Scientific Publications 2004
2004. "High-level ab initio calculations for the four low-lying families of minima of (H2O)(20): 1. Estimates of MP2/CBS binding energies and comparison with empirical potentials ." Journal of Chemical Physics 121(6):2655-2663. Abstract We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest lying isomers within each of the four major families of minima of (H2O)20. These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CBS estimates are: -200.1 kcal/mol (dodecahedron, 30 hydrogen bonds), -212.6 kcal/mol (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds) and –217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). The energetic ordering of the various (H2O)20 isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within < 1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3-5%.
2004. "High-Resolution Solid-State Nuclear Magnetic Resonance Experiments on Highly Radioactive Ceramics." Review of Scientific Instruments 75(12):5232-5236. Abstract A triple containment magic-angle spinning rotor insert system has been developed and a sample handling procedure formulated for safety analyzing highly radioactive solids by high resolution solid state NMR. The protocol and containment system have been demonstrated for magic angle spinning (MAS) experiments on ceramic samples containing 5-10 wt% 239Pu and 238Pu at rotation speeds of 3500 Hz. The technique has been used to demonstrate that MASNMR experiments can be used to measure amorphous atomic number fractions produced during accelerated internal radioactive decay. This will allow incorporated ν-emitters with short half-lives to be used to model the long-term radiation tolerance of potential ceramic radioactive waste forms. It is believed to be the first example of MASNMR spectroscopy on samples containing fissionable isotopes.
2004. "Yeast mating for combinatorial Fab library generation and surface display." FEBS letters 564(1-2):24-34. Abstract Yeast display of antibody fragments has proven to be an efficient and productive means for directed evolution of single chain Fv (scFv) antibodies for increased affinity and thermal stability, and more recently for the display and screening of a non-immune library. In this paper, we describe an elegant and simple method for constructing large combinatorial Fab libraries for display on the surface of Saccharomyces cerevisiae, from modestly sized, and easily constructed, heavy and light chain libraries. To this end, we have constructed a set of yeast strains and a two vector system for heavy chain and light chain surface display of Fab fragments with free native amino termini. Through yeast mating of the haploid libraries, a very large heterodimeric immune Fab library was displayed on the diploids and high affinity antigen specific Fabs were isolated from the library.
2004. "An Aqueous Thermodynamic Model for the Complexation of Nickel with EDTA Valid to high Base Concentration." Journal of Solution Chemistry 33(9):1161-1180. doi:10.1023/B:JOSL.0000048051.48779.0c Abstract An aqueous thermodynamic model is developed which accurately describes the effects of high base concentration on the complexation of Ni2+ by ethylenedinitrilotetraacetic acid (EDTA). The model is primarily developed from an extensive data on the solubility of Ni(OH)2(c) in the presence of EDTA and in the presence and absence of Ca2+ as the competing metal ion. The solubility data for Ni(OH)2(c) were obtained in solutions ranging in NaOH concentration from 0.01 to 11.6m, and in Ca 2+ concentrations extending to saturation with respect to portlandite, Ca(OH)2. Owing to the inert nature of the Ni-EDTA complexation reactions, solubility experiments were approached from both the oversaturation and undersaturation direction and over time frames extending to 413 days. The final aqueous thermodynamic model is based upon the equations of Pitzer, accurately predicts the observed solubilities to concentrations as high as 11.6m NaOH, and is consistent with UV-Vis spectroscopic studies of the complexes in solution.
2004. "Noncovalent Functionalization of Carbon Nanotubes with Molecular Anchors using Supercritical Fluids ." Journal of Physical Chemistry B 108(25):8737-8741. Abstract In this article we describe a facile and effective method for the modification of multi wall carbon nanotubes with molecular anchor molecules using supercritical fluids. Through choice of deposition conditions the degree of loading in these nanotube-anchor structures can be controlled to achieve sub-monolayer, monolayer, or greater-than-monolayer coverage. This level of control represents a potential advantage of supercritical fluids over liquid solvents for anchor deposition. Employment of the described technique is expected to enable the direct addition of desired chemical functionality to many carbon nanotube structures for a variety of applications.
2004. "Identification of Sporulated and Vegetative Bacteria using Statistical Analysis of Fourier Transform Mid-Infrared Transmission Data ." Applied Spectroscopy 58(2):203-211. Abstract A combined mid-infrared spectroscopic/statistical modeling approach for the discrimination and identification, at the strain level, of both sporulated and vegetative bacterial samples is presented. Transmission mode spectra of bacteria dried on ZnSe windows were collected using a Fourier-transform mid-infrared (FTIR) spectrometer. Five Bacillus bacterial strains (B. atrophaeus 49337, B. globigii, B. thuringiensis ssp. kurstaki, B. subtilis 49780, and B. subtilis 6051) were used to construct a reference spectral library and to parameterize a four-step statistical model for the systematic identification of bacteria. The statistical methods used included principal-component analysis (PCA), classification and regression trees (CART), and Mahalanobis-distance calculations. Internal cross-validation studies successfully classified 100% of the samples into their correct physiological state (sporulated or vegetative) and identified 67% of the samples correctly as to their bacterial strain. Analysis of thirteen blind samples, which included reference and other bacteria, nonbiological materials, and mixtures of both nonbiological and bacterial samples, yielded comparable accuracy. The chief advantage of this approach is the accurate identification of unknown bacteria, including spores, in a matter of minutes.
2004. "Activation of the Sulfhydryl Group by Mo Centers: Kinetics of Reaction of Benzyl Radical with a Binuclear Mo(mu-SH)Mo Complex and with Arene and Alkane Thiols." Journal of the American Chemical Society 126(21):6680-6691. Abstract This paper provides evidence from kinetic experiments and electronic structure calculations of a significantly reduced S-H bond strength in the Mo(mu-SH)Mo function in the homogeneous catalyst model, CpMo(mu-S)2(mu-SH)2MoCp (1, Cp = eta(5)-cyclopentadienyl).
2004. "A Film Depositional Model of Permeability for Mineral Reactions in Unsaturated Media." Vadose Zone Journal (3):1414-1424. Abstract A new modeling approach based on the biofilm models of Taylor et al. (1990, Water Resources Research, 26, 2153-2159) has been developed for modeling changes in porosity and permeability in saturated porous media and implemented in an inorganic reactive transport code. Application of the film depositional models to mineral precipitation and dissolution reactions requires that calculations of mineral films be dynamically changing as a function of time dependent reaction processes. Since calculations of film thicknesses do not consider mineral density, results show that the film porosity model does not adequately describe volumetric changes in the porous medium. These effects can be included in permeability calculations by coupling the film permeability models (Mualem and Childs and Collis-George) to a volumetric model that incorporates both mineral density and reactive surface area. Model simulations demonstrate that an important difference between the biofilm and mineral film models is in the translation of changes in mineral radii to changes in pore space. Including the effect of tortuosity on pore radii changes improves the performance of the Mualem permeability model for both precipitation and dissolution. Results from simulation of simultaneous dissolution and secondary mineral precipitation provides reasonable estimates of porosity and permeability. Moreover, a comparison of experimental and simulated data show that the model yields qualitatively reasonable results for permeability changes due to solid-aqueous phase reactions.
2004. "Lanthanide Selective Sorbents: Self-Assembled Monolayers on Mesoporous Supports (SAMMS) ." Journal of Materials Chemistry 14(22):3356-3363. Abstract Through the marriage of mesoporous ceramics with self-assembled monolayer chemistry, the genesis of a powerful new class of environmental sorbent materials has been realized. By coating the mesoporous ceramic backbone with a monolayer terminated with a lanthanide-specific ligand, it is possible to couple high lanthanide binding affinity with the high loading capacity (resulting from the extremely high surface area of the support). This lanthanide-specific ligand field is created by pairing a “hard” anionic Lewis base with a suitable synergistic ligand, in a favorable chelating geometry. Details of the synthesis, characterization, lanthanide binding studies, binding kinetics, competition experiments and sorbent regeneration studies are summarized.
2004. "Lanthanide Selective Sorbents: Self-Assembled Monolayers on Mesoporous Supports (SAMMS)." Journal of Materials Chemistry 14(22):3356-3363. Abstract Through the marriage of mesoporous ceramics with self-assembled monolayer chemistry, the genesis of a powerful new class of environmental sorbent materials has been realized. By coating the mesoporous ceramic backbone with a monolayer terminated with a lanthanide-specific ligand, it is possible to couple high lanthanide binding affinity with the high loading capacity (resulting from the extremely high surface area of the support). This lanthanide-specific ligand field is created by pairing a “hard” anionic Lewis base with a suitable synergistic ligand, in a favorable chelating geometry. Details of the synthesis, characterization, lanthanide binding studies, binding kinetics, competition experiments and sorbent regeneration studies are summarized
2004. "Terminal Ligand Influence on the Electronic Structure and Intrinsic Redox Properties of the [Fe4S4]2+ Cubane Clusters." Inorganic Chemistry 43(12):3647-3655. Abstract We used photoelectron spectroscopy (PES) to study how the terminal ligands influence the electronic structure and redox properties of the [4Fe-4S] cubane in several series of ligand-substituted analogue complexes: [Fe4S4CI4-x(CN)x]2-, [Fe4S4CI4-x(SCN)x]2-, [Fe4S4CI4-x(OAc)x]2-, [Fe4S4(SC2H5)4-x(OPr)x]2-, and [Fe4S4(SC2H5)4-x(CI)x]2-(x=0-4). All the ligand-substituted complexes gave similar PES spectra as the parents, suggesting that the mixed-ligand coordination does not perturb the electronic structure of the cubane core significantly.