Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2019 Feb 15

PMID 30763086

Citations 12

Authors

Koen M Visscher

Daan P Geerke

Affiliations

Soon will be listed here.

Abstract

In this work we propose a strategy based on quantum mechanical (QM) calculations to parametrize a polarizable force field for use in molecular dynamics (MD) simulations. We investigate the use of multiple atoms-in-molecules (AIM) strategies to partition QM determined molecular electron densities into atomic subregions. The partitioned atomic densities are subsequently used to compute atomic dispersion coefficients from effective exchange-hole-dipole moment (XDM) calculations. In order to derive values for the repulsive van der Waals parameters from first principles, we use a simple volume relation to scale effective atomic radii. Explicit inclusion of higher order dispersion coefficients was tested for a series of alkanes, and we show that combining C and C attractive terms together with a C repulsive potential yields satisfying models when used in combination with our van der Waals parameters and electrostatic and bonded parameters as directly obtained from quantum calculations as well. This result highlights that explicit inclusion of higher order dispersion terms could be viable in simulation, and it suggests that currently available QM analysis methods allow for first-principles parametrization of molecular mechanics models.

Citing Articles

van der Waals Radii of Free and Bonded Atoms from Hydrogen (Z = 1) to Oganesson (Z = 118).

Charry J, Tkatchenko A J Chem Theory Comput. 2024; 20(17):7469-7478.

PMID: 39208255 PMC: 11391583. DOI: 10.1021/acs.jctc.4c00784.

Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions.

Thurlemann M, Boselt L, Riniker S J Chem Theory Comput. 2023; .

PMID: 36633918 PMC: 9878731. DOI: 10.1021/acs.jctc.2c00661.

Perspective on the Current State-of-the-Art of Quantum Computing for Drug Discovery Applications.

Blunt N, Camps J, Crawford O, Izsak R, Leontica S, Mirani A J Chem Theory Comput. 2022; 18(12):7001-7023.

PMID: 36355616 PMC: 9753588. DOI: 10.1021/acs.jctc.2c00574.

A collection of forcefield precursors for metal-organic frameworks.

Chen T, Manz T RSC Adv. 2022; 9(63):36492-36507.

PMID: 35539031 PMC: 9075174. DOI: 10.1039/c9ra07327b.

New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy.

Manz T, Chen T, Cole D, Limas N, Fiszbein B RSC Adv. 2022; 9(34):19297-19324.

PMID: 35519408 PMC: 9064874. DOI: 10.1039/c9ra03003d.

References

Geerke D, van Gunsteren W . Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters. J Phys Chem B. 2007; 111(23):6425-36. DOI: 10.1021/jp0706477. View

Verstraelen T, Vandenbrande S, Heidar-Zadeh F, Vanduyfhuys L, Van Speybroeck V, Waroquier M . Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development. J Chem Theory Comput. 2016; 12(8):3894-912. DOI: 10.1021/acs.jctc.6b00456. View

Boulanger E, Huang L, Rupakheti C, MacKerell Jr A, Roux B . Optimized Lennard-Jones Parameters for Druglike Small Molecules. J Chem Theory Comput. 2018; 14(6):3121-3131. PMC: 5997559. DOI: 10.1021/acs.jctc.8b00172. View

Riniker S . Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. J Chem Inf Model. 2018; 58(3):565-578. DOI: 10.1021/acs.jcim.8b00042. View

Vosmeer C, Kiewisch K, Keijzer K, Visscher L, Geerke D . A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities. Phys Chem Chem Phys. 2014; 16(33):17857-62. DOI: 10.1039/c4cp02401j. View

Verhoef D, Visscher K, Vosmeer C, Cheung K, Reitsma P, Geerke D . Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors. Nat Commun. 2017; 8(1):528. PMC: 5597622. DOI: 10.1038/s41467-017-00647-9. View

Becke A, Johnson E . Exchange-hole dipole moment and the dispersion interaction revisited. J Chem Phys. 2007; 127(15):154108. DOI: 10.1063/1.2795701. View

Bultinck P, Van Alsenoy C, Ayers P, Carbo-Dorca R . Critical analysis and extension of the Hirshfeld atoms in molecules. J Chem Phys. 2007; 126(14):144111. DOI: 10.1063/1.2715563. View

Tkatchenko A, Scheffler M . Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys Rev Lett. 2009; 102(7):073005. DOI: 10.1103/PhysRevLett.102.073005. View

10.

Oostenbrink C, Villa A, Mark A, van Gunsteren W . A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004; 25(13):1656-76. DOI: 10.1002/jcc.20090. View

11.

Cerutti D, Rice J, Swope W, Case D . Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization. J Phys Chem B. 2013; 117(8):2328-38. PMC: 3622952. DOI: 10.1021/jp311851r. View

12.

Huang J, Lopes P, Roux B, MacKerell Jr A . Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J Phys Chem Lett. 2014; 5(18):3144-3150. PMC: 4167036. DOI: 10.1021/jz501315h. View

13.

Manz T, Sholl D . Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials. J Chem Theory Comput. 2015; 8(8):2844-67. DOI: 10.1021/ct3002199. View

14.

Visscher K, Vosmeer C, Luirink R, Geerke D . A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols. J Comput Chem. 2017; 38(8):508-517. DOI: 10.1002/jcc.24702. View

15.

Huang L, Roux B . AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON TARGET DATA. J Chem Theory Comput. 2013; 9(8). PMC: 3819940. DOI: 10.1021/ct4003477. View

16.

Chodera J, Mobley D, Shirts M, Dixon R, Branson K, Pande V . Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol. 2011; 21(2):150-60. PMC: 3085996. DOI: 10.1016/j.sbi.2011.01.011. View

17.

Robustelli P, Piana S, Shaw D . Developing a molecular dynamics force field for both folded and disordered protein states. Proc Natl Acad Sci U S A. 2018; 115(21):E4758-E4766. PMC: 6003505. DOI: 10.1073/pnas.1800690115. View

18.

Wang L, Martinez T, Pande V . Building Force Fields: An Automatic, Systematic, and Reproducible Approach. J Phys Chem Lett. 2015; 5(11):1885-91. PMC: 9649520. DOI: 10.1021/jz500737m. View

19.

Zou W, Nori-Shargh D, Boggs J . On the covalent character of rare gas bonding interactions: a new kind of weak interaction. J Phys Chem A. 2012; 117(1):207-12. DOI: 10.1021/jp3104535. View

20.

Walters E, Mohebifar M, Johnson E, Rowley C . Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. J Phys Chem B. 2018; 122(26):6690-6701. DOI: 10.1021/acs.jpcb.8b02814. View