Colby Chemistry

Molecular Structure Calculations

The simple theories of bonding that we learn in General Chemistry are powerful and useful. These theories are simple models that help us 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 our chemical structure as we compare our Lewis structures and hybridization arguments with the molecular orbitals.

The Molecular Structure Input Form will allow you to calculate molecular properties such as bond lengths, angles, atomic charges, the dipole moment, bond orders, and molecular orbital energies. The best Lewis structure that fits the molecular orbitals will also be calculated, so you can directly compare with your prediction. 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.

Molecular orbital theory is based on approximations also. Your calculations will be done with some of the best available calculation methods (DFT for geometry and molecular orbital energies and ab initio for properties). These calculations take time; 1-2 hours in some cases. If you don't want to wait for the calculations, try some of the example calculations listed below. Answer some Study Questions to help your understanding of some interesting chemistry.

Example Molecular Orbital Results

LiH     LiF     BeH₂     BH     diborane     BF     BF₃
C₂     N₂     NO     NO^-     NO⁺     O₂     O₂ singlet     O₂^-     CO     NF     SO     ClO
H₂O     O₃     CO₂     NCN^2-     NO₂     NO₂⁺     NO₂^-     N₂O     ONOOH     NOCl     ONCl
FOOF     F₃^-     Cl₃^-
AlH₃     AlF₃     AlCl₃     AlCl₄^-     ClAlO
SiH₄     SiH₃SiH₃     CH₂SiH₂     SiO₂     SiCl₂O     CH₃SiOCl
PCl₃     S₄     SO₂     SO₃     SF₂     SF₄     ClO₂

Acids

Onium Ions: NH₄⁺     H₃O⁺     H₂F⁺     PH₄⁺     H₃S⁺     H₂Cl⁺
Hydrides: HF     HCl     HCN     HNCO     HOCN     HNCS     HSCN     HN₃
        H₂N₂     H₂N=N     N₂H₄     P₂H₄     H₂S
Oxyacids: HON     HNO     HNO₂     HNO₃     H₂O₂     HOF     HOCl
        HClO₃     HSOH     H₃PO₂

Anions

Hydride Conjugates: F^-     Cl^-     OH^-     CN^-     NCO^-     NCS^-     CNS^-     N₃^-
        HN₂^-     N₂H₃^-     P₂H₃^-     HS^-
Oxyanions: NO^-     NO₂^-     NO₃^-     HO₂^-     OF^-     OCl^-
        ClO₃^-     HOS^-     HSO^-     CO₃^2-     CO₃O^2-     H₂PO₂^-     PO₄^3-     SO₄^2-     ClO₄^-

Organics

ethane     ethylene     acetylene     H₂C=C, vinylidene
formaldehyde     formic acid     formate ion     formoylperoxide     formamide
        formylchloride
methanol     methylamine     methylammonium ion     acetonitrile     methylisocyanide     diazomethane
        methylphosphine     methylthiol     chloromethane
        nitrosomethane     methane sulfonate ion     methane sulfonyl chloride
chloroethane     acetaldehyde     ketene     acetylfluoride     acetylchloride     oxalylchloride
gauche-difluoroethane     anti-difluoroethane     gauche-dichloroethane     anti-dichloroethane
        1,1,1-trifluoroethane
hydroxylamine    hydroxylammonium ion    CH₂NH-methanimine    CH₂NH₂⁺-methaniminonium ion    NH₂CN-cyanamide
NH₃->O     CH₃NH₂->O     CH₂NH->O     H₂N₂->O
PH₃->O     CH₃PH₂->O     H₂S->O     CH₃SH->O     H₂S->O₂
CH₃Li     LiNH₂     LiNH₂-dimer     LiNHCH₃

Reactive Intermediates

OH radical     HOO radical
methylene singlet (CH₂)     methylene triplet (CH₂)     methyl radical (CH₃)     ethyl radical (CH₃CH₂)     HCC^-
CH₃NH^-     CH₃O^-     CH₂OH⁺     CH₃CO⁺     N₂H⁺     CH₂CHO^-     CF₂ singlet     H₂CF⁺     H₂CCl⁺
HCONH^-     N₃³⁺ singlet     N₃³⁺ triplet

Hydrogen Bonded and Neutral Complexes

H₂O dimer NH₃ dimer HF...water HF...NH₃ H₂O...H₂S H₂S...H₂O H₂O...formaldehyde HCN...formaldehyde water...CO water...superoxide^- water...HCONH^-
CO₂...water CH₃radical...H₂

Ion-Molecule Complexes

Li⁺..H₂O FHF^-

Atomic and Ionic Energies

atomic energies cation energies anion energies

Weird, Wacky, High Energy Structures

HCl^- HNCO-cyclic BH₄⁺ AlH₄⁺

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This work was supported by an Academic Research Infrastructure Grant from the National Science Foundation, no. 9512457.

About the calculation methods