Category Archives: Chemistry

COVID’s Metamorphoses: RCSB Coronavirus resources

The CDC and WHO are giving us good advice on what do in this Plague Year.  The Research Collaboratory for Structural Bioinformatics (RCSB) is showing us the molecule causing the havoc.  Check out the structures of the various flavors of Coronavirus at The Protein Database (PDB).  Click on the images, most of which will go to detailed pages including 3D models that can be spun in the browser.  Knowledge will be power in dealing with this beast and let’s offer thanks to the research groups who took the lead in characterizing it which must have come at considerable risk to themselves.  When it mutates, and it will, they and others will undoubtedly don their capes and do the measurements again.

It is damnably, horrifyingly beautiful in David Goodsell’s artistic rendering of it infecting a lung:

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-019

 

License: CC-BY-4.0
Image used unmodified and there is no endorsement from or by the artist

Spectral response: The science and emotion of color

The web’s archive of older industrial films is a recurring delight.  Jam Handy, Coronet, and other firms crafted these with an attention to detail, calm explanation, and rigorous science that is harder(*) to find today when most equivalents are about sales rather than fundamentals.  Jeff Quitney has uploaded a wonderful 1954 cleaned-up film to his Vimeo page on color theory and practice by the Interchemical Corporation.  It begins with the importance of color to society – especially in packaging goods and people – and then gives a marvelous account of the optics involved.   I’ve worked in the field for years but I learned to see things (pun intended) differently thanks to it.

The second film from 2016 looks at color in packaging through its emotional impact and its influence on design and designers.  ‘Color In Sight’  resembles like Hustwit’s ‘Helvetica.’  A number of prominent designers talk about how they use and think about color in order to evoke a response, surface a memory, or reveal a part of the spectrum to the color-blind.   I have no idea what I’d say to a nail-polish maker but Suzi Weiss-Fischmann (8m18s in) comes off  as a fun seatmate on a long plane trip.  I had a similar feeling about  Helvetica’s Paula Scher.   Interestingly, it is produced by TeaLeaves, a Canadian company specializing in very high-end teas for hotels.  Judging by their Youtube page, they must spend a fortune on short films – many of which have little outward bearing on their products.  I’ve never understood the appeal of tea but the videos are well worth a look.

(*) But not impossible by any means.

Vimeo Channel: Jeff Quitney

 

Youtube Channel: TeaLeaves

 

An elegant weapon for a more civilized age: In praise of chalk

Modern ejumacation has gone multimedia and Powerpoint, often multimedia within Powerpoint.  Some like 3Blue1Brown are brilliant at it (the multimedia, not Powepoint), others less so.  Here’s a random assortment of lectures where good old chalk and boards prevail: E&M from IIT Madras, chemistry and cryptography from Ruhr Universität, Bochum, Fields Medalist Cédric Villani on something-or-the-other, and an early calm-for-him presentation by Jens Fehlau on the Leibniz integration rule made famous by Feynman.  Finally, a tribute to a popular chalk, recently discontinued.

Youtube Channel: nptelhrd

 

Youtube channel: ChemieRub

 

Youtube channel: Introduction to Cryptography by Christof Paar

Youtube channel: Institut des Hautes Études Scientifiques (IHÉS)

Youtube channel: Flammable Maths

Youtube channel: Great Big Story

 

Photo Chemistry: The silver behind the silver screen

We have megapixel cameras in our phones and gigapixel cameras on our telescopes.  Before digital took over photography (and the world,) we had film.  Light struck silver and made a mark and behind it all was some marvelous physical chemistry.  It is still awe-inspiring to think of how these processes came about when knowledge and instrumentation were not nearly as advanced as today.  Each step could have millions of alternatives and sorting them through brute force would take the age of the universe.  Yet somehow it all came together and spawned industries.  The American Chemical Society takes us through the science as it was in 1940.

Vimeo Channel: Jeff Quitney

Scrubbing bubbles: The pros and cons of cavitation

We routinely use ultrasonic cleaners to decontaminate all kinds of surfaces.  A little solvent, some buzzing, and jewelry, electronic parts, and pen nibs get degunked effectively.  Cavitation is responsible.  It is also responsible for damaging surfaces such as ship propellers and pump impellers.  The first video explains the physical chemistry behind the process and its (mostly) destructive effects.  The second shows it applied to cleaning vegetables which, surprisingly, is a research problem funded by the National Science Foundation.  Both videos show closeups of bubble collapse making the cleaning/damage mechanism much easier to understand.

Youtube Channel: IET Institute for Energy Technology

Youtube Channel: National Science Foundation

Addendum 7 April 2019: More detailed super-slowmo  videos from the EPFL group featured in the first video.
Source: CAVITATION BUBBLES IN VARIABLE GRAVITY

Seawater: Armando Hasudungan on carbohydrates

The reputation of carbohydrates waxes and wanes depending on trends in nutritional science and public interpretation.   Chemical facts that I learned years ago still hold.  Take one carbon, two hydrogen, and one oxygen, CH2O (or seawater, ha!) and repeat in quantity n to get the empirical formula for the carbohydrate family: (CH2O)n .  From there it quickly gets very interesting and very complicated.  These handed molecules can form five- and six-membered rings and the rings can join together in marvelously intricate ways.   Beyond mere aesthetics they form through sugars, starches, and cellulose the code, fuel, and structure of life.   Here is Armando Hasudungan explaining more than what I once knew but since have much forgotten about these compounds.  His channel is a gold mine for aged chemists and aspiring medical students.

Youtube Channel: Armando Hasudungan

 

Maintaining standards: The triple-point cell

Our society depends on standards in countless, mostly invisible ways.   If we can’t agree on how to measure weight, length, temperature, or time we can kiss manufacturing and our manufactured world with its specified, engineered, and interchangeable parts goodbye.   Actually creating and maintaining these standards is hard and the methods change over the years.  The meter was once defined in relation to earthly distances until the realization that the earth changes over time.  Now it is defined in relation to the speed of light which we are pretty sure does not.  The second used to be defined in terms of the day, now it is based on a fundamental property of the cesium atom.  The kilogram has just been redefined in terms of Planck’s constant which then turns into a combination of the second and the meter.

Making any of these measurements is difficult and requires a lot of fancy equipment, often involving lasers, vacuum chambers, electromagnets, and/or racks of electronics.  Here’s how NIST’s new F2 atomic clock works schematically and here’s a package from its inventor on the details.   As the F2 becomes a practical albeit sophisticated standard, even fancier methods are under development for the future.

The Kelvin, fundamental unit of temperature, is a nice exception to this complexity.  It is defined in relation to the triple point of water; that temperature at which the liquid, solid, and vapor phases of isotopically controlled, gas and contaminant-free water are in equilibrium.  Measure this and the Kelvin is 1/273.16 of that.   The aptly named triple point cell requires appropriate water, a skilled glassblower, and some patience.   Thermometers can be calibrated against this standard within and across laboratories.

The Fluke Corporation, despite its name, has long been a respected supplier of a wide variety of test and measurement equipment and they sell such a triple point cell.  In the right hands, it can allow the temperature of 0.01C (the Centigrade and Kelvin are equivalent) to be measured with an uncertainty better than ± 0.0001 °C.  Here’s Fluke’s Matt Newman showing how it is done and not a laser to be seen.

Addendum 20 February 2019: The Kelvin has also been redefined as of November 2018.  It is now tied to Boltzmann’s constant, k.  NIST says that not much will change for the moment since the triple point cell is a known, reliable tool.

 

Fun damentals: RCSB’s Protein 101

These videos provide excellent overviews of proteins and enzymes – what they are and why they are important.  They are produced by the Research Collaboratory for Structural Bioinformatics (RCSB), a part of the worldwide Protein Data Bank Archive.  The RCSB site has additional educational information for non-specialists through its PDB-101 subdomain including curricula for teachers, video challenges for high school students, and a “molecule of the month” providing interactive views into complex protein structures.

Youtube Channel: RCSBProteinDataBank