Recommendations for chemistry software

[Moogie]

Hi

Can anyone recommend any tools for creating resources for teaching chemistry and molecular sciences? I used rasmol many years ago but I believe that has been superceded by Jmol so i will download that and have a look. I know Isis Draw is free. I have downloaded it and will investigate

I would like to draw:
organic chemistry reaction mechanisms
reaction profile diagrams
electron orbitals

At a more basic level it would be animate molecular movement (with the atoms respresented as simple circles) to show things like:
-why reaction rates speed up as concentration increases due to collision theory
-animate diffusion
-to show 'pressure' in terms of molecular collisions against a container wall

thanks

 

[alxm]

Rasmol and JMol are fairly different, in that the former is mainly for looking at PDB structures and JMol isn't.

Isis Draw and ChemDraw are what's typically used for reaction mechanisms. There's a free Linux one (forgot the name at the moment) too, but it's not as good, yet at least. Reaction profiles you can use any vector graphics program, but the aforementioned programs can do it, even if I don't think they have any built-in functionality for it. All you need is some lines.

Drawing orbitals is quite different. To draw the orbitals, you first have to know what they are, which means you need quantum-chemistry software and the related visualization software, such as GaussView, Molden, Spartan, Maestro.

 

[Moogie]

Thanks for your reply. Don't you load pdb files into Jmol then? I thought you did. How does it draw molecules then? Do you give it a molecular formula and it renders it for you?

 

[Borek]

animate diffusion

Go to http://www.chembuddy.com/?left=all&right=download

Ignore commercial software in the upper part of the page (well - feel free to try these programs for free for 30 days) and scroll down to diffusion and fractal electrodeposition simulator.

 

[alxm]

Don't you load pdb files into Jmol then? I thought you did. How does it draw molecules then? Do you give it a molecular formula and it renders it for you?

Ah, I should've been more specific I suppose. Yes, JMol is for rendering 3d structures, such as pdb files. I just meant that Rasmol is more geared towards (and suitable for) protein structures than JMol is. If I were to look at a protein I'd use rasmol, but if i wanted to look at an organic molecule I'd use JMol.

(Well, actually I've written my own software which is similar in functionality to JMol, so I use that)

How's business going, Borek?

 

[Moogie]

Really? What's your software? I won a prize when I was at university for an investigation into the use of molecular visualisation tools to aid the teaching of '3D' subjects. There wasn't that much around those days then. Except rasmol of course

 

[Borek]

How's business going, Borek?

Not enough to be the sole source of income, enough for a nice vacations now and then