Computed 3-D Structures

Katherine C. Hafner,
Ann Marie Martin, Nimit Patel, Mariya Shevchuk, Nathan Kau, Abbie Tran, Joseph Tseytlin,
Daniel S. Graham, Yvonne Niyonzima, Sarah E. Wollman, Avi M. Newman, Ashley M. Zhang,
Sonia F. Dermer, Ethan N. Ho, Sejal Aggarwal, Emily W. Jin, Sarah Pan,
Michael Y. Liou, Jennifer K. Skerritt, Helen M. Park, Niranjan B. Ravi,
Stuart C. Ness, Daniel X. Du, Jeffrey W. Qiu, Alexander H. Yang,
Thomas C. Allison, Karl K. Irikura, and Joel F. Liebman

Summary.  The three-dimensional 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 for single 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 density functional theory (DFT). DFT is a quantum mechanical model in which electrons are included explicitly.  The details (below) are a popular choice that is a good compromise between reliability and computational efficiency.

Technical details.  Initial structures were from two sources: (1) the 2-D MOL files previously available in the WebBook, and (2) generated from chemical names using ChemBioDraw [1,2].  After cleanup, the 2-D structures were converted to crude 3-D structures using Chem3D Pro [1,2].  After cleanup, the crude 3-D structures were refined in two stages, using the Gaussian quantum chemistry software [1,3].  The first refinement was energy minimization using PM6, a semiempirical molecular orbital method in which many integrals are replaced by empirical parameters [4].  The final refinement was energy minimization using the hybrid B3LYP functional [5,6,7] within the framework of Kohn-Sham DFT. Atom-centered, Gaussian basis sets were used [8]:  the Pople-style 6-31G(d) sets for lighter atoms (Z ≤ 36; up to Kr) and the Stuttgart-Dresden ("SDD") pseudopotentials and matching basis sets for heavier atoms. Following energy minimization, it was verified that all harmonic vibrational frequencies were real-valued, which indicates that the structure represents a local minimum in energy. The structures are provided in the WebBook in SD-file format [1].  Each structure has been reviewed by at least one person.

How to view 3-D structures.  Click on the "Java" or "Javascript" link to view a structure within your web browser. Structure files may also be downloaded using the "SD file" link and viewed using many desktop software packages.

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

References

  1. [1]  Certain commercial materials and equipment are identified in this document 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.
  2. [2]  CambridgeSoft / PerkinElmer Informatics, Waltham, MA.
  3. [3]  Gaussian, Inc., Wallingford, CT.
  4. [4]  J.J.P. Stewart  "Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements"; J. Mol. Model. 2007, 13, 1173-1213. (doi: 10.1007/s00894-007-0233-4)
  5. [5]  A.D. Becke  "Density-functional thermochemistry. III. The role of exact exchange"; J. Chem. Phys., 1993, 98, 5648-5652. (doi: 10.1063/1.464913)
  6. [6]  C. Lee, W. Yang, R.G. Parr  "Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density"; Phys. Rev. B, 1988, 37, 785-789. (doi: 10.1103/PhysRevB.37.785)
  7. [7]  P.J. Stephens, F.J. Devlin, C.F. Chabalowski, M.J. Frisch  "Ab Initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields"; J. Phys. Chem., 1994, 98, 11623-11627. (doi: 10.1021/j100096a001)
  8. [8]  These and other basis sets are available, with literature references, at the Pacific Northwest National Laboratory's Basis Set Exchange.

Last revised 9 Feb. 2015