Biomedical subjects

Randall W Hall

Publications and source records attributed to Randall W Hall.

7 recordsLinked to original sources

PubMed2007

Structural characterization of Al10O6iBu16(mu-H)2, a high aluminum content cluster: further studies of methylaluminoxane (MAO) and related aluminum complexes.

The first structurally characterized isobutyl-containing aluminoxane compound is presented. The Al10O6iBu16(mu-H)2 (I) cluster is produced from neat octakis-isobutyltetraluminoxane (Al4O2iBu8) at 80 degrees C in 6-8 h followed by slow crystallization. The crystal is triclinic (space group P1) with the molecule lying on an inversion center. This aluminoxane contains both nearly linear, 154(2) degrees, aluminum-bridging hydrides and three-coordinate aluminum sites. Solid-state 27Al magic-angle spinning (MAS) NMR experiments were done at 19.6 and 40 T (833 MHz and 1.703 GHz, 1H) and at 30-35 kHz spinning speeds, leading to the determination of the Cq and eta values for the two four-coordinate Al sites and a lower limit of Cq for the three-coordinate Al site. Geometry-optimized restricted Hartree-Fock calculations at the double-zeta level of an idealized structure (methyl substituted, D2h geometry) yielded Cq and eta in close agreement with experiment; Cq agrees within 3 MHz.

Journal Article↗

PubMed2006

Methyaluminoxane (MAO) polymerization mechanism and kinetic model from ab initio molecular dynamics and electronic structure calculations.

MAO is the co-catalyst in metallocene catalytic systems, which are widely used in single-site olefin polymerization due to their high stereoselectivity. To date, the structures of the catalytically active compound or compounds in MAO have eluded researchers. Although many structural models have been proposed, none are generally accepted. In this study, aspects of the formation mechanism of MAO are addressed. Molecular dynamics simulations at the MP2 level of theory were carried out for presumed elementary steps in MAO formation via hydrolysis of trimethylaluminum (TMA). Methane production was observed, in agreement with experiment, as well as intermediate species that are consistent with the known structural features of MAO and similar to isolated and structurally characterized aluminoxanes. A (CH3)3Al-OH2 species, which we denote as TMA-OH2, containing a stable Al-O single bond emerged as the building block molecule. From this species, a hexameric cage was formed and activation barriers for the various reactions were calculated. Three distinct channels were identified for growth beyond the hexameric cage. It was concluded that MAO formation is a step polymerization through a bifunctional monomer, with [(CH3)Al-O] as the structural unit and a kinetic model was proposed. The structures that emerged were in agreement with the crystallographic evidence for aluminoxanes and support the experimental data regarding the MAO chemical composition.

Journal Article↗

PubMed2005

Simulation of electronic and geometric degrees of freedom using a kink-based path integral formulation: application to molecular systems.

A kink-based path integral method, previously applied to atomic systems, is modified and used to study molecular systems. The method allows the simultaneous evolution of atomic and electronic degrees of freedom. The results for CH4, NH3, and H2O demonstrate this method to be accurate for both geometries and energies. A comparison with density functional theory (DFT) and second-order Moller-Plesset (MP2) level calculations show the path integral approach to produce energies in close agreement with MP2 energies and geometries in close agreement with both DFT and MP2 results.

Journal Article↗

PubMed2005

Divergence, recombination and retention of functionality during protein evolution.

We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates). These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality--even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

Evolution, Molecular↗

PubMed2004

Tools and strategies for processing diffusion-ordered 2D NMR spectroscopy (DOSY) of a broad, featureless resonance: an application to methylaluminoxane (MAO).

UNLABELLED: DOSY has been extremely successful in many studies of molecular weight distributions, especially when the components are separable along the chemical shift axis. However, an unresolved NMR resonance yields the familiar problem of overlapping exponential decays. In a study of methylaluminoxane (MAO), a set of data processing and simulation tools were developed: read Bruker data files (Matlab); preliminary non-linear least-squares fit with f-test (Matlab); movie generation of the fits (Matlab); conversion of diffusion coefficients to molecular masses through molecular volumes (Gaussian-98); and simulation of DOSY data sets for various molecular mass distributions (Mathematica). These tools are presented here and briefly compared with other DOSY analysis methods. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00216-003-2457-1. The following Matlab and Mathematica files are made available: Plot_Raw_DOSY.m, Fit_Two_Component.m (which calls One_Gaussian_LEASTSQ.m, Two_Gaussian_LEASTSQ.m, and pFTest.m), and DOSY_theory.nb. Note: Matlab v5.2 optimization toolbox, as supplied, lacked a confidence interval subroutine; upon our request, confint.m was provided to the authors by Mathworks, Inc. Newer versions of Matlab have a similar program already included in the optimization.

Journal Article↗

PubMed2004

High-field 19.6T 27Al solid-state MAS NMR of in vitro aluminated brain tissue.

The combination of (27)Al high-field solid-state NMR (19.6T) with rapid spinning speeds (17.8 kHz) is used to acquire (27)Al NMR spectra of total RNA human brain temporal lobe tissues exposed to 0.10 mM Al(3+) (as AlCl(3)) and of human retinal pigment epithelial cells (ARPE-19), grown in 0.10 mM AlCl(3). The spectra of these model systems show multiple Al(3+) binding sites, good signal/noise ratios and apparent chemical shift dispersions. A single broad peak (-3 to 11 ppm) is seen for the aluminated ARPE-19 cells, consistent with reported solution-state NMR chemical shifts of Al-transferrin. The aluminated brain tissue has a considerably different (27)Al MAS NMR spectrum. In addition to the transferrin-type resonance, additional peaks are seen. Tentative assignments include: -9 to -3 ppm, octahedral AlO(6) (phosphate and water); 9 ppm, condensed AlO(6) units (Al-O-Al bridges); 24 ppm, tetrahedral AlO(3)N and/or octahedral Al-carbonate; and 35 ppm, more N-substituted aluminum and /or tetrahedral AlO(4). Thus, brain tissue is susceptible to a broad range of coordination by aluminum. Furthermore, the moderate (27)Al C(Q) values (all less than 10 MHz) suggest future NMR studies may be performed at 9.4T and a spin rate of 20 kHz.

Aluminum↗

PubMed2003

Microscopic theory of network glasses.

A theory of the glass transition of network liquids is developed using self-consistent phonon and liquid state approaches. The dynamical transition and entropy crisis characteristic of random first-order transitions are mapped as a function of the degree of bonding and density. Using a scaling relation for a soft-core model to crudely translate the densities into temperatures, theory predicts that the ratio of the dynamical transition temperature to the laboratory transition temperature rises as the degree of bonding increases, while the Kauzmann temperature falls explaining why highly coordinated liquids are "strong" while van der Waals liquids without coordination are "fragile."

Journal Article↗