Introduction: Home Made Molecular Model Kit
Students of organic chemistry have an ongoing need for a comprehensive molecular model kit throughout their high school and university studies. There are many different types and makes of kit available commercially, but generally they are either too restricted in the range of compounds which can be built from them, or else are rather expensive if they have a large number and variety of components.
A very versatile kit can easily be made up using cheap and plentiful household items, at a fraction of the cost of commercial kits. The basic components are plastic Christmas decorations, in the form of strings of small beads, usually metallised in silver, gold, red, green or blue. Two sizes are common, 6 mm and 12 mm diameter. The other items are bamboo satay skewers, 2.5 mm in diameter ( available in most supermarkets ) and plastic tubing with internal diameter 2.5 mm. The tubing may be vinyl, polyurethane or any other moderately flexible plastic. The ink tubes from some types of ball point pens can also be salvaged for this purpose. Other materials needed are a set of acrylic poster paints ( black, white, red, blue, green and yellow are the main colours needed ), plus some clear craft glue suitable for wood and plastics and a spray can of clear acrylic lacquer..
Some tools will also be needed, including a small electric drill, a fine hacksaw, a sharp hobby knife, small paint brushes and a protractor. To make the atom centres, it is necessary to drill holes at the required angles into the plastic Christmas decorations ( referred to hereafter as “balls” ) and glue in short lengths of bamboo skewer, after which the atom centres are painted in the appropriate colours. Drilling the holes accurately will require the use of a simple jig made from a block of wood, so that the stubs can be set up at the common bond angles of 90 0, 109 0, or 120 0. Three types of atom geometry are sufficient for most organic compounds, tetrahedral, octahedral and trigonal bipyramidal. The trigonal bipyramid jig is simpler to make, so let's begin with that.
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A hole 10 mm in diameter and 5 mm deep is drilled into a wooden block, and angles of 120 0 are marked off around the circumference of the hole . The edge of the hole is chamfered with a countersink or a sharp knife so that a 12 mm ball will sit snugly in the hole.
A 2.5 mm diameter hole is drilled vertically through the centre of the 10 mm hole.
Using the same drill, a hole is then drilled diametrically through the centre of a ball and a 27 mm length of bamboo skewer glued into this. The ball with its protruding prongs is now located by inserting one of the prongs into the hole in the jig
The three “equatorial” holes are then drilled into the ball following the 120 0angle marks. Three 12 mm lengths of bamboo skewer are glued into these holes to complete a trigonal bipyramid atom centre.
The octahedral jig is identical to this, except that four equatorial holes at 90 0are needed.
To make a tetrahedral jig, another hole 10 mm in diameter and 5 mm deep is drilled into a wooden block, and an angle of 109.5 0is marked off on the circumference of the hole. A 12 mm ball is then located in the hole and drilled with two holes at an angle of 109.5 0 as indicated by the marks.
Two 12 mm lengths of bamboo skewer are glued into these holes. You will then need a cylindrical piece of plastic, such as the cap from a felt tip marker, in which has been cut two slots so that the prongs will slide into the slots. The atom centre is inserted with the prongs pointing vertically downwards and a marking pen is used to draw a line on the ball perpendicular to the plane of the two prongs.
The ball is then removed from the jig, and another hole is drilled into the block at an angle of 54.5 0from the horizontal , so that one of the two prongs on the atom centre can be inserted with the marker line level with the circumference of the 12 mm hole, having the two 109.5 0 marks exactly opposite the prongs.
The remaining two 109.5 0holes are now drilled in line with the marks , and two more 12 mm lengths of bamboo skewer glued into the holes. The result will be a tetrahedral atom centre having four bonds at angles of 109.5 0 These are used for sp3 hybridised atoms, such as the carbon atom in methane. Atom centres for sp3 nitrogen, oxygen and sulphur can be made on the same jig, but using only the required number of prongs. I prefer to leave the extra prongs in place to represent lone pairs of electrons (where applicable ).
Once the jigs are constructed, you are ready to begin building and painting a stock of atom centres for the model kit. A minimum starting kit would need about 20 carbons, made up of 12 sp3 tetrahedra, 6 sp2 trigonal bipyramids and 2 sp octahedral atoms in black, 8 nitrogens ( 4 sp3 , 2 sp2 and 2 sp in blue), 6 oxygens ( 4 sp3 & 2 sp2 in red ) and 36 hydrogens ( 6 mm balls, with a single prong, white ). A few fluorine ( blue-green ) and chlorine ( yellow-green ) atoms may also be useful.
You will also need a collection of bond tubes cut to suitable lengths, depending on the scale of the models you wish to build. A convenient scale is 30 mm = 100 pm, so for most bonds found in organic molecules, a standard length of 35 mm would be satisfactory. Two 12 mm diameter balls connected by 35 mm of tubing will have a distance of 47 mm between the atom centres, which corresponds to 157 pm on this scale. The pi bonding tubes are cut to a length of 75 mm.
Whether you just use clear tubing for all bonds, or paint the tubing to match the atom colours is a matter of choice. I prefer to use coloured tubing for the sigma bonds only, and clear tubing for pi bonds. The tubing may need to be undercoated with a solvent based primer before applying acrylic colour coats, otherwise the acrylic may flake off. A final coat of clear acrylic lacquer will prevent the parts from becoming soiled from handling.
A home made kit constructed in this fashion will have some minor dimensional variations compared to mass-produced injection moulded products, but is quite adequate for any non-quantitative studies of the geometry of organic molecules up to graduate levels. Stereochemistry is mainly concerned with the relative positions of atoms, rather than precise values of distances and angles. Computer modelling programs are more suitable for quantitative studies.
CONSTRUCTION OF MODELS WITH THE KIT
This kit will allow construction of organic molecules with sigma and pi bonding depicted, using atom centres with the appropriate geometry and sections of tubing to represent the bonding electrons. Some examples will illustrate the general construction procedure. If you want to know more about bonding in organic molecules, a brief tutorial is attached in the file VSEPR Bonding.pdf
Example 1 : Cyclohexane( sigma bonds only )
Parts needed : 6 black tetrahedral atom centres ( carbon ), 12 white hydrogen atoms and 18 sigma bond tubes. Using the sigma bond tubes pushed over the atom prongs, join the 6 carbon atoms in a 6-membered ring in the chair conformation, and connect 2 hydrogens to the remaining prongs of each carbon atom. The model may be flexed to convert between different conformations of the ring.
Example 2 : Ethylene( Double bond )
Parts needed : 2 trigonal bipyramid carbons, 4 hydrogens, 5 sigma bond tubes & 2 pi bond tubes
Connect the carbons and hydrogens in the sigma bonded framework, then attach the pi bonds to the axial prongs of the carbon atoms as shown.
Example 3 : Benzene ( Delocalised double bonds )
Parts needed : 6 black trigonal bipyramid atoms centres ( carbon ), 6 white hydrogen atom centres, 12 sigma bonding tubes and 6 long pi bonding tubes.
Using the sigma bonding tubes and the equatorial prongs of the carbon atoms, join the 6 carbons in a planar ring and attach one hydrogen to each remaining equatorial prong.. The long pi bonding tubes are now attached to the axial prongs of the carbons, alternating above and below the ring to represent the delocalised pi bonds.
Example 4 : Acetonitrile ( Cyanomethane )( Triple bonds )
Parts needed : 1 tetrahedral carbon, 1 octahedral carbon, 1 octahedral nitrogen, 3 hydrogens, 6 sigma bond tubes and 4 pi bond tubes.
Using the sigma bond tubes, form the linear structure C-C-N with the octahedral carbon in the centre, and attach 3 hydrogens to the tetrahedral carbon.. Attach the 4 pi bond tubes to the remaining prongs of the carbon atoms, and their other ends to the adjacent nitrogen atom prongs, forming four curved pi bonds as shown.
Example 5 : Ketene ( Ethenone )( 2 Double bonds to the same carbon atom )
Parts needed : 1 trigonal bipyramid carbon, 1 octahedral carbon, 1 trigonal bipyramid oxygen, 2 hydrogens, 4 sigma bond tubes & 4 pi bond tubes.
Using the sigma bonds, assemble the linear structure C-C-O with the octahedral carbon in the centre. Attach 2 hydrogens to the trigonal carbon, using the equatorial prongs. Attach the 4 pi bond tubes to the remaining prongs of the octahedral carbon. Two of these pi bond tubes are attached to the trigonal bipyramidal carbon's axial prongs, and two to the oxygen's axial prongs.
Step 10: Home Made Molecular Model Kit
Example 6 : Chlorophyll A ( Example of a large molecule built with this kit)
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