A theoretical study of the characterization and the absorption spectrum of Mg: Tetracycline complexes in aqueous environment.

The complex formed by the tetracycline (TC) molecule with the Mg ion is able to prevent the replication of the genetic material in the bacterial ribosome, making an excellent antibiotic. In general, the absorption and emission spectra of TC are very sensitive to the host ions and the pH of the solvent that the set is immersed. However, the theoretical absorption spectrum available in the literature is scarce and limited to simple models that do not consider the fluctuations of the liquid. Our aim is to obtain the electronic absorption spectrum of TC and the complex Mg:TC in the ratio 1:1 and 2:1. Moreover, we analyze the changes in intensity and shifts of the bands in the systems listed. We performed the simulation using the classical Monte Carlo technique with the Lennard-Jones plus Coulomb potential applied to each atom of the both TC molecule and the Mg:TC complexes in water. The electronic absorption spectrum was obtained from the time-dependent density functional theory using different solvent models. In general, we obtained a good qualitative description of the spectra when compared with the experimental results. The Mg atom shifts the first band by 4 nm in our models, in excellent agreement to the experimental result of 4 nm. The second absorption band is found here to be useful for the characterization of the position where the ion attaches to the TC.

Reactions of atomic and molecular ions with acetone, 1,1,1- trifluoroacetone, and hexafluoroacetone: An investigation of the effects of molecular structure on the dynamics and kinetics of ion-molecule reactions

A selected ion flow tube study of the reactions of a series of gas-phase atomic cations (S⁺, Xe⁺, O⁺, Kr⁺, N⁺, Ar⁺ and Ne⁺) and molecular ions (SF _n⁺ (n = 1-5), CF_n⁺ (n = 1-3), CF₂Cl⁺, H₃O⁺, NO⁺, N ₂O⁺, CO₂⁺, CO⁺, and N₂⁺) spanning a large range of recombination energies (6.3-21.6 eV), with acetone, 1,1,1-trifluoroacetone, and hexafluoroacetone has been undertaken with the objective of exploring the nature of the reaction ion chemistry as the methyl groups in acetone are substituted for CF₃. The reaction rate coefficients and product ion branching ratios for all 66 reactions, measured at 298 K, are reported. The experimental reaction rate coefficients are compared to theoretically calculated collisional values. Several distinct reaction processes were observed among the large number of reactions studied, including charge transfer (non-dissociative and dissociative), abstraction, ion-molecule associations and, in the case of the reactions involving the reagent ion H₃O⁺, proton transfer. 

Theoretical investigation of atomic and electronic structures of Ga(2)O(3)(ZnO)(6)

Transparent conducting oxides (TCO) are widely used in technological applications ranging from photovoltaics to thin-film transparent field-effect transistors. In this work we report a first-principles investigation, based on density-functional theory, of the atomic and electronic properties of Ga(2)O(3)(ZnO)(6) (GZO(6)), which is a promising candidate to be used as host oxide for wide band gap TCO applications. We identify a low-energy configuration for the coherent distribution of the Ga and Zn atoms in the cation positions within the experimentally reported orthorhombic GZO(6) structure. Four Ga atoms are located in four-fold sites, while the remaining 12 Ga atoms in the unit cell form four shared Ga agglomerates (a motif of four atoms). The Zn atoms are distributed in the remaining cation sites with effective coordination numbers from 3.90 to 4.50. Furthermore, we identify the natural formation of twin-boundaries in GZO(6), which can explain the zigzag modulations observed experimentally by high-resolution transmission electron microscopy in GZO(n) (n=9). Due to the intrinsic twin-boundary formation, polarity inversion in the ZnO tetrahedrons is present which is facilitated by the formation of the Ga agglomerates. Our analysis shows that the formation of fourfold Ga sites and Ga agglomerates are stabilized by the electronic octet rule, while the distribution of Ga atoms and the formation of the twin-boundary help alleviate excess strain. Finally we identify that the electronic properties of GZO(6) are essentially determined by the electronic properties of ZnO, i.e., there are slight changes in the band gap and optical absorption properties.

Local and average structure in zinc cyanide: towards an understanding of the atomistic origin of negative thermal expansion

Neutron diffraction at 11.4 and 295 K and solid-state 67Zn NMR are used to determine both the local and average structures in the disordered, negative thermal expansion (NTE) material, Zn(CN)2. Solid-state NMR not only confirms that there is head-to-tail disorder of the C≡N groups present in the solid, but yields information about the relative abundances of the different Zn(CN)4-n(NC)n tetrahedral species, which do not follow a simple binomial distribution. The Zn(CN)4 and Zn(NC)4 species occur with much lower probabilities than are predicted by binomial theory, supporting the conclusion that they are of higher energy than the other local arrangements. The lowest energy arrangement is Zn(CN)2(NC)2. The use of total neutron diffraction at 11.4 K, with analysis of both the Bragg diffraction and the derived total correlation function, yields the first experimental determination of the individual Zn−N and Zn−C bond lengths as 1.969(2) and 2.030(2) Å, respectively. The very small difference in bond lengths, of ~0.06 Å, means that it is impossible to obtain these bond lengths using Bragg diffraction in isolation. Total neutron diffraction also provides information on both the average and local atomic displacements responsible for NTE in Zn(CN)2. The principal motions giving rise to NTE are shown to be those in which the carbon and nitrogen atoms within individual Zn−C≡N−Zn linkages are displaced to the same side of the Zn···Zn axis. Displacements of the carbon and nitrogen atoms to opposite sides of the Zn···Zn axis, suggested previously in X-ray studies as being responsible for NTE behavior, in fact make negligible contribution at temperatures up to 295 K.

Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new PNP inhibitors. © 2005 Elsevier Inc. All rights reserved.

Genetic diversity and population structure of the New World screwworm fly from the Amazon region of Brazil

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

Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Local order and electronic structure of Pb1-xLaxZr0.40Ti0.60O3 materials and its relation with ferroelectric properties

The knowledge of electronic and local structures is a fundamental step towards understanding the properties of ferroelectric ceramics. X-ray absorption near-edge structure (XANES) of Pb1-xLaxZr0.40Ti0.60O3 ferroelectric samples was measured in order to know how the local order and electronic structure are related to their ferroelectric property, which was tailored by the substitution of lead by lanthanum atoms. The analysis of XANES spectra collected at Ti K- and L-edges XANES showed that the substitution of Pb by La leads to a decrement of local distortion around Ti atoms on the TiO6 octahedron. The analysis of O K-edge XANES spectra showed that the hybridization between O 2p and Pb 6sp states is related to the displacement of Ti atoms in the TiO6 octahedra. Based on these results, it is possible to determine that the degree of ferroelectricity in these samples and the manifestation of relaxor behavior are directly related to the weakening of O 2p and Pb 6sp hybridization. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4720472]

Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

Dynamical Casimir effect and the structure of vacuum in quantum field theory

Some of the most interesting phenomena that arise from the developments of the modern physics are surely vacuum fluctuations. They appear in different branches of physics, such as Quantum Field Theory, Cosmology, Condensed Matter Physics, Atomic and Molecular Physics, and also in Mathematical Physics. One of the most important of these vacuum fluctuations, sometimes called "zero-point energy", as well as one of the easiest quantum effect to detect, is the so-called Casimir effect. The purposes of this thesis are: - To propose a simple retarded approach for dynamical Casimir effect, thus a description of this vacuum effect when we have moving boundaries. - To describe the behaviour of the force acting on a boundary, due to its self-interaction with the vacuum.

From eventual to atomic and locally atomic CC programs: A concurrent semantics

We present a concurrent semantics (i.e. a semantics where concurrency is explicitely represented) for CC programs with atomic tells. This allows to derive concurrency, dependency, and nondeterminism information for such languages. The ability to treat failure information puts CLP programs also in the range of applicability of our semantics: although such programs are not concurrent, the concurrency information derived in the semantics may be interpreted as possible parallelism, thus allowing to safely parallelize those computation steps which appear to be concurrent in the net. Dually, the dependency information may also be interpreted as necessary sequentialization, thus possibly exploiting it to schedule CC programs. The fact that the semantical structure contains dependency information suggests a new tell operation, which checks for consistency only the constraints it depends on, achieving a reasonable trade-off between efficiency and atomicity.

X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.

Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-ray structure of porcine fIXa described here shows the atomic origins of the disease, while the spatial distribution of mutation sites suggests a structural model for factor X activation by phospholipid-bound fIXa and cofactor VIIIa. The 3.0-A-resolution diffraction data clearly show the structures of the serine proteinase module and the two preceding epidermal growth factor (EGF)-like modules; the N-terminal Gla module is partially disordered. The catalytic module, with covalent inhibitor D-Phe-1I-Pro-2I-Arg-3I chloromethyl ketone, most closely resembles fXa but differs significantly at several positions. Particularly noteworthy is the strained conformation of Glu-388, a residue strictly conserved in known fIXa sequences but conserved as Gly among other trypsin-like serine proteinases. Flexibility apparent in electron density together with modeling studies suggests that this may cause incomplete active site formation, even after zymogen, and hence the low catalytic activity of fIXa. The principal axes of the oblong EGF-like domains define an angle of 110 degrees, stabilized by a strictly conserved and fIX-specific interdomain salt bridge. The disorder of the Gla module, whose hydrophobic helix is apparent in electron density, can be attributed to the absence of calcium in the crystals; we have modeled the Gla module in its calcium form by using prothrombin fragment 1. The arched module arrangement agrees with fluorescence energy transfer experiments. Most hemophilic mutation sites of surface fIX residues occur on the concave surface of the bent molecule and suggest a plausible model for the membrane-bound ternary fIXa-FVIIIa-fX complex structure: fIXa and an equivalently arranged fX arch across an underlying fVIIIa subdomain from opposite sides; the stabilizing fVIIIa interactions force the catalytic modules together, completing fIXa active site formation and catalytic enhancement.

Molecular dynamics simulation of organic-inorganic nanocomposites: Layering behavior and interlayer structure of organoclays

Isothermal-isobaric (NPT) molecular dynamics simulation has been performed to investigate the layering behavior and structure of nanoconfined quaternary alkylammoniums in organoclays. This work is focused on systems consisting of two clay layers and a number of alkylammoniums, and involves the use of modified Dreiding force field. The simulated basal spacings of organoclays agree satisfactorily with the experimental results in the literature. The atomic density profiles in the direction normal to the clay surface indicate that the alkyl chains within the interlayer space of montmorillonite exhibit an obvious layering behavior. The headgroups of long alkyl chains are distributed within two layers close to the clay surface, whereas the distributions of methyl and methylene groups are strongly dependent on the alkyl chain length and clay layer charge. Monolayer, bilayer, and pseudo-trilayer structures are found in organoclays modified with single long alkyl chains, which are identical to the structural models based on the measured basal spacings. A pseudo-quadrilayer structure, for the first time to our knowledge, is also identified in organoclays with double long alkyl chains. In the mixture structure of paraffin-type and multilayer, alkyl chains do not lie flat within a single layer but interlace, and also jump to the next layer in pseudo-trilayer as well as next nearest layer in pseudo-quadrilayer.