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Exploring Chemsoft Software

Exploring Chemsoft Software. Ernst J. Schumacher University of Bern, Switzerland and Arlen Viste Augustana College (SD) 25 Aug 2004. Exploring Chemsoft Software.

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Exploring Chemsoft Software

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  1. Exploring Chemsoft Software Ernst J. Schumacher University of Bern, Switzerland and Arlen Viste Augustana College (SD) 25 Aug 2004

  2. Exploring Chemsoft Software In memory of Prof. Wayne P. Anderson (1942-2003)Bloomsburg University (PA)colleague and friend in MoleCVUEfan of Linux and GAMESS http://facstaff.bloomu.edu/wpa/http://ed.augie.edu/~webmo/

  3. Molecular Modeling on an Undergraduate Budget This presentation will explore three software packages which are freely available on the Chemsoft website in Switzerland. http://www.chemsoft.ch/These provide very convenient graphical interfaces (scripts) for PC-GAMESS (recent DFT version of Alex Granovsky), GAMESS (US), and Fda (non-relativistic atomic structure). These packages are in the spirit of Wayne P. Anderson, who developed and published a convenient graphical interface for PC-GAMESS shortly before his untimely death in July 2003. http://jchemed.chem.wisc.edu/JCEDLib/WebWare/collection/reviewed/WW017/

  4. Exploring Chemsoft Software http://www.chemsoft.ch/ FDA Atomic Structure Dialect script by EJS for code of David J. Hesterberg (1995) based on Hermann and Skillman (1963) PCGam and RunPcg Dialect scripts by EJS for PC-GAMESS (v. 6.4, Alex Granovsky, 2004)RunPcg style inspired by Wayne Anderson Cygam and WingRun Dialect scripts by EJS for GAMESS (compiled under Cygwin by Nuno Bandeira in collaboration with E J Schumacher 2003-2004)WingRun style inspired by Wayne Anderson

  5. Exploring Chemsoft Software Ernst Schumacher Prof. Emeritus University of Berne Switzerland With son and grandson http://www.chemsoft.ch/ http://www.dcb.unibe.ch/groups/schumacher/

  6. Exploring Chemsoft Software FDAFinite Difference Atomic Structure calculations Carbon http://www.dcb.unibe.ch/groups/schumacher/qc/fda.htm

  7. FDA This little script lets you compute energies and orbitals of atoms for any electron configuration you might fancy: Atoms in ground state, atomic ions, ionization potentials, electron affinities, inner excitations for X-ray terms, outer excitations for UV/VIS spectra. The computing engine is the program FDA which is based on an SCF procedure using a Density Functional method and the Xalpha functional proposed in the sixties by Herman & Skillman (1963). The source code from David J. Heisterberg (1995) is further developed (and corrected) and FDA gives more accurate results. It is written in C/C++ and can be compiled e.g. with Visual C/C++, 6.0. http://server.ccl.net/cgi-bin/ccl/message.cgi?1995+04+13+010http://www.ccl.net/cca/software/SOURCES/Cpp/atomic-DF/index.shtml

  8. FDA Carbon -- Total density: r2R2 vs r1 bohr = 0.5292 Å

  9. FDA Carbon -- Orbitals: rR vs r

  10. FDA Orbital Summary -- Carbon nl occ E KE <1/r> <r> 1s 2.00 -10.8710 16.5840 5.7583 0.2643 2s 2.00 -0.6769 1.8255 0.9670 1.5010 2p 2.00 -0.3555 1.4282 0.8313 1.6628 Energy Summary kinetic energy = 39.6755 potential energy = -77.0810 one-electron energy = -51.0043 two-electron energy = 13.5987 total energy = -37.4055 virial ratio = -1.9428 Energy units1 Hartree = 2625.5 kJ/mol = 627.51 kcal/mol = 27.211 eV

  11. FDA Silicon -- Total density: r2R2 vs r

  12. FDA Tin -- Total density: r2R2 vs r

  13. FDA Uuq (Z = 114) -- Total density: r2R2 vs r

  14. PCGam The PCgam script is a simple frontend for composing and running PC Gamess jobs on single CPU systems or in parallel on SMP and/or separated nodes. A new version 6.4 of PC GAMESS has been released on 09 March 2004, running under a Windows (98SE, ME, NT, 2K, XP) or Linux environments. Alex A. Granovsky, Lomonosov State University, Moscow, has developed it and added a rich set of 25 Functionals with fast DFT algorithms. Included are a FASTDIAG.dll and various instructions for the different executables optimized for a number of CPU's. An even faster version 6.5 will be released shortly. It has linear scaling for large molecules.

  15. PCGam PCGam Dialect script singlet CH2 B3LYP1/6-311+G(d,p) http://www.chemsoft.ch/qc/pcgam.html

  16. PCGam structure visualization with Jmol Energy units 1 Hartree = 2625.5 kJ/mol = 627.51 kcal/mol = 27.211 eV =219470 cm-1 http://srdata.nist.gov/cccbdb/ CH2 singlet CH2 triplet 101.5 o B3LYP1134.1 o Herzberg 102.4 o NIST 135.5 o ground state Energy -39.1472226265 a.u. Energy -39.1665909580 a.u.

  17. PCGam visualization with Molekel CH2 singlet Electron density Electron density surfacewith electrostatic potential

  18. PCGam visualization with Molekel CH2 singlet HOMO - 2 HOMO - 1 HOMO

  19. RUNpcg RUNpcg is a 'Dialect' GUI used in conjunction with PC Gamess (Alex A. Granovsky, 2004). RUNpcg allows one to build a molecule, save it, run PC Gamess, and view the structure directly from the output or as a .pdb or .xyz file using free software that can be downloaded off the Internet. By using the 'Configuration File', one can customize the interface to one’s own system. The style of RUNpcg is inspired by Wayne P. Anderson’s pcgRUN 1.0 (J Chem Ed, 2003, implemented in Tcl/Tk). Just one piece of software has been borrowed from WPA. This is 'gamout2pdb.exe', a FORTRAN binary which produces three files based on PC GAMESS output, 'molecule.pdb', 'molecule.ent' identical to the previous, and 'molecule.xyz'.

  20. RUNpcg PC GAMESS 6.4Alex Granovsky C6H6 D6h B3LYP1/6-31G(d) Optimize Hessian Raman

  21. RUNpcg Input

  22. RUNpcg Advanced

  23. RUNpcg Visualization with Molekel

  24. RUNpcg NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION -------------------------------------------------------- 6 7 8 9 10 FREQUENCY: 19.51 415.23 415.23 619.20 619.20 IR INTENSITY: 0.00000 0.00000 0.00000 0.00000 0.00000 RAMAN INTENSITY: 13.117 0.006 0.009 3.989 4.113 DEPOLARIZATION: 0.750 0.750 0.476 0.727 0.691 11 12 13 14 15 FREQUENCY: 694.42 718.07 864.51 864.51 968.85 IR INTENSITY: 1.83527 0.00000 0.00000 0.00000 0.00000 RAMAN INTENSITY: 0.000 0.000 5.952 5.952 0.009 DEPOLARIZATION: 0.155 0.750 0.750 0.750 0.626 16 17 18 19 20 FREQUENCY: 968.85 1010.83 1015.50 1021.15 1067.84 IR INTENSITY: 0.00000 0.00000 0.00002 0.00000 0.07878 RAMAN INTENSITY: 0.013 0.000 54.945 0.000 0.000 DEPOLARIZATION: 0.352 0.750 0.098 0.316 0.750 21 22 23 24 25 FREQUENCY: 1067.84 1184.90 1207.39 1207.39 1356.31 IR INTENSITY: 0.07857 0.00000 0.00000 0.00000 0.00000 RAMAN INTENSITY: 0.000 0.000 10.411 15.804 0.000 DEPOLARIZATION: 0.750 0.025 0.700 0.373 0.001 26 27 28 29 30 FREQUENCY: 1386.39 1530.30 1530.30 1654.90 1654.90 IR INTENSITY: 0.00000 0.15280 0.15279 0.00000 0.00000 RAMAN INTENSITY: 0.000 0.000 0.000 11.791 11.691 DEPOLARIZATION: 0.181 0.750 0.750 0.735 0.750 31 32 33 34 35 FREQUENCY: 3151.21 3160.03 3160.03 3176.97 3176.97 IR INTENSITY: 0.00000 0.00000 0.00000 1.23177 1.23170 RAMAN INTENSITY: 0.000 136.160 136.106 0.000 0.000 DEPOLARIZATION: 0.662 0.749 0.750 0.750 0.750 36 FREQUENCY: 3191.27 IR INTENSITY: 0.00001 RAMAN INTENSITY: 344.428 DEPOLARIZATION: 0.115

  25. RUNpcg IR and Raman spectrum

  26. RUNpcg Mode 181016 cm-1(unscaled) Mode 261386 cm-1(unscaled) (Modes 1-6 are translation + rotation) Mode 36: 3191 cm-1 (unscaled)

  27. WingRUN WingRUN is a 'Dialect' GUI used in conjunction with a special version of the original "GAMESS", version 19 May 2004 R3, running in a Windows environment (98SE, ME, NT, 2K, XP) with the help of Cygwin1.dll but without the necessity of a full Cygwin installation. Nuno A.G. Bandeira, Lisbon, has compiled a WinGamess version with special compilation/linking scripts, available from GAMESS-US. WingRUN allows one to build a molecule, save it, run Gamess, and view the structure directly from the output or as a .pdb or .xyz file using free software that can be downloaded off the Internet. By using the 'Configuration File', one can customize the interface to one’s own system. An earlier version, Cygam, similar in type to Pcgam, has now been discontinuedThe style of WingRUN, similar to RUNpcg, is inspired by Wayne P. Anderson’s pcgRUN 1.0.

  28. WingRUN GAMESS 19 May 2004 R3compiled under Cygwin by Nuno A. G. Bandeira CH4 Td 6-31G(d) Optimize Hessian Raman

  29. WingRUN CH4 electron density with MEP

  30. WingRUN CH4 IR and Raman spectrum

  31. WingRUN Property from CH41641.out NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION -------------------------------------------------------- 1 2 3 4 5 FREQUENCY: 0.03 0.03 0.03 3.86 3.86 IR INTENSITY: 0.00000 0.00000 0.00000 0.00000 0.00000 RAMAN INTENSITY: 0.000 0.000 0.000 0.000 0.000 DEPOLARIZATION: 0.359 0.363 0.339 0.451 0.454 6 7 8 9 10 FREQUENCY: 3.86 1487.94 1487.94 1487.94 1702.60 IR INTENSITY: 0.00000 0.24303 0.24303 0.24303 0.00000 RAMAN INTENSITY: 0.000 2.642 2.641 2.641 32.667 DEPOLARIZATION: 0.609 0.750 0.750 0.750 0.750 11 12 13 14 15 FREQUENCY: 1702.60 3197.23 3301.74 3301.74 3301.74 IR INTENSITY: 0.00000 0.00000 0.94215 0.94216 0.94216 RAMAN INTENSITY: 32.667 134.601 65.026 65.026 65.026 DEPOLARIZATION: 0.750 0.000 0.750 0.750 0.750 (Modes 1-6 are translation + rotation)

  32. WingRUN (Modes 1-6 are translation + rotation) Mode 7 T2 1488 cm-1 unscaled Mode 11 E 1703 cm-1 unscaled Mode 12 A1 3197 cm-1 unscaled Mode 13 T2 3302 cm-1 unscaled

  33. Protonation of CH4 PCgam scriptPC GAMESS 6.5(Alex A. Granovsky) DFT Calculations on CH4 and CH5+ (2 confomers)B3LYP1/6-311+G(d,p)

  34. Protonation of CH4 1 a.u. = 1 Hartree = 2625.5 kJ/mol = 627.51 kcal/mol = 27.211 eV CH4 Energy-40.5344787375 a.u. CH5+ Energy-40.7443648344 a.u. CH5+ Energy-40.7467844215 a.u.

  35. Exploring Chemsoft Software Molecular builders ArgusLab 3.1 and 4.0(Windows)currently free for academic use http://www.arguslab.com/

  36. Exploring Chemsoft Software Molecular builders ACD ChemSketch

  37. Exploring Chemsoft Software Molecular builders Marvin (online demo)from ChemAxon http://ed.augie.edu/~viste/builder/index.html

  38. Exploring Chemsoft Software Molecular builders GhemicalA molecular modelling package released under the GNU GPLLinux http://www.uku.fi/~thassine/ghemical/http://bioinformatics.org/ghemical/http://www.vigyaancd.org/

  39. Exploring Chemsoft Software PCgam scriptPC GAMESS 6.5(Alex A. Granovsky) DFT Calculations on CO, COH+, HCO+B3LYP1/6-311+G(d,p)

  40. Exploring Chemsoft Software CO polarity CO CO electron density with mep Dipole momentC- O+ CO HOMO mep scale Calculated dipole moment: 0.072 Debye with C- O+Expt: 0.1222 D with C- O+ (electric resonance molecular beam expt)[Frank Jensen, Introduction to Computational Chemistry, 1999, p. 286] Mulliken charges C = +0.019 O = -0.019Löwdin charges C = +0.095 O = -0.095

  41. Exploring Chemsoft Software Protonation of CO CO Energy-113.3505430503 a.u. COH+ Energy-113.5205749573 a.u. HCO+ Energy-113.5831658647 a.u. 1 a.u. = 1 Hartree = 2625.5 kJ/mol = 627.51 kcal/mol = 27.211 eV

  42. Molecular Modeling on an Undergraduate BudgetExploring Chemsoft Software Summary This presentation has explored three software packages which are freely available on the Chemsoft website in Switzerland. http://www.chemsoft.ch/ These provide convenient graphical interfaces (Dialect scripts) for PC-GAMESS (recent DFT version of Alex Granovsky), GAMESS (US), and Fda (non-relativistic atomic structure). These packages are in the spirit of Wayne P. Anderson.

  43. Exploring Chemsoft Software

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