Calculated optical spectrum of model oxyheme complex

The optical spectrum of a model oxyheme complex has been calculated using a new intermediate neglect of differential overlap (INDO-SCF-CI ) method that allows for the inclusion of configuration interaction and transition metals. In addition to the porphyrin π→π* transitions common to all heme proteins, four weak x,y polarized transitions observed only in oxyheme complexes have been calculated and assigned to excitations involving the lowest-empty highly delocalized (Oπ, dπ) orbital. Two broad z-polarized bands observed in the single-crystal polarized absorption spectra of oxymyoglobin and hemoglobin have also been calculated. Controversy exists over the assignment of these transitions and, in particular, over the extent of involvement of the oxygen ligand. Our calculations assign the weaker near-IR visible band mainly to the d σ dπ→ dπ* excitations and the more intense UV band mainly to a_2u → dσ* excitations. While significant participation (25%) of the highly delocalized (Oπ, dπ) virtual orbital is also found, these z-polarized transitions need not be totally unique to oxyheme complexes, in keeping with experimental observation.     

A theoretical study of the electromagnetic properties of ferrocene and the ferrocenium ion

An iterative extended Hückel molecular orbital calculation was used to obtain wave functions for the ground state of ferrocene and several low lying states of the ferrocenium ion. Photoemission spectra in terms of relative ionization potentials and the electric field gradient at the iron nucleus were calculated for ferrocene andg values and the electric field gradient were calculated for the ferrocenium ion. These values are in good agreement with experiment. The nature of the molecular orbitals was compared with results of previous semi-empirical andab initio calculations.     

Calculated electronic spectra of model ferric cytochrome P450 complexes

Restricted open-shell ground state properties and electronic spectra of two closely related low-spin, ferric, 6-coordinate, model cytochrome P450 complexes, one with a methyl mercaptide and the other a mercaptan as the second axial ligands, have been calculated with a newly modified, semiempirical INDO-SCF-CI method. The sensitivity of the calculated spectra to protonation of the sixth axial ligand, and the ability of the method to predict characteristic spectral features for the complexes investigated, are determined. Assignment of transitions, including xy- and z-polarized transitions, are made and compared with experimental observations where available. In particular, the origin of the anomalous split Soret spectrum observed in low-spin ferric complexes with mercaptide but not a mercaptan is investigated. Finally, a two part hypothesis is presented which provides a general explanation for the origin of both the observed split Soret and the red-shifted normal Soret in various ferrous and ferric P450 complexes in terms of the ground state orbital characters and simple symmetry considerations.     

Low spin ferric hemoglobin complexes

A caloulation has been made of the energy eigenfunotions and eigenvalues of low spin ferric ion in complexes with a strong cubic crystal field including the effects of tetragonal and rhombic distortions and of spin-orbit coupling among the ground state components and with excited states. Using the resultant, spin-orbit coupled eigenfunotions as a basis set, the magnetic susceptibility, the components of magnetic field energy, and the lattice and valence contributions to an electric field gradient at the iron nucleus were all calculated as a function of rhombic, tetragonal, and spin-orbit coupling strength used as parameters: R, u and . All of the calculated results agree reasonable well with experiment for the values of parameters R=1000 cm^–1, u=2000 cm^–1 and the free ion value (=420 cm^–1. These values of parameters were selected for the excellent fit they gave of the calculated values of g _x, g_y and g _z compared with the experimental ones obtained from single crystal electron spin resonance of ferrihemoglobin azide. With them, a value of 2.29 Bohr magnetons was calculated for the effective magnetic moment compared to the experimental value of 2.35. The total field gradient calculated under the same conditions, predicts a nuclear quadrupole moment Q in the range of. 107 –127. Barns, which is smaller than the range predicted from the high spin ferric ion results. Reasons for this discrepancy are discussed.

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Zusammenfassung Ausgehend von einem starken kubischen Ligandenfeld und unter Berücksichtigung tetragonaler (R) und rhombischer (u) Verzerrung sowie der Spin-Bahn-Kopplung () werden Eigenfunktionen und Energien fur Low-Spin-Ferrihämoglobinkomplexe berechnet. Mit den Parametern R=1000 cm^–1, u=2000 cm^–1, =420 cm^–1 erhält man für Suszeptibilität, elektrischen Feldgradienten am Fe und g-Werte gute Übereinstimmung mit experimentellen Daten. Aus dem berechneten Feldgradienten folgt ein Quadrupolmoment des Fe⁵⁷ von 0.107–0.127 Barn, im Gegensatz zu den viel höheren Resultaten bei High-Spin-Fe(III)-Verbindungen; diese Diskrepanz wird diskutiert.

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Résumé Les fonctions propres et les énergies du complexe Ferrihémoglobine «low spin» sont calculées pour un fort champ de ligandes à symétrie cubique, en tenant compte des distortions tétragonale (R) et rhomboédrique (u), ainsi que du couplage spin-orbite (). Avec les parametres R=1000 cm^–1, u=2000 cm^–1, =420 cm^–1, on trouve pour la susceptibilité, le gradient du champ électrique à l'emplacement de Fe et le facteur g des valeurs en bon accord avec les données expérimentales. On déduit du gradient de champ calculé un moment quadrupolaire de Fe⁵⁷ de 0,107 à 0,127 Barn, en désaccord avec les résultats beaucoup plus élevés obtenus à partir des associations Fe (III) «high spin». Ce désaccord fait l'objet d'une discussion.

     

Comparative study of free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam by free energy simulation,AMSOL, and Poisson Boltzmann methods

Free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam were determined using (1) free energy simulation, (2) AMSOL-SM2 semiempirical methods, and (3) Poisson-Boltzmann methods. The goals of this study were threefold: (1) to compare the results obtained from the three different methods, (2) to investigate the effect of inclusion of intraperturbed group interactions on free energy simulation estimates of solvation free energy differences, and (3) to investigate to what extent differences in free energies of solvation among three of these inhibitors could account for observed differences in their enzyme binding free energies. In general, relative solvation free energies obtained from the free energy simulations and AMSOL-SM2 methods give comparable results (i.e., the same rank ordering and similar quantitative results, differing significantly from results obtained using Poisson-Boltzmann methods). The free energy simulation studies suggest that the neglect of intraperturbed group interactions had little effect on rank order of free energies of solvation of the polar phenylimidazoles. The relative desolvation free energies of the three inhibitors of P450cam—1-phenylimidazole (1-PI), 2-phenylimidazole (2-PI), and 4-phenylimidazole (4-PI)—with known enzyme bound X-ray structures parallel that of their known binding affinities and could account for most of the differences in the free energies of binding of these three inhibitors to P450cam. The origin of the difference of the free energies of solution of these three inhibitors is primarily the additional interaction between solvent and N(SINGLE BOND)H group in the imidazole ring of 2- and 4-phenylimidazole that is absent in the 1-phenylimidazole isomer. This hypothesis is substantiated by a second comparison of the relative solvation free energies of 4-phenylimidazole with its methylated derivative, 3-methyl-4-phenylimidazole, also lacking an N(SINGLE BOND)H group. © 1996 by John Wiley & Sons, Inc.     

Confined modified realizability

We present a refinement ofthe bounded modified realizability which provides both upper and lower bounds for witnesses. Our interpretation is based on a generalisation of Howard/Bezem's notion of strong majorizability. We show how the bounded modified realizability coincides with (a weak version of) our interpretation in the case when least elements exist (e.g. natural numbers). The new interpretation, however, permits the extraction of more accurate bounds, and provides an ideal setting for dealing directly with data types whose natural ordering is not well‐founded (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Application of molecular orbital theory to the interpretation of mass spectra study of substituent effect on a series of acetophenones

Semi-empirical molecular orbital calculations have been used to study the substituent effect on the intensity of the m/e 43 peak ([COCH₃]+) in the mass spectra of a series of 25 substituted acetophenones. The two most relevant molecular properties calculated appear to be the ionization potential and the bond density of the fragmenting bond. A semi-logarithmic plot of relative peak intensities[the ratio of m/e (43/[M]⁺)] versus the ratio of ionization potential to bond density for these compounds produced a linear relationship with a correlation coefficient of 0.90 from the INDO method and 0.93 from the IEHT method. The use of two different semi-empirical methods to calculate ionization potentials and bond densities, together with the qualitative agreement between the two methods and with available experimental data, substantiates the correlations obtained. In addition, the molecular orbital calculations were used to understand the anomalous behavior of the teritary butyl and para-phenyl substitutes.     

Preparative mass‐spectrometry profiling of minor concentrated metabolites in Salicornia gaudichaudiana Moq by high‐speed countercurrent chromatography and off‐line electrospray mass‐spectrometry injection

Salicornia species have just been introduced to the European market as a vegetable named ‘samphire’, ‘green asparagus’, or ‘sea asparagus’. Due to its increasing attention, and associated value, minor compounds of Salicornia gaudichaudiana Moq were investigated. The use of countercurrent chromatography and mass spectrometry enabled the search for known, as well as potentially novel natural products. Their identification was achieved based on molecular weights and mass‐spectrometric fragmentation data. Low detection limits enabled the visualization of all compounds with their identification in almost real time close to the preparative countercurrent chromatography experiment. A list of known natural products from Salicornia genus guided the identification process of compounds occurring in Salicornia gaudichaudiana Moq by tandem mass spectrometry fragment comparison. The natural product classes were divided into four groups: chlorogenic acid derivatives; flavonoid derivatives; pentacyclic triterpenoid saponins; and other compounds.     

Harrington’s conservation theorem redone

Leo Harrington showed that the second-order theory of arithmetic WKL ₀ is -conservative over the theory RCA ₀. Harrington’s proof is model-theoretic, making use of a forcing argument. A purely proof-theoretic proof, avoiding forcing, has been eluding the efforts of researchers. In this short paper, we present a proof of Harrington’s result using a cut-elimination argument.