Insight into the Formation of Cocrystals of Flavonoids and 4,4′-Vinylenedipyridine: Heteromolecular Hydrogen Bonds, Molar Ratio, and Structural Analysis

2021 ◽  
Author(s):  
Yanhong Zhang ◽  
Bin Zhu ◽  
Wei-Jie Ji ◽  
Chun-Yang Guo ◽  
Minghuang Hong ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Molar Ratio ◽  
Insight Into

scholarly journals Insight into the origin of SARS-CoV-2 through structural analysis of receptor recognition: a molecular simulation study

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 8718-8729
Author(s):  
Jixue Sun ◽  
Meijiang Liu ◽  
Na Yang
Keyword(s):  
Molecular Dynamics ◽  
Structural Analysis ◽  
Molecular Dynamics Simulations ◽  
Molecular Simulation ◽  
Simulation Study ◽  
Receptor Recognition ◽  
Dynamics Simulations ◽  
Insight Into

The origin of SARS-CoV-2 through structural analysis of receptor recognition was investigated by molecular dynamics simulations.

scholarly journals Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fengbin Wang ◽  
Ordy Gnewou ◽  
Charles Modlin ◽  
Leticia C. Beltran ◽  
Chunfu Xu ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Synthetic Peptide ◽  
Quaternary Structure ◽  
De Novo ◽  
Rational Approach ◽  
Lateral Interactions ◽  
Protein Assemblies ◽  
Self Assembling ◽  
Arginine Residues ◽  
Insight Into

AbstractThe exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

scholarly journals Crystal structure of the new hybrid material bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate

2015 ◽  
Vol 71 (11) ◽  
pp. 1384-1387
Author(s):  
Marwen Chouri ◽  
Habib Boughzala
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Molar Ratio ◽  
Water Molecules ◽  
Site Symmetry ◽  
Two Dimensional ◽  
Slow Evaporation ◽  
Solution Ph

The title compound bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate, (C6H14N2)2[Bi2Cl10]·2H2O, was obtained by slow evaporation at room temperature of a hydrochloric aqueous solution (pH = 1) containing bismuth(III) nitrate and 1,4-diazabicyclo[2.2.2]octane (DABCO) in a 1:2 molar ratio. The structure displays a two-dimensional arrangement parallel to (100) of isolated [Bi2Cl10]4−bioctahedra (site symmetry -1) separated by layers of organic 1,4-diazoniabicyclo[2.2.2]octane dications [(DABCOH2)2+] and water molecules. O—H...Cl, N—H...O and N—H...Cl hydrogen bonds lead to additional cohesion of the structure.

Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method

2021 ◽  
Vol 11 (1) ◽  
pp. 127-134
Author(s):  
Nhung Ngo Thi Hong ◽  
Huong Dau Thi Thu ◽  
Trung Nguyen Tien
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Energy Surface ◽  
Covalent Bond ◽  
Electrostatic Energy ◽  
Substantial Contribution ◽  
Structure Stability ◽  
Dispersion Terms ◽  
Insight Into

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.

Isomorphous rare-earth tris[bis(2,6-diisopropylphenyl) phosphate] complexes and their catalytic properties in 1,3-diene polymerization and in the inhibited oxidation of polydimethylsiloxane

2018 ◽  
Vol 74 (5) ◽  
pp. 590-598 ◽  
Author(s):  
Mikhail E. Minyaev ◽  
Alexander N. Tavtorkin ◽  
Sof'ya A. Korchagina ◽  
Galina N. Bondarenko ◽  
Andrei V. Churakov ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Catalytic Properties ◽  
Molar Ratio ◽  
High Catalytic Activity ◽  
Catalytic Systems ◽  
Neodymium Complex ◽  
Butadiene Polymerization ◽  
Bond Network ◽  
Phosphate Ligands ◽  
Monodentate Coordination

Crystals of mononuclear tris[bis(2,6-diisopropylphenyl) phosphato-κO]pentakis(methanol-κO)lanthanide methanol monosolvates of lanthanum, [La(C24H34O4P)3(CH3OH)5]·CH3OH, (1), cerium, [Ce(C24H34O4P)3(CH3OH)5]·CH3OH, (2), and neodymium, [Nd(C24H34O4P)3(CH3OH)5]·CH3OH, (3), have been obtained by reactions between LnCl3(H2O) n (n = 6 or 7) and lithium bis(2,6-diisopropylphenyl) phosphate in a 1:3 molar ratio in methanol media. Compounds (1)–(3) crystallize in the monoclinic P21/c space group and have isomorphous crystal structures. All three bis(2,6-diisopropylphenyl) phosphate ligands display a κO-monodentate coordination mode. The coordination number of the metal atom is 8. Each [Ln{O2P(O-2,6-iPr2C6H3)2}3(CH3OH)5] molecular unit exhibits four intramolecular O—H...O hydrogen bonds, forming six-membered rings. The unit forms two intermolecular O—H...O hydrogen bonds with one noncoordinating methanol molecule. All six hydroxy H atoms are involved in hydrogen bonding within the [Ln{O2P(O-2,6-iPr2C6H3)2}3(CH3OH)5]·CH3OH unit. This, along with the high steric hindrance induced by the three bulky diaryl phosphate ligands, prevents the formation of a hydrogen-bond network. Complexes (1)–(3) exhibit disorder of two of the isopropyl groups of the phosphate ligands. The cerium compound (2) demonstrates an essential catalytic inhibition in the thermal decomposition of polydimethylsiloxane in air at 573 K. Catalytic systems based on the neodymium complex tris[bis(2,6-diisopropylphenyl) phosphato-κO]neodymium, (3′), which was obtained as a dry powder of (3) upon removal of methanol, display a high catalytic activity in isoprene and butadiene polymerization.

Synthese und Kristallstrukturen einiger Tetramethylstibonium-Hydrogendicarboxylate / Synthesis and Crystal Structures of Some Tetramethylstibonium Hydrogendicarboxylates

1982 ◽  
Vol 37 (11) ◽  
pp. 1393-1401 ◽  
Author(s):  
Beatrix Milewski-Mahrla ◽  
Hubert Schmidbaur
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Spectroscopic Data ◽  
Molar Ratio ◽  
Ionic Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Carboxylate Oxygen ◽  
Donor Acceptor ◽  
New Compounds

Reactions of pentamethylantimony (CH3)5Sb with carboxylic acids in the molar ratio 1:2 afford one equivalent of methane and essentially quantitative yields of crystalline tetramothylstibonium hydrogendicarboxylates. Six new compounds of this series have been synthesized using benzoic, o-phthalic, salicylic, 4-ethoxy-salicylic, oxalic, and malic acid, and characterized by analytical and spectroscopic data. An ionic structure with strong hydrogen bonds in the anionic components is proposed.The crystal structures of the hydrogen-dibenzoato (1), hydrogen-ortho-plithalato (2) and 4-ethoxy-hydrogen-salicylate (3) were determined by single crystal X-ray diffraction. The compounds can be described as having ionic lattices with some donor-acceptor inter­actions between the stibonium centers and the carboxylate oxygen atoms. The anions are characterized by strong hydrogen bonds O...H...O. Thus, the (CH3)4Sb-tetrahedron in 1 is distorted by two benzoate oxygon atoms (at 304(2) and 340(2) pin). The cation in 2 is largely undistorted and the anion has a hydrogenphthalate hydrogen bond of d(O...H...O) = 232 pm. The cation-anion contact in 3 is as short as d(Sb-O) = 289 pm rendering the Sb atom pentacoordinate.

scholarly journals 1,1′,3,3′-Tetramesitylquinobis(imidazole)-2,2′-dithione

IUCrData ◽  
2019 ◽  
Vol 4 (9) ◽  
Author(s):  
Jayaraman Selvakumar ◽  
Kuppuswamy Arumugam
Keyword(s):  
Crystal Structure ◽  
Molecular Weight ◽  
Solid State ◽  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Cell Volume ◽  
Title Compound ◽  
Unit Cell Volume ◽  
Density Peaks ◽  
Solvent Molecules

The solid-state structural analysis of the title compound [systematic name: 5,11-disulfanylidene-4,6,10,12-tetrakis(2,4,6-trimethylphenyl)-4,6,10,12-tetraazatricyclo[7.3.0.03,7]dodeca-1(9),3(7)-diene-2,8-dione], C44H44N4O2S2 [+solvent], reveals that the molecule crystallizes in a highly symmetric cubic space group so that one quarter of the molecule is crystallographically unique, the molecule lying on special positions (two mirror planes, two twofold axes and a center of inversion). The crystal structure exhibits large cavities of 193 Å3 accounting for 7.3% of the total unit-cell volume. These cavities contain residual density peaks but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent molecules to the scattering was removed using a solvent mask and is not included in the reported molecular weight. No classical hydrogen bonds are observed between the main molecules.

Understanding distortions of inorganic substructures in chloridobismuthates(III)

2021 ◽  
Vol 77 (5) ◽  
Author(s):  
Maciej Bujak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Inorganic Anions ◽  
Cambridge Structural Database ◽  
Molar Ratio ◽  
Organic Cations ◽  
Hybrid Crystals ◽  
Structural Database ◽  
Distortion Parameters

The molar ratio variations of organic and inorganic reactants of chloridobismuthates(III) with N,N-dimethylethane-1,2-diammonium, [(CH3)2NH(CH2)2NH3]2+, and N,N,N′,N′-tetramethylguanidinium, [NH2C{N(CH3)2}2]+, cations lead to the formation of four different products, namely, tris(N,N-dimethylethane-1,2-diammonium) bis[hexachloridobismuthate(III)], [(CH3)2NH(CH2)2NH3]3[BiCl6]2 (1), catena-poly[N,N-dimethylethane-1,2-diammonium [[tetrachloridobismuthate(III)]-μ-chlorido]], {[(CH3)2NH(CH2)2NH3][BiCl5]} n (2), tris(N,N,N′,N′-tetramethylguanidinium) tri-μ-chlorido-bis[trichloridobismuthate(III)], [NH2C{N(CH3)2}2]3[Bi2Cl9] (3), and catena-poly[N,N,N′,N′-tetramethylguanidinium [[dichloridobismuthate(III)]-di-μ-chlorido]], {[NH2C{N(CH3)2}2][BiCl4]} n (4). The hybrid crystals 1–4, containing relatively large but different organic cations, are composed of four distinct anionic substructures. They are built up from isolated [BiCl6]3− octahedra in 1, from face-sharing bioctahedral [Bi2Cl9]3− units in 3, from polymeric corner-sharing {[BiCl5]2−} n chains in 2 and from edge-sharing {[BiCl4]−} n chains in 4. The distortions shown by the single [BiCl6]3− polyhedra in 1–4 are associated with intrinsic interactions within the anionic substructures and the organic...inorganic substructures interactions, namely, N/C—H...Cl hydrogen bonds. The first factor is the stronger, which is evident in comparison of the experimentally determined geometrical and calculated distortion parameters for the isolated octahedron in 1 to the more complex inorganic substructures in 2–4. The formation of N—H...Cl hydrogen bonds, in terms of their number and strength, is favoured for 1 and 3 containing relatively easily accessed hydrogen-bond acceptors of isolated [BiCl6]3− and [Bi2Cl9]3− units. The studies of the deviations from regularity of the [BiCl6]3− octahedra within inorganic substructures were supported by a survey of the Cambridge Structural Database, which confirmed the role played by different factors in the variations in geometry of the inorganic anions.

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