Exploring Chemsoft Software Ernst J. Schumacher University of Bern, Switzerland and Arlen Viste...

Exploring Chemsoft Software

Ernst J. SchumacherUniversity of Bern, Switzerland

and Arlen VisteAugustana College (SD)

25 Aug 2004


In memory of Prof. Wayne P. Anderson (1942-2003)

Bloomsburg University (PA)colleague and friend in MoleCVUE

fan of Linux and GAMESS

http://facstaff.bloomu.edu/wpa/http://ed.augie.edu/~webmo/

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/

Exploring Chemsoft Software http://www.chemsoft.ch/

FDAAtomic StructureDialect script by EJS for code of David J. Hesterberg (1995) based on Hermann and Skillman (1963)

PCGam and RunPcg Dialect scripts by EJS forPC-GAMESS (v. 6.4, Alex Granovsky, 2004)RunPcg style inspired by Wayne Anderson

Cygam and WingRun Dialect scripts by EJS forGAMESS (compiled under Cygwin by Nuno Bandeira in collaboration with E J Schumacher2003-2004)WingRun style inspired by Wayne Anderson


Ernst Schumacher

Prof. Emeritus

University of Berne

Switzerland

With son and grandson

http://www.chemsoft.ch/

http://www.dcb.unibe.ch/groups/schumacher/


FDAFinite Difference Atomic Structure calculations

Carbon

http://www.dcb.unibe.ch/groups/schumacher/qc/fda.htm

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

FDA

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

FDA

Carbon -- Orbitals: rR vs r

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

FDA

Silicon -- Total density: r2R2 vs r

FDA

Tin -- Total density: r2R2 vs r

FDA

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

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.

PCGam

PCGam Dialect script

singlet CH2

B3LYP1/6-311+G(d,p)

http://www.chemsoft.ch/qc/pcgam.html

PCGam structure visualization with Jmol

CH2 singlet CH2 triplet 101.5 o B3LYP1 134.1 o

Herzberg 102.4 o NIST 135.5 o ground state

Energy -39.1472226265 a.u. Energy -39.1665909580 a.u.

http://srdata.nist.gov/cccbdb/

Energy units 1 Hartree = 2625.5 kJ/mol = 627.51 kcal/mol = 27.211 eV =219470 cm-1

PCGam visualization with Molekel

CH2 singlet

Electron density Electron density surfacewith electrostatic potential

PCGam visualization with Molekel

CH2 singlet

HOMO - 2 HOMO - 1 HOMO

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'.

RUNpcg

PC GAMESS 6.4Alex Granovsky

C6H6

D6h

B3LYP1/6-31G(d)

Optimize

Hessian

Raman

RUNpcg

Input

RUNpcg

Advanced

RUNpcg

Visualization with Molekel

RUNpcgNORMAL 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





36 FREQUENCY: 3191.27 IR INTENSITY: 0.00001 RAMAN INTENSITY: 344.428 DEPOLARIZATION: 0.115

RUNpcg

IR and Raman spectrum

RUNpcg

Mode 181016 cm-1

(unscaled)

Mode 261386 cm-1

(unscaled)

Mode 36: 3191 cm-1 (unscaled)

(Modes 1-6 are translation + rotation)

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.

WingRUN

GAMESS 19 May 2004 R3compiled under Cygwin by Nuno A. G. Bandeira

CH4

Td6-31G(d)OptimizeHessianRaman

WingRUN

CH4 electron density with MEP

WingRUN

CH4 IR and Raman spectrum

WingRUN

Property from CH41641.out

NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION --------------------------------------------------------





WingRUN

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


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)

Protonation of CH4

CH4 Energy

-40.5344787375 a.u.

CH5+ Energy

-40.7443648344 a.u.

CH5+ Energy

-40.7467844215 a.u.

1 a.u. = 1 Hartree = 2625.5 kJ/mol = 627.51 kcal/mol = 27.211 eV


Molecular builders

ArgusLab 3.1 and 4.0(Windows)

currently free for academic use

http://www.arguslab.com/


Molecular builders

ACD ChemSketch


Molecular builders

Marvin (online demo)from ChemAxon

http://ed.augie.edu/~viste/builder/index.html


Molecular builders

GhemicalA molecular modelling package released under the GNU GPL

Linux

http://www.uku.fi/~thassine/ghemical/http://bioinformatics.org/ghemical/http://www.vigyaancd.org/


PCgam scriptPC GAMESS 6.5(Alex A. Granovsky)

DFT Calculations on CO, COH+, HCO+

B3LYP1/6-311+G(d,p)


CO polarity

CO mep scale CO electron density with mep

Dipole momentC- O+

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]

CO HOMO

Mulliken charges C = +0.019 O = -0.019Löwdin charges C = +0.095 O = -0.095


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

Molecular Modeling on an Undergraduate Budget Exploring 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.

Exploring Chemsoft Software Ernst J. Schumacher University of Bern, Switzerland and Arlen Viste...

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