Modulating the electronic structure of amino acids: interaction of model lewis acids with anthranilic acid

On the basis of theoretical B3LYP calculations, Yáñez and co-workers (J. Chem. Theory Comput. 2012, 8, 2293) illustrated that beryllium ions are capable of significantly modulating (changing) the electronic structures of imidazole. In this computational organic chemistry study, the interaction of this β-amino acid and five model Lewis acids (BeF1+, Be2+, AlF2(1+), AlF2+, and Al3+) were investigated. Several aspects were addressed: natural bond orbitals, including second order perturbation analysis of intra-molecular charge delocalization and the natural population analysis atomic charges; molecular geometries; selected infrared stretching frequencies (C-N, C-O, and N-H), and selected ¹H-NMR chemical shifts. The data illustrate that this interaction can weaken the H-O bond and goes beyond strengthening the intra-molecular hydrogen bond (N...H-O) to cause a spontaneous transfer of the proton to the nitrogen atom in five cases generating zwitterion structures. Many new features are observed. Most importantly, the zwitterion structures include a stabilizing hydrogen bond (N-H...O) that varies in relative strength according to the Lewis acid. These findings explain the experimental observations of α-amino acids (for example: J. Am. Chem. Soc. 2001, 123, 3577) and are the first reported fundamental electronic structure characterization of β-amino acids in zwitterion form.

Magnetic structure of Li2CuO2: From ab initio calculations to macroscopic simulations

The magnetic structure of the edge-sharing cuprate compound Li2CuO2 has been investigated with highly correlated ab initio electronic structure calculations. The first- and second-neighbor in-chain magnetic interactions are calculated to be 142 and -22 K, respectively. The ratio between the two parameters is smaller than suggested previously in the literature. The interchain interactions are antiferromagnetic in nature and of the order of a few K only. Monte Carlo simulations using the ab initio parameters to define the spin model Hamiltonian result in a Nel temperature in good agreement with experiment. Spin population analysis situates the magnetic moment on the copper and oxygen ions between the completely localized picture derived from experiment and the more delocalized picture based on local-density calculations.

Relativistic effects in physics and chemistry of element 105. [Part] I.

A detailed study of the electronic structure and bonding of the pentahalides of group 5 elements V, Nb, Ta, and element 105, hahnium (and Pa) has been carried out using relativistic molecular cluster Dirac-Slater discrete-variational method. A number of calculations have been performed for different geometries and molecular bond distances. The character of the bonding has been analyzed using the Mulliken population analysis of the molecular orbitals. It is shown that hahnium is a typical group 5 element. In a great number of properties it continues trends in the group. Some peculiarities in the electronic structure of HaCl_5 result from relativistic effects.

Relativistic effects in physics and chemistry of element 105. [Part] III.

Electronic structures of MOCl_3 and MOBr_3 molecules, where M = V, Nb, Ta, Pa, and element 105, hahnium, have been calculated using the relativistic Dirac-Slater discrete variational method. The character of bonding has been analyzed using the Mulliken population analysis of the molecular orbitals. It was shown that hahnium oxytrihalides have similar properties to oxytrihalides of Nb and Ta and that hahnium has the highest tendency to form double bond with oxygen. Some peculiarities in the electronic structure of HaOCl_3 and HaOBr_3 result from relativistic effects. Volatilities of the oxytrihalides in comparison with the corresponding pentahalides were considered using results of the present calculations. Higher ionic character and lower covalency as well as the presence of dipole moments in MOX_3 (X = Cl, Br) molecules compared to analogous MX_5 ones are the factors contributing to their lower volatilities.

The effects of landscape modifications on the long-term persistence of animal populations

Background: The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Methodology/Principal Findings: Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Significance: Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

PCR-based markers diagnostic for spring and winter seasonal growth habit in barley

Toward the ultimate goal of replacing field-based evaluation of seasonal growth habit, we describe the design and validation of a multiplex polymerase chain reaction assay diagnostic for allelic status at the barley (Hordeum vulgare ssp. vulgare L.) vernalization locus, VRN-H1 By assaying for the presence of all known insertion–deletion polymorphisms thought to be responsible for the difference between spring and winter alleles, this assay directly tests for the presence of functional polymorphism at VRN-H1 Four of the nine previously recognized VRN-H1 haplotypes (including both winter alleles) give unique profiles using this assay. The remaining five spring haplotypes share a single profile, indicative of function-altering deletions spanning, or adjacent to, the putative “vernalization critical” region of intron 1. When used in conjunction with a previously published PCR-based assay diagnostic for alleles at VRN-H2, it was possible to predict growth habit in all the 100 contemporary UK spring and winter lines analyzed in this study. This assay is likely to find application in instances when seasonal growth habit needs to be determined without the time and cost of phenotypic assessment and during marker-assisted selection using conventional and multicross population analysis.

Can retired galaxies mimic active galaxies? Clues from the Sloan Digital Sky Survey

The classification of galaxies as star forming or active is generally done in the ([O III]/H beta, [N II]/H alpha) plane. The Sloan Digital Sky Survey (SDSS) has revealed that, in this plane, the distribution of galaxies looks like the two wings of a seagull. Galaxies in the right wing are referred to as Seyfert/LINERs, leading to the idea that non-stellar activity in galaxies is a very common phenomenon. Here, we argue that a large fraction of the systems in the right wing could actually be galaxies which stopped forming stars. The ionization in these `retired` galaxies would be produced by hot post-asymptotic giant branch stars and white dwarfs. Our argumentation is based on a stellar population analysis of the galaxies via our STARLIGHT code and on photoionization models using the Lyman continuum radiation predicted for this population. The proportion of LINER galaxies that can be explained in such a way is, however, uncertain. We further show how observational selection effects account for the shape of the right wing. Our study suggests that nuclear activity may not be as common as thought. If retired galaxies do explain a large part of the seagull`s right wing, some of the work concerning nuclear activity in galaxies, as inferred from SDSS data, will have to be revised.

Axial ligand influence on geometries, charge distributions and electronic structures of iron tetraazamacrocycle [Fe((II))TIM(X)(Y)](2+) complexes assessed by Density Functional Theory

We employed the Density Functional Theory along with small basis sets, B3LYP/LANL2DZ, for the study of FeTIM complexes with different pairs of axial ligands (CO, H(2)O, NH(3), imidazole and CH(3)CN). These calculations did not result in relevant changes of molecular quantities as bond lengths, vibrational frequencies and electronic populations supporting any significant back-donation to the carbonyl or acetonitrile axial ligands. Moreover, a back-donation mechanism to the macrocycle cannot be used to explain the observed changes in molecular properties along these complexes with CO or CH(3)CN. This work also indicates that complexes with CO show smaller binding energies and are less stable than complexes with CH(3)CN. Further, the electronic band with the largest intensity in the visible region (or close to this region) is associated to the transition from an occupied 3d orbital on iron to an empty pi* orbital located at the macrocycle. The energy of this Metal-to-Ligand Charge Transfer (MLCT) transition shows a linear relation to the total charge of the macrocycle in these complexes as given by Mulliken or Natural Population Analysis (NPA) formalisms. Finally, the macrocycle total charge seems to be influenced by the field induced by the axial ligands. (C) 2011 Elsevier Ltd. All rights reserved.

Investigating the Nature of Noble Gas-Copper Bonds by the Quantum Theory of Atoms in Molecules

We investigated noble gas copper bonds in linear complexes represented by the NgCuX general formula in which Ng and X stand for a noble gas (neon, argon, krypton, or xenon) and a halogen (fluorine, chlorine or bromine), respectively, by coupled cluster methods and modified cc-pVQZ basis sets. The quantum theory of atoms in molecules (QTAIM) shows a linear relation between the dissociation energy or noble gas-copper bonds and the amount of electronic charge transferred mainly from the noble gas to copper during complexation. Large changes in the QTAIM quadrupole moments of copper and noble gases resulting from this bonding and a comparison between NgCuX and NgNaCl systems indicate that these noble gas-copper bonds should be better interpreted as predominantly covalent. Finally, QTAIM atomic dipoles of noble gases in NgNaCl systems agree satisfactorily with atomic dipoles given by a simple model for these NgNa van der Waals bonds.

Plantas antagonistas no manejo de Meloidogyne incognita, em solo arenoso de área de cultivo de olerícolas

The aim of this study was to evaluate the efficiency of antagonistic plants on nematode control in vegetables growing areas. The experiment was conducted in two periods in randomized complete block design in plots 1.5 x 1.4 m, corresponding to experimental units and randomly cultivated with the different plants. From each plot 100 cm(3) of soil and 10 g of tomato root were collected for estimating the initial population of the first and second experiment, respectively. Sixteen antagonistic plant seedlings of velvet bean (Stizolobium aterrimum), sunn plant (Crotalaria spectabilis) and pigeon pea (Cajanus cajan) were transferred to the plots and tomato (Solanun lycopersicum) cultivar Santa Clara was used as a control. After 116 days, two root systems and 100 cm(3) of soil were collected from each plot for a final nematode population analysis. Lettuce seedlings (Lactuca sativa) were transferred to the plots and evaluated after 28 and 42 days, respectively, for galls and eggs on the root system and fresh and dry weight of shoots,. Each treatment consisted of 6 replicates and the means were compared by LSD test (p<0.05). Meloidogyne incognita was found in the first survey. After the crop of the antagonistic plants, the M. incognita population in the root systems and the final population (soil + root) were statistically lower than in the control, which demonstrates the antagonistic effect of these plants on the nematode population. There were also a reduced number of galls on the lettuce cultivated after the antagonistic plants when compared to the control. The velvet bean and sunn plant showed an increase in dry shoot weight of the lettuce cultivated after the antagonists, respectively, in the first and second experiments.

Genetic structure of the ornamental tetra fish species Piabucus melanostomus Holmberg, 1891 (CHARACIDAE, IGUANODECTINAE) in the Brazilian Pantanal wetlands inferred by mitochondrial DNA sequences

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

Theoretical study of MgO(001) surfaces: Pure, doped with Fe, Ca, and Al, and with and without adsorbed water

Ab initio calculations of large cluster models have been performed in order to study water adsorption at the five-fold coordinated adsorption site on pure Mg(001) and MgO(001) surfaces doped with Fe, Ca, and Al. The geometric parameters of the adsorbed water molecule have been optimized preparatory to analysis of binding energies, charge transfer, preferential sites of interaction, and bonding distances. We have used Mulliken population analysis methods in order to analyze charge distributions and the direction of charge transfer. We have also investigated energy gaps, HOMO energies, and SCF orbital energies as well as the acid-base properties of our cluster model. Numerical results are compared, where possible, with experiment and interpreted in the framework of various analytical models. (C) 2001 John Wiley & Sons, Inc.

A joint theoretical and kinetic investigation on the fragmentation of (N-halo)-2-amino cycloalkanecarboxylates

A combined theoretical and experimental study to elucidate the molecular mechanism for the Grob fragmentation of different (N-halo)-2-amino cyclocarboxylates with the nitrogen atom in exocyclic position: (N-Cl)-2-amino cyclopropanecarboxylate (1), (N-Cl)-2-amino cyclobutanecarboxylate (2), (N-Cl)-2-amino cyclopentanecarboxylate (3) and (N-Cl)-2-amino cyclohexanecarboxylate (4), and the corresponding acyclic compounds, (N-Cl)-2-amino isobutyric acid (A), (N-Cl)-2-amino butyric acid (B), has been carried out. The kinetics of decomposition for these compounds and related bromine derivatives were experimentally determined by conventional and stopped-flow UV spectrophotometry. The reaction products have been analyzed by GC and spectrophotometry. Theoretical analysis is based in the localization of stationary points (reactants and transition structures) on the potential energy surface. Calculations were carried out at B3LYP/6-31+G* and MP2/6-31+G* computing methods in the gas phase, while solvent effects have been included by means the self-consistent reaction field theory, PCM continuum model, at MP2/6-31+G* and MP4/6-31+G*//MP2/6-31+G* calculation levels. Based on both experimental and theoretical results, the different Grob fragmentation processes show a global synchronicity index close to 0.9, corresponding to a nearly concerted process. At the TSs, the N-Cl bond breaking is more advanced than the C-C cleavage process. An antiperiplanar configuration of these bonds is reached at the TSs, and this geometrical arrangement is the key factor governing the decomposition. In the case of 1 and 2 the ring strain prevents this spatial disposition, leading to a larger value of the activation barrier. Natural population analysis shows that the polarization of the N-Cl and C-C bonds along the bond-breaking process can be considered the driving force for the decomposition and that a negative charge flows from the carboxylate group to the chlorine atom to assist the reaction pathway. A comparison of theoretical and experimental results shows the relevance of calculation level and the inclusion of solvent effects for determining accurate unimolecular rate coefficients for the decomposition process. © 2002 Published by Elsevier Science B.V.

Genetic conservation of Brazilian fishes - Present state and perspectives

Natural environments have been worldwide affected by the growing impact of anthropogenic actions that promote the reduction or the extinction of several vertebrate species. Aquatic ecosystems represent one of the most affected environments and many fish species and/or populations have been increasingly fragmented distributed due to habitat degradation, predatory fishing, introduction of exotic species, river sedimentation, deforestation, pollution, reduction of food resource, and construction of hydroelectric dams. Actually, more than 150 Brazilian fish species, including freshwater, estuary and coastal species, can be considered threatened. Information on the diversity, conservation biology and population analysis on threatened species or populations, with several DNA markers, can be extremely useful for the success of fish species-recovery and maintenance programs. Although DNA analysis in Neotropical fish species are just beginning, they tend to increase with the widespread attention to the use of molecular approaches to minimize problems related to the risk of extinction. The accumulation of information on biology and pattern of genetic variation of fish species, associated with ecological and demographic data, and also education and respect to the nature, constitutes a crucial task to develop efficient conservation strategies in order to preserve the genetic diversity in aquatic environments.

Caracterização dos diamantes da província kimberlítica de Juína (MT), e distritos diamantíferos de Espigão D'Oeste (RO), Cacoal (RO) e Diamantina (MG)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)