The image presented here is of the molecule alanine. The geometry of the molecule was
optimized using Gaussian98, after which a full population analysis
was performed at the 6-31G** level of theory.
The electron density for the whole molecule was calculated using an in-house program (Rhocalc04). Additionally,
fuzzy electron density fragments were created based on some of the methods (MEDLA, ADMA) used by the research group.
These electron density files were visualized using the powerful MOLCAD II module of the SYBYL molecular modelling package.
This module allows for the mapping of an image upon a surface. In this case, the surfaces of the alanine molecule have been mapped with an image of the Memorial University of Newfoundland clock tower.
Reference for Gaussian 98
- M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery Jr., R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennuchi, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, A.G. Baboul, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B.G. Johnson, W. Chen, M.W. Wong, J.L. Andres, M. Head-Gordon, E.S. Replogle, and J.A. Pople, Gaussian 98 (Revision A.9), Gaussian, Inc., Pittsburgh, PA (1998).
References for the 6-31G** basis set
- P.C. Hariharan and J.A. Pople, Theoret. Chimica Acta, 28, 213 (1973).
- M.M. Francl, W.J. Petro, W.J. Hehre, J.S. Binkley, M.S. Gordon, D.J. DeFrees and J.A. Pople, J. Chem. Phys., 77, 3654 (1982).
- V. Rassolov, J.A. Pople, M. Ratner and T.L. Windus, J. Chem. Phys., 109, 1223 (1998).
References for MOLCAD II
- M. Waldherr-Teshner, T. Goetze, W. Heiden, M. Knoblauch, H. Volhardt, and J. Brinkmann, "MOLCAD - Computer Aided Visualization and Manipulation of Models in Molecular Science", in Second Eurographics Workshop on Visualization in Scientific Computing, Delft, Netherlands (1991).
- J. Brinkmann, M. Keil, T.E. Exner, R. Marhöfer, and G. Moeckel, "Molecular Models: Visualization", in The Encyclopedia of Computational Chemistry, P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.J. Schaefer III, and P.R. Schreiner, Eds., John Wiley & Sons, Chichester (1998).
- J. Brinkmann, M. Keil, T.E. Exner, and R. Marhöfer, J. Mol. Model., 6, 328 (2000).
- SYBYL 6.7, Tripos, Inc., 1699 South Hamley Road, St. Louis, MO, 63144 (2000).
This page was created by Peter Warburton. Please send comments to him at firstname.lastname@example.org.