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Journal articles on the topic 'Hydrogen bonding; Crystallography'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Malaspina, Lorraine A., Alessandro Genoni, Dylan Jayatilaka, et al. "The advanced treatment of hydrogen bonding in quantum crystallography." Journal of Applied Crystallography 54, no. 3 (2021): 718–29. http://dx.doi.org/10.1107/s1600576721001126.

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Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the t

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2

Alshahateet, Solhe F., Mohan M. Bhadbhade, Roger Bishop, and Marcia L. Scudder. "Different solvents yield alternative crystal forms through aromatic, halogen bonding and hydrogen bonding competition." CrystEngComm 17, no. 4 (2015): 877–88. http://dx.doi.org/10.1039/c4ce02109f.

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X-ray crystallography shows that entirely different structures are produced when the dichlorodiquinoline derivative is crystallised from aprotic dimethylformamide or from protic solvents like methanol or acetic acid, demonstrating the importance of solvent choice in yielding alternative crystal forms.

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3

Stevens, Joanna, Stephan Byard, Lauren Newton, et al. "Core level crystallography: Probing H-bonding through nitrogen XPS and NEXAFS." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C560. http://dx.doi.org/10.1107/s205327331409439x.

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Determining the location of hydrogen is not always straightforward, despite its potential for wide-reaching effects, such as altering physicochemical properties and biological/chemical processes. Proton transfer can be considered a simple chemical reaction, with a continuum from neutral to protonated states, and short, strong H-bonds (SSHB) and disordered systems between the two extremes. X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) intrinsically probe the local environment, with sensitivity to the chemical state of the atom and, importantly, na

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4

Gudkovskikh, Sergey V., and Mikhail V. Kirov. "Topological crystallography of gas hydrates." Acta Crystallographica Section A Foundations and Advances 71, no. 4 (2015): 444–50. http://dx.doi.org/10.1107/s2053273315008864.

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A new approach to the investigation of the proton-disordered structure of clathrate hydrates is presented. This approach is based on topological crystallography. The quotient graphs were built for the unit cells of the cubic structure I and the hexagonal structure H. This is a very convenient way to represent the topology of a hydrogen-bonding network under periodic boundary conditions. The exact proton configuration statistics for the unit cells of structure I and structure H were obtained using the quotient graphs. In addition, the statistical analysis of the proton transfer along hydrogen-b

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5

Emami, Marzieh, Katarzyna Anna Ślepokura, Monika Trzebiatowska, Nader Noshiranzadeh, and Vasyl Kinzhybalo. "Oxyanion clusters with antielectrostatic hydrogen bonding (AEHB) in tetraalkylammonium hypodiphosphates." CrystEngComm 20, no. 35 (2018): 5209–19. http://dx.doi.org/10.1039/c8ce00880a.

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6

Singh, Praveen, Ranjeet Kumar, and Ashish Kumar Tewari. "Hydrogen bonding framework in imidazole derivatives: Crystal structure and Hirshfeld surface analysis." European Journal of Chemistry 11, no. 1 (2020): 50–59. http://dx.doi.org/10.5155/eurjchem.11.1.50-59.1945.

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A series of imidazole derivatives (1-3) were synthesized with three component reaction among benzil, ammonium acetate and formaldehyde/aromatic aldehyde at 110 °C without a catalyst and solvent. These synthesized imidazole derivatives have shown intermolecular hydrogen bonding such as N-H···N and O-H···N. The imidazole 1 and 2 exhibited N-H···N intermolecular hydrogen bonding while imidazole 3 exhibited O-H···N intermolecular hydrogen bonding. The hydrogen bonds in imidazoles were studied by X-ray crystallography and Hirshfeld Surface Analysis at dnorm surface which show the visible red spots,

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7

Minezaki, Y., and N. Niimura. "Hydrogen bonding study of HEW-lysozyme by neutron protein crystallography." Seibutsu Butsuri 39, supplement (1999): S111. http://dx.doi.org/10.2142/biophys.39.s111_2.

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8

Kerr, Hannah E., Lorna K. Softley, Kuthuru Suresh, Paul Hodgkinson, and Ivana Radosavljevic Evans. "Structure and physicochemical characterization of a naproxen–picolinamide cocrystal." Acta Crystallographica Section C Structural Chemistry 73, no. 3 (2017): 168–75. http://dx.doi.org/10.1107/s2053229616011980.

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Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-methoxynaphthalen-2-yl)propanoic acid–pyridine-2-carboxamide (1/1), C14H14O3·C6H6N2O]. The pharmaceutically rele

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9

Moon, Dohyun, and Jong-Ha Choi. "Crystal structure of 1,4,8,11-tetramethyl-1,4,8,11-tetraazoniacyclotetradecane bis[chloridochromate(VI)] dichloride from synchrotron X-ray data." Acta Crystallographica Section E Crystallographic Communications 76, no. 4 (2020): 523–26. http://dx.doi.org/10.1107/s2056989020003059.

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The crystal structure of title compound, (C14H36N4)[CrO3Cl]2Cl2, has been determined by synchrotron radiation X-ray crystallography at 220 K. The macrocyclic cation lies across a crystallographic inversion center and hence the asymmetric unit contains one half of the organic cation, one chlorochromate anion and one chloride anion. Both the Cl− anion and chlorochromate Cl atom are involved in hydrogen bonding. In the crystal, hydrogen bonds involving the 1,4,8,11-tetramethyl-1,4,8,11-tetraazoniacyclotetradecane (TMC) N—H groups and C—H groups as donor groups and three O atoms of the chlorochrom

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10

Coates, Leighton. "A crystallographic study of the Toho-1 β-lactamase acylation mechanism". Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1207. http://dx.doi.org/10.1107/s2053273314087920.

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β-lactam antibiotics have been used effectively over several decades against many types of highly virulent bacteria. The predominant cause of resistance to these antibiotics in Gram-negative bacterial pathogens is the production of serine β-lactamase enzymes. A key aspect of the class A serine β-lactamase mechanism that remains unresolved and controversial is the identity of the residue acting as the catalytic base during the acylation reaction. Multiple mechanisms have been proposed for the formation of the acyl-enzyme intermediate that are predicated on understanding the protonation states a

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11

Pandurangan, Komala, Jonathan A. Kitchen, Salvador Blasco, Francesca Paradisi, and Thorfinnur Gunnlaugsson. "Supramolecular pyridyl urea gels as soft matter with antibacterial properties against MRSA and/or E. coli." Chem. Commun. 50, no. 74 (2014): 10819–22. http://dx.doi.org/10.1039/c4cc04028g.

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The development of a family of twelve aryl pyridyl ureas, their crystallography and the ability of a number of these to form hydrogen bonding supramolecular gels with antimicrobial properties are described.

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12

Golden, Emily A., and Alice Vrielink. "Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function." Australian Journal of Chemistry 67, no. 12 (2014): 1751. http://dx.doi.org/10.1071/ch14337.

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Neutron crystallography allows direct localization of hydrogen positions in biological macromolecules. Within enzymes, hydrogen atoms play a pivotal role in catalysis. Recent advances in instrumentation and sample preparation have helped to overcome the difficulties of performing neutron diffraction experiments on protein crystals. The application of neutron macromolecular crystallography to a growing number of proteins has yielded novel structural insights. The ability to accurately position water molecules, hydronium ions, and hydrogen atoms within protein structures has helped in the study

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13

Logan, Derek T. "Hunting down hydrogen: applying neutron macromolecular crystallography to galectins." Biochemist 41, no. 2 (2019): 20–23. http://dx.doi.org/10.1042/bio04102020.

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Galectins are a medically important family of small, soluble carbohydrate-binding proteins that have been implicated in a wide variety of diseases, and are therefore targets for the development of new drugs. Many X-ray crystal structures of small molecules in complex with galectins have been determined and have given invaluable information on how natural ligands and synthetic inhibitors are recognized. However, until now the hydrogen-bonding patterns involved in ligand recognition have been a matter of informed guesswork, as X-ray crystallography can't reliably tell us where hydrogen atoms are

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14

GUPTA, PALVI, and KAMNI. "BIOLOGICAL ACTIVITY PREDICTIONS AND HYDROGEN BONDING ANALYSIS IN QUINOLINES." International Journal of Modern Physics: Conference Series 22 (January 2013): 603–11. http://dx.doi.org/10.1142/s2010194513010738.

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The paper has been designed to make a comprehensive review of a particular series of organic molecular assembly in the form of compendium. An overview of general description of fifteen quinoline derivatives has been given. The biological activity spectra of quinoline derivatives have been correlated on structure activity relationships base which provides the different Pa (possibility of activity) and Pi (possibility of inactivity) values. Expositions of the role of intermolecular interactions in the identified derivatives have been discussed with the standard distance and angle cut-off criteri

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15

Rajni Kant, V. "Crystallography of steroids: a comparative analysis of geometrical features and hydrogen bonding." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C381. http://dx.doi.org/10.1107/s0108767308087837.

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16

Jackson, TW, M. Kojima, and RM Lambrecht. "Preparation of Rhenium Diamino Dithiolate Complexes. The X-Ray Crystal Structure of Oxo(1,1,8,8-tetraethyl-3,6-diazaoctane-1,8-dithiolato)rhenium." Australian Journal of Chemistry 46, no. 7 (1993): 1093. http://dx.doi.org/10.1071/ch9931093.

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The complexes oxo (1,1,8,8-tetraethyl-3,6-diazaoctane-1,8-dithiolato)rhenium[ ReO ( tedadt )], oxo (1,1,8,8-tetraethyl-4,4-dimethyl-3,6-diazaoctane-1,8-dithiolato)rhenium [ ReO ( tedmdadt )] and (1,1,4,4,8,8-hexamethyl-3,6-diazaoctane-1,8-dithiolato) oxorhenium [ ReO ( hmdadt )] were prepared. The crystal structure of the complex ReO ( tedadt ) was determined by X-ray crystallography to be a hydrogen-bonded dimer . This is the first example of intermolecular hydrogen bonding in rhenium diamino dithiolate ( dadt ) complexes.

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17

Hardin, Ellington, Nguyen, et al. "A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors." Inorganics 7, no. 10 (2019): 119. http://dx.doi.org/10.3390/inorganics7100119.

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Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray

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18

Smith, Graham, Urs D. Wermuth, Peter C. Healy, and Jonathan M. White. "Molecular Recognition in Proton-Transfer Compounds of Brucine with Achiral Substituted Salicylic Acid Analogues." Australian Journal of Chemistry 59, no. 5 (2006): 320. http://dx.doi.org/10.1071/ch06074.

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The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have t

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19

Stevens, Joanna, Stephen Byard, Colin Seaton, Ghazala Sadiq, Roger Davey, and Sven Schroeder. "H-bonds and Protons in Molecular Crystals: Insight from Combined XPS/ssNMR/XRD." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C531. http://dx.doi.org/10.1107/s2053273314094686.

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Physicochemical properties of molecular crystals are significantly influenced by non-covalent interactions and proton transfer. A well known application is the tuning of solubility, bioavailability and stability of pharmaceutical actives through co-crystal (hydrogen-bonding) or salt (ionic, Brønsted acceptors) formation. X-ray Photoelectron Spectroscopy (XPS) is an intrinsically local structural probe, providing information on the chemical state and chemical environment of atoms in molecules and crystals through the photoemission of core level electrons. We have recently studied a wide range o

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20

Wang, Bei, Ai-Quan Jia, Hong-Mei Yang, Jing-Long Liu, and Qian-Feng Zhang. "Encapsulation of ferrocenes by hydrogen-bonded pyrogallol[4]arene dimers." Zeitschrift für Naturforschung B 73, no. 8 (2018): 597–600. http://dx.doi.org/10.1515/znb-2018-0083.

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AbstractThe treatment of C-iso-butylpyrogallarene (PgC4) or C-ethylpyrogallarene (PgC2) with ferrocene (FcH) in a 2:1 molar ratio under different reaction conditions afforded the host–guest compounds FcH@(PgC4)2·CH3OH·3H2O (1) and FcH@(PgC2)2·3EtOH·2H2O (2), respectively. Complexes 1 and 2 are both pyrogallarene dimers providing capsule-type voids. Single crystal X-ray crystallography was used to investigate the role of hydrogen bonding networks in the assembly of the two host–guest systems.

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21

Marks, Laurence. "Competitive Chloride Chemisorption Disrupts Hydrogen Bonding Networks: DFT, Crystallography, Thermodynamics, and Morphological Consequences." Corrosion 74, no. 3 (2017): 295–311. http://dx.doi.org/10.5006/2555.

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The consequence for aqueous corrosion of chloride ions in an aqueous environment on the surface structure and thermodynamics of hydroxylated magnesia (001) and alpha-alumina (001) and (100) is analyzed using density functional methods. It is shown that there is competitive chemisorption between hydroxide and chloride, with the chloride disrupting the hydrogen bonding network on the surface. There is a significant crystallographic dependence, as well as dependencies upon the environment in terms of the pH and chloride molarity. An analysis of the results in terms of existing, competing models i

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22

Chen, Julian C. H., B. Leif Hanson, S. Zoë Fisher, Paul Langan, and Andrey Y. Kovalevsky. "Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography." Proceedings of the National Academy of Sciences 109, no. 38 (2012): 15301–6. http://dx.doi.org/10.1073/pnas.1208341109.

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The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be r

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23

Chen, Julian C. H., and Clifford J. Unkefer. "Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography." IUCrJ 4, no. 1 (2017): 72–86. http://dx.doi.org/10.1107/s205225251601664x.

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The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge Nati

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24

Büchler, Jochen, Cacilia Maichle-Mössmer, and Karl-Artur Kovar. "Enantioselektive Gewinnung und Kristallstruktur des Ecstasy-Analogons N-Ethyl-3,4-methylendioxyamphetamin-HCl (MDE) und seiner beiden Hauptmetaboliten MDA und HME / Enantioselective Production and Crystal Structure of the Ecstasy Analogue N-Ethyl-3,4- methylenedioxyamphetamine-HCl (MDE) and its Major Metabolites MDA and HME." Zeitschrift für Naturforschung B 55, no. 12 (2000): 1124–30. http://dx.doi.org/10.1515/znb-2000-1204.

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A synthetic route to the production of the pure enantiomers of the ecstasy-analogue N-Ethyl- 3,4-methylenedioxyamphetamine (MDE) and its major metabolites MDA and HME is presented. The crystal and molecular structure of these compounds has been determined by X-ray crystallography. The hydrogen bonding in the crystal lattice is examined and significant differences were found by comparing (R)- and (S)-MDA-HCl.

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25

Laliberté, Dominic, Thierry Maris, and James D. Wuest. "Molecular tectonics Use of urethanes and ureas derived from tetraphenylmethane and tetraphenylsilane to build porous chiral hydrogen-bonded networks." Canadian Journal of Chemistry 82, no. 2 (2004): 386–98. http://dx.doi.org/10.1139/v03-208.

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Tetraphenylmethane, tetraphenylsilane, and simple derivatives with substituents that do not engage in hydrogen bonding typically crystallize as close-packed structures with essentially no space available for the inclusion of guests. In contrast, derivatives with hydrogen-bonding groups are known to favor the formation of open networks that include significant amounts of guests. To explore this phenomenon, we synthesized six new derivatives 5a5e and 6a of tetraphenylmethane and tetraphenylsilane with urethane and urea groups at the para positions, crystallized the compounds, and determined the

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26

Dong, Ming-Ming, Deng-Yong Zhu, Yan Zhao, Xiao-Yuan Li, and Shuang-Quan Zang. "A Two-fold Interpenetrated Diamondlike 3D Metal-Organic Cd(II) Complex Based on 5-Iodo-isophthalic Acid and 1,3-Bi(4-pyridyl)propane." Zeitschrift für Naturforschung B 67, no. 5 (2012): 499–503. http://dx.doi.org/10.5560/znb.2012-0065.

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A metal-organic framework based on 5-iodo-isophthalic acid (5-iipaH2) and the ancillary nitrogen ligand 1,3-bi(4- pyridyl)propane (bpp), namely [Cd(5-iipa)(bpp)(H2O)]n (1), has been synthesized, and characterized by IR spectroscopy, elemental analysis, thermogravimetry, and X-ray crystallography. Complex 1shows a two-fold interpenetrating 3D diamond-like architecture that is stabilized by hydrogen bonding, μ...μ, I...μ, and C-H...p interactions.

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27

Dzambaski, Zdravko, Milovan Stojanovic, Marija Baranac-Stojanovic, Dragica Minic, and Rade Markovic. "Thermal solid-state Z/E isomerization of 2-alkylidene-4-oxothiazolidines: Effects of non-covalent interactions." Journal of the Serbian Chemical Society 76, no. 3 (2011): 317–28. http://dx.doi.org/10.2298/jsc100607038d.

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Configurational isomerization of stereo-defined 5-substituted and unsubstituted 2-alkylidene-4-oxothiazolidines 1 in the solid state, giving the Z/E mixtures in various ratios, was investigated by 1H-NMR spectroscopy, X-ray powder crystallography and differential scanning calorimetry (DSC). The Z/E composition can be rationalized in terms of non-covalent interactions, involving intermolecular and intramolecular hydrogen bonding and directional non-bonded 1,5-type S...O interactions. X-Ray powder crystallography, using selected crystalline (Z)-4- oxothiazolidine substrates, revealed transformat

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28

Curry, Kenneth, Hugh McLennan, Steven J. Rettig, and James Trotter. "The synthesis and X-ray structures of the geometric isomers of 1-amino-1,2-cyclopentanedicarboxylic acid." Canadian Journal of Chemistry 71, no. 1 (1993): 76–83. http://dx.doi.org/10.1139/v93-011.

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The geometric isomers of 1-amino-1,2-cyclopentanedicarboxylic acid were isolated as the hydrolysis products of 2-cyclopentanecarboxylic acid-5,5′-hydantoin. The hydantoin ester was formed from ethyl -2-oxocyclopentanecarboxylate via a Bucherer–Bergs reaction. Hydrolysis of the hydantoin at elevated temperatures gave a mixture of trans- and cis-1 -amino-1,2-cyclopentanedicarboxylic acids indicating epimerization during hydrolysis. The trans product has not been described previously and the cis not extensively characterized. X-ray crystallography reveals that both isomers are zwitterionic in the

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29

McArdle, Patrick. "Oscail, a program package for small-molecule single-crystal crystallography with crystal morphology prediction and molecular modelling." Journal of Applied Crystallography 50, no. 1 (2017): 320–26. http://dx.doi.org/10.1107/s1600576716018446.

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Oscail is a program for small-molecule crystallography which includes crystal morphology prediction and an interface to molecular modelling. The Oscail graphical user interface can drive SHELX and Superflip for structure solution and SHELXL for structure refinement. The lattice analysis includes hydrogen bonding, halogen bonding and van der Waals contact stacking. Other facilities include interactive bar charts of space-group frequencies in the Cambridge Structural Database, powder diffraction pattern calculation and reduced cell cluster analysis of structures. The graphics output includes the

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30

Lai, Chih-Hsuan, Co-Chih Chang, Huai-Chia Chuang, Tse-Hua Tan, and Ping-Chiang Lyu. "Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases." International Journal of Molecular Sciences 21, no. 20 (2020): 7515. http://dx.doi.org/10.3390/ijms21207515.

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Cysteine-based protein tyrosine phosphatases (Cys-based PTPs) perform dephosphorylation to regulate signaling pathways in cellular responses. The hydrogen bonding network in their active site plays an important conformational role and supports the phosphatase activity. Nearly half of dual-specificity phosphatases (DUSPs) use three conserved residues, including aspartate in the D-loop, serine in the P-loop, and asparagine in the N-loop, to form the hydrogen bonding network, the D-, P-, N-triloop interaction (DPN–triloop interaction). In this study, DUSP22 is used to investigate the importance o

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31

Chen, Julian, Bryant Hanson, S. Fisher, et al. "Ultra-high resolution neutron and X-ray crystallography: structure of crambin." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1206. http://dx.doi.org/10.1107/s2053273314087932.

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Neutron diffraction data to 1.1 Å was collected on a crystal of the small protein crambin at the Protein Crystallography Station (PCS) at Los Alamos, the highest resolution neutron structure of a protein to date, and a technical benchmark for the instrument. 95 % of the hydrogen atoms in the protein structure were resolved. The data allowed for the refinement of anisotropic temperature factors for selected deuterium atoms within the protein. Hydrogen bonding networks ambiguous in room temperature, ultra-high resolution (0.84 Å) electron density maps are clarified in the nuclear density maps. T

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32

Smith, Graham, Colin H. L. Kennard, and Karl A. Byriel. "The Preparation and Crystal Structures of a Series of Urea Adducts: with Fumaric Acid (2 : 1), with Itaconic Acid (1 : 1) and with Cyanuric Acid (1 : 1)." Australian Journal of Chemistry 50, no. 10 (1997): 1021. http://dx.doi.org/10.1071/c97123.

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The adducts of a series of compounds with urea (ur) have been prepared and their crystal structures determined by X-ray crystallography. These are the adducts with the unsaturated aliphatic acids fumaric acid [(fumaric acid)(ur)2] (1) and itaconic acid [(itaconic acid)(ur)] (2), and with cyanuric acid [(cyanuric acid)(ur)] (3). All structures have extensive hydrogen-bonding systems in which most of the urea donor and acceptor sites are involved.

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Smith, Graham, Katherine E. Baldry, Colin H. L. Kennard, and Karl A. Byriel. "The Preparation and Crystal Structure of the 1 : 1 Adduct of Glycine with Urea." Australian Journal of Chemistry 50, no. 7 (1997): 737. http://dx.doi.org/10.1071/c96205.

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The 1 : 1 adduct of the a-amino acid glycine with urea has been prepared and its crystal structure determined by X-ray crystallography and refined to a residual R 0·028 for 776 observed reflections. Crystals are monoclinic, pace group P21 with two molecules in a cell of dimensions a 7·364(1), b 4·8703(2), c 8·494(1) Å, β 98·555(7)°. The polymeric structure is based on a primary cyclic hydrogen-bonded nine-membered ring involving both the carboxyl oxygen and an amino hydrogen of the zwitterionic glycine molecule with the urea amine hydrogen and oxygen respectively. These repeat down the twofold

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34

Caldararu, Octav, Francesco Manzoni, Esko Oksanen, Derek T. Logan, and Ulf Ryde. "Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data." Acta Crystallographica Section D Structural Biology 75, no. 4 (2019): 368–80. http://dx.doi.org/10.1107/s205979831900175x.

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Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calcul

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35

Smith, Graham, Raymond C. Bott, A. David Rae, and Anthony C. Willis. "The Modulated Crystal Structure of the Molecular Adduct of 2,4,6-Trinitrobenzoic Acid with 2,6-Diaminopyridine." Australian Journal of Chemistry 53, no. 6 (2000): 531. http://dx.doi.org/10.1071/ch00072.

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The 1 : 1 adduct of 2,4,6-trinitrobenzoic acid (tnba) with 2,6-diaminopyridine (2,6-dap), [(2,6-dap)+(tnba)-], has been prepared and the low-temperature crystal structure has been determined by X-ray crystallography. A modulated structure has been identified and refined by using a stacking fault model that requires reflection data to be put on three scales depending on an index condition. Crystals are triclinic, space group P1–, with Z 8 in a cell of dimensions a 13.538(3), b 14.516(4), c 16.480(4) Å; α 97.17(2), β 105.69(2), γ 106.09(2)˚. The structure involves proton transfer from the tnba m

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36

Vinken, Esther, Ann E. Terry, Anne B. Spoelstra, Cor E. Koning, and Sanjay Rastogi. "Influence of Superheated Water on the Hydrogen Bonding and Crystallography of Piperazine-Based (Co)polyamides." Langmuir 25, no. 9 (2009): 5294–303. http://dx.doi.org/10.1021/la804046r.

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37

Ogawa, Yu, Philip-Kunio Naito, and Yoshiharu Nishiyama. "Hydrogen-bonding network in anhydrous chitosan from neutron crystallography and periodic density functional theory calculations." Carbohydrate Polymers 207 (March 2019): 211–17. http://dx.doi.org/10.1016/j.carbpol.2018.11.042.

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38

Grosu, Ioana Georgeta, Xenia Filip, Maria O. Miclăuș, and Claudiu Filip. "Hydrogen-Mediated Noncovalent Interactions in Solids: What Can NMR Crystallography Tell About?" Molecules 25, no. 16 (2020): 3757. http://dx.doi.org/10.3390/molecules25163757.

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Hydrogen atoms play a crucial role in the aggregation of organic (bio)molecules through diverse number of noncovalent interactions that they mediate, such as electrostatic in proton transfer systems, hydrogen bonding, and CH–π interactions, to mention only the most prominent. To identify and adequately describe such low-energy interactions, increasingly sensitive methods have been developed over time, among which quantum chemical computations have witnessed impressive advances in recent years. For reaching the present state-of-the-art, computations had to rely on a pool of relevant experimenta

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39

Gholivand, Khodayar, and Hamid Reza Mahzouni. "Solid-state and gas-phase structures of two conformers of N-(4-methylphenyl)-N′,N′′-bis(morpholinyl) phosphoric triamide; insights from X-ray crystallography and DFT calculations." Acta Crystallographica Section B Structural Science 67, no. 3 (2011): 238–43. http://dx.doi.org/10.1107/s0108768111010470.

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A phosphoric triamide with the formula (4-CH3—C6H4NH)P(O)(NC4H8O)2 has been synthesized and characterized. X-ray crystallography at 120 K reveals that the title compound is composed of two symmetrically independent molecules in the solid state. Density functional theory (DFT) calculations reveal that two conformers A and B are very close to each other from an energy point of view. Thus there is equal chance that the presence of two conformers in the lattice may lead to hydrogen-bonded chains with an ABABAB arrangement. Hydrogen bonds of the type OP...H—N (OP being the phosphoryl O atom) are es

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40

Seidel, Rüdiger W., Nils Nöthling, Richard Goddard, and Christian W. Lehmann. "Structural Elucidation of Enantiopure and Racemic 2-Bromo-3-Methylbutyric Acid." Chemistry 2, no. 3 (2020): 691–99. http://dx.doi.org/10.3390/chemistry2030044.

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Halogenated carboxylic acids have been important compounds in chemical synthesis and indispensable research tools in biochemical studies for decades. Nevertheless, the number of structurally characterized simple α-brominated monocarboxylic acids is still limited. We herein report the crystallization and structural elucidation of (R)- and rac-2-bromo-3-methylbutyric acid (2-bromo-3-methylbutanoic acid, 1) to shed light on intermolecular interactions, in particular hydrogen bonding motifs, packing modes and preferred conformations in the solid-state. The crystal structures of (R)- and rac-1 are

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41

Sofetis, Andreas, Giannis S. Papaefstathiou, Aris Terzis, Catherine P. Raptopoulou, and Theodoros F. Zafiropoulos. "Preparation, Crystal Structure and Spectroscopic Characterization of [Ga(OH)(SO4)(terpy)(H2O)] · H2O (terpy=2,2’:6’,2-Terpyridine): The First Characterized Gallium(III) Sulfato Complex." Zeitschrift für Naturforschung B 59, no. 3 (2004): 291–97. http://dx.doi.org/10.1515/znb-2004-0310.

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The reaction of Ga2(SO4)3·18H2O and excess 2,2′:6′,2″-terpyridine (terpy) in MeOH / H2O leads to [Ga(OH)(SO4)(terpy)(H2O)]·H2O (1·H2O] in good yield. The structure of the complex has been determined by single-crystal X-ray crystallography. The GaIII atom in 1·H2O is 6-coordinate and ligation is provided by one terdentate terpy molecule, one monodentate sulfate, one terminal hydroxide and one terminal H2O molecule; the coodination polyhedron about the metal is described as a distorted octahedron. There is an extensive hydrogen-bonding network in the crystal structure which generates corrugated

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42

Kruszynski, Rafal. "Intermolecular interactions in 2,4-dinitrophenylhydrazine hydrochloride hydrate: X-ray structural and quantum mechanical study." Open Chemistry 6, no. 4 (2008): 542–48. http://dx.doi.org/10.2478/s11532-008-0067-7.

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Abstract2,4-dinitrophenylhydrazine hydrochloride hydrate (I) was determined by X-ray crystallography, and the intermolecular interaction energies were calculated in terms of Natural Bond Orbital analysis. The asymmetric unit of (I) consists of a dinitrophenylhydrazinium cation, a chloride anion and a water molecule. The interatomic distances and angles in (I) show no unusual values. In the structure there are intermolecular N—H⊎⊎⊎O, N—H⊎⊎⊎Cl, O—H⊎⊎⊎Cl, C—H⊎⊎⊎O hydrogen bonds with bonding energy ranging form 16.03 to 0.76 kcal mol−1. These hydrogen bonds create the following N1 motifs: 6D, S(5)

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43

Czernek, Jiří, and Jiří Brus. "Polymorphic Forms of Valinomycin Investigated by NMR Crystallography." International Journal of Molecular Sciences 21, no. 14 (2020): 4907. http://dx.doi.org/10.3390/ijms21144907.

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A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a confor

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Schrader, Tobias, Andreas Ostermann, Michael Monkenbusch, et al. "BioDiff - a neutron diffractometer for protein crystallography." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1215. http://dx.doi.org/10.1107/s2053273314087841.

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The research reactor Heinz Maier-Leibnitz (FRM II) is a modern high flux neutron source which feeds some 30 state of the art neutron beam instruments. Currently 24 are operational, others in commissioning or under construction. The newly built neutron single crystal diffractometer BIODIFF is especially designed to collect data from crystals with large unit cells. The main field of application is the structural analysis of proteins, especially the determination of hydrogen atom positions. BIODIFF is a joint project of the Jülich Centre for Neutron Science (JCNS) and the FRM II. Typical scientif

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Xu, Ya-Ping, Wen-Tong Chen, Cai Yi, Jian-Gen Huang, Ding-Wa Zhang, and Yin-Feng Wang. "A Novel Manganese Complex with Mixed Ligands: Preparation, Structure, Photoluminescent and Semiconductive Properties." Journal of Chemical Research 42, no. 3 (2018): 148–52. http://dx.doi.org/10.3184/174751918x15212927064594.

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A manganese complex with mixed ligands, [Mn(2,2′-biim)2(4,4′-bipy)] n[Mn(2,2′-biim)3]2 n6 n(ClO4)•8 nH2O (2,2′-biim = 2,2′-biimidazole; 4,4′-bipy = 4,4′-bipyridine), has been obtained by a hydrothermal procedure and its structure determined by single-crystal X-ray crystallography. A two-dimensional (2-D) supramolecular layer is established through hydrogen-bonding interactions. Solid-state photoluminescence measurement reveals that this complex shows a blue light emission. Solid-state diffuse reflectance determination uncovers the presence of a narrow optical band gap of 2.18 eV in this comple

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46

Wong, MG, JM Gulbis, MF Mackay, DJ Craik, and PR Andrews. "Anisatin: a Crystallographic, N.M.R. and Theoretical Conformation Study." Australian Journal of Chemistry 41, no. 7 (1988): 1071. http://dx.doi.org/10.1071/ch9881071.

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The convulsant compound anisatin has been studied by 1H n.m.r ., and X- ray crystallography, to establish its molecular geometry. The n.m.r . measurements included an analysis of proton-proton vicinal coupling constants and saturation transfer experiments which monitored exchange of the hydroxy groups of anisatin. The former analysis was used to obtain a solution conformation via the Karplus equation while the latter experiments yield information on intramolecular hydrogen bonding. The experimental geometry is compared to that obtained by several theoretical methods, including MINDO/3, MNDO, A

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Albino, Marjorie, Monique Body, Christophe Legein, et al. "NMR Crystallography, Hydrogen Bonding and Optical Properties of the Novel 2D Hybrid Oxyfluorotitanate [H2taz]2·(Ti5O5F12)." Crystal Growth & Design 18, no. 11 (2018): 6873–84. http://dx.doi.org/10.1021/acs.cgd.8b01085.

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48

Filip, Xenia, Ioana-Georgeta Grosu, Maria Miclăuş, and Claudiu Filip. "NMR crystallography methods to probe complex hydrogen bonding networks: application to structure elucidation of anhydrous quercetin." CrystEngComm 15, no. 20 (2013): 4131. http://dx.doi.org/10.1039/c3ce40299a.

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Tanski, Joseph. "Integrating Chemical Crystallography into Advanced Undergraduate Laboratories." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1382. http://dx.doi.org/10.1107/s2053273314086173.

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As scientific educators, it is important to mentor students in using state-of-the-art instrumentation and in the communication of new knowledge. Just as chemical crystallography and complimentary spectroscopic techniques such as NMR can be fast, effective tools to experimentally determine the structure of molecules and enhance students learning of molecular structure, they can also provide an inspiring opportunity for students to write short, scientific journal style reports that can be edited and published in collaboration with a mentor. This contribution will focus on incorporating X-ray cry

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Huang, Lin, Jia Wang, Andrew M. Watkins, Rhiju Das, and David M. J. Lilley. "Structure and ligand binding of the glutamine-II riboswitch." Nucleic Acids Research 47, no. 14 (2019): 7666–75. http://dx.doi.org/10.1093/nar/gkz539.

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Abstract We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, expl

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