Thoughts on Excerpt from My Chem Prof's Textbook?

[Qube]

What are your thoughts on this excerpt from my chem prof's textbook?

ON FORMULA WRITING
In this writing chemical formulas are used which keep with structure of species. This is of particular importance since structure is the most important property of any chemical species which has covalent bonds (i.e., molecule and polyatomic ion). For example, consider the following common names/formulas (which keep with structure):

hydroxide ion, HO^-
sulfuric acid, (HO)₂SO₂
hydrogen peroxide, HOOH
ammonia, H₃N
ammonium ion, H₄N⁺
hydrated aluminum ion, Al(OH₂)₆³⁺

Likely you have seen the formulas for these species written as:
OH^-
H₂SO₄
H₂O₂
NH₃
NH₄⁺
and Al(H₂O)₆³⁺, respectively.

However, these “traditional” formulas are wrong with respect to structure and should not be written as such in the chemical literature – tradition be damned!

To illustrate, hydroxide ion is produced by the deprotonation of water (HOH) which cleaves an H-O bond heterolytically to produce H⁺ and & OH^-. In other words, this heterolytic bond-breaking process converts the originally-shared bonding electron pair between H and O into a nonbonding electron pair residing in the valence environment of the oxygen atom thereby creating a “-” charge. This can be readily verified by formal charge analysis (see Ch. 9, p. 11) and is expected since O is much more electronegative than H (see Ch. 9, p. 6). Furthermore, standard formula-writing practice dictates that a chemical formula has the symbol for the more electropositive element written before the symbol for the more electronegative element. Thus, for hydroxide ion, HO^-is correct and OH^- is grossly incorrect.

Similarly, ammonia should be written as H₃N and ammonium ion should be written as H₄N⁺ since N is more electronegative than H and since the nitrogen atom bears the “+” charge created by addition of H⁺ to H₃N.

I have a few problems with the beginning of the text and a huge problem with the bolded statement.

I understand the intentions of my teacher - structure - is highly important in chemistry. Not so much emphasized in general chemistry but very important in organic chemistry (i.e. how do you know whether you're getting a nasal decongestant or an illegal drug?)

However, I find his emphasis on formal charge analysis a bit misguided. He has continually stated that one of his main goals is to ready us for the rigors of organic and analytical chem.

The problem is that the central conceit of orgo is: nucleophile attacks electrophile.

When you write hydroxide ion the way he does, that's okay, because the formal charge - which is nothing more than what its name suggests - a mere formalism - is mostly born by the oxygen (not the hydrogen). Keeping this in mind allows one to understand why, say, potassium hydroxide can absorb carbon dioxide and give a false positive test when testing for carboantes - the nucleophilic oxygen in hydroxide ion attacks the electrophilic carbon in carbon dioxide.

But when he says something like nitrogen bears the "+" charge - that's just creating a chemistry unicorn in place of killing another chemistry unicorn. Yes, nitrogen in ammonium ion bears the positive formal charge. But no, the nitrogen in ammonium ion is NOT electrophilic. That would be the hydrogens in the ammonium ion. Those are the ones with the partial positive charge.

Same thing with hydronium ion. Why write one formula "correctly" while leaving the other implying the wrong things - which can be problematic - especially in organic class? Bottom line is that if one uses formal charge to determine nucleo/electrophilicity, one will be screwed over on a regular basis.

Now, I understand his argument for writing the electropositive element first. But this is simply more tradition, some of which he has already damned. He even breaks his own rule: he actually writes:

$NC^{-}$

rather than

$CN^{-}$

which he once derided as "lousy" chemistry.

Here, however, the textbook have done it right, according to one of his rules - write the most electropositive element first!

But he still derides this example of formula writing as WRONG because hey, the negative formal charge rests on the carbon! True! And it just so happens that in the cyanide ion, the partial negative charge also rests on the carbon!

But what about the hydronium ion? He insists on writing

$H_{3}O^{+}$

instead of

$H^{+}$

because it is chemical fact that the bare proton is hydrated in water solution - that's just Coulombically (very highly) favorable.

True, there is a positive formal charge on the oxygen! But why not write:

$OH_{3}^+$, which keeps even more with structure? This actually shows that the hydrogens on the hydronium ion are electrophilic! If anything, at least

$H^{+}$

Makes it clear that there is a positive charge on the hydrogen proton and that it is electrophilic!

The point of my post is:

1) I'm about to take this up with my former general chemistry professor. So are my points factually accurate at the very least?

2) Who do you side with?

3) Bottom line: I appreciate his ridding us of those pesky chemical unicorns that populate the pages of general chemistry textbooks but at the same time, he's creating more misconceptions himself. Take ammonium ion: the hydrogens are the ones that are bearing the partial positive charge, and in organic chemistry, no one cares about formalisms! You can think that the nitrogen bears the positive charge but in reality the nitrogen isn't going to be as electrophilic as the hydrogens. And as he says himself, the only thing that matters is experimental fact. Not what one might write down on paper or what one might think. He's not even consistent with his own damn rules (cyanide example).

4) I don't have a personal beef with him; I just want to show him that I've been thinking about this stuff just like he has. His course has been 10% philosophy, 10% myth busting, and 80% good chemistry.

 

[Yellowflash]

I did not read the whole thing, but most people write ammonia as NH subscript 3 and ammonium as NH subscript 4 superscript +.

 

[Yanick]

I personally thing the entire thing is trivial. Learning a fieeld means learning the little quirks in notation and naming etc. No way around it. Anyone studying chemistry should get the inkling by the end of Gen Chem that representations of molecules, whether lewis structures with resonance or empirical formulas etc, are simplified means of describing dynamic and complicated systems. I think your time is better spent learning more chemistry than tryingbto reinvent the wheel.

 

[Qube]

I think your time is better spent learning more chemistry than tryingbto reinvent the wheel.

Things are easier to learn when they are less arbitrary. Think about English. Native speakers know the quirks because they've been using it since day 1. However, non-native speakers can study rules and books and all that, but all its quirks make it more of a practiced talent rather than one which can be studied. And if you pull your regular Joe off the street who speaks fluent English, he probably can't explain the rules of English at all. He might use English correctly most of the time, perhaps forgetting when to use the objective case whom when appropriate, but people understand him.

And in science, we need people who are the opposite of Joe - people who understand - not people who may be able to answer a few multiple choice questions correctly.

I also firmly believe that writing hydroxide ion as HO^- rather than OH^- is preferable because that doesn't take any additional blood, sweat, tears, or ink and conveys a more right idea.

In addition, his preaching about the formulas is directly forcing us to appreciate and learn about chemistry. Rather than blindly accept, on faith, the traditions passed down by chemists, we are forced to at least superficially analyze the structures of the formulas and think about them for more than a passing moment.

When I presented his style of formula writing to a group of about 100 high schoolers from one of the top high schools in America (ranked #5 recently by some magazine and has been in the top 10 consistently for the last decade) ... only two or three could actually figure out a formal charge. These were people who had taken AP and IB Chemistry for a year if not two. And again, only two or three people could even draw out phosphoric acid. When you write it as H₃PO₄ instead of (HO)₃PO you aren't helping them draw out phosphoric acid. When we write formulas like hydroxide ion according to the textbooks we obscure deeper chemical meaning. Even if we want to keep writing it the traditional way, it is at least good to think for a second about where that negative charge really is. But most general chemistry textbooks don't do that! If you want to show me one that does, good luck.

Bottom line though: if one's going to reinvent the wheel, as you say, one might as well reinvent it right. He wants to reinvent it in a way to facilitate a deeper understanding of organic chemistry. I say that requires rethinking formula writing even further.

 

[Qube]

Anyone studying chemistry should get the inkling by the end of Gen Chem that representations of molecules, whether lewis structures with resonance or empirical formulas etc, are simplified means of describing dynamic and complicated systems.

Right, but how many do?

I was an A student in Gen Chem I. Average grade was a C. Most of the class dropped out.

I drew methane with 90 degree bond angles.

I wrote hydroxide ion as OH^-.

I didn't know what formal charge was.

Etc.

As my gen chem 2 prof once said, he asked an entire class to draw out sulfuric acid once.

No one got it.

Everyone had hydrogens bonded to the sulfur or something to that effect.

 

[Yanick]

Drawing a Lewis structure of methane with 90 degree bond angles isn't wrong because Lewis structures were never meant to totally convey the full picture. They are an approximation to show connectivities quickly and easily. Formal charges are also approximations, just as oxidation numbers are, empirical/molecular formulas etc. Each has their place and you learn what place that is as you progress through your studies.

In acid-base chemistry you just write HA and A^-, in biochemistry you write OAc for acetate, in quantum chemistry you may look at potential maps or mostly numbers on a screen, in organic you stare at dots, sticks and arrows. Just as in physics you imagine perfect spheres flying through vacuums and colliding elastically etc.

Your examples of of HS kids and undergrads stinking at chemistry after taking one or two classes is an example, IMO, of everything that is wrong with education today. Kids are taught to pass exams, not to think. A top 5 HS is probably the biggest culprit. Every HS (and some undergrads) kid I've mentored from one of those schools was amazing at following directions but not much beyond. I digress though.

I still think the while thing is a bit trivial.

 

[Qube]

Drawing a Lewis structure of methane with 90 degree bond angles isn't wrong because Lewis structures were never meant to totally convey the full picture. They are an approximation to show connectivities quickly and easily. Formal charges are also approximations, just as oxidation numbers are, empirical/molecular formulas etc. Each has their place and you learn what place that is as you progress through your studies.

In acid-base chemistry you just write HA and A^-, in biochemistry you write OAc for acetate, in quantum chemistry you may look at potential maps or mostly numbers on a screen, in organic you stare at dots, sticks and arrows. Just as in physics you imagine perfect spheres flying through vacuums and colliding elastically etc.

Your examples of of HS kids and undergrads stinking at chemistry after taking one or two classes is an example, IMO, of everything that is wrong with education today. Kids are taught to pass exams, not to think. A top 5 HS is probably the biggest culprit. Every HS (and some undergrads) kid I've mentored from one of those schools was amazing at following directions but not much beyond. I digress though.

I still think the while thing is a bit trivial.

What better to shift the focus from passing standardized exams (which are basically bound to following chemical convention for risk of mass confusion and hysteria) than at least writing formulas differently to cause students to think a bit more? I was a C student in chemistry in HS and now I think I'm a bit improved - hey - at least I'm here thinking about this stuff at this level (correctly too). That must be worth something.

What would you suggest as a solution for improving chemical literacy?

 

[Qube]

Drawing a Lewis structure of methane with 90 degree bond angles isn't wrong because Lewis structures were never meant to totally convey the full picture. They are an approximation to show connectivities quickly and easily. Formal charges are also approximations, just as oxidation numbers are, empirical/molecular formulas etc. Each has their place and you learn what place that is as you progress through your studies.

In acid-base chemistry you just write HA and A^-, in biochemistry you write OAc for acetate, in quantum chemistry you may look at potential maps or mostly numbers on a screen, in organic you stare at dots, sticks and arrows. Just as in physics you imagine perfect spheres flying through vacuums and colliding elastically etc.

Right, we approximate real-life phenomena. But if we can better approximate real-life phenomena, why not? I suppose it is a pain to equate HO^- with OH^- but that is hardly impossible and it helps with understanding - if one draws out the hydroxide ion and labels the formal and partial charges, boom. There you go.

Also about Lewis pictures - it's not that hard to use wedges and dashes or at least draw methane like a retrovirus to at least convey the idea that the bond angles are not 90 degrees. It seems trivial but drawing them with 90 degree bond angles gives students the wrong idea.

I think the main thing I've learned from chemistry is that chemists are lazy :P.

But really, the main reason people hate classes (or at least one reason) is that "it doesn't make sense." Math "doesn't make sense." Physics "doesn't make sense." Chemistry "doesn't make sense." Not making sense implies that the presentation of the subject is arbitrary. So if we can make things less arbitrary, wouldn't that be a win?

 

[Yanick]

You can write things however you want as long as people understand what you mean. Beyond the first year of Gen Chem everyone should know what a hydroxide or hydroxyl group is. In my opinion, the important point is not whether we put the minus on the right or left, it is the fact that drawing symbols on a page, of any kind, is a simplification of the actual object as it exists in nature.

No matter how you slice it the reality of the situation is that charges behave more like gradients in molecules, take a look at any electrostatic potential map. There are no clear cut boundaries where the positive or negative charges reside fully. There are transitions from more positive to more negative and such. If you want to get extremely technical you should be drawing 90% probability distributions of the electrons as calculated through QM. It is pointless however because five quick strokes of a pen is enough to show someone the relevant acid/base chemistry, connectivity or molecular charge on a hydroxide. Your example of drawing methane is fine if you are talking specifically about the spatial orientation of the nuclei but again, it is not always necessary. It is also a trivial example. Go find a 25 carbon molecule with several functional groups and try drawing out all of the dashes and wedges. Try figuring out how to show NADH/NAD+ in a molecular formula by staying true to the "true nature" of the molecule. If you have these kinds if problems wait until you get to analytical chemistry where no one cares about structure at all (mostly). Call your molecule X, make some assumptions about its presence/absence etc and do your calculations. Even better is wait for something like biochem where you will just write AcCoA or CoA-SH. Read some of the literature about hemes where everything is called compound 0-III.

Again, it is good you are thinking about these things to begin with. You should understand the benefits and limitations of any model you learn. I just think arguing about something like where we decide to write the plus sign in ammonium is trivial and your time is better spent learning and thinking about other things.