New Version of the Theoretical Databank of Transferable Aspherical Pseudoatoms, UBDB2011--towards Nucleic Acid Modelling
作者： Katarzyna N. Jarzembska , Paulina M. Dominiak
DOI: 10.1107/S0108767311042176
关键词:
摘要: The theoretical databank of aspherical pseudoatoms (UBDB) was recently extended with over 100 new atom types present in RNA, DNA and some other molecules great importance biology pharmacy. atom-type definitions were modified keys added to provide a more precise description the atomic charge-density distribution. X-H bond lengths updated according recent neutron diffraction studies implemented LSDB program as well used for modelling appropriate types. UBDB2011 extensively tested. Electrostatic interaction energies calculated on basis models compared corresponding results obtained directly from wavefunctions at same level theory (SPDFG/B3LYP/6-31G** SPDFG/B3LYP/aug-cc-pVDZ). Various small complexes analysed cover most different types, i.e. adenine-thymine guanine-cytosine hydrogen bonding, guanine-adenine stacking contacts, group neutral charged species nucleic acid bases interacting amino side chains. energy trends are preserved (R(2) > 0.9); however values differ between two methods by about 4 kcal mol(-1) (1 = 4.184 kJ mol(-1)) average. What is noticeable that replacement one set another purely quantum chemical approach leads electrostatic difference, magnitude. work opens up possibility applying macromolecules contain DNA/RNA fragments. This study shows can be estimated structure refinements carried out. However, method limitations apparent.
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