Trajectory studies of energy transfer: CH3NC with He,Xe, H2 and N2

A trajectory program was used to simulate the collisions of CH₃NC with He, Xe, H₂ and N₂. Calculated energy transfer is in accord with experiment. The pattern of CH₃NC vibrational mode energization is found to be noticeably non-random. The approximate sampling methods used in thermal unimolecular trajectory studies produce a more uniform state distribution.     

Determination of affinity constants and response factors of the noncovalent dimer of gramicidin by electrospray ionization mass spectrometry and mathematical modeling

The dimerization of gramicidin, a 15-residue membrane peptide, in solution can be viewed as a model for protein-protein interactions. We reported previously that the dimer can be observed when electrosprayed from organic solvents and that the abundances of the dimer depends on the dielectric constant of the solvent. Here, we report an effort to determine an affinity constant for the dimerization of gramicidin by using gas-phase abundance. Two issues affecting the determination are the electrospray-induced dissociation of the dimer and discrimination in the electrospray of the dimer compared with the monomer. Other methods developed for the purpose of determining affinity from mass spectral abundance do not address the dissociation of the complex in the gas phase or can not be applied for cases of low affinity constant, K(a). We present a mathematical model that uses the ratio of the signal intensities of the dimer and the monomer during a titration. The model also incorporates the dissociation and an electrospray ionization-response factor of the dimer for extracting the affinity constant for the dimerization of gramicidin. The dimerization constants from the new method agree within a factor of two with values reported in the literature.     

Facilitated transport from ternary cation mixtures through water—chloroform—water membrane systems containing macrocyclic ligands

Cation fluxes were determined for various three-component, equimolar mixtures of alkali metal, alkaline earth, and Pb²⁺ cations in a H₂O---CHCl₃---H₂O liquid membrane system incorporating macrocyclic polyethers as carriers. Carrier ligands studied were 18-crown-6, dicyclohexano-18-crown-6, 1,10-diaza-18-crown-6, 21-crown-7, dibenzo-24-crown-8, and cryptand [2.2.2]. Correlations were found between transport and relative cation:polyether cavity radii, the type of substituents present on the polyether ring, and the type and number of donor atoms present. All the ligands studied transported Pb²⁺ at higher rates than the other Mⁿ⁺ in the mixtures. Transport behavior in these multi-cation systems can be predicted from Mⁿ⁺—polyether complex stability constant data in most cases.     

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.     

Siloxyaluminate and Siloxygallate Complexes as Models for Framework and Partially Hydrolyzed Framework Sites in Zeolites and Zeotypes

Anionic molecular models for nonhydrolyzed and partially hydrolyzed aluminum and gallium framework sites on silica, M[OSi(OtBu)₃]₄⁻ and HOM[OSi(OtBu)₃]₃⁻ (where M=Al or Ga), were synthesized from anionic chlorides Li{M[OSi(OtBu)₃]₃Cl} in salt metathesis reactions. Sequestration of lithium cations with [12]crown-4 afforded charge-separated ion pairs composed of monomeric anions M[OSi(OtBu)₃]₄⁻ with outer-sphere [([12]crown-4)₂Li]⁺ cations, and hydroxides {HOM[OSi(OtBu)₃]₃} with pendant [([12]crown-4)Li]⁺ cations. These molecular models were characterized by single-crystal X-ray diffraction, vibrational spectroscopy, mass spectrometry and NMR spectroscopy. Upon treatment of monomeric [([12]crown-4)Li]{HOM[OSi(OtBu)₃]₃} complexes with benzyl alcohol, benzyloxide complexes were formed, modeling a possible pathway for the formation of active sites for Meerwin–Ponndorf–Verley (MPV) transfer hydrogenations with Al/Ga-doped silica catalysts.     

Electrostatic energy of a complex and infinitely extended electronic system

Formulae concerning the evaluation of the total electrostatic energy per supercell in an infinitely extended system made up of identical atoms are developed in a consistent manner, which emphasizes and takes care of several delicate points connected with the occurrence of divergent and spurious constant terms. The treatment is carried out within a k-space formulation of density functional theory and special attention is devoted to a consistent re-derivation of the Madelung energy result of the Wigner solid associated with a realistic identical atom system. Two formulae of practical interest for computer applications are obtained and discussed.     

Composite Likelihood Inference in a Discrete Latent Variable Model for Two-Way “Clustering-by-Segmentation” Problems

We consider a discrete latent variable model for two-way data arrays, which allows one to simultaneously produce clusters along one of the data dimensions (e.g., exchangeable observational units or features) and contiguous groups, or segments, along the other (e.g., consecutively ordered times or locations). The model relies on a hidden Markov structure but, given its complexity, cannot be estimated by full maximum likelihood. Therefore, we introduce a composite likelihood methodology based on considering different subsets of the data. The proposed approach is illustrated by simulation, and with an application to genomic data.     

A computational DFT analysis of OH chemisorption on catalytic Pt(111) nanoparticles

In this article, various energies and geometries of pure platinum nanoparticles and those of platinum nanoparticles with adsorbed OH were investigated. Fourteen different platinum clusters of 3–40 atoms were studied using spin-unrestricted density functional theory (DFT) with a double numerical plus polarization basis set. This range of sizes gave enough information for establishing the general trends that were the primary goal of the study. Three different shapes of platinum clusters were presented, and the effect of cluster size on binding energy, total energy, and HOMO–LUMO energy gap was investigated. Subsequently, same calculations were performed for those selected Pt clusters with OH adsorbate on the surface. The results show that the stability of both the pure clusters and the clusters with adsorbed OH molecule increases with an increase of cluster size. This fact indicates that direct influence of the size of Pt cluster on the reaction rate is possible, and the understanding of how cluster size would affect binding energy is important. As expected, the effect of cluster size on total energy of molecule was shown to be a linear function independent of cluster type. We also found that optimized (stable) Pt clusters were bigger in size than that of the initial clusters, or clusters with bulk geometry.