Hyperactive Molecules: Part 1

  1. The first published paper with "clickable" chemical diagrams and animated molecules: P. Camilleri, D. Eggleston, H. S. Rzepa and M. L. Webb, J. Chem. Soc., Chem. Commun, 1994, 1135.

  2. The first published paper with Hyperactive Molecules using chemical MIME: D. O'Hagan and H. S. Rzepa, J. Chem. Soc., Chem. Commmun. , 1994, 2029.

  3. See "Chemical Applications of the World-Wide-Web": H. S. Rzepa, B. J. Whitaker and M. J. Winter, J. Chem. Soc., Chem. Commun., 1994, 1907 for a more detailed dicsussion.

  4. See the PDB database in action at the National Institutes of Health. (P. C. Fitzgerald). File size: various, but can be > 500,000.

  5. Three dimensional structure of the α pokeweed antiviral protein at 2.3 angstroms resolution" (PDB coordinates taken from H.Ago,J.Kataoka,H.Tsuge,N.Habuka,E.Inagaki,M.Noma, and M.Miyano, to be published). PDB File size: 182617.

  6. The C60 molecule (does your browser display the subscripts?). XYZ File size: 2252.

  7. Chymotrypsin Inhibitor 2 (A serine protease). The 2D noesy nmr spectrum of CI2 shows a number of cross peaks related to homoresidue, adjacent residue and cross residue contacts. (H. S. Rzepa). PDB File size: 36994.

  8. Mopac and Gaussian style input files showing how 1,3 dithiane may be oxidised by peracid (P. C. B. Page and H. S. Rzepa, to be published). MOPAC File size: 1575. Gaussian File size: 1894.

  9. Mapping a potential Energy Surface for cyclohexane 1,3-diol into MOPAC geometries (C. J. Leach and H. S. Rzepa, submitted as an abstract to the First Electronic Computational Chemistry Conference). The isometric contour map shows the COSMO calculated aqueous solvation energy as a function of the orientation of the two OH groups. Various hotspots (indicated with circles) indicate that MOPAC coordinates for that geometry can be downloaded and visualised. Note the prominent ridges in the contour map corresponding to intramolecular hydrogen bonds. File size: various, but less than 2000.

  10. A normal vibrational mode of Carbon Dioxide, read from a MOPAC FORCE calculation (O. Casher and H. S. Rzepa, unpublished). Mopac output File size: 8905.

  11. A Gaussian style output (verbose log) file showing a sequence of 15 successive geometry optimisation cycles as an animation. (O. Casher, D. O'Hagan, C. Rosenkranz, H. S . Rzepa, N.A. Zaidi, J. Chem. Soc., Chem. Commun, 1993, 1337). The second image shows the alternative pre-processed XYZ format for the Gaussian optimisation in the preceeding example (thanks to Raul E. Cachau).To activate the animation click on the image and select "animate" from the "Extras" drop down menu in Xmol. Gaussian output File size: 891326. XYZ File size: 12180.

  12. The protein Triose phosphate isomerase. His-95 in this remarkable enzyme has a highly anomalous pKa, being significantly lower than expected. This effect can be quantitatively modelled by the use of neural networks (S. Green, H. S. Rzepa and H. Broughton, J. Chem. Soc., Chem. Commun, 1992, 1178). PDB File size: 329508.

  13. An ATM SuperJanet based collaborative molecular visualisation session using Explorer EyeChem. To participate, you will need to enter the Remote IP address of a participating centre in the DISPLAY widgit that appears. In the two windows that appear you will be able to rotate, and discuss the molecules as a joint collaboration. (O. Casher, B. J. Whitaker and H. S. Rzepa, demonstrated on July 13, 1994 and on Channel 4 News on 27 July 1994). PDB File size: 329508.

  14. EyeChem visualisation of the Molecular Orbitals of Benzene. (O. Casher and H. S. Rzepa, unpublished). Mopac file size: 51200.

  15. Stereoscopic CAChe visualisations for those with access to a Macintosh CAChe worksystem and the CAChe Visualiser or Editor software. (H. S. Rzepa, unpublished). CAChe File size: 21305.

  16. This is a host-guest complex as described in W. C. Still et al, J. Am. Chem. Soc. (1994), 116, 3593, for which the high degree of enantioselectivity was predicted using free energy perturbation before it was synthesized. A success story in computer-aided molecular design! Macromodel (V4.5) File size: 8579.

  17. This molecular "snowflake" is an example of a cyclically hydrogen bonded alcohol. Such "hexamers" are quite rare compared with tetramers. Note the extraordinary perfect "chair" conformation adopted by this structure. (M. Foreman, H. S. Rzepa, D. J. Williams, and A. White, submitted for publication). MOPAC File size: 19100.

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