Molecular Structure Calculations

Molecular Structure Calculations

Colby Chemistry, Paul J. Schupf Computational Chemistry Lab

The simple theories of bonding that we learn in General Chemistry are powerful and useful. These theories, which include Lewis structures, VSEPR, and hybridization, are simple models that help predict chemical properties. However, Lewis dot structures and hybridization are approximations that may or may not match reality. We should verify the usefulness of our simple predictions with molecular orbital theory. If the theoretical calculations are done carefully, we can learn a lot about chemical structure by comparing our Lewis structures and hybridization arguments with the molecular orbitals.

The calculations in this database include bond lengths, angles, atomic charges, the dipole moment, bond orders, and molecular orbital energies. The best Lewis structure that fits the molecular orbitals is also calculated, so you can directly compare with your predictions. This best Lewis structure is presented with formal electron pair localized bonds and the hybridization of the atomic orbitals used to form these localized bonds. The Chime plugin is needed to see the 3-D structure of the molecules in these pages. See the link at the bottom of the page for the Chime plugin.

Molecular orbital theory is based on approximations also. These calculations are done with some of the best available calculation methods (DFT for geometry and molecular orbital energies and ab initio for properties). We use Alain St-Amant's DeFT program (University of Ottawa).

The Molecular Structure Input Form, see below, will allow you to do calculations for molecules not in the database. These calculations take time; 1-2 hours in some cases.

You can use the Formula Search page or browse the links below. As of 07/12/05 there are 1056 structures in the database.
A Best Lewis Structure and Donor Acceptor Interactions Tutorial is available to help you interpret those output sections. These Lewis structure calculations are done using NBO Analysis.
Answer some Study Questions to help your understanding of some interesting chemistry.

Example Molecular Orbital Results

LiH LiF LiCl LiOH LiCN LiBr C₂ N₂ NO O₂ CO F₂

Many More Diatomic molecules and ions

H₃⁺     Li₂O     BeH₂     BeCl₂     diborane     BH₃     BH₂CN     BH₂SH
BF₃     BF₃2-     BF₄⁺     BF₂O^-     BCl₃     BH₃NH₃     BH₃CO     BH₃PH₃     BO₂NO
C₃     C₅     H₂O     H₃O⁺     H₄O⁺     O₃     O₄     CO₂     OCS     cyclic CO₂     CO₂^-     HCO⁺     HOC⁺
N₃ radical     N₃ quartet     HN₃     N₃^-     NCO     HNCNH     CNNO
NO₂     NO₂⁺     NO₂^-     HOON     NOO^-     NO₂^- triplet     NO₂²⁺     NO₃^-     NO₃^-triplet     NO₂O^-
N₂O     cyclic N₂O     cyclic N₂O₂     N₂O₄     NO₂NO
ONOOH     N₂H₂     N₂H₂ triplet     H₂NN     H₂NN triplet     NH₂F     NHF₂     NF₃     NF₄^-     N₂F₂     N₂F₄     BNHF
HNCl⁺     NH₂Cl     N₃Cl     NCl₂     NCl₃     NOCl     ONCl     NClO     ClNO₂     ClNOO     t-ClONO     OCl₂
OF₂     FOO•     FOOF     FNO₂     FOON     F₃^-     Cl₃^-     Cl₃F     ClF₂⁺
AlH₃     AlF₃     AlCl₃     Al₂Cl₆
SiH₄     SiH₃SiH₃     SiO₂
P₂     PCl₃     SO₂     SO₃     SO₃^-     SOCl₂     SO₂Cl₂     ClO₂     ClOO     ClO₂⁺     ClO₂^-     ClOO^-
FClO     FClO₂     K₂O

Many More Binary Hydrides and their Anions, Cations, and Radicals
Many More Triatomic molecules and their Anions, Cations, and Radicals
Many More Period 3 Compounds, Al, Si, P, S, and Cl
Many More Period 4 Compounds, Ga, Ge, As, Se, and Br

Acids

Onium Ions: NH₄⁺     NH₃F⁺     NH₃Cl⁺     H₃O⁺     H₃O₂⁺     H₂F⁺     PH₄⁺     H₃S⁺     H₂Cl⁺     H₂CN⁺
Hydrides: HF     HCl     HCN     HCN triplet     HNC     HNCO     HOCN     HONC     HCNO     HNCS     HSCN     HN₃
        H₂N₂     H₂N=N     N₂H₄     H₂O₂     P₂H₄     H₂S     H₂S₂
Oxyacids: H₂CO₃     HON     HNO     HNO₂     HNO₃     H₂O₂     HOF     HOCl
        HClO₃     HClO₄     H₃PO₂     H₃PO₃     H₃PO₄     HSOH     H₂SO₃     H₂SO₄

Anions

Hydride Conjugates: F^-     Cl^-     OH^-     CN^-     NCO^-     CNO^-     NCS^-     CNS^-     NSC^-     N₃^-     HN₂^-     N₂H₃^-     HOO^-
P₂H₃^-     HS^-
Oxyanions: HCO₃^-     CO₃^2-     CO₃OH^-     CO₃O^2-     NO^-     NO₂^-     NO₃^-     HO₂^-     O₂^2-     OF^-     OCl^-     ClO₂^-
        ClO₃^-     ClO₄^-     H₂PO₂^-     H₂PO₃^-     H₂PO₄^-     HPO₄^2-     PO₄^3-     HOS^-     HSO^-
        HSO₃^-    SO₃^2-    HSO₄^-    SO₄^2-     S₂O₃^2-

Many More Hydroxyl Compounds, Donor-Acceptor Oxides, Oxyacids, and Anions
Many More Formally Double Bonded Hydroxyl Compounds, Donor-Acceptor Oxides, and Oxyacids (e.g.Carbonic and Nitric acid)

Organics

ethane ethylene acetylene H₂C=C, vinylidene
methanol formaldehyde formic acid methylamine CF₃Cl

Many More Carbon Compounds, Organics, and Organic Reagents
Many More Organic Radical Cations, Neutral Radicals, Cations, and Anions

Oxides

NH₃->O CH₃NH₂->O CH₂NH->O CH₃OH->O CH₂O->O CH₂O->O triplet H₂N₂->O
PH₃->O CH₃PH₂->O H₂S->O CH₃SH->O CH₃F->O CH₃OF CH₃Cl->O H₂S->O₂

Reactive Intermediates

OH radical     HOO radical     H₂O₂⁺ radical     HCO₃ radical     CO₃^- radical     CO₃OH^-     CO₃O^2-     peroxodicarbonate dianion, O₂COOCO₂^2-
methylene singlet (CH₂)     methylene triplet (CH₂)     methyl radical (CH₃)     CH₃⁺
    ethyl radical (CH₃CH₂)     CH₃CH₂⁺     ethylene triplet     cyclopropane radical     HCC•     HCC^-
CH₃NH^-     CH₃OH⁺     CH₃OH₂⁺     CH₃O^-     CH₃O radical     CH₂OH⁺     CH₃CO⁺     CH₂CHO^-
CF₂ singlet     CF₂ triplet     CF₃•     CF₃⁺     CCl₂ singlet     CCl₂ triplet
CHCl singlet     CHCl triplet     CHBr singlet     CHBr triplet
H₂CF⁺     CH₂Cl⁺     CH₂Cl^-     trans-C₂H₄Cl₂⁺     Cl₂C=C singlet
allyl⁺     allyl radical     allyl^-     allylalcohol radical     allylchloride radical     1-chloropropane radical
HCONH^-     N₃ radical     N₃³⁺ singlet     N₃³⁺ triplet     N₂H⁺

Hydrogen Bonded and Neutral Complexes

H₂O dimer     NH₃ dimer     HF...water     HF...NH₃     HCl...NH₃     H₂O...H₂S     H₂S...H₂O     SO₂...H₂O     H₂O...formaldehyde
HCN...formaldehyde     HCN...H₂CC     water...CO     water...HPO₂     CO₂...H₂     CO₂...CO₂
CO₂...water     H₂O...SO₃     H₂S...SO₃     PCl₃...Cl₂     Cl₂...Cl ₂     CH₃radical...H₂     H₂O...Cl•

Ion-Molecule Complexes

Li⁺..H₂O     Li⁺..(H₂O)₂     BeCl₂²⁺     water...superoxide^-
Be²⁺...H₂C=CH₂ unsymmetrical     Be²⁺...H₂C=CH₂ symmetrical     Be⁺...H₂C=CH₂ unsymmetrical     Be⁺...H₂C=CH₂ symmetrical
FHF^-     CO₂F^-     H₂...OH^-     water...HCONH^-     O₃...Br^-
H₃O⁺...H₂O     H₃O⁺...CO₂     H₃O⁺...N₂     H₃O⁺...HO•     NO⁺...H₂O     NO⁺...N₂     NO⁺...O₂

Atomic and Ionic Energies

atomic energies cation energies anion energies

Weird, Wacky, High Energy Structures

HCl^- H₃Cl CH₄²⁺ COH₂ CH₂..HCl CH₃OHCH⁺ HNCO-cyclic C₄N₂ CO₂O^2- CO₂^2- BH₄⁺ AlH₄⁺ FClPCl PF₄⁺F^- ClF₄^-

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Molecular Structure Input Form

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This work was supported by an Academic Research Infrastructure Grant from the National Science Foundation, no. 9512457. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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