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One Hydrogen Bond—Two Ways To Build a Structure. The Role of N–H···O Hydrogen Bonds in Crystal Structures of N,N-Dimethylglycine

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    One Hydrogen Bond—Two Ways To Build a Structure. The Role of N–H···O Hydrogen Bonds in Crystal Structures of N,N-Dimethylglycine
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    † REC-008 Novosibirsk State University, Novosibirsk, Russia
    ‡ Institute of Solid State Chemistry and Mechanochemistry, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
    § National Institute of Chemistry, Ljubljana, Slovenia
    *Elena V. Boldyreva E-mail: [email protected]
    *Eugene A. Kapustin E-mail: [email protected]
    *Vasily S. Minkov E-mail: [email protected]
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    Crystal Growth & Design

    Cite this: Cryst. Growth Des. 2014, 14, 4, 1851–1864
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    https://doi.org/10.1021/cg5000183
    Published February 24, 2014
    Copyright © 2014 American Chemical Society
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    Abstract

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    Crystal structures of amino acids are considered to mimic important interactions in peptides; therefore the studies of the structure-forming factors in these systems attract much attention. N,N-Dimethylglycine is an interesting model compound that was used to test the role of the N–H···O hydrogen bonds in forming the head-to-tail chains, the main structural unit in the crystals of amino acids. It was hypothesized previously [Kolesov, B. A.; Boldyreva, E. V. J. Raman Spectrosc. 2010, 41, 670−677] that additional side N–H···O hydrogen bonds play an important role in forming the head-to-tail chains of amino acid zwitterions linked via N–H···O hydrogen bonds between the charged −NH3+ and −COO– terminal groups. The twice methylated amino group of N,N-dimethylglycine is able to form only one N–H···O hydrogen bond in the crystal structure, so this hypothesis could be tested. In the present article, we describe the crystal structures of two polymorphs of N,N-dimethylglycine, in which the zwitterions are packed in two different ways. In one polymorph (orthorhombic, Pbca), they form finite four-membered ring motifs not linked to each other via any hydrogen bonds but only by weak van der Waals interactions. However, in the second polymorph (monoclinic, P21/n, which was never described before), the zwitterions do form infinite head-to-tail chains though the N–H···O bond is the only interaction and is not assisted via any additional hydrogen bonds. The effect of cooling on the two crystal structures was followed by single-crystal X-ray diffraction combined with polarized Raman spectroscopy of oriented single crystals, in order to compare the response of the N–H···O bonds to temperature variations. The crystal structure of the monoclinic polymorph with infinite chain motifs compresses anisotropically on cooling, whereas that of the orthorhombic polymorph with finite ring motifs undergoes a reversible single-crystal to single-crystal phase transition at ∼200 K accompanied by nonmerohedral twinning, reducing the space symmetry to monoclinic (P21/b) and doubling the asymmetric unit from two to four molecules. This phase transition could not be detected by Raman spectroscopy and DSC. The temperature dependent structure and relative stability of both polymorphs were studied by periodic DFT calculations. The monoclinic polymorph appears to be more stable (by 0.8–1.2 kcal/mol, depending on the density), but with the increasing density and decreasing temperature, the difference decreases. The phase transition of the orthorhombic polymorph has no detectable impact on its relative stability.

    Copyright © 2014 American Chemical Society

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    Supporting Information

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    The structural data for two polymorphs of N,N-dimethylglycine with coordinates of all non-H atoms refined based on X-ray single-crystal diffraction experiments and with coordinates of H atoms optimized using DFT calculations. This material is available free of charge via the Internet at http://pubs.acs.org. The structural data for two polymorphs of N,N-dimethylglycine were deposited as CIFs at the Cambridge Crystallographic Database (CCDC Nos. 978985–978993 for DMG-I and 978975–978983 for DMG-II) and can be downloaded freely from the following site: http://www.ccdc.cam.ac.uk.

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    Cited By

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    This article is cited by 15 publications.

    1. Rohit Bhowal, Suprakash Biswas, Athulbabu Thumbarathil, Apurba L. Koner, Deepak Chopra. Exploring the Relationship between Intermolecular Interactions and Solid-State Photophysical Properties of Organic Co-Crystals. The Journal of Physical Chemistry C 2019, 123 (14) , 9311-9322. https://doi.org/10.1021/acs.jpcc.8b10643
    2. Marcin Podsiadło, Anna Olejniczak, and Andrzej Katrusiak . Structure–Property Relations and Polymorphism in Compressed Methylamines. Crystal Growth & Design 2017, 17 (4) , 2218-2222. https://doi.org/10.1021/acs.cgd.7b00203
    3. Anaid G. Flores-Huerta, Alexandre Tkatchenko, and Marcelo Galván . Nature of Hydrogen Bonds and S···S Interactions in the l-Cystine Crystal. The Journal of Physical Chemistry A 2016, 120 (24) , 4223-4230. https://doi.org/10.1021/acs.jpca.6b03167
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    5. Timothy J. Giese, Maria T. Panteva, Haoyuan Chen, and Darrin M. York . Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field. Journal of Chemical Theory and Computation 2015, 11 (2) , 451-461. https://doi.org/10.1021/ct500799g
    6. Ian F. Bruce-Smith, Boris A. Zakharov, Jernej Stare, Elena V. Boldyreva, and Colin R. Pulham . Structural Properties of Nickel Dimethylglyoxime at High Pressure: Single-Crystal X-ray Diffraction and DFT Studies. The Journal of Physical Chemistry C 2014, 118 (42) , 24705-24713. https://doi.org/10.1021/jp508939g
    7. Andrea Daolio, Patrick Scilabra, Giancarlo Terraneo, Giuseppe Resnati. C(sp3) atoms as tetrel bond donors: A crystallographic survey. Coordination Chemistry Reviews 2020, 413 , 213265. https://doi.org/10.1016/j.ccr.2020.213265
    8. A.M. Petrosyan, V.V. Ghazaryan, G. Giester, M. Fleck, Z. Tylczyński, M. Wiesner. Halogenides of dimethylglycine in comparison with respective salts of glycine, sarcosine and betaine. Journal of Molecular Structure 2018, 1158 , 106-121. https://doi.org/10.1016/j.molstruc.2018.01.017
    9. Pavel S. Zelenovskiy, Anton O. Davydov, Alexander S. Krylov, Andrei L. Kholkin. Raman study of structural transformations in self‐assembled diphenylalanine nanotubes at elevated temperatures. Journal of Raman Spectroscopy 2017, 48 (11) , 1401-1405. https://doi.org/10.1002/jrs.5084
    10. Alexander P. Voronin, German L. Perlovich, Mikhail V. Vener. Effects of the crystal structure and thermodynamic stability on solubility of bioactive compounds: DFT study of isoniazid cocrystals. Computational and Theoretical Chemistry 2016, 1092 , 1-11. https://doi.org/10.1016/j.comptc.2016.07.022
    11. Carl Henrik Görbitz. Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs. Crystallography Reviews 2015, 21 (3) , 160-212. https://doi.org/10.1080/0889311X.2014.964229
    12. Mohammad Alauddin, Himansu S. Biswal, Eric Gloaguen, Michel Mons. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides. Physical Chemistry Chemical Physics 2015, 17 (3) , 2169-2178. https://doi.org/10.1039/C4CP04449E
    13. E. A. Kapustin, V. S. Minkov, E. V. Boldyreva. Sarcosine and betaine crystals upon cooling: structural motifs unstable at high pressure become stable at low temperatures. Physical Chemistry Chemical Physics 2015, 17 (5) , 3534-3543. https://doi.org/10.1039/C4CP05094K
    14. Eugene A. Kapustin, Vasily S. Minkov, Elena V. Boldyreva. Effect of pressure on methylated glycine derivatives: relative roles of hydrogen bonds and steric repulsion of methyl groups. Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 2014, 70 (3) , 517-532. https://doi.org/10.1107/S205252061401035X
    15. E. A. Kapustin, V. S. Minkov, E. V. Boldyreva. Oxidative stress of H 2 O 2 on N,N-dimethylglycine: formation of perhydrate crystals and more. CrystEngComm 2014, 16 (44) , 10165-10168. https://doi.org/10.1039/C4CE01835D
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    Crystal Growth & Design

    Cite this: Cryst. Growth Des. 2014, 14, 4, 1851–1864
    Click to copy citationCitation copied!
    https://doi.org/10.1021/cg5000183
    Published February 24, 2014
    Copyright © 2014 American Chemical Society
    Request reuse permissions

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