Connecting Thermodynamics of Alkali Ion Exchange on the Quartz (101) Surface with Density Functional Theory Calculations.

Periodic plane-wave density functional theory (DFT) calculations were performed on the α-quartz (SiO2) (101) surface to model exchange of adsorbed Li+ and either Na+, K+, or Rb+ in inner- and outer-sphere adsorbed, and aqueous configurations, which are charge-balanced with 2 Cl-. SiO- or SiOH groups represented the adsorption surface sites. The SiO- models included 58 H2O and 2 H3O+ molecules to approximate an aqueous environment, whereas the SiOH models had 59 H2O and 1 H3O+ molecules. The goal of this work is to calculate the heats of exchange for these alkali ions and to compare the results with those measured by flow microcalorimetry to ascertain the most probable mechanisms for these cations exchanging on the α-quartz (101) surface. Energy minimizations of each alkali ion adsorbed as outer-sphere complexes on SiOH surface sites, and as inner- and outer-sphere complexes on SiO- surface sites, were used to determine the energy of exchange (ΔEex) with Li+ for comparison with experimentally determined ΔHex values. Here, we present a novel method for calculating ΔEex using the difference in energies of geometry-optimized end member models. The aqueous and surface structures produced are similar to those observed experimentally. Although the trend for the calculated ΔEex values is consistent with those from the heats of exchange measured experimentally, the magnitude of our modeled ΔEex results is significantly larger than select experimental data from the literature [Peng, L. Zeta-Potentials and Enthalpy Changes in the Process of Electrostatic Self-Assembly of Cations on Silica Surface. Powder Technol. 2009, 193(1), 46-49]; we discuss the reasons for this discrepancy herein. The relative energy differences of the various configurations modeled have implications for the measurements of the surface charge via potentiometric titrations due to the more active role of alkali cations in quartz surface chemistry that have been previously considered as inert background electrolytes.

Gibbsite (100) and Kaolinite (100) Sorption of Cadmium(II): A Density Functional Theory and XANES Study of Structures and Energies.

Due to the potential toxicity of cadmium (Cd2+) and its presence in various waste products found in the environment, it is necessary to develop methods to attenuate and remediate Cd2+ waste. Sorption of Cd2+ to mineral surfaces is a potential route to accomplish this goal. This work focused on improving our molecular-scale understanding of the chemistry of Cd2+ interactions with gibbsite and kaolinite mineral surfaces. Plane-wave density functional theory (DFT) energy minimization calculations and molecular dynamics simulations were used to study the adsorption energies and the nature of the bonds between Cd2+ and the mineral surfaces for possible inner- and outer-sphere surface complexes. Models resulting from the DFT calculations were used to calculate theoretical XANES spectra that were compared with experimental Cd LIII XANES of aqueous Cd2+ as a proxy for outer-sphere Cd2+ hydrated complexes associated with the mineral surfaces. These studies suggest that Cd2+ would favorably bond to the (100) surfaces of both kaolinite and gibbsite through a bidentate mononuclear interaction. However, the results indicate that mixtures of surface complexes on these minerals are likely.

Quantum Calculations on Plant Cell Wall Component Interactions.

Density functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M05-2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components. Solvation effects were examined by modeling the interactions in the gas phase, in explicit H2O, and in polarized continuum models (PCM) of solvation. PCMs were used to represent water, methanol, and chloroform. The results predict the relative ranges of each type of interaction and when specific configurations will be strongly preferred. Structures and energies are useful as a basis for testing classical force fields and as guidance for coarse-grained models of PCWs.

Sum-frequency-generation vibration spectroscopy and density functional theory calculations with dispersion corrections (DFT-D2) for cellulose Iα and Iß.

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 Iß. This paper compares SFG spectra of laterally aligned cellulose Iα and Iß 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 Iß 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.

Identification and characterization of a cellulose binding heptapeptide revealed by phage display.

Cellulose nanowhiskers (CNWs) were used in conjunction with phage display technology to identify polypeptides which bind the crystalline region of cellulose. A consensus peptide WHWTYYW was identified to efficiently bind the CNWs. The binding affinities of specific phage particles were assessed using biopanning assays and enzyme-linked immunosorbent assay (ELISA). The WHWTYYW peptide was synthesized and isothermal titration calorimetry (ITC) analysis showed that the peptide exhibited a binding constant of ∼10(5) M(-1) toward the crystalline CNWs. In order to understand how the affinity of this peptide differs for noncrystalline cellulose, binding properties were characterized using cello-oligosaccharides as substrates. Binding analysis was performed using UV spectroscopy and fluorescence quenching experiments. The specific molecular interactions of the WHWTYYW peptide with cellohexaose were examined using nuclear magnetic resonance (NMR). Interactions of this peptide with crystalline cellulose were also investigated using classical molecular modeling and quantum mechanical calculations of (13)C NMR chemical shifts. The NMR experiments and calculations indicate that the WHWTYYW peptide exhibits a bent structure when bound, allowing the Y5 amino acid to form a CH/π stacking interaction and H-bond with the glucose ring of cellulose.

Evaluation of potential reaction mechanisms leading to the formation of coniferyl alcohol α-linkages in lignin: a density functional theory study.

Five potential reaction mechanisms, each leading to the formation of an α-O-4-linked coniferyl alcohol dimer, and one scheme leading to the formation of a recently proposed free-radical coniferyl alcohol trimer were assessed using density functional theory (DFT) calculations. These potential reaction mechanisms were evaluated using both the calculated Gibbs free energies, to predict the spontaneity of the constituent reactions, and the electron-density mapped Fukui function, to determine the most reactive sites of each intermediate species. The results indicate that each reaction in one of the six mechanisms is thermodynamically favorable to those in the other mechanisms; what is more, the Fukui function for each free radical intermediate corroborates with the thermochemical results for this mechanism. This mechanism proceeds via the formation of two distinct free-radical intermediates, which then react to produce the four α-O-4 stereoisomers.

Comparison of multistandard and TMS-standard calculated NMR shifts for coniferyl alcohol and application of the multistandard method to lignin dimers.

Coniferyl alcohol is a monomeric building block of lignin, the second most abundant biopolymer. During lignification, the monomer forms a variety of linkages through free radical additions. A large NMR database has been constructed that reports the (1)H and (13)C chemical shifts for thousands of lignin oligomers. Herein, Boltzmann averaged (1)H and (13)C GIAO NMR calculations were performed on coniferyl alcohol and four of its dimers, ß-O-4, ß-ß, ß-5, and 5-5, to compare the calculated chemical shifts with experiment. Six B3LYP/6-311++G(d,p) energy-minimized conformational isomers of coniferyl alcohol were subjected to single-point GIAO NMR calculations. Initially, four NMR shift calculation methods were compared: three were performed using the TMS-standard method at the HF/6-311+G(2d,p), B3LYP/6-311+G(2d,p), and mPW1PW91/6-31G(d) theory levels, and the fourth was performed with a multistandard approach using a mPW1PW91/6-31G(d) theory level. For the multistandard method, benzene was used as the standard for aromatic C and H atoms and methanol was used for aliphatic C and H atoms. The hydroxyl-H of methanol was used as the standard for hydroxyl-H atoms. The Boltzmann averaged results for six conformers showed that the multistandard method is more accurate for coniferyl alcohol and its dimers than the often used TMS-standard method, based on the mean unsigned, root-mean-squared, and maximum errors, as well as linear correlations between observed and calculated values. The (13)C results were more accurate than the (1)H results, due to poorer agreement between calculated hydroxyl-H results and observed data. Further Boltzmann-averaged, multistandard NMR calculations compared the (13)C and (1)H chemical shifts with experiment for the four stereoisomers of the ß-O-4 dimer, as well as the 5-5, ß-5, and ß-ß dimers of coniferyl alcohol. The (13)C results correlated well with experiment (r(2)>0.99) for all dimers and showed small statistical errors, compared with experiment. The correlation with experiment for (1)H NMR was generally inferior to the (13)C NMR results for the dimers.

MP2, density functional theory, and molecular mechanical calculations of C-H...pi and hydrogen bond interactions in a cellulose-binding module-cellulose model system.

Exploring non-covalent interactions, such as C-H...pi stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-Hcdots, three dots, centeredpi (sugar-aromatic stacking) and H-bonds, between methyl beta-d-glucopyranoside and l-tyrosine-a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between -24 and -38kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-Hcdots, three dots, centeredpi stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-Hcdots, three dots, centeredO4 approximately 2A, e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the sigma *(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is approximately 13kJ/mol. This H-bond interaction plays an important role in controlling the CH/pi interaction geometry. Therefore, the C-Hcdots, three dots, centeredpi dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/pi interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-Hcdots, three dots, centeredpi interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine C(delta1)-C(epsilon1) and C(delta2)-C(epsilon2) bonds in the complex, the calculated IR spectra show red shifts of 12cm(-1) (MP2/6-31G(d)) and 5cm(-1) (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed (1)H NMR chemical shifts due to the C-Hcdots, three dots, centeredpi interaction.