Category Archives: Geochemistry

How Do Silica Tetrahedra Work? – A #UREES101 #GoodQuestion

Most common rock-forming minerals on Earth belong to a group of minerals called silicates. Silicates are distinguished from other minerals by the silica tetrahedron (sometimes called the silicate tetrahedron), a structural unit composed of one silicon atom surrounded by four oxygen atoms that bond directly to the silicon. This gives it the chemical formula of SiO4.

The silica tetrahedron is a four-sided pyramid-like structure, where the faces of the pyramid are all equilateral triangles and the corners (or vertices) are where the oxygen atoms are. The silicon atom is in the very center of the tetrahedron.

The silica tetrahedron, as a molecular diagram and as a solid. CREDIT: Hbf878 Public Domain

The silica tetrahedron looks a little different when the individual sizes of the atoms are considered.

A space-filling atomic model of the silica tetrahedron.
CREDIT: Helgi CC By-SA 3.0
A space-filling atomic model of the silica tetrahedron, with the atoms labeled.
CREDIT: Helgi CC By-SA 3.0

The question came up in class today: How does a silica tetrahedron thing bond? How does it work?

Sadly, I had no answer. In the nearly 30 years I’ve been studying geology, it never occurred to me to ask that simple question. How – thermodynamically, chemically, physically – is it possible for a silica tetrahedron to exist. It’s always just simply been. The tetrahedron is. Just like air. It just is.

Well, that’s about as satisfying of an answer as “because I told you so,” or “because it’s always been that way.” Useless.

So, I looked for answers.

Those of us with a chemistry background agreed that at a first pass, since silicon lies just below carbon on the periodic table, it will behave in roughly the same way. Carbon is able to form four covalent bonds at once (Methane, CH4 being the simplest example of this) which results in the tetrahedral shape. Methane is tetrahedral, with a carbon atom in the middle and hydrogen atoms on the four corners.

Methane shown three different ways. Upper left: molecular sketch; Upper right: stick drawing; Bottom: space-filling model. Blue is carbon, white is hydrogen.
CREDIT Effeietsanders CC By 2.5 nl

The tetrahedral shape works great for methane, because each hydrogen atom “wants” another electron, and the carbon atom “wants” four more electrons. By sharing electrons (covalent bonding), the carbon and the hydrogen are “happy” and methane is a stable molecule.

Covalently bonded hydrogen and carbon in a molecule of methane.
CREDIT DynaBlast CC By-SA 2.5

Does this work with the silicate tetrahedron? No. Not quite. Like carbon, the silicon in the center of the silica tetrahedron “wants” four more electrons. However, the oxygens (unlike hydrogen in methane), each “want” two electrons.

The result is that the silica tetrahedron (SiO4) has a strong negative charge and should properly be written SiO44-. This little detail is often glossed over when silicates are introduced in introductory classes (just like mine, oops). But it’s because of this charge that silicates come in so many varieties and forms.

Silica tetrahedra may remain independent in a mineral (as in the nesosilicates) or they may bond to each other in pairs (sorosilicates), rings (cyclosilicates), chains (inosilicates), sheets (phyllosilicates), or as a complex three-dimensional network (tectosilicates). When the tetrahedra bond to one another the charge is then reduced. The remaining charge (or the entire 4- charge, in the case of nesosilicates) is taken up with anions (atoms with positive charges) such as magnesium, iron, potassium, calcium, and aluminum.

The details of how the various silicates form etc. would be a different blog post. But I hope that this one at least satisfies our collective curiosity about how the silica tetrahedron can even be a thing.

Infrared Light and the Quality of Fossil Preservation – #365papers – 2018 – 62

Beasley, Bartelink, Taylor, and Miller, 2014, Comparison of transmission FTIR, ATR, and DRIFT spectra: implications for assessment of bone bioapatite diagenesis: Journal of ARchaeological Science, v. 46, p. 16-22.

What’s it about?

One of the challenges of studying the chemistry of fossil bones and teeth is being confident that the chemistry of the fossils is unaltered from its original state (that is, the bones and teeth still faithfully record the chemistry of the living animal they came from). During the process of fossilization, the mineral and chemical structure of bones and teeth are altered from what they were in life, a process called diagenesis.Continue reading “Infrared Light and the Quality of Fossil Preservation – #365papers – 2018 – 62”

Clay Keeps Records of Ancient Water – #365papers – 2018 – 56

Mix and Chamberlain, 2014, Stable isotope records of hydrologic change and paleotemperature from smectite in Cenozoic western North America: Geochimica et Cosmochimica Acta, v. 141, p. 532-546

What’s it about?

Smectite is a specific kind of clay mineral, common in volcanic ash. This kind of clay incorporates water during its formation, which, as the authors show, can provide a record of what surface water was like when the clay formed. Continue reading “Clay Keeps Records of Ancient Water – #365papers – 2018 – 56”

Migrating Marsupials of the Pleistocene – #365papers – 2018 – 44

Price, Ferguson, Webb, Feng, Higgins, Nguyen, Zhao, Joannes-Boyau, and Louys, 2017, Seasonal migration of marsupial megafauna in Pleistocene Sahul (Australia-New Guinea): Proceedings of the Royal Society B, v. 284: 20170785

What’s it about?

Seasonal migrations are seen in many large mammals. In modern animals, however, such migrations are not observed in marsupials. The authors put together geochemical data from rocks and fossil to show that the massive wombat-like extinct marsupial Diprotodon migrated seasonally as far as 100 km each way.Continue reading “Migrating Marsupials of the Pleistocene – #365papers – 2018 – 44”

Methods for Extracting Proteins from Fossils: Paleoproteomics – #365papers – 2018 – 38

Cleland and Schroeter, 2018, A comparison of common mass spectrometry approaches for paleoproteomics: Journal of Proteome Research, DOI: 10.1021/acs.jproteome.7b00703

What’s it about?

Recently, there has been great discussion about the extraction of proteins from fossils. This paper outlines various methods, and their strengths and weaknesses, for extracting proteins from ancient bones.Continue reading “Methods for Extracting Proteins from Fossils: Paleoproteomics – #365papers – 2018 – 38”

Using Glass to Estimate Altitude – #365papers – 2018 – 37

Dettinger and Quade, 2015, Testing the analytical protocols and calibration of volcanic glass for the reconstruction of hydrogen isotopes in paleoprecipitation, in DeCelles, Ducea, Carrapa, and Kapp, eds., Geodynamics of a Cordilleran Orogenic System: The Central Andes of Argentina and Northern Chile: Geological Society of America Memoir 212, p. 261-276.

What’s it about?

Isotopes of oxygen and hydrogen from water can give us insights into the altitude at which that water fell to the ground as rain. Some of this water can become incorporated into volcanic glass (in ash), preserving the isotopic values of the original water.Continue reading “Using Glass to Estimate Altitude – #365papers – 2018 – 37”

Interpreting Cretaceous Environments from Multiple Sources – #365papers – 2018 – 32

Bojar, Csiki, and Grigorescu, 2010, Stable isotope dirstibution in Maastrichtian vertebrates and paleosols from the Hateg Basin, South Carpathians: Palaeogeography, Palaeoclimatology, Palaeoecology, v. 293, p. 329-342.

What’s it about?

Some late Cretaceous-aged (AKA Maastrichtian) rocks from Romania contain fossilized soils (paleosols), dinosaur bones and teeth, and dinosaur eggshells. The authors use geochemical analysis, specifically stable isotope analysis, from all of these materials to build a fairly complete picture of what the region was like at the time that those dinosaurs were alive. What they found was that the environment was relatively warm and dry, and that the dinosaurs didn’t appear to utilize different parts of the habitat, but instead lived side-by-side.Continue reading “Interpreting Cretaceous Environments from Multiple Sources – #365papers – 2018 – 32”

How Can We Know When The Earth’s Atmosphere Became Oxygenated? – #365papers – 2018 – 31

Eickmann, Hofmann, Wille, Bui, Wing, and Schoenberg, 2018, Isotopic evidence for oxygenated Mesoarchaean shallow oceans: Nature Geoscience, v. 11, p. 133–138.

What’s it about?

Sulfur and iron atoms come in different sizes, called isotopes. The relative amounts of these isotopes can tell us a lot. In this paper, isotopes of sulfur are used to recognize active metabolism of microbes that use sulfur in their metabolic processes. These results, combined with results from isotopes of iron, provide evidence not only of the activities of life, but also show that there was some oxygen in the atmosphere at that time, enough to oxygenate shallow water but not deep water of the ocean.Continue reading “How Can We Know When The Earth’s Atmosphere Became Oxygenated? – #365papers – 2018 – 31”

Sabertooth, Sabertooth, How Do Your Teeth Grow? – #365papers – 2018 – 30

Feranec, 2004, Isotopic evidence of saber-tooth development, growth rate, and diet from the adult canine of Smilodon fatalis from Rancho La Brea: Palaeogeography, Palaeoclimatology, Palaeoecology, v. 206, p. 303-310.

What’s it about?

Sabertoothed mammals are so named because of their massive, elongate canines. A natural question to ask is, how does it get so long? The major ideas are that the teeth grow for a very long time (which would affect how the animals survived before the teeth were fully grown), that they grew very quickly, or some combination.

The author uses isotopes of oxygen from the tooth enamel of some adult sabertooth tigers (Smilodon fatalis) to estimate how long it tooth the tooth to grow. This he compares with known growth rates and timing of development of modern lions and tigers to see how it compares. Continue reading “Sabertooth, Sabertooth, How Do Your Teeth Grow? – #365papers – 2018 – 30”

Something Something Sulfides Cobbles Granite and Collision – #365papers – 2018 – 27

Whalen, Zagorevski, McNicoll, and Rogers, 2013, Geochemistry, U-Pb geochronology, and genesis of granitoid clasts in transported volcanogenic massive sulfide ore deposits, Buchans, Newfoundland: Canadian Journal of Earth Sciences, v. 50, p. 1116-1133.

What’s it about?

This paper is about some massive sulfide deposits (good places to finding sulfur, zinc, iron, and lead) that occur in the middle of Newfoundland. The deposits come in several forms and are associated with some igneous rocks (granites). The authors explore whether the different forms of deposits and their associated granites all occurred at the same time, from the same original volcanic source, or are from different sources.Continue reading “Something Something Sulfides Cobbles Granite and Collision – #365papers – 2018 – 27”