Analytical allowance for dependence of anharmonic coefficients and stretching vibration frequencies of hydroxyl groups on geometry of hydrogen bonds

1990 ◽  
Vol 53 (3) ◽  
pp. 996-1001
Author(s):  
V. V. Sivchik ◽  
R. G. Zhbankov
Keyword(s):  
Hydrogen Bonds ◽  
Hydroxyl Groups ◽  
Vibration Frequencies ◽  
Stretching Vibration

On the structural diversity anions coordinate to the butterfly-shaped [(R2Sn)3O(OH)2]2+ cations and vice versa

2014 ◽  
Vol 92 (6) ◽  
pp. 496-507 ◽  
Author(s):  
Hans Reuter ◽  
Hilko Wilberts
Keyword(s):  
Hydrogen Bonds ◽  
Iodine Atom ◽  
Structural Parameters ◽  
Structural Diversity ◽  
Hydroxyl Groups ◽  
Equatorial Position ◽  
Chelating Ligands ◽  
Trigonal Bipyramidal Coordination ◽  
Trigonal Bipyramidal ◽  
Oxygen Framework

The syntheses and crystal structures of [(t-Bu2Sn)3O(OH)2]CO3·3MeOH, 1a, [(t-Bu2Sn)3O(OH)2]CO3·3H2O·acetone, 1b, [(t-Bu2Sn)3O(OH)2][I]2·[(t-Bu2Sn(OH)I]2·2DMSO, 1c, and [(Cy2Sn)3O(OH)2][I]2·2DMSO, 2a, all containing the trinuclear [(R2Sn)3O(OH)2]2+ ion have been described. The butterfly shape of this cation is derived from two annulated, four-membered tin–oxygen rings with a central μ3-oxygen atom and trigonal-bipyramidally coordinated tin atom both belonging to both rings and two μ2-hydroxyl groups and two outer, four-fold coordinated tin atoms. In 1a and 1b, the carbonate anions interact with the outer tin atoms of the cations as bidentate chelating ligands in the classical syn–syn coordination mode, and vice versa. In this way, both outer tin atoms expand their coordination sphere from four to five, with the consequence that bond angles and lengths within the cation are determined by the axial and equatorial position of the oxygen atoms within the trigonal-bipyramidal coordination on all three tin atoms. 1c consists of two different building units, an up to now unknown hydroxide iodide of composition [(t-Bu2Sn(OH)I]2 with hydrogen-bonded DMSO molecules and a [(t-Bu2Sn)3O(OH)2]2+ cation with one coordinated and one isolated, via hydrogen bonds connected iodine ion. The hydroxide iodine is built up of two five-fold coordinated tin atoms linked via two hydroxyl groups with exocyclic iodine atoms occupying axial positions at the trigonal-biypramidally coordinated tin atoms. The unprecedented coordination of the iodine ion to the [(t-Bu2Sn)3O(OH)2]2+ cation takes place between both outer tin atoms, resulting in a five-fold, trigonal-bipyramidal coordination at these tin atoms, too. Structural parameters within the so-formed [(t-Bu2Sn)3O(OH)2I]+ complex are very similar to those of 1a and 1b, with the exception of a significant lengthening of the tin–oxygen bonds opposite to the bridging iodine atom. 2a represents the first example of the [(R2Sn)3O(OH)2]2+ cation without R = t-butyl, so far. In the solid, it consists of two crystallographic independent [(Cy2Sn)3O(OH)2][I]2 building units, each connected to two DMSO molecules via hydrogen bonds. Both building units are very similar with respect to their conformation. Each of the iodine anions coordinates with only one of the two outer tin atoms, one in an inwards, one in an outwards to the tin-oxygen framework directed position. These tin atoms are therefore also trigonal-bipyramidally coordinated as in 1a−1c, but because of steric reasons one of the trigonal-bipyramids has changed its orientation within the tin–oxygen framework, accompanied by enormous changes of bond lengths and angles therein.

Crystal structure of rivastigmine hydrogen tartrate Form I (Exelon®), C14H23N2O2(C4H5O6)

2016 ◽  
Vol 31 (2) ◽  
pp. 97-103 ◽  
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Strong Hydrogen Bond ◽  
Hydroxyl Groups ◽  
A Chain ◽  
Tartrate Anion

The crystal structure of rivastigmine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rivastigmine hydrogen tartrate crystallizes in space group P21 (#4) with a = 17.538 34(5), b = 8.326 89(2), c = 7.261 11(2) Å, β = 98.7999(2)°, V = 1047.929(4) Å3, and Z = 2. The un-ionized end of the hydrogen tartrate anions forms a very strong hydrogen bond with the ionized end of another anion to form a chain. The ammonium group of the rivastigmine cation forms a strong discrete hydrogen bond with the carbonyl oxygen atom of the un-ionized end of the tartrate anion. These hydrogen bonds form a corrugated network in the bc-plane. Both hydroxyl groups of the tartrate anion form intramolecular O–H⋯O hydrogen bonds. Several C–H⋯O hydrogen bonds appear to contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1501.

scholarly journals Molecular interactions in nanocellulose assembly

2017 ◽  
Vol 376 (2112) ◽  
pp. 20170047 ◽  
Author(s):  
Yoshiharu Nishiyama
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Molecular Modelling ◽  
Hydroxyl Group ◽  
Enthalpy Of Sublimation ◽  
Dispersion Force ◽  
Hydroxyl Groups ◽  
Range Interaction ◽  
Simple Arithmetic ◽  
London Dispersion

The contribution of hydrogen bonds and the London dispersion force in the cohesion of cellulose is discussed in the light of the structure, spectroscopic data, empirical molecular-modelling parameters and thermodynamics data of analogue molecules. The hydrogen bond of cellulose is mainly electrostatic, and the stabilization energy in cellulose for each hydrogen bond is estimated to be between 17 and 30 kJ mol −1 . On average, hydroxyl groups of cellulose form hydrogen bonds comparable to those of other simple alcohols. The London dispersion interaction may be estimated from empirical attraction terms in molecular modelling by simple integration over all components. Although this interaction extends to relatively large distances in colloidal systems, the short-range interaction is dominant for the cohesion of cellulose and is equivalent to a compression of 3 GPa. Trends of heat of vaporization of alkyl alcohols and alkanes suggests a stabilization by such hydroxyl group hydrogen bonding to be of the order of 24 kJ mol −1 , whereas the London dispersion force contributes about 0.41 kJ mol −1  Da −1 . The simple arithmetic sum of the energy is consistent with the experimental enthalpy of sublimation of small sugars, where the main part of the cohesive energy comes from hydrogen bonds. For cellulose, because of the reduced number of hydroxyl groups, the London dispersion force provides the main contribution to intermolecular cohesion. This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.

Synthesis, spectroscopic (FT–IR and UV–Vis), crystallographic and theoretical studies, and a molecular docking simulation of an imatinib-like template

2019 ◽  
Vol 75 (12) ◽  
pp. 1681-1689
Author(s):  
Rodolfo Moreno-Fuquen ◽  
Kevin Arango-Daraviña ◽  
Esteban Garcia ◽  
Juan-C. Tenorio ◽  
Javier Ellena
Keyword(s):  
Crystal Growth ◽  
Hydrogen Bonds ◽  
Docking Simulation ◽  
Myelogenous Leukemia ◽  
Amino Group ◽  
Protein Residues ◽  
Function Analyzer ◽  
Stretching Vibration ◽  
Donor Acceptor ◽  
Ft Ir

The aim of the present study was to report the crystal structure and spectroscopic, electronic, supramolecular and electrostatic properties of a new polymorph of 4-(pyridin-2-yl)pyrimidin-2-amine (C9H8N4). The compound was synthesized under microwave irradiation. The single-crystal X-ray structure analysis revealed an angle of 13.36 (8)° between the planes of the rings, as well as molecules linked by Nsp 2—H...N hydrogen bonds forming dimers along the crystal. The material was analyzed by FT–IR vibrational spectroscopy, while a computational approach was used to elucidate the vibrational frequency couplings. The existence of Nsp 2—H...N hydrogen bonds in the crystal was confirmed spectroscopically by the IR peaks from the N—H stretching vibration shifting to lower wavenumbers in the solid state relative to those in the gas phase. The supramolecular studies confirmed the formation of centrosymmetric R 2 2(8) rings, which correspond to the formation of dimers that stack parallel to the b direction. Other weak C—H...π interactions, essential for crystal growth, were found. The UV–Vis spectroscopic analysis showed a donor–acceptor process, where the amino group acts as a donor and the pyridine and pyrimidine rings act as acceptors. The reactive sites of the molecule were identified and their quantitative values were defined using the electrostatic potential model proposed in the multifunctional wave function analyzer multiwfn. The calculated interaction energies between pairs of molecules were used to visualize the electrostatic terms as the leading factors against the dispersion factors in the crystal-growth process. The docking results showed that the amino group of the pyrimidine moiety was simultaneously anchored by hydrogen-bonding interactions with the Asp427 and His407 protein residues. This compound could be key for the realization of a series of syntheses of molecules that could be used as possible inhibitors of chronic myelogenous leukemia.

scholarly journals A Robust, Tough and Multifunctional Polyurethane/Tannic Acid Hydrogel Fabricated by Physical-Chemical Dual Crosslinking

Polymers ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 239 ◽  
Author(s):  
Jie Wen ◽  
Xiaopeng Zhang ◽  
Mingwang Pan ◽  
Jinfeng Yuan ◽  
Zhanyu Jia ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Tensile Strength ◽  
Polyethylene Glycol ◽  
Hydrogen Bonds ◽  
Tannic Acid ◽  
Hydroxyl Groups ◽  
Self Healing ◽  
Physical Chemical ◽  
Biomedical Field ◽  
Physical Crosslinking

Commonly synthetic polyethylene glycol polyurethane (PEG–PU) hydrogels possess poor mechanical properties, such as robustness and toughness, which limits their load-bearing application. Hence, it remains a challenge to prepare PEG–PU hydrogels with excellent mechanical properties. Herein, a novel double-crosslinked (DC) PEG–PU hydrogel was fabricated by combining chemical with physical crosslinking, where trimethylolpropane (TMP) was used as the first chemical crosslinker and polyphenol compound tannic acid (TA) was introduced into the single crosslinked PU network by simple immersion process. The second physical crosslinking was formed by numerous hydrogen bonds between urethane groups of PU and phenol hydroxyl groups in TA, which can endow PEG–PU hydrogel with good mechanical properties, self-recovery and a self-healing capability. The research results indicated that as little as a 30 mg·mL−1 TA solution enhanced the tensile strength and fracture energy of PEG–PU hydrogel from 0.27 to 2.2 MPa, 2.0 to 9.6 KJ·m−2, respectively. Moreover, the DC PEG–PU hydrogel possessed good adhesiveness to diverse substrates because of TA abundant catechol groups. This work shows a simple and versatile method to prepare a multifunctional DC single network PEG–PU hydrogel with excellent mechanical properties, and is expected to facilitate developments in the biomedical field.

scholarly journals Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa

2005 ◽  
Vol 61 (1) ◽  
pp. 58-68 ◽  
Author(s):  
Stephen A. Moggach ◽  
David R. Allan ◽  
Carole A. Morrison ◽  
Simon Parsons ◽  
Lindsay Sawyer
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Ambient Pressure ◽  
Crystal Form ◽  
Hydroxyl Groups ◽  
Orthorhombic Space Group ◽  
Crystal Forms ◽  
Hydrogen Bonded

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH...carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the —CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O...O separation of 2.918 (4) Å and an O...O...O angle of 148.5 (2)°; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7)°. Elsewhere in the structure one NH...O interaction reaches an N...O separation of 2.691 (13) Å at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH...OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH...carboxyl interactions, which have an O...O separation of 2.62 (2) Å. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCαCO torsion angle from −178.1 (2)° at 4.8 GPa to −156.3 (10)° at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH...O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.

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