Structural solvation, structure

In some solutions, the solute and the solvent molecules form an inhomogeneous structure (solvation structure), in which the solute and solvent molecules are strongly bound each other. The liquid jet method enables to isolate clusters in the gas phase maintaining the solvation structure, because free solvent molecules (almost bound-free to the solvation structure) in the solution are likely to desert the solvation structure as a solvated cluster in the gas phase on volume expansion of the droplets. In reality, the size-distribution of a hydrated methanol cluster ion, H CH30H(H20) j, produced from a methanol solution in water shows a linear increase in the abundance with n, whereas the abundance of H CH30H(H20) i produced by attachment of a methanol molecule onto water clusters in the gas phase is almost constant regardless of n. This finding indicates that a methanol molecule is mainly solvated by the water molecules in a solution. Namely, the size-distribution of the gas phase clusters thus produced provides structural information of the solutions. 

A major advance in force measurement was the development by Tabor, Win-terton and Israelachvili of a surface force apparatus (SFA) involving crossed cylinders coated with molecularly smooth cleaved mica sheets [11, 28]. A current version of an apparatus is shown in Fig. VI-4 from Ref. 29. The separation between surfaces is measured interferometrically to a precision of 0.1 nm the surfaces are driven together with piezoelectric transducers. The combination of a stiff double-cantilever spring with one of a number of measuring leaf springs provides force resolution down to 10 dyn (10 N). Since its development, several groups have used the SFA to measure the retarded and unretarded dispersion forces, electrostatic repulsions in a variety of electrolytes, structural and solvation forces (see below), and numerous studies of polymeric and biological systems. 

In either case, the structure of the solvation shell has to be calculated by otiier methods supplied or introduced ad hoc by some fiirther model assumptions, while charge distributions of the solute and within solvent molecules are obtained from quantum chemistry. 

The quality of the results that can be obtained with point charge or dipole models depends critically on the input solvation shell structure. In view of the computer power available today, taking the most rigorous route... 

There is one important caveat to consider before one starts to interpret activation volumes in temis of changes of structure and solvation during the reaction the pressure dependence of the rate coefficient may also be caused by transport or dynamic effects, as solvent viscosity, diffiision coefficients and relaxation times may also change with pressure [2]. Examples will be given in subsequent sections. 

R), i.e. there is no effect due to caging of the encounter complex in the common solvation shell. There exist numerous modifications and extensions of this basic theory that not only involve different initial and boundary conditions, but also the inclusion of microscopic structural aspects [31]. Among these are hydrodynamic repulsion at short distances that may be modelled, for example, by a distance-dependent diffiision coefficient... 

The analysis of recent measurements of the density dependence of has shown, however, that considering only the variation of solvent structure in the vicinity of the atom pair as a fiinction of density is entirely sufficient to understand tire observed changes in with pressure and also with size of the solvent molecules [38]. Assuming that iodine atoms colliding with a solvent molecule of the first solvation shell under an angle a less than (the value of is solvent dependent and has to be found by simulations) are reflected back onto each other in the solvent cage, is given by... 

The well defined contact geometry and the ionic structure of the mica surface favours observation of structural and solvation forces. Besides a monotonic entropic repulsion one may observe superimposed periodic force modulations. It is commonly believed that these modulations are due to a metastable layering at surface separations below some 3-10 molecular diameters. These diflftise layers are very difficult to observe with other teclmiques [92]. The periodicity of these oscillatory forces is regularly found to correspond to the characteristic molecular diameter. Figure Bl.20.7 shows a typical measurement of solvation forces in the case of ethanol between mica. 

H3O" is strictly the oxonium ion actually, in aqueous solutions of acid this and Other solvated-proton structures exist, but they are conveniently represented as... 

The SMD simulations were based on an NMR structure of the Ig domain 127 of the cardiac titin I-band (Improta et ah, 1996). The Ig domains consist of two /9-sheets packed against each other, with each sheet containing four strands, as shown in Fig. 8b. After 127 was solvated and equilibrated, SMD simulations were carried out by fixing one terminus of the domain and applying a force to the other in the direction from the fixed terminus to the other terminus. Simulations were performed as described by Eq. (1) with V = 0.5 A/ps and if = 10 ksT/A 414 pN/A. The force-extension profile from the SMD trajectory showed a single force peak as presented in Fig. 8a. This feature agrees well with the sawtooth-shaped force profile exhibited in AFM experiments. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

The most ambitious approaches to the protein folding problem attempt to solve it from firs principles (ab initio). As such, the problem is to explore the coirformational space of th molecule in order to identify the most appropriate structure. The total number of possibl conformations is invariably very large and so it is usual to try to find only the very lowes energy structure(s). Some form of empirical force field is usually used, often augmente with a solvation term (see Section 11.12). The global minimum in the energy function i assumed to correspond to the naturally occurring structure of the molecule. 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

The solvation thermodynamics have been interpreted in a classical study by Frank and Evans in terms of the iceberg model . This model states that the water molecules around an nonpolar solute show an increased quasi-solid structuring. This pattern would account for the strongly negative... 

Many semiempirical methods have been created for modeling organic compounds. These methods correctly predict many aspects of electronic structure, such as aromaticity. Furthermore, these orbital-based methods give additional information about the compounds, such as population analysis. There are also good techniques for including solvation elfects in some semiempirical calculations. Semiempirical methods are discussed further in Chapter 4. 

A number of types of calculations can be performed. These include optimization of geometry, transition structure optimization, frequency calculation, and IRC calculation. It is also possible to compute electronic excited states using the TDDFT method. Solvation effects can be included using the COSMO method. Electric fields and point charges may be included in the calculation. Relativistic density functional calculations can be run using the ZORA method or the Pauli Hamiltonian. The program authors recommend using the ZORA method. 

The HE, GVB, local MP2, and DFT methods are available, as well as local, gradient-corrected, and hybrid density functionals. The GVB-RCI (restricted configuration interaction) method is available to give correlation and correct bond dissociation with a minimum amount of CPU time. There is also a GVB-DFT calculation available, which is a GVB-SCF calculation with a post-SCF DFT calculation. In addition, GVB-MP2 calculations are possible. Geometry optimizations can be performed with constraints. Both quasi-Newton and QST transition structure finding algorithms are available, as well as the SCRF solvation method. 

OPW (orthogonalized plane wave) a band-structure computation method P89 (Perdew 1986) a gradient corrected DFT method parallel computer a computer with more than one CPU Pariser-Parr-Pople (PPP) a simple semiempirical method PCM (polarized continuum method) method for including solvation effects in ah initio calculations... 

Protein tertiary structure is also influenced by the environment In water a globu lar protein usually adopts a shape that places its hydrophobic groups toward the interior with Its polar groups on the surface where they are solvated by water molecules About 65% of the mass of most cells is water and the proteins present m cells are said to be m their native state—the tertiary structure m which they express their biological activ ity When the tertiary structure of a protein is disrupted by adding substances that cause the protein chain to unfold the protein becomes denatured and loses most if not all of Its activity Evidence that supports the view that the tertiary structure is dictated by the primary structure includes experiments m which proteins are denatured and allowed to stand whereupon they are observed to spontaneously readopt their native state confer matron with full recovery of biological activity... 

Fig. 1. The structure of the electrical double layer where Q represents the solvent CD, specifically adsorbed anions 0, anions and (D, cations. The inner Helmholtz plane (IHP) is the center of specifically adsorbed ions. The outer Helmholtz plane (OHP) is the closest point of approach for solvated cations or molecules. O, the corresponding electric potential across the double layer, is also shown.

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