Biomedical subjects

Ian R Gould

Publications and source records attributed to Ian R Gould.

17 recordsLinked to original sources

PubMed2007

Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations.

The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries.

Alcohol Dehydrogenase↗

PubMed2006

Fragmentation of 2,2,2-triphenylethoxychlorocarbene: evidence for ultrafast fragmentation-rearrangement in excited diazirines.

[reaction: see text] Photolysis of 3-(2,2,2-triphenylethoxy)-3-chlorodiazirine gives 2,2,2-triphenylethoxychlorocarbene which fragments with 1,2-phenyl migration and loss of CO and Cl(-) to yield the 1,1,2-triphenylethyl cation and thence 1,1,2-triphenylethene by proton loss. However, ps and fs laser flash photolysis provides evidence that up to 25% of the alkene product stems from carbocation that arises directly from excited diazirine rather than from the carbene.

Journal Article↗

PubMed2006

Molecular dynamics simulations of LysRS: an asymmetric state.

We report molecular dynamics simulations of the Escherichia coli Lysyl-tRNA synthetase LysU isoform carried out as a benchmark for mutant simulations in in silico protein engineering efforts. Unlike previous studies of aminoacyl-tRNA synthetases, LysU is modelled in its full dimeric form with explicit solvent. While developing a suitable simulation protocol, we observed an asymmetry that persists despite improvements to the model. This prediction has directly led to experiments that establish a functional asymmetry in nucleotide binding by LysU. The development of a simulation protocol and validation of the model are presented here. The observed asymmetry is described and the role of protein flexibility in developing the asymmetry is discussed.

Adenosine Triphosphate↗

PubMed2006

Structural characterization of the 1-butyl-3-methylimidazolium chloride ion pair using ab initio methods.

Ab initio theoretical methods are used to investigate the gas-phase ion pairs of the ionic liquid 1-butyl-3-methylimidazolium chloride. Multiple stable conformers with the chloride anion positioned (in-plane) around the imidazolium ring or above the C2-H bond are determined. The relative energy ordering of the conformers is examined at the B3LYP, MP2, and CCSD(T) levels. Zero-point energies, BSSE, and basis set effects are examined. For accurate results, correlation (dispersion) effects must be included. The most stable conformers are essentially degenerate and have the chloride H-bonding to, or lying above, the C2-H bond. Other conformers are found to lie approximately 30 and approximately 60 kJ mol(-1) higher in energy. Results are compared with those from recent simulations and experimental studies. The effect of the chloride anion on rotation of the butyl chain is investigated and found to lower some rotational barriers while enhancing others. The origin of the rotational barriers is determined. The number and type of hydrogen bonds formed between the imidazolium cation and chloride anion is found to vary significantly among conformers. No evidence of a possible intra C(alkyl)-H...pi interaction is obtained; however, hints of a Cl...pi interaction are found. The vibrational spectrum of each conformer is examined, and the origin of multiple (H-bonding) features in the vibrational spectrum of the ionic liquid explained.

Journal Article↗

PubMed2006

Glyoxylate as a backbone linkage for a prebiotic ancestor of RNA.

The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate (the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group in modern RNA. Although in low yields ( approximately 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions, provided that metal ions are present (e.g., Mg2+), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 degrees C), i.e. under "drying conditions". Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge. Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate.

Chromatography, High Pressure Liquid↗

PubMed2005

Multiplexed DNA sequencing-by-synthesis.

We report a new DNA sequencing-by-synthesis method in which the sequences of DNA templates, hybridized to a surface-immobilized array of DNA primers, are determined by sensing the number of nucleotides by which the primers in each array spot are extended in sequential DNA polymerase-catalyzed nucleotide incorporation reactions, each with a single fluorescein-labeled deoxyribonucleoside triphosphate (dNTP) species. The fluorescein label is destroyed after each readout by a photostimulated reaction with diphenyliodonium chloride. A DNA polymerase with enhanced ability to incorporate, and to extend beyond, modified nucleotides is used. Self-quenching of adjacent fluorescein labels, which impedes readout of homopolymeric runs, is avoided by diluting the labeled dNTP with unlabeled reagent. Misincorporation effects have been quantified and are small; however, low-level contamination of dNTPs with other nucleotides mimics misincorporation and can produce significant false-positive signals. These impurities are removed by polymerase-catalyzed incorporation into complementary "cleaning duplexes." Here, we demonstrate the accurate sequence readout for a small array of known DNA templates, the ability to quantify homopolymeric runs, and a short sequencing example of sections of the wild-type and mutant BRCA1 gene. For a 20,000-spot array, readout rates in excess of 6000 bases per minute are projected.

Amino Acid Sequence↗

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.

Journal Article↗

PubMed2005

A quantitative curve-crossing model for radical fragmentation.

The kinetics of bond fragmentation for a series of N-methoxypyridyl radicals are analyzed in terms of a simple curve-crossing model that includes bond stretching and bond bending coordinates. The model accurately reproduces the reaction surfaces calculated using density functional theory (DFT) and also the experimental reaction energy barriers. The reactions proceed on the ground state surface by avoidance of a conical intersection, which is clearly illustrated by the model. A value for the electronic coupling matrix element responsible for splitting the upper and lower surfaces of 0.9 eV is obtained. The model illustrates the molecular features that allow barrierless fragmentation from a formally pi radical.

Journal Article↗

PubMed2005

Effect of adiabaticity on electron dynamics in zinc myoglobin.

Electron-vibration coupling in zinc substituted myoglobin has been calculated using a quantum mechanical/molecular mechanical method. The methodology has been tested by a direct comparison of the calculated optical observables, the steady-state optical spectra and three-pulse-photon-echo-peak-shift (3PEPS) function, to those experimentally measured showing a qualitative agreement. A range of experiments and calculations were performed to explain the discrepancies, which lead to the conclusion that the discrepancy originates from adiabatic coupling of the two nearly degenerate electronic transitions.

Animals↗

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.

Journal Article↗

PubMedDate not supplied

Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

Amines↗