Periodic DFT calculations to compute the attributes of a quantum material: honeycomb ruthenium trichloride.

Quantum spin liquids (QSLs) have become prominent materials of interest in the pursuit of fault-tolerant materials for quantum computing applications. This is due to the fact that these materials are theorized to host an interesting variety of quantum phenomena such as quasi-particles that may behave as anyons as a result of the high entangled nature of the spin states within the systems. Computing the electronic and magnetic properties of these materials is necessary in order to understand the underlying interactions of the materials.

Exploration of functionalizing graphene and the subsequent impact on PFAS adsorption capabilities via molecular dynamics.

Per- and polyfluoroalkyl substances (PFAS) are extremely stable compounds due to their strong C-F bonds. They are used in water and stain proof coatings, aqueous film forming foams for fire suppression, cosmetics, paints, adhesives, etc. PFAS have been found in soils and waterways around the world due to their widespread usage and recalcitrance to degradation.

Preferential Adsorption of Prominent Amino Acids in the Urease Enzyme of on Arid Soil Components: A Periodic DFT Study.

The urease enzyme is commonly used in microbially induced carbonate precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) to heal and strengthen soil. Improving our understanding of the adsorption of the urease enzyme with various soil surfaces can lead to advancements in the MICP and EICP engineering methods as well as other areas of soil science. In this work, we use density functional theory (DFT) to investigate the urease enzyme's binding ability with four common arid soil components: quartz, corundum, albite, and hematite.

Properties and Mechanisms for PFAS Adsorption to Aqueous Clay and Humic Soil Components.

The proliferation of poly- and perfluorinated alkyl substances (PFASs) has resulted in global concerns over contamination and bioaccumulation. PFAS compounds tend to remain in the environment indefinitely, and research is needed to elucidate the ultimate fate of these molecules. We have investigated the model humic substance and model clay surfaces as a potential environmental sink for the adsorption and retention of three representative PFAS molecules with varying chain length and head groups.

Computational Investigation on Interactions between Some Munition Compounds and Humic Substances.

Humic acid substances (HAs) in natural soil and sediment environments affect the retention and degradation of insensitive munition compounds and legacy high explosives (MCs): 2,4-dinitroanisole (DNAN), DNiNH, -methyl--nitroaniline (nMNA), 1-nitroguanidine (NQ), 3-nitro-1,2,4-triazol-5-one (NTO; neutral and anionic forms), 2,4,6-trinitrotoluene (TNT), and 1,3,5-trinitro-1,3,5-triazinane (RDX). A humic acid model compound has been considered using molecular dynamics, thermodynamic integration, and density functional theory to characterize the munition binding ability, ionization potential, and electron affinity compared to that in the water solution. Humic acids bind most compounds and act as both a sink and source for electrons.

Predicting the Impact of Aqueous Ions on Fate and Transport of Munition Compounds in the Environment.

A model framework for natural water has been developed using computational chemistry techniques to elucidate the interactions between solvated munition compounds and eight common ions in naturally occurring water sources. The interaction energies, residence times, coordination statistics, and surface preferences of nine munition-related compounds with each ion were evaluated. The propensity of these interactions to increase degradation of the munition compound was predicted using accelerated replica QM/MM simulations.

Impact of Water-Dilution on the Solvation Properties of the Ionic Liquid 1-Methyltriethoxy-3-ethylimidazolium Acetate for Model Biomass Molecules.

Many studies have suggested that the processing of lignocellulosic biomass could provide a renewable feedstock to supplant much of the current demand on petroleum sources. Currently, alkyl imidazolium-based ionic liquids (ILs) have shown considerable promise in the pretreatment, solvation, and hydrolysis of lignocellulosic materials although their high cost and unfavorable viscosity has limited their widespread use. Functionalizing these ILs with an oligo(ethoxy) tail has previously been shown through experiment to decrease the IL's viscosity resulting in enhanced mass transport characteristics, in addition to other favorable traits including decreased inhibition of some enzymes.

In silico insights into the solvation characteristics of the ionic liquid 1-methyltriethoxy-3-ethylimidazolium acetate for cellulosic biomass.

Lignocellulosic biomass is a domestically grown, sustainable, and potentially carbon-neutral feedstock for the production of liquid fuels and other value added chemicals. This underutilized renewable feedstock has the potential to alleviate some of the current socio-economic dependence on foreign petroleum supplies while stimulating rural economies. Unfortunately, the potential of biomass has largely been underdeveloped due to the recalcitrant nature of lignocellulosic materials.

The impact of active site protonation on substrate ring conformation in Melanocarpus albomyces cellobiohydrolase Cel7B.

The ability to utilize biomass as a feedstock for liquid fuel and value-added chemicals is dependent on the efficient and economic utilization of lignin, hemicellulose, and cellulose. In current bioreactors, cellulases are used to convert crystalline and amorphous cellulose to smaller oligomers and eventually glucose by means of cellulase enzymes. A critical component of the enzyme catalyzed hydrolysis reaction is the degree to which the enzyme can facilitate substrate ring deformation from the chair to a more catalytically active conformation (e.

Elucidating the conformational energetics of glucose and cellobiose in ionic liquids.

A major challenge for the utilization of lignocellulosic feedstocks for liquid fuels and other value added chemicals has been the recalcitrant nature of crystalline cellulose to various hydrolysis techniques. Ionic liquids (ILs) are considered to be a promising solvent for the dissolution and conversion of cellulose to simple sugars, which has the potential to facilitate the unlocking of biomass as a supplement and/or replacement for petroleum as a feedstock. Recent studies have revealed that the orientation of the hydroxymethyl group, described via the ω dihedral, and the glycosidic bond, described via the φ-ψ dihedrals, are significantly modified in the presence of ILs.

Computational evaluation of the dynamic fluctuations of peripheral loops enclosing the catalytic tunnel of a family 7 cellobiohydrolase.

The size and character of the peripheral loops enclosing the active site for cellulase enzymes is believed to play a major role in dictating many critical enzymatic properties. For many cellulases it is observed that fully enclosed active sites forming a tunnel are more conducive to cellobiohydrolase activity and the ability to processively move along the substrate. Conversely, a more open active site groove is indicative of endoglucanase activity.