Eufrozina A. Hoffmann

Harmonic vibrational frequency scaling factors for the new NDDO Hamiltonians: RM1 and PM6

Scaling factors have been derived to obtain fundamental vibrational frequencies with the recently introduced semiempirical molecular orbital methods RM1 and PM6, implemented in MOPAC2007. A least-squares approach is used with a training set comprised of 90 singlet-state molecules and 922 distinct vibrations, extracted from the NIST Computational Chemistry Comparison and Benchmark Database (CCCBDB). Results are presented both for the conventional Scott-Radom type single-factor fitting, and for a multi-factor linear model: Semiempirical Semiglobal Self-consistently Scaled Quantum Mechanical (S4QM). The new NDDO methods in conjunction with the multi-linear fitting are shown to yield improved prediction of vibrational frequencies. To demonstrate the performance of S4QM//PM6 for calculating vibrational spectra, the examples of indene, indazole and four tetrachlorinated p-dibenzodioxins are presented.

On the possible roles of N-terminal His-rich domains of Cu,Zn SODs of some Gram-negative bacteria

The Cu,Zn superoxide dismutases (Cu,Zn SOD) isolated from some Gram-negative bacteria possess a His-rich N-terminal metal binding extension. The N-terminal domain of Haemophilus ducreyi Cu,Zn SOD has been previously proposed to play a copper(II)-, and may be a zinc(II)-chaperoning role under metal ion starvation, and to behave as a temporary (low activity) superoxide dismutating center if copper(II) is available. The N-terminal extension of Cu,Zn SOD from Actinobacillus pleuropneumoniae starts with an analogous sequence (HxDHxH), but contains considerably fewer metal binding sites. In order to study the possibility of the generalization of the above mentioned functions over all Gram-negative bacteria possessing His-rich N-terminal extension, here we report thermodynamic and solution structural analysis of the copper(II) and zinc(II) complexes of a peptide corresponding to the first eight amino acids (HADHDHKK-NH(2), L) of the enzyme isolated from A. pleuropneumoniae. In equimolar solutions of Cu(II)/Zn(II) and the peptide the MH(2)L complexes are dominant in the neutral pH-range. L has extraordinary copper(II) sequestering capacity (K(D,Cu)=7.4×10(-13)M at pH 7.4), which is provided only by non-amide (side chain) donors. The central ion in CuH(2)L is coordinated by four nitrogens {NH(2),3N(im)} in the equatorial plane. In ZnH(2)L the peptide binds to zinc(II) through a {NH(2),2N(im),COO(-)} donor set, and its zinc binding affinity is relatively modest (K(D,Zn)=4.8×10(-7)M at pH 7.4). Consequently, the presented data do support a general chaperoning role of the N-terminal His-rich region of Gram-negative bacteria in copper(II) uptake, but do not confirm similar function for zinc(II). Interestingly, the complex CuH(2)L has very high SOD-like activity, which may further support the multifunctional role of the copper(II)-bound N-terminal His-rich domain of Cu,Zn SODs of Gram-negative bacteria. The proposed structure for the MH(2)L complexes has been verified by semiempirical quantum chemical calculations (PM6), too.

Theoretical characterization of gas-liquid chromatographic stationary phases with quantum chemical descriptors

Quantitative structure-property relationship (QSPR) solvent model has been developed for the McReynolds constants (prototypical solutes) on 36 gas-liquid chromatographic stationary phases. PM6 semiempirical quantum chemical calculations combined with conductor-like screening model (COSMO) has been utilized. From 276 descriptors considered, forward stepwise variable selection, followed by best subset selection, yielded linear regression models containing six purely quantum chemical and two hybrid, topologically based descriptors. Internal (leave-one-out and bootstrap) as well as external validation methods confirmed the predictive power of these structure-driven models across all 10 McReynolds constants, with 40 Kováts-index units overall root-mean-square prediction error estimate.

Quantum chemical characterization of Abraham solvation parameters for gas-liquid chromatographic stationary phases

Quantum chemical based investigation is presented on the Abraham solvation parameters for 23 molecular (non-polymeric) GLC stationary phases. PM6 semiempirical calculations combined with conductor-like screening model (COSMO) have been utilized. Comprehensive search for an optimal model was carried out, based on best subset selection from 86 variables considered. A unified quantitative structure-property relationship model has been developed for all five Abraham parameters reported. The selected set of five structure-driven descriptors was subjected to statistical analyses, and was shown to be useful for stationary phase classification.