Tag: Pique the Geek

NMR (Nuclear Magnetic Resonance) spectrometry is one of the big guns in organic chemistry and biochemistry for determining how atoms are strung together in molecules.  There are many different kinds, but the two of greatest utility to chemists are proton NMR and carbon-13 NMR.  A friend of mine asked me for some help for his daughter who is studying the subject in Organic Chemistry right now, so I thought that I might as well use it as a topic for this series.

Before we get deep into the subject, note that some authors refer to NMR spectrometry and others to NMR spectroscopy.  I prefer the former term because the connotation of spectroscopy, to me at least, has to do with lenses, prisms, and diffraction gratings, making it an optical method.  There are no analogous devices in NMR, so I prefer spectrometry.

All NMR has some features in common, so we might as well cover the basics first.  By the way, this has nothing to do with nuclear energy, and the only radiation present is in the radiofrequency range, so it will not fry you.

This is heavily connected with quantum mechanics, but I shall try to use analogies that are more easily visualized than a bunch of equations.  I do not intend for this to be a graduate level abstract.

Of all foodstuffs, milk is unique in that it provides all of the nutritional needs for infant mammals.  In addition to nutrition, it also supplies essential antibodies the first few days to newborns.  Milk is unique to mammals, and is one of the reasons that mammals had the evolutionary advantage that they had when they arose during the age of reptiles.

However, humans are also unique in that we are one of the few mammals who continue to take it after infancy, and the only species that continues to take it after adolescence and into adulthood.  Milk is far from the perfect food for adults, but certainly can be part of healthy diet.

Humans are also unique in that we are the only species that takes milk in a natural setting from other species.  By that I mean that we actively collect it, not like giving the cat a saucer of milk.  The nutritive value of milk is species specific, and our habit to taking cows’ milk (for the most part) is quite unnatural.

Last time we talked about trichonomiasis, a sexually transmitted infection (STI) that often produces no symptoms.  Chlamydia is another STI that often causes no symptoms, at least initially.  We shall investigate this condition this week and then move to topics other than STIs next time.

This infection is usually caused in humans by the bacterium Chlamydia trachomatis and is found only in humans.  Unlike trichomoniasis, women are more often asymptomatic than are men.  Estimates are that around 75% of women present with no symptoms whislt around 50% of men do have symptoms, almost the opposite from our infection of the week last time.

Although this is a serious subject, let us keep it a bit light.  After the fold in a song by Todd Rundgren called “You Left me Sore”.  Although most likely written about gonorrhea, it is still apt in this case.

Trichomoniasis is probably the most commonly spread sexually transmitted disease (STD) in the US at present, yet hardly anyone has heard of it.  The main reason is that there are many “silent” cases, with no symptoms at all.

The purpose of this piece is to raise awareness of this infection in the hope of doing a small part to have people get themselves tested.  Unlike HPV Strains 16 and 18, it is not strongly linked to cervical cancer, there is evidence that it can increase the risk of this disease to a small extent, but any increase in risk for cervical cancer is too big an increase.  By the way, we covered HPV some time ago, here.

Fortunately, after diagnosis it is easily treated and cured in the course of a week or two, depending on the regimen used.  We shall get into that near the end of the piece.

This is sort of an unusual piece for me, because many years ago, before the former Mrs. Translator and I were an item, I became infected with this parasite.  As we cover the subject, I shall insert my personal observations where appropriate.

Last week we discussed the production and uses of aluminum, and that piece got a lot of comment traffic and made the Kos Recommended List, which I value greatly.  Some of the comments asked questions and made me decide to write a follow up piece, because some of the questions were excellent in their own right, and some of them also caused me to think a bit further about our use of this material.

Tonight we shall concentrate on a few more uses of aluminum, why it is so unique, and less environmentally damaging ways to produce it.  It turns out that there is an experimental process to refine aluminum that does not produce nearly as much carbon dioxide as the Hall-Héroult process, and might be more energy efficient as well.

There is no time like the present, so let us get started!  That is unless you have an objection.

Aluminum (or aluminium to our UK friends) is one of the most useful metals that are commonly available.  Unlike other metals such as iron, copper, and the like, aluminum has been used in large quantities only fairly recently.  Actually, alumimium is the better name, because it is in keeping with the naming of most metallic elements with the “ium” ending.  However, we shall use the US term.  Interestingly, the brilliant British chemist Sir Humphrey Davy called it aluminum, but he never produced the actual metal.  In addition, his first name for it was alumium, and folks from My Little Town who were older used that name!  That really should be the systematic name for it.

Aluminum compounds have been known for centuries, but the free metal only since around 1825 and even then in an impure form.  It was not until very late in the 19th century that aluminum was produced on a large scale, using a process that is essentially identical with the process being used even now.

Christendom, like other religions before it, assimilated former religions to forge its own traditions.  This is very much the rule rather than the exception when a new religion begins to dominate an older one.  It is easier to get people to come to your point of view if do not change things too much.

There are a number of pagan traditions that were assimilated into the Christmas tradition, and not all of them were done simultaneously.  For example, the Yule log is much  more recent than celebrating Christmas on 25 December (and that date is not universal, by the way).  Let us look as some of our customs that are not Christian at all.

The popular TeeVee show NCIS purports to use science to solve most of the difficult bits of its cases, almost always murders.  Since this is about a TeeVee show, I was torn betwixt posting this piece here or on Popular Culture, but chose here because it will get a little geeky.

Before I continue, let me tell you that I like the program very much, not so much for the science but for excellent script writing and character development.  I think that it is important to recognize a well crafted program.  Since most viewers are not technically proficient, the science is not a problem for them.

But it is for me.  I am reminded of another popular TeeVee show from years, the Jack Klugman one called Quincy, M. E., that relied heavily on fictionalized scientific methods.  I had a boss at one time who coined a phrase that I shall reveal later.

Sodium hydroxide, aka lye, is one of the most important basic chemicals used in industry, and until not too long ago, for several home uses.  It can still be found in a few consumer products, but because of its usefulness as a chemical reagent for clandestine preparation of methamphetamine, is hard to get now without a legitimate business reason.  However, I found some at Lowe’s a couple of years ago (under a different label) for opening drains.  I wanted some to show my relatives how to make soap.

A significant amount of this material is still used for making soap, but its uses are so widespread and pervasive that soapmaking is just a small fraction of the applications for this material.  Industrially it is used when a strong, cheap base is needed, because it is amongst the strongest and cheapest, other than perhaps calcium hydroxide (lime), but sodium hydroxide is very soluble in water where calcium hydroxide is not.

The way that atoms bond together to form molecules has been a question asked since scientists came to the consensus that atoms do indeed exist.  Work progressed rapidly after the turn of the 20th century from both theoretical and experimental breakthroughs.  To keep the discussion easy to visualize, we shall consider only diatomic molecules, but the concepts are good for any number of atoms.  One of the great advances was the development of the idea that chemical bonds can either be covalent, where each atom shares bonding electrons equally, or ionic, where one atom donates an electron to another atom entirely.

Actually, pure ionic bonds do not exist because all bonds have at least a little bit of covalent character.  Pure covalent bonds are common, common examples being the nitrogen and oxygen of the atmosphere.  There is a very cool way to predict where a particular bond falls in the covalent to ionic spectrum, and that is to use electronegativity values.