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Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization

Rahaman, Obaidur and van Duin, Adri C. T. and Goddard, William A., III and Doren, Douglas J. (2011) Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization. Journal of Physical Chemistry B, 115 (2). pp. 249-261. ISSN 1520-6106. PMCID PMC3042430. https://resolver.caltech.edu/CaltechAUTHORS:20110301-145945403

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Abstract

Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine−water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF → ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/jp108642r DOIArticle
http://pubs.acs.org/doi/full/10.1021/jp108642rPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042430/PubMed CentralArticle
ORCID:
AuthorORCID
van Duin, Adri C. T.0000-0002-3478-4945
Goddard, William A., III0000-0003-0097-5716
Additional Information:© 2011 American Chemical Society. Received: September 10, 2010; Revised Manuscript Received: November 18, 2010. Publication Date (Web): December 17, 2010. A.C.T.v.D. and W.A.G. acknowledge NSF-funding DMR 0427177: ITR for the development of the ReaxFF water-potential. A.C.T.v.D. acknowledges funding from KISK startup Grant No. C000032472. D.J.D. and O.R. acknowledge support from NIH under P42 ES010344-06A2.
Funders:
Funding AgencyGrant Number
NSFDMR-0427177
KISKC000032472
NIHP42 ES010344-06A2
Issue or Number:2
PubMed Central ID:PMC3042430
Record Number:CaltechAUTHORS:20110301-145945403
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110301-145945403
Official Citation:Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization Obaidur Rahaman, Adri C. T. van Duin, William A. Goddard III, Douglas J. Doren The Journal of Physical Chemistry B 2011 115 (2), 249-261
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22589
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:03 Mar 2011 17:11
Last Modified:03 Oct 2019 02:38

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