An optimized potential function for base-stacking interactions is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole-monopole approximation (MMA) is compared to the more refined segmented multipole-multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima.The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima.The attractive part of the Lennard-Jones 6-12 potential is compared to and parameterized against the expressions for the second-order interaction terms composed of multipole-bond polarizability for the polarization energy and transition-dipole bond polariz abilities for approximation of the dispersion energy. The repulsive part of the Lennard-Jones potential is compared to a Kitaygorodski-type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function.Stacking minima calculated with the optimized potential method are compared with various perturbation-type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.

The SN2 reaction between ammonia and formic acid has been studied as a model reaction for peptide bond formation using the semiempirical MNDO and ab initio molecular orbital methods. Two reaction mechanisms have been examined, i.e., a stepwise and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies have been calculated for all geometry optimized reaction species to determine the thermodynamics and kinetics of each reaction. The stepwise mechanism was found to be more favorable than the concerted one by both MNDO and ab initio calculations. However, the ab initio method predicts both mechanisms to be fairly competitive with free energies of activation of about 50 kcal/mol. Despite excellent agreement between both methods in the calculated entropies and thermal energies, the minimum basis set character of MNDO leads to values of free energy of activation much higher than those obtained by the ab initio method. The basis set dependence and effect of correlation of the computed ab initio results and the relative effects of polarization and correlation were also investigated by using a number of basis sets up to 6-31G** and estimates of correlation energy by Moller-Plesset perturbation theory up to fourth order. Correlation energy was found to be a significant factor in the stabilization of transition states.

Determinations of the salt sensitivity of enzymes extracted from the halophilic alga Dunaliella viridis revealed that pentose phosphate isomerase, ribulose diphosphate carboxylase, glucose-6-phosphate dehydrogenase, and phosphohexose isomerase were inhibited by NaCl concentrations far lower than that in the growth medium (3.75 M). The inhibition was reversible and was not prevented by preparing the extracts in the presence of salt. Potassium, lithium, and cesium chlorides were equally inhibitory. In contrast, whole cells require rather high levels of NaCl for optimal growth, whereas growth is inhibited by low levels of the other cations. The results suggest a specific mechanism for the exclusion of sodium from the interior of the cell. The basis of the salt tolerance of the halophilic bacteria appears to be a distinctive form of enzymatic protein which is resistant to inactivation by high levels of salt and, in fact, requires substantial concentrations of salt for full enzymatic activity (6). The halophilic species of the green alga Dunaliella grow in concentrated salt solutions, but the basis of this salt tolerance is unknown. The present report describes the effects of sodium chloride and other salts on the growth of Dunaliella viridis and on the activity of several enzymes from this halophilic species.

Glassy structures of water were generated by rapidly quenching configurations of 64 and 343 molecules of liquid water. The potential energy was then expanded through quadratic order around local minima generated this way and properties of the resulting harmonic system were calculated. The results were used to test the extent to which the structure of liquid water is similar to that of a harmonic aqueous glass. The radial distribution functions for the glass are remarkably similar to those of the liquid. The vibrational density of states for the glassy water exhibits a gap between 300 and 400 cm-1. The normal modes below 300 cm-1 correspond to molecular translations while the modes above 400 cm-1 are ascribed to molecular librations. Translational modes are almost entirely responsible for the broadening of oxygen-oxygen radial distribution function of the quenched configuration. They are also primarily responsible for the broadening of other radial distribution functions. Vibrational density of states leads to classical and quantum free energies for the harmonic system equal -9.62 +/- 0.12 and -8.89 +/- 0.12 kcal/mol, respectively, at T = 300 K. Both free energies were found to be insensitive to sample size and to the configurational differences between the quenched structures.

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