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Journal of Computer-Aided Molecular Design

, Volume 31, Issue 4, pp 349–363 | Cite as

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

  • Meagan C. Small
  • Asaminew H. Aytenfisu
  • Fang-Yu Lin
  • Xibing He
  • Alexander D. MacKerellJr.
Article

Abstract

The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

Keywords

Potential energy function CHARMM Molecular dynamics Molecular mechanics Electronic polarization Glycan 

Notes

Acknowledgements

Financial support from the NIH to ADM (GM072558) and computational support from the University of Maryland Computer-Aided Drug Design Center, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number OCI-1053575, are acknowledged.

Compliance with ethical standards

Conflict of interest

ADM Jr., is co-founder and Chief Scientific Officer of SilcsBio LLC.

Supplementary material

10822_2017_10_MOESM1_ESM.pdf (327 kb)
Supplementary material 1 (PDF 327 KB)

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Copyright information

© Springer International Publishing Switzerland 2017

Authors and Affiliations

  • Meagan C. Small
    • 1
  • Asaminew H. Aytenfisu
    • 1
  • Fang-Yu Lin
    • 1
  • Xibing He
    • 1
  • Alexander D. MacKerellJr.
    • 1
  1. 1.Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreUSA

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