Theoretical studies of hydrogen-bonded complexes using semiempirical methods

Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach

This work examines the ability of semiempirical methods to describe the structure of liquid water. Particularly, the standard AM1 and PM3 methods together with recently developed PM3-PIF and PM3-MAIS parametrizations have been considered. We perform molecular dynamics simulations for a system consisting of 64 or 216 water molecules in a periodic cubic box. The whole system is described quantum mechanically. Calculations with 64 molecules have been carried out using standard SCF techniques whereas calculations with 216 molecules have been done using the divide and conquer approach. This method has also been used in one simulation case with 64 molecules for test purposes. Within this scope, the molecular dynamics program ROAR have been coupled with a linear scaling semiempirical code (DivCon) implemented in a parallel MPI version. The predicted liquid water structure using either AM1 or PM3 is shown to be very poor due to well-known limitations of these methods describing hydrogen bonds. In contrast, PM3-PIF and PM3-MAIS calculations lead to results in reasonably good agreement with experimental data. The best results for the heat of vaporization are obtained with the PM3-PIF method. The average induced dipole moment of the water molecule in the liquid is underestimated by all semiempirical techniques, which seems to be related to the NDDO approximation and to the use of minimal basis sets. A brief discussion on charge-transfer effects in liquid water is also presented.

Quantification of the influence of single-point mutations on haloalkane dehalogenase activity: a molecular quantum similarity study

Controlled modifications in certain protein amino acid residues can lead to changes in their function and stability. Amino acid structural features and their relation to these changes were examined by using quantum molecular similarity techniques. The effect of deliberate mutations in position 172 of the haloalkane dehalogenase enzyme, yielding to variations on the dehalogenation of 1,2-dibromoethane, was studied qualitatively and quantitatively using molecular quantum similarity techniques. A valuable classification of the residues according to their effect on activity was obtained by representing the optimal two-dimensional classical scaling solution. In addition, satisfactory quantitative relationships were found, comparable to those attained by previous studies on this same data set using other techniques. Molecular quantum similarity analysis provides a consistent, unbiased, and homogeneous set of molecular descriptors and is a feasible alternative to the use of physicochemical properties.