Abstract
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.
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References
Pilbrow JR (1990) Transition ion electron paramagnetic resonance. Clarendon, Oxford
Mabbs FE, Collison DC (1992) Electron paramagnetic resonance of transition metal compounds. Elsevier, Amsterdam
Basosi R, Antholine WE, Hyde JS (1993) Multifrequency ESR of copper biophysical applications. In: Berliner LJ, Reuben J (eds) Biological magnetic resonance, vol 13. Plenum Press, New York
Moebius K, Savitsky A (2008) High field EPR spectroscopy of proteins and their model systems: characterization of transient paramagnetic states. Royal Society of Chemistry, Cambridge
Misra S (2011) Multifrequency electron paramagnetic resonance: theory and applications. Wiley-VCH, Weinheim
Sarker B (2005) Electrochemistry spectroelectrochemistry and multifrequency EPR of dinuclear transition metal complexes containing nitrogen-rich bridging ligands. Logos, Berlin
Grinberg O, Berliner LJ (eds) (2004) Very high frequency (VHF) ESR/EPR in biological magnetic resonance, vol 22. Kluwer Academic/Plenum, New York
Hanson GR, Brunette AA, McDonell AC, Murray KS, Wedd AG (1981) Electronic properties of thiolate compounds of oxomolybdenum (V) and their tungsten and selenium analogues. Effects of 17-O, 98-Mo and 95-Mo isotope substitution upon ESR spectra. J Am Chem Soc 103:1953–1959
Lebedev YS (1994) Very-high-field EPR and its applications. Appl Magn Reson 7:339–369
Brunel LC (1996) Recent developments in high frequency/high magnetic field CW EPR. Applications in chemistry and biology. Appl Magn Reson 11:417–423
Reijerse EJ, VanDam PJ, Klaassen AAK, Hagen WR, VanBentum PJM, Smith GM (1998) Concepts in high-frequency EPR—applications to bio-inorganic systems. Appl Magn Reson 14:153–167
Schweiger A, Jeschke G (2001) Principles of pulse electron paramagnetic resonance. Oxford University Press, Oxford
(a) Kaess H, Rautter J, Zweygart W, Struck A, Scheer H, Lubitz W (1994) EPR, ENDOR, and TRIPLE resonance studies of modified bacteriochlorophyll cation radicals. J Phys Chem 98:354–363; (b) Kaess H, Rautter J, Boenigk B, Hoefer P, Lubitz W (1995) 2D ESEEM of the 15N-Labeled radical cations of bacteriochlorophyll a and of the primary donor in reaction centers of rhodobacter sphaeroides. J Phys Chem 99:436–448; (c) Lendzian F, Huber M, Isaacson RA, Endeward B, Plato M, Bonigk B, Mobius K, Lubitz W, Feher G (1993) The electronic structure of the primary donor cation radical in rhodobacter sphaeroides R-26: ENDOR and TRIPLE resonance studies in single crystals of reaction centers. Biochim Biophys Acta 1183:139–160; (d) Käβ H, Bittersmann-Weidlich E, Andréasson L-E, Bönigk B, Lubitz W (1995) ENDOR and ESEEM of the 15N labelled radical cations of chlorophyll a and the primary donor P700 in photosystem I. Chem Phys 194:419–432
Thomann H, Bernardo M (2007) Electron–nuclear multiple resonance spectroscopy. Encyclopedia of magnetic resonance. Wiley, pp 1–17.onlinelibrary.wiley.com/doi/10.1002/9780470034590.emrstm0153/full
Feher G (1956) Observation of nuclear magnetic resonances via the electron spin resonance line. Phys Rev 103:834–835
Kevan L, Kispert LD (eds) (1979) Electron spin double resonance spectroscopy. Wiley-Interscience, New York
Dorio MM, Freed JH (eds) (1979) Multiple electron spectroscopy. Plenum Press, New York
Abragam A, Bleaney B (1970) Electron paramagnetic resonance of transition ions. Clarendon, Oxford
Bencini A, Gatteschi D (1990) EPR of exchange coupled systems. Springer, Berlin
Smith TD, Pilbrow JR (1974) The determination of structural properties of dimeric transition metal ion complexes from EPR spectra. Coord Chem Rev 13:173–278
Taylor PC, Baugher JF, Kriz HM (1975) Magnetic resonance spectra in polycrystalline solids. Chem Rev 75:203–240
Swalen JD, Gladney HM (1964) Computer analysis of electron paramagnetic resonance spectra. IBM J Res Dev 8:515–526
Swalen JD, Lusebrink TRL, Ziessow D (1973) Computer applications in magnetic resonance. Magn Reson Rev 2:165–184
Vancamp HL, Heiss AH (1981) Computer applications in electron paramagnetic resonance. Magn Reson Rev 7:1–40
Gaffney BJ, Silverstone HJ (1993) Simulation of the EMR spectra of the high-spin iron in proteins. In: Berliner LJ, Reuben J (eds) Biological magnetic resonance. Plenum Press, New York, pp 1–101
Brumby S (1980) Numerical analysis of EPR spectra. 3. Iterative least-squares analysis of significance plots. J Magn Reson 39:1–9
Brumby S (1980) Numerical analysis of EPR spectra. 4. Spectra of 1- and 2-methylnaphthalene anions. J Magn Reson 40:157–165
Wang D, Hanson GR (1996) New methodologies for computer simulation of paramagnetic resonance spectra. Appl Magn Reson 11:401–415
Hanson GR, Gates KE, Noble CJ, Mitchell A, Benson S, Griffin M, Burrage K (2003) XSophe - Sophe - XeprView a computer simulation software suite for the analysis of continuous wave EPR spectra. In: Shiotani M, Lund A (eds) EPR of free radicals in solids: trends in methods and applications. Kluwer Press, Dordrecht, pp 197–237
Hanson GR, Gates KE, Noble CJ, Griffin M, Mitchell A, Benson S (2004) XSophe-Sophe-XeprView. A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra. J Inorg Biochem 98:903–916
Griffin M, Muys A, Noble C, Wang D, Eldershaw C, Gates KE, Burrage K, Hanson GR (1999) XSophe, a computer simulation software suite for the analysis of electron paramagnetic resonance spectra. Mol Phys Rep 26:60–84
Heichel M, Höfer P, Kamlowski A, Griffin M, Muys A, Noble C, Wang D, Hanson GR, Eldershaw C, Gates KE, Burrage K (2000) XSophe-Sophe-XeprView Bruker’s professional CW-EPR simulation suite. Bruker Rep 148:6–9
Hanson GR (2005) XSophe release notes, 1.1.4.1. Bruker Biospin, Germany, pp 1–79. www.cai.uq.edu.au/epr/simulation/XSophe
Stoll S, Schweiger A (2006) EasySpin, a comprehensive software package for spectral simulation and analysis in EPR. J Magn Reson 178:42–55
Hanson GR, Noble CJ, Benson S (2009) Molecular Sophe, an integrated approach to the structural characterization of metalloproteins, the next generation of computer simulation software in high resolution EPR: applications to metalloenzymes and metals in medicine. In Hanson GR, Berliner LJ (eds) Biol Magn Reson 28:105–173
(a) Berliner LJ, Eaton SS, Eaton GR (eds) (2001) Distance measurements in biological systems by EPR. Biological magnetic resonance, vol 19. Kluwer Academic Press, New York; (b) Jeschke G, Pannier M, Spiess HW (2001) Double electron-electron resonance methodical advances and application to disordered systems, pp 493–512, ibid
Wang D, Hanson GR (1995) A new method for simulating randomly oriented powder spectra in magnetic resonance: the Sydney Opera House(SOPHE) method. J Magn Reson A 117:1–8
Hanson GR, Noble CJ, Benson S (2010) Molecular Sophe. An integrated computer simulation software suite for the analysis of CW and pulsed EPR spectra user manual v 2.1.6, pp 1–152. www.cai.uq.edu.au/epr/simulation/MoSophe
(a) Schenk G, Boutchard CL, Carrington LE, Noble CJ, Moubaraki B, de Jersey BJ, Hanson GR, Hamilton S (2001) A purple acid phosphatase from sweet potato contains an antiferromagnetically coupled binuclear Fe-Mn center. J Biol Chem 276:19084–19088; (b) Mitić N, Noble CJ, Gahan LR, Hanson GR, Schenk G (2009) Metal ion mutagenesis – conversion of a purple acid phosphatase from sweet potato to a neutral phosphatase with the formation of an unprecedented catalytically competent MnIIMnIIactive site. J Am Chem Soc 131:8173–8179
Yoon J, Mirica LM, Stack TD, Solomon EI (2004) Spectroscopic demonstration of a large antisymmetric exchange contribution to the spin-frustrated ground state of a D3 symmetric hydroxy-bridged trinuclear Cu(II) complex: ground-to-excited state superexchange pathways. J Am Chem Soc 126:12586–12595
Atanasov M, Comba P, Hanson GR, Hausberg S, Helmle S, Wadepohl H (2011) Cyano-bridged homodinuclear copper(II) complexes. Inorg Chem 50:6890–6901
Jeener J (1982) Superoperators in magnetic resonance. Adv Magn Reson 10:1–51
Hofer P (1994) Distortion-free electron-spin-echo envelope-modulation spectra of disordered solids obtained from two-dimensional and three-dimensional HYSCORE experiments. J Magn Reson A 111:77–86
Pilbrow JR (1984) Lineshapes in frequency-swept and field-swept epr for spin 1/2*. J Magn Reson 58:186–203
(a) Sinclair GR (1988) Modelling strain broadened EPR spectra. PhD thesis, Monash University, Victoria, Australia; (b) Pilbrow JR, Sinclair GR, Hutton DR, Troup GJ (1983) Asymmetric lines in field-swept EPR: Cr3+looping transitions in ruby. J Magn Reson 52:386–399
Gates KE, Griffin M, Hanson GR, Burrage K (1998) Computer simulation of magnetic resonance spectra employing homotopy. J Magn Reson 135:104–112
Griffin M (2002) The computer simulation of electron paramagnetic resonance spectra employing homotopy. PhD thesis, The University of Queensland, Queensland, Australia
(a) Belford RL, Nilges MJ (1979) EPR symposium 21st Rocky mountain conference, Denver, CO; (b) Maurice AM (1980) Acquisition of anisotropic information by computational analysis of isotropic EPR spectra. PhD thesis, University of Illinois, Urbana, IL; (c) Nilges MJ (1979) Electron paramagnetic resonance studies of low symmetry nickel(I) and molybdenum(V) complexes. PhD thesis, University of Illinois, Urbana, IL
Alderman DW, Solum MS, Grant DM (1986) Methods for analyzing spectroscopic line shapes. NMR solid powder patterns. J Chem Phys 84:3717–3725
Mombourquette MJ, Weil JA (1992) Simulation of magnetic resonance powder spectra. J Magn Reson 99:37–44
Craciun C (2010) Application of the SCVT orientation grid to the simulation of CW EPR powder spectra. Appl Magn Reson 38:279–293
Gribnau MCM, van Tits JLC, Reijerse EJ (1990) An efficient general algorithm for the simulation of magnetic resonance spectra of orientationally disordered solids. J Magn Reson 90:474–485
van Veen G (1969) Simulation and analysis of EPR spectra of paramagnetic ions in powders. J Magn Reson 38:91–109
Nettar D, Villafranca NI (1985) A program for EPR powder spectra simulation. J Magn Reson 64:61–65
Scullane MI, White LK, Chasteen ND (1982) An efficient approach to computer simulation of EPR spectra of high-spin Fe(III) in rhombic ligand fields. J Magn Reson 47:383–397
McGavin DG, Mombourquette MJ, Weil JA (1993) EPR ENDOR user’s manual. University of Saskatchewan, Saskatchewan
Belford GG, Belford RL, Burkhalter JF (1973) Eigenfields: a practical direct calculation of resonance fields and intensities for field-swept fixed-frequency spectrometers. J Magn Reson 11:251–265
Su BQ, Liu DY (1989) Computational geometry – curves and surface modelling. Academic, Singapore
Shaltiel D, Low W (1961) Anisotropic broadening of linewidth in the paramagnetic resonance spectra of magnetically dilute crystals. Phys Rev 124:1062–1067
(a) Kivelson D, (1960) Theory of ESR linewidths of free radicals. J Chem Phys 33:1094–1106; (b) Wilson R, Kivelson D (1966) ESR linewidths in solution. I. Experiments on anisotropic and spin—rotational effects. J Chem Phys 44:154–168; (c) Wilson R, Kivelson D (1966) ESR linewidths in solution. III. Experimental study of the solvent dependence of anisotropic and spin—rotational effects. J Chem Phys 44:4440–4444; (d) Atkins PW, Kivelson D (1966) ESR linewidths in solution. II. Analysis of spin—rotational relaxation data. J Chem Phys 44:169–174
(a) Froncisz W, Hyde JS (1980) Broadening by strains of lines in the g‐parallel region of Cu2+EPR spectra. J Chem Phys 73:3123–3131; (b) Hyde JS, Froncisz W (1982) The role of microwave frequency in EPR spectroscopy of copper complexes. Ann Rev Biophys Bioeng 11:391–417
(a) Drew SC, Hill JP, Lane I, Hanson GR, Gable RW, Young CG (2007) Synthesis, structural characterization and multifrequency electron paramagnetic resonance studies of mononuclear thiomolybdenyl complexes. Inorg Chem 46:2373–2387; (b) Drew SC, Young CG, Hanson GR (2007) A density functional study of the electronic structure and spin Hamiltonian parameters of mononuclear thiomolybdenyl complexes. Inorg Chem 46:2388–2397
Sproules S, Banerjee P, Weyhermüller T, Yan Y, Donahue JP, Wieghardt K (2011) Monoanionic molybdenum and tungsten tris(dithiolene) complexes: a multifrequency EPR study. Inorg Chem 50:7106–7122
(a) Wilson GL, Greenwood RJ, Pilbrow JR, Spence JT, Wedd AG (1991) Molybdenum(V) sites in xanthine oxidase and relevant analog complexes: comparison of molybdenum-95 and sulfur-33 hyperfine coupling. J Am Chem Soc 113:6803–6812; (b) Greenwood RJ, Wilson GL, Pilbrow JR, Wedd AG (1993) Molybdenum(V) sites in xanthine oxidase and relevant analog complexes: comparison of oxygen-17 hyperfine coupling. J Am Chem Soc 115:5385–5392
(a) Oliver SW, Smith TD, Hanson GR, Lahey N, Pilbrow JR, Sinclair GR (1987) Electron spin resonance study of the copper (II) and cobalt (II) chelates of 2,3;7,8;12,13;17,18-tetrakis-(9,10-dihydroanthracene-9,10-diyl)porphyrazine. J Chem Soc Faraday Trans 1(84):1475–1489; (b) Nielsen P, Toftlund H, Bond AD, Boas JF, Pilbrow JR, Hanson GR, Noble CJ, Riley MJ, Neville SM, Moubaraki B, Murray KS (2009) Systematic study of spin crossover and structure in [Co(terpyRX)2](Y)2systems, (terpyRX = 4′-alkoxy-2,2′:6′,2″-terpyridine, X = 4, 8, 12, Y = BF −4 , ClO −4 , PF −6 , BPh −4 ). Inorg Chem 48:7033–7047
Antholine WE, Bennett B, Hanson GR (2011) Copper coordination environments. In: Misra SK (ed) Mutltifrequency electron paramagnetic resonance. Wiley-VCH/Verlag/GmbH, Berlin, pp 647–718
Wenzel RF, Kim YW (1965) Linewidth of the electron paramagnetic resonance of (Al2O3)1-x(Cr2O3)x. Phys Rev 140:A1592–A1598
(a) Comba P, Dovalil N, Haberhauer G, Hanson GR, Kato Y, Taura T (2010) Complex formation and stability of westiellamide derivatives with copper(II). J Biol Inorg Chem 15:1129–1135; (b) Comba P, Dovalil N, Hanson GR, Linti G (2011) Synthesis and CuII coordination chemistry of a patellamide derivative – consequences of the change from the natural thiazole/oxazoline to the artificial imidazole heterocycles. Inorg Chem 50:5165–5174; (c) Comba P, Dovalil N, Gahan LR, Haberhauer G, Hanson GR, Noble CJ, Seibold B, Vadivelu P (2012) CuIIcoordination chemistry of patellamide derivatives. Possible biological functions of cyclic pseudo-peptides. Chem Eur J 18:2578--2590
(a) Misra SK (1976) Evaluation of spin-Hamiltonian parameters from EPR data by the method of least-squares fitting. J Magn Reson 23:403–410; (b) Misra SK (1986) Evaluation of spin Hamiltonian parameters from ESR data of single crystals. Mag Reson Rev 10:285–331; (c) Misra SK (1983) Evaluated of spin Hamiltonian parameters of electron-nuclear spin-coupled systems from EPR data by the method of least-squares fitting. Physica 121B:193–201; (d) Misra SK, Subramanian S (1982) Calculation of parameter errors in the analysis of electron paramagnetic resonance data. J Phys C 15:7199–7207
Spin Hamiltonian parameters are constrained to a portion of P-space as this will prevent the generation of a NULL spectrum
Hooke R, Jeeves TA (1961) ‘Direct search’ solution of numerical and statistical problems. J Assoc Comput Mach 8:212–229
Spendley W, Hext GR, Himsworth FR (1962) Sequential application of simplex designs in optimisation and evolutionary operation. Technometrics 4:441–461
(a) Nicholson DM, Chowdhary A, Schwartz L (1984) Monte Carlo optimization of pair distribution functions: application to the electronic structure of disordered metals. Phys Rev B 29:1633–1637; (b) Bohachevsky IO, Johnson ME, Myron LS (1986) Generalized simulated annealing for function optimization. Technometrics 28:209–217; (c) Corana A, Marchesi M, Martini C, Ridella S (1987) Minimizing multimodal functions of continuous variables with the “simulated annealing” algorithm. ACM Trans Math Software 13:262–280; (d) Heynderickx H, De Raedt H, Schoemaker D (1986) Simulated anneal method for the determination of spin Hamiltonian parameters from ESR data. J Magn Reson 70:134–139
Basosi R, Della Lunga G, Pogni R (1996) Resolution enhancement of nitrogen hyperfine patterns in the EPR spectra of Cu(II) complexes: FT analysis of Cu(II)(His-Gly)2. Appl Magn Reson 11:437–442
Noble CJ, Hanson GR (2011) Personal communication
Micallef A, Hanson GR (2011) Personal communication
Acknowledgments
We would like to thank past members of the Sophe group, including Dr. Kevin Gates, Dr. Mark Griffin, Dr. Anthony Mitchell, Andrae Muys, Dr. Deming Wang for their contributions to the computer simulation software suites described herein.
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Hanson, G.R., Noble, C.J., Benson, S. (2013). XSophe – Sophe – XeprView and Molecular Sophe: Computer Simulation Software Suites for the Analysis of Continuous Wave and Pulsed EPR and ENDOR Spectra. In: Lund, A., Shiotani, M. (eds) EPR of Free Radicals in Solids I. Progress in Theoretical Chemistry and Physics, vol 24. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4893-4_5
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