How well can new-generation density functional methods describe stacking interactions in biological systems? Export

@article{citeulike:3352040, abstract = {We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.}, author = {Zhao, Yan and Truhlar, Donald G.}, citeulike-article-id = {3352040}, citeulike-linkout-0 = {http://dx.doi.org/10.1039/b507036h}, citeulike-linkout-1 = {http://www.rsc.org/Publishing/Journals/article.asp?doi=b507036h}, doi = {10.1039/b507036h}, journal = {Phys. Chem. Chem. Phys.}, keywords = {dna\_stacking, dna\_stretching}, number = {14}, pages = {2701--2705}, posted-at = {2008-09-29 11:24:07}, priority = {2}, publisher = {The Royal Society of Chemistry}, title = {How well can new-generation density functional methods describe stacking interactions in biological systems?}, url = {http://dx.doi.org/10.1039/b507036h}, volume = {7}, year = {2005} }

TY - JOUR ID - citeulike:3352040 L3 - citeulike-article-id:3352040 N2 - We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role. IS - 14 JF - Phys. Chem. Chem. Phys. EP - 2705 TI - How well can new-generation density functional methods describe stacking interactions in biological systems? PB - The Royal Society of Chemistry VL - 7 SP - 2701 KW - dna_stacking KW - dna_stretching AU - Zhao, Yan AU - Truhlar, Donald PY - 2005/// UR - http://dx.doi.org/10.1039/b507036h ER -