S. Benson

Molecular Sophe: An Integrated Approach to the Structural Characterization of Metalloproteins: The Next Generation of Computer Simulation Software

Herein we describe an integrated approach — Molecular Sophe — for determination of the molecular structure of redox active cofactors in metalloproteins from an analysis of their high-resolution EPR spectra. Molecular Sophe involves the computer simulation of continuous-wave and orientation-selective pulsed EPR and electron nuclear double resonance(ENDOR) spectra. As aids to the correct analysis of these spectra, calculation of energy level diagrams, transition roadmaps, and transition surfaces can also be performed. This approach, based on molecularstructure, promises to revolutionize the three-dimensional molecular (geometric and electronic) characterization of paramagnetic materials using a combination of high-resolution EPR spectroscopy and quantum chemistry calculations.

XSophe — Sophe — XeprView

The XSophe-Sophe-XeprView computer simulation software suite provides scientists with an easy-to-use research tool for the analysis of isotropic, randomly orientated and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra. XSophe provides an X Windows graphical user interface to the Sophe programme allowing; the creation of multiple input files, the local and remote execution of Sophe and display of Sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme with a number of innovative technologies including; the Sophe partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation line width model, parallelisation (OpcnMP — for SGI computers running the lrix operating system) and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. The output of CW EPR spectra (1D and 2D) from the Sophe programme can be visualised in conjunction with the experimental spectrum in XeprView or Xepr. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly orientated EPR spectra and can he viewed with a netscape browser and an OpenInventor scene graph viewer.

XSophe – Sophe – XeprView and Molecular Sophe: Computer Simulation Software Suites for the Analysis of Continuous Wave and Pulsed EPR and ENDOR Spectra

Herein we provide a description of the XSophe-Sophe-XeprView and Molecular Sophe computer simulation software suites for the analysis of continuous wave (CW) and pulsed EPR spectra. While the XSophe-Sophe-XeprView computer simulation software suite employs a traditional structural approach through calculation of the spin Hamiltonian parameters which are then compared with other compounds or parameters obtained from computational chemistry calculations, Molecular Sophe utlizes an integrated molecular structure approach. Both computer simulation suites are completely general, employ matrix diagonalization, the mosaic misorientation linewidth model and provide additional tools (calculation of energy level diagrams, transition roadmaps and transition surfaces) aiding scientists in their analysis of complex CW or pulsed EPR spectra. Molecular Sophe enables the computer simulation of continuous wave and orientation selective pulsed EPR and electron nuclear double resonance (ENDOR) spectra. The molecular structure approach employed within Molecular Sophe, promises to revolutionize the 3-dimensional molecular (geometric and electronic) characterization of paramagnetic species using a combination of high resolution EPR spectroscopy and quantum chemistry calculations.