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 (SiO) (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 HO and 2 HO molecules to approximate an aqueous environment, whereas the SiOH models had 59 HO and 1 HO molecules.

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 (Cd) and its presence in various waste products found in the environment, it is necessary to develop methods to attenuate and remediate Cd waste. Sorption of Cd to mineral surfaces is a potential route to accomplish this goal. This work focused on improving our molecular-scale understanding of the chemistry of Cd interactions with gibbsite and kaolinite mineral surfaces.

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.

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).

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).

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.

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.

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...