Birefringence Terminology

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ldflan
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Birefringence Terminology

Post by ldflan »

I am trying to figure out the proper terminology to describe the optical qualities of Calcium Oxalate (druse) biocrystals ("CaOx") that occur in many type of angiosperms, in my case rose tissue.

Many researchers describe biogenic CaOx crystals as being anisotropic and strongly birefringent, but this seems a problematic description to me. If you rotate a biogenic CaOx crystal under crossed polarizers, it displays no extinction orientations whatsoever. So it's not anisotropic as I understand the term.

Moreover, the brilliant "birefringence" CaOx biocrystals show is white under crossed polarizers using white light. With the addition of a full wave retarder plate, the CaOx biocrystals I am working with show the same interference color (apple green) again regardless of crystal orientation.

Does anyone know the proper terminology to describe such a state of affairs?

I am not really sure whether this is even properly called birefringence as it is completely independent of crystal orientation, and does not depend on the specific morphology of the CaOx biocrystal being under observation. These biocrystals are known to be chiral (even though non-biogenic CaOx crystals are not), but I find no reference to them being optically active.

Thanks for any help you can give me!

Leonard

Duke
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Re: Birefringence Terminology

Post by Duke »

I've had some experience in study of kidney stone.
I've done XRD, SEM -EDS -EBSD & optical microscopy study of one sample I've received, mainly from "scientific curiosity".
Since I'm not qualified in medicine (other than 1 eyar course of biochemistry in the Uni, my specialty is chemical analysis) to publish such researches, and not in the right mood for it anyway.
I'll share some results here.
Fragment of the kidney stone, SEM/BSE 50x.
Kidney_stone_BSE_50x.jpg
*Full resolution*
Nikon BD Plan 5x DIC
Kidney_stone_DIC_0nm.jpg
*Full resolution*
Nikon BD Plan 5x POL
Kidney_stone_PL.jpg
*Full resolution*
SEM/BSE 4000x.
Kidney_stone_BSE_4000x.jpg
*Full resolution*
SEM/EDS 4000x Oxygen Ka x-ray line map
Kidney_stone_Oxygen_Ka.jpg
SEM/EDS 4000x Carbon Ka x-ray line map
Kidney_stone_Carbon_Ka.jpg
You are free to make your judgement, if I had to describe the structure based on mineralogical classification as below.
The macrostructure shows concentric texture, similar to agate. The microstructure of the sample is cryptocrystalline. It consists of thin alternating layers of submicron thickness of sheet-like crystals of COD (calcium oxalate dihydrate) and COM (calcium oxalate monohydrate), occasionally there are inclusions of other salts (phosphates, urates). There is some sort of prevailed orientation on for crystals in the layers on one of the crystalline axis, like one direction is fixed (defined by position of concentric suface), while the other two axises remain somewhat free.
As crystals are very thin, there's no way to observe and study or describe their individual optical properties using classic approaches of polarizing microscopy.
I think what means by "researchers describe biogenic CaOx crystals as being anisotropic and strongly birefringent", there's no way it based on optical section data (as layers are concentric, and shape is round, so as result, any section would look like tree trunk cross-cut with mosaic rings of crystal aggregates that would only produce diffuse scattered polarized light), so it's either quote known optical crystallographic data on these compounds, either they was able so subtract individual layers and measure their properties (there's some cleavage going on between layers), I believe that is possible to chip such sheets in case of relatively large stone.
“Thoroughly conscious ignorance is the prelude to every real advance in science.” - JCM

Pau
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Re: Birefringence Terminology

Post by Pau »

Leonard,

I'm not able to solve your question because of lack of experience with Oxalate and not enough knowledge, but maybe could help to clarify few points

- Chirality demostrates in solution (often not easily without a precision polarimeter), not sure up to what point it could be related with birefringence.

- Most birefringent crystals are isotropic in some directions (axis) so they are not birefringent it those directions

- Interference colors are related with the thickness of the crystals, when they are thick you often have high interference order that are pale gray or pale yellow (see the Michael-Levy chart)

The dry external onion skin leaves have nice oxalate crystals into the cells, you could compare them.
Pau

ldflan
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Re: Birefringence Terminology

Post by ldflan »

Duke -

Thank you for the thoughtful reply and the images. Nucleation and crystallization processes for CaOx are probably very different in plants and animals, but it seems very clear that the biogenic CaOx crystals in plants incorporate macromolecules on some kind of net or sheath composed of protein and carbohydrate. My own guess is that starch is the main nucleation network for druse, and is likely that CaOx is in some sense layered on in crystals. Recent findings show it being added and removed in a metabolic cycle.

The druse crystals look very much like complete crystals, but your term cryptocrystalline might best describe them.

Given the apparent structure of plant CaOx crystals, I wonder if the term mesocrystalline is appropriate?

In any case, If I understand it, then, what we likely have is a whole mess of microcrystals that each is anisotropic, but they are all packed together so that individual interference colors are indistinguishable.



Leonard
Last edited by ldflan on Fri Feb 26, 2021 11:17 am, edited 1 time in total.

ldflan
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Re: Birefringence Terminology

Post by ldflan »

Thanks, Pau.

Optical activity can be demonstrated in solids as well as solutions. D and L rotary quartz, for example.

Here, maybe if the assembly of microcrystals that form a druse crystal are laid down by the responsible plastids in a helical pattern, we might have a similar polarity rotation effect? Reaching, I know...

The other thing is that the crystallization chamber presumably contains a fairly saturated solution of CaOx, perhaps in a very thin layer, which might cause rotation as would be seen in a solution? This doesn't explain why samples processed through paraffin behave the same, though.

Leonard

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Re: Birefringence Terminology

Post by Pau »

ldflan wrote:
Fri Feb 26, 2021 11:05 am
Optical activity can be demonstrated in solids as well as solutions. D and L rotary quartz, for example.
Sure, although I think that this refers to different causes: organic molecules chirality is caused by the spatial asymmetry of their molecular structure while in quartz this is just impossible and optical rotation is only due to the crystalline structure. I ignore if chiral molecules can induce optical rotation of their crystals
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Re: Birefringence Terminology

Post by Pau »

In this Javier's recent post you can see the oxalate crystals I was referring to, take a look at the linked full size image and you will see few one at extinction:
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ldflan
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Re: Birefringence Terminology

Post by ldflan »

Pau wrote:
Fri Feb 26, 2021 11:43 am
ldflan wrote:
Fri Feb 26, 2021 11:05 am
Optical activity can be demonstrated in solids as well as solutions. D and L rotary quartz, for example.
Sure, although I think that this refers to different causes: organic molecules chirality is caused by the spatial asymmetry of their molecular structure while in quartz this is just impossible and optical rotation is only due to the crystalline structure. I ignore if chiral molecules can induce optical rotation of their crystals
I think maybe it's clearer to talk about "optical activity" here, since "chirality" is used alone to described a structural relationships, not necessarily the quality of rotating light polarity. I think.

In any case, yes, the cause may be different between molecules in solution and crystals. But, since some crystals can induce optical rotation (however it happens) depending on the orientation (d or l) of the component molecules, then it seems at least potentially important. Also as I understand it, chemically-synthesized CaOx is not birefringent.... So that's a puzzle.

I think Duke's idea above, if I understand it correctly, is likely the answer, probably not optical activity per se. Need to look at some cryptocrystalline minerals in thin section to see if they behave the same as druse.

Leonard

ldflan
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Re: Birefringence Terminology

Post by ldflan »

Pau wrote:
Fri Feb 26, 2021 11:53 am
In this Javier's recent post you can see the oxalate crystals I was referring to, take a look at the linked full size image and you will see few one at extinction:
Some of the twinned crystals do show a clear extinction point. These are pretty simple forms compared to rosa. Hmmm.

Leonard

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Re: Birefringence Terminology

Post by Duke »

Sorry if my answer was a bit confusing, at first I was quickly browsing through the topic from my phone, and didn't read closely enough, I've read 'tissue' end 'biogenic', but missed the part 'rose', indicating that this topic is about COM crystals, observed in the thin sections of the plants. Animal or human tissue COM crystals are always polycrystaline. There're often definitely observed monocrystals in plant sections, but there are twinning crystals, polycrystaline particles are not uncommon as well.
COM.jpeg
This morphology differs in from plant to plant and, and even in the same plant from tissue to tissue.
Such star-shaped or nail-aggregate polycrystaline particles are formed from small unarranged crystals, and they produce diffused light with no evident extinction.
Birefringence basically means different refraction index for different directions in the crystal. All crystals, aside from cubic syngony, will be technically birefringent. Calcium oxalate monohydrate is of monoclinic syngony, that does mean it's optically double axis crystal, and by the looking molecule and coordinate number, there's no chance it optical properties would be close for different directions, or in other words it would have strong anisotropy. Really regardless of is it naturally occurring or synthetic. Here's link for the paper on the subject https://www.jstor.org/stable/24532601 .
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ldflan
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Re: Birefringence Terminology

Post by ldflan »

Duke -

"Animal or human tissue COM crystals are always polycrystaline. There're often definitely observed monocrystals in plant sections, but there are twinning crystals, polycrystaline particles are not uncommon as well."

I am not sure it makes any difference, but di- and tri-hydrated forms of calcium oxalate are common in Plantae as well. The exact composition in terms of water is not the main factor determining morphology, it seems. As you suggest below, crystal morphology is controlled basically at the cellular level, is very diverse, and in many cases seems highly evolved for multiple functions.

"This morphology differs in from plant to plant and, and even in the same plant from tissue to tissue."

Yes, just so, as does the relative distribution differ by plant and tissue types. These qualities can prove taxonomically useful.

"Such star-shaped or nail-aggregate polycrystaline particles are formed from small unarranged crystals, and they produce diffused light with no evident extinction."

Yes, usually called druse. But I would not call them "unarranged." In most cases these druse clusters or rosettes (middle picture above is a simple example) show clear higher order specific to genus, predictable numbers of lobes, etc.

In Rosa, the druse rosettes show no extinction point, which make sense given their polycrystalline composition as you say.

But I am finding that even seemingly individual triclinic CaOx crystals, as well as relatively simple-seeming bipyramidal prisms, likewise show no extinction. I suppose that they must be composed in a highly ordered fashion of individual microcrystals.

It follows that the microcrystals must also be arranged at nucleation with either random axes or (more likely) cellularly-dictated but varying axes. (Starch helices might be expected.)

"Calcium oxalate monohydrate is of monoclinic syngony, that does mean it's optically double axis crystal, and by the looking molecule and coordinate number, there's no chance it optical properties would be close for different directions, or in other words it would have strong anisotropy. Really regardless of is it naturally occurring or synthetic."

Thanks for that, and the link demonstrating the fact. I will see if I can find the reference to synthetic CaOx crystals not showing anisotropy. There was only one reference I can recall, and it seems logical that it would be wrong.

Your insights are much appreciated!

Leonard

ldflan
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Re: Birefringence Terminology

Post by ldflan »

DSC09400 RSZ.jpg
R. blanda leaflet, 400x DIC
2020-12-03-13.28.47 ZS DMap (2) 1024.jpg
R. blanda leaflet, 100x, Crossed polarizers and full wave retarder. Image stack of 11.

And this is interesting: figures 3-4 show developing rosette type druse crystals. The authors don't note it, but at very early stages the crystals show classic maltese cross interference, but this disappears at a point of later development.

https://www.researchgate.net/publicatio ... eae_Leaves


Leonard

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