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. In this paper, the structural, electronic, and magnetic properties including lattice parameters, bandgap, Heisenberg coupling constants, and Curie temperatures for α-RuCl3, a promising candidate for the Kitaev QSL model, are computed using periodic density functional theory. Furthermore, various parameters of the calculations (i.e. functional choice, basis set, k-point density, and Hubbard correction) are varied in order to determine what effect, if any, the computational setup has on the computed properties. The results of this study indicate that PBE functional with Hubbard corrections of 1.5-2.5 eV with a k-point density of 3.0 points per Å-1 appear to be the best parameters to compute Heisenberg coupling constants for α-RuCl3. These parameters with the addition of spin orbit coupling works well for computing Curie temperatures for α-RuCl3. Distinct differences are noted in the computations of the bulk structure vs. monolayer structures, indicating that interactions between the layers play a role in the material properties and changes to the inter-layer spacing may result in interesting and unique magnetic properties that require further investigation.

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. Development of selective adsorbent materials is necessary to effectively capture a vast family of PFAS structures in order to remediate PFAS contamination in the environment. The work herein is focused on extracting design principles from molecular dynamics simulations of PFAS with functionalized graphene materials. Simulations examined how PFBA, PFOA, and PFOS interact with graphene, graphene oxide, nitrogen group-functionalized graphene oxide, partially fluorinated graphene flakes, and fully fluorinated flakes. Five flakes were used in each simulation to examine how interactions between flakes may lead to competitive interactions with respect to PFAS or formation of pores. Our study revealed that both the clustering mechanisms of the flakes and functional groups on the flake play a role in PFAS adsorption. The most effective functionalizations for PFAS adsorption are as follows: pristine graphene ≈ fully fluorinated > graphene oxide ≈ partially fluorinated > amine and amide functionalized graphene oxide flake. Long chain PFAS and sulfonate PFAS had higher propensity to adsorb to the materials compared to short chain PFAS and carboxylic head groups.

Preferential Adsorption of Prominent Amino Acids in the Urease Enzyme of Sporosarcina pasteurii 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. As the urease enzyme cannot directly be simulated with DFT due to its size, the amino acids comprising at least 5% of the urease enzyme were simulated instead. An adsorption model incorporating the Gibbs free energy was used to determine the existence of amino acid-mineral binding modes. It was found that the nine simulated amino acids bind preferentially to the different soil components. Alanine favors corundum, glycine and threonine favor hematite, and aspartic acid favors albite. It was found that, under the standard environmental conditions considered here, amino acid binding to quartz is unfavorable. In the polymeric form where the side chains would dominate the binding interactions, hematite favors aspartic acid through its R-OH group and corundum favors glutamic acid through its R-Ket group. Overall, our model predicts that the urease enzyme produced by Sporosarcina pasteurii can bind to various oxides found in arid soil through its alanine, glycine, aspartic/glutamic acid, or threonine residues.

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. Utilizing molecular dynamics simulation, we quantify the ability of pyrophyllite and the humic substance to favorably adsorb these PFAS molecules from aqueous solution. We have observed that the hydrophobic nature of the pyrophyllite surface makes the material well suited for the sorption of medium- and long-tail PFAS moieties. Similarly, we find a preference for the formation of a monolayer on the surface for long-chain PFAS molecules at high concentration. Furthermore, we discussed trends in the adsorption mechanisms for the fate and transport of these compounds, as well as potential approaches for their environmental remediation.

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), DNi-NH4+, N-methyl-p-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. Ionization potentials suggest that HAs are more susceptible to oxidation than the MCs studied. The electron affinity of HAs is very conformation-dependent and spans the same range as the munition compounds. When HAs and MCs are complexed, the HAs tend to radicalize first, thus buffering MCs against reductive as well as oxidative attacks.

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. The degradation prediction data qualitatively align with previous quantum mechanical studies. The results suggest that primary ions of interest for fate and transport modeling of munition compounds in natural waters may follow the relative importance of SO42-, Cl- ≫ HCO3-, Na+, Mg2+ > Ca2+, K+, and NH4+.

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. Additionally, the use of cosolvents to mitigate the cost and unfavorable traits of ILs is an area of growing interest with particular attention on water as the presence of water in biomass processes is inevitable. Through the use of biased and unbiased molecular dynamics (MD) simulations, this study provides a molecular-level perspective of the various solvent-solvent and solvent-solute interactions in binary mixtures of water and 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM+] [OAc-]) in the presence of model cellulose compounds (i.e., glucose and cellobiose). It is observed that at ∼75% w/w IL and water a transition in the nanostructure of the solvent occurs between water-like and IL-like solvation characteristics. It is shown that H-bonding interactions between the anion and water are a major driving force that significantly impacts the solvent properties of the IL as well as conformational preferences of the cellulosic model compound. In addition, it is found that the oligo(ethoxy) cation tail is responsible for the reduction in the propensity for tail aggregation as compared to alkyl tails of similar length, which, combined with increased ionic shielding, results in increased diffusion and enhanced water-like solvation characteristics.

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. Task-specific ionic liquids (ILs) have shown considerable promise as an alternative non-aqueous solvent for solvation and deconstruction of lignocellulose in the presence of metal chloride catalyst or enzymes. Recently it has been hypothesized that adding oxygen atoms to the tail of an imidazolium cation would alleviate some of the negative characteristics of the ILs by increasing mass transport properties, and decreasing IL deactivation of enzymes, while at the same time retaining favorable solvation characteristics for lignocellulose. Reported here are fully atomistic molecular dynamic simulations of 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM(+)] [OAc(-)]) that elucidate promising molecular-level details pertaining to the solvation characteristics of model compounds of cellulose, and IL-induced side-chain and ring puckering conformations. It is found that the anion interactions with the saccharide induce alternate ring puckering conformations from those seen in aqueous environments (i.e.(1)C4), while the cation interactions are found to influence the conformation of the ω dihedral. These perturbations in saccharide structures are discussed in the context of their contribution to the disruption of hydrogen bonding in cellulosic architecture and their role in solvation.

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.g. skewed boat) at the -1 subsite. Presented here is an evaluation of the impact of the protonation state for critical active site residues (i.e. Glu212, Asp214, Glu217, and His228) in Melanocarpus albomyces (Ma) Cellobiohydrolase Cel7B on the substrate's orientation and ring conformation. It is found that the protonation state of the active site can disrupt the intra-enzyme hydrogen bonding network and enhance the sampling of various ring puckering conformations for the substrate ring at the +1 and -1 subsites. In particular it is observed that the protonation state of Asp214 dictates the accessibility of the glycosidic bond to the catalytic acid/base Glu217 by influencing the φ/ψ dihedral angles and the puckering of the ring structure. The protonation-orientation-conformation analysis has revealed an active site that primarily utilizes two highly coupled protonation schemes; one protonation scheme to orient the substrate and generate catalytically favorable substrate geometries and ring puckering conformations and another protonation scheme to hydrolyze the glycosidic bond. In addition to identifying how enzymes utilize protonation state to manipulate substrate geometry, this study identifies possible directions for improving catalytic activity through protein engineering.

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. In this study, we explore the energetics driving the orientational preference of the ω dihedral and the φ-ψ dihedrals for glucose and cellobiose in water and three imidazolium based ILs. It is found that interactions between the cation and the ring oxygen in glucose directly impact the conformational preference of the ω dihedral shifting the distribution towards the gauche-trans (GT) conformation and creating an increasingly unfavorable gauche-gauche (GG) conformation with increasing tail length. This discovery modifies the current hypothesis that intramolecular hydrogen bonding is responsible for the shift in the ω dihedral distribution and illuminates the importance of the cation's character. In addition, it is found that the IL's interaction with the glycosidic bond results in the modification of the observed φ-ψ dihedrals, which may have implications for hydrolysis in the presence of ILs. The molecular level information gained from this study identifies the favorable IL-sugar interactions that need to be exploited in order to enhance the utilization of lignocellulosic biomass as a ubiquitous feedstock.

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. For both cellobiohydrolases and endoglucanases, the loop regions have been implicated in the ability of the enzyme to bind substrate, influence the pKa of active site residues, modulate the catalytic activity, and influence thermal stability. Reported here are constant pH molecular dynamics (CpHMD) simulations that investigate the role of dynamic fluctuations, substrate interactions, and residue pKa values for the peripheral loops enclosing the active site of the cellobiohydrolase Melanocarpus albomyces Cel7B. Two highly flexible loop regions in the free enzyme have been identified, which impact the overall dynamical motions of the enzyme. Charge interactions between Asp198 and Asp367, which reside on two adjacent loops, were found to influence the overall loop conformations and dynamics. In the presence of a substrate the protonation of Asp367, Asp198, and Tyr370 were found to stabilize substrate binding and control the movement of two peripheral loops onto the active site containing the substrate (i.e., clamping down). The substrate-induced response of the loop regions secures the cellulose polymer in the catalytic tunnel and creates an environment that is conducive to hydrolysis of the glycosidic bond.