Thermally induced fluid reversed hexagonal (H(II)) mesophase

In the present study we characterized the microstructures of the Lc and HII phases in a glycerol monooleate (GMO)/tricaprylin (TAG)/water mixture as a function of temperature. We studied the factors that govern the formation of a low-viscosity HII phase at relatively elevated temperatures (>35 degrees C). This phase has very valuable physical characteristics and properties. The techniques used were differential scanning calorimetry (DSC), wide- and small-angle X-ray scattering (WAXS and SAXS, respectively), NMR (self-diffusion and (2)H NMR), and Fourier transform infrared (FTIR) spectroscopies. The reverse hexagonal phase exhibited relatively rapid flow of water in the inner channels within the densely packed cylindrical aggregates of GMO with TAG molecules located in the interstices. The existence of two water diffusion peaks reflects the existence of both mobile water and hydration water at the GMO-water interface (hydrogen exchange between the GMO hydroxyls and water molecules). Above 35 degrees C, the sample became fluid yet hexagonal symmetry was maintained. The fluidity of the HII phase is explained by a significant reduction in the domain size and also perhaps cylinder length. This phenomenon was characterized by higher mobility of the GMO, lower mobility of the water, and a significant dehydration process.     

Molecular structure of cis-trifluoromethylmercury-bis(triphenylphosphine)trifluoromethylplatinum(II)

Conclusions An x-ray structure study has shown that the CF₃HgPt(CF₃)[P(C₆H₅)₃]₂ molecule exists in cis configuration. The length of the Hg-Pt bond has been determined for the first time as 2.569(2) Å.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 3, pp. 621–627, March, 1978.     

An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Structural and dynamical properties of Zn(II) in aqueous solution were investigated, based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation at double-zeta Hartree-Fock quantum mechanical level including the first and second hydration shells into the QM region. The inclusion of the second shell in the QM region resulted in significant changes in the properties of the hydrate. The first shell coordination number was found to be 6, the second shell consists of approximately 14 water molecules. The structural properties were determined in terms of RDF, ADF, tilt and theta angle distributions, while dynamics were characterized by mean ligand residence times, ion-ligand stretching frequencies and the vibrational and librational motions of water ligands.     

Molecular dynamics simulation of the renin inhibitor H142 in water

Summary H142 is a synthetic decapeptide designed to inhibit renin, an enzyme acting in the regulation of blood pressure. The inhibiting effect of H142 is caused by a reduction of a-Leu-Val-peptide bond (i. e. C(=O)-NHCH₂-NH). The conformational and dynamical properties of H142 and its unreduced counterpart (H142n) was modelled by means of molecular dynamics simulations. Water was either included explicitly in the simulations or as a dielectric continuum. When water molecules surround the peptides, they remain in a more or less extended conformation through the simulation. If water is replaced by a dielectric continuum, the peptides undergo a conformational change from an extended to a folded state. It is not clear whether this difference is a consequence of a too short simulation time for the water simulations, a force-field artifact promoting extended conformations, or if the extended conformation represents the true conformational state of the peptide. A number of dynamic properties were evaluated as well, such as overall rotation, translational diffusion, side-chain dynamics and hydrogen bonding.     

Molecular dynamics simulation of structure H clathrate-hydrates of binary guest molecules

Molecular dynamics (MD) simulations are performed to study the stability of structure H clathrate-hydrates of methane+large-molecule guest substance (LMGS) at temperatures of 270, 273, 278 and 280 K under canonical (NVT-) ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane (2-MB), 2,3-dimethylbutane (2,3-DMB), neohexane (NH), methylcyclohexane (MCH), adamantane and tert-butyl methyl ether (TBME). In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.     

Molecular dynamics simulations of Cu(II) and the PHGGGWGQ octapeptide

The interaction between Cu2+ and the copper-binding octapeptide region in the human prion protein has been investigated by molecular dynamics simulations. In total four different nonbonded and bonded models were used in the study. Charge sets containing atomic partial charges were developed for these models. Out of the considered models, the bonded model performed physically in the most correct way. The simulations with the bonded model showed that the water molecules in the axial position are very labile. The tryptophan indole ring can remain in a stable position on top of the equatorial coordination plane of copper without water mediation. Strong aromatic interaction was observed between the imidazole and indole rings. The nonbonded models showed a tendency for water-mediated interaction between the copper ion and different carbonyl oxygen atoms. In the case of the bonded model, a carbonyl group could also interact directly with the copper ion in one of the apical position.     

Structure and dynamics of the lincomycin-copper(II) complex in water solution by (1)H and (13)C NMR studies

The copper(II) complex of lincomycin in water solution at pH = 7.15 was characterized by (1)H and (13)C NMR and UV-vis spectroscopy. A 1:1 complex is formed in these conditions. The temperature dependence of spin-lattice relaxation rates was measured, showing that all protons behave in a similar fashion and slow exchange conditions prevail. The spin-lattice relaxation rate enhancements were interpreted by the Solomon-Bloembergen-Morgan theory. Reorientational dynamics of the complex was approximated by evaluating the motional correlation time of free lincomycin in water solution. The observed proton and carbon relaxation rate enhancements allowed us to calculate copper-proton and copper-carbon distances that were used for building a molecular model of the complex. The obtained data provide an interpretation of the relatively high stability constant.     

Molecular dynamics study of the stability of methane structure H clathrate hydrates

Molecular dynamics simulations are used to study the stability of structure H (sH) methane clathrate hydrates in a 3 x 3 x 3 sH unit cell replica. Simulations are performed at experimental conditions of 300 K and 2 GPa for three methane intermolecular potentials. The five small cages of the sH unit cell are assigned methane guest occupancies of one and large cage guest occupancies of one to five are considered. Radial distribution functions, unit cell volumes, and configurational energies are studied as a function of large cage CH(4) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies. Large cage occupancy of five is the most stable configuration for a Lennard-Jones united-atom potential and the Tse-Klein-McDonald potential parametrized for condensed methane phases and two for the most stable configuation for the Murad and Gubbins potential.     

Molecular dynamics simulations of binary structure H hydrogen and methyl-tert-butylether clathrate hydrates

Binary structure H (sH) hydrogen and methyl-tert-butylether (MTBE) clathrate hydrates are studied with molecular dynamics simulations. Simulations on a 3 x 3 x 3 sH unit cell with up to 4.7 mass % hydrogen gas are run at pressures of 100 bars and 2 kbars at 100 and 273 K. For the small and medium cages of the sH unit cell, H2 guest molecule occupancies of 0, 1 (single occupancy), and 2 (double occupancy) are considered with the MTBE molecule occupying all of the large cages. An increase of the small and medium cage occupancies from 1 to 2 leads to a jump in the unit cell volume and configurational energy. Calculations are also set up with 13, 23, and 89 of the MTBE molecules in the large cages replaced by sets of three to six H2 molecules, and the effects on the configurational energy and volume of the simulation cell are determined. As MTBE molecules are replaced with sets of H2 guests in the large cages, the configurational energy of the unit cell increases. At the lower temperature, the energy and volume of the clathrate are not sensitive to the number of hydrogen guests in the large cages; however, at higher temperatures the repulsions among the H2 guest molecules in the large cages cause an increase in the system energy and volume.     

Molecular dynamics simulations of hydration shell on montmorillonite (001) in water

Molecular dynamics simulations (MDS) of montmorillonite (001)/water interface system were used for studying the hydration shell on the montmorillonite surface in this work. The study was performed on the simulation of concentration profile and self‐diffusion coefficients. The results have shown that there was a hydration shell on the surface with the thickness of approximately 1.74 nm, which was composed of six ordered water molecule layers, including ordered layers and transition layers. The water molecules in the shell were closely and orderly arranged than those in bulk water, leading to a higher concentration of water molecules. Copyright © 2016 John Wiley & Sons, Ltd.     

Paramagnetic carbonyl cobalt(II) complexes. Molecular structure of bromocarbonyl-1,1,1-tris(diphenylphosphinomethyl)ethanecobalt(II) tetraphenylborate

Carbon monoxide or cyclohexyl isonitrile (L) react with the dinuclear five-coordinated derivatives of 1,1,1-tris(diphenylphosphinomethyl)ethane, (triphos), [(triphos)Co(μ-X)₂Co(triphos)](BPh₄)₂ (X = halide) to give complexes of formula [(triphos)Co(L)X]BPh₄. The latter are rare examples of paramagnetic cobalt(II) carbonyl complexes. The molecular structure of [(triphos)Co(CO)Br]BPh₄ has been determined from counter diffraction data. The crystals are monoclinic, space group P2₁/a with cell dimensions a 20.225(8), b 20.664(9), c 13.301(5); β 97.24(5)°, D_c = 1.338 g cm^?3 for Z = 4. Full-matrix least squares refinement led to the conventional R factor of 0.057 for 3648 observed reflections. The molecular structure consists of five-coordinate [(triphos)Co(CO)Br]⁺ cations of intermediate geometry and BPh^?₄ anions.     

从分子构造到分子构型和分子构象（中）

我们从(上)文看到,化学家们最初认为物质的性质只决定于物质的分子组成,后来逐渐认识到物质的性质除决定于物质的分子组成外,还决定于分子构造.     

Molecular structure of cyanidin metal complexes: Al(III) versus Mg(II)

Metal complexation by anthocyanins is a very efficient mechanism for protecting plants. While Mg is an essential metal for life, typically found bound to anthocyanins, Al interferes with the metabolism of the former. Density functional theory and the polarizable continuum model are used to study cyanin (the simplest anthocyanin bearing a catechol unit) complexes with Mg(II) and Al(III), considering different metal ligand stoichiometries. Results obtained for metal-binding energies indicate that Al(III) complexes are always more stable than those of Mg(II). Furthermore, reaction energies for the metal exchange process show that free Al(III) (hexaaquo complex) is always able to displace Mg(II). This displacement is more favored when the metal ligand ratio decreases. Thus, anthocyanins are implied in suppressing Al(III) toxicity by enabling its accumulation and reducing its migration to ecosystems. The characteristics of Al(III)?Ccyanidin and Mg(II)?Ccyanidin bonds are investigated using the quantum theory of atoms in molecules. We find these complexes are more stabilized by ion?Cdipole electrostatic interactions than by electron pair sharing, as predicted by the Hard and Soft Acids Theory. Globally, two factors increase the covalent character: replacement of Mg(II) by Al(III) and replacement of water by cyanidin ligands.     

Molecular sheets in the crystal structure of a Ba(II) complex with imidazole-4,5-dicarboxylate and water ligands

The structure of poly-tetraaquabis(μ-Himidazole-4,5-dicarboxylato-N,O;-O′)barium(II) dihydrate, Ba(C₅H₃N₂O₄)₂(H₂O)₄·2H₂O is built of molecular sheets in which singly-deprotonated imidazole-4,5-dicarboxylate [H(4,5-IDA)] bridges metal ions using its N, O bonding moiety and one oxygen atom of its second carboxylate group. Each barium(II) is coordinated by N, O bonding moieties of two ligands, two carboxylate oxygen atoms of two other ligands and four waters. The coordination number of Ba(II) is ten, and the coordination polyhedron contains fourteen faces. A network of hydrogen bonds is responsible for the stability of the crystal.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

New mesomorphic organocyclosiloxanes II. Thermal behaviour and mesophase structure of organocyclohexasiloxanes

Investigations of thermotropic phase transitions performed on organocyclosiloxanes [PhSi(O)OSiR]₆, where R is Me₃, Me₂(CH₂Cl) or Me₂(CH≃CH₂), have revealed that all these hexamers are mesomorphic compounds. The hexamers exhibit uncommon polymesomorphic behaviour forming two quite different mesomorphic structures. The molecular arrangement in the low temperature (LT) modification is characterized by two-dimensional (2D) long-range order with hexagonal packing. The X-ray diffraction pattern and peculiarities of molecular packing in the crystal lead us to suggest that the LT-mesophase is columnar, presumably of the Col_hd type. The LT-mesophase is formed by dimeric moieties, which associate with each other in column-like substructures, the ring planes not orthogonal to the stack axis. The high temperature (HT) mesophase is a plastic crystal (3D-order), where molecules take up positions in a face-centred cubic lattice. This is a very uncommon example of thermal behaviour for plastic crystals that provides a unique opportunity to bridge the gap between plastic crystalline and liquid crystalline mesomorphic behaviour. The thermal and structural properties of the mesophases depend upon the type of side groups of the hexamers. The size of the ring also affects the phase behaviour and the mesomorphic structure. This conclusion is consistent with data obtained by us earlier for cyclotetrasiloxanes.     

Molecular structure and bonding in octamethylporphyrin tin(II), SnN4C28H28

Gas-phase electron diffraction was applied for the molecular structure determination of octamethylporphyrin tin(II), SnN(4)C(28)H(28), at the temperature of 706(10) K. The molecule was found to possess C(4v) symmetry with the Sn atom 1.025(30) ? above the plane of the N atoms and the following main internuclear distances (r(h1), ?): Sn-N = 2.301(9), C(α)-N = 1.360(8), C(α)-C(β) = 1.453(4), C(α)-C(m) = 1.395(4), C(β)-C(CH3) = 1.498(4). Quantum chemical calculations, DFT (B3LYP, BP86, PBE, PBE0) with cc-pVDZ, cc-pVTZ and cc-pVQZ basis sets reproduce the experimental bond distances with accuracy within 0.03 ?. According to NBO(B3LYP/cc-pVTZ) analysis, the direct donation gives a prevailing contribution to Sn-N bonding, decreasing the net charge on Sn from formal +2 to +1.28. The substitution effects at the pyrrole rings are discussed. The ability of different theoretical methods to predict the structure of this compound is analyzed.     

Bonding properties and electronic structures of glycylglycinato copper(II) complexes. Molecular structure of acetylhistaminegly-cylglycinatocopper(II) dihydrate

Summary Mixed ligand diglycinatocopper(II) complexes of the Cu(glygly)L·nH₂O type, where glygly stands for [NH₂-CH₂ CONCH₂CO₂]^2– and L for imidazole (n = 1.5), N-methylimidazole (n = 1), 2-methylimidazole (n = 2), 4-methylimidazole (n = 2), 4-phenylimidazole (n = 2), N-acetylhistamine (n = 2) and NH₃ (n = 2), were prepared and characterized by elemental analyses, i.r., vis. and e.p.r. spectroscopic measurements. The molecular structure of [Cu(glygly)(achmH)]·2H₂O (achmH = acetylhistamine) was determined using three dimensional XRD data. The structure consists of distorted square planar [Cu(glygly)-(achmH)] units interconnected via the peptide oxygen at the apex to complete a square pyramidal structure, Cu—O-(peptide) 2.477(2) Å. The H₂O molecules, not binding directly to the copper ion, involve in intermolecular hydrogen bonding with the copper units. The dianionic glygly ligand and the imidazole ring bind strongly to the central copper ion with Cu—N(amino) 2.045(6) Å, Cu—N-(peptide) 1.891(5) Å, Cu—O(carboxylate) 2.001(4) Å and Cu—N(imidazole) 1.956(5) Å. The dihedral angle between the imidazole nucleus and the CuN₃O xy plane is 6.0°. Similar structures with a CuN₃O coordination plane are proposed for the imidazole complexes, based on spectroscopic data. The bonding properties of the glygly ligand and the unidentate imidazole ligands are elucidated and discussed with reference to the electronic structures of the complexes deduced from Gaussian analyses.