Scientific Publications 2004
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2004. "Relative Proton Affinities from Kinetic Energy Release Distributions for Dissociation of Proton-Bound Dimers: 2. Diamines as a Test Case." International Journal of Mass Spectrometry 233:223-231. Abstract Dissociation of proton-bound dimers containing diamines is often characterized by a substantial entropy difference between the two competing reaction channels. Kinetic energy release distributions (KERDs) upon dissociation of diamine-containing dimers are utilized along with Finite Heat Bath theory analysis to obtain relative proton affinities of monomeric species composing the dimer. When dissociation of a proton-bound dimer is not associated with reverse activation barrier our method provides reliable relative energetics and dynamics.
2004. "Raman Under Nitrogen. The High-Resolution Raman Spectroscopy of Crystalline Uranocene, Thorocene, and Ferrocene." Journal of Chemical Physics 120(6):2708-2718. Abstract The utility of recording Raman spectroscopy under liquid nitrogen, a technique we call Raman Under Nitrogen (RUN), is demonstrated for ferrocene, uranocene and thorocene. Using RUN, low temperature (liquid nitrogen cooled) Raman spectra for these compounds exhibit higher resolution than previous studies and new vibrational features are reported. The first Raman spectra of crystalline uranocene at 77 K are reported using excitation from argon (5145 Å) and krypton (6764 Å) ion lasers. The spectra obtained showed bands corresponding to vibrational transitions at 212, 236, 259, 379, 753, 897, 1500, and 3042 cm-1 , assigned to ring-metal-ring stretching, ring-metal tilting, out-ofplane CCC bending, in-plane CCC bending, ring-breathing, C-H bending, CC stretching and CH stretching, respectively. The assigned vibrational bands are compared to those of uranocene in THF and thorocene. All vibrational frequencies of the ligands, except the 259 cm-1 out-of-plane CCC bending mode, were found to increase upon coordination. A broad polarizable band centered about ~460 cm-1 was also observed. The 460 cm-1 band is greatly enhanced relative to the vibrational Raman transitions with excitation from the krypton ion laser, which is indicative of an electronic resonance Raman process as has been shown previously. The electronic resonance Raman band is observed to split into three distinct bands at 450, 461 and 474 cm-1 with 6764 Å excitation. Relativistic density functional theory (DFT) is used to provide theoretical interpretations of the measured spectra.
2004. "A Direct Route towards Assembly of Nanoparticle-Carbon Nanotube Composite Materials ." Langmuir 20(14):6019-6025. Abstract The exploration of nanoparticle-structured thin films as sensing materials desires maximum accessibility of analytes and effective mass transport within the nanostructure. This paper explores the viability of creating nanoparticle-carbon nanotube (CNTs) as composite interfacial materials to enhance such properties. We report findings of an investigation of the assembly of monolayer-protected gold nanoparticles on multi-walled CNTs. A simple and effective route has been demonstrated for assembling nanoparticles of 2-5 nm core sizes onto CNTs with controllable coverage and interparticle spatial properties. The composite nanomaterials can be dispersed in organic solvent and cast on interdigitated microelectrode surface. The skeleton-like nanocomposite materials have been examined for chemiresistor sensing of volatile organic compounds. The response profiles and sensitivities of the nanocomposites determined for the sorption of a series of vapors have been shown to exhibit different or enhanced sensing properties in comparison with similar but nanotube-free nanoparticle assemblies. The observation of these results can be attributed to a combination of three factors, the increased accessibility of analytes to the nanostructure, the enhanced mass transport characteristics, and the unique electronic properties of the nanocomposite materials. Implications of the findings to the design of nanostructured sensing materials are also discussed.
2004. "Probing Ion Channel Conformational Dynamics Using Simultaneous Single-Molecule Ultrafast Spectroscopy and Patch-Champ Electric Recording." Applied Physics Letters 84(10):1792-1794. Abstract A new approach to probing single-molecule ion channel kinetics and conformational dynamics, patch-clamp confocal fluorescence microscopy (PCCFM), uses simultaneous ultrafast fluorescence spectroscopy and single-channel electric current recording.
2004. "Structural Criteria for the Rational Design of Selective Ligands: Convergent Hydrogen Bonding Sites for the Nitrate Anion." Journal of the American Chemical Society 126(25):7925-7934. Abstract Molecular hosts for anion complexation are often constructed by combining two or more hydrogen bonding functional groups, D–H. The deliberate design of complementary host architectures requires knowledge of the optimal geometry for the hydrogen bonds formed between the host and the guest. Herein, we present a detailed study of the structural aspects of hydrogen bonding interactions with the NO3– anion. A large number of crystal structures are analyzed to determine the number of hydrogen bond contacts per anion and to further characterize the structural aspects of these interactions. Electronic structure calculations are used to determine stable geometries and interaction energies for NO3– complexes with several simple molecules possessing D–H groups, including water, methanol, N-methylformamide, and methane. Theoretical results are reported at several levels of density functional theory, including BP86/DN**, B3LYP/TZVP, and B3LYP/TZVP+, and at MP2/aug-cc-pVDZ. In addition, MP2 binding energies for these complexes were obtained at the complete basis set limit by extrapolating from single point energies obtained with larger correlation-consistent basis sets. The results establish that NO3– has an intrinsic hydrogen bonding topography in which there are six optimal sites for proton location. The structural features observed in crystal structures and in the optimized geometries of complexes are explained by a preference to locate the D–H protons in these positions. For the strongest hydrogen bonding interactions, the N–O•••H angle is bent at an angle of 115 ± 10°, and the hydrogen atom lies in the NO3– plane giving O–N–O•••H dihedral angles of 0 and 180°. In addition, the D-H vector points towards the oxygen atom, giving D–H•••O angles that are near linear, 170 ± 10°. Due to steric hindrance, simple alcohol O–H and amide N–H donors form 3:1 complexes with NO3–, with H•••O distances of 1.85 ± 0.5 Å. Thus, the optimal cavity radius for a tridentate host, defined as the distance from the center to the D–H hydrogen atoms, is 2.65 ± 0.15 Å.
2004. "Acetone Chemistry on Oxidized and Reduced TiO2(110)." Journal of Physical Chemistry B 108(49):18932-18941. Abstract The chemistry of acetone on the oxidized and reduced surfaces of TiO₂(110) was examined using temperature programmed desorption (TPD) and high resolution electron energy loss spectroscopy (HREELS). The reduced surface was prepared with about 7% oxygen vacancy sites by annealing in ultrahigh vacuum (UHV) at 850 K, and the oxidized surface was prepared by exposure of the reduced surface to molecular oxygen at 95 K followed by heating the surface to a variety of temperatures between 200 and 500 K. Acetone adsorbs molecularly on the reduced surface with no evidence for either decomposition or preferential binding at vacancy sites. Based on HREELS, the majority of acetone molecules adsorbed in an ƞ¹ configuration at Ti⁴⁺ sites through interaction of lone pair electrons on the carbonyl oxygen atom. Repulsive acetone-acetone interactions shift the desorption peak from 345 K at low coverage to 175 K as the first layer saturates with a coverage of ~ 1 ML. In contrast, about 7% of the acetone adlayer decomposes when the surface is pretreated with molecular oxygen. Acetate is among the detected decomposition products, but only comprises about 1/3rd of the amount of acetone decomposed and its yield depends on the temperature at which the O₂ exposed surface was preheated to prior to acetone adsorption. Aside from the small level of irreversible decomposition, about 0.25 ML of acetone is stabilized to 375 K by coadsorbed oxygen. These acetone species exhibit an HREELS spectrum unlike that of ƞ¹-acetone or of any other species proposed to exist from the interaction of acetone with TiO₂ powders. Based on the presence of extensive ¹⁶O/¹⁸O exchange between acetone and coadsorbed oxygen in the 375 K acetone TPD state, it is proposed that a polymeric form of acetone forms on the TiO₂(110) surface through nucleophilic attack of oxygen on the carbonyl carbon atom of acetone, and is propagated to neighboring ƞ¹-acetone molecules. This process is initiated at temperatures as low as 135 K based on HREELS. Although the dominant thermal pathway of this surface species is to liberate acetone in UHV, it may be a key intermediate in acetone thermal and photolytic chemistry on TiO₂ surfaces.
2004. "Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data." Bioinformatics 20(14):2296-2304. Abstract Peptide identification following tandem mass spectrometry is usually achieved by matching the mass spectrum of an unidentified peptide to those available in a database. This methodology will be successful only if the peptide under investigation belongs to an available database. We present a proposal to use a Genetic Algorithm (GA) to construct amino acid sequences of peptides using only spectral features and then discuss some of the problems associated with this approach. The GA can potentially overcome some of the problems associated with real MS/MS data like incomplete or unclearly defined peaks and may prove to be a valuable tool in the proteomics field.
2004. "Thermodynamic Model for the Solubility of TcO2•xH2O(am) in the Aqueous Tc(IV) - Na+ - Cl- - H+ - OH- - H2O System." Journal of Solution Chemistry 33(2):199-226. Abstract Solubility studies of TcO2•xH2O(am) have been conducted as a function of H+ concentration from 1 x 10-5 to 6 M HCl and as function of chloride concentration from 1 x 10-3 to 5 M NaCl. These experiments were conducted under carefully controlled reducing conditions such that the preponderance of Tc is present in solution is in the reduced oxidation state and was determined to be Tc(IV) by XANES analysis. The aqueous species and solid phases were characterized using a combination of techniques including thermodynamic analyses of solubility data, XRD, and XANES, EXAFS, and UV-Vis spectroscopies. Chloride was found to significantly affect Tc(IV) concentrations through 1) the formation of Tc(IV) chloro complexes [i.e., TcCl4(aq) and TcCl62-] and a stable compound [data suggests this compound to be TcCl4(am)] in highly acidic and relatively concentrated chloride solutions, and 2) its interactions with the positively charged hydrolyzed Tc(IV) species in solutions of relatively low acidity and high chloride concentrations. A thermodynamic model was developed, which included hitherto unavailable chemical potentials of Tc(IV)-chloro species and Pitzer ion-interaction parameters for Tc(IV) hydrolyzed species with bulk electrolyte ions used in this study. The thermodynamic model presented in this paper is consistent with the extensive data reported in this study and with the reliable literature data, and is applicable to a wide range in H+ and Cl- concentrations and ionic strengths.
2004. "Determination of Surface Exciton Energies by Velocity Resolved Atomic Desorption." Surface Science 564(1-3):62-70. Abstract We have developed a new method for determining surface exciton band energies in alkali halides based on velocity-resolved atomic desorption (VRAD). Using this new method, we predict the surface exciton energies for K1, KBr, KC1, and NaC1 within +0.15 eV. Our data, combined with the available EELS data for alkali fluorides, demonstrate a universal linear correlation with the inverse inter-atomic distance in these materials. The results suggest that surface excitons exist in all alkali halides and their excitation energies can be predicted from the known bulk exciton energies and the obtained correlation plot.
2004. "Higher-Order Equation-of-Motion Coupled-Cluster Methods." Journal of Chemical Physics 121(1):51-59. Abstract The equation-of-motion coupled-cluster (EOM-CC) methods with cluster and linear excitation operators truncated after double, triple, or quadruple excitation level (EOM-CCSD, EOM-CCSDT, and EOM-CCSDTQ) for excitation energies, excited-state dipole moments, and transition moments, and also related Λ equation solvers for coupled-cluster (CC) methods through and up to connected quadruple excitation (CCSD, CCSDT, and CCSDTQ) have been implemented into programs that execute in parallel, taking advantage of spin, spatial (real Abelian), and permutation symmetries simultaneously and fully (within the spin-orbital formalisms). This has been achieved by virtue of the new implementation paradigm of using an algebraic and symbolic manipulation program that automated the formula derivation and implementation altogether. The EOM-CC methods and CC Λ equations introduce a new class of second quantized ansatz with a de-excitation operator ( ), an arbitrary number of excitation operators ( ), and a physical (e.g., the Hamiltonian) operator ( ), the tensor contraction expressions of which can be performed in the order of or at the minimal peak operation cost. Any intermediate tensor resulting from either contraction order is shown to have at most six groups of permutable indices, which finding is used to guide the computer-synthesized programs to fully exploit the permutation symmetry of any tensor to minimize the arithmetic and memory costs.
2004. "Combined Coupled-Cluster and Many-body Perturbation Theories: Automated Derivation and Parallel Implementation." Journal of Chemical Physics 121(24):12197-12207. doi:10.1063/1.1814932 Abstract Various approximations of combined coupled-cluster (CC) and many-body perturbation theories (MBPT) have been derived and implemented into parallel execution programs that take account of spin, spatial (real Abelian), and permutation symmetries within the spin-orbital formalisms for closed- and open-shell molecules. The models range from CCSD(T), CCSD[T], CCSD(2)T, CCSD(2)TQ, CCSDT(2)Q to the completely renormalized CCSD(T) and CCSD[T], where CCSD (CCSDT) is the CC with connected single and double (and triple) excitation operators and subscripted or parenthesized 2, T, and Q indicate the order of perturbation or the rank of connected excitation operators in the correction. The derivation and implementation have been semi-automated by the algebraic and symbolic manipulation program. The computer-synthesized subroutines generate the tensors with the highest rank in a block-wise manner so that they never need to be stored in their entirety, reusing the other pre-calculated intermediate tensors defined also prioritizing the memory optimization (subroutines for these are also computer synthesized). Consequently, the overall memory cost for the perturbation corrections of connected triple and quadruple excitation operators scales as O(n4) and O(n6), respectively (n is the number of orbitals). For systems with different multi-reference character in their wave functions, we found the order of accuracy is roughly CCSD < CR-CCSD(T) ≈ CCSD(2)T ≈ CCSD(T) < CCSD(2)TQ ≈ CCSDT < CCSDT(2)Q, whereas CR-CCSD(T) is effective for extreme cases of quasi-degeneracy (particularly for stretched single bonds) and the operation costs of CCSD(2)TQ and CCSDT(2)Q in the present implementations scale as rather steep O(n9). The perturbation correction part of the CCSD(T)/cc-pVDZ calculations for azulene exhibited a 45-fold speedup upon a 64-fold increase in the number of processors to 512 processors.
2004. "Third-order Douglas-Kroll Relativistic Coupled-Cluster Theory through Connected Single, Double, Triple, and Quadruple Substitutions: Applications to Diatomic and Triatomic Hydrides." Journal of Chemical Physics 120(7):3297-3310. Abstract Coupled-cluster methods including through and up to the connected single, double, triple, and quadruple substitutions (CCSD, CCSDT, and CCSDTQ) have been automatically derived and implemented for sequential and parallel executions for use in conjunction with a one-component third-order Douglas-Kroll (DK3) approximation for relativistic corrections. A combination of the converging electron-correlation methods, the accurate relativistic reference wave functions, and the use of systematic basis sets tailored to the relativistic approximation has been shown to predict the experimental singlet-triplet separations within 0.02 eV (0.5 kcal/mol) for five triatomic hydrides (CH2, NH2+, SiH2, PH2+, and AsH2+), the experimental bond lengths within 0.002 angstroms, rotational constants within 0.02 cm-1, vibration-rotation constants within 0.01 cm-1, centrifugal distortion constants within 2 %, harmonic vibration frequencies within 9 cm-1 (0.4 %), anharmonic vibrational constants within 2 cm-1, and dissociation energies within 0.03 eV (0.8 kcal/mol) for twenty diatomic hydrides (BH, CH, NH, OH, FH, AlH, SiH, PH, SH, ClH, GaH, GeH, AsH, SeH, BrH, InH, SnH, SbH, TeH, and IH) containing main-group elements across the second through fifth periods of the periodic table. In these calculations, spin-orbit effects on dissociation energies, which were assumed to be additive, were estimated from the measured spin-orbit coupling constants of atoms and diatomic molecules, and an electronic energy in the complete-basis-set, complete-electron-correlation limit has been extrapolated by the formula which was in turn based on the exponential-Gaussian extrapolation formula of the basis set dependence.
2004. "Sodium Nitrate Particles: Physical and Chemical Properties During Hydration and Dehydration, and Implications for Aged Sea Salt Aerosols." Journal of Aerosol Science 35(7):869-887. Abstract Experiments probing the phase and behavior of NaNO3 particles at different relative humidities, important for elucidating the role these play in the chemistry and radiative properties of marine regions, are presented. Changes in NaNO3 particles during hydration were studied using environmental scanning electron mircoscopy (ESEM) and conventional SEM coupled with energy dispersive X-ray analysis (SEM/EDX). Mixtures of NaNO3 and NaCI, which are typical of partially processed sea salt particles, were also studied. Complementary studies using long path FTIR were carried out to determine the extent of water association with NaNO3 aerosols, and for comparison, NaC1, MgC12, and NH4NO3, as a function of relative humidity. The combination of these techniques shows that NaNO3 particles exist as unusual metastable, amorphous solids at low relative humidity that undergo continuous hygroscopic growth with increasing relative humidity. While other evidence for this phenomenon has been reported, this is the first direct observation using ESEM.
2004. "Review of Developments in Portable Hydrogen Production Using Microreactor Technology." Chemical Reviews 104(10):4767-4789. Abstract This paper reviews work that is being done in the area of hydrogen production for low power fuel cell applications (0.1-500W). It focuses on fuel reforming for these low power applications. It reviews many of the state of the art work being done.
2004. "Control System for an Ion Trap Mass Spectrometer." Scientific Computing & Instrumentation (April 2004):18-20. Abstract This paper describes the development of a control system for an ion trap mass spectrometer that is both inexpensive and flexible, allowing application of ion trap technology to a number of research areas. This project is part of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy national scientific user facility, located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. EMSL offers a comprehensive array of cutting-edge resources that are available to its users. Among these resources are a number of custom-built ion trap mass spectrometers (ITMS) that are are devoted to stuides in scientific areas including atmopsheric chemistry, diesel catalysis, biological applications as well as applications in defense and homeland security. The primary thrust of this effort is to develop a basic hardware and software platform for ion trap mass spectrometry (ITMS) that will allow the construction and deployment of systems with capabilities tailored to the specific needs of a variety of scientific applications. The emphasis will be on the use of chemical ionization techniques to address the need for highly sensitive and specific measurements as well as analytical needs dictated by research areas such as atmospheric chemistry, catalysis, materials science, biology, and inhalation toxicology. This ITMS platform can also be used to develop and deploy systems for critical applications such as chemical weapons detection and nuclear proliferation monitoring.
2004. "Placing Single-Molecule T4 Lysozyme Enzymes on a Bacterial Cell Surface: Toward Probing Single-Molecule Enzymatic Reaction in Living Cells." Biophysical Journal 87:656-661. Abstract TheT4 lysozyme enzymatic hydrolyzation reaction of bacterial cell walls is an important biological process, and single-molecule enzymatic reaction dynamics had been studied under physiological condition using purified E. Coli cell walls as substrates. Here, we report progress toward characterizing the T4 lysozyme enzymatic reaction on a living bacterial cell wall using a combined single-molecule placement and spectroscopy. Placing a dye-labeled single T4 lysozyme molecule on a targeted cell wall by using a hydrodynamic micro-injection approach, we monitored single-molecule rotational motions during binding, attachment to, and dissociation from the cell wall by tracing single-molecule fluorescence intensity time trajectories and polarization. The single-molecule attachment duration of the T4 lysozyme to the cell wall during enzymatic reactions was typically shorter than photobleaching time under physiological conditions.
2004. "Correlated Topographic and Spectroscopic Imaging by Combined Atomic Force Microscopy and Optical Microscopy." Journal of Luminescence 107(1-4):4-12. Abstract Near-field scanning microscopy is a powerful approach to obtain topographic and spectroscopic characterization simultaneously for imaging biological and nanoscale systems. To achieve optical imaging at high spatial resolution beyond the diffraction limit, aperture-less metallic scanning tips have been utilized to enhance the laser illumination local electromagnetic field at the apex of the scanning tips.
2004. "High Resolution 1H NMR Spectroscopy of Metabolically Active Microorganisms Using Non-Destructive Magic Angle Spinning." Spectroscopy 19(12):98-103. Abstract It is shown that the resolution of the 1H NMR metabolite spectra of densely packed microbial cells or biofilms attached to solid surfaces can be significantly enhanced with the so-called PASS R.F pulse sequence combined with slow (40-100 Hz) magic angle spinning of the sample. Hence this technique can be used to study biofilm metabolism under environmentally relevant conditions in a minimally invasive way.
2004. "Direct Speciation of Phosphorus in Alum-Amended Poultry Litter: Solid-State 31P NMR Investigation ." Environmental Science and Technology 38(3):674-681. Abstract Amending poultry litter (PL) with aluminum sulfate (alum) has proven to be effective in reducing water-soluble phosphorus (P) in the litter and in runoff from fields that have received PL applications; it has therefore been suggested as a best management practice. Although its effectiveness has been demonstrated on a macroscopic scale in the field, little is known about P speciation in either alumamended or unamended litter. This knowledge is important for the evaluation of the long-term stability and bioavailability of P, which is a necessary prerequisite for the assessment of the sustainability of intensive poultry operations. Both solidstate MAS and CP-MAS 31P NMR as well as 31P{27Al}- TRAPDOR were used to investigate P speciation in alumamended and unamended PL. The results indicate the presence of a complex mixture of organic and inorganic orthophosphate phases.Acalcium phosphate phase, probably a surface precipitate on calcium carbonate, could be identified in both unamended and alum-amended PL, as well as physically bound HPO4 2-. Phosphate associated with Al was found in the alum-amended PL, most probably a mixture of a poorly ordered wavellite and phosphate surface complexes on aluminum hydroxide that had been formed by the hydrolysis of alum. However, a complex mixture of organic and inorganic phosphate species could not be resolved. Phosphate associated with Al comprised on average 40 ( 14% of the total P in alum-amended PL, whereas calcium phosphate phases comprised on average 7 ( 4% in the alum-amended PL and 14 ( 5% in the unamended PL.
