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     

Sandwich-type transition metal complexes [(CBO)n]2M with carbon boronyl ligands (CBO)n (n=4–6)

A density functional theory investigation on a series of sandwich-type transition metal complexes [(CBO)_n]₂M (n=4–6; M=transition metals) with carbon boronyls (CBO)_n as effective aromatic ligands has been presented in this work at B3LYP level. The ground-states of these complexes possess staggered D_nd symmetries, while the corresponding eclipsed D_nh structures exist as transition states with slightly higher energies (within 5.8 kJ/mol). Carbon boronyl complexes [(CBO)_n]₂M are confirmed to be much more stable than their boron carbonyl isomers [(BCO)_n]₂M, which, on the other hand, take eclipsed ground-states with D_nh symmetries. The carbon boronyl complexes [(BCO)_n]₂M proposed in this work parallelize the well-known sandwich-type hydrocarbon complexes [C_nH_n]₂M in coordination chemistry with boronyl groups –BO isolobal to –H atoms in corresponding ligands.     

A kinetic stability study of <Emphasis Type="Italic">M</Emphasis>N<Subscript>5</Subscript> (<Emphasis Type="Italic">M</Emphasis>=Li,Na, K,and Rb)

A structure and kinetic stability study on some complexes with the general formula MN₅, where M are the alkali-metal atoms, Li, Na, K, and Rb, has been carried by using hybrid density functional methods. Complex B (C_2v) with two points of attachment to the N₅ ring is the most energetically favored for all metals considered here. Pyramidal structures A (C_5v) are kinetically unstable and they rapidly rearrange to the most stable planar structures B. At the QCISD(T)/6-311 + G*//B3LYP/6-311 + G* + ZPE (B3LYP/6-311 + G*) level, the decomposition barrier heights of LiN₅-B, NaN₅–B, KN₅-B, and RbN₅-B are predicted to be 19.9, 22.0, 22.5, and 23.0 kcal/mol, respectively. In addition, the rate constants of the decomposition reaction MN₅-B MN₃ + N₂ (M + Li, Na, K, and Rb) are also predicted using conventional transition state theory and canonical variational transition state theory, respectively.     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

Studies on the properties of ionic liquid EMIInCl4

This paper reports that an ionic liquid (IL) has been prepared by directly mixing InCl₃ and 1-methyl-3-ethylimidazolium chloride (EMIC) with molar ratio 1/1 under dry argon atmosphere. The densities, and surface tension of the pure IL were determined at temperature range of 293.15 to 343.15 ± 0.1 K. The volumetric properties and the properties of surface for ionic liquid based on group III were discussed by Glasser's theory and Yang's interstice model.     

Volumetric Properties of the Ternary System 1,4-Dioxane + Butyl Acrylate + Ethyl Acrylate and Its Binary Butyl Acrylate + Ethyl Acrylate at 298.15 K

Densities of the ternary system 1,4-dioxane + butyl acrylate + ethyl acrylate and its binary butyl acrylate + ethyl acrylate have been measured in the whole composition range, at 298.15 K and atmospheric pressure, using an Anton Paar DMA 5000 oscillating U-tube densimeter. The calculated excess molar volumes of the binary system are positive and were correlated with the Redlich–Kister equation and with a series of Legendre polynomials. Several models were used to correlate the ternary behavior from the excess molar volume data of their constituent binaries and were found equally good to fit the data. The best fit was based on a direct approach, without information on the component binary systems.     

Effect of mobile phase density gradients on efficiency in packed column supercritical fluid chromatography

Summary The efficiency of packed columns was measured as a function of flow rate, temperature, outlet density, and the density differential across the column, unsing pure carbon dioxide as the mobile phase. Although density differentials are often blamed for a serious loss in efficiency in packed column supercritical fluid chromatography, the results show that efficiency was not a function of the density differential. Peak shapes suggest that apparent loss in efficiency is actually due to inadequate solubility of the solute in carbon dioxide.     

Transition metal clusters and supported species with metal-carbon bonds from first-principles quantum chemistry

We discuss the impact of density functional electronic structure calculations for understanding the organometallic chemistry of transition metal (TM) surface complexes and clusters. Examples will cover three types of systems, mainly of interest in the context of heterogeneous catalysis: (i) supported carbonyl complexes of rhenium on MgO and of rhodium in zeolites, (ii) TM clusters with CO ligands and adsorbates, and (iii) metal clusters exhibiting chemical bonds with atomic carbon. The first group of case studies promotes the concept that surface groups of oxide supports are bonded to TM complexes in the same way as common (poly-dentate) ligands are bonded in coordination compounds. The second group of examples demonstrates various “ligand effects” of TM clusters. Finally, we illustrate how carbido centers stabilize TM clusters and modify the propensity for adsorption at the surface of such clusters.     

Grid-free DFT implementation of local and gradient-corrected XC functionals

Following an approach to density functional theory calculations based on the matrix representation of operators, we implemented a scheme as an alternative to traditional grid-based methods. These techniques allow integrals over exchange-correlation operators to be evaluated through matrix manipulations. Both local and gradient-corrected functionals can be treated in a similar way. After deriving all the required expressions, selected examples with various functionals are given. Received: 7 March 1998 / Accepted: 21 May 1998 / Published on line: 6 August 1998     

Theoretical DFT and experimental Raman and NMR studies on thiophene, 3-methylthiophene and selenophene

The results of extended MO calculations using density functional theory (DFT) approximation supported by experimental Raman, ¹H and ¹³C NMR studies on thiophene are reported. Raman spectra of liquid thiophene were re-examined and the performance of a hybrid B3PW91 density functional was compared with the ab initio restricted Hartree–Fock (RHF) method. With the basis sets of the 6-311++G^** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.

Additionally, the results on thiophene were extended by calculations on 3-methylthiophene and selenophene. In this case, a significant change in geometry and charge distribution in thiophene ring due to a methyl group substituent or replacement of sulphur by selene atom was observed.

A linear correlation between the predicted harmonic vibrational frequencies (scaled using SQM method) and experimental ones for thiophene, selenophene and 3-methylthiophene was shown. The theoretically calculated spectra have satisfactorily reproduced the available experimental spectra for thiophene and selenophene.