Impact of intermolecular hydrogen bond on structural properties of phenylboronic acid: quantum chemical and X-ray study

2008 ◽  
Vol 21 (6) ◽  
pp. 472-482 ◽  
Author(s):  
Michał K. Cyrański ◽  
Aneta Jezierska ◽  
Paulina Klimentowska ◽  
Jarosław J. Panek ◽  
Andrzej Sporzyński
Keyword(s):  
Hydrogen Bond ◽  
Structural Properties ◽  
Quantum Chemical ◽  
Phenylboronic Acid ◽  
Intermolecular Hydrogen Bond ◽  
X Ray

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

Synthesis of ReItricarbonyl complexes with various sulfur- and oxygen-donating ligands: crystal structures of two ReIdinuclear structures bridged by S atoms

2018 ◽  
Vol 74 (10) ◽  
pp. 1116-1122
Author(s):  
Pheello I. Nkoe ◽  
Hendrik G. Visser ◽  
Chantel Swart ◽  
Alice Brink ◽  
Marietjie Schutte-Smith
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
Metal Centre ◽  
Pyridine Ligand ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Mononuclear Complexes

The synthesis and characterization of two dinuclear complexes, namelyfac-hexacarbonyl-1κ3C,2κ3C-(pyridine-1κN)[μ-2,2′-sulfanediyldi(ethanethiolato)-1κ2S1,S3:2κ3S1,S2,S3]dirhenium(I), [Re2(C4H8S3)(C5H5N)(CO)6], (1), and tetraethylammoniumfac-tris(μ-2-methoxybenzenethiolato-κ2S:S)bis[tricarbonylrhenium(I)], (C8H20N)[Re2(C7H7OS)3(CO)6], (2), together with two mononuclear complexes, namely (2,2′-bithiophene-5-carboxylic acid-κ2S,S′)bromidotricarbonylrhenium(I), (3), and bromidotricarbonyl(methyl benzo[b]thiophene-2-carboxylate-κ2O,S)rhenium(I), (4), are reported. Crystals of (1) and (2) were characterized by X-ray diffraction. The crystal structure of (1) revealed two Re—S—Re bridges. The thioether S atom only bonds to one of the ReImetal centres, while the geometry of the second ReImetal centre is completed by a pyridine ligand. The structure of (2) is characterized by three S-atom bridges and an Re...Re nonbonding distance of 3.4879 (5) Å, which is shorter than the distance found for (1) [3.7996 (6)/3.7963 (6) Å], but still clearly a nonbonding distance. Complex (1) is stabilized by six intermolecular hydrogen-bond interactions and an O...O interaction, while (2) is stabilized by two intermolecular hydrogen-bond interactions and two O...π interactions.

scholarly journals Synthesis of ferrocene amides and esters from aminoferrocene and 2-substituted ferrocenecarboxylic acid and properties thereof

2016 ◽  
Vol 40 (11) ◽  
pp. 9441-9447 ◽  
Author(s):  
Palabindela Srinivas ◽  
Sunchu Prabhakar ◽  
Floris Chevallier ◽  
Ekhlass Nassar ◽  
William Erb ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Functional Groups ◽  
Intermolecular Hydrogen Bond ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Structure ◽  
Ferrocenecarboxylic Acid

The X-ray diffraction structure of the ferrocene ester FcE-1 showed the presence of an intermolecular hydrogen bond between the amide functional groups.

scholarly journals New Insights Into the Structure of Hydroxylated and Alkylated Glycols: A Comparative X-ray Diffraction, Raman and Molecular Dynamics Study of Ethane-1,2-Diol, 2-Methoxyethan-1-ol and 1,2-Dimethoxy Ethane

2020 ◽  
Author(s):  
Lorenzo Gontrani ◽  
Pietro Tagliatesta ◽  
Antonio Agresti ◽  
Sara Pescetelli ◽  
Marilena Carbone
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Room Temperature ◽  
Intermolecular Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Gauche Conformation ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Diffraction Patterns ◽  
Intramolecular Hydrogen

In this study, we report a detailed experimental and theoretical investigation of three glycols, namely ethane-1,2-diol, 2-methoxyethan-1-ol and 1,2-dimethoxy ethane. For the first time, the X-Ray spectra of the latter two liquids was measured at room temperature, and they were compared with the newly measured spectrum of ethane-1,2-diol. The experimental diffraction patterns were interpreted very satisfactorily with molecular dynamics calculations, and suggest that in liquid ethane-1,2-diol most molecules are found in gauche conformation, with intramolecular hydrogen bond between the two hydroxyl groups. Intramolecular H-bonds are established in the mono-alkylated diol, but the interaction is weaker. The EDXD study also evidences strong intermolecular hydrogen-bond interactions, with short O···O correlations in both systems, while longer methyl-methyl interactions are found in 1,2-dimethoxy ethane. X-Ray studies are complemented by micro Raman investigations at room temperature and at 80°C, that confirm the conformational analysis predicted by X-Ray experiments and simulations.

X-ray molecular orbital analysis. II. Application to diformohydrazide, (NHCHO)2

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Kiyoaki Tanaka ◽  
Yuko Wasada-Tsutsui
Keyword(s):  
Hydrogen Bond ◽  
Electron Density ◽  
Molecular Orbital ◽  
Intermolecular Hydrogen Bond ◽  
Saddle Points ◽  
Electron Densities ◽  
Multiple Diffraction ◽  
Molecular Plane ◽  
X Ray ◽  
Structure Factors

The molecular orbitals (MOs) of diformohydrazide have been determined from the electron density measured by X-ray diffraction. The experimental and refinement procedures are explained in detail and the validity of the obtained MOs is assessed from the crystallographic point of view. The X-ray structure factors were measured at 100 K by a four-circle diffractometer avoiding multiple diffraction, the effect of which on the structure factors is comparable to two-centre structure factors. There remained no significant peaks on the residual density map and the R factors reduced significantly. Among the 788 MO coefficients, 731 converged, of which 694 were statistically significant. The C—H and N—H bond distances are 1.032 (2) and 1.033 (3) Å, respectively. The electron densities of theoretical and experimental MOs and the differences between them are illustrated. The overall features of the electron density obtained by X-ray molecular orbital (XMO) analysis are in good agreement with the canonical orbitals calculated by the restricted Hartree Fock (RHF) method. The bonding-electron distribution around the middle of each bond is well represented and the relative phase relationships of the π orbitals are reflected clearly in the electron densities on the plane perpendicular to the molecular plane. However, differences are noticeable around the O atom on the molecular plane. The orbital energies obtained by XMO analysis are about 0.3 a.u. higher than the corresponding canonical orbitals, except for MO10 to MO14 which are about 0.7 a.u. higher. These exceptions are attributed to the N—H...O′′ intermolecular hydrogen bond, which is neglected in the MO models of the present study. The hydrogen bond is supported by significant electron densities at the saddle points between the H(N) and O′′ atoms in MO7, 8, 14 and 17, and by that of O′′-p extended over H(N) in MO21 and 22, while no peaks were found in MO10, 11, 13 and 15. The electron density of each MO clearly exhibits its role in the molecule. Consequently, the MOs obtained by XMO analysis give a fundamental quantum mechanical insight into the real properties of molecules.

Synthesis, Photophysics and Theoretical Calculation of (E)-2-(benzo[d] thiazol-2-yl)-3-(3-methoxyphenyl)acrylonitrile

2020 ◽  
Vol 17 (9) ◽  
pp. 688-693
Author(s):  
Pei-Chieh Wu ◽  
Chih-Hsien Chen
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Emission Intensity ◽  
Intermolecular Hydrogen Bond ◽  
Aromatic Rings ◽  
Organic Nanoparticles ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
New Type ◽  
The Stability

In this study, a new type of luminogen with aggregation-induced-emission (AIE) behavior was designed and synthesized. The result of single-crystal X-ray structure showed a planar structure in which the dihedral angle between two aromatic rings is less than 30o. Moreover, two different intermolecular hydrogen bond interactions supported the stability of the crystal structure. After the formation of organic nanoparticles in poor solubility solvent, the emission intensity of the desired product was increased and the enhancement achieved was 14-fold. This new design of luminogen provided further understanding of the AIE mechanism.

An X-ray crystallographic and density functional theory study of (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one

2013 ◽  
Vol 69 (3) ◽  
pp. 258-262
Author(s):  
Kate J. Akerman ◽  
Orde Q. Munro
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Intramolecular Hydrogen Bond ◽  
Density Functional ◽  
Intermolecular Hydrogen Bond ◽  
Functional Theory ◽  
One Dimensional ◽  
X Ray ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

The Schiff base enaminones (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one, C13H17NO4S, (I), and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one, C15H21NO2, (II), were studied by X-ray crystallography and density functional theory (DFT). Although the keto tautomer of these compounds is dominant, the O=C—C=C—N bond lengths are consistent with some electron delocalization and partial enol character. Both (I) and (II) are nonplanar, with the amino–phenol group canted relative to the rest of the molecule; the twist about the N(enamine)—C(aryl) bond leads to dihedral angles of 40.5 (2) and −116.7 (1)° for (I) and (II), respectively. Compound (I) has a bifurcated intramolecular hydrogen bond between the N—H group and the flanking carbonyl and hydroxy O atoms, as well as an intermolecular hydrogen bond, leading to an infinite one-dimensional hydrogen-bonded chain. Compound (II) has one intramolecular hydrogen bond and one intermolecular C=O...H—O hydrogen bond, and consequently also forms a one-dimensional hydrogen-bonded chain. The DFT-calculated structures [in vacuo, B3LYP/6-311G(d,p) level] for the keto tautomers compare favourably with the X-ray crystal structures of (I) and (II), confirming the dominance of the keto tautomer. The simulations indicate that the keto tautomers are 20.55 and 18.86 kJ mol−1lower in energy than the enol tautomers for (I) and (II), respectively.

scholarly journals Effects of Silane Debonder on the Properties of Fluff Pulp and the Study of Relevant Mechanism

2016 ◽  
Vol 11 (2) ◽  
pp. 155892501601100
Author(s):  
Yongjian Xu Shaanxi ◽  
Yuzhen Ning Shaanxi ◽  
Leigang Zuo ◽  
Hao Sun Shaanxi
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Great Influence ◽  
Xrd Analysis ◽  
Absorption Capacity ◽  
Hydroxyl Groups ◽  
Pulp Fibers ◽  
X Ray ◽  
Ft Ir ◽  
Intramolecular Hydrogen

The influence of silane debonder on the properties of fluff pulp fibers was investigated. The results showed that the burst index and internal bond strength of pulp sheet decreased with the increasing debonder loading. The density and zero-span tensile strength didn't change significantly when the debonder was added. The absorption capacity of fiber increased with increasing the de-bonder loading and achieved a maximum value of 10.3 g·g-1 when the debonder loading was 2.5%. The relevant mechanism was studied by X-ray Diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, and energy dispersive X-ray analysis (EDAX). XRD analysis indicated that the debonder had no great influence on the crystal structure of fiber. FT-IR analysis results showed that it was easier to break the intermolecular hydrogen bond than the intramolecular hydrogen bond with the incorporation of debonder. Therefore, the proportion of intramolecular hydrogen was increased. The EDAX results indicated that the debonder can decrease the binding force of fiber by shielding the hydroxyl groups and preventing the formation of hydrogen bonds.

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