SpecDis is a handy 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. Additionally, a prelimininary support for ADF calculations has been added.
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 and Gaussian09
- Boltzmann weighting of ORD values
- Similarity Factors for UV and CD spectra
We are grateful to Dr. Pescitelli (University of Pisa; Italy) for helpfull discussions and beta testing of SpecDis.
SpecDis is tested under Windows 2000, XP SP3, Vista SP1, Windows 7 SP1 and Suse Linux Enterprise Server 11.3. 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 4.6, png plotting will work with gnuplot 4.6 and higher only!
If you have any questions or suggestions feel free to send an email to email@example.com .
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 1.61, University of Wuerzburg, Germany, 2013.
SpecDis: Quantifying the Comparison of Calculated and Experimental Electronic Circular Dichroism Spectra, T. Bruhn, A. Schaumlöffel, Y. Hemberger, G. Bringmann, Chirality 2013, 25, 243–249.
SpecDis is offered as-is, without any warranty!
Download SpecDis together with a preliminary manual as a zip archive from the following links:
Windows 7, 64Bit: Win7_64b.zip
Windows XP, 32Bit: WinXP_32b.zip
Linux GTK2, 64Bit: Linux_GTK2_64b.zip
After unzipping under Linux the SpecDis binary has to be made executable by using:
chmod ugo+x SpecDis_gtk2_64b
Major changes since version 1.60
- gnuplot directory has to be set in the settings for the Linux version, too. Otherwise it wont work
- shrinking of names for gnuplot has been corrected and will now shorten the names correctly
- if an experimental CD Spectrum is loaded, the units at the y-axis for gnuplot will always be set to CD[mdeg], if absolute values are found the units will be changed to this
- some corrections in the ORD-plotting routines have been done
- Preliminary reading of UV and CD calculations of ADF (version 2012.1) has been added (but there is no 'automatic extraction')
- Loading of 'solvent shifts' from ORCA has been removed
- Before plotting UV or CD spectra, SpecDis checks if all curves have different names, if not it will stop the plotting routines
- Possibility to convert wavelength to eV has been added in the gnuplot settings of UV curves. This has an impact on the plotted eps or png files only, data files are still given in nm!!
Major changes since version 1.53
- SpecDis has been converted from Delphi to free pascal using Lazarus, it is more platform independent now and we can now provide a version for Linux, too.
- The 'sum spectra' code has been improved, weighting factors are displayed now, error messages are shown in the new memo field.
- When using multiplot, SpecDis now gives the possibility to replace curves in the Compare menu, a window for this opens automatically when you try to load a new spectrum
- ORD values from g09 calculations are read now by SpecDis, keep in mind that alphaD values will not be calculated automatically by g09 and that 589.3 nm has to be given in the wavelength section (CPHF Keyword)
- Compatibility for semicolon-separated CD data has been added
- Loading of experimental files has been changed: SpecDis displays a Warning when errors have occured during the loading routine, but the data that was readable will now be displayed
- SpecDis shows the used scaling factors in a new memo field on the right side of the window, a factor of 1 means that no scaling has been applied
- Removed a bug in the experimental-spectra loading routine, SpecDis now correctly compares CD and UV spectra
- SpecDis tries to determine the units of experimental CD spectra measured with JASCO spectrometers (displayed only in gnuplot graphics) and recognizes the units of calculations (see Plot settings for CD)
- Several possibilities to change the output of gnuplot (CD and UV) have been added:
- select fonts and sizes
- add a second y axis if calc and exp CD are compared
- labels at the axes can be changed
- change names of curves
- squared or non-squared plots
- choose whether shifts and band width should be displayed
- position of the legend inside or outside the plot
- tics inside or outside the plot
- zero line in CD spectra as full or dotted curve
- white or transparent background for png's
- user defined y ranges
Parts of these changes can be saved in the SpecDis.ini file when using the save-settings button in the settings window (File --> settings)
- The png plotting terminal of gnuplot has been changed to pngcairo, this only works with gnuplot version 4.6 and later!
- The eps plotting has been slightly modified and now works with gnuplot version 4.6 and later, too
- Files that caused SpecDis to crash will no longer be uneditable (this occured as long as SpecDis was still open after the crash)
Publications using SpecDis (Selection)
Applications of SpecDis from our group:
E. C. Tatsis, A. Schaumlöffel, A. C. Warskulat, G. Massiot, B. Schneider, G. Bringmann, Nudicaulins, Yellow Flower Pigments of Papaver nudicaule: Revised Constitution and Assignment of Absolute Configuration, Org. Lett. 2013, 15, 156-159.
N. Jansen, B. Ohlendorf, A. Erhard, T. Bruhn, G. Bringmann, J. Imhoff, Helicusin E, Isochromophilone X and Isochromophilone XI: New Chloroazaphilones Produced by the Fungus Bartalinia robillardoides Strain LF550, Mar. Drugs 2013, 11, 800-816.
A. Schaumlöffel, M. Groh, A. Speicher, G. Bringmann; Stereochemical Assignment of Cyclic Bisbibenzyl by HPLC-CD on a Chiral Phase and Quantum-Chemical CD Calculations, Eur. J. Org. Chem. 2012, 6878-6887.
A. Goel, A. Kumar, Y. Hemberger, A. Raghuvanshi, R. Jeet, G. Tiwari, M. Knauer, J. Kureel, A. K. Singh, A. Gautam, R. Trivedi, D. Singh, G. Bringmann, Synthesis, optical resolution, absolute configuration, and osteogenic activity of cis-pterocarpans, Org. Biomol. Chem. 2012, 10, 9583-9592.
J. Li, M.-Y. Li, T. Bruhn, D. C.G. Götz, Q. Xiao, T. Satyanandamurty, J. Wu, G. Bringmann, Andhraxylocarpins A-E: Structurally Intriguing Limonoids from Mangroves, Xylocarpus granatum and Xylocarpus moluccensis, Collected in the Estuaries of Andhra Pradesh, Chem. Eur. J. 2012, 18, 14342–14351.
C. Almeida, Y. Hemberger, S. Bouhired, L. Natesan, S. Kehraus, K. Dimas, M. Gütschow, G. Bringmann, G.M. König; Marilines A-D, Novel Phthalimidines from the Sponge-Derived Fungus Stachylidium sp.; Chem. Eur. J. 2012, 18, 8827-8834.
G. Bringmann, D. Goetz T. Bruhn; The Online Stereoanalysis of Chiral Compounds by HPLC-ECD Coupling in Combination with Quantum-Chemical Calculations; in Comprehensive Chiroptical Spectroscopy (N. Berova, P. Polavarapu, K. Nakanishi, R.W. Woody, Eds.), Vol. 2, John Wiley & Sons, 2012, pp. 355-420.
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:
G. Pescitelli, D. Padula, F. Santoro, Intermolecular exciton coupling and vibronic effects in solid-state circular dichroism: a case study, Phys. Chem. Chem. Phys. 2013, 15, 795-802.
G. Mazzeo, E. Santoro, A. Andolfi, A. Cimmino, P. Troselj, A. G. Petrovic, S. Superchi, A. Evidente, N. Berova, Absolute Configurations of Fungal and Plant Metabolites by Chiroptical Methods. ORD, ECD, and VCD Studies on Phyllostin, Scytolide, and Oxysporone, J. Nat. Prod. 2013, DOI:10.1021/np300770s.
S. Wang, J. Li, J. Sun, K.-W. Zeng, J.-R. Cui, Y. Jiang, P.-F. Tu, NO inhibitory guaianolide-derived terpenoids from Artemisia argyi, Fitoterapia 2013, 85, 169-175.
X.-H. Liu, F.-P. Miao, M.-F. Qiao, R. H. Cichewicz, N.-Y. Ji, Terretonin, ophiobolin, and drimane terpenes with absolute configurations from an algicolous Aspergillus ustus, RSC Adv. 2013, 3, 588-595.
X.-D. Li, F.-P. Miao, X.-R. Liang, B.-G. Wang, N.-Y. Ji, Two halosesquiterpenes from Laurencia composita, RSC Adv. 2013, 3, 1953-1956.
S. N. Ebrahimi, S. Zimmermann, J. Zaugg, M. Smiesko, R. Brun, M. Hamburger, Abietane Diterpenoids from Salvia sahendica - Antiprotozoal Activity and Determination of Their Absolute Configurations, Planta Med. 2013, 79, 150-156.
M. A. Beniddir, M.-T. Martin, M.-E. Tran Huu Dau, P. Rasoanaivo, F. Guéritte, M. Litaudon, Bisindole alkaloid artifacts from Gonioma malagasy, Tetrahedron Lett. 2013, 54, 2115-2119.
Y. Zhang, X.-M. Li, Z. Shang, C.-S. Li, N.-Y. Ji, B.-G. Wang, Meroterpenoid and Diphenyl Ether Derivatives from Penicillium sp. MA-37, a Fungus Isolated from Marine Mangrove Rhizospheric Soil, J. Nat. Prod. 2012, 75, 1888-1895.
S.-X. Yang, J.-M. Gao, H. Laatsch, J.-M. Tian, G. Pescitelli, Absolute Configuration of Fusarone, a New Azaphilone from the Endophytic Fungus Fusarium sp. Isolated from Melia azedarach, and of Related Azaphilones, Chirality 2012, 24, 621-627.
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.
G. Pescitelli, Solid-state Circular Dichroism and Hydrogen Bonding, Part 2: The Case of Hypothemycin Re-investigated, Chirality 2012, 24, 718–724.
Y. Fu, Y. Zhang, H. He, L. Hou, Y. Di, S. Li, X. Luo, X.-J. Hao, Strynuxlines A and B, ALkaloids with an Unprecedented Carbon Skeleton from Strychnos nux-vomica, J. Nat. Prod. 2012, DOI:10.1021/np300339r.
F.-P. Miao, X.-R. Liang, X.-L. Yin, G. Wang, N.-Y. Ji, Absolute Configurations of Unique Harziane Diterpenes from Trichoderma Species, Org. Lett. 2012, 14, 3815-3817.
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.
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, 134, 7117–7125.
V. Costantino, E. Fattorusso, A. Mangoni, C. Perinu, R. Teta, E. Panza, A. Ianaro; Tedarenes A and B: Structural and Stereochemical Analysis of Two New Strained Cyclic Diarylheptanoids from the Marine Sponge Tedania ignis; J. Org. Chem. 2012, 77, 6377−6383.
Y. Fua, H. Hea, Y. Dia, S. Lia, Y. Zhanga, X. Hao; Mekongenines A and B, two new alkaloids from Bousigonia mekongensis; Tetrahedron Lett. 2012, 53, 3642–3646.
G. Pescitelli, R. Woody; The Exciton Origin of the Visible Circular Dichroism Spectrum of Bacteriorhodopsin; J. Phys. Chem. B 2012, 116, 6751–6763.
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.
T. Kurtán, R. Jia, Y. Li, G. Pescitelli, Y.-W. Guo, Absolute Configuration of Highly Flexible Natural Products by the Solid-State ECD/TDDFT Method: Ximaolides and Sinulaparvalides, Eur. J. Org. Chem. 2012, 6722-6728.
I. Jastrzębska, M. Górecki, J. Frelek, R. Santillan, L. Siergiejczyk, J. W. Morzycki, Photoinduced Isomerization of 23-Oxosapogenins: Conformational Analysis and Spectroscopic Characterization of 22-Isosapogenins, J. Org. Chem. 2012, 77, 11257-11269.
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.
G. Bagdžiūnas, E. Butkus, S. Stončius, Synthesis of Diastereomeric Bicyclo[3.3.1]nonane Dibenzoyl Esters and Study of Their Chiroptical Properties, Chirality 2012, 24, 810-816.
P. W. Elsinghorst, T. Cavlar, A. Müller, A. Braune, M. Blaut, M. Gütschow; The Thermal and Enzymatic Taxifolin–Alphitonin Rearrangement; J. Nat. Prod. 2011, 74, 2243-2249.
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.