Molecules

Molecular structures

There's a dearth of decent resources for molecular drawings out there. (Update: at least until PubChem arrived). This is my little contribution to plugging that gap. The files are all available in (at least) PNG graphical format, and ISIS Draw SKC format, which you can manipulate to your heart's content (providing you install ISIS Draw of course). There are also a few Brookhaven protein database format (PDB) files you can view using Chime, Jmol, or similar. The JPG files are generally screen-dumps of the PDB files, and the GIFs are animated spinning images of the PDB files.

All the PNG, SKC and JPG files were made by me, and you may do what you will with them. The small molecular PDB files have been generated from SMILES strings, generally downloaded from PubChem, 3D-ed using CORINA, and diddled with by hand to reinstate the multiple bonds that PDB doesn't really support. The larger molecules (mostly proteins) have been downloaded from sites allowing free redistribution (mostly the RCSM databank). The GIFs were made using pdb2gif, and the membrane cutaways are reproduced from H. Heller, M. Schäfer & K. Schulten (1993) Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases. Journal of Physical Chemistry 97 8343-8360.

The orbitals were generated using Orbital Viewer, followed by some tarting with a Perl script to generate a faked PDB file from the (x,y,z) data. The orbitals are arranged with the x-axis horizontal, y-axis vertical, and z-axis coming out of the plane of the screen. Each orbital has 5000 points from the relevant distribution in a hydrogen or carbon atom (for hybrids and molecular orbitals). f-orbitals are those of the general set, not the cubic set. The quantum numbers and a little more data are in the headers of the PDB file, should you want them.

Of all the pages I have ever written, this one has the largest chance of being packed full of errors, so caveat surfer. In particular, the stereochemistry of items that are not explicitly labelled with an IUPAC descriptor may well be unspecified. Drawing the sugars nearly killed me, so there will almost certainly be mistakes in some of the more obscure ones.

| Alcohols | Aldehydes and ketones | Alkaloids | Alkanes | Alkenes | Alkynes | Amides | Amines | Amino acids | Arenes | Arsenic compounds | Azo compounds | Biochemical pathways | Boron compounds | Carbamates | Carboxylic acids | Cofactors | Cyanides | Esters | Ethers | Halogen compounds | Lipids | Nitroarenes and anilines | Nucleotides | Orbitals | Phenols | Phosphorus compounds | Phthalates | Polymers | Porphyrins | Proteins | Silicon compounds | Sugars | Sulfur compounds | Terpenes |

Alcohols

Aldehydes and ketones

Alkaloids

Alkanes

Alkenes

Alkynes

Amides

Amines

Amino acids

Arenes

Arsenic compounds

Azo compounds

Biochemical pathways

Boron compounds

Carbamates

Carboxylic acids

Cofactors

Cyanides

Esters

Ethers

Halogen compounds

Lipids

Nitroarenes and anilines

Nucleotides

Orbitals

Phenols

Phosphorus compounds

Phthalates

Polymers

Porphyrins

Proteins

Silicon compounds

Sugars

Sulfur compounds

Terpenes

Peer Review.
This page has been peer reviewed by 9 people. Many thanks to Martin Redovich, Sebastian Curth, J. Dean, Dennis Turner, Michael Bobrick, James Nairne, Todd Williams, Jean-Luc Pruvost, Jean-Philippe Demers, and Shana for pointing out some of the the most appalling errors.