Computational study of bond dissociation enthalpies for substituted β-O-4 lignin model compounds

The biopolymer lignin is a potential source of valuable chemicals. Phenethyl phenyl ether (PPE) is representative of the dominant β-O-4 ether linkage. DFT is used to calculate the Boltzmann-weighted carbon-oxygen and carbon-carbon bond dissociation enthalpies (BDEs) of substituted PPE. These values are important for understanding lignin decomposition. Exclusion of all conformers that have distributions of less than 5% at 298 K impacts the BDE by less than 1 kcal mol(-1). We find that aliphatic hydroxyl/methylhydroxyl substituents introduce only small changes to the BDEs (0-3 kcal mol(-1)). Substitution on the phenyl ring at the ortho position substantially lowers the C-O BDE, except in combination with the hydroxyl/methylhydroxyl substituents, for which the effect of methoxy substitution is reduced by hydrogen bonding. Hydrogen bonding between the aliphatic substituents and the ether oxygen in the PPE derivatives has a significant influence on the BDE. CCSD(T)-calculated BDEs and hydrogen-bond strengths of ortho-substituted anisoles, when compared with M06-2X values, confirm that the latter method is sufficient to describe the molecules studied and provide an important benchmark for lignin model compounds.     

Hydrogenolysis of β-O-4 lignin model dimers by a ruthenium-xantphos catalyst

Hydrogenolysis reactions of so-called lignin model dimers using a Ru-xantphos catalyst are presented (xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene). For example, of some nine models studied, the alcohol, 2-(2-methoxyphenoxy)-1-phenylethanol (), with 5 mol% Ru(H)(2)(CO)(PPh(3))(xantphos) () in toluene-d(8) at 135 °C for 20 h under N(2), gives in ～95% yield the C-O cleavage hydrogenolysis products, acetophenone () and guaiacol (), and a small amount (<5%) of the ketone, 2-(2-methoxyphenoxy)-1-phenylethanone (), as observed by (1)H NMR spectroscopy. The in situ Ru(H)(2)(CO)(PPh(3))(3)/xantphos system gives similar findings, confirming a recent report (J. M. Nichols et al., J. Am. Chem. Soc., 2010, 132, 12554). The active catalyst is formulated 'for convenience' as 'Ru(CO)(xantphos)'. The hydrogenolysis mechanism proceeds by initial dehydrogenation to give the ketone , which then undergoes hydrogenolysis of the C-O bond to give and . Hydrogenolysis of to and also occurs using the Ru catalyst under 1 atm H(2); in contrast, use of 3-hydroxy-2-(2-methoxyphenoxy)-1-phenyl-1-propanone (), for example, where the CH(2) of has been changed to CHCH(2)OH, gives a low yield (≤15%) of hydrogenolysis products. Similarly, the diol substrate, 2-(2-methoxyphenoxy)-1-phenyl-1,3-propanediol (), gives low yields of hydrogenolysis products. These low yields are due to formation of the catalytically inactive complexes Ru(CO)(xantphos)[C(O)C(OC(6)H(4)OMe)[double bond, length as m-dash]C(Ph)O] () and/or Ru(CO)(xantphos)[C(O)CH[double bond, length as m-dash]C(Ph)O] (), where the organic fragments result from dehydrogenation of CH(2)OH moieties in and . Trace amounts of Ru(CO)(xantphos)(OC(6)H(4)O), a catecholate complex, are isolated from the reaction of with . Improved syntheses of and lignin models are also presented.     

Selective electrochemical CO bond cleavage of β-O-4 lignin model compounds mediated by iodide ion

The electrochemically oxidative cleavage of lignin β-O-4 model compounds mediated by iodide ion has been studied. The results indicate that electrolytic conditions play a predominant role in determining the distribution of cleavage products. The preparative-scale electrolysis proceeds in a simple undivided cell, employing a catalytic amount of NaI as the redox mediator and supporting electrolyte in methanol. Under these conditions, the C_βO bond is selectively cleaved with 2,2-dimethoxy-2-arylacetaldehyde being the main product. In some cases, the reaction gives a good yield of cleavaged products. The results further demonstrate that the indirect electrolysis mediated by halide is a versatile approach for chemical transformation.     

Degradation of ²-O-4 lignin model and related compounds by the ascomyceteChrysonilia sitophila (TFB 27441 strain)

Growth of the ascomyceteChrysonilia sitophila during degradation of lignin model dimers and monomers was compared to a glucose control. An inhibition of growth by Cα-carbonyl monomers and stimulation by β-O-4 lignin model and vanillyl alcohol were observed. A comparison of the degradation by this ascomycete with the basidiomycetePhanerochaete chrysosoporium showed similarities in relation to the type of degradation caused.     

On the active site of mononuclear B1 metallo β-lactamases: a computational study

Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called ‘3H’ and ‘DCH’ sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum–classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the εεδ and δεδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.     

Chromophore production in lignin model compounds — Anaerobic reactions

The anaerobic photochemistry of a number of plausible lignin model compounds (i.e. I: 3,4-Dimethoxy-α-(2-methoxyphenoxy)-β-hydroxypropiophenone;II: 1-(3,4-Dimethoxyphenyl)-2-(2-methoxyphenoxy)-propan-1,3-diol;Pol A: Poly(4-methoxyacrylophenone);Pol B: Poly(3,4-dimethoxyacrylophenone);St 1: 3,5-Dimethoxy-4-hydroxystilbene; andSt 2: 3,5,3′,5′-Tetramethoxy-4-hydroxystilbene) was studied, thin films of these materials being exposed to long-wave (λ≥300 nm) radiation under high vacuum conditions (10^?6 torr). In all cases, the only low molecular weight products formed were methane and ethane, and quantum yields were estimated for these reactions. All materials underwent colouration (yellow) and a number of changes were also observed in both the absorbing and emitting characteristics. The colouration was attributed to the presence ofo-quinones which were formed (by further photolysis) from the phenoxy radicals, which were, in turn, produced by O?CH₃ fission, the resulting methyl radicals being the precursors of methane and ethane. The stilbenes were in all cases much more reactive (by a factor of about 100); however, they also absorbed higher intensities of radiation in the 300<λ<350 nm region on account of the greater extent of red-shifting of the longest-wave π-π′ aromatic transitions. Gel permeation data indicate the formation of products of cyclization and isomerization of stilbenes and the dimerization of phenoxy radicals while new absorbances in the infrared and¹³C NMR confirm the presence ofo-quinones in all the models.     

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.     

Synthesis ofa trimeric lignin model compound composed ofol-O-4 and β-O-4 linkages under microwave irradiation

A trimeric lignin model compound composed of α-O-4 and β-O-4 linkages was prepared by the microwave-assisted synthesis, which consisted of three steps： （a） the synthesis of 3-methoxy-4- benzyloxyacetophenone （2） from acetovanillone （1）, （b） the bromination of compound 2 to produce 3- methoxy-4-benzyloxy-α-bromoacetophenone （3）, and （c） followed by a nucleophilic substitution of compound （3） to obtain 3-methoxy-4-benzyloxy-α-（3-methoxy-4-（1-propenyl）phenol）-acetophenone （4）. The target product was characterized by MS, 1H NMR and 13C NMR spectroscopy. It was found that the trimeric compound synthesized can be used as a preferable lignin model compound because it contains guaiacyl structural unit （3-methoxy-4-hydroxy phenyl propane） linked by α-O-4 and β-O-4 linkages. In addition, under the conditions of microwave irradiation, the reaction time of each step is significantly reduced, and the selectivity of target product is greatly improved. The yields of each step and the overall sequence are 95.31%. 87.3%. 90.6% and 75.4% （95.31%× 87.3% × 90.6%）. respectively.     

Oxidative addition of the Cα-Cβ bond in β-O-4 linkage of lignin to transition metals using a relativistic pseudopotential-based ccCA-ONIOM method

A multi-level multi-layer QM/QM method, the relativistic pseudopotential correlation-consistent composite approach within an ONIOM framework (rp-ccCA-ONIOM), was applied to study the oxidative addition of the C(α)-C(β) bond in an archetypal arylglycerol β-aryl ether (β-O-4 linkage) substructure of lignin to Ni, Cu, Pd and Pt transition metal atoms. The chemically active high-level layer is treated using the relativistic pseudopotential correlation-consistent composite approach (rp-ccCA), an efficient methodology designed to reproduce an accuracy that would be obtained using the more computationally demanding CCSD(T)/aug-cc-pCV∞Z-PP, albeit at a significantly reduced computational cost, while the low-level layer is computed using B3LYP/cc-pVTZ. The thermodynamic and kinetic feasibilities of the model reactions are reported in terms of enthalpies of reactions at 298 K (ΔH°(298)) and activation energies (ΔH-act). The results obtained from the rp-ccCA:B3LYP hybrid method are compared to the corresponding values using CCSD(T) and several density functionals including B3LYP, M06, M06 L, B2PLYP, mPWPLYP and B2GP-PLYP. The energetics of the oxidative addition of C?C bond in ethane to Ni, Cu, Pd and Pt atoms are also reported to demonstrate that the rp-ccCA method effectively reproduces the accuracy of the CCSD(T)/aug-cc-pCV∞Z method. Our results show that in the catalytic activation of the C(α)-C(β) bond of β-O-4, the use of platinum metal catalysts will lead to the most thermodynamically favored reaction with the lowest activation barrier.     

Combined computational and experimental study on the inclusion complexes of β-cyclodextrin with selected food phenolic compounds

Phenolic compounds, such as caffeic acid, trans-ferulic, acid and p-coumaric acid that are commonly found in food products, are beneficial for human health. Cyclodextrins can form inclusion complexes with various organic compounds in which the physiochemical properties of the included organic molecules are changed. In this study, inclusion complexes of three phenolic compounds with β-cyclodextrin were investigated. The complexes were characterized by various analytical methods, including nuclear magnetic resonance (NMR) spectroscopy, Fourier IR (FT-IR) spectroscopy, mass spectrometry, differential scanning calorimetry, and scanning electron microscopy. Results showed that the phenolic compounds used in this study were able to form inclusion complexes in the hydrophobic cavity of β-cyclodextrin by non-covalent bonds. Their physicochemical properties were changed due to the complex formation. In addition, a computational study was performed to find factors that were responsible for binding forces between flavors and β-cyclodextrin. The quantum-mechanical calculations supported the results obtained from experimental studies. Thus, ΔH_f for the complex of p-coumaric acid and β-cyclodextrin has been found as ??11.72 kcal/mol, which was about 3 kcal/mol more stable than for inclusion complexes of other flavors. Energies of frontier orbitals (higher occupied molecular orbital (HOMO) and lower unoccupied molecular orbital (LUMO)) were analyzed, and it was found that H-L gap for the complex of p-coumaric acid and β-cyclodextrin had the largest value (8.19 eV) in comparison to other complexes, which confirmed the experimental findings of the most stabile complex.

     

Four polyanionic compounds in the K–Au–Ga system: a case study in exploratory synthesis and of the art of structural analysis

The K-Au-Ga system has been investigated at 350 °C for <50 at. % K. The potassium gold gallides K(0.55)Au(2)Ga(2), KAu(3)Ga(2), KAu(2)Ga(4) and the solid solution KAu(x)Ga(3-x) (x = 0-0.33) were synthesized directly from the elements via typical high-temperature reactions, and their crystal structures were determined by single crystal X-ray diffraction: K(0.55)Au(2)Ga(2) (I, I4/mcm, a = 8.860(3) ?, c = 4.834(2) ?, Z = 4), KAu(3)Ga(2) (II, Cmcm, a = 11.078(2) ?, b = 8.486(2) ?, c = 5.569(1) ?, Z = 4), KAu(2)Ga(4) (III, Immm, a = 4.4070(9) ?, b = 7.339(1) ?, c = 8.664(2) ?, Z = 2), KAu(0.33)Ga(2.67) (IV, I-4m2, a = 6.0900(9) ?, c = 15.450(3) ?, Z = 6). The first two compounds contain different kinds of tunnels built of puckered six- (II) or eight-membered (I) ordered Au/Ga rings with completely different cation placements: uniaxial in I and III but in novel 2D-zigzag chains in II. III contains only infinite chains of a potassium-centered 20-vertex polyhedron (K@Au(8)Ga(12)) built of ordered 6-8-6 planar Au/Ga rings. The main structural feature of IV is dodecahedral (Au/Ga)(8) clusters. Tight-binding electronic structure calculations by linear muffin-tin-orbital methods were performed for idealized models of I, II, and III to gain insights into their structure-bonding relationships. Density of states curves reveal metallic character for all compounds, and the overall crystal orbital Hamilton populations are dominated by polar covalent Au-Ga bonds. The relativistic effects of gold lead to formation of bonds of greater population with most post-transition elements or to itself, and these appear to be responsible for a variety of compounds, as in the K-Au-Ga system.     

Is the Beckmann rearrangement a concerted or stepwise reaction? A computational study

[reaction: see text] RB3LYP calculations were performed on the Beckman rearrangement by the use of three substrates, acetone oxime (1), acetophenone oxime (2), and cyclohexanone oxime (3). Acidic solvents were modeled by H+ (CH3COOH)3 and H3O+ (H2O)6, and reaction paths were determined precisely. For 1, a two-step process involving a sigma-type cationic complex was obtained. For 2, a three-step process with pi- and sigma-type complexes was found in H+ (CH3COOH)3 and a two-step process involving a sigma-type cationic complex was obtained in H3O+ (H2O)6. However, for 3, a concerted process without pi and sigma complexes was calculated, which leads to the product, epsilon-caprolactam. Three different mechanisms were explained in terms of FMO theory.     

The origin of diastereoselectivity in the Michael addition reaction: a computational study of the interaction between CH-acidic Schiff base and α,β-unsaturated ketones

Theoretical quantum chemical computations were applied in answering a question set from the experiment: why the Michael addition to chalcones is a highly diastereoselective process? Density functional theory methods were used to examine the mechanistic pathways for the Michael reaction of [(diphenylmethylene)amino]acetonitrile—CH-acidic Schiff base with α,β-unsaturated ketones (enones). Transition state structures, prereactive complexes and reaction path energetics for different channels of the reaction are determined. The theoretical predictions reveal that the difference in the stabilization of the prereactive complex explains adequately the experimental findings for diastereoselectivity of the addition to benzylideneacetophenone (chalcone), compared to the nonselective process in the case of 4,4-dimethyl-1-phenyl-1-pentene-3-one.     

Cleavage/cross-coupling strategy for converting β-O-4 linkage lignin model compounds into high valued benzyl amines via dual C–O bond cleavage

Lignin is the most recalcitrant of the three components of lignocellulosic biomass. The strength and stability of the linkages have long been a great challenge for the degradation and valorization of lignin biomass to obtain bio-fuels and commercial chemicals. Up to now, the selective cleavage of C–O linkages of lignin to afford chemicals contains only C, H and O atoms. Our group has developed a cleavage/crosscoupling strategy for converting 4-O-5 linkage lignin model compounds into high value-a...     

A practical and efficient green synthesis of β-aminophosphoryl compounds via the aza-Michael reaction in water

Biphasic systems room temperature imidazolium ionic liquid (RTIL)/water or water as a solvent significantly accelerate the addition of amines to vinylphosphoryl compounds hence opening green and effective synthesis of β-aminophosphoryl compounds in excellent yields over short reaction times. The application of water, being the cheapest and most non-toxic solvent, without any catalyst or co-solvent, is more advantageous as it provides a simple isolation procedure for products having high purity (> 95% according to the NMR data) via simple freeze-drying and does not require extraction with organic solvents. The solubility of the starting phosphorus substrate in water does not play crucial role in the reaction as it was demonstrated using water insoluble diphenylvinylphosphine oxide. In contrast to typical procedures, using a reactant ratio (vinylphosphoryl compound: amine) of 2:1 readily resulted in double phosphorylation of primary amines, including polyamines, in water.     

Cleavage/cross-coupling strategy for converting β-O-4 linkage lignin model compounds into high valued benzyl amines via dual C–O bond cleavage

Lignin is the most recalcitrant of the three components of lignocellulosic biomass. The strength and stability of the linkages have long been a great challenge for the degradation and valorization of lignin biomass to obtain bio-fuels and commercial chemicals. Up to now, the selective cleavage of C–O linkages of lignin to afford chemicals contains only C, H and O atoms. Our group has developed a cleavage/crosscoupling strategy for converting 4-O-5 linkage lignin model compounds into high value-a...     

Bifurcation analysis of reaction–diffusion Schnakenberg model

Bifurcations of spatially nonhomogeneous periodic orbits and steady state solutions are rigorously proved for a reaction–diffusion system modeling Schnakenberg chemical reaction. The existence of these patterned solutions shows the richness of the spatiotemporal dynamics such as oscillatory behavior and spatial patterns.     

Optimal homotopy analysis method for the non-isothermal reaction–diffusion model equations in a spherical catalyst

We consider the Lane–Emden boundary value problems which appear in chemical applications, biochemical applications, and scientific disciplines. The Lane–Emden problem is transformed into an equivalent integral equation. The optimal homotopy analysis method is used to solve two specific models. The first problem models reaction–diffusion equation in a spherical catalyst, while the second problem models the reaction–diffusion process in a spherical biocatalyst. We obtain reliable analytical solutions of the concentrations and the effectiveness factors. Numerical results and graphs show the reliability and efficiency applicability of the employed method.