title: SSC: a tool for constructing libraries for systematic screening of conformers.
abstract: Even a relatively small molecule with 10-20 atoms might have a few local minima, which correspond to different conformers. The number of local minima quickly increases with molecular size and the most common algorithms, driven by calculated forces, frequently identify a minimum, which is closest to the initial structure, rather than the most stable conformer. Here we discuss how to perform a systematic search of the conformational space for a chain-like molecule. Our approach is fully automated and a user has control which chemical bonds will be probed and with which increments. Moreover, whole fragments of the molecule, which are adjacent to each selected rotational bond, are rotated in a properly selected cylindrical coordinate system and unchemical hybridizations and some "clashes" between neighboring groups, which are common when standard Z-matrices are used, are avoided. A library of potentially relevant conformers is created with a tool, which we call SSC, denoting Systematic Screening of Conformers. Each member of the library is prescreened at a predefined level of theory and the most promising conformers are identified. Finally, they are further evaluated at a higher level of theory to identify the most stable structures and their physicochemical properties. As an example, we demonstrate the results of this approach for 2'-deoxycytidine.
authors: Chemistry--School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom. s.ling@hw.ac.uk
authors: Sanliang
authors: S
authors: Ling
authors: Maciej
authors: M
authors: Gutowski
mesh_terms: D000465:Algorithms; D003841:Deoxycytidine / Q000737:chemistry; D008968:Molecular Conformation; D054852:Small Molecule Libraries / Q000737:chemistry*
chemical_list: D054852:Small Molecule Libraries; D003841:Deoxycytidine