Simon Benson

Publications (6)3.35 Total impact

• Article: XSophe-Sophe-XeprView. A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra.

  Graeme R Hanson, Kevin E Gates, Christopher J Noble, Mark Griffin, Anthony Mitchell, Simon Benson
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  ABSTRACT: The XSophe-Sophe-XeprView computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D=0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10 (-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.
  Journal of Inorganic Biochemistry 06/2004; 98(5):903-16. · 3.35 Impact Factor
• Article: XSophe: An integrated molecular approach to the analysis of continuous wave and pulsed EPR spectra from metalloprotein

  Anthony Mitchell, Christopher J. Noble, Simon Benson, Kevin E. Gates, Graeme R. Hanson
• Article: Strategies for the computer simulation of the electron paramagnetic resonance spectra of exchange coupled transition metal systems

  Christopher J. Noble, Simon Benson, Graeme R. Hanson
• Article: Molecular Sophe An Integrated Computer Simulation Software Suite for the Analysis of CW and Pulsed EPR Spectra

  Christopher J. Noble, Anthony Mitchell, Simon Benson, Graeme R. Hanson
• Article: iResonanz: An EPR Simulation Environment

  Simon Benson, Christopher J. Noble, Graeme R. Hanson
• Article: Application of CW and pulsed EPR, MoSophe and DFT calculations in unravelling the electronic structure of the molybdenum(V) centre in dimethylsulfoxide reductase

  Simon Drew, Ian Lane, Christopher J. Noble, Charles G Young, Simon Benson, Graeme R. Hanson
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  ABSTRACT: Dimethylsulfoxide reductase, a bacterial molybdenum oxotransferase, belongs to the Type-III Clade of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes and catalyses the conversion of DMSO to dimethylsulfide (DMS) with an accompanying two electron transfer. The molybdenum cofactor within DMSO reductase contains an organic component known as molybdopterin (MGD) which is a modified pterin providing an ene-dithiolene side chain responsible for ligating the Mo. The active site of the DMSO reductase contains two MGD ligands, a single oxo group and the amino acid ligand Serine in a trigonal prismatic geometry. A continuous wave (CW) EPR spectrum attributable to the Low-g Type-I Mo(V) species and a sulfur centered radical were observed upon dithionite reduction of dimethylsulfoxide reductase from the photosynthetic bacterium Rhodobacter capsulatus (Lan et al., 2007a&b), of the naturally abundant and 95Mo enriched Low-g Type-I Mo(V) CW EPR spectrum reveals that while the magnitudes of the principal components of the g and A matrices resemble the Slow Mo(V) center found in desulfo xanthine oxidase, their orientation is quite different and the largest 95Mo hyperfine component is associated with the smallest g value rather than the largest g value. The coordination sphere of the Low-g Type-I Mo(V) species consists of an an ene-dithiolene (P-MGD), Ser-147 and a protonated oxo group, which form the base of a square pyramid. In conjunction with the results obtained from a multifrequency CW EPR and density functional theory (ORCA) of a series of thiomolybdenyl complexes (Drew et al., 2007a&b), the g and triclinic A(95Mo) matrices are consistent with the unpaired electron located in a |dx2-y2> ground state molecular orbital in which the x and y axes are located between Mo-ligand bonds. In addition to the Low-g Type-I Mo(V) species, the CW EPR spectrum exhibits an orthorhombic signal (gz = 2.0545, gy = 2.0182, gx = 1.999) with small 95Mo (A2 = 5.0x10-4 cm-1) hyperfine coupling on the gy resonance. Both 3-pulse ESEEM and HYSCORE spectra revealed the presence of one or more weakly coupled protons and isotropic hyperfine coupling (Aiso(14N) = 6.7 MHz) to a single nitrogen nucleus. The CW- and pulsed-EPR results are consistent with an unpaired electron centered on sulfur atom (S1) of Q-MGD which is delocalized onto the pyranopterin ring system. These results implicate sulfur centered radicals in the stabilization of the charge on the molybdenum ion in DMSO reductase and/or electron transfer between the native electron donor DorC and the Mo center via the Q-MGD. Analysis of the continuous wave and pulsed electron paramagnetic resonance spectra and EPR potentiometric titration experiments reveal that the Mo(V) High-g Unsplit Type-2 species is the intermediate species formed during the catalytic reduction of DMSO reductase from Rhodobacter capsulatus. The spin Hamiltonian parameters for the Mo(V) High-g Unsplit Type-2 species obtained from naturally abundant and 95Mo enriched DMSO reductase reveal that the unpaired electron is present in a |dz2> ground state molecular orbital and that the geometry of the active site Mo centre is trigonal prismatic. Since the tigonal prismatic geometry of the Mo centre is retained upon reduction of the resting (Mo(VI)), to Mo(V) and Mo(IV) the active site within DMSO reductase is an example of an entatic state. The Mo(V) High-g Split species, previously proposed to be catalytically relevant in the reductive direction, has been shown to be involved in the oxidative half reaction.