Journal of Computer-Aided Molecular Design

, Volume 14, Issue 2, pp 123–134 | Cite as

Molden: a pre- and post-processing program for molecular and electronic structures*

  • G. Schaftenaar
  • J.H. Noordik


Molden is a software package for pre- and postprocessing of computational chemistry program data. Interfacing to the ab initio programs Gamess-US/UK and Gaussian and to the semi-empirical package MOPAC is provided. The emphasis is on computation and visualization of electronic and molecular properties but, e.g., reaction pathways can be simulated as well. Some molecular properties of interest are processed directly from the output of the computational chemistry programs, others are calculated in MOLDEN before display. The package features different options to display MOLecular electronic DENsity, each focusing on a different structural aspect: molecular orbitals, electron density, molecular minus atomic density and the Laplacian of the electron density. To display difference density, either the spherically averaged atomic density or the oriented ground state atomic density can be used for a number of standard basis sets. The quantum mechanical electrostatic potential or a distributed multipole expansion derived electrostatic potential can be calculated and atomic charges can be fitted to these potentials calculated on Connolly surface(s). Reaction pathways and molecular vibrations can be visualized. Input structures can be generated with a Z-matrix editor. A variety of graphics languages is supported: XWindows, postscript, VRML and Povray format.

animation charge distribution electrostatic potential molecular density visualization 


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  1. 1.
    Frish, M.J., Trucks, G.W., Head-Gordon, M., Gill, P.M.W., Wong, M.W., Foresman, J.B., Johnson, B.G., Schlegel, H.B., Robb, M.A., Replogle, E.S., Gomperts, R., Andres, J.L., Raghavachari, K., Binkley, J.S., Gonzalez, C., Martin, R.L., Fox, D.J., Defrees, D.J., Baker, J., Stewart, J.J.P. and Pople, J.A., Gaussian94. Gaussian, Inc., Pittsburgh, PA, 1995.Google Scholar
  2. 2.
    Schmidt, M.W., Boatz, J.A., Baldridge, K.K., Koseki, S., Gordon, M.S., Elbert, S.T. and Lam, B., GAMESS, Program No. 115. Indiana University, Bloomington, IN.Google Scholar
  3. 3.
    Guest, M.F., Kendrick, J., van Lenthe, J.H., Shoeffel, K. and Sherwood, P., GAMESS-UK Users Guide and Reference Manual. Computing for Science (CFS) Ltd, Daresbury Laboratory, 1994.Google Scholar
  4. 4.
    Stewart, J.J.P., QCPE Bull., 10 (1990) 86.Google Scholar
  5. 5.
    Nielsen, A.B. and Holder, A.J., GaussView User' Reference. Gaussian, Inc., Pittsburgh, PA.Google Scholar
  6. 6.
    Tripos Associated Inc., St. Louis, MO.Google Scholar
  7. 7.
    Molecular Simulations Inc., San Diego, CA, Cerius User Guide, March 1997.Google Scholar
  8. 8.
    Schaftenaar, G., QCPE Bull., 12 (1992) 3.Google Scholar
  9. 9.
    Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E., Bryce, M.D., Rogers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.Google Scholar
  10. 10.
    Wishart, D.S., Willard, L., Richards, F.M. and Sykes, B.D., VADAR: A Comprehensive Program Suite for Protein Structural Analysis. Protein Engineering Network of Centres of Excellence, University of Alberta, 1993.Google Scholar
  11. 11.
    Allen, F.H., Bellard, S.A., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B.G., Kennard, O., Motherwell, W.D.S., Rodgers, J.R. and Watson, D.G., Acta Crystallogr., Sect. B, 35 (1979) 2331.Google Scholar
  12. 12.
    Allen, F.H., Johnson, O., Macrae, C.F., Smith, J.M., Motherwell, W.D.S., Galloy, J.J., Watson, D.G., Rowland, R.S., Edgington, P.R., Garner, S.E., Davies, J.E. and Mitchell, G.F., CSD System Documentation. Cambridge Crystallographic Data Centre, Cambridge, U.K., 1992.Google Scholar
  13. 13.
    Minnesota Supercomputer Center, Inc., Minneapolis MN, XMol Users Manual, 1994.Google Scholar
  14. 14.
    Chemical Design Ltd, Oxon, England, Chem-X Reference Guide, Volume III, 1993.Google Scholar
  15. 15.
    GRAPHICS INTERCHANGE FORMAT Version 89a. CompuServe Inc., Columbus, OH, 1990.Google Scholar
  16. 16.
    Stewart, R.F., J. Chem. Phys., 51 (1969) 4569.Google Scholar
  17. 17.
    Hirshfeld, F.L., Acta Crystallogr., Sect. B, 27 (1971) 769.Google Scholar
  18. 18.
    Kunze, K.L. and Hall, M.B., J. Am. Chem. Soc., 108 (1986) 5122.Google Scholar
  19. 19.
    Schwarz, W.H.E., Ruedenberg, K. and Mensching, L., J. Am. Chem. Soc., 111 (1989) 6926.Google Scholar
  20. 20.
    Hirshfeld, F.L., Crystallography Reviews, Vol. 2, Electron density distributions in molecules, Gordon and Breach, London, 1989.Google Scholar
  21. 21.
    Bader, R.F.W., Keaveny, I. and Cade, P.E., J. Chem. Phys., 47 (1967) 3381.Google Scholar
  22. 22.
    Schwarz, W.H.E., Valtazanos, P. and Ruedenberg, K., Theor. Chim. Acta, 68 (1985) 471.Google Scholar
  23. 23.
    Roothaan, C.C.J., Rev. Mod. Phys., 23 (1951) 69.Google Scholar
  24. 24.
    Fleming, I., Frontier Orbitals and Organic Chemical Reactions, Wiley, New York, NY, 1976.Google Scholar
  25. 25.
    Bader, R., Atoms in molecules-A Quantum Theory, Oxford University Press, Oxford, 1990.Google Scholar
  26. 26.
    Bader, R.F.W., Popelier, P.L.A. and Keith, T.A., Angewandte Chemie, Intl. Ed. Eng., 33 (1986) 620.Google Scholar
  27. 27.
    Bader, R.F.W., Gough, K.M., Laidig, K.E. and Keith, T.A., Mol. Phys., 75 (1992) 1167.Google Scholar
  28. 28.
    Bader, R.F.W., Gillespie, R.J. and MacDougall, P.J., J. Am. Chem. Soc., 110 (1988) 7239.Google Scholar
  29. 29.
    Clementi, E. and Davis, D.R., J. Chem. Phys., 45 (1966) 2593.Google Scholar
  30. 30.
    Stone, A.J., Chem. Phys. Lett., 83 (1981) 233.Google Scholar
  31. 31.
    Price, S.L., Stone, A.J. and Alderton, M., Mol. Phys., 52 (1984) 987.Google Scholar
  32. 32.
    Buckingham, A.D. and Fowler, P.W., Can. J. Chem., 63 (1985) 2018.Google Scholar
  33. 33.
    Price, S.L. and Stone, A.J., J. Chem. Phys., 86 (1987) 2859.Google Scholar
  34. 34.
    Mitchell, J.B.O., Nandi, C.L., Thornton, J.M., Price, S.L., Singh, J. and Snarey, M., J. Chem. Soc., Faraday Trans., 89 (1993) 2619.Google Scholar
  35. 35.
    Price, S.L., Lo Celso, F., Treichel, J.A. and Goodfellow, J.M., J. Chem. Soc., Faraday Trans., 89 (1993) 3407.Google Scholar
  36. 36.
    Coombes, D.S., Price, S.L., Willock, D.J. and Leslie, M., J. Chem. Phys., 100 (1996) 7352.Google Scholar
  37. 37.
    Stone, A.J., Dullweber, A., Popelier, P.L.A. and Wales, D.J., Orient: a program for studying interactions between molecules, version 3.2, University of Cambridge, 1995.Google Scholar
  38. 38.
    Willock, D.J., Price, S.L., Leslie, M. and Catlow, C.R.A., J. Comput. Chem., 16 (1995) 628.Google Scholar
  39. 39.
    Boys, S.F., Proc. R. Soc., 200 (1950) 542.Google Scholar
  40. 40.
    Saunders, V., Computational Techniques in Quantum Chemistry and Molecular Physics. An Introduction to Molecular Integral Evaluation, Reidel, Dordrecht, 1975.Google Scholar
  41. 41.
    Bonaccorsi, R., Scrocco, E. and Tomasi, J., J. Chem. Phys., 54 (1970) 5270.Google Scholar
  42. 42.
    Dupuis, M., Rys, J. and King, H.F., J. Chem. Phys., 65 (1976) 111.Google Scholar
  43. 43.
    King, H.F. and Dupuis, M., J. Comput. Phys., 21 (1976) 144.Google Scholar
  44. 44.
    Besler, B.H., Merz, K.M. and Kollman, P.A., J. Comput. Chem., 11 (1990) 431.Google Scholar
  45. 45.
    Bayly, C.I., Cieplak, P., Cornell, W.D. and Kollman, P.A., J. Phys. Chem., 97 (1993) 10269.Google Scholar
  46. 46.
    Francl, M.M., Carey, C. and Chirlian, L.E., J. Phys. Chem., 17 (1996) 367.Google Scholar
  47. 47.
    URL: Scholar
  48. 48.
    Werner, H.J. and Knowles, P.J., User' manual for MOLPRO. Institut für Theoretische Chemie, Universität Stuttgart and School of Chemistry, University of Birmingham, 1996.Google Scholar
  49. 49.
    Baerends, E.J., Ellis, D.E. and Ros, P., Chem. Phys., 2 (1973) 41.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • G. Schaftenaar
    • 1
  • J.H. Noordik
    • 1
  1. 1.CAOS/CAMM Center, Faculty of ScienceNijmegen University, ToernooiveldNijmegenThe Netherlands

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