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Mindat Chemical Formulae: Inconsistency, Error, or Other?

Posted by Steve Hardinger  
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Steve Hardinger February 03, 2019 07:43PM
I've aways been puzzled by the way chemical formulae are presented here on Mindat, and (in some cases) other sites/publications as well. Specifically, the use of parentheses.

It appears to me that parentheses are used to groups together atoms that together form an anionic unit, such as the molybdate in wulfenite, Pb(MoO4) or the tungstate in scheelite, Ca(WO4).

I see that parentheses are used to enclose an anion when the anion must be separated from other anions for the sake of clarifying arrangement and bonding, for example giving the formula or descloizite as PbZn(VO4)(OH) instead of PbZnVO4OH.

But what about calcite, whose formula is (invariably) written as CaCO3? Why not Ca(CO3) for the sake of consistency?

It might be argued that this is just an inconsistency that needs to be addressed here on Mindat (and elsewhere).

However (as someone once failed to convince me) that the parentheses are not used "everyone of course knows these atoms are grouped together." If so then what about people (beginners mostly, I assume) **don't** know? For the beginner the inconsistent use of parenthesis probably causes more confusion about mineral chemical structure and representation within chemical formulae than it causes clarity.

From a chemist's perspective (mine) CaCO3 is correct and Pb(MO4) is incorrect. However a chemist's rules for writing a formula depend upon what is being conveyed (and what is being conveyed is not always clear in the context of the writing). An inorganic chemist will agree with CaCO3 but an organic chemist (a chemist for whom carbon is most important) the correct way to write a formula is carbon first with all other elements in alphabetical order. Thus calcite becomes CCaO3. Of course the latter only gives the atomic ratios, and fails to suggest any aspect of molecular structure.

So I get that mineralogists and chemists may have different rules, but what about the inconsistency in just mineralogy?
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Jolyon & Katya Ralph February 03, 2019 07:49PM
I personally don't like the use of parentheses in simple formulas such as PbMoO4

Occasionally I go in and remove them, and someone comes along and adds them back :)
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Jolyon & Katya Ralph February 03, 2019 07:49PM
I personally don't like the use of parentheses in simple formulas such as PbMoO4

Occasionally I go in and remove them, and someone comes along and adds them back :)
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Erik Vercammen February 03, 2019 07:59PM
Parentheses can clarify the structure: see FeWO4 that is an oxide of iron and wolfram and Ca[WO4] that is a wolframate of calcium.
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Jolyon & Katya Ralph February 03, 2019 08:27PM
> Parentheses can clarify the structure

Why do we need that when we have the structure detailed on the page below it. IF you need to explain the structure of the minerals clearly the formula is not the place to do it!
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Ralph Bottrill February 03, 2019 08:47PM
We are inconsistent, but it’s not just Mindat. In general mineralogists and geologists assume all readers have sufficient chemistry to understand most minerals have anion groups in their structure and only use parentheses where the structure gets a little complicated. We all assume everyone will see a formula KAlSi3O8 and infer it’s a silicate without parentheses, but you really need them with eg. epidote, tourmalines etc., though I’m not sure we need the two or three different types shown for some (eg. See epidote).
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Uwe Kolitsch February 03, 2019 08:53PM
The IMA list is inconsistent in that respect, but they are working on it (as part of the work on group nomenclature).

PS This was discussed several times before (use search option of the forum).
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Frank K. Mazdab February 03, 2019 09:29PM
I guess I missed it... where is the structure detailed on the calcite page?

And as for the difference between "multiple oxides" and "anionic groups", the distinction has sometimes seemed a bit arbitrary to me. Spinel is a "multiple oxide" where Mg and Al sit in various tetrahedral and octahedral vacancies in a lattice of CCP oxygens; conversely, forsterite is a "silicate" where Mg and Si sit in various tetrahedral and octahedral vacancies in a lattice of HCP oxygens. What's the big difference? Ringwoodite, chemically [but not structurally] the same as forsterite, is a spinel but apparently isn't a multiple oxide like its brethren in the spinel family... it seems to be considered a nesosilicate, although maybe it shouldn't be? It seems in ABO4 compounds when one cation occupies a much larger coordination site than the other, the small one gets to be in an anionic group (e.g. VIIICa[IVWO4]), but when the two cations sit in similar or identical sized sites (VIFeVIWO4), the whole thing is a multiple oxide (but to be clear in this particular case, since W sits in a WO6 octahedron, bracketing the [WO4] would not convey a correct sense of the structure anyway).

In any case, VICa[IIICO3] may look busy for calcite, but it does nicely show what's going on... trigonal planar CO3 groups whose oxygens coordinate a much larger Ca. I'll keep including the brackets (and occasionally the C.N. too), but if others delete them, I'm nonetheless not so hardcore to feel I need to add them back in... I think... lol.
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Frank K. Mazdab February 03, 2019 09:44PM
Ralph, good point. And your bracketless KAlSi3O8 example brings to mind why I like to use parentheses/brackets when I teach mineral formulas.

Without brackets, beginning students don't understand why NaAlSi2O6 is a pyroxene but seemingly similar KAlSi2O6 is a framework silicate.

Add in the brackets, and NaAl[Si2O6] jumps out as a [T2O6] mineral (a chain silicate), and K[AlSi2O6] jumps out as a [TxO2x] mineral (a framework silicate). Adding in C.N. makes the difference even more compelling (and addresses the sometimes question I get that the added brackets seem "arbitrarily placed").

If one of the goals of mindat is mineralogy education (and I believe it is), then there is something to be said for maybe adding the brackets/parentheses and potentially even some C.N. to what we view as even simple formulas.

Edit: and I agree the curly brackets around the {A1A2} and {M1M2M3} groups in the epidote group seem odd and out of place... perhaps just simple parentheses around those groups if the atoms are different (and omitted altogether if the constituent atoms are identical), as is done for the amphiboles.



Edited 1 time(s). Last edit at 02/03/2019 09:58PM by Frank K. Mazdab.
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Steve Hardinger February 03, 2019 09:45PM
Perhaps the solution to the inconsistency is to decide what a mineral chemical formula is trying to say, and then develop a system which consistently says this. Does Mindat have to be inconsistent just because the IMA is inconsistent? (If Johnny jumps off the Brooklyn Bridge do you have to jump off the Brooklyn Bridge, too?)
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Jolyon & Katya Ralph February 03, 2019 09:56PM
For simple items such as Calcite and Barite I think it's totally overkill to add them.

> Without brackets, beginning students don't understand why NaAlSi2O6 is a pyroxene but seemingly similar KAlSi2O6 is a framework silicate.

I think it's safer to say you can't deduce anything about the structure from the formula and give that as a good example - if people come to expect everything to be spoonfed to them with brackets and they come across forumlas written without them they'll soon end up in trouble.
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Alfredo Petrov February 03, 2019 10:06PM
I agree with Frank and Steve. A mineral formula must indeed depict something of the structure, and it should at least be consistent within structural groups, which it currently is not. We have different species written with different formula styles even within the same group! The cop-out is that "that's the way the IMA does it, so it's "official"". But as I've often pointed out, there is not an "official" way to write formulae, there are different styles for different purposes, and the very idea of having an "official formula" is as silly as an "official bread dough recipe".
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Frank K. Mazdab February 03, 2019 10:26PM
Whether adding brackets around simple formulas is overkill or not may well be a matter of personal preference, but all I can say about the sentiment of that last sentence is "yikes!" Add the brackets around those two minerals and you can deduce their structures, at least to a first degree. That's the elegance of it. And that's true for many other minerals too. One can look at the formula for a mineral and sometimes determine that the purported crystal system is impossible (or more commonly the other way around), because some unexpected prime number in the formula can't be reconciled with a high symmetry.

Maybe it is spoon-feeding. But I guess all education starts as spoon-feeding. When people later come across a formula without brackets, they don't "get in trouble"... they apply knowledge and experience. It's their earlier exposure to the formulas with brackets that will allow them to figure what's going on with a new unfamiliar formula. Anyway, no worries... mindat may simply be a data repository and it's good to know there are other resources out there to get ancillary information (but it seems kind of unfortunate that it wouldn't all be here)... so to my surprise, mineralogy education may not be a focus of this site.

By the way, why do we include a birefringence value in the optical data? You know that can just be simply calculated by subtracting the high and low refractive indices... this spoon-feeding has got to stop... LOL.



Edited 1 time(s). Last edit at 02/03/2019 11:36PM by Frank K. Mazdab.
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Jolyon & Katya Ralph February 03, 2019 11:27PM
Also, as for Wolframite, although it can be classed as a oxide it certainly is a tungstate too (although with W in 6 fold orientation rather than 4-fold)

If you look at the structure of Wolframite/Ferberite all the oxygen surrounds the W, and each Fe is surrounded 6 [WO6] groups.

> Maybe it is spoon-feeding. But I guess all education starts as spoon-feeding.

I was being a little harsh. My concerns are that if we were to do our own thing with a formula convention that isn't generally followed in the scientific literature it would generate confusion.

Maybe we need to have multiple formula fields, a plain formula (which is probably the one collectors would put on their labels), and a structurally-divided formula.

Then I'd be happy to have CaCO3 and Ca[CO3] side by side, and we can all have everything we want.

But wait... there's another problem here...

Why aren't we doing

Ca2+[CO3]2-


At the moment we have no easy way of searching for minerals that contain an element at a specific oxidation state. Nor can we easily search for specific ions such as [WO4] (which shouldn't bring up ferberite!)

We need to think about not just something to be displayed, but something that can potentially contain hidden codes to allow us to index and search on these. We may not care to show that Calcium is always 2+, but we do want to be able in the future do a search for, eg, any oxychloride of a 2+ cation.
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Frank K. Mazdab February 03, 2019 11:55PM
Hi Jolyon,

I appreciate your additional thoughts on this. An extra field or two as you suggest would seem to offer sufficient flexibility. For example, we already have IMA formula and "formula"... offering an additional "structural formula" field would be great.

And I hadn't considered how formal oxidation state is sometimes but not always presented, but agree that some way of accommodating it (whether hidden for searches, or in cases where there's a question about an element like Fe, Mn, Cr, etc., potentially both hidden and visually) would be useful.
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Volker Betz February 04, 2019 12:28AM
Almost 50 years ago... I had to give a seminar presentation concerning chemical nomenclature. Wulfenite as a chemical is lead molybdate Pb[MoO4], so the parentheses have a reason. To use simplified formulas for minerals is very common but does not describe reality.

Mineral crystals are often not pure chemicals. So for example wulfenite from Mezica (Slovenia) is in reality about

Pb0.94Mo0.06[MoO4]

see;
http://www.academia.edu/download/46968074/On_the_symmetry_of_wulfenite_PbMoO4_fr20160702-7493-73hiyo.pdf

So writing formulas simple is just describing something ideal, not reality, loss of information and rather far from pcecision.
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Keith Compton February 04, 2019 01:18AM
Sure glad I don't include mineral formulae on my labels !! ((-:)
Always thought I could simply look it up (e.eg: in Fleishers) if I didn't know or couldn't remember.
Now I'll never even be able to remember Calcite !! ))-:) Thanks J !!!

But seriously - perhaps it would be good to include alternate formulae - stay one or two steps ahead of the IMA



Edited 1 time(s). Last edit at 02/04/2019 01:19AM by Keith Compton.
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Alfredo Petrov February 04, 2019 02:03AM
The general custom is to only include valencies for those elements that can have multiple valencies in minerals, like Fe, V, U, etc, so it isn't necessary to write it for Ca because everyone knows that it's Ca2+ (well, everyone who had enough chemistry in school to read a formula anyway; the rest of our users will ignore all types of formulae). It would look a bit silly to start including valencies for every element.
I agree that we need multiple formulae options.
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Ralph Bottrill February 04, 2019 12:22PM
I agree with optional multiple formulae, as we have discussed in previous threads. As Volker says, sometimes as well as showing theoretical formulae (and structural formulae) we need empirical ones also, to indicate typical element solid solutions. Some mineral groups are terribly inconsistent in this regard, with a shambolic mixture of the two. Eg see pyroxenes and micas. We can still list the “official” IMA formula but can often do better! And of course we are an educational site and really need to do our best in this regard; not everything should be dumbed down for the uneducated masses!
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Donald Lapham February 04, 2019 05:14PM
Would it help any for Mindat to have a small section devoted to Chemistry with a mineralogical bent? Perhaps a periodic table with valence state information and some indications of tendencies such as "Chalcophilicity"or "Lithophilicity"?
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Benjamin Oelkers May 16, 2019 12:29PM
The possibility to expand the search functionality towards valencies and/or coordination numbers is something that I personally like quite a bit. And as Jolyon said, that would likely mean (internally) representing the formulae in a different way that can be used for multiple things. I don't know whether anything is already planned in this direction, but some kind of expanded internal format that can easily be parsed would be my suggestion. Something along the lines of:

CaCO3
ct:< Ca,1,2+,VI>an:<[< C,1,4+,III>],1,2-,VI>

Each position would be enclosed in <> (which is not already used in typical formulae), giving element or structural unit, stoichiometric coefficient, total charge, and coordination number in that order. Nesting can easily be done, unknown position can be filled with a placeholder (here ?). (Each?) cation and anion is preceded by ct: or an:, respectively.

Parsing for a simplified formula would ignore the third and fourth position of every entry as well as drop brackets with stoichiometric coefficient 1, giving the usual
CaCO3

Indication of valencies can be done by also using the third position of each entry (of course, whitelisting or blacklisting could be used to avoid unwanted "simple" valencies from showing). This would result in
Ca2+[C4+O32-]2- (all charges) or, e.g.,
Ca2+[CO3]2- (charges only for complete structural units).

Indication of coordination numbers can be achieved by using the fourth position of each entry. Again, some data might still best be left hidden, which could be filtered by blacklisting or some other method.
VICaVI[IIICIIIO3] (all c.n.)
VICaVI[CO3] (c.n. only for complete structural units).

Mixed sites could be represented in a similar way, based on the example above:
Pb0.94Mo0.06[MoO4]
ct:< Pb|Mo,0.94|0.06,2+|?,VIII>an:<[< Mo,1,6+,IV>],1,2-,VIII>

Please note that this is only a rough idea, but it could be a starting point for a system that is easy enough to both automate and use manually and flexible enough to allow for automatic generation of various formulae and various search functions. You could also use simple strings, making data handling rather easy. Spaces after < in the examples above are only needed for the string to show correctly on the messageboard! ;-)
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Donald B Peck May 16, 2019 04:19PM
At first glance, something along the lines of Benjamin's proposal seems to have merit, but I hope that such a change would be in addition to the formula that already exists. Many (most?) users find mineralogical formulae to be a bit daunting anyway, and Benjamin's suggestion would, I think, be overwhelming. And speaking of overwhelming, creating Ben's expressions across the mindat dataset might be quite a challenge. Another major problem: since the format is not a general standard one, how would the reader of mindat learn/know how to interpret it?
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Benjamin Oelkers May 16, 2019 04:37PM
The idea would be to have such a system in place working in the background. The formula on each mineral page would be displayed just as it is at the moment, the difference being that it would be easy to have a button (or something similar) which would change the formula from one appearance (e.g., "simple") to another one (e.g., "with valencies"). Any additional search functionality would also not involve the user handling the formula (or even its parts) directly, but it would use the (additional) information stored in something like the proposed format.

Of course, I agree that the main hurdle is to prepare formulae in the format needed. But quite a bit of that work could (more or less easily) be automated - maybe around 75%? (Just guessing here.)
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Benjamin Oelkers May 16, 2019 04:40PM
You might be familiar with the CIF data format for crystal structures - that format also uses a text-based, easily machine-readable approach. Unless you want to work with a structure in detail, e.g., while preparing it, you will not need to handle that format directly, but the program of your choice will handle it for you. The idea here is rather similar, albeit much much simpler.
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Doug Daniels May 17, 2019 02:38AM
Looks a bit complicated. You give a simple example using calcite; think I can follow the logic on it. However, what about the oxygen? How do you account for it? Let's not even get into some of the silicate groups: tourmalines, amphiboles, micas, etc. Seems like such a system might be of use to some professionals (maybe). And, with some of the cations (e.g., Cu, Fe, Mn.....) , and anion oddities (what is the valence of sulfur in pyrite?) who's going to go in and determine the valence state? And we now have something like 5000 species? Not too sure about this idea, but that's just me.
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Frank K. Mazdab May 17, 2019 03:44AM
Hi Doug... the valence of S in pyrite is still -2, but because the two sulfurs are bonded to each other, the whole S2 group has an effective valence of -2:

-S-S-

It's the same as with the oxygens in hydrogen peroxide. All is still OK with pyrite... :-)
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Doug Daniels May 17, 2019 07:40AM
Dang...we had arguments about such things when I was in grad school (do a reaction to show how pyrite degrades to iron oxide and sulfuric acid....). It's not a simple -2 valence... certainly with hydrogen peroxide (and, lets throw in sodium hypochlorite - "cholox") . It's a weird working of them durned electrons.... With pyrite, it can be stable, or not; (and...why???) with other things, well....
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Frank K. Mazdab May 17, 2019 08:49AM
A lot going on there in your post, but pyrite really is VIFe2+VI[S2]2-, which is structurally similar to halite (the "rock salt" structure), with the Fe in the equivalent Na positions, and the S-S dumbbells in the equivalent Cl positions with their long axes oriented along the cube body diagonals. However, the non-sphericity of the S-S pair lowers the symmetry of pyrite relative to that of its NaCl, MgO and PbS brethren, so pyrite is perhaps more properly considered as "derived from the rock salt structure". And in marcasite, the S-S dumbbells aren't aligned along the cube diagonals (so the cubic symmetry is totally destroyed), but the non-spherical dumbbells are instead aligned in the a-b plane of an orthorhombic lattice. It's pretty cool how these minerals all derived from one simple structure. Calcite is put together in an equivalent way, but here the non-spherical equilateral triangular CO32- groups destroy all the 4-fold symmetry of the cube (or, more properly, destroy three of the four 3-fold rotational axes of a generic isometric crystal), leaving only one 3-fold rotation axis left. That sole remaining 3-fold rotation axis, which was once one of the body diagonals of a cube, is what's left that reduces calcite down to just trigonal symmetry.



Edited 1 time(s). Last edit at 05/17/2019 08:58AM by Frank K. Mazdab.
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Cecil Cosse May 17, 2019 10:33AM
pppp
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Benjamin Oelkers May 17, 2019 11:33AM
Doug, Frank,
Thank you for commenting on this. Just to add some minor correction to the pyrite question: Pyrite is indeed VIFe2+VI[S2]2-, just as Frank said, but that makes each individual sulfur atom have a charge (or oxidation state, if you prefer) of -1: [S1-2]2-

Doug, you are certainly right that implementing such a system would be a lot of work. However, you would not need to give all possible information from the beginning, all fields could be filled with placeholders to begin with. Some script could then bring up formulae with missing information to someone willing to fill it in, maybe using a user-friendly UI of some description. I was really just playing around with ideas for a more powerful backbone for chemical formulae - in essence, no regular user should see any of that, but only enjoy the (easily automatable) output generated from it.
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Łukasz Kruszewski May 17, 2019 08:59PM
"It appears to me that parentheses are used to groups together atoms that together form an anionic unit, such as the molybdate in wulfenite, Pb(MoO4) or the tungstate in scheelite, Ca(WO4).

I see that parentheses are used to enclose an anion when the anion must be separated from other anions for the sake of clarifying arrangement and bonding, for example giving the formula or descloizite as PbZn(VO4)(OH) instead of PbZnVO4OH.

But what about calcite, whose formula is (invariably) written as CaCO3? Why not Ca(CO3) for the sake of consistency?"

Both types of formulas are accepted, though using parentheses in case of simple salts like CaCO3, CaWO4, or PbMoO4 is not practiced in chemistry.

Also, a single way of writting chemical (or crystallochemical) formulas is non-existent. So is for the compound names. Even though IUPAC recommends some single names, there are almost always other names, that are treated like synonyms, and also unnecessary/spare names.

It might be argued that this is just an inconsistency that needs to be addressed here on Mindat (and elsewhere).

"However (as someone once failed to convince me) that the parentheses are not used "everyone of course knows these atoms are grouped together." If so then what about people (beginners mostly, I assume) **don't** know? For the beginner the inconsistent use of parenthesis probably causes more confusion about mineral chemical structure and representation within chemical formulae than it causes clarity."

Parentheses are, indeed, needed when there are more ions (both cations and ions), but one of their main role is strictly mathematical, i.e., if there are more than 1 ions per formula unit, e.g., in dolomite: CaMg(CO3)2.

"From a chemist's perspective (mine) CaCO3 is correct and Pb(MO4) is incorrect. However a chemist's rules for writing a formula depend upon what is being conveyed (and what is being conveyed is not always clear in the context of the writing). An inorganic chemist will agree with CaCO3 but an organic chemist (a chemist for whom carbon is most important) the correct way to write a formula is carbon first with all other elements in alphabetical order. Thus calcite becomes CCaO3. Of course the latter only gives the atomic ratios, and fails to suggest any aspect of molecular structure."

"CCaO3" is just another way of writing the formula. Personally I've never liked this formulation, because it mixes everything. I thus prefer crystallochemical formulas, e.g., in the case of alunogen:

* simplified formula: Al2(SO4)3*17H2O
* crystallochemical formula: [Al2(H2O)6]2(SO4)3*5H2O

The latter formula not only explains how are the Al3+ cations surrounded, but also diversifies water into structural (or tightly-bound) water and crystallization water. The latter formulation also expresses thermal behaviour of such compounds, which first give-off the second H2O type, and then the first one.
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Jolyon & Katya Ralph May 18, 2019 08:50AM
> makes each individual sulfur atom have a charge
> (or oxidation state, if you prefer) of -1

I think that when you're looking at the S2 in pyrite it doesn't make any sense whatsoever to say that the individual sulfur atoms have a charge of -1 because they are not individuals!

Is the charge of Carbon in Calcium Carbide CaC2 -1 also?

It may be true statistically and for certain calculations but it absolutely not a real explanation of how the carbon is bonded.


When I do the anion/cation search there won't be any option to select S-1 but there will be for S-22.



Edited 1 time(s). Last edit at 05/18/2019 08:50AM by Jolyon & Katya Ralph.
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Benjamin Oelkers May 18, 2019 10:10AM
You are certainly right that there is no isolated S1-. I think the point here is to distinguish between the number of electrons each atom in a compound formally has, its oxidation state, and the real distribution of electrons in the compound, (usually) resulting in charges on some atoms.

The oxidation state (which I should have exclusively referred to) of sulfur in pyrite is -I, that is just a result of the stoichiometry. The same goes for CaC2 - carbon is in the oxidation state -I.

However, that does not mean that such ions can exist in isolated form, compare methane, for example: carbon has the oxidation state -IV in this case! The oxidation state does not even imply that there is a meaningful way to break a compound down into the corresponding ions - again, compare the methane example.

The real charges on each atom, on the other hand, are usually not very nicely defined in condensed matter. For very ionic bonding, we expect to "see" (either measure or calculate by theoretical means) high (effective) charges on anion and cation, respectively. Still, there is always some contribution of covalent bonding even in sodium chloride, resulting in effective charges of slightly less than 1+ and 1-. That is why we just draw a line somewhere between ionic compounds, for which we only account for ionic bonding and round the charges up to nice whole numbers (NaCl), and covalent compounds, for which we only account for covalent bonding and round the charges off to zero (CH4).

So, in conclusion: There is no isolated S- ion in pyrite (or likely anywhere else in condensed matter), the oxidation state of sulfur is -I, the formal charge of the disulfide anion is 2-, and the real/effective charge of sulfur in pyrite is very likely even less than 1-, because there is quite some metallic character to this compound, suggesting less localized electrons - of course, that also means that the effective charge on iron is also less than 2+.



Edited 1 time(s). Last edit at 05/18/2019 10:10AM by Benjamin Oelkers.
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Frank K. Mazdab May 18, 2019 11:45AM
I have to reluctantly admit that as a mathematical construct, Benjamin's assessment that the individual sulfur valence in pyrite calculates to -1 is actually correct. Still, it's a formalism that nonetheless periodically bothers me for reasons akin to what Jolyon points out, particularly when one looks at more esoteric species than just S22-. For example, the S in S3- would by this construct have a valence of -1/3; the S in carrrollite is somewhere between -1.5 (2008) and -1.75 (2009), and the two S in thiosulfate (S2O32-) from just math appear to be +2 each, but could conceivably be +6 and -2, and indeed from bond length measurements are actually more likely a perhaps unexpected +5 and -1. That's an awful lot of potential choices for a sulfur valence drop-down menu... :-/
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Benjamin Oelkers May 18, 2019 11:52AM
I just found a detailed analysis on the charge distribution in pyrite and marcasite:

Schmøkel et al., Chemical Science 2014, 5, 1408-1421 (DOI: 10.1039/c3sc52977k).

They conclude that the effective charge on sulfur is about -1/3 and that on iron about +2/3 instead of -1 and +2 as a purely ionic bonding would suggest. I find it intriguing to see how much our simplified interpretation of bonding can sometimes deviate from in-depth studies!
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Benjamin Oelkers May 18, 2019 11:58AM
For selection purposes, I would suggest to just keep it simple, and use just a few categories like S2-, Sx2-, SO42-, SO32- and SxOy2- (for the S,O-containing anions). That is in essence the same thing that the various mineral classification systems do, isn't it?
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Łukasz Kruszewski May 18, 2019 12:02PM
Benjamin,

you may also want to check some Cu sulfides pages. Some years ago I've introduced some informations about the "extended" formulas, which show distribution of various Cu states. But there is more... Similar charge issues have to do with... fluorite.... Quite recently some Polish studies have shown, that Ca "is not 2+" and F "is not 1-" in CaF2:

https://www.ncbi.nlm.nih.gov/pubmed/28762974

But this all only confirms, that there is no a SINGLE formula representation of any particular structure.

I this field, I like Robert A. Wilson and his anti-IS ideas: there is nothing like "IS" in science, actually. There MIGHT BE.... or things ARE SUPPOSED TO BE, etc.



Edited 1 time(s). Last edit at 05/18/2019 12:04PM by Łukasz Kruszewski.
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Łukasz Kruszewski May 18, 2019 12:03PM
Benjamin, also thanks for this interesting link. I will update the pyrite and marcasite pages now.
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Frank K. Mazdab May 18, 2019 12:12PM
I like brackets, even for simple formulas, to ensure that our newbie amateur mineralogists appreciate that, for example, K[AlSi2O6] is more closely related to Na[AlSiO4] than it is to NaAl[Si2O6], despite the latter's subscript-identical formula.
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Benjamin Oelkers May 18, 2019 12:47PM
Łukasz,
thank you for the link, that will certainly be a nice read.

For me, using oxidation states is a powerful tool as long as you keep in mind that it is a simplification derived to fit numerous cases and uses, but without any strict physical meaning. That is also why in chemical training, you will usually be faulted for using "oxidation state" and "charge" interchangeably... :-)

Frank,
I strongly support using brackets to differentiate between alumosilicates and aluminium-containing silicates!
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Jolyon & Katya Ralph May 18, 2019 01:20PM
Searching for complex families of anions eg the SxOy category that Benjamin suggests is a hugely important.

BUT.. we're really missing the whole point of this.

The main point is to be able to search, for example, for minerals with Mn4+ instead of Mn2+, or for minerals that contain sulfite groups, etc etc.


My problem with putting [ ] in formula to help amateur mineralogists appreciate the difference between minerals has always been that the if you're looking at the formula alone to tell this you're really doing it wrong! In the case of the aluminosilicates that Frank brings up I really don't mind too much, but we do need some better way of dealing with this in general.

The concept of an encoding system for formulae that allows a more complex structural formula and a 'simple' formula to be generated from the same data is very appealing. The big concern is the work involved in converting 5500+ entries into this syntax.


I like the idea also of having something interactive. remember, we're on a computer, this isn't a book.

So, perhaps you could have a formula displayed as

CaWO4

but when you move your mouse over the different elements in the formula (or touch them on a touch device) they are highlighted and explained, and you can click a button to switch it to a more detailed format.

Trying just to throw a few brackets and parentheses in to the formulas in the hope that somehow that's going to explain everything isn't going to work!



Edited 1 time(s). Last edit at 05/18/2019 01:21PM by Jolyon & Katya Ralph.
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Łukasz Kruszewski May 18, 2019 05:15PM
Sounds like a bunch of great ideas. But, indeed, a large work to be done.... Regarding the valencies search: things quite often go changed in mineralogy and this also includes the valencies knowledge (e.g., due to the more and more common use of XANES/EXAFS but also some new techniques including a special microprobe). On the other hand, maybe we could have the "general" (mindat) formula, and something like "extended formula"? And, for instance, a simple chemical search and an extended one?
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Łukasz Kruszewski May 18, 2019 05:23PM
Addressing the issue of normal and square brackets (and other ones): although chemistry does have special meaning of these types, this may be a "philosophy" question if, or rather to which extent, mineralogy should follow it. One answer is the more and more often multidisciplinary character of the nature sciences today (which would suggest a strict following the IUPAC recommendations). On the other hand, this has to do with the type, or level/hierarchy, of the formula in question. I think the general/mindat formula could use the bracket regarding to the large-than-one-occupancy cases, and to complex ions like [AsO3(OH)]. The meaning of the square bracket in a simplified formula is sometimes different than in a crystallochemical formula. A good example is the betpakdalite supergroup or some titanosilicates with block-like structure, where the particular blocks (and not necessarily ions) or other parts like sheets or chains are represented in square brackets.

I think we also need to remember that there are cases in chemistry when some simple anions are reported in square brackets. A good example here is the silicates. I must say I do not see a need of putting them in square brackets and not in the standard ones, but I assume this might have to do with the nature of the silicate anions (i.e., a lacking confirmation of the true presence of at least some of the siliceous acids), but I may be wrong here.
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