Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase

Uroporphyrinogen III decarboxylase catalyzes the fifth step in heme biosynthesis: the elimination of carboxyl groups from the four acetate side chains of uroporphyrinogen III to yield coproporphyrinogen III. The enzyme acts by successively protonating each of the four pyrrole rings present in the substrate, thereby allowing decarboxylation of their side chains, but the identity of the proton donors has not been established yet. Tyr164 has been suggested as a proton donor, and Asp86 has been proposed to act either as a proton donor or as an intermediate-stabilizing residue. We have performed density-functional calculations to study this reaction mechanism, and found that the rate-limiting step is substrate protonation, rather than decarboxylation. Surprisingly, whereas Tyr164 is unable to protonate the substrate, this protonation can be effected by a nearby arginine residue (Arg37), with a free energy barrier of 21.4 kcal.mol(-1), in remarkable agreement with the experimental value of 19.5 kcal.mol(-1). The central positioning of this residue in close proximity to all four pyrrole rings in the substrate may play a key role in the sequential activation of each of these moieties.     

Formal total synthesis of β-pipitzol

(±)-$\text{O}$-methylperezone ($\text{1b}$) was obtained by selective oxidative demethylation of (±)-leucoperezone trimethyl ether ($\text{4a}$). Compound ($\text{4a}$) was prepared by condensation of 2,3,5-trimethoxytoluene ($\text{5e}$) with 6-methyl-5-hepten-2-one, followed by reductive removal of the tertiary alcohol. The aromatic precursor $\text{5e}$ was prepared in four steps from 2,3-dimethoxytoluene ($\text{5a}$) and, alternatively, in three steps from 5-bromoveratraldehyde ($\text{6a}$). Racemic $\text{1b}$ and $\text{4a}$ were directly compared with the optically active molecules prepared from natural R(-)-perezone ($\text{1a}$).     

Fused Mesoionic Heterocycles: Synthesis of 1,2,4-triazolo(4,3-b)-1,2,4-triazole derivatives

A number of mesoionic compounds derivatives of the bicyclic system 1,2,4-triazolo(4,3-b)-1,2,4-triazole have been prepared from 4-amino-1-methyl-3,5-bis(methylthio)-1,2,4-triazolium iodide and aryl isothiocyanates.     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

A DFT study on the 1,3-dipolar cycloaddition reactions of C-(methoxycarbonyl)-N-methyl nitrone with methyl acrylate and vinyl acetate

In the 1,3-dipolar cycloaddition of glyoxylic nitrones with electron-poor and electron-rich alkenes, the configurational instability of the nitrone leads to parallel models when regio- and stereoselectivities are rationalized. The energetics of the cycloaddition reactions have been investigated through molecular orbital calculations at the B3LYP/6-31-G(d) theory level. By studying different reaction channels and reagent conformations, leading to a total of sixteen transition structures for each dipolarophile, the regio- and stereochemical preferences of the reaction are discussed.     

Holo- and hemidirected lead(II) in the polymeric [Pb(4)(mu-3,4-TDTA)2(H2O)2]*4H2O complex. N,N,N',N'-tetraacetate ligands derived from o-phenylenediamines as sequestering agents for lead(II)

The coordinating ability of the ligands 3,4-toluenediamine-N,N,N',N'-tetraacetate (3,4-TDTA), o-phenylenediamine-N,N,N',N'-tetraacetate (o-PhDTA), and 4-chloro-1,2-phenylenediamine-N,N,N',N'-tetraacetate (4-Cl-o-PhDTA) (H4L acids) toward lead(II) is studied by potentiometry (25 degrees C, I = 0.5 mol x dm(-3) in NaClO4), UV-vis spectrophotometry, and 207Pb NMR spectrometry. The stability constants of the complex species formed were determined. X-ray diffraction structural analysis of the complex [Pb4(mu-3,4-TDTA)4(H2O)2]*4H2O (1) revealed that 1 has a 2-D structure. The layers are built up by the polymerization of centrosymmetric [Pb4L2(H2O)2] tetranuclear units. The neutral layers have the aromatic rings of the ligands pointing to the periphery, whereas the metallic ions are located in the central part of the layers. In compound 1, two types of six-coordinate lead(II) environments are produced. The Pb(1) is coordinated to two nitrogen atoms and four carboxylate oxygens from the ligand, whereas Pb(2) has an O6 trigonally distorted octahedral surrounding. The lead(II) ion is surrounded by five carboxylate oxygens and a water molecule. The carboxylate oxygens belong to four different ligands that are also joined to four other Pb(1) ions. The selective uptake of lead(II) was analyzed by means of chemical speciation diagrams as well as the so-called conditional or effective formation constants K(Pb)eff. The results indicate that, in competition with other ligands that are strong complexing agents for lead(II), our ligands are better sequestering agents in acidic media.     

A ferrocene-based heteroditopic ligand for electrochemical sensing of cations and anions

A ferrocene-based heteroditopic receptor containing urea and crown ether units shows electrochemical responses to dihydrogenphosphate and fluoride anions. K+ cations can only be detected in the presence of dihydrogenphosphate.     

Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential V(A) on a one-atom density rho(A) or rho(B). To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale.     

Stereoselective synthesis of 4 alpha-hydroxy-8,12-guaianolides from santonin

Hydroxyester 2, easily obtained from santonin (1), has been transformed into 10 alpha-hydroxyguai-3-en-8,12-olide 6, a good intermediate for the synthesis of natural 8,12-guaianolides. Compound 6 was obtained from 2 by photochemical rearrangement of its acetyl derivative 7, stereoselective hydrogenation on Pd/C, reduction, regioselective elimination, hydrolysis, and lactonization. The synthesis of the natural guaianolides 3-5 was carried out in two sequences in which the regioselective elimination of a hydroxyl group at C10 with triflic anhydride or SOCl2 to afford, respectively, the endo or exo double bond on C10 and the regioselective opening of the C3-C4 alpha-epoxide were the key steps.     

Constant neutral loss scanning for the characterization of glycerol phosphatidylcholine phospholipids

The product-ion spectra of the sodiated molecules of glycerol phosphatidylcholine phospholipids (GPC) were obtained, using fast-atom bombardment (FAB) as the ionization method, in a tandem mass spectrometer. The product-ion spectra of these sodiated molecules of GPCs were found to differ significantly from those of the protonated GPC molecules. This difference is due to the absence of the ion of m/z 184 (protonated-phosphocholine moiety) and to the presence of an ion resulting from the loss of trimethylamine (m=59 Da) from the polar head group, which is the dominant fragmentation. This characteristic neutral loss provides a means of identification of this class of phospholipids and of differentiation from other phospholipid classes in complex mixtures by performing a constant-neutral-loss scan of 59.