Quantum-chemical modeling of hydrogen bonds in α-glycine

Abstract

Quantum chemistry was used to simulate a fragment of α-glycine crystal consisting of 5 and 6 glycine molecules. The α-glycine crystal fragment model was constructed using X-ray diffraction data contained in the Cambridge Crystallographic Database (CCDC). Theoretical IR spectra were obtained. It was shown that in a fragment of a crystal, glycine molecules in zwitterionic form form N-H...O hydrogen bonds of different strength, which correspond to different frequencies of stretching vibrations νst (N-H) of the NH3+ group. Full optimization of glycine crystal fragments consisting of a small number of molecules, regardless of the method of calculation, leads to the agglomeration of the structure. The system forms the maximum possible number of the most durable hydrogen bonds, thereby lowering the overall energy of the system, which leads to disruption of the crystal structure of the fragment, distortion of the parameters of hydrogen bonds in the crystal, and, consequently, to an unsystematic shift in the frequencies of N-H vibrations. To avoid this process, further modeling was performed by partially optimizing the geometry of the crystal fragment, with the positions of heavy nitrogen atoms, carbon and oxygen atoms being fixed, and only the positions of hydrogen atoms involved in the formation of hydrogen bonds were varied. Using the DFT/B3LYP/6-311G** method, the energies of donor–acceptor interaction in a fragment of a crystal, as well as its oscillation frequencies, are calculated. The calculated frequencies are consistent with the three experimental frequencies in the indicated X-ray region. A comparison was made between the calculated and experimental frequencies of the stretching vibrations of the N-H group of the NH3+ group. According to the geometric characteristics of the HB and the energy of donor-acceptor interaction between the lone electron pairs of oxygen atoms and the *(N-H) loosening orbitals, it was found that the hydrogen bonds of N-H...O between molecules in one layer are stronger than between molecules in different layers of a crystal.

Glycine: The Gift that Keeps on Giving

“…[52,[127][128][129][130][131][132] The number of theoretical works dedicated to the interactions of glycine with its environment in the gas phase, various fluids and in various crystal structures is as large as that of various experimental studies on this compound. [48,50,52,73,91,93,[133][134][135] However, it is hardly possible to select an obviously dominating type of the interaction. In a text-book by Kitaigorodsky [136] a layer in the glycine structure is shown as an example of a "close packing principle", so that van der Waals interactions are optimized.…”