Molecular Properties of Water

The quadrupole may be approximated as a dipole in which an excess of positive charge, 8+, is separated over a distance x from an equal excess of negative charge, 8. The dipolar moment 

FIG U RE 4.3 Three-dunensional structure of ice H2O (S). Each oxygen atom is at the center of four oxygen atoms at a separation distance of 0.276 nm. 

As the temperature increases, more hydrogen bonds are disrupted resulting in a further breakdown of the regular structure, so that the density increases reaching a maximum at 4°C. Then, beyond d C, the density gradually decreases due to an overcompensating effect of thermal expansion. 

As mentioned, breakdown of the regular structure leads to a decreased water volume. Stated in the reversed way a reduced volume (for instance, by exerting a pressure) leads to a breakdown of structure which manifests itself by, for example, a lower viscosity. This is the reason why, in contradiction to essentially aU other liquids, water has a lower viscosity at higher pressure, at least in the temperature range between 0°C and 30°C and at pressures below 1000atm. 

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Water, as we have seen, is the major component of living systems, and it interacts with many biomolecules. Some molecules are water-loving, or hydrophilic, others are water-abhorring, or hydrophobic, and still others are amphi-pathic, or in between. What properties of a molecule make it hydrophilic or hydrophobic First, consider the molecular properties of water and how water interacts with itself. 

Table 3-10. Comparison of the molecular properties of water in the gas phase. All results are in a.u.

Davidson, E. R., and D. Feller (1984). Molecular properties of water. Chem. Phys. Lett. 104, 54. 

Building up from microscopic basics to observed complex functions, this insightful monograph explains and describes how the unique molecular properties of water give rise to its structural and dynamical behavior, which in turn translates into its role in biological and chemical processes. 

Studying the MM approach based on a quasi-component distribution function had led to the formulation of what I shall refer to as the principal molecular property of water, or for short, the principle. While the importance of the structure of water and the underlying hydrogen bonds were recognized long ago, the new and more fundamental aspect of the intermolecular interactions which can explain both the structure and the outstanding properties of water were recognized much later. 

Some of the important physical and molecular properties of water and hydrogen peroxide are compared in the following tabulation ... 

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

The input file for an STO-3G calculation of the bond distances, energies, and other molecular properties of the isolated water molecule in the gaseous state at 0 kelvins is... 

The molecular and liquid properties of water have been subjects of intensive research in the field of molecular science. Most theoretical approaches, including molecular simulation and integral equation methods, have relied on the effective potential, which was determined empirically or semiempirically with the aid of ab initio MO calculations for isolated molecules. The potential parameters so determined from the ab initio MO in vacuum should have been readjusted so as to reproduce experimental observables in solutions. An obvious problem in such a way of determining molecular parameters is that it requires the reevaluation of the parameters whenever the thermodynamic conditions such as temperature and pressure are changed, because the effective potentials are state properties. 

A good understanding of the properties of water is thus essential as we move to more complicated systems. We have been involving in the study of aqueous solution of many important biological molecules, such as acetylcholine, Gramicidin, deoxydinucleoside phosphate and proflavin, and DNA, etc., first at the Monte Carlo level and slowly moving to the molecular dynamics simulations. We will discuss some of the new results on the hydration structure and the dynamics of B- and Z-DNA in the presence of counterions in the following. 

The coefficients Co, nnd C2 (denoted as mq, ai, and aj in Ref. 33) are influenced by various molecular properties of the solvent and an ion, including their electron-donating or accepting abilities. Hence, these coefficients are specific to the ion. Nevertheless, they may be considered as common to a family of ions such as the polyanions whose surface atoms, directly interacting with solvents, are oxygens. This is the case for hydrated cations or anions whose surfaces are composed of some water molecules that interact with outer water molecules in the W phase or with organic solvents in the O phase. 

In a, P-unsaturated carbonyl compounds and related electron-deficient alkenes and alkynes, there exist two electrophilic sites and both are prone to be attacked by nucleophiles. However, the conjugated site is considerably softer compared with the unconjugated site, based on the Frontier Molecular Orbital analysis.27 Consequently, softer nucleophiles predominantly react with a, (i-unsaturated carbonyl compounds through conjugate addition (or Michael addition). Water is a hard solvent. This property of water has two significant implications for conjugate addition reactions (1) Such reactions can tolerate water since the nucleophiles and the electrophiles are softer whereas water is hard and (2) water will not compete with nucleophiles significantly in such... 

The background theory that underlies the FEP method as well as the molecular mechanics force fields that relate molecular structure to energy are reviewed in section one of the book. Section two describes the use of free energy calculations for determining molecular properties of ligands, including solvation, as calculated using both implicit and explicit water... 

Over the years, a large number of models of water structure have been developed in an attempt to reconcile all the known physical properties of water and to arrive at a molecular description of water that accounts correctly for its behavior over a large range of thermodynamic conditions. Early models of water structure have been categorized by Fennema (1996) and Ball (2001) into three general types mixture, uniformist, and interstitial. Mixture models are based on the concept of intermolecular hydrogen bonds... 

Five organic solvents [acetonitrile, methanol, tetrahydrofuran (THF), acetone, and dimethylformamide], which are homogeneously miscible with water, have been used as modifiers to study the relationship of the selectivity of the solvent to the molecular properties of analytes. The polar interaction... 

Normal-phase liquid chromatography is thus a steric-selective separation method. The molecular properties of steric isomers are not easily obtained and the molecular properties of optical isomers estimated by computational chemical calculation are the same. Therefore, the development of prediction methods for retention times in normal-phase liquid chromatography is difficult compared with reversed-phase liquid chromatography, where the hydrophobicity of the molecule is the predominant determinant of retention differences. When the molecular structure is known, the separation conditions in normal-phase LC can be estimated from Table 1.1, and from the solvent selectivity. A small-scale thin-layer liquid chromatographic separation is often a good tool to find a suitable eluent. When a silica gel column is used, the formation of a monolayer of water on the surface of the silica gel is an important technique. A water-saturated very non-polar solvent should be used as the base solvent, such as water-saturated w-hexane or isooctane. 

An important aspect of the study of water under electrochemical conditions is that one is able to continuously modify the charge on the metal surface and thus apply a well-defined external electric field, which can have a dramatic effect on adsorption and on chemical reactions. Here we briefly discuss the effect of the external electric field on the properties of water at the solution/metal interface obtained from molecular dynamics computer simulations. A general discussion of the theoretical and experi-... 

Independent of the molecular properties of contaminants, the subsurface solid phase constituents are a major factor that control the adsorption process. Both the mineral and organic components of the solid phases interact differentially with ionic and nonionic pollutants, and in all cases, environmental factors, such as temperature, subsurface water content, and chemistry, affect the mechanism, extent, and rate of contaminant adsorption. 

The solubility of contaminants in subsurface water is controlled by (1) the molecular properties of the contaminant, (2) the porous media solid phase composition, and (3) the chemistry of the aqueous solution. The presence of potential cosolvents or other chemicals in water also affects contaminant solubility. A number of relevant examples selected from the literature are presented here to illustrate various solubility and dissolution processes. 

Figure 9,1 Molecular interaction potentials in Stockmayer s (1941) model for H2O vapor, (a) antiparallel dipolar moments (b) parallel dipolar moments. Reprinted from D. Eisemberg and W. Kauzmann, The Structures and Properties of Water, 1969, by permission of Oxford University Press.

The metal-solution interface as the locus of the deposition processes. This interface has two components a metal and an aqueous ionic solution. To understand this interface, it is necessary to have a basic knowledge of the structure and electronic properties of metals, the molecular structure of water, and the structure and properties of ionic solutions. The structure and electronic properties of metals are the subject matter of solid-state physics. The structure and properties of water and ionic solutions are (mainly) subjects related to chemical physics (and physical chemistry). Thus, to study and understand the structure of the metal-solution interface, it is necessary to have some knowledge of solid-state physics as well as of chemical physics. Relevant presentations of these subjects are given in Chapters 2 and 3. 

No single treatise can provide a sufficiently thorough account of the properties of water Yet, the kinetics and thermodynamics of every biochemical process are linked to the molecular interactions of water with macromolecules, membranes, metabohtes, anions, cations, protons and even electrons. For this reason, this handbook provides a brief overview of the structure and general properties of this most fascinating of all solvents. Where deemed appropriate, references are provided for further reading by those motivated to examine these topics at greater depth. 

Meng, E. C., and P. A. Kollman, Molecular dynamics studies of the properties of water around simple organic solutes , J. Phys. Chem., 100, 11460-11470(1996). 

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