Neighboring Water Molecules Research Articles

An analysis of hydrated proton diffusion in ab initio molecular dynamics

A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore, the correlations of the neighboring water atoms are identified as the fourth water approaches the hydronium. Finally, the temperature effects on structural and dynamical properties are studied.

Properties of water hydrating the galactolipid and phospholipid bilayers: a molecular dynamics simulation study.

Molecular dynamics simulations of 1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayers were carried out to compare the effect of the lipid head group's chemical structure on the dynamics and orientational order of the water molecules hydrating the bilayer. The effect of the bilayers on the diffusion of water is strong for the neighbouring water molecules i.e., those located not further than 4 Å from any bilayer atom. This is because the neighbouring water molecules are predominantly hydrogen bonded to the lipid oxygen atoms and their mobility is limited to a confined spatial volume. The choline group of DOPC and the galactose group of MGDG affect water diffusion less than the polar groups located deeper in the bilayer interface, and similarly. The latter is an unexpected result since interactions of water with these groups have a vastly different origin. The least affected by the bilayer lipids is the lateral diffusion of unbound water in the bilayer plane (x,y-plane) - it is because the diffusion is not confined by the periodic boundary conditions, whereas that perpendicular to the plane is. Interactions of water molecules with lipid groups also enforce certain orientations of water dipole moments. The profile of an average water orientation along the bilayer normal for the MGDG bilayer differs from that for the DOPC bilayer. In the DOPC bilayer, the ordering effect of the lipid head groups extends further into the water phase than in the MGDG bilayer, whereas inside the bilayer/water interface, ordering of the water dipoles in the MGDG bilayer is higher. It is possible that differences in the profiles of an average water orientation across the bilayer in the DOPC and MGDG bilayers are responsible for differences in the lateral pressure profiles of these bilayers.

Structure and Dynamics of Ferrocyanide and Ferricyanide Anions in Water and Heavy Water: An Insight by MD Simulations and 2D IR Spectroscopy.

Combined computational and experimental techniques were employed to investigate at the microscopic level the structural and dynamic properties of ferro- and ferricyanide ions in aqueous solution. The characterization of the structural patterns and multiscale dynamics taking place within the first solvation spheres in water and heavy water solvents was first achieved through extensive molecular dynamics simulations, performed with refined force fields, specifically parametrized for the cyanide ions under investigation. The information gained about the solute-solvent interactions is then validated through the successful comparison of computed and measured waiting-time-dependent 2D IR spectra. The vibrational patterns resulting from 2D IR measurements were rationalized in terms of the interaction between the ion and the neighboring water molecules described by simulation. It was found that, within the first solvation sphere, the stronger interactions of the solvent with the ferro species are responsible for a delay in the relaxation dynamics, which becomes more and more evident on longer time scales.

Cross sections, stopping powers, and energy loss rates for rotational and phonon excitation processes in liquid water by electron impact

We calculated cross sections, stopping powers, and energy loss rates for rotational and phonon-mode excitations caused by the impact of an electron in an energy region from 0.1 meV to 100 eV injected into liquid water. The spatial distribution of the decelerated electron depends on these cross sections. We performed calculations assuming an optical approximation with the dielectric functions that are experimentally reported in the literature. We observed that the cross sections lie below 1×10−16 cm2 over the considered energy region. The values for rotational excitation processes in the liquid phase are less by three orders of magnitude than those in the gas phase because of the screening effect of neighboring water molecules on the interaction between the incident electron and water molecules. These results suggest that the cross sections in the liquid phase are significantly different from those in the gas phase. The values for phonon-mode excitations in the liquid phase are close to those reported for amorphous ice. Furthermore, we observed that the stopping power shows a maximum around 200 meV, and the energy loss rates, which are derived from the stopping power, depend significantly on the electron energy, particularly below 1 eV. The values obtained here will allow us to precisely estimate the decelerating process of an electron in liquid water to predict radiation effects such as chemical processes in water radiolysis or biomolecular damage induction strongly involved in low energy electron processes.

Trona at extreme conditions: A pollutant-sequestering material at high pressures and low temperatures

Single-crystal X-ray diffraction of trona, Na 3 CO 3 HCO 3 ·2H 2 O, was measured between 100 and 340 K at ambient pressures, and the infrared and Raman spectra of this material characterized to ~25 GPa. The thermal expansion of trona is greatest in the b direction, which is due to a particularly large expansion of the long Na 2 -O 1 and the short Na 2 -O 4 bonds within the sodium septahedron in the trona structure. This crystallographic direction is associated with the distance between neighboring carbonate groups and neighboring water molecules within the structure. The dimensions of the carbonate group undergo no systematic changes over this temperature range, and the disordered hydrogen atom within the structure does not order at temperatures down to 100 K. Thus, detailed changes in the geometry of the sodium polyhedra primarily modulate the response of trona to decreases in temperature. The infrared and Raman spectra undergo discontinuous and reversible changes at ~7 and ~14.5 GPa: the former of these phase transitions is likely associated with a shift primarily in the sodium-oxygen polyhedra, while the latter also involves shifts in bonding of the carbonate groups. New assignments are suggested for portions of the vibrational spectrum based on the high-pressure results. Resonance effects between different vibrational modes are observed, including the observation of a transmission maximum associated with a resonant interaction between the carbonate symmetric stretching vibration and a broad mode at similar frequencies. The behavior of trona under extreme conditions is useful for understanding CO 2 -vapor-saturated alkali-rich systems, and late-stage peralkaline magmatic processes and, in its usage as both a sorbent and scrubber of SO 2 and CO 2 in flue gasses and lignite coals.

Molecular dynamics studies on the influences of a gradient electric field on the water chain in a peptide nanotube.

The structure and transportation characteristics of the water chain inside a 8×cyclo-(WL)4 peptide nanotube (PNT) were simulated under a gradient electric (GE) field. The gradient was defined by the ratio of a constant (Ea) and the z-directional length (Lz) of the simulation box. Ea varies from 0.0 to 0.9 V nm(-1). As the gradient increases, the probabilities of finding two water molecules in an α-plane zone and three in a midplane region increase. To accommodate more water molecules, the axial array of channel water molecules becomes more compact. Meanwhile, the H-bonded network between the channel water is greatly intensified when Ea increases from 0.3 to 0.9 V nm(-1). Nevertheless, the proportion of strong H-bonds does not increase significantly following the formation of a more compact axial array of water molecules. When Ea reaches 0.9 V nm(-1), the water molecule in an α-plane zone may be dragged by its neighboring water molecules into the midplane region, resulting in a significant deviation from the channel axis. With the augment of the gradient, the dipoles of channel water are gradually oriented along the tube axis in the sequence from gap 1 to 7, namely along the direction of the electric field. Nevertheless, even when E a reaches 0.9 V nm(-1), the dipole orientation of the channel water is not complete, and dipole flips still occur in gap 7. Under a GE field, the rightward and leftward hopping rates of channel water are no longer equal to each other, i.e., channel water performs an asymmetric transportation.

Intrinsic autocorrelation time of picoseconds for thermal noise in water.

Whether thermal noise is colored or white is of fundamental importance. In conventional theory, thermal noise is usually treated as white noise so that there are no directional transportations in the asymmetrical systems without external inputs, since only the colored fluctuations with appropriate autocorrelation time length can lead to directional transportations in the asymmetrical systems. Here, on the basis of molecular dynamics simulations, we show that the autocorrelation time length of thermal noise in water is ~10 ps at room temperature, which indicates that thermal noise is not white in the molecular scale while thermal noise can be reasonably assumed as white in macro- and meso-scale systems. The autocorrelation time length of thermal noise is intrinsic, since the value is almost unchanged for different temperature coupling methods. Interestingly, the autocorrelation time of thermal noise is correlated with the lifetime of hydrogen bonds, suggesting that the finite autocorrelation time length of thermal noise mainly comes from the finite lifetime of the interactions between neighboring water molecules.

Effects of the translational and rotational degrees of freedom on the hydration of simple solutes.

Molecular dynamics simulations with separate thermostats for rotational and translational motion were used to study the effect of these degrees of freedom on the structure of water around model solutes. To describe water molecules we used the SPC/E model. The simplest solute studied here, the hydrophobe, was represented as a Lennard-Jones particle. Since direct interaction between the hydrophobe and water molecules has no angular dependence the influence of the increase of the rotational temperature on the solvation of a hydrophobe is only indirect. In the next step the central solute was assumed to be charged with either a positive or a negative charge to mimic an ion in water. Hence, depending on the charge of the ion, the neighboring water molecules assumed different angular distributions. The principal conclusions of this work are: (i) an increase of the translational temperature always decreases the height of the first peak in the solute-water radial distribution function; (ii) an increase of the rotational temperature yields an increase in the first peak in the solute-water radial distribution function for hydrophobes and cations; (iii) in contrast to this, the solvation peak decreases around ions with sufficiently large negative charge; and (iv) an increase of the rotational temperature affects cations in an opposite way to anions. For this reason complex molecules with a small net charge may not be very sensitive to variation of the rotational temperature.

Theoretical Study of Water Cluster Catalyzed Decomposition of Formic Acid

We have performed a number of quantum chemical simulations to examine water cluster catalyzed decomposition of formic acid. The decomposition of formic acid consists of two competing pathways, dehydration, and decarboxylation. We use the Gaussian 4 method of the Gaussian09 software to locate and optimize a transition state of the decomposition reaction and obtain the activation energy. The decomposition starts by transferring a proton of a formic acid to a water molecule. The de Broglie wavelength of a proton is similar to the width of the potential barrier of the decomposition reaction at low temperature. The tunneling, in which a proton penetrates the potential barrier, enhances the decomposition rate. Water molecules serve as the catalyst in the decomposition and reduce the activation energy. The relay of a proton from a water molecule to a neighboring water molecule is accomplished with little change of the geometry of a molecule, resulting in the reduction of the activation energy. Two water molecules are actively involved in the decomposition reaction to reduce the activation energy. We have also examined the effect of water clusters with three, four, and five water molecules on the decomposition reaction. The noncovalent distance between a hydrogen atom of a water molecule and an oxygen atom of a neighboring water molecule decreases in a water cluster due to the cooperative many-body interactions. A water molecule in a water cluster becomes a better proton donor as well as a better proton acceptor. The activation energy of the decomposition is further decreased by the catalytic effect of a water cluster. We calculate the reaction rate using the transition state theory corrected by the tunneling effect of a proton. The calculated reaction rate of the decarboxylation is smaller than that of the dehydration when less than three water molecules are included in the simulation. However, the major product of the decomposition of a formic acid becomes carbon dioxide and hydrogen molecule formed by the decarboxylation when a water cluster with more than four water molecules serves as catalyst in the decomposition of formic acid.

Entropy gain due to water release upon ligand binding

Experimental thermodynamic data of the ligand-receptor association showed that the entropy changes upon binding are positive and large enough to be important driving forces of the binding process for a considerable number of ligand-receptor complexes [1]. The expected source behind such an entropy increase is the release of the water molecules from the binding pocket and from around the ligand to get more freedom in the bulk phase. However, this important source of entropy is usually ignored due to the lake of a method to compute it. Therefore, we developed a method to compute the entropic gain due to water release upon ligand binding. Water molecules close to a charged residue are restricted from free rotation due to the interaction between their dipole moments and the electric field. This restriction result in a decrease in their entropy. The loss of entropy can be gained again when the water molecules displaced from area that under the electric field upon the binding process. To compute the loss of entropy due to the electric field, we developed a method based on the knowledge of the electric field which affects the rotation of the water molecules using the continuum electrostatic methods. This provides a possibility for the calculation of the entropic loss from the partition function of the water molecules under an electric field. For monovalent ions, the computed loss in entropy upon solvation correlates well with experimentally measured one. The loss of entropy of water close to hydrophobic molecules (Hydrophobic entropy) cannot be explained by the effect of the electric field from the molecule because the magnitude of the electric field is not strong enough to restrict the mobility of the water molecules. However, the loss in entropy results from the asymmetric interactions of the water molecules with the hydrophobic molecules and the neighbour water molecules. To compute the hydrophobic entropy we developed an empirical method which is derived from a linear relation between the hydration entropy of small hydrophobic molecules and the hydrophobicity of the water molecules around the surface of the small molecule. A training data set of 142 small molecules shows a significant linear relation between the hydrophobic entropy and the computed hydrophobicity.

Characteristics of selenate in aqueous solution – An ab initio QMCF-MD study

An ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) study of the selenate ion in water was performed at the Hartree Fock/6-31G (d,p) level of theory. The intramolecular geometry, structure and dynamics of the hydration shell and the vibrational frequency modes calculated via velocity autocorrelation functions are presented. The resulting bond distances as well as angles and vibrational frequencies are in good agreement with experimental data. The structure and dynamics reveal the hydrogen bonding network between the ion and neighboring water molecules and exchange processes in the hydration sphere characterize the ion as a structure-forming anion.

Hydration Structure of CO2-Absorbed 2-Aminoethanol Studied by Neutron Diffraction with the 14N/15N Isotopic Substitution Method

Neutron diffraction measurements were carried out for CO2-absorbed aqueous 11 mol % 2-aminoethanol (MEA) D2O solutions (corresponding to 30 wt % MEA solution) in order to obtain information on both the intramolecular structure and intermolecular hydration structure of the MEA carbamate molecule in the aqueous solution. Neutron scattering cross sections observed for (MEA)0.11(D2O)0.89, (MEA)0.11(D2O)0.89(CO2)0.06, and (MEA)0.11(D2O)0.89(DCl)0.11 solutions with different (14)N/(15)N ratios were used to derive the first-order difference function, ΔN(Q), which involves environmental structural information around the nitrogen atom of the MEA molecule. Intramolecular geometry and intermolecular hydration structure of MEA, protonated MEA (MEAD(+)), and MEA carbamate (MEA-CO2) molecules were obtained through the least-squares fitting of the observed Δ(N)(Q) in the high-Q region and the intermolecular difference function, Δ(N)(inter)(Q), respectively. In the aqueous solution, the MEA molecule takes the gauche conformation (dihedral angle, ∠NCCO = 45 ± 3°), suggesting that an intramolecular hydrogen bond is formed. On the other hand, values of the dihedral angle ∠NCCO determined for MEAD(+) and MEA-CO2 molecules were 193 ± 4° and 214 ± 8°, respectively. These results imply that the intermolecular hydrogen bonds are dominated for MEAD(+) and MEA-CO2 molecules. The intermolecular nearest neighbor N···O(D2O) distance for the MEA molecule was determined to be 3.13 ± 0.01 Å, which suggests weak intermolecular interaction between the amino-nitrogen atom of MEA and water molecules in the first hydration shell. The nearest-neighbor N···O(D2O) distances for MEAD(+) and MEA-CO2 molecules, 2.79 ± 0.03 and 2.87 ± 0.04 Å, clearly indicate strong hydrogen bonds are formed among the amino group of these molecules and neighboring water molecules.

Mobility of Water in a Confined Proteinaceous Environment

Bulk water mobility is mainly determined by hydrogen bonds to neighboring water molecules. Mobility of confined water may be very different, especially when the hydrogen bonds are scarcely formed inside a protein and/or are geometrically distorted due to the position of the amino acids. Here we assessed intra-proteinaceous water mobility in terms of the water diffusion coefficient D by exploiting the fact that D governs the unitary permeability pf of water channels [1]. We measured the per-channel increment in proteoliposome water permeability [2], which was determined in a broad range of channel concentrations by the aid of stopped-flow experiments. Via fluorescence correlation spectroscopy, both the number of proteoliposomes and the number of protein-containing micelles were counted after solubilization, providing the number of reconstituted fluorescently labeled human aquaporin-1, bacterial aquaporin-Z, or bacterial aquaglyceroporin GlpF per proteoliposome. For all three proteins, pf exceeded previous estimates by more than an order of magnitude indicating that the intra-proteinaceous D is much larger than D of bulk water. The result suggests that in silico modeling of confined water may be more challenging than thus far imagined.[1] Saparov et al. Phys.Rev.Lett. 96 (14):148101, 2006.[2] Hoomann et al. Proc.Natl.Acad.Sci.U.S.A. 110 (26):10842-10847, 2013.

Multiscale Simulation of Liquid Water Using a Four-to-One Mapping for Coarse-Graining.

We present a multiresolution simulation scheme for the solvent environment where four atomistic water molecules are mapped onto one coarse-grained bead. Soft restraining potentials are used to allow a resolution exchange of four water molecules into a single coarse-grained site. We first study the effect of adding restraining potentials in liquid water using full all-atom simulations. The usage of very soft restraining potentials to bundle four nearest neighbor water molecules does not disrupt the hydrogen bonding patterns in the liquid water. The structural properties of the first solvation shell around hydrophobic, hydrophilic, and ionic solutes are well preserved when soft restraining potentials are added. By modeling a bundle of four water molecules as a single molecule, a smooth transition and free exchange between coarse-grained and all-atom resolution is possible by using the adaptive resolution scheme (AdResS).

Dissociation of HCl into Ions on Wet Hydroxylated (0001) α-Quartz

The acidification of surfaces in the natural and built environments is important to atmospheric science because the process can enhance chemistry at surfaces and increase the release of highly reactive products into the gas phase. We present the results of an ab initio molecular dynamics study using density functional theory of HCl ionic dissociation on the hydroxylated (0001) α-quartz surface. We observed that at temperatures in the range of 250–300 K, HCl ionizes rapidly on a surface wetted with a water monolayer. It seems that ionization is enhanced by lattice mismatch between the silica and water layer. The first proton transfer to a neighboring water molecule initiates proton migration within the water adlayer via the Grotthuss mechanism. Spectroscopic signatures for the ionization are calculated and are in fair agreement with experiment.

Reaction kinetics for the oxygen hydrogenation process on Pt(111) derived from temperature-programmed XPS

Oxygen hydrogenation under ultra high vacuum conditions at the platinum surface was explored using temperature-programmed X-ray photoelectron spectroscopy. Through modeling of the oxygen consumption, information on the reaction kinetics was obtained indicating that the reaction rate of the oxygen hydrogenation process depends on the hydrogen diffusion and on the lifetime of hydroxyl intermediates. The reaction rate is, however, enhanced when an autocatalytic process stabilizes the hydroxyl intermediates through hydrogen bonding to neighboring water molecules. The overall activation energy for the hydrogenation of atomic oxygen to form water was determined to be 0.20eV with a frequency factor of only 103s−1.

Relaxation of Electronically Excited Hydrogen Peroxide in Liquid Water: Insights from Auger-Electron Emission

Autoionization electron spectroscopy is applied to study nonradiative relaxation processes of hydrogen peroxide aqueous solution irradiated by soft X-rays. The high kinetic energy part of the oxygen 1s H2O2(aq) Auger-electron spectrum reveals dicationic final states with considerably lower energy than for neat liquid water. Assisted by quantum chemical calculations, it is argued that such lower-energy states arise from two fundamentally different relaxation processes. One is (local) Auger decay, yielding H2O22+(aq) species, and here the low final-state energy arises from charge delocalization across the molecular O–O bond. Alternatively, nonlocal dicationic states can form, corresponding to a charge-separated complex comprising H2O2 and a neighboring water molecule. Different charge-separation mechanisms, depending on whether or not proton dynamics of the core-level excited or ionized H2O2 molecule is involved, are discussed. We also present for the first time the partial electron yield X-ray absorption s...

Study of interatomic Coulombic decay of Ne(H2O)n (n = 1,3) clusters using equation-of-motion coupled-cluster method

Interatomic Coulombic decay (ICD) is an efficient and ultrafast radiationless decay mechanism which can be initiated by removal of an electron from the inner-valence shell of an atom or molecule. Generally, the ICD mechanism is prevailed in weakly bound clusters. A very promising approach, known as CAP/EOM-CC, consists of the combination of complex absorbing potential (CAP) with the equation-of-motion coupled-cluster (EOM-CC) method, is applied for the first time to study the nature of the ICD mechanism. We have applied this technique to determine the lifetime of an auto-ionized, inner-valence excited state of the NeH2O, Ne(H2O)2, and Ne(H2O)3 systems. The lifetime is found to be very short and decreases significantly with the number of neighboring water molecules.

Hydronium dynamics in the perchloric acid clathrate hydrate

Clathrate hydrates are nanoporous crystalline materials made of a network of hydrogen-bonded water molecules (forming host cages) stabilized by the presence of foreign (generally hydrophobic) guest molecules. The encapsulation of strong acids such as perchloric acid (with an acid to water ratio of 5.5) leads to an ionic clathrate structure formed with perchlorate anions within cationic cages. The excess protons, at the origin of the large protonic conductivity of the compound, are delocalized over the cage sub-structure through a Grotthus mechanism. Such ionic crystal constitutes a good model system for investigating the spatial and time characteristics of the elementary steps of the proton conduction. In this paper, the dynamics of hydronium ions are investigated by means of incoherent quasi-elastic neutron scattering (QENS) experiments performed by tuning the observation time to the timescale of the probed dynamical process met in the perchloric acid clathrate hydrate at 220 K. Thanks to the specific versatility of time-of-flight spectrometer, two elementary processes have been identified for modeling the hydronium ion dynamics: hydronium reorientations coupled to intermolecular proton transfer. The hydronium ions undergo reorientations with a characteristic time of 42 ± 8 ps while the proton transfer within the hydrogen bond between hydronium ion and neighboring water molecule occurs with a characteristic time of 1.4 ± 0.3 ps. A previous high-resolution QENS investigation has shown that water molecules surrounding the hydronium ions undergo reorientations with a characteristic time of 0.7 ± 0.1 ns at 220 K. Such experimental results outline the key role played by the relaxation of the water molecules surrounding the hydronium ions prior to any proton transfer.

Molecular Dynamics Study of Water and Ions Transported during the Nanopore Calcium Silicate Phase: Case Study of Jennite

AbstractDurability is an important property that determines the long-term behavior of cement-based materials. Water and ions are transported in nanopores of calcium-silicate-hydrate (C-S-H) gels, the main element in cement-based material, which significantly influences the durability of cement. Because of its structural similarity, jennite, an important mineral analog of C-S-H gel, is first taken to investigate the transport behavior at a molecular level. In this paper, structural and dynamical properties of the water/ions and the jennite interface are studied by the molecular dynamics (MD) simulation method. On the (001) surface of jennite, water molecules diffusing in the channel between silicate chains demonstrate the following structural water features: large density, good orientation preference, ordered interfacial organization, and low diffusion rate. The channel water molecules have more H-bonds connected with the neighboring water molecules and solid surface. As the distance from the channel incre...