Competitive Adsorption of Acetic Acid and Water on Kaolinite

Mineral dust is prevalent in the atmosphere as a result of emissions from natural and anthropogenic sources. As mineral dust particles undergo long-distance transport, they are exposed to trace gases and water vapor. We have characterized the interactions of acetic acid on kaolinite using diffuse reflectance infrared Fourier transform spectroscopy and molecular modeling to determine the chemisorbed species present. After the addition of acetic acid, gas-phase water was introduced to explore how water vapor competes with acetic acid for surface sites. We found that four chemisorbed acetate species are present on kaolinite after exposure to acetic acid in which acetate bonds through a monodentate, bidenatate, or bidentate bridging linkage with an aluminum atom. These species exhibit varying levels of stability after the introduction of water, indicating that water vapor affects the adsorption of organic acids. These results indicate that the type of chemisorbed species determines its stability toward competitive adsorption, which has potential implications for atmospheric composition and ice nucleation

Quantum Mechanical Modeling of CO₂ Interactions with Irradiated Stoichiometric and Oxygen-Deficient Anatase TiO₂ Surfaces: Implications for the Photocatalytic Reduction of CO₂

The conversion of CO₂ using light energy (CO₂ photoreduction) has the potential to produce useful fuels or valuable chemicals while decreasing CO₂ emissions from the use of fossil fuels. Identifying the mechanism and the active sites involved in the formation of negatively charged CO₂ species on TiO₂ surfaces represents a significant advance in our understanding of CO₂ photoreduction. To understand the role of the TiO₂ surface acting as a photocatalyst mediating CO₂ photocatalytic reduction, excited-state ab initio calculations of CO₂ adsorbed on clusters from the (010), (101), and (001) anatase surface planes were performed. Both post-Hartree−Fock calculations on small model surface clusters as well as density-functional theory (DFT) calculations on larger clusters indicate that conduction band electrons in irradiated, stoichiometric TiO₂ surfaces may not be transferred to CO₂. On the other hand, oxygen vacancies may act as the active sites for CO₂ photoreduction

Position-Specific ²H/H Equilibrium Isotopic Fractionation Factors in Alkane, Alkene, and Aromatic Molecules: A Density Functional Theory Approach

Advances in position-specific deuterium (2H) analyses provide powerful and accurate means for evaluating organic H isotopic signatures and fractionation factors. Density functional theory can aid in determining 2H–H equilibrium fractionation factors at specific positions on organic compounds. This work evaluates a DFT method that provides improved accuracy with respect to experimental data over previous methods while allowing for calculations on higher molecular weight compounds that are useful organic geochemical markers (biomarkers). We used computational quantum chemistry and applied the density functional theory method B3LYP and multiple basis sets. Based on accuracy criteria, we selected the basis set, 6-311++G(d,p), to calculate 2H–H equilibrium fractionation factors (α) on primary, secondary, tertiary, sp2, and aromatic C atoms for a model set that included methane, ethane, propane, 2-methylbutane, 2,3-dimethylpentane, 2,4-dimethylpentane, 2,6-dimethyloctane, 2,6,10,14-tetramethylpentadecane (pristane), 2,6,10,14-tetramethylhexadecane (phytane), twist-boat and chair cyclohexane, axial and equatorial methylcyclohexane, 2-heptanone, (E) and (Z) 2-pentene, and benzene with water. Two conformers each of cyclohexane, 2-pentene, and pristane were used to explore how thermodynamic weighting using the Boltzmann partition function could improve the α results for models of organic compounds that occur in more than one isomeric form. The B3LYP method coupled with the 6-311++G(d,p) basis set provided the most accurate α results, when compared with results from B3LYP coupled with 17 other basis sets. The calculated equilibrium α values for 2H on primary, secondary, and tertiary C atoms follow the observed trend in the deuterium preference for carbon–hydrogen bonds relative to water: α3° > α2° > α1°. Further, ln(β) values predicted from the DFT calculations also agree with fractionation estimated within 4%, as calculated using observed FTIR vibrational frequencies. Application of B3LYP/6-311++G(d,p) will aid in the assessments of position-specific 2H–H equilibrium fractionation factors (α) for comparison with experimental studies. Estimated position-specific alpha values can be scaled with temperature and used to predict molecular-averaged delta values, such as determined using compound-specific isotope analyses (CSIA). The ability to adjust position and molecular-averaged calculations for dominant isomeric forms makes this a useful approach to study equilibrium H isotope distributions in larger compounds of organic geochemical, biogeochemical, and environmental interest

How Cellulose ElongatesA QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA

The catalytic mechanism of bacterial cellulose synthase was investigated by using a hybrid quantum mechanics and molecular mechanics (QM/MM) approach. The Michaelis complex model was built based on the X-ray crystal structure of the cellulose synthase subunits BcsA and BcsB containing a uridine diphosphate molecule and a translocating glucan. Our study identified an S_N2-type transition structure corresponding to the nucleophilic attack of the nonreducing end O₄ on the anomeric carbon C₁, the breaking of the glycosidic bond C₁–O₁, and the transfer of proton from the nonreducing end O₄ to the general base D343. The activation barrier found for this S_N2-type transition state is 68 kJ/mol. The rate constant of polymerization is estimated to be ∼8.0 s^–1 via transition state theory. A similar S_N2-type transition structure was also identified for a second glucose molecule added to the growing polysaccharide chain, which aligned with the polymer 180° rotated compared to the initially added unit. This study provides detailed insights into how cellulose is extended by one glucose molecule at a time and how the individual glucose units align into cellobiose repeating units

X‑ray Absorption Spectroscopic Quantification and Speciation Modeling of Sulfate Adsorption on Ferrihydrite Surfaces

Sulfate adsorption on mineral surfaces is an important environmental chemical process, but the structures and respective contribution of different adsorption complexes under various environmental conditions are unclear. By combining sulfur K-edge XANES and EXAFS spectroscopy, quantum chemical calculations, and surface complexation modeling (SCM), we have shown that sulfate forms both outer-sphere complexes and bidentate–binuclear inner-sphere complexes on ferrihydrite surfaces. The relative fractions of the complexes vary with pH, ionic strength (<i>I</i>), and sample hydration degree (wet versus air-dried), but their structures remained the same. The inner-sphere complex adsorption loading decreases with increasing pH while remaining unchanged with <i>I</i>. At both <i>I</i> = 0.02 and 0.1 M, the outer-sphere complex loading reaches maximum at pH ∼5 and then decreases with pH, whereas it monotonically decreases with pH at <i>I</i> = 0.5 M. These observations result from a combination of the ionic-strength effect, the pH dependence of anion adsorption, and the competition between inner- and outer-sphere complexation. Air-drying drastically converts the outer-sphere complexes to the inner-sphere complexes. The respective contributions to the overall adsorption loading of the two complexes were directly modeled with the extended triple layer SCM by implementing the bidentate–binuclear inner-sphere complexation identified in the present study. These findings improve our understanding of sulfate adsorption and its effects on other environmental chemical processes and have important implications for generalizing the adsorption behavior of anions forming both inner- and outer-sphere complexes on mineral surfaces

A New Hypothesis for the Dissolution Mechanism of Silicates

A novel mechanism for protonating bridging O atoms (O_br) and dissolving silica is proposed that is consistent with experimental data and quantum mechanical simulations of the α-quartz (101)/water interface. The new hypothesis is that H⁺-transfer occurs through internal surface H-bonds (i.e., SiOH–O_br) rather than surface water H-bonds and that increasing ionic strength, <i>I</i>, favors formation of these internal H-bonds, leading to a larger pre-exponential factor, <i>A</i>, in the Arrhenius equation, <i><i>k</i> = A</i> exp­(<i>−</i>Δ<i>E</i>_a/<i>RT</i>), and higher rates of dissolution. Projector-augmented planewave density functional theory (DFT) molecular dynamics (MD) simulations and static energy minimizations were performed on the α-quartz (101) surface and with pure water, with Cl^–, Na⁺, and Mg²⁺. Classical molecular dynamics were performed on α-quartz (101) surface and pure water only. The nature of the H-bonding of the surface silanol (SiOH) groups with the solution and with other surface atoms is examined as a test of the above hypothesis. Statistically significant increases in the percentages of internal SiOH–O_br H-bonds, as well as the possibility of O_br protonation with H-bond linkage to silanol group, are predicted by these simulations, which is consistent with the new hypothesis. This new hypothesis is discussed in relation to experimental data on silicate dissolution

A New Hypothesis for the Dissolution Mechanism of Silicates

A novel mechanism for protonating bridging O atoms (O_br) and dissolving silica is proposed that is consistent with experimental data and quantum mechanical simulations of the α-quartz (101)/water interface. The new hypothesis is that H⁺-transfer occurs through internal surface H-bonds (i.e., SiOH–O_br) rather than surface water H-bonds and that increasing ionic strength, <i>I</i>, favors formation of these internal H-bonds, leading to a larger pre-exponential factor, <i>A</i>, in the Arrhenius equation, <i><i>k</i> = A</i> exp­(<i>−</i>Δ<i>E</i>_a/<i>RT</i>), and higher rates of dissolution. Projector-augmented planewave density functional theory (DFT) molecular dynamics (MD) simulations and static energy minimizations were performed on the α-quartz (101) surface and with pure water, with Cl^–, Na⁺, and Mg²⁺. Classical molecular dynamics were performed on α-quartz (101) surface and pure water only. The nature of the H-bonding of the surface silanol (SiOH) groups with the solution and with other surface atoms is examined as a test of the above hypothesis. Statistically significant increases in the percentages of internal SiOH–O_br H-bonds, as well as the possibility of O_br protonation with H-bond linkage to silanol group, are predicted by these simulations, which is consistent with the new hypothesis. This new hypothesis is discussed in relation to experimental data on silicate dissolution

Initiation, Elongation, and Termination of Bacterial Cellulose Synthesis

Cellulose is the major component of the plant cell wall and composed of β-linked glucose units. Use of cellulose is greatly impacted by its physical properties, which are dominated by the number of individual cellulose strand within each fiber and the average length of each strand. Our work described herein provides a complete mechanism for cellulose synthase accounting for its processivity and mechanism of initiation. Using ionic liquids and gel permeation chromatography, we obtain kinetic constants for initiation, elongation, and termination (release of the cellulose strand from the enzyme) for two bacterial cellulose synthases (Gluconacetobacter hansenii and Rhodobacter sphaeroides). Our results show that initiation of synthesis is primer-independent. After initiation, the enzyme undergoes multiple cycles of elongation until the strand is released. The rate of elongation is much faster than that of steady-state turnover. Elongation requires cyclic addition of glucose (from uridine diphosphate-glucose) and then strand translocation by one glucose unit. Translocations greater than one glucose unit result in termination requiring reinitiation. The rate of the strand release, relative to the rate of elongation, determines the processivity of the enzyme. This mechanism and the measured rate constants were supported by kinetic simulation. With the experimentally determined rate constants, we are able to simulate steady-state kinetics and mimic the size distribution of the product. Thus, our results provide for the first time a mechanism for cellulose synthase that accounts for initiation, elongation, and termination

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

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