Determining typical interatomic distances for hydrogen bonds in a lithium sulfate hydrate. Removing all van der Waals contacts from the adjacency matrix.
Home / FAQ / Determining typical interatomic distances for hydrogen bonds in a lithium sulfate hydrate. Removing all van der Waals contacts from the adjacency matrix.
1. Open a Crystal Data window for a lithium sulfate hydrate (Ref. Code 22347) with all allocated hydrogen
atoms (Compound/Edit or double left click or click F4).
2. Open Adjacency matrix tab and find all hydrogen bonds (H) in the list. Find typical interatomic
distances for the hydrogen bonds O-H…O. What range do they vary in? (see the values of R in Å)
3. Find all contacts H…O corresponding to Van der Waals bonding. What are their distances?
4. Remove all the "non H" H…O contacts using local menu (Delete Selected or Change Type/No bond
commands). Save the changes. Pay attention that the Reference Code field contains the Collection Code
of the structure in ICSD.
5. Open a Crystal Data window for a lithium sulfate hydrate without allocated hydrogen atoms. Look at the
typical interatomic distances corresponding to O…O hydrogen bonds. For example, compound with Ref. Code 18173 shows O1…O5 2.870 Å vdW
6. If instead of going on Change Type (step 4 above) you click on Information, you will get, e.g. for
structures 22347 (with H, left) and 18173 (without H, right) the following self-explanatory windows:
Perform the algorithm for lithium selenate hydrates. Are there any differences in interatomic
distances O…O for hydrogen bonds in lithium sulfate and selenate hydrates?
The distances O…O for hydrogen bonds in lithium selenate is 2.87 Å; 3.00-2.881 Å are typical
ranges for O…O distances in hydrogen bonds in lithium sulfate.