Structural and Optoelectronic Properties of the α-, β-, and γ-Glycine Polymorphs and the Glycine Dihydrate Crystal: A DFT Study

Rodriguez, Jhonatan Santamaria; Costa, Gabriela Maria Cavalcanti; Silva, M. B. da; Silva, B. P.; Honório, L. J.; Lima‐Neto, Pedro de; Santos, R. C. R.; Caetano, E. W. S.; Alves, H. W. Leite; Freire, V. N.

doi:10.1021/acs.cgd.9b00593

Cited by 14 publications

(14 citation statements)

References 78 publications

(111 reference statements)

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“…In general, PBE + D3 calculations provided a good description of the structural parameters, probably due the gradient corrected exchange-correlation functional. Rodríguez et al reported PBE + TS results, in which the unit cell volume error was only 0.37% for the α phase and a maximum deviation of 1.4% in the lattice parameters was obtained for the α and β-glycine, whereas noncorrected PBE functional overestimated the lattice parameters, leading to higher deviations in comparison to the experimental data.…”

Section: Resultsmentioning

confidence: 99%

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What Rules the Relative Stability of α-, β-, and γ-Glycine Polymorphs?

Xavier

Silva

Bauerfeldt

2020

Crystal Growth & Design

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Theoretical calculations based on the density functional theory, using the PBE functional with the D3 dispersion correction under periodic boundary conditions, have been employed aiming to investigate the properties of α-, β-, and γ-glycine. Structural parameters have been predicted with a maximum error of 1.42% for lattice parameters and 2.53% for the unit-cell volume, for the α phase. Band structure calculations suggest the band gap values of 4.80, 5.01, and 5.23 eV for the α, β, and γ phases, respectively. Quasi-harmonic calculations have been performed and the Gibbs free energy function has been calculated in a wide range of temperature and pressures, suggesting the stability ordering γ > α > β, at room temperature, and the γ to α-glycine phase transition temperature of 442.55 K, at 1 bar, in agreement with the experimental findings. Moreover, a deviation from the experimental value of only 0.44 J mol–1 K–1 is observed for the predicted S(α→γ) at 298.15 K. Finally, calculated sublimation enthalpies of 140.58, 138.09, and 141.70 kJ mol–1 (α, β, and γ-glycine, respectively), at 298.15 K and 1 bar, have also shown good agreement with the experimental values.

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Section: Resultsmentioning

confidence: 99%

“…Accurate result for the stability ranking has been reported from PBE calculations including the Grimme’s dispersion correction scheme (D2), using a genetic algorithm code . However, such results could not be reproduced by the CPAZ , + TS calculations in the work of Rodríguez et al…”

Section: Introductionmentioning

confidence: 99%

What Rules the Relative Stability of α-, β-, and γ-Glycine Polymorphs?

Xavier

Silva

Bauerfeldt

2020

Crystal Growth & Design

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“…[34] glycine at ambient and high pressures was attempted many times. [48][49][50][51][52] Some recent papers propose the structures of some new polymorphs, but their existence has never been confirmed experimentally. [53,54] In all the glycine polymorphs there is a common structureforming motif -a head-to-tail hydrogen-bonded chain formed by the glycine zwitter-ions (Figure 4a).…”

Section: Figurementioning

confidence: 99%

“…[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.…”

Section: Intermolecular Interactionsmentioning

confidence: 99%

Glycine: The Gift that Keeps on Giving

Boldyreva

2021

Israel Journal of Chemistry

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Glycine is a small molecule. It cannot change its conformation and is achiral. Despite the apparent simplicity, glycine shows endless diversity in its behavior over many phenomena. It was the first amino acid for which polymorphism was reported, first on crystallization and then on hydrostatic compression. The polymorphs differ in their physical properties and their biological activity. Glycine clusters persist in solution, leading to "solution memory". Phenomena at interfaces are critically important for crystal growth, dissolution, and for physical properties, which can be at times unexpected, like polarity in centrosymmetric αpolymorph. It is a great pleasure to remind of these remarkable phenomena in a special issue honoring professors Meir Lahav and Leslie Leiserowitz, who pioneered the study of the behavior of this unique molecule in many respects, and showed how complex and non-trivial phenomena can be at interfaces: between phases and between research fields.

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“…At temperatures higher than 440 K, αglycine becomes more stable than γ-glycine. The crystal structure and relative stabilities of the glycine polymorphs have been studied extensively, using different computational methods [81][82][83][84][85][86][87].…”

Section: Glycinementioning

confidence: 99%

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Tom,

Rose,

Bier

et al. 2019

Preprint

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Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. For all polymorphs, the final pool either contained the experimental structure, or structures with similar lattice parameters, symmetry, and packing motifs.

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Structural and Optoelectronic Properties of the α-, β-, and γ-Glycine Polymorphs and the Glycine Dihydrate Crystal: A DFT Study

Cited by 14 publications

References 78 publications

What Rules the Relative Stability of α-, β-, and γ-Glycine Polymorphs?

What Rules the Relative Stability of α-, β-, and γ-Glycine Polymorphs?

Glycine: The Gift that Keeps on Giving

Genarris 2.0: A Random Structure Generator for Molecular Crystals

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