Visualizing Electrons in Atoms and Molecules

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Visualizing Electronsin Atoms and Molecules
In honor of Milton P. Hanson 40 years colleague
and friend
Arlen Viste 17 April 2004
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Visualizing Electrons in Atoms and Molecules
and 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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Visualizing Electrons in Atoms and Molecules
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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Visualizing Electrons in Atoms and Molecules
FDAFinite Difference Atomic Structure
calculations
Carbon
http//www.dcb.unibe.ch/groups/schumacher/qc/fda.h
tm
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Visualizing Electrons in Atoms and Molecules
Carbon -- Total density r2R2 vs r1 bohr
0.5292 Å
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Visualizing Electrons in Atoms and Molecules
Carbon -- Orbitals rR vs r
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Visualizing Electrons in Atoms and Molecules
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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Visualizing Electrons in Atoms and Molecules
Silicon -- Total density r2R2 vs r
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Visualizing Electrons in Atoms and Molecules
Germanium -- Total density r2R2 vs r
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Visualizing Electrons in Atoms and Molecules
Tin -- Total density r2R2 vs r
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Visualizing Electrons in Atoms and Molecules
Lead -- Total density r2R2 vs r
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Visualizing Electrons in Atoms and Molecules
Uuq (Z 114) -- Total density r2R2 vs r
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Visualizing Electrons in Atoms and Molecules
singlet CH2
http//www.chemsoft.ch/qc/pcgam.html
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Visualizing Electrons in Atoms and Molecules
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
B3LYP
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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Visualizing Electrons in Atoms and Molecules
CH2 singlet
Electron density
Electron density surfacewith electrostatic
potential
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Visualizing Electrons in Atoms and Molecules
CH2 singlet
HOMO - 2
HOMO - 1
HOMO
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Visualizing Electrons in Atoms and Molecules
Benzenediazonium ionC6H5N2
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Visualizing Electrons in Atoms and Molecules
Benzenediazonium ion, C6H5N2
Electron density surface
Electron density surface withelectrostatic
potential
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Visualizing Electrons in Atoms and Molecules
Benzenediazonium ionMolecular Orbitals
HOMO
HOMO - 1
LUMO
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Visualizing Electrons in Atoms and Molecules
Benzenediazonium ionMolecular Orbitals
HOMO - 2
HOMO - 3
HOMO - 4
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Visualizing Electrons in Atoms and Molecules
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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Visualizing Electrons in Atoms and Molecules
Molecular builders ArgusLab 3.1 and
4.0(Windows)free for academic use
http//www.arguslab.com/
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Visualizing Electrons in Atoms and Molecules
Molecular builders Marvin (online demo)from
ChemAxon
http//ed.augie.edu/viste/builder/index.html
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Visualizing Electrons in Atoms and Molecules
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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Visualizing Electrons in Atoms and Molecules
Molecular builders PyMolLinux, Mac,
WindowsPyMOL is a USER-SPONSORED molecular
modeling system with an OPEN-SOURCE foundation.
PyMol builder
Jmol display
http//pymol.sourceforge.net/http//pymol.sourcef
orge.net/obtaining.htmlhttp//jmol.sourceforge.ne
t/
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Visualizing Electrons in Atoms and Molecules
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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Visualizing Electrons in Atoms and Molecules
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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Visualizing Electrons in Atoms and Molecules
Best wishes to Milt and Marj!