Submitted by Chip Nataro / Lafayette College on Mon, 04/23/2012 - 09:29
My Notes
Categories
Description

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.

Learning Goals

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
Evaluation Methods

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.

Evaluation Results

One honor's thesis student has been successful at calculating %Vbur values.

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Adam Johnson / Harvey Mudd College

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

Thu, 05/03/2012 - 23:00 Permalink
Joanne Stewart / Hope College

Following up on Adam's concept, I wondered if anyone had connected cone angles with %Vbur in some meaningful comparison?

Joanne

Mon, 05/14/2012 - 15:06 Permalink
Chip Nataro / Lafayette College

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.

Mon, 11/21/2016 - 17:39 Permalink
Tropp / University of Southern Mississippi

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.

 

 

 

Wed, 02/15/2017 - 20:44 Permalink
Chip Nataro / Lafayette College

Hi Joshua,

Nope it seems the site is down. I will contact Luigi to see what is happening.

Wed, 02/15/2017 - 21:47 Permalink
Chip Nataro / Lafayette College

Just heard back from Luigi, their server crashed. They hope to have the site back up in a few days.

Thu, 02/16/2017 - 00:24 Permalink
Tropp / University of Southern Mississippi

Thank you very much,

 

I can't wait to use it!

 

Josh

Thu, 02/16/2017 - 01:10 Permalink
Chip Nataro / Lafayette College

I just heard back from Luigi, the server is back online. Good luck!

Mon, 02/20/2017 - 09:16 Permalink
Alan Goldman / Rutgers University

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.

Tue, 08/04/2020 - 01:02 Permalink
Chip Nataro / Lafayette College

In reply to 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.

Tue, 08/04/2020 - 08:23 Permalink