James D. Kubicki

Photoinduced activation of CO2 on Ti-based heterogeneous catalysts: Current state, chemical physics-based insights and outlook

This article is a review of the current knowledge of the chemical physics of carbon dioxide (CO2) conversion to fuels using light energy and water (CO2 photoreduction) on titania (TiO2)-based catalysts and Ti-species in porous materials. Fairly comprehensive literature reviews of CO2 photoreduction are available already. However, this article is focused on CO2 photoreduction on Ti-based catalysts, and incorporates fundamental aspects of CO2 photoreduction, knowledge from surface science studies of TiO2 and the surface chemistry of CO2. Firstly, the current state of development of this field is briefly reviewed, followed by a description of and insights from surface state and surface site approaches. Using examples such as metal-doping of TiO2, dye-sensitization, oxygen vacancies in TiO2 and isolated-Ti centers in microporous/mesoporous materials, the utility of these approaches to understand photoinduced reactions involved in CO2activation is examined. Finally, challenges and prospects for further development of this field are presented. Enhanced understanding of the CO2 : TiO2 system, with a combination of computational and experimental studies is required to develop catalysts exhibiting higher activity towards CO2 photoreduction.

Kinetics of Water-Rock Interaction

Analysis of Rates of Geochemical Reactions.- Transition State Theory and Molecular Orbital Calculations Applied to Rates and Reaction Mechanisms in Geochemical Kinetics.- The Mineral-Water Interface.- Kinetics of Sorption-Desorption.- Kinetics of Mineral Dissolution.- Data Fitting Techniques with Applications to Mineral Dissolution Kinetics.- Nucleation, Growth, and Aggregation of Mineral Phases: Mechanisms and Kinetic Controls.- Microbiological Controls on Geochemical Kinetics 1: Fundamentals and Case Study on Microbial Fe(III) Oxide Reduction.- Microbiological Controls on Geochemical Kinetics 2: Case Study on Microbial Oxidation of Metal Sulfide Minerals and Future Prospects.- Quantitative Approaches to Characterizing Natural Chemical Weathering Rates.- Geochemical Kinetics and Transport.- Isotope Geochemistry as a Tool for Deciphering Kinetics of Water-Rock Interaction.- Kinetics of Global Geochemical Cycles.

Attenuated total reflectance Fourier-transform infrared spectroscopy of carboxylic acids adsorbed onto mineral surfaces

Abstract A suite of naturally-occurring carboxylic acids (acetic, oxalic, citric, benzoic, salicylic and phthalic) and their corresponding sodium salts were adsorbed onto a set of common mineral substrates (quartz, albite, illite, kaolinite and montmorillonite) in batch slurry experiments. Solution pH’s of approximately 3 and 6 were used to examine the effects of pH on sorption mechanisms. Attenuated total reflectance Fourier-transform infrared (ATR FTIR) spectroscopy was employed to obtain vibrational frequencies of the organic ligands on the mineral surfaces and in solution. UV/visible spectroscopy on supernatant solutions was also employed to confirm that adsorption from solution had taken place for benzoic, salicylic and phthalic acids. Molecular orbital calculations were used to model possible surface complexes and interpret the experimental spectra. In general, the tectosilicates, quartz and albite feldspar, did not chemisorb (i.e., strong, inner-sphere adsorption) the carboxylate anions in sufficient amounts to produce infrared spectra of the organics after rinsing in distilled water. The clays (illite, kaolinite and montmorillonite) each exhibited similar ATR FTIR spectra. However, the illite sample used in this study reacted to form strong surface and aqueous complexes with salicylic acid before being treated to remove free Fe-hydroxides. Chemisorption of carboxylic acids onto clays is shown to be limited without the presence of Fe-hydroxides within the clay matrix.

Dissolution of nepheline, jadeite and albite glasses: toward better models for aluminosilicate dissolution

Abstract SLB acknowledges many educational and entertaining conversations with Hal Helgeson (ranging from kinetics to bent head morphologies) over the last 17 years. To investigate the effects of changing the Al/Si ratio on plagioclase dissolution without complications of varying Na/Ca content or exsolution, three glasses with varying Al/Si ratios (albite, jadeite, and nepheline glasses) were synthesized and dissolved. Many similarities in dissolution behavior between plagioclase crystals and this suite of glasses were observed: 1) dissolution was slowest at near-neutral pH and increased under acid and basic conditions; 2) dissolution rate at all pH values increased with increasing Al/Si ratio; 3) the pH dependence of dissolution was higher for the phase with Al/Si = 1 than the phase with Al/Si = 0.3; 4) after acid leaching, the extent of Al depletion of the altered surface increased with increasing bulk Al/Si ratio from Al/Si = 0.3 (albite glass) to 0.5 (jadeite glass), but then decreased in nepheline glass (Al/Si = 1.0), which dissolved stoichiometrically with respect to Al; and 5) little to no Al depletion of the surface of any glass occurred at pH > 7. In contrast with some observations for plagioclase dissolution, however, log (rate) increased linearly with Al content, and n, the slope of the log (rate) − pH curve at low pH, varied smoothly from albite glass to jadeite glass to nepheline glass (n = −0.3, −0.6, and −1.0, respectively). These results, plus the observation that the slope calculated at high pH, m, did not differ between glasses (m = 0.4 ± 0.1), may be consistent with an identical mechanism controlling dissolution of albite, jadeite, and nepheline glasses, although no Si-rich layer can develop on nepheline because of the lack of SiOSi linkages. Such a conclusion is consistent with a transition state for these aluminosilicates at high pH consisting of a deprotonated Q3Si hydroxyl group (where Qvx refers to an x atom in a tetrahedral site with v bridging oxygens) or a five-coordinate Si site after nucleophilic attack by OH−. At low pH, bridging oxygens between Q4Si and Q4Al may be rate limiting if they are slower to hydrolyze than QvSiQwSi linkages (v,w≤ 3). According to this mechanism, dissolution rate increases from albite to jadeite to nepheline glass because hydrolysis of AlOSi bonds become more energetically favorable as the number of Al atoms per Si tetrahedron increases, a phenomenon documented here by geometry optimizations by use of ab initio methods. A model wherein Q4AlQ4Si linkages are faster to hydrolyze than lower connectivity linkages between Si atoms (QvSiQwSi, v,w≤ 3) may also explain aspects of this data. Further computational and experimental measurements are needed to distinguish the models.

Tertiary model of a plant cellulose synthase

A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure of a bacterial cellulose-synthesizing protein validates the overall fold of the modeled glycosyltransferase (GT) domain. The coaligned plant and bacterial GT domains share a six-stranded β-sheet, five α-helices, and conserved motifs similar to those required for catalysis in other GT-2 glycosyltransferases. Extending beyond the cross-kingdom similarities related to cellulose polymerization, the predicted structure of cotton CESA reveals that plant-specific modules (plant-conserved region and class-specific region) fold into distinct subdomains on the periphery of the catalytic region. Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose–synthesis complexes that are characteristic of plants. Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in Arabidopsis thaliana to their analogous positions in the modeled structure. Most of these mutation sites are near the predicted catalytic region, and the confluence of other mutation sites supports the existence of previously undefined functional nodes within the catalytic core of CESA. Overall, the predicted tertiary structure provides a platform for the biochemical engineering of plant CESAs.

Models of natural organic matter and interactions with organic contaminants

Adsorption of organic contaminants onto soils, sediments and other particulates has the potential to be a major controlling factor in their bioavailability, fate and behavior in the environment. Models for estimating the amount and stability of sorbed organic contaminants based on the fraction of organic carbon in a soil or sediment can oversimplify the process of sorption in the environment. In order to help understand sorption of organic contaminants in soils and sediments, we modeled various components of natural organic matter (NOM) that are possible substrates for sorption. These substrates include soot particles, lignin, humic and fulvic acids. The molecular scale interactions of selected aromatic hydrocarbons with different substrates were also simulated. Results of the simulations include the 3-D structures of the NOM components, changes in structure with protonation state and solvation and the sorption energy between PAH and substrate. This last parameter is an indicator of the amount of contaminant that will sorb and the energy required to free the contaminant from the substrate. Although the simulation results presented in this paper represent a first-order examination of NOM and contaminant interactions, the findings highlight a number of essential features that should be included in future molecular models of NOM and contaminant sorption.

Development of a reactive force field for iron-oxyhydroxide systems.

We adopt a classical force field methodology, ReaxFF, which is able to reproduce chemical reactions, and train its parameters for the thermodynamics of iron oxides as well as energetics of a few iron redox reactions. Two parametrizations are developed, and their results are compared with quantum calculations or experimental measurements. In addition to training, two test cases are considered: the lattice parameters of a selected set of iron minerals, and the molecular dynamics simulation of a model for alpha-FeOOH (goethite)-water interaction. Reliability and limitations of the developed force fields in predicting structure and energetics are discussed.

Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework.

The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 A of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 degrees C that agrees quantitatively with the experimentally determined value (5.4+/-0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees C into quantitative agreement with the experimental value (4.8+/-0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 degrees C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite (alpha-SnO2) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.

Comparisons of multilayer H2O adsorption onto the (110) surfaces of alpha-TiO2 and SnO2 as calculated with density functional theory.

Mono- and bilayer adsorption of H2O molecules on TiO2 and SnO 2 (110) surfaces has been investigated using static planewave density functional theory (PW DFT) simulations. Potential energies and structures were calculated for the associative, mixed, and dissociative adsorption states. The DOS of the bare and hydrated surfaces has been used for the analysis of the difference between the H2O interaction with TiO2 and SnO 2 surfaces. The important role of the bridging oxygen in the H2O dissociation process is discussed. The influence of the second layer of H2O molecules on relaxation of the surface atoms was estimated.

Sum-Frequency-Generation Vibration Spectroscopy and Density Functional Theory Calculations with Dispersion Corrections (DFT-D2) for Cellulose Iα and Iβ

Sum-frequency-generation (SFG) vibration spectroscopy selectively detects noncentrosymmetric vibrational modes in crystalline cellulose inside intact lignocellulose. However, SFG peak assignment in biomass samples is challenging due to the complexity of the SFG processes and the lack of reference SFG spectra from the two crystal forms synthesized in nature, cellulose Iα and Iβ. This paper compares SFG spectra of laterally aligned cellulose Iα and Iβ crystals with vibration frequencies calculated from density functional theory with dispersion corrections (DFT-D2). Two possible hydrogen-bond networks A and B ( Nishiyama et al. Biomacromolecules 2008 , 9 , 3133 ) were investigated for both polymorphs. From DFT-D2 calculations the energetically favorable structures for cellulose Iα and Iβ had CH2OH groups in tg conformations and network A hydrogen bonding. The calculated frequencies of C-H stretch modes agreed reasonably well with the peak positions observed with SFG and were localized vibrations; thus, peak assignments to specific alkyl groups were proposed. DFT-D2 calculations underestimated the distances between hydrogen-bonded oxygen atoms compared to the experimentally determined values; therefore, the OH stretching calculated frequencies were ~100 cm(-1) lower than observed. The SFG peak assignments through comparison with DFT-D2 calculations will guide the SFG analysis of the crystalline cellulose structure in plant cell walls and lignocellulose biomass.