Role of water in some biological processes.

The state of intracellular water has been a matter of controversy for a long time for two reasons. First, experiments have often given conflicting results. Second, hitherto, there have been no plausible grounds for assuming that intracellular water should be significantly different from bulk water. A collective behavior of water molecules is suggested here as a thermodynamically inevitable mechanism for generation of appreciable zones of abnormal water. At a highly charged surface, water molecules move together, generating a zone of water perhaps 6 nm thick, which is weakly hydrogen bonded, fluid, and reactive and selectively accumulates small cations, multivalent anions, and hydrophobic solutes. At a hydrophobic surface, molecules move apart and local water becomes strongly bonded, inert, and viscous and accumulates large cations, univalent anions, and compatible solutes. Proteins and many other biopolymers have patchy surfaces which therefore induce, by the two mechanisms described, patchy interfacial water structures, which extended appreciable distances from the surface. The reason for many conflicting experimental results now becomes apparent. Average values of properties of water measured in gels, cells, or solutions of proteins are often not very different from the same properties of normal water, giving no indication that they are averages of extreme values. To detect the operation of this phenomenon, it is necessary to probe selectively a single abnormal population. Examples of such experiments are given. It is shown that this collective behavior of water molecules amounts to a considerable biological force, which can be equivalent to a pressure of 1,000 atm (1.013 x 10(5) kPa). It is suggested that cells selectively accumulate K+ ions and compatible solutes to avoid extremes of water structure in their aqueous compartments, but that cation pumps and other enzymes exploit the different solvent properties and reactivities of water to perform work of transport or synthesis.     

Physical aspects of the weakly hydrated protein surface.

We review the physical properties of water on the surface of weakly hydrated proteins and present some theoretical models used to understand them. The first part concerns mainly structural properties and introduces a model for two-dimensional clusters of water molecules. The second part is devoted to dynamical properties of the hydrated protein surface. Dielectric measurements which provide an evidence for proton conductivity due to the percolation of the network of surface water molecules and for the glass dynamics of migrating protons when temperature is lowered are reviewed. These results can be associated with the concept of frustration and analyzed with two models, an Ising model to describe the proton jumps and the model of two-dimensional surface water which exhibits a glassy dynamiques of the water molecules. Biological implications of these properties of hydration water are briefly discussed.     

The surface tension of water calculated from a random network model

The surface tension (excess surface free energy) of water is an important factor in many biological and chemical systems. It is often invoked to correlate or explain the low solubility of nonpolar compounds in water as well as the so-called hydrophobic effect of nonpolar molecules aggregating in water. While water's surface tension is not easily obtained from theory, the random network model (RNM) of Henn and Kauzmann (H-K), which described water's well-known, anomalous thermodynamic properties, can be used successfully to calculate the surface tension of water at atmospheric pressure between temperatures of 0 and 100 degrees C. Agreement with observed values, particularly at lower temperatures, is good, although the H-K RNM is too ice-like in nature to allow for the rapid drop off of surface tension with increasing temperature. Suggestions are offered for improving the model. In addition, an alternative explanation for the preferred orientation of surface water molecules is proposed based on water's H-bonding and attendant intramolecular, zero-point distortion energy.     

On the structure of molecularly imprinted polymers by modifying charge on functional groups through molecular dynamics simulations

Molecularly imprinted polymers (MIPs) have been widely applied in many fields owing to their advantages. The recognition mechanism between target molecules and MIPs and the influence of dominant factor on the recognition process are still poorly understood. In this paper, a cubic methacrylate-based MIP model was constructed, and the charge on carboxyl group atoms was changed artificially to investigate the recognition process. It is found that the diffusion coefficients of the target molecules (cholesterol) are not affected by polymer network structure. The recognition process is mainly determined by the mesh sizes of the polymer network. In addition, the structure of modified MIP systems was also discussed from the viewpoints of radial distribution function and hydrogen bonds system. These results suggest that the polymer matrix structure would be enhanced with an increase in charge. Thus, it influences the structure of the water molecules in the system a little.     

Molecular dynamics simulations of interaction between sub-bituminous coal and water

The high moisture content of sub-bituminous coal is associated with the interactions between coal and water. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of sub-bituminous coal according to XPS results. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxy and carbonyl is similar.     

Gastropod nacre: structure, properties and growth--biological, chemical and physical basics

The biogenic polymer/mineral composite nacre is a non-brittle biological ceramic, which self-organizes in aqueous environment and under ambient conditions. It is therefore an important model for new sustainable materials. Its highly controlled structural organization of mineral and organic components at all scales down to the nano- and molecular scales is guided by organic molecules. These molecules then get incorporated into the material to be responsible for properties like fracture mechanics, beauty and corrosion resistance. We report here on structure, properties and growth of columnar (gastropod) nacre with emphasis on the genus Haliotis in contrast to sheet nacre of many bivalves.     

X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutions

The presence of ions in water provides a rich and varied environment in which many natural processes occur with important consequences in biology, geology and chemistry. This article will focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct information regarding the radial pair distribution functions of many cations and anions in solution. This information can subsequently be used to calculate coordination numbers and to determine ion-water conformation in great detail. As well as enabling comparisons to be made amongst ions in particular groups in the periodic table, such information can also be contrasted with results provided by molecular dynamics (MD) simulation techniques. To illustrate the power of these 'difference' methods, reference will be made to the alkali group of ions, all of which have been successfully investigated by the above methods, with the exception of the radioactive element francium. Additional comments will be made on how NDIS measurements are currently being combined with MD simulations to determine the structure around complex ions and molecules, many of which are common in biological systems.     

Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data

The implications of protein-water interactions are of importance for understanding the solution behavior of proteins and for analyzing the fine structure of proteins in aqueous solution. Starting from the atomic coordinates, by bead modeling the scattering and hydrodynamic properties of proteins can be predicted reliably (Debye modeling, program HYDRO). By advanced modeling techniques the hydration can be taken into account appropriately: by some kind of rescaling procedures, by modeling a water shell, by iterative comparisons to experimental scattering curves (ab initio modeling) or by special hydration algorithms. In the latter case, the surface topography of proteins is visualized in terms of dot surface points, and the normal vectors to these points are used to construct starting points for placing water molecules in definite positions on the protein envelope. Bead modeling may then be used for shaping the individual atomic or amino acid residues and also for individual water molecules. Among the tuning parameters, the choice of the scaling factor for amino acid hydration and of the molecular volume of bound water turned out to be crucial. The number and position of bound water molecules created by our hydration modeling program HYDCRYST were compared with those derived from X-ray crystallography, and the capability to predict hydration, structural and hydrodynamic parameters (hydrated volume, radius of gyration, translational diffusion and sedimentation coefficients) was compared with the findings generated by the water-shell approach CRYSOL. If the atomic coordinates are unknown, ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions.     

On the properties of aqueous amide solutions through classical molecular dynamics simulations

The structure and dynamics of infinitely diluted aqueous amide solutions is studied for 13 compounds in the NVT ensemble using classical molecular dynamics simulations. The aim of this work is to provide valuable insights into the effect of amides on liquid water properties in order to understand the amides role in the kinetic inhibition of clathrate hydrate formation in natural gas mixtures. The OPLS-AA forcefield is used to describe the amides, with parameters obtained through fitting of computed B3LYP/6-311++g^{* *} data when not available in the literature, and the SPC-E model is applied for water molecules. Structural properties of the solutions are analyzed via calculated radial distribution functions and dynamic properties are studied with the computed mean square displacements and velocity autocorrelation functions. Most of the studied compounds show a remarkable structuring effect on the surrounding water with strong interactions resulting from hydrogen bonding between solute and solvent molecules. Hydrophobic and hydrophilic synergistic effects influence the amide–water interaction and the properties of the water solvation shells around amides.     

Exploring the structure and dynamics of nano-confined water molecules using molecular dynamics simulations

Confinement effects can lead to drastic changes in the structural and dynamical properties of water molecules. In this work, we have performed classical molecular dynamics simulations of endohedral fullerenes of type (H₂O)_n@C_m (n = 1, 12, 21, 62, 108 and m = 60, 180, 240, 500 and 720) to explore the effects of spherical confinement on water properties. It is shown that these confined water molecules can form distinct solvation pattern depending upon the available space inside the fullerene cavity. For the systems with smaller diameter, cage-like structure is predominant whereas bulk-like structure is observed for larger fullerenes. The orientational relaxation of these confined water molecules showed slower relaxation as the cavity diameter increases except for the (H₂O)₂₁@C₂₄₀. In this case, stable cage-like structure hinders the overall dynamics of the trapped water molecules. Finally, we have calculated the hydrogen bond lifetimes from the hydrogen bond time correlation functions and compared with that of bulk water.     

Interactions between macromolecules and ions: The Hofmeister series

The Hofmeister series, first noted in 1888, ranks the relative influence of ions on the physical behavior of a wide variety of aqueous processes ranging from colloidal assembly to protein folding. Originally, it was thought that an ion's influence on macromolecular properties was caused at least in part by 'making' or 'breaking' bulk water structure. Recent time-resolved and thermodynamic studies of water molecules in salt solutions, however, demonstrate that bulk water structure is not central to the Hofmeister effect. Instead, models are being developed that depend upon direct ion-macromolecule interactions as well as interactions with water molecules in the first hydration shell of the macromolecule.     

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.     

Molecular dynamics simulations of nonionic surfactant adsorbed on subbituminous coal model surface based on XPS analysis

A molecular dynamics (MD) simulation was conducted to study the adsorption behaviour of a nonionic surfactant adsorbed on low-rank coal. Owing to the complicated chemical component and structure of the coal surface, a modified graphite surface with hydroxyl, carboxyl, and carbonyl groups was utilised for a representation of the subbituminous coal surface model. The compositions of the hydroxyl, carbonyl, and carboxyl groups on the coal surface were found to be at a proportion of 25:3:5 according to the X-ray photoelectron spectroscopy (XPS) results. The interaction of nonylphenol ethoxylate with 8 ethylene oxide groups (NPEO-8) using this coal model in an aqueous phase was then simulated. It was revealed that the nonionic surfactant molecules were adsorbed at the interface between water and coal. This agminated structure of the surfactant molecules on the surface of the coal demonstrated an attachment of the surfactant ethoxylate groups to these solid surfaces and an extension of the remaining hydrophobic portions into the solution. Therefore, a coal surface with greater hydrophobicity was created. The dynamic properties of the water molecules characterised through self-diffusion coefficients indicate greater water mobility resulting from the existence of NPEO-8.     

Unified approach to partition functions of RNA secondary structures

RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences.     

Changes in CNT-confined water structural properties induced by the variation in water molecule orientation

Using a (8, 8) carbon nanotube (CNT) as a model for nanochannel, we studied the effects of carbonyl (–CO) groups and external electric field on the properties of confined water molecules by molecular dynamics simulation. We analysed the density profiles, the distribution of orientation and the hydrogen bonds of water molecules in the axial and radial directions of the CNT. The results show that –CO groups are more powerful than electric fields on controlling water properties, and property changes induced by –CO groups are less affected by electric fields. Meanwhile, the particular behaviour of water molecules induced by the –CO groups is not limited near the –CO groups, but also expands to the whole CNT.     

X-ray studies of water structure in 2 Zn insulin crystal

The water structure of rhombohedral 2 Zn insulin crystal which contains about 280 water molecules and 0.55-0.60 mol citrate molecules per dimer has been studied by X-ray crystallographic refinement with 1.1 A resolution data. Atomic parameters of 83 fully occupied and 258 partially occupied water molecules and 0.3 mol of citrate were obtained. Full matrix least-squares method with isotropic temperature factor was used for the refinement of partially occupied water molecules. The water molecules in this crystal exist in one of the three states: fully occupied water, partially occupied water and water continuum, and a schematic model of water structure in protein crystal was proposed. The flexibility of water molecules is described.     

Mineralization of type I collagen

It was previously found that the lateral spacing of the collagen molecules in wet mineralized tissues is exactly proportional to the inverse wet density. Several properties were investigated and the same type of relationship was observed each time. A possible explanation is offered. It is hypothesized that mineral is deposited initially in the extrafibrillar space so as to isolate the fibrils. Further deposition reduces the net free fibril volume thereby decreasing the spacing between collagen molecules. The linear relationship is derived from density considerations together with limitations on the collagen packing structure described as the generalized packing model. Three experimental situations were studied: lateral spacing wet tissue versus density; lateral spacing dry tissue versus density; and lateral spacing versus water content. The observed variations of the spacing can be attributed to a structure where the mass of the tissue remains constant but the volume decreases linearly with increasing mineral content.