Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Department of Physical Chemistry, Chair and Department of Physical Pharmacy and Bioanalysis, Banacha 1, Warsaw, 02-093, Poland.
Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Department of Biomaterials Chemistry, Chair and Department of Inorganic and Analytical Chemistry, Banacha 1, Warsaw, 02-093, Poland.
J Comput Chem. 2018 May 30;39(14):853-861. doi: 10.1002/jcc.25161. Epub 2018 Jan 5.
Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc.
甘氨酸是一种常见的氨基酸，其在固态下的化学性质相对复杂。尽管已经知道结晶甘氨酸有几种多晶型物（α、β、δ、γ、ε），但对于 NMR 光谱学来说，最重要的是一种多晶型物，它被用作校准光谱仪性能的标准品，因此受到了实验方法和理论计算的广泛研究。甘氨酸的巨大科学兴趣导致了大量晶体学信息文件（CIFs）被储存在剑桥结构数据库（CSD）中。本研究的目的是评估在不同结晶实验条件（温度、压力和α-甘氨酸的辐射源）下获得的α-甘氨酸晶体结构对周期性 DFT 计算结果的影响。为此，总共进行了 136 次α-甘氨酸 NMR 参数的 GIPAW 计算，之前进行了四种结构准备方法（“SP”、“仅 H”、“完整”、“完整+细胞”）。对在各种实验条件下获得的具有代表性的 34 组结构进行这些计算的结果分析表明，尽管这些结构通常具有较好的准确性（大多数结构的 R<0.05），但使用未优化结构进行的周期性 DFT 计算结果存在显著差异。所研究的 NMR 参数的标准偏差值在大多数情况下随着优化参数数量的增加而减小。最准确的结果（计算）通常是使用仅优化了氢原子位置的结构获得的。©2018Wiley Periodicals, Inc.
