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Byline: Ramon Carbo-Dorca (1), Patrick Bultinck (2) Keywords: Mulliken population analysis; atomic charge; electron density; density function; LCAO MO Abstract: Using an approach alternative to that of Mayer, this paper shows that a Hermitian operator can be found, such that, in a molecule atomic populations can be obtained as its expectation values. In this way, atomic charges can be computed within a quantum mechanical correct definition. When working within the LCAO MO framework, it is found that Mulliken populations appear as the appropriate expectation values of the charge operator. Author Affiliation: (1) Institut de Quimica Computacional, Universitat de Girona, Girona, 17071, Catalonia, Spain (2) Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281, B-9000, Gent, Belgium Article History: Registration Date: 27/10/2004

Quantum mechanical methods are used to study the reactions caused by catalyzing the antibody 10F11 substrate. Functional theory and empirical docking methods are employed to investigate the substrate and transition state binding to the active site of the antibody.

Byline: Ramon Carbo-Dorca (1), Patrick Bultinck (2) Keywords: Hohenberg--Kohn theorem; Density Functional Theory Abstract: A general theorem concerning the spectral relationship of two non-commuting Hermitian matrices is demonstrated. Discussion and analysis of such finding leads to consider its tight connection with respect of the Hohenberg--Kohn theorem (HKT), cornerstone of DFT theory. The present analysis shows that not only HKT can be considered a particular case of the proposed theorem, but also the validity of the studied spectral relationship can be extended from quantum mechanical ground state to excited states as well. Author Affiliation: (1) Institute of Computational Chemistry, University of Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain (2) Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000, Gent, Belgium Article History: Registration Date: 08/10/2004

The article consists of the general overview on the quantum similarities of quantitative structure-activity relationships. The topics of interest include the theoretical background and the role of the quantum mechanical density function, and the applicability of quantum similarity.

Ab initio quantum mechanical and density functional theory calculations, along with an isodensity surface-polarized continuum model, were used to examine cytosine methylation reaction. An approach for estimating the pKa of the cytosine N3 in the reaction intermediates and transition states and on the calculated reaction profiles is also introduced. According to pKa calculations, the pKa of N3 of the ring increases from five to 18 during the attack of methyl thiolate on C6 of the cytosine. This declines from 17 to five in the next reaction stage where C5 of the cytosine is methylated. Proton transfers in cytosine methylation are believed to occur between Glu119 of the active site and N3 of the cytosine.

The ring opening of the epoxide inhibitors catalyzed by the catalytic elements of the glycosidases, the nucleophile and the acid/base catalyst was studied for a better understanding of the mechanism of the epoxide ring opening. A model system consisting of methyloxirane, formate and formic acid was used. Results indicate that efficient ring opening reaction requires both the nucleophile and the acid/base catalyst.

A new quantum mechanical approach has been applied to isomeric radicals from the addition of hydrogen atoms to thymine. Post-Hartree-Fock or density functional electronic computations are included in the computational protocol. Hybrid Hartree-Fock/density functional models gave reliable results, and there was good agreement between the computed hyperfine coupling constants and experimental data.

A modeled version of the (Ru(H...H)(Csub5Mesub5)(dppm))+ complex has been studied at electronic structure level and with quantum treatment of the nuclei. Density function theory (DFT) electronic structure calculations cannot alone reproduce reported geometry of the elongated dihydrogen ligand of the complex, but quantum nuclear motion calculations can explain the geometries correctly.

Density functional theory and multiconfigurational quantum chemical studies were performed to differentiate nitride versus oxide in polymetallic uranium molecules containing [(N).sup.3-] and [(O).sup.2-]. The crystallographic data obtained provide insight into the electronic structure and unique chemical bonding of uranium polymetallic compounds.

A combination of various QM and MM studies is employed to explain the various effects of solvents on the photoreactivity of valerophenone. The formation of different shift in the excited states of the compound because of the different reactions with different mechanisms is also discussed.

Density functional theory and correlated ab initio quantum mechanical methods were used to locate and analyze alkene hydroboration transition structures for 10-R-9-borabicyclo[3.3.2]decane reagents. The analysis results for the 10-R group and borabicyclo[3.3.2]decane ring conformation effects provide better insight into the origin of asymmetric selectivity.

The mechanism for [H.sub.2] cleavage in NeFe-hydrogenase is reinvestigated with large models by using both hybrid density functional theory (DFT) by itself, or in a quantum mechanics (QM)/molecular mechanics (MM) scheme following the ONIOM approach. The studies have shown that the ONIOM results for the reaction mechanism in NiFe-hydrogenase had to be corrected by large model DFT results, which is due to overestimation of polarization effects of the QM region by the MM region.

The nature of the Fe-[O.sub.2] bonding in oxy-myoglobin is examined by hybrid quantum mechanical/molecular mechanical calculations and gas-phase calculations using density functional theory (DFT). The protein has strengthened the [Fe.sup.III]-[O.sub.2.sup.-] character of the complex, thus affecting its bonding features and the oxygen binding affinity of Mb.

The SM8 quantum mechanical aqueous continuum solvation model is applied on a 17-molecule test set for predicting free energies of solvation. The sensitivity of the SM8 model to the choices of molecular geometry, charge model and density functional model is discussed.

The application and the limitations of using quantum mechanics for chemical studies and calculations by employing different software packages are discussed. Though, the calculations are shown to be not completely accurate, they are shown to be fine enough for practical applications.

Quantum mechanical calculations are used to study puckering in various uridine compounds in a continuous medium which mimics the dielectric properties of water. It is observed that north puckering is favored in 2'-OH than in 2'-OC[H.sub.3] compounds due to the orientation of 2' group and the presence of water molecule.