Atomic positions solvent effect

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

Baechler and coworkers204, have also studied the kinetics of the thermal isomerization of allylic sulfoxides and suggested a dissociative free radical mechanism. This process, depicted in equation 58, would account for the positive activation entropy, dramatic rate acceleration upon substitution at the a-allylic position, and relative insensitivity to changes in solvent polarity. Such a homolytic dissociative recombination process is also compatible with a similar study by Kwart and Benko204b employing heavy-atom kinetic isotope effects. 

Spectroscopy provides a window to explain solvent effects. The solvent effects on spectroscopic properties, that is, electronic excitation, leading to absorption spectra in the nltraviolet and/or visible range, of solutes in solution are due to differences in the solvation of the gronnd and excited states of the solute. Such differences take place when there is an appreciable difference in the charge distribution in the two states, often accompanied by a profonnd change in the dipole moments. The excited state, in contrast with the transition state discussed above, is not in equilibrium with the surrounding solvent, since the time-scale for electronic excitation is too short for the readjustment of the positions of the atoms of the solute (the Franck-Condon principle) or of the orientation and position of the solvent shell around it. 

The distribution of charge changes radically with conditions. For the largest, counter ions there appears to be an almost even distribution of charge over the a and Y positions, but with the ion Li+, particularly in the nonsolvating solvent benzene, the charge and presumably also the Li atom are positioned closer to the end carbon atom. The small effect of temperature on the shifts would appear to discourage any attempt to explain the intermediate positions of some of these shifts in terms of ionic-covalent equilibrium, or 1 2 - 1 4 equilibria. 

Since fluorine is the most electronegative element, it should inductively destabilize carbocations. The stability of fluoromethyl cations in the gas phase decreases in the order CFH2+ > CF2H+ > CF3+ > CH3+. The trend in solution, however, could be different, due to solvent effects, ion pairing, and so on. Indeed, fluorine has been shown to provide stabilization for carbocations. The existence of CH3CF2+, in contrast to the elusive ethyl cation CH3CH2+, is a clear evidence that replacement of H atoms by F atoms provides stabilization for carbocations.524 Furthermore, it was found that in perfluorobenzyl cation C6F5CF2+ fluorine atoms in resonance positions (ortho and para) are more deshielded than those in meta positions.536 This indicates carbocation stabilization by back-donation. 

Russell, G. A. Solvent effects in the reactions of free radicals and atoms. II. Effects of solvents on the position of attack of chlorine atoms upon 2,3-dimethylbutane, isobutane and 2-deuterio-2-methyl-propane. J. Amer. chem. Soc. 80, 4987 (1958). 

What is the reason for this apparent discrepancy It is a solvent effect. In aqueous solution (Figure 9.6), the OH group at the anomeric C atom of the glucose becomes so voluminous due to hydration that it strives for the position in which the steric interactions are as weak as possible. Thus, it moves into the equatorial position—with a AG° value of approximately -1.6 kcal/mol—to avoid a gauche interaction with the six-membered ring skeleton. (Remember that axially oriented substituents on the chair conformer of cyclohexane are subject to two gauche interactions with the two next-to-nearest C. —C bonds. They therefore have a... 

Disorder may strongly influence the precision with which all atomic positions in that crystal can be measured, and it is often difficult to obtain a model that accounts adequately for the disorder. Consequently diffraction effects resulting from disorder may be compensated for b (erroneous) shifts in other parameters that involve ordered atoms. Bond distances may appear unusually long or short and bond angles may be atypical. These effects almost certainly result from inadequacies in the model. If the disorder occurs in only a small fraction of the content of the asymmetric unit, it is presumed that the conformation of the (well-ordered) remainder of the asymmetric unit (molecule) is driving the crystal packing rather than vice versa. Disorder is often observed in solvent of crystallization, since there may be space in the crystal structure for the solvent molecules to organize in one of several manners. ... 

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