Exploring Chemsoft Software

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Exploring Chemsoft Software
Ernst J. Schumacher University of Bern,
Switzerland and Arlen Viste Augustana College
(SD) 25 Aug 2004
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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.ed
u/webmo/
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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/colle
ction/reviewed/WW017/
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Exploring Chemsoft Software http//www.chemsoft.c
h/
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
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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/
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Exploring Chemsoft Software
FDAFinite Difference Atomic Structure
calculations
Carbon
http//www.dcb.unibe.ch/groups/schumacher/qc/fda.h
tm
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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
?19950413010http//www.ccl.net/cca/software/SO
URCES/Cpp/atomic-DF/index.shtml
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FDA
Carbon -- Total density r2R2 vs r1 bohr
0.5292 Å
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FDA
Carbon -- Orbitals rR vs r
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FDA
Orbital Summary -- Carbon nl occ E
KE lt1/rgt ltrgt 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
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FDA
Silicon -- Total density r2R2 vs r
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FDA
Tin -- Total density r2R2 vs r
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FDA
Uuq (Z 114) -- Total density r2R2 vs r
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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.
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PCGam
PCGam Dialect script singlet CH2 B3LYP1/6-311G(d,
p)
http//www.chemsoft.ch/qc/pcgam.html
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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
B3LYP1
134.1 o Herzberg 102.4 o
NIST 135.5 o ground
state Energy -39.1472226265 a.u.
Energy -39.1665909580 a.u.
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PCGam visualization with Molekel
CH2 singlet
Electron density
Electron density surfacewith electrostatic
potential
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PCGam visualization with Molekel
CH2 singlet
HOMO - 2
HOMO - 1
HOMO
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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 ones own system. The
style of RUNpcg is inspired by Wayne P.
Andersons 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'.
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RUNpcg
PC GAMESS 6.4Alex Granovsky C6H6 D6h B3LYP1/6-31G
(d) Optimize Hessian Raman
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RUNpcg
Input
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RUNpcg
Advanced
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RUNpcg
Visualization with Molekel
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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
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3191.27 IR INTENSITY 0.00001 RAMAN
INTENSITY 344.428 DEPOLARIZATION
0.115
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RUNpcg
IR and Raman spectrum
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RUNpcg
Mode 181016 cm-1(unscaled)
Mode 261386 cm-1(unscaled)
(Modes 1-6 are translation rotation)
Mode 36 3191 cm-1 (unscaled)
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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 ones 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. Andersons
pcgRUN 1.0.
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WingRUN
GAMESS 19 May 2004 R3compiled under Cygwin by
Nuno A. G. Bandeira CH4 Td 6-31G(d) Optimize Hes
sian Raman
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WingRUN
CH4 electron density with MEP
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WingRUN
CH4 IR and Raman spectrum
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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)
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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
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Protonation of CH4
PCgam scriptPC GAMESS 6.5(Alex A.
Granovsky) DFT Calculations on CH4 and CH5
(2 confomers)B3LYP1/6-311G(d,p)
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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.
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Exploring Chemsoft Software
Molecular builders ArgusLab 3.1 and
4.0(Windows)currently free for academic use
http//www.arguslab.com/
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Exploring Chemsoft Software
Molecular builders ACD ChemSketch
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Exploring Chemsoft Software
Molecular builders Marvin (online demo)from
ChemAxon
http//ed.augie.edu/viste/builder/index.html
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Exploring Chemsoft Software
Molecular builders GhemicalA molecular modelling
package released under the GNU GPLLinux
http//www.uku.fi/thassine/ghemical/http//bioin
formatics.org/ghemical/http//www.vigyaancd.org/
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Exploring Chemsoft Software
PCgam scriptPC GAMESS 6.5(Alex A.
Granovsky) DFT Calculations on CO, COH,
HCOB3LYP1/6-311G(d,p)
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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-
OExpt 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
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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
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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.
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Exploring Chemsoft Software