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.
![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikCbx57yqOx1ct_LrOPfblvJZo0FJi67naRNRy5LLJkf_IvdBdigSBp3h8nU1IB_kkvx6bygB2ZN88PFF87KiaYo7SpH9Vr81Txhzfjbrjq67Gr3o3cH-7OJ8GOR-P4A_lv7ejd79aJWw/s400/Cellobiose_Bild_03.png)
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.
![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLOE-n4ux1Rb_SyVZgLSzN7L2GjbV6BGLyBq5ZtiHBEPUNHVV0ZgYB64_g5kOkmBvixv_o_5aOS-R0z3-5JgEVex3z0njoOoUwedFpF8g30SEJiYVy9FFNkiTrEm_ZNTm1YhaGKZFqW8o/s400/Cellobiose_Bild_02.png)
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.
![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZMsUrxmzYb2EngGuRBbhlo6EtJbzqXU_gW5OeucSO35vTX7IU2vKSZhyphenhyphenb5DXT1-jGs6PNYifbvaxSW8e_tfURMTWNF90qjZUHjiEprF0Llai58pW3DlgFoKtTg-rch0TY-thwMJlqTnc/s400/Cellobiose_Bild_01.png)
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:
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
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)
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
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