Molecular Modeling

Molecular Modeling

Being able to visualize what molecules look like is really useful as you can build up a 3d picture.

Modeling

Molymods are expensive but can really help with various chemistry related skills.

Visualization

Rasmol is a piece of software that can visualize molecules, it is mostly used for biology but can be used to view Hydrocarbons and other molecules.

Available for:- Windows, Linux and Apple

Check out the Biology for links and instructions. In the mean time the video below may be useful.

How to Video

Following some feedback I have found a nice how to video that gives basic introduction to building with Molymods.

Ethanol is an Alcohol so has single bonds (C2H5OH)

Ethene is an Alkene so has a double bond (C2H4)

Ethene showing double bond

Modeling on a budget.

It should be possible to use different colored modeling clay (Plasticine) and bendy drinking straws, cut to size, to try and do the same job as the Molymod kits.

Bonds

Straight bonds could be about 1 - 2"
For double bonds, you could use the bendy portion. Look where the bend is,measure from bend to the end of the straw (this is the short portion) and note the length, then measure from the other end of the bend and cut. So they are both roughly equal.

With the bendy straws cut about 1" either side of the bend. Use two or three to form a double (or triple bond) and if you cut the straight part about 2" the use this for single bonds.

Plastercine Atoms

For the Atoms

Black - Carbon
Red - Oxygen
White - Hydrogen
Green - Halogens (Fl, Cl etc)
Lt Blue - Nitrogen

So same convention as for Molymods (see video as this is standard colour coding)

To help illustrated. I have managed to do this with Bluetack and old drinking straws.


Single Bond


Double bond

Clearly this doesn’t illustrate bond angles, but at least you hopefully get to build some simple molecules.

You may have to fight a younger sibling for the Plasticine though, just say it is for science.

Suppliers

To add some context to this

Science Daily : June 24, 2020

Space fill molecules

With the Molymod kits it is also possible to build models using space-fill connectors. More useful for single bonds. Here are the first 5 Alkanes in the Nomenclature series.

So now having obtained some Modelling clay, I set about making Methane CH_4.

This photo is from my personal blog.

MY MOLECULE MODELLING VIDEOS

I have uploaded videos of various molecules being built from my Molymod kit. This can be found on my Peer Tube account.

Constructive comments and contributions welcome.