Kitamo Molecular Models Ball-And-Stick Model Design Guide

KitaMo Molecular Models Ball-and-Stick Model Design Guide

Draft Version. Issue Date 10 April 2012.

WARNING:

Please bear in mind that our models are not toys. Allow children to handle them only with adult supervision. Although they are built with structural integrity, they can easily be damaged by mishandling.

KitaMo Molecular Models are custom-made to your specifications.

This Guide is intended to help you prepare the specifications for your Ball-and-Stick Molecular Model.

If your requirements are not discussed in this guide, please let us know: [email protected].

Do not quench your inspiration and your imagination; do not become the slave of your model. Vincent Van Gogh

KitaMo Molecular Models are custom-built using precisely-machined parts. They are not assembled from commercially available kits, resulting in accurate structures.

Ball-and-Stick models are typically built on a scale of 1 Angstrom per centimeter (10 million times actual size), a compact scale that allows for easy handling and requires little display space.

The tools and techniques used to produce such miniatures may be adapted to build larger scale models.

To order a custom-made molecular model, the following information are required:

structure, scale, color scheme, accuracy and display preference.

Structural Information about the molecule. From this the number of atoms, the number of bonds, the bond angles and the bond lengths can all be determined. Such information may be provided using atomic coordinates preferably in an electronic file format that can be read by JMol (e.g., PDB). For simpler models, a drawing with all the necessary dimensions may be sufficient.

Scale in Angstroms per centimeter. Given the scale, the actual dimensions of the finished model can be determined.

Plastic beads for atoms

KitaMo Molecular Models use colored polystyrene beads to represent the atoms. Holes are drilled into the beads at precise angles and locations.

Bead colors. There are no standard colors for the elements and the choice of colors is completely arbitrary. However, the atom color assignments used by some popular model kits have found widespread use over the years (See Appendix A).

Bead sizes. KitaMo models are built using beads of the same or different sizes. The latter allows the relative sizes of the atoms/ions to be shown. Available bead diameters are 4, 5, 6, 8, 10 and 12 millimeters.

Metal Links for Bonds

KitaMo Molecular Models use stainless steel wire to represent the bonds. These wires are cut to precise lengths, inserted into the bead holes, and fixed permanently in place with epoxy or cyanoacrylate adhesive.

By default, only one wire is used to link two beads regardless of the number of chemical bonds. More links may be added to represent multiple bonds.

Models are assembled for static display. As an option, single bonds can be allowed to rotate, allowing for conformation changes.

Bond colors. The simplest models are constructed using plain unpolished 0.7 mm diameter stainless steel wire. Bond colors can be added to enhance the appearance of the model, or to distinguish between bond types (e.g., covalent bonds are colored while hydrogen bonds are bare metal). Color is added by slipping vinyl tubing over the wire. The tubing outside diameter is 1.5 mm.

Availability is currently limited to the following colors: black, blue, red, yellow, orange, green and white.

If bond colors are used, there are two options: (1) Using the same color for all the bonds; (2) Inherited bond colors, where each bond has two colors, each color being inherited from the parent atom, and resulting in a demarcation line halfway between the bond.

Since the tubing and the beads are not from the same supplier, color matching is not guaranteed for inherited bond colors.

Accuracy

It is during assembly that the final accuracies are realized. The best achievable tolerances are ± 1 degree for the bond angles and ± 0.2 mm for the bond lengths. For highly symmetrical structures, accuracy is very important. However, if the structure allows, the tolerances can be relaxed to ± 3 degrees for the bond angles and ± 0.5 mm for the bond lengths. In this case, the model would be easier to make and this translates to lower cost.

Display Preference

Depending on how the model will be used/displayed, provisions for a stand or some other mounting method may be necessary (e.g., picture frame, bookend). In certain cases, like the DNA double helix, the stand is required to support the model.

Cosmetics

While care is taken during construction, cosmetic imperfections may be present in the finished model. These do not affect the structural integrity of the model and in most cases are subtle and almost unnoticeable.

Some of these cosmetic imperfections are permanent due to the nature of the materials/methods used:

- Mold marks. Beads always come with a mold parting seam and an injection mark.

- Color mismatch for Inherited Bond Colors.

Other imperfections can be corrected, at additional cost, to improve the physical appearance of the model. See Appendix B for details.

Appendix A: The CPK Color Scheme

The CPK Color Scheme is used by CPK molecular models designed by chemists Robert Corey, Linus Pauling and Walter Koltun.

Element Color

Hydrogen (H) white Carbon (C) black Nitrogen (N) dark blue Oxygen (O) red Fluorine (F), Chlorine (Cl) green Bromine (Br) dark red* iodine (I) dark violet* Noble gases (He, Ne, Ar, Xe, Kr) cyan Phosphorus (P) orange Sulfur (S) yellow Boron (B) and most transition metals peach, salmon Alkali metals (Li, Na, K, Rb, Cs) violet Alkaline earth metals (Be, Mg, Ca, Sr, Ba, Ra) dark green Titanium (Ti) gray* Iron (Fe) orange Other elements pink

* this color is not available for KitaMo Molecular Models

Appendix B: Correcting Model Imperfections

Some cosmetic imperfections take time to correct and by default are left uncorrected on the model. These can be corrected, at additional cost, to improve the physical appearance of the model.

Bead Holes. Beads are originally made with an axial hole (about 1.6 mm diameter). At least one end of the hole is always used for bonding. The unused end is kept open, leaving a dimple. Remedy: This dimple can be filled with colored resin to improve the spherical surface contour, however color matching between the bead and the resin is not guaranteed.

Random traces of excess adhesive at bond roots. Adhesive is clear or light tan in color and the best effort is always used to minimize adhesive build-up, however some noticeable amount may still be left. Remedy: All bond roots are meticulously cleaned up to remove unwanted traces of adhesive.

Gaps at bead/colored bond interface. The spherical bead surface and the squarely-cut end of the bond color tubing do not exactly mate, resulting in a noticeable gap. Remedy: The gap is filled clear with adhesive, resulting in a filleted contour.