Molecular mobility of nitroxide spin probes in glassy polymers. Quasi‐libration model

ESR spectra of three spin probes with different molecular volumes: 2,2,6,6‐tetramethyl‐4‐oxopiperidine‐1‐oxyl, di‐p‐anisylnitroxide, and nitroxide derivative of fullerene in glassy polystyrene, polyvinyl trimethylsilane, and Teflon AF‐2400 were calculated numerically within the model of quasi‐libration motions. Temperature ranges, where the model is capable to reproduce spectra within experimental errors, were defined. It was found that simulation of X‐band ESR spectra allows to determine quasi‐libration amplitudes around molecular axes X and Y with accuracy ～ 3° and around Z axis with accuracy ～ 15–20°. A shape of distribution of quasi‐libration amplitudes was also determined qualitatively by ESR spectra simulations. It was established that the average amplitude of quasi‐libration motion depends on the free volume of each polymer and geometrical molecular volume of a spin probe. Quasi‐libration amplitudes increase as the temperature increases, and reach the value of 40 degrees. We found that upon further temperature increase, quasi‐libration model becomes inapplicable for quantitative numerical spectra simulation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 107–120, 2009     

Insights into the reaction mechanism of soluble epoxide hydrolase from theoretical active site mutants

Density functional theory calculations of active site mutants are used to gain insights into the reaction mechanism of the soluble epoxide hydrolases (sEHs). The quantum chemical model is based on the X-ray crystal structure of the human soluble epoxide hydrolase. The role of two conserved active site tyrosines is explored through in silico single and double mutations to phenylalanine. Full potential energy curves for hydrolysis of (1S,2S)-beta-methylstyrene oxide are presented. The results indicate that the two active site tyrosines act in concert to lower the activation barrier for the alkylation step. For the wild-type and three different tyrosine mutant models, the regioselectivity of epoxide opening is compared for the substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide. An additional part of our study focuses on the importance of the catalytic histidine for the alkylation half-reaction. Different models are presented to explore the protonation state of the catalytic histidine in the alkylation step and to evaluate the possibility of an interaction between the nucleophilic aspartate and the catalytic histidine.     

Theoretical study of the full reaction mechanism of human soluble epoxide hydrolase

The complete reaction mechanism of soluble epoxide hydrolase (sEH) has been investigated by using the B3LYP density functional theory method. Epoxide hydrolases catalyze the conversion of epoxides to their corresponding vicinal diols. In our theoretical study, the sEH active site is represented by quantum-chemical models that are based on the X-ray crystal structure of human soluble epoxide hydrolase. The trans-substituted epoxide (1S,2S)-beta-methylstyrene oxide has been used as a substrate in the theoretical investigation of the sEH reaction mechanism. Both the alkylation and the hydrolytic half-reactions have been studied in detail. We present the energetics of the reaction mechanism as well as the optimized intermediates and transition-state structures. Full potential energy curves for the reactions involving nucleophilic attack at either the benzylic or the homo-benzylic carbon atom of (1S,2S)-beta-methylstyrene oxide have been computed. The regioselectivity of epoxide opening has been addressed for the two substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide.     

UV LASER INDUCED RNA-PROTEIN CROSSLINKS AND RNA CHAIN BREAKS IN TOBACCO MOSAIC VIRUS RNA in situ

The efficiency of RNA-protein crosslink and RNA chain break formation under nanosecond or picosecond UV-laser pulse irradiation of tobacco mosaic virus was determined. It was found that on high-intensity UV-laser irradiation the quantum yields of both reactions increase considerably as compared to the usual (low-intensity) UV-irradiation. The RNA-protein crosslink quantum yield was found to be 1.8 x 10(-5) and 1.2 x 10(-4) and that of RNA chain breaks 1.7 x 10(-4) and 8.9 x 10(-4) for nanosecond and picosecond irradiation, respectively.     

Charge Transfer Complex Role in the Formation of Chlorobenzene in the γ‐Irradiated Carbon Tetrachloride‐Benzene System

The formation of carbon tetrachloride‐benzene charge transfer complex was confirmed by UV and NMR spectrometric studies. A change in UV spectrum of benzene is observed upon addition of carbon tetrachloride. Whereas the appearance of new bands supports the formation of charge transfer complex. NMR study shows that, chemical shift of benzene pmr signal depends on the CCl₄‐C₆H₆ molar ratio. This observation is another criterion for the formation of benzene‐carbon tetrachloride charge transfer complex. Job's Continuous Variation method indicates that a 2:1 CCl₄‐C₆H₆ charge transfer complex (2:1 CTC) is formed. The association constants (K_2:1) of (2:1 CTC) was found to be 0.0197 M^?2. The maximum concentration of (2:1 CTC) was found to be in samples with 2:1 CCl₄‐C₆H₆ molar ratio (33% benzene mole). On the other hand the maximum yield of chlorobenzene was obtained, also, upon radiolysis of CCl₄‐C₆H₆ samples at a 2:1 molar ratio (33% benzene mole). Therefore, it could be concluded that (2:1 CTC) participates in the formation of chlorobenzene upon radiolysis of the benzene‐carbon tetrachloride system. This conclusion was supported by the dependence of the chlorobenzene yield of a γ‐irradiated carbon tetrachloride‐benzene system (2:1 molar ratio) on irradiation time according to a third order kinetic equation with a very good linearity (R² = 0.9977). Accordingly, the rate constant for the chlorobenzene formation under this condition was found to be ≈ 5.5 × 10^?7 L².mol^?2.h^?1. We propose a radiation chemical mechanism in which the 2:1 CTC plays a role in the formation of chlorobenzene.     

Catalytic mechanism of limonene epoxide hydrolase, a theoretical study

The catalytic mechanism of limonene epoxide hydrolase (LEH) was investigated theoretically using the density functional theory method B3LYP. LEH is part of a novel limonene degradation pathway found in Rhodococcus erythropolis DCL14, where it catalyzes the hydrolysis of limonene-1,2-epoxide to give limonene-1,2-diol. The recent crystal structure of LEH was used to build a model of the LEH active site composed of five amino acids and a crystallographically observed water molecule. With this model, hydrolysis of different substrates was investigated. It is concluded that LEH employs a concerted general acid/general base-catalyzed reaction mechanism involving protonation of the substrate by Asp101, nucleophilic attack by water on the epoxide, and abstraction of a proton from water by Asp132. Furthermore, we provide an explanation for the experimentally observed regioselective hydrolysis of the four stereoisomers of limonene-1,2-epoxide.     

Formal C−H Carboxylation of Unactivated Arenes

A formal C−H carboxylation of unactivated arenes using CO₂ in green solvents is described. The present strategy combines a sterically controlled Ir-catalyzed C−H borylation followed by a Cu-catalyzed carboxylation of the in situ generated organoboronates. The reaction is highly regioselective for the C−H carboxylation of 1,3-disubstituted and 1,2,3-trisubstituted benzenes, 1,2- or 1,4-symmetrically substituted benzenes, fluorinated benzenes and different heterocycles. The developed methodology was applied to the late-stage C−H carboxylation of commercial drugs and ligands.