Optimized Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters Based on Liquid-State Data

Kantonen, Sophie M; Hs, Muddana; Nm, Henriksen; Wang, L; Gilson, Michael K.

doi:10.26434/chemrxiv.9121367.v1

Cited by 3 publications

(2 citation statements)

References 63 publications

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“…A modification to the RESP protocol has recently been proposed which found that predictions of liquid densities and enthalpies of vaporization were improved when the LJ parameters were re-optimized to the new partial charges. 83 In this respect, the very recent method of Kantonen et al for efficiently fitting LJ parameters for MBIS partial charges, 84 should prove to be useful.…”

Section: Discussionmentioning

confidence: 99%

Alchemical Hydration Free-Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On–the–Fly Polarization Approach

Kelly

Smith

2020

J. Chem. Theory Comput.

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We present a methodology using fixed charge force fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges using QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large druglike molecules. We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential (RESP), and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an average absolute deviation (AAD) of 6.3 kJ• mol −1 in comparison with the AM1-BCC result of 8.6 kJ•mol −1 . AM1-BCC is within experimental uncertainty on 10% of the data compared to 30% with our method. We conjecture that results can be further improved by using Lennard-Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.

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Section: Discussionmentioning

confidence: 99%

Alchemical Hydration Free-Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On–the–Fly Polarization Approach

Kelly

Smith

2020

J. Chem. Theory Comput.

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Section: Potential Ff Modificationsmentioning

confidence: 99%

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On-the-Fly Approach

Kelly¹,

Smith²

2020

Preprint

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<div>We present a methodology using fixed charge force-fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges using QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug-like molecules. We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential (RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an Average Absolute Deviation (AAD) of 6.3 kJ·mol−1 in comparison with the AM1-BCC result of 8.6 kJ·mol−1. AM1-BCC is within experimental uncertainty on 10% of the data compared to 30% with our method. We conjecture that results can be further improved by using Lennard-Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.</div>

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Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An OTFP Approach

Kelly

Smith²

2019

Preprint

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We present a methodology using fixed charge force–fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges use QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug–like molecules.We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential(RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an AAD that is 2.98 kJ·mol−1(0.71 kcal·mol−1) lower than AM1–BCC. AM1–BCC is within experimental uncertainty on 10% of thedata compared to 40% with our method. We conjecture that results can be further improved by using Lennard–Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.<br>

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Optimized Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters Based on Liquid-State Data

Cited by 3 publications

References 63 publications

Alchemical Hydration Free-Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On–the–Fly Polarization Approach

Alchemical Hydration Free-Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On–the–Fly Polarization Approach

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On-the-Fly Approach

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An OTFP Approach

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