Discrete Water Molecules Research Articles

Hydrogen atom and hydride transfer in the reactions of chromium(IV) and chromium(V) complexes with rhodium hydrides. Crystal structure of a superoxorhodium(III) product.

The aquachromyl ion, Cr(IV)aqO2+, reacts with the hydrides L(H2O)RhH2+ (L = L1 = [14]aneN4 and L2 = meso-Me6-[14]aneN4) in aqueous solutions in the presence of molecular oxygen to yield Cr(aq)3+ and the superoxo complexes L(H2O)RhOO2+. At 25 degrees C, the rate constants are approximately 10(4) M(-1) s(-1) (L = L1) and 1.12 x 10(3) M(-1) s(-1) (L = L2). Both reactions exhibit a moderate deuterium isotope effect, kRhH/kRhD = approximately 3 (L1) and 3.3 (L2), but no solvent isotope effect, kH2O/kD2O = 1. The proposed mechanism involves hydrogen atom abstraction followed by the capture of LRh(H2O)2+ with molecular oxygen. There is no evidence for the formation of L(H2O)Rh2+ in the reaction between L(H2O)RhH2+ and (salen)CrVO+. The proposed hydride transfer is supported by the magnitude of the rate constants (L = L1, k = 8,800 M(-1) s(-1); (NH3)4, 2,500; L2, 1,000) and isotope effects (L = L1, kie = 5.4; L2, 6.2). The superoxo complex [L1(CH3CN)RhOO](CF3SO3)2.H2O crystallizes with discrete anions, cations, and solvate water molecules in the lattice. All moieties are linked by a network of hydrogen bonds of nine different types. The complex crystallized in the triclinic space group P1 with a = 9.4257(5) A, b = 13.4119(7) A, c = 13.6140(7) A, alpha = 72.842(1)degrees, beta = 82.082(1) degrees, gamma = 75.414(1) degrees, V = 1587.69(14) A3, and Z = 2.

SYNTHESIS, CRYSTAL STRUCTURE AND LUMINESCENCE STUDIES OF A LANTHANIDE COORDINATION POLYMER WITH A NEW DOUBLE BETAINE LIGAND

A novel europium(III) coordination polymer with a new double betaine derivative. {[Eu(L1)(NO3)(H2O)3](NO3)2 3.5H2O}n (L= l,3-bis(pyridinio-4-carboxylato)-propane) has been synthesized and its structure determined. Its luminescence properties have also been studied. The title metal carboxylate coordination polymer contains centrosymmetric dimeric units in which each pair of metal ions is linked by a pair of syn-anti carboxylato-O.O' groups, and each pair of such dimeric units is bridged by the backbones of L1 ligands to form infinite double chains in the b direction. These metal carboxylate chains are further cross-linked by hydrogen bonds among both coordinated and discrete nitrate anions, aqua ligands and lattice water molecules to form a three-dimensional network. Luminescent data show that the L1 ligand is a good energy donor and the complex has a relatively long luminescent lifetime.

The particle concept: placing discrete water molecules during protein-ligand docking predictions

Water is known to play a significant role in the formation of protein-ligand complexes. In this paper, we focus on the influence of water molecules on the structure of protein-ligand complexes. We present an algorithmic approach, called the particle concept, for integrating the placement of single water molecules in the docking algorithm of FLEXX. FLEXX is an incremental construction approach to ligand docking consisting of three phases: the selection of base fragments, the placement of the base fragments, and the incremental reconstruction of the ligand inside the active site of a protein. The goal of the extension is to find water molecules at favorable places in the protein-ligand interface which may guide the placement of the ligand. In a preprocessing phase, favorable positions of water molecules inside the active site are calculated and stored in a list of possible water positions. During the incremental construction phase, water molecules are placed at the precomputed positions if they can form additional hydrogen bonds to the ligand. Steric constraints resulting from the water molecules as well as the geometry of the hydrogen bonds are used to optimize the ligand orientation in the active site during the reconstruction process. We have tested the particle concept on a series of 200 protein-ligand complexes. Although the average improvement of the prediction results is minor, we were able to predict water molecules between the protein and the ligand correctly in several cases. For instance in the case of HIV-1 protease, where a single water molecule between the protein and the ligand is known to be of importance in complex formation, significant improvements can be achieved.

The particle concept: placing discrete water molecules during protein‐ligand docking predictions

The particle concept: placing discrete water molecules during protein‐ligand docking predictions

Influence of solvation on the hydrogen bond in hydrogen malonate An ab initio and semiempirical study

The energy difference ΔE EZ in vacuo between the closed (E) and open (Z) forms of the hydrogen malonate ion was computed at the ab initio HF/6–31G(d,p), 6–311++G(d,p), DFT B3LYP/6–31G(d, p) and B3LYP/6–311++G(d,p) levels. The effects of the polar environment were simulated by attaching discrete water molecules, by the self-consistent reaction field model (SCRF) and by the combination of both approaches. These simulations were done at the HF/6–31G(d,p) level. The SCRF approach applied to both forms of the HM tetrahydrate yields the free energy difference of −0.73 kcal mol −1, slightly favouring the open form; this contrasts the stabilization by ~20kcal mol −1 of the E form in vacuo. The metric parameters of the intramolecular hydrogen bond indicate a slight weakening of the intramolecular H-bond by the influence of hydration. Calculations at the PM3 level did not reproduce the ab initio computed ΔE EZ values.

An effective fragment method for modeling solvent effects in quantum mechanical calculations

An effective fragment model is developed to treat solvent effects on chemical properties and reactions. The solvent, which might consist of discrete water molecules, protein, or other material, is treated explicitly using a model potential that incorporates electrostatics, polarization, and exchange repulsion effects. The solute, which one can most generally envision as including some number of solvent molecules as well, is treated in a fully ab initio manner, using an appropriate level of electronic structure theory. In addition to the fragment model itself, formulae are presented that permit the determination of analytic energy gradients and, therefore, numerically determined energy second derivatives (hessians) for the complete system. Initial tests of the model for the water dimer and water-formamide are in good agreement with fully ab initio calculations.

Hexaaquatitanium(III) Tris(p-Toluenesulfonate) Trihydrate

The crystal structure of [Ti(H 2 O) 6 ](p-CH 3 C 6 H 4 SO 3 ) 3 .3H 2 O consists of discrete cations, anions and solvate water molecules, all linked by a hydrogen-bonding network. Each Ti ion lies on an inversion centre and shows essentially octahedral coordination with Ti−O bonds in the range 2.018 (5)-2.046 (6) A

Structure and energetics of protein-carbohydrate complexes

During the past year, several new coordinate sets for protein-carbohydrate complexes have appeared. The data fall into two important categories: complexes of lectins other than legume and chemotaxis proteins, and high-resolution refinements that allow placement of discrete water molecules. These data should lead to a better understanding of the role of water in protein-carbohydrate complexation. Interest in the energetics of association is growing, and calorimetrically determined thermodynamic parameters are now available for a host of protein-carbohydrate complexations. The impact of recent structural and energetic studies on proposed models of protein-carbohydrate association is discussed.

Effects of water and onium ion phase-transfer catalyst on the rate of liquid-phase oxidation of hydrocarbons

The liquid-phase oxidations of tetralin, cumene, cyclohexene and methylcyclohexane were investigated in the presence of water and different types of surfactants. It was found that water first increases, then decreases, the rate of oxidation. Aromatic compounds are oxidised more readily than non-aromatic ones. [H 2O] max is mostly determined by the concentration of hydroperoxide present, and it does not depend on the nature of the hydrocarbon. H 2O and D 2O have similar catalytic effects; both inhibit the oxidation when applied in a larger excess. Anionic and non-ionic surfactants reduce the catalytic effect of water, because access to the hydroperoxide molecules by the water droplets is considerably hindered by the surrounding surfactant ions or molecules. In contrast, cationic surfactants catalyse the oxidation, their efficiencies largely depend on the nature of their anions. It is assumed that the water catalysis arises from the H-bonding interaction of the hydroperoxide with the discrete or less-associated water molecules. Water and onium ion have a joint catalytic effect. The onium-ion pair attacks at the more nucleophilic O-atom of the hydroperoxide, while the outer O-atom is activated by water, through Hbond formation.

Interbilayer repulsion in nonionic surfactant-water lamellar phases.

We report a simulation study using the RIB modification of the Gibbs' ensemble, for a model membrane system in which the surfaces have embedded dipoles, and are separated by a fluid of discrete TIPS2 water molecules. The separation between the layers is allowed to vary, as is the number of water molecules in the membrane which is in equilibrium with a vapour phase, the whole system being kept at constant (N, V, T). The simulations were performed at 298 K and two systems were studied: in the first, the surface dipoles were modelled as OH groups attached to hydrocarbon chains; in the second, the charge on the O and H atoms was arbitrarily doubled to 0-734e

Structural dynamics of calmodulin and troponin C

We present the results of computational simulation studies of the structures of calmodulin (CAM) and troponin C (TNC). Possible differences between the structures of these molecules in the crystal and in solution were suggested by results from some recent experimental studies, which implied that their conformations in solution may be more compacted than the characteristic dumbbell shape observed in the crystal. The molecular dynamics simulations were carried out with the CHARMM system of programs, and the environment was modeled with a distance-dependent dielectric permittivity and discrete water molecules surrounding the proteins at starting positions identified in the crystals of CAM and TNC. Methods of macromolecular structure analysis, including linear distance plots, distance matrices and a matrix representation of hydrogen bonding, were used to analyze the nature, the extent and the source of structural differences between the computed structures of the molecules and their conformations in the crystal. Following the longest simulation, in which intradomain structure was conserved, the crystallographically observed dumbbell structure of the molecule changed due to a kinking or bending in the region of the central tether helix connecting the two Ca(2+)-binding domains which moved into close proximity. The resulting structure correlates with experimental observations of complexes between CAM and peptides such as melittin and mastoparan. Analysis of the corresponding pair distance distribution functions in comparison to experimental results suggests the dynamic existence of a non-negligible fraction of the compacted structure in aqueous solutions of CAM. In this more nearly globular shape, CAM reveals to the environment two interior pockets that contain a number of hydrophobic residues, in agreement with NMR data suggesting involvement of such residues in the binding of inhibitors and proteins to CAM.

Solid-state and solution conformation of a new cobalt dimer µ-form-amido-bis[penta-amminecobalt(III)] pentachloride monohydrate: X-ray and kinetic studies

The crystal and molecular structure of the title compound has been determined by three-dimensional X-ray analysis. Crystals are triclinic, space group P, with Z= 2 in a unit cell of dimensions: a= 6.981(8), b= 14.346(8), c= 11.992(6)A, α= 99.41(4), β= 103.68(9), γ= 93.11(7)°. The structure was solved by the heavy-atom method and refined by full-matrix least-squares calculations to R 0.082 for 922 observed reflections measured by diffractometer. The crystal structure consists of discrete cations, anions, and water molecules separated by normal distances. In the cation the octahedrally co-ordinated cobalt atoms are linked by the bidentate formamido-ligand which has a cis-conformation of the NH and CH groups. Co–N(formamido) Is 1.94(2), and the mean of the other Co–N bonds is 1.99(2)A. Other bond lengths are Co–O 1.92(2), C–O 1.26(3), and C–N 1.34(4)A.The cation is shown to have the same cis-conformation in solution (from nuclear Overhauser studies) as that found in the solid state. Kinetics of reduction show that the complex is reduced by an initial outer-sphere mechanism.

Discrete water molecules in the vicinity of two oppositely charged ions

An attempt is made to describe the water molecules in contact with an ion pair in an aqueous solution. One possible arrangement consisting of 10 nonpolarizable water dipoles is considered and a comparison of various energy terms is made in order to decide what factors are most important. The two ions and their attached water dipoles are enclosed in a spheroidal cavity embedded in a dielectric continuum to represent the bulk of the water. It is shown that the energy associated with the water molecules lying in the central region between the two ions is practically unaffected by the cavity size. On the other hand, although the behavior of the "outer" water molecules is extremely sensitive to the cavity size it is a good approximation to the more precise statistical problem to place them in the position of minimum potential energy.