An acronym in cheminformatics: SMILES for simplified molecular input line entry system

SMILES stands for simplified molecular input line entry system [1]. SMILES is a chemical notation system with a small chemical grammar for the encoding of molecular structures based on the principles of molecular graph theory.

SMILES is a user-friendly chemical language that allows input of molecular structures in molecular editors, databases, search engines and property estimation tools. For example, ChemSpider [2] accepts SMILES entries (also: nomenclature-based names, registry number or InChI). Looking for aspirin (2-(acetyloxy)benzoic acid)? Type the SMILES notation CC(=O)Oc1ccccc1C(=O)O into the search field. Notice that the six carbon atoms of the aromatic benzene ring have been entered in lower case to identify them as aromatic-ring members. Also, hydrogen atoms have not been explicitly specified, since their occurrence is deduced based on valence rules.

What is “hiding” behind the notation FC12C3(F)C4(F)C1(F)C5(F)C4(F)C3(F)C25F?
Correct, it is perfluorocubane (1,2,3,4,5,6,7,8-octafluorocubane). ChemSpider is finding it either way and it is your choice to type the SMILES notation or a name.

Computers “love” SMILES since they can automatically derive a connection table from the linear notation code, which is essential to draw the assocoated structure or to calculate molecular descriptors. Given a name such as 2-(acetyloxy)benzoic acid would require automatic structure interpretation on a much higher level—not so easy for a computer. And giving aspirin will cause a computer headache, speaking in human terms.

Keywords: molecular graphs, molecular connectivity, molecular data exchange

References
[1] David Weininger: SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
DOI: 10.1021/ci00057a005.
[2] ChemSpider starting guide: How do you find compounds? [www.chemspider.com/GettingStarted.aspx].

The Leet seismograph, named after L. Don Leet

The Leet seismograph is named after its developer, the geoscientist Dr. L. Don Leet, who has been chairman of the Division of Geological Sciences at Harvard University, Director of the Harvard Seismographic Station [1] and was a co-founder of the Vibration Engineering Company, where he developed the first three-component portable seismograph in the 1940s [2,3].

In his earthquake-seismology book, which Don Leet wrote together with his wife Florence [1], he describes how he was lured down from Boston to New Mexico in 1945 to record seismic waves from explosion tests. It turned out that those testing experiments involved nothing less than atomic bomb explosions: “Among the seismographs recording this event were four portable Leet seismographs, one operating by remote control five miles from the bomb. The largest motion registered on it was produced by a type of surface earth wave (the ‘hydrodynamic’) that had not previously been recognized. Another type of earth wave also was recorded on this same record. Its vibration had a particle motion (‘coupled’) that I had first recognized and reported in 1939, when it had been recorded from dynamite blasts. These two surface waves have since been identified on records from dynamite blasts and from nuclear blasts, but not on records from earthquakes.”

When the relationship between the United States and the Soviet Union began to get shaky, recording of underground earth waves became a matter of international security and headline news and speculations about seismic events spread around the globe almost as fast as their recordable waves.

Keywords: history of seismology, atomic bombs, nuclear explosion, artificial earthquakes

References
[1] L. Don and Florence Leet: Earthquake • Discoveries in Seismology. Dell Publishing Co., Inc, 750 Third Avenue, New York, N. Y. , 10017, USA, 1964; pages 178 and 181.
[2] GeoSonics Vibra-Tech: History [www.geosonicsvibratech.com/history.html].
[3] History of Explosives and Blasting, see entry for 1950: first portable 3 component monitor developed, the Leet Seismograph weighs 65 lbs [www.explosives.org/HistoryofExplosives.htm].

Is your surname on the map of the United States?

This year's February issue of National Geographic features a map of the United States with surnames covering territory from Hawaii to Maine and Alaska to Florida. This namescape is supposed to give the viewer an idea of the distribution of common last names, reflecting North America's immigration history. The surnames have different colors indicating their language-based origin from countries in Europe and Asia.

Overall, there is lot of blue—from light to dark for England, Wales and Scotland. Green names in the Boston area belong to Irish folks. French names are scattered along the Canadian border in Maine and around New Orleans. Spanish names dominate in the southern parts of California and Florida. Scandinavian and German names are found frequently west of Lake Michigan. Interestingly, the surname Miller is sometimes displayed in the “German color.” German newcomers apparently anglicized—or should we say americanized—their surname from Müller to Miller.

You'll look in vain for names that would specifically indicate Native American, African American and Jewish origin! Well, Native Americans are not (recent) immigrants; but don't they have names? During the time of slavery, black people often took (or got?) the name of their owner and today's descendants, therefore, have often British-sounding names. The Jewish population, like many other ethnic groups, are concentrated in particular parts of the country, which do not show up in sufficient detail. Little Italy neighborhoods and Basque Shepherd communities are too small for surname presence on the grand scale. Imagine, printing a similar map for New York or Los Angeles: the printer would probably run out of colors—and even letters.

Keywords: immigration, naturalization, integration, population dynamics, ethnic diversity, name persistence, name change

Reference
What's in a Surname? National Geographic February 2011 [blogs.ngm.com/blog_central/2011/01/whats-in-a-surname.html].

Acronym in chemistry and business: BASF for Badische Anilin und Soda Fabrik

BASF is a German-language acronym for Badische Anilin und Soda Fabrik, a chemical company with its headquarters in Ludwigshafen, Germany. The word Fabrik means factory. The inner phrase Anilin und Soda refers to aniline and sodium carbonate, which were the critical start-up products in the 1860s: Aniline was manufactured in a plant in Mannheim and sodium carbonate at a soda and mineral acid factory at Ludwigshafen on the other bank of the Rhine [1]. The adjective Badische specifies the location: Baden, which was a Grand Duchy then, is today part of the twin-state Baden-Württemberg in southwest Germany. Mannheim is—after Stuttgart— the second largest city of this state. Ludwighafen belongs to the state of Rhineland-Palatine. The company, however, is not confined to two German states: it is present worldwide and even became the largest chemical company through major acquisitions. The BASF was chosen as C&EN's 2010 company of the year [2].

Keynotes: chemical history, business strategies, recovery from recession

References
[1] Fred Aftalion: A History of the International Chemical Industry. Translated from the original French edition by Otto Theodor Bentley. University pf Pennsylvania Press, Philadelphia, 1991; page 41. (Note that this reference confuses the rivers Main and Rhine.)
[2] Alexander H. Tullo and C&EN Northeast News Bureau: Company Of The Year. Chemical & Engineering News January 3, 2011, 89 (1), page 15. Background: BASF: The Chemical Company?

The bigram “ionic liquid” and related terms in the Ngram Viewer

The Google Books Ngram Viewer provides interesting options to analyze the frequency of use of words and phrases (n-grams) over time—relative, as a percentage of all other n-grams occurring in a corpus of books published in a selected language. By simultaneously generating time-percentage graphs for a set of different terms, one can easily compare their “importance” relative to each other and establish their culturomics.

Let's see how it works for chemistry. I choose the term “ionic liquid” to check if the graph reflects the recent growth in the design and application of ionic liquids. The graph clearly indicates a rise from almost zero up to 0.00001% between 1998 and 2008. This growth trend parallels the one found in an analysis of journal publications [1]. Interestingly, the synonymous term “liquid salt,” although used before the appearance of the term “ionic liquid”, continues on after 1998 at the same low percentage as before 1998. The 4-grams “room temperature ionic liquid” and “task specific ionic liquid” are too specific and do not produce a graph. However, their acronyms “RTIL” and “TSIL” do, following the trend of the parent term “ionic liquid”, while the unigram “RTIL” has a much higher frequency than “TSIL”.

For a final “ionoculturomics” diagram, I entered the unigrams “cation”, “anion” and “zwitterion”. As expected, the percentage for the term “zwitterion” stays near zero over the whole time range from 1900 to 2008. The shapes of the “cation” and “anion” graph are very similar, showing a maximum around 1980 and declining thereafter. Consistently over time, the term “cation” is used almost twice as often as the term “anion”. I don't have an explanation for that.

Reference
[1] Figure 1: “The rise in publications concerning ionic liquids as a function of time, as determined using SciFinder” in the Preface of the book entitled “ Ionic Liquids in Synthesis,” edited by P. Wasserscheid and T. Welton. Wiley-VCH Verlag, Weinheim, Germany, 2003.

Culturomics, a portmanteau blending the words “culture” and “genomics”

The noun culturomics is a portmanteau derived from the words culture and genomics. While in genomics the sequences of DNA base pairs are studied, in culturomics the changes in meaning and frequencies of word sequences (n-grams) in written documents over time are the subjects of curiosity. John Bohannon describes how Jean-Baptiste Michel and Erez Lieberman Aiden came up with the term culturomics [1]: “In a nod to data-intensive genomics, Michel and Lieberman Aiden call this nascent field ‘culturomics’.”

This nascent field has already been applied to investigate cultural trends and linguistic phenomena in a large corpus of digitized English-language texts published between 1800 and 2000 [2,3]. The culture of culturomics can be followed via tweets at the Cultural Observatory [4]. And if you want to track the evolution of your favorite phrase or a strange word, you are invited to use the Ngram Viewer [5]. But there is no absolute warranty that your favorite book has been scanned, digitized and n-gramatized!

References and n-gram exploration
[1] John Bohannon: Google Opens Books to New Cultural Studies. Science 17. December 2010, 330, page 1600. DOI: 10.1126/science.330.6011.1600.
[2] J.-B. Michel, Y. K. Shen, A. P. Aiden, A. Veres, M. K. Gray, The Google Books Team, J. P. Pickett, D. Hoiberg, D. Clancy, P. Norvig, J. Orwant, J. Orwant, S. Pinker, M. A. Nowak and E. Lieberman Aiden: Quantitative Analysis of Culture Using Milions of Digitized Books. Science Published Online 16. December 2010. DOI: 10.1126/science.1199644.
[3] Culturomics: www.culturomics.org.
[4] @culturomics: twitter.com/culturomics.
[5] Google labs Books Ngram Viewer: ngrams.googlelabs.com.

Gaia hypothesis named after the Greek goddess of Earth

The Gaia hypothesis was named by the British scientist James Lovelock after the Greek goddess of Earth. Lovelock followed a suggestion of novelist William Golding to name his hypothesis that explains life through its initiating capacity rather than its adapting behavior [1]: “Lovelock's insight stood that notion [of simple adaption] on its head, giving to life the function, exercised over billions of years, of establishing and maintaining conditions conclusive to its own welfare.”

Synonymous terms such as Gaia theory, Gaia principle, Gaia metaphor or Gaian paradigm of Earth are in common use [2]. Gaian thinking embraces complex systems as a whole before attending to specific domains. Self-regulating systems play a key role in gaian understanding of nature. Mutual evolution of the living and non-living world and processes of self-regulation fight tendencies toward entropy and create order out of chaos. After all, Gaia was born from Chaos, according to Greek mythology [3].

The Gaia principle includes interdisciplinary teaching and working, complementing science with philosophy, ethics and perspectives in discussing and solving global problems.

References
[1] David E. Moody: Gaia Comes of Age. Natural History December 2010/ January 2011, 119(3), 40-42.
[2] The Gaia Theory • Model and Metaphor for the 21st Century [www.gaiatheory.org].
[3] Ron Leadbetter: Gaia [www.pantheon.org/articles/g/gaia.html].