Complex formation in solutions of oppositely charged polyelectrolytes at different polyion compositions and salt content

The formation of complexes in solutions containing positively charged polyions (polycations) and a variable amount of negatively charged polyions (polyanions) has been investigated by Monte Carlo simulations. The polyions were described as flexible chains of charged hard spheres interacting through a screened Coulomb potential. The systems were analyzed in terms of cluster compositions, structure factors, and radial distribution functions. At 50% charge equivalence or less, complexes involving two polycations and one polyanion were frequent, while closer to charge equivalence, larger clusters were formed. Small and neutral complexes dominated the solution at charge equivalence in a monodisperse system, while larger clusters again dominated the solution when the polyions were made polydisperse. The cluster composition and solution structure were also examined as functions of added salt by varying the electrostatic screening length. The observed formation of clusters could be rationalized by a few simple rules.

Displacement of methane by coadsorbed carbon dioxide is facilitated in narrow carbon nanopores

By using simulation methods, we studied the adsorption of binary CO2-CH4 mixtures on various CH4 preadsorbed carbonaceous materials (e.g., triply periodic carbon minimal surfaces, slit-shaped carbon micropores, and Harris's virtual porous carbons) at 293 K. Regardless of the different micropore geometry, two-stage mechanism of CH4 displacement from carbon nanospaces by coadsorbed CO2 has been proposed. In the first stage, the coadsorbed CO2 molecules induced the enhancement of CH4 adsorbed amount. In the second stage, the stronger affinity of CO2 to flat/curved graphitic surfaces as well as CO2-CO2 interactions cause the displacement of CH4 molecules from carbonaceous materials. The operating conditions of CO2-induced cleaning of the adsorbed phase from CH4 mixture component strongly depend on the size of the carbon micropores, but, in general, the enhanced adsorption field in narrow carbon ultramicropores facilitates the nonreactive displacement of CH4 by coadsorbed CO2. This is because in narrow carbon ultramicropores the equilibrium CO2/CH4 selectivity (i.e., preferential adsorption toward CO2) increased significantly. The adsorption field in wider micropores (i.e., the overall surface energy) for both CO2 and CH4 is very similar, which decreases the preferential CO2 adsorption. This suppresses the displacement of CH4 by coadsorbed CO2 and assists further adsorption of CH4 from the bulk mixture (i.e., CO2/CH4 mixing in adsorbed phase).

Time-resolved gas-phase kinetic, quantum chemical, and RRKM studies of reactions of silylene with alcohols

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of 1-silacyclopent-3-ene and phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with methanol, ethanol, 1-propanol, 1-butanol and 2-methyl-1-butanol. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at room temperature. In the study with methanol several buffer gases were used. All five reactions showed pressure dependences characteristic of third body assisted association reactions. The rate constant pressure dependences were modelled using RRKM theory, based on Eo values of the association complexes obtained by ab initio calculation (G3 level). Transition state models were adjusted to fit experimental fall-off curves and extrapolated to obtain k∞ values in the range 1.9 to 4.5 × 10-10 cm3 molecule-1 s-1. These numbers, corresponding to the true bimolecular rate constants, indicate efficiencies of between 16 and 67% of the collision rates for these reactions. In the reaction of SiH2 + MeOH there is a small kinetic component to the rate which is second order in MeOH (at low total pressures). This suggests an additional catalysed reaction pathway, which is supported by the ab initio calculations. These calculations have been used to define specific MeOH-for-H2O substitution effects on this catalytic pathway. Where possible our experimental and theoretical results are compared with those of previous studies.

Hydrogen bonding in the gas-phase: the molecular structures of 2‑hydroxybenzamide (C7H7NO2) and 2‑methoxybenzamide (C8H9NO2), obtained by gas-phase electron diffraction and theoretical calculations

The structures of 2-hydroxybenzamide(C7H7NO2) and 2-methoxybenzamide (C8H9NO2) have been determined in the gas-phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d,p)) predict four stable conformers for both 2-hydroxybenzamide and 2-methoxybenzamide. For both compounds, evidence for intramolecular hydrogen bonding is presented. In 2-hydroxybenzamide, the observed hydrogen bonded fragment is between the hydroxyl and carbonyl groups, while in 2-methoxybenzamide, the hydrogen bonded fragment is between one of the hydrogen atoms of the amide group and the methoxy oxygen atom.

Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

Background: Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe- set, consisting of up to 16 probe-pairs. Signal intensities across probe- pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology. Results: Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice. Conclusion: This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.

Determination of orientations of aromatic groups in self-assembled peptide fibrils by polarised Raman spectroscopy

In this paper we describe a novel combination of Raman spectroscopy, isotope editing and X-ray scattering as a powerful approach to give detailed structural information on aromatic side chains in peptide fibrils. The orientation of the tyrosine residues in fibrils of the peptide YTIAALLSPYS with respect to the fibril axis has been determined from a combination of polarised Raman spectroscopy and X-ray diffraction measurements. The Raman intensity of selected tyrosine bands collected at different polarisation geometries is related to the values and orientation of the Raman tensor for those specific vibrations. Using published Raman tensor values we solved the relevant expressions for both of the two tyrosine residues present in this peptide. Ring deuteration in one of the two tyrosine side chains allowed for the calculation to be performed individually for both, by virtue of the isotopic shift that eliminates band overlapping. Sample disorder was taken into account by obtaining the distribution of orientations of the samples from X-ray diffraction experiments. The results provide previously unavailable details about the molecular conformation of this peptide, and demonstrate the value of this approach for the study of amyloid fibrils.

Redox behavior of the model catalyst Pd/CeO2-x/Pt(111)

Photoelectron spectroscopy and scanning tunneling microscopy have been used to investigate how the oxidation state of Ce in CeO2-x(111) ultrathin films is influenced by the presence of Pd nanoparticles. Pd induces an increase in the concentration of Ce3+ cations, which is interpreted as charge transfer from Pd to CeO2-x(111) on the basis of DFT+U calculations. Charge transfer from Pd to Ce4+ is found to be energetically favorable even for individual Pd adatoms. These results have implications for our understanding of the redox behavior of ceria-based model catalyst systems.

Scanning tunneling microscopy and molecular dynamics study of the Li2TiO3(001) surface

We have investigated the (001) surface structure of lithium titanate (Li2TiO3) using auger electron spectroscopy (AES), low-energy electron diffraction (LEED), and scanning tunneling microscopy (STM). Li2TiO3 is a potential fusion reactor blanket material. After annealing at 1200 K, LEED demonstrated that the Li2TiO3(001) surface was well ordered and not reconstructed. STM imaging showed that terraces are separated in height by about 0.3 nm suggesting a single termination layer. Moreover, hexagonal patterns with a periodicity of ∼0.4 nm are observed. On the basis of molecular dynamics (MD) simulations, these are interpreted as a dynamic arrangement of Li atoms.

A theoretical investigation of a-Fe2O3–Cr2O3 solid solutions

We have examined the thermodynamic stability of a-Fe2O3–Cr2O3 solid solutions as a function of temperature and composition, using a combination of statistical mechanics with atomistic simulation techniques based on classical interatomic potentials, and the addition of a model magnetic interaction Hamiltonian. Our calculations show that the segregation of the Fe and Cr cations is marginally favourable in energy compared to any other cation distribution, and in fact the energy of any cation configuration of the mixed system is always slightly higher than the combined energies of equivalent amounts of the pure oxides separately. However, the positive enthalpy of mixing is small enough to allow the stabilisation of highly disordered solid solutions at temperatures of B400 K or higher. We have investigated the degree of cation disorder and the effective cell parameters of the mixed oxide as functions of temperature and composition, and we discuss the effect of magnetic interactions and lattice vibrations on the stability of the solid solution.

Electronic charge transfer between ceria surfaces and gold adatoms: a GGA+U investigation

We use density functional theory calculations with Hubbard corrections (DFT+U) to investigate electronic aspects of the interaction between ceria surfaces and gold atoms. Our results show that Au adatoms at the (111) surface of ceria can adopt Au0, Au+ or Au� electronic configurations depending on the adsorption site. The strongest adsorption sites are on top of the surface oxygen and in a bridge position between two surface oxygen atoms, and in both cases charge transfer from the gold atom to one of the Ce cations at the surface is involved. Adsorption at other sites, including the hollow sites of the surface, and an O–Ce bridging site, is weaker and does not involve charge transfer. Adsorption at an oxygen vacancy site is very strong and involves the formation of an Au� anion. We argue that the ability of gold atoms to stabilise oxygen vacancies at the ceria surface by moving into the vacancy site and attracting the excess electrons of the defect could be responsible for the enhanced reducibility of ceria surfaces in the presence of gold. Finally, we rationalise the differences in charge transfer behaviour from site to site in terms of the electrostatic potential at the surface and the coordination of the species.

Structure and stress of Re(11%21); chiral terraces at a racemic surface

The surface structure and morphology of the clean Re(11%21) surface has been investigated through combined low energy electron diffraction intensity analysis of data taken at multiple angles of incidence, scanning tunneling microscopy, and first-principles density functional calculations. The results show how this globally racemic surface terminates in two chirally distinct terraces, which show largescale out-of-plane atomic relaxations and in-plane lateral movement of the uppermost atoms. We further identify and discuss the initial stages of step bunching upon adsorption of oxygen that leads ultimately to the large-scale faceting of the surface. Finally, we present calculations of surface stress and the response to applied surface strain, which suggest routes to the exertion of control over the expression of chirality at the surface.

Dinitrogen release from arylpentazole: A picosecond time-resolved infrared, spectroelectrochemical, and DFT computational study

p-(Dimethylamino)phenyl pentazole, DMAP-N5 (DMAP = Me2N−C6H4), was characterized by picosecond transient infrared spectroscopy and infrared spectroelectrochemistry. Femtosecond laser excitation at 310 or 330 nm produces the DMAP-N5 (S1) excited state, part of which returns to the ground state (τ = 82 ± 4 ps), while DMAP-N and DMAP-N3 (S0) are generated as double and single N2-loss photoproducts with η ≈ 0.14. The lifetime of DMAP-N5 (S1) is temperature and solvent dependent. [DMAP-N3]+ is produced from DMAP-N5 in a quasireversible, one-electron oxidation process (E1/2 = +0.67 V). Control experiments with DMAP-N3 support the findings. DFT B3LYP/6-311G** calculations were used to identify DMAP-N5 (S1), DMAP-N3 +, and DMAP-N in the infrared spectra. Both DMAP-N5 (S1) and [DMAP-N5]+ have a weakened N5 ring structure.

Substitutional and orientational disorder in organic crystals: a symmetry-adapted ensemble model

Modelling of disorder in organic crystals is highly desirable since it would allow thermodynamic stabilities and other disorder-sensitive properties to be estimated for such systems. Two disordered organic molecular systems are modeled using a symmetry-adapted ensemble approach, in which the disordered system is treated as an ensemble of the configurations of a supercell with respect to substitution of one disorder component for another. Computation time is kept manageable by performing calculations only on the symmetrically inequivalent configurations. Calculations are presented on a substitutionally disordered system, the dichloro/dibromobenzene solid solution, and on an orientationally disordered system, eniluracil, and the resultant free energies, disorder patterns, and system properties are discussed. The results are found to be in agreement with experiment following manual removal of physically implausible configurations from ensemble averages, highlighting the dangers of a completely automated approach to organic crystal thermodynamics which ignores the barriers to equilibration once the crystal has been formed.

Ozonolysis of methyl oleate monolayers at the air–water interface: oxidation kinetics, reaction products and atmospheric implications

Ozonolysis of methyl oleate monolayers at the air–water interface results in surprisingly rapid loss of material through cleavage of the C[double bond, length as m-dash]C bond and evaporation/dissolution of reaction products. We determine using neutron reflectometry a rate coefficient of (5.7 ± 0.9) × 10−10 cm2 molecule−1 s−1 and an uptake coefficient of [similar]3 × 10−5 for the oxidation of a methyl ester monolayer: the atmospheric lifetime is [similar]10 min. We obtained direct experimental evidence that <2% of organic material remains at the surface on atmospheric timescales. Therefore known long atmospheric residence times of unsaturated fatty acids suggest that these molecules cannot be present at the interface throughout their ageing cycle, i.e. the reported atmospheric longevity is likely to be attributed to presence in the bulk and viscosity-limited reactive loss. Possible reaction products were characterized by ellipsometry and uncertainties in the atmospheric fate of organic surfactants such as oleic acid and its methyl ester are discussed. Our results suggest that a minor change to the structure of the molecule (fatty acid vs. its methyl ester) considerably impacts on reactivity and fate of the organic film.

A DFT study of the structures, stabilities and redox behaviour of the major surfaces of magnetite Fe3O4

The renewed interest in magnetite (Fe3O4) as a major phase in different types of catalysts has led us to study the oxidation–reduction behaviour of its most prominent surfaces. We have employed computer modelling techniques based on the density functional theory to calculate the geometries and surface free energies of a number of surfaces at different compositions, including the stoichiometric plane, and those with a deficiency or excess of oxygen atoms. The most stable surfaces are the (001) and (111), leading to a cubic Fe3O4 crystal morphology with truncated corners under equilibrium conditions. The scanning tunnelling microscopy images of the different terminations of the (001) and (111) stoichiometric surfaces were calculated and compared with previous reports. Under reducing conditions, the creation of oxygen vacancies in the surface leads to the formation of reduced Fe species in the surface in the vicinity of the vacant oxygen. The (001) surface is slightly more prone to reduction than the (111), due to the higher stabilisation upon relaxation of the atoms around the oxygen vacancy, but molecular oxygen adsorbs preferentially at the (111) surface. In both oxidized surfaces, the oxygen atoms are located on bridge positions between two surface iron atoms, from which they attract electron density. The oxidised state is thermodynamically favourable with respect to the stoichiometric surfaces under ambient conditions, although not under the conditions when bulk Fe3O4 is thermodynamically stable with respect to Fe2O3. This finding is important in the interpretation of the catalytic properties of Fe3O4 due to the presence of oxidised species under experimental conditions.