Intermediate motions as studied by solid-state separated local field NMR experiments

In this report, the application of a class of separated local field NMR experiments named dipolar chemical shift correlation (DIPSHIFT) for probing motions in the intermediate regime is discussed. Simple analytical procedures based on the Anderson-Weiss (AW) approximation are presented. In order to establish limits of validity of the AW based formulas, a comparison with spin dynamics simulations based on the solution of the stochastic Liouville-von-Neumann equation is presented. It is shown that at short evolution times (less than 30% of the rotor period), the AW based formulas are suitable for fitting the DIPSHIFT curves and extracting kinetic parameters even in the case of jumplike motions. However, full spin dynamics simulations provide a more reliable treatment and extend the frequency range of the molecular motions accessible by DIPSHIFT experiments. As an experimental test, molecular jumps of imidazol methyl sulfonate and trimethylsulfoxonium iodide, as well as the side-chain motions in the photoluminescent polymer poly[2-methoxy-5-(2(')-ethylhexyloxy)-1,4-phenylenevinylene], were characterized. Possible extensions are also discussed. (c) 2008 American Institute of Physics.

Intermediate motions and dipolar couplings as studied by Lee-Goldburg cross-polarization NMR: Hartmann-Hahn matching profiles

In this article, we evaluate the use of simple Lee-Goldburg cross-polarization (LG-CP) NMR experiments for obtaining quantitative information of molecular motion in the intermediate regime. In particular, we introduce the measurement of Hartmann-Hahn matching profiles for the assessment of heteronuclear dipolar couplings as well as dynamics as a reliable and robust alternative to the more common analysis of build-up curves. We have carried out dynamic spin dynamics simulations in order to test the method's sensitivity to intermediate motion and address its limitations concerning possible experimental imperfections. We further demonstrate the successful use of simple theoretical concepts, most prominently Anderson-Weiss (AW) theory, to analyze the data. We further propose an alternative way to estimate activation energies of molecular motions, based upon the acquisition of only two LG-CP spectra per temperature at different temperatures. As experimental tests, molecular jumps in imidazole methyl sulfonate, trimethylsulfoxonium iodide, and bisphenol A polycarbonate were investigated with the new method.

DNA alters the bilayer structure of cationic lipid diC14-amidine: A spin label study

Cationic lipids-DNA complexes (lipoplexes) have been used for delivery of nucleic acids into cells in vitro and in vivo. Despite the fact that, over the last decade, significant progress in the understanding of the cellular pathways and mechanisms involved in lipoplexes-mediated gene transfection have been achieved, a convincing relationship between the structure of lipoplexes and their in vivo and in vitro transfection activity is still missing. How does DNA affect the lipid packing and what are the consequences for transfection efficiency is the point we want to address here. We investigated the bilayer organization in cationic liposomes by electron spin resonance (ESR). Phospholipids spin labeled at the 5th and 16th carbon atoms were incorporated into the DNA/diC14-amidine complex. Our data demonstrate that electrostatic interactions involved in the formation of DNA-cationic lipid complex modify the packing of the cationic lipid membrane. DNA rigidifies the amidine fluid bilayer and fluidizes the amidine rigid bilayer just below the gel-fluid transition temperature. These effects were not observed with single nucleotides and are clearly related to the repetitive charged motif present in the DNA chain and not to a charge-charge interaction. These modifications of the initial lipid packing of the cationic lipid may reorient its cellular pathway towards different routes. A better knowledge of the cationic lipid packing before and after interaction with DNA may therefore contribute to the design of lipoplexes capable to reach specific cellular targets. (c) 2009 Elsevier B.V. All rights reserved.

Exploring new molecular species on the (1)[H, Se, F] singlet potential energy surface: Energetics, structures, IR spectra, and heats of formation

Structural, energetic, and vibrational properties of new molecular species, HSeF and HFSe, the associated transition state, and dissociation fragments are investigated using a state-of-the-art theoretical approach, CCSD(T)/CBS. HSeF is a normal covalently bonded molecule 38.98 kcal mol (1) more stable than the complex HF-Se, which shows an unusual structure with a central fluorine atom and a bond angle of 101.8 degrees.A barrier (Delta G(#)) of 49.01 kcal mol (1) separates the two species. Vibrational frequencies are also quite distinct. Heats of formation are evaluated for the diatomic fragments and HSeF. Final Delta(f)H values depend on the experimental accuracy of those of Se(g) and H(2)Se. (c) 2009 Elsevier B.V. All rights reserved.

New Molecular Species of Potential Interest to Atmospheric Chemistry: Isomers on the [H, S(2), Br] Potential Energy Surface

This work reports a state-of-the-art theoretical characterization of four new sulfur-bromine species and five transition states on the [H, S(2), Br] potential energy surface. Our highest level theoretical approach employed the method coupled cluster singles and doubles with perturbative contributions of connected triples, CCSD(T), along with the series of correlation-consistent basis sets and with extrapolation to the complete basis set (CBS) limit in the optimization of the geometrical parameters and to quantify the energetic quantities. The structural and vibrational frequencies here reported are unique and represent the most accurate investigation to date of these species. The global minimum corresponds to a skewed structure HSSBr with a disulfide bond; this is followed by a pyramidal-like structure, SSHBr, 18.85 kcal/mol above the minimum. Much higher in energy, we found another skewed structure, HSBrS (50.29 kcal/mol), with one S-Br dative-type bond, and another pyramidal-like one, HBrSS (109.80 kcal/mol), with two S-Br dative-type bonds. The interconversion of HSSBr into SSHBr can occur via a transfer of either the hydrogen or the bromine atom but involves a very high barrier of about 43 kcal/mol. These molecules are potentially a new route of coupling the sulfur and bromine chemistry in the atmosphere, and conditions of high concentration of H(2)S like in volcanic eruptions might contribute to their formation. We note that HSSBr can act as a reservoir molecule for the reaction between the radicals HSS and Br. Also, an assessment of the methods DFT/B3LYP/CBS and MP2/CBS relative to CCSD(T)/CBS provides insights on the expected performance of these methods on the characterization of polysulfides and also of more complex systems containing disulfide bridges.

Molecular markers and genetic diversity of Plasmodium vivax

Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.

Homeotropic surface anchoring and the layer-thinning transition in free-standing films

In this work, we investigate the interplay between surface anchoring and finite-size effects on the smectic-isotropic transition in free-standing smectic films. Using an extended McMillan model, we study how a homeotropic anchoring stabilizes the smectic order above the bulk transition temperature. In particular, we determine how the transition temperature depends on the surface ordering and film thickness. We identify a characteristic anchoring for which the transition temperature does not depend on the film thickness. For strong surface ordering, we found that the thickness dependence of the transition temperature can be well represented by a power-law relation. The power-law exponent exhibits a weak dependence on the range of film thicknesses, as well as on the molecular alkyl tail length. Our results reproduce the main experimental findings concerning the layer-thinning transitions in free-standing smectic films.

Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation

The antimicrobial peptide indolicidin (IND) and the mutant CP10A in hydrated micelles were studied using molecular dynamics simulations in order to observe whether the molecular dynamics and experimental data could be sufficiently correlated and a detailed description of the interaction of the antimicrobial peptides with a model of the membrane provided by a hydrated micelle system could be obtained. In agreement with the experiments, the simulations showed that the peptides are located near the surface of the micelles. Peptide insertions agree with available experimental data, showing deeper insertion of the mutant compared with the peptide IND. Major insertion into the hydrophobic core of the micelle by all tryptophan and mutated residues of CP10A in relation to IND was observed. The charged residues of the terminus regions of both peptides present similar behavior, indicating that the major differences in the interactions with the micelles of the peptides IND and CP10A occur in the case of the hydrophobic residues.

Leishmania-Specific Surface Antigens Show Sub-Genus Sequence Variation and Immune Recognition

Background: A family of hydrophilic acylated surface (HASP) proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic) and intracellular (amastigote) stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia) have lost HASP genes from their genomes. Methods/Principal Findings: We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia) species, L. (V.) braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L.) mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o) HASPs) are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family. Conclusions/Significance: These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are surface-exposed on amastigotes (although L. (L.) major parasites also express HASPB on the metacyclic plasma membrane). The central repetitive domains of the HASPs are highly variant in their amino acid sequences, both within and between species, consistent with a role in immune recognition in the host.

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

First-principles study of the adsorption of atomic and molecular hydrogen on BC(2)N nanotubes

The adsorption of atomic and molecular hydrogen on armchair and zigzag boron carbonitride nanotubes is investigated within the ab initio density functional theory. The adsorption of atomic H on the BC(2)N nanotubes presents properties which are promising for nanoelectronic applications. Depending on the adsorption site for the H, the Fermi energy moves toward the bottom of the conduction band or toward the top of the valence band, leading the system to exhibit donor or acceptor characteristics, respectively. The H(2) molecules are physisorbed on the BC(2)N surface for both chiralities. The binding energies for the H(2) molecules are slightly dependent on the adsorption site, and they are near to the range to work as a hydrogen storage medium.

Surface Plasmon-Induced Band Gap in the Photocurrent Response of Organic Solar Cells

A 260 nm layer of organic bulk heterojunction blend of the polymer poly(3-hexylthiophene) (P3HT) and the fullerene [6,6]-phenyl C(61)-butyric (PCBM) was spin-coated in between aluminum and gold electrodes, respectively, on top of a laser inscribed azo polymer surface-relief diffraction grating. Angle-dependent surface plasmons (SPs) with a large band gap were observed in the normalized photocurrent by the P3HT-PCBM layer as a function of wavelength. The SP-induced photocurrents were also investigated as a function of the grating depth and spacing.

Transition-metal 13-atom clusters assessed with solid and surface-biased functionals

First-principles density-functional theory studies have reported open structures based on the formation of double simple-cubic (DSC) arrangements for Ru(13), Rh(13), Os(13), and Ir(13), which can be considered an unexpected result as those elements crystallize in compact bulk structures such as the face-centered cubic and hexagonal close-packed lattices. In this work, we investigated with the projected augmented wave method the dependence of the lowest-energy structure on the local and semilocal exchange-correlation (xc) energy functionals employed in density-functional theory. We found that the local-density approximation (LDA) and generalized-gradient formulations with different treatment of the electronic inhomogeneities (PBE, PBEsol, and AM05) confirm the DSC configuration as the lowest-energy structure for the studied TM(13) clusters. A good agreement in the relative total energies are obtained even for structures with small energy differences, e. g., 0.10 eV. The employed xc functionals yield the same total magnetic moment for a given structure, i.e., the differences in the bond lengths do not affect the moments, which can be attributed to the atomic character of those clusters. Thus, at least for those systems, the differences among the LDA, PBE, PBEsol, and AM05 functionals are not large enough to yield qualitatively different results. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3577999]

Full-dimensional analytical ab initio potential energy surface of the ground state of HOI

Extensive ab initio calculations using a complete active space second-order perturbation theory wavefunction, including scalar and spin-orbit relativistic effects with a quadruple-zeta quality basis set were used to construct an analytical potential energy surface (PES) of the ground state of the [H, O, I] system. A total of 5344 points were fit to a three-dimensional function of the internuclear distances, with a global root-mean-square error of 1.26 kcal mol(-1). The resulting PES describes accurately the main features of this system: the HOI and HIO isomers, the transition state between them, and all dissociation asymptotes. After a small adjustment, using a scaling factor on the internal coordinates of HOI, the frequencies calculated in this work agree with the experimental data available within 10 cm(-1). (C) 2011 American Institute of Physics. [doi: 10.1063/1.3615545]

High performance gold nanorods and silver nanocubes in surface-enhanced Raman spectroscopy of pesticides

The behavior of Au nanorods and Ag nanocubes as analytical sensors was evaluated for three different classes of herbicides. The use of such anisotropic nanoparticles in surface-enhanced Raman scattering (SERS) experiments allows the one to obtain the spectrum of crystal violet dye in the single molecule regime, as well as the pesticides dichlorophenoxyacetic acid (2,4-D), trichlorfon and ametryn. Such metallic substrates show high SERS performance at low analyte concentrations making them adequate for use as analytical sensors. Density functional theory (DFT) calculations of the geometries and vibrational wavenumbers of the adsorbates in the presence of silver or gold atoms were used to elucidate the nature of adsorbate-nanostructure bonding in each case and support the enhancement patterns observed in each SERS spectrum.