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Chemical name reference

Posted by Jeff Joy  
Jeff Joy October 09, 2018 12:36AM
Today the database displays the chemical formula, but not the searchable chemical name. (Perhaps I am missing existing functionality of the database?) I would propose a new field for this purpose.
For example if I typed in ‘manganese oxide’ I would hopefully get back those minerals for which this compound is the constituent molecule. Of course there may be many oxides as well as polymorphs, etc which creates many targets but that’s the point. I may ‘think’ that I know what the results would be, but may be surprised by the actual results.
Again using this example, a use of this information might include exhaustive exploration of manganese-rich sites for undiscovered species, knowing that a complete list with photos was at hand as a starting point.
Other uses of this ‘reverse lookup’ come to mind, such as as when you simply can’t recall the proper name of a mineral but can describe it in IUPAC terms.
Public thoughts welcomed here.
Doug Daniels October 09, 2018 01:07AM
Just a thought or two - sure I could come up with others as this rolls around in my mind. Part of the problem would be with how someone puts in a "word description" of the chemical composition of a mineral. Your example of manganese oxide sounds simple, but would likely exclude any hydroxides/hydroxyoxides (see? how do you name the composition?).
Manganese carbonate would definitely be simple. But, think about the silicates - can you come up with a simple chemical name for a tourmaline, an amphibole, a zeolite? How you might name the compound, and how it would potentially be written into the database, may be two different things, so you would likely miss some potential matches.
Erik Vercammen October 09, 2018 04:07AM
You can already search minerals with chemical components (elements) in the search functions 'minerals by chemistry'.
Benjamin Oelkers October 09, 2018 01:20PM
I would agree that it likely is easiest to just use the search via elements ("minerals by chemistry"). Although a precise and unequivocal chemical name can of course be generated for every substance that is described by a chemical formula, that would indeed become quite cumbersome quite quickly as mentioned above.

Maybe something a little more in line with the original idea: How about a search function that allows for usual chemical entities (e.g., ions)? What I mean by that is that you would put in "manganese oxide" as stated above, and get all minerals containing manganese (in cationic form) and oxide (O2-), but not silicates, phosphates, etc. While this result can be obtained by tweaking the search via elements (e.g., exclude Si and P), it would indeed be helpful to get something like that in a simple way.

In principle, a similar mechanism to the search via elements could be used by adding buttons with O2-, OH-, CO32-, SO42-, etc. However, this would need the relevant structural data to be parsed/extracted from a "good" chemical formula or name... Maybe the IMA's chemical formula is a good candidate for this?
Keith Compton October 09, 2018 08:53PM

I'm not quite sure what you are after but have you tried searching via using the periodic table to find what you are after?

Go to the top search bar then select the "More" button, then select the "The Elements" button.

Select the element from the Periodic Table that you are interested in and the elements that you want associated in the formula and work your way through them.

It is a neat way of searching and also learning about minerals in a different way.

Kevin Conroy October 09, 2018 09:01PM
I wonder if you search Pb, Cr and Al if the result would return "Pub Crawl"?
Keith Compton October 09, 2018 09:05PM

At least the pub would have "BeEr" and "WINe" of course :-))


Edited 1 time(s). Last edit at 10/09/2018 09:08PM by Keith Compton.
Doug Daniels October 09, 2018 09:12PM
I'd go to that PuB.
Alan Pribula October 09, 2018 10:57PM
This is enough to drive someone BaNa2S.
Jeff Weissman October 09, 2018 11:00PM
Now, don't be CuTe
Alfredo Petrov October 09, 2018 11:00PM
This is too much! Y'all seriously need to forget about minerals for a while and go out and look at some rickardite realgar.
Doug Daniels October 10, 2018 12:02AM
Clever, Alfredo...clever.....
Jeff Joy October 10, 2018 12:56AM
Clearly I was unaware of the genie that I had unleashed ;-))

To respond to Doug’s initial reply, a query on ‘manganese oxide’ should rightly exclude ‘manganese hydroxide’ as it is a different species. This is just the point of the current search by element function’s dilemma, and why I made this posting. If I were to search on both Mn and O the results include a huge list inclusive of all species with these elements. A proper result for this search indeed, but not the one I desire if I ask for all minerals containing the chemical formula ‘manganese oxide’. There are only maybe four proper chemical combinations of manganese and oxygen that fit this description and that naturally occur as minerals, and I would wish only these to be reported as the desired results.
To Benjamin’s points, query by the ionic and valence states and then dealing with the ones that are non-ionic/covalent seems to be a complex methodology. However - hitchhiking on this notion, one might deviate from pure IUPAC nomenclature and use familiar mineral terms where commonly agreed. For example it may be sufficient to describe SIO4 as ‘Silicate’ as a practical matter. This can then be extended to alumosilicates, beryllosilicates, borosilicates and so forth so as not to dig deeper than needed while describing sufficiently to differentiate say, tourmalines from of zeolites.
Yes, a God of chemical nomenclature will have to rule for a time as initial names are handed out but of course the bulk of work is one-time, with new species being relatively rarely named.
[edit] Hey’s Mineral Index looks to have the right balance between detail and simplicity when constructing a named query. So for ex. if one queried ‘Fe’ and ‘aluminosilicate’ one should properly get ‘Almandine’ as a response. While “Iron Aluminosilicate” is not a real chemical compound name, it follows the idea of using ‘shorthand’ for mineral names.

Edited 1 time(s). Last edit at 10/10/2018 01:27AM by Jeff Joy.
Michael Hatskel October 10, 2018 01:27AM
In many cases, the Hey's Classification works just fine for me. For your particular example with MnOx / MnOHx, category 7.18.3 should work.

When using the 'Minerals by Chemistry' search, I found it helpful to first select the "Elements to Include" and the "Mineral Class", then play with the "Essential Elements Only?" field, and then, if necessary to further polish the search results, add the "Elements to Exclude".


Edited 1 time(s). Last edit at 10/10/2018 01:28AM by Michael Hatskel.
David Von Bargen October 10, 2018 09:47AM
The chemical search here does have the option to exclude certain elements from the search. Although when searching for manganese oxides, most geologists would include both manganese oxides, hydroxides and a bunch of amorphous material.

When you are looking for things like sulfates or carbonates, you would need to get into the various classification systems around (but they are not being kept up)

Search for just Mn and O

Jeff Joy October 11, 2018 02:21AM
Michael and David, thanks for your replies, and yes, you are both showing ways to get there using existing tools, but as one can see from the cumbersome exclusion field in David’s search by chemistry example, it leaves something to be desired. I also agree that the Haye’s classification allows one to drill down as Michael’s example shows, but it requires a decision-tree query down multiple levels until one arrives at some desired level of specificity. Again, doable but tedious.

I had hoped for an easy one step query by name with results that matched just that formula (or description).

Well, we’ve beaten this horse about as far as he will go, so it’s time to quit, but thanks for playing, and will see you all next time around ;-)

Edited 1 time(s). Last edit at 10/11/2018 02:23AM by Jeff Joy.
David Von Bargen October 11, 2018 10:09AM
The exclusion field is easy to generate - just hit the "Exclude unselected elements"
Jolyon & Katya Ralph October 11, 2018 10:54AM
Going back to the original question, I think there is certainly a benefit in having more traditional chemical names for some minerals (when you get to things like complex silicates it becomes a little less relevent)

So things like Manganese III Oxide for Bixbyite.

These become useful when trying to track down synthetic analogues of these compounds.
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