In the aqueous systems we’re talking about, the strength of an acid is related to its tendency to liberate protons. An acid’s tendency to dissociate into protons is related to the thermodynamic stability of its “conjugate base” - the acid, minus a proton. These electronegative substituents withdraw some electron density from the negative charge on the conjugate base, giving a more potent acid.

This is one part of how these compounds seem to work; these mild acids help slough off dead skin cells, revealing the smoother skin underneath. Trichloroacetic acid is much stronger than acetic or even glycolic acid, and is, thus, only used by professionals.

Salicylic acid is another acid used in skin care; its hydroxyl group likely helps stabilize the conjugate base by virtue of its electronegativity alone, but it also can participate in a “hydrogen bond” (to a first approximation, the sharing of a proton between two electronegative atoms - usually oxygen, nitrogen, or fluorine). This gives a pretty good energetic “bonus,” stabilizing the conjugate base, salicylicate. A picture will hopefully help - the putative hydrogen bond is denoted by a dotted line:

Skin care is one of those fields that is full of crackpot ingredients (and incredibly overpriced ones), but these are among the few ingredients that are actually up to something.

Creatine actually occurs endogenously, and it is synthesized by the liver. An enzyme called creatine kinase exists in the body to move a phosphate from ATP to creatine, making N-phosphocreatine and ADP. This reaction is not very thermodynamically favorable - you will only make 1 molecule of phosphocreatine for every 1000 molecules of ATP or so. This is good, because your body needs the ATP for other things (you’ve probably heard of ATP as the “universal energy currency” of the body) as well. Phosphorylation of creatine only happens when your body has a large excess of ATP.

The reverse reaction takes place too, and, as you might guess, phosphocreatine still would prefer to transfer its phosphate to ADP, regenerating ATP. It’s favored in the low-ATP regime - such as during the last repetition of a weightlifting set. This latter reaction is shown below:

Phosphocreatine/creatine/creatine kinase/ATP/ADP is a system that allows your body to deliver energy very, very quickly. The slow system that generates most of this ATP is glycolysis, which breaks up sugar into useful carbon precursors for the body, as well as CO₂ and substantial amounts of energy. It requires oxygen, creatine phosphate-delivered energy does not directly. It is from this that the approximate distinction between “aerobic” and “anaerobic” activity comes from - anaerobic activity, like weightlifting, gets energy delivered rapidly from ATP/Creatine phosphate and related systems . Aerobic activity uses energy sufficiently slowly that it can be carried on for longer periods of time, with glycolysis & related systems supplying a good chunk of the energy. Both systems are, of course, in effect constantly to one degree or another, whether you’re biking or benching - it’s not a black/white distinction.

Have a good weekend!

Artifical sweeteners fall into two broad classes, “nutritive” and “non-nutritive.” Nutritive ones have some food value (Calories or kilojoules). The best example of this is aspartame, which is a peptide and actually has the same ~4 Calories/gram as sugars. It is a dietetic sweetener because it is many times stronger than sugar, so you get a negligible amount of Calories - just under one in most 12oz/355mL diet sodas, so most are labeled as zero calories (or, in one memorable case, they chose to round up, giving “one awesome calorie.” Why not the usual couple hundred, then, eh?)

Acesulfame is a “non-nutritive” artifical sweetener. It shares this designation with saccharin and cyclamate, among others. I am completely uninformed as to structure-taste relationships - it makes sense to me that, say, sucralose tastes sweet, since it’s structurally so close to a sugar. Aspartame I don’t get. Acesulfame, saccharin, and cyclamates, either. You’ll notice that they all share a common structural feature, a sulfamic acid moiety. Couldn’t tell you why, though. Anyone?

Image public domain, sourced from Wikipedia

Taq was crucial to the development of PCR,the process by which large pieces of DNA are copied today, pretty much exclusively, and the subject of Kary Mullis’ 1993 Nobel. To copy DNA by PCR, it needs to be repeatedly “melted” (separated into single strands by heating), “annealed” (fused back into double strands), and “extended” (copied by the DNA polymerase, Taq here). The idea here is that you do this ~30 times and get 2 copies, then 4, then 8…then 2^30, or about a billion.
The trouble with this is that the melting phase requires sufficiently intense heating that most enzymes are damaged (unfolded, or “denatured”). Since PCR requires tens of cycles, enzyme denaturation is a problem. Initially, the polymerase from E.Coli, the workhorse of modern molecular biology was used. Cetus, the company with which Mullis and co-workers developed PCR, was planning a system to add fresh polymerase after every cycle - ~30 times - it works, but it’s not an elegant solution.

Fortunately, Taq, as you’ve probably surmised, lives in hot water. It’s enzyme has evolved to withstand an amazing amount of heat (relatively speaking), and the near-boiling temperatures used in PCR barely make it break a sweat (well, not quite. it lasts about half an hour near boiling, so you can only use it for one ~30 cycle PCR reaction).

Taq polymerase has made genetic engineering and molecular biology possible today. Another thermophilic polymerase from Pyrococcus furiosus (Furiosus. Don’t you love science?) has come into favor today because of its enhanced stability and decreased tendency to make copying errors. The thermostable polymerases are something without which molecular biology would pretty much grind to a halt.

After all, once you have a ring, it’s going to behave very much like a macroscopic ring; no passing through the side or anything. And to get two rings to loop together, they need to be oriented properly when the loop is made. This seemed unlikely to me, so I moved on to doodling other things.

Fortunately, someone had tried. If I remember correctly, the first catenanes were made by a plain old ring-forming reaction (i.e., one that forms monomers). The reasoning was that if you had a big enough ring, a high enough concentration that the ring-formers were pretty crowded, etc., you had to get SOME molecules oriented just right and make some catenane (as opposed to monomeric rings). Sure enough, it worked (although the yield was, predictably, quite poor).

Nowadays, the field of supramolecular chemistry is growing prodigously. As our knowledge of intermolecular interactions progresses, we are gradually getting better at better at orienting molecules in dilute solution and assembling unlikely-seeming shapes. A Self-assembly and pre-organization strategy is often used to pursue catenanes today.

See you tomorrow.

Thiols have a prodigous appetite for metal, especially mercury. This led to a second name for them: mercaptans (describing their ability to capture mercury).

All this leads up to a truly unusual thiol: grapefruit mercaptan. You’ll notice it looks like another terpene, like carvone and damascone. Grapefruit mercaptan is such a singular compound because it is a nice-smelling thiol. It’s another one I haven’t smelled, but I’m told it’s very complex and grapefruity. It’s also unique because not many things synthesize thiols on purpose (thiols being reactive and stinky - skunks are a notable exception here).

The Wikipedia article notes that this is a bit of a thorn in the flavor industry’s side - almost ALL thiols stink, and this is a notable exception. Thiols have a nasty habit of oxidizing to form dimers in the presence of oxygen (R-SH -> R-S-S-R), and even if grapefruit mercaptan doesn’t stink, its decomposition products probably do. All these leads to a not-so-hot flavoring agent.

Here’s the structure:

See you Monday.

Perfumers (and biologists) still are looking for structure-odor rules, which prove to be continuously elusive. As I’ve mentioned before, one problem here is language; describing odor is hard!

I won’t even try at this one (anyway, I’ve never smelled it neat): beta-damascone:

Depending whom you ask, beta-damascone can be described by any of the following descriptors:

• fruity
• floral
• blackcurrant
• plum
• rose
• honey
• tobacco
• berry
• alcoholic
• green
• woody
• minty

You might begin to get an idea of what such an amalgam would be like, but probably not until you smelled it. Remember, all these “notes” come from ONE molecule: not a plant extract of many molecules.

Beta-damascone also looks like another terpene. This isn’t too surprising, since they are ubiquitous natural products.

See you tomorrow.