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Supercell calculations of the geometry and lattice energy of α-glycine crystal

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Abstract

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.

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Acknowledgments

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.

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  1. Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil

    Neubi F. Xavier Jr, Antônio M. Da Silva Jr & Glauco Favilla Bauerfeldt

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Xavier, N.F., Da Silva, A.M. & Bauerfeldt, G.F. Supercell calculations of the geometry and lattice energy of α-glycine crystal. J Mol Model 25, 244 (2019). https://doi.org/10.1007/s00894-019-4124-2

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