An Unprecedented Neolignan Skeleton from Chimarrhis turbinata

A lignan with a new skeleton named chimarrhinin (1) was isolated from an extract of the leaves of Chimarrhis turbinata, a Rubiaceae plant species. (13)C NMR spectrometric techniques including 1D and 2D experiments and HRESIMS provided unequivocal structural confirmation of this new C(6).C(3) skeleton type. The relative configuration of 1 was established by 2D (1)H-H analysis and J couplings, while its conformation was evaluated through molecular modeling using the RM1 semiempirical method, with the aid of coupling constants obtained by NMR analysis. The antioxidant activity of the new derivative 1 and two known and previously isolated phenolic derivatives (2 and 3) was investigated. An IC(50) value of 7.50 +/- 0.5 mu mol L(-1) was obtained for the new derivative 1, while 2 and 3 showed IC(50) values of 18.60 +/- 0.4 and 18.50 +/- 0.6 mu mol, respectively.

Origin of the spectral shifts among the early intermediates of the rhodopsin photocycle.

A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one correspondence between the structures of the different early intermediates (dark, batho, BSI, lumi) involved in the initial steps of the rhodopsin photoactivation mechanism and their optical spectra. A systematic analysis of the results based on a correlation-based feature selection algorithm shows that the origin of the color shifts among these intermediates can be mainly ascribed to alterations in intrinsic properties of the chromophore structure, which are tuned by several residues located in the protein binding pocket. In addition to the expected electrostatic and dipolar effects caused by the charged residues (Glu113, Glu181) and to strong hydrogen bonding with Glu113, other interactions such as π-stacking with Ala117 and Thr118 backbone atoms, van der Waals contacts with Gly114 and Ala292, and CH/π weak interactions with Tyr268, Ala117, Thr118, and Ser186 side chains are found to make non-negligible contributions to the modulation of the color tuning among the different rhodopsin photointermediates.

Análise conformacional de modelos de lignina

The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level.

UDP-N-acetilglicosamina enolpiruvil transferase: determinação dos estados de protonação de resíduos de aminoácidos do sítio ativo pelo método PM6

UDP-N-acetylglucosamine-enolpyruvyl transferase (MurA) catalyzes the reaction between phosphoenol pyruvate and UDP-N-acetylglucosamine. We present a theoretical approach using the semiempirical PM6 method for defining protonation state of three active site residues, K22, H125, and K160. Prior comparison with neutron diffraction data showed that PM6 accurately predicted protonation states of active site residues of b-trypsin and D-xylose isomerase. Using the same methodology with MurA crystallographic data, we conclude that when reaction intermediate is located at the active site, H125 and K22 are in protonated form and K160 in neutral form.

Theoretical study of omeprazole behavior: Racemization barrier and decomposition reaction

omeprazole is a substituted benzimidazole which suppresses gastric-acid secretion by means of H+, K+-ATPase inhibition. It is an optically active drug with the sulfur of the sulfoxide being the chiral center. This pro-drug can be easily converted into its respective sulfenamide at low pH. In this work, omeprazole has been studied in relation to racemization barrier and decomposition reaction. Quantum chemistry coupled to PCA chemometric method were used to find all minimum energy structures. Conformational analysis and calculation of racemization barriers were carried out by PM3 semiempirical method (Gaussian 98). The average racemization energy barrier for all minimum energy structures (43.56 kcal mol(-1)) can be related to the velocity constant in Eyring's equation. The enormous half-life time at 100 degrees C (9.04 x 10(4) years) indicates that the process cannot be observed in human time scale. on the other hand, the difference of free energy change (Delta(Delta G) = -266.78 kcal mol(-1)) for the decomposition reaction shows that the process is favorable to the sulfenamide formation. The highly negative Delta(Delta G) obtained for the decomposition reaction shows that this process is extremely exothermic. This result explains why omeprazole decomposes and does not racemize. (C) 2008 Wiley Periodicals, Inc.

An Unprecedented Neolignan Skeleton from Chimarrhis turbinata

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A partial least squares regression study with antioxidant flavonoid compounds

The quantitative structure-activity relationship of a set of 19 flavonoid compounds presenting antioxidant activity was studied by means of PLS (Partial Least Squares) regression. The optimization of the structures and calculation of electronic properties were done by using the semiempirical method AMI. A reliable model (r(2) = 0.806 and q(2) = 0.730) was obtained and from this model it was possible to consider some aspects of the structure of the flavonoid compounds studied that are related with their free radical scavenging ability. The quality of the PLS model obtained in this work indicates that it can be used in order to design new flavonoid compounds that present ability to scavenge free radicals.

Secondary protons in the atmosphere at different latitudes

We present a semiempirical method to study the production and propagation of atmospheric secondary protons with energy>100 Mev, moving in the vertical direction. The derived production functions are fitted by the least-square method for the only previously published splash (SP) and return (RE) albedos observed data using the same instrument and measurement sites. The closed agreements between the measurement data and the calculations over a wide range of atmospheric depths lead to a possible extension of the method for other latitudes. The spectra of SP and RE intensities versus the geomagnetic cut-off reveal similar behaviour as assumed earlier by the theory for those components in the Earth's magnetic field. © 1993 Società Italiana di Fisica.

Multiple minima hypersurfaces procedures for biomimetic ligands screening

In this work the interaction of the pesticide carbaryl with two groups of biomimetic ligands, peptides and MIPs was screened by multiple minima hypersurfaces (MMH) procedures, through the AM1 semiempirical method. Data related to the properties of the molecular association of the complex biomimetic ligand-pesticide were obtained and compared with another molecular modeling algorithm named Leapfrog, as included in the Sybyl software package, and experimental results from the literature, remarking good correlation between them. All important MMH program parameters (cells number, box size, conformers) were studied and optimized with the aim of getting the minimum computation time without losing the correlation with experimental data. The data demonstrated that MMH approach can be used as a fast biomimetic ligand screening tool for MIPs. In the case of peptides the computation time was not comparable with the molecular dynamics methods conventionally used for this approach. © 2011 Springer Science+Business Media B.V.

Theoretical study of molecular and electronic structures of 5(1) knot systems: two-layered ONIOM calculations

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Métodos Semi-Empíricos: princípios básicos e aplicações

Pós-graduação em Física - IGCE

Theoretical and experimental studies on the electronic, optical, and structural properties of poly-pyrrole-2-carboxylic acid films

A theoretical approach is used here to explain experimental results obtained from the electrosynthesis of polypyrrole-2-carboxylic acid (PPY-2-COOH) films in nonaqueous medium. An analysis of the Fukui function (reactivity index) indicates that the monomer (pyrrole-2-carboxylic acid, PY-2-COOH), and dimers and trimers are oxidized in the C4 or C5 positions of the heterocyclic ring of the PY-2-COOH structure. After calculating the heat of formation using semiempirical Austin Model 1 post-Hartree-Fock parameterization for dimer species, both C4 and C5 positions adjacent to the aromatic rings of PPY-2-COOH were considered the most susceptible ones to oxidative coupling reactions. The ZINDO-S/CI semiempirical method was used to simulate the electronic transitions typically seen in the UV-VIS-NIR range in monomer and oligomers with different conjugation lengths. The use of an electrochemical quartz crystal microbalance provides sufficient information to propose a polymerization mechanism of PY-2-COOH based on molecular modeling and experimental results.

Molecular interaction between perthiolated [beta]-cyclodextrin (CD) and the guests molecules adamantaneacetic acid (AD) and ferroceneacetic acid (FC); and the effect of the interaction on the electron transition of CD anchored particles

The molecular interactions between the host molecule, perthiolated beta-cyclodextrin (CD), and the guest molecules, adamantaneacetic acid (AD) and ferroceneacetic acid (FC), have been inestigated theoretically in both the gas and aqueous phases. The major computations have been carried out at the theoretical levels, RHF/6-31G and B3LYP/6- 31G. MP2 electronic energies were also computed based at the geometries optimized by both the RHF and B3LYP methods in the gas phase to establish a better estimate of the correlation effect. The solvent phase computations were completed at the RHF/6-31G and B3LYP/6-31G levels using the PCM model. The most stable structures optimized in gas phase by both the RHF and B3LYP methods were used for the computations in solution. A method to systematically manipulate the relative position and orientation between the interacting molecules is proposed. In the gas phase, six trials with different host-guest relative positions and orientations were completed successfully with the B3LYP method for both the CD-AD and CD-FC complexes. Only four trials were completed with RHF method. In the gas phase, the best results from the RHF method gives for the association Gibbs free energy (ΔG°) values equal to -32.21kj/mol for CD-AD and -25.73kj/mol for CD-FC. And the best results from the B3LYP method have ΔG° equal to -47.57kj/mol for CD-AD and -41.09kj/mol for CD-FC. The MP2 correction significantly lowers ΔG° based on the geometries from both methods. For the RHF structure, the MP2 computations lowered ΔG° to -60.64kj/mol for CD-AD and -54.10 for CD-FC. For the structure from the B3LYP method, it was reduced to -59.87 kj/mol for CD-AD and -54.84 kj/mol for CDFC. The RHF solvent phase calculations yielded following results: ΔG°(aq) equals 107.2kj/mol for CD-AD and 111.4kj/mol for CD-FC. Compared with the results from the RHF method, the B3LYP method provided clearly better solvent phase results with ΔG° (aq) equal to 38.64kj/mol for CD-AD and 39.61kj/mol for CD-FC. These results qualitatively explain the experimental observations. However quantitatively they are in poor agreement with the experimental values available in the literature and those recently published by Liu et al. And the reason is believed to be omission of hydrophobic contribution to the association. Determining the global geometrical minima for these very large systems was very difficult and computationally time consuming, but after a very thorough search, these were identified. A relevant result of this search is that when the complexes, CD-AD and CD-FC, are formed, the AD and FC molecules are only partially embedded inside the CD cavity. The totally embedded complexes were found to have significantly higher energies. The semiempirical method, ZINDO, was employed to investigate the effect of complexation on the first electronic excitation of CD anchored to a metal nano-particle. The computational results revealed that after complexation to FC, the transition intensity declines to about 25% of the original value, and after complexation with AD, the intensity drops almost 50%. The tighter binding and transition intensity of CD-AD qualitatively agrees with the experimental result that the addition of AD to a solution of CD and FC restores the fluorescence of CD that was quenched by the addition of FC. A method to evaluate the “hydrophobic force” effect is proposed for future work.

Agent-based model for the effect of curing temperature on cement hydration

The agent-based model presented here, comprises an algorithm that computes the degree of hydration, the water consumption and the layer thickness of C-S-H gel as functions of time for different temperatures and different w/c ratios. The results are in agreement with reported experimental studies, demonstrating the applicability of the model. As the available experimental results regarding elevated curing temperature are scarce, the model could be recalibrated in the future. Combining the agent-based computational model with TGA analysis, a semiempirical method is achieved to be used for better understanding the microstructure development in ordinary cement pastes and to predict the influence of temperature on the hydration process.

Efficiency of hysteresis rods in small spacecraft attitude stabilization

A semiempirical method for predicting the damping efficiency of hysteresis rods on-board small satellites is presented. It is based on the evaluation of dissipating energy variation of different ferromagnetic materials for two different rod shapes: thin film and circular cross-section rods, as a function of their elongation. Based on this formulation, an optimum design considering the size of hysteresis rods, their cross section shape, and layout has been proposed. Finally, the formulation developed was applied to the case of four existing small satellites, whose corresponding in-flight data are published. A good agreement between the estimated rotational speed decay time and the in-flight data has been observed.