Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with¹³C CPMAS NMR as a Verification Method

Abstract

The ALJAR03 software was implemented performing searches in the dihedral angle conformational space of disaccharides. The angles φ, ψ, and ω around glycosidic linkages, as well as the orientations of hydroxymethyl and hydroxyl groups, were considered. The energy maps were calculated using the MM+ force field. The searches were performed using a genetic algorithm (GA) combined with systematic grid search (GS). The application of a genetic algorithm-assisted grid search (GAAGS) approach yielded a significant reduction in the number of structures to be sampled in order to find the best low-energy conformation, as compared with the standard systematic grid search. Thus, time-consuming gauge-independent atomic orbital (GIAO) calculations of shielding constants can be rationalized and limited to some selected conformations. 13 C CP-MAS NMR chemical shifts for solid gentiobiose were measured and compared with the respective (GIAO DFT) shielding constants calculated for the crystallographic structure and for low-energy conformers. The differences in shielding are associated with the conformational effects (different arrangements of exocyclic groups) and hydrogen bonds. The best agreement (R 2 = 0.99) between the experimental and calculated chemical shifts was for the XRD structure and for the best conformer (R 2 = 0.98). Their geometries differ in the orientation of OH groups.

Phenyl galactopyranosides – 13 C CPMAS NMR and conformational analysis using genetic algorithm

“…Chemical shifts (d) are reported in ppm downfield from TMS. Conformational analysis was performed using genetic algorithm-assisted grid search method (GAAGS), which combines the standard grid search technique with genetic algorithm [34]. It encompassed preparation of potential energy maps of compounds 1-4 with respect of values of torsion angles around glycosidic bond.…”

“…In the GAAGS method this is realized by genetic algorithm. This method was successfully used in [34,36]. The specially developed software was adapted to cooperate with TINKER 6.3 molecular mechanics package [37].…”

Structural studies of two capsaicinoids: dihydrocapsaicin and nonivamide. 13C and 15N MAS NMR supported by genetic algorithm and GIAO DFT calculations

“…Special soware (ALJAR05) was developed for the calculations and used as described earlier. 6 Each conformation was rst optimized using molecular mechanics (MMFF94 force eld) to classify the conformers found by the genetic algorithm methodology.…”