Equivalent potential of water for electronic structure of asparagine

The equivalent potential of water for the electronic structure of asparagine(Asn) is constructed by using the first‐principles, all‐electron, ab initio calculation. The process is composed of three steps. The first step is to determine the geometric structure of Asn+nH₂O system with a minimum energy. The second step is to calculate the electronic structure of Asn with the potential of water molecules by using the self‐consistent cluster‐embedding (SCCE) method, based on the result obtained in the first step. The last step is to calculate the electronic structure of Asn with the potential of dipole after replacing water molecules with dipoles. The results show that the major effect of water molecules on Asn' electronic structure be raising the occupied electronic states by 0.034 Ry on average and narrowing energy gap by 0.91%. The effect of water on the electronic structure of Asn can be well simulated by using dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Mild solution synthesis of plate-like and rod-like ZnO crystals

Micro-disks and micro-rods of ZnO were successfully synthesized by a mild solution process using zinc chloride as starting material. The morphology of the ZnO crystals changed substantially, depending on the concentrations of the Zn²⁺ ion and organic additives in the solution. A plate-like Zn₅(OH)₈Cl₂·H₂O precursor with a layered structure could be produced in solutions with high concentrations of chloride ions. The thermal stability, including phase composition and morphology, of the as-prepared Zn₅(OH)₈Cl₂·H₂O in air and water was investigated.     

L‐Leucylglycine 0.67‐hydrate and [(4S)‐2,2‐dimethyl‐4‐(2‐methylpropyl)‐5‐oxoimidazolidin‐3‐ium‐1‐yl]acetate

Crystals of L‐leucylglycine (L‐Leu–Gly) 0.67‐hydrate, C₈H₁₆N₂O₃·0.67H₂O, (I), were obtained from an aqueous solution. There are three symmetrically independent dipeptide zwitterionic molecules in (I) and they are parallel to one another. The hydrogen‐bond network composed of carboxylate and amino groups and water molecules extends parallel to the ab plane. Hydrophilic regions composed of main chains and hydrophobic regions composed of the isobutyl groups of the leucyl residues are aligned alternately along the c axis. An imidazolidinone derivative was obtained from L‐Leu–Gly and acetone, viz. [(4S)‐2,2‐dimethyl‐4‐(2‐methylpropyl)‐5‐oxoimidazolidin‐3‐ium‐1‐yl]acetate, C₁₁H₂₀N₂O₃, (II), and was crystallized from a methanol–acetone solution of L‐Leu–Gly. The unit‐cell parameters coincide with those reported previously for L‐Leu–Gly dihydrate revealing that the previously reported values should be assigned to the structure of (II). One of the imidazolidine N atoms is protonated and the ring is nearly planar, except for the protonated N atom. Protonated N atoms and deprotonated carboxy groups of neighbouring molecules form hydrogen‐bonded chains. The ring carbonyl group is not involved in hydrogen bonding.     

How Water Accelerates Bivalent Ion Diffusion at the Electrolyte/Electrode Interface

The effect of H₂O in electrolytes and in electrode lattices on the thermodynamics and kinetics of reversible multivalent‐ion intercalation chemistry based on a model platform of layered VOPO₄ has been investigated. The presence of H₂O at the electrolyte/electrode interface plays a key role in assisting Zn²⁺ diffusion from electrolyte to the surface, while H₂O in the lattice structure alters the working potential. More importantly, a dynamic equilibrium between bulk electrode and electrolyte is eventually reached for H₂O transport during the charge/discharge cycles, with the water activity serving as the key parameter determining the direction of water movement and the cycling stability.     

Cyclic lipoundecapeptide tensin from Pseudomonas fluorescens strain 96.578

The crystal structure of the non‐ribosomal lipoundecapeptide tensin from Pseudomonas fluorescens has been solved as an ethyl acetate/bis‐water solvate (tensin ethyl acetate dihydrate, C₆₇H₁₁₅N₁₂O₂₀·C₄H₈O₂·2H₂O) to a resolution of 0.8 Å. The primary structure of tensin is β‐hydroxydecanoyl‐d ‐Leu‐d ‐Asp‐d ‐allo‐Thr‐d ‐Leu‐d ‐Leu‐d ‐Ser‐l ‐Leu‐d ‐Gln‐l ‐Leu‐l ‐Ile‐l ‐Glu. The peptide is a lactone linking the Thr3 O_γ atom to the C‐terminal C atom. The stereochemistry of the β‐hydroxy acid has been shown to be S. The peptide shows structural resemblance to the non‐ribosomal cyclic lipopeptide fengycin from Bacillus subtilis. The structure of tensin is essentially helical (3₁₀‐helix), with the cyclic peptide wrapping around a hydrogen‐bonded water molecule. The lipopeptide is amphipathic in good agreement with its function as a biosurfactant.     

Effect of Solvation on Chemical Reactions,I. Addition of a Single Water Molecule to the H− + H2O → OH− + H2 Reaction

The gas phase chemical reaction, H^? + H₂O → H₂ + OH, and the effect of an additional water molecule on the reaction, H^?(H₂O) + H₂O → H₂ + OH(H₂O), have been investigated. The optimal structures and energies of the reactants, products, two stable intermediates, and the transition state connecting the two intermediates have been determined. The additional water molecule does not affect the potential surface congruently: it destabilizes the H(H₂O) minimum, but stabilizes the H₂ ?OH minimum and the transition state connecting the two intermediates. However, it stabilizes the products more than the H₂ ?OH^? minimum. Finally, in line with the reduction in the barrier height, the transition state for the H(H₂0) to H₂ ?OH^? isomerization moves further along the reaction path.     

Ionization-recombination equilibrium in cold cluster plasma under conditions of retardation by high energy barrier

The kinetics of charge separation in a cold plasma was studied with the degradation reaction in molecular clusters HCl(H₂O) _n + m(H₂O) ? H₃O⁺(H₂O) _{n + m ?1}Cl^?, taken as an example, which precedes chlorine adsorption on the ice surface in the stratosphere. The formation of a vast population of H⁺, Cl^? ion pairs stabilized in water clusters ensures the intense binding of chlorine in ice microcrystals that occur in stratospheric clouds. The accumulation of chlorine in the stratosphere is recognized as the main cause of the destruction of the protective ozone layer. The ion buildup effect is a result of the balance between opposite ionization and recombination processes in the presence of a high energy barrier that retards ion recombination in water clusters. A kinetic equation for the process was obtained and its solution was analyzed. The parameters of the barrier were calculated by computer simulation.     

Geometry Optimization of Ba2+(H2O)n Clusters Using a Fast Hybrid Global Optimization Algorithm

A global optimization called fast hybrid global optimization algorithm was proposed based on genetic algorithm, fast simulated algorithm and conjugated gradient algorithm. We employ it to search the global minimum energy structures of Ba²⁺(H₂O)_n clusters for n = 1–30 within the TIP4P model. The results show that Ba²⁺(H₂O)_n clusters have the n+0 structure while n = 1–8. When n is in the range 9 ≤ n ≤ 18, the number of water molecules in the first shell around the barium ion is 8 and the other water molecules arrange in the outer shell. In the global minimum structure of Ba²⁺(H₂O)₁₉, the number of the first shell water molecules adds up to 9, and the value is kept until n = 30. According to the computational results, a conclusion that hydration numbers for Ba²⁺ is 9 can be drawn, which is in agreement with the result by a Monte Carlo simulation.     

Supramolecular Adduct of γ-Cyclodextrin and [{Re<Subscript>6</Subscript>Q<Subscript>8</Subscript>}(H<Subscript>2</Subscript>O)<Subscript>6</Subscript>]<Superscript>2+</Superscript> (Q=S,Se)

Slow evaporation of water solution of [{Re₆S₈}(H₂O)₆]²⁺ generated in situ from [{Re₆S₈}(OH)₆]^4– in presence of γ-cyclodextrin (CD) leads to crystallization of {[{Re₆S₈}(H₂O)₆] ? [γ-CD]}(NO₃)₂·12H₂O (1·12H₂O) supramolecular complex, which was characterized by single-crystal X-ray diffraction crystallography, IR-spectroscopy, thermogravimetric and elemental analyses. X-ray analysis confirms the formation of 1:1 {[{Re₆S₈}(H₂O)₆] ? [γ-CD]}²⁺ inclusion compound in the solid state. However, no adduct formation was detected between [{Re₆S₈}(H₂O)₆]²⁺ and γ-cyclodextrin in solution, according to ¹H NMR spectroscopy. In the case of in situ generated [{Re₆Se₈}(H₂O)₆]²⁺ the reaction solution with γ-cyclodextrin is unstable and during the crystallization only amorphous precipitate has been obtained.     

Enthalpies of solution of tetramethyl-ammonium chloride in aqueous-organic binary solvent systems

Enthalpies of solution of tetramethylammonium chloride in H₂O+acetone, H₂O+DMSO, and H₂O+2,2,2-trifluoroethanol (TFE) are reported. The enthalpies of solution for the frist two solvent systems are positive for all compositions investigated, whereas for the H₂O+TFE systemsH_s becomes large and negative as the mole fraction of TFE is increased past 0.2. The enthalpy-of-solution data are rationalized on the basis of solvent structural effects and solvation.     

Über die Struktur vonM(BF4)2·6H2O fürM=Mg2+, Zn2+, Cd2+

The IR and Raman spectra ofM(BF₄)₂·6H₂O forM=Mg²⁺, Zn²⁺ and Cd²⁺ in the range 4000–140 cm^?1 were recorded, as were theirDTA andTG curves up to 500°C. The data obtained confirm the presence of the water complex [M(H₂O)₆]²⁺ and of the complex anion BF₄ ^? in these compounds. It was also established that the six water molecules in Mg(BF₄)₂·6H₂O and in Zn(BF₄)₂·6H₂O are not crystallographically equivalent, and that hydrogen bonds of the type H₂O...H₂O...F₄B and H₂O...H₂O...H₂O participate in the structure. The energy of the hydrogen bonds H₂O...F₄B for the three crystal hydrates was also calculated. The thermal and thermogravimetric data are in agreement with and confirm the spectroscopic data.     

Formation of aqua and tetraammine Cu(II) complexes inside the cavities of cucurbit[6,8]urils: A DFT forecast

Results of DFT calculations of the structure and thermodynamics of formation of aqua and tetraammine Cu(II) complexes inside CB[n] (n = 6,8) are presented in this study. Formation thermodynamics of the complexes in the cavitands was evaluated by taking into account the most probable number of water molecules inside CB[n]. In this methodology, the complexation was first considered as a substitution reaction in which the guest complex displaces partially or completely the water molecules that are located inside the cavity. The water molecules present in the cavitand were shown to play an important role in the fixation of the guest complex inside the cavity due to the hydrogen bonds with the oxygen portals. The hydration of Cu(II) ion inside CB[6] leads to the formation of an inclusion compound with the formula {[Cu(H₂O)₄]²⁺·2H₂O}@CB[6] while in CB[8] {[Cu(H₂O)₆]²⁺·4H₂O}@CB[8] is formed. For the binding of tetraammine Cu(II) complex, CB[8] was determined to be a significantly more suitable “container” than CB[6]. Both a direct embedding of this complex into the CB[8] and another mechanism in which ammonia molecules replace the water molecules in the Cu(II) aqua complex, preexisting in CB[8] were determined to be thermodynamically possible. Both these lead to the formation of the resultant inclusion compound described by the formula {[Cu(NH₃)₄(H₂O)₂]²⁺·4H₂O}@CB[8].     

A Monte Carlo simulation of Fe2+ aqueous solvation

A Monte Carlo simulation of Fe²⁺ aqueous solvation, at 298 K, including 100 water molecules, has been done using periodic boundary conditions under the minimum image conversion. The energy has been calculated in the pair-potential approach, employing the MCY potential for the H₂OH₂O interaction and an ab initio analytical potential generated by us for the Fe²⁺H₂O interaction. The examination of interaction energies and of the radial distribution functions clearly show that the first hydration shell is formed by eight water molecules. By classifying the generated configurations into different significant structures of the solvent, it has been found that the eight water molecules of the first hydration shell are situated in a lightly distorted D_4d structure which maximizes the water—solute stabilization and minimizes the water—water repulsion. Finally, the validity of our theoretical predictions is discussed.     

Synthesis and Crystal Structures of Alkali and Alkaline Earth Metal Complexes of 3,5-Dinitropyrazolyl-4-carboxylate

The synthesis and crystal structures of 3,5-dinitro-1H-pyrazolyl-4-carboxylic acid (H₂dnpzc) and its four complexes with Ca²⁺, Ba²⁺, Na⁺ and K⁺ are reported in this paper. Ca(dnpzc) · 5H₂O exhibits a 1D polymeric structure, whereas Ba(dnpzc) · 4H₂O possesses a 2D structure. The structure of Na₂(dnpzc) · 4H₂O consists of 2D layers of [Na(dnpzc)]^–_n and 1D chains of [Na(H₂O)₃]⁺_n. K₂(dnpzc) · H₂O has a true 3D structure. It was observed that the doubly deprotonated ligand (dnpzc^2–) can act as a versatile bridge to form polymeric structures by varying combinations of its 8 potential donor atoms (two carboxy O atoms, two pyrazolyl N atoms and four nitro O atoms). Particularly in the structure of K₂(dnpzc) · H₂O, all the 8 donor atoms of dnpzc^2– take part in the coordination and as many as 10 potassium atoms are connected by one ligand.     

Theoretical study of the desorption of neutral and ionic alkali metal atoms from the excited Li+(H2O)n = 1-4 and Na+(H2O)n = 1-4 cluster models: Electronic excitation charge transfer

In this work, the potential energy curves of several low-lying excited states of M⁺(H₂O)_{n = 1-4} (M = Li and Na) clusters with one M─O bond, related to the stretching of their M─O bond, were calculated in the gas phase. The time-dependent density functional theory and direct-symmetry-adapted cluster-configuration interaction were used in this study separately. Theoretical calculations showed that the charge transfer occurred between M⁺ and (H₂O)_n in the excited clusters so that the neutral metal atom was obtained at the dissociation limit of the potential curves. The excited potential curves of clusters were also calculated in the presence of the electrostatic field of water (EFW), and it was found that the charge transfer was blocked in the presence of EFW. The effect of the size of the (H₂O)_n cluster on the shape of the excited potential curves was investigated to observe how the M─O bond was affected in the excited states depending on the (H₂O)_n size. It was found that the increase in the size of the (H₂O)_n cluster increased the number of bonding excited potential curves. The difference between the electron density of the excited and ground electronic states was calculated to see how the charge transfer was affected by the size of the (H₂O)_n cluster.     

Synthese,Kristallstruktur und thermischer Abbau von Mg(H2O)6[B12H12] · 6 H2O

Synthesis, Crystal Structure, and Thermal Decomposition of Mg(H₂O)₆[B₁₂H₁₂] · 6 H₂O By reaction of an aqueous solution of the free acid (H₃O)₂[B₁₂H₁₂] with MgCO₃ and subsequent isothermic evaporation of the resulting solution to dryness, colourless, bead‐shaped single crystals of the dodecahydrate of magnesium dodecahydro closo‐dodecaborate Mg(H₂O)₆[B₁₂H₁₂] · 6 H₂O (cubic, F4₁32; a = 1643.21(9) pm, Z = 8) emerge. The crystal structure is best described as a NaTl‐type arrangement in which the centers of gravity of the quasi‐icosahedral [B₁₂H₁₂]^2— anions (d(B—B) = 178—180 pm, d(B—H) = 109 pm) occupy the positions of Tl^— while the Mg²⁺ cations occupy the Na⁺ positions. A direct coordinative influence of the [B₁₂H₁₂]^2— units at the Mg²⁺ cations is however not noticeable. The latter are octahedrally coordinated by six water molecules forming isolated hexaaqua complex cations [Mg(H₂O)₆]²⁺ (d(Mg—O) = 206 pm, 6×). In addition, six “zeolitic” water molecules are located in the crystal structure for the formation of a strong O—H^δ+···^δ—O‐hydrogen bridge‐bonding system. The evidence of weak B—H^δ—···^δ+H—O‐hydrogen bonds between water molecules and anionic [B₁₂H₁₂]^2— clusters is also considered. Investigations on the dodecahydrate Mg[B₁₂H₁₂] · 12 H₂O (≡ Mg(H₂O)₆[B₁₂H₁₂] · 6 H₂O) by DTA/TG measurements showed that its dehydration takes place in two steps within a temperature range of 71 and 76 °C as well as at 202 °C, respectively. Thermal treatment eventually leads to the anhydrous magnesium dodecahydro closo‐dodecaborate Mg[B₁₂H₁₂].     

catena‐Poly[[[triaquazinc(II)]‐μ‐2‐nitroterephthalato‐κO1:κ2O4,O4′] monohydrate]

The title complex, {[Zn(C₈H₃NO₆)(H₂O)₃]·H₂O}_n, has a one‐dimensional chain structure. The two carboxylate groups of the dianionic 2‐nitroterephthalate ligand adopt mono‐ and bidentate chelating modes. The Zn atom shows distorted octahedral coordination, bonded to three O atoms from two carboxylate groups and three O atoms of three non‐equivalent coordinated water molecules. The one‐dimensional chains are aggregated into two‐dimensional layers through inter‐chain hydrogen bonding. The whole three‐dimensional structure is further stabilized by inter‐layer hydrogen bonds.     

Water exchange rates and mechanisms in tetrahedral [Be(H2O)4]2+ and [Li(H2O)4]+ complexes using DFT methods and cluster‐continuum models

The water exchange reactions in aquated Li⁺ and Be²⁺ ions were investigated with density functional theory calculations performed using the [Li(H₂O)₄]⁺·14H₂O and [Be(H₂O)₄]²⁺·8H₂O systems and a cluster‐continuum approach. A range of commonly used functionals predict water exchange rates several orders of magnitude lower than the experimental ones. This effect is attributed to the overstabilization of coordination number four by these functionals with respect to the five‐coordinated transition states responsible for the associative ( A ) or associative interchange ( I_a ) water exchange mechanisms. However, the M06 and M062X functionals provide results in good agreement with the experimental data: M062X/TZVP calculations yield a concerted I_a mechanism for the water exchange in [Be(H₂O)₄]²⁺·8H₂O that gives an average residence time of water molecules in the first coordination sphere of 260 μs. For [Li(H₂O)₄]⁺·14H₂O the water exchange reaction is predicted to follow an A mechanism with a residence time of inner‐sphere water molecules of 25 ps.     

Synthesis,X-ray crystal structure,thermal and solution studies of a centrosymmetric metal–organic polymer based on proton transfer methodology

A 3-D metal–organic coordination polymer based on pyrazine-2,3-dicarboxylic acid (pzdcH₂) formulated as {[Mn(pzdc)(H₂O)₂] · 2H₂O} _n (1), was obtained by the treatment of MnCl₂ · 6H₂O with pzdcH₂, 8-hydroxy quinoline (8-HQ), and 2-amino-4-methyl pyridine (ampy). In this study, we describe the synthesis, elemental analysis, IR spectroscopy, TG analysis, and single X-ray diffraction. The X-ray single crystal structure reveals that the chemical environment around each Mn(II) is a distorted octahedral by participating one nitrogen, five oxygens from three (pzdc)^2? and two water molecules, O₅MnN. The centrosymmetric 1-D ladder-like structure of 1 is bridged by oxygens of (pzdc)^2?, and Mn–pzdc–Mn bonds are the rungs for our ladder structure. In the crystal structure, intermolecular O–H ··· O hydrogen bonds result in the formation of a supramolecular structure, effective for the stabilization of the structure. The thermal decomposition of 1 indicates that it is quite thermally stable. The protonation constants of ampy, 8-HQ and pzdcH₂ as the building blocks of proton transfer systems including pzdcH₂-ampy and pzdcH₂-8-HQ and the corresponding stability constants of these systems were determined by potentiometric study. The stoichiometry and stability constants of complexes of pzdcH₂-ampy and pzdcH₂-8-HQ with Mn²⁺ were investigated by this method in aqueous solution. The results obtained from solution study are comparable with the solid state results.