Literature DB >> 27524378

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

Ian J Nessler1, Jacob M Litman2, Michael J Schnieders3.   

Abstract

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol-1. For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol-1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol-1) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol-1). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

Entities:  

Year:  2016        PMID: 27524378      PMCID: PMC5102770          DOI: 10.1039/c6cp02595a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  58 in total

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Authors:  J P Lommerse; W D Motherwell; H L Ammon; J D Dunitz; A Gavezzotti; D W Hofmann; F J Leusen; W T Mooij; S L Price; B Schweizer; M U Schmidt; P Verwer; D E Williams
Journal:  Acta Crystallogr B       Date:  2000-08

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Authors:  William L Jorgensen; Erin M Duffy
Journal:  Adv Drug Deliv Rev       Date:  2002-03-31       Impact factor: 15.470

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Authors:  Mats H M Olsson; Gongyi Hong; Arieh Warshel
Journal:  J Am Chem Soc       Date:  2003-04-30       Impact factor: 15.419

4.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

Review 5.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

6.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

Authors:  J Gao; X Xia
Journal:  Science       Date:  1992-10-23       Impact factor: 47.728

Review 7.  The computational prediction of pharmaceutical crystal structures and polymorphism.

Authors:  Sarah L Price
Journal:  Adv Drug Deliv Rev       Date:  2004-02-23       Impact factor: 15.470

8.  Dual-topology/dual-coordinate free-energy simulation using QM/MM force field.

Authors:  Hao Hu; Weitao Yang
Journal:  J Chem Phys       Date:  2005-07-22       Impact factor: 3.488

9.  Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.

Authors:  Celeste Sagui; Lee G Pedersen; Thomas A Darden
Journal:  J Chem Phys       Date:  2004-01-01       Impact factor: 3.488

10.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

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  1 in total

1.  Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Authors:  Guilherme Duarte Ramos Matos; Daisy Y Kyu; Hannes H Loeffler; John D Chodera; Michael R Shirts; David L Mobley
Journal:  J Chem Eng Data       Date:  2017-04-24       Impact factor: 2.694

  1 in total

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