Current Version: SpecDis v1.53

SpecDis is a small tool to process the results of quantum-chemical CD or UV calculations. It supports diverse software packages like ORCA, Gaussian03, Gaussian09, Turbomole (escf, ricc2),  or Grimme´s DFT/MRCI software package.

SpecDis can visualize the computational results and has several possibilities to further process the spectra. Some of the features of SpecDis are:

• compare calculated CD or UV spectra directly with experimental data (up to 5 curves)
• Gauss and Lorentz curve generation
• provide an enantiomeric CD spectrum
• applying a "UV shift"
• arithmetic or Boltzmann weighted summation of spectra
• determining a similarity factor
• plot spectra with gnuplot in a "what you see is what you get" manner
• export spectral curves as *.xy files that can be processed with other software like Excel or Origin
• plot UV and CD traces of HPLC runs
• automatic extraction of heats of formation and spectral data from output files
• preliminary handling of ORD calculations with gaussian03
• Boltzmann weighting of ORD values

 

Acknowledgments:

We are grateful to Dr. Pescitelli (University of Pisa; Italy) for helpfull discussions and beta testing of SpecDis.

 

System Requirements

SpecDis is tested under Windows 2000, XP SP3, Vista SP1, and Windows 7 SP1. For Windows Vista and Windows 7 Specdis has to be installed on a partioned disk other than c:\, otherwise one might get administrator-right problems.

The Interface to Gnuplot is tested up to version 4.4

 

Screenshot of SpecDis.

Major changes since version 1.51

• removed several bugs in the drawing routine of bar spectra, sometimes bar spectra were mirrored or values were much to large, now everything should be drawn correctly.
• removed a bug in reading of ricc2-files: if all rotational strength values found in the file were zero, SpecDis gave an error message, this has been corrected
• the newer versions of ORCA (2.8 rev 2360 and later) give rotational strength values from mrci calculations in sgs units, the loading routine has been recoded so that SpecDis recognizes whether the values have to be converted or not
• Extraction of heats from Gaussian files extended to B97D and CAM-B3LYP calculations
• XY-Curves (Menus CD and UV spectrum) will now be saved only in the nm ranges that are specified in SpecDis, the nm stepsize is given (and changeable) in the settings 
• removed a color bug that sometimes appeared when comparing with experimental CD spectra (the labeling had colors different to black)
• removed a bug that occured when reading g09 files: If g09 gives the error message 'Excited state symmetry could not be determined.' SpecDis was unable to read the log-files
• removed a bug that occured when reading g09 files: If g09 does not give the message
  'This state for optimization and/or second-order correction.
   Copying the excited state density for this state as the 1-particle RhoCI density.'
  SpecDis was unable to read the log-files

Major changes since version 1.50

• solved some issues with Windows 7 and Windows Vista, SpecDis should now work properly
• solved a problem with Gaussian09-Rev-B.01 files
• now up to five chromatograms or CD/UV spectra can be compared
• *.log and *.out files can be loaded directly as second (third, forth, fifth) spectrum
• rotational strength values from the ORCA mrci_module will be converted from a.u. to 10-40*sgs units automatically
• changed the file format of plotted chromatograms from ps to eps
• chromatogram plots are no longer in landscape but in portrait format
• added the possibility to plot 3D chromatograms with gnuplot (UV traces only)
• possibility to use different shifts for calculated spectra has been added (tools --> multi shift)

Major changes since version 1.45

• changed the range of the displayed spectra to 100-1100nm
• added support for Gaussian09 files
• added support for Turbomole ricc2 files 
• results of g03 calculations no longer need the #P keyword
• UV, CD and ORD spectra can be plotted as png
• replaced the 'non-relative units' checkbox by 'auto scaling'
• improved the 'extract spectra' tool, the routine will now also look for escf, ricc2, and g09 files
• substantially improved the plotting routines
• drag & drop with HPLC-data works now correctly
• calculation of Lorentzian or Gauss curves for UV spectra corrected (sometimes absolute values were too high)
• ... and several more minor bugs have been removed
  
  

Download

You can freely download this software, but if you use it for publications please cite SpecDis as:

T. Bruhn, A. Schaumlöffel, Y. Hemberger, G. Bringmann, SpecDis version 1.53, University of Wuerzburg, Germany, 2012.

Download SpecDis together with a short manual  as a rar-archive from the following link:

If you have any questions or suggestions feel free to send an email to bruhn@chemie.uni-wuerzburg.de, hemberger@chemie.uni-wuerzburg.de, or schaumloeffel@chemie.uni-wuerzburg.de.

Publications using SpecDis (Selection)

Applications of SpecDis from our group:

S. Loesgen, T. Bruhn, K. Meindl, I. Dix, B. Schulz, A. Zeeck, G. Bringmann; (+)-Flavipucine, the Missing Member of the Pyridione Epoxide Family of Fungal Antibiotics; Eur. J. Org. Chem. 2011, 5156–5162.

C. Brückner, D. C. G. Götz, S. P. Fox, C. Ryppa, J. R. McCarthy, T. Bruhn, J. Akhigbe, S. Banerjee, P. Daddario, H. W. Daniell, M. Zeller, R. W. Boyle, G. Bringmann; Helimeric Porphyrinoids: Stereostructure and Chiral Resolution of meso-Tetraarylmorpholinochlorins; J. Am. Chem. Soc. 2011, 133, 8740–8752.

C. Büchold, Y. Hemberger, C. Heindl, A. Welker, B. Degel, T. Pfeuffer, P. Staib, S. Schneider, P. J. Rosenthal, J. Gut, J. Morschhäuser, G. Bringmann, T. Schirmeister; New cis-Configured Aziridine-2-carboxylates as Aspartic Acid Protease Inhibitors; ChemMedChem 2011, 6, 141–152.

L. Liu, T. Bruhn, L. Guo, D. C. G. Götz, R. Brun, A. Stich, Y. Che, G. Bringmann; Chloropupukeanolides C–E: Cytotoxic Pupukeanane Chlorides with a Spiroketal Skeleton from Pestalotiopsis fici; Chem. Eur. J. 2011, 17, 2604-2613.

L. Du, J. Ai, D. Li, T. Zhu, Y. Wang, M. Knauer, T. Bruhn, H. Liu, M. Geng, Q. Gu, G. Bringmann; Aspergiolides C and D: Spirocyclic Aromatic Polyketides with Potent Protein Kinase c-Met Inhibitory Effects; Chem. Eur. J. 2011, 17, 1319–1326.

G. Bringmann, G. Lang, T. Bruhn, K. Schäffler, S. Steffens, R. Schmaljohann, J. Wiese, J. F. Imhoff; Sorbifuranones A-C, sorbicillinoid metabolites from Penicillium strains isolated from Mediterranean sponges; Tetrahedron 2010, 66, 9894-9901.

G. Bringmann, T. Gulder, B. Hertlein, Y. Hemberger, F. Meyer; Total Synthesis of the N,C-Coupled Naphthylisoquinoline Alkaloids Ancistrocladinium A and B and Related Analogues; J. Am. Chem. Soc. 2010, 132, 1151-1158.

M. Xu , T. Bruhn, B. Hertlein, R. Brun, A. Stich, J. Wu, G. Bringmann; Shuangancistrotectorines A-E, Dimeric Naphthylisoquinoline Alkaloids with Three Chiral Biaryl Axes from the Chinese Plant Ancistrocladus tectorius; Chem. Eur. J. 2010, 16, 4206-4216.

D. C. G. Götz, T. Bruhn, M. O. Senge, G. Bringmann; Synthesis and Stereochemistry of Highly Unsymmetric beta,meso-Linked Porphyrin Arrays; J. Org. Chem. 2009, 74, 8005-8020.

G. Bringmann, K. Maksimenka, T. Bruhn, M. Reichert, T. Harada, R. Kuroda; Quantum chemical CD calculations of dioncophylline A in the solid state; Tetrahedron 2009, 65, 5720-5728.

G. Bringmann, T. Bruhn, K. Maksimenka, Y. Hemberger; The Assignment of Absolute Stereostructures through Quantum Chemical Circular Dichroism Calculations; Eur. J. Org. Chem. 2009, 2717-2727.

G. Bringmann, D. C. G. Götz, T. A. M. Gulder, T. H. Gehrke, T. Bruhn, T. Kupfer, K. Radacki, H. Braunschweig, A. Heckmann, C. Lambert; Axially Chiral beta-beta'-Bisporphyrins: Synthesis and Configurational Stability Tuned by the Central Metals; J. Am. Chem. Soc. 2008, 130, 17812-17825.

Applications of SpecDis by other groups:

L. You, G. Pescitelli, E. V. Anslyn, L. Di Bari; An Exciton-Coupled Circular Dichroism Protocol for the Determination of Identity, Chirality, and Enantiomeric Excess of Chiral Secondary Alcohols; J. Am. Chem. Soc. 2012, published online, DOI:10.1021/ja301252h.

G. Pescitelli, R. Woody; The Exciton Origin of the Visible Circular Dichroism Spectrum of Bacteriorhodopsin; J. Phys. Chem. B 2012, published online, DOI:10.1021/jp212166k.

L. Wang, H.-P. He, Y.-T. Di, Y. Zhang, X.-J. Hao; Catharoseumine, a new monoterpenoid indole alkaloid possessing a peroxy bridge from Catharanthus roseus; Tetrahedron Lett. 2012, 53, 1576-1578.

S. A. Neff, S. U. Lee, Y. Asami, J. S. Ahn, H. Oh, J. Baltrusaitis, J. B. Gloer, D. T. Wicklow; Aflaquinolones A–G: Secondary Metabolites from Marine and Fungicolous Isolates of Aspergillus spp; J. Nat. Prod. 2012, 75, 464–472.

J. M. Dragna, G. Pescitelli, L. Tran, V. M. Lynch, E. V. Anslyn, L. Di Bari; In Situ Assembly of Octahedral Fe(II) Complexes for the Enantiomeric Excess Determination of Chiral Amines Using Circular Dichroism Spectroscopy; J. Am. Chem. Soc. 2012, 134, 4398−4407.

H. Hussain, K. Krohn, I. Ahmed, S. Draeger, B. Schulz, S. Di Pietro, G. Pescitelli; Phomopsinones A–D: Four New Pyrenocines from Endophytic Fungus Phomopsis sp; Eur. J. Org. Chem. 2012, 1783–1789.

A. Debbab, A. H. Aly, R. Edrada-Ebel, V. Wray, A. Pretsch, G. Pescitelli, T. Kurtan, P. Proksch; New Anthracene Derivatives – Structure Elucidation and Antimicrobial Activity; Eur. J. Org. Chem. 2012, 1351-1359.

P.-M. Allard, M.-T. Martin, M.-E. Tran Huu Dau, P. Leyssen, F. Guéritte, M. Litaudon; Trigocherrin A, the First Natural Chlorinated Daphnane Diterpene Orthoester from Trigonostemon cherrieri; Org. Lett. 2011, 14, 342-345.

P.-M. Allard, E. T. H. Dau, C. Eydoux, J.-C. Guillemot, V. Dumontet, C. Poullain, B. Canard, F. Guéritte, M. Litaudon; Alkylated Flavanones from the Bark of Cryptocarya chartacea As Dengue Virus NS5 Polymerase Inhibitors; J. Nat. Prod. 2011, 74, 2446-2453.

James W. Walton, Lorenzo Di Bari, David Parker, Gennaro Pescitelli, Horst Puschmann and Dmitry S. Yufit; Structure, resolution and chiroptical analysis of stable lanthanide complexes of a pyridylphenylphosphinate triazacyclononane ligand; Chem. Commun. 2011, 47, 12289-12291.

H. Hussain, I. Ahmed, B. Schulz, S. Draeger, U. Flörke, G. Pescitelli, K. Krohn; Solid-state circular dichroism and hydrogen bonding: Absolute configuration of massarigenin A from Microsphaeropsis sp; Chirality 2011, 23, 617-623.

I. Ahmed, H. Hussain, B. Schulz, S. Draeger, D. Padula, G. Pescitelli, T. van Ree, K. Krohn; Three New Antimicrobial Metabolites from the Endophytic Fungus Phomopsis sp.; Eur. J. Org. Chem. 2011, 2867–2873.

I. N. Siddiqui, A. Zahoor, H. Hussain, I. Ahmed, V. U. Ahmad, D. Padula, S. Draeger, B. Schulz, K. Meier, M. Steinert, T. Kurtán, U. Flörke, G. Pescitelli, K. Krohn; Diversonol and Blennolide Derivatives from the Endophytic Fungus Microdiplodia sp.: Absolute Configuration of Diversonol; J. Nat. Prod. 2011, 74, 365–373.

S. H. Shim, J. Baltrusaitis, J. B. Gloer, D. T. Wicklow; Phomalevones A−C: Dimeric and Pseudodimeric Polyketides from a Fungicolous Hawaiian Isolate of Phoma sp. (Cucurbitariaceae); J. Nat. Prod. 2011, 74, 395–401.

L. E. Schmidt, S. T. Deyrup, J. Baltrusaitis, D. C. Swenson, D. T. Wicklow, J. B. Gloer; Hymenopsins A and B and a Macrophorin Analogue from a Fungicolous Hymenopsis sp.; J. Nat. Prod. 2010, 73, 404-408.

T. Paululat, A. Kulik, H. Hausmann, A. D. Karagouni, H. Zinecker, J. F. Imhoff, H. P. Fiedler; Grecocyclines: New Angucyclines from Streptomyces sp. Acta 1362; Eur. J. Org. Chem. 2010, 2010, 2344-2350.

M. Masullo, C. Bassarello, G. Bifulco, S. Piacente; Polyisoprenylated benzophenone derivatives from the fruits of Garcinia cambogia and their absolute configuration by quantum chemical circular dichroism calculations; Tetrahedron 2010, 66, 139-145.

T. Funaioli, M. Cavazza, M. Zandomeneghi, F. Pietra; On the Chiroptical Behavior of Conjugated Multichromophoric Compounds of a New Pseudoaromatic Class: Bicolchicides and Biisocolchicides; PLoS One 2010, 5, e10617.