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Top of Page MOLecular ARCHitecture+ - MolArch+ and MOLCAD Graphics Gallery
MolArch+ Sample Image
MolArch+ Sample Image
Top of Page Computational Methods
Computational Details

Only basic information is given here, for a more detailed description of the procedures used see Ref. [1].

Molecular Geometries

All geometry analysis were performed using molecular mechanics and the PIMM88 and PIMM91 force field program [2]. Molecular dynamics simulations were carried out with the GROMOS [3] or CHARMM [4] force field. Solid-state geometries were obtained from the Cambridge Crystallographic data file (CCDF) [5] or are related to our own work [6].

Molecular Surfaces and Hydrophobicity Patterns

Calculation of the molecular contact surfaces [7], the molecular electrostatic potential profiles (MEP) [8], and the molecular lipophilicity patterns (MLP) [9] was performed with the MOLCAD molecular modeling program [10], the computational basics are given by Brickmann et al. in Ref. [8,9]. Surface coloring was achieved using texture mapping techniques [11], graphics were photographed from the computer screen of a SILICON-GRAPHICS workstation.

Molecular Graphics and Ribbon Models

All molecular graphics with blue or black backgrounds including all ribbon models were generated using the MolArch+ program in combination with the POVRAY Persistence of Vision(tm) Ray Tracer.

Top of Page References
  1. S. Immel, Ph.D. Thesis, Technical University of Darmstadt, 1995.
  2. (a) H. J. Lindner, PIMM88 - Closed Shell PI-SCF-LCAO-MO- Molecular Mechanics Program, Technical University of Darmstadt, 1988. - (b) H. J. Lindner, Tetrahedron 1974, 30, 1127-1132. - (c) A. E. Smith, Ph.D. Thesis, Technical University of Darmstadt, 1989. - (d) A. E. Smith and H. J. Lindner, J. Comput.-Aided Mol. Des. 1991, 5, 235-262.
  3. (a) W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Nijenborgh 16, Groningen, The Netherlands, 1987. - (b) W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem. 1990, 102, 1020-1055; Angew. Chem. Int. Ed. Engl. 1990, 29, 992-1023.
  4. (a) B. R. Brooks, R. E.Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comp. Chem. 1983, 4, 187-217. - (b) CHARMM - Chemistry at HARvard Macromolecular Mechanics, 1996; http://yuri.harvard.edu/.
  5. (a) Cambridge Crystallographic Data File, Version 5.09, 1995. - (b) F. H. Allen, S. A. Bellard, M. D. Brice, B. A. Cartwright, A. Doubleday, H. Higgs, T. Hummelink, B. G. Hummelink-Peters, O. Kennard, W. D. S. Motherwell, J. R. Rodgers, and D. G. Watson, Acta Crystallogr., Sect. B, 1979, 35, 2331-2339. - (c) F. H. Allen, O. Kennard, and R. Taylor, Acc. Chem. Res. 1983, 16, 146-153.
  6. For additional informations see the list of publications.
  7. (a) F. M. Richards, Ann. Rev. Biophys. Bioeng. 1977, 6, 151-176; Carlsberg. Res. Commun. 1979, 44, 47-63. - (b) M. L. Connolly, J. Appl. Cryst. 1983, 16, 548-558; Science 1983, 221, 709-713. (c) B. Lee and F. M. Richards, J. Mol. Biol. 1971, 55, 379-400.
  8. (a) P. K. Weiner, R. Langridge, J. M. Blaney, R. Schaefer, and P. A. Kollman, Proc. Natl. Acad. Sci. USA 1982, 79, 3754-3758. - (b) C. E. Dykstra, Chem. Rev. 1993, 93, 2339- 2353.
  9. W. Heiden, G. Moeckel, and J. Brickmann, J. Comput.-Aided Mol. Des. 1993, 7, 503-514.
  10. (a) J. Brickmann, MOLCAD - MOLecular Computer Aided Design, Technical University of Darmstadt, 1992. The major part of the MOLCAD program is included in the MOLCAD-module of the SYBYL package of TRIPOS Associates, St. Louis, USA. - (b) J. Brickmann and M. Waldherr-Teschner, Labo (Hoppenstedt Verlag, Darmstadt) 1989, 10, 7-14; Informationstechnik (Oldenburg Verlag, Muenchen) 1991, 33, 83-90. - (c) J. Brickmann, J. Chim. Phys. 1992, 89, 1709-1721. - (d) M. Waldherr-Teschner, T. Goetze, W. Heiden, M. Knoblauch, H. Vollhardt, and J. Brickmann, in: Advances in Scientific Visualization (Eds.: F. H. Post, A. J. S. Hin), Springer Verlag, Heidelberg, 1992, pp. 58-67. - (e) J. Brickmann, T. Goetze, W. Heiden, G. Moeckel, S. Reiling, H. Vollhardt, and C.-D. Zachmann, Interactive Visualization of Molecular Scenarios with MOLCAD/SYBYL, in: Data Visualization in Molecular Science - Tools for Insight and Innovation (Ed.: J. E. Bowie), Addison-Wesley Publishing Company Inc., Reading, Mass., 1995, pp. 83-97.
  11. M. Teschner, C. Henn, H. Vollhardt, S. Reiling, and J. Brickmann, J. Mol. Graphics 1994, 12, 98-105.

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