Space-filling model

<h2 id="history">History</h2>

<p>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 <a href="/facts/Thermal_ellipsoid/rs75Fjvz">these crystallographic models</a>); most often, however, crystallographers present the locations of atoms derived from crystallography via "<a href="/facts/Thermal_ellipsoid/rs75Fjvz">thermal ellipsoids</a>" whose cut-off parameters are set for convenience both to show the atom locations (with <a href="/facts/Anisotropy/YMqTQWVB">anisotropies</a>), 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.
</p><p>In 1952, Robert Corey and Linus Pauling described accurate scale models of molecules which they had built at <a href="/facts/California_Institute_of_Technology/3FPcp7BL">Caltech</a>.<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a>  In their models, they envisioned the surface of the molecule as being determined by the <a href="/facts/Van_der_Waals_radius/PNoSTW41">van der Waals radius</a> of each atom of the molecule, and crafted atoms as <a href="/facts/Hardwood/KQT6MN8W">hardwood</a> spheres of diameter proportional to each atom's van der Waals radius, in the scale 1 inch = 1 <a href="/facts/Angstrom/T5mjdd97">Å</a>.  To allow bonds between atoms a portion of each sphere was cut away to create a pair of matching flat faces, with the cuts dimensioned so that the distance between sphere centers was proportional to the lengths of standard types of chemical bonds.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a>  A connector was designed—a <a href="/facts/Threaded_bushing/rNbmYEzf">metal bushing</a> 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 <a href="/facts/Hydrogen_bond/85V86IIg">hydrogen bonds</a>.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a>[<i>verification needed</i>]<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a>
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<p>In 1965, Walter L. Koltun designed and patented a simplified system with molded plastic atoms of various <a href="/facts/CPK_coloring/vaubNxqx">colours</a>, which were joined by specially designed snap connectors; this simpler system accomplished essentially the same ends as the Corey-Pauling system,<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a><a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> 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.
</p><p>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 <a href="/facts/Accessible_surface_area/5khd22je">accessible to solvent</a>, 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.
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<h2 id="see-also">See also</h2>
<ul><li><a href="/facts/Ball-and-stick_model/0FQhyys8">Ball-and-stick model</a></li>
<li><a href="/facts/Van_der_Waals_surface/EEJSxIx0">Van der Waals surface</a></li>
<li><a href="/facts/CPK_coloring/vaubNxqx">CPK coloring</a></li>
<li><a href="/facts/Molecular_graphics/rLuIm8hP">Molecular graphics</a></li>
<li><a href="/facts/List_of_software_for_molecular_mechanics_modeling/RabeF7vR">Software for molecular modeling</a></li>
<li><a href="/facts/Molecular_design_software/BsLuzcbr">Molecular design software</a></li></ul>

<h2 id="external-links">External links</h2>
<ul><li><a href="http://www.mpipks-dresden.mpg.de/mpi-doc/quantumchemistry/ChemieAlltag/page1.html">More on molecular models and a couple of examples from chemistry and biology</a>  (article is in German)</li></ul>
<h2 id="gallery">Gallery</h2>

<h2 id="references">References</h2>

<ol>
<li id="fn:1"><p>Corey, Robert B.; Pauling, Linus (1953). "Molecular models of amino acids, peptides, and proteins" (PDF). Review of Scientific Instruments. 8 (24): 621–627. Bibcode:1953RScI...24..621C. doi:10.1063/1.1770803. Retrieved 9 March 2020. <a href="https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf" target="_blank">https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li>
<li id="fn:2"><p>Corey, Robert B.; Pauling, Linus (1953). "Molecular models of amino acids, peptides, and proteins" (PDF). Review of Scientific Instruments. 8 (24): 621–627. Bibcode:1953RScI...24..621C. doi:10.1063/1.1770803. Retrieved 9 March 2020. <a href="https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf" target="_blank">https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li>
<li id="fn:3"><p>Corey, Robert B.; Pauling, Linus (1953). "Molecular models of amino acids, peptides, and proteins" (PDF). Review of Scientific Instruments. 8 (24): 621–627. Bibcode:1953RScI...24..621C. doi:10.1063/1.1770803. Retrieved 9 March 2020. <a href="https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf" target="_blank">https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li>
<li id="fn:4"><p>Corey, Robert B.; Pauling, Linus (1953). "Molecular models of amino acids, peptides, and proteins" (PDF). Review of Scientific Instruments. 8 (24): 621–627. Bibcode:1953RScI...24..621C. doi:10.1063/1.1770803. Retrieved 9 March 2020. <a href="https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf" target="_blank">https://collections.nlm.nih.gov/ext/document/101584639X114/PDF/101584639X114.pdf</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li>
<li id="fn:5"><p>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. <a href="/w/index.php?title=Polyvinyl_plastic&action=edit&redlink=1" target="_blank">/w/index.php?title=Polyvinyl_plastic&action=edit&redlink=1</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li>
<li id="fn:6"><p>Koltun, Walter L. (1965). "Precision space-filling atomic models". Biopolymers. 3 (6): 665–679. doi:10.1002/bip.360030606. ISSN 0006-3525. <a href="https://onlinelibrary.wiley.com/doi/10.1002/bip.360030606" target="_blank">https://onlinelibrary.wiley.com/doi/10.1002/bip.360030606</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li>
<li id="fn:7"><p>US patent 3170246, Koltun, Walter L., "Space filling atomic units and connectors for molecular models", issued 1965-02-23
 <a href="https://patents.google.com/patent/US3170246A" target="_blank">https://patents.google.com/patent/US3170246A</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li>
</ol>

Space-filling model open-in-new

Space-filling model