New Computational Methods and Developments for Molecular Response Properties in Condensed Matter

Abstract

In this thesis we are aimed by the purpose of describe three important cases of chemical interest and show how theoretical and computational methods can be useful, even needful to explore and solve very significative applications. The commons theme of this work are represented by the well known Density Functional Theory and the Polarizable Continuum Model used for all the cases reported . As we will able to recall the first is one of the most diffused theoretical approach in computational chemistry studies whenever the electronic structure has to be solved. The second one represents a wide diffuse model which is able to describe with good accuracy molecular interactions in condensed matter. Both of them provide the most common computational configuration in organic, and oreganometallic studies. In this thesis we are going to describe few examples which spread from the study of condensed matters under extremely high pressure to a biological application on DNA nucleobase systems, moving through some typical organometallic problems. Focusing on our issues we are going to present a new computational QM method for the study of structural properties (i.e. equilibrium geometry) of molecular systems under very high pressure. The procedure is based on the Polarizable Continuum Model , usually used to study molecular solutes under standard pressure conditions. The presented development considers two critical items: the definition of the pressure and the elaboration of an analytical code for the calculation of molecular gradient. The method has been developed at HF and DFT levels, with computational costs comparable with those of similar calculations in vacuo. The numerical examples regarding the equilibrium geometries and conformational energies (DFT level) of 1,3-butadiene under high pressure give an indication of the potentialities of the approach and of the problems to which it may be applied. The next argument regards several application in the field of inorganic chemistry. We will shortly describe a computational procedure where we investigate some spectroscopical properties of some luminescence silver complexes. In this, we will describe a time dependent density functional study of several excited states. Moreover we will study the correlation between stretching vibration and Mulliken charges in some rhodium complexes. But most of this section will be dedicate to a very practical application in chemistry that is the chemical reaction path determination. Aimed by unclear experimental evidences provided by the catalytic investigation of an half sandwich Ru(II) complex, we performed a deep exploration of the mechanism through which the pre catalysts operate. Several data obtained by high-resolution MS (ESI) have been explained by a combined ”Density Functional /Polarizable Continuum Model” study. The results reveal that the complexes containing PNH2 operate through a bifunctional mechanism analogous to that proposed for diamines and amino alcohol ligands, but with some new aspects that are important to point out. Finally an efficient computational method has been identified which uses Density Functional Theory, Polarizable Continuum Models with a modified UFF cavity and Boltzmann weighting of tautomers to predict the site-specific and global pKa of DNA nucleobases and their oxidation products. The method has been used to evaluate the acidity of Gh and Sp, two highly mutagenic guanine oxidation products. The trend observed for the pKa values of Gh (9.64 and 8.15) is consistent with the experimentally observed values for guanidine cation (13.7) and hydantoin (9.16). The pKa1(calc) value for deprotonation of Sp cation (Sp+-->Sp) is very close to the experimentally observed pKa1 for 8-oxoG and is consistent with the similarity in their structures. The data suggest that the imide (N7) proton in Sp is considerably more acidic than that in Gh, possibly due to the presence of the through-space electronic e ects of the carbonyl group located at C6. This difference in the acidity of Gh and Sp may be an indication of their potential toxicity and mutagenicity in vivo and remains a fertile area for experimental study.