Solvation discrete

There are now several structural studies on cobalt(II) crown ether and cryptand complexes (Table 78), which show the coordination mode to be markedly sensitive to the macrocycle cavity diameter. Both 12-crown-4 and 15-crown-5 (cavity diameters 120-150 pm and 170-220 pm respectively) can include ions to form structures in which every ether oxygen atom is bound to the metal. In contrast Co—O (ether) bonding is destabilized in the larger 18-crown-6 and dicyclohexyl-18-crown 6 polyethers. In the blue complexes obtained from the reaction of these compounds with C0CI2 the role of the cyclic polyether is to solvate discrete [Co(H20)6] cations and [CoC ] " anions and there are no direct Co—O (ether) bonds.A similar effect is seen in the Co" complex of a 27-membered-ring macrocycle where the pentacoordinate structure (267) features only one long Co—O (ether) bond. " ... 

Specific solute-solvent interactions involving the first solvation shell only can be treated in detail by discrete solvent models. The various approaches like point charge models, siipennoleciilar calculations, quantum theories of reactions in solution, and their implementations in Monte Carlo methods and molecular dynamics simulations like the Car-Parrinello method are discussed elsewhere in this encyclopedia. Here only some points will be briefly mentioned that seem of relevance for later sections. 

The mixed solvent models, where the first solvation sphere is accounted for by including a number of solvent molecules, implicitly include the solute-solvent cavity/ dispersion terms, although the corresponding tenns between the solvent molecules and the continuum are usually neglected. Once discrete solvent molecules are included, however, the problem of configuration sampling arises. Nevertheless, in many cases the first solvation shell is by far the most important, and mixed models may yield substantially better results than pure continuum models, at the price of an increase in computational cost. 

This strnctnring of liqnids into discrete layers when confined by a solid surface has been more readily observable in liquid systems other than water [1,55]. In fact, such solvation forces in water, also known as hydration forces, have been notoriously difficult to measure due to the small size of the water molecule and the ease with which trace amounts of contamination can affect the ordering. However, hydration forces are thought to be influential in many adhesive processes. In colloidal and biological systems, the idea that the hydration layer mnst be overcome before two molecules, colloidal particles, or membranes can adhere to each other is prevalent. This implies that factors affecting the water structure, such as the presence of salts, can also control adhesive processes. 

Equation (34.10) describes the dependence of the activation free energy on the free energy of transition AF for electron transfer between two discrete energy levels (one in the donor, Eq, and one in the acceptor, e ). The quantity AF involves the difference of these electron energies, the solvation free energies of the reaction products, wfi and the initial reactants, wf and the works required to bring the reaction products, w, and the reactants, w,., from infinity to a given interreactant distance 34. 

In either neat dioxane or THF, carbene-ether ylides are observed as a broad IR absorption band between 1560 and 1610 cm , distinct from the IR bands of the free carbenes. With discrete spectroscopic signatures for the free carbene and its corresponding ether ylides, TRIR spectroscopy was used to confirm that the effects described above with dilute ether in Freon-113 were due to specific solvation of the carbene (Scheme 4.6, Reaction 2) rather than a pre-equilibration with the coordinating solvent (Scheme 4.6, Reaction 3) or reactivity of the ylide itself (Scheme 6, Reaction 4). In Freon-113 containing 0.095M THF simultaneous TRIR observation of both the free carbene (x = ca. 500 ns) and the carbene-THF ylide (x = ca. 5ps) was possible7 The observation that lifetimes of these species were observed to be so different conclusively demonstrates that the free carbene and the carbene-THF ylide are not in rapid equilibrium and that Reaction 3 of Scheme 4.6 is not operative. By examining the kinetics of the carbene 34 at 1635 cm directly in Freon-113 with small amounts of added dioxane, it was observed that the rate of reaction with TME was reduced, consistent with Reaction 2 (and not Reaction 4) of Scheme 4.6. 

Figure 14-1. Left Relative errors (RELE) in the force as a function of radial distance from the center of the active dynamical region for the VEP-RVM charge-scaling method [80] for the solvated hammerhead ribozyme at different discretization levels [151] of die co surface. Right The projected total electrostatic potential due to the fully solvated hammerhead ribozyme projected onto die YEP surface [80]...

The coordination of transition metal ions in acidic chloroaluminate melts has not been firmly established. However, in the case of AICb-EtMelmCI. the E0 values of simple redox systems that are electrochemically accessible in both acidic and basic melt, e.g., Hg(II)/Hg [51], Sb(III)/Sb [52], and Sn(II)/Sn [53] exhibit a large positive potential shift on going from basic melt, where metal ions are known to exist as discrete anionic chloride complexes, to acidic melt. Similar results were observed for Cu(I) in AlCh-NaCl [48]. This dramatic decrease in electrochemical stability isprima facie evidence that metal ions in acidic melt are probably only weakly solvated by anionic species such as AICI4 and AECI-. Additional evidence for this is derived from the results of EXAFS measurements of simple metal ions such Co(II), Mn(II), and Ni(II) in acidic AlCh-EtMelmCl, which indicate that each of these ions is coordinated by three bidentate AICI4 ions to give octahedrally-coordinated species such as [ M (AIC14) 2 ] [54]. Most transition metal chloride compounds are virtually... 

For molecules and molecular ions, such as the cations of 8-methyl-N5-deazapterin and 8-methyl-pterin, the charge distribution (which is represented in MD simulations by a set of discrete atomic charges) will be dependent on the chosen quantum chemical model. Differences in the charge distributions of these cations may influence both the relative binding and solvation thermodynamics. Consequently, we studied the relative solvation thermodynamics of similar DHFR-binding molecular ions.30 Atomic charges... 

It can be seen from Table 26.1 that various methods used to model the effect of a solvent can be broadly classified into three types (1) those which treat the solvent as continuous medium, (2) those which describe the individual solvent molecules (discrete/explicit solvation), and (3) combinations of (1) and (2) treatments. The following section provides a brief introduction to continuum models. 

Quantitative models of solute-solvent systems are often divided into two broad classes, depending upon whether the solvent is treated as being composed of discrete molecules or as a continuum. Molecular dynamics and Monte Carlo simulations are examples of the former 8"11 the interaction of a solute molecule with each of hundreds or sometimes even thousands of solvent molecules is explicitly taken into account, over a lengthy series of steps. This clearly puts a considerable demand upon computer resources. The different continuum models,11"16 which have evolved from the work of Bom,17 Bell,18 Kirkwood,19 and Onsager20 in the pre-computer era, view the solvent as a continuous, polarizable isotropic medium in which the solute molecule is contained within a cavity. The division into discrete and continuum models is of course not a rigorous one there are many variants that combine elements of both. For example, the solute molecule might be surrounded by a first solvation shell with the constituents of which it interacts explicitly, while beyond this is the continuum solvent.16... 

Relative Free Energies of Solvation in Water, in kcal/mole, Obtained by Classical Discrete Molecular Solvent Methods... 

Relative Free Energies Of Solvation in Water, in kcal/mole," Obtained by a QM/MM Discrete Molecular Solvent Method, Using The AMI Solute Hamiltonian. The Estimated Error Bars for The Calculated Values Are 0.5 Kcal/Mole... 

The level of accuracy that can be achieved by these different methods may be viewed as somewhat remarkable, given the approximations that are involved. For relatively small organic molecules, for instance, the calculated AGsoivation is now usually within less than 1 kcal/mole of the experimental value, often considerably less. Appropriate parametrization is of key importance. Applications to biological systems pose greater problems, due to the size and complexity of the molecules,66 156 159 161 and require the use of semiempirical rather than ab initio quantum-mechanical methods. In terms of computational expense, continuum models have the advantage over discrete molecular ones, but the latter are better able to describe solvent structure and handle first-solvation-shell effects. 

There are three types of chiral auxiliary that are used chiral derivatizing agents (CDAs), chiral lanthanide shift reagents (CLSRs) and chiral solvating agents (CSAs)75. Chiral derivatizing agents (CDAs), such as the enantiomers of o -methoxy-o -(trifluoromethyl)phenylacetic acid (MTPA, 83)76, require the separate formation of discrete... 

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