Atomistic surface erosion and thin film growth modelled over realistic time scales

We present results of atomistic modelling of surface growth and sputtering using a multi-time scale molecular dynamics-on-the-fly kinetic Monte Carlo scheme which allows simulations to be carried out over realistic experimental times. The method uses molecular dynamics to model the fast processes and then calculates the diffusion barriers for the slow processes on-the-fly, without any preconceptions about what transitions might occur. The method is applied to the growth of metal and oxide materials at impact energies typical for both vapour deposition and magnetron sputtering. The method can be used to explain growth processes, such as the filling of vacancies and the formation of stacking faults. By tuning the variable experimental parameters on the computer, a parameter set for optimum crystalline growth can be determined. The method can also be used to model sputtering where the particle interactions with the surface occur at a higher energy. It is shown how a steady state can arise in which interstitial clusters are continuously being formed below the surface during an atom impact event which also recombine or diffuse to the surface between impact events. For fcc metals the near surface region remains basically crystalline during the erosion process with a pitted topography which soon attains a steady state roughness.     

Electron affinity of Al13: a correlated electronic structure study

Neutral and anionic 13-atom aluminum clusters are studied with high-level, fully ab initio methods: second-order perturbation theory (MP2) and coupled cluster theory with singles, doubles, and perturbative triples (CCSD(T)). Energies and vibrational frequencies are reported for icosahedral and decahedral isomers, and are compared with density functional theory results. At the MP2 level of theory, with all of the basis sets employed, the icosahedral structure is energetically favored over the decahedral structure for both the neutral and anionic Al(13) clusters. Hessian calculations imply that only the icosahedral structures are potential energy minima. The CCSD(T)/aug-cc-pVTZ adiabatic electron affinity of Al(13) is found to be 3.57 eV, in excellent agreement with experiment.     

O-H stretch overtone excitation of ethyl hydroperoxide conformers

We present laser photoacoustic spectra of ethyl hydroperoxide (EHP) for 3-6 quanta of O-H stretch. Spectra are consistent with ab initio spectral simulations that take into account the influence of torsional motion about the O-O bond on O-H stretch overtone excitation. Experimental and simulated spectra share two trends. First, spectral features due to torsional excitation, including hot bands, become more prominent with increasing O-H stretch excitation, as has been shown previously for similar molecules such as methyl hydroperoxide. Second, contributions from the two different EHP conformers become clearly distinguishable at higher O-H stretch excitation, mainly due to the role of torsional motion. Results are consistent with a higher energy separation (330 cm(-1)) between the lower energy anti and the higher energy gauche conformers than predicted by electronic structure calculations (137 cm(-1)). Calculated absorption intensities are consistently higher than experimental values by ~30% but within the experimental uncertainty. With each additional O-H stretch overtone, the dropoff in calculated integrated absorption intensities at room temperature becomes less extreme, with a 14-fold dropoff from 3ν(OH) to 4ν(OH) and an 8-fold decrease from 5ν(OH) to 6ν(OH).     

Inductive effect: a quantum theory of atoms in molecules perspective

Substituent effects are ubiquitous in chemistry and the most fundamental is the inductive effect. In this study, the so-called inductive effect was probed in derivatives of bicyclo[1.1.1]pentane-1-carboxylic acid using the isodesmic reaction energy of the acid-base deprotonation, calculated at the PBE0/6-31++G(d,p) level of theory (used throughout). Although structure, molecular orbitals, and nuclear magnetic shielding parameters are discussed, the main focus of this study is the use of the quantum theory of atoms in molecules to analyze the electron density distribution. It was observed that the effect propagates via the manipulation of atomic dipole moments controlled by that of the substituent. As the dipole moment conforms to the principle of atomic transferability, it is found that the substituent dipole determined in simple systems (e.g., R-H) can be used to describe the effect upon the bicyclo[1.1.1]pentane-1-carboxylic acid system.     

Density functional theory study of the role of anions on the oxidative decomposition reaction of propylene carbonate

The oxidative decomposition mechanism of the lithium battery electrolyte solvent propylene carbonate (PC) with and without PF(6)(-) and ClO(4)(-) anions has been investigated using the density functional theory at the B3LYP/6-311++G(d) level. Calculations were performed in the gas phase (dielectric constant ε = 1) and employing the polarized continuum model with a dielectric constant ε = 20.5 to implicitly account for solvent effects. It has been found that the presence of PF(6)(-) and ClO(4)(-) anions significantly reduces PC oxidation stability, stabilizes the PC-anion oxidation decomposition products, and changes the order of the oxidation decomposition paths. The primary oxidative decomposition products of PC-PF(6)(-) and PC-ClO(4)(-) were CO(2) and acetone radical. Formation of HF and PF(5) was observed upon the initial step of PC-PF(6)(-) oxidation while HClO(4) formed during initial oxidation of PC-ClO(4)(-). The products from the less likely reaction paths included propanal, a polymer with fluorine and fluoro-alkanols for PC-PF(6)(-) decomposition, while acetic acid, carboxylic acid anhydrides, and Cl(-) were found among the decomposition products of PC-ClO(4)(-). The decomposition pathways with the lowest barrier for the oxidized PC-PF(6)(-) and PC-ClO(4)(-) complexes did not result in the incorporation of the fluorine from PF(6)(-) or ClO(4)(-) into the most probable reaction products despite anions and HF being involved in the decomposition mechanism; however, the pathway with the second lowest barrier for the PC-PF(6)(-) oxidative ring-opening resulted in a formation of fluoro-organic compounds, suggesting that these toxic compounds could form at elevated temperatures under oxidizing conditions.     

Structure-enantioselectivity effects in 3,4-dihydropyrimido[2,1-b]benzothiazole-based isothioureas as enantioselective acylation catalysts

The catalytic activity and enantioselectivity in the kinetic resolution of (±)-1-naphthylethanol with a range of structurally related 3,4-dihydropyrimido[2,1-b]benzothiazole-based catalysts is examined. Of the isothiourea catalysts screened, (2S,3R)-2-phenyl-3-isopropyl substitution proved optimal, giving good levels of selectivity in the kinetic resolution of a number of secondary alcohols (S values up to >100 at ~50% conversion). Low catalyst loadings (0.10-0.25 mol%) of the optimal isothiourea can be used to generate enantiopure alcohols (>99% ee) in good yields.     

Single cell 3-D platform to study ligand mobility in cell-cell contact

Lateral mobility and dimensionality have both been shown to influence cellular behavior, but have yet to be combined and applied in a single in vitro platform to address, e.g., cell adhesion in a setting mimicking the three-dimensional environment of neighboring cells in a reductionist way. To study the effect of the lateral mobility of cell adhesive ligands in three dimensions we present and characterize a platform, which enables patterning of single cells into microwells presenting a cell membrane mimetic interface pre-patterned to its walls. Soluble E-cadherin extracellular domains coupled through an optimized streptavidin-antibody linkage to lipids in a supported lipid bilayer (SPB) were presented on the microwell walls as either laterally mobile or immobile ligands. The fluidity was controlled through a small change in temperature by choosing phospholipids for the SPB with a lipid phase transition temperature around 30 °C. The platform thus enabled the investigation of cell adhesion to either laterally immobile or mobile E-cadherin ligands presented on the same cell membrane mimetic surface. Chinese hamster ovary (CHO) cells engineered to express E-cadherin that were cultured on the platform demonstrated that enhanced cadherin lateral mobility significantly decreased the formation of actin bundles and resulted in more diffuse actin organization, while constraining the cell shape to that of the microwell. This example highlights the potential to use in vitro cell culture platforms to mimic direct cell-cell interaction in a controlled environment that nevertheless captures the dynamic nature of the native cell environment.     

Organic base effects in NHC promoted O- to C-carboxyl transfer; chemoselectivity profiles, mechanistic studies and domino catalysis

The O- to C-carboxyl transfer of oxazolyl carbonates promoted by triazolinylidenes, generated in situ with NEt(3), shows a markedly different rate and chemoselectivity profile to the same reaction promoted by triazolinylidenes generated using KHMDS. The mechanism of these pathways has been probed through extensive crossover studies to understand this process. The use of NEt(3) as a base allows domino multi-step reaction sequences to be developed, although chiral NHCs only generate modest levels of asymmetric induction (<15% ee) in these domino reaction processes.     

Unraveling the relationship between structure and stabilization of triarylpyridines as G-quadruplex binding ligands

A series of novel 2,4,6-triarylpyridines have been synthesized and their interactions with intramolecular G-quadruplexes have been measured by F?rster Resonance Energy Transfer (FRET) melting and Fluorescent Intercalator Displacement (FID) assays. A few of these compounds exhibit stabilization of G4-DNA that is comparable to other benchmark G4-DNA ligands with fair to excellent G4-DNA vs. duplex selectivity and significant cytotoxicity towards HeLa cells. The nature of the 4-aryl substituents along with side chain length governs the G4-DNA stabilization ability of the compounds. In addition, we demonstrate that there is a strong correlation between the ability of the compounds to stabilize the same G4-DNA sequence in K(+) and Na(+) conditions and a strong correlation between the ability of the compounds to stabilize different G4-DNA sequences in K(+) or Na(+) buffer.     

Inorganic approaches for radiolabelling biomolecules with fluorine-18 for imaging with positron emission tomography

Conventional methods for radiolabelling biomolecules such as proteins and peptides with fluorine-18 for PET imaging rely on carbon-fluorine bond formation and are complex and inefficient. Several non-carbon elements form strong bonds (i.e. with high bond enthalpy) with fluorine, but with lower activation energy for their formation compared to carbon-fluorine bonds, whilst preserving a relatively high kinetic stability. In particular, by incorporating boron-, aluminium- and silicon-containing prosthetic groups into biomolecules, promising results have recently been achieved in the radiolabelling with F-18-fluoride under mild aqueous conditions, affording a level of convenience, efficiency and specific activity potentially superior to those offered by conventional C-F bond formation methods. The promise already shown by these early studies heralds a new branch of bioconjugate radiochemistry involving a wider range of "fluoridephilic" elements for synthesis of PET molecular imaging agents.