Calculated ionization potentials of the linear alkanes

The equivalent orbital (EO) method is investigated and used for predicting outer and inner ionization potentials of the linear alkanes. The calculated ionization potentials are in good agreement with those observed in photoelectron spectra provided that a set of 12 parameters is used in the theory. An optimization technique is used to find the best values for thle parameters and a single transferable parameter set can be found which is applicable to all the n-alkanes. A good fit to the experimental results can only be obtained if the uppermost molecular orbital of the n-alkanes is an antisymmetrical orbital built up from CH equivalent orbitals.

A microscopic view of substitution reactions solvated by ionic liquids

The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl(-) and Br(-) reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties. (c) 2008 American Institute of Physics.

DFT and electrochemical studies on nortriptyline oxidation sites

A study on the possible sites of oxidation and epoxidation of nortriptyline was performed using electrochemical and quantum chemical methods; these sites are involved in the biological responses (for example, hepatotoxicity) of nortriptyline and other similar antidepressants. Quantum chemical studies and electrochemical experiments demonstrated that the oxidation and epoxidation sites are located on the apolar region of nortriptyline, which will useful for understanding the molecule`s activity. Also, for the determination of the compound in biological fluids or in pharmaceutical formulations, we propose a useful analytical methodology using a graphite-polyurethane composite electrode, which exhibited the best performance when compared with boron-doped diamond or glassy carbon surfaces.

Synthesis and evaluation of sesquiterpene lactone inhibitors of phospholipase A(2) from Bothrops jararacussu

Several sesquiterpene lactone were synthesized and their inhibitive activities on phospholipase A(2) (PLA(2)) from Bothrops jararacussu venom were evaluated. Compounds Lac01 and Lac02 were efficient against PLA(2) edema-inducing, enzymatic and myotoxic activities and it reduces around 85% of myotoxicity and around 70% of edema-inducing activity. Lac05-Lac08 presented lower efficiency in inhibiting the biological activities studied and reduce the myotoxic and edema-inducing activities around only 15%. The enzymatic activity was significantly reduced. The values of inhibition constants (K(1)) for Lac01 and Lac02 were approximately 740 mu M, and for compounds Lac05-Lac08 the inhibition constants were approximately 7.622-9.240 mu M. The enzymatic kinetic studies show that the sesquiterpene lactones inhibit PLA(2) in a non-competitive manner. Some aspects of the structure-activity relationships (topologic, molecular and electronic parameters) were obtained using ab initio quantum calculations and analyzed by chemometric methods (HCA and PCA). The quantum chemistry calculations show that compounds with a higher capacity of inhibiting PLA(2) (Lac01-Lac04) present lower values of highest occupied molecular orbital (HOMO) energy and molecular volume (VOL) and bigger values of hydrophobicity (LogP). These results indicate some topologic aspects of the binding site of sesquiterpene lactone derivatives and PLA(2). (C) 2010 Elsevier Ltd. All rights reserved.

A first-principles density-functional calculation of the electronic and vibrational structure of the key melanin monomers

We report first-principles density-functional calculations for hydroquinone (HQ), indolequinone (IQ), and semiquinone (SQ). These molecules are believed to be the basic building blocks of the eumelanins, a class of biomacromolecules with important biological functions (including photoprotection) and with the potential for certain bioengineering applications. We have used the difference of self-consistent fields method to study the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, HL. We show that HL is similar in IQ and SQ, but approximately twice as large in HQ. This may have important implications for our understanding of the observed broadband optical absorption of the eumelanins. The possibility of using this difference in HL to molecularly engineer the electronic properties of eumelanins is discussed. We calculate the infrared and Raman spectra of the three redox forms from first principles. Each of the molecules have significantly different infrared and Raman signatures, and so these spectra could be used in situ to nondestructively identify the monomeric content of macromolecules. It is hoped that this may be a helpful analytical tool in determining the structure of eumelanin macromolecules and hence in helping to determine the structure-property-function relationships that control the behavior of the eumelanins.

Synthesis, spectroscopic characterization, DFT studies and biological assays of a novel gold(I) complex with 2-mercaptothiazoline

A new gold(I) complex with 2-mercaptothiazoline (MTZ) with the coordination formula [AuCN(C(3)H(5)NS(2))] was synthesized and characterized by chemical and spectroscopic measurements, OFT studies and biological assays. Infrared (IR) and (1)H, (13)C and (15)N nuclear magnetic resonance (NMR) spectroscopic measurements indicate coordination of the ligand to gold(I) through the nitrogen atom. Studies based on OFT confirmed nitrogen coordination to gold(I) as a minimum of the potential energy surface with calculations of the hessians showing no imaginary frequencies. Thermal decomposition starts at temperatures near 160 degrees C, leading to the formation of Au as the final residue at 1000 degrees C. The gold(I) complex with 2-mercaptothiazoline (Au-MTZ) is soluble in dimethyl sulfoxide (DMSO), and is insoluble in water, methanol, ethanol, acetonitrile and hexane. The antibacterial activities of the Au-MTZ complex were evaluated by an antibiogram assay using the disc diffusion method. The compound showed an effective antibacterial activity against Staphylococcus aureus (Gram-positive) and Escherichia coli and Pseudomonas aeruginosa (Gram-negative) bacterial cells. Biological analysis for evaluation of the cytotoxic effect of the Au-MTZ complex was performed using HeLa cells derived from human cervical adenocarcinoma. The complex presented a potent cytotoxic activity, inducing 85% of cell death at a concentration of 2.0 mu mol L(-1). (C) 2011 Elsevier Ltd. All rights reserved.

Basis set convergence in Hartree-Fock calculations of some diatomic molecules containing first and second-row atoms

Investiga-se a convergência de conjuntos de bases em direção ao limite numérico da energia Hartree-Fock (HF) total para as seqüências hierárquicas dos conjuntos de bases XZP e ccpVXZ. Para as duas hierarquias, melhoramentos significativos são obtidos com cada incremento em X. Para estimar o limite do conjunto de base completo, uma forma exponencial foi usada. Entre as várias aproximações consideradas aqui, uma extrapolação exponencial de três parâmetros aplicada aos resultados TZP, QZP e 5ZP deu os limites do conjunto de bases mais precisos. Em adição, energias HF dos orbitais moleculares ocupados mais altos de algumas moléculas diatômicas foram calculadas com o conjunto 5ZP e comparadas com as correspondentes obtidas com o conjunto cc-pV5Z e com um método numérico HF.

Febrifugine derivative antimalarial activity: quantum mechanical predictors

Plasmodium falciparum resistant strain development has encouraged the search for new antimalarial drugs. Febrifugine is a natural substance with high activity against P. falciparum presenting strong emetic property and liver toxicity, which prevent it from being used as a clinical drug. The search for analogues that could have a better clinical performance is a current topic. We aim to investigate the theoretical electronic structure by means of febrifugine derivative family semi-empirical molecular orbital calculations, seeking the electronic indexes that could help the design of new efficient derivatives. The theoretical results show there is a clustering in well-defined ranges of several electronic indexes of the most selective molecules. The model proposed for achieving high selectivity was tested with success.

Perylene Diimide acceptors: Fabrication and characterization of electron-only, hole-only devices and solar cells

The thrust towards energy conservation and reduced environmental footprint has fueled intensive research for alternative low cost sources of renewable energy. Organic photovoltaic cells (OPVs), with their low fabrication costs, easy processing and flexibility, represent a possible viable alternative. Perylene diimides (PDIs) are promising electron-acceptor candidates for bulk heterojunction (BHJ) OPVs, as they combine higher absorption and stability with tunable material properties, such as solubility and position of the lowest unoccupied molecular orbital (LUMO) level. A prerequisite for trap free electron transport is for the LUMO to be located at a level deeper than 3.7 eV since electron trapping in organic semiconductors is universal and dominated by a trap level located at 3.6 eV. Although the mostly used fullerene acceptors in polymer:fullerene solar cells feature trap-free electron transport, low optical absorption of fullerene derivatives limits maximum attainable efficiency. In this thesis, we try to get a better understanding of the electronic properties of PDIs, with a focus on charge carrier transport characteristics and the effect of different processing conditions such as annealing temperature and top contact (cathode) material. We report on a commercially available PDI and three PDI derivatives as acceptor materials, and its blends with MEH-PPV (Poly[2-methoxy 5-(2-ethylhexyloxy)-1,4-phenylenevinylene]) and P3HT (Poly(3-hexylthiophene-2,5-diyl)) donor materials in single carrier devices (electron-only and hole-only) and in solar cells. Space-charge limited current measurements and modelling of temperature dependent J-V characteristics confirmed that the electron transport is essentially trap-free in such materials. Different blend ratios of P3HT:PDI-1 (1:1) and (1:3) show increase in the device performance with increasing PDI-1 ratio. Furthermore, thermal annealing of the devices have a significant effect in the solar cells that decreases open-circuit voltage (Voc) and fill factor FF, but increases short-circuit current (Jsc) and overall device performance. Morphological studies show that over-aggregation in traditional donor:PDI blend systems is still a big problem, which hinders charge carrier transport and performance in solar cells.

Ionic, paramagnetic and photophysical properties of a new biohybrid material incorporating copper perchlorate

The sol-gel method was employed in the synthesis of di-urethane cross-linked poly(-caprolactone) (d-PCL(530)/siloxane biohybrid ormolytes incorporating copper perchlorate, (Cu(ClO4)2). The highest ionic conductivity of the d PCL(530)/siloxanenCu(ClO4)2 system is that with n = 10 (1.4 x 10-7 and 1.4 x 10-5 S cm-1, at 25 and 100 ºC, respectively). In an attempt to understand the ionic conductivity/ionic association relationship, we decide to inspect the chemical environment experienced by the Cu2+ ions in the d-PCL(530)/siloxane medium. The observed EPR spectra are typical of isolated monomeric Cu2+ ions in axially distorted sites. The molecular orbital coefficients obtained from the EPR spin Hamiltonian parameters and the optical absorption band suggests that bonding between the Cu2+ and its ligand in the ormolytes are moderately ionic. Investigation by photoluminescence spectroscopy did not evidence or allow selective excitation of transitions corresponding to complexed Cu2+ species.

How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers?

We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95 + + (d,p) basis sets at both the Hartree-Fock and second-order Møller-Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone

Investigation of classical epidemiological links between patients harbouring identical, non-predominant meticillin-resistant Staphylococcus aureus genotypes and lessons for epidemiological tracking.

According to molecular epidemiology theory, two isolates belong to the same chain of transmission if they are similar according to a highly discriminatory molecular typing method. This has been demonstrated in outbreaks, but is rarely studied in endemic situations. Person-to-person transmission cannot be established when isolates of meticillin-resistant Staphylococcus aureus (MRSA) belong to endemically predominant genotypes. By contrast, isolates of infrequent genotypes might be more suitable for epidemiological tracking. The objective of the present study was to determine, in newly identified patients harbouring non-predominant MRSA genotypes, whether putative epidemiological links inferred from molecular typing could replace classical epidemiology in the context of a regional surveillance programme. MRSA genotypes were defined using double-locus sequence typing (DLST) combining clfB and spa genes. A total of 1,268 non-repetitive MRSA isolates recovered between 2005 and 2006 in Western Switzerland were typed: 897 isolates (71%) belonged to four predominant genotypes, 231 (18%) to 55 non-predominant genotypes, and 140 (11%) were unique. Obvious epidemiological links were found in only 106/231 (46%) patients carrying isolates with non-predominant genotypes suggesting that molecular surveillance identified twice as many clusters as those that may have been suspected with classical epidemiological links. However, not all of these molecular clusters represented person-to-person transmission. Thus, molecular typing cannot replace classical epidemiology but is complementary. A prospective surveillance of MRSA genotypes could help to target epidemiological tracking in order to recognise new risk factors in hospital and community settings, or emergence of new epidemic clones.

O uso de cálculos teóricos como ferramenta para a detecção de moléculas no meio interestelar: o caso dos carbenos CnNH (n=1, 3 e 5)

This work reviews some applications of ab initio molecular orbital calculations to the elucidation of structures of interstellar molecules. The case of the CnNH (n=1, 3 and 5 ) carbenes is extensively analyzed and discussed. Theoretical conformational analysis and predicted values for the rotational constants and dipole moments of the singlet state of C5NH are reported for the first time and a comparison is performed with results previously obtained for C3NH and CNH.

Estudo químico-computacional da reatividade de aziridinona e diaziridinona através de cálculos semi-empíricos

The results of semiempirical molecular orbital calculations performed on aziridinone and diaziridinone employing the MNDO, AM1, and PM3 molecular models are presented. The AM1 method, which best reproduces ground-state molecular properties, is used to calculate electronic parameters and the use of these parameters for the evaluation of reactivity is discussed.

Unambiguous assessments of reaction paths for selected pericyclic reactions

Four commonplace concerted reactions are examined using (i) correlation diagrams, (ii) frontier molecular orbital analyses for transition states, (iii) Zimmerman-Dewar analyses for transition states and (iv) modified Zimmerman-Dewar analyses for transition states. Only the latter approach is consistently satisfactory.