dynamics simulations while remains consistent with SAPT energy decompositions, utilizing both <i>ab initio</i> data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.</p>

scholarly journals AMOEBA+ Classical Potential for Modeling Molecular Interactions

2019 ◽  
Author(s):  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren
Keyword(s):  
Organic Molecules ◽  
Intermolecular Forces ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
General Applicability ◽  
The Past ◽  
Physical Environments ◽  
Classical Potential ◽  
Dynamics Simulations

<p>Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to the Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model developed based on the AMOEBA+ framework captures various liquid phase properties in molecular dynamics simulations while remains consistent with SAPT energy decompositions, utilizing both <i>ab initio</i> data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.</p>

AMOEBA+ Classical Potential for Modeling Molecular Interactions

2019 ◽  
Author(s):  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren
Keyword(s):  
Organic Molecules ◽  
Intermolecular Forces ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
General Applicability ◽  
The Past ◽  
Physical Environments ◽  
Classical Potential ◽  
Dynamics Simulations

<p>Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to the Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model developed based on the AMOEBA+ framework captures various liquid phase properties in molecular dynamics simulations while remains consistent with SAPT energy decompositions, utilizing both <i>ab initio</i> data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.</p>

scholarly journals AMOEBA+ Classical Potential for Modeling Molecular Interactions

2019 ◽  
Author(s):  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren
Keyword(s):  
Organic Molecules ◽  
Intermolecular Forces ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
General Applicability ◽  
The Past ◽  
Physical Environments ◽  
Classical Potential ◽  
Dynamics Simulations

<p>Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to the Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model developed based on the AMOEBA+ framework captures various liquid phase properties in molecular dynamics simulations while remains consistent with SAPT energy decompositions, utilizing both <i>ab initio</i> data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.</p>

scholarly journals Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2170 ◽  
Author(s):  
Adam Duster ◽  
Chun-Hung Wang ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Model System ◽  
Water Model ◽  
Quantum Mechanical ◽  
Many Body ◽  
Adaptive Partitioning ◽  
Pap Method ◽  
Dynamics Simulations

In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system.

Data-Driven Many-Body Models with Chemical Accuracy for CH4/H2O Mixtures

2020 ◽  
Author(s):  
Marc Riera ◽  
Alan Hirales ◽  
Raja Ghosh ◽  
Francesco Paesani
Keyword(s):  
Liquid Phase ◽  
Quantitative Description ◽  
Liquid Mixtures ◽  
Many Body ◽  
Energy Functions ◽  
Potential Energy Functions ◽  
Dynamics Simulations ◽  
Body Potential ◽  
Small Clusters ◽  
Many Body Interactions

<div> <div> <div> <p>Many-body potential energy functions (PEFs) based on the TTM-nrg and MB-nrg theoretical/computational frameworks are developed from coupled cluster reference data for neat methane and mixed methane/water systems. It is shown that that the MB-nrg PEFs achieve subchemical accuracy in the representation of individual many-body effects in small clusters and enables predictive simulations from the gas to the liquid phase. Analysis of structural properties calculated from molecular dynamics simulations of liquid methane and methane/water mixtures using both TTM-nrg and MB-nrg PEFs indicates that, while accounting for polarization effects is important for a correct description of many-body interactions in the liquid phase, an accurate representation of short-range interactions, as provided by the MB-nrg PEFs, is necessary for a quantitative description of the local solvation structure in liquid mixtures. </p> </div> </div> </div>

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

The Impact of War on Population Health

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Turkan Ahmet
Keyword(s):  
Health Care ◽  
Health Status ◽  
Health Care Services ◽  
Negative Effects ◽  
The Past ◽  
Care Services ◽  
Physical Environments ◽  
The Social ◽  
Personal Experiences ◽  
The Impact

The past few decades of ongoing war in Iraq has had a dramatic impact on the health of Iraq’s population. Wars are known to have negative effects on the social and physical environments of individuals, as well as limit their access to the available health care services. This paper explores the personal experiences of my family members, who were exposed to war, as well as includes information that has been reviewed form many academic sources. The data aided in providing recommendations and developing strategies, on both local and international levels, to improve the health status of the populations exposed to war.

scholarly journals Not Just Transporters: Alternative Functions of ABC Transporters in Bacillus subtilis and Listeria monocytogenes

2021 ◽  
Vol 9 (1) ◽  
pp. 163
Author(s):  
Jeanine Rismondo ◽  
Lisa Maria Schulz
Keyword(s):  
Bacillus Subtilis ◽  
Listeria Monocytogenes ◽  
Abc Transporters ◽  
Organic Molecules ◽  
Atp Hydrolysis ◽  
The Past ◽  
Wide Range ◽  
Regulatory Functions ◽  
Complex Organic ◽  
Detoxification Mechanisms

ATP-binding cassette (ABC) transporters are usually involved in the translocation of their cognate substrates, which is driven by ATP hydrolysis. Typically, these transporters are required for the import or export of a wide range of substrates such as sugars, ions and complex organic molecules. ABC exporters can also be involved in the export of toxic compounds such as antibiotics. However, recent studies revealed alternative detoxification mechanisms of ABC transporters. For instance, the ABC transporter BceAB of Bacillus subtilis seems to confer resistance to bacitracin via target protection. In addition, several transporters with functions other than substrate export or import have been identified in the past. Here, we provide an overview of recent findings on ABC transporters of the Gram-positive organisms B. subtilis and Listeria monocytogenes with transport or regulatory functions affecting antibiotic resistance, cell wall biosynthesis, cell division and sporulation.

scholarly journals The Non-Relativistic Many-Body Quantum-Mechanical Hamiltonian with Diamagnetic Current-Current Interaction

2021 ◽  
Author(s):  
Ladislaus Alexander Bányai
Keyword(s):  
Solid State ◽  
Analogous Result ◽  
Charged Particles ◽  
Coulomb Gauge ◽  
Quantum Mechanical ◽  
Photon Propagator ◽  
Coulomb Interactions ◽  
Many Body ◽  
Transverse Current ◽  
Current Interaction

AbstractWe extend the standard solid-state quantum mechanical Hamiltonian containing only Coulomb interactions between the charged particles by inclusion of the (transverse) current-current diamagnetic interaction starting from the non-relativistic QED restricted to the states without photons and neglecting the retardation in the photon propagator. This derivation is supplemented with a derivation of an analogous result along the non-rigorous old classical Darwin-Landau-Lifshitz argumentation within the physical Coulomb gauge.

Sign in / Sign up

Export Citation Format

Share Document