Hydrogen-bonded Network Of Water Molecules Research Articles

A Dinuclear Vanadyl–Oxalate Compound

The title compound, bis(tetraphenylphosphonium) μ-oxalato-O 1 ,O 2 :O 1' ,O 2' -bis[aqua(oxalato-O 1 ,O 2 )oxovanadium(IV)] octahydrate, [(C 6 H 5 ) 4 P] 2 [V 2 O 2 (C 2 O 4 ) 3 (H 2 O) 2 ].8H 2 O, consists of an anionic vanadyl dimer linked by an oxalate ligand and additionally coordinated by two non-bridging oxalate and two water molecules. Both the bridging and non-bridging oxalates act as bidenate chelating ligands, forming five-membered rings with the metal centres. The V IV atoms are six-coordinated, forming a distorted octahedral geometry. A two-dimensional O-H...O hydrogen-bonding network of water molecules and oxalate O atoms stabilizes the structure.

Topological and spatial structure in the liquid-water–acetonitrile mixture

We have studied the structure of the liquid-water--acetonitrile mixture using molecular configurations obtained by molecular dynamics simulation. Spatial distribution functions have been used to analyze the local structures surrounding the molecules. The effective hydrogen-bond definition has been used to study basic hydrogen-bond properties and topological properties of the hydrogen-bond network. The topology of the network depends on the acetonitrile concentration. Up to a critical concentration, there is an infinite network of hydrogen-bonded water molecules. At higher concentrations, the network cannot be supported, and finite water clusters form. In order to characterize the networks and clusters, we have calculated some properties of loops and chains of water molecules. The patterns of hydrogen bonds surrounding the molecules and the size distribution of the clusters have also been calculated. We suggest that this approach can be useful when studying the structure of other liquid mixtures where hydrogen bonds are an important mode of interaction.

Bifurcated Bridging Cyano Group and Network of Hydrogen-bonded Water Molecules in a Novel Framework Host Inclusion Compound Triaquacadmium(II) Tricyanocuprate(I)-Acetonitrile (1/1)

Abstract The dimeric structure unit of [Cu2(CN)6]4− in the title inclusion compound involves two bifurcated CN groups respectively linked to two Cu(I) at the C and a Cd(II) at the N to form the framework host accommodating the CH3CN whose orientation is regulated with the hydrogen bonds among the guest and the waters of coordination in the host.

Structure refinement of large-pore aluminophosphate molecular sieve, H1, by Rietveld methods

The structure of HI, a large-pore molecular sieve, is analyzed using X-ray powder diffraction data collected on two samples from separate preparations. Data for one of the samples, H1-A, prepared using a combination of tributylamine and dipentylamine was collected using a synchrotron source, whereas for the other sample prepared using dipropylamine (H1-B), radiation from a rotating anode was used. The space group for these crystals is P6 3 cm with a = 18.9702(3) and c = 8.1163(2) Å for H1-A and a = 18.9923(4) and c = 8.1206(3) Å for H1-B. Final agreement indices were Rp = 0.086 and Rwp = 0.122 for Hl-A and Rp = 0.087 and Rp = 0.112 for Hl-B. The framework structure of Hl in these two samples is similar to that of VPI-5 except that the 6-membered rings in HI contain disordered phosphate groups. The structure is described on the basis of two partially occupied models: The first one is a regular VPI-5 framework with an occupancy of about 0.75, and the other is a different orientation of the groups in the 6-membered ring with occupancy of about 0.25. The Al atom of the 4-ring is 6-coordinated by four framework oxygens and two water molecules. The large channel is occupied by a network of hydrogen-bonded water molecules. These studies together with our earlier results on dehydrated samples show that HI has two partially occupied structures, but that their populations vary from one preparation to the other. The disorder model for HI clearly distinguishes it from VPI-5, which does not display this disorder.

Active site dynamics of acyl‐chymotrypsin

The motions of water molecules, the acyl moiety, the catalytic triad, and the oxyanion binding site of acyl-chymotrypsin were studied by means of a stochastic boundary molecular dynamics simulation. A water molecule that could provide the nucleophilic OH- for the deacylation stage of the catalysis was found to be trapped between the imidazole ring of His-57 and the carbonyl carbon of the acyl group. It makes a hydrogen bond with the N epsilon 2 of His-57 and is held in place through a network of hydrogen-bonded water molecules in the active site. The water molecule was found as close as 2.8 A to the carbonyl carbon. This appears to be due to the constraints imposed by nonbonded interaction in the active site. Configurations were found in which one hydrogen of the trapped water shared a bifurcated hydrogen bond with His-57-N epsilon 2 and Ser-195-O gamma, with the water oxygen very close to the carbonyl carbon. The existence of such a water molecule suggests that large movement of the His-57 imidazole ring between positions suitable for providing general-base catalyzed assistance and for providing general-acid catalyzed assistance may not be required during the reaction. The simulation indicates that the side chains of residues involved in catalysis (i.e., His-57, Ser-195, and Asp-102) are significantly less flexible than other side chains in the protein. The 40% reduction in rms fluctuations is consistent with a comparable reduction calculated from the temperature factors obtained in the X-ray crystallographic data of gamma-chymotrypsin. The greater rigidity of active site residues seems to result from interconnected hydrogen bonding networks among the residues and between the residues and the solvent water in the active site.

Contribution of hydrogen bonding to lipid-lipid interactions in membranes and the role of lipid order: Effects of cholesterol, increased phospholipid unsaturation, and ethanol

It is proposed that increased phospholipid unsaturation in membranes and perturbation by agents such as ethanol weaken interlipid hydrogen bonding involving water and that the process is independent of effects on lipid order. To investigate this, the rates of phospholipid desorption, as a measure of the strength of interlipid interactions, from "donor" lipid vesicles was determined. This was accomplished using (7-nitrobenzo-2-oxa-1,3-diazole-4-yl)aminohexanoate (C6-NBD) labeled phospholipids, the rate of desorption being followed from changes in fluorescence with time. The rates of desorption of the NBD-phospholipids from phosphatidylcholine (PC) donor vesicles was in the order phosphatidylcholine (PC) > phosphatidylserine (PS) > phosphatidylethanolamine (PE), the slower rates in the PS and PE reflecting direct interlipid hydrogen bonding. For PC, the interlipid hydrogen bonding was restricted to the "hydration layer", the network of hydrogen-bonded water molecules extending between phospholipid head groups. The rate of C6-NBD-PC desorption was elevated with higher levels of donor PC sn-2 unsaturation, due the increased head group spacing weakening the lipid-lipid interactions that occur via the hydration layer. Ethanol also increased the rate of NBD-phospholipid desorption from donor PC vesicles in the order PC > PS > PE, showing that PC interactions, here limited to the weaker hydrogen-bonded water molecule network, were more susceptible compared to stronger, direct interlipid hydrogen bonds involving PE and PS. The relative magnitude of the ethanol-induced increase in the desorption rate was amplified with higher levels of donor lipid sn-2 unsaturation. Cholesterol had little effect on the rate of phospholipid desorption.(ABSTRACT TRUNCATED AT 250 WORDS)

Deletion of the .OMEGA.-loop in the active site of staphylococcal nuclease. I. Effect on catalysis and stability

The high-resolution X-ray structure of wild-type staphylococcal nuclease (E43 SNase) suggests that Glu 43 acts a general basic catalyst to assist the attack of water on a phosphodiester substrate [Loll, P., & Lattman, E. E. (1989) Proteins: Struct., Funct., Genet. 5, 183]. Glu 43 is located at the base of the solvent-exposed and conformationally mobile omega-loop in the active site of E43 SNase having the sequence Glu43-Thr44-Lys45-His46-Pro47-Lys48- Lys49-Gly50-Val51-Glu52, where the gamma-carboxylate of Glu 52 is hydrogen bonded to the amide hydrogen of Glu 43. With a metabolic selection for SNase activity produced in an Escherichia coli host, we detected an unexpected deletion of residues 44-49 of the omega-loop of E43 SNase in cassette mutagenesis experiments designed to randomize codons 44 and 45 in the omega-loop and increase the activity of the previously described E43D mutation (D43 SNase). A high-resolution X-ray structure of D43 SNase has revealed that the E43D substitution significantly changes the structure of the omega-loop, reduces the interaction of the essential Ca2+ ion with its active-site ligands, and diminishes the network of hydrogen-bonded water molecules in the active site [Loll, P., & Lattman, E. E. (1990) Biochemistry 29, 6866]. This deletion of six amino acids from the omega-loop generates a protein (E43 delta SNase) having a partially solvent-exposed, surface beta-turn with the sequence Glu43-Gly50-Val51-Glu52; the structure of this beta-turn is addressed in the following article [Baldisseri et al. (1991) Biochemistry (following paper in this issue)].(ABSTRACT TRUNCATED AT 250 WORDS)

Two-dimensional proton conduction at a membrane surface: Influence of molecular packing and hydrogen bonding

Evidence for two-dimensional protonic charge transport along a monolayer/water interface is presented, supporting the concept of localised charge transport along membrane surface. Charge transport proceeds only at and above a critical molecular packing density, and probably occurs via a network of hydrogen-bonded water molecules and lipid headgroups.

Computer Counting of the Number of Water Molecules in the First Layer of Crystalline Water Clathrate

Abstract Semiempirical calculation of the number of water molecules in the first layer of water clathrates in crystalline state was developed by computer aided construction of hydrogen-bonded network of water molecules. In the generalized thermodynamic considerations on four possible types of “unit clathrate,” van der Waals stabilization energy, “strain” energy of the unit clathrate, and entropy term due to the motional freedom of the guest were taken into account for the calculation of free energy change for the formation of the water clathrate. The results of calculations on 37 hydrophobic organic molecules well represented the trend of the reported experimental data of X-ray studies. The present calculation also disclosed such a large unfavorable strain energy (8.72 kcal·mol−1) of pentakaidecahedron that it counteracts the van der Waals stabilization. The result is in a good agreement with the fact that pentakaidecahedral cavity is rarely seen in the gas hydrates. Most importantly, these semiempirical calculations of the energetics of water clathrates afforded valuable new insights into water assembly and may be extended to give better understandings of structured water in biological system and of water clusters that develop around apolar solutions in water.