This page provides links to the structures of molecules discussed in class. The structures come from a variety of sources which are indicated if known. The coordinates of the structures are in the pdb (Brookhaven protein database) format which can be read by the viewer RasMol. Pomona students can download the Berkeley version of RasMol from the directory v:\public\rasmol.

MOPAC is a package which solve the Schroedinger wave equation and calculates molecular orbitals of the valence electrons. The core electrons are handled empirically.

1. Molecules used to illustrate the Lewis electron dot method.
   • ammonia, NH₃(g) (MOPAC structure)
   • hydrazine, N₂H₄(g), nitrogen-nitrogen single bond (MOPAC structure)
   • diimide, N₂H₂(g), nitrogen-nitrogen double bond (MOPAC structure, trans isomer shown)
   • nitrogen, N₂(g), nitrogen-nitrogen triple bond (MOPAC structure, trans isomer shown)

2. Molecules used to illustrate VSEPR
   (The Berkeley site is the source of these structures.)
   • linear molelcule (sp): CO₂
   • trigonal planar (sp²): SO₂
   • tetrahedral (sp³): CH₄
   • trigonal bipyramid (dsp³): PF₅, ClF₃, SF₄
   • octahedral (d²sp³): SF₆

3. Molecules used to illustrate hybridization, conformers, and isomers
   • 1,2-difluoroethane, CH₂FCH₂F, trans conformer (MOPAC structure)
   • 1,2-difluoroethane, CH₂FCH₂F, gauche conformer (MOPAC structure)
   • 1,2-difluoroethylene, CHFCHF, trans (E) geometrical isomer (MOPAC structure)
   • 1,2-difluoroethylene, CHFCHF, cis (Z) geometrical isomer (MOPAC structure)
   • difluoroacetylene, FCCF (MOPAC structure)
   • the two enantiomers (optical isomers) of 2-butanol: R and S
   • 1,3-difluoroallene, CHFCCHF, R optical isomer (MOPAC structure)

4. Molecules used to illustrate transition-metal complexes
   • cis and trans diamminedichloroplatinum(II), square planar complexes
   • delta and lambda tris(ethylenediamine)cobalt(III) cation, a pair of optical isomers (enantiomers)
   • the crystal structure of the EDTA complex of manganese(II). Source: the Cambridge Structural Database System.

5. Crystal structures of binary ionic substances

   The bond lengths are not drawn in several of these structures so to show the atoms in Rasmol, set the DISPLAY option to "space filling" or "balls and sticks". The structures have been downloaded from a Navy site and were converted from the xyz format to the pdb format. Rasmol can display structures in the xyz format but your browser must be set to recognize the MIME type (chemical) and subtype (x-xyz) and extension (xyz).

   • cubic closest packing (ccp) structure
   • hexagonal closest packing (hcp) structure
   • sodium chloride structure. The sodium cations fill all of the octahedral holes in a ccp lattice of chloride anions. The coordination number of each ion is 6.
   • zinc sulfide (sphalerite) structure. The zinc cations fill half of the tetrahedral holes in a ccp lattice of sulfide anions. The coordination number of each type of ion is 4.
   • fluorite structure. In the classic fluorite structure exhibited by the mineral fluorite, CaF₂, the fluoride anions fill all of the tetrahedral holes in a ccp lattice of calcium ions. The case examined in class was Li₂S which has the antifluorite structure in which the lithium cations fill all the tetrahedral holes in a ccp lattice of sulfide anions.

6. Network covalent solids

   These structures were also downloaded from the Navy site.

   • diamond. The unit cell and only a small portion of the infinite lattice is shown.
   • graphite. A small portion of four sheets is shown. Strong covalent bonds exist within a sheet and weak forces between the sheets.

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Last updated, 8 August 1997