Molecular dynamics study of the active site of methylamine dehydrogenase

We have obtained AMBER94 force-field parameters for the TTQ cofactor of the enzyme methylamine dehydrogenase (MADH). This enzyme catalyzes the oxidation of methylamine to produce formaldehyde and ammonia. In the rate-determining step of the catalyzed reaction, a proton is transferred from the methyl group of the substrate to residue Asp76. We used the new parameters to perform molecular dynamics simulations of MADH in order to characterize the dynamics of the active site prior to the proton-transfer step. We found that only one of the oxygen atoms of Asp76 can act as an acceptor of the proton. The other oxygen interacts with Thr122 via a strong hydrogen bond. In contrast, because of the rotation the methyl group of the substrate, the three methyl hydrogen atoms are alternately in position to be transferred. The distance that the proton has to travel presents a broad distribution with a peak between 1.0 and 1.1 A and reaches values as short as 0.8 A. The fluctuation of the distance between the donor and the acceptor has the largest frequency component at 50 cm(-1), but the spectrum presents a rich structure between 10 and 400 cm(-1). The more important peaks appear below 250 cm(-1).     

Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase.

The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions--an area of great current interest--for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified-to either of the carboxylate oxygen atoms of the catalytic base (Asp428beta)-and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5+/-0.9 kcal mol(-1) for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal mol(-1). In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474beta(MADH)/Thr172beta(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471beta(MADH)/Phe169beta(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions.     

On the mechanism of reaction of radicals with tirapazamine

Ketyl radicals produced by photolysis of ketones or di-tert-butyl peroxide (DTBP) in alcohol solvents react rapidly with tirapazamine (TPZ). The acetone ketyl radical (ACOH) reacts with TPZ with an absolute second-order rate constant of (9.7 +/- 0.4) x 108 M-1 s-1. The reaction kinetics can be followed by monitoring the bleaching of TPZ absorption at 475 nm or the formation of a reaction product which absorbs at 320 and 410 nm. The ACOD radical reacts with TPZ in 2-propanol-OD with an absolute rate constant of (6.7 +/- 0.5) x 108 M-1 s-1, corresponding to a kinetic isotope effect (KIE) of 1.4. Deuteration of the radical on carbon (ACOH-d6) retards the reaction of the radical with TPZ even further (absolute rate constant = (4.8 +/- 0.04) x 108 M-1 s-1). This result corresponds to a KIE of 2.0. Radicals derived from dioxane and diisopropyl ether by flash photolysis of DTBP in ethereal solvent react with TPZ more slowly than do ketyl radicals. It is concluded that ketyl radicals react, in part, with TPZ in organic solvents by transfer of a hydrogen atom from the OH and CH3 groups of the ketyl radical to the oxygen atom at the N4 position of TPZ to form acetone or acetone enol and a radical derivative of TPZ (TPZH). The latter species absorbs at 320 and 405 nm, has a lifetime of hundreds of microseconds in alcohol solvents, and decays by disproportionation to form TPZ and a reduced heterocycle. The reduced heterocycle eventually forms a desoxytirapazamine by a polar mechanism. The results are supported by density functional theory calculations. It is proposed that dioxanyl radical will also react, in part, with TPZ by transfer of a hydrogen atom from the carbon adjacent to the radical center to the oxygen atom at the N4 position of TPZ. This produces the enol ether and the previously mentioned TPZH radical. It is further posited that ether radicals react a bit more slowly than ketyl radicals because they lack the second mode of hydrogen transfer (from the OH group) that is present in the ACOH radical. Our data are permissive of the possibility that ether radicals add to TPZ at a rate that is competitive with beta-hydrogen atom transfer.     

Model studies of 6,7-indolequinone cofactors of quinoprotein amine dehydrogenases

The electronic effects of the C-4 substituent on the physicochemical properties and reactivity of the 6,7-inodolequinone cofactors (CTQ and TTQ) have extensively been investigated with use of a series of C-4 substituted 6,7-inodolequinone derivatives (1-4). The one-electron reduction potentials of the 6,7-inodolequinone derivatives decrease with increasing the electron donating ability of the C-4 substituent (with the following order of E degrees': 4>1>2>3). The reaction of indolequinones 1-3 with benzylamine proceeds stepwise through the iminoquinone and the product-imine intermediates to give aminophenol as the final product as the case of TTQ model compound 4. The rate constants of each step have been determined by the detailed kinetic analysis, and the kinetic deuterium isotope effects have also been examined to confirm the rate-determining step. The reactivity of CTQ model compound 1 toward the amines is by one order of magnitude lower than that of TTQ model compound 4. The reactivity of indolequinones 2 and 3 is further decreased due to their stronger electron-donating substituents at C-4. A more important difference between CTQ model compound 1 and TTQ model compound 4 is the reactivity of the iminoquinone intermediate: the reaction of the CTQ model compound with amines stops at the iminoquinone formation stage at room temperature, whereas the reaction of the TTQ model compound with amines proceeds up to the aminophenol formation. Thus, the energy barrier for the rearrangement of the iminoquinone to the product-imine is higher in the CTQ model system than in the TTQ model system.     

Evidence for substrate activation of electron transfer from methylamine dehydrogenase to amicyanin

Electron transfer (ET) from methylamine dehydrogenase (MADH) to amicyanin may be true or gated ET, depending upon the redox form of MADH. ET from the substrate-reduced aminoquinol form of MADH is gated, and the reaction rate is dependent on the presence of monovalent cations. This ET reaction has been studied in buffer free of monovalent cations. The reaction rate is orders of magnitude less than with saturating concentrations of monovalent cation. Analysis of the temperature dependence of this slow reaction, however, reveals that it is a true ET reaction. The rate of MADH reduction by substrate and the steady-state rate of substrate-dependent reduction of amicyanin by MADH were examined in different buffers. The results reveal that, in the steady state, the protonated methylammonium substrate performs the role previously attributed to monovalent cations in regulating the rate and mechanism of ET from MADH. The two putative cation binding sites previously observed in the crystal structure of MADH may now be assigned distinct roles, one as a catalytic substrate binding site and the other as a noncatalytic regulatory substrate binding site.     

Donor–acceptor (donor) polymers with differently conjugated side groups at the acceptor units for photovoltaics

Four new donor–acceptor (donor) [D–A(D)], PBDT‐PTQ, PBDT‐PTTQ, PBDT‐TQ, and PBDT‐TTQ, bearing the same backbone of alternative benzodithiophene (BDT) and quinoxaline units but with phenylene thienyl, phenylene di‐thienyl, thienyl and di‐thienyl groups (other donors), respectively, at the acceptor quinoxaline units, were designed and synthesized to investigate the impacts of the conjugated side chains at the acceptor units on the photovoltaic properties of polymers. The power conversion efficiencies (PCEs) of the polymer solar cells (PSCs) based on PBDT‐TQ:[6,6]‐phenyl‐C‐70‐butyric acid methyl ester (PC70BM) and PBDT‐PTQ:PC70BM reach to 4.39 and 3.58%, respectively, which are 43 and 17% higher, respectively, than that of a reported alkylphenyl substituted polymer with the same main chain. However, the PCEs based on PBDT‐TTQ and PBDT‐PTTQ, in which an additional thiophene is added at a side chain of PBDT‐TQ and PBDT‐PTQ, respectively, decline. The mechanism how the conjugated side chains affect the performance of the PSCs is also discussed. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

Model Studies of TTQ-Containing Amine Dehydrogenases

The reactions of a TTQ model compound [1, 3-methyl-4-(3'-methylindol-2'-yl)indole-6,7-dione] with several amines have been investigated in organic media to obtain mechanistic information on the action of quinoprotein methylamine and aromatic amine dehydrogenases. It has been found that compound 1 acts as an efficient catalyst for the autorecycling oxidation of benzylamine by molecular oxygen in CH(3)OH. In order to evaluate the oxidation mechanism of amines by 1, the product analyses and kinetic studies have been carried out under anaerobic conditions. In the first stage of the reaction of 1 with amines, 1 is converted into an iminoquinone-type adduct (so-called substrateimine), which was isolated and characterized by using cyclopropylamine as a substrate. The observed NOE of the isolated product indicates clearly that the addition position of the amine is C-6 of the quinone. The molecular orbital calculations suggest that the thermodynamic stability of the carbinolamine intermediate is a major factor to determine such regioselectivity; the C-6 carbinolamine is more stable than the C-7 counterpart by 2.9 kcal/mol. The reactivity of several primary amines and the electronic effect of the p-substituents of benzylamine derivatives in the iminoquinone formation suggest that the addition step of the amine to the quinone is rate-determining. When amines having an acidic alpha-proton such as benzylamine derivatives are employed as substrates, formation of the iminoquinone adduct was followed by rearrangement to the productimine. The kinetic analysis has revealed that this rearrangement consists of noncatalyzed and general base-catalyzed processes. Large kinetic isotope effects of 7.8 and 9.2 were observed for both the noncatalyzed and general base-catalyzed processes, respectively, since these steps involve a proton abstraction from the alpha-position of the substrate. In the reaction with benzhydrylamine, the product imine was isolated quantitatively and well characterized by several spectroscopic data. In the case of benzylamine, the product imine is further converted into the aminophenol derivative by the imine exchange reaction with excess benzylamine. These results indicate clearly that the amine oxidation by compound 1 proceeds via a transamination mechanism as suggested for the enzymatic oxidation of amines by TTQ cofactor.     

Computational study (PM3) of the hydration of dipentylpyridine-2,5-dicarboxylate

Carbonyl oxygens are the main elements of dialkyl pyridine dicarboxylate which are able to form hydrates with water molecules. Oxygens of the alkoxyl groups and pyridine nitrogens can be only considered as additional elements to enhance the molecule hydrophilicity. The hydration is, however, limited in two phase extraction systems. The carbonyl oxygen at position 2 and the pyridine nitrogen can be considered as the hydrophilic center of dipentyl pyridine-2,5-dicarboxylate while the hydrophilic character of the ester group at position 5 can be neglected due to steric effects and the lack of any interaction with water molecules. The same probably concerns the alkoxyl oxygen at position 2. Hydrophilic effects of both the carbonyl oxygens at position 2 and the pyridine nitrogen and the location of the second hydrophobic substituent directly on the opposite side of the pyridine ring (at position 5) in respect to the ester group at position 2 predominate the structure for effective hydration adsorption and decreasing of the interfacial tension at hydrocarbon/water interfaces in comparison to various dipentyl pyridine dicarboxylates having other positions of the ester groups.     

Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: oxidation of tryptamine by aromatic amine dehydrogenase

Proton tunneling dominates the oxidative deamination of tryptamine catalyzed by the enzyme aromatic amine dehydrogenase. For reaction with the fast substrate tryptamine, a H/D kinetic isotope effect (KIE) of 55 +/- 6 has been reported-one of the largest observed in an enzyme reaction. We present here a computational analysis of this proton-transfer reaction, applying combined quantum mechanics/molecular mechanics (QM/MM) methods (PM3-SRP//PM3/CHARMM22). In particular, we extend our previous computational study (Masgrau et al. Science 2006, 312, 237) by using improved energy corrections, high-level QM/MM methods, and an ensemble of paths to estimate the tunneling contributions. We have carried out QM/MM molecular dynamics simulations and variational transition state theory calculations with small-curvature tunneling corrections. The results provide detailed insight into the processes involved in the reaction. Transfer to the O2 oxygen of the catalytic base, Asp128beta, is found to be the favored reaction both thermodynamically and kinetically, even though O1 is closer in the reactant complex. Comparison of quantum and classical models of proton transfer allows estimation of the contribution of hydrogen tunneling in lowering the barrier to reaction in the enzyme. A reduction of the activation free energy due to tunneling of 3.1 kcal mol-1 is found, which represents a rate enhancement due to tunneling by 2 orders of magnitude. The calculated KIE of 30 is significantly elevated over the semiclassical limit, in agreement with the experimental observations; a semiclassical value of 6 is obtained when tunneling is omitted. A polarization of the C-H bond to be broken is observed due to the close proximity of the catalytic aspartate and the (formally) positively charged imine nitrogen. A comparison is also made with the related quinoprotein methylamine dehydrogenase (MADH)-the much lower KIE of 11 that we obtain for the MADH/methylamine system is found to arise from a more endothermic potential energy surface for the MADH reaction.     

Stereoelectronic factors in the stereoselective epoxidation of glycals and 4-deoxypentenosides

Glycals and 4-deoxypentenosides (4-DPs), unsaturated pyranosides with similar structures and reactivity profiles, can exhibit a high degree of stereoselectivity upon epoxidation with dimethyldioxirane (DMDO). In most cases, the glycals and their corresponding 4-DP isosteres share the same facioselectivity, implying that the pyran substituents are largely responsible for the stereodirecting effect. Fully substituted dihydropyrans are subject to a "majority rule", in which the epoxidation is directed toward the face opposite to two of the three groups. Removing one of the substituents has a variable effect on the epoxidation outcome, depending on its position and also on the relative stereochemistry of the remaining two groups. Overall, we observe that the greatest loss in facioselectivity for glycals and 4-DPs is caused by removal of the C3 oxygen, followed by the C5/anomeric substituent, and least of all by the C4/C2 oxygen. DFT calculations based on polarized-π frontier molecular orbital (PPFMO) theory support a stereoelectronic role for the oxygen substituents in 4-DP facioselectivity, but less clearly so in the case of glycals. We conclude that the anomeric oxygen in 4-DPs contributes toward a stereoelectronic bias in facioselectivity whereas the C5 alkoxymethyl in glycals imparts a steric bias, which at times can compete with the stereodirecting effects from the other oxygen substituents.     

Mechanisms of formation of 8-oxoguanine due to reactions of one and two OH* radicals and the H2O2 molecule with guanine: A quantum computational study

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.     

Probing Bis‐FeIV MauG: Experimental Evidence for the Long‐Range Charge‐Resonance Model

The biosynthesis of tryptophan tryptophylquinone, a protein‐derived cofactor, involves a long‐range reaction mediated by a bis‐Fe^IV intermediate of a diheme enzyme, MauG. Recently, a unique charge‐resonance (CR) phenomenon was discovered in this intermediate, and a biological, long‐distance CR model was proposed. This model suggests that the chemical nature of the bis‐Fe^IV species is not as simple as it appears; rather, it is composed of a collection of resonance structures in a dynamic equilibrium. Here, we experimentally evaluated the proposed CR model by introducing small molecules to, and measuring the temperature dependence of, bis‐Fe^IV MauG. Spectroscopic evidence was presented to demonstrate that the selected compounds increase the decay rate of the bis‐Fe^IV species by disrupting the equilibrium of the resonance structures that constitutes the proposed CR model. The results support this new CR model and bring a fresh concept to the classical CR theory.     

Chain-Cleavage and hydrolysis of activated polyethylene glycol derivatives: Evidence for competitive processes

Studies have been carried out with the tosylate of the monomethyl ether of polyethylene glycol (MeO–PEG–OTs) and with low molecular weight models to assess whether the neighboring oxygen at position 3 or 6 provides the driving force for hydrolytic cleavage of these activated derivatives. Our results reveal that MeO–PEG–OTs undergoes hydrolysis by competitive pathways. Water directly displaces the tosylate group to give the original PEG alcohol and the oxygen at position 6 nucleophilically displaces the tosylate group to give a cyclic oxonium ion as an intermediate. This intermediate can react by three pathways. First, it can lead to the production of the original PEG alcohol by attack of water on a ring carbon; second, dioxane and a lower molecular weight PEG alcohol is produced by water attack at the nonring carbon next to the charged oxygen; and third dioxane can be displaced by the oxygen atom at position 6 in the chain.     

Pyrimethamine analogs as strong inhibitors of double and quadruple mutants of dihydrofolate reductase in human malaria parasites

Pyrimethamine acts against malarial parasites by selectively inhibiting their dihydrofolate reductase-thymidylate synthase. Resistance to pyrimethamine in Plasmodium falciparum is due to point mutations in the DHFR domain, initially at residue 108 (S108N), with additional mutations imparting much greater resistance. Our previous work, the development of a simple rational drug design strategy to overcome such resistance, used suitable meta-substituents in the pyrimethamine framework to avoid the unfavorable steric clash with mutant side chains at position 108. Interestingly, the meta-chloro analog of pyrimethamine not only overcame the resistance due to S108N, but also that contributed by the more remote mutation, C59R. The present work improves on this by means of other meta-substituents. Against wild type DHFR, double mutant types A16V + S108T and C59R + S108T, and the highly pyrimethamine/cycloguanil-resistant quadruple-mutant form N51I + C59R + S108N + I164L, pyrimethamine itself gave Ki values of 1.5, 2.4, 72.3 and 859 nM, respectively. The meta-substituted analogs, especially the meta-bromo analog, were much more powerful inhibitors of these DHFRs, including the quadruple-mutant form (meta-bromo analog, Ki 5.1 nM). For comparison, the dihydropyrazine antifolate, WR99210, gave Ki values of 0.9, 3.2, 0.8 and 0.9 nM, respectively. Ki values were also measured against recombinant human DHFR, as were their activities against the growth of Plasmodium falciparum cultures bearing the double mutations (FCB and K1 strains) and quadruple mutation (V1/S) and the wild type (3D7). The meta-analogs were highly active against all of these, with the meta-bromo again being the strongest, having an IC50 of 37 nM against V1/S, compared to > 5000 nM for pyrimethamine itself and 1.1 nM for WR99210.     

Density-functional-theory studies of the infrared spectra of titanium carbide nanocrystals

The infrared (IR) spectra of cuboidic titanium carbide (TiC) nanocrystals have been studied at the density-functional-theory (DFT) level using the Becke-Perdew (BP) functional and triple-zeta quality basis sets augmented by one set of polarization functions (TZVP). The accuracy of the calculations was checked by DFT calculations using the Perdew-Burke-Ernzerhof hybrid functional (PBE0) and up to quadruple-zeta quality basis sets augmented by one set of polarization functions (QZVP). The calculated IR spectrum for Ti(14)C(13) (3 x 3 x 3) is found to be in fair agreement with the experimental IR spectrum obtained by infrared resonance-enhanced multiphoton ionization (IR-REMPI) measurements, whereas, for Ti(18)C(18) (4 x 3 x 3) and Ti(32)C(32) (4 x 4 x 4), the calculated IR spectra differ significantly from the experimental ones. The smallest TiC cluster (Ti(4)C(4), 2 x 2 x 2) considered has not been reported in any mass-spectrometer studies. The present DFT calculations show that the vibrational modes related to the in-plane vibrations of solid TiC are not observed in the IR-REMPI spectra of nanocrystals larger than Ti(14)C(13). Contrary to solid TiC, the studied TiC nanocrystals are nonmetallic with optical gaps of 0.62 eV (0.55 eV) and 0.028 eV (0.027 eV) for Ti(32)C(32) and Ti(108)C(108) (6 x 6 x 6), calculated at the time-dependent density-functional-theory (TDDFT) level using the BP functional. The HOMO-LUMO gaps obtained in the BP DFT calculations are given within parentheses. At the PBE0 DFT level, the HOMO-LUMO gaps for Ti(32)C(32) and Ti(108)C(108) are 1.74 and 0.32 eV, respectively.     

Fragmentation of oxime and silyl oxime ether odd‐electron positive ions by the McLafferty rearrangement: new insights on structural factors that promote α,β fragmentation

The McLafferty rearrangement is an extensively studied fragmentation reaction for the odd‐electron positive ions from a diverse range of functional groups and molecules. Here, we present experimental and theoretical results of 12 model compounds that were synthesized and investigated by GC‐TOF MS and density functional theory calculations. These compounds consisted of three main groups: carbonyls, oximes and silyl oxime ethers. In all electron ionization mass spectra, the fragment ions that could be attributed to the occurrence of a McLafferty rearrangement were observed. For t‐butyldimethylsilyl oxime ethers with oxygen in a β‐position, the McLafferty rearrangement was accompanied by loss of the t‐butyl radical. The various mass spectra showed that the McLafferty rearrangement is relatively enhanced compared with other primary fragmentation reactions by the following factors: oxime versus carbonyl, oxygen versus methylene at the β‐position and ketone versus aldehyde. Calculations predict that the stepwise mechanism is favored over the concerted mechanism for all but one compound. For carbonyl compounds, C–C bond breaking was the rate‐determining step. However, for both the oximes and t‐butyldimethylsilyl oxime ethers with oxygen at the β‐position, the hydrogen transfer step was rate limiting, whereas with a CH₂ group at the β‐position, the C–C bond breaking was again rate determining. n‐Propoxy‐acetaldehyde, bearing an oxygen atom at the β‐position, is the only case that was predicted to proceed through a concerted mechanism. The synthesized oximes exist as both the (E)‐ and (Z)‐isomers, and these were separable by GC. In the mass spectra of the two isomers, fragment ions that were generated by the McLafferty rearrangement were observed. Finally, fragment ions corresponding to the McLafferty reverse charge rearrangement were observed for all compounds at varying relative ion intensities compared with the conventional McLafferty rearrangement. Copyright © 2012 John Wiley & Sons, Ltd.     

Effect of the oxygen transfer coefficient on xylitol production from sugarcane bagasse hydrolysate by continuous stirred-tank reactor fermentation

The effect of the oxygen transfer coefficient on the production of xylitol by biocon version of xylose present in sugarcane bagasse hemicellulosic hydrolysate using the yeast Candiada guilliermondii was investigated. Continuous cultivation was carried out in a 1.25-L fermentor at 30°C, pH 5.5, 300 rpm, and a dilution rate of 0.03/h, using oxygen transfer coefficients of 10,20, and 30/h. The results showed that the microbial xylitol production (11 g/L) increased by 108% with the decrease in the oxygen volumetric transfer coefficient from 30 to 20/h. The maximum values of xylitol productivity (0.7g/[L…h]) and yield (0.58 g/g) were obtained at k _L a 20/h.     

Toward an understanding of the selectivity in domino reactions. A DFT study of the reaction between acetylenedicarboxylic acid and 1, 3-Bis(2-furyl)propane

The mechanism of the domino reaction between acetylenedicarboxylic acid and 1,3-bis(2-furyl)propane has been theoretically studied in the framework of density functional theory. This domino process comprises two consecutive cycloaddition reactions: the first one is initialized by the nucleophilic attack of the C5 position of the furan ring to a conjugate position of acetylenedicarboxylic acid to give a zwitterionic intermediate, which by a subsequent ring-closure process affords an oxanorbornadiene intermediate. The second reaction is an intramolecular concerted cycloaddition of this intermediate to give the final dioxapentacyclic adduct. For the second cycloaddition, which corresponds to the step controlling the selectivity, eight alternative reaction pathways are found. Chemoselectivity, facial selectivity, and stereoselectivity of this domino reaction are related with the different approach modes of the tethered furan to the oxanorbornadiene system of the intermediate. The most favorable pathway takes place along an endo/syn approach of the furan ring relative to the bridged oxygen atom of the oxanorbornadiene system, with participation of the substituted double bond. An analysis of energetic contributions to the potential energy barriers for the intramolecular cycloadditions identifies the different factors controlling the reactive channels. Selectivity outcome is reproduced by these calculations.     

Rotational isomerism about acyl–oxygen bond in two envelope conformations and vibrational spectral analysis of cyclopentyl acetate—a combined theoretical and experimental study

The s-cis and s-trans isomers resulting from the rotation about the acyl–oxygen bond of two envelope conformations with C5 (neighbour to substituted carbon C4) and C4 as apical atoms in the five-membered ring and vibrational spectra of cyclopentyl acetate are studied with density functional molecular orbital theory at the B3LYP/6-311++G** level. In the case of C5 at the flap and –OAc group in the axial position, it is found that the s-cis isomer (1:s-cis) is more stable than the s-trans isomer (1:s-trans) by 7.46 kcal/mol. The s-cis–s-trans rotational barrier is 15 kcal/mol. The other two conformers with C4 at the flap and –OAc group in the equatorial position, the relative energies of the s-cis and s-trans isomers (2:s-cis and 2:s-trans) with respect to 1:s-cis are found to be 0.45 and 8.21 kcal/mol, respectively. The infrared spectra (200–3200 cm⁻¹) in gas and liquid phase and Raman spectra (3200–150 cm⁻¹) in liquid phase for cyclopentyl acetate and 10 of its isotopomers are recorded. The calculated spectra of all conformers along with the observed spectra has helped study the effect of rotational isomerism on the vibrational spectra. The normal coordinate analysis in terms of non-redundant local coordinates is done for vibrational assignments of the 57 normal modes. The experimental and theoretical results are compared to the corresponding quantities of some similar molecules.