Gas‐phase reactions of Cl atoms with hydrochloroethers: relative rate constants and their correlation with substituents' electronegativities

Rate constants for the reactions of Cl atoms with CH₃OCHCl₂ and CH₃OCH₂CH₂Cl were determined at (296 ± 2) K and atmospheric pressure using synthetic air as bath gas. Decay rates of these organic compounds were measured relative to the following reference compounds: CH₂ClCH₂Cl and n‐C₅H₁₂. Using rate constants of 1.33 × 10^?12 and 2.52 × 10^?10 cm³ molecule^?1 sec^?1 for the reaction of Cl atoms with CH₂ClCH₂Cl and n‐C₅H₁₂, respectively, the following rate coefficients were derived: k(Cl + CH₃OCHCl₂) = (1.05 ± 0.11) × 10^?12 and k(Cl + CH₃OCH₂CH₂Cl) = (1.14 ± 0.10) × 10^?10, in units of cm³ molecule^?1 s^?1. The rate constants obtained were compared with previous literature data and a correlation was found between the rate coefficients of some CH₃OCHR¹R² + Cl reactions and ΔElectronegativity of ? CHR¹R². Copyright © 2008 John Wiley & Sons, Ltd.     

Inelastic electron scattering and energy-selective negative ion reactions in molecular films on silicon surfaces

Careful control of plasma chemistry, particularly the negative ion production and reaction channels, could lead to nanoscale patterning, growth, and etching strategies. Since the energies of anion and electron surface collisions are relatively low (<10 eV) in plasmas, these interactions are essentially damage free with respect to the buried interface and subsurface region. Thus, renewed interest has arisen that takes advantage of negative ion surface chemistry in film deposition and nanopatterning. We review (i) the transient negative ion states such as shape and dissociative electron attachment resonances produced during electron molecule scattering, (ii) the many body interactions and substrate-effects on the resonance energies, widths and cross sections and (iii) examples of post-dissociation interactions of the reactive fragments and anions that may lead to controlled etching or growth. Specifically, we summarize past and recent studies on electron scattering with gas- and condensed-phase H₂O, CF₄, SiCl₄ and O₂ targets. We then discuss recent examples of energy selective oxidation and fluorination of hydrogen terminated silicon surfaces and comment on the general applicability of low-energy electrons and negative ion surface chemistry in film deposition, nanopatterning and growth strategies.     

Interactions of speaking condition and auditory feedback on vowel production in postlingually deaf adults with cochlear implants

This study investigates the effects of speaking condition and auditory feedback on vowel production by postlingually deafened adults. Thirteen cochlear implant users produced repetitions of nine American English vowels prior to implantation, and at one month and one year after implantation. There were three speaking conditions (clear, normal, and fast), and two feedback conditions after implantation (implant processor turned on and off). Ten normal-hearing controls were also recorded once. Vowel contrasts in the formant space (expressed in mels) were larger in the clear than in the fast condition, both for controls and for implant users at all three time samples. Implant users also produced differences in duration between clear and fast conditions that were in the range of those obtained from the controls. In agreement with prior work, the implant users had contrast values lower than did the controls. The implant users' contrasts were larger with hearing on than off and improved from one month to one year postimplant. Because the controls and implant users responded similarly to a change in speaking condition, it is inferred that auditory feedback, although demonstrably important for maintaining normative values of vowel contrasts, is not needed to maintain the distinctiveness of those contrasts in different speaking conditions.     

Co-regulation of a large and rapidly evolving repertoire of odorant receptor genes

The olfactory system meets niche- and species-specific demands by an accelerated evolution of its odorant receptor repertoires. In this review, we describe evolutionary processes that have shaped olfactory and vomeronasal receptor gene families in vertebrate genomes. We emphasize three important periods in the evolution of the olfactory system evident by comparative genomics: the adaptation to land in amphibian ancestors, the decline of olfaction in primates, and the delineation of putative pheromone receptors concurrent with rodent speciation. The rapid evolution of odorant receptor genes, the sheer size of the repertoire, as well as their wide distribution in the genome, presents a developmental challenge: how are these ever-changing odorant receptor repertoires coordinated within the olfactory system? A central organizing principle in olfaction is the specialization of sensory neurons resulting from each sensory neuron expressing only ~one odorant receptor allele. In this review, we also discuss this mutually exclusive expression of odorant receptor genes. We have considered several models to account for co-regulation of odorant receptor repertoires, as well as discussed a new hypothesis that invokes important epigenetic properties of the system.     

Spectral tuning of shortwave-sensitive visual pigments in vertebrates

Of the four classes of vertebrate cone visual pigments, the shortwave-sensitive SWS1 class shows some of the largest shifts in lambda(max), with values ranging in different species from 390-435 nm in the violet region of the spectrum to < 360 nm in the ultraviolet. Phylogenetic evidence indicates that the ancestral pigment most probably had a lambda(max) in the UV and that shifts between violet and UV have occurred many times during evolution. In violet-sensitive (VS) pigments, the Schiff base is protonated whereas in UV-sensitive (UVS) pigments, it is almost certainly unprotonated. The generation of VS pigments in amphibia, birds and mammals from ancestral UVS pigments must involve therefore the stabilization of protonation. Similarly, stabilization must be lost in the evolution of avian UVS pigments from a VS ancestral pigment. The key residues in the opsin protein for these shifts are at sites 86 and 90, both adjacent to the Schiff base and the counterion at Glu113. In this review, the various molecular mechanisms for the UV and violet shifts in the different vertebrate groups are presented and the changes in the opsin protein that are responsible for the spectral shifts are discussed in the context of the structural model of bovine rhodopsin.     

Bacterial characterization using protein profiling in a microchip separations platform

A rapid microanalytical protein-based approach to bacterial characterization is presented. Chip gel electrophoresis (CGE) coupled with LIF detection was used to analyze lysates from different bacterial cell lines to obtain signature profiles of the soluble protein composition. The study includes Escherichia coli, Bacillus subtilis, and Bacillus anthracis (Delta Sterne strain) vegetative cells as well as endospores formed from the latter two species as model organisms to demonstrate the method. A unified protein preparation protocol was developed for both cell types to streamline the benchtop process and aid future automation. Cells and spores were lysed and proteins solubilized using a combination of thermal and chemical lysis methods. Reducing agents, necessary to solubilize spore proteins, were eliminated using a small-scale rapid size-exclusion chromatography step to eliminate interference with down-stream protein labeling. This approach was found to be compatible with nonspore cells (i.e., vegetative cells) as well, not adversely impacting the protein signatures. Data are presented demonstrating distinct CGE protein signatures for our model organisms, suggesting the potential for discrimination of organisms on the basis of empirical protein patterns. The goal of this work is to develop a fast and field-portable method for characterizing bacteria via their proteomes.     

Hydrogen bonded OH-stretching vibration in the water dimer

We have calculated the frequencies and intensities of the hydrogen-bonded OH-stretching transitions in the water dimer complex. The potential-energy curve and dipole-moment function are calculated ab initio at the coupled cluster with singles, doubles, and perturbative triples level of theory with correlation-consistent Dunning basis sets. The vibrational frequencies and wavefunctions are found from a numerical solution to a one-dimensional Schr?dinger equation. The corresponding transition intensities are found from numerical integration of these vibrational wavefunctions with the ab initio calculated dipole moment function. We investigate the effect of counterpoise correcting both the potential-energy surface and dipole-moment function. We find that the effect of using a numeric potential is significant for higher overtones and that inclusion of a counterpoise correction for basis set superposition error is important.     

Preparation and characterization of standard reference material 3276, carrot extract in oil

The National Institute of Standards and Technology (NIST), the Food and Drug Administration (FDA) Center for Drug Evaluation and Research (CDER) and Center for Food Safety and Applied Nutrition (CFSAN), and the National Institutes of Health (NIH), Office of Dietary Supplements (ODS) are collaborating to produce a series of standard reference materials (SRMs) for dietary supplements. Standard reference material (SRM) 3276 Carrot Extract in Oil is one in this series, with values assigned for trans-alpha-carotene, trans- and total beta-carotene, delta- and gamma-tocopherol, and twelve fatty acids. Results for carotenoids and tocopherols were obtained by use of combinations of liquid chromatography (LC), on columns of differing selectivity, with absorbance and mass spectrometric (MS) detection. Fluorescence detection also was used for the tocopherols. Results for fatty acids were obtained by use of gas chromatography (GC) with both flame-ionization and mass-spectrometric detection. This material is intended for use as a primary control material when assigning values to in-house (secondary) control materials and for validation of analytical methods for measurement of these analytes in similar matrices.     

Templated assembly of biomembranes on silica microspheres using bacteriorhodopsin conjugates as structural anchors

Membrane proteins are some of the most sophisticated molecules found in nature. These molecules have extraordinary recognition properties; hence, they represent a vast source of specialized materials with potential uses in sensing and screening applications. However, the strict requirement of the native lipid environment to preserve their structure and functionality presents an impediment in building biofunctional materials from these molecules. In general, the purification protocols remove the native lipid support structures found in the cellular environment that stabilize the membrane proteins. Furthermore, the membrane protein structure is often highly complex, typified by large, multisubunit complexes that not only span the lipid bilayer but also contain large (>2 nm) cytoplasmic and extracellular domains that protrude from the membrane. The present study is focused on using a biomimetic approach to build a stable, fluid microenvironment to be used to incorporate larger membrane proteins of interest into a tether-supported lipid bilayer membrane adequately spaced above a substrate passivated to liposome fusion and nonspecific adsorption. Our aim is to reintroduce the supporting structures of the native cell membrane using self-assembled supramolecular complexes constructed on microspheres in an artificial cytoskeleton motif. Central to our architecture is to utilize bacteriorhodopsin (bR), a transmembrane protein, as a biomembrane anchoring molecule to be tethered to surfaces of interest as a sparse structural element in the design. Compared to a typical lipid tether, which inserts into one leaflet of the lipid bilayer, bR anchoring provides an over 8-fold greater hydrophobic surface area in contact with the bilayer. In the work presented here, the silica microsphere surface was biofunctionalized with streptavidin to make it a suitable supporting interface. This was achieved by self-assembly of (p-aminophenyl)trimethoxysilane on the silica surface followed by subsequent conjugation of biotin-PEG3400 (PEG = poly(ethylene glycol) and PEG2000 for further passivation and the binding of streptavidin. We have conjugated bR with biotin-PEG3400 through amine-based coupling to use it as a tether. The biotin-PEG-bR conjugate was further labeled with Texas Red to facilitate localization via fluorescence imaging. Confocal microscopy was utilized to analyze the microsphere surface at different stages of surface modification by employing fluorescent staining techniques. Sparely tethered supported lipid bilayer membranes were constructed successfully on streptavidin-functionalized silica particles (5 mum) using a detergent-based method in which tethered bR nucleates self-assembly of the bilayer membrane. The fluidity of the supported membranes was analyzed using fluorescence recovery after photobleaching in confocal imaging detection mode. The phospholipid diffusion coefficients obtained from these studies indicated that nativelike fluidity was achieved in the tether-supported membranes, thus providing a prospective microenvironment for insertion of membrane proteins of interest.     

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

Markov State Models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov State Models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.