On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.     

Beiträge zur Chemie der Pyrrolo[3,2-c]azepine und der Pyrrolo [3,2-b]azepine

Some chemical transformations in the series of the pyrrolo [3,2-b]azepines and the pyrrolo[3,2-c]azepines are reported: alkylation at the pyrrolo nitrogen and/or the azepino nitrogen, reduction of the lactam group by means of LiAlH₄, preparation of lactim ethers and amidines, substitution in position 2 by MANNICH reaction, bromination and condensation with oxalyl chloride or chloral hydrate, and the cyclocondensation with dimethylmalonyl chloride. The structures of the 2-substitution products have been evaluated by NMR.-spectroscopy.     

Epoxides,cyclic sulfites,and sulfate from natural pentacyclic triterpenoids: theoretical calculations and chemical transformations

Several triterpenic derivatives, with the A-ring functionalized, were semisynthesized from oleanolic and maslinic acids. The reactivities of sulfites, sulfate, and epoxides in these triterpene compounds were investigated under different reaction conditions. Moreover, contracted A-ring triterpenes (five-membered rings) were obtained, by different treatments of the sulfate 7. From the epoxide 8, deoxygenated and halohydrin derivatives were semisynthesized with several nucleophiles. Ozonolysis and Beckmann reactions were used to yield 4-aza compounds, from five-membered ring olanediene triterpenes. The X-ray structure of sulfate 7 is given and compared with density functional theory geometries. Theoretical (13)C and (1)H chemical shifts (gauge-invariant atomic orbital method at the B3LYP/6-31G*//B3LYP/6-31G* level) and (3)J(H,H) coupling constants were calculated for compounds 5-9 and 34-36, identifying the (R)- or (S)-sulfur and alpha- or beta-epoxide configurations together with 4-aza or 3-aza structures.     

Lead(II) thiocyanate complexes with bibracchial lariat ethers: an X-ray and DFT study

Compounds of formula [Pb(L2)(NCS)2] (1) and [Pb(L4)(SCN)2] (2) (where L2 is the lariat crown ether N,N'-bis(3-aminobenzyl)-4,13-diaza-18-crown-6 and L4 is the Schiff-base lariat crown ether N,N'-bis(3-(salicylaldimino)benzyl)-4,13-diaza-18-crown-6) were isolated and structurally characterized by X-ray diffraction analyses. The X-ray crystal structures of both compounds show the metal ion coordinated to the six donor atoms of the crown moiety, leaving the corresponding pendant arms uncoordinated. The coordination sphere of lead(II) is completed by two thiocyanate groups that coordinate either through their nitrogen (1) or sulfur (2) atoms. The organic receptor adopts a syn conformation in 1, while in 2 it shows an anti conformation. To rationalize these unexpected different conformations of the L2 and L4 receptors in compounds 1 and 2, as well as the different binding modes found for the thiocyanate ligands, we have carried out theoretical calculations at the DFT (B3LYP) level. These calculations predict the syn conformation being the most stable in both 1 and 2 complexes. So, the anti conformation found for 2 in the solid state is tentatively attributed to the presence of intermolecular pi-pi interactions between phenol rings, for which the dihedral angle between the least-squares planes of both rings amounts to 2.6 degrees and the distance between the center of both rings is 3.766 A. On the other hand, the analysis of the electronic structure has revealed that the Pb-ligand bonds present highly ionic character in this family of compounds. They also suggest a greater transfer of electron density from the NCS- ligands when they coordinate through the less electronegative S atom. The Pb-SCN covalent bond formation mainly occurs due to an effective overlap of the occupied 3p z orbitals of the S atoms and the unoccupied 6p z AO of the Pb atom, while the Pb-NCS bonding interaction is primarily due to the overlap of the 6s and 7s AO of Pb with sp(1.10) hybrids of the N donor atoms. Our electronic structure calculations can rationalize the different coordination of the thiocyanate groups in compounds 1 and 2: the simultaneous formation of two Pb-SCN bonds is more favorable for S-Pb-S angles close to 180 degrees , for which the overlap between the occupied 3p z orbitals of the S atoms and the unoccupied 6 pz AO of the Pb atom is maximized.     

Recherches sur la structure électronique de composés soufrés (méthode L.C.A.O. améliorée)

Improved L.C.A.O. method primitively built for conjugated molecules holding only atoms of second row in the periodic classification is extended to molecules holding atoms of the third row. The application is done for thiophen, thioketones, SO₂ and SO₃. d orbitals are not introduced in this study. Discussion about results shows that d orbitals must be introduced when the sulphur atom is strongly positively charged like in sulphur oxides.     

Effect of absolute laser phase on reaction paths in laser-induced chemical reactions

Potential surfaces, dipole moments, and polarizabilities are calculated by ab initio methods [unrestricted MP2(full)/6-311++G(2d,2p)] along the reaction paths of the F+CH4 and Cl+CH4 reaction systems. It is found that in general dipole moments and polarizabilities exhibit peaks near the transition state. In the case of X=F these peaks are on the products side and in the case of X=Cl they are on the reactants side indicating an early transition state in the case of fluorine and a late transition state in the case of chlorine. An analysis of the geometric changes along the reaction paths reveals a one-to-one correspondence between the peaks in the electric properties and peaks in the rate of change of certain internal geometric coordinates along the reaction path. Interaction with short infrared intense laser fields pulses leads to the possibility of interferences between the dipole and polarizability laser-molecule interactions as a function of laser phase. The larger dipole moment in the Cl+CH4 reaction can lead to the creation of deep wells (instead of energy barriers) and new strongly bound states in the transition state region. This suggests possible coherent control of the reaction path as a function of the absolute phase of the incident field, by significant modification of the potential surfaces along the reaction path and, in particular, in the transition state region.     

A thieno-2H-chromene alpha-amino acid derivative: synthesis and photochromic properties

[structure: see text] A new photochromic thieno-2H-chromene alpha-amino acid derivative was prepared by C-N palladium-catalyzed cross-coupling of a bromothieno-2H-chromene with the aminated aromatic side chain of the methyl ester of a N,N-diprotected amino acid. Its good photochromic properties demonstrated by flash photolysis and continuous irradiation indicate a possible application in ophthalmic lenses. It may also be inserted into peptides to give photoinduced reversible structural changes.     

Consequence of boar edible tissue consumption on urinary profiles of nandrolone metabolites. II. Identification and quantification of 19-norsteroids responsible for 19-norandrosterone and 19-noretiocholanolone excretion in human urine

In previous work (Le Bizec et al., Rapid Commun. Mass Spectrom. 2000; 14: 1058), it was demonstrated that a boar meal intake could lead to possible false accusations of abuse of 17beta-nortestosterone in antidoping control. The aim of the present study was to identify and quantify endogenous 19-norsteroids in boar edible tissue at concentrations that can alter the steroid urinary profile in humans, and lead to excretion of 19-norandrosterone (19-NA) and 19-noretiocholanolone (19-NE). The samples were analysed in two laboratories. The methodologies used for extraction and detection (GC/MS(EI) and LC/MS/MS(APCI+)) are compared and discussed. 19-Norandrostenedione (NAED), 17beta- and 17alpha-nortestosterone (bNT, aNT), and 17beta- and 17alpha-testosterone (bT, aT) were quantified. The largest concentrations of NAED and bNT were observed in testicles (83 and 172 microg/kg), liver (17 and 63 microg/kg) and kidney (45 and 38 microg/kg). A correlation between the bNT and NAED content of a typical meal prepared with boar parts and the excreted concentrations of 19-NA and 19-NE in human urine was demonstrated.     

Can the presence of chemically inert species modify the face selectivity in asymmetric induction by cyclodextrins?

Reduction of-cyclodextrin (-CD) aromatic ketone (acetophenone and acetonaphthones) inclusion compounds were carried out in the presence of a large number of chemically inert species as potential co-guests. In several cases, it was observed that stoichiometric molar ratios of these compounds to ketone significantly modify the chiral induction yielding the inverted alcohol enantiomer and increasing the face selectivity. The results were found to depend strongly on the respective structure and shape of both the ketone and the additive, and on the molar ratio of-CD:ketone:third compound. These observations suggest the formation of a three-component inclusion complex in which the geometry of binding of the substrate and its mobility are changed with respect to the binary system.     

New designs for inhibitors of the NF-κB: DNA binding

We present a series of new inhibitors of the association between nuclear factor kappa B (NF-B) and the corresponding B site in DNA. They were designed using the lead compound 15-deoxy-^12,14 -prostaglandin J₂ (PGJ2), which is a natural product with demonstrated inhibitory efficiency for this system. First, the binding mode of PGJ2 to NF-B was unraveled by GOLD docking calculation. Subsequently, substitutions were made to PGJ2 to optimize its association with NF-B. Care was taken not to strongly increase the reactivity of the new compounds, and to keep the overall shape, size and hydrophilicity of the lead compound, which should render them a similar bioavailability. Molecular mechanics calculations were performed to decide on the suitability of the substitutions, and to evaluate the energies of association with NF-B. Density functional theory calculations were performed also to study the overall reactivity of the substituted drugs towards NF-B. Important general conclusions were obtained, concerning the improvement of these natural inhibitors; namely, a set of rational methodologies were deduced to improve the association between the PGJ2 derivatives and NF-B, and their efficiency demonstrated by generating a set of substituted complexes, some of them with a very much increased affinity for NF-B, opening new doors to enlarge the therapeutic capabilities of this class of drugs.