Tuesday, 12 June 2007

Cellobiose

Cellobiose is interesting because it is the building block of cellulose. As I understand it, the important structural feature is the hydrogen bond between the ring O and the 4' OH. It gives rigidity to cellulose strands.

In my GAMESS 3-21G calculation the hydrogen bond has a bonding order of .08 which is not really a lot. But this may just be a problem of the calculation. I don't know how to add extra functions just to the atoms I am interested in. And even the way I did it, it took 3 hours of geometry optimisation and it wasn't even quite stationary then.

This post is mostly to show a few nice pictures, though. I like making them and it seems that most of the google hits are going for them. Here's another one.

To give credit to all the nice free (or formerly free) programs I used: The structure was drawn, MM optimised and semi-empirically optimised in ArgusLab. Then I rearranged the structure with PyMOL's sculpting function to get the O and OH together. Structure optimisation in GAMESS, data extraction in ChemCraft, pictures again in PyMOL.

3 comments:

Anonymous said...

You can probably use semi empirical methods and still arrive at a stationary point which is pretty good. I think you will see the hydrogen bonding

Felix said...

actually I ran the geometry optimisation for some more time and now I have a stationary point. where the hydrogen bond length is 1.96 and the order .073

I ran the same starting geometry with AM1, PM3 and MNDO. It was much faster (5 minutes compared to 6 hours) but the results are totally different: MNDO - no H-bond at all (distance 2.90)
AM1 - maybe an H-bond (distance 2.27)
PM3 - they moved even closer together (1.85)

Troy Benjegerdes said...

Can I get your GAMESS input file for this? I want to try some higher-order methods on some of the bigger computers we have.

.. troy (at) scl (dot) ameslab (dot) gov