Chemical Nomenclature

Looking at the ingredient list of some popular processed foods will produce a puzzled look on the typical hacker’s face. Tricalcium phosphate, thiamine mononitrate, zinc proteinate, pyridoxine hydrocloride… just who the hell comes up with these names anyway? It turns out that there is a method to the madness of chemical name structures. Some of them are well known, such as sodium chloride (NaCl) and hydrogen peroxide (H2O2). Others… not so much. In the early years of chemistry, chemical substances were named after their appearance, affects and uses. Baking soda, laughing gas and formic acid (formic is Latin for ant, and responsible for the sting in an ant bite) to name a few. As more and more chemical substances were discovered over time, a more structured naming convention was needed. Today, the above are known as sodium bicarbonate (NaHCO3), nitrous oxide (N2O) and a type of carboxylic acid (R – COOH, think of the “R” as a variable) respectively.

In today’s article, we’re going to talk about this naming structure, so that next time you admire the back of soup can, you won’t look so puzzled. We’ll also cover several common definitions that every novice biohacker should be familiar with as well.

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Chemical Formulas 101

It seems like every other day we hear about some hacker, tinkerer, maker, coder or one of the many other Do-It-Yourself engineer types getting their hands into a complex field once reserved to only a select few. Costs have come down, enabling common everyday folks to equip themselves with 3D printers, laser cutters, CNC mills and a host of other once very expensive pieces of equipment. Getting PCB boards made is literally dirt cheap, and there are more inexpensive Linux single board computers than we can keep track of these days. Combining the lowering hardware costs with the ever increasing wealth of knowledge available on the internet creates a perfect environment for DIYers to push into ever more specific scientific fields.

One of these fields is biomedical research. In labs across the world, you’ll find a host of different machines used to study and create biological and chemical compounds. These machines include DNA and protein synthesizers, mass spectrometers, UV spectrometers, lyophilizers, liquid chromatography machines, fraction collectors… I could go on and on.

These machines are prohibitively expensive to the DIYer. But they don’t have to be. We have the ability to make these machines in our garages if we wanted to. So why aren’t we? One of the reasons we see very few biomedical hacks is because the chemistry knowledge needed to make and operate these machines is generally not in the typical DIYers toolbox. This is something that we believe needs to change, and we start today.

In this article, we’re going to go over how to convert basic chemical formulas, such as C9H804 (aspirin), into its molecular structure, and visa versa. Such knowledge might be elementary, but it is a requirement for anyone who wishes to get started in biomedical hacking, and a great starting point for the curious among us.

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“You Sank my Dysprosium!”: Periodic Table Battleship

Kids these days, they have it so easy. Back in the old days, we learned our elements the hard way, by listening to “The Elements” by Tom Lehrer over and over until the vinyl wore out on the LP. Now, thanks to [Karyn], kids can learn the elements by playing “Battleship” – no tongue-twisting lyrics required.

For anyone familiar with the classic “Battleship” game, you’ll wonder why no one thought of this before. [Karyn]’s version of the game is decidedly low-tech, but gets the job done. She printed out four copies of the periodic table, added letters to label the rows, and laminated them. A pair of tables goes into a manila file folder, the tops get clipped together, and dry-erase markers are used to mark out blocks of two to five elements to represent the ships of the Elemental Navy on the lower table. Guesses at the location of the enemy ships can be made by row and series labels for the elementally challenged, or better yet by element name. Hits and misses are marked with Xs and Os on the upper table, and play proceeds until that carrier hiding in the Actinide Archipelago is finally destroyed.

This is pure genius in its simplicity and practicality, but of course there’s room for improvement. The action-packed video after the break reveals some structural problems with the file folders, so that’s an obvious version 2.0 upgrade. And you can easily see how this could be used for other tabular material – Multiplication Table Battleship? Sounds good to us. And if your nippers catch the chemistry bug from this, be sure to take a deeper dive into the structure of the periodic table with them.

Now, if you’ll excuse me: “There’s antimony, arsenic, aluminum, selenium, and hydrogen and oxygen and nitrogen and rhenium….”

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7th Period of the Periodic Table Complete

For the last fifty or so years, the periodic table has been incomplete. Elements after uranium on the periodic table have been synthesized for the past few decades, but there were always a few missing blocks in the periodic table. These elements, with atomic numbers of 113, 115, 117, and 118 comprise the missing parts of period 7 – the lowest row – of the periodic table. Now, IUPAC, the International Union of Pure and Applied Chemistry, has announced the verification of the discoveries of the last four elements of the seventh period of the periodic table.

With the announcement of the verification of discovery for these elements, they will get a name. Currently elements 113, 115, 117, and 118 are known as Ununtrium, Ununpentium, Ununseptium, and Ununoctium, respectively. What these elements will be named depends on the proposals by the discoverers of these elements.

Element 113 was discovered by researchers at the RIKEN laboratory in Japan, and these researchers will be able to propose a name and atomic symbol for their discovery. Elements 115, 117, and 118 were discovered through a partnership between the Joint Institute for Nuclear Research in Dubna, Russia, Lawrence Livermore National Laboratory in California, and Oak Ridge National Laboratory in Oak Ridge, Tennessee. Researchers at these three laboratories will propose names and atomic symbols for these three elements.

It should be noted that Lawrence Livermore National Laboratories and the Joint Institute for Nuclear Research in Dubna each have their own element named after them: Lawrencium and Dubnium, with atomic numbers 103 and 105, respectively. Having element 113, 115, and 118 named after Oak Ridge National Laboratory wouldn’t be a bad proposal, and would be rather fitting given the laboratory’s influence on the last half-century of physics.

Of particular interest is the naming of element 118. Because element 118 falls within group 18 of the periodic table, it is a noble gas, with a particular naming pattern. each of the elements in group 18 end with the suffix ~on, instead of the suffix for the rest of the periodic table, ~ium (helium is the exception to this rule due to historical precedent). Whether element 118 will use the ~on or ~ium suffix is up to debate; current IUPAC rules say all new elements should end with ~ium, but recommendations have been published to name all group 18 elements with the ~on suffix.

This is not the end of the periodic table by any means. It is possible that elements with higher atomic numbers can be synthesized. However, experiments to synthesize element 119 have so far come up short, and the predicted properties of element 119 put it at the limits of what current technology is able to detect.

Don’t Understand the Periodic Table? It’s Just a Quantum Truth Table

In the wee hours of the late 17th century, Isaac Newton could be found locked up in his laboratory prodding the secrets of nature. Giant plumes of green smoke poured from cauldrons of all shapes and sizes, while others hissed  and spat new and mysterious chemical concoctions, like miniature volcanoes erupting with knowledge from the unknown. Under the eerie glow of twinkling candle light, Newton would go on to write over a million words on the subject of alchemy. He had to do so in secret because the practice was frowned upon at that time.  In fact, it is now known that alchemy was the ‘science’ in which he was chiefly interested in. His fascination with turning lead into gold via the elusive philosopher’s stone is now evident. He had even turned down a professorship at Cambridge and instead opted for England’s Director of Mint, where he oversaw his nation’s gold repository.

Not much was known about the fundamental structure of matter in Newton’s time. The first version of the periodic table would not come along for more than a hundred and forty years after his death. With the modern atomic structure not surfacing for another 30 years after that. Today, we know that we can’t turn lead into gold without setting the world on fire. Alchemy is recognized as a pseudoscience, and we opt for modern chemistry to describe the interactions between the elements. Everyone walking out of high school knows what atoms and the periodic table are. They know what the sub-atomic particles and their associated electric charges are. In this article, we’re going to push beyond the basics. We’re going to look at atomic structure from a quantum mechanical view, which will give you a new understanding of why the periodic table looks the way it does. In fact, you can construct the entire periodic table using nothing but the quantum numbers.

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