Scientific Publications 2005
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B
2005. "Stabilization of very rare tautomers of uracil by an excess electron." Physical Chemistry Chemical Physics. PCCP 7(10):2116-2125. Abstract We characterized valence-type and dipole-bound anionic states of uracil using various electronic structure methods. We found that the most stable anion is related to neither the canonical 2,4-dioxo nor a rare imino-hydroxy tautomer. Instead, it is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, , is characterized by an electron vertical detachment energy (VDE) of 1267 meV and it is adiabatically stable with respect to the canonical neutral by 3.93 kcal/mol. It is also more stable by 2.32 and 5.10 kcal/mol than the dipole-bound ( ) and valence anion ( ), respectively, of the canonical tautomer. The VDE values for and are 73 and 506 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2499 meV has a proton transferred from N3H to C5 ( ). It is less stable than the neutral canonical tautomer by 1.38 kcal/mol. The mechanism of formation of anionic tautomers with the carbon C5 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of anionic tautomers with carbon atoms protonated might be unstable upon an excess electron detachment. Indeed, the neutral systems resulting from electron detachment from and evolve along barrier-free decomposition pathways to a linear or a bicyclo structure, respectively, which might be viewed as lesions to RNA. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; remains the most stable, being followed by , and .
2005. "Anion of the Formic Acid Dimer as a Model for Intermolecular Proton Transfer Induced by a [pi]* Excess Electron." Journal of Chemical Physics 122(20):article #204304. Abstract The neutral and anionic formic acid dimers have been studied at the second order Møller-Plesset and coupled cluster level of theory with single, double, and perturbative triple excitations with augmented, correlation consistent basis sets of double- and triple-zeta quality. Scans of the potential energy surface for the anion were performed at the density functional level of theory with a hybrid B3LYP functional and a high quality basis set. Our main finding is that the formic acid dimer is susceptible to intermolecular proton transfer upon an excess electron attachment. The unpaired electron occupies a * orbital, the molecular moiety that accommodates an excess electron “buckles”, and a proton is transferred to the unit where the excess electron is localized. In consequence of these geometrical transformations the electron vertical detachment energy becomes substantial, 2.35 eV. The anion is barely adiabatically unstable with respect to the neutral at 0 K. However, at standard conditions and in terms of Gibbs free energy, the anion is more stable than the neutral by 0.04 eV. The neutral and anionic dimers display different IR characteristics. In summary, the formic acid dimer can exist in two quasidegenerate states (neutral and anionic), which can be viewed as “zero” and “one” in the binary system. These two states are switchable and distinguishable.
2005. "Summary of ISO/TC 201 Standard: XVIII, ISO 19318: 2004 – Surface Chemical Analysis – X-Ray Photoelectron Spectroscopy - Reporting of Methods Used for Charge Control and Charge Correction." Surface and Interface Analysis 37(5):524?526. Abstract X-ray photoelectron spectroscopy (XPS) is widely used for characterization of surfaces of materials. Elements in the sample (with the exception of hydrogen and helium) are identified from comparisons of the binding energies of their core levels, determined from measured photoelectron spectra, with tabulated values of these binding energies for the various elements. Information on the chemical state of the detected elements can frequently be obtained from small variations (typically between 0.1 eV and 10 eV) of the core-level binding energies from the corresponding values for the pure elements. Reliable determination of chemical shifts often requires that the binding-energy scale of the XPS instrument be calibrated with an uncertainty that could be as small as 0.1 eV. The surface potential of an insulating specimen will generally change during an XPS measurement due to surface charging, and it is then difficult to determine binding energies with the accuracy needed for elemental identification or chemical-state determination. There are two steps in dealing with this problem. First, experimental steps can be taken to minimize the amount of surface charging (charge-control methods). Second, corrections for the effects of surface charging can be made after acquisition of the XPS data (charge-correction methods). Although the buildup of surface charge can complicate analysis in some circumstances, it can be creatively used as a tool to gain information about a specimen.
2005. "Summary: Update to ASTM Guide E 1523 to Charge Control and Charge Referencing Techniques in X-ray Photoelectron Spectroscopy." Journal of Vacuum Science and Technology A--Vacuum, Surfaces and Films 23(3):577-578. Abstract An updated version of the ASTM guide E1523 to the methods to charge control and charge referencing techniques in x-ray photoelectron spectroscopy has been released by ASTM. The guide is meant to acquaint x-ray photoelectron spectroscopy (XPS) users with the various charge control and charge referencing techniques that are and have been used in the acquisition and interpretation of XPS data from surfaces of insulating specimens. The current guide has been expanded to include new references as well as recommendations for reporting information on charge control and charge referencing. The previous version of the document had been published in 1997.
2005. "Simple Method for Estimating and Comparing of X-Ray Damage Rates." Journal of Vacuum Science and Technology A--Vacuum, Surfaces and Films 23(6):1740-1744. doi:10.1116/1.2073387 Abstract This note describes an approach for estimating and comparing rates or thresholds for x-ray induced specimen damage during surface analysis. The method uses a common reference material to compare x-ray damage rates reported in the literature and in publications to the rates of damage that may occur on a specific instrument. Although the method makes several assumptions that are only partially valid, results from a few damage data-sets appear acceptably consistent when comparing estimates to a time for 10% damage or signal change.
2005. "Challenges in Applying Surface Analysis Methods to Nanoparticles and Nanostructured Materials." Journal of Surface Analysis 12(2):101-108. Abstract Nanostructured materials of various types and forms are formulated in a variety of novel ways and increasingly subject to many types of chemical and physical analysis. Since nanomaterial systems contain a relatively large amount of surface or interface area, it should be natural to characterize them using tools designed to analyze surfaces and interfaces. We have found that nanoparticles and other nanostructured materials present a variety of challenges. This paper reviews environmental effects on measurements of Ce-oxide nanoparticles and nanoporous silica films and focuses on efforts to quantify the ion damage and sputter rates for the Fe-oxide nanoparticles. We have found that nanoparticles appear more readily damaged and to have sputter rates that exceed “bulk” materials. To verify such effects, we need to know many details about size, size distribution, density, and shape that are not always easily obtained.
2005. "Substitutional Nitrogen in Nanodiamond and Bucky-Diamond Particles." Journal of Physical Chemistry B 109(36):17107-17112. doi:10.1021/jp0524126 Abstract The inclusion of dopants (such as nitrogen) in diamond nanoparticles is expected to be important for use in future nanodevices, such as qubits for quantum computing. Although most commercial diamond nanoparticles contain a small fraction of nitrogen, it is still unclear whether it is located within the core or at the surface of the nanoparticle. Presented here are density functional tight binding simulations examining the configuration, potential energy surface, and electronic charge of substitutional nitrogen in nanodiamond and bucky-diamond particles. The results predict that nitrogen is likely to be positioned at the surface of both hydrogenated nanodiamond and (dehydrogenated) bucky-diamond, and that the coordination of the dopants within the particles is dependent upon the surface structure.
2005. "Density Functional Study of H-induced Defects as Nucleation Sites in Hybrid Carbon Nanomaterials." Chemistry of Materials 17(3):527-535. doi:10.1021/cm0488682 S0897-4756(04)08868-4 Abstract The abstract for this product is not available at this time.
2005. "Anatase and Rutile Surfaces with Adsorbates Representativeof Acidic and Basic Conditions." Surface Science 582:173-188. doi:10.1016/j.susc.2005.03.014 Abstract Presented here are density functional theory results of the structure and energetics of selected low index stoichiometric surfaces of the anatase and rutile titanium dioxide polymorphs, passivated with complete monolayers of adsorbates chosen to represent acidic and basic conditions. The adsorbates differ in each case by varying the hydrogen to oxygen ratio with respect to a neutral, water-terminated surface. The results are compared for each of the 30 surfaces examined here, to identify relationships between surface chemistry, surface free energy, surface stress and (upper-most) surface tri-layer reconstructions. Within our model, the results show that termination with water consistently results in the lowest values of surface free energy, but not necessarily the lowest surface stress.
2005. "Modeling the Morphology and Phase Stability of TiO₂ Nanocrystals in Water." Journal of Chemical Theory and Computation 1(1):107-116. Abstract The potential of titanium dioxide nanoparticles for advanced photochemical applications has prompted a number of studies to analyze the size, phase, and morphology dependent properties. Previously we have used a thermodynamic model of nanoparticles as a function of size and shape to predict the phase stability of titanium dioxide nanoparticles, with particular attention given to the crossover of stability between the anatase and rutile phases. This work has now been extended to titanium dioxide nanoparticles in water, to examine the effects of various adsorption configurations on the equilibrium shape and the phase transition. Density functional calculations have been used to accurately determine surface energies and surface tension of low index hydrated stoichiometric surfaces of anatase and rutile, which are presented along with a brief outline of the surface structure. We have shown that morphology of TiO₂ nanocrystals is affected by the presence of water, resulting in variations in the size of the (001) and (001) truncation facets in anatase, and a reduction in the aspect ratio of rutile nanocrystals. Our results also highlight that the consideration of hydrated nanocrystal surfaces is necessary to accurately predict the correct size dependence of the anatase to rutile phase transition.
2005. "Equilibrium Morphology of Face-Centered Cubic Gold Nanoparticles >3 nm and the ShapeChanges Induced by Temperature." Journal of Physical Chemistry B 109(51):24465-24472. doi:10.1021/jp054279n Abstract Many of the unique properties of metallic nanoparticles are determined not only by their finite size but also by their shape, defined by the crystallographic orientation of the surface facets. These surfaces (and therefore the nanoparticles themselves) may differ in a number of ways, including surface atom densities, electronic structure, bonding, chemical reactivities, and thermodynamic properties. In the case of gold, it is known that the melting temperature of nanoparticles strongly depends on the crystal size and that the shape may alter considerably (and yet somewhat unpredictably) during annealing. In this work we use first principle calculations and a thermodynamic model to investigate the morphology of gold nanoparticles in the range 3-100 nm. The results predict that the equilibrium shape of gold nanoparticles is a modified truncated octahedron and that the (size-dependent) melting of such particles is preceded by a significant change in the nanoparticle’s morphology.
2005. "What Determines the Sticking Probability of Water Molecules on Ice?" Physical Review Letters. doi:10.1103/PhysRevLett.95.223201 Abstract We present both experimental and theoretical studies of the sticking of water molecules on ice. The sticking probability is unity over a wide range in energy (0.5 eV–1.5 eV) when the molecules are incident along the surface normal, but drops as the angle increases at high incident energy. This is explained in terms of the strong orientational dependence of the interaction of the molecule with the surface and the time required for the reorientation of the molecule. The sticking probability is found to scale with the component of the incident velocity in the plane of the surface, unlike the commonly assumed normal or total energy scaling.
2005. "Bacterial wall structure and implications for interaction with metal ions and minerals." Journal of Nuclear and Radiochemical Sciences 6(1):7-10. Abstract New techniques in the rapid freezing of cells, so that they are vitrified, and cryo-transmission electron microscopy (cryoTEM) of the frozen hydrated thin-sections from the vitrified cells are showing their true native structure. Unlike other forms of TEM, frozen hydrated thin-sections cannot be contrasted by heavy-metal tains (such as U, Pb, and Os) and their contrast is via the inherent density of the constituent molecules within the cells. Therefore, these frozen sections show the true mass distribution within the biomatter. Another cryoTEM technique, reezesubstitution, also produces thin sections for viewing by TEM, but these are plastic sections of heavy-metal stained cells. The heavy-metal ions of the stain complex to the available reactive sites of the biomatter. When such images are compared to those from the frozen hydrated sections, a clear interpretation of native structure and its metal reactivity can be made. These types of observations will be invaluable for the study of microbemetal/radionuclide interactions.
2005. "Planar-to-Tubular Structural Transition in Boron Clusters: B20 as the Embryo of Single-Walled Boron Nanotubes." Proceedings of the National Academy of Sciences of the United States of America 102(4):961-964. Abstract Experimental and computational simulations revealed that boron clusters, which favor planar (2D) structures up to 18 atoms, prefer three-dimensional (3D) structures beginning at 20 atoms. Using global optimization methods, we found that the B20 neutral cluster has a double-ring tubular structure with a diameter of 5.2 Å. In the B20- anion, the tubular structure is shown to be isoenergetic to 2D structures, which were observed and confirmed by photoelectron spectroscopy. The 2D to 3D structural transition observed at B20, reminiscent to the ring-to-fullerene transition at C20 in carbon clusters, suggests it may be considered as the embryo of the thinnest single-walled boron nanotubes.
2005. "All-Metal Aromaticity and Antiaromaticity." Chemical Reviews 105(10):3716-3757. Abstract Metals and organic molecules are at the opposite sides in chemistry. Thus one may think that chemical bonding models, such as aromaticity, developed in organic chemistry will not be applicable in systems involving metallic elements. Yet in recent years there have been significant advances in extending the aromaticity and antiaromaticity concepts into the realm of metal clusters and alloys. These new developments have shown that aromaticity and antiaromaticity in metal systems have frequently multiple nature, being o-aromatic/antiaromatic and n-aromatic/antiaromatic, which is not found in organic aromatic/antiaromatic molecules.
2005. "A Multispectrum Analysis of the v2 Band of H12C14N: Part II. Theoretical Calculations of Self-Broadening, Self-Induced Shifts, and Their Temperature Dependences." Journal of Molecular Spectroscopy 231(1):85-95. Abstract A semiclassical theory based upon the Robert-Bonamy formalism has been developed in order to explain the experimental measurements of self-broadening, self-induced pressure shift coefficients in the v1, v2, 2v2 bands of H12C14N and the 2v1 band of H13C14N as well as the temperature dependences of these parameters with special emphasis on the v2 band. Our calculations include only electrostatic interactions and neglect the vibrational dependence of the isotropic part of the intermolecular potential, which probably has a weak contribution to the HCN self-shifts for the bands investigated in this study. The agreement between theory and measurements is good in the cases of self-broadening coefficients and their variation with temperature, as well as the self-shift coefficients determined at room temperature. However, the observed temperature dependence of self-shift coefficients in the v2 band is different from that derived theoretically.
2005. "The Solution Conformation of Triarylmethyl Radicals." Journal of Magnetic Resonance 172(2):254-267. Abstract Hyperfine coupling tensors to 1H, 2H and natural abundance 13C were measured using X-band pulsed electron nuclear double resonance (ENDOR) spectroscopy for two triarylmethyl (trityl) radicals used in electron paramagnetic resonance imaging and oximetry: methyl tris(8-carboxy-2,2,6,6-tetramethyl-benzo[1,2d:4,5-d’]bis(1,3)dithiol-4-yl and methyl tris(8-carboxy-2,2,6,6-tetramethyl(-d3)-benzo[1,2d:4,5-d’]bis(1,3)dithiol-4-yl. Quantum chemical calculations using Density Functional Theory predict a structure that reproduces the experimentally determined hyperfine tensors. The radicals are propeller-shaped with the three aryl rings nearly mutually orthogonal. The central carbon atom carrying most of the unpaired electron spin density is completely surrounded by the sulfur atoms in the radical and is completely shielded from solvent. This structure explains features of the electron spin relaxation of these radicals and suggests ways in which the radicals can be chemically modified to improve their characteristics for imaging and oximetry.
2005. "Track Structure in DNA Irradiated with Heavy Ions ." Radiation Research 163(4):447-454. Abstract The spatial properties of trapped radicals produced in heavy ion-irradiated solid DNA at 77 K have been probed using pulsed Electron Paramagnetic Double Resonance (PELDOR or DEER) techniques. Salmon testes DNA hydrated to twelve water molecules per nucleotide was irradiated with 40Ar ions of energy 100 MeV/nucleon and LET ranging from 300 to 400 keV/μ. Irradiated samples were maintained at cryogenic temperature at all times. PELDOR measurements were made using a refocused echo detection sequence that allows dipolar interaction between trapped radicals to be observed. The EPR spectrum is attributed to electron loss/gain DNA base radicals and neutral carbon-centered radicals that likely arise from sugar damage. We find a radical concentration of 13.5*1018 cm-3 in the tracks and a track radius of 6.79 nm. The cross section of these tracks is 144 nm2 yielding a lineal radical density of 2.6 radicals/nm. Based upon the yields previously determined for particles having calculated LET values of 300 – 400 keV/mm and our measured lineal density, we obtain an LET of 270 keV/mm, which is in good agreement with the calculated range of values. These measurements of radical density and spatial extent provide the first direct experimental determination of track characteristics in irradiated DNA.
2005. "The Serine-rich Domain from Crk-associated Substrate (p130Cas) is a Four-helix Bundle." Journal of Biological Chemistry 280(23):21908-21914. Abstract p130Cas (Crk-associated substrate) is a docking protein that is involved in assembly of focal adhesions and concomitant cellular signaling. It plays a role in physiological regulation of cell adhesion, migration, survival and proliferation, as well as in oncogenic transformation. The molecule consists of multiple protein-protein interaction motifs including a serine-rich region that is positioned between Crk and Src-binding sites. This study reports the first structure of a functional domain of Cas. The solution structure of the serine-rich region has been determined by nuclear magnetic resonance spectroscopy (NMR) demonstrating that this is a stable domain that folds as a four-helix bundle, a protein-interaction motif.
2005. "Influence of substituents on the strength of aryl C-H•••anion hydrogen bonds ." Organic Letters 7(22):5031-5034. Abstract When electron withdrawing substituents are present aryl C–H groups become powerful hydrogen bond donors, forming stronger complexes than obtained with conventional O–H and N–H groups.
2005. "Conformational Analysis and Rotational Barriers of Alkyl- and Phenyl-Substituted Urea Derivatives ." Journal of Physical Chemistry A 109(5):832-842. Abstract Potential energy surfaces (PES) for rotation about the N-C(sp3) or N-C(aryl) bond and energies of stationary points on PES for rotation about the C(sp2)-N bond are reported for methylurea, ethylurea, isopropylurea, t-butylurea and phenylurea using the B3LYP/DZVP2 and MP2/aug-cc-pVDZ methods. The analysis of alkylureas reveals cis and (less stable) trans isomers that adopt anti geometries, whereas syn geometries do not correspond to stationary points. In contrast, the analysis of phenylurea reveals that the lowest energy form at the MP2 level is a trans isomer in a syn geometry. The fully optimized geometries are in good agreement with crystal structure data, and PESs are consistent with the experimental dihedral angle distribution. Rotation about the C(sp2)-N bond in alkylureas and phenylurea is slightly more hindered (8.6-9.4 kcal/mol) than the analogous motion in the unsubstituted molecule (8.2 kcal/mol). At the MP2 level of theory, the maximum barriers to rotation for the methyl, ethyl, isopropyl, t-butyl and phenyl groups are predicted to be 0.9, 6.2, 6.0, 4.6 and 2.4 kcal/mol, respectively. The results are used to benchmark the performance of the MMFF94 force field. Systematic discrepancies between MMFF94 and MP2 results were improved by modification of several torsional parameters.
2005. "Solution-state NMR Investigation of DNA Binding Interactions in Escherichia coli Formamidopyrimidine-DNA Glycosylase (Fpg): A Dynamic Description of the DNA/Protein Interface ." DNA Repair 4(3):327-339. Abstract Formamidopyrimidine-DNA glycosylase (Fpg) is a base excision repair protein that removes oxidative DNA lesions. Recent crystal structures of Fpg bound to DNA revealed residues involved in damage recognition and enzyme catalysis, but failed to shed light on the dynamic nature of the processes. To examine the structural and dynamic changes that occur in solution when Fpg binds DNA, NMR spectroscopy was used to study Escherichia coli Fpg free and bound to a double-stranded DNA oligomer (13-PD) containing propanediol, a non-hydrolyzable abasic-site analogue. Only 209 out of a possible 252 (83%) free-precession HSQC cross peaks were observed and 180 of these were assignable, indicating that ~30% of the residues undergo intermediate timescale motion that makes them intractable in backbone assignment experiments. DNA titration experiments revealed line broadening and chemical shift perturbations for backbone amides nearby and distant from the DNA binding surface, but failed to quench the intermediate time-scale motion observed for free Fpg. CPMG-HSQC experiments revealed millisecond to microsecond motion for the backbone amides of D91 and H92 that was quenched upon binding 13-PD. Collectively, these observations reveal that, in solution, Fpg contains highly flexible regions. The dynamic nature of Fpg, especially at the DNA binding surface, may be key to its processive search mechanism.
2005. "Ab Initio Electronic Structure Study of One-Electron Reduction Of Polychlorinated Ethylenes ." Journal of Physical Chemistry A 109(26):5905-5916. Abstract Polychlorethylene radicals, anions, and radical anions are potential intermediates in the reduction of polychlorinated ethylenes (C2Cl4, C2HCl3, trans-C2H2Cl2, cis-C2H2Cl2, 1,1-C2H2Cl2, C2H3Cl). Ab initio electronic structure methods were used to calculate the thermochemical properties, Hof(298.15K), So(298.15K,1 bar),GS(298.15K, 1 bar) of 37 different polychloroethylene-yl radicals, anions, and radical anion complexes: C2HyCl3-y•, C2HyCl3-y-, and C2HyCl4-y-• for y = 0,1,2,3 for the purpose of characterizing reduction mechanisms of polychlorinated ethylenes. In this study 8 radicals, 7 anions, and 22 radical anions were found to have stable structures, i.e minima on the potential energy surfaces. This multitude of isomers for C2HyCl4-y-• radical anion complexes are *, *, and -H…Cl- structures. Several stable * radical anionic structures were obtained for the first time through the use of restricted open-shell theories. On the basis of the calculated thermochemical estimates, the overall reaction energetics (in the gas phase and aqueous phase) for several mechanisms of the first electron reduction of the polychlorinated ethylenes were determined. In almost all of the gas-phase reactions, the thermodynamically most favorable pathways involve —HCl- complexes of the C2HyCl4-y-• radical anion, in which a chloride ion is loosely bound to a hydrogen of a C2HxCl2-x• radical. The exception is for C2Cl4, in which the most favorable anionic structure is a loose * radical anion complex, with a nearly iso-energetic * radical anion. Solvation significantly changes the product energetics with the thermodynamically most favorable pathway leads to C2HyCl3-y• + Cl-. The results suggest that a higher degree of chlorination favors reduction, and that reduction pathways involving the C2HyCl3-y- anions are high energy pathways.
