Space-filling model

Source: Wikipedia, the free encyclopedia.
This article is about the model in chemistry. For space-filling curves in geometry, see Space-filling curve.
conformational "pose" of a population of molecules, which, because of low Gibbs energy
barriers to rotation about its carbon-carbon bonds (giving the carbon "chain" great flexibility), normally is composed of a very large number of different such conformations (e.g., in solution).
An example of a three-dimensional, space-filling model of a complex molecule, THC, the active agent in marijuana.

In

radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic nuclei, all in the same scale. Atoms of different chemical elements
are usually represented by spheres of different colors.

Space-filling calotte models are also referred to as

conformers. On the other hand, these models mask the chemical bonds between the atoms, and make it difficult to see the structure of the molecule that is obscured by the atoms nearest to the viewer in a particular pose. For this reason, such models are of greater utility if they can be used dynamically, especially when used with complex molecules (e.g., see the greater understanding of the molecules shape given when the THC
model is clicked on to rotate).

History

Space-filling models arise out of a desire to represent molecules in ways that reflect the electronic surfaces that molecules present, that dictate how they interact, one with another (or with surfaces, or macromolecules such as enzymes, etc.). Crystallographic data are the starting point for understanding static molecular structure, and these data contain the information rigorously required to generate space-filling representations (e.g., see these crystallographic models); most often, however, crystallographers present the locations of atoms derived from crystallography via "thermal ellipsoids" whose cut-off parameters are set for convenience both to show the atom locations (with anisotropies), and to allow representation of the covalent bonds or other interactions between atoms as lines. In short, for reasons of utility, crystallographic data historically have appeared in presentations closer to ball-and-stick models. Hence, while crystallographic data contain the information to create space-filling models, it remained for individuals interested in modeling an effective static shape of a molecule, and the space it occupied, and the ways in which it might present a surface to another molecule, to develop the formalism shown above.

In 1952, Robert Corey and Linus Pauling described accurate scale models of molecules which they had built at

metal bushing that threaded into each sphere at the center of each flat face. The two spheres were then firmly held together by a metal rod inserted into the pair of opposing bushing (with fastening by screws). The models also had special features to allow representation of hydrogen bonds.[1][verification needed][2]

electropositive areas to red for electronegative areas. The surface was generated by calculating the energy of interaction of a spherical point positive charge (e.g., a proton, H+,) with the molecule's atoms and bonding electrons, in a series of discrete computational steps. Here, the electrostatic surface emphasizes the electron deficiency of the sulfur atom, suggesting interactions in which it might engage, and chemical reactions
it might undergo.

In 1965, Walter L. Koltun designed and patented a simplified system with molded plastic atoms of various colours, which were joined by specially designed snap connectors; this simpler system accomplished essentially the same ends as the Corey-Pauling system,[4][5] and allowed for the development of the models as a popular way of working with molecules in training and research environments. Such colour-coded, bond length-defined, van der Waals-type space-filling models are now commonly known as CPK models, after these three developers of the specific concept.

In modern research efforts, attention returned to use of data-rich crystallographic models in combination with traditional and new computational methods to provide space-filling models of molecules, both simple and complex, where added information such as which portions of the surface of the molecule were readily accessible to solvent, or how the electrostatic characteristics of a space-filling representation—which in the CPK case is almost fully left to the imagination—could be added to the visual models created. The two closing images give examples of the latter type of calculation and representation, and its utility.

See also

References

  1. ^
    doi:10.1063/1.1770803
    . Retrieved 9 March 2020.
  2. ^ In the same paper Corey and Pauling also briefly describe a much simpler but less accurate type of model, with rubber-like polyvinyl plastic spheres in the scale 1 inch = 2Å and connected by snap fasteners. See Corey & Pauling, 1953, op. cit.
  3. ^ Baker, N.A., Sept, D., Joseph, S., Holst, M.J. & McCammon, J.A., 2001, "Electrostatics of nanosystems: Application to microtubules and the ribosome," Proc. Natl. Acad. Sci. U.S.A. 98: pp. 10037-10041, see [1], and "Calculating Electrostatics". Archived from the original on 2015-06-24. Retrieved 2015-06-23., and [2], accessed 23 June 2015.
  4. ISSN 0006-3525
    .
  5. ^ US patent 3170246, Koltun, Walter L., "Space filling atomic units and connectors for molecular models", issued 1965-02-23 
A space-filling model of cyclohexane C
6H
12. Carbon atoms, partially masked, are in grey, and hydrogen atoms are presented as white spheres.
Retrieved from "https://en.wikipedia.org/w/index.php?title=Space-filling_model&oldid=1292167265"