Novel lignin polymerization pathway leading to branching in the structure.

The chemical structure of lignin has been shrouded in controversies, with a particularly prevalent issue pertaining to the degree of branching in it. The present work computationally demonstrates that the predominant ß-O-4 linkage comprising lignin can act as a branching point via an α-O-γ lignin linkage, altering how the community thinks of the lignin structure from a fundamental and valorization perspective.

Determining surface-specific Hubbard-U corrections and identifying key adsorbates on nickel and cobalt oxide catalyst surfaces.

NiO is a popular transition metal oxide (TMO) with high thermal and chemical stability and Co3O4 is a relatively more reducible TMO due to weaker metal-oxygen bonds. Both are often used as catalysts in a variety of chemical transformations. Density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) are used to investigate catalysis on TMO surfaces, yet both techniques have their own limitations. The accuracy of DFT highly depends on the choice of Hubbard U correction. The bulk-property optimized U value of 5.3 eV for NiO and different U values for Co3O4, without any consensus, are often used in the literature to simulate surface catalysis. However, U values optimized using bulk properties often fail to reproduce surface-adsorbate interactions on TMOs. Similarly, there exists arbitrariness in assigning observed XPS shifts to different surface species on these metal oxides. Hence, a synergistic application of XPS and DFT+U is implemented to determine the surface specific U values for NiO and Co3O4, and to identify adsorbed surface moieties corresponding to experimentally observed XPS shifts. For the NiO (100) surface, the U value of ∼2 eV is able to reproduce the experimentally observed XPS O1s core level binding energy shifts correctly, instead of the bulk property optimized and commonly used U value of 5.3 eV. Using this surface specific U value of 2 eV, the experimentally observed XPS shifts are assigned. Similarly, for Co3O4 (100) surface, ∼3 eV of U value could successfully predict the experimentally observed XPS shifts and corresponding adsorbates. The surface adsorbates and configurations suggested in this work will help analyze experimental XPS data and the surface specific U values will ensure accurate predictions of adsorption and reaction energetics on these catalysts.

Mechanistic Investigation into the Formation of Humins in Acid-Catalyzed Biomass Reactions.

Humins are carbonaceous, polymeric byproducts formed during the acid-catalyzed condensed phase transformation of biomass-derived moieties and are responsible for significant carbon loss and catalyst deactivation. There exists very limited knowledge about their formation chemistry and composition. Infrared spectra of humins formed during the dehydration of glucose/fructose to 5-HMF show that the furan ring and the hydroxy methyl group of 5-HMF are present in humins, but the carbonyl group is not. Based on this, aldol addition and condensation between 5-HMF and other derived species are proposed as the main reactions that initiate humin formation. Hence, in this work, density functional theory (DFT)-based calculations are performed to compute the reaction pathways, activation barriers, and reaction free energies associated with all elementary reaction steps in the 5HMF-initiated, acid-catalyzed reactions leading to humin formation. The humin formation is initiated with the rehydration of HMF to form 2,5-dioxo-6-hydroxy-hexanal or DHH (key promoter of humin formation), followed by its keto-enol tautomerization and aldol addition and condensation with HMF. The rate-determining step in this pathway is the aldol-addition reaction between the DHH-derived enols with 5-HMF. Within the implicit solvation approximation, the formation of the 5-HMF-DHH dimer is slightly endergonic, whereas the 5-HMF rehydration leading to DHH is thermodynamically downhill. This mechanistic understanding of initiation reactions for humins could pave the way to screen and design solvent and catalyst systems to deter their formation.

Origins of covalent linkages within the lignin-carbohydrate network of biomass.

Covalent linkages between lignin and the surrounding carbohydrate network, often referred to as lignin-carbohydrate complexes (LCCs), have been proposed to affect the organization of the biomass microstructure and directly correlate with the recalcitrant nature of biomass. However, the existence and frequency of these LCC linkages remain controversial and largely unknown, primarily due to the harsh experimental techniques available to characterize them. During the predominant lignin polymerization pathway a reactive intermediate is formed. Though this intermediate can covalently bind to the surrounding cellulose/hemicellulose matrix, it has been traditionally assumed to react exclusively with water, leading to purely physical interactions between lignin and cellulose/hemicellulose in the cell wall. This work, for the first time, provides direct evidence of the molecular mechanism of the formation of benzyl ether and benzyl ester LCC linkages via the speculated lignin polymerization pathway. The formation of these LCC linkages showed thermodynamic favorability, while remaining kinetically facile, compared to the previously assumed mechanism of the lignin intermediate reacting with water. The present work suggests that the surrounding carbohydrate matrix could play a role in the organization of lignin deposition and these covalent linkages could be a key factor in biomass recalcitrance.

Understanding the Effect of Solvent Environment on the Interaction of Hydronium Ion with Biomass Derived Species: A Molecular Dynamics and Metadynamics Investigation.

The addition of aprotic solvents results in higher reactivities and selectivities in many key aqueous phase biomass reactions, including the acid-catalyzed conversion of fructose to 5-hydroxyl methyl furfural (HMF). The addition of certain co-solvents inhibits the formation of humins via preferential solvation of key functional groups and can alter reaction kinetics. An important factor in this context is the relative stability of the hydronium ion (the catalyst) in the vicinity of the biomass moiety as compared to that in bulk, as it could determine its efficacy in the protonation step. Hence, in the present work, molecular dynamics (MD) simulations of HMF (the model product) and fructose (the model reactant) in acidic water and water-DMSO mixtures are performed to analyze their interaction with the hydronium ions. We show that the presence of DMSO favors the interaction of the hydronium ion with fructose, whereas it has a detrimental effect on the interaction of hydronium ion with HMF. Well-tempered metadynamics (WT-MTD) simulations are performed to determine the relative stability of the hydronium ion in the immediate vicinity of fructose and HMF, as compared to that in the bulk solvent phase, as a function of solvent composition. We find that DMSO improves the stabilization of the hydronium ions in the first solvation shell of fructose compared to that in the bulk solvent. On the other hand, hydronium ions become less stable in the immediate vicinity of HMF, as the concentration of DMSO increases.

Molecular Clustering in Formaldehyde-Methanol-Water Mixtures Revealed by High-Intensity, High-q Small-Angle Neutron Scattering.

Methanol-Water (mw) mixtures, with or without a solute, display a nonideal thermodynamic behavior, typically attributed to the structure of the microphase. However, experimental observation of the microphase structures at the molecular length scale has been a challenge. We report the presence of molecular clusters in mw and formaldehyde-methanol-water (fmw) mixtures using small-angle neutron scattering (SANS) experiments and molecular dynamics (MD) simulations. Hydrophobic clusters of methanol in mw and formaldehyde-methanol in fmw mixtures were observed at low methanol compositions (xm ≤ 0.3). A three-dimensional hydrogen-bonded network of water with the solute is observed at xm = 0.5. Linear chains of methanol surrounding the formaldehyde and water molecules were observed at high methanol compositions (xm ≥ 0.7). The calculated size of the molecular clusters (r ≈ 0.5 nm, spherical) from the SANS data and their volume fraction closely matched the MD simulation results.

Unraveling the Impact of High-Order Silk Structures on Molecular Drug Binding and Release Behaviors.

Silk continues to amaze: over the past decade, new research threads have emerged that include the use of silk fibroin for advanced pharmaceutics, including its suitability for drug delivery. Despite this ongoing interest, the details of silk fibroin structures and their subsequent drug interactions at the molecular level remain elusive, primarily because of the difficulties encountered in modeling the silk fibroin molecule. Here, we generated an atomistic silk model containing amorphous and crystalline regions. We then exploited advanced well-tempered metadynamics simulations to generate molecular conformations that we subsequently exposed to classical molecular dynamics simulations to monitor both drug binding and release. Overall, this study demonstrated the importance of the silk fibroin primary sequence, electrostatic interactions, hydrogen bonding, and higher-order conformation in the processes of drug binding and release.

Influence of Alkali and Alkaline-Earth Metals on the Cleavage of Glycosidic Bond in Biomass Pyrolysis: A DFT Study Using Cellobiose as a Model Compound.

Fast pyrolysis is a promising technology for the production of renewable fuels and chemicals from lignocellulosic biomass. The product distribution (bio-oil, char) and the composition of bio-oil are significantly influenced by the presence of naturally occurring alkali and alkaline-earth metals (AAEMs). In this paper, we investigate, at the molecular level, the influence of Na(I), K(I), Ca(II), and Mg(II) ions on glycosidic bond breaking reactions using density functional theory. Glycosidic bond breaking reactions are categorized as direct C-O breaking mechanisms, namely, transglycosylation, glycosylation, and ring contraction and the two-step pathways, which include the mannose pathway, dehydration, and ring opening. Our calculations show that in the absence of metal, transglycosylation and dehydration pathways (activation barriers ∼55 kcal.mol-1) are kinetically most facile. The linkage type (α- or ß-1,4) has an insignificant effect on kinetics of glycosidic bond cleavage. Mg(II) ions have a pronounced effect on lowering the activation barriers of glycosylation, ring contraction, and the mannose pathway, requiring activation enthalpies of 32-52 kcal.mol-1. Conversely, Mg(II) and Ca(II) ions inhibit the dehydration pathway. Na(I) and K(I) ions do not significantly influence the activation barriers of glycosidic bond cleavage reactions, as the reduction is only about 5-10 kcal.mol-1. Thus, AAEM ions exhibit different catalytic effects on glycosidic bond breaking reactions.

Understanding the role of hydrogen bonding in Brønsted acidic ionic liquid-catalyzed transesterification: a combined theoretical and experimental investigation.

Brønsted acidic ionic liquids (BAILs) can play a dual role, as a solvent and as a catalyst, in many reactions. However, molecular details of the catalytic mechanism are poorly understood. We present here a density functional theory (DFT) study for the catalytic mechanism of the transesterification of methyl ester (ME) with trimethylolpropane (TMP), in the presence of three representative BAILs, namely, N-methylimidazole-IL, pyridinium-IL, and triethylamine-IL. The deprotonation of the BAIL cation and the transesterification step are investigated. Key inter- and intra-molecular hydrogen bonds (HBs) that govern the catalytic performance of BAILs were identified and analyzed using natural bond orbital (NBO) and atoms in molecule (AIM) methods. For the deprotonation of BAILs, it was found that the intermolecular O-HO HB between the hydroxyl group of TMP and the oxygen of the sulfonic group of BAIL was indispensable for proton transfer. DFT computed free energy barriers for the transesterification step are in excellent agreement with the experimental results only after taking into account the BAIL cation-anion interaction in terms of HBs in which the O-HO between the hydroxyl group of the anion and the oxygen of the sulfonic group of the cation was the strongest HB, suggesting the role of the anion in governing the catalytic activity of BAILs. The existence of the HBs suggested by DFT calculations was further validated using in situ FTIR experiments/ATR-FTIR.

Biomass Oxidation: Formyl C-H Bond Activation by the Surface Lattice Oxygen of Regenerative CuO Nanoleaves.

An integrated experimental and computational investigation reveals that surface lattice oxygen of copper oxide (CuO) nanoleaves activates the formyl C-H bond in glucose and incorporates itself into the glucose molecule to oxidize it to gluconic acid. The reduced CuO catalyst regains its structure, morphology, and activity upon reoxidation. The activity of lattice oxygen is shown to be superior to that of the chemisorbed oxygen on the metal surface and the hydrogen abstraction ability of the catalyst is correlated with the adsorption energy. Based on the present investigation, it is suggested that surface lattice oxygen is critical for the oxidation of glucose to gluconic acid, without further breaking down the glucose molecule into smaller fragments, because of C-C cleavage. Using CuO nanoleaves as catalyst, an excellent yield of gluconic acid is also obtained for the direct oxidation of cellobiose and polymeric cellulose, as biomass substrates.

First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects.

Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cun where n = 2-12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barrier for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C-H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH3 and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CHx (x = 1-3) species and recombination of H with CHx have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.

Crystallization-induced red emission of a facilely synthesized biodegradable indigo derivative.

We report a new class of crystallization-induced red-emitting luminogen based on a synthetic biodegradable indigo derivative, Indigoid-B. This compound, upon an ultrasonic treatment, formed well-defined microcrystals that showed striking crystallization-induced emission (CIE) in mixed solvents of tetrahydrofuran-water.

Solvation dynamics and energetics of intramolecular hydride transfer reactions in biomass conversion.

Hydride transfer changes the charge structure of the reactant and thus, may induce reorientation/reorganization of solvent molecules. This solvent reorganization may in turn alter the energetics of the reaction. In the present work, we investigate the intramolecular hydride transfer by taking Lewis acid catalyzed glucose to fructose isomerization as an example. The C2-C1 hydride transfer is the rate limiting step in this reaction. Water and methanol are used as solvents and hydride transfer is simulated in the presence of explicit solvent molecules, treated quantum mechanically and at a finite temperature, using Car-Parrinello molecular dynamics (CPMD) and metadynamics. Activation free energy barrier for hydride transfer in methanol is found to be 50 kJ mol(-1) higher than that in water. In contrast, in density functional theory calculations, using an implicit solvent environment, the barriers are almost identical. Analysis of solvent dynamics and electronic polarization along the molecular dynamics trajectory and the results of CPMD-metadynamics simulation of the hydride transfer process in the absence of any solvent suggest that higher barrier in methanol is a result of non-equilibrium solvation. Methanol undergoes electronic polarization during the hydride transfer step. However, its molecular orientational relaxation is a much slower process that takes place after the hydride transfer, over an extended timescale. This results in non-equilibrium solvation. Water, on the other hand, does not undergo significant electronic polarization and thus, has to undergo minimal molecular reorientation to provide near equilibrium solvation to the transition state and an improved equilibrium solvation to the post hydride shift product state. Hence, the hydride transfer step is also observed to be exergonic in water and endergonic in methanol. The aforementioned explanation is juxtaposed to enzyme catalyzed charge transfer reactions, where the enhanced solvation of the transition and product states by enzymes, due to electrostatic interactions, reduces the activation free energy barrier and the free energy change of the reaction. Similarly, we suggest that, in the intramolecular hydride shift, improved solvation of the transition state and of the product state by water is achieved due to minimal polarization and reorientation, and (near) equilibrium solvation.

Insights into the Cr(III) catalyzed isomerization mechanism of glucose to fructose in the presence of water using ab initio molecular dynamics.

The mechanism of glucose ring opening and isomerization to fructose, catalyzed by the Lewis acid catalyst CrCl3 in the presence of water, is investigated using Car-Parrinello molecular dynamics with metadynamics. Minimum energy pathways for the reactions are revealed and the corresponding free energy barriers are computed. Addition of glucose replaces two water molecules in the active [Cr(H2O)5OH](+2) complex, with two hydroxyl groups of glucose taking their place. Ring opening and isomerization reactions can only proceed if the first step involving the deprotonation of glucose is accompanied by the protonation of the OH(-) group in the partially hydrolyzed metal center ([Cr(C6H12O6)(H2O)3OH](+2) → [Cr(C6H11O6)(H2O)4](+2)). This provides further evidence that the partially hydrolyzed [Cr(H2O)5OH](+2) is the active species catalyzing ring opening and isomerization reactions and that unhydrolyzed Cr(+3) may not be able to catalyze the reactions. After the ring opening, the isomerization reaction proceeds via deprotonation, followed by hydride shift and the back donation of the proton from the metal complex to the sugar. Water molecules outside the first coordination sphere of the metal complex participate in the reaction for mediating the proton transfer. The hydride shift in the isomerization is the overall rate limiting step with a free energy barrier of 104 kJ mol(-1). The simulation computed barrier is in agreement with experiments.

Extraction of (9,8) single-walled carbon nanotubes by fluorene-based polymers.

Selective polymer wrapping is a promising approach to obtain high-chiral-purity single-walled carbon nanotubes (SWCNTs) needed in technical applications and scientific studies. We showed that among three fluorene-based polymers with different side-chain lengths and backbones, poly[(9,9-dihexylfluorenyl-2,7-diyl)-co-(9,10-anthracene)] (PFH-A) can selectively extract SWCNTs synthesized from the CoSO4 /SiO2 catalyst, which results in enrichment of 78.3 % (9,8) and 12.2 % (9,7) nanotubes among all semiconducting species. These high-chiral-purity SWCNTs may find potential applications in electronics, optoelectronics, and photovoltaics. Furthermore, molecular dynamics simulations suggest that the extraction selectivity of PFH-A relates to the bending and alignment of its alkyl chains and the twisting of its two aromatic backbone units (biphenyl and anthracene) relative to SWCNTs. The strong π-π interaction between polymers and SWCNTs would increase the extraction yield, but it is not beneficial for chiral selectivity. Our findings suggest that the matching between the curvature of SWCNTs and the flexibility of the polymer side chains and the aromatic backbone units is essential in designing novel polymers for selective extraction of (n,m) species.

Insights into the interplay of Lewis and Brønsted acid catalysts in glucose and fructose conversion to 5-(hydroxymethyl)furfural and levulinic acid in aqueous media.

5-(Hydroxymethyl)furfural (HMF) and levulinic acid production from glucose in a cascade of reactions using a Lewis acid (CrCl3) catalyst together with a Brønsted acid (HCl) catalyst in aqueous media is investigated. It is shown that CrCl3 is an active Lewis acid catalyst in glucose isomerization to fructose, and the combined Lewis and Brønsted acid catalysts perform the isomerization and dehydration/rehydration reactions. A CrCl3 speciation model in conjunction with kinetics results indicates that the hydrolyzed Cr(III) complex [Cr(H2O)5OH](2+) is the most active Cr species in glucose isomerization and probably acts as a Lewis acid-Brønsted base bifunctional site. Extended X-ray absorption fine structure spectroscopy and Car-Parrinello molecular dynamics simulations indicate a strong interaction between the Cr cation and the glucose molecule whereby some water molecules are displaced from the first coordination sphere of Cr by the glucose to enable ring-opening and isomerization of glucose. Additionally, complex interactions between the two catalysts are revealed: Brønsted acidity retards aldose-to-ketose isomerization by decreasing the equilibrium concentration of [Cr(H2O)5OH](2+). In contrast, Lewis acidity increases the overall rate of consumption of fructose and HMF compared to Brønsted acid catalysis by promoting side reactions. Even in the absence of HCl, hydrolysis of Cr(III) decreases the solution pH, and this intrinsic Brønsted acidity drives the dehydration and rehydration reactions. Yields of 46% levulinic acid in a single phase and 59% HMF in a biphasic system have been achieved at moderate temperatures by combining CrCl3 and HCl.

Fructose-water-dimethylsulfoxide interactions by vibrational spectroscopy and molecular dynamics simulations.

The solvation of fructose in dimethyl sulfoxide (DMSO) and DMSO-H(2)O (or DMSO-D(2)O) mixtures was investigated using vibrational spectroscopy (Raman, ATR/FTIR) and molecular dynamics (MD) simulations. The analysis of the fructose hydroxyl hydrogen-DMSO oxygen radial distribution function showed that the coordination number of DMSO around the furanose form of fructose is ~3.5. This number is smaller than the number of hydroxyl groups of fructose because one DMSO molecule is shared between two hydroxyl groups and because intramolecular hydrogen bonds are formed. In the case of fructose-DMSO mixtures, a red shift of the Raman S═O asymmetric stretch is observed, which indicates that fructose breaks the DMSO clusters through strong hydrogen bonding between the hydrogen atoms of its hydroxyl groups and the oxygen atom of DMSO. The Raman scattering cross sections of the DMSO S═O stretch when a DMSO molecule interacts with another DMSO molecule, a fructose molecule, or a water molecule were estimated from the spectra of the binary mixtures using the coordination numbers from MD simulations. It was also possible to use these values together with the MD-estimated coordination numbers to satisfactorily predict the effect of the water fraction on the Raman scattering intensity of the S═O stretching band in ternary mixtures. MD simulations also showed that, with increasing water content, the DMSO orientation around fructose changed, with the sulfur atom moving away from the carbohydrate. The deconvolution of the fructose IR OH stretching region revealed that the hydroxyls of fructose can be separated into two groups that participate in hydrogen bonds of different strengths. MD simulations showed that the three hydroxyls of the fructose ring form stronger hydrogen bonds with the solvent than the remaining hydroxyls, providing an explanation for the experimental observations. Finally, analysis of ATR/FTIR spectra revealed that, with increasing water content, the average hydrogen-bond enthalpy of the fructose hydroxyls decreases by ~2.5 kJ/mol.

Understanding solvent effects in the selective conversion of fructose to 5-hydroxymethyl-furfural: a molecular dynamics investigation.

Selective conversion of fructose to 5-hydroxymethyl-furfural (HMF) involves the participation of high-boiling solvents like dimethyl sulfoxide (DMSO). In order to replace DMSO with low-boiling solvents, it is imperative that we understand the effect of DMSO solvation in protecting (i) HMF from rehydration and humins formation reactions and (ii) fructose from side reactions, other than its dehydration to HMF. In the present work, molecular dynamics simulations of HMF and fructose in water and in water-DMSO mixtures are carried out using the OPLS-AA force field. Radial pair distribution functions, coordination numbers and the hydrogen-bond network between the HMF/fructose molecule and the solvent molecules are analysed. The local 3-dimensional picture of the arrangement of solvent molecules around the solute, which cannot be accessed from pair distribution functions, is also computed. We show preferential coordination of DMSO around HMF and explain how this could provide a shielding effect to the HMF molecule, thus protecting it from further rehydration to levulinic acid and formic acid and from humins formation. In the case of fructose, the presence of DMSO also reduces the number of water molecules in the immediate vicinity of fructose. Though fewer water molecules coordinate around fructose, they are bound strongly to it. Analysis of the local 3-dimensional arrangement of DMSO molecules suggests that it protects the fructose molecule from side reactions that would lead to condensation or reversion products. However, the presence of DMSO molecules does not hamper the water molecules coming into contact with the oxygen atom of the hydroxyl groups of fructose, which is required for a proton transfer from water to fructose, to initiate the dehydration reaction to HMF.