HELICOBACTER PYLORI INFECTION IN PATIENTS WITH DIFFERENT GASTROINTESTINAL DISEASES FROM NORTHERN BRAZIL.

Background: The mechanisms whereby Helicobacter pylori produces different pathological manifestations in the stomach and duodenum are not fully understood. Considering the geographic diversity in the prevalence of virulence factors of this microorganism and their association with the development of different diseases, the search for pathogenicity markers such as CagA and VacA alleles by molecular techniques has intensified.

Objectives: To investigate the presence of H.

Benchmarks of electronically excited states: basis set effects on CASPT2 results.

Vertical excitation energies and one-electron properties are computed for the valence excited states of 28 medium-sized organic benchmark molecules using multistate multiconfigurational second-order perturbation theory (MS-CASPT2) and the augmented correlation-consistent aug-cc-pVTZ basis set. They are compared with previously reported MS-CASPT2 results obtained with the smaller TZVP basis. The basis set extension from TZVP to aug-cc-pVTZ causes rather minor and systematic shifts in the vertical excitation energies that are normally slightly reduced (on average by 0.

Benchmark of Electronically Excited States for Semiempirical Methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2.

Semiempirical configuration interaction (CI) calculations with eight different Hamiltonians are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies and one-electron properties are computed using the same geometries as in our previous ab initio benchmark study on electronically excited states. The CI calculations for the standard methods (MNDO, AM1, PM3) and for the orthogonalization-corrected methods (OM1, OM2, OM3) include single, double, triple, and quadruple excitations (CISDTQ) using the graphical unitary group approach (GUGA) as implemented in the MNDO code.

Influence of the LOV domain on low-lying excited states of flavin: a combined quantum-mechanics/molecular-mechanics investigation.

The ground and low-lying excited states of flavin mononucleotide (FMN) in the light, oxygen, and voltage sensitive (LOV) domain of the blue-light photosensor YtvA of Bacillus subtilis were studied by means of combined quantum-mechanical/molecular-mechanical (QM/MM) methods. The FMN cofactor (without the side chain) was treated with density functional theory (DFT) for the geometry optimizations and a combination of DFT and multireference configuration interaction (MRCI) for the determination of the excitation energies, while the protein environment was represented by the CHARMM force field. In addition, several important amino acid side chains, including the reactive cysteine residue, were included in the QM region in order to probe their influence on the spectral properties of the cofactor in two protein conformations.

Benchmarks for Electronically Excited States: A Comparison of Noniterative and Iterative Triples Corrections in Linear Response Coupled Cluster Methods: CCSDR(3) versus CC3.

CCSDR(3) calculations of vertical excitation energies are reported for a set of 24 molecules and 121 excited valence singlet states from a recently published benchmark of organic molecules. The same geometries (MP2/6-31G*) and basis set (TZVP) were employed as in our previous linear response CC2, CCSD, and CC3 calculations. The CCSDR(3) results are compared against the CCSD and CC3 results.

Benchmarks for electronically excited states: time-dependent density functional theory and density functional theory based multireference configuration interaction.

Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole moments are computed using the same geometries (MP2/6-31G(*)) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio results, and, in particular, against the proposed best estimates for 104 singlet and 63 triplet vertical excitation energies.

Benchmarks for electronically excited states: CASPT2, CC2, CCSD, and CC3.

A benchmark set of 28 medium-sized organic molecules is assembled that covers the most important classes of chromophores including polyenes and other unsaturated aliphatic compounds, aromatic hydrocarbons, heterocycles, carbonyl compounds, and nucleobases. Vertical excitation energies and one-electron properties are computed for the valence excited states of these molecules using both multiconfigurational second-order perturbation theory, CASPT2, and a hierarchy of coupled cluster methods, CC2, CCSD, and CC3. The calculations are done at identical geometries (MP26-31G*) and with the same basis set (TZVP).