Limited Number Of Water Molecules Research Articles

Electric nuclear quadrupole coupling reveals dissociation of HCl with a few water molecules

Investigating the dissociation of acids in the presence of a limited number of water molecules is crucial for understanding various elementary chemical processes. In our study, focusing on HCl(H 2 O) n clusters (where HCl is hydrogen chloride and H 2 O is water) formed in a cold and isolated jet expansion, we used the nuclear quadrupole coupling tensor obtained through rotational spectroscopy to decipher the nature of the hydrogen-chlorine (H-Cl) chemical bond in a microaqueous environment. For n = 1 to 4, the H-Cl bond is covalent. At n = 5 and 7, the contact ion pair of H 3 O + Cl − is spontaneously formed within the hydrogen bond networks of book and cube acid-water clusters, respectively.

Addressing the Effectiveness and Molecular Mechanism of the Catalytic CO2 Hydration in Aqueous Solutions by Nickel Nanoparticles.

Hydration of carbon dioxide in water solution is the rate limiting step for the CO2 mineralization process, a process which is at the base of many carbon capture and utilization (CCU) technologies aiming to convert carbon dioxide to added-value products and mitigate climate change. Here, we present a combined experimental and computational study to clarify the effectiveness and molecular mechanism by which nickel nanoparticles, NiNPs, may enhance CO2 hydration in aqueous solutions. Contrary to previous literature, our kinetic experiments recording changes of pHs, conductivity, and dissolved carbon dioxide in solution reveal a minimal effect of the NiNPs in catalyzing CO2 hydration. Our atomistic simulations indicate that the Ni metal surface can coordinate only a limited number of water molecules, leaving uncoordinated metal sites for the binding of carbon dioxide or other cations in solution. This deactivates the catalyst and limits the continuous re-formation of a hydroxyl-decorated surface, which was a key chemical step in the previously suggested Ni-catalyzed hydration mechanism of carbon dioxide in aqueous solutions. At our experimental conditions, which expand the investigation of NiNP applicability toward a wider range of scenarios for CCU, NiNPs show a limited catalytic effect on the rate of CO2 hydration. Our study also highlights the importance of the solvation regime: while Ni surfaces may accelerate carbon dioxide hydration in water restricted environments, it may not be the case in fully hydrated conditions.

Where Are Sodium Ions in AOT Reverse Micelles? Fluoride Anion Probes Nanoconfined Ions by 19F Nuclear Magnetic Resonance Spectroscopy.

Confining water to nanosized spaces creates a unique environment that can change water's structural and dynamic properties. When ions are present in these nanoscopic spaces, the limited number of water molecules and short screening length can dramatically affect how ions are distributed compared to the homogeneous distribution assumed in bulk aqueous solution. Here, we demonstrate that the chemical shift observed in 19F NMR spectroscopy of fluoride anion, F-, probes the location of sodium ions, Na+, confined in reverse micelles prepared from AOT (sodium dioctyl sulfosuccinate) surfactants. Our measurements show that the nanoconfined environment of reverse micelles can lead to extremely high apparent ion concentrations and ionic strength, beyond the limit in bulk aqueous solutions. Most notably, the 19F NMR chemical shift trends we observe for F- in the reverse micelles indicate that the AOT sodium counterions remain at or near the interior interface between surfactant and water, thus providing the first experimental support for this hypothesis.

Smog chamber simulation on heterogeneous reaction of O3 and NO2 on black carbon under various relative humidity conditions

In this study, heterogeneous formation of nitrate from O3 reaction with NO2 on black carbon (BC) and KCl-treated BC surface in the presence of NH3 was simulated under 30–90% RH conditions by using a laboratory smog chamber. We found that O3 and NO2 in the chamber quickly reacted into N2O5 in the gas phase, which subsequently hydrolyzed into HNO3 and further neutralized with NH3 into NH4NO3 on the BC surface, along with a small amount of N2O5 decomposed into NO and NO2 through a reaction with the BC surface active site. Meanwhile, the fractal BC aggregates restructured and condensed to spherical particles during the NH4NO3 coating process. Compared to that during the exposure to NO2 or O3 alone, the presence of strong signals of CH2O+, CH2O2+ and CH4NO+ during the simultaneous exposure to both NO2 and O3 suggested a synergetic oxidizing effect of NO2 and O3, which significantly activated the BC surface by forming carbonyl, carboxylic and nitro groups, promoted the adsorption of water vapor onto the BC surface and enhanced the NH4NO3 formation. Under <75 ± 2% RH conditions the coating process of NH4NO3 on the BC surface consisted of a diffusion of N2O5 onto the surface and a subsequent hydrolysis, due to the limited number of water molecules adsorbed. However, under 90 ± 2% RH conditions N2O5 directly hydrolyzed on the aqueous phase of the BC surface due to the multilayer water molecules adsorbed, which caused an instant NH4NO3 formation on the surface without any delay. The coating rate of NH4NO3 on KCl-treated BC particles was 3–4 times faster than that on the pure BC particles at the initial stage, indicating an increasing formation of NH4NO3, mainly due to an enhanced hygroscopicity of BC by KCl salts.

Quantum Calculations on the Role of Two Amino Acid Groupings that Include Three Positive, Two Negative Charged Residues on the Transport of Protons in the Voltage Sensing Domain of the KV1.2 Potassium Channel

The upper part of the voltage sensing domain (VSD) of the Kv1.2 channel is very similar to the upper part of the Hv1 proton channel, so the transport of protons in the VSD is possible. Our calculations have shown how two sets of five charged amino acids, each with two acid and three basic residues, hence with net one positive charge each, plus three polar but uncharged residues, are critical elements of the proton pathway, together with a limited number of water molecules. The upper group consists of (using numbering from the 3Lut pdb structure) R297,T184,E183,R300,Y266, R303,E226,S176; the lower section includes D259,K306,R309, R240,E236, W232,H310,S169. F233 is an additional critical residue: but rotating it facilitates the motion of a proton through what would otherwise seem a hydrophobic block. An electric field is needed to start the proton cascade from the upper section, which drives protons through the lower section, then along the cytoplasmic surface of the membrane, to the gate. A mutation, F233W, left shifts the gating current curve (MacKinnon and coworkers). In addition to finding the path through the VSD, our calculations explain this left shift, as well as the right shift found with F233E. The calculations show minimal shifts in structure with the field, of the order of 1 Å, but these are enough to produce electrostatic effects that lower the barrier to the proton's progress. Calculations with the protons in several positions have shown the relative energy, and the barriers, to proton transitions along the path. In particular the F233W mutant lowers the activation energy of proton transfer from K306 to D259.

Quantum Calculations on the Transport of Protons in the Voltage Sensing Domain of the Kv1.2 Potassium Channel: Multiple Paths, Charged Groups, and a Switch

The upper part of the voltage sensing domain (VSD) of the Kv1.2 potassium channel resembles the upper part of the Hv1 proton channel, suggesting that transport of protons in the VSD is possible. Our calculations have shown how two sets of amino acids, each with two acid and three basic residues, hence with net one positive charge each, plus three polar but uncharged residues, and a limited number of water molecules, are critical elements of the proton pathway. The upper group consists of (numbering from the 3Lut pdb structure) R297:T184:E183:R300:Y266:R303:E226:S176; the lower section includes D259:K306:R309:R240:E236:W232:H310:S169, in each case, plus water. F233 is an additional critical residue: rotating it facilitates the motion of a proton through what would otherwise seem a hydrophobic block; in effect it acts as a switch. An electric field starts the proton cascade from the upper section, which drives protons through the lower section; the cascade continues, in a nearly field-free environment, along the cytoplasmic surface of the membrane, to the gate. A mutation within the VSD, F233W, left shifts the gating current curve (MacKinnon and coworkers). In addition to finding the path through the VSD, our calculations explain this left shift by lower activation energy of proton transfer from K306 to D259, then on to H310; we also explain the right shift found with F233E. The calculations show minimal shifts in structure with the field, of the order of 1 Å, but these are enough to produce electrostatic effects that lower the barrier to the proton's progress. Calculations with the protons in several positions have shown the relative energy, and the barriers, to proton transitions along the path.

Silica-Based Materials as Drug Adsorbents: First Principle Investigation on the Role of Water Microsolvation on Ibuprofen Adsorption

Silica-based materials find applications as excipients and, particularly for those of mesoporous nature, as drug delivery agents for pharmaceutical formulations. Their performance can be crucially affected by water moisture, as it can modify the behavior of these formulations, by limiting their shelf life. Here we describe the role of water microsolvation on the features of ibuprofen adsorbed on a model of amorphous silica surface by means of density functional theory (DFT) simulations. Starting from the results of the simulation of ibuprofen in interaction with a dry hydrophobic amorphous silica surface, a limited number of water molecules has been added to study the configurational landscape of the microsolvated system. Structural and energetics properties, as well as the role of dispersive forces, have been investigated. Our simulations have revealed that the silica surface exhibits a higher affinity for water than for ibuprofen, even if several structures coexist at room temperature, with an active competition of ibuprofen and water for the exposed surface silanols. Dispersive interactions play a key role in this system, as pure DFT fails to correctly describe its potential energy surface. Indeed, van der Waals forces are the leading contribution to adsorption, independently of whether the drug is hydrogen-bonded directly to the surface or via water molecules.

Structural Basis for the Exceptional Stability of Bisaminoacylated Nucleotides and Transfer RNAs

At least one bisaminoacyl-tRNA is synthesized in nature (by Thermus thermophilus phenylalanyl-tRNA synthetase), and many disubstituted tRNAs have been prepared in vitro. Such misacylated tRNAs are able to participate in protein synthesis, even though they lack the free 2'-OH group of the 3'-terminal adenosine moiety. Their ready participation in protein synthesis implies significant chemical reactivity. The basis for this reactivity has been documented previously. Surprisingly, the aminoacyl moieties of these tRNAs also exhibit exceptional chemical stability. In the present report, bisaminoacylated nucleotides are investigated computationally and experimentally to define the basis for the stability of such species. Molecular modeling of bisalanyl-AMP in the absence of solvent and in the presence of a limited number of water molecules revealed two common features among the low-energy structures. The first was the presence of H-bonding interactions between the two aminoacyl moieties. The second was the presence of a H-bonding interaction between the 2'-O-alanyl moiety and the N-3 atom of the adenine nucleobase, typically mediated through a water molecule. The prediction of an interaction between an aminoacyl moiety and the adenine nucleobase was confirmed experimentally by comparing the behavior of bisalanyl-AMP and bisalanyl-UMP in the presence of model nucleophiles. This study suggests a possible role for the adenosine moiety at the 3'-end of aminoanyl-tRNAs in controlling the stability and reactivity of the aminoacyl moiety and has important implications for the reactivity and stability of normal aminoacyl-tRNAs.

How does microhydration impact on structure, spectroscopy and formation of disulfide radical anions? An ab initio investigation on dimethyldisulfide

The effect of microhydration on the one-electron uptake of a prototypical disulfide is examined at the MP2/DZP++ level of theory. After systematic generation of low-lying conformers of dimethyldisulfide–water clusters (DMDS: nH 2O, n = 1–5), either neutral or anionic, it is found that their energy ranking is governed by the increasing strength of the three hydrogen bonds involved, namely, water-neutral DMDS bonds, intra-water bonds and water–anionic DMDS bonds. Their optimal values are respectively 3.5, 4.5 and 11.4 kcal/mol. The inclusion of a limited number of water molecules has a non-negligible impact on structure and UV–Vis absorption of DMDS radical anion. Furthermore, its formation is favored by up to 1.04 eV when explicitly solvated by five water molecules.

Theoretical study of the structure and electronic spectra of fully protonated emeraldine oligomers

AbstractPolyaniline (PANI) is one of the most studied conducting polymers. Obtained in its conducting form (known as “emeraldine salt”) by chemical or electrochemical oxidation of aniline in aqueous acidic medium, this polymer manifests an array of attractive properties. Nevertheless, these properties still need to be described at the molecular level. Intense theoretical investigations during the past few years aim at explaining the chain organization, conductivity mechanism, and other structural and spectral characteristics. Most studies adopt simplified models in which hydration effect is underestimated, since all simulations are performed either in vacuum or in the presence of a limited number of water molecules. The present computational study sheds light on the molecular organization of a number of model PANI hydrated clusters with different alignment and multiplicity, which can explain the experimentally recorded UV/VIS spectra. The influence of hydration and interaction with adjacent oligomers is estimated. Short‐chain doubly protonated emeraldine oligomers are used as model systems. The calculations are performed at the semi‐empirical (AM1) and/or molecular mechanics (AMBER96) level. Proper configurations of the clusters are selected using Monte Carlo simulations. Electron correlation (CIS) is accounted for upon evaluation of the absorption spectra of the clusters. The relative strength of the interchain coupling is estimated by simulation of PANI clusters consisting of two PANI tetramers in water. Comparison to experimental results is made. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Fast Lipid Disorientation at the Onset of Membrane Fusion Revealed by Molecular Dynamics Simulations

Membrane fusion is a key event in vesicular trafficking in every cell, and many fusion-related proteins have been identified. However, how the actual fusion event occurs has not been elucidated. By using molecular dynamics simulations we found that when even a small region of two membranes is closely apposed such that only a limited number of water molecules remain in the apposed area (e.g., by a fusogenic protein and thermal membrane fluctuations), dramatic lipid disorientation results within 100 ps-2 ns, which might initiate membrane fusion. Up to 12% of phospholipid molecules in the apposing layers had their alkyl chains outside the hydrophobic region, lying almost parallel to the membrane surface or protruding out of the bilayer by 2 ns after two membranes were closely apposed.

Anion activation by quaternary onium salts and polyether ligands in homogeneous and heterogeneous systems

Abstract

Monte carlo simulation of the hydration shell of double‐helical amylose: A left‐handed antiparallel double helix fits best into liquid water structure

AbstractThe conformation of double‐helical amylose is influenced by its water environment [A. Imberty, H. Chanzy, S. Perez, A. Buléon, and V. Tran (1988) Journal of Molecular Biology, Vol. 201, pp. 365–378; A. Imberty and S. Perez (1988) Biopolymers, Vol. 27, 1205–1221]. For several low‐energy conformations of left‐handed amylose double helices, we performed Monte Carlo simulations of the (N, V, T)‐ensemble of configurations of water molecules surrounding a single duplex. The crucial point of this simulation is the use of cylindrical periodical boundary conditions with a relatively small asymmetric unit comprising a limited number of water molecules. The output data consists of local maxima of water density in the space near the macromolecule and information on one‐ and two‐membered water bridges between polar groups of amylose as well as energetic characteristics of the system under study.A left‐handed antiparallel‐stranded conformation of the amylose double helix (rise and twist per glucose unit are 0.343 nm and –58.1°) corresponds to the global minimum of intraduplex potential energy W. Schulz and H. Sklenar (1993) Biopolymers, submitted; W. Schulz, H. Sklenar, W. Hinrichs, and W. Saenger (1993) Biopolymers, to be published. We found that this conformation is favored also by its hydration shell characteristics in comparison to parallel‐stranded structures. Three hydration sites per glucose unit in the vicinity of HO6, O6, and O3 could be identified. Regular water bridges forming a network around the duplex were observed. A moderate change of the helical parameters within the family of left‐handed antiparallel structures (to a rise and twist per glucose unit of 0.233 nm and –45°) does not have noteworthy consequences for the characteristics of the hydration shell. The location of the hydration sites with respect to the polar groups of amylose and the observed water bridges are in excellent agreement with the hydration geometry of the heavily hydrated antiparallel‐stranded left‐handed double helix of p‐nitrophenyl α‐maltohexose described in a high‐resolution crystal study [W. Hinrichs, G. Büttner, M. Steifar, Ch. Betzel, V. Zabel, B. Pfannermüller, and W. Saenger (1987) Science, Vol. 238, pp. 205–208; W. Hinrichs and W. Saenger (1990) Journal of the American Chemical Society, Vol. 112, pp. 2789–2796].In the case of parallel‐stranded (nonsymmetric or symmetric) double helices, only one hydration site near the (H) O3 group could be identified. No systematic water bridges with sufficient high probability were observed. The sum of the average potential energies of the amylose–water and water–water interactions is not favourable in comparison with the energy for antiparallel‐stranded double helices. The water‐water interaction is high, i.e., parallel‐stranded amylose breaks the structure of liquid water. This effect would explain the insolubility of natural amylose in cold water and support the occurrence of parallel‐stranded double helices in crystallites of starch granules and in amylose microcrystals having only low water content [see Imberty et al. (1988) and Imberty and Perez ( 1988) above]. Symmetric parallel‐stranded double helices have very well‐exposed polar groups and their conformation should be favored in crystals by the ability to form extensively interduplex hydrogen bonds directly or via single water molecules. Single water molecules incorporated into the crystal would compensate for the shortage of donors of hydrogen bonds on the surface of the symmetric parallel‐stranded double helix. Indeed, in accordance with diffraction data see Imberty and Perez (1988) above; also A. Imberty, H. Chanzy, S. Perez, A. BulBon, V. Tran (1987) Macromolecules, Vol. 20, pp. 2636–26381 a critical amount of water increases the crystallinity of amylose and only symmetric parallel‐stranded double helices would fit into a crystallographic unit cell with c = 1.05 nm. The unfavorable hydration of parallel‐stranded double‐helical amylose would increase the stability of natural starch granules (e.g., in seeds) and, therefore, be biologically sensible. © 1992 John Wiley &amp; Sons, Inc.

Structure of the hydration shells of oligo(dA‐dT)·oligo(dA‐dT) and oligo(dA)·oligo(dT) tracts in B‐type conformation on the basis of Monte Carlo calculations

Monte Carlo simulations [(N, V, T)-ensemble] were performed for the hydration shell of poly(dA-dT).poly(dA-dT) in canonical B form and for the hydration shell of poly(dA).poly(dT) in canonical B conformation and in a conformation with narrow minor groove, highly inclined bases, but with a nearly zero-inclined base pair plane (B' conformation). We introduced helical periodic boundary conditions with a rather small unit cell and a limited number of water molecules to reduce the dimensionality of the configuration space. The coordinates of local maxima of water density and the properties of one- and two-membered water bridges between polar groups of the DNA were obtained. The AT-alternating duplex hydration mirrors the dyad symmetry of polar group distribution. At the dApdT step, a water bridge between the two carbonyl oxygens O2 of thymines is formed as in the central base-pair step of Dickerson's dodecamer. In the major groove, 5-membered water chains along the tetranucleotide pattern d(TATA).d(TATA) are observed. The hydration geometry of poly(dA).poly(dT) in canonical B conformation is distinguished by autonomous primary hydration of the base-pair edges in both grooves. When this polymer adopts a conformation with highly inclined bases and narrow minor groove, the water density distribution in the minor groove is in excellent agreement with Dickerson's spine model. One local maximum per base pair of the first layer is located near the dyad axis between adjacent base pairs, and one local maximum per base pair in the second shell lies near the dyad axis of the base pair itself. The water bridge between the two strands formed within the first layer was observed with high probability. But the water molecules of the second layer do not have a statistically favored orientation necessary for bridging first layer waters. In the major groove, the hydration geometry of the (A.T) base-pair edge resembles the main features of the AT-pair hydration derived from other sequences for the canonical B form. The preference of the B' conformation for oligo(dA).oligo(dT) tracts may express the tendency to common hydration of base-pair edges of successive base pairs in the grooves of B-type DNA. The mean potential energy of hydration of canonical B-DNA was estimated to be -60 to -80 kJ/mole nucleotides in dependence on the (G.C) contents. Because of the small system size, this estimation is preliminary.

Effect of hydration on the acidities of substituted methylammonium ions

Calculations at the ab initio level on the hydration equilibria of substituted methylamines, XCH 2NH 2 and of their ammonium salts are reported. These results allow the calculation of the acidities of the methylammonium ions in the presence of a limited number of water molecules. Such results are compared to calculated and experimental results for the gas phase and experimental results in aqueous solution. Calculated results for three molecules per methylammonium ion and one per methylamine approach those found for aqueous solution.

Effect of hydration on the acidities of substituted acetic acids

We report calculations at the ab-initio level on the hydration equilibria of substituted acetates XCH 2CO 2 − + nH 2O ⇌ XCH 2CO 2 − with nH 2O up to n = 3. Results are also given for the hydration energies of the corresponding acetic acids. These results allow the calculation of the acidities of the acetic acids in the presence of a limited number of water molecules. Such results are compared to experimental figures in the gas phase and in aqueous solution. Results for three water molecules per acetate ion and one per acetic acid molecule approach those found for aqueous solution.

Nucleophilic aromatic substitution promoted by lipophilic quaternary 'onium salts under phase-transfer conditions and in low polarity anhydrous solvents. A kinetic study

A kinetic study of aromatic nucleophilic substitutions by N3– and SCN– has been carried out under phase-transfer catalysis (p.t.c.) conditions and in anhydrous chlorobenzene in the presence of hexadecyltributylphosphonium azide and thiocyanate. Under p.t.c. conditions, reactions follow a pseudo-first-order kinetic equation, and kobs is linearly related to the nucleophile concentration in the organic phase. In most reactions, the rate-determining step is attack by the nucleophile on the substrate. However in a few cases the process is controlled by diffusion of the anions through the interface. Passing from p.t.c. conditions to chlorobenzene solution leads to 5–7- and 2–3-fold increases in reaction rates with N3– and SCN–, respectively. This behaviour is analogous to that observed in the aliphatic series, and is probably due to the limited number of water molecules accompanying the anions in the organic phase under p.t.c. conditions. Nucleofugicity scales are related to the polarizability of the nucleophile, and with N3– and SCN– they are F Br ≳ I ≳ Cl and Br > I > F ≳ Cl, respectively. Reaction products, including those derived from successive decomposition of N3 and SCN groups, have been identified.

Phase-transfer mechanism and nucleophilicity of halide ions in an aqueous–organic two-phase system

Nucleophilic substitution by halide ions in n-octyl methanesulphonate catalysed by hexadecyltri-butylphosphonium halides in a water–chlorobenzene two-phase system occurs in the organic phase; the reactivity range (Cl–:Br–:I–= 0·6:1·1:1) is largely determined by the specific solvation of the anion by a limited number of water molecules.

Freezing of the water content of porous membranes

A theoretical and experimental study of the freezing of water in a porous membrane is presented. A membrane is considered as a set of very fine capillaries of radius r and thickness e with a thick ice-water interface, consisting of several molecular layers. The effect of the number N of molecules comprising the interface on the melting temperature T is studied in terms of the thermodynamics of small systems. Experimental results on the ice melting point of calibrated membranes are given. It was found that the rate of decreasing of the melting point versus pore radius is different from the previous rate by the Kelvin relation, and it is shown that interfacial phenomena have an important effect when the pore radius decreases. The problems of freezing the water contained in a very fine capillary were studied as a model of the freezing of living cells, and in particular as a model of the effects of freezing on cell membranes, an event that is common to all cryobiological problems. Although the experimental and theoretical results presented here are not directly transposable to actual living membranes, a model of a semipermeable membrane containing distilled water is examined. The characteristic parameter of such membranes is the mean pore radius. Many studies were done in this field (2, 17, 18) in relation to the fundamental function of the cell membrane (3, 4, 16). In a very schematic manner, one can assume that the pores in the biological membranes have a radius of 10 −10 − 10 −6 m (i.e., vegetables stomata). In this type of fine capillary, we have a limited number of water molecules. The thermodynamic relations of the Kelvin type, used to calculate the equilibrium temperature, are not valid in this case because the interface and its radius of curvature are no longer fixed. In a macroscopic system, the interface is defined as the surface which separates two different phases. The solid phase, i.e., ice, is characterized by a certain molecular ordering forming a well-defined crystalline structure (9). The liquid phase is characterized by a different molecular ordering, still imperfectly understood (7, 19). In a system with a small number of molecules, the problem is completely different. There are no more macroscopic effects to average out the phenomena appearing at the molecular level. Since there are no bulk effects, the surface effects, which are negligible in a macroscopic: system, become an essential parameter. In particular, it is difficult to assume that the interface is a discontinuous surface as in the larger systems. On the contrary, the interface is probably composed of a variable number of molecular layers depending on the size of the system under consideration. This assumption is introduced in the theoretical model developed in the following section, a model derived from the thermodynamics of small systems (12).