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Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation |
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| Authors: | Hui Li Dmitri G. Fedorov Takeshi Nagata Kazuo Kitaura Jan H. Jensen Mark S. Gordon |
| Affiliation: | 1. Department of Chemistry, University of Nebraska‐Lincoln, Lincoln, Nebraska 68588;2. National Institute of Advanced Industrial Science and Technology, 1‐1‐1 Umezono, Tsukuba, Ibaraki 305‐8568, Japan;3. Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo‐ku, Kyoto 606‐8501, Japan;4. Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark;5. Ames Laboratory, US‐DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011 |
| Abstract: | The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6‐31G* level) is used to optimize the solution structure of the 304‐atom Trp‐cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the α‐helix, β‐turn and the extended form in solution are elucidated for polyalanine. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 |
| Keywords: | fragment molecular orbital polarizable continuum model geometry optimization polyalanine Trp‐cage miniprotein solution structure |