Hyperactive Molecules: Part 2

  1. Molecular Dynamics trajectories showing a right hand alpha helix unfolding. (Thanks to Raul E. Cachau, cachau@ncifcrf.gov). To activate the animation click on the image and select "animate" from the "Extras" drop down menu in Xmol. XYZ File size: 126680.

  2. An animation of the reaction path calculation for phosphoryl transfer (H. S. Rzepa and M. Y. Yi, J. Chem. Soc., Chem. Commun., 1989, 1502 ). Mopac Output File size: 126680.

  3. The 2D NOESY Spectrum of Barnase. Click first on the image of the protein to activate the Rasmol viewer. Then click on coloured cross-peaks in the 2D spectrum to find out which two residues are associated with the close contact giving rise to the peak. Only these two residues will be coloured in the RasMol display. The effect can be seen most clearly if the ribbon display is on. (M. Hargreaves, H. S. Rzepa, R.Sayle, B. J. Whitaker, to be published). PDB File Size: 177471.

  4. The NOESY 2D NMR spectrum of the hairpin loop oligonucleotide CGCGTTTTCGCG, taken from K. M. Banks, D. R. Hare and B. R. Reid, Biochemistry, 1989, 28, 6996. Click first on the image of the DNA loop to activate the Rasmol viewer. Click then on coloured cross-peaks in the 2D NOESY spectrum to trace out the NOE connectivity. There are two types of nOe cross-peak. Those arising between close approach of the anomeric and aromatic protons of the SAME base, and those arising out of proximity between an anomeric proton and aromatic proton of DIFFERENT bases. Verify for yourselves that the highlighted protons are indeed within 4.2A of eachother! (M. Hargreaves, H. S. Rzepa, R.Sayle, B. J. Whitaker, to be published). PDB File size: 62451.

  5. The reaction of methoxy anion and methyliodide. To activate the animation click on the image and select "animate" from the "Extras" drop down menu in Xmol. (Part of the XMol distribution examples). XYZ File size: 32748.

  6. A Kinemage display, starting with flavodoxin, as an example of the "doubly-wound beta sheet" or "nucleotide-binding domain" structure, in the Alpha/Beta category of tertiary structure. Flavodoxin contains a central, twisted beta sheet (in seagreen) of 5 parallel strands, with FMN bound at the C-terminal end of the central strands. Animate to switch to triose phosphate isomerase ("TIM"), the classic example of a singly-wound parallel beta barrel structure, also called a "TIM barrel" or a (BetaAlpha)8 barrel. It contains a central barrel of 8 parallel beta strands (seagreen), surrounded by a ring of 8 alpha-helices (pink). The chain winds around the barrel by one strand at a time, and each connection joins adjacent beta strands by a righthanded crossover connection or a "beta-alpha-beta loop". (Thanks to Stephen White). KIN File size: 189872.

  7. The example shows a portion of the fluorescence excitation spectrum of jet-cooled cyclclobutanone (J. Zhang, W.-Y. Chiang and J. Laane, J. Chem. Phys., 1994, 100 3455). The labelled series of peaks correspond to a vibrational progression of the v=26 mode, which is an out-of-plan wag of the carbonyl group. If you have XMol configured, clicking on, or near, the labels will activate Xmol. Clicking on the "animate" menu entry from the "Extras" drop-down menu in Xmol will start the animation. (M. Hargreaves, H. S. Rzepa, R.Sayle, B. J. Whitaker, to be published). XYZ File Fize:

  8. Click first on the image of the Pentaantennary Large Asilio Glycan to activate the Rasmol viewer. Click then in the coloured regions to find out the cleaving bond. Taken from T. Taguchi, A. Seko, K. Kitajima, Y. Muto, S. Inoue, K. -H. Khoo, H. R. Morris, A. Dell and Y. Inoue, J. Biological Chemistry, 1994, 269, 8762.

  9. Total Synthesis of (+)-Papuamine: Determination of the Absolute Stereochemistry of the Natural Product. (Anthony G.M. Barrett, Mark L. Boys and Terri L. Boehm, J. Chem. Soc., Chem. Commun., 1994, in press).

  10. An illustration of the Citric Acid cycle, with connections to numerous databases of relevant information. (Peter Murray-Rust and Gudge Chandramohan). File Sizes: small.

  11. Clickable NOESY spectrum of InterLeukin-8. Click first on the image of the protein to bring up RasMol, and then on individual peaks to highlight the inter-chain contacts. (Martin Hargreaves, Glaxo, Greenford). PDB File Size: 205578.

  12. The reaction centre of the purple bacterium Rhodopseudomonas viridis Click first on the thumbnail image above to start the Rasmol viewer. Then, for a more detailed explanation of this system, including the mechanism of electron transfer through the complex, click here. You will need to acquire the csml script to be able to markup the structure.

  13. An illustration of a Mathematica Notebook, used at Imperial College Chemistry department for remedial Maths teaching. The MIME type used is application/x-mathematica which should be mapped in your browser to the Mathematica Front end, which needs to be resident on your local machine. Note that "molecular modelling" Mathematica programs are also available.

  14. The Racemization of Octahelicene is rationalised using the AM1 SCF-MO method. An extensive discussion is available in the original reference by J.H. Borkent. Ampac file size: 153995.

  15. The SCOP Project: Structural Classification of Proteins. Authors: A. Murzin, S. E. Brenner, T. J. P. Hubbard and C. Chotia, MRC Laboratory of Molecular Biology and Centre for Protein Engineering, Cambridge.

  16. Hyperactive Molecules at Bristol University Chemistry Department (thanks to Karl N Harrison, Bristol University).

  17. Infra Red Spectra in the JCAMP-DX format and IR Spectral Readers. Author: R. J. Lancashire, Dept. Chemistry, University of West Indies, Jamaica.

  18. A Hyperactive talk, delivered at Birkbeck College, London (5 Dec 1994) and Reading Iniversity (14 December 1994) by Henry Rzepa.

  19. A 300 MHz NMR spectrum annotated using CSML by Michael Haak at the University of Oldenburg.

  20. A Hyperactive Molecule Gallery at the Computer Chemistry Center Erlangen (Author: A. Dransfield

  21. Hyperactive Reaction schemes and search queries in "TGF" format (thanks to Osman Güner of MDL for these). For more examples, click here.

  22. Examples of Hyperactive Molecules using VRML and JAVA Applets: Author Henry Rzepa. Requires either a VRML Browser or a Java compliant browser.

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