NDLI: Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

Content Provider	Springer Nature Link
Author	Pieffet, Gilles Petukhov, Pavel A.
Copyright Year	2009
Abstract	The accuracy of molecular dynamics (MD) simulations is limited by the availability of parameters for the molecular system of interest. In most force fields, parameters of common chemical groups are already present. With the development of novel small organic molecules as probes to study biological systems, more chemical groups require parameterization. An azide group is often used in studies of biological systems but computational studies are still impeded by the lack of parameters. In this paper, we present a set of molecular mechanics (MM) parameters for aromatic and aliphatic azido groups, and their application in MD simulations of a photoaffinity probe currently used in our laboratory for mapping binding modes available in the active site of histone deacetylases. The parameters were developed for the generalized Amber force field (GAFF) using density functional theory (DFT) calculations at B3LYP 6-311G(d) level. The parameters were validated by geometry optimization and MD simulations.
Starting Page	1291
Ending Page	1297
Page Count	7
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	15
Issue Number	11
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2009-03-14
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Force field Parameterization Azido groups Molecular dynamics Molecular mechanics Photoaffinity probes Computer Application in Life Sciences Life Sciences Health Informatics Molecular Medicine Biomedicine general Computer Applications in Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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