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Biomedical subjects

Noel M O'Boyle

Publications and source records attributed to Noel M O'Boyle.

8 recordsLinked to original sources

A density functional theory study of the electronic properties of Os(II) and Os(III) complexes immobilized on Au(111).

We present a density functional theory (DFT) study of an osmium polypyridyl complex adsorbed on Au(111). The osmium polypyridyl complex [Os(bpy)2(P0P)Cl]n+ [bpy is 2,2'-bipyridine, P0P is 4,4'-bipyridine, n = 1 for osmium(II), and n = 2 for osmium(III)] is bound to the surface through the free nitrogen of the P0P ligand. The calculations illuminate electronic properties relevant to recent comprehensive characterization of this class of osmium complexes by electrochemistry and electrochemical scanning tunneling microscopy. The optimized structures for the compounds are in close agreement with crystallographic structures reported in the literature. Oxidation of the complex has little effect on these structural features, but there is a substantial reordering of the electronic energy levels with corresponding changes in the electron density. Significantly, the highest occupied molecular orbital shifts from the metal center to the P0P ligand. The surface is modeled by a cluster of 28 gold atoms and gives a good description of the effect of immobilization on the electronic properties of the complexes. The results show that the coupling between the immobilized complex and the gold surface involves electronic polarization at the adsorbate/substrate interface rather than the formation of a covalent bond. However, the cluster is too small to fully represent bulk gold with the result that, contrary to what is experimentally observed, the DFT calculation predicts that the gold surface is more easily oxidized than the osmium(II) complex.

Algorithms↗

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

Catalysis↗

PYCHEM: a multivariate analysis package for python.

UNLABELLED: We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. AVAILABILITY: http://sourceforge.net/projects/pychem

Algorithms↗

MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.

Catalysis↗

Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems.

Rational design of supramolecular systems for application in photonic devices requires a clear understanding of both the mechanism of energy and electron transfer processes and how these processes can be manipulated. Central to achieving these goals is a detailed picture of their electronic structure and of the interaction between the constituent components. We review several approaches that have been taken towards gaining such understanding, with particular focus on the physical techniques employed. In the discussion, case studies are introduced to illustrate the key issues under consideration.

Chemical Phenomena↗

Ground- and excited-state electronic structure of an emissive pyrazine-bridged ruthenium(II) dinuclear complex.

The synthesis, characterization, and electrochemical, photophysical, and photochemical properties of the binuclear compounds [(Ru(H8-bpy)2)2((Metr)2Pz)](PF6)2 (1) and [(Ru(D8-bpy)2)2((Metr)2Pz)](PF6)2 (2), where bpy is 2,2'-bipyridine and H2(Metr)2Pz is the planar ligand 2,5-bis(5'-methyl-4'H-[1,2,4]triaz-3'-yl)pyrazine, are reported. Electrochemical and spectro-electrochemical investigations indicate that the ground-state interaction between each metal center is predominantly electrostatic and in the mixed-valence form only a low level of ground-state delocalization is present. Resonance Raman, transient, and time-resolved spectroscopies enable a detailed assignment to be made of the excited-state photophysical properties of the complexes. Deuteriation is employed to both facilitate spectroscopic characterization and investigate the nature of the lowest excited states.

Journal Article↗

Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes.

The synthesis and characterisation of [Ru(bipy)(2)(L1)](2+) and the homodinuclear complexes [M(bipy)(2)(L1)M(bipy)(2)](4+)(where M = Ru or Os), employing the ditopic ligand, 1,4-phenylene-bis(1-pyridin-2-ylimidazo[1,5-a]pyridine)(L1), are reported. The complexes are identified by elemental analysis, UV/Vis, emission, resonance Raman, transient resonance Raman and (1)H NMR spectroscopy, mass spectrometry and electrochemistry. The X-ray structure of the complex [Ru(bipy)(2)(L1)(bipy)(2)Ru](PF(6))(4) is also reported. DFT calculations, carried out to model the electronic properties of the compounds, are in good agreement with experiment. Minimal communication between the metal centres is observed. The low level of ground state electronic interaction is rationalized in terms of the poor ability of the phenyl spacer in facilitating superexchange interactions. Using the electronic and electrochemical data a detailed picture of the electronic properties of the RuRu compound is presented.

Journal Article↗

Synthesis and characterisation of ruthenium complexes containing a pendent catechol ring.

A series of [Ru(bipy)2L]+ and [Ru(phen)2L]+ complexes where L is 2-[5-(3,4-dimethoxyphenyl)-4H-1,2,4-triazol-3-yl]pyridine (HL1) and 4-(5-pyridin-2-yl-4H-1,2,4-triazol-3-yl)benzene-1,2-diol (HL2) are reported. The compounds obtained have been characterised using X-ray crystallography, NMR, UV/Vis and emission spectroscopies. Partial deuteriation is used to determine the nature of the emitting state and to simplify the NMR spectra. The acid-base properties of the compounds are also investigated. The electronic structures of [Ru(bipy)2L1]+ and Ru(bipy)2HL1]2+ are examined using ZINDO. Electro and spectroelectrochemical studies on [Ru(bipy)2(L2)]+ suggest that proton transfer between the catechol and triazole moieties on L2 takes place upon oxidation of the L2 ligand.

Catechols↗