Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis

2017 ◽  
Vol 78 ◽  
pp. 48-60 ◽  
Author(s):  
Natarajan Sathiyamoorthy Venkataramanan ◽  
Ambigapathy Suvitha ◽  
Yoshiyuki Kawazoe
2012 ◽  
Vol 68 (8) ◽  
pp. o2357-o2357 ◽  
Author(s):  
María-Guadalupe Hernández Linares ◽  
Sylvain Bernès ◽  
Marcos Flores-Alamo ◽  
Gabriel Guerrero-Luna ◽  
Anselmo A. Martínez-Gallegos

Diosgenin [or (22R,25R)-spirost-5-en-3β-ol] is the starting material of the Marker degradation, a cheap semi-synthesis of progesterone, which has been designated as an International Historic Chemical Landmark. Thus far, a single X-ray structure for diosgenin is known, namely its dimethyl sulfoxide solvate [Zhanget al.(2005).Acta Cryst.E61, o2324–o2325]. We have now determined the structure of the hemihydrate, C27H42O3·0.5H2O. The asymmetric unit contains two diosgenin molecules, with quite similar conformations, and one water molecule. Hydroxy groups in steroids and water molecules form O—H...O hydrogen-bondedR54(10) ring motifs. Fused edge-sharingR(10) rings form a backbone oriented along [100], which aggregates the diosgenin molecules in the crystal structure.


2020 ◽  
Vol 20 (8) ◽  
pp. 4799-4806
Author(s):  
Peng Xie ◽  
Shubin Jin ◽  
Chenggang Sun ◽  
Yushu Xie

We performed MD simulations to examine dimethyl sulfoxide (DMSO) nanocluster structures in NaCl aqueous solution with different concentrations (0.45 g/100 mL, 0.9 g/100 mL, 1.8 g/100 mL, 2.7 g/100 mL, and 3.6 g/100 mL). Results showed that interaction between Na+ and DMSO at the first solvation shells was weakened due to acceleration rotational influence of ion driven by NaCl concentration. We investigated the tetrahedral order parameter and average H-B number of water molecules. These results indicated that NaCl influenced the solvation structure of water cluster, but that of DMSO was not affected by NaCl. We also found that Na+ was prior solvated by water solution in these mixture systems, and Cl− only existed in the water cluster in our simulation systems. Consequently, we herein proposed a decentralized model that depicts microphysical structure images of DMSO in NaCl aqueous solution systems.


2014 ◽  
Vol 70 (6) ◽  
pp. m200-m201 ◽  
Author(s):  
Ricardo A. Gutiérrez-Márquez ◽  
Carmela Crisóstomo-Lucas ◽  
Reyna Reyes-Martínez ◽  
Simón Hernández-Ortega ◽  
David Morales-Morales

The title compound, [PdCl2(C18H24N2)]·(CH3)2SO·H2O, the PdIIion is in a distorted square-planar geometry. The Pd—N bond distances are 2.022 (2) and 2.027 (2) Å, the Pd—Cl bond distances are 2.2880 (7) and 2.2833 (7) Å, and the ligand bite angle is 80.07 (9)°. The dimethyl sulfoxide and water molecules form linear chains along [100] by O—H...O and O—H...S hydrogen bonds, generating eight- and 12-membered rings. C—H...Cl interactions link the chains, forming a three-dimensional arrangement. In addition, the 4,4-di-tert-butyl-2,2′-bipyridine ligand exhibits π–π stacking interactions [centroid–centroid distances = 3.8741 (15) and 3.8353 (15) Å]. The DMSO solvent is disordered and was refined with an occupancy ratio of 0.866 (3):0.134 (3).


2012 ◽  
Vol 9 (2) ◽  
pp. 76-79
Author(s):  
D.F. Marin

The paper presents results on acceleration of molecular dynamics simulations with the usage of GPUs. A system of water molecules is considered as an example of polar liquid. The intermolecular interaction is modeled with the usage of Coulomb and truncated Lennard-Jones potentials. Results of computational experiments on acceleration and performance of the developed code are presented.


2015 ◽  
Vol 71 (12) ◽  
pp. 1457-1461 ◽  
Author(s):  
Graham Smith ◽  
Daniel E. Lynch

The crystal structures of two erbium(III) complexes with 4-aminobenzoic acid (4-ABAH), namely bis(μ2-4-aminobenzoato-κ2O:O′)bis[bis(4-aminobenzoato-κ2O,O′)diaquaerbium(III)] dihydrate, [Er2(C7H6NO2)6(H2O)4]·2H2O, (I), and 4-chloro-3-nitrobenzoic acid (CLNBAH), namely poly[hexakis(μ2-4-chloro-3-nitrobenzoato-κ2O:O′)bis(dimethyl sulfoxide-κO)dierbium(III)], [Er2(C7H3ClNO4)6(C2H6OS)2]n, (II), have been determined. In the structure of solvatomorphic compound (I), the symmetry-related irregular ErO8coordination polyhedra in the discrete centrosymmetric dinuclear complex comprise two monodentate water molecules and six carboxylate O-atom donors, four from two bidentate carboxylateO,O′-chelate groups and two from the bis-monodentateO:O′-bridging group of the third 4-ABA anion. The Er—O bond-length range is 2.232 (3)–2.478 (3) Å and the Er...Er separation in the dinuclear complex unit is 4.7527 (4) Å. One of the coordinating water molecules is involved in an intra-unit O—H...O hydrogen-bonding association with an inversion-related carboxylate O-atom acceptor. In contrast, the anhydrous compound (II) is polymeric, based on centrosymmetric dinuclear repeat units comprising ErO7coordination polyhedra which involve four O-atom donors from two bidentateO:O′-bridging carboxylate groups, one O-atom donor from the monodentate dimethyl sulfoxide ligand and two O-atom donors from the third bridging CLNBA anion. The latter provides the inter-unit link in the one-dimensional coordination polymer extending along [100]. The Er—O bond-length range in (II) is 2.239 (6)–2.348 (6) Å and the Er...Er separation within the dinuclear unit is 4.4620 (6) Å. In the crystal of (I), extensive inter-dimer O—H...O and N—H...O hydrogen-bonding interactions involving both the coordinating water molecules and the solvent water molecules, as well as the amine groups of the 4-ABA anions, give an overall three-dimensional network structure. Within this structure are also weak π–π ring interactions between two of the coordinating ligands [ring-centroid separations = 3.676 (3) and 3.711 (2) Å]. With (II), only weak intra-polymer C—H...O, C—H...Cl and C—H...S interactions are present.


Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3666
Author(s):  
Liu ◽  
Zhang ◽  
Huang ◽  
Wu ◽  
Ouyang

The effects of hydrogen bonds on the molecular structure of water-tetrahydrofuran (H2O–THF), water-dimethyl sulfoxide (H2O–DMSO), and water-tetrahydrofuran-dimethyl sulfoxide (H2O–THF–DMSO) in binary aqueous solutions and ternary aqueous solutions were studied using Raman spectroscopy. The results indicate that in the binary aqueous solution, the addition of THF and DMSO will generate hydrogen bonds with water molecules, resulting in changes in the peak positions of S=O bonds and C–O bonds. Compared with the binary aqueous solutions, the hydrogen bonds between DMSO and THF, and the hydrogen bonds between DMSO and H2O in the ternary aqueous solutions are competitive, and the hydrogen bond competition is susceptible to water content. In addition, the formation of hydrogen bonds will destroy the fully hydrogen-bonded water and make it change to the partially hydrogen-bonded water. By fitting the spectra into the three Gaussian components assigned to water molecules with different hydrogen bonding (HB) environments, these spectral features are interpreted by a mechanism that H2O in different solution systems has equal types of water molecules with similar HB degrees-fully hydrogen-bonded H2O (FHW) and partially hydrogen-bonded H2O (PHW). The ratio of the intensity transition from FHW to PHW is determined based on Gaussian fitting. Therefore, the variation of hydrogen bond competition can be supplemented by the intensity ratio of PHW/FHW ((IC2 + IC3)/IC1). This study provides an experimental basis for enriching the hydrogen bonding theory of multivariate aqueous solution systems.


1968 ◽  
Vol 9 (2) ◽  
pp. 855-858
Author(s):  
P. A. Bazhulin ◽  
L. Singurel ◽  
A. V. Chekunov

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