hydrogen bonds
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Shanchen Li ◽  
Yang Chen ◽  
Zhihui Li ◽  
Junhua Zhao ◽  
Ning Wei

IUCrData ◽  
2022 ◽  
Vol 7 (1) ◽  
Lin Liu ◽  
Zheng-Bo Han

In the title compound, [Cu(C9H6N3O2)2(C2H7N)2], the Cu2+ cation is situated on an inversion center and is coordinated by the N atoms of two dimethylamine ligands and the carboxylate O atoms of two 4-(1,2,4-triazol-1-yl)benzoate anions, leading to a slightly distorted square-planar N2O2 coordination environment. In the crystal, intermolecular N—H...N hydrogen bonds between the amine function and the central N atom of the triazole ring lead to the formation of ribbons parallel to [1\overline{1}1]. Weak intermolecular C—H...O hydrogen-bonding interactions are also observed that consolidate the crystal packing.

Nate Schultheiss ◽  
Jeremy Holtsclaw ◽  
Matthias Zeller

Substituted triazines are a class of compounds utilized for scavenging and sequestering hydrogen sulfide in oil and gas production operations. The reaction of one of these triazines under field conditions resulted in the formation of the title compound, 2-(1,3,5-dithiazinan-5-yl)ethanol, C5H11NOS2, or MEA-dithiazine. Polymorphic form I, in space group I41/a, was first reported in 2004 and its extended structure displays one-dimensional, helical strands connected through O—H...O hydrogen bonds. We describe here the form II polymorph of the title compound, which crystallizes in the orthorhombic space group Pbca as centrosymmetric dimers through pairwise O—H...N hydrogen bonds from the hydroxyl moiety to the nitrogen atom of an adjacent molecule.

Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Saranphong Yimklan ◽  
Yothin Chimupala ◽  
Sutsiri Wongngam ◽  
Nippich Kaeosamut

A three-dimensional coordination polymer, poly[hexaaqua(μ4-glutarato)bis(μ3-sulfato)dineodymium(III)], [Nd2(H2O)6(glutarato)(SO4)2] n (glutarato2– = C5H6O4 2–), 1, consisting of cationic {Nd2(H2O)6(SO4)2} n 2n+ layers linked by bridging glutarate ligands, was synthesized by the microwave-heating technique within few minutes. The crystal structure of 1 consists of two crystallographically independent TPRS-{NdIIIO9} (TPRS is tricapped trigonal–prismatic geometry) units that form an edge-sharing dinuclear cluster interconnected to neighbouring dimers by the μ3-SO4 2– anions, yielding a cationic two-dimensional {Nd2(H2O)6(SO4)2} n 2n+ sheet. Adjacent cationic layers are then linked via the μ4-glutarato2– ligands into a three-dimensional coordination network. Strong O—H...O hydrogen bonds are the predominant interaction in the crystal structure.

2022 ◽  
Vol 0 (0) ◽  
Christoph Ludwig Teske ◽  
Huayna Terraschke ◽  
Sebastian Mangelsen ◽  
Wolfgang Bensch

Abstract The title compounds were prepared by precipitation from acidic solutions of the reactants in acetone/water. Bi(S2CNH2)2Cl (1) crystallizes in the non-centrosymmetric trigonal space group P32 with a = 8.6121(3) and c = 11.1554(4) Å, Z = 3; Bi(S2NH2)2SCN (2) in P21/c (monoclinic) with a = 5.5600(2), b = 14.3679(5), c = 12.8665(4) Å, and β = 90.37(3)°. In the crystal structure of 1 Bi3+ is in a sevenfold coordination of two bidentate and one monodentate S2CHNH2 − anions with an asymmetric coordination pattern of five Bi–S and two Bi–Cl− bonds. The linkage of these polyhedra via common Cl–S edges leads to a 1D polymeric structure with undulated chains propagating in the direction [001]. These chains are linked by strong and medium strong hydrogen bonds forming the 3D crystal structure. In the crystal structure of 2 the Bi3+ cation is in an eightfold coordination. The polyhedron can be described as a significantly distorted tetragonal anti-prism, capped by an additional S atom. Two of these prisms share a common quadrilateral face to form a “prism-double” (Bi2S10N2). These building units are linked by common edges, and the resulting 1D infinite angulated chains propagate along [100]. By contrast to organo-dithiocarbamate compounds, where C–H···X bridges are dominant, the interchain connections in the crystal structures of 1 and 2 are formed exclusively via N–H···S, N–H···Cl, and N–H···N interactions, generating the 3D networks. A significant eccentricity of the Bi3+ cation in the crystal structures of both complexes is observed. Both compounds emit light in the orange range of the electromagnetic spectrum.

2022 ◽  
Vol 12 (1) ◽  
Shengmin Zhou ◽  
Yuanhao Liu ◽  
Sijian Wang ◽  
Lu Wang

AbstractShort hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.

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