In order to define the atoms which comprise a group, a file, gausssum2.2/Groups.txt, should be created with a format similar to the following:
atoms Ru 1 bpy1 2-11,14,17,22,27,34-35,42-43,50,57 bpy2 12,16,18-19,25-26,28-30,39-41,44-46,54-56,58,61 bpy3 13,15,20-21,23-24,31-33,36-38,47-49,51-53,59-60
The first line needs to be either "atoms", "orbitals", "allatoms" or "allorbitals". If it is "allatoms" or "allorbitals", then no further input is required and a separate group will be made for each atom or each orbital. Otherwise, as in the example above, you need to describe which atoms or which orbitals are in each group. The numbers correspond to the order of the atoms/orbitals in the output file. An easy way to obtain these for Gaussian calculations is to open the output file in GaussView and turn on the labels. Groups.txt needs to obey the following rules:
Every atom in the molecule must be listed
No atom may be listed more than once
A single point calculation should be done with the following keywords: (Gaussian) pop=full iop(3/33=1,3/36=-1), (GAMESS) NPRINT=3. This creates a large log file containing information on the overlap matrix among other things. (Note: the 3/36=-1 option for Gaussian prevents the calculation and printing of the multipole matrices; this is purely to keep the output file size as small as possible. In some cases, for example SCRF calculations, the multipole matrices must be calculated - if so, leave out the 3/36=-1. It will not affect the calculation of the PDOS.)
Using GaussSum open the log file and choose Orbitals. Pick the DOS option. See the previous section for information on the options.
Click on the GaussSum logo. GaussSum calculates the percent contributions of each of the groups to each of the molecular orbitals. This may take a few minutes.
Afterwards, the partial density of states spectra (PDOS) are plotted. Note that each one is stacked on top of the previous one, which means that the line at the greatest height is equal to the sum of all of the partial density of states, and hence equal to the total density of states spectrum. The stacking order is undefined. Information on the spectra is written to gausssum2.2/DOS_spectrum.txt which can be used to plot your own graphs.
Information on the molecular orbitals and the percent contributions of the groups is written to gausssum2.2/orbital_data.txt. The last few columns of orbital_data.txt contain more accurate values for the percent contributions and are used by the Electronic transitions operation. You should not edit this file if you wish to use the information in it to calculate the changes in charge density associated with electronic transitions, as described in Chapter 8, How do I get the UV-Vis or circular dichroism spectrum of a molecule?.
Note that the percent contributions are calculated based on Mulliken Population Analysis (MPA). MPA has some well-known deficiencies which can lead to unphysical values such as negative percentage contributions. If this happens for an orbital in which you are interested, remember that the exact figures are less important than the trend across a group of compounds.
Creation of PDOS spectra is also supported for unrestricted calculations with Gaussian. The spectrum plotted is of the total DOS broken down by the contribution of each of the groups. orbital_data.txt contains information on the breakdown of the alpha and beta electrons by group.
Table of Contents
Open a log file that is the result of a TD-DFT calculation. For best results, a Gaussian TD-DFT calculation should include the following keyword "IOP(9/40=2)".
Choose the Electronic transitions from the list of operations on the left.
Choose the start and end (in nm) of the convoluted spectrum, as well as the number of points you wish to have in the calculated spectrum. FWHM refers to the full width at half-maximum of the gaussian curves used to convolute the spectrum. FWHM should be entered in cm-1.
After you have set the various parameters, click on the GaussSum logo to run convolute the spectrum.
The details are written to gausssum2.2/UVSpectrum.txt and gausssum2.2/UVData.txt. The file UVData.txt contains information on the contribution of singly-excited configurations to each electronic transition.
If there is a file in the gausssum2.2 directory called orbital_data.txt containing information on the percent contributions of various groups (e.g. ligands and metal centers) to the various molecular orbitals, GaussSum will use that data. It will calculate, for each transition, the change in charge density on each group. This information will be added to gausssum2.2/UVData.txt. (For more information, please see "How to find the % contribution of a group to each molecular orbital".)
Table of Contents
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If you use GaussSum to obtain results for publication, please cite it as follows:
N. M. O'Boyle, A. L. Tenderholt and K. M. Langner. J. Comp. Chem., 2008, 29, 839-845.
Here is a list of some papers that cite GaussSum.
Ligand-Selective Photodissociation from [Ru(bpy)(4AP)4]2+: a Spectroscopic and Computational Study Luca Salassa, Claudio Garino, Giovanni Salassa, Carlo Nervi, Roberto Gobetto, Carlo Lamberti, Diego Gianolio, Ranieri Bizzarri and Peter J. Sadler Inorg. Chem., 2009, 48 (4), pp 1469-1481
Localised to intraligand charge-transfer states in cyclometalated platinum complexes: an experimental and theoretical study into the influence of electron-rich pendants and modulation of excited states by ion binding David L. Rochester, Stephanie Develay, Stanislav Zali, J. A. Gareth Williams, Dalton Trans., 2009, (10),1728-1741
Synthetic, structural, photophysical and computational studies of -conjugated bis- and tris-1,3,2-benzodiazaboroles and related bis(boryl) dithiophenes Lothar Weber, Vanessa Werner, Mark A. Fox, Todd B. Marder, Stefanie Schwedler, Andreas Brockhinke, Hans-Georg Stammler, Beate Neumann, Dalton Trans., 2009, (8),1339-1351
The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory Ricardo A. Matute and Renato Contreras, Guillermo Prez-Hernndez and Leticia Gonzlez J. Phys. Chem. B, 2008, 112 (51), pp 16253-16256
Comparison of adsorption mechanism on colloidal silver surface of alafosfalin and its analogs Journal of Raman Spectroscopy Edyta Podstawka, Marcin Andrzejak, Pawelstrok Kafarski, Leonard M. Proniewicz Volume 39, Issue 9, Date: September 2008, Pages: 1238-1249
Computational and Spectroscopic Studies of New Rhenium(I) Complexes Containing Pyridylimidazo[1,5-a]pyridine Ligands: Charge Transfer and Dual Emission by Fine-Tuning of Excited States Luca Salassa, Claudio Garino, Andrea Albertino, Giorgio Volpi, Carlo Nervi, Roberto Gobetto and Kenneth I. Hardcastle Organometallics, 2008, 27 (7), pp 1427-1435
A Computational Study of the Ground and Excited State Structure and Absorption Spectra of Free-Base N-Confused Porphine and Free-Base N-Confused Tetraphenylporphyrin Shubham Vyas, Christopher M. Hadad and David A. Modarelli J. Phys. Chem. A, 2008, 112 (29), pp 6533-6549
Determination of Absolute Configuration of Chiral Hemicage Metal Complexes Using Time-Dependent Density Functional Theory Frederick J. Coughlin, Karl D. Oyler, Robert A. Pascal, Jr., and Stefan Bernhard Inorg. Chem., 2008, 47 (3), pp 974-979
Effect of an aliphatic spacer group on the adsorption mechanism of phosphonodipeptides containing N-terminal glycine on the colloidal silver surface Journal of Raman Spectroscopy Volume 39, Issue 10, Date: October 2008, Pages: 1396-1407 Edyta Podstawka, Pawelstrok Kafarski, Leonard M. Proniewicz
Effect of an aliphatic spacer group on the adsorption mechanism on the colloidal silver surface of L-proline phosphonodipeptides Journal of Raman Spectroscopy Edyta Podstawka, Pawelstrok Kafarski, Leonard M. Proniewicz Volume 39, Issue 12, Date: December 2008, Pages: 1726-1739
Electronic structure and reactivity analysis for a set of Zn-chelates with substituted 8-hydroxyquinoline ligands and their application in OLED Ricardo Vivas-Reyes, Francisco Nunez-Zarur, Emiliano Martinez Organic Electronics, Volume 9, Issue 5, October 2008, Pages 625-634
A laser flash photolysis, matrix isolation, and DFT investigation of (?6-C6H5Y)Cr(CO)3 (Y = NH2, OCH3, H, CHO, or CO2CH3) Mohammed A.H. Alamiry, Peter Brennan, Conor Long, Mary T. Pryce, Journal of Organometallic Chemistry, Volume 693, Issue 17, 15 August 2008, Pages 2907-2914
Mechanism of Forster-type hopping of charge transfer and excitation energy transfer along blocked oligothiophenes by Si-atoms Yong Ding, Xiangsi Wang, Fengcai Ma Chemical Physics, Volume 348, Issues 1-3, 2 June 2008, Pages 31-38
Mechanism of Ligand Photodissociation in Photoactivable [Ru(bpy)2L2]2+ Complexes: A Density Functional Theory Study Luca Salassa, Claudio Garino, Giovanni Salassa, Roberto Gobetto and Carlo Nervi J. Am. Chem. Soc., 2008, 130 (29), pp 9590-9597
Nature of Charge Carriers in Long Doped Oligothiophenes: The Effect of Counterions Natalia Zamoshchik, Ulrike Salzner and Michael Bendikov J. Phys. Chem. C, 2008, 112 (22), pp 8408-8418
Photoinduced Se?C Insertion Following Photolysis of (?5-C4H4Se)Cr(CO)3. A Picosecond and Nanosecond Time-Resolved Infrared, Matrix Isolation, and DFT Investigation Peter Brennan, Michael W. George, Omar S. Jina, Conor Long, Jennifer McKenna, Mary T. Pryce, Xue-Zhong Sun and Khuong Q. Vuong Organometallics, 2008, 27 (15), pp 3671-3680
Quantum chemical studies on the potentially important imidates Tarek M. El-Gogary Journal of Molecular Structure: THEOCHEM, Volume 861, Issues 1-3, 30 July 2008, Pages 62-67
Reversible Intramolecular C?C Bond Formation/Breaking and Color Switching Mediated by a N,C-Chelate in (2-ph-py)BMes2 and (5-BMes2-2-ph-py)BMes2 Ying-Li Rao, Hazem Amarne, Shu-Bin Zhao, Theresa M. McCormick, Sanela Marti, Yi Sun, Rui-Yao Wang and Suning Wang J. Am. Chem. Soc., 2008, 130 (39), pp 12898-12900
Ruthenium-carbonyl complexes of 1-alkyl-2-(arylazo)imidazoles: Synthesis, structure, spectra and redox properties T.K. Mondal, S.K. Sarker, P. Raghavaiah, C. Sinha Polyhedron, Volume 27, Issue 13, 10 September 2008, Pages 3020-3028
Spectroscopic and theoretical studies on axial coordination of bis(pyrrol-2-ylmethyleneamine)phenyl complexes Jia-Mei Chen, Wen-Juan Ruan, Liang Meng, Feng Gao, Zhi-Ang Zhu Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 71, Issue 1, 1 November 2008, Pages 191-198
Structural Properties of l-X-l-Met-l-Ala Phosphonate Tripeptides: A Combined FT-IR, FT-RS, and SERS Spectroscopy Studies and DFT Calculations Edyta Podstawka, Pawe? Kafarski and Leonard M. Proniewicz J. Phys. Chem. A, 2008, 112 (46), pp 11744-11755
Structures and Bonding on a Colloidal Silver Surface of the Various Length Carboxyl Terminal Fragments of Bombesin Edyta Podstawka, Yukihiro Ozaki and Leonard M. Proniewicz Langmuir, 2008, 24 (19), pp 10807-10816
Structure?Property Relationships of Polyselenoethers [?(CH2)ySe?]x (y = 1, 2, and 3) and Related Polyethers and Polysulfides Yuji Sasanuma, Akinori Watanabe and Kenta Tamura J. Phys. Chem. B, 2008, 112 (32), pp 9613-9624
Structure, spectra and electrochemistry of ruthenium-carbonyl complexes of naphthylazoimidazole Inorganica Chimica Acta, Volume 361, Issue 8, 2 June 2008, Pages 2431-2438 Tapan Kumar Mondal, Joydev Dinda, Jack Cheng, Tian-Huey Lu, Chittaranjan Sinha
Structure, Stereodynamics and Absolute Configuration of the Atropisomers of Hindered Arylanthraquinones Lodovico Lunazzi, Michele Mancinelli and Andrea Mazzanti J. Org. Chem., 2009, 74 (3), pp 1345-1348
Synthesis, Separation, and Circularly Polarized Luminescence Studies of Enantiomers of Iridium(III) Luminophores Frederick J. Coughlin, Michael S. Westrol, Karl D. Oyler, Neal Byrne, Christina Kraml, Eli Zysman-Colman, Michael S. Lowry and Stefan Bernhard Inorg. Chem., 2008, 47 (6), pp 2039-2048
Theoretical analysis on the electronic structures and properties of PPV fused with electron-withdrawing unit: Monomer, oligomer and polymer Yangwu Fu, Wei Shen, Ming Li Polymer, Volume 49, Issue 10, 13 May 2008, Pages 2614-2620
Computational Study of Iron(II) Systems Containing Ligands with Nitrogen Heterocyclic Groups R. A. Kirgan and D. P. Rillema J. Phys. Chem. A, 2007, 111 (50), pp 13157-13162
Electronic Spectroscopy of Nonalternant Hydrocarbons Inside Helium Nanodroplets Ozgur Birer, Paolo Moreschini, Kevin K. Lehmann, and Giacinto Scoles J. Phys. Chem. A, 2007, 111 (49), pp 12200-12209
Spectroscopic and Computational Studies of a Ru(II) Terpyridine Complex: The Importance of Weak Intermolecular Forces to Photophysical Properties Claudio Garino, Roberto Gobetto, Carlo Nervi, Luca Salassa, Edward Rosenberg, J. B. Alexander Ross, Xi Chu, Kenneth I. Hardcastle, and Cristiana Sabatini Inorg. Chem., 2007, 46 (21), pp 8752-8762
Influence of the Substituted Side Group on the Molecular Structure and Electronic Properties of TPP and Related Implications on Organic Zeolites Use Godefroid Gahungu, Bin Zhang, and Jingping Zhang J. Phys. Chem. B, 2007, 111 (19), pp 5031-5033
Syntheses and structures of mononuclear lutetium imido complexes with very short Lu-N bonds Tarun K. Panda, Soren Randoll, Cristian G. Hrib, Peter G. Jones, Thomas Bannenberg, Matthias Tamm, Chem. Commun., 2007, (47),5007-5009
A DFT/TDDFT study of the structural and spectroscopic properties of Al(III) complexes with 4-nitrocatechol in acidic aqueous solution Jean-Paul Cornard, Christine Lapouge, Jean-Claude Merlin Chemical Physics, Volume 340, Issues 1-3, 9 November 2007, Pages 273-282
Adsorption mechanism of physiologically active l-phenylalanine phosphonodipeptide analogues: Comparison of colloidal silver and macroscopic silver substrates E. Podstawka, A. Kudelski, L.M. Proniewicz Surface Science, Volume 601, Issue 21, 1 November 2007, Pages 4971-4983
Theoretical studies on electrochemistry of p-aminophenol Yuanzhi Song Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 67, Issues 3-4, July 2007, Pages 611-618
Intramolecular hydrogen bonding and photoinduced intramolecular proton and electron transfer in 2-(2'-hydroxyphenyl)benzothiazole Dongjie Sun, Jinghai Fang, Guanghua Yu, Fengcai Ma Journal of Molecular Structure: THEOCHEM, Volume 806, Issues 1-3, 31 March 2007, Pages 105-112
Photophysical properties and computational investigations of tricarbonylrhenium(I)[2-(4-methylpyridin-2-yl)benzo[d]-X-azole]L and tricarbonylrhenium(I)[2-(benzo[d]-X-azol-2-yl)-4-methylquinoline]L derivatives (X = N-CH3, O, or S; L = Cl-, pyridine) Andrea Albertino, Claudio Garino, Simona Ghiani, Roberto Gobetto, Carlo Nervi, Luca Salassa, Edward Rosenberg, Ayesha Sharmin, Guido Viscardi, Roberto Buscaino, Gianluca Croce, Marco Milanesio Journal of Organometallic Chemistry, Volume 692, Issue 6, 15 February 2007, Pages 1377-1391
A Density Functional Theory Study of the Electronic Properties of Os(II) and Os(III) Complexes Immobilized on Au(111). O'Boyle, N. M.; Albrecht, T.; Murgida, D. H.; Cassidy, L.; Ulstrup, J.; Vos, J. G., Inorg. Chem., 2007, 46, 117.
Photophysical and electrochemical properties of new ortho-metalated complexes of rhodium(III) containing 2,2-dipyridylketone and 2,2-dipyridylamine. An experimental and theoretical study Wei Lin Su, Yu Cheng Yu, Mei Ching Tseng, Shao Pin Wang and Wen Liang Huang Dalton Trans., 2007, 3440.
Photochemical cis-trans Isomerization of cis-(eta6-1,2-Diphenylethene)Cr(CO)3 and the Molecular Structure of trans-(eta6-1,2-Diphenylethene)Cr(CO)3 A. Coleman, S.M. Draper, C. Long, and M.T. Pryce Organometallics, 2007, 26, 4128.
Density Functional Studies on the Effects of Hydrogen Bonding on the Formation of a Charge-Transfer Complex between p-Benzoquinone and 2,6-Dimethoxyphenol Bangal, P. R. J. Phys. Chem. A.; (Article); 2007; 111(25); 5536-5543.
Lone Pair-pi and pi-pi Interactions Play an Important Role in Proton-Coupled Electron Transfer Reactions DiLabio, G. A.; Johnson, E. R. J. Am. Chem. Soc.; (Article); 2007; 129(19); 6199-620
Intramolecular hydrogen bonding and photoinduced intramolecular proton and electron transfer in 2-(2'-hydroxyphenyl)benzothiazole. D. Sun, J. Fang, G. Yu and F. Ma. J. Mol. Struct. THEOCHEM, 2007, 806, 105.
Photophysical properties and computational investigations of tricarbonylrhenium(I)[2-(4-methylpyridin-2-yl)benzo[d]-X-azole]L and tricarbonylrhenium(I)[2-(benzo[d]-X-azol-2-yl)-4-methylquinoline]L derivatives (X = N--CH3, O, or S; L = Cl-, pyridine). A. Albertino, C. Garino, S. Ghiani, R. Gobetto, C. Nervi, L. Salassa, E. Rosenberg, A. Sharmin, G. Viscardi, R. Buscaino, G. Croce, and M. Milanesio, J. Organomet. Chem., 2007, 692, 1377.
Electronic transitions and bonding properties in a series of five-coordinate "16-electron" complexes [Mn(CO)3(L2)]- (L2 = chelating redox-active p-donor ligand). F. Hartl, P. Rosa, L. Ricard, P. Le Floch and S. Zalis. Coord. Chem. Rev., 2007, 251, 557.
Theoretical studies on electrochemistry of p-aminophenol Y. Song Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2007, 67, 611.
The electronic and structural properties of nonclassical bicyclic thiophene: Monomer, oligomer and polymer W. Shen, M. Li, R. He, J. Zhang and W. Lei Polymer, 2007, 48, 3912-3918
Spectroscopic and computational studies on self-assembly complexes of bis(pyrrol-2- ylmethyleneamine) ligands linked by alkyl spacers with Cu(II) W. Li, Y. Wang, L. Yang, A. Szeghalmi, Y. Ye, J. Ma, M. Luo, J.-m. Hu and W. Kiefer J. Raman. Spectros., 2007, 38, 483-495.
CO2 Fixation and Transformation by a Dinuclear Copper Cryptate under Acidic Conditions J.-M. Chen, W. W., X.-L. Feng and T.-B. Lu Chemistry - An Asian Journal, 2007, 2, 710-719.
A DFT study of the chemisorption of methoxy on clean and low oxygen precovered Ru(0 0 0 1) surfaces M.N.D.S. Cordeiro, A.S.S. Pinto and J.A.N.F. Gomes Surface Science, 2007, 601, 2473-2485
Syntheses, crystallography and spectroelectrochemical studies of ruthenium azomethine complexes M.Z. Al-Noaimi, H. Saadeh, S.F. Haddad, M.I. El-Barghouthi, M. El-khateeb and R.J. Crutchley Polyhedron, 2007, 26, 3675.
Field-induced conformational changes in bimetallic oligoaniline junctions J.C. Sotelo, L. Yan, M. Wang and J.M. Seminario Phys. Rev. A, 2007, 75, 022511
Density functional theoretical study of Cun, Aln (n = 4-31) and copper doped aluminum clusters: Electronic properties and reactivity with atomic oxygen C. Lacaze-Dufaure, C. Blanc, G. Mankowski and C. Mijoule Surface Science, 2007, 601, 1544-1553
Electronic Structure and Excited States of Rhenium(I) Amido and Phosphido Carbonyl-Bipyridine Complexes Studied by Picosecond Time-Resolved IR Spectroscopy and DFT Calculations. Gabrielsson, A.; Busby, M.; Matousek, P.; Towrie, M.; Hevia, E.; Cuesta, L.; Perez, J.; Zalis, S.; Vlcek, A., Jr., Inorg. Chem., 2006, 45, 9789.
Spectroscopic and Computational Studies on the Coordination-Driven Self-Assembly Complexes (ZnL)2 and (NiL)2 [L= Bis(2,4-dimethyldipyrrin-3-yl)methane]. Li, W.; Wang, Y.-B.; Yang, L.-Y.; Shan, X.-F.; Cai, X.; Szeghalmi, A.; Ye, Y.; Ma, J.-S.; Luo, M.-D.; Hu, J.; Kiefer, W., J. Phys. Chem. B., 2006, 110, 21958.
The hydrogen bond in the acetylene-2(HF) complex: A theoretical study about intramolecular and unusual PI...H interactions using DFT and AIM calculations. B.G. Oliveira, R.C.M.U. Araujo, A.B. Carvalho, E.F. Lima, W.L.V. Silva, M.N. Ramos and A.M. Tavares, J. Mol. Struct. THEOCHEM, 2006, 775, 39.
Calculation of standard electrode potential of half reaction for benzoquinone and hydroquinone. Y. Song, J. Xie, Y. Song, H. Shu, G. Zhao, X. Lv and W. Xie, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2006, 65, 333.
A theoretical quantum study on the distribution of electrophilic and nucleophilic active sites on Ag(100) surfaces modeled as Finite Clusters. C. H. Rios-Reyes, R. L. Camacho-Mendoza and L. H. Mendoza-Huizar, J. Mex. Chem. Soc., 2006, 50, 19.
Computational studies of the interactions between emeraldine and palladium atom. B. Bialek, Surf. Sci., 2006, 600, 1679.
Excited States of Nitro-Polypyridine Metal Complexes and Their Ultrafast Decay. Time-Resolved IR Absorption, Spectroelectrochemistry, and TD-DFT Calculations of fac-[Re(Cl)(CO)3(5-Nitro-1,10-phenanthroline)]. A. Gabrielsson, P. Matousek, M. Towrie, F. Hartl, S. Zalis, and A. Vlcek, Jr., J. Phys. Chem. A, 2005, 109, 6147.
Molecular geometry, electronic structure and optical properties study of meridianal tris(8-hydroxyquinolinato)gallium(III) with ab initio and DFT methods. G. Gahungu, and J. Zhang, J. Mol. Struct. THEOCHEM, 2005, 755, 19.
CH/N Substituted mer-Gaq3 and mer-Alq3 Derivatives: An Effective Approach for the Tuning of Emitting Color. G. Gahungu and J. Zhang. J. Phys. Chem. B, 2005, 109, 17762.
Ground- and excited-state electronic structure of an emissive pyrazine-bridged ruthenium(II) dinuclear complex. W.R. Browne, N.M. O'Boyle, W. Henry, A.L. Guckian, S. Horn, T. Fett, C.M. O'Connor, M. Duati, L. De Cola, C.G. Coates, K.L. Ronayne, J.J. McGarvey, and J.G. Vos, J. Am. Chem. Soc., 2005, 127, 1229.
Bimetallic Clusters Pt6Au: Geometric and Electronic Structures within Density Functional Theory W. Quan Tian, M. Ge, F. Gu, and Y. Aoki, J. Phys. Chem. A, 2005, 109, 9860.
Ground vs. excited state interaction in ruthenium-thienyl dyads: implications for through bond interactions in multicomponent systems. W. Henry, W.R. Browne, K.L. Ronayne, N.M. O'Boyle, J.G. Vos, and J.J. McGarvey, J. Mol. Struct., 2005, 735-736, 123.
(NH3CH2CH2NH3)Ag2SnS4: a quaternary sulfide-containing chiral layers. Y. An, B. Menghe, L. Ye, M. Ji, X. Liu, and G. Ning, Inorg. Chem. Commun., 2005, 8, 301.
Ligand-to-Diimine/Metal-to-Diimine Charge-Transfer Excited States of [Re(NCS)(CO)3(alpha-diimine)] (alpha-diimine = 2,2'-bipyridine, di-iPr-N,N-1,4-diazabutadiene). A Spectroscopic and Computational Study. A.M. Blanco Rodriguez, A. Gabrielsson, M. Motevalli, P. Matousek, M. Towrie, J. Syebera, S. Zalis, and Antonin Vlcek, Jr., J. Phys. Chem. A, 2005, 109, 5016.
DFT and HF Studies of the Geometry, Electronic Structure, and Vibrational Spectra of 2-Nitrotetraphenylporphyrin and Zinc 2-Nitrotetraphenylporphyrin. W. Li, Y.-B. Wang, I. Pavel, Y. Ye, Z.-P. Chen, M.-D. Luo, J.-M. Hu, and W. Kiefer, J. Phys. Chem. A, 2004, 108, 6052.
Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes. A.L. Guckian, M.Doering, M. Ciesielski, O. Walter, J. Hjelm, N.M. O'Boyle, W. Henry, W.R. Browne, J.J. McGarvey, and J.G. Vos, Dalton Trans., 2004, 3943.
Ab initio study of the electronic and structural properties of the crystalline polyethyleneimine polymer. G. Herlem and B. Lakard, J. Chem. Phys., 2004, 120, 9376.
Open the file you wish to search and choose Find from the list of operations on the left.
Either choose one of the default search terms or choose Custom. If you choose Custom, enter a search term into the box. Note: you can change the default search terms using the Settings dialog box.
Click on the GaussSum logo to start the script.
If you wish to find all lines containing either TERM_A or TERM_B, then use the following notation, TERM_A%TERM_B, for the search term. Any number of terms may be combined in this way.
Table of Contents
This chapter describes how to install and run GaussSum on computers running Windows or Linux. Note that there are two choices for installing in Windows. One is to install an all-in-one bundle of Python/Numpy/PIL/GaussSum (the easier method), the other is to install the GaussSum sources and the required libraries separately.
Download the quite large all-in-one bundle from here. Extract the zip file into something like C:\Program Files\GaussSum2.2. To run, just doubleclick on GaussSum.exe. You may find it useful to create a shortcut on your desktop to GaussSum.exe (to do so, right-click on an empty part of the desktop, choose New -> Shortcut, browse to the folder where you installed GaussSum and choose GaussSum.exe). If you want to set a startup folder, right-click on the icon, choose Properties -> Shortcut -> Start in:, and type the name of the startup folder.
Table of Contents
This chapter has been divided into three sections. The first section describes how to extract information on the eigenvalues and symmetries of the molecular orbitals. The second section describes how to extract information on the contributions of groups of atoms to each of the molecular orbitals. The third section describes how to extract information on the nature of the overlap between different groups of atoms.
Open the log file containing the relevant information and choose Orbitals from the list of operations on the left. Pick the DOS option.
The boxes labeled "Start" and "End" are the start and end points (in eV) of the density of states spectrum. The box labeled "FWHM" is the full width at half-maximum (in eV) of the gaussian curves used to convolute the DOS and COOP spectra.
Click on the GaussSum logo to start the script. The molecular orbital information is written to gausssum2.2/orbital_data.txt.
The density of states (DOS) spectrum is convoluted using Gaussian curves of unit height and the specified full width at half-maximum. Gnuplot is then used to plot the spectrum. The details are written to gausssum2.2/DOS_spectrum.txt.
If you tick the box labelled "Create originorbs.txt?", a file gausssum2.2/orginorbs.txt will be created which can be used to plot the orbital energies as a series of bars, one above the other, using a program such as Origin (Windows) or Grace (Linux). See the worked example on the GaussSum web site for more information.
Unrestricted calculations are supported for Gaussian. The same files are created but with the data broken down into sections for alpha and beta electrons. The DOS spectrum plotted is also different, containing an alpha DOS, a beta DOS and a (scaled) total DOS. If you ticked the box to create originorbs.txt, the beta eigenvalues are listed after all of the alpha eigenvalues.
GaussSum requires Python, which is a programming language commonly used for scripting.
Go to the Python 2.7 install page. Download and run the Windows installer, Python-2.7.3.msi. Install it into something like C:\Python2.7. GaussSum also works well with Python 2.5 and 2.6.
GaussSum requires Numpy, which is a Python extension that allows efficient matrix algebra.
Go to the Numpy download page. Download and run the Windows installer for your version of Python.
In order to create .png images, GaussSum requires the Python Imaging Library, which is a Python package that allows image manipulation.
Go to the PIL download page. Download the run the Windows installer for your version of Python.
The scripts can be found here. Extract the zip file into something like C:\Program Files\GaussSum (note: Gnuplot is included in this zip file in the sub folder gnuplot400).
Create a shortcut on your desktop to GaussSum.py (to do this, right-click on an empty part of the desktop, choose New -> Shortcut, browse to the folder where you installed GaussSum and choose GaussSum.py). To change the icon, right-click on the icon, choose Properties -> General -> Change Icon -> Browse. Find the folder where you installed GaussSum and choose GaussSum.ico. In addition, change the program used to open GaussSum by following these instructions: right-click on the icon, choose Properties -> General -> Opens with -> Change -> PythonW. If you want to set a startup folder, right-click on the icon, choose Properties -> Shortcut -> Start in:, and type the name of the startup folder.
If you have any questions or requests, or if you wish to be added to the mailing list for information on new versions and bug fixes, please send an email to gausssum-help@lists.sourceforge.net.
An EDDM is a representation of the changes in electron density that occur for a given electronic transition. It is calculated using the information on the single-excited configurations that contribute to each transition. The relative contribution is based on the square of the configuration's coefficient. Note that for some programs (e.g. Gaussian) these squares are not guaranteed to sum to 1.0 and so should not be regarded as scientifically accurate. However, they should be sufficient for the purposes of generating a diagram.
After you have plotted the UV-Vis or circular dichroism spectrum, copy a checkpoint file (or formatted checkpoint file) into the gausssum2.2 directory. Then select "Electronic transitions" and choose the "Create EDDM script?" option. Click on the GaussSum logo to convolute the spectrum and generate gausssum2.2/eddm.bat (gausssum2.2/eddm.sh on Linux).
Next you need to set the environment variable G03DIR to the directory containing the Gaussian binaries. To generate the EDDM, at a command prompt run "eddm.bat N", where N is the transition number (starting from 1 for the lowest energy transition).
(Gaussian,GAMESS)
Next, open a log file containing the results of a freq calculation. It isn't necessary to specify whether you wish to calculate the IR or the Raman spectrum - the IR spectrum will always be calculated, and if you ran a freq=raman job, then the Raman activity and Raman intensity spectra will be calculated.
Choose Frequencies from the list of operations on the left.
Parameters for Frequencies
The spectra will be calculated for wavelengths between Start and End. The units of Start and End are cm-1.
This parameter determines the number of points in the calculated spectra.
The Full Width at Half Maximum of each peak.
You can choose either a general or individual scaling factor (see below).The calculated frequencies are multiplied by the scaling factor. The scaled frequencies are then used to generate the spectra.
(Only available for Raman) The value of the excitation wavelength is used to calculate the Raman intensities from the Raman activity (see below) using the equation described by Krishnakumar et al. (J. Mol. Struct., 2004, 702, 9) and Keresztury et al. (Spectrochimica Acta, 1993, 49A, 2007).
(Only available for Raman) This value determines the temperature used in the Raman intensity equation (see above).
Click on the GaussSum icon to run the script.
The spectra are convoluted with Lorentzian curves and then plotted with Gnuplot.
Information on the each spectrum and on the normal modes are written to gausssum2.2/IRSpectrum.txt and gausssum2.2/RamanSpectrum.txt.
The first few lines of an example IRSpectrum.txt are shown below. Tabs are used to separate each column of information. This allows easy import into spreadsheet software (e.g. Excel), just by right-clicking on the file and choosing "Open with".
Spectrum Normal Modes Freq (cm-1) IR act Mode Label Freq (cm-1) IR act Scaling factors Unscaled freq 8 0.000612391353264 1 A 466.3941 0.0 1.0 466.3941 16 0.000624493504806 2 A 466.3945 0.0 1.0 466.3945 24 0.000636968752613 3 A 698.2427 0.0 1.0 698.2427 32 0.000649832766662 4 A 698.2429 0.0 1.0 698.2429
If you want to use individual scaling factors, you should open a previously created IRSpectrum.txt or RamanSpectrum.txt and edit the column titled 'Scaling Factors'. You can do this in (for example) Excel, and then save as 'Tab Delimited'. Run the Frequencies option again but choose individual scaling factors this time. The new IRSpectrum.txt or RamanSpectrum.txt will contain the scaled frequencies.
A number of people provided helpful feedback during the development of GaussSum. The following names are listed in no particular order:
shaloncai reported an error in the data written in UVData.txt.
Rudy Coquet reported an error in the data written in CDSpectrum.txt.
Fabrizia Fabrizi de Biani reported an error in the labels used in UVData.txt.
Tong Glenna reported an error in the major and minor contributions in UVData.txt.
Christos Garoufalis reported a problem parsing PC-GAMESS files with large basis sets.
Emmanuel Koukaras reported a bug in the output of DOS_spectrum.txt, as well as a problem plotting the COOP.
Xinyu Huang reported a bug plotting the PDOS.
Yafei Dai reported problems parsing Gaussian files with "pop=regular".
Charles Bradshaw reported problems plotting the vibrational frequencies for GAMESS calculations.
Juan Sotelo-Campos pointed out that the COOP was only being calculated for alpha orbitals in unrestricted calculations.
Dr. Carlo Nervi, Torino, who found a bug in EDDM.py
James Hepburn, Aberdeen, who found that Hyperchem code had been neglected
Prof Ziyang Liu, Zhejiang University, P.R.China, who found a bug in the output of MO.py for unrestricted calculations
Fred Coughlin, Princeton, U.S., who found a couple of bugs in my code for CD spectra
Li Daobing and Jordan Mantha who have packaged GaussSum up for Debian and Ubuntu users
Neil Berry, Liverpool, who helped to increase GaussSum support for GAMESS files
Julien Chiron, Faculté des Sciences de Saint Jérôme, Marseille, France helped me add support for GAMESS and is perhaps the first Mac user of GaussSum (see screenshots)
Avril Coghlan, formerly of Trinity College Dublin, Ireland, thought of the name (it rhymes with awesome!) and suggested various web page improvements
Elmar Gerwalin, University of Kaiserslautern, Germany, who helped me enormously in getting GaussSum (a) to run in Linux and (b) to work for other people's calculations
Denis G. Golovanov, Russian Academy of Sciences, Moscow and his non-symmetry-containing logfile provided another challenge to GaussSum
Guillaume Herlam, Université de Franche-Comté, Besançon, France who requested and tested COOP diagrams
Roma Oakes, Queens University Belfast, made many useful comments regarding the initial development, especially regarding IR_Raman.py
Ullrich Siehl, University of Ulm, Germany, who made a number of suggestions that lead to the creation of version 0.9.
In order to create GaussSum, I had to learn a few things. I found the following resources very helpful:
O'Reilly's The Definitive Guide to DocBook came in handy when writing the documentation.
O'Reilly's Learning Python was obviously a wise investment.
Fredrik Lundh's An Introduction to Tkinter was invaluable in creating the GUI for GaussSum.
The digital hermit's page helped me create the GaussSum logo.
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Click on "File", "Settings". Check the path to the Gnuplot executable. You can test this by clicking on the "Test" button, which should display the GaussSum logo drawn using Gnuplot.
Note that the default location used by GaussSum for Gnuplot under Linux is "/usr/bin/gnuplot", but yours may be located in "/usr/local/bin/gnuplot". Under Windows, the default location used is the Gnuplot distribution bundled with GaussSum (e.g. "C:\Program Files\GaussSum-2.2\gnuplot400\bin\wgnuplot.exe"). However, if you are upgrading from an earlier version of GaussSum, the new version of GaussSum will use the configuration file of the earlier version, and so you will need to correct the path to Gnuplot.
If you still have problems, please let me know by sending an email to gausssum-help@lists.sourceforge.net.
GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information.
It is written by Noel O'Boyle and is available for free under the GNU Public License. For up-to-date information, please see http://gausssum.sf.net.
GaussSum version 2.2 can do the following:
display all lines containing a certain phrase follow the progress of the SCF convergence follow the progress of a geometry optimisation extract molecular orbital information, including contributions of groups of atoms to the molecular orbitals plot the density of states spectrum (and the partial density of states, in the case of groups of atoms) plot the crystal orbital overlap population (COOP) spectrum, which gives information on the bonding/anti-bonding nature of an overlap between atoms/groups extract information on the UV-Vis transitions, including the change in the charge density of groups of atoms plot the UV-Vis spectrum and the circular dichroism spectrum extract information on IR and Raman vibrations plot the IR and Raman spectra, which may be scaled using general or individual scaling factors Handle compressed log files (.zip, .gz, .bz2) as easily as regular log files. Release Notes for Version 2.2.6.1: Bugfix for 2.2.6. Gnuplot location undefined for new users of GaussSum (Guillaume Lamoureux). Release Notes for Version 2.2.6: A patch from Thomas Pijper was integrated to enable calculation of Raman intensities (from Raman activity). Support has been added for calculating charge density changes for unrestricted calculations (requested by Phil Schauer). Blank lines in Groups.txt are now ignored. Release Notes for Version 2.2.5: Parser updated to cclib r923 (Ben Stein, Marius Retegan). Removed minus signs in output for TD-DFT (previously these indicated the sign of the contribution). Corrected equation used for circular dichroism to match that from Stephens and Harada (see circular dichroism docs for ref). Thanks to Li-She Gan for identifying this problem and pointing me to this paper. Release Notes for Version 2.2.4: Parser updated to cclib r912 (Tiago Silva). Release Notes for Version 2.2.3: Fix serious bug with EDDM (Carlo Nervi, Carlos Silva Lopez). Parser updated to cclib r884 (Mahesh Kumar, Dan Matusek). Release Notes for Version 2.2.2: Fix problems with Linux version (Daniel Liedert). Minor doc fixes (Irena Efremenko). Release Notes for Version 2.2.1: Fix bug in importing cclib (Daniel Liedert). Parser updated to handle Gaussian09 CD output (Rino Pescitelli). Release Notes for Version 2.2.0: Update in parsing library (to cclib r877) Added support for creating EDDM maps with Gaussian Release Notes for Version 2.1.6: Can now handle unrestricted TD-DFT calculations correctly (previously there were errors in the contribution descriptions in UVData.txt). Release Notes for Version 2.1.5: Updated cclib to cclib 0.9+ (r840). Fixed problem reparsing GeoOpts. Fixed problem with exe on Windows with default Gnuplot and Docs locations. Release Notes for Version 2.1.4: Bugfixes for UVData.txt which had incorrect % contributions of singly-excited configurations and incorrect changes in electron density of groups. Release Notes for Version 2.1.3: Bugfixes for incorrect data for energies in CDSpectrum.txt and incorrect units in heading in UVData.txt. Updated cclib to cclib 0.8 beta Release Notes for Version 2.1.2: Bugfix for off-by-one error in orbital names in major and minor contributions in UVData.txt. Release Notes for Version 2.1.1: Updated the code to save results to gausssum2.1 subfolder, along with some minor documentation fixes Release Notes for Version 2.1.0: Major update in parsing library (upgraded from cclib 0.6.1 to cclib 0.8dev) Jaguar log files now supported Compressed log files (.zip, .gz., .bz2) supported Underlying code now uses Numpy for numerical calculation, rather than the deprecated Numeric Fixed error in the output of DOS_spectrum.txt where the 'Total' column was equal to the values for the first group Fixed problem plotting the COOP Release Notes for Version 2.0.6: Plotting the PDOS was failing due to 'type' issues with Numeric arrays (due to changes in cclib 0.6.1). Release Notes for Version 2.0.5: Parsing was failing for Gaussian files with "pop=regular". Release Notes for Version 2.0.4: Plotting vibrational frequencies now works for GAMESS calculations that have imaginary frequencies (bug fix in cclib). Release Notes for Version 2.0.3: Plotting vibrational frequencies now works for frequencies that don't have symmetry labels. Release Notes for Version 2.0.2: COOP now works for unrestricted calculations.
Release Notes for Version 2.0: main differences compared to GaussSum 1.0
This is the first release of GaussSum that uses cclib to parse output files. Calculation of the DOS and COOP uses matrix algebra now, and is almost instant. Images can now be saved as .png files. Groups can be described in terms of atomic orbitals now (and not just atoms).
Crystal Orbital Overlap Population (COOP) diagrams were first developed by Huckel. They are especially used in the area of extended solids. They are equivalent to a multiplication of the DOS spectrum and the overlap population (positive or negative) between two groups. In this way, the bond between two groups can be described as bonding or antibonding with respect to each of the molecular orbitals.
Exactly the same information as for creating a PDOS diagram is needed for creating a COOP diagram. That is, you need a log file which is the result of a single-point calculation containing the same keywords as described in "How to find the % contribution of a group to each molecular orbital". You also need a file
Choose COOP after picking Orbitals. The options for creating a COOP diagram are the same as for creating a DOS or PDOS diagram.
Click on the GaussSum logo to calculate the COOP. Information on the overlap is written to
Open a log file that is the result of a TD-DFT calculation. For best results, a Gaussian TD-DFT calculation should include the following keyword "IOP(9/40=2)".
From the list of operations on the left, choose Electronic transitions.
Choose the start and end (in nm) of the convoluted spectrum, as well as the number of points you wish to have in the calculated spectrum. Sigma refers to the width of the band at 1/e height for the gaussian curves used to convolute the spectrum. The units for sigma are eV. (The equation used is Equation 8 from Stephens and Harada, Chirality, 2010, 22, 229-233. Delta in that equation is Sigma/2.)
After you have set the various parameters, click on the GaussSum logo to convolute the spectrum. The details are written to
Using GaussSum open the file you want to examine. Usually this will be the output file of a job which is currently running.
Choose Monitor GeoOpt and click on the GaussSum logo to run the script.
Two graphs will be plotted. The first is of energy vs optimisation step. The second is the deviation from the targets vs optimisation step.
The deviation is found by considering the convergence criteria. Each of the current values is divided by the target values. The log is taken of any results greater than 1. The deviation is then calculated by summing the logs. Note that convergence is achieved when the progress value equals 0.
You may wish to leave out the initial points, so as to focus on the last few points. You can do this by entering a non-zero value into the box labeled "Leave out the first n points", and re-running the script.
Check to see if you already have Gnuplot, by typing 'which gnuplot' in a shell window. If Gnuplot is installed, you need to make sure that it is version 4.0 or newer ('gnuplot --version').
If you need to install Gnuplot, rpms are available from rpmfind.net and gzipped tar files from SourceForge. If you are using Debian Linux, Gnuplot will be downloaded and installed if you issue the following command as root: 'apt-get install gnuplot'.
Check to see if you already have Python, by typing 'which python' in a shell window.
If you have Python, type 'python'. The version number should be displayed. If this is less than 2.4, the scripts may not work with your currently installed Python version. (Press 'CTRL+D, ENTER' to exit.)
If you need to install Python, follow the appropriate instructions for your system at www.python.org. You should install the latest version of Python 2.7 (although Python 2.5 and 2.6 also work fine with GaussSum). If you are using Debian Linux, Python will be downloaded and installed if you issue the following command as root: 'apt-get install python python-tk'.
Numpy is an extension to Python that allows efficient matrix manipulation. You should try to find a binary package for your system rather than compiling it yourself (check your package management system). If you are using Debian Linux, Numpy will be downloaded and installed if you issue the following command as root: 'apt-get install python-numpy python-numpy-ext'.
The Python Imaging Library is a Python package that allows manipulation of images. GaussSum requires PIL to handle PNG images. You can get PIL 1.1.7 from here under "Python Imaging Library 1.1.7 Source Kit (all platforms)". This should be untarred into a folder in the usual way, using 'tar zxvf Imaging-1.1.7.tar.gz'. Next, go into the folder created and (as root) install the package as follows: 'python setup.py install'. If you are using Debian Linux, the Python Imaging Library will be downloaded and installed if you issue the following command as root: 'apt-get install python-imaging python-imaging-tk'.
Download a gzipped tar of GaussSum here. This should be untarred into a folder in the usual way, using 'tar zxvf GaussSum-2.2.6.1.tar.gz'.
If you wish to be added to the mailing list for information on new versions and bug fixes, please send an email to gausssum-help@lists.sourceforge.net.
For Gaussian to print SCF convergence information, it is necessary to specify additional print, by using #P in the route section.
Using GaussSum, open the file you want to examine. Usually this will be the output file of a job which is currently running.
Choose Monitor SCF and click on the GaussSum logo to run the script. A graph will be plotted of the progress of the SCF convergence versus step number. Details of the SCF cycles are written to the screen. Where there is information on several SCF convergence cycles in a log file (e.g. in the case of a geometry optimisation), GaussSum plots the one closest to the end of the file.
The progress of the SCF convergence is calculated by considering the convergence criteria. For example, for Gaussian, these criteria are the RMS density, MAX density and change in energy. Each of the current values is divided by the target values. The log is taken of any results greater than 1. The 'progress value' is then calculated by summing the logs. Note that convergence is achieved when the progress value equals 0.
You may wish to leave out the initial points, so as to focus on the last few points. You can do this by entering a non-zero value into the box labeled "Leave out the first n points", and re-running the script.
Note that, at the moment, this procedure does not work for SCF=QC (Gaussian).
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GaussSum-2.2.6.1/Docs/pr01.html 0000664 0001750 0001750 00000020027 12117172552 014451 0 ustar noel noel
GaussSum-2.2.6.1/Docs/ch07s03.html 0000664 0001750 0001750 00000007551 12117172552 014765 0 ustar noel noel
GaussSum-2.2.6.1/Docs/ch08s02.html 0000664 0001750 0001750 00000006250 12117172552 014760 0 ustar noel noel
Groups.txt describing the groups of interest in the molecule (see "How to find the % contribution of a group to each molecular orbital"). The rules for Groups.txt are not as strict in this case: no atom can be listed twice, but not every atom needs to be listed.
gausssum2.2/COOP_data.txt and gausssum2.2/COOP_spectrum.txt.
GaussSum-2.2.6.1/Docs/ch05.html 0000664 0001750 0001750 00000006165 12117172552 014435 0 ustar noel noel
gausssum2.2/CDSpectrum.txt.
GaussSum-2.2.6.1/Docs/ch01s03.html 0000664 0001750 0001750 00000015753 12117172552 014762 0 ustar noel noel
GaussSum-2.2.6.1/Docs/ch04.html 0000664 0001750 0001750 00000007353 12117172552 014434 0 ustar noel noel
GaussSum-2.2.6.1/GaussSum.py 0000775 0001750 0001750 00000001473 12117172552 014241 0 ustar noel noel #!/usr/bin/env python
# -*- coding: cp1252 -*-
#
# Copyright (C) 2006-2009 Noel O'Boyle