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

@article{citeulike:4190531, abstract = {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.}, author = {Pieffet, Gilles and Petukhov, Pavel}, citeulike-article-id = {4190531}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/s00894-009-0488-z}, citeulike-linkout-1 = {http://www.springerlink.com/content/552k310732276020}, doi = {10.1007/s00894-009-0488-z}, journal = {Journal of Molecular Modeling}, keywords = {amber, fluorescence, md, modeling, spectroscopy, theory}, posted-at = {2009-09-15 14:25:43}, priority = {2}, title = {Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies}, url = {http://dx.doi.org/10.1007/s00894-009-0488-z} }

TY - JOUR ID - citeulike:4190531 L3 - citeulike-article-id:4190531 N2 - 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. JF - Journal of Molecular Modeling TI - Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies KW - amber KW - fluorescence KW - md KW - modeling KW - spectroscopy KW - theory AU - Pieffet, Gilles AU - Petukhov, Pavel UR - http://dx.doi.org/10.1007/s00894-009-0488-z ER -