Biomedical subjects

Ian R Gould

Publications and source records attributed to Ian R Gould.

8 recordsLinked to original sources

PubMed2005

Efficient unimolecular deprotonation of aniline radical cations.

[reaction: see text] Deprotonation of the radical cations of aromatic amines, such as anilines, generally occurs much more slowly than other fragmentation reactions. Here we report a stereoelectronic effect involving twisting of the anilino group out of the plane of the benzene ring that results in a significantly increased rate of reactivity toward deprotonation. Quantitative studies of the rate constants for deprotonation as a function of aniline radical cation pKa (Brønsted plots) demonstrate that the effect is not simply due to a change in the reaction thermodynamics. By combining this stereoelectronic effect with covalent attachment of carboxylate as a base, aniline radical cations that undergo unimolecular deprotonation with rate constants as high as 10(8) s(-1), even in unfavorable protic media, are described.

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PubMed2005

Density functional theory predicts the barriers for radical fragmentation in solution.

[reaction: see text] N-Methoxypyridyl radicals formed by one-electron reduction of the corresponding cationic heterocycles undergo N-O bond cleavage. Experimental activation free energies for a series of these bond fragmentations are compared to corresponding barriers determined from electronic structure calculations. The DFT barriers agree well with those from experiment, being smaller than the latter values by an average value of ca. 1 kcal/mol, for rate constants varying over almost 3 orders of magnitude, or within ca. 3 kcal/mol over 8 orders of magnitude of rate constant. For a model compound, the B3PW91/6-31+G hybrid density functional method is also found to be in good agreement with the MCSCF-MRMP2 method. One of the reactions is found by DFT to have no minimum for the reactant radical, consistent with a truly barrierless reaction.

Journal Article↗

PubMed2005

A combined QM and MM investigation into guanine quadruplexes.

This paper reports on the application of quantum mechanical (QM) energy calculations, QM optimisations and MD simulations to explore the stability of a human telomeric guanine quadruplex, containing potassium and sodium cations. G-quadruplexes are of great biological interest as it has been suggested that they offer a novel path to cancer inhibition. By understanding the stability and geometry of these DNA features gives us the ability to design ligands which can bind and stabilise the G-quadruplex. There are significant structural differences between the potassium containing crystal structure of human telomeric G-quadruplex and the sodium containing NMR structure; in this paper, we investigate the energetics and dynamics of the potassium derived crystal structure and a model for the sodium containing structure. QM investigations upon the 12 G-quadruplex core, extracted from the human potassium quadruplex crystal structure, indicate that replacement of the potassium cations with sodium yields an energetically more favourable structure. However, attempts to geometry optimise both structures at the QM level proved unsuccessful, the structure of the partially optimised potassium containing G-quadruplex retains significant structural integrity with respect to the original crystal structure, whilst the sodium containing G-quadruplex shows significant structural distortion. QM investigation of the 12 G-quadruplex core containing no cations unsurprisingly yields a highly unfavourable energetic structure. MD simulations on the complete quadruplex structure, containing potassium cations, yields a remarkably stable structure after 4ns of simulation, the most significant deviation from the original crystal structure being the loss of the capping potassium cation from the structure. MD simulation of the sodium containing quadruplex for 4ns show significant structural reorganisation compared with the original potassium containing crystal structure.

Crystallization↗

PubMed2004

Barrierless electron transfer bond fragmentation reactions.

The ultrafast N-O bond fragmentation in a series of N-methoxypyridyl radicals, formed by one-electron reduction of the corresponding N-methoxypyridiniums, has been investigated as potentially barrierless electron-transfer-initiated chemical reactions. A model for the reaction involving the electronic and geometric factors that control the shape of the potential energy surface for the reaction is described. On the basis of this model, molecular structural features appropriate for ultrafast reactivity are proposed. Femtosecond kinetic measurements on these reactions are consistent with a kinetic definition of an essentially barrierless reaction, i.e., that the lifetime of the radical is a few vibrational periods of the fragmenting bond, for the p-methoxy-N-methoxypyridyl radical.

Journal Article↗

PubMed2003

Selective solid state photooxidant.

Irradiation of biphenyl encapsulated in the cavities of a NaZSM-5 zeolite framework has been reported to result in the formation of an extremely long-lived radical cation. Here, we show that such zeolite encapsulated radical cations can act as irreversible one-electron oxidants for simple alkenes and dienes, in a solid-state analogue to solution-phase cosensitization. Compared to the well-known semiconductor photooxidizers, such as titanium dioxide, the NaZSM-5 zeolite-based solid photooxidants exhibit enhanced selectivity based on oxidation potential, molecular size and shape, and Lewis base character.

Journal Article↗

PubMed2003

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment.

BACKGROUND: Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. RESULTS: Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. CONCLUSIONS: The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-tRNA synthetases, and may play an important functional role. We suggest a manner in which catalytic efficiency could be improved by LysU operating in an alternating sites mechanism.

Adenosine Triphosphate↗

PubMed2003

Associative return electron transfer. A bond-coupled electron transfer in the photoreactions of cyclopropylamines.

The dynamics of the geminate radical-ion pairs formed by electron transfer to the excited states of cyanoanthracenes from 2-phenylcyclopropylamines are dominated by exothermic bond cleavage of the amine radical cations. Quantitative studies of product formation as a function of the energetics of the photochemical and corresponding thermal reactions provide support for a novel mechanism in which return electron transfer in the geminate pair occurs in concert with bond formation from the ring-opened radical cations. This bond-coupled electron transfer process is referred to as an associative return electron transfer reaction. The important features of the associative electron transfer process that explain the experimental observations are described in terms of potential energy surfaces and competition between adiabatic and non-adiabatic deactivation paths.

Journal Article↗

PubMed2002

Kinetics of reductive N-O bond fragmentation: the role of a conical intersection.

N-alkoxyheterocycles can act as powerful one-electron acceptors in photochemical electron-transfer reactions. One-electron reduction of these species results in formation of a radical that undergoes N-O bond fragmentation to form an alkoxy radical and a neutral heterocycle. The kinetics of this N-O bond fragmentation reaction have been determined for a series of radicals with varying substituents and extents of delocalization. Rate constants varying over 7 orders of magnitude are obtained. A reaction potential energy surface is described that involves avoidance of a conical intersection. A molecular basis for the variation of the reaction rate constant with radical structure is given in terms of the relationship between the energies of the important molecular orbitals and the reaction potential energy surface. Ab initio and density functional electronic structure calculations provide support for the proposed reaction energy surface.

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