Katherine C. Hafner,
Daniel S. Graham,
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, Mariya S. Shevchuk,
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 . 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 : 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 . Each structure has been reviewed by at least one person.
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.
Last revised 9 Feb. 2015