An experimental and computational study of the reaction between pent-3-en-2-yl radicals and oxygen molecules: switching from pure stabilisation to pure decomposition with increasing temperature.

We have used laser-photolysis-photoionization mass spectrometry, quantum chemical calculations, and master equation simulations to investigate the kinetics of the reaction between (E/Z)-pent-3-en-2-yl a resonance-stabilised hydrocarbon radical, and molecular oxygen. The time-resolved experiments were performed over a wide temperature range (240-750 K) at relatively low pressures (0.4-7 Torr) under pseudo-first-order conditions (excess [O2]). Helium bath gas was used in most experiments, but nitrogen was employed in a few measurements to investigate the effect of a heavier collider on the kinetics of the studied reaction. The experimental traces were directly used to optimise parameters in the master equation model using the recently implemented trace fitting feature in the MESMER program. At low temperatures (T < 300 K), the reaction proceeds by barrierless recombination reactions to form peroxyl adducts, and the radical traces are single-exponential. Between 326 K and 376 K, equilibration between the reactants and the peroxyl adducts is observed, and the radical traces are multi-exponential. Interestingly, at temperatures above 500 K, single-exponential decays were again observed, although the reaction is much slower than at low temperatures. The master equation simulations revealed that at both low and high temperatures, the radical decay rate is governed by a single eigenvalue. At low temperatures, this eigenvalue corresponds to recombination reactions, and at high temperatures to the phenomenological formation of bimolecular products. Between low and high temperatures (the exact temperature thresholds depend on [O2]), there is a region of avoided crossing in which the rate coefficient "jumps" from one eigencurve to the other. Although chemically significant eigenvalues are not well separated from internal energy relaxation eigenvalues at elevated temperatures (600 K at 0.01 bar, 850 K at 100 bar), we observed that many of the Bartis-Widom rate coefficients produced by the master equation model were valid up to 1500 K. Our simulations predict that the most important reaction channel at high temperatures is the formation of (E/Z)-penta-1,3-diene and hydroperoxyl. The experimentally constrained master equation model was used to simulate the title reaction over a wide range of conditions. To facilitate the use of our results in autoignition and combustion models, modified Arrhenius representations are given for the most important reaction channels.

Solving the discrepancy between the direct and relative-rate determinations of unimolecular reaction kinetics of dimethyl-substituted Criegee intermediate (CH3)2COO using a new photolytic precursor.

We have performed direct kinetic measurements of the thermal unimolecular reaction of (CH3)2COO in the temperature range 243-340 K and pressure range 5-350 Torr using time-resolved UV-absorption spectroscopy. We have utilized a new photolytic precursor, 2-bromo-2-iodopropane ((CH3)2CIBr), which photolysis at 213 nm in the presence of O2 produces acetone oxide, (CH3)2COO. The results show that the thermal unimolecular reaction is even more important main loss process of (CH3)2COO in the atmosphere than direct kinetic studies have suggested hitherto. The current experiments show that the unimolecular reaction rate of (CH3)2COO at 296 K and atmospheric pressure is 899 ± 42 s-1. Probably more importantly, current measurements bring the direct and relative-rate measurements of thermal unimolecular reaction kinetics of (CH3)2COO into quantitative agreement.

Tuning the stability of alkoxyisopropyl protection groups.

Five different 2-alkoxypropan-2-yl groups are introduced as acid-labile protecting groups for the 5'- and 3'-hydroxy groups of a 2'-deoxynucleoside. All studied protecting groups were readily introduced with good to excellent yields using the appropriate enol ether as a reagent and 0.5 to 1 mol % p-toluenesulfonic acid as a catalyst. The protected compounds could be purified by silica gel column chromatography without degradation. The compatibility of these protecting groups in parallel use with benzoyl and silyl groups was verified. The stabilities of the different alkoxy acetal protecting groups were compared by following the kinetics of their hydrolysis at 25.0 °C in buffered solutions through an HPLC method. In the pH range 4.94 to 6.82 the hydrolysis reactions are of first order in the hydronium ion. The rate of hydrolysis correlates with the electron-donating or electron-withdrawing ability of the corresponding alkoxy group. The studied 2-alkoxypropan-2-yl groups and the relative rate constants for their cleavage from the 5'-hydroxy group of 2'-deoxythymidine were: cyclohexyloxy (k rel = 7.7), isopropoxy (7.4), methoxy (1), benzyloxy (0.6) and 2,2,2-trifluoroethyloxy (0.04). The attachment of the same groups to the 3'-hydroxy group are from 1.3 to 1.9-fold more stable. The most reactive of these acetone-based acetal groups are faster removed than a dimethoxytrityl group, and they are easier to cleave completely in solution. The structural variation allows steering of the stability and lipophilicity of the compounds in some range.

Stability of Criegee intermediates formed by ozonolysis of different double bonds.

The formation of Criegee intermediates by ozonolysis of different species containing C═N and C═P bonds is studied computationally. Electronic structure calculations are carried out for the energetics of ozonolysis, and the lifetime of the Criegee intermediate formed is computed by transition state theory. All calculations are carried out for formation of CH2OO, the simplest Criegee intermediate. Extremely large differences are found for the lifetime of CH2OO depending on the specific C═N, C═P, and C═C precursor, due to the great variations in the exoergicity of the ozonolysis. The largest lifetimes of CH2OO are found to be up to a millisecond range for a Schiff base precursor, being orders of magnitude greater than for C═C and C═P precursors at the same conditions. The results provide insights into the role of the precursor in determining the stability of the Criegee species formed and suggest an approach for preparing Criegee intermediates of relatively long lifetimes.

Isomerization and decomposition of a Criegee intermediate in the ozonolysis of alkenes: dynamics using a multireference potential.

The isomerization and decomposition dynamics of the simplest Criegee intermediate CH2 OO have been studied by classical trajectory simulations using the multireference ab initio MR-PT2 potential on the fly. A new, accelerated algorithm for dynamics with MR-PT2 was used. For an initial temperature of 300 K, starting from the transition state from CH2 OO→CH2 O2 , the system reaches the dioxirane structure in around 50 fs, then isomerizes to formic acid (in ca. 2800 fs), and decomposes into CO+H2 O at around 2900 fs. The contributions of different configurations to the multiconfigurational total electronic wave function vary dramatically along the trajectory, with diradical contributions being important for transition states corresponding to H-atom transfers, while being only moderately significant for CH2 OO. The implications for reactions of Criegee intermediates are discussed.

Direct Kinetic Measurements of a Cyclic Criegee Intermediate; Unimolecular Decomposition of c-(CH2)5COO.

We report the first direct kinetic measurements of a cyclic stabilized Criegee Intermediate. We have measured the unimolecular reaction rate coefficient of cyclohexanone oxide (c-(CH2)5COO) in the temperature 213-296 K and pressure 7-50 Torr ranges using absorption spectrometry. The c-(CH2)5COO was produced by the photolysis of c-(CH2)5CIBr at 213 nm in the presence of O2. We compare the measured fast c-(CH2)5COO unimolecular rate coefficient, 1998 ± 147 s-1 at 296 K, with the literature calculations for the structurally similar E-nopinone oxide formed in ß-pinene ozonolysis. The kuni(c-(CH2)5COO)/kuni(E-nopinone oxide) ratio calculated using transition-state theory and density functional theory agrees well with this comparison. We have also measured the bimolecular rate coefficient of the reaction between c-(CH2)5COO and trifluoroacetic acid at 253 K and 10 Torr and obtained the value (8.7 ± 1.0) × 10-10 cm3 molecule-1 s-1. This very large value agrees with previous kinetic measurements for reactions between stabilized Criegee intermediates and halogenated organic acids.

On the factors affecting product distribution in laccase-catalyzed oxidation of a lignin model compound vanillyl alcohol: experimental and computational evaluation.

Laccases (EC 1.10.3.2) are multicopper oxidases, which can oxidize phenolic substrates by the concomitant reduction of oxygen to water. The phenolic substructures of lignin are also oxidized by laccases, resulting mainly in various polymerized products. Several model compound studies indicate that variations in the reaction media, such as the pH and the enzyme dosage used, have an impact on the observed product distribution of laccase promoted oxidation, but no detailed study has been reported to explain these results. In the present study, a monomeric lignin model compound, vanillyl alcohol, was oxidized in laccase-catalyzed reactions by varying the pH, enzyme dosage and temperature. The energies of all the observed products and potential intermediates were calculated by applying density functional theory (DFT) and the polarizable continuum solvation model (PCM). The observed predominant product at pH 4.5 to 7.5 was clearly the 5-5' dimer, although the thermodynamic product according to the calculated free energies was vanillin, the difference being 5.6 kcal mol(-1). The hydrogen bonding is shown to give an additional stabilizing effect on the transition state leading to the 5-5' dimer, but also a kinetic barrier reduces the formation of vanillin. Based on the calculated pKa-values of the proposed intermediates we suggest that the rearomatization reactions of the quinones formed in the radical reactions under mildly acidic and neutral conditions would preferentially occur through deprotonation rather than through protonation.

Is coproporphyrin III a copper-acquisition compound in Paracoccus denitrificans?

Paracoccus denitrificans is a soil bacterium which can respire aerobically and also denitrify if oxygen is absent. Both processes are highly dependent on copper enzymes and copper is therefore likely to be an essential trace element for the bacterium. If copper is not easily available, a copper-acquisition mechanism would be highly beneficial. In this paper, we have addressed the question of whether Paracoccus secretes a copper-acquisition compound functionally analogous to that found in some methanotrophs. Bacteria were grown both in copper-containing and copper-deficient denitrification media, cells were removed by centrifugation and the supernatant was analysed using chromatography and spectroscopy. Bacterial growth yield in the absence of copper was 70-80% of that in the copper-containing medium. A notable difference between the two culture conditions was that spent copper-deficient medium was pigmented, whereas the copper-containing medium was not. Spectrophotometry indicated that a red compound with an absorption maximum at 405 nm was produced under copper-limited conditions. In addition to the strong 405 nm maximum, the visible spectrum of the purified red molecule had weaker maxima at 535 nm and 570 nm, features typical of metallated tetrapyrroles. Mass spectrometry showed that the purified pigment had a molecular mass of 716.18. Moreover, the fine structure of the mass spectrum suggested the presence of zinc and was consistent with the chemical formula of C(36)H(36)N(4)O(8)Zn. The presence of zinc was also demonstrated using inductively coupled plasma atomic emission spectroscopy. Fragmentation analysis with mass spectrometry showed the release of consecutive 59 Da fragments, assignable to four -CH(2)-COOH moieties. Thin layer chromatography as well as NMR analysis of the C-13/N-15 labelled red pigment suggested that it is predominantly zinc coproporphyrin III with a minor fraction of metal-free coproporphyrin III. We propose that in a copper-poor environment P. denitrificans secretes coproporphyrin III for copper chelation and subsequent uptake of the bound copper into the cell. Consistent with this idea, cell yields of copper-deficient cultures grown in the presence of 1 microM copper-coproporphyrin III were 90-95% of the yields of cultures grown in the normal copper-containing media. Coproporphyrin III may work as a copper-acquisition compound in P. denitrificans.

A novel approach to solid phase chemical synthesis of oligonucleotide mRNA cap analogs.

A novel approach for the synthesis of 5-capped 2'-O-methyloligoribonucleotides on a disulfide-tethered solid support is described. The key step of the synthesis is ZnCl2 promoted coupling of m7GDP imidazolide to a fully deprotected oligonucleotide 5'-phosphate on-support. By this methodology m7G5'pppm2'Apm2'Upm2'Ap has been prepared.

A solid supported reagent for internucleoside H-phosphonate linkage formation.

A fast and convenient procedure for synthesis of dinucleoside H-phosphonates is obtained through use of the novel polystyrene supported 5-carboxy-5-methyl-2-oxo-2-chloro-1,3,2-diaoxaphosphorinane reagent. Virtually quantitative H-phosphonate condensations are obtained leading to excellent isolatedyields and with only a simple filtration as the purification procedure. This provides for a convenient and high-yielding procedure that should be suited for solution-phase synthesis of oligonucleotides.

On the reactions of two fungal laccases differing in their redox potential with lignin model compounds: products and their rate of formation.

Laccases (EC 1.10.3.2) are multicopper oxidases able to oxidize phenolic compounds such as lignin-related polyphenols. Since the discovery that so-called mediators effectively extend the family of laccase substrates, direct interactions between lignin-like materials and laccase have gained much less attention. In this work, the aim was to characterize oxidation products formed in direct laccase-catalyzed oxidation of different guaiacylic and syringylic lignin model compounds with two different laccases: a low redox potential Melanocarpus albomyces laccase and a high redox potential Trametes hirsuta laccase. By following the formation of different, mainly biphenylic (5-5) and benzylic oxidation products, it was found that although both of these enzymes generated practically the same pattern of products with particular types of syringyl and guaiacyl compounds, in some cases a clear difference in the rates of their formation was observed. The results also confirm further to the suggestions that syringylic compounds are able to act as mediators in their own oxidation reactions and also that in some instances acetylation of phenolic material may produce altered, unexpected structures.

2,2-Bis(ethoxycarbonyl)- and 2-(alkylaminocarbonyl)-2-cyano-substituted 3-(pivaloyloxy)propyl groups as biodegradable phosphate protections of oligonucleotides.

Oligonucleotides bearing biodegradable phosphate protecting groups have been synthesized on a solid support. For this purpose, two dimeric building blocks, viz. 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2,2-bis(ethoxycarbonyl)-3-(pivaloyloxy)propyl]-P-thiothymidylyl-(3',5')-thymidine 3'-[O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite] (1) and 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2-cyano-2-(2-phenylethylaminocarbonyl)-3-(pivaloyloxy)propyl]thymidylyl-(3',5')-thymidine 3'-(H-phosphonate) (2), were prepared. Phosphoramidite 1 was incorporated into an phosphorothioate oligothymidylate sequence on a base-labile hydroquinone-O,O'-diacetic acid linker (Q-linker) and on a photolabile 4-alkoxy-5-methoxy-2-nitrobenzyl carbonate linker (11). H-Phosphonate 2 was, in turn, incorporated into an oligothymidylate sequence only on the photolabile linker. Kinetics of the removal of the protecting groups by porcine liver esterase and subsequent retro aldol condensation/phosphate elimination were then studied. While the pro-oligonucleotide that contained only one phosphate protection gave the deprotected phosphorothioate oligonucleotide in a quantitative yield, the enzymatic step was markedly decelerated upon increasing the number of protection groups, and hence chain cleavage started to compete.

Synthesis of phosphate-branched oligonucleotides.

A solid-phase synthesis for phosphate-branched oligonucleotides is described. The method is based on coupling of a single nucleoside phosphorodiamidite to terminal hydroxyl functions of two solid-supported oligonucleotides. After oxidation of the phosphite triester obtained to a phosphate triester, the third branch is assembled by conventional phosphoramidite chemistry.

Solid-phase synthesis of oligonucleotide glycoconjugates bearing three different glycosyl groups: orthogonally protected bis(hydroxymethyl)-N,N'-bis(3-hydroxypropyl)malondiamide phosphoramidite as key building block.

Diethyl O,O'-(methoxymethylene)bis(hydroxymethyl)malonate (3) was observed to undergo a stepwise aminolysis when treated with 3-aminopropanol. This allowed convenient preparation of bis(hydroxymethyl)-N,N'-bis(3-hydroxypropyl)malondiamide bearing orthogonal levulinyl (Lev) and tert-butyldiphenylsilyl (TBDPS) protections at the two N-hydroxypropyl groups (8). One of the hydroxylmethyl functions was then protected with a 4,4'-dimethoxytrityl (DMTr) group, and the other one was phosphitylated to obtain a methyl N,N-diisopropylphosphoramidite (1). This building block was used for the synthesis of oligonucleotide glycoconjugates (25 and 26) carrying three different sugar units. After conventional phosphoramidite chain assembly of the sequence containing 1, the 5'-terminal DMTr group was removed and an appropriate glycosyl 6-O-phosphoramidite was coupled. The remaining protections of the branching unit were removed in the order of Lev and TBDPS, and the exposed hydroxyl functions were reacted one after another with the desired glycosyl 6-O-phosphoramidites. Global deprotection and cleavage of the conjugate from the support were achieved by conventional ammonolysis.

Facile determination of the protecting group location of Nim-protected histidine derivatives by 1H-15N heteronuclear correlation NMR.

The positioning of the imidazole protecting group of several histidine derivatives was determined by means of (1)H-(15)N heteronuclear multiple-bond correlation NMR experiments. The cross-peak originated from the three-bond correlation between the histidine side-chain H(beta) and the imidazole N(pi) was used for the identification of the N(pi) signal in the (15)N spectrum. Therefore, based on the fact that the signal of the substituted imidazole nitrogen appears always at lower chemical shift (delta) than the unsubstituted one, the position of the blocking group could easily be inferred. The obtained data confirmed previous findings that were accomplished with other less generally applicable spectroscopic or crystallographic techniques.

An Orthogonally Protected alpha,alpha-bis(aminomethyl)-beta-alanine building block for the construction of glycoconjugates on a solid support.

Synthetic glycoclusters are extensively used as mimetics of naturally occurring, multivalent carbohydrate ligands in various glycobiological applications. Their preparation, however, is far from trivial, and it still is a limiting factor in the study of carbohydrate binding. We herein report the synthesis of an orthogonally protected building block, N-Alloc-N'-Boc-N' '-Fmoc-alpha,alpha-bis(aminomethyl)-beta-alanine (1), and its use in the preparation of triantennary peptide glycoclusters (21-24) on a solid support. The assembly of the clusters involves removal of the amino protections of the solid-supported branching unit 1 in the order Fmoc, Boc, and Alloc, and subsequent coupling of peracetylated O-(glycopyranosyl)-N-Fmoc-L-serine pentafluorophenyl esters (galactose, glucose, mannose, and ribose) to each amino group exposed.