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1

Baias, Maria, Renny Mathew, Ivan Sergeyev, Karolina Uchman, Melanie Rosay, Fabien Aussenac, Werner Maas, Chris J. Pickard, and Bart Kahr. "NMR crystallography advancements for exploring polymorphism." Acta Crystallographica Section A Foundations and Advances 75, a1 (July 20, 2019): a278. http://dx.doi.org/10.1107/s0108767319097277.

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2

Tirkkonen, B., A. Aukrust, E. Couture, D. Grace, Y. Haile, K. M. Holm, H. Hope, Å. Larsen, H. Sivertsen Lunde, and C. E. Sjøgren. "Physicochemical characterisation of mangafodipir trisodium." Acta Radiologica 38, no. 5 (September 1997): 780–89. http://dx.doi.org/10.1080/02841859709172411.

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Purpose: To determine the structure and various physicochemical properties of man-gafodipir (MnDPDP) trisodium, the active ingredient of Teslascan, a new organ-specific contrast medium for MR imaging. Material and Methods: The structure of MnDPDP trisodium crystals was determined by X-ray crystallography. The possible existence of polymorphism in MnDPDP trisodium was evaluated by powder X-ray diffraction, optical microscopy, thermal analysis and IR spectroscopy. In addition, various spectroscopic techniques and physicochemical measurements were used for characterisation of MnDPDP trisodium. Results: The crystallographic data obtained for MnDPDP trisodium show that the general core structure of the MnDPDP anion is similar to that seen in related substances. The metal coordination geometry is a distorted octahedron defined by 2 phenolate oxygens, 2 carboxylate oxygens and 2 amine nitrogens. The unit cell contains 2 MnDPDP anions, 6 sodium ions and 50 water molecules. The various spectroscopic data are consistent with the structure determined by X-ray crystallography. The product (Teslascan) has low viscosity, is isotonic with blood and has a physiological pH. Conclusion: MnDPDP trisodium is a crystalline, hygroscopic solid which is readily soluble in water. No evidence of polymorphism was seen in the samples studied.
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3

Katrusiak, Andrzej. "High-pressure crystallography." Acta Crystallographica Section A Foundations of Crystallography 64, no. 1 (December 21, 2007): 135–48. http://dx.doi.org/10.1107/s0108767307061181.

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Since the late 1950's, high-pressure structural studies have become increasingly frequent, following the inception of opposed-anvil cells, development of efficient diffractometric equipment (brighter radiation sources both in laboratories and in synchrotron facilities, highly efficient area detectors) and procedures (for crystal mounting, centring, pressure calibration, collecting and correcting data). Consequently, during the last decades, high-pressure crystallography has evolved into a powerful technique which can be routinely applied in laboratories and dedicated synchrotron and neutron facilities. The variation of pressure adds a new thermodynamic dimension to crystal-structure analyses, and extends the understanding of the solid state and materials in general. New areas of thermodynamic exploration of phase diagrams, polymorphism, transformations between different phases and cohesion forces, structure–property relations, and a deeper understanding of matter at the atomic scale in general are accessible with the high-pressure techniques in hand. A brief history, guidelines and requirements for performing high-pressure structural studies are outlined.
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4

G, Nithya, Sudha R, and Charles C. Kanakam. "Polymorphic behavior of an organic compound." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (April 1, 2017): 259. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.16702.

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Objective: Polymorphic crystals were exhibited in many organic compounds. The frequency changes, relative intensities, band contours, and numberof bands were observed in the spectra of different polymorphism which may be due to molecule-molecule interactions in the crystal unit cells. Theshape of a molecule at its site in the unit cell is distorted by molecular interactions.Methods: The identification of a pure crystal form and to quantify a mixture of two forms infrared and Raman spectra of different crystalline formsof the same organic compound can be used. 2’-chloro-4-methoxy-3-nitro benzil (1) was synthesized and its two polymorphic forms were obtainedby recrystallization from the solvents acetone/chloroform and ethanol. The polymorphism present in the compound was confirmed by single crystalX-ray crystallography and differential scanning calorimetry.Results: The polymorph 1.1 crystallizes as triclinic P-1 space group in the solvent acetone – chloroform and the polymorph 1.2 crystallizes asmonoclinic P21/c space group in the solvent ethanol.Discussion: The intermolecular lattice energy and the interplay of molecular conformation in the crystallization and stability of polymorphs areidentified by X-ray crystal structures of conformational polymorphs.Keywords: Conformational polymorphism, Organic compounds, Single crystal growth, X-ray diffraction.
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5

Cogoni, M., B. D'Aguanno, L. N. Kuleshova, and D. W. M. Hofmann. "A powerful computational crystallography method to study ice polymorphism." Journal of Chemical Physics 134, no. 20 (May 28, 2011): 204506. http://dx.doi.org/10.1063/1.3593200.

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6

Gholivand, Khodayar, Farzaneh Afshar, Zahra Shariatinia, and Karim Zare. "Polymorphism for a novel phosphoramidate; NMR and X-ray crystallography." Structural Chemistry 21, no. 3 (February 11, 2010): 629–36. http://dx.doi.org/10.1007/s11224-010-9592-z.

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7

Wang, Jungang, Yang Gao, Jiachen Xiang, Miao Wang, and Anxin Wu. "X-ray studies of conformation: observation of conformational polymorphism of a glycoluril clip." CrystEngComm 17, no. 11 (2015): 2245–49. http://dx.doi.org/10.1039/c5ce00066a.

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8

Kálmán, Alajos. "Morphotropism: link between the isostructurality, polymorphism and (stereo)isomerism of organic crystals." Acta Crystallographica Section B Structural Science 61, no. 5 (September 23, 2005): 536–47. http://dx.doi.org/10.1107/s0108768105023189.

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An ongoing analysis of the supramolecular self-assembly of disubstituted cycloalkanes has led to the discovery of seven packing patterns built up from hydrogen-bonded homo- and heterochiral chains of racemic molecules, associated in either antiparallel or parallel arrays [Kálmán et al. (2001). Acta Cryst. B57, 539–550]. Two further patterns have been revealed in the close packing of analogous alicyclic β-amino acids [Fábián et al. (2005). Cryst. Growth Des. 5, 773–782]. Since each pattern is represented by at least one crystal structure, the chemical similarity and crystallographic forms of these crystals have facilitated the recognition that these patterns differ by one or two rotation(s) of the common motifs (e.g. dimers, tetramers, helices etc.), or the whole pattern may rotate through 180° in an oblique unit cell. Such non-crystallographic – with the exception of polymorphism – virtual rotations as a whole may be denoted by the expression morphotropism. According to Kitaigorodskii [(1961), Organic Chemical Crystallography, pp. 222–231. New York: Consultants Bureau], morphotropism is an attempt to keep the packing coefficient above 0.6 whenever there are alternative possibilities for the structures of closely related molecules. It has been found that crystals of stereoisomers are also frequently related by such virtual rotations. Similarly, non-crystallographic rotations effect bridges between homostructural crystals [Kálmán et al. (1993b). Acta Cryst. B49, 1039–1049] and occasionally hallmark the polymorphism of organic compounds [Kálmán et al. (2003) J. Am. Chem. Soc. 125, 34–35]. In polymorphs, however, such rotations really transform one molecule into another in order to achieve a better packing mediated by solvents, temperature etc.
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9

Dubrovinsky, Leonid. "Polymorphism and electronic transformations of deep Earth minerals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C37. http://dx.doi.org/10.1107/s2053273314099628.

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While powder X-ray diffraction studies stepped over a megabar in pressure already in the 1970s, single crystal experiments remained much rarer and covered until recently a very limited pressure range barely reaching 15 GPa. Recent technological advances resulted in a revolutionary breakthrough in the high-pressure crystallography. The structure solution and the full refinement are now possible at pressures over 100 GPa. A comprehensive understanding of the iron- and aluminum-bearing magnesium silicate perovskite (Pv) and post-perovskite (PPv, CaIrO3-type) crystal structures and their evolution under pressure and temperature is vital for evaluating seismic data of the Earth's lower mantle. We investigated materials with different compositions and iron oxidation states by means of single-crystal X-ray diffraction at pressures over 150 GPa and temperatures over 2500 K, and by Mössbauer spectroscopy. By structural studies of Pv at extreme conditions, we found (a) no spin state crossover in ferric iron occupying the bicapped trigonal prism ("A" crystallographic site), and (b) no crystal-chemically significant amount of ferric iron in the octahedral "B-site at any conditions of our experiments. We synthesized single crystals of PPv, refined their structure and distribution of iron between the structural sites. We demonstrated that incorporation of ferric iron and aluminum significantly increases the compressibility of magnesium silicate Pv and PPv. Based on experimental data we constrained the thermal equation of state for Pv and PPv with a variable content of iron (ferrous and ferric) and aluminum. We concluded that variation of Fe3+/ΣFe can lead to significant changes of Pv bulk sound velocity (over 1%) demonstrating that the oxidation state of iron is a critical parameter for interpretation of seismic tomography data.
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10

Kálmán, Alajos, and László Fábián. "Structural similarities in tetraaryltins described by virtual non-crystallographic rotations or translations: Kitaigorodskii's morphotropism is revisited." Acta Crystallographica Section B Structural Science 63, no. 3 (May 16, 2007): 411–17. http://dx.doi.org/10.1107/s0108768107010968.

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Recently Kálmán [(2005), Acta Cryst. B61, 536–547] revealed that semirigid molecules or their patterns held together e.g. by hydrogen bonds may perform non-crystallographic rotations (through 180, 90° etc.) around themselves whenever a substitution, ring enlargement or isomerization destroys the existing close packing, i.e. the novel substituent or the enlarged ring can no longer fit in the hollows formed between the molecules. In other words, the old and new arrangements of such chemically similar molecules can be converted into each other by virtual rotations. However, when a semirigid molecule without substitution, but under the influence of solvents, temperature etc., is fully or partly rearranged in the solid state, the corresponding non-crystallographic rotation (hereinafter ncr) is real and gives rise to polymorphism. Such polymorphs are hallmarked by full or partial isostructurality and show that ncrs always occur together with isostructurality. First Kitaigorodskii [(1961), Organic Chemical Crystallography, New York: Consultants Bureau] reported on the structural similarity of three tetraaryltins, (p-RC6H4)4Sn, R = H, CH3, CH3O, which is terminated by the larger C2H5O group. A revisit to these structures revealed that the tetragonal → monoclinic conversion termed by Kitaigorodskii as a `morphotropic step' is also performed by an ncr. Similarly, other tetraaryltins in the literature are related by ncrs or the nc translation of the semirigid tetrahedra, or they remain isostructural. Since one of the definitions of morphotropism, a word of Greek origin, is `turn of form', the ncrs of semirigid molecules can be denoted – following Kitaigorodskii – by this word, whereas its alternative definition in the morphological crystallography of `unidirectional changes' [applied by Groth (1870). Ber. Chem. Ges. 3, 449–457] covers the non-crystallographic translations described first in this work.
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11

Hargittai, Istvan. "Jack D. Dunitz (1923–2021): a chemists’ crystallographer." Structural Chemistry 33, no. 1 (October 30, 2021): 291–97. http://dx.doi.org/10.1007/s11224-021-01846-3.

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AbstractJack D. Dunitz (1923–2021) was Professor of Chemical Crystallography at the Swiss Federal Institute of Technology, Zurich. He received his degrees from Glasgow University, was at the ETH Zurich since 1957, and retired in 1990. His research interests included crystal structure analysis as a tool for solving chemical problems, polymorphism, solid state reactions, and a broad area of structural variations during chemical events under the umbrella term of structure correlation.
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12

Czernek, Jiri, Martina Urbanova, and Jiri Brus. "NMR Crystallography of the Polymorphs of Metergoline." Crystals 8, no. 10 (September 25, 2018): 378. http://dx.doi.org/10.3390/cryst8100378.

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Two polymorphs of the drug compound metergoline (C25H29N3O2) were investigated in detail by solid-state NMR measurements. The results have been analysed by an advanced procedure, which uses experimental input together with the results of quantum chemical calculations that were performed for molecular crystals. In this way, it was possible to assign the total of 40 1H–13C correlation pairs in a highly complex system, namely, in the dynamically disordered polymorph with two independent molecules in the unit cell of a large volume of 4234 Å3. For the simpler polymorph, which exhibits only small-amplitude motions and has just one molecule in the unit cell with a volume of 529.0 Å3, the values of the principal elements of the 13C chemical shift tensors were measured. Additionally, for this polymorph, a set of crystal structure predictions were generated, and the {13C, 1H} isotropic and 13C anisotropic chemical shielding data were computed while using the gauge-including projector augmented-wave approach combined with the “revised Perdew-Burke-Ernzerhof“ exchange-correlation functional (GIPAW-RPBE). The experimental and theoretical results were combined in an application of the newly developed strategy to polymorph discrimination. This research thus opens up new routes towards more accurate characterization of the polymorphism of drug formulations.
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13

Lewis, Lori, Peter Troost, Donald Lavery, and Koichi Nishikida. "Pharmaceutical Polymorphism Studies by Infrared Spectroscopic Imaging." Microscopy and Microanalysis 7, S2 (August 2001): 158–59. http://dx.doi.org/10.1017/s1431927600026866.

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Many drugs are known to crystallize in different polymorphic forms or as solvates. Solubility, melting point, density, hardness, optical properties, vapor pressure, and a host of other physical properties may all vary with polymorphic form. Not only do the various crystal structures of a given pharmaceutical compound affect the efficacy of the drug, but they may also carry enormous legal implications. Much product revenue can depend upon the identification and patent protection of certain polymorphic forms. Thus, the control of crystallization is a very important process parameter, and techniques such as X-ray crystallography, infrared spectroscopy, Raman spectroscopy, and polarized light microscopy are routinely used in the characterization of crystalline drugs.This presentation will involve the investigation of a variety of pharmaceutical polycrystalline films using infrared (IR) spectroscopic imaging. Preliminary data was collected using a conventional FT-IR microscope with visible polarized light capabilities. Correlating data was then collected using a commercially available IR imaging microscope.
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14

Songkerdthong, Jetnipat, Phimphaka Harding, and David J. Harding. "Conformational polymorphism in a cobalt(II) dithiocarbamate complex." Acta Crystallographica Section C Structural Chemistry 76, no. 9 (August 28, 2020): 921–26. http://dx.doi.org/10.1107/s205322962001164x.

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Two conformational polymorphs of (N,N-dibutyldithiocarbamato-κ2 S,S′)[tris(3,5-diphenylpyrazol-1-yl-κN 2)hydroborato]cobalt(II), [Co(C45H34BN6)(C9H18NS2)] or [TpPh2Co(S2CNBu2)], 1, are accessible by recrystallization from dichloromethane–methanol to give orthorhombic polymorph 1a, while slow evaporation from acetonitrile produces triclinic polymorph 1b. The two polymorphs have been characterized by IR spectroscopy and single-crystal X-ray crystallography at 150 K. Polymorphs 1a and 1b crystallize in the orthorhombic space group Pbca and the triclinic space group P-1, respectively. The polymorphs have a trans (1a) and cis (1b) orientation of the butyl groups with respect to the S2CN plane of the dithiocarbamate ligand, which results in an intermediate five-coordinate geometry for 1a and a square-pyramidal geometry for 1b. Hirshfeld surface analysis reveals minor differences between the two polymorphs, with 1a exhibiting stronger C—H...S interactions and 1b favouring C—H...π interactions.
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15

Rezgui, Dellel, Christopher Williams, Sharon A. Savage, Stuart N. Prince, Oliver J. Zaccheo, E. Yvonne Jones, Matthew P. Crump, and A. Bassim Hassan. "Structure and function of the human Gly1619Arg polymorphism of M6P/IGF2R domain 11 implicated in IGF2 dependent growth." Journal of Molecular Endocrinology 42, no. 4 (February 4, 2009): 341–56. http://dx.doi.org/10.1677/jme-08-0154.

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The mannose 6-phosphate/IGF 2 receptor (IGF2R) is comprised of 15 extra-cellular domains that bind IGF2 and mannose 6-phosphate ligands. IGF2R transports ligands from the Golgi to the pre-lysosomal compartment and thereafter to and from the cell surface. IGF2R regulates growth, placental development, tumour suppression and signalling. The ligand IGF2 is implicated in the growth phenotype, where IGF2R normally limits bioavailability, such that loss and gain of IGF2R results in increased and reduced growth respectively. The IGF2R exon 34 (5002A>G) polymorphism (rs629849) of the IGF2 specific binding domain has been correlated with impaired childhood growth (A/A homozygotes). We evaluated the function of the Gly1619Arg non-synonymous amino acid modification of domain 11. NMR and X-ray crystallography structures located 1619 remote from the ligand binding region of domain 11. Arg1619 was located close to the fibronectin type II (FnII) domain of domain 13, previously implicated as a modifier of IGF2 ligand binding through indirect interaction with the AB loop of the binding cleft. However, comparison of binding kinetics of IGF2R, Gly1619 and Arg1619 to either IGF2 or mannose 6-phosphate revealed no differences in ‘on’ and ‘off’ rates. Quantitative PCR, 35S pulse chase and flow cytometry failed to demonstrate altered gene expression, protein half-life and cell membrane distribution, suggesting the polymorphism had no direct effect on receptor function. Intronic polymorphisms were identified which may be in linkage disequilibrium with rs629849 in certain populations. Other potential IGF2R polymorphisms may account for the correlation with childhood growth, warranting further functional evaluation.
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Kunimoto, Ko-Ki, Kouji Kimura, Takatomo Takai, Hitoshi Senda, Motoo Shiro, Akio Kuwae, and Kazuhiko Hanai. "Polymorphism of 4-Fluorophenylpyruvic Acid Studied by X-Ray Crystallography and Vibrational Spectroscopy." Spectroscopy Letters 33, no. 4 (July 2000): 509–22. http://dx.doi.org/10.1080/00387010009350135.

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17

Satange, Roshan, Chien-Ying Chuang, Stephen Neidle, and Ming-Hon Hou. "Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation." Nucleic Acids Research 47, no. 16 (July 30, 2019): 8899–912. http://dx.doi.org/10.1093/nar/gkz653.

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Abstract DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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18

Yu, Lian. "Color Changes Caused by Conformational Polymorphism: Optical-Crystallography, Single-Crystal Spectroscopy, and Computational Chemistry." Journal of Physical Chemistry A 106, no. 3 (January 2002): 544–50. http://dx.doi.org/10.1021/jp013019c.

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19

Mollica, Giulia. "New sensitivity-enhanced NMR crystallography approaches to investigate crystallization and polymorphism in organic materials." Acta Crystallographica Section A Foundations and Advances 75, a2 (August 18, 2019): e608-e608. http://dx.doi.org/10.1107/s2053273319089484.

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20

Obal, G., F. Trajtenberg, F. Carrión, L. Tomé, N. Larrieux, X. Zhang, O. Pritsch, and A. Buschiazzo. "Conformational plasticity of a native retroviral capsid revealed by x-ray crystallography." Science 349, no. 6243 (June 4, 2015): 95–98. http://dx.doi.org/10.1126/science.aaa5182.

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Retroviruses depend on self-assembly of their capsid proteins (core particle) to yield infectious mature virions. Despite the essential role of the retroviral core, its high polymorphism has hindered high-resolution structural analyses. Here, we report the x-ray structure of the native capsid (CA) protein from bovine leukemia virus. CA is organized as hexamers that deviate substantially from sixfold symmetry, yet adjust to make two-dimensional pseudohexagonal arrays that mimic mature retroviral cores. Intra- and interhexameric quasi-equivalent contacts are uncovered, with flexible trimeric lateral contacts among hexamers, yet preserving very similar dimeric interfaces making the lattice. The conformation of each capsid subunit in the hexamer is therefore dictated by long-range interactions, revealing how the hexamers can also assemble into closed core particles, a relevant feature of retrovirus biology.
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21

Gomes, Ligia R., John Nicolson Low, Fernando Cagide, and Fernanda Borges. "Polymorphism in the structure of N-(5-methylthiazol-2-yl)-4-oxo-4H-chromene-3-carboxamide." Acta Crystallographica Section E Crystallographic Communications 73, no. 8 (July 13, 2017): 1154–61. http://dx.doi.org/10.1107/s2056989017009902.

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Chromone derivatives have been extensively studied recently because of to their promising biological activities. The new title chromone–thiazole hybrid presented here, C14H10N2O3S, is a candidate as a selective ligand for adenosine receptors. The compound has been synthesized and characterized by the usual spectroscopic means (NMR and EM/IE) and its structure elucidated by X-ray crystallography, which revealed the presence of packing polymorphism. The two polymorphs (one with space group P21/n and one with P21/c) show slightly different conformations and the major change induced by crystallization regards the intramolecular contacts defining the supramolecular structure. Those differences been highlighted by Hirshfeld surface analysis mapped over d norm and ESP.
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22

Fili, S., A. Valmas, M. Norrman, G. Schluckebier, D. Beckers, T. Degen, J. Wright, et al. "Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol." IUCrJ 2, no. 5 (August 4, 2015): 534–44. http://dx.doi.org/10.1107/s2052252515013159.

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This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50–8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.
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Karavassili, Fotini, Alexandros Valmas, Maria Dimarogona, Anastasia E. Giannopoulou, Stavroula Fili, Mathias Norrman, Gerd Schluckebier, Detlef Beckers, Andrew N. Fitch, and I. Margiolaki. "Exploring the complex map of insulin polymorphism: a novel crystalline form in the presence of m-cresol." Acta Crystallographica Section D Structural Biology 76, no. 4 (March 25, 2020): 366–74. http://dx.doi.org/10.1107/s2059798320002545.

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In this study, the first crystal structure of a novel crystal form of human insulin bound to meta-cresol in an acidic environment is reported. The combination of single-crystal and powder X-ray diffraction crystallography led to the detection of a previously unknown monoclinic phase (P21). The structure was identified from the powder patterns and was solved using single-crystal diffraction data at 2.2 Å resolution. The unit-cell parameters at pH 6.1 are a = 47.66, b = 70.36, c = 84.75 Å, β = 105.21°. The structure consists of two insulin hexamers per asymmetric unit. The potential use of this insulin form in microcrystalline drugs is discussed.
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24

Bryce, David L. "Solid-State NMR at the University of Ottawa." Canadian Journal of Chemistry 93, no. 5 (May 2015): 485–91. http://dx.doi.org/10.1139/cjc-2014-0559.

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This article describes some highlights of the research which has been carried out in my laboratory at the University of Ottawa over the period covering 2005 to 2014. My research is in the general areas of solid-state NMR, applications of quantum chemistry, and biomolecular NMR. The format will follow that of my 2014 Canadian Society for Chemistry Keith Laidler Award presentation given in Vancouver in June 2014 at the 97th Canadian Chemistry Conference and Exhibition. Following a brief introduction, I will present some of our most interesting and exciting recent advances according to the following six themes: 1. Fundamental solid-state NMR. 2. Materials characterization and NMR crystallography. 3. Pharmaceuticals and polymorphism. 4. Non-covalent interactions: Halogen bonds. 5. Biomolecular NMR. 6. Software development.
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Thirugnanasambandam, Arunachalam, Selvam Karthik, Gunanithi Artheswari, and Namasivayam Gautham. "DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC)." Acta Crystallographica Section D Structural Biology 72, no. 6 (May 25, 2016): 780–88. http://dx.doi.org/10.1107/s2059798316006306.

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High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals. The decanucleotide d(GCATGCATGC) was previously reported to assume a single-stranded double-fold structure. In one of the two crystal structures described here the decamer assumes both the double-fold conformation and, simultaneously, the more conventional B-type double-helical structure. In the other crystal the sequence assumes the A-type double-helical conformation. These results, taken together with CD spectra, which were recorded as the decamer was titrated against four metal ions and spermine, indicate that the molecule may exist as a mixed population of structures in solution. Small differences in the environmental conditions, such as the concentration of metal ion, may decide which of these crystallizes out. The results also support the idea that it may be possible for DNA to change its structure to suit the binding requirements of proteins or drugs.
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26

Claramunt, R. M., M. Á. García, M. Á. Farrán, C. I. Nieto, M. C. Torralba, M. R. Torres, I. Alkorta, and J. Elguero. "Polymorphism in 8-hydroxyquinolin-2(1H)-one by X-ray crystallography, solid-state NMR and DFT calculations." Acta Crystallographica Section A Foundations of Crystallography 67, a1 (August 22, 2011): C816—C817. http://dx.doi.org/10.1107/s010876731107930x.

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27

Smirnova, Valeriya Yu, Anna A. Iurchenkova, and Denis A. Rychkov. "Computational Investigation of the Stability of Di-p-Tolyl Disulfide “Hidden” and “Conventional” Polymorphs at High Pressures." Crystals 12, no. 8 (August 17, 2022): 1157. http://dx.doi.org/10.3390/cryst12081157.

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The investigation of molecular crystals at high pressure is a sought-after trend in crystallography, pharmaceutics, solid state chemistry, and materials sciences. The di-p-tolyl disulfide (CH3−C6H4−S−)2 system is a bright example of high-pressure polymorphism. It contains “conventional” solid–solid transition and a “hidden” form which may be obtained only from solution at elevated pressure. In this work, we apply force field and periodic DFT computational techniques to evaluate the thermodynamic stability of three di-p-tolyl disulfide polymorphs as a function of pressure. Theoretical pressures and driving forces for polymorphic transitions are defined, showing that the compressibility of the γ phase is the key point for higher stability at elevated pressures. Transition state energies are also estimated for α → β and α → γ transitions from thermodynamic characteristics of crystal structures, not exceeding 5 kJ/mol. The β → γ transition does not occur experimentally in the 0.0–2.8 GPa pressure range because transition state energy is greater than 18 kJ/mol. Relations between free Gibbs energy (in assumption of enthalpy) of phases α, β, and γ, as a function of pressure, are suggested to supplement and refine experimental data. A brief discussion of the computational techniques used for high-pressure phase transitions is provided.
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Eliopoulos, E., G. Goulielmos, M. Matalliotakis, D. Vlachakis, T. Niewold, and M. Zervou. "THU0017 ATTEMPTS TO LINK EXONIC GENE POLYMORPHISMS TO SYSTEMIC LUPUS ERYTHEMATOSUS (SLE)-ASSOCIATED PROTEIN MODIFIED FUNCTIONALITY: A STRUCTURAL BIOLOGY APPROACH." Annals of the Rheumatic Diseases 79, Suppl 1 (June 2020): 221.1–222. http://dx.doi.org/10.1136/annrheumdis-2020-eular.1144.

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Background:Gene association studies and genome wide association studies (GWAS) have played a primary role in depicting genetic contributions to systemic lupus erythematosus (SLE) development, while accommodating the exonic polymorphisms on the protein structure level, when available, enhances our understanding of protein function modification or depletion. Linking human genetics with therapeutic targets requires the biological function of the causal gene and variant to be known.Objectives:To investigate recently identified SLE-associated functional gene polymorphisms, such asPARP1,ITGAM, TNFAIP3, NCF1, PON1, IFIH1, SH2B3andTYK2[1-4] by correlation to protein structure and function.Methods:Three-dimensional (3D) homology modeling and molecular mechanics/dynamics studies were applied for the localization of the polymorphisms under study on the respective proteins. The mutants were constructed using molecular modeling with the program Maestro (Schrodinger, LLC), which was also used to analyze the conformational changes caused by the mutation. All figures depicting 3D models were created using the molecular graphics program PyMOL V.2.2 [5].Results:Modeling revealed that rs1136410 SNP encodes the less common polymorphism Val762Ala onPARP1that reduces enzymatic activity of Poly(ADP-ribose) polymerase 1 (Figure 1),ITGAMpolymorphism rs1143679 (Arg77His) on Integrin alpha M, component of the macrophage-1 antigen complex affects protein surface recognition,TNFAIP3rs2230926 polymorphism encodes Cys instead of Phe at residue 127 of the ubiquitin editing A20 protein, while rs201802880 polymorphism of the neutrophil cytosolic factor 1 (NCF1) gene modifies the function of the cytosolic subunit of neutrophil NADPH oxidase with the mutation Arg90His.PON1is involved in the oxidative stress process that cause tissue damage observed in SLE and anti-phospholipid syndrome (APS). ThePON1Gln192Arg mutation (rs662 SNP) affects shape and recognition of the ligand recognition site as part of the evolutionary process, whileIFIH1(rs35667974) helicase C domain1 mutant I923V is located on an essential RNA beta loop interacting directly with the nucleic acid (Figure 2). Finally, the rs3184504 SNP ofSH2B3gene generates mutant Arg262Trp on SH2 adapter protein 3, acting as a signaling pathway involved in autoimmune disorders, while inTYK2 gene, one of the Janus kinases, the rs35018800 producing mutant Ala928Val modifies the ADP binding site.Figure 1.Details of the Val762 interaction where V762A mutation occurs in PARP1protein.Figure 2.Nucleic acid interacting IFIH1 helicase beta-loop where I923V mutation occurs (in purple).Conclusion:Based on several examples, we have tried to define a rational link from SLE-associated gene polymorphisms to structure and to modified function, including metagenomic analysis of SNPs, protein crystallography, protein molecular modeling, molecular mechanics and dynamics. Locating, shaping and understanding the target protein interaction interface plays a decisive role in most cases and provides clues for further pharmacological or medical actions [6].References:[1]Hur JW et al (2006). Rheumatology 45:711-7[2]Maiti AK et al (2014). Hum Mol Genet 23:4161-76[3]Shimane K et al (2010). Arthritis Rheum. 62:574-9[4]Linge P et al (2019). Ann Rheum Dis. 2019 Nov 8. pii: annrheumdis-2019-215820[5]Schrödinger LLC: The PyMOL Molecular Graphics System 2016 version 2.2. Available from: pymol.org/2/support.html[6]Plenge RM et al (2013). Nat Rev Drug Discov 12:581–94Disclosure of Interests:None declared
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29

Scally, Stephen W., Soi-Cheng Law, Yi Tian Ting, Jurgen van Heemst, Jeremy Sokolove, Aaron J. Deutsch, E. Bridie Clemens, et al. "Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis." Annals of the Rheumatic Diseases 76, no. 11 (August 11, 2017): 1915–23. http://dx.doi.org/10.1136/annrheumdis-2017-211300.

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ObjectiveThe pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a common motif, the ‘shared susceptibility epitope (SE)’. Here, the electropositive P4 pocket of HLA-DRB1 accommodates self-peptide residues containing citrulline but not arginine. HLA-DRB1 His/Phe13β stratifies with ACPA-positive RA, while His13βSer polymorphisms stratify with ACPA-negative RA and RA protection. Indigenous North American (INA) populations have high risk of early-onset ACPA-positive RA, whereby HLA-DRB1*04:04 and HLA-DRB1*14:02 are implicated as risk factors for RA in INA. However, HLA-DRB1*14:02 has a His13βSer polymorphism. Therefore, we aimed to verify this association and determine its molecular mechanism.MethodsHLA genotype was compared in 344 INA patients with RA and 352 controls. Structures of HLA-DRB1*1402-class II loaded with vimentin-64Arg59-71, vimentin-64Cit59-71 and fibrinogen β−74Cit69-81 were solved using X-ray crystallography. Vimentin-64Cit59-71-specific and vimentin59-71-specific CD4+ T cells were characterised by flow cytometry using peptide-histocompatibility leukocyte antigen (pHLA) tetramers. After sorting of antigen-specific T cells, TCRα and β-chains were analysed using multiplex, nested PCR and sequencing.ResultsACPA+ RA in INA was independently associated with HLA-DRB1*14:02. Consequent to the His13βSer polymorphism and altered P4 pocket of HLA-DRB1*14:02, both citrulline and arginine were accommodated in opposite orientations. Oligoclonal autoreactive CD4+ effector T cells reactive with both citrulline and arginine forms of vimentin59-71 were observed in patients with HLA-DRB1*14:02+ RA and at-risk ACPA- first-degree relatives. HLA-DRB1*14:02-vimentin59-71-specific and HLA-DRB1*14:02-vimentin-64Cit59-71-specific CD4+ memory T cells were phenotypically distinct populations.ConclusionHLA-DRB1*14:02 broadens the capacity for citrullinated and native self-peptide presentation and T cell expansion, increasing risk of ACPA+ RA.
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Allen, Frank H., and W. D. Samuel Motherwell. "Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry." Acta Crystallographica Section B Structural Science 58, no. 3 (May 29, 2002): 407–22. http://dx.doi.org/10.1107/s0108768102004895.

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The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.
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Velásquez-González, Omar, Camila Campos-Escamilla, Andrea Flores-Ibarra, Nuria Esturau-Escofet, Roberto Arreguin-Espinosa, Vivian Stojanoff, Mayra Cuéllar-Cruz, and Abel Moreno. "Crystal Growth in Gels from the Mechanisms of Crystal Growth to Control of Polymorphism: New Trends on Theoretical and Experimental Aspects." Crystals 9, no. 9 (August 26, 2019): 443. http://dx.doi.org/10.3390/cryst9090443.

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A gel can be considered to be a two-phase (liquid and solid) system, which lacks flow once it reaches a stationary state. The solid phase is usually a tridimensional polymeric mesh, while the liquid phase is usually found in three forms: contained in great cavities, retained in the capillary pores between micelles, or adsorbed on the surface of a micelle. The influence of the use of gels in crystal growth is diverse and depends on the type of gel being used. A decrease in solubility of any solute in the liquid may occur if the solvent interacts extensively with the polymeric section, hence, the nucleation in gels in these cases apparently occurs at relatively low supersaturations. However, if the pore size is small enough, there is a possibility that a higher supersaturation is needed, due to the compartmentalization of solvents. Finally, this may also represent an effect in the diffusion of substances. This review is divided into three main parts; the first evaluates the theory and practice used for the obtainment of polymorphs. The second part describes the use of gels into crystallogenesis of different substances. The last part is related to the particularities of protein crystal polymorphism, as well as modern trends in gel growth for high-resolution X-ray crystallography.
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Wesela-Bauman, Grzegorz, Simon Parsons, Sergiusz Luliński, Janusz Serwatowski, and Krzysztof Woźniak. "Structure-properties relationship in Borinic Systems at high and normal pressure." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1264. http://dx.doi.org/10.1107/s205327331408735x.

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Recently we were focused on the synthetic, physicochemical and theoretical evaluation of the properties of borinic 8-oxyquinolinates.[1,2] Such systems are of interest of many groups in the world, as borinic derivatives are promising materials for the preparation of luminescent layers in organic light emitting diodes (OLEDs).[3] Our aim is to trace the impact of structure on properties of the system. Hence we have conducted polymorph screening for highly strain aromatic heteroleptic borinic system. As a result, we are presenting, the very first examples of polymorphism in the group of aromatic borinic 8-oxyquinolinate complexes [(2-fluoro-3-pyridyl) (2,2`-biphenyl)borinic 8-oxyquinolinate)]. We wanted to extend our investigations on high-pressure crystallography. These investigations were prompted by results obtained by other groups which analysed crystal structures of AlQ3, GaQ3 and InQ3 under low and high pressure. Such studies helped to trace a connection between the motifs present in the crystal phases and optical properties of these complexes as a consequence of orbital interactions. On this basis we were interested in investigation of the influence of high pressure on the packing of synthesized and characterized (2-fluoro-3-pyridyl) (4-iodophenyl)borinic 8-oxyquinolinate.
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Yeh, Vivien, Alice Goode, and Boyan B. Bonev. "Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR." Biology 9, no. 11 (November 12, 2020): 396. http://dx.doi.org/10.3390/biology9110396.

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Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
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34

Hannan, J., K. Young, G. Szakonyi, M. J. Overduin, S. J. Perkins, X. Chen, and V. M. Holers. "Structure of complement receptor (CR) 2 and CR2-C3d complexes." Biochemical Society Transactions 30, no. 6 (November 1, 2002): 983–87. http://dx.doi.org/10.1042/bst0300983.

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Using X-ray crystallography, we have determined the structure of the first two short consensus repeats (SCRs) of human complement receptor (CR) 2 in complex with C3d. These studies revealed: (i) a primary site of interaction for C3d within SCR2 of CR2, (ii) a hydrophobic patch holding SCR1 to SCR2 in a rigid V-shape, (iii) a dimer formed by interactions between SCR1 of each molecule, (iv) several non-linear sequences on C3d that interact with CR2 and (v) mutations of C3d amino acids within the co-crystal interface that resulted in decreased binding. In addition, a polymorphism that results in decreased C3d binding and introduces a new glycosylation site predicted to disrupt the dimer interface was found in the New Zealand White autoimmune mouse strain. Although the co-crystal complex results are in agreement with a subset of prior studies, our additional findings, which demonstrate an extended SCR1-SCR2 structure in solution and differences in the kinetics of ligand-receptor interactions with longer forms of CR2, have suggested a more complex receptor-ligand interaction. To characterize this interaction further, several approaches directed at the determination of solution phase interactions as well as the analysis of the three-dimensional structure of CR2 alone and key CR2 mutants will be necessary.
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Volkmann, Niels, David DeRosier, Paul Matsudaira, and Dorit Hanein. "An Atomic Model of Actin Filaments Cross-Linked by Fimbrin and Its Implications for Bundle Assembly and Function." Journal of Cell Biology 153, no. 5 (May 21, 2001): 947–56. http://dx.doi.org/10.1083/jcb.153.5.947.

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Actin bundles have profound effects on cellular shape, division, adhesion, motility, and signaling. Fimbrin belongs to a large family of actin-bundling proteins and is involved in the formation of tightly ordered cross-linked bundles in the brush border microvilli and in the stereocilia of inner ear hair cells. Polymorphism in these three-dimensional (3D) bundles has prevented the detailed structural characterization required for in-depth understanding of their morphogenesis and function. Here, we describe the structural characterization of two-dimensional arrays of actin cross-linked with human T-fimbrin. Structural information obtained by electron microscopy, x-ray crystallography, and homology modeling allowed us to build the first molecular model for the complete actin–fimbrin cross-link. The restriction of the arrays to two dimensions allowed us to deduce the spatial relationship between the components, the mode of fimbrin cross-linking, and the flexibility within the cross-link. The atomic model of the fimbrin cross-link, the cross-linking rules deduced from the arrays, and the hexagonal packing of actin bundles in situ were all combined to generate an atomic model for 3D actin–fimbrin bundles. Furthermore, the assembly of the actin–fimbrin arrays suggests coupling between actin polymerization, fimbrin binding, and crossbridge formation, presumably achieved by a feedback between conformational changes and changes in affinity.
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36

Panini, Piyush, K. N. Venugopala, Bharti Odhav, and Deepak Chopra. "Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 70, no. 4 (July 31, 2014): 681–96. http://dx.doi.org/10.1107/s2052520614006209.

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A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.
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37

Aree, Thammarat. "Inclusion Scenarios and Conformational Flexibility of the SSRI Paroxetine as Perceived from Polymorphism of β-Cyclodextrin–Paroxetine Complex." Pharmaceuticals 15, no. 1 (January 14, 2022): 98. http://dx.doi.org/10.3390/ph15010098.

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Depression, a global mental health problem, is prevalent during the coronavirus disease 2019 (COVID-19) pandemic and can be efficiently treated by selective serotonin reuptake inhibitors (SSRIs). Our study series aims at forwarding insights on the β-cyclodextrin (β-CD)–SSRI inclusion complexes by X-ray crystallography combined with density functional theory (DFT) calculation. Here, we report a new crystal form (II) of the 1:1 β-CD–paroxetine (PXT) complex, which is inspired by the reported 2:1 β-CD–PXT complex (crystal form I), reflecting an elusive phenomenon of the polymorphism in CD inclusion complexes. The β-CD–PXT polymorphism stems from the PXT conformational flexibility, which is defined by torsion angles κ, ε around the -CH2–O- group bridging the A- and C–D-rings, of which those of PXT in I and II are totally different. While PXT (II) in an open V-shaped conformation that has the B-ring shallowly inserted in the β-CD cavity, PXT (I) in a closed U-shaped structure is mostly entirely embedded in the β-CD dimeric cavity, of which the A-ring is deeply inserted in the main β-CD cavity. However, PXT molecules in both crystal forms are similarly maintained in the CD cavity via host–guest N–H···O5/O6 H-bonds and C/O–H···π(B/C) interactions and β-CDs have similar 3D arrangements, channel (II) vs. screw-channel (I). Further theoretical explorations on the β-CD–PXT thermodynamic stabilities and the PXT conformational stabilities based on their potential energy surfaces (PESs) have been completed by DFT calculations. The 2:1 β-CD–PXT complex with the greater presence of dispersion interactions is more energetically favorable than the unimolar complex. Conversely, whereas free PXT, PXT (II) and PXT in complex with serotonin transporter are more energetically stable, PXT (I) is least stable and stabilized in the β-CD cavity. As SSRIs could lessen the COVID-19 severity, the CD inclusion complexation not only helps to improve the drug bioavailability, but also promotes the use of antidepressants and COVID-19 medicines concurrently.
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38

Nyanguile, Origène, Benoit Devogelaere, Leen Vijgen, Walter Van den Broeck, Frederik Pauwels, Maxwell D. Cummings, Hendrik L. De Bondt, et al. "1a/1b Subtype Profiling of Nonnucleoside Polymerase Inhibitors of Hepatitis C Virus." Journal of Virology 84, no. 6 (January 13, 2010): 2923–34. http://dx.doi.org/10.1128/jvi.01980-09.

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ABSTRACT The RNA-dependent RNA polymerase (NS5B) of hepatitis C virus (HCV) is an unusually attractive target for drug discovery since it contains five distinct drugable sites. The success of novel antiviral therapies will require nonnucleoside inhibitors to be active in at least patients infected with HCV of subtypes 1a and 1b. Therefore, the genotypic assessment of these agents against clinical isolates derived from genotype 1-infected patients is an important prerequisite for the selection of suitable candidates for clinical development. Here we report the 1a/1b subtype profiling of polymerase inhibitors that bind at each of the four known nonnucleoside binding sites. We show that inhibition of all of the clinical isolates tested is maintained, except for inhibitors that bind at the palm-1 binding site. Subtype coverage varies across chemotypes within this class of inhibitors, and inhibition of genotype 1a improves when hydrophobic contact with the polymerase is increased. We investigated if the polymorphism of the palm-1 binding site is the sole cause of the reduced susceptibility of subtype 1a to inhibition by 1,5-benzodiazepines by using reverse genetics, X-ray crystallography, and surface plasmon resonance studies. We showed Y415F to be a key determinant in conferring resistance on subtype 1a, with this effect being mediated through an inhibitor- and enzyme-bound water molecule. Binding studies revealed that the mechanism of subtype 1a resistance is faster dissociation of the inhibitor from the enzyme.
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Li, Lenong, Yasameen Muzahim, and Marlene Bouvier. "Suppression of antigen presentation by the adenovirus E3-19K protein; a crystallographic analysis of E3-19K/MHC I interaction (106.37)." Journal of Immunology 188, no. 1_Supplement (May 1, 2012): 106.37. http://dx.doi.org/10.4049/jimmunol.188.supp.106.37.

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Abstract The cell-surface presentation of viral antigens by MHC class I molecules is critical for eliminating infected cells. In turn, viruses have evolved strategies to interfere with the process of antigen presentation. The adenovirus (Ad) E3-19K protein binds to and retains MHC class I molecules in the endoplasmic reticulum (ER), blocking their egress to the cell surface. We characterized for the first time interaction between Ad type 2 (Ad2) E3-19K and HLA-A2 using x-ray crystallography. Our structure to 2.1Å resolution reveals that Ad2 E3-19K interacts with the N-terminus of the α1-helix and C-terminus of the α2-helix of HLA-A2, i.e., the C-terminal end of the groove. E3-19K binds away from the opening of the groove. This mode of binding is entirely consistent with our biochemical studies of E3-19K/MHC I interaction, including the ability of E3-19K to associate with mature and immature MHC class I molecules. Importantly, the Ad2 E3-19K/HLA-A2 structure reveals how E3-19K uses it variable and conserved regions to bind to MHC I, and how it accommodates polymorphism in MHC I. Our structure also allows to understand the ability of E3-19K of different Ad serotypes and subgroups to associate with MHC I in an allele- and locus-specific manner. Overall, the Ad2 E3-19K/HLA-A2 structure reveals determinants in E3-19K that are critical for targeting MHC class I molecules. It also permits to better understand how E3-19K has evolved to subvert antigen presentation.
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40

Bour, Hélène, Olivier Michielin, Philippe Bousso, Jean-Charles Cerottini, and H. Robson MacDonald. "Dramatic Influence of Vβ Gene Polymorphism on an Antigen-Specific CD8+ T Cell Response In Vivo." Journal of Immunology 162, no. 8 (April 15, 1999): 4647–56. http://dx.doi.org/10.4049/jimmunol.162.8.4647.

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Abstract According to recent crystallographic studies, the TCR-αβ contacts MHC class I-bound antigenic peptides via the polymorphic V gene-encoded complementarity-determining region 1β (CDR1β) and the hypervariable (D)J-encoded CDR3β and CDR3α domains. To evaluate directly the relative importance of CDR1β polymorphism on the fine specificity of T cell responses in vivo, we have taken advantage of congenic Vβa and Vβb mouse strains that differ by a CDR1 polymorphism in the Vβ10 gene segment. The Vβ10-restricted CD8+ T cell response to a defined immunodominant epitope was dramatically reduced in Vβa compared with Vβb mice, as measured either by the expansion of Vβ10+ cells or by the binding of MHC-peptide tetramers. These data indicate that Vβ polymorphism has an important impact on TCR-ligand binding in vivo, presumably by modifying the affinity of CDR1β-peptide interactions.
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41

Slim, Rola, Florence Torremocha, Thierry Moreau, Anne Pizard, Steven C. Hunt, Albert Vuagnat, Gordon H. Williams, Francis Gauthier, Xavier Jeunemaitre, and François Alhenc-Gelas. "Loss-of-Function Polymorphism of the Human Kallikrein Gene with Reduced Urinary Kallikrein Activity." Journal of the American Society of Nephrology 13, no. 4 (April 2002): 968–76. http://dx.doi.org/10.1681/asn.v134968.

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ABSTRACT. Kallikrein is synthesized in the distal tubules and produces kinins, which are involved in the regulation of vascular tone in the kidney. Urinary kallikrein activity has been reported to be partly inherited and to be reduced in essential hypertension. In a systematic search for molecular variants of the human kallikrein gene, nine single-nucleotide polymorphisms were identified. Five of those polymorphisms, including two nonsynonymous substitutions in exon 3, i.e., Arg53His (allelic frequency in Caucasian subjects, 0.03) and Gln121Glu (allelic frequency, 0.33), were studied in a normotensive group and two independent hypertensive groups for which 24-h urinary kallikrein activity had been measured. A significant decrease in urinary kallikrein activity was observed for the subjects who were heterozygous for the Arg53His polymorphism, compared with the other subjects. This finding was consistent in the two hypertensive groups and was observed with several kallikrein enzymatic assays. The Gln121Glu polymorphism and the other polymorphisms were not associated with changes in urinary kallikrein activity. None of the polymorphisms was associated with hypertension. Recombinant kallikrein variants were synthesized and enzymatically characterized, using native kininogen and kininogen-derived synthetic peptide substrates. No important effect was observed after Gln121 mutation, but there was a major decrease in enzyme activity when Arg53 was replaced by histidine. A model of kallikrein derived from crystallographic data suggested that Arg53 can affect substrate binding. The identification of a subset of subjects with genetically reduced kallikrein activity as a result of an amino acid mutation could facilitate analysis of the role of the kallikrein-kinin system in renal and vascular diseases.
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42

Yoon, Youngkwan, Jin Young Koo, Jongwon Oh, Soyoung Kim, Hee Cheul Choi, and Seok Min Yoon. "Surface-guided polymorphism control of titanyl phthalocyanine single crystals." Inorganic Chemistry Frontiers 7, no. 11 (2020): 2178–87. http://dx.doi.org/10.1039/d0qi00228c.

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43

Ueda, Masafumi, and Yasuhiro Mazaki. "Synthesis and crystal structure of a sulphur-bridged molecular hoop consisting of 5,7,12,14-tetrathiapentacene." RSC Advances 12, no. 18 (2022): 10870–74. http://dx.doi.org/10.1039/d2ra00489e.

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5,7,12,14-Tetrathiapentacene (TC[2]TTP) was synthesized by an intramolecular Friedel–Crafts-type condensation, adopting a honeycomb structure with columnar stacking. X-ray crystallography revealed polymorphisms with organic solvents incorporated into its internal cavity.
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Spiteri, Lorella, Ulrich Baisch, and Liana Vella-Zarb. "Understanding Conformational Polymorphism in Ganciclovir: A Holistic Approach." Chemistry 3, no. 1 (January 26, 2021): 126–37. http://dx.doi.org/10.3390/chemistry3010010.

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We present a holistic crystallographic study of the antiviral ganciclovir, including insights into its solid-state behavior, which could prove useful during drug development, making the process more sustainable. A newly developed methodology was used incorporating a combination of statistical and thermodynamic approaches, which can be applied to various crystalline materials. We demonstrate how the chemical environment and orientation of a functional group can affect its accessibility for participation in hydrogen bonding. The difference in the nature and strength of intermolecular contacts between the two anhydrous forms, exposed through full interaction maps and Hirshfeld surfaces, leads to the manifestation of conformational polymorphism. Variations in the intramolecular geometry and intermolecular interactions of both forms of ganciclovir were identified as possible predictors for their relative thermodynamic stability. It was shown through energy frameworks how the extensive supramolecular network of contacts in form I causes a higher level of compactness and lower enthalpy relative to form II. The likelihood of the material to exhibit polymorphism was assessed through a hydrogen bond propensity model, which predicted a high probability associated with the formation of other relatively stable forms. However, this model failed to classify the stability of form I appropriately, suggesting that it might not have fully captured the collective impacts which govern polymorphic stability.
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45

Barnett, S. A., and D. R. Allan. "The high-pressure and low-temperature structural behaviour of 2,2,2-trifluoroethanol." CrystEngComm 21, no. 30 (2019): 4501–6. http://dx.doi.org/10.1039/c9ce00485h.

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46

Guzei, Ilia A., and Charmaine Arderne. "Polymorphism of dinitro[tris(2-aminoethyl)amine]cobalt(III) chloride." Acta Crystallographica Section C Structural Chemistry 71, no. 8 (July 15, 2015): 695–700. http://dx.doi.org/10.1107/s205322961501270x.

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Three polymorphs of bis(nitrito-κN)[tris(2-aminoethyl)amine-κ4N,N′,N′′,N′′′]cobalt(III) chloride, [Co(NO2)2(C6H18N4)]Cl, have been structurally characterized in the 100–300 K temperature range. Two orthorhombic polymorphs are related by a solid-state enantiotropic order–disorder k2 phase transition atca152 K. The third, monoclinic, polymorph crystallizes as a nonmerohedral twin. In the structure of the high-temperature (300 K) orthorhombic polymorph, the CoIIIcomplex cation resides on a crystallographic mirror plane, whereas the Cl−anion occupies a crystallographic twofold axis. In the unit cell of the monoclinic polymorph, the cationic CoIIIcomplex is in a general position, whose charge is balanced by two halves of two Cl−anions, each residing on a crystallographic twofold axis.
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47

Laughlin, Gary J. "Polymorphism and “Universal Seeding,” or Disappearing Polymorphs." Microscope 69, no. 4 (2022): ii. http://dx.doi.org/10.59082/zcbn1840.

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Any chemical compound showing polymorphism can crystallize with different internal lattices that will give correspondingly different external crystal morphologies, different optical crystallographic properties, and different physical properties. Ludwig and Adelheid Kofler and their successors in Innsbruck, Austria, along with Walter C. McCrone and his successors in the U.S., expounded the topic of polymorphism, especially as it was investigated with the polarized light microscope equipped with a hot stage.
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48

Kant, Rajni. "Pharmaceutical Drug Polymorphism: A Case Study of Three Novel Drugs." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C544. http://dx.doi.org/10.1107/s2053273314094558.

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Polymorphism is more widespread in pharmaceutical solids, with estimates of 30-50% in drug-like molecules, compared to 4-5% polymorphic crystals in the Cambridge Structural Database (Nangia, 2007). Most of the drug molecules are formulated and marketed in crystalline form and many of these are highly functionalized and can self-organize in several ways in the solid state with nearly the same lattice energies. Though a lot of work is going on in the field of pharmaceutical drug polymorphism and its possible application in the field of crystal engineering, yet there are difficulties in getting polymorphs of many important molecules. The present work deals with a comparative crystallographic study on the existing polymorphic forms of three medicinally important molecules, Aspirin, Paracetamol and Norfloxacin which are known to have a wide spectrum of medicinal activities. Broadly, the present study accounts for the following observations: (i) Choice of the solvent system, its purity and its reaction mechanism with solute under ideal condition of growth/crystallization. (ii) The interaction of grown material with X-rays should be very healthy in the sense that maximum number of planes in a given crystal should diffract the incoming X-ray beam. This aspect is once again related to quality single crystal growth. Fairly good interaction of a compound with X-rays leads to better refined structure, yielding a very high level of confidence between the chemical and computed structure. (iii) Analysis of a molecule's ability to exhibit biological activities by employing some suitable empirical and clinical modes. (iv) Most of physical properties of a grown material depend on how the molecules have been packed in the unit cell and how the derived knowledge of intra and intermolecular interactions is applied for engineering a crystal of choice.
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49

Borisov, S. V., S. A. Magarill, and N. V. Pervukhina. "Crystallographic Analysis of TiO2 Polymorphism (Brookite, Anatase, Rutile)." Journal of Structural Chemistry 60, no. 11 (November 2019): 1783–89. http://dx.doi.org/10.1134/s0022476619110118.

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50

Heimgert, Jaqueline, Florian Morsbach, Martin Kleinschmidt, and Guido J. Reiss. "Synthesis, Structural Characterization, Conformational and Topological Classification of Different Salts in the 2,2-Dimethylpropane-1,3-diamine/HCl/H2O-System." Solids 3, no. 3 (June 28, 2022): 385–96. http://dx.doi.org/10.3390/solids3030027.

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The reaction of 2,2-dimethylpropane-1,3-diamine (dmpn) with an excess of concentrated aqueous hydrochloric acid yielded colorless crystals of 2,2-dimethylpropane-1,3-diaminium dichloride, dmpnH2Cl2 (1), in addition to small amounts of a monohydrate, dmpnH2Cl2∙H2O (2). The compounds were studied via X-ray crystallography, IR and Raman spectroscopy, NMR spectroscopy and thermal analysis. Single crystal structure determinations on 1 and 2 showed that dmpnH2Cl2 exists in two polymorphic forms, 1a and 1b. The crystal structure of 1b showed to be much more complex than that of 1a. In the crystal structure of 2, four (dmpnH2)2+ cations and eight chloride anions form a cage constructed by N−H∙∙∙Cl hydrogen bonds. In the center of these cages water dimers with a O∙∙∙O distance of 2.776 (8) Å are present. In addition, a conformational analysis of the 2,2-dimethylpropane-1,3-diaminium cation was performed. The results are compared to the experimental findings of 1a, 1b, 2 and other related hydrogen bonded salt structures from the Cambridge crystallographic structure database (CCDC). Last, a topological classification of the solid-state structures of 1a and 2 was performed and the simplified topological networks are discussed.
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