A study of neolignan compounds with biological activity against Paracoccidioides brasiliensis by using quantum chemical and chemometric methods

Métodos quimiométricos (estatísticos) são empregados para classificar um conjunto de compostos derivados de neolignanas com atividade biológica contra a Paracoccidioides brasiliensis. O método AM1 (Austin Model 1) foi utilizado para calcular um conjunto de descritores moleculares (propriedades) para os compostos em estudo. A seguir, os descritores foram analisados utilizando os seguintes métodos de reconhecimento de padrões: Análise de Componentes Principais (PCA), Análise Hierárquica de Agrupamentos (HCA) e o método de K-vizinhos mais próximos (KNN). Os métodos PCA e HCA mostraram-se bastante eficientes para classificação dos compostos estudados em dois grupos (ativos e inativos). Três descritores moleculares foram responsáveis pela separação entre os compostos ativos e inativos: energia do orbital molecular mais alto ocupado (EHOMO), ordem de ligação entre os átomos C1'-R7 (L14) e ordem de ligação entre os átomos C5'-R6 (L22). Como as variáveis responsáveis pela separação entre compostos ativos e inativos são descritores eletrônicos, conclui-se que efeitos eletrônicos podem desempenhar um importante papel na interação entre receptor biológico e compostos derivados de neolignanas com atividade contra a Paracoccidioides brasiliensis.

Raman spectroscopy and DFT calculations of para-coumaric acid and its deprotonated species

An electronic and vibrational spectroscopic analysis of p-coumaric acid (HCou) and its deprotonated species was performed by UV-vis and Raman, respectively, and the results were supported by density functional theory (OFT) calculations. Electronic UV-vis spectral data of HCou solutions show that the deprotonation of the carboxyl group (Cou(-)) leads to a blue shift of the lowest energy electronic transition in comparison to the neutral species, whereas the subsequent deprotonation of the phenolic moiety (Cou(2-)) carries out to a more delocalized chromophore. The DFT geometric parameters calculations suggest that the variation in the electronic delocalization for the three organic species is due to different contribution of a quinoid structure that is significantly distorted in the case of Cou(2-). The Raman data of HCou and its sodium salts show that the main spectral features that allow to differentiate the three organic species are those involving the styrene nu(C=C)(sty) vibration at 1600cm(-1) region. Even though the Raman spectra of the sodium salts of Cou(-) and Cou(2-) anions show subtle differences, the appearing of a band at ca. 1598cm(-1) in the Na(2)Cou spectrum, assigned to a mode involving the carboxylate asymmetric stretching, nu(as)(COO), and the styrene stretching, nu(C=C)(sty), is quite characteristic, as confirmed by the theoretical Raman spectrum. Considering that p-coumaric acid is an archetypical phenolic compound with several biological activities that essentially depend upon the medium pH, Raman spectroscopy results reported in this work can provide a proper way to characterize such important phytochemical compound in different protonation states. In order to complement the characterization of the sodium salts, X-ray diffraction (XRD) and thermal analysis were performed. (C) 2011 Elsevier B.V. All rights reserved.

Thermodynamic behavior of the binaries 1-butilpryridinium tetrafluoroborate with water and alkanols: their interpretation using 1H-NMR spectroscopy and quantum-chemistry calculations

[EN]Here we present experimental data of different properties for a set of binary mixtures composed of water or alkanols (methanol to butanol) with an ionic liquid (IL), butylpyridinium tetrafluoroborate [bpy][BF4]. Solubility data (xIL,T) are presented for each of the mixtures, including water, which is found to have a small interval of compositions in IL, xIL, with immiscibility. In each case, the upper critical solubility temperature (UCST) is determined and a correlation was observed between the UCST and the nature of the compounds in the mixtures. Miscibility curves establish the composition and temperature intervals where thermodynamic properties of the mixtures, such as enthalpies Hm E and volumes Vm E, can be determined.

Large-scale coupled-cluster calculations

Coupled-cluster theory provides one of the most successful concepts in electronic-structure theory. This work covers the parallelization of coupled-cluster energies, gradients, and second derivatives and its application to selected large-scale chemical problems, beside the more practical aspects such as the publication and support of the quantum-chemistry package ACES II MAB and the design and development of a computational environment optimized for coupled-cluster calculations. The main objective of this thesis was to extend the range of applicability of coupled-cluster models to larger molecular systems and their properties and therefore to bring large-scale coupled-cluster calculations into day-to-day routine of computational chemistry. A straightforward strategy for the parallelization of CCSD and CCSD(T) energies, gradients, and second derivatives has been outlined and implemented for closed-shell and open-shell references. Starting from the highly efficient serial implementation of the ACES II MAB computer code an adaptation for affordable workstation clusters has been obtained by parallelizing the most time-consuming steps of the algorithms. Benchmark calculations for systems with up to 1300 basis functions and the presented applications show that the resulting algorithm for energies, gradients and second derivatives at the CCSD and CCSD(T) level of theory exhibits good scaling with the number of processors and substantially extends the range of applicability. Within the framework of the ’High accuracy Extrapolated Ab initio Thermochemistry’ (HEAT) protocols effects of increased basis-set size and higher excitations in the coupled- cluster expansion were investigated. The HEAT scheme was generalized for molecules containing second-row atoms in the case of vinyl chloride. This allowed the different experimental reported values to be discriminated. In the case of the benzene molecule it was shown that even for molecules of this size chemical accuracy can be achieved. Near-quantitative agreement with experiment (about 2 ppm deviation) for the prediction of fluorine-19 nuclear magnetic shielding constants can be achieved by employing the CCSD(T) model together with large basis sets at accurate equilibrium geometries if vibrational averaging and temperature corrections via second-order vibrational perturbation theory are considered. Applying a very similar level of theory for the calculation of the carbon-13 NMR chemical shifts of benzene resulted in quantitative agreement with experimental gas-phase data. The NMR chemical shift study for the bridgehead 1-adamantyl cation at the CCSD(T) level resolved earlier discrepancies of lower-level theoretical treatment. The equilibrium structure of diacetylene has been determined based on the combination of experimental rotational constants of thirteen isotopic species and zero-point vibrational corrections calculated at various quantum-chemical levels. These empirical equilibrium structures agree to within 0.1 pm irrespective of the theoretical level employed. High-level quantum-chemical calculations on the hyperfine structure parameters of the cyanopolyynes were found to be in excellent agreement with experiment. Finally, the theoretically most accurate determination of the molecular equilibrium structure of ferrocene to date is presented.

Quantum chemical investigation on iodine oxides and their role in the formation of atmospheric aerosols

En esta contribución se presenta un estudio teórico de diferentes reacciones químicas entre óxidos de iodo y agua que pueden contribuir a la formación de partículas en la atmósfera. Mediante el uso de cálculos quimicocuánticos ab initio con tratamiento de la correlación electrónica se han obtenido propiedades termodinámicas para caracterizar esas reacciones

On the absorbance changes in the photocycle of the photoactive yellow protein: A quantum-chemical analysis

Spectral changes in the photocycle of the photoactive yellow protein (PYP) are investigated by using ab initio multiconfigurational second-order perturbation theory at the available structures experimentally determined. Using the dark ground-state crystal structure [Genick, U. K., Soltis, S. M., Kuhn, P., Canestrelli, I. L. & Getzoff, E. D. (1998) Nature (London) 392, 206–209], the ππ* transition to the lowest excited state is related to the typical blue-light absorption observed at 446 nm. The different nature of the second excited state (nπ*) is consistent with the alternative route detected at 395-nm excitation. The results suggest the low-temperature photoproduct PYPHL as the most plausible candidate for the assignment of the cryogenically trapped early intermediate (Genick et al.). We cannot establish, however, a successful correspondence between the theoretical spectrum for the nanosecond time-resolved x-ray structure [Perman, B., Šrajer, V., Ren, Z., Teng, T., Pradervand, C., et al. (1998) Science 279, 1946–1950] and any of the spectroscopic photoproducts known up to date. It is fully confirmed that the colorless light-activated intermediate recorded by millisecond time-resolved crystallography [Genick, U. K., Borgstahl, G. E. O., Ng, K., Ren, Z., Pradervand, C., et al. (1997) Science 275, 1471–1475] is protonated, nicely matching the spectroscopic features of the photoproduct PYPM. The overall contribution demonstrates that a combined analysis of high-level theoretical results and experimental data can be of great value to perform assignments of detected intermediates in a photocycle.

Emergence of half-metallicity in suspended NiO chains: Ab initio electronic structure and quantum transport calculations

Contrary to the antiferromagnetic and insulating character of bulk NiO, one-dimensional chains of this material can become half metallic due to the lower coordination of their atoms. Here we present ab initio electronic structure and quantum transport calculations of ideal infinitely long NiO chains and of more realistic short ones suspended between Ni electrodes. While infinite chains are insulating, short suspended chains are half-metallic minority-spin conductors that displays very large magnetoresistance and a spin-valve behavior controlled by a single atom.

Physico-chemical calculations,

Mode of access: Internet.

Chemical calculations,

"Fourth edition, May 1929."

The physical and chemical properties of eumelanin

In this article, we review the current state of knowledge concerning the physical and chemical properties of the eumelanin pigment. We examine properties related to its photoprotective functionality, and draw the crucial link between fundamental molecular structure and observable macroscopic behaviour. Where necessary, we also briefly review certain aspects of the pheomelanin literature to draw relevant comparison. A full understanding of melanin function, and indeed its role in retarding or promoting the disease state, can only be obtained through a full mapping of key structure-property relationships in the main pigment types. We are engaged in such an endeavor for the case of eumelanin.

Quantum yield calculations for strongly absorbing chromophores

This article demonstrates that a commonly-made assumption in quantum yield calculations may produce errors of up to 25% in extreme cases and can be corrected by a simple modification to the analysis.

Chlorine contribution to quantitative structure and activity relationship models of disinfection by -products' quantum chemical descriptors and toxicities

Quantitative Structure-Activity Relationship (QSAR) has been applied extensively in predicting toxicity of Disinfection By-Products (DBPs) in drinking water. Among many toxicological properties, acute and chronic toxicities of DBPs have been widely used in health risk assessment of DBPs. These toxicities are correlated with molecular properties, which are usually correlated with molecular descriptors. The primary goals of this thesis are: (1) to investigate the effects of molecular descriptors (e.g., chlorine number) on molecular properties such as energy of the lowest unoccupied molecular orbital (E LUMO) via QSAR modelling and analysis; (2) to validate the models by using internal and external cross-validation techniques; (3) to quantify the model uncertainties through Taylor and Monte Carlo Simulation. One of the very important ways to predict molecular properties such as ELUMO is using QSAR analysis. In this study, number of chlorine (NCl ) and number of carbon (NC) as well as energy of the highest occupied molecular orbital (EHOMO) are used as molecular descriptors. There are typically three approaches used in QSAR model development: (1) Linear or Multi-linear Regression (MLR); (2) Partial Least Squares (PLS); and (3) Principle Component Regression (PCR). In QSAR analysis, a very critical step is model validation after QSAR models are established and before applying them to toxicity prediction. The DBPs to be studied include five chemical classes: chlorinated alkanes, alkenes, and aromatics. In addition, validated QSARs are developed to describe the toxicity of selected groups (i.e., chloro-alkane and aromatic compounds with a nitro- or cyano group) of DBP chemicals to three types of organisms (e.g., Fish, T. pyriformis, and P.pyosphoreum) based on experimental toxicity data from the literature. The results show that: (1) QSAR models to predict molecular property built by MLR, PLS or PCR can be used either to select valid data points or to eliminate outliers; (2) The Leave-One-Out Cross-Validation procedure by itself is not enough to give a reliable representation of the predictive ability of the QSAR models, however, Leave-Many-Out/K-fold cross-validation and external validation can be applied together to achieve more reliable results; (3) E LUMO are shown to correlate highly with the NCl for several classes of DBPs; and (4) According to uncertainty analysis using Taylor method, the uncertainty of QSAR models is contributed mostly from NCl for all DBP classes.

Chlorine Contribution to Quantitative Structure and Activity Relationship Models of Disinfection By-Products' Quantum Chemical Descriptors and Toxicities

Quantitative Structure-Activity Relationship (QSAR) has been applied extensively in predicting toxicity of Disinfection By-Products (DBPs) in drinking water. Among many toxicological properties, acute and chronic toxicities of DBPs have been widely used in health risk assessment of DBPs. These toxicities are correlated with molecular properties, which are usually correlated with molecular descriptors. The primary goals of this thesis are: 1) to investigate the effects of molecular descriptors (e.g., chlorine number) on molecular properties such as energy of the lowest unoccupied molecular orbital (ELUMO) via QSAR modelling and analysis; 2) to validate the models by using internal and external cross-validation techniques; 3) to quantify the model uncertainties through Taylor and Monte Carlo Simulation. One of the very important ways to predict molecular properties such as ELUMO is using QSAR analysis. In this study, number of chlorine (NCl) and number of carbon (NC) as well as energy of the highest occupied molecular orbital (EHOMO) are used as molecular descriptors. There are typically three approaches used in QSAR model development: 1) Linear or Multi-linear Regression (MLR); 2) Partial Least Squares (PLS); and 3) Principle Component Regression (PCR). In QSAR analysis, a very critical step is model validation after QSAR models are established and before applying them to toxicity prediction. The DBPs to be studied include five chemical classes: chlorinated alkanes, alkenes, and aromatics. In addition, validated QSARs are developed to describe the toxicity of selected groups (i.e., chloro-alkane and aromatic compounds with a nitro- or cyano group) of DBP chemicals to three types of organisms (e.g., Fish, T. pyriformis, and P.pyosphoreum) based on experimental toxicity data from the literature. The results show that: 1) QSAR models to predict molecular property built by MLR, PLS or PCR can be used either to select valid data points or to eliminate outliers; 2) The Leave-One-Out Cross-Validation procedure by itself is not enough to give a reliable representation of the predictive ability of the QSAR models, however, Leave-Many-Out/K-fold cross-validation and external validation can be applied together to achieve more reliable results; 3) ELUMO are shown to correlate highly with the NCl for several classes of DBPs; and 4) According to uncertainty analysis using Taylor method, the uncertainty of QSAR models is contributed mostly from NCl for all DBP classes.

Probing the interactions between ionic liquids and water: experimental and quantum chemical approach

For an adequate choice or design of ionic liquids, the knowledge of their interaction with other solutes and solvents is an essential feature for predicting the reactivity and selectivity of systems involving these compounds. In this work, the activity coefficient of water in several imidazolium-based ionic liquids with the common cation 1-butyl-3-methylimidazolium was measured at 298.2 K. To contribute to a deeper insight into the interaction between ionic liquids and water, COSMO-RS was used to predict the activity coefficient of water in the studied ionic liquids along with the excess enthalpies. The results showed good agreement between experimental and predicted activity coefficient of water in ionic liquids and that the interaction of water and ionic liquids was strongly influenced by the hydrogen bonding of the anion with water. Accordingly, the intensity of interaction of the anions with water can be ranked as the following: [CF3SO3](-) < [SCN](-) < [TFA](-) < Br(-) < [TOS](-) < Cl(-) < [CH3SO3](-) [DMP](-) < [Ac](-). In addition, fluorination and aromatization of anions are shown to reduce their interaction with water. The effect of temperature on the activity coefficient of water at infinite dilution was measured by inverse gas chromatography and predicted by COSMO-RS. Further analysis based on COSMO-RS provided information on the nature of hydrogen bonding between water and anion as well as the possibility of anion-water complex formation.

Ultraviolet Photodissociation of the N-Methylpyridinium Ion: Action Spectroscopy and Product Characterization

The ultraviolet photodissociation of gas-phase N-methylpyridinium ions is studied at room temperature using laser photodissociation mass spectrometry and structurally diagnostic ion-molecule reaction kinetics. The C5H5N-CH3+ (m/z 94), C5H5N-CD3+ (m/z 97), and C5D5N-CH3+(m/z 99) isotopologues are investigated, and it is shown that the N-methylpyridinium ion photodissociates by the loss of methane in the 36 000 - 43 000 cm(-1) (280 - 230 nm) region. The dissociation likely occurs on the ground state surface following internal conversion from the SI state. For each isotopologue, by monitoring the photofragmentation yield as a function of photon wavenumber, a broad vibronically featured band is recorded with origin (0-0) transitions assigned at 38 130, 38 140 and 38 320 cm(-1) for C5H5N-CH3+ C5H5N-CD3+ and C5D5N-CH3+, respectively. With the aid of quantum chemical calculations (CASSCF(6,6)/aug-cc-pVDZ), most of the observed vibronic detail is assigned to two in-plane ring deformation modes. Finally, using ion-molecule reactions, the methane coproduct at m/z 78 is confirmed as a 2-pyridinylium ion.