A predictive pattern of computed barriers for C-h hydroxylation by compound I of cytochrome p450

The communication presents DFT calculations of 10 different C-H hydroxylation barriers by the active species of the enzyme cytochrome P450. The work demonstrates the existence of an excellent barrier-bond energy correlation. The so-obtained equation of the straight line is demonstrated to be useful for predicting barriers of related C-H activation processes, as well as for assessing barrier heights within the protein environment. This facility is demonstrated be estimating the barrier of camphor hydroxylation by P450cam.     

Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism

The stereospecific cytochrome P450-catalyzed hydroxylation of the C(5)-H((5-exo)) bond in camphor has been studied theoretically by a combined quantum mechanical/molecular mechanical (QM/MM) approach. Density functional theory is employed to treat the electronic structure of the active site (40-100 atoms), while the protein and solvent environment (ca. 24,000 atoms) is described by the CHARMM force field. The calculated energy profile of the hydrogen-abstraction oxygen-rebound mechanism indicates that the reaction takes place in two spin states (doublet and quartet), as has been suggested earlier on the basis of calculations on simpler models ("two-state reactivity"). While the reaction on the doublet potential energy surface is nonsynchronous, yet effectively concerted, the quartet pathway is truly stepwise, including formation of a distinct intermediate substrate radical and a hydroxo-iron complex. Comparative calculations in the gas phase demonstrate the effect of the protein environment on the geometry and relative stability of intermediates (in terms of spin states and redox electromers) through steric constraints and electronic polarization.     

The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations

The primary oxidant of cytochrome P450 enzymes, Compound I, is hard to detect experimentally; in the case of cytochrome P450(cam), this intermediate does not accumulate in solution during the catalytic cycle even at temperatures as low as 200 K (ref 4). Theory can play an important role in characterizing such elusive species. We present here combined quantum mechanical/molecular mechanical (QM/MM) calculations of Compound I of cytochrome P450(cam) in the full enzyme environment as well as density functional studies of the isolated QM region. The calculations assign the ground state of the species, quantify the effect of polarization and hydrogen bonding on its properties, and show that the protein environment and its specific hydrogen bonding to the cysteinate ligand are crucial for sustaining the Fe-S bond and for preventing the full oxidation of the sulfur.     

Total synthesis of (R)- and (S)-turmerone and (7S,9R)-bisacumol by an efficient chemoenzymatic approach

An enantioselective synthesis of (R)-, (S)-turmerone and (7S,9R)-bisacumol is described. The enantiomerically pure key intermediates, a substituted butanoate ester and acid are utilized in the synthesis of both enantiomers of turmerone. The lipase catalyzed resolution studies of the acetate of bisacumol have been exploited towards the total synthesis of the naturally occurring cytotoxic sesquiterpene, (7S,9R)-bisacumol with high diastereoselectivity (94% de).     

Some answers to frequently asked questions about the distortive tendencies of π-electronic system

The paper reviews briefly the various computational strategies, which have been devised by different groups to probe the symmetrizing vs distortive propensities of the π-bonding species of polyenes. All methods point to the same conclusion that the π-bonding components of benzene, allyl, aromatic annulenes and related species have intrinsic distortive tendencies; these species maintain bond-equalized geometries due to the symmetrizing driving force of the corresponding σ frames. Some frequently asked questions, that deal with the compatibility of the π-distortivity scenario with the greater body of experimental data regarding aromatic stability and π-delocalization, are addressed. Many of these questions are immediately answered, once the notion is accepted that delocalized π-systems possess a duality: their π-component is distortive and at the same time resonance stabilized relative to the localized structure with the same geometry. The notion of distortive π-electronic components of polyenes is shown to find a natural place in the wider context of a unified model of electronic delocalization that is valid for both conjugated π- and σ-electronic systems.     

Gelation of ionic liquid-based electrolytes with silica nanoparticles for quasi-solid-state dye-sensitized solar cells

For the first time silica nanoparticles were used to solidify ionic liquids. These ionic liquid-based quasi-solid-state electrolytes were successfully employed for regenerative photoelectrochemical cells that yielded 7% efficiency at AM 1.5 sunlight in combination with an amphiphilic ruthenium polypyridyl photosensitizer.     

A high molar extinction coefficient sensitizer for stable dye-sensitized solar cells

An amphiphilic heteroleptic polypyridyl ruthenium complex with a high molar extinction coefficient was synthesized and demonstrated as an efficient, thermostable sensitizer in nanocrystalline dye-sensitized solar cells.     

Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery

Natural product analogs are significant sources for therapeutic agents. To capitalize efficiently on the effective features of naturally occurring substances, a natural product-based library production platform has been devised at Aurigene for drug lead discovery. This approach combines the attractive biological and physicochemical properties of natural product scaffolds, provided by eons of natural selection, with the chemical diversity available from parallel synthetic methods. Virtual property analysis, using computational methods described here, guides the selection of a set of natural product scaffolds that are both structurally diverse and likely to have favorable pharmacokinetic properties. The experimental characterization of several in vitro ADME properties of twenty of these scaffolds, and of a small set of designed congeners based upon one scaffold, is also described. These data confirm that most of the scaffolds and the designed library members have properties favorable to their utilization for creating libraries of lead-like molecules.These authors have contributed equally to this work.     

pi bonding in second and third row molecules: testing the strength of Linus's blanket

The flexibility of valence bond (VB) theory provides a new method of calculating pi-bond energies in the double-bonded species H(m)A=BH(n), where A, B = C, N, O, Si, P, S. This new method circumvents the problems usually associated with obtaining pi-bond strengths by targeting only the pi bond, while all other factors remain constant. In this manner, a clean separation between sigma- and pi effects can be achieved which highlights some expected trends in bond strength upon moving from left to right and up and down the Periodic Table. Intra-row pi bonds conform to the classic statement by Pauling [L. Pauling, The Natiure of the Chemical Bond, Cornell University Press, Ithaca, 1960, 3rd edition] regarding the relationship of heteronuclear bond strengths to their homonuclear constituents whereas inter-row pi bonds do not. This variance with Pauling's statement is shown to be due to the constraining effect of the underlying sigma bonds which prevents optimal p(pi)-p(pi) overlap. While Pauling's statement was based on the assumption that the resonance energy (RE) would be large for heteronuclear and small for homonuclear bonds, we have found large REs for all bonds studied herein; this leads to the conclusion that REs are dependent not only on the electronegativity difference but also the electronegativity sum of the constituent atoms. This situation where the bond is neither covalent nor ionic but originates in the covalent-ionic mixing has been termed charge shift (CS) bonding [S. Shaik, P. Maitre, G. Sini, P. C. Hiberty, J. Am. Chem. Soc. 1992, 114, 7861]. We have shown that CS bonding extends beyond single sigma bonds in first row molecules, thus supporting the idea that CS-bonding is a ubiquitous bonding form.