Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations

Abstract

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.

Periodic DFT Calculations—Review of Applications in the Pharmaceutical Sciences

“…For example, in one of our earlier studies we have performed a series of similar NMR parameters calculations for α glycine using all available crystal structures from Cambridge Crystallographic Data Centre (CCDC). In this large group (39) of crystal structures, calculated NMR parameters using low quality structure obtained from the PXRD differed significantly from the ones obtained using structures originating from SCXRD experiments, even after performing geometry optimization ( Figure 1) [71].…”

A theoretical NMR study of polymorphism in crystal structures of azoles and benzazoles

“…This work shows the limitations of the combined use of solid-state NMR (SSNMR) and GIPAW calculations to clarify problems related to tautomerism, polymorphism, and desmotropy. [7][8][9][52][53][54][55] When the molecule bears a heavy-atom substituent, either an empirical model using a dummy variable or ZORA-SO calculations are necessary to account for the experimental chemical shifts, especially for atoms directly bonded to an heavy atom, such as bromine and iodine.…”

Can We Predict the Pressure Induced Phase Transition of Urea? Application of Quantum Molecular Dynamics

“…Fortunately, calculations on molecular crystals using density functional theory (DFT) based programs that enable to include the periodic boundary conditions of a studied system and a planewave basis set, such as CASTEP [9], have proven to be very accurate. Still, in most of the reported studies on the relative stability of the polymorphic forms solely the lattice energies [10][11][12] or, in less number of cases, free energy differences [13,14] of the structures are being calculated and compared. While those computational studies are indeed very interesting and appreciated, since their results enable the insight into the structure and stability of polymorphic forms, accurate phase transition modeling-defined here as a possibility to predict the changes in the crystal structure when exposed to the high pressure-is a much more complicated and challenging task.…”