Importance of electronegativity differences and surface structure in molecular dissociation reactions at transition metal surfaces

The dissociative adsorption of N-2 has been studied at both monatomic steps and flat regions on the surfaces of the 4d transition metals from Zr to Pd. Using density functional theory (DFT) calculations, we have determined and analyzed the trends in both straight reactivity and structure sensitivity across the periodic table. With regards to reactivity, we find that the trend in activation energy (Ea) is determined mainly by a charge transfer from the surface metal atoms to the N atoms during transition state formation, namely, the degree of ionicity of the N-surface bond at the transition state. Indeed, we find that the strength of the metal-N bond at the transition state (and therefore the trend in Ea) can be predicted by the difference in Mulliken electronegativity between the metal and N. Structure sensitivity is analyzed in terms of geometric and electronic effects. We find that the lowering of Ea due to steps is more pronounced on the right-hand side of the periodic table. It is found that for the early transition metals the geometric and electronic effects work in opposition when going from terrace to step active site. In the case of the late 4d metals, however, these effects work in combination, producing a more marked reduction in Ea.

Methane transformation to carbon and hydrogen on Pd(100): Pathways and energetics from density functional theory calculations

Density functional theory with gradient corrections has been employed to study the reaction pathways and the reaction energetics for the transformations of CH4 to C and H on a Pd(100) surface. On examination of transition state structures identified in each elementary reaction, a clear relationship between the valencies of the CHx fragments and the locations of the transition states emerges. The higher the valency of the CHx fragment, the higher the coordination number of the CHx with the surface atoms. The calculated reaction energetics are in good agreement with the experiments. In addition, calculation results are also used to illustrate an interesting issue concerning the CH3 stability on Pd surfaces. (C) 2002 American Institute of Physics.

Crystal structure and ab initio calculations of a cyano-carbamimidic acid ethyl ester

The structure of one tautomer (amine form) of cyano-carbamimidic acid ethyl ester or (amino-ethoxy-methylidene)aminoformonitrile (CAS: 13947-84-7) was determined by single crystal X-ray diffraction. Ab initio quantum chemical calculations at the B3LYP, MP2 and G3 levels were performed to investigate the stability and the formation of the different tautomers and conformers. The calculations indicate that the amine form is the more stable tautomer, showing a high degree of election conjugation. The most stable amine conformer located by the calculations corresponds to the crystallized structure. On the contrary, in the less stable imine form, the conjugation is separated by a N2-C2 single bond. (C) 2007 Elsevier B.V. All rights reserved.

Prediction of the formation and stabilities of energetic salts and ionic liquids based on ab initio electronic structure calculations

A computational approach to predict the thermodynamics for forming a variety of imidazolium-based salts and ionic liquids from typical starting materials is described. The gas-phase proton and methyl cation acidities of several protonating and methylating agents, as well as the proton and methyl cation affinities of many important methyl-, nitro-, and cyano- substituted imidazoles, have been calculated reliably by using the computationally feasible DFT (B3LYP) and MP2 (extrapolated to the complete basis set limit) methods. These accurately calculated proton and methyl cation affinities of neutrals and anions are used in conjunction with an empirical approach based on molecular volumes to estimate the lattice enthalpies and entropies of ionic liquids, organic solids, and organic liquids. These quantities were used to construct a thermodynamic cycle for salt formation to reliably predict the ability to synthesize a variety of salts including ones with potentially high energetic densities. An adjustment of the gas phase thermodynamic cycle to account for solid- and liquid-phase chemistries provides the best overall assessment of salt formation and stability. This has been applied to imidazoles (the cation to be formed) with alkyl, nitro, and cyano substituents. The proton and methyl cation donors studied were as follows: HCl, HBr, HI, (HO)(2)SO2, HSO3CF3 (TfOH), and HSO3(C6H4)CH3 (TsOH); CH3Cl, CH3Br, CH3I, (CH3O)(2)SO2, CH3SO3CF3 (TfOCH3) and CH3SO3(C6H4)CH3 (TsOCH3). As substitution of the cation with electron-withdrawing groups increases, the triflate reagents appear to be the best overall choice as protonating and methylating agents. Even stronger alkylating agents should be considered to enhance the chances of synthetic success. When using the enthalpies of reaction for the gas-phase reactants (eq 6) to form a salt, a cutoff value of - 13 kcal mol(-1) or lower (more negative) should be used as the minimum value for predicting whether a salt can be synthesized.

Short pulse laser-induced dissociation of vibrationally cold, trapped molecular ions

An electrostatic trapping scheme for use in the study of light-induced dissociation of molecular ions is outlined. We present a detailed description of the electrostatic reflection storage device and specifically demonstrate its use in the preparation of a vibrationally cold ensemble of deuterium hydride (HD+) ions. By interacting an intense femtosecond laser with this target and detecting neutral fragmentation products, we are able to elucidate previously inaccessible dissociation dynamics for fundamental diatomics in intense laser fields. In this context, we present new results of intense field dissociation of HD+ which are interpreted in terms of recent theoretical calculations.

Correlated electron-ion dynamics in metallic systems

In this paper we briefly discuss the problem of simulating non-adiabatic processes in systems that are usefully modelled using molecular dynamics. In particular we address the problems associated with metals, and describe two methods that can be applied: the Ehrenfest approximation and correlated electron-ion dynamics (CEID). The Ehrenfest approximation is used to successfully describe the friction force experienced by an energetic particle passing through a crystal, but is unable to describe the heating of a wire by an electric current. CEID restores the proper heating.

Photo-double detachment from the F- ion

The correlated process of photodetaching two electrons from the F- ion following the absorption of a single photon has been investigated over an energy range 20-62 eV. In the experiment, a beam of photons from the Advanced Light Source was collinearly merged with a counter-propagating beam of F- ions from a sputter ion source. The F+ ions produced in the interaction region were detected, and the normalized signal was used to monitor the relative cross section for the double-detachment reaction. An absolute scale for the cross section was established by measuring the spatial overlap of the two beams and by determining the efficiency for collection and detection of the F+ ions. The measured cross section is compared with R-matrix and random phase approximation calculations. These calculations show that the Auger decay of the 2s2p(6) core-excited state of the F atom plays a minor role in the production of F+ ions and that double detachment is likely to be dominated by simultaneous correlated ejection of two valence electrons at energies well above threshold.

Many-body theory calculations of positron binding to negative ions

A many-body theory approach developed by the authors [Phys. Rev. A 70, 032720 (2004)] is applied to positron bound states and annihilation rates in atomic systems. Within the formalism, full account of virtual positronium (Ps) formation is made by summing the electron-positron ladder diagram series, thus enabling the theory to include all important many-body correlation effects in the positron problem. Numerical calculations have been performed for positron bound states with the hydrogen and halogen negative ions, also known as Ps hydride and Ps halides. The Ps binding energies of 1.118, 2.718, 2.245, 1.873 and 1.393 eV and annihilation rates of 2.544, 2.482, 1.984, 1.913 and 1.809 ns^{-1}, have been obtained for PsH, PsF, PsCl, PsBr and PsI, respectively.

Comment on “Electron transport through correlated molecules computed using the time-independent Wigner function: Two critical tests”

The many-electron-correlated scattering (MECS) approach to quantum electronic transport was investigated in the linear-response regime [I. Bâldea and H. Köppel, Phys. Rev. B 78, 115315 (2008). The authors suggest, based on numerical calculations, that the manner in which the method imposes boundary conditions is unable to reproduce the well-known phenomena of conductance quantization. We introduce an analytical model and demonstrate that conductance quantization is correctly obtained using open system boundary conditions within the MECS approach.

Elucidating the molecular physiopathology of acute respiratory distress syndrome in severe acute respiratory syndrome patients

Acute respiratory distress syndrome (ARDS) is a severe form of acute lung injury. It is a response to various diseases of variable etiology, including SARS-CoV infection. To date, a comprehensive study of the genomic physiopathology of ARDS (and SARS) is lacking, primarily due to the difficulty of finding suitable materials to study the disease process at a tissue level (instead of blood, sputa or swaps). Hereby we attempt to provide such study by analyzing autopsy lung samples from patient who died of SARS and showed different degrees of severity of the pulmonary involvement. We performed real-time quantitative PCR analysis of 107 genes with functional roles in inflammation, coagulation, fibrosis and apoptosis: some key genes were confirmed at a protein expression level by immunohistochemistry and correlated to the degree of morphological severity present in the individual samples analyzed. Significant expression levels were identified for ANPEP (a receptor for CoV), as well as inhibition of the STAT1 pathway, IFNs production and CXCL10 (a T-cell recruiter). Other genes unassociated to date with ARDS/SARS include C1Qb, C5R1, CASP3, CASP9, CD14, CD68, FGF7, HLA-DRA, ICF1, IRF3, MALAT-1, MSR1, NFIL3, SLPI, USP33, CLC, GBP1 and TACI. As a result, we proposed to therapeutically target some of these genes with compounds such as ANPEP inhibitors, SLPI and dexamethasone. Ultimately, this study may serve as a model for future, tissue-based analyses of fibroinflammatory conditions affecting the lung. (C) 2009 Elsevier B.V. All rights reserved.

Clinical and molecular characteristics of hereditary non-polyposis colorectal cancer families in Southeast Asia

Hereditary non-polyposis colorectal cancer (HNPCC), predominantly due to germline MLH1/MSH2 mutations, is the commonest form of hereditary colorectal cancer (CRC), but data in Asians are sparse. We sequenced the MLH1/MSH2 coding and promoter core regions in CRC patients diagnosed below age 40, and/or with multiple primary cancers or familial cancer clustering suggestive of HNPCC, and correlated deleterious mutations with clinical and tumour features. Forty-six Chinese, Malay and Indian kindreds participated. Of the 153 cancers reported in the 46 kindreds, stomach (14%) and urogenital cancers (13%) were the most common extracolonic cancers, whereas endometrial cancer comprised only 7%. Eleven different MLH1 and 12 MSH2 mutations were identified, including nine novel and four recurring mutations in the Chinese. One Indian was a compound heterozygote for an MLH1 and MSH2 mutation. The MLH1/MSH2 mutation data in the Malays and the Indians represents the first in these ethnic groups. Factors strongly associated with deleterious mutations were the Amsterdam criteria, family history of stomach or multiple primary cancers, and MSI-high tumours, whereas family history of endometrial cancer and young cancer age alone correlated poorly. Distinct clinical and molecular characteristics were identified among Asian HNPCC kindreds and may have important clinical implications.

Molecular Modeling on Inhibitor Complexes and Active-Site Dynamics of Cytochrome P450 C17, a Target for Prostate Cancer Therapy

A molecular model for the P450 enzyme cytochrome P450 C17 (CYP17) is presented based on sequence alignments of multiple template structures and homology modeling. This enzyme plays a central role in the biosynthesis of testosterone and is emerging as a major target in prostate cancer, with the recently developed inhibitor abiraterone currently in advanced clinical trials. The model is described in detail, together with its validation, by providing structural explanations to available site-directed mutagenesis data. The CYP17 molecule in this model is in the form of a triangular prism, with an edge of similar to 55 angstrom and a thickness of similar to 37 angstrom. It is predominantly helical, comprising 13 alpha helices interspersed by six 3(10) helices and 11 beta-sheets. Multinanosecond molecular dynamics simulations in explicit solvent have been carried out, and principal components analysis has been used to reveal the details of dynamics around the active site. Coarse-grained methods have also been used to verify low-frequency motions, which have been correlated with active-site gating. The work also describes the results of docking synthetic inhibitors, including the drug abiraterone and the natural substrate pregnenolone, in the CYP17 active site together with molecular dynamics simulations on the complexes. (C) 2010 Elsevier Ltd. All rights reserved.

Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.

Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150–200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such quadruplex structures, with external TTA loops positioned to potentially interact with other macromolecules. This study reports on possible arrangements for these quadruplex dimers and tetramers, which can be formed from 8 or 16 telomeric DNA repeats, and on a methodology for modeling their interactions with small molecules. A series of computational methods including molecular dynamics, free energy calculations, and principal components analysis have been used to characterize the properties of these higher-order G-quadruplex dimers and tetramers with parallel-stranded topology. The results confirm the stability of the central G-tetrads, the individual quadruplexes, and the resulting multimers. Principal components analysis has been carried out to highlight the dominant motions in these G-quadruplex dimer and multimer structures. The TTA loop is the most flexible part of the model and the overall multimer quadruplex becoming more stable with the addition of further G-tetrads. The addition of a ligand to the model confirms the hypothesis that flat planar chromophores stabilize G-quadruplex structures by making them less flexible.