Adjacent Water Molecules Research Articles

Molecular dynamics simulation of the proton transport in water

AbstractThe proton transport in water is treated within a mixed molecular dynamic (MD) and Monte Carlo (MC) scheme. Therein the migration of a positive charge is treated as a two step process; (i) as a displacement of a hydronium ion and (ii) as a proton transfer between a hydronium ion and an adjacent water molecule. Both, the hydronium ion and the water molecules are treated as rigid molecules. It is found that the determining step for the proton transport rate is the dissociation rate of H5O2+ complexes. In these complexes the O‐O distance is only 2.4–2.5 Å while the corresponding distance for two water molecules in solution is 2.83 Å. In the H5O2+ complex the proton does no longer belong to a single water molecule, but is delocalized between the two oxygen atoms. This situation is modelled by an exchange of the water and the hydronium every time step with a probability p = 1/2.

Structure and dynamics of primary hydration shell of phosphatidylcholine bilayers at subzero temperatures

Deuterium NMR relaxation and intensity measurements of the 2H-labeled H2O/dimyristoyl phosphatidylcholine bilayer were performed to understand the molecular origin of the freezing event of phospholipid headgroup and the structure and dynamics of unfrozen water molecules in the interbilayer space at subzero temperatures. The results suggest that about one to two water molecules associated with the phosphate group freeze during the freezing event of phospholipid headgroups, whereas about five to six waters near the trimethylammonium group behave as a water cluster and remain unfrozen at temperatures as low as -70 degrees C. In addition, temperature-dependent T1 and T2 relaxation times suggest that dynamic coupling occurs not only between the phosphate group and its bound water, but also between the methyl group and the adjacent water molecules. Based on these observations, the primary hydration shell of phosphatidylcholine headgroup at subzero temperatures is suggested to consist of two distinct regions: a clathrate-like water cluster, most likely a water pentamer, near the hydrophobic methyl group, and hydration water molecules associated with the phosphate group.

Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP)

We have determined the structure of the homotrimeric dUTPase from Escherichia coli, completed with an inhibitor and substrate analogue, dUDP. Three molecules of dUDP are found symmetrically bound per trimer, each in a shallow cleft between adjacent subunits, interacting with evolutionary conserved residues. The interactions of the uracil ring and the deoxypentose with the protein are consistent with the high specificity of the enzyme with respect to these groups. The positions of the two phosphate groups and adjacent water molecules are discussed in relation to the mechanism and kinetics of catalysis. The role that dUTPase plays in DNA metabolism makes the enzyme a potential target for chemotherapeutic drugs: the results presented here will aid in the design and development of inhibitory compounds.

Cyclo(L-alanyl-L-seryl).H2O and Cyclo(glycyl-L-seryl)

We have determined the crystal structures of two diketopiperazines, cyclo(l-alanyl-l-seryl).H2O, (cis-6-hydroxymethyl-3-methyl-2,5- piperazinedione hydrate, C6H10N2O3.H2O and cyclo(glycyl-l-seryl), 3-hydroxymethyl-2,5-piperazinedione, C5H8N2O3. The crystal structure of cyclo(l-alanyl-l-seryl).H2O [cyclo(l-Ala-l-Ser)] consists of a peptide backbone that is hydrogen bonded to two adjacent diketopiperazine rings, forming extended chains through the crystal. The serine hydroxyl of cyclo(l-Ala-l-Ser) is hydrated by two adjacent water molecules in the crystal. In contrast, the crystal structure of cyclo(Glycyl-l-seryl) [cyclo(Gly l-Ser)] is held together by a three-dimensional network of hydrogen bonds. The serine hydroxyl of cyclo(Gly l-Ser) participates in two hydrogen bonds with the peptide backbone of neighboring molecules.

Molecular dynamics investigation of the surface/bulk equilibrium in an ethanol–water solution

Molecular dynamics simulations of the vapour/solution interface, initiated from an ethanol–water mixture at a mole fraction of ethanol, Xe= 0.1, have been performed. Rapid redistribution of ethanol molecules to the free surface was observed during simulations of two different sized systems. Inspection of the calculated surface structure reveals that after redistributing the ethanol molecules are preferentially oriented such that the alkyl group points out of the solution. A ‘depletion layer’ of enhanced water density beneath the ethanol surface excess was revealed by the simulation. Analysis of the structure involving molecules close to the surface shows that water molecules are arranged to maximize the hydrogen bonding between the oriented ethanol and the adjacent water molecules. The enhanced water density beneath the interface results from this optimization. The surface tension calculated from the simulation is ca. 50% higher than the results of macroscopic experimental measurements. This overestimation is attributed to shortcomings in both the potential function and the simulation methodology. The number density profiles of the ethanol surface excess were compared with results from neutron reflectivity measurements. The calculated profiles agree better with the experimental measurements at the calculated surface tension (i.e. Xe= 0.022) than those reported for Xe= 0.1 mixtures.

Multiphoton Ionization of Liquid Water with 3.0−5.0 eV Photons

We report a picosecond laser study of the transient absorption of hydrated electrons generated by the 3−5 eV multiphoton ionization of liquid water. The geminate kinetics indicate that eaq- is produced by at least three different mechanisms over this energy range. Power dependence of the signal amplitude shows a two-photon threshold for 4.0 eV excitation and a three-photon threshold absorption at 3.47 eV, consistent with two- or three-photon excitation of the Ã(1B1) lowest excited state. For (three-photon) excitation in the range 3.02−3.47 eV very little (≤15%) geminate recombination is observed while for the (two-photon) excitation at shorter wavelengths significant recombination (≥55%) is observed. In the region of 3.85−4.54 eV, photon-energy-independent kinetics indicate that eaq- is produced via two-photon excitation of the à state followed by an ionization process in which the electrons do not obtain any excess kinetic energy. For photon energies in the range of 4.75−5.05 eV, the escape fraction increases slightly, consistent with two-photon excitation of higher energy states. Simulation with a diffusion model shows that the electron is ejected at least 25 Å farther into the bulk for the 3.02−3.47 eV photon energies relative to two-photon ionization in the 3.67−5.0 eV range. We conclude that the larger distances result from a (3 + 1)-photon resonance-enhanced multiphoton ionization (REMPI) process, made possible by visible/near-UV absorption of the water excited states. Possible mechanisms of the water ionization are discussed. A new mechanism is proposed to explain the production of solvated electrons from excitation of the Ã(1B1) state of liquid water, well below the Born−Oppenheimer ionization threshold. On the basis of the gas phase properties of this state, we assume a direct dissociation to give OH radical and H atoms, with the excess energy almost entirely transferred to kinetic energy of the H atoms: H2O* → OH + H(hot). It is proposed that the hot H atoms immediately react with an adjacent water molecule to form hydronium ion and a solvated electron, in a process analogous to the thermal reaction of H atoms with water at elevated temperatures: H(hot) + H2O → H3O+ + eaq-.

Sticky ions in biological systems.

Aqueous gel sieving chromatography on Sephadex G-10 of the Group IA cations (Li+, Na+, K+, Rb+, Cs+) plus NH4+ as the Cl- salts, in combination with previous results for the halide anions (F-, Cl-, Br-, I-) as the Na+ salts [Washabaugh, M.W. & Collins, K.D. (1986) J. Biol. Chem. 261, 12477-12485], leads to the following conclusions. (i) The small monovalent ions (Li+, Na+, F-) flow through the gel with water molecules attached, whereas the large monovalent ions (K+, Rb+, Cs+, Cl-, Br-, I-) adsorb to the nonpolar surface of the gel, a process requiring partial dehydration of the ion and implying that these ions bind the immediately adjacent water molecules weakly. (ii) The transition from strong to weak hydration occurs at a radius of about 1.78 A for the monovalent anions, compared with a radius of about 1.06 A for the monovalent cations (using ionic radii), indicating that the anions are more strongly hydrated than the cations for a given charge density. (iii) The anions show larger deviations from ideal behavior (an elution position corresponding to the anhydrous molecular weight) than do the cations and dominate the chromatographic behavior of the neutral salts. These results are interpreted to mean that weakly hydrated ions (chaotropes) are "pushed" onto weakly hydrated surfaces by strong water-water interactions and that the transition from strong ionic hydration to weak ionic hydration occurs where the strength of ion-water interactions approximately equals the strength of water-water interactions in bulk solution.

Investigation of the Crystal Structure of γ-CaSO4, CaSO4 · 0.5 H2O, and CaSO4 · 0.6 H2O by Powder Diffraction Methods

The crystal structures of soluble anhydrite, γ-CaSO4, and the two calcium sulfate subhydrates, CaSO4 · 0.5 H2O and CaSO4 · 0.6 H2O, were investigated by powder diffraction methods; using synchrotron X ray radiation and neutron powder diffraction, and the positions of the water molecules in the structure were determined. γ-CaSO4 is orthorhombic, space group C222 (N°21) with a = 12.0777(7), b = 6.9723(4), c = 6.3040(2) Å (from the neutron diffraction data), and Z = 6. The structure contains two different chains of CaO8 coordination polyhedra (mean Ca-O = 2,460 Å) held together by SO2-4 ions. CaSO4 · 0.5 H2O (SH1) is monoclinic, space group I121 (No. 5) with a = 12.0317(4), b = 6.9269(2), c = 12.6712(3) Å, β = 90.27(1)° (from the neutron diffraction data), and Z = 12. The structure contains chains of alternating CoO8 and CaO9 coordination polyhedra held together by the SO2-4 ions. The average Ca-O distances in the CoO8 and in the CaO9 coordination polyhedra are 2.469 and 2.500 Å, respectively. A monoclinic structure is proposed for CaSO4 · 0.6 H2O (SH2), space group I121 (No. 5) with a = 11.9845(4), b = 6.9292(2), c = 12.7505(3) Å, β = 90° (from the neutron diffraction data), and Z = 12. The structure contains chains of CaO8 and chains of CaO9 coordination polyhedra, both held together by the SO2-4 ions. The average Ca-O distances in the CoO8 and in the CaO9 coordination polyhedra are 2.538 and 2.494 Å, respectively. All of the three structures have channels where the water molecules associated with the CoO9 polyhedra are located in the case of subhydrates. In the case of the hemihydrate, the water molecules form hydrogen bonds with oxygen atoms of the sulfate tetrahedra of 2.85-3,03 Å. In the case of CaSO4 · 0.6 H2O, two adjacent water molecules in the channels are linked by a strong hydrogen bond (O-H = 1.9 Å).

Comparison of temperature, pressure and isotope effects on the proton jump between the hydroxide and oxonium ion

The limiting molar conductances Λ° of potassium deuteroxide KOD in D2O and potassium hydroxide KOH in H2O were determined at 5 and 45°C as a function of pressure to clarify the difference in the temperature, pressure and isotope effects on the proton jump between an OD− (OH−) and a D3O+ (H3O+) ion. The excess conductances of the OD− ion in D2O and the OH− ion in H2O, λ E 0 (OD-) and λ E 0 (OH-), increase with increasing temperature and pressure as in the case of the excess deuteron and proton conductances, λ E 0 (D+) and λ E 0 (H+). However, the temperature effect on the excess conductance is larger for the OD−(OH−) ion than for the D3O+ (H3O+) ion but the pressure effect is much smaller for the OD− (OH−) ion than for the D3O+ (H3O+) ion. These findings are correlated with larger activation energies and less negative activation volumes found for the OD− (OH−) ion than for the D3O+ (H3O+) ion. Concerning the isotope effect, the value of λ E 0 (OH-)/λ E 0 (OD-) deviates considerably from\(\surd 2\) at each temperature and pressure in contrast with that of λ E 0 (H+)/λ E 0 (D+), although both of them decrease with increasing temperature and pressure. These results are discussed mainly in terms of the difference in repulsive force between the OD− (OH−) or the D3O+ (H3O+) ion and the adjacent water molecule, the difference in strength of hydrogen bonds in D2O and H2O, and their variations with temperature, pressure, and isotope.

Partial molar volumes, expansibilities, and compressibilities of oligoglycines in aqueous solutions at 18–55°C

AbstractWe have determined the partial molar volumes, expansibilities, and adiabatic compressibilities of glycine, diglycine, triglycine, tetraglycine, and pentaglycine over the temperature range 18–55°C. These data were analyzed and interpreted in terms of the hydration of these short oligoglycines and their constituent groups. From our results, we have estimated the contributions of the peptide group to the partial molar volume and the partial molar adiabatic compressibility of these oligoglycines. Based on these data, we propose that each of the polar atomic groups of the peptide bond forms approximately two hydrogen bonds with adjacent water molecules. Furthermore, the temperature dependence of the partial molar volume suggests that water that solvates the polar groups of a peptide linkage behaves more like a “normal” liquid than does bulk water, which exhibits its well‐known anomalous liquid properties. © 1994 John Wiley & Sons, Inc.

Substrate dependence of electron-stimulated O− yields from dissociative electron attachment to physisorbed O2

We present measurements of O− electron stimulated desorption yields obtained under identical experimental conditions from 0.15 monolayers (ML) of O2 deposited onto disordered substrates consisting of 4 ML of either Kr, Xe, C2H6, C2H4, N2O, CH3Cl, or H2O, all condensed on Pt (polycrystalline). The resulting O− yield functions, for incident electron energies below 20 eV, are compared to that obtained from the O2/Kr solid; this allows us to assess the order of magnitude effects of the local substrate environment on dissociative electron attachment (DEA) via the 2Πu and gas phase forbidden 2Σ+g,u resonances of O−2. We note that, in addition to electron energy losses in the substrate prior to DEA to O2 and post-dissociation interactions of the O− with the substrate molecules, charge or energy transfer from the O−2 transient anion to a substrate molecule, and capture of the incident electron into a dissociative anion resonance of the substrate molecule may contribute to a reduced O− yield from the physisorbed O2. In the case of O2 deposited on amorphous ice, we find that the O− signal from DEA to O2 is completely absent for electron energies below 14 eV; we attribute this to a complete quenching of the dissociative O−2(2Πu, 2Σ+) resonances by the adjacent water molecules.

Quenching of the dissociative electron attachment resonances of O2 physisorbed on amorphous ice

Measurements of electron stimulated desorption (ESD) yields of O−, at incident electron energies below 20 eV, from 0.15 monolayers (ML) of O2 physisorbed at 20 K on a variety of molecular solids have been performed. It is observed that for O2 condensed on 4 ML of H2O, the O− signal from dissociative electron attachment (DEA) to O2 is entirely absent. We attribute this to a complete quenching of the dissociative 2Πu, 2Σ+g, and 2Σ+u, resonances of O−2 by the adjacent water molecules.

Pressure and temperature effects on the excess deuteron and proton conductance

The limiting molar conductances Λ° of deuterium chloride DCl in D2O were determined as a function of pressure and temperature in order to examine the proton-jump mechanism in detail. The excess deuteron conductances λ°E(D +), as estimated by the equation [λ°E(D +) = Λ°(DCl/D 2 O) − Λ°(KCl/D 2 O)], increases with an increase in the pressure and temperature as well as the excess proton conductance [λ°E(H +) = Λ°(HCl/H 2 O) − Λ°(KCl/H 2 O)]. The isotope effect on the excess conductances, however, depends on the pressure and temperature contrary to the model proposed by Conway et al.: λ°E(H +)/λ°E(D +) decreases with increasing pressure and temperature. The magnitude of the decrease with pressure becomes more prominent at lower temperature. These results are discussed in terms of the pre-rotation of adjacent water molecules, the bending of hydrogen bonds with pressure, and the difference in strength of hydrogen bonds between D2O and H2O.

Solvent transoport across cation-exchange membranes under a temperature difference and under an osmotic pressure difference

Solvent transport across cation-exchange membranes was measured for water and aqueous salt solutions under a temperature difference and under an osmotic pressure difference. Perfluorosulfonic acid-type membrane Nafion® 417, perfluorocarboxylic acid-type membrane Flemion® AR1.25, and hydrocarbonsulfonic acid-type membranes Neosepta® C66-5T, C66-10F, CM-1 and CM-2 were used. The water flux across cation-exchange membranes in the H +-form is higher than that in other cation forms because the hydrogen ions can exchange with the hydrogen of the adjacent water molecules and thus contribute to the water transport across the membrane as the proton jumps in conductivity. The direction of thermoosmosis across cation-exchange membranes in the Li +-form is from the hot side to the cold side, although in general thermoosmosis across hydrophilic charged membranes occurs towards the hot side.

Electron-transfer-induced acidity/basicity and reactivity changes of purine and pyrimidine bases. Consequences of redox processes for DNA base pairs.

Changes in the oxidation state of the DNA bases, induced by oxidation (ionization) or by reduction (electron capture), have drastic effects on the acidity or basicity, respectively, of the molecules. Since in DNA every base is connected to its complementary base in the other strand, any change of the electric charge status of a base in one DNA strand that accompanies its oxidation or reduction may affect also the other strand via proton transfer across the hydrogen bonds in the base pairs. The free energies for electron transfer to or from a base can be drastically altered by the proton transfer processes that accompany the electron transfer reactions. Electron-transfer (ET) induced proton transfer sensitizes the base opposite to the ET-damaged base to redox damage, i.e., damage produced by separation of charge (ionization) has an increased change of being trapped in a base pair. Of the two types of base pair in DNA, A-T and C-G, the latter is more sensitive to both oxidative and reductive processes than the former. Proton transfer induced by ET does not only occur between the heteroatoms (O and N) of the base pairs (intra-pair proton transfer), but also to and from adjacent water molecules in the hydration shell of DNA (extra-pair proton transfer). These proton transfers can involve carbon and as such are likely to be irreversible. It is the A-T pair which appears to be particularly prone to such irreversible reactions.

Proton transport at the monolayer-water interface

It is shown that when monolayers of stearic acid, palmitic acid, DPPC, or DPPS are compressed above some critical area A c a lateral conduction mechanism is initiated at the monolayer/water interface. The interfacial conductance increases on further increasing the molecular packing density in the monolayer. All compounds also show major changes in surface potential at A c the potential becoming more positive in all cases. It is argued that this is a consequence of structural reorganisation at the headgroup/water interface causing a significant reduction in the local permittivity. The critical area, A c, is approximately double the molecular areas estimated from the pressure-area isotherm, and experiments with stearic acid monolayers show that A c decreases significantly when the chaotropic ion SCN −, which is known to disrupt the molecular structure of water, is added to the subphase. It is likely, therefore, that the structural changes occurring at A c involve the formation of a hydrogen bonded network between monolayer headgroups and adjacent water molecules at the monolayer/water interface. It is suggested that the conduction mechanism initiated at A c arises from proton hopping along this hydrogen-bond network.

Solutions of organic solutes. Part 4.—Structure and the effect of solute concentration on the volume

The chemical thermodynamic (CT) model and dielectric theory have been used for an analysis of [∂(∂V/∂text-decoration:overlinen2)/∂text-decoration:overlinen2]T, p, text-decoration:overlinen, the volume differential with respect to solute concentration, for aqueous solutions of dipolar compounds at 25 °C (24 solutes). There are three main components of this function, arising from: (1) the response of the solute-cavity volume (including packing and dynamic requirements) to changes in concentration, (2) changes in the dipole compressional effects and (3) the change in the static-dielectric orientational correlation function (g1) of the solvent, water. For the amino acids the third term is negligible. The orientational correlation functions of the solute (g2) and solvent were estimated and considered in relation to electrical packing factors, the cavity field and the polar work associated with solvation. The relationship of g2 to the number of adjacent water molecules showed distinct solute classifications in terms of the relative effects on orientation and relaxation of neighbouring water molecules.

Kinetic and magnetic resonance studies of active-site mutants of staphylococcal nuclease: factors contributing to catalysis.

To determine the origin of the overall approximately 10(16)-fold rate enhancement of DNA hydrolysis catalyzed by staphylococcal nuclease, the effects of single mutations that alter the amino acid residue at each of the essential positions Asp-21, Asp-40, Thr-41, Arg-35, and Arg-87 have been examined. Metal ion and substrate analogue binding were quantitated by EPR, by the paramagnetic effects of Mn2+ on 1/T1 of water protons, and by fluorescence titrations, yielding the six dissociation constants of the ternary enzyme-Mn2+-3',5'-pdTp and enzyme-Ca2+-3',5'-pdTp complexes. The kinetic parameters kcat, KACa, KMCa, KSDNA, KMDNA, and KIMn were determined by monitoring the rate of DNA hydrolysis. By thermodynamic and kinetic criteria, Mn2+ binds tightly to the Ca2+ binding site of the enzyme but is at least 36,000-fold less effective than Ca2+ in activating the enzyme. Alterations of the liganding residues in the D40G, D40E, T41P, D21E, and D21Y mutants generally weaken the binding of Ca2+ less than or equal to 12.7-fold and of Mn2+ less than or equal to 5.4-fold, exert little effect on the KSDNA or KMDNA (less than or equal to 3.2-fold), and raise the affinity of the enzyme and its metal complexes for 3',5'-pdTp by factors less than or equal to 13.5-fold. Small changes in the ligand geometry are also reflected in the Mn2+ complexes of the liganding mutants (i.e., those in which the metal-liganding amino acids have been altered) by decreases in the electron-spin relaxation time of Mn2+. Inhibitory effects on kcat are noted in all of the liganding mutants with D40E, D40G, T41P, D21E, and D21Y showing 12-, 30-, 37-, 1500-, and greater than or equal to 29,000-fold reductions, respectively. The greater than or equal 10(3)-fold larger inhibitory effects on kcat of enlarging Asp-21 as compared to enlarging Asp-40 are ascribed to the displacement of the adjacent water molecule which attacks the phosphodiester. Mutations of each of the essential Arg residues to Gly (R35G and R87G) reduce kcat by factors greater than or equal to 35,000 but weaken metal binding less than or equal to 9-fold.(ABSTRACT TRUNCATED AT 400 WORDS)

The systematic characterization by aqueous column chromatography of solutes which affect protein stability.

We have systematically characterized, by aqueous column chromatography on a size exclusion cross-linked dextran gel (Sephadex G-10), 12 solutes, 11 of which are known to affect protein stability. Six are chaotropes (water structure breakers) and destabilize proteins, while five are polar kosmotropes (polar water structure makers) and stabilize proteins. Analysis of the chromatographic behavior of these neutral (ethylene glycol, urea), positively charged (Tris, guanidine, as the hydrochloride salts) and negatively charged (SO2-4, HPO2-4, F-, Cl-, Br-, Cl3CCO-2, I-, SCN-, as the sodium salts, in order of elution) solutes at pH 7 as a function of sample concentration (up to 0.6 M), supporting electrolyte, and temperature yields four conclusions, based largely on the behavior of the anions. Chaotropes adsorb to the gel according to their position in the Hofmeister series, with the most chaotropic species adsorbing most strongly. ++Chaotropes adsorb to the gel less strongly in the presence of chaotropes (a salting in effect) and more strongly in the presence of polar kosmotropes (a salting out effect). Polar kosmotropes do not adsorb to the gel, and are sieved through the gel according to their position in the Hofmeister series, with the most kosmotropic species having the largest relative hydrodynamic radii. The hydrodynamic radii of polar kosmotropes is increased by chaotropes and decreased by polar kosmotropes. These results suggest that a chaotrope interacts with the first layer of immediately adjacent water molecules somewhat less strongly than would bulk water in its place; a polar kosmotrope, more strongly.

Structure of .BETA.-cyclodextrin inclusion complex with nicotinamide.

The crystal structure of the β-cyclodextrin-nicotinamide (1 : 1) complex hexahydrate was determined by the X-ray method. The β-cyclodextrin ring is round in shape with seven intramolecular hydrogen bonds between secondary hydroxyl groups. The nicotinamide molecule is included in the host β-cyclodextrin cavity with the pyridine moiety being located at the center of the cavity. The amido group protrudes outside from the primary hydroxyl side of β-cyclodextrin and forms hydrogen bonds with adjacent β-cyclodextrin and water molecules.