Scientific Publications 2008
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2008. "Acetaldehyde photochemistry on TiO2(110)." Surface Science 602(13):2238-2249. doi:10.1016/j.susc.2008.04.045 Abstract The ultraviolet (UV) photon induced decomposition of acetaldehyde absorbed on the oxidized retile TIO2(110) surface was studied with photon stimulated desorption (PSD) and theral programmed desorption (TPD). Acetaldehyde desorbs molecularly from TiO2(110) with minor decomposition channels yielding butene on the reduced TiO2 surface and acetate on the oxidized TiO2 surface. Acetaldehyde absorbed on oxidized TiO2(110) undergoes a facile thermal reaction to form a photoactive acetaldehyde-oxygen complex. UV irradiation of the acetaldehyde-oxygen complex resulting in the ejection of methyl radical into gas phase and conversion of the surface bound fragment to formate.
2008. "Acetaldehyde Photochemistry on TiO2(110)." Surface Science 602(13):2238-2249. Abstract The ultraviolet (UV) photon induced decomposition of acetaldehyde adsorbed on the oxidized rutile TiO2(110) surface was studied with photon stimulated desorption (PSD) and thermal programmed desorption (TPD). Acetaldehyde desorbs molecularly from TiO2(110) with minor decomposition channels yielding butene on the reduced TiO2 surface and acetate on the oxidized TiO2 surface. Acetaldehyde adsorbed on oxidized TiO2(110) undergoes a facile thermal reaction to form a photoactive acetaldehyde-oxygen complex. UV irradiation of the acetaldehyde-oxygen complex initiated photofragmentation of the complex resulting in the ejection of methyl radical into gas phase and conversion of the surface bound fragment to formate.
2008. "Influence of O2-induced surface roughening on the chemistry of water on TiO2(110)." Surface Science 602(8):1507-1516. Abstract The impact of oxygen induced regrowth of TiO2 on the reduced rutile TiO2(110) surface has been studied using temperature programmed desorption (TPD) of adsorbed water multilayers. Pre-exposure of UHV annealed TiO2(110) surfaces to O2 at temperatures from 300 to 850 K induced changes in subsequent water TPDs that were interpreted in terms of the rougher surface morphologies resulting from the regrowth process. Water TPD from TiO2(110) previously oxidized at 300 K exhibited a new peak at *312 K due to reaction of water with O adatoms. These O adatoms were produced by dissociative adsorption of O2 at O-vacancy sites. Additionally, oxygen reacted (slowly) with surface Ti2O3 strands at RT. Water TPD from surfaces pre-oxidized at higher temperatures (P500 K) exhibited features reflective of desorption from rough surfaces, namely loss of peak resolution and eventual merger of the second layer and ice peaks, formation of a high temperature tail on the second layer peak, and broadening of the first layer TPD peak. The multiplicity of kinetically different adsorption sites on the roughened TiO2(110) surfaces contributed to the widening of the desorption features. Published by Elsevier B.V.
2008. "A New Interpretation of the Scanning Tunneling Microscope Image of Graphite." Chemical Physics 348(1-3):233-236. doi:10.1016/j.chemphys.2008.03.019 Abstract In this work, highly-resolved scanning tunneling microscopy images of graphite basal plane are obtained and theoretical computations are performed to explain the resolution of only half the atoms in STM images of graphite. Our experimental and computational findings indicate that the bright elliptical spots observed in trigonal STM images of graphite may not correspond to carbon positions but to p-states localized above alternate carbon–carbon bonds. This interpretation is based on STM experiments that suggest that the elliptical shape of the bright spots may not be a tip artifact and on simulated STM images of a graphite using orthorhombic unit cells that are in excellent agreement with experimentally obtained images.
2008. ""Depth-Profiling" and Quantitative Characterization of the Size, Composition, Shape, Density, and Morphology of Fine Particles with SPLAT, a Single-Particle Mass Spectrometer." Journal of Physical Chemistry A 112(4):669-677. doi:10.1021/jp077308y Abstract A significant fraction of atmospheric particles are composed of inorganic substances that are mixed or coated with organics. The behavior of these particles depends on the particle internal composition and on the arrangement of the specific constituents in each particle. It is important to know which constituent is on the surface and whether it entirely covers the particle surface. We present a study that demonstrates that an instrumental system that includes an ultra-sensitive single particle mass spectrometer that is coupled with a differential mobility analyzer can be used to quantitatively measure in real-time individual particle composition, size, density, shape and determine which substance is on the surface and whether it entirely covers the particle. Here we use liquid dioctyl phthalate to coat NaCl seeds and generate spherical particles that are encapsulated with the organic coat and pyrene, a solid poly aromatic hydrocarbon, to produce aspherical particles with pyrene nodules and exposed NaCl cores. We show that the behavior of the mass spectral intensities as a function of laser fluence yields information that can be used to determine the morphological distribution of individual particles constituents.
2008. "A New Real-Time Method for Determining Particles Sphericity and Density: Application to Secondary Organic Aerosol Formed by Ozonolysis of alpha-Pinene." Environmental Science & Technology 42(21):8033-8038. doi:10.1021/es8013562 Abstract Particle volumes are most often obtained by measuring particle mobility size distributions and assuming that the particles are spherical. These volumes are then converted to mass loads by using particle densities that are commonly either assumed or estimated from the measured mobility and vacuum aerodynamic diameters assuming again that the particles are spherical. Depending on the system, these assumptions can introduce significant errors. We present a new method that can be applied to any particle system to determine in real-time whether the particles are spherical or not. We use our 2nd generation single particle mass spectrometer (SPLAT II) to measure with extremely high precision the vacuum aerodynamic size distributions of particles classified by differential mobility analyzer (DMA) and demonstrate that the line shape of these distributions provide a way to unambiguously distinguish between spherical and aspherical particles. Moreover, the very same experimental system is used to obtain in addition to individual particle size, its density, composition and dynamic shape factor. We illustrate the application of this method to secondary organic aerosols formed as a result of ozonolysis of α-pinene in the presence and absence of an OH scavenger and find these particles to be spherical with densities of 1.198±0.004 gcm-3 and 1.213±0.003 gcm-3 respectively.
2008. "ClusterSculptor: Software for Expert-Steered Classification of Single Particle Mass Spectra." International Journal of Mass Spectrometry 275(1-3):1-10. doi:10.1016/j.ijms.2008.04.033 Abstract To take full advantage of the vast amount of highly detailed data acquired by single particle mass spectrometers requires that the data be organized according to some rules that have the potential to be insightful. Most commonly statistical tools are used to cluster the individual particle mass spectra on the basis of their similarity. Cluster analysis is a powerful strategy for the exploration of high-dimensional data in the absence of a-priori hypotheses or data classification models, and the results of cluster analysis can then be used to form such models. More often than not, when examining the data clustering results we find that many clusters contain particles of different types and that many particles of one type end up in a number of separate clusters. Our experience with cluster analysis shows that we have a vast amount of non-compiled knowledge and intuition that should be brought to bear in this effort. We will present new software we call ClusterSculptor that provides comprehensive and intuitive framework to aid scientists in data classification. ClusterSculptor uses k-means as the overall clustering engine, but allows tuning its parameters interactively, based on a non-distorted compact visual presentation of the inherent characteristics of the data in high-dimensional space. ClusterSculptor provides all the tools necessary for a high-dimensional activity we call cluster sculpting. ClusterSculptor is designed to be coupled to SpectraMiner, our data mining and visualization software package. The data are first visualized with SpectraMiner and identified problems are exported to ClusterSculptor, where the user steers the reclassification and recombination of clusters of tens of thousands particle mass spectra in real-time. The resulting sculpted clusters can be then imported back into SpectraMiner. Here we will greatly improved single particle chemical speciation in an example of application of this new tool to a number of particle types of atmospheric importance.
2008. "Chemisorption-Induced Structural Changes and Transition from Chemisorption to Physisorption in Au6(CO)n-(n=4-9)." Journal of Physical Chemistry C 112(31):11920-11928. doi:10.1021/jp803161b Abstract The interactions of CO with gold clusters are essential to understanding the catalytic mechanisms of CO oxidation on supported gold nanoparticles. Here we report a photoelectron spectroscopy and theoretical study of CO adsorption on a well-defined Au6− cluster in Au6(CO)n− (n = 4-9). Previous studies have shown that the first three CO successively bind the three apex sites of the triangular Au6−. The current work reveals that the forth CO induces a major structural change to create more apex sites to accommodate the additional CO. Definitive spectroscopic evidence is obtained for the chemisorption saturation at Au6(CO)6 −, in which Au6 has rearranged to accommodate the six CO adsorbates. The photoelectron spectra of larger clusters from Au6(CO)7 − to Au6(CO)9 − are observed to be almost identical to that of Au6(CO)6 −, suggesting that the additional CO’s are simply physisorbed onto the Au6(CO)6 − core. Quasirelativistic density functional calculations are performed on both Au6(CO)n and Au6(CO)n − (n = 4-6). The theoretical results are used to interpret the experimental observations and provide insight into the nature of CO interactions with gold clusters. The Au6 cluster is shown to be highly fluxional upon multiple CO adsorptions, stabilizing structures with more apex sites to accommodate the additional CO’s. The CO-induced structural transformation is analogous to structural flexibility and mobility in heterogeneous catalysis. The observations of the propensity of CO toward apex sites and CO-induced structural changes in small gold clusters m
2008. "Probing the Electronic and Structural Properties of Chromium Oxide Clusters (CrO3)n- and (CrO3)n (n=1-5): Photoelectron Spectroscopy and Density Functional Calculations." Journal of the American Chemical Society 130(15):5167-5177. Abstract Photoelectron spectroscopy has been conducted for a series of (CrO3)n- (n = 1-5) clusters and compared with density functional calculations. Well-resolved photoelectron spectra were obtained for (CrO3)n- (n = 1-5) at 193 nm (6.424 eV) and 157 nm (7.866 eV) photon energies, allowing for accurate measurements of the electron binding energies, low-lying electronic excitations for n = 1 and 2, and the energy gaps. Density functional and molecular orbital theory (CCSD(T)) calculations were performed to locate the ground and low-lying excited states for the neutral clusters and to calculate the electron binding energies of the anionic species. The experimental and computational studies firmly establish the unique low-spin, non-planar, cyclic ring structures for (CrO3)n and (CrO3)n- for n ≥ 3. The structural parameters of (CrO3)n are shown to converge rapidly to those of the bulk CrO3 crystal. The extra electron in (CrO3)n- (n ≥ 2) is shown to be largely delocalized over all Cr centers, in accord with the relatively sharp ground state photoelectron bands. The measured energy gaps of (CrO3)n exhibit a sharp increase from n = 1 to n = 3 and approach to the bulk value of 2.25 eV at n = 4 and 5, consistent with the convergence of the structural parameters.
2008. "Probing the Electronic Structure and Chemical Bonding of Gold Oxides and Sulfides in AuOn- and AuSn- (n=1, 2)." Journal of the American Chemical Society 130(28):9156-9167. doi:10.1021/ja802408b Abstract The Au-O and Au-S interactions are essential in nanogold catalysis and nanotechnology, for which mono-gold oxide and sulfide clusters serve as the simplest molecular models. We report a combined photoelectron spectroscopy and ab initio study on AuO− and AuO2− and their valent isoelectronic AuS− and AuS2− species to probe their electronic structure and to elucidate the Au-O and Au-S chemical bonding. Vibrationally-resolved spectra were obtained at different photon energies, providing a wealth of electronic structure information for each species. Similar spectra were observed for AuO− and AuS− and for the linear OAuO− and SAuS− species. A bent isomer was also observed as Au(S2)− in the AuS2− spectra, whereas a similar Au(O2)− complex was not observed in the case of AuO2−. High-level ab initio calculations were conducted to aid spectral assignments and provide insight into the chemical bonding in the AuX− and AuX2− molecules. Excellent agreement is achieved between the calculated electronic excitations and the observed spectra. Configuration interactions and spin-orbit couplings were shown to be important and were necessary to achieve good agreement between theory and experiment. Strong covalent bonding was found in both the AuX− and the XAuX− species with multiple bonding characters. While Au(S2)− was found to be a low-lying isomer with a significant binding energy, Au(O2)− was shown to be unbound consistent with the experimental observation. The latter is understood in the context of the size-dependent reactivity of Aun− clusters with O2.
2008. "Identification of protein-protein interaction and topologies in living cells by chemical cross-linking and mass spectrometry." Molecular & Cellular Proteomics. MCP 8(3):409-420. doi:10.1074/mcp.M800232-MCP200 Abstract Current chemical cross-linking methods are commonly employed for mapping sites of interaction and three-dimensional structure in purified, known protein complexes. When applied in vivo in combination of co-immunoprecipitation methods, information on the sites of interaction between proteins are unattainable due to overwhelming sample complexity. We present results from a novel cross-linking strategy that allow simultaneous protein-protein interaction and surface topology measurement in vivo without any prior knowledge of the system. The strategy consists of: (i) cross-linking reaction: intact cell labeling with protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by 2D-LC/MS/MS; and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. This strategy was applied to Shewanella oneidensis MR-1 bacterial cells and successfully identified a protein-protein interaction between SecA and a small outer membrane lipoprotein as well as their sites of interaction in vivo.
2008. "Quantum Chemical Calculations of the Cl- + CH3I → CH3Cl + I- Potential Energy Surface." Journal of Physical Chemistry A 113(10):1976-1984. doi:10.1021/jp808146c Abstract Electronic structure theory calculations, using MP2 theory and the DFT functionals OPBE, OLYP, HCTH407, BhandH, and B97-1, were performed to characterize the structures, vibrational frequencies, and energies for stationary points on the Cl- + CH3I → ClCH3 + I- potential energy surface. The aug-cc-pVDZ and aug-cc-pVTZ basis sets, with an effective core potential (ECP) for iodine, were employed. Single-point CCSD(T) calculations were performed to obtain the complete basis set (CBS) limit for the reaction energies. DFT was found to give significantly longer halide ion/carbon atom bond lengths for the ion-dipole complexes and central barrier transition state, than MP2. BhandH, with either the aug-cc-pVDZ and aug-cc-pVTZ basis sets, gives good agreement with the experimental structures for both CH3I and CH3Cl. The frequencies of CH3I and CH3Cl, obtained with the different level of theory and basis sets, are in excellent agreement with experiment. The major difference between the MP2 and DFT frequencies is for the imaginary frequency of the central barrier. Using the aug-cc-pVTZ basis the MP2 value for this frequency ranges from 1.26 - 1.59 times larger than those for the DFT functional. Thus, the MP2 and DFT theories have different PES shapes in the vicinity of the [Cl--CH3--I]- central barrier. The CCSD(T)/CBS energies are in good agreement with experiments for the complexation energies and reaction exothermicity, with a small 1 kcal/mol difference for the latter. The CCSD(T)/CBS central barrier height is lower than values deduced by using statistical theoretical models to fit the Cl- + CH3I → ClCH3 + I- experimental rate constant, which is consistent with the expected non-statistical dynamics for the reaction. The BhandH energies are in overall best agreement with the CCSD(T) values, with a largest difference of only 0.7 kcal/mol.
2008. "Micro-Raman and Micro-Infrared Spectroscopic Studies of Pb- and Au-Irradiated ZrSiO4: Optical Properties, Structural Damage and Amorphization ." Physical Review. B, Condensed Matter and Materials Physics 77(14):144110. doi:10.1103/PhysRevB.77.144110 Abstract The optical properties of damaged, periodic and aperiodic domains created by Pb+ (280 keV) and Au4+ (10 MeV) implantation of zircon were studied using micro-infrared (IR) and micro-Raman spectroscopy. The Pb+- and Au4+-irradiations caused a dramatic decrease in the IR reflectivity similar to that observed for metamict natural zircon. The irradiation with 10 MeV Au4+ ions (to fluences of 1x10^15 Au4+ ions/cm2) also results in the formation of an amorphized phase similar to that observed in metamict zircon. These results show that high-energy, heavy-ion irradiations provide a good simulation of the ballistic effects of the recoil nucleus of an alpha-decay event, and in both cases, the result is the creation of aperiodic domains. Additional IR and Raman features were recorded in samples irradiated with 280 keV Pb+ ions (to fluences of 1x10^14 and 1x10^15 Pb+ ions/cm2), indicating the formation of an irradiation-induced new phase(s). The frequencies of the features are consistent with lead silicates, ZrO2 and SiO2. The results show that spectral features of the Au4+- and Pb+-irradiated zircon are different from those of quenched ZrSiO4 melts, and the finding further confirms that the amorphous state produced by high-energy ion irradiations is structurally different from the glassy state that results from quenching a high temperature melt. In contrast to significant changes in the frequency and width of the Raman 3 band observed in metamict zircon, the Pb+- and Au4+-irradiations do not cause similar variations, indicating that the remaining zircon crystalline domains in irradiated samples have a crystalline structure with fewer defects than those of metamict zircon.
2008. "A Perspective on the Maillard Reaction and the Analysis of Protein Glycation by Mass Spectrometry: Probing the Pathogenesis of Chronic Disease." Journal of Proteome Research 8(2):754-769. Abstract The Maillard reaction, starting from the glycation of protein and progressing to the formation of advanced glycation end-products (AGEs), is implicated in the development of complications of diabetes mellitus, as well as in the pathogenesis of cardiovascular, renal, and neurodegenerative diseases. In this perspective review, we provide on overview on the relevance of the Maillard reaction in the pathogenesis of chronic disease and discuss traditional approaches and recent developments in the analysis of glycated proteins by mass spectrometry. We propose that proteomics approaches, particularly bottom-up proteomics, will play a significant role in analyses of clinical samples leading to the identification of new markers of disease development and progression.
2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(19):3027-3034. doi:10.1002/rcm.3703 Abstract Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.
2008. "Fabrication of Transparent Capacitive Structure by Self-Assembled Thin Films." Journal of Nanoscience and Nanotechnology 8(6):3008-3012. doi:10.1166/jnn.2008.075 Abstract An approach to fabricating transparent electronic devices by using nanomaterial and nanofabrication is presented in this paper. A see-through capacitor is constructed from selfassembled silica nanoparticle layers that are stacked on the transparent substrate. The electrodes are made of indium tin oxide. Unlike the traditional processes used to fabricate such devices, the self-assembly approach enables one to synthesize the thin film layers at lower temperature and cost, and with a broader availability of nanomaterials. The vertical dimension of the selfassembled thin films can be precisely controlled, as well as the molecular order in the thin film layers. The shape of the capacitor is generated by planar micropatterning. The quartz crystal demonstrates the steady growth of the silica nanoparticle multilayer. In addition, because the nanomaterial synthesis and the device fabrication steps are separate, the device is not affected by the harsh conditions required for the material synthesis. A clear pattern is allowed over a large area on the substrate. The prepared capacitive structure has an optical transparency higher than 92% over the visible spectrum. The capacitive impedance is measured at different frequencies and fit the theoretical results. As one of the fundamental components, this type of capacitive structure can serve in the transparent circuits, interactive media and sensors, as well as being applicable to other transparent devices.
2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides ." Analytical Chemistry 80(24):9822-9829. doi:10.1021/ac801704j Abstract Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an on-line wash of column-bound glycated peptides using 50 mM ammonium acetate. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (3) precursor-ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. In general, acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor-ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number glycated peptides identified by LC-MS/MS.
2008. "Atomic Collision and Ionization Effects in Oxides." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 266(12-13):2828-2833. doi:10.1016/j.nimb.2008.03.197 Abstract Irradiation with ions and electrons provides accelerated study of radiation damage in nuclear materials, such as those proposed for immobilization of actinides and long-lived fission products. The effects of ion irradiation in SrTiO3, Sm2Ti2O7 and Sr2Nd8(SiO4)6O2, as representative materials, are studied using 1 MeV Au+ ions. The irradiation-induced disorder, due to atomic collisions processes, increases nonlinearly with irradiation dose and is well described by a disorder accumulation model that includes contributions from amorphous domains, point defects and defect clusters. Ionization from 200 keV electrons induces recrystallization at the amorphous/crystalline (a/c) interface that exhibits several distinct stages associated with residual defect annihilation near the interface, epitaxial regrowth at the interface, and a surface-stabilized amorphous state. Understanding ionization effects and the coupled effects of electronic and atomic dynamics on material behavior is a challenging area for scientific research.
2008. "On the Diurnal Cycle of Deep Convection, High-Level Cloud, and Upper Troposphere Water Vapor in the Multiscale Modeling Framework." Journal of Geophysical Research. D. (Atmospheres) 113:D16105 (19 pp). doi:10.1029/2008JD009905 Abstract The Multiscale Modeling Framework (MMF), also called ‘‘superparameterization’’, embeds a cloud-resolving model (CRM) at each grid column of a general circulation model to replace traditional parameterizations of moist convection and large-scale condensation. This study evaluates the diurnal cycle of deep convection, high-level clouds, and upper troposphere water vapor by applying an infrared (IR) brightness temperature (Tb) and a precipitation radar (PR) simulator to the CRM column data. Simulator results are then compared with IR radiances from geostationary satellites and PR reflectivities from the Tropical Rainfall Measuring Mission (TRMM). While the actual surface precipitation rate in the MMF has a reasonable diurnal phase and amplitude when compared with TRMM observations, the IR simulator results indicate an inconsistency in the diurnal anomalies of high-level clouds between the model and the geostationary satellite data. Primarily because of its excessive high-level clouds, the MMF overestimates the simulated precipitation index (PI) and fails to reproduce the observed diurnal cycle phase relationships among PI, high-level clouds, and upper troposphere relative humidity. The PR simulator results show that over the tropical oceans, the occurrence fraction of reflectivity in excess of 20 dBZ is almost 1 order of magnitude larger than the TRMM data especially at altitudes above 6 km. Both results suggest that the MMF oceanic convection is overactive and possible reasons for this bias are discussed. However, the joint distribution of simulated IR Tb and PR reflectivity indicates that the most intense deep convection is found more often over tropical land than ocean, in agreement with previous observational studies.
2008. "Scintillation Response of CaF2 to H and He over a Continuous Energy Range." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 266(12-13):2750-2753. doi:10.1016/j.nimb.2008.03.110 Abstract Recent demands for new radiation detector materials with improved -ray detection performance at room temperature have prompted research efforts on both accelerated material discovery and efficient techniques that can be used to identify material properties relevant to detector performance. New material discovery has been limited due to the difficulties of large crystal growth to completely absorb energies; whereas high-quality thin films or small crystals of candidate materials can be readily produced by various modern growth techniques. In this work, an ion-scintillator technique is demonstrated that can be applied to study scintillation properties of thin films and small crystals. The scintillation response of a benchmark scintillator, europium-doped calcium fluoride (CaF2:Eu), to energetic proton and helium ions is studied using the ion-scintillator approach based on a time of flight (TOF) telescope. Excellent energy resolution and fast response of the TOF telescope allow quantitative measurement of light yield, nonlinearity and energy resolution over an energy range from a few tens to a few thousands of keV.
2008. "Vacancy Assisted Diffusion of Alkoxy Species on Rutile TiO2(110)." Physical Review Letters 101(15):156103. doi:10.1103/PhysRevLett.101.156103 Abstract The catalytic and photocatalytic properties of TiO2 have attracted widespread interest in a variety of applications, such as air purification, self-cleaning glass, water splitting, solar cells and wastewater treatment. In many cases the catalytic chemistry of reducible oxides is dominated by oxygen vacancy sites. For reduced rutile TiO2(110)-1×1, the bridge-bonded oxygen (BBO) vacancies (BBOV’s) are the most prevalent surface defects and, as has been shown, they can readily dissociate small molecules such as H2O, O2, and alcohols.Here we demonstrate for the first time that BBOV’s can also catalyze the transport of adsorbed species which is a key ingredient in heterogeneous catalytic processes. Specifically, we show that at elevated temperatures (≥ 400 K), mobile BBOV’s can assist the diffusion of alkoxy groups formed by the dissociation of alcohols at BBOV’s. This type of mechanism is likely applicable to other adsorbates bound to BBO atoms of TiO2(110).
2008. "A Prototype for Graphene Material Simulation: Structures and Interaction Potentials ofCoronene Dimers." Journal of Physical Chemistry C 112(11):4061-4067. doi:10.1021/jp710918f Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Graphene sheets are the building blocks of carbon nanotubes and a variety of functionalized nanomaterials. Methods to be used for computer-aided design of such materials or for the study of aromatic-aromatic interactions in biopolymers and other soft materials should be validated for smaller systems where reliable estimates of interaction energies are available. In this work, we first validated the M06-2X functional against the S22 database of noncovalent interaction energies of biological importance. We then applied the M06-2X functional to study aromatic-aromatic interactions in coronene dimers. We located six stationary points on the potential energy surface of coronene dimer, we calculated the potential energy curves for the sandwich, T-shaped, and parallel-displaced configurations of this prototype of aromatic-aromatic interactions, and we found that a parallel displaced configuration is the global minimum. The potential curves for the coronene dimers will aid the development of new force fields and potential energy functions that are computationally efficient and capable of modeling large graphene or aromatic clusters.
2008. "Benchmark Data for Interactions in Zeolite Model Complexes and Their Use forAssessment and Validation of Electronic Structure Methods." Journal of Physical Chemistry C 112(17):6860-6868. doi:10.1021/jp7112363 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We present benchmark binding energies for five zeolite model complexes, with four of the adsorbates bound noncovalently and one covalently. The binding energies were determined as the sum of the infinite-basis-set limit of Møller-Plesset second-order perturbation theory (MP2) energies and a CCSD(T) correction term evaluated with the aug-cc-pVDZ basis set. The basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X ) D and T and separate extrapolation of the Hartree- Fock and correlation energies. We found that correlation contributions beyond MP2 to the final binding energies are small; their magnitude is in the range of 0.02-1.0 kcal/mol. For the MP2 method to describe the interactions in these zeolite model systems accurately, one needs to use a basis set at least the size of aug-cc-pVTZ in conjunction with counterpoise corrections. Final binding energies (kcal/mol) of the model complexes are in the range of 3.5-19.5 kcal/mol, and they were used as reference data to test 6 wave function methods and 41 density functionals. Among the tested density functional methods, M06-L/6-31+G(d,p) gives a mean unsigned error (MUE) without counterpoise correction of 0.87 kcal/mol. With counterpoise corrections, the M06-2X and M05-2X functionals give the best performance. The MUE with counterpoise corrections for the M06-2X/6-311+G(2df,2p)//MP2/6-311+G(2df,2p) level of theory is 0.39 kcal/mol. With the DFT/6-31+G- (d,p) geometries and the 6-311+G(2df,2p) basis set, M05-2X and M06-2X give MUEs with counterpoise corrections of 0.40 and 0.52 kcal/mol, respectively. Tests against the binding energies of four complexes (two noncovalent and two covalent) of the adsoption of isobutene on a large 16T zeolite model cluster confirmed that M06-L, M06, M05-2X, and M06-2X are very promising quantum mechanical methods for hybrid quantum mechanical/molecular mechanical (QM/MM) simulations of zeolites. In fact the performance of these four Minnesota functionals, as compared to other high-quality functionals, is relatively even better for the larger 16T clusters than for the smaller 3T ones.
2008. "Computational characterization and modeling of buckyball tweezers:density functional study of concave–convex π•••π interactions." Physical Chemistry Chemical Physics. PCCP 10:2813-2818. doi:10.1039/b717744e Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The geometries and binding energies of a recent buckyball tweezers (C60H28) and its supramolecular complexes are investigated using recently developed density functionals (M06-L and M06-2X) that include an accurate treatment of medium-range correlation energy. The pincer part of the tweezers, corannulene, has a strong attractive interaction with C60. However, due to the entropy penalty, the calculated gas-phase free energy of association of the C60@corannulene supramolecule is positive 3.5 kcal mol-1; and this entropy penalty explains why it is difficult to observe C60@corannulene supramolecule experimentally. By using a p-extended tetrathiafulvalene (TTF), in particular 9,10-bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracene (TTFAQ or C20H10S4), as the pincer part, we modeled a new buckyball tweezers. The geometries and binding energies of the new buckyball tweezers and its supramolecular complexes are also calculated. Due to fact that the attractive interaction between TTFAQ and C60 is weaker than that between corannulene and C60, the gas-phase binding free energy in the C60@C60H 32S8 supramolecular complex is smaller than that in the C60@C60H28 supramolecule. We also discuss solvent effects.
2008. "Construction of a Generalized Gradient Approximation by Restoring the Density-gradient Expansion and Enforcing a Tight Lieb-Oxford Bound." Journal of Chemical Physics 128(18):184109. doi:10.1063/1.2912068 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Recently, a generalized gradient approximation (GGA) to the density functional, called PBEsol, was optimized (one parameter) against the jellium-surface exchange-correlation energies, and this, in conjunction with changing another parameter to restore the first-principles gradient expansion for exchange, was sufficient to yield accurate lattice constants of solids. Here, we construct a new GGA that has no empirical parameters, that satisfies one more exact constraint than PBEsol, and that performs 20% better for the lattice constants of 18 previously studied solids, although it does not improve on PBEsol for molecular atomization energies (a property that neither functional was designed for). The new GGA is exact through second order, and it is called the second-order generalized gradient approximation (SOGGA). The SOGGA functional also differs from other GGAs in that it enforces a tighter Lieb–Oxford bound. SOGGA and other functionals are compared to a diverse set of lattice constants, bond distances, and energetic quantities for solids and molecules (this includes the first test of the M06-L meta-GGA for solid-state properties). We find that classifying density functionals in terms of the magnitude µ of the second-order coefficient of the density gradient expansion of the exchange functional not only correlates their behavior for predicting lattice constants of solids versus their behavior for predicting small-molecule atomization energies, as pointed out by Perdew and co-workers
2008. "Density Functionals with Broad Applicability in Chemistry." Accounts of Chemical Research 41(2):157-167. doi:10.1021/ar700111a Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by mediumrange correlation energy, such as van der Waals attraction, aromatic-aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid) functionals, Hartree-Fock exchange. We have developed four new functionals that overcome the above-mentioned difficulties: (a) M06, a hybrid meta functional, is a functional with good accuracy “across-theboard” for transition metals, main group thermochemistry, medium-range correlation energy, and barrier heights; (b) M06- 2X, another hybrid meta functional, is not good for transition metals but has excellent performance for main group chemistry, predicts accurate valence and Rydberg electronic excitation energies, and is an excellent functional for aromatic-aromatic stacking interactions; (c) M06-L is not as accurate as M06 for barrier heights but is the most accurate functional for transition metals and is the only local functional (no Hartree-Fock exchange) with better across-the-board average performance than B3LYP; this is very important because only local functionals are affordable for many demanding applications on very large systems; (d) M06-HF has good performance for valence, Rydberg, and charge transfer excited states with minimal sacrifice of ground-state accuracy. In this Account, we compared the performance of the M06-class functionals and one M05-class functional (M05-2X) to that of some popular functionals for diverse databases and their performance on several difficult cases. The tests include barrier heights, conformational energy, and the trend in bond dissociation energies of Grubbs’ ruthenium catalysts for olefin metathesis. Based on these tests, we recommend (1) the M06-2X, BMK, and M05-2X functionals for main-group thermochemistry and kinetics, (2) M06-2X and M06 for systems where main-group thermochemistry, kinetics, and noncovalent interactions are all important, (3) M06-L and M06 for transition metal thermochemistry, (4) M06 for problems involving multireference rearrangements or reactions where both organic and transition-metal bonds are formed or broken, (5) M06-2X, M05-2X, M06-HF, M06, and M06-L for the study of noncovalent interactions, (6) M06-HF when the use of full Hartree-Fock exchange is important, for example, to avoid the error of self-interaction at longrange, (7) M06-L when a local functional is required, because a local functional has much lower cost for large systems.
2008. "Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions." Journal of Chemical Theory and Computation 4(11):1849-1868. doi:10.1021/ct800246v Abstract The hybrid meta density functionals M05-2X and M06-2X have been shown to provide broad accuracy for main group chemistry. In the present article we make the functional form more flexible and improve the self-interaction term in the correlation functional to improve its self-consistent-field convergence. We also explore the constraint of enforcing the exact forms of the exchange and correlation functionals through second order (SO) in the reduced density gradient. This yields two new functionals called M08-HX and M08-SO, with different exact constraints. The new functionals are optimized against 267 diverse main-group energetic data consisting of atomization energies, ionization potentials, electron affinities, proton affinities, dissociation energies, isomerization energies, barrier heights, noncovalent complexation energies, and atomic energies. Then the M08-HX, M08-SO, M05-2X, and M06-2X functionals and the popular B3LYP functional are tested against 250 data that were not part of the original training data for any of the functionals, in particular 164 main-group energetic data in 7 databases, 39 bond lengths, 38 vibrational frequencies, and 9 multiplicity-changing electronic transition energies. These tests include a variety of new challenges for complex systems, including large-molecule atomization energies, organic isomerization energies, interaction energies in uracil trimers, and bond distances in crowded molecules (in particular, cyclophanes). The M08-HX functional performs slightly better than M08-SO and M06-2X on average, significantly better than M05- 2X, and much better than B3LYP for a combination of main-group thermochemistry, kinetics, noncovalent interactions, and electronic spectroscopy. More important than the slight improvement in accuracy afforded by M08-HX is the conformation that the optimization procedure works well for data outside the training set. Problems for which the accuracy is especially improved by the new M08-HX functional include large-molecule atomization energies, noncovalent interaction energies, conformational energies in aromatic peptides, barrier heights, multiplicity-changing excitation energies, and bond lengths in crowded molecules.
2008. "How Well Can New-Generation Density Functionals Describe the Energetics ofBond-Dissociation Reactions Producing Radicals?" Journal of Physical Chemistry A 112(6):1095-1099. doi:10.1021/jp7109127 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The performance of various density functionals has been tested for three sets of reaction energies involving radicals. It is shown that two recently designed functionals, M05-2X and M06-2X, provide the best performance. These functionals provide useful and affordable methods for future mechanistic studies involving organic radicals.
2008. "Direct Observation of the Active Center for Methane Dehydroaromatization Using an Ultrahigh Field 95Mo NMR Spectroscopy." Journal of the American Chemical Society 130(12):3722-3723. doi:10.1021/ja7110916 Abstract Direct conversion of methane to value-added chemicals remains a challenge from both scientific and industrial points of view. In 1993, Wang et al. reported that methane can be transformed into aromatics on Mo/HZSM-5 catalysts under non-oxidative condition.1 Although remarkable progress has been made in the studies of the methane dehydroaromatization (MDA) reaction since that time, the reaction mechanism is still being debated,2 mainly due to the lack of understanding of the active center on Mo/HZSM-5 catalysts.3 It has been hypothesized that molybdenum may migrate into zeolitic channels and anchor on Brönsted acid sites during the synthesis. However, it is unclear whether the active molybdenum species are small crystallites or isolated exchanged species.
2008. "Aromaticity and Antiaromaticity in Transition-Metal Systems." Physical Chemistry Chemical Physics. PCCP 10(2):257-267. doi:10.1039/b713646c Abstract Aromaticity is an important concept in chemistry primarily for hydrocarbon compounds, but it has been extended to compounds containing transition-metal atoms. Recent findings of aromaticity and antiaromaticy in all-metal clusters have stimulated further researches in describing the chemical bonding, structures, and stability in transition-metal clusters and compounds on the basis of aromaticity and antiaromaticity, which are reviewed here. The presence of d-orbitals endows much more diverse chemistry, structure, and chemical bonding to transition-metal clusters and compounds. One interesting feature is the existence of a new type of -aromaticity, in addition to - and -aromaticity that are only possible for main group compounds. Another striking characteristic in the chemical bonding of transition-metal systems is the multi-fold nature of aromaticity, antiaromaticity, or even conflicting aromaticity. Separate sets of counting rules have been proposed for cyclic transition-metal systems to account for the three types of -, -, and -aromaticity/antiaromaticity. The diverse transition-metal clusters and compounds reviewed here indicate that multiple aromaticity and antiaromaticity may be much more common in chemistry than one would anticipate. It is hoped that the current review will stimulate interest in further understanding the structure and bonding, on the basis of aromaticity and antiaromaticity, of other known or unknown transition-metal systems, such as the active sites of enzymes or other biomolecules, which contain transition-metal atoms and clusters.
