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These slides present a walkthough of performing a Percent Buried Volume (%Vbur) calculation. The %Vbur is a measurement of the bulk of a ligand coordinated to a transiton metal. The calculation uses the crystal structure of a compound to determine how much space a ligand occupies. It does this by placing the metal at the center of a sphere and then calculates the volume of that sphere occupied by the ligand. Originally developed for N-heterocyclic carbene (NHC) ligands, it has also been applied to mono- and bidentate phosphines.
| Attachment | Size |
|---|---|
| Updated 5 slides | 296.5 KB |
| Original 5 slides for the older version of the site | 362.98 KB |
| Videos for original 5 slides | 4.36 MB |
This presentation was a step-by-step guide to performing a %Vbur calculation using a crystal structure from the literature. With the newer graphical version of the site that information is no longer useful. However, the 5 slides should give you the backgrounded needed to understand what this calculation is all about.
Evaluation
The SambVca software will either report a %Vbur value or it will not. The value will only be reported if the data is in the correct format and if the proper information is input. The recommendation would be to try the calculation of some of the Au(PR3)Cl compounds reported by Nolan to determine if calculation has been mastered.
One honor's thesis student has been successful at calculating %Vbur values.
Chip,
This looks like a very useful concept that I had not seen before. One procedural note that I missed on my first viewing: there are movies embedded in the pptx file (the same movies that are attached as the zip file). I only saw the black screen and was wondering what the problem is.
I teach Tolman cone angle as a method for thinking about sterics but the %Vbur seems like a much more meaningful (albeit harder to calculate) number. I can see myself using this for my own ligands in my research as well as in my teaching.
Adam
Following up on Adam's concept, I wondered if anyone had connected cone angles with %Vbur in some meaningful comparison?
Joanne
The site has recently been upgraded to version 2.0. Usually I am resistant to change but in this case I can say without a doubt it made a huge difference! It is now all graphical. And even better, it includes a library which you can use to see exactly how to go about doing these calculations. I am have modified the 5 slides to keep some of the background information. I am not going to update any of the info on how to do the calculations because the site provides you with that info now. I liked these calculations before, I love them now.
I have tried to log into the website provided here and in the paper and it won't let me access it.
https://www.molnac.unisa.it/OMtools/sambvca2.0/index.html
I keep getting notifications such as:
"The site cannot be reached" or "refused to connect"
Was the site developed for a particular type of computer (Mac or PC), or for a particular internet browser?
I haven't seen any retraction or modification of the original or 2016 paper so I was wondering why I could not connect. Has anyone else had these issues?
Thank you for the help.
Hi Joshua,
Nope it seems the site is down. I will contact Luigi to see what is happening.
Just heard back from Luigi, their server crashed. They hope to have the site back up in a few days.
Thank you very much,
I can't wait to use it!
Josh
I just heard back from Luigi, the server is back online. Good luck!
Echoing Joanne's question (8 years later) "if anyone had connected cone angles with %Vbur in some meaningful comparison?" and wondering why 3.5 Å is the magic number for the sphere and how different it would be at other distances for various ligands.
In reply to Echoing Joanne's question (8… by Alan Goldman / Rutgers University
The best answer I have Alan is from the paper on version 2 of SambVca (OGM 2016, 35, 2286) in which the authors state "Considering that typical metal−ligand bond distances are within 2.0−2.5 Å, a value of 3.5 Å to define the first coordination sphere around the metal is expected to account for the space roughly comprising the van der Waals volume occupied by the atoms coordinated to the metal." They also report that changes in that distance to certainly impact the %Vbur but that the overall trend remains. I take it as for something to access the metal center, it has to get reasonable close to the center. So, why not use a reasonably short radius and consider accessability to the metal within that sphere.