Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction of flow. Under the ideal solvent conditions, torsional twisting of the chain and aperiodic cyclical dynamics are observed for the end of the oligomer. Under poor solvent conditions, a metastable helix forms in the end of the chain despite the lack of any attractive potential between beads in the oligomeric chain. The formation of the helix is postulated to be the result of a solvent induced chain collapse that has been confined to a single dimension by a strong flow field.     

Kinetics and mechanisms of hydrolysis and aminolysis of thioxocephalosporins

The effect of replacing the beta-lactam carbonyl oxygen in cephalosporins by sulfur on their reactivity has been investigated. The second-order rate constant for alkaline hydrolysis of the sulfur analogue is 2-fold less than that for the natural cephalosporin. The thioxo derivative of cephalexin, with an amino group in the C7 side chain, undergoes beta-lactam ring opening with intramolecular aminolysis by a reaction similar to that for cephalexin itself. However, the rate of intramolecular aminolysis for the S-analogue is 3 orders of magnitude greater than that for cephalexin. Furthermore, unlike cephalexin, intramolecular aminolysis in the S-analogue occurs up to pH 14 with no competitive hydrolysis. The rate of intermolecular aminolysis of natural cephalosporins is dominated by a second-order dependence on amine concentration, whereas that for thioxocephalosporins shows only a first-order term in amine. The Bronsted beta(nuc) for the aminolysis of thioxo-cephalosporin is +0.39, indicative of rate-limiting formation of the tetrahedral intermediate with an early transition state with relatively little C-N bond formation.     

CH-stretching overtone spectroscopy of 1,1,1,2-tetrafluoroethane

We have recorded the vibrational absorption spectrum of 1,1,1,2-tetrafluoroethane (HFC-134a) in the fundamental and first five CH-stretching overtone regions with the use of Fourier transform infrared, dispersive long-path, intracavity laser photoacoustic, and cavity ringdown spectroscopies. We compare our measured total oscillator strengths in each region with intensities calculated using an anharmonic oscillator local mode model. We calculate intensities with 1D, 2D, and 3D Hamiltonians, including one or two CH stretches and two CH stretches with the HCH bending mode, respectively. The dipole moment function is calculated ab initio with self-consistent-field Hartree-Fock and density functional theories combined with double- and triple-zeta-quality basis sets. We find that the basis set choice affects the total intensity more than the choice of the Hamiltonian. We achieve agreement between the calculated and measured total intensities of approximately a factor of 2 or better for the fundamental and first five overtones.     

A New Mechanism for β‐Lactamases: Class D Enzymes Degrade 1β‐Methyl Carbapenems through Lactone Formation

β‐Lactamases threaten the clinical use of carbapenems, which are considered antibiotics of last resort. The classical mechanism of serine carbapenemase catalysis proceeds through hydrolysis of an acyl‐enzyme intermediate. We show that class D β‐lactamases also degrade clinically used 1β‐methyl‐substituted carbapenems through the unprecedented formation of a carbapenem‐derived β‐lactone. β‐Lactone formation results from nucleophilic attack of the carbapenem hydroxyethyl side chain on the ester carbonyl of the acyl‐enzyme intermediate. The carbapenem‐derived lactone products inhibit both serine β‐lactamases (particularly class D) and metallo‐β‐lactamases. These results define a new mechanism for the class D carbapenemases, in which a hydrolytic water molecule is not required.     

The structure and thermal motion of simple liquids—I

The characteristics of the liquid state are discussed qualitatively in terms or the forces between molecules, and their thermal motion. Experimental methods available for studying structure and thermal motions on a microscopic scale are outlined.

In particular the relation of the static pair distribution function to neutron and x-ray scattering is considered and the general features of the results presented.     

Spinodal decomposition in a model colloid-polymer mixture in microgravity

We study phase separation in a deeply quenched colloid-polymer mixture in microgravity on the International Space Station using small-angle light scattering and direct imaging. We observe a clear crossover from early-stage spinodal decomposition to late-stage, interfacial-tension-driven coarsening. Data acquired over 5 orders of magnitude in time show more than 3 orders of magnitude increase in domain size, following nearly the same evolution as that in binary liquid mixtures. The late-stage growth approaches the expected linear growth rate quite slowly.     

Investigation of high sensitivity GC-FTIR as an analytical tool for structural identification

As part of a detailed investigation into the application of GC-FTIR in industrial and environmental analysis, representative sets of samples have been analyzed in parallel using commercial high-sensitivity instruments. Two of the instruments utilize low temperature storage of the GC eluate to extend the time available for FTIR analysis, yielding greater sensitivity than that possible by conventional ‘light-pipe’ GC-FTIR. In certain circumstances, instruments using both types of sample storage give rise to spectra exhibiting features characteristic of the interface used. Chromatographic resolution was found not to be significantly degraded by use of either sample storage interface. Particular advantages were found in having parallel flame ionization detection and mass spectrometry; this enabled the location of smaller components and gave greater certainty of identification.     

Mode-coupling theory for multiple-time correlation functions of tagged particle densities and dynamical filters designed for glassy systems

The theoretical framework for higher-order correlation functions involving multiple times and multiple points in a classical, many-body system developed by Van Zon and Schofield [Phys. Rev. E 2002, 65, 011106] is extended here to include tagged particle densities. Such densities have found an intriguing application as proposed measures of dynamical heterogeneities in structural glasses. The theoretical formalism is based upon projection operator techniques which are used to isolate the slow time evolution of dynamical variables by expanding the slowly evolving component of arbitrary variables in an infinite basis composed of the products of slow variables of the system. The resulting formally exact mode-coupling expressions for multiple-point and multiple-time correlation functions are made tractable by applying the so-called N-ordering method. This theory is used to derive for moderate densities the leading mode coupling expressions for indicators of relaxation type and domain relaxation, which use dynamical filters that lead to multiple-time correlations of a tagged particle density. The mode coupling expressions for higher order correlation functions are also successfully tested against simulations of a hard sphere fluid at relatively low density.     

Electronic effects induced by single hydrogen atoms on the Ge(001) surface

The properties of an isolated dangling bond formed by the chemisorption of a single hydrogen atom on a dimer of the Ge(001) surface are investigated by first-principles density functional theory (DFT) calculations, and scanning tunneling microscopy (STM) measurements. Two stable atomic configurations of the Ge-Ge-H hemihydride with respect to the neighboring bare Ge-Ge dimers are predicted by DFT. For both configurations, the unpaired electron of the HGe(001) system is found to be delocalized over the surface, rendering the isolated dangling bond of the hemihydride unoccupied. However, local surface charge accumulation, such as may occur during STM imaging, leads to the localization of two electrons onto the hemihydride dangling bond. The calculated surface densities of states for one of the charged Ge-Ge-H hemihydride configurations are found to be in good agreement with atomic-resolution STM measurements on n-type Ge(001). Comparison with a Si-Si-H hemihydride of the Si(001) surface shows similarities in structural properties, but substantial differences in electronic properties.