Arrangement Of Water Molecules Research Articles

Catalytic activity of water molecules in gas‐phase glycine dimerization

AbstractThe dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known as cis and trans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas‐phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of the cis transition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm‐based configurational sampling, density functional theory geometries, and domain‐based local pair natural orbital coupled‐cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concerted cis mechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.

Movement of water in compacted bentonite and its relation with swelling pressure

A testing procedure was proposed to study water movement in compacted bentonite and the development of swelling pressure (ps) when compacted bentonite specimens were wetted. In this procedure, a multi-ring mold was introduced for ps measurements, after which the specimen was sliced for X-ray diffraction to find movement of water in the interlayer space of montmorillonite. Results revealed a relation between four phases of ps development and evolution of four states of interlayer water molecule arrangement of montmorillonite (L): when ps reached its first peak in phase I, L moved from 1 row water arrangement (1w) to at least 2w; when ps decreased and re-increased in phases II or III, L moved from 2w to at least 3w; and when ps reached a steady state in phase IV, L = 3w. The w distribution in the compacted bentonite was also measured as water absorption time increased. Based on those results, the global water movement was estimated in terms of diffusivity (D) following a method employing Boltzmann transform. Results of comparisons implied that D calculated using this method matched experimental data well and the method was rather easily handled.

Eu3+ luminescent ions detect water density anomaly

It is well known that water density varies anomalously with temperature. However, nowadays there is still a lack of agreement on the causes of this phenomenon. In this work, we use Eu3+ luminescent ion as a probe to investigate the changes in the arrangement of water molecules around the temperature of maximum density. The slight changes in the arrangement of water molecules in the first coordination sphere of Eu3+ ions due to the water density anomaly affect the variation with temperature of Eu3+ ions emission spectra and intensity decay time. This is the first time, to the best of our knowledge, that the effect of the anomaly in the density of water is detected by a luminescent material. From these experimental results we can infer that possibly the anomaly could be caused by variation in the length of hydrogen bonds between molecules with temperature for both water and heavy water.

The contribution of surfaces to the Raman spectrum of snow

We investigated if the Raman spectrum of snow is affected by the highly differentiated snow morphology. The latter is subjected to continuous changes driven by the variation of ambient parameters, mainly temperature and humidity as snow progresses from freshly deposited, to compact, to icy. We measured the Raman spectrum of snow grains of different size and morphology on the temperature interval between −5.5 °C and −0.5 °C approaching the melting point. We found systematic differences with respect to bulk ice Ih in the OH-stretching band of snows with different histories. We attribute the observed spectral differences to the change of the molecular arrangement of water molecules between bulk and surface sites. We investigate this characteristic via molecular dynamics DFT simulations of bulk ice and of three thin slabs cut along specific surfaces. We analysed the simulated Raman spectra and compared their distinguishing features to those of experimental spectra of snow. The Raman features of the OH-stretching band allow to distinguish among layers inside a snowpack, each layer being characterized by a different specific surface area. This is relevant to estimate the mechanical stability of the snowpack itself. The influence of UV-A irradiation on snow is discussed.

Change of Hydration Patterns upon RNA Melting Probed by Excitations of Phosphate Backbone Vibrations.

The water hydration shell has a decisive impact on the structural and functional properties of RNA. Changes of the RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process that is barely characterized. To discern hydration geometries around the backbone phosphate groups of an RNA double helix at the molecular level, we combine two-dimensional infrared spectroscopy of phosphate vibrations with theoretical simulations. There are three distinct coexisting hydration motifs of the RNA A-helix: an ordered chain-like arrangement of water molecules with links between neighboring phosphate groups, separate local hydration shells of up to six water molecules, and hydrated phosphate/counterion contact pairs. RNA disordering upon melting is connected with a transition from predominantly ordered water structures to local hydration shells around phosphate units. Structural fluctuations are dominated by librational water motions occurring on a 300 fs time scale, without exchange between hydration motifs.

Effects of concentration and pressure on the aqueous solvation structure of ammonia and composition dependent ion solvation scenario in water-ammonia mixtures

The hydrogen bonding structure of water and its dynamics in aqueous ammonia solution is investigated by using classical molecular dynamics simulations. We have considered eight different mole-fraction of ammonia, ranging from xNH3 = 0.02 to 0.30, and the pressure variation is carried out on the concentrated ammonia solution (xNH3=0.30), ranging from P = 0.1 MPa to 800 MPa, at 293K. The radial distribution function indicates that the addition of ammonia facilitates the structural organization of water, which is further supported by increasing values of asphericity parameter. But, the tetrahedral order parameter values suggest an angularly disordered arrangement of water molecules. The self-diffusion coefficient values of water pass through shallow minima, whereas it increases for ammonia with ammonia concentration in the solution. The application of pressure causes a sharp decline in translation mobility of ammonia compared to water, but at very high pressure (above 600 MPa), both the species diffuse at the same rate. The rotational relaxation of ammonia is approximately three times faster than water in the solution, which further increases along with concentration as well as pressure. A similar trend is also observed in the case of structural reorganization of water-water and water-ammonia hydrogen bonds. The water-water and water-ammonia hydrogen-bond lifetimes are increasing with ammonia concentration, whereas it passes through shallow maxima with the application of pressure. In this study, we have compared two different Lennard-Jones (LJ) combination rule, which causes negligible differences in the calculated properties. The solvation scenario of different ionic (Na+, Cl−) and neutral (Cl0) solutes are also analyzed along with the coordination number. It is observed that the hydration shell of ion is mainly dominated by water molecules in the solution.

The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom‐up investigation

AbstractThe geometry of surrounding water molecules on the side chain of glycine, alanine, α‐aminoisobutyric acid, α‐aminobutyric acid, valine, and related hydrocarbons has been analyzed combining bottom‐up and quantum chemical methodologies. To minimize the cavity size and to prevent water‐water hydrogen bonding loss, the water molecules adopt a shape, resembling the one found in crystal structure of gas clathrate hydrates, with water molecules tangentially oriented to the surface of hydrophobic side chain. The cage is directly hydrogen bonded to the backbone's polar groups, thus hydration shells around hydrophobic and hydrophilic groups are folded together in amphiphilic molecules. The hydrophobe enclathration implies a substantial freedom degree reduction which makes it entropically disfavored. This disadvantageous entropic contribution is partially compensated by the favorable van der Waals interactions with guest in stabilizing clathrate hydrate formation. The water shell around the side chain relates intimately with the side‐chain rotational isomerism. Present data are correlated with the experimental determined populations of the three rotamers, yielding promising results for both α‐aminobutyric acid and valine.

A primary model of THz and far-infrared signal generation and conduction in neuron systems based on the hypothesis of the ordered phase of water molecules on the neuron surface I: signal characteristics

In this paper, we use the theory of quantum optics and electrodynamics to study the electromagnetic field problem in the nervous system based on the assumption of an ordered arrangement of water molecules on the neuronal surface. Using the Lagrangian of the water molecule-field ion, the dynamic equations for neural signal generation and transmission are derived. Perturbation theory and the numerical method are used to solve the dynamic equations, and the characteristics of high-frequency signals (the dispersion relation, the time domain of the field, the frequency domain waveform, etc.) are discussed. This model predicts some intrinsic vibration modes of electromagnetic radiation on the neuronal surface. The frequency range of these vibration modes is in the THz and far-infrared ranges.

PH dependence of water anomaly temperature investigated by Eu(III) cryptate luminescence.

Although water has been extensively studied, not all of its unique properties have been fully understood. There is still controversy about the temperature at which hydrogen bonds are broken or weakened, producing the anomalous temperature dependence of many water properties. Different temperatures between 23 and 48 °C have been reported, but no study has scrutinized the reasons for this discrepancy. We suggest the determining role of pH in the alteration of the water anomaly temperature. We employed a luminescent europium trisbipyridine cryptate, which is highly sensitive to changes in the arrangement of water molecules and whose luminescence intensity and lifetime are not significantly influenced by variations over a broad pH range. Our results revealed an increase of the crossover temperature from circa 35 °C at pH 3.5 to circa 45 °C at pH 7 to 9, which explains the discrepancies of previous studies. The pH dependence of water anomaly temperature is an important property for a better understanding of water and water-based systems and applications.

Substrate recognition by bacterial solute-binding protein is responsible for import of extracellular hyaluronan and chondroitin sulfate from the animal host.

Glycosaminoglycans (GAGs) such as hyaluronan and chondroitin in animal extracellular matrices contain disaccharide-repeating units. In a Gram-negative pathogenic Streptobacillus moniliformis, which belongs to Fusobacteria phylum and resides in rodent oral cavities, the solute-binding protein (Smon0123)-dependent ATP-binding cassette transporter imports unsaturated hyaluronan/chondroitin disaccharides into the cytoplasm after GAG lyase-dependent depolymerization. Here we show substrate recognition of unsaturated hyaluronan disaccharide by Smon0123. Moreover, Smon0123 exhibited no affinity for unsaturated chondroitin disaccharides containing three sulfate groups, distinct from non-sulfated, mono-sulfated, and di-sulfated chondroitin disaccharides previously identified as substrates. Crystal structure of Smon0123 with unsaturated hyaluronan disaccharide demonstrates that several residues, including Trp284 and Glu410, are crucial for binding to unsaturated hyaluronan/chondroitin disaccharides, whereas arrangements of water molecules at binding sites are found to be substrate dependent through comparison with substrate-bound structures determined previously. These residues are well conserved in Smon0123-like proteins of fusobacteria, and probably facilitate the fusobacterial residence in hyaluronan-rich oral cavities.

Dynamics and Spectral Response of Water Molecules around Tetramethylammonium Cation.

Till now, there has been ambiguity about the structural heterogeneity inside a solute solvation shell and the dynamical response of the surrounding solvent molecules. To address the dynamics and spectral response of solvent molecules, we performed first-principles molecular dynamics simulations for the comprehensive study of water's hydroxyl stretch frequency evolution due to environmental variations (also called "spectral diffusion") in the vicinity of a hydrophobe, tetramethylammonium (TMA) cation. The N-Ow radial distribution function (RDF), spatial distribution function (SDF), and combined distribution function (CDF) were calculated to provide information about the arrangement of water molecules around TMA. In the probability distribution plot of the cosine of the angle (θ) between Ow-Hw and NTMA-Ow bond vectors, the hydrogen atoms are observed being oriented toward TMA and the oxygen atoms aligned away. The decaying dynamics of the orientation autocorrelation function (OACF) reveals the reorientation time is more inside the solvation shell (4.1 ps) as compared to bulk (2.8 ps), matching with the trend obtained from water's orientational dynamics in tetraalkylammonium salts. Wavelet transform of the obtained trajectory was used to calculate the time-dependent vibrational stretching frequencies of the OH modes of water molecules. The normalized frequency distribution in the aqueous solvation shell of TMA, tagging a particular water molecule within the N-Ow cutoff distance 5.5 Å, displays an intense peak at 3661 cm-1 representing non-hydrogen bonded or dangling or free OH modes. Simulations around aromatic solutes and Raman-MCR studies in the hydration shell of hydrophobic TBA reported a distinctive dangling OH band at 3660 cm-1 (range: 3661 ± 2 cm-1). Besides dangling water molecules in the first hydration layer of ammonium nitrogen, few OH modes are strongly hydrogen-bonded having an average frequency at 3300 cm-1. The predominance of dangling hydroxyl modes around apolar hydrophobic TMA was further explored by comparing the dangling lifetime (∼0.68 ps) with the lifespan of hydrogen bonded OH modes (∼0.48 ps). At our simulation temperature 330 K, a significant fraction of the water molecules in the vicinity of TMA ion are free or dangling, and a few of them form an ordered structure with enhanced hydrogen bonding. Structural analysis, orientation correlation, frequency fluctuations, dangling, and hole dynamics calculations provide the evidence of the existence of dangling OH modes dominating over highly ordered strong hydrogen bonded structure in the cationic TMA solvation shell at an elevated temperature.

Conformation-Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid.

The structure and dynamics of water molecules around the carboxylate and amino groups of γ-aminobutyric acid (GABA), a primary neurotransmitter in mammals, are investigated by means of ab initio molecular dynamics simulation. Zwitterionic GABA has two major conformations in water, namely, the open and the closed conformations. The angle-averaged one-dimensional structures of water in the solvation shells around the carboxylate and amino groups are found to be quite similar for the closed and open conformations of the solute. The two-dimensional structural correlations, which describe the solvation shell structure with better resolution, reveal some differences in the arrangement of water molecules around the solute for its open and closed conformations. It is found that the dynamics of solvation shells in the two conformations vary only slightly. However, the existence of trapped water between the oppositely charged carboxylate and amino groups of GABA in its closed form is found to give rise to a very different dynamical behavior as compared to the overall solvation shell in the same conformation as well as that in the open conformation. Thus, dynamical heterogeneity at a local level is induced by a change in the conformation of zwitterionic GABA. Such trapped water is not seen in the open form of the solute. A similar type of "connecting water" has also been observed for microsolvated β-alanine in a recent experimental and theoretical study ( Ghassemizadeh J. Phys. Chem. B , 2019 , 123 , 4392 - 4399 ). Thus, the current study shows the variation of binding properties of water with the change in the conformation of zwitterionic GABA, which in turn changes the dynamics of water at a local level. The conformation-induced changes in the water dynamics constitute an example of dynamical heterogeneity of water, which is normally observed in the presence of large biomolecules like proteins, DNA, etc.

Effect of Layer Charge Density on Hydration Properties of Montmorillonite: Molecular Dynamics Simulation and Experimental Study.

Four kinds of Ca-montmorillonite with different layer charge density were used to study the effect of charge density on their hydration properties by molecular dynamics simulation and experiments. The research results of Z-density distribution of water molecules, Hw (hydrogen in water molecules), and Ca in the interlayer of montmorillonite show that the hydration properties of montmorillonite are closely related to its layer charge density. If the charge density is low, the water molecules in the interlayers are mainly concentrated on the sides of the central axis about –1.3 Å and 1.5 Å. As the charge density increases from 0.38semi-cell to 0.69semi-cell, the water molecules are distributed −2.5 Å and 2.4 Å away from the siloxane surface (Si-O), the concentration of water molecules near the central axis decreases, and at the same time, Ca2+ appears to gradually shift from the vicinity of the central axis to the Si-O surface on both sides in the montmorillonite layer. The simulation results of the radial distribution function (RDF) of the Ca-Hw, Ca-Ow (oxygen in water molecules), and Ca-Ot (the oxygen in the tetrahedron) show that the Ca2+ and Ow are more tightly packed together than that of Hw; with the increase of the charge density, due to the fact that the negative charge sites on the Si-O surface increase, under the action of electrostatic attraction, some of the Ca2+ are pulled towards the Si-O surface, which is more obvious when the layer charge density of the montmorillonite is higher. The results of the RDF of the Ot-Hw show that with the increase of charge density, the number of hydrogen bonds formed by Ot and Hw in the interlayers increase, and under the action of hydrogen bonding force, the water molecules near the central axis are pulled towards the two sides of Si-O surface. As a result, the arrangement of water molecules is more compact, and the structure is obvious. Correspondingly, the self-diffusion coefficient shows that the higher the layer charge density, the lower the self-diffusion coefficient of water molecules in interlayers is and the worse the hydration performance of montmorillonite. The experimental results of the experiments fit well with the above simulation results.

Isothermal Kinetic Investigation of the Water-Cations Interaction in Natural Clinoptilolite

The kinetics of water adsorption by a natural zeolite (clinoptilolite) sample has been investigated by high-frequency AC current intensity measurements. According to the achieved kinetic results, cations should play a relevant role in the clinoptilolite hydration, in fact most of adsorbed water stay in the cationic sites. The water molecules associate withcation one-by-one. In particular, the forced adsorption of water molecules in a wet atmosphere is a quite slow process, while water desorption in air or dry atmosphere is a spontaneous and fast process. The observed increase of cation mobility could be adequately explained by assuming an arrangement of water molecules between the cation and the negatively charged oxygens contained in the cationic site. Such molecular arrangement could increase the strength of both dipole-cation and hydrogen bond interactions.

Isothermal Kinetic Investigation of the Water-Cations Interaction in Natural Clinoptilolite

The kinetics of water adsorption by a natural zeolite (clinoptilolite) sample has been investigated by high-frequency AC current intensity measurements. According to the achieved kinetic results, cations should play a relevant role in the clinoptilolite hydration, in fact most of adsorbed water stay in the cationic sites. The water molecules associate withcation one-by-one. In particular, the forced adsorption of water molecules in a wet atmosphere is a quite slow process, while water desorption in air or dry atmosphere is a spontaneous and fast process. The observed increase of cation mobility could be adequately explained by assuming an arrangement of water molecules between the cation and the negatively charged oxygens contained in the cationic site. Such molecular arrangement could increase the strength of both dipole-cation and hydrogen bond interactions.

In Situ Study of Molecular Structure of Water and Ice Entrapped in Graphene Nanovessels.

Water is ubiquitous in natural systems, ranging from the vast oceans to the nanocapillaries in the earth crust or cellular organelles. In bulk or in intimate contact with solid surfaces, water molecules arrange themselves according to their hydrogen (H) bonding, which critically affects their short- and long-range molecular structures. Formation of H-bonds among water molecules designates the energy levels of certain nonbonding molecular orbitals of water, which are quantifiable by spectroscopic techniques. While the molecular architecture of water in nanoenclosures is of particular interest to both science and industry, it requires fine spectroscopic probes with nanometer spatial resolution and sub-eV energy sensitivity. Graphene liquid cells (GLCs), which feature opposing closely spaced sheets of hydrophobic graphene, facilitate high-resolution transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS) measurements of attoliter water volumes encapsulated tightly in the GLC nanovessels. We perform in situ TEM and EELS analysis of water encased in thin GLCs exposed to room and cryogenic temperatures to examine the nanoscale arrangement of the contained water molecules. Simultaneous quantification of GLC thickness leads to the conclusion that H-bonding strengthens under increased water confinement. The present results demonstrate the feasibility of nanoscale chemical characterization of aqueous fluids trapped in GLC nanovessels and offer insights on water molecule arrangement under high-confinement conditions.

The effect of electric fields in methane hydrate growth and dissociation: A molecular dynamics simulation

Molecular dynamics simulation was employed to examine the growth and dissociation process of methane hydrate in the presence of static/oscillation electric fields at T = 260 K and P = 100 bars. The intensity of electric field was in range of 1.0–2.0 v/nm, and the frequency of applied e/m field was in range of 2.45 GHz–1.0 THz. Electric field would be a factor controlling the hydrate growth and dissociation because the migration of water molecules may be affected. Total energy of simulation system, final system configurations, hydrate-like methane numbers, radial distribution functions, H-bond numbers with simulation time, and dipole moment were analyzed. There is intensity threshold for e-field to exert an effect on methane hydrate. Static electric fields above the intensity threshold (1.5 v/nm) could push hydrate dissociation by inducing the arrangement of water molecules along the field. Cosine oscillation electric fields could promote both methane hydrate growth and dissociation, and there are different critical field magnitudes for different frequency e-fields to play positive roles in methane hydrate growth or dissociation. In order to promote methane hydrate dissociation, higher the e-field magnitude will need as the e-field frequency is higher.

Molecular dynamics simulation of characteristic water molecular arrangement on graphene surface and wetting transparency of graphene

Graphene has received a lot of attention for its excellent physical and chemical properties, and the unique wettability of graphene is still under investigation. Most of previous studies focused on graphene or carbon nanotubes, and less of them on the comparison of wettability between graphene and other materials to reveal the characteristic wettability of graphene. In the present study, the wettability of monolayer graphene, copper and silica are studied by using the molecular dynamics simulation, in which the contact angle and the water molecule arrangement (i.e. density distribution and angle distribution of water molecules) on the substrates are analyzed. The results show that although both copper and graphene are weak hydrophilic materials, there are two neat layers of water molecule structure on the surface of graphene, and water molecules are disordered on the surface of copper. Silica is a kind of strong hydrophilic material and graphene is a kind of weak hydrophilic material, but both of them have two layers of dense water molecule layer, which are in different states, on the surface. On the silica surface, the two layers of water molecules, whose densities are greatly different, are close to the substrate, and hydrogen bonds are randomly arranged, which is very different from the arrangement of water molecules on the graphene surface. By making a comparison of wettability among the three materials, the characteristic water molecule arrangement on graphene surface is obtained: there exist two layers of water molecules on the surface of graphene. Within the dense layer of water molecules near the substrate, the angles between the O−H bonds of water molecule and the vertical direction of substrate focus on 90°, while the hydrogen bonds on the surface are almost perpendicular to the substrate. Furthermore, it is found that adding a layer of graphene on copper (the main force between water molecules and copper is van der Waals force) will have a less influence on copper wettability. However, adding a layer of graphene on silica (the main force between water molecule and silica is from chemical bonds) will have a significant influence on the wettability of silica, i.e. not only the upper contact angle increases significantly, but also the arrangement of water molecules on the surface of the substrate becomes similar to that of graphene. These simulated results are found to be in agreement with the experimental results of Rafiee et al. [Rafiee J, Mi X, Gullapalli H, Thomas A V, Yavari F, Shi Y, Ajayan P M, Koratkar N A 2012 <i>Nature</i> <b>11</b> 217]. This work can provide a theoretical guidance for further developing the applications of graphene in microstructure design.

Crystal structure, large distortion of the Zn tetrahedron, and statistical displacement of water molecules in skorpionite

The crystal structures of skorpionite from the Skorpion zinc deposit in Namibia [Ca3Zn2(PO4)2CO3(OH)2·H2O; monoclinic; a = 19.0715(8), b = 9.3321(3), c = 6.5338(3) Å, β = 92.6773(12)°; space group C2/c] and [a = 19.0570(14), b = 9.3346(5), c = 6.5322(4) Å, β = 92.752(2)°; space group Cc] are analyzed using single–crystal X–ray diffraction and refined to yield R values of 0.0253 and 0.0272 for 1576 and 2446 unique reflections with Fo > 4σ(Fo), respectively. Hydrogen atoms in the structure determined by the difference Fourier method. Although two space groups, C2/c and Cc, are possible, the Cc space group without center of symmetry is more likely the structure of skorpionite, which shows that skorpionite is a ferroelectric mineral. The disordered structure is induced in skorpionite by twinning and/or domain structures because of the relaxation of the natural polarization caused by the arrangement of polarized water molecules. The space group Cc model without the center of symmetry eliminates the need for statistical distribution. Bond valence sum calculations and hydrogen bond networks can be explained in detail by the model. In the complicated structure caused by the chemical composition, the local structure with a non–ideal coordination environment is observed near the Zn sites. Hydrogen atoms are continuously arranged with regular arrangements of water molecules in the tunnel structure.

Interactions of RNA and Water probed by 2D-IR Spectroscopy

Combined experimental-theoretical investigation of ultrafast hydration dynamics of an A-form RNA double helix in water reveals an ordered arrangement of water molecules and provides boundary conditions for the ion atmosphere around the polyanionic RNA.