Thursday, February 26, 2009

doublets of doublets: I'm beggining to see!

Poking around in some books on nmr today I found someone who directly addresses the doublet of doublets phenomenon. You can't imagine how happy I was to see this.

I'm beginning to get it. As usual, Straumanis is right. The book explains that in most situations, nearest neighbor hydrogens are similar enough to one another that the splitting occurs in a way that follows the rules for splitting we have learned. In a few situations, though, when the neighbors are very different from one another (as expressed by something called their coupling constant), they split the signal sort of separately and generate a doublet of doublets.

The book provides an example that looks a lot like the fluorinated benze we were examining, except it has a nitro (NO2) group across from the F.

The fluorine is the reason for the different coupling constant in our molecule, but I am still sorting out the details of what role it plays. I also still don't have complete clarity about why these coupling constants could vary when the coupling has all been explained to me using the quantized spin states (as I tried to describe in my earlier post).

south Deschutes: voting on the nitrate fix

There are strong opinions on both sides of the conversation regarding the ballot initiative called the groundwater ordinance referendum. For the uninitiated, a clear and brief description of the situation can be found here.

I'd like to think I'm a well informed voter, but there are a lot of things going on behind this ballot.

  • What is the real relationship between nitrates and health problems?
  • What is the relationship between nitrates in groundwater and environmental problems?
  • Is nitrate mitigation going to protect the health of groundwater in more general ways?
  • If nitrate pollution is a real threat to health or the environment, what regulation is appropriate?
  • Why is this vote in front of us, after extended study and an ordinance passed by the county board of commissioners? Is it appropriate to have the public decide on such a technical issue?
  • What alternative solutions exist?

Any post that tried to address all of these issues would be long and probably set off a firestorm. I only want to comment on the first item on my list of questions. Unfortunately, even with a Ph.D. in biochemistry, I am confused about how to answer this one.

Nitrate can look like a real problem, if you consider the following health effects, pilfered from the EPA consumer fact sheet on nitrates/nitrites:

Short-term: Excessive levels of nitrate in drinking water have caused serious illness and sometimes death. The serious illness in infants is due to the conversion of nitrate to nitrite by the body, which can interfere with the oxygen-carrying capacity of the childs blood. This can be an acute condition in which health deteriorates rapidly over a period of days. Symptoms include shortness of breath and blueness of the skin.

Long-term: Nitrates and nitrites have the potential to cause the following effects from a lifetime exposure at levels above the MCL: diuresis, increased starchy deposits and hemorrhaging of the spleen.

Then there is this quote, pulled from a web page of the department of health and human services:

A large proportion of hemoglobin in young infants is in the form of fetal hemoglobin. Fetal hemoglobin is more readily oxidized to methemoglobin (MHg) by nitrites than is adult hemoglobin. In addition, in infants, NADH-dependent methemoglobin reductase, the enzyme responsible for reduction of induced MHg back to normal hemoglobin, has only about half the activity it has in adults.

But last week I just happened across this, from American Scientist, a publication of Sigma Xi that I respect an awful lot.

Just answering the first concern about nitrates: are they a real health concern? is proving difficult. I could vote based on the precautionary principle, but I realize the economic impact to families living in that area would be huge.

The more I have to vote on these voter initiatives, the less I like the initiative system.

Wednesday, February 25, 2009

doublets of doublets

I am still not able to resolve the doublet of doublets question that came up Tuesday. But since I promised, I am going to try to explain as well as I can what I'm thinking about it. If you are reading this, give yourself a break if you don't know how an nmr picks up signals. If you are reading this and do understand nmr, I would be delighted to have you help me improve my understanding.

Here's what I (think I) know:

Spin 1/2 nuclei, such as hydrogen, have spin that gives them magnetic moments.
The spin states in such nuclei are described as being either "up" or "down," and are quantized.
Inside the nmr, an applied magnetic field aligns spin states and then an applied radiofrequency signal can cause spin flips at particular frequencies. These spin flips cause absorbances which are converted to signals, generating the spectrum.
The chemical shift for a given set of equivalent hydrogens indicates what frequency is required to generate this absorbance, which varies depending on the environment that nucleus sits in.
Hydrogens that are nmr equivalent absorb at exactly the same frequency.

Still with me? Good. I am about to address splitting:

Absorbance peaks are split due to interactions that occur through bonds, but between nuclei of the hydrogen(s) generating a particular peak and those which are described as "nearest neighbors." We have learned how to identify nearest neighbors, so I won't go into that here.
The splitting occurs because the neighboring nuclei have a minor but real effect on chemical shift. Their spins can be in or out of phase with those that are generating the signal, adding to or subtracting from the chemical shift.
For every nucleus involved in these relationships, there is a particular number of possible spin-state alignments, which happens to equal the number of nearest neighbors plus one.
Therefore the peaks are split into that many (neighbor Hs plus 1) like we learned, and forms a set that varies in intensity like a Pascal's triangle.

Now, finally, for the confusion about the doublets of doublets:

Occasionally one hydrogen attached to a carbon is nmr inequivalent to another on the same carbon. For example, two hydrogens on an sp2-hybridized carbon could qualify, if the stuff on the other end of the alkene is distributed asymmetrically.

In this case it makes perfect sense to me that these hydrogens would each have a slightly different chemical shift, and that each one would be split by a nearest neighbor, generating an overlapping "doublet of doublets," rather than the triplet signal you would otherwise expect.

I can't understand the other example Straumanis gives, however, which involves hydrogens around an aromatic ring that has a single fluorine substituent. There are 3 groups of equivalent hydrogens on this structure: those at C1 adn C5, those at C2 and C4, and one at C3. He seems to argue that because the H at C1 exists in a different environment than the one at C4, that the signal from the H at C3 will split into a doublet of doublets.

If peak splitting is based purely on the spin-state interactions of the nuclei, what environment those nearest neighbor hydrogens are in doesn't seem to have anything at all to do with it.

Signals from hydrogens on aromatic rings do tend to get all overlappy and scrunched up, so he could be perfectly correct, but I can't sort out why. I think I need to send the question to him, or to a group of others I know are using the workbook.

Friday, February 20, 2009

who is absolutely hot?

Nova, the classic PBS program that recently rebroadcast it's awesome Absolute Zero show, publishes an "occasional column" (what a great idea!) that has recently addressed the possibility that there is an corresponding Absolute Hot. Thanks, Krokodile, for the link.

Thursday, February 12, 2009

Wednesday, February 11, 2009

I don't think this requires any
description at all.

Thanks to "Million Moments"
for sharing.

JACS is not quite so fun

No similar news items from JACS, the Journal of the ACS. Oh, well. Then again, there is always Chemical and Engineering News, which has good online articles and links to other resources. ACS just is not enthusiastic about opening access to their journals to the public, except in small ways.

Somewhere in my online ramblings I tripped into this, which may be of interest to those who are interested in all the fuss about Thimerosal and autism.

ES&T: what's NOT available on line?

The ACS journal Environmental Science and Technology (ES&T) appears to have lots of great content available free on the web. Oh, joy! Now if I could only find more time and more energy, I could get around to reading this stuff.

Here is an example article: this one is on the presence of pharmaceuticals in drinking water.

And here is another, on nitrate contamination in drinking water.

Could it be that other ACS publications have similar resources available on the web? I'm a little embarrassed to admit I don't know: I'm going looking right now.

Thursday, February 5, 2009

chemistry in the news: good news!

OPB reports on a chemical that appears to repel pine bark beetles, a real scourge in the pine forests on the east side of the Cascades. It is called verbenone, and is a terpene produced by lots of plants, including those of the genus Verbena.

our local National Teach-In is tomorrow!

The National Teach-In on Global Warming Solutions is going on now. Tomorrow several institutions in Central Oregon will be involved. OSU-Cascades, Central OR CC and at least one area High School are gathering from 11 am till 2 pm to talk, teach, eat, and discuss.

Everyone is of course welcome. From 1:30 until 2 the actual dialog will occur, featuring a number of students and City Counselors from Bend.

Hope to see you there!


This morning's news included a story suggesting that Nazi hunters at the Simon Wiesenthal Center have determined a certain war criminal, Aribert Heim, probably died and was buried in Egypt in the early '90s. He was apparently involved in "medical" experiments that sound awful--including deliberately injecting people with poison.

When I heard the story I immediately was taken back to a class yesterday, where the conversation led to the meaning of "phenol" and I casually mentioned that phenol, while rated as toxic by chemical supply houses, happens to be the ingredient in Chloraseptic throat spray. Ha ha ha, I chuckled, "How is it both medicine and poison?" and then I looked a bit deeper into this compound. It has a fascinating rap sheet.

Phenol is not only used as a topical antiseptic in Chloraseptic, it also:
  • is considered toxic and mutagenic, and carries a health warning of "3" (highest is 4) on the NFPA label
  • is the source of the odor best known as hospital smell
  • is a raw material in phenolic resins, which included the historically important polymer, Bakelite
In addition to all this, it was also used by the Nazis to kill people by injection.

So wasn't it a coincidence to learn all this yesterday, and then wake this morning to the story of the Nazi doctor who may have committed these horrific acts with, perhaps, this very compound.