Статті в журналах: "Hydrogen Bond Length"

1

Ferraris, G., and G. Ivaldi. "Bond valence vs bond length in O...O hydrogen bonds." Acta Crystallographica Section B Structural Science 44, no. 4 (August 1, 1988): 341–44. http://dx.doi.org/10.1107/s0108768188001648.

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2

Chandler, Graham S., Magdalena Wajrak, and R. Nazim Khan. "Neutron diffraction structures of water in crystalline hydrates of metal salts." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 71, no. 3 (May 26, 2015): 275–84. http://dx.doi.org/10.1107/s2052520615005387.

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Neutron diffraction structures of water molecules in crystalline hydrates of metal salts have been collected from the literature up to December 2011. Statistical methods were used to investigate the influence on the water structures of the position and nature of hydrogen bond acceptors and cations coordinated to the water oxygen. For statistical modelling the data were pruned so that only structures with oxygen as hydrogen acceptors, single hydrogen bonds, and no more than two metals or hydrogens coordinated to the water oxygen were included. Multiple linear regression models were fitted with the water OH bond length and bond angle as response variables. Other variables describing the position and nature of the acceptors and ions coordinated to the waters were taken as explanatory variables. These variables were sufficient to give good models for the bond lengths and angles. There were sufficient structures involving coordinated Mg^{2+} or Cu^{2+} for a separate statistical modelling to be done for these cases.

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3

ZHANG, FANGFANG, and DONGFENG XUE. "CHEMICAL BONDING BEHAVIORS OF N—H⋯O HYDROGEN BONDS OF ${\rm{NH}}_4^ + \cdots {\rm{O}}$ SYSTEMS IN INORGANIC CRYSTALS." Modern Physics Letters B 23, no. 31n32 (December 30, 2009): 3943–50. http://dx.doi.org/10.1142/s0217984909022046.

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The original length d0 of N — H and H ⋯ O bonds in various inorganic [Formula: see text] systems was comprehensively studied from a chemical bond viewpoint. Two linear relationships between d0 and the average bond lengths of each [Formula: see text] system, d0, N - H , versus [Formula: see text] and d0, H ⋯ O versus [Formula: see text] were respectively established. It is indicated that d0 is affected by the crystalline environment evidently, therefore, the valence electron distribution of hydrogen atom which depends on the lengthening degree of the original bond length is strongly affected by the chemical environment of hydrogen atoms. The obtained valence electron distributions of hydrogen are in a good agreement with the bond valence sum rule, and their overall applicability to ammonium ion interactions was discussed.

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4

Корабельников, Д. В., та Ю. Н. Журавлев. "Структура и колебательные свойства гидратов оксианионных кристаллов из первых принципов". Физика твердого тела 60, № 10 (2018): 2014. http://dx.doi.org/10.21883/ftt.2018.10.46533.072.

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AbstractStructural parameters and IR spectra of hydrates of lithium and sodium perchlorates, calcium sulfate hydrate (gypsum), and lithium nitrate hydrate are calculated ab initio using the density functional theory. The bond lengths in the water molecules are established as functions of length and energy of hydrogen bonds. The relationship between lengths of intra-anionic and hydrogen bonds is considered. The splitting of intramolecular vibrations of water is highlighted. The stretching vibration frequency of water is determined as a function of length and energy of hydrogen bonds. The combined (mixed) vibrations of anions and molecules of water with frequencies below 1400 cm^–1 are feasible as well.

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5

Olesen, Solveig Gaarn, and Steen Hammerum. "Redshift or Adduct Stabilization—A Computational Study of Hydrogen Bonding in Adducts of Protonated Carboxylic Acids." European Journal of Mass Spectrometry 15, no. 2 (April 2009): 239–48. http://dx.doi.org/10.1255/ejms.970.

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It is generally expected that the hydrogen bond strength in a D–H•••A adduct is predicted by the difference between the proton affinities (Δ PA) of D and A, measured by the adduct stabilization, and demonstrated by the infrared (IR) redshift of the D–H bond stretching vibrational frequency. These criteria do not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The Δ PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength.

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6

Stenfors, Brock A., Richard J. Staples, Shannon M. Biros, and Felix N. Ngassa. "Crystal structure of 1-[(4-methylbenzene)sulfonyl]pyrrolidine." Acta Crystallographica Section E Crystallographic Communications 76, no. 3 (February 28, 2020): 452–55. http://dx.doi.org/10.1107/s205698902000208x.

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The molecular structure of the title compound, C11H15NO2S, features a sulfonamide group with S=O bond lengths of 1.4357 (16) and 1.4349 (16) Å, an S—N bond length of 1.625 (2) Å, and an S—C bond length of 1.770 (2) Å. When viewing the molecule down the S—N bond, both N—C bonds of the pyrrolidine ring are oriented gauche to the S—C bond with torsion angles of −65.6 (2)° and 76.2 (2)°. The crystal structure features both intra- and intermolecular C—H...O hydrogen bonds, as well as intermolecular C—H...π and π–π interactions, leading to the formation of sheets parallel to the ac plane.

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7

Cornilescu, Gabriel, Benjamin E. Ramirez, M. Kirsten Frank, G. Marius Clore, Angela M. Gronenborn, and Ad Bax. "Correlation between3hJNC‘and Hydrogen Bond Length in Proteins." Journal of the American Chemical Society 121, no. 26 (July 1999): 6275–79. http://dx.doi.org/10.1021/ja9909024.

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8

Ueda, Takahiro, Shigenori Nagatomo, Hirotsugu Masui, Nobuo Nakamura, and Shigenobu Hayashi. "Hydrogen Bonds in Crystalline Imidazoles Studied by 15N NMR and ab initio MO Calculations." Zeitschrift für Naturforschung A 54, no. 6-7 (July 1, 1999): 437–42. http://dx.doi.org/10.1515/zna-1999-6-715.

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Abstract Intermolecular hydrogen bonds of the type N-H...N in crystals of imidazole and its 4-substituted and 4,5-disubstituted derivatives were studied by 15N CP/MAS NMR and an ab initio molecular orbital (MO) calculation. In the 15N CP/MAS NMR spectrum of each of the imidazole derivatives, two peaks due to the two different functional groups, >NH and =N-, were observed. The value of the 15N isotropic chemical shift for each nitrogen atom depends on both the length of the intermolecular hydrogen bond and the kind of the substituent or substituents. It was found that the difference between the experimen-tal chemical shifts of >NH and =N-varies predominantly with the hydrogen bond length but does not show any systematic dependence on the kind of substituent. The ab initio MO calculations suggest that the hydrogen bond formation influences the 15N isotropic chemical shift predominantly, and that the difference between the 15N isotropic chemical shift of >NH and =N-varies linearly with the hydrogen bond length.

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9

XIONG, ZICHANG, JUN GAO, DONGJU ZHANG, and CHENGBU LIU. "HYDROGEN BOND NETWORK OF 1-ALKYL-3-METHYLIMIDAZOLIUM IONIC LIQUIDS: A NETWORK THEORY ANALYSIS." Journal of Theoretical and Computational Chemistry 11, no. 03 (June 2012): 587–98. http://dx.doi.org/10.1142/s0219633612500381.

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Hydrogen bond is a key factor in the determination of structures and properties of room-temperature ionic liquids. Connections of these hydrogen bonds form a network. In this work, we analyzed the hydrogen bond network of 1-alkyl-3-methylimidazolium ionic liquids using network theory. A two-dimensional view of the hydrogen bond network has been generated, the connection pattern shown that the average length of line shape connection is 2.44 to 2.77 for six 1-alkyl-3-methylimidazolium ionic liquids, and the connection patterns are different for short and long alkyl side chain length. The degree of each ion was calculated and analyzed. The nodes with zero degree were adopted to detect the boundary of the clusters in the ionic liquids, which have no hydrogen bond connected with neighbor ions. This work indicates that the network analysis method is useful for understanding and predicting the structure and function of RTILs.

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10

Tiritiris, Ioannis, Stefan Saur, and Willi Kantlehner. "Crystal structure of (ethoxyethylidene)dimethylazanium ethyl sulfate." Acta Crystallographica Section E Crystallographic Communications 71, no. 12 (November 7, 2015): o916. http://dx.doi.org/10.1107/s2056989015020678.

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In the title salt, C6H14NO+·C2H5SO4−, the C—N bond lengths in the cation are 1.2981 (14), 1.4658 (14) and 1.4707 (15) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.3157 (13) Å shows double-bond character, indicating charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H...O hydrogen bonds between H atoms of the cations and O atoms of neighbouring ethyl sulfate anions are present, generating a three-dimensional network.

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11

Yang, Dapeng, Min Jia, Xiaoyan Song та Qiaoli Zhang. "Elaborating a new excited state intramolecular proton transfer (ESPT) mechanism for a new π-conjugated dye 2, 2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol)". Canadian Journal of Chemistry 96, № 3 (березень 2018): 351–57. http://dx.doi.org/10.1139/cjc-2017-0628.

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In this work, the excited state dynamical behavior of a novel π-conjugated dye 2,2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol) (C1) has been investigated. Two intramolecular hydrogen bonds of C1 are tested to pre-existing in the ground state via AIM and reduced density gradient. Using a time-dependent density functional theory (TDDFT) method, it has been substantiated that the intramolecular hydrogen bonds of C1 should be strengthened in the S1 state via analyzing fundamental bond length, bond angles, and corresponding infrared vibrational modes. The most obvious variation of these two hydrogen bonds is the O4–H5···N6 bond, which might play important roles in excited state behavior for the C1 system. Furthermore, based on electronic excitation, charge transfer could occur. Just due to this kind of charge re-distribution, two hydrogen bonds should be tighter in the first excited state, which is consistent with the variation of hydrogen bond lengths. Thus, the phenomenon of charge transfer is reasonable evidence for confirming the occurrence of the excited state proton transfer (ESPT) process in the S1 state. Our theoretically constructed potential energy surfaces of C1 show that excited state single proton transfer should occur along with the O4–H5···N6 hydrogen bond rather than the O1–H2···N3 bond. We not only clarify the ESIPT mechanism for C1 but put forward new affiliation and explain a previous experiment successfully.

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12

Yang, Dapeng, Yonggang Yang, and Yufang Liu. "A theoretical study on the red- and blue-shift hydrogen bonds of cis-trans formic acid dimer in excited states." Open Chemistry 11, no. 2 (February 1, 2013): 171–79. http://dx.doi.org/10.2478/s11532-012-0143-x.

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AbstractThe excited states of cis-trans formic acid dimer and its monomers have been investigated by time-dependent density functional theory (TDDFT) method. The formation of intermolecular hydrogen bonds O1-H1...O2=C2 and C2-H2...O4=C1 induces bond length lengthening of the groups related to the hydrogen bond, while that of the C2-H2 group is shortened. It is demonstrated that the red-shift hydrogen bond O1-H1...O2=C2 and blue-shift hydrogen bond C2-H2...O4=C1 are both weakened when excited to the S1 state. Moreover, it is found that the groups related to the formation of red-shift hydrogen bond O1-H1...O2=C2 are both strengthened in the S1 state, while the groups related to the blue-shift hydrogen bond C2-H2...O4=C1 are both weakened. This will provide information for the photochemistry and photophysical study of red- and blue-shift hydrogen bond.

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13

Wolfe, Saul, B. Mario Pinto, Vikram Varma, and Ronald Y. N. Leung. "The Perlin Effect: bond lengths, bond strengths, and the origins of stereoelectronic effects upon one-bond C–H coupling constants." Canadian Journal of Chemistry 68, no. 7 (July 1, 1990): 1051–62. http://dx.doi.org/10.1139/v90-164.

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The magnitude of a one-bond C–H coupling constant depends upon the chemical environment of the hydrogen atom and, especially, upon its stereochemical relationship to vicinal lone electron pairs. However, a lone electron pair is not essential for the observation of a stereoelectronic effect, since even cyclohexane exhibits different axial and equatorial C–H coupling constants. We propose the name "Perlin Effect" to describe such observations. An analysis of the extensive experimental data regarding the Perlin Effect reveals that, in cyclohexane and in six-membered rings having one or more heteroatoms of the first row attached to the carbon of interest, 1JC–H is always larger for an equatorial hydrogen than for an axial hydrogen. The magnitude of the Perlin Effect is reduced when the carbon carrying the hydrogen of interest is attached to first row and second row atoms or heteroatoms, and it reverses when the carbon atom carries two heteroatoms from below the first row.The existence of the Perlin Effect in nuclear magnetic resonance spectra is reminiscent of an infrared effect known as the Bohlmann bands, whose origin has previously been explained by quantitative perturbational molecular orbital (PMO) theory in terms of the effects of lone electron pairs upon the lengths and strengths and, therefore, the chemical reactivities of vicinal C—H bonds. Since the magnitude of a one-bond C–H coupling constant is expected to vary inversely with bond length, the origins of the Perlin Effect and of the Bohlmann bands would seem to be the same, i.e., the longer (weaker) C—H bond has the smaller one-bond coupling constant. This expectation has now been confirmed: for 25 molecules, representing a total of 35 different kinds of C—H bonds, the bond lengths, stretching force constants, and charge distributions have been determined from fully optimized 6-31G* molecular orbital calculations. In nine of ten cases for which experimental data exist for pairs of diastereomeric or diastereotopic hydrogens, the shorter C—H bond of the pair has the larger coupling constant; in the tenth case, the experimental difference is only 1–2 Hz. Moreover, a global analysis of the data in terms of the equation J = A + BqCqH + C/r, where J is an experimental coupling constant, q is a total atomic charge, and r is a C—H bond length, correlates 23 different types of C—H bonds linearly with a correlation coefficient of 0.915. The C parameter is the leading term of the correlation. Among the systems studied theoretically are eight molecules of the type CH3CHXY (Y = OH, SH; X = F, Cl, OH, SH), which are representative of systems containing both endocyclic and exocyclic first row and second row anomeric effects. The exocyclic effect is found to be very similar for first row and second row substituents, but the endocyclic effect is larger for the first row substituent. Both findings agree with experimental data in solution. Finally, quantitative PMO analysis has been employed to analyse the origins of the different C—H bond lengths in the various molecules of the study. Keywords: anomeric effect, PMO analysis, NMR, stereochemistry, molecular orbital calculations.

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14

Flörke, Ulrich, and Birte Drewes. "(2R,3R,4S,5R)-2-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-methyltetrahydrofuran-3,4-diol." Acta Crystallographica Section E Structure Reports Online 69, no. 11 (October 16, 2013): o1646—o1647. http://dx.doi.org/10.1107/s1600536813027931.

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The molecular structure of the title compound, C11H13IN4O3, shows a ribofuranosyl–pyrrolo O—C—N—C torsion angle of 59.1 (3)°, with the central C—N bond length being 1.446 (3) Å. The C—I bond length is 2.072 (2) Å. The amino group is coplanar with the attached aromatic ring [C—N—C—N torsion angle = −178.8 (2)°] and forms an intramolecular N—H...I hydrogen bond. In the crystal, O—H...N and N—H...O hydrogen bonds link the molecules into puckered layers parallel to (001). These layers are bound to each other by secondary I...O interactions [3.2250 (17) Å], forming a three-dimensional framework.

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15

Li, Shenshen, and Jijun Xiao. "Molecular Dynamics Simulations for Effects of Fluoropolymer Binder Content in CL-20/TNT Based Polymer-Bonded Explosives." Molecules 26, no. 16 (August 12, 2021): 4876. http://dx.doi.org/10.3390/molecules26164876.

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In order to better understand the role of binder content, molecular dynamics (MD) simulations were performed to study the interfacial interactions, sensitivity and mechanical properties of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT) based polymer-bonded explosives (PBXs) with fluorine rubber F2311. The binding energy between CL-20/TNT co-crystal (1 0 0) surface and F2311, pair correlation function, the maximum bond length of the N–NO2 trigger bond, and the mechanical properties of the PBXs were reported. From the calculated binding energy, it was found that binding energy increases with increasing F2311 content. Additionally, according to the results of pair correlation function, it turns out that H–O hydrogen bonds and H–F hydrogen bonds exist between F2311 molecules and the molecules in CL-20/TNT. The length of trigger bond in CL-20/TNT were adopted as theoretical criterion of sensitivity. The maximum bond length of the N–NO2 trigger bond decreased very significantly when the F2311 content increased from 0 to 9.2%. This indicated increasing F2311 content can reduce sensitivity and improve thermal stability. However, the maximum bond length of the N–NO2 trigger bond remained essentially unchanged when the F2311 content was further increased. Additionally, the calculated mechanical data indicated that with the increase in F2311 content, the rigidity of CL-20/TNT based PBXs was decrease, the toughness was improved.

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16

Dai, Ho Quoc, Nguyen Ngoc Tri, Nguyen Thi Thu Trang, and Nguyen Tien Trung. "Remarkable effects of substitution on stability of complexes and origin of the C–H⋯O(N) hydrogen bonds formed between acetone's derivative and CO2, XCN (X = F, Cl, Br)." RSC Adv. 4, no. 27 (2014): 13901–8. http://dx.doi.org/10.1039/c3ra47321j.

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17

Hushvaktov, H., A. Jumabaev, G. Murodov, A. Absanov, and G. Sharifov. "Aggregation of Molecules in Liquid Ethylene Glycol and Its Manifestation in Experimental Raman Spectra and Non-Empirical Calculations." Ukrainian Journal of Physics 65, no. 4 (April 17, 2020): 298. http://dx.doi.org/10.15407/ujpe65.4.298.

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Intra- and intermolecular interactions in liquid ethylene glycol have been studied using the Raman spectroscopy method and non-empirical calculations. The results of non-empirical calculations show that an intermolecular hydrogen bond is formed between the hydrogen atom of the OH group in one ethylene glycol molecule and the oxygen atom in the other molecule. The formation of this bond gives rise to a substantial redistribution of charges between those atoms, which, nevertheless, insignificantly changes the bond length. In the corresponding Raman spectra, the presence of hydrogen bonds between the ethylene glycol molecules manifests itself as the band asymmetry and splitting.

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18

Joo, Hea-Chung, Ki-Min Park, and Uk Lee. "Crystal structure of the Anderson-type heteropolyoxometalate; K2[H7CrIIIMo6O24]·8H2O: a redetermination revealing the position of the extra H atom in the polyanion." Acta Crystallographica Section E Crystallographic Communications 71, no. 2 (January 17, 2015): 157–60. http://dx.doi.org/10.1107/s2056989015000390.

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The title compound contains a symmetric hydrogen bond in which the H atom does not lie on a crystallographic centre of symmetry. The structure of K2[H7CrIIIMo6O24]·8H2O, namely dipotassium heptahydrogen hexamolybdochromate(III) octahydrate, previously reported by Lee [Acta Cryst. (2007), E63, i5–i7], has been redetermined in order to locate the position of the seventh H atom in the anion. Six of the H atoms are bonded to the six μ3-O atoms and form hydrogen bonds of medium strength either to water molecules or to the terminal O atoms of other polyanions. The seventh H atom forms a very short hydrogen bond between two μ2-O atoms on adjacent polyanions. This short bond, together with two normal hydrogen bonds, link the two crystallographically distinct centrosymmetric polyanions into chains along [011], while the length of this bond [2.461 (3) Å] suggests that the H atom lies at its centre, but unusually for such a bond, this point is not a crystallographic centre of symmetry.

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19

Ngo Thi Hong, Nhung, Huong Dau Thi Thu, and Trung Nguyen Tien. "Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method." Vietnam Journal of Catalysis and Adsorption 11, no. 1 (October 5, 2021): 126–33. http://dx.doi.org/10.51316/jca.2022.020.

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Nine stable structures of complexes formed by interaction of guanine with thymine were located on potential energy surface at B3LYP/6-311++G(2d,2p). The complexes are quite stable with interaction energy from -5,8 to -17,7 kcal.mol-1. Strength of complexes are contributed by hydrogen bonds, in which a pivotal role of N−H×××O/N overcoming C−H×××O/N hydrogen bond, up to to 3.5 times, determines stabilization of complexes investigated. It is found that polarity of N/C−H covalent bond over proton affinity of N/O site governs stability of hydrogen bond in the complexes. The obtained results show that the N/C−H×××O/N red-shifting hydrogen bonds occur in all complexes, and a larger magnitude of an elongation of N−H compared C-H bond length accompanied by a decrease of its stretching frequency is detected in the N/C−H×××O/N hydrogen bond upon complexation. The SAPT2+ analysis indicates the substantial contribution of attractive electrostatic energy versus the induction and dispersion terms in stabilizing the complexes.

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20

Orpen, A. Guy. "Metal Complex Geometries in Small-Molecule Crystals." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1194–98. http://dx.doi.org/10.1107/s0907444998007744.

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The origins, scope and utility of compilations of metal–ligand and intraligand bond lengths based on the Cambridge Structural Database are discussed. The limitations on the apparent uncertainty of metal–ligand bond lengths derived from crystallographic data and recent evidence of metal-assisted hydrogen bonding involving ligands are reviewed in the light of the transferability of bond-length values from one crystal structure determination.

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21

Kapoor, Utkarsh, Arjita Kulshreshtha, and Arthi Jayaraman. "Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding." Polymers 12, no. 11 (November 23, 2020): 2764. http://dx.doi.org/10.3390/polym12112764.

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In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

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22

Ordinartsev, Artem A., Andrey A. Petrov, Konstantin A. Lyssenko, Andrey V. Petrov, Eugene A. Goodilin, and Alexey B. Tarasov. "Crystal structure of new formamidinium triiodide jointly refined by single-crystal XRD, Raman scattering spectroscopy and DFT assessment of hydrogen-bond network features." Acta Crystallographica Section E Crystallographic Communications 77, no. 7 (June 8, 2021): 692–95. http://dx.doi.org/10.1107/s2056989021005673.

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A novel triiodide phase of the formamidinium cation, CH5N2 +·I3 −, crystallizes in the triclinic space group P\overline{1} at a temperature of 110 K. The structure consists of two independent isolated triiodide ions located on inversion centers. The centrosymmetric character of I3 − was additionally confirmed by the observed pronounced peaks of symmetrical oscillations of I3 − at 115–116 cm−1 in Raman scattering spectra. An additional structural feature is that each terminal iodine atom is connected with three neighboring planar formamidinium cations by N—H...I hydrogen bonding with the N—H...I bond length varying from 2.81 to 3.08 Å, forming a deformed two-dimensional framework of hydrogen bonds. A Mulliken population analysis showed that the calculated charges of hydrogen atoms correlate well with hydrogen-bond lengths. The crystal studied was refined as a three-component twin with domain ratios of 0.631 (1):0.211 (1):0.158 (1).

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23

Benoit, Magali, and Dominik Marx. "The Shapes of Protons in Hydrogen Bonds Depend on the Bond Length." ChemPhysChem 6, no. 9 (September 12, 2005): 1738–41. http://dx.doi.org/10.1002/cphc.200400533.

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24

Bruni, F., C. Di Mino, S. Imberti, S. E. McLain, N. H. Rhys, and M. A. Ricci. "Hydrogen Bond Length as a Key To Understanding Sweetness." Journal of Physical Chemistry Letters 9, no. 13 (June 19, 2018): 3667–72. http://dx.doi.org/10.1021/acs.jpclett.8b01280.

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25

Wang, Li Min, and Chuan Xia. "Theory Study on Structure Property of N-Ethyl Morpholinium Ionic Liquid of Different Alkyl Length." Advanced Materials Research 301-303 (July 2011): 170–74. http://dx.doi.org/10.4028/www.scientific.net/amr.301-303.170.

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The ionic liquid is a green solvent and catalyst, its application is abroad. By using at density functional theory (DFT) at B3LYP/6-31G* levels, The N-ethyl morpholinium ionic liquid with different alkyl length have been studied. The computed results indicate that the ionic liquid formed by ethyl N-ethyl morpholinium and a chlorine ion has nine structures and eighteen positions. Three hydrogen bonds have been formed in each position, the hydrogen bond between chlorine ion and hydrogen atom in morpholinium ring is strongest and shortest. The hydrogen bond between chlorine ion and hydrogen atom in ethyl is weaker, which can strengthen the stability of ion pair. The nine structures of the ionic liquid formed by ethyl N-ethyl morpholinium and a chlorine ion are compared, the ionic liquid of MO1,2NC和MO1,2LC is more stable, the energy released of MO1,2LC is biggest, the energy released of MO1,2NB is smallest. For ethyl N-ethyl morpholinium, propyl N-ethyl morpholinium and butyl N-ethyl morpholinium, as the alkyl length becomes longer, the binding energy between chlorine ion and morpholinium with different alkyl length becomes weaker.

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26

Li, Wei, Ruchun Yang, and Qiang Xiao. "(2R,3S,4R,5R)-5-(4-Amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-4-fluoro-2-(hydroxymethyl)tetrahydrofuran-3-ol." Acta Crystallographica Section E Structure Reports Online 70, no. 2 (January 8, 2014): o120. http://dx.doi.org/10.1107/s1600536813034995.

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Анотація:

The title compound, C11H12FIN4O3, is composed of a 7-carbapurine moiety connectedviaan N atom to 2-deoxy-2-fluoro-β-D-ribose. The conformation about the N-glycosydic bond is −antiwith χ = −129.0 (11)°. The glycosydic N—C bond length is 1.435 (14) Å. The sugar ring adopts anNconformation with an unsymmetrical twist O-endo-C-exo (oT4). The conformation around the C—C bond is +sc, with a torsion angle of 53.0 (12)°. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming chains propagating along theaaxis. These chains are linkedviaO—H...I and C—H...O hydrogen bonds, forming layers lying parallel to thecaxis.

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27

Rivera, Augusto, Juan Manuel Uribe, Jaime Ríos-Motta, Hector Jairo Osorio, and Michael Bolte. "Evidence for stereoelectronic effects in the N—C—N group of 8,10,12-triaza-1-azoniatetracyclo[8.3.1.18,12.02,7]pentadecane 4-nitrophenolate 4-nitrophenol monosolvate from the protonation of aminal (2R,7R)-1,8,10,12-tetraazatetracyclo[8.3.1.18,12.02,7]pentadecane: X-ray and natural bond orbital analysis." Acta Crystallographica Section C Structural Chemistry 71, no. 4 (March 14, 2015): 284–88. http://dx.doi.org/10.1107/s2053229615004829.

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Анотація:

The title molecular salt, C11H21N4+·C6H4NO3−·C6H5NO3, (II), crystallizes with two independent three-component aggregates in the asymmetric unit. In the cations, the cyclohexane rings fused to the cage azaadamantane systems both adopt a chair conformation. In the crystal structure, the aggregates are connected by C—H...O hydrogen bonds, forming a supramolecular unit enclosing anR44(24) ring motif. These units are linkedviaC—H...O and C—H...N hydrogen bonds, forming a three-dimensional network. Even hydrogen-bond formation to one of the N atoms is enough to induce structural stereoelectronic effects in the normal donor→acceptor direction. The C—N bond distances provide structural evidence for a strong anomeric effect. The structure also displays O—H...O and N—H...O hydrogen bonding. Geometric optimization and natural bond orbital (NBO) analysis of (II) were undertaken by utilizing DFT/B3LYP with the 6-31+G(d,p) basis set. NBO second-order perturbation theory calculations indicate donor–acceptor interactions between nitrogen lone pairs and the antibonding orbital of the C—C and C—N bonds for the protonated polyamine, in agreement with the occurrence of bond-length and bond-angle changes within the aminal cage structure.

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28

Häußler, Angelika, Thomas M. Klapötke, and Holger Piotrowski. "Experimental and Theoretical Study on the Structure of Nitramide H2NNO2." Zeitschrift für Naturforschung B 57, no. 2 (February 1, 2002): 151–56. http://dx.doi.org/10.1515/znb-2002-0204.

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Анотація:

Nitramide was investigated by multinuclear NMR spectroscopy, X-ray-diffraction and computational methods. The crystal structure analysis at various temperatures reveals a planar conformation of the molecule with a N-N bond length corresponding to a bond order between one and two. Hydrogen bonds connect the nitramide molecules side-on and end-on. This leads to the formation of layers in the crystal. Calculations were performed to explain the shorter N-N bond length in the crystal compared to the gas phase. The nitramide trimer is used as a model.

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29

Zarei, Mohammad, Abdolvahab Seif, Khaled Azizi, Mohanna Zarei, and Jamil Bahrami. "Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study." International Journal of Modern Physics C 27, no. 10 (August 29, 2016): 1650119. http://dx.doi.org/10.1142/s0129183116501199.

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Анотація:

In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

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30

Datta, Riya, V. Ramya, M. Sithambaresan, and M. R. Prathapachandra Kurup. "Crystal structure of 4-{(E)-[2-(pyridin-4-ylcarbonyl)hydrazin-1-ylidene]methyl}phenyl acetate monohydrate." Acta Crystallographica Section E Crystallographic Communications 71, no. 2 (January 3, 2015): o79—o80. http://dx.doi.org/10.1107/s2056989014027819.

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The asymmetric unit of the title compound, C15H13N3O3·H2O, comprises a 4-{(E)-[2-(pyridin-4-ylcarbonyl)hydrazinylidene]methyl}phenyl acetate molecule and a solvent water molecule linked by O—H...O and O—H...N hydrogen bonds from the water molecule and a C—H...O contact from the organic molecule. The compound adopts anEconformation with respect to the azomethine bond and the dihedral angle between the pyridine and benzene rings is 21.90 (7)°. The azomethine bond [1.275 (2) Å] distance is very close to the formal C=N bond length, which confirms the azomethine bond formation. An extensive set of O—H...O, O—H...N, N—H...O and C—H...O hydrogen bonds builds a two-dimensional network progressing along thecaxis.

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31

Gagné, Olivier Charles, Patrick H. J. Mercier, and Frank Christopher Hawthorne. "A priori bond-valence and bond-length calculations in rock-forming minerals." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 74, no. 6 (December 1, 2018): 470–82. http://dx.doi.org/10.1107/s2052520618010442.

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Within the framework of the bond-valence model, one may write equations describing the valence-sum rule and the loop rule in terms of the constituent bond valences. These are collectively called the network equations, and can be solved for a specific bond topology to calculate its a priori bond valences. A priori bond valences are the ideal values of bond strengths intrinsic to a given bond topology that depend strictly on the formal valences of the ion at each site in the structure, and the bond-topological characteristics of the structure (i.e. the ion connectivity). The a priori bond valences are calculated for selected rock-forming minerals, beginning with a simple example (magnesiochromite, = 1.379 bits per atom) and progressing through a series of gradually more complex minerals (grossular, diopside, forsterite, fluoro-phlogopite, phlogopite, fluoro-tremolite, tremolite, albite) to finish with epidote (= 4.187 bits per atom). The effects of weak bonds (hydrogen bonds, long Na+—O2− bonds) on the calculation of a priori bond valences and bond lengths are examined. For the selected set of minerals, a priori and observed bond valences and bond lengths scatter closely about the 1:1 line with an average deviation of 0.04 v.u. and 0.048 Å and maximum deviations of 0.16 v.u. and 0.620 Å. The scatter of the corresponding a priori and observed bond lengths is strongly a function of the Lewis acidity of the constituent cation. For cations of high Lewis acidity, the range of differences between the a priori and observed bond lengths is small, whereas for cations of low Lewis acidity, the range of differences between the a priori and observed bond lengths is large. These calculations allow assessment of the strain in a crystal structure and provide a way to examine the effect of bond topology on variation in observed bond lengths for the same ion-pair in different bond topologies.

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32

Hudiyanti, D., V. N. R. Putri, Y. Hikmahwati, S. M. Christa, P. Siahaan, and D. S. B. Anugrah. "Interaction of Phospholipid, Cholesterol, Beta-Carotene, and Vitamin C Molecules in Liposome-Based Drug Delivery Systems: An In Silico Study." Advances in Pharmacological and Pharmaceutical Sciences 2023 (January 4, 2023): 1–10. http://dx.doi.org/10.1155/2023/4301310.

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This paper investigates the interaction within a liposome-based drug delivery system in silico. Results confirmed that phospholipids, cholesterol, beta-carotene, and vitamin C in the liposome structures interact noncovalently. The formation of noncovalent interactions indicates that the liposomal structures from phospholipid molecules will not result in chemical changes to the drug or any molecules encapsulated within. Noncovalent interactions formed include (i) moderate-strength hydrogen bonds with interaction energies ranging from −73.6434 kJ·mol−1 to −45.6734 kJ·mol−1 and bond lengths ranging from 1.731 Å to 1.827 Å and (ii) van der Waals interactions (induced dipole-induced dipole and induced dipole-dipole interactions) with interaction energies ranging from −4.4735 kJ·mol−1 to −1.5840 kJ·mol−1 and bond lengths ranging from 3.192 Å to 3.742 Å. The studies for several phospholipids with short hydrocarbon chains show that changes in chain length have almost no effect on interaction energy, bond length, and partial atomic charge.

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33

Ahmed, Zahoor, Hasan Zulfiqar, Lixia Tang, and Hao Lin. "A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins." International Journal of Molecular Sciences 23, no. 17 (September 4, 2022): 10116. http://dx.doi.org/10.3390/ijms231710116.

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Анотація:

Thermophilic proteins have various practical applications in theoretical research and in industry. In recent years, the demand for thermophilic proteins on an industrial scale has been increasing; therefore, the engineering of thermophilic proteins has become a hot direction in the field of protein engineering. However, the exact mechanism of thermostability of proteins is not yet known, for engineering thermophilic proteins knowing the basis of thermostability is necessary. In order to understand the basis of the thermostability in proteins, we have made a statistical analysis of the sequences, secondary structures, hydrogen bonds, salt bridges, DHA (Donor–Hydrogen–Accepter) angles, and bond lengths of ten pairs of thermophilic proteins and their non-thermophilic orthologous. Our findings suggest that polar amino acids contribute to thermostability in proteins by forming hydrogen bonds and salt bridges which provide resistance against protein denaturation. Short bond length and a wider DHA angle provide greater bond stability in thermophilic proteins. Moreover, the increased frequency of aromatic amino acids in thermophilic proteins contributes to thermal stability by forming more aromatic interactions. Additionally, the coil, helix, and loop in the secondary structure also contribute to thermostability.

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34

Fábry, Jan, Michaela Fridrichová, Michal Dušek, Karla Fejfarová, and Radmila Krupková. "Two polymorphs of bis(2-carbamoylguanidinium) fluorophosphonate dihydrate." Acta Crystallographica Section C Crystal Structure Communications 68, no. 2 (January 6, 2012): o71—o75. http://dx.doi.org/10.1107/s0108270111053133.

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Анотація:

Two polymorphs of bis(2-carbamoylguanidinium) fluorophosphonate dihydrate, 2C2H7N4O+·FO3P2−·2H2O, are presented. Polymorph (I), crystallizing in the space groupPnma, is slightly less densely packed than polymorph (II), which crystallizes inPbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen-bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation ofR44(10) graph-set motifs. These motifs extend along theaaxis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three-dimensional hydrogen-bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen-bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen-bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).

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35

Leskovac, Vladimir, Svetlana Trivic, Draginja Pericin, Mira Popovic, and Julijan Kandrac. "Short hydrogen bonds in the catalytic mechanism of serine proteases." Journal of the Serbian Chemical Society 73, no. 4 (2008): 393–403. http://dx.doi.org/10.2298/jsc0804393l.

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The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

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36

Djomo, Edith Dimitri, Frédéric Capet, Justin Nenwa, Michel M. Bélombé та Michel Foulon. "Crystal structure of 4-(dimethylamino)pyridiniumcis-diaquabis(oxalato-κ2O,O′)ferrate(III) hemihydrate". Acta Crystallographica Section E Crystallographic Communications 71, № 8 (15 липня 2015): 934–36. http://dx.doi.org/10.1107/s2056989015013213.

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Анотація:

The FeIIIions in the hybrid title salt, (C7H11N2)[Fe(C2O4)2(H2O)2]·0.5H2O, show a distorted octahedral coordination environment, with four O atoms from two chelating oxalate dianions and two O atoms from twocisaqua ligands. The average Fe—O(oxalate) bond length [2.00 (2) Å] is shorter than the average Fe—O(water) bond length [2.027 (19) Å]. The ionic components are connectedviaintermolecular N—H...O and O—H...O hydrogen bonds into a three-dimensional network.

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37

Kim, Dae-Woong, Jong Won Shin та Dohyun Moon. "Crystal structure oftrans-(1,8-dibutyl-1,3,6,8,10,13-hexaazacyclotetradecane-κ4N3,N6,N10,N13)bis(perchlorato-κO)copper(II) from synchrotron data". Acta Crystallographica Section E Crystallographic Communications 71, № 2 (10 січня 2015): 136–38. http://dx.doi.org/10.1107/s2056989014028047.

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The structure of the title compound, [Cu(ClO4)2(C16H38N6)] has been determined from synchrotron data, λ = 0.62988 Å. The asymmetric unit comprises one half of the CuIIcomplex as the CuIIcation lies on an inversion center. It is coordinated by the four secondary N atoms of the macrocyclic ligand and the mutuallytransO atoms of the two perchlorate ions in a tetragonally distorted octahedral geometry. The average equatorial Cu—N bond length is significantly shorter than the average axial Cu—O bond length [2.010 (4) and 2.569 (1) Å, respectively]. Intramolecular N—H...O hydrogen bonds between the macrocyclic ligand and uncoordinating O atoms of the perchlorate ligand stabilize the molecular structure. In the crystal structure, an extensive series of intermolecular N—H...O and C—H...O hydrogen bonds generate a three-dimensional network.

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38

Oh, In-Hwan, Yoo-Jung Sohn, Martin Meven, and Gernot Heger. "Neutron Diffraction Investigation on the Symmetrical Hydrogen Bond in K3H(SO4)2." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1114. http://dx.doi.org/10.1107/s2053273314088858.

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In this work, we present a structure investigation on K3H(SO4)2 by single crystal neutron diffraction. Letovicite with a chemical composition (NH4)3H(SO4)2 belongs to a large family of M3(H,D)(XO4)2 compounds, where M = K+, Rb+, (NH4)+, Cs+, Tl+ and X = Se6+ and S6+. This compound crystallizes in the monoclinic space group A2/a with a = 9.789(7) Å, b = 5.6815(9) Å, c = 14.703(2) Å and β = 103.03(4)0at 300K. At 2.3K, the lattice parameters are a = 9.687(20) Å, b = 5.648(13) Å, c = 14.613(9) Å and β = 103.23(14)0. Data at 2.3K were measured up to (sinθ/λ) = 0.807Å-1 with the single crystal neutron diffractormeter HEiDi at the FRM-II, Germany. H/D shows a dynamic disorder at high temperature, which can be related to very high proton conductivity. In letovicite, two types of disorder related with hydrogen atoms are reported [1]. Although letovicite shows various phase transitions owing to the proton ordering at low temperature, K3H(SO4)2, without the possibility of an orientational disorder of NH4+, undergoes no phase transition at low temperature. At room temperature, the title compound is isostructural to lectovicite, and has an inversion center in the middle of the SO4-H-SO4 dimer. The bond length, 2.483(3) Å, and bond angle, 1800, support the hypothesis that the disordered proton shows a double-well potential, if the distance between the oxygen atoms of the hydrogen bond Ro-o are longer than a critical bond length rc(2.47 Å for protons and 2.40 Å for deuterons) [2]. However, it is not easy to determine if the hydrogen bond is a low-barrier hydrogen bond (LBHB) or centered hydrogen bond (centered HB). Based on an analysis of the anisotropic parameters, the bond lengths and elongation of the hydrogen atom toward the two oxygen atoms by neutron single crystal diffraction experiments at 300K and 2.3K, it seems that the hydrogen bond in the title compound can be classified as a centered hydrogen bond or intermediate form between a cigar-like shape and the disk-like shape [3].

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39

Boyarskaya, Dina, Margarita Avdontceva, and Tatiana Chulkova. "Synthesis and crystal structure of 2-isocyano-4-methylphenyl diphenylacetate: a rare case of an easily accessible odourless isocyanide." Acta Crystallographica Section C Structural Chemistry 71, no. 2 (January 31, 2015): 155–58. http://dx.doi.org/10.1107/s2053229615001588.

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Acidic hydrogen containing 2-isocyano-4-methylphenyl diphenylacetate, C22H17NO2, (I), was synthesized by the base-promoted reaction between 5-methylbenzoxazole and diphenylacetyl chloride. Achiral (I) crystallizes in the chiralP212121space group. The C[triple-bond]N bond length is 1.164 (2) Å and the angle between the OCO and 2-isocyano-4-methylphenyl planes is 69.10 (16)°. Molecules are linkedviaC=O...Hphenyland bifurcated N[triple-bond]C...Hphenyl/N[triple-bond]C...Hmethinehydrogen bonds, forming one-dimensional arrays.

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40

Wilson, Lucie, R. Bicca de Alencastro, and C. Sandorfy. "Hydrogen bonding of n-alcohols of different chain lengths." Canadian Journal of Chemistry 63, no. 1 (January 1, 1985): 40–45. http://dx.doi.org/10.1139/v85-007.

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Анотація:

The anesthetic potency of n-alcohols exhibits a somewhat irregular dependence on the length of the hydrocarbon chain. An attempt has therefore been made to ascertain if this is related to the relative tendency for hydrogen bond formation by these alcohols. No such relationship was found. The result was rather that the degree of association by hydrogen bond formation of dissolved alcohols appears to be independent of the chain length, that is of the extent of other interactions that exist in these solutions.

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41

Wang, Weizhou, Yu Zhang, and Baoming Ji. "The nature of the bond-length change upon molecule complexation." Collection of Czechoslovak Chemical Communications 75, no. 3 (2010): 243–56. http://dx.doi.org/10.1135/cccc2009532.

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Анотація:

The nature of the bond-length change upon molecule complexation has been investigated at the MP2/aug-cc-pVTZ level of theory. Our results have clearly shown that the X–Y bond-length change upon complex formation is determined mainly by the electrostatic attractive interaction and the charge-transfer interaction. In the case of strongly polar bond, the electrostatic interaction always causes bond elongation while in the case of weakly polar bond it causes bond contraction. The charge-transfer interaction generally results in the X–Y bond elongation; either it is a more polar bond or it is a less polar bond. Employing this simple “electrostatic interaction plus charge-transfer interaction” explanation, we explained and predicted many interesting phenomena related to the bond-length change upon molecule complexation. In addition, the difference between the origin of the bond-length change upon hydrogen-bonded complex formation and the origin of the bond-length change upon halogen-bonded complex formation was also discussed.

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42

Fortes, A. D., I. G. Wood, and K. S. Knight. "The crystal structure of perdeuterated methanol monoammoniate (CD3OD·ND3) determined from neutron powder diffraction data at 4.2 and 180 K." Journal of Applied Crystallography 42, no. 6 (October 3, 2009): 1054–61. http://dx.doi.org/10.1107/s0021889809035705.

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Анотація:

The crystal structure of perdeuterated methanol monoammoniate, CD3OD·ND3, has been solved from neutron powder diffraction data collected at 4.2 and 180 K. The crystal structure is orthorhombic, space groupPbca(Z= 8), with unit-cell dimensionsa= 11.02320 (7),b= 7.66074 (6),c= 7.59129 (6) Å,V= 641.053 (5) Å3[ρcalc= 1162.782 (9) kg m−3] at 4.2 K, anda= 11.21169 (5),b= 7.74663 (4),c= 7.68077 (5) Å,V= 667.097 (4) Å3[ρcalc= 1117.386 (7) kg m−3] at 180 K. The crystal structure was determined byab initiomethods from the powder data; atomic coordinates and anisotropic displacement parameters were subsequently refined by the Rietveld method toRp< 3% at both temperatures. The crystal comprises a sheet-like structure in thebccrystallographic plane, consisting of strongly hydrogen bonded elements; these sheets are stacked along theaaxis, and adjacent sheets are linked by what may be comparatively weak C—D...O hydrogen bonds. Within the strongly bonded sheet structure, ND3molecules are tetrahedrally coordinated by the hydroxy moieties of the methanol molecule, accepting one hydrogen bond (O—D...N) of length ∼1.75 Å, and donating three hydrogen bonds (N—D...O) of length 2.15–2.25 Å. Two of the methyl deuterons appear to participate in weak interlayer hydrogen bonds (C—D...O) of length 2.7–2.8 Å. The hydrogen bonds are ordered at both 4.2 and 180 K. The relative volume change on warming from 4.2 to 180 K, ΔV/V, is +4.06%, which is comparable to, but more nearly isotropic (as determined from the relative change in axial lengths,e.g.Δa/a) than, that observed in deuterated methanol monohydrate.

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43

Mascal, Mark, Christopher E. Marjo, and Alexander J. Blake. "Breakdown of the hydrogen bond strength–length analogy: a revision." Chemical Communications, no. 17 (2000): 1591–92. http://dx.doi.org/10.1039/b002361m.

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44

Parra, Rubén D. "Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study." Molecules 28, no. 17 (August 24, 2023): 6217. http://dx.doi.org/10.3390/molecules28176217.

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Анотація:

DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH2 group or seven CH2 groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.

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45

White, Curtis W., and Jaime M. Martell. "Hydrogen Abstraction from Fluorinated Ethyl Methyl Ether Systems by OH Radicals." Advances in Physical Chemistry 2016 (February 10, 2016): 1–10. http://dx.doi.org/10.1155/2016/3740278.

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Анотація:

A systematic computational investigation of hydrogen abstraction by OH from the full series of fluorinated ethyl methyl ethers (EME) containing at least one H and one F, C2HnX5-nOCHmX3-m (n=0–5, m=0–3; and n=m=0 not allowed), including 147 reactants and 469 transition states, has been carried out, employing the MP2/6-31G(d) level of theory. Results for optimized geometries, including evidence of intramolecular hydrogen bonding in transition states, and barrier heights are presented. Trends pertaining to the number of fluorines substituted, key bond lengths, barrier heights, and key bond angles were found with good correlations and were investigated. An increase in the number of F increases the barrier height of the reaction. An increase in some parameters such as C–H length of TS, relative change in C–H from reactants to TS, ∠COC of reactants, ∠HOH in the TS, and relative change in ∠HOH between TS and free water bond angle also correlates with increased barrier height. An increase in other parameters like C–H length in the reactants and hydrogen bonding can decrease the barrier height.

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46

Ramasami, Ponnadurai, and Thomas A. Ford. "Ab initio studies of the vibrational spectra of some hydrogen-bonded complexes of fluoroacetylene." Canadian Journal of Chemistry 88, no. 8 (August 2010): 716–24. http://dx.doi.org/10.1139/v10-028.

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Ab initio molecular orbital theory has been used to compute the properties of a number of hydrogen-bonded complexes between fluoroacetylene as proton donor and ammonia, water, hydrogen fluoride, phosphine, hydrogen sulfide, and hydrogen chloride as proton acceptors. The properties considered were the vibrational spectra, the molecular structures, the hydrogen-bond energies, and the electron densities, and one of the aims of the study was to ascertain whether there was any evidence of blue-shifting hydrogen-bond character in the complexes formed. The adducts with NH3, H2O, PH3, and H2S were of the conventional CH···X kind (X = N, O, P, S), with hydrogen-bond energies decreasing in the order NH3 > H2O > PH3 ≈ H2S. Those formed with HF and HCl showed the presence of three alternative structures; in addition to the CH···F(Cl) complexes, adducts of the F(Cl)H···F and F(Cl)H···π type were also found to be stationary points on the potential energy surfaces, with stabilities in the order F(Cl)H···π > CH···F(Cl) > F(Cl)H···F. The hydrogen-bond energies of the CH···X series correlated with the gas-phase basicities of the proton acceptors; moreover, the CH bond-length changes, the wavenumber shifts, the complex–monomer infrared intensity ratios of the CH stretching modes, and the amounts of charge transferred on complex formation were all found to track with the hydrogen-bond energies. All those properties considered here are consistent with the formation of red-shifting hydrogen bonds, to the exclusion of the blue-shifting alternatives.

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Aranburu Leiva, Ane I., Sophie L. Benjamin, Stuart K. Langley, and Ryan E. Mewis. "Crystal structure of 2,4-di-tert-butyl-6-(hydroxymethyl)phenol." Acta Crystallographica Section E Crystallographic Communications 72, no. 11 (October 25, 2016): 1614–17. http://dx.doi.org/10.1107/s2056989016016753.

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The title compound, C15H24O2, is an example of a phenol-based pendant-arm precursor. In the molecule, the phenol hydroxy group participates in an intramolecular O—H...O hydrogen bond with the pendant alcohol group, forming anS(6) ring. This ring adopts a half-chair conformation. In the crystal, O—H...O hydrogen bonds connect molecules related by the 31screw axes, forming chains along thecaxis. The C—C—O angles for the hydroxy groups are different as a result of the type of hybridization for the C atoms that are involved in these angles. The C—C—O angle for the phenol hydroxy group is 119.21 (13)°, while the angle within the pendant alcohol is 111.99 (13)°. The bond length involving the phenolic oxygen is 1.3820 (19) Å, which contrasts with that of the alcoholic oxygen which is 1.447 (2) Å. The former is conjugated with the aromatic ring and so leads to the observed shorter bond length.

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48

Trabelsi, Sonia, Manel Essid, Thierry Roisnel, Mohamed Rzaigui, and Houda Marouani. "Propane-1,2-diammonium chromate(VI)." Acta Crystallographica Section E Structure Reports Online 70, no. 3 (February 8, 2014): m84—m85. http://dx.doi.org/10.1107/s1600536814002463.

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In the title molecular salt, (C3H12N2)[CrO4], each chromate anion accepts six N—H...O and C—H...O hydrogen bonds from nearby propane-1,2-diammonium cations. Three of the four O atoms of the chromate anion accept these bonds; the remaining Cr—O bond length is notably shorter than the others. In the crystal, the anions and cations stack in layers lying parallel to (100): the hydrogen-bonding pattern leads to a three-dimensional network.

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49

Ibrahimova, N. Z., S. M. Rustemova, G. M. Jafarov та I. U. Lyatifov. "HYROGEN BOND IN CRYSTAL STRUCTURE OF SALTS OF SYMMETRIC POLYMETHYLFERRICINIUM CATİONS (SYM.[(CH3)mC5H5–m]2Fe+X – , m=3,4,5 or МеnFc+X – , n = 6, 8, 10; X– = PF6 – , BF4 – , Br3 – )". Chemical Problems 21, № 3 (2023): 203–10. http://dx.doi.org/10.32737/2221-8688-2023-3-203-210.

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The article explains reasons of elongation (0.019 Å) of the bond between iron–cyclopentadienyl ring in the 1,2,4,1,2,4-hexamethylferricinium (sym. Ме6Fc+ ) cation formed due to the one-electron oxidation of iron atom of sym.1,2,4,1,2,4-hexamethylferrocene (sym. Ме6Fc) molecule which is 2-2.5 times smaller (0.04–0.05 Å) than that observed in pairs of ferrocene/ferricinium (Fc/Fc+ ), sym. octamethylferrocene/sym.octamethylferricinium (Ме8Fc/Me8Fc+ ) and decamethylferrocene/decamethylferricinium (Ме10Fc/Ме10Fc+ ). For this purpose, X-ray structural parameters characterizing the interaction between cation and anion in the sym.Ме6Fc+PF6 – complex was compared with appropriate parameters in Ме8Fc+BF4 – , Ме10Fc+Br3 and Ме10Fc+PF6 – complexes; and it was mooted that there is an F …H type hydrogen bond in this complex taking into account the length of the non-valent F…H contact (bond) in the sym. Ме6Fc+PF6 – complex. The lengths of Р–F bonds and F–P–F angles of the PF6 – anion in the listed 4 sandwich complexes were compared with appropriate parameters in the РF6 – anion of the LiРF6 crystal. It has been unequivocally proved that F…H hydrogen bonds exist in the sym.Ме6Fc+PF6 – complex.

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Petrova, M., R. Muhamadejev, B. Vigante, G. Duburs, and Edvards Liepinsh. "Intramolecular hydrogen bonds in 1,4-dihydropyridine derivatives." Royal Society Open Science 5, no. 6 (June 2018): 180088. http://dx.doi.org/10.1098/rsos.180088.

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1,4-Dihydropyridine (1,4-DHP) derivatives have been synthesized and characterized by 1 H, 13 C, 15 N nuclear magnetic resonance (NMR) spectroscopy, secondary proton/deuterium 13 C isotope shifts, variable temperature 1 H NMR experiments and quantum-chemical calculation. The intramolecular hydrogen bonds NH⋯O=C and CH⋯O=C in these compounds were established by NMR and quantum-chemical studies The downfield shift of the NH proton , accompanied by the upfield shift of the 15 N nuclear magnetic resonance signals, the shift to the higher wavenumbers of the NH stretching vibration in the infrared spectra and the increase of the 1 J( 15 N, 1 H) values may indicate the shortening of the N–H bond length upon intramolecular NH⋯O=C hydrogen bond formation.

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