Ikaite, a mineral named after the Ika Fjord in southwest Greenland

The mineral ikaite is named after the Ika Fjord, now spelled Ikka Fjord, in southwest Greenland. This fjord is about 12 km long and forms the southern border of Ivigtut Peninsula, which is bordered on the north by Arsuk Fjord [1].
Ikaite is a metastable hexahydrate of calcium carbonate with formula CaCO₃·6H₂O [2]. It forms in lake and sea water in glaciomarine environments at temperatures near 0°C and converts to calcite at higher temperatures. The metastability of this mineral has been illustrated with the description of the treatment of the first samples, secured by a diver in 1962 near skerries (tiny islands) in the Ikka Fjord [1]:

Samples taken fresh from skerries appear as white porous material that is rather friable but forms coherent masses, which disintegrate within a few hours into a wet powder. These and other observations showed that samples had to be stored and shipped with special care. The excellent samples obtained in August from the bottom of small pillars were shipped to Copenhagen in the refrigator aboard the M. S. Nanok S of the Royal Greenland Trading Company.

Ikaite has also been found in ocean floor sediments off the coast of Antartica (in 1982) and in minor amounts in Mono Lake, Mono County in eastern California [3]. Present understanding of the geochemistry of ikaite explains the existence of today's tufa columns at lakes in the Great Basin area, including Pyramid Lake (Nevada) and Mono Lake, as a result of climate warming that pseudomorphed ikaite into tufa since the end of the ice age, when ancient Lake Lahontan and other lakes began their gradual desiccation.

Keywords: mineralogy, geography, Greenland, Mono Lake, history

References and suggested reading
[1] Hans Pauly: “Ikaite”, a new mineral from Greenland. Artic 1963, 16, pp. 264-264.
pubs.aina.ucalgary.ca/artic/Arctic16-4-263.pdf.
[2] The mineral and locality database: Ikaite. www.mindat.org/min-2007.html.
[3] Timothy Tierney: Geology of the Mono Basin. Kutsavi Press, Lee Vining, California, 2000; pp. 59-60.
[4] J. L. Bischoff, J. A. Fitzpatrick and R. J. Rosenbauer: The Solubility and Stabilization of ikaite (CaCO₃·6H₂O) from 0°C to 25°C: Environmental and Paleoclimatic Implications for Thinolite Tufa. J. Geol. January 1993, 101 (1), pp. 21-33.
Abstract: www.jstor.org/pss/30066092.
[5] B. Buchardt, C. Israelson, P. Seaman and G. Stockmann: Ikaite Tufa Towers in Ikka Fjord, Southwest Greenland: Their Formation by Mixing of Seawater and Alkaline Spring Water. J. Sediment. Res. January 2001, 71 (1), pp. 176-189.
DOI: 10.1306/042800710176.

Hazenite, a mineral named after earth scientist Robert M. Hazen

Hazenite is a hydrous alkali magnesium phosphate with the formula KNaMg₂(PO₄)₂·14H₂O [1,2]. This mineral was discovered and described by Hexiong Yang of the University of Arizona and named after Robert M. Hazen, a senior staff scientist at the Carnegie Institution's Geophysical Laboratory and Clarence Robinson Professor of Earth Science at George Mason University [3].

Hazenite is a white, vitreous, and transparent mineral (see picture on page 64 in [3]). It is precipitated by microbes in the highly alkaline Mono Lake in Mono County, California. Hazenite, like many minerals on Earth, owes its existence to life. Current knowledge of the formation process of hazenite supports the hypothesis/fact of co-dependence and co-evolution of organisms and minerals. The subtitle of a recent article by Robert Hazen summarizes this view [3]:

Looking at the mineral kingdom through the lens of deep time leads to a startling conclusion: most mineral species owe their existence to life.

The lifeless matter is, from the viewpoint of a large time-scale, becoming alive. Geology is going to recognize terms like species and kingdom that are commonly associated with biological nomenclature and taxonomy.

Synonym/code for hazenite: IMA2007-061 [2].

Keywords: earth science, mineralogy, geochemistry, biology, history

References
[1] Carnegie Institution for Science: Hazenite officialy approved as a new mineral. hazen.gl.ciw.edu/node/270.
[2] The mineral and locality database: Hazenite. www.mindat.org/min-38992.html.
[3] Robert M. Hazen: Evolution of Minerals. Scientific American March 2010, 302 (3), pp. 58-65.

Don't (mis)match Deutsch and Dutch!

Drop the two letters e and s from the German word Deutsch and you get Dutch. This is what a Danish student of German did—according to his teacher—while he tried to short-cut his homework assignment (see Däne verwechselte Deutsch und Dutch). The Danish German teacher Frank Lacay at the private Ådalen school of Ishøj near Copenhagen, Danemark, proved that his pupil, who thought he had translated some Danish text into German (as he was supposed to do by means of his acquired German language skills), in fact translated the given text into Dutch language by using an on-line translation tool on the Internet. By checking on-line translation services himself, the teacher found it obvious that the schoolboy used such a service and clicked Dutch instead of Deutsch: the text of the delivered “homework” translation and the Dutch-triggered machine output were identical.

The best machine is counterproductive when you press the wrong button. But even if you stay button-accurate, I doubt that there is a reliable “best translation” machine—at least not for text embedded in context. Anyway, it is always fun to try, as long as you press the relevant keys and think ahead of the machine …

And this is for the schoolboys:
Deutsch is the German word for the English word German,
Holländisch is the German word for the English word Dutch,
Niederländisch is a German-language synonym for Holländisch,
Dänisch is the German word for the English word Danish.

Short notations for α-amino acids and peptides based on one-letter code (1LC)

A three-letter code (3LC) is typically applied to encode molecular structures that contain sequences of the proteinogenic amino acids. The notations for such structures can further be shortened by about 75% (also omitting hyphens in the sequence notation) when one-letter codes (1LCs) are used. Both, 3LCs and 1LCs for the proteinogenic amino acids can be looked up by their names in different languages (English, French, German, Italian, Portuguese and Spanish) and in context of thermodynamic property links.
The synthetic pentapeptide pentigetide, for which the 3LC-based encoding has previously been demonstrated (see Short notations for α-amino acids and peptides based on three-letter code (3LC) ) being Asp-Ser-Asp-Pro-Arg, shrinks to DSDPR by using the 1LC system.
1LC-based notations are very efficient for sequence search and similarity-based modeling of peptides and derivatives in large libraries.

Note: The design of an encoding system for derivatives of amino acid sequences needs a syntax that distiguishes between amino acid 1LCs and one-letter chemical element symbols. Ambiguities arise for the following letters:

• C: cysteine (carbon)
• F: phenylalanine (fluorine)
• H: histidine (hydrogen)
• I: isoleucine (iodine)
• K: lysine (potassium)
• N: asparagine (nitrogen)
• O: pyrrolysine (oxygen)
  
• P: proline (phosphorus)
  
• S: serine (sulfur)
• U: selenocysteine (uranium)
  
• V: valine (vanadium)
• Y: tyrosine (yttrium)
  

Finally, the 1LC for aspartic acid (D) may conflict with the symbol for the hydrogen isotope deuterium.

Short notations for α-amino acids and peptides based on three-letter code (3LC)

α-Amino acids are the building blocks of biomolecules such as peptides and proteins as well as supramolecular structures that are of interest in materials science and nanotechnology. Abbreviations and short notations are frequently used for the “standard” and other amino acids. For the 22 proteinogenic amino acids, which include the 20 standard amino acids plus pyrrolysine and selenocysteine, three-letter codes (3LCs) are in common use. These 3LCs are applied to encode peptides as linear notations. For example, the notation for the synthetic pentapeptide pentigetide [1],

Asp-Ser-Asp-Pro-Arg,

indicates that the molecule consists of a sequence of the L-enantiomers of the α-amino acids aspartic acid (Asp), serine (Ser), aspartic acid (Asp), proline (Pro) and arginine (Arg). The four hyphens in the notation “symbolize” peptide bonds that each connect the carboxylic group of the left-side amino acid residue to the amino group at the C_α-atom of the right-side amino acid residue. The Chemical Abstract name for pentigetide is [1]:

N²-[1-[N-(N-L-α-aspartyl-L-seryl)-L-α-aspartyl]-L-prolyl]-L-arginine.

Pentigetide is an oligopeptide. Many biomolecules, polypeptides and other biopolymers contain more than five amino acid units and the efficiency of the 3LC is immediately appreciated when encoding their molecular structure.

References
[1] Entry 7086 on page 1130 in The Merck Index, Eleventh Edition, Merck & Co. Inc., Rahway, NJ, U.S.A., 1989.
[2] Bibliography and links: Notations for amino acids.

Amino acids in English, French, German, Italian, Portuguese and Spanish

The twenty standard amino acids have one-word names in the languages English, French, German, Italian, Portuguese and Spanish. The only exceptions are the names aspartic acid (Asp) and glutamic acid (Gln), whose molecules contain an additional -COOH group in the side chain. For comparison, the names of standard amino acids are presented in an overview table along with their short notations, the three-letter codes (3LCs) and one-letter codes (1LCs):

Names of α-amino acids in different languages.

With the exception of Asp and Gln, the one-word names are composed from a stem and an ending. The stem spelling is very similar, sometimes undistinguishable, while comparing names of a given amino acid across the considered languages. The endings show language-specific patterns. German names have the ending in (or an in Tryptophan), not having the terminal e of their English and French counterparts that end in ine; with the exception of tryptophan ending in an in German and English and in ane in French. The Italian, Portuguese and Spanish names have the ending na. Here, again, the names of tryptophan make for an exception: the ending is no in these three languages.

The English term amino acid in other languages:
French: acide aminé
German: Aminosäure
Italian: amminoacido
Portuguese: aminoácido
Spanish: aminoácido

Click chemistry, a term now recognized in many branches of chemistry

The term click chemistry refers to a synthetic strategy that focuses on “ easy-to-make” chemical compounds and materials from modular “blocks.” In 2001, Sharpless, Kolb, and Finn introduced this term to label a chemical synthesis approach conceptualized to advance fast, modular, process-driven design and application-oriented molecular discovery [1/de,1/en]. They defined a set of criteria that a useful process (reaction scheme) must meet in the context of click chemistry:

The reaction must be modular, wide in scope, give very high yields, generate only inoffensive byproducts that can be removed by nonchromatographic methods, and be stereospecific (but not necessarily enantio-selective). The required process characteristics include simple reaction conditions (ideally, the process should be insensitive to oxygen and water), readily available starting materials and reagents, the use of no solvent or a solvent that is benign (such as water) or easily removed, and simple product isolation. Purification—if required—must be by nonchromatographic methods, such as crystallization or distillation, and the product must be stable under physiological conditions.

In various aspects, the goals of click chemistry overlap with those of sustainable chemistry (green chemistry). Although originally demonstrated and discussed within applications in biochemistry and medicine, click chemistry today is recognized in many other areas including materials science, biotechnology, nanotechnology and photovoltaics. References to selected articles, communicating and reviewing research in and applications of click chemistry in such fields, are given below.

Keywords: chemical synthesis, library synthesis, thermodynamics, kinetics, pharmaceutical chemistry, drug design, material design, chemical reaction types, cycloaddition, nucleophile addition

References
[1/de] H. C. Kolb, M. G. Finn and K. B. Sharpless: Click Chemie: diverse chemische Funktionalität mit einer Handvoll guter Reaktionen. Angew. Chem. 2001, 113 (11), pp. 2056-2075.
DOI: 10.1002/1521-3757(20010601)113:11<2056::aid-ange2056>3.0.CO;2-W.
[1/en] H. C. Kolb, M. G. Finn and K. B. Sharpless: Click Chemistry: Diverse Chemical Function from a Few Good Reactions. Angew. Chem. Int. Ed. 2001, 40, pp. 2004-2021.
DOI: 10.1002/1521-3773(20010601)40:11<2004::aid-anie2004>3.0.CO;2-5.
[2] A. J. Dirks, J. J. L. M. Cornelissen, F. L. van Delft, J. C. M. van Hest, R. J. M. Nolte, A. E. Rowan and F. P. J. T. Rutjes: From (bio)Molecules to Biohybrid Materials with the Click Chemistry Approach. QSAR & Combinatorial Science 2007, 26 (11-12), pp. 1200-1210.
DOI: 10.1002/qsar.200740085.
[3] W. Zhan, W. Wu, J. Hua, Y. Jing, F. Meng and He Tian: Photovoltaic properties of new cyanine-naphthalimide dyads synthesized by ‘Click’ chemistry. Tetrahedron Lett. 2007, 48 (14), pp. 2461-2465.
DOI: 10.1016/j.tetlet.2007.02.034.
[4] J. Lutz and H. G. Bömer: Modern trends in polymer bioconjugates design. Prog. Polym. Sci. 2008, 33 (1), pp. 1-39.
DOI: 10.1016/j.progpolymsci.2007.07.005.
[5] Special Issue: Click Chemistry in Polymer Science. Macromol. Rapid Commun. 2008. Table of Contents.
[6] D. Kunz: Klick-Chemie. Synthesen, die gelingen. Chemie in unserer Zeit (ChiuZ) 2009, 43 (4), pp. 224-230.
DOI: 10.1002/ciuz.200900475.