Predicting Crystalline Packing Arrangements of Molecules That Form Hydrogen-Bonded Tapes

A procedure based on simulated annealing Monte Carlo (SAMC) was used to predict the crystal structures of hydrogen-bonded organic molecules that form molecular tapes. This procedure was optimized to select structures with good hydrogen-bond geometries; it allowed for deformations in molecular conformation due to packing pressures. Biasing the SAMC procedure to select structures with good hydrogen bonds improves the efficiency of generating hydrogen-bonding motifs significantly. This procedure, written in the syntax of the CHARMM molecular modeling program, correctly predicted the crystalline structures of three test molecules derived from diketopiperazine: (C5DKP = 3,6-(cyclotetramethylene)-2,5-diketopiperazine; Me4DKP = 3,6-(tetramethyl)-2,5-diketopiperazine; (Me2C6)2DKP = 3,6-(4,4-dimethylcyclohexane)-2,5-diketopiperazine). The computational and experimental results were compared using powder diffraction patterns, visualization, and values of Ck* (a measure of the crystalline packing efficiency).