Using light to describe the ancient world

Archive for February, 2011

Spectroscopy of fossil bone 2: Infrared Splitting Factor

Calculating the infrared crystallinity index, modified from Shemesh (1990).

Infrared spectroscopy is probably the second most commonly used spectroscopic technique applied to fossils. Infrared spectroscopy, or mid-infrared spectroscopy if you want to be picky, is fairly simple in principal: a range of infrared wavelengths are directed at a sample, and the wavelengths that are NOT absorbed are collated at a detector. Hence, an infrared spectrum tells you about the wavelengths that are absorbed by your sample, where specific wavelengths are absorbed by specific vibrational modes (see #Spectroscopy of fossil bone Part 1). In other words, an infrared spectrum gives you the molecular components in your sample: it’s a chemical fingerprint.

Focussing in on an individual band within an infrared spectrum can give you even more chemical data. The position of a band can tell you about the average chemical environment that a vibrational mode occurs in, and the width of a band tells you about the variation across the chemical environments. For example, the phosphate molecule has a vibrational mode where all of the oxygens stretch away from the central phosphorus in sync (=symmetric stretch). If this phosphate is in a mineral lattice, then it will be surrounded by neighbouring ions. Minerals are made up of repeated unit cells, so we have lots of phosphate in the mineral lattice, all eager to symmetrically stretch. If the ions surrounding phosphate are all the same, and the phosphate is in the same lattice site throughout the mineral, then the symmetric stretch will occur within a consistent environment. If you substitute half of the surrounding ions with a different type of ion, then you will change the chemical environment surrounding some of the phosphate. Symmetric stretching will now occur in multiple environments, which we can interpret from the position and width of spectral bands.

This is how infrared spectroscopy is applied to fossils. Infrared spectroscopy makes good use of non-degenerate vibrational modes. We describe a vibrational mode by the type of movement it makes, but there is room for interpretation. Consider the antisymmetric bending of phosphate (see #Spectroscopy of fossil bone Part 1). Phosphate is an anion with a central phosphorus atom bound to four oxygen atoms. During an antisymmetric bend, two of the oxygen atoms are pulled in one direction, while the other two are pulled in another. The chemical environments encountered by each oxygen pair during an antisymmetric bend might differ, and then change again during the next bend. Think of the bending oxygens as feelers that are probing their chemical environment. The chemical environment encountered during an antisymmetric bend will affect the position and width of that vibrational mode, and each stretching geometry of the vibrational mode is recorded as a band on an infrared spectrum. This means that the set of spectral bands produced by the antisymmetric bending of phosphate within bone mineral can tell you about the chemical structure of fossil bone. The variation between the antisymmetic bending bands will be smallest when the mineral has a homogeneous chemical composition, with variation being larger when the mineral is more chemically variable. Shemesh (1990) developed a crystallinity index (CIFTIR) from the antisymmetric bending bands: higher CIFTIR values indicate a more homogenous crystal lattice. Natural bone mineral straight from the animal is chemically heterogeneous and has CIFTIR values less than 3.8. Bone is chemically altered during burial however, and the heterogeneous chemistry is replaced with a standardised, geologically robust chemistry. Hence, altered bone has a high CIFTIR value (Shemesh 1990). The crystallinity index developed by Shemesh (1990) has seen wide use, and is also referred to as the Infrared Splitting Factor of fossil bone.

Shemesh, A. 1990. Crystallinity and diagenesis of sedimentary apatites. Geochimica et Cosmichimica Acta 54: 2433–2438.


#News: Fossil pine forests

Pine resin hardens to form amber, and can be diagnosed using Infrared spectroscopy. Image from Wikimedia Commons (details below).

Gums and resins “exuded” by seed-bearing plants (Gymnosperms) are compositionally distinct, and can be diagnosed using infrared (IR) spectroscopy. Ralf Tappert and colleagues used IR spectroscopy to distinguish the resin produced by pine trees (Pinaceae) from other conifers, and provided identities for gums and other resins as well. Exuded resin hardens into amber and survives through geologic time. Tappert et al. (2011) have therefore provided a method for identifying fossil pine forests.

Tappert R, Wolfe AP, McKellar RC, Tappert MC and Muehlenbachs K (2011). Characterizing Modern and Fossil Gymnosperm Exudates Using Micro-Fourier Transform Infrared Spectroscopy. International Journal of Plant Sciences 172: 120-138.

Image link: resin

Spectroscopy of fossil bone Part 1: Phosphate

Vibrational modes (dance moves) of phosphate.

Bone is a matrix of organic matter supported on a mineral scaffold. Bone mineral (biological apatite) contains an abundance of calcium, as we all know, but is mostly phosphate by weight. Phosphate is an anion formed from one phosphorus atom bound to four oxygen atoms – the oxygens try to keep as far away from each other as possible, and give phosphate a tetrahedral arrangement. Although the oxygens are tethered to the central phosphorus atom, they are free to move, and move they do. Oxygen dance moves are well choreographed and can be prompted under the right conditions. For example, all of the oxygens can stretch away from the phosphorus at the same time (ν1), or they can all bend in the same direction (ν2), or two can stretch while the other two contract (ν3), or two can bend one way while they other two bend the opposite way (ν4). Each of these dance moves is called a vibrational mode, and may be induced when phosphate is irradiated with a laser. Over the next few posts I will explore how these vibrational modes report important information about the preservation of fossils.

Recommended reading

Smith, E. and Dent, G. 2005. Modern Raman Spectroscopy, a practical approach. John Wiley and Sons (Chichester). Find it on Google Books

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