The Proof Is in the Calculation

Dec 12, 2009 - of the machinery. This is a little different from “traditional” theory in which a model is developed and tested by comparing it to ...
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Research: Science and Education

JCE Concept Connections

The Proof Is in the Calculation The paper by Roger L. DeKock et al. on pp 1459–1464 gives its interesting results by analyzing proven mathematical models (ab initio molecular modeling calculations) for aspects that correspond to physical phenomena (H-bond and covalent bond distances). Instead of developing mathematical arguments leading to a unique model of a system or a solution to a problem, these explorations focus on the results of the calculations, not the development of the machinery. This is a little different from “traditional” theory in which a model is developed and tested by comparing it to experiments. Here, the calculations are the experiment. Comparing the results of the calculations when the parameters are changed is analogous to studying the results of a lab experiment when experimental conditions are changed. In this JCE Concept Connection, Randall Wildman of the JCE staff focuses on other materials available from JCE in which similarly important conclusions are drawn by experimenters working in the computer room, not in the lab.

Molecular Modeling The ring at the end of the carotene molecule flaps back and forth, contrary to its double bond being conjugated with the linear portion of the molecule (which is rigid). This one may surprise the students. See: http://www.jce.divched.org/JCEWWW/Features/MonthlyMolecules/2008/Feb/index.html

The energy of helium bonding is explored the only way it can be, nonexperimentally. http://www.jce.divched.org/Journal/Issues/2007/May/abs860.html Applications of molecular modeling for use by students, as applied to organic chemistry, are demonstrated here:



http://www.jce.divched.org/Journal/Issues/2009/Aug/abs955.html

This is a nice molecular modeling resource list so you can implement these ideas (another JCE Concept Connection): http://www.jce.divched.org/Journal/Issues/2009/Aug/abs958.html

Crystal Structure Explorations Simply calculating the locations of members of a crystalline lattice can reveal unexpected structures within. This is done with copper compounds and reveals remarkable similarities between different compounds, and vice versa: http://www.jce.divched.org/Journal/Issues/2009/Aug/abs980.html Topography based on SEM data of surfaces showing the outlines of individual atoms is generated and explored in this software program. Instances of lattice imperfections, atom replacements through doping, thermal effects, and more can be seen at:

http://www.jce.divched.org/JCESoft/jcesoftSubscriber/FlyingOverAtoms/index.htm

Direct calculation of the packing efficiency of the hcp lattice (not just an intuitive presentation of why it must be the same as the fcc) is clearly demonstrated below. Beautiful graphics and a particularly interesting conclusion paragraph exist here: http://www.jce.divched.org/JCEWWW/Articles/FillingHCP/FillingHCP.html This is an article analyzing the ccp, but using the rhombohedral primitive cell instead of the cubic cell: http://www.jce.divched.org/Journal/Issues/2008/Jan/abs90.html

Laboratory Simulations Photoelectron effect spectroscopy measures bond characteristics. Here, spectra are simulated using ab initio calculations, generating photoelectric spectra for the students to practice assigning the peaks:

http://www.jce.divched.org/Journal/Issues/2008/Dec/abs1672.html

This experiment generates HPLC spectra to give students practice on optimizing HPLC settings: http://www.jce.divched.org/ Journal/Issues/2008/Sep/abs1265.html. See a similar example for GC: http://www.jce.divched.org/Journal/Issues/2007/Sep/ abs1488.html. This simulation obtains phase diagrams: http://www.jce.divched.org/Journal/Issues/2008/Jun/abs879.html.

Process Simulation Michaelis–Menten kinetics through simulation of reactant, product concentrations over the course of a reaction:

http://www.jce.divched.org/Journal/Issues/2007/Mar/abs434.html

A statistical simulation of chromatography, suitable for demonstrating the principles to primary and secondary students:

http://www.jce.divched.org/HS/Journal/Issues/2009/Jan/abs19.html

Webware showing different points of two-component phase diagram for six different systems:

http://www.jce.divched.org/Journal/Issues/2009/May/abs653.html

Molecular and Fluid Dynamics “Classic” molecular dynamics modeling, in a package that is suitable for educators:

http://www.jce.divched.org/Journal/Issues/2008/Aug/abs1071.html

A Web-based kinetics simulator that explores intractable kinetic systems, great for analyzing oscillating reactions, is available at: http://www.jce. divched.org/Journal/Issues/2008/Aug/abs1146.html. For another kinetic simulator used by students to model oscillating reactions, see: http:// www.jce.divched.org/Journal/Issues/2009/Sep/abs1072.html.

A spreadsheet-based demonstration of diffusion is at: http://www.jce.divched.org/Journal/Issues/2009/May/abs651.html and an in-class chromatography simulation using people as the “analyte” is at: http://www.jce.divched.org/Journal/Issues/2008/Nov/abs1512.html.

Explore the wealth of JCE resources.

www.JCE.DivCHED.org

© Division of Chemical Education  •  www.JCE.DivCHED.org  •  Vol. 86  No. 12  December 2009  •  Journal of Chemical Education

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