Crystal structure prediction of flexible molecules with genetic algorithms and a standard force field

JULIO C. FACELLI; SEONAH KIM; ANITA M. ORENDT; MARTA B. FERRARO; IAN PIMIENTA; VÍCTOR BAZTERRA

BAHIA BLANCA -ARGENTINA

Congreso; IV REUNION de la ASOCIACION ARGENTINA DE CRISTALOGRAFIA; 2008

ASOCIACION ARGENTINA DE CRISTALOGRAFIA

<!-- @page { size: 8.5in 11in; margin: 0.79in } P { margin-bottom: 0.08in } --> In this presentation we describe our distributed computing framework for crystal structure prediction, MGAC (Modified Genetic Algorithms for Crystal and Cluster Prediction) and its application to predict the structure of flexible molecules using GAFF (Generalized Amber Force Field). MGAC is capable of performing crystal structure searches for flexible molecules within any space group and with an arbitrary number of molecules in the asymmetric unit. The distributed computing framework includes a series of tightly integrated computer programs for generating the molecule’s force field, sampling possible crystal structures using a distributed parallel genetic algorithm, locally minimization of the structures and classifying, sorting and archiving the most relevant ones. Our results indicate the method consistently can find the experimentally known structures when the GAFF force field reproduce the torsional energetics of the molecule, but unfortunately in some cases GAFF exhibit serious errors in describing this energetics. The quality of the positive matches is depicted in the figure. <!-- @page { size: 8.5in 11in; margin: 0.79in } P { margin-bottom: 0.08in } --> which depicts the matching between the predicted and experimental structures of norephedrine (racemic 2-amino-1-phenyl-1-propanol). This matching corresponds to a RMS of 0.315 Å over a cluster of 15 molecules using the COMPACK, method. Both the experimental and predicted structure belong to the P21/c symmetry group, the predicted cell parameters are (experimental values between parenthesis), a = 12.447 Å (12.507 Å), b = 8.293 Å (8.771 Å), c =7.808 (8.130 Å) and  = 104.63˚ (106.20˚).