Supercell calculations of the geometry and lattice energy of α-glycine crystal
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Evidence about the presence of glycine in the interstellar medium (ISM) has been motivating studies aiming the understanding of the chemical behavior of this amino acid in such environment. Since glycine is expected to be predominantly found in the ISM in solid phase, this work focuses on the search for a theoretical methodology for obtaining a molecular cluster for α-glycine that provides a good description of the geometry of the unit cell and lattice energy. Calculations have been performed using the B3LYP-D3, PBE0-D3, and WB97X-D3 functionals, with def2-SVP, def2-TZVP, def2-TZVPP, and def2-QZVPP basis sets for two models: (a) the unit cell, containing 4 glycine units, and (b) the 2 × 1 × 2 expanded cell, with 16 glycine units. Corrections for the basis set superposition error have also been applied. No significant changes in geometries and lattice energy predictions from the different functionals and basis sets have been observed for each model. Nevertheless, results obtained for the larger molecular cluster are in better agreement with the experimental data. The best lattice energy prediction, obtained for the 2 × 1 × 2 supercell at the B3LYP-gCP-D3/def2-TZVPP level, is − 15.35 kcal mol−1, with a root mean square deviation of the predicted Cartesian coordinates of the inner molecules (with respect to the experimental α-glycine unit cell geometry) of 0.966 Å. This methodology is finally recommended for future studies of similar molecular cluster, and the predicted geometry is proposed for further studies aiming to describe glycine surface reactions in the ISM.
Keywordsα-Glycine Interstellar medium Molecular crystal Lattice energy
The authors would like to acknowledge Conselho Nacional de Desenvolvimento e Pesquisa (CNPq) for the scholarship and the LNCC–SINAPAD–Santos Dumont (sdumont2018/chamada1/paper182342) for the ongoing project. The authors also thank Prof. Chaudhuri for providing Cartesian coordinates of the optimized tetramer reported in Ref. 27.
- 1.Elsila JE, Glavin DP, Dworkin JP (2009) Cometary glycine detected in samples returned by Stardust. Meteorit Planet Sci 44:1323–1330. https://doi.org/10.1111/j.1945-5100.2009.tb01224.x CrossRefGoogle Scholar
- 23.Szeleszczuk Ł, Pisklak DM, Zielińska-Pisklak M (2018) 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. J Comput Chem 39:853–861. https://doi.org/10.1002/jcc.25161 CrossRefPubMedGoogle Scholar
- 56.Brandenburg JG, Grimme S (2013) Dispersion corrected Hartree–Fock and density functional theory for organic crystal structure prediction. Springer-Verlag, Berlin Heidelberg, Berlin, pp 1–23Google Scholar
- 69.Gavezzotti A (2008) Computational contributions to crystal engineering. CrystEngComm. https://doi.org/10.1039/b802431f