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     NCN2-     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-     CO32-     CO3O2-     H2PO2-     PO43-     SO42-     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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Molecular Structure Input Form

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Results Here


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

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