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Visualizing Electrons in Atoms and Molecules. In honor of Milton P. Hanson 40 years colleague and friend. Arlen Viste 17 April 2004. Visualizing Electrons in Atoms and Molecules.

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visualizing electrons in atoms and molecules
Visualizing Electronsin Atoms and Molecules

In honor of Milton P. Hanson

40 years colleague and friend

Arlen Viste

17 April 2004

visualizing electrons in atoms and molecules2
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.edu/~webmo/

visualizing electrons in atoms and molecules3
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/

visualizing electrons in atoms and molecules4
Visualizing Electrons in Atoms and Molecules

FDAFinite Difference Atomic Structure calculations

Carbon

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

visualizing electrons in atoms and molecules5
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

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

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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

visualizing electrons in atoms and molecules10
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 B3LYP134.1 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 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.

visualizing electrons in atoms and molecules22
Visualizing Electrons in Atoms and Molecules

Molecular builders

ArgusLab 3.1 and 4.0(Windows)free for academic use

http://www.arguslab.com/

visualizing electrons in atoms and molecules23
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://bioinformatics.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.sourceforge.net/obtaining.htmlhttp://jmol.sourceforge.net/

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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- 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

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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