Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation.
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 alpha-helix, beta-turn and the extended form in solution are elucidated for polyalanine.
Li
Hui
H
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA. hli4@unl.edu
Fedorov
Dmitri G
DG
Nagata
Takeshi
T
Kitaura
Kazuo
K
Jensen
Jan H
JH
Gordon
Mark S
MS
D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012996:Solutions
D010455:Peptides; D011506:Proteins; D012996:Solutions; C019529:polyalanine