Climate Science Glossary

Term Lookup

Enter a term in the search box to find its definition.

Settings

Use the controls in the far right panel to increase or decrease the number of terms automatically displayed (or to completely turn that feature off).

Term Lookup

Settings


All IPCC definitions taken from Climate Change 2007: The Physical Science Basis. Working Group I Contribution to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, Annex I, Glossary, pp. 941-954. Cambridge University Press.

Home Arguments Software Resources Comments The Consensus Project Translations About Donate

Twitter Facebook YouTube Pinterest

RSS Posts RSS Comments Email Subscribe


Climate's changed before
It's the sun
It's not bad
There is no consensus
It's cooling
Models are unreliable
Temp record is unreliable
Animals and plants can adapt
It hasn't warmed since 1998
Antarctica is gaining ice
View All Arguments...



Username
Password
Keep me logged in
New? Register here
Forgot your password?

Latest Posts

Archives

OA not OK part 13: Polymorphs - the son of Poseidon

Posted on 5 August 2011 by Doug Mackie

This post is number #13 in a series about ocean acidification. Other posts: Introduction, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, Summary 1 of 2, Summary 2 of 2.

Welcome to the 13th post in our series about ocean acidification. In post 3, we said that there are several types of calcium carbonate. In this post, we describe the types of calcium carbonate used in by marine organisms to make their shells.

Shelled fauna first show up in fossil records for the early Cambrian period – about 540 million years ago, some 60 million years after the evolution of multicellular organisms.

Why calcium carbonate for shells? If truth be told, it isn't always calcium carbonate; other bio-minerals are also used. Radiolaria and diatoms, are single-celled photosynthetic algae that have skeletons made of silica, as do most sponges. Vertebrates, on the other hand, favour various phosphates.

But calcium carbonate is the most common marine biomineral. Why? In a single sentence, calcium carbonate is hard, (mostly) insoluble, and cheap. Actually, there are several forms of calcium carbonate and we may as well get the distinctions clear now.

Biological calcium carbonate comes in two main forms, or polymorphs poly = many, morph = form): aragonite and calcite. A third form, vaterite, is quite soluble and is rare in biology.

Aragonite is found, for example, in thecosomata pteropods (small free swimming sea snails) and corals. Calcite is found, for example, in coccolithophores and foraminifera. Molluscs can use either or both polymorphs.

cocco and foram

Figure 7. (L to R). Emiliana huxleyi a common coccolithophore about 5 microns across, (image ORNL ), fossil foraminifera from New Zealand about 500 microns across, (image Te Ara).

Without going into great detail (fascinating though it is) we will say that the polymorphs differ in the way the molecules stack when they form crystals. As an analogy, think of stacking balls in a box. Figure 8 shows two of the several ways to stack spheres. The left panels show 2 ways to lay the bottom layer and the right panels show 2 ways to lay the top layer. In the top row of boxes, each ball not on an edge touches 4 neighbours in a given layer (plus 4 in each layer above and below). In the second row of boxes each ball not on an edge touches 6 neighbours in a given layer (plus 3 in each layer above and below). That is balls in both ways of stacking have the same number of neighbours – though the neighbourhood makeup is different.

Figure 8 packing of spheres

Figure 8. Some ways to pack spheres. Left panels give two ways to lay the first layer. Right gives second layer - laid as for first layer. These are NOT representations of aragonite and calcite.

Note that these figures do NOT represent aragonite or calcite. It would take a lot of subtle technical terms to adequately explain their actual crystal structure, but the basic principles exemplified in the figures holds. You can see that the spheres in the bottom boxes are packed more tightly than the spheres in the top boxes. This sort of packing difference explains why aragonite is denser (2.95 grams per cubic centimetre) than calcite (2.71). The packing arrangement (including things like the length of bonds between molecules and the makeup of the neighbours) also controls the attributes like solubility. In the case of CaCO3, the polymorph aragonite is always more soluble than calcite.

text box aragonite more soluble

 

xl structure aragonite and calcite

Figure 9. Crystal structures of carbonate molecules in calcite (L) and aragonite (R). Carbonate groups are shown as 'Y' shape sticks. Black = carbon, red = oxygen. The differences are primarily in the way the CO32– molecules align or are staggered so calcium atoms omitted for clarity.

aragonite

 

calcite xyx rotation

Figure 10. Animations of the unit cells for crystal structures of aragonite (top) and calcite (bottom). Carbonates shown as 'Y' shape sticks. Black = carbon, red = oxygen, blue = calcium. The black boxes outline the unit cell

The unit cell is the repeating unit of the crystal. This is the same principle as wallpaper pattern groups. A simple repeating unit is used to build up the pattern. Sometimes a simple pattern is reproduced within a short space, other times it takes much longer before the pattern repeats. It turns out that the calcite unit cell is 3x longer than the aragonite unit cell and that the calcite unit cell contains partial CO32- (hence the funny looking non Y shapes at the edges).

Don't think that the molecules are mostly empty space. The 'stick' form structures are given because they highlight spatial relationships between the CO32- molecules. Space-fill representations show the electrical sphere of influence of each atom (Figure 11) but obscure the molecule to molecule positioning.

calcitearagonite

Figure 11. Space filling sphere representations of unit cell for calcite (left) and aragonite (right).

How is the stability of calcium carbonate shells affected by the particular polymorph? In post 2 we mentioned that lower energy reaction products are favoured by thermodynamics. For 2 or more polymorphs we can illustrate this graphically. The thick blue line in Figure 12 shows the relative energy of calcium carbonate with respect to packing conditions. The two dips in the line correspond to two states where a compound is stable. Imagine placing a ball in each dip - aragonite (pink ball) and calcite (green ball). The green ball (calcite) is well and truly sunk in its pocket and is thus stable. Aragonite is formally described as metastable: the pink ball mostly stays put, but a gentle push could get it roll down to calcite.

Polymorph stability

Figure 12. Stability of polymorphs of calcium carbonate. The schematic illustrates the generic concept of polymorphs but is not accurate for aragonite vs. calcite. For one thing, the relative stabilities depend on temperature, pH etc.

Ever since Rutherford chemists have had a funny idea about what 'gentle' is and in this case a 'gentle push' means heating to a couple of hundred of degrees and/or sitting around for a few million years. So in the real world, under most conditions, aragonite shells are as stable as calcite shells. We will, of course return, to 'most conditions' and what the choice of polymorph means for organisms in a later post.

Rutherford was one of ours (a kiwi) but this post couldn't have been written without an Australian who was 25 years when he got his prize, he'd be a 121 now if he hadn't died.

In the next post we discuss the main processes that shift and transform carbon in the ocean: photosynthesis and respiration.

Written by Doug Mackie, Christina McGraw , and Keith Hunter . This post is number 13 in a series about ocean acidification. Other posts: Introduction , 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, Summary 1 of 2, Summary 2 of 2.

 

posts

booklet

0 0

Bookmark and Share Printable Version  |  Link to this page | Repost this Article Repost This

Comments

Comments 1 to 11:

  1. You can see that the spheres in the bottom boxes are packed more tightly than the spheres in the top boxes.

    If this is refering to the sample illustration (not the calcite and aragonite), I'm not sure that's true. If I'm not mistaken, the top row is face-centered cubic (FCC). If you rotate it, you can find layers with hexagonal packing. Those would go in a repeating cycle of 3 layers - the second row would be FCC if the third layer's atoms don't line up with either the first or second row. If they line up with the first row, it's hexagonal closest packed (HCC). I think they both have the same density - if the interatomic distances are the same, which I suppose might not be the case given particulars about bonding geometry (?) for an actual substance.

    If you space out the atoms in each layer in the first row then I think you would get BCC...

    ---

    Sorry I know this is beside the point but I just thought it was interesting.
    0 0
  2. CORRECTION
    ...the second row would be FCC if the third layer's atoms don't line up with either the first or second **layer**.
    0 0
  3. Thanks Patrick. It is important to distinguish between a lattice and a crystal.

    The balls in the top row of figures are not close packed and form a body centred cubic (bcc), this has a packing efficiency (for identical spheres) of 68%. For the bottom row of figures if we place the 3rd layer directly above the bottom layer we get face centred cubic (fcc), or if we place the third layer in the hollows we get hexagonal close packed (hcp). Fcc and hcp have the same packing efficiency for identical spheres of 74%.

    Thus, for the given box frame 3 layers of the top boxes would contain 16 + 9 + 16 = 41 spheres, while 3 layers of the bottom set (as fcp or hcp) would contain 14 + 14 + 14 = 42 spheres.
    0 0
  4. This is a great series, thanks, Doug. I'm learning lots.

    PS: If anyone figures out the significance of the last link in your post, can they claim bragging rights?
    0 0
  5. lattice vs crystal - yes, but if if all these spheres are identical then the fig 8 top will form (if the third square layer is aligned with the first) an FCC structure with all spheres at lattice points (the lattice cell top and bottom faces are at 45 degrees to the box; the rest of the faces stand 'vertical' (assuming a downward view); if the third layer added in the bottom of fig 8 is aligned with neither the first nor second but the fourth layer is aligned with the first, you get the same FCC structure, but rotated so that it is a cube standing on a corner. Both FCC and HCC have coordination number of 12 and have the same density (because HCC would just have the third layer added to the bottom of fig 8 be aligned with the first - it would be at the same height above the first layer; all the hexagonal layers in either FCC (which I think has hexagonal layers in four different directions, each being a diagonal running between opposite corners of the FCC cube) and in HCC have the same packing density within themselves and the same spacing between layers); the number of spheres per layer shown in the figure doesn't indicate the density because they don't fully fill the box.

    I think the coordination number (for spheres of equal size centered on lattice points) in BCC is 8, and none of the spheres in a layer touch each other (if we're looking at layers parallel to the faces of the cubes); they only contact spheres in the layers above and below.
    0 0
    Moderator Response: Patrick, please stay on topic. Future posts by you that are off-topic or irrelevant will be deleted. Thanks for your cooperation.
  6. Patrick, you are not adding anything. Please keep on topic. I will not have this thread derailed.
    0 0
  7. Sorry.
    0 0
  8. Andy

    Naming rights: William Lawrence Bragg 1890-1971

    http://en.wikipedia.org/wiki/William_Lawrence_Bragg.

    He and his father were pioneers in X-Ray Diffraction and X-Ray Crystallography, he was the youngest ever Nobel prize winner at 25

    What he might have thought of Billy Bragg and his music, dunno? Doug's reference to Billy is certainly cryptic.
    0 0
  9. Small correction: radiolaria are Protozoa, i.e. animals (in fact the smallest of all animals), unlike diatoms which are photosynthetic.
    0 0
  10. mea culpa on that one. Keith pointed that out that in the proofing rounds several weeks ago. I thought I had fixed it. Recapitulated etchings here.
    0 0

  11. second summary post

    0 0

You need to be logged in to post a comment. Login via the left margin or if you're new, register here.



The Consensus Project Website

TEXTBOOK

THE ESCALATOR

(free to republish)

THE DEBUNKING HANDBOOK

BOOK NOW AVAILABLE

The Scientific Guide to
Global Warming Skepticism

Smartphone Apps

iPhone
Android
Nokia

© Copyright 2014 John Cook
Home | Links | Translations | About Us | Contact Us