Computed 3-D Structures

Karl Irikura

Note: This document is out of date and will be updated shortly. New structures computed using more rigorous methods have been added to the site. In addition the file format used for structures has been changed from the MOL file to the SD file and the JMOL viewer has been provided. The computational method described in this document is only valid for those structures labeled as “PM3.”

Summary.  The 3D structures in the NIST Chemistry WebBook were generated computationally, not from experiments.  Many molecules in the WebBook are "floppy", that is, they can be deformed in certain ways using very little energy.  For example, the central C-C bond in n-butane can be rotated easily to obtain different "conformational isomers".  Even for floppy molecules, only one representative structure is provided.  The theoretical model does not include solvent or other medium effects, so the structures are intended to be for molecules in the gas phase, not the condensed phase.

Brief description of the theoretical model.  Each structure has been optimized for minimum energy.  However, the structure provided may not represent the global energy minimum.  The molecular energy was computed using the semiempirical molecular orbital theory [1,2] known as PM3 [3].  PM3 is a quantum mechanical theory in which electrons are included explicitly.  It is not an "ab initio" theory because many of the detailed integrals have been replaced by empirical parameters.  The values of these parameters were adjusted to reproduce, as well as possible, experimental data for a large set of molecules.  Four gas-phase properties were used in the parameterization:  enthalpy of formation, dipole moment, ionization energy, and molecular geometry (i.e., structure) [4].  Parameters were not reoptimized to reflect new values of any of these properties such as those found elsewhere in the NIST Chemistry WebBook.

Technical details.  Initial structures were the 2-D MOL files previously available in the WebBook.  3-D structures were generated using the Alchemy 2000 desktop software package [5,6] and its native molecular-mechanics force field.  When the necessary parameters were available, the structures were then reoptimized using the MM3 force field [7] and the simulated annealing algorithm included in the Tinker software package [8,6].  Final optimization, at the PM3 level, was done using the version of MOPAC6 [9] bundled with the Alchemy 2000 package or, in some cases, the Gaussian 94 software package [10,6].  The structures are provided in the WebBook in MOL format [6].  All structures have been reviewed at least once [11].

How to view 3-D structures.  MOL files may be downloaded and viewed using many desktop software packages.

Disclaimer.  The 3-D structures are not intended to be used in critical applications.  We disclaim all responsibility for any loss or damage that may result from such use.


  1. [1]  M. J. S. Dewar The Molecular Orbital Theory of Organic Chemistry; McGraw-Hill: New York, 1969.
  2. [2]  W. Thiel  "Thermochemistry from semiempirical molecular orbital theory"; In Computational Thermochemistry:  Prediction and Estimation of Molecular Thermodynamics (ACS Symposium Series 677); Irikura, K. K., Frurip, D. J., Eds.; American Chemical Society: Washington, DC, 1998; pp 142-161.
  3. [3]  J. J. P. Stewart  "Optimization of parameters for semiempirical methods.  I. Method"; J. Comput. Chem. 1989, 10, 209-220.
  4. [4]  J. J. P. Stewart  "Optimization of parameters for semiempirical methods.  II. Applications"; J. Comput. Chem. 1989, 10, 221-264.
  5. [5Alchemy 2000, version 2.  Tripos, Inc., St. Louis, MO, 1998.
  6. [6]  Certain commercial materials and equipment are identified in this paper in order to specify procedures completely.  In no case does such identification imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the material or equipment identified is necessarily the best available for the purpose.
  7. [7]  J. P. Bowen, N. L. Allinger  "Molecular mechanics:  the art and science of parameterization"; In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1991; Vol. 2; pp 81-97.
  8. [8TINKER, version 3.6.  J. W. Ponder et al.  Washington Univ. School of Medicine, St. Louis, MO, 1998.
  9. [9]  J. J. P. Stewart.  MOPAC Manual, sixth edition.  United States Air Force Academy: Colorado Springs, CO, 1990.
  10. [10Gaussian 94, revision E.2. M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, M. Head-Gordon, C. Gonzalez, J. A. Pople  Gaussian, Inc., Pittsburgh, PA, 1995.
  11. [11]  Structures checked by K. K. Irikura and J. F. Liebman, 1998-1999.

Last revised 13 Jan. 2000

NIST, National Institute of Standards and Technology Material Measurement Laboratory Standard Reference
Data Program