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


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   


Hydride Conjugates: F-     Cl-     OH-     CN-     NCO-     CNO-     NCS-     CNS-     NSC-     N3-     HN2-     N2H3-     HOO-    
P2H3-     HS-    
Oxyanions: HCO3-     CO32-     CO3OH-     CO3O2-     NO-     NO2-     NO3-     HO2-     O22-     OF-     OCl-     ClO2-    
        ClO3-     ClO4-     H2PO2-     H2PO3-     H2PO4-     HPO42-     PO43-     HOS-     HSO-    
        HSO3-    SO32-    HSO4-    SO42-     S2O32-    

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)


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


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-     CO3O2-     peroxodicarbonate dianion, O2COOCO22-    
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     CO2O2-     CO22-     BH4+     AlH4+     FClPCl     PF4+F-     ClF4-    

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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