Solvent Conformational Transition

At 25°C, the cyclohexane molecules mainly have the chair form. The equilibrium concentration of the isomeric twist form is —10 mol dm On ionization, the solvent cation-radicals in the chair form are predominant. Electron transfer between the chair form of the cyclohexane cation-radicals and the chair-shaped surrounding cyclohexane (neutral) molecules is very fast, since it requires minimum reorganization energy. However, the chair-form cation-radical sometimes approaches a minor part of the neutral molecules in the twisted form. Because the twisted cyclohexane has lower IP, the twist-shaped molecules scavenge the cation-radicals in the chair form. 

As noted, the twisted conformer, which has a lower IP, rapidly scavenges the chair form of the cation-radical. Being endothermic, the backward transfer is relatively slow, and equilibrium is reached in 20-30 min. Thus, the electron transfer can be described as a series of periods of very fast hole migration between the chair forms and intermittent migration with the participation of the twist forms. 

It is important that both the twisted and chair forms of the cylclohexane cation-radical react with a solute, for example, with perylene. Therefore, generation of the perylene cation-radical is characterized with bimodal kinetics under these conditions. 

No such confusion arises for decalins. In decalin mixtures, a reversible electron-transfer reaction takes place  

Becanse of the high concentration of isomeric molecules ( 0.1 mol dm ), this equilibrium is established instantaneously. The IP of trans-AtcaYm is 0.02 eV lower than the IP of cw-decalin (9.24 eV versus 9.26 eV). Therefore, the electron-transfer eqnilibrinm is shifted slightly to the left side. Thns, in terms of charge-transfer kinetics, the two ions behave as a single species. It shonld be worth noting that decalin has only two isomeric forms, cis and trans. On the contrary, n-nonane exists in the multitude of conformations. The rate constant of electron exchange between parent nentral molecules of nonane and its cation-radicals is much lower, namely, 2 orders lower than the diffnsion-controlled limit (Borovkov et al. 2007). 

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The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

The study of slow protein dynamics is a fascinating field with still many unknowns. We have presented a number of computational techniques that are currently being used to tackle those questions. Most promising for our case seems the development of methods that combine an implicit solvent description with techniques to induce conformational transitions. 

The quantity of primary interest in our thermodynamic construction is the partial molar Gibbs free energy or chemical potential of the solute in solution. This chemical potential reflects the conformational degrees of freedom of the solute and the solution conditions (temperature, pressure, and solvent composition) and provides the driving force for solute conformational transitions in solution. For a simple solute with no internal structure (i.e., no intramolecular degrees of freedom), this chemical potential can be expressed as... 

Uversky, V. N., Narizhneva, N. V., Kirschstein, S. O., Winter, S., and Lober, G. (1997). Conformational transitions provoked by organic solvents in beta-lactoglobulin Can a molten globule like intermediate be induced by the decrease in dielectric constant FoldingDes. 2, 163-172. 

There are substantial difficulties in the interpretation of temperature-dependent shifts of protein spectra because of the thermal lability of proteins and the possibility of temperature-dependent conformational transitions. Low-temperature studies in aqueous solutions revealed that for many of the proteins investigated the observed shifts of the fluorescence spectra within narrow temperature ranges were probably the result of cooperative conformational transitions, and not of relaxational shifts/100 1 Spectral shifts have also been observed for proteins in glass-forming solvents, 01) but here there arise difficulties associated with the possible effects of viscous solvents on the protein dynamics. 

Fig. 5.11 T-dependence of the solvent viscosity (dashed line) and the characteristic time deduced for the conformational transitions in PIB (filled diamond). The solid line through the points corresponds to the fit to an Arrhenius law. (Reprinted with permission from [186]. Copyright 2001 American Chemical Society)...

The influence of the solvent on chiroptical properties of synthetic polymers is dramatically illustrated in the case of poly (propylene oxide). Price and Osgan had already shown, in their first article, that this polymer presents optical activity of opposite sign when dissolved in CHCI3 or in benzene (78). The hypothesis of a conformational transition similar to the helix-coil transition of polypeptides was rejected because the optical activity varies linearly with the content of the two components in the mixture of solvents. Chiellini observed that the ORD curves in several solvents show a maximum around 235 nm, which should not be attributed to a Cotton effect and which was interpreted by a two-term Drude equation. He emphasized the influence of solvation on the position of the conformational equilibrium (383). In turn, Furakawa, as the result of an investigation in 35 different solvents, focused on the polarizability change of methyl and methylene groups in the polymer due to the formation of a contact complex with aromatic solvents (384). 

Jennings, D.E., Kuznetsov, Y.A., Timoshenko, E.G. and Dawson, K.A. (2000) A lattice model Monte Carlo study of coil-globule and other conformational transitions of polymer, amphiphile, and solvent. J. Chem. Phys., 112, 7711-7722. 

Hen egg-white lysozyme, lyophilized from aqueous solutions of different pH from pH 2.5 to 10.0 and then dissolved in water and in anhydrous glycerol, exhibits a cooperative conformational transition in both solvents occurring between 10 and 100°C (Burova, 2000). The thermal transition in glycerol is reversible and equilibrium follows the classical two-state mechanism. The transition enthalpies AHm in glycerol are substantially lower than in water, while transition temperatures Tm are similar to values in water, but follow similar pH dependences. The transition heat capacity increment ACp in glycerol does not depend on the pH and is 1.25 0.31 kj (mol K) 1 compared to 6.72 0.23 kj (mol K)-1 in water. Thermodynamic analysis of the calorimetric data reveals that the stability of the folded conformation of lysozyme in glycerol is similar to that in water at 20-80°C but exceeds it at lower and higher temperatures. 

In order to calculate ensemble averages the explicit time-dependence of the exciton Hamiltonian is replaced by stochastic processes. If drastic changes of Jmn appear due to CC conformational transitions it is hard to apply this approach (Refs. [33] and [34] introduced a dichotomically fluctuating transfer coupling to cover such large conformational transitions). Instead, as it will be demonstrated here, it is more appropriate to directly generate the time-dependence of the exciton parameters Em and Jmn by MD simulations. Then, a microscopic account for solvent effects as well as a detailed description of solvent induced conformational transitions is possible. 

If the intensity of the CD band at 222 nm, which can be considered a function of the a-helix content, is plotted as a function of methanol concentration, it is observed that addition of methanol induces a coil—>a-helix transition in the macromolecular conformation (Figure 7). However, the amount of methanol needed to induce the conformational transition is different for the sample irradiated at 340 (cis azo units) and that irradiated at 417 nm (trans azo units). Therefore, two separate curves are observed for the two samples. At solvent compositions in the range between the two curves, alternating irradiation at 340 and 417 nm gives rise to folding or unfolding of the macromolecular chains. The photoresponse occurs only in a selected and nar-... 

Since amphiphilic polymers contain monomeric units having hydropho-bic/hydrophilic character, they can exhibit conformational transitions induced by temperature, solvent composition, or pH variation [96]. Because of the presence of the two opposing interactions towards the solvent in which they are immersed, amphiphiles can self-assemble, forming a variety of supramolecular structures. Understanding the physics of self-association... 

Micka et al. [169] were the first who simulated a multichain HPE system. They studied regular copolymers with alternating neutral and charged monomers (with a charge fraction of / = 1/3) in a poor solvent in the presence of monovalent counterions. The paper by Micka et al. [169] nicely demonstrated that the necklace microstructures exhibit a variety of conformational transitions as a function of polymer concentration. The end-to-end distance was found to be a nonmonotonic function of concentration and showed a strong minimum in the semidilute regime. 

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