Tag Archives: ft-ir

An alternative analysis to FT-IR to study deuterium exchange

Via figshare:

Deuterium Content of Deuterium Depleted Water: 1st Trial. Anthony Salvagno, Scott Jasechko. figshare.
Retrieved 21:24, Jul 20, 2012 (GMT)

A few days ago I made a new friend named Scott Jasechko. We met to discuss the possibility of creating a TED branded forum to UNM. We got to talking about our research and it turned out that our research interests are very much aligned and he studies water isotope amounts with relation to natural water around the planet. He’s about to publish his findings and once that goes through I’ll link to that.

It turned out that his lab has a device that can very accurately measure small concentrations of deuterium and oxygen-18 in water samples. I told him about my DDW experiments and how deuterium exchange may affect my experiments, but that I can’t quantitatively measure it’s affect or the process in general. So we got to talking and he wanted to help me out.

The data linked above is the results of the mini-collaboration that I predict will turn into more. Scott used his Picarro cavity ring down spectroscope, which means very little to me right now, to analyze the water samples I gave him. The water was used in these two experiments (each word is a separate link). And was then stored in our desiccator (with drierite to reduce moisture exchange) until yesterday (July 19, 2012).

Surprisingly, the data shows very little change from what Sigma claims (less than 1 part per million D to H) to yesterday, showing very little exchange. There are two things to consider here: (1) the machine wasn’t calibrated for such low levels of D, which skew the readings (since they actually give us negative ratios), and (2) volume may play a part in exchange.

I don’t understand the mechanism very well but I suspect that surface interactions play the largest role in deuterium exchange. Once deuterium is introduced into the sample, then I would guess diffusion takes over, but this is probably slower in nature than evaporation/other mechanisms that are involved on the surface. Basically this is a thermodynamics problem that I would need to spend 3 months thinking about to compare with experimental analysis (since that is how long the Thermo class is, 1 semester).

The follow up to this experiment should be better organized. Obviously we’ll need to redo this experiment. Scott and I are also performing another experiment where Scott has left the lid off the samples I gave him so he can see if there is a new value the spectroscope provides. From here we may want to do some longer time analysis and some other studies that we’ll have to plan. I’ll start a new thread for that, in the mean-time I hope he’ll introduce himself in the comments of this post.

Some other notes:

  • I geeked out when I realized the power of this sort of collaboration. If I hadn’t been affiliated with TEDxABQ and thus this new idea of TEDxUNM (not officially licensed), I would have never met Scott. These are the sorts of collaborations that I hope can be introduced because of the Open Research IGERT proposal.
  • I mega-geeked out when I realized I can do a project planning thread with someone here at the university in another lab that can also participate in the project! Open science at the core all the way.
  • I super-mega-geeked out when I realized that I implemented a crucial aspect of ONS. As I wrote this post I wondered what experiments I had used the water for. Then I realized that it’s all documented and that I can show everyone what those experiments are. It’s not enough that I have it recorded by date, but also that you all saw those experiments in real-time and their use in future experiments has been realized. That’s a major win for ONS.

FT-IR scans from Alex

Alex uploaded the data sets to FigShare per my request. Here is her notebook entry regarding the subject, here is the data set on FigShare:

FTIR spectra DDW, DI, D20 raw data 2-2-2012. alexandria haddad. Figshare.
Retrieved 21:12, February 04, 2012

And here is the jpeg of the scans:

FTIR DDW, DI, D20 2-2-2012. alexandria haddad. Figshare.
Retrieved 20:37, February 04, 2012


FT-IR Training and Experiments

Since mid December, I’ve been urging Alex to set up FT-IR training with Stephen Myers and being the go-getter that she is, she has set up a few training sessions. You can see her notes from that here.

I spoke with her at the beginning of the week to try and plan the future of these experiments. We have a couple of experiments that we would like to try out which wouldn’t be all that time consuming, and I’m leaving her in charge of all of it (she’s big time now!).

Yesterday was just step 1. We went to examine 4 samples. We wanted to analyze (3mL of each): DDW, D2O, DI, and DDW + 1uL of D2O (which was roughly equivalent to the standard mean ocean water).

I haven’t looked at the data in any real detail yet, but by eye the DDW and DI looked very similar, and there was almost no difference between that and DDW+1ul D2O (but I thought it was slightly discernable). Because of this we tried 3mL of DDW with 70ul of D2O added (which is roughly 2% by volume D2O), and this was obviously different in profile (but barely). As per usual, the pure D2O sample was very different.

Hopefully Alex will get the data on FigShare today (I could do it myself easily, but I would like her to experience the awesomeness).

Mini rant in 3… 2… 1… I gotta get her to be on top of her notebook a little better. I keep telling her to notebook frequently about everything, and that she just needs to get into the habit of doing it. She agrees but then doesn’t notebook. Grrrr… I was hoping to do this post yesterday but alas Alex didn’t post until after my bedtime so here it is now. Once she enters the lab I’ll be all over her like a tiger on a gazelle licking lilacs in the wilted meadow of frozen tundra. With regards to posting to figshare, of course. Rant over.

Anyways the plan for the project is as follows:

  1. Understand the spectroscopy results as they correlate to the physical properties of the water molecules (H2O and D2O and HOD). This will be major literature searching on Alex’s part with aid by myself.
  2. FT-IR analysis of D2O/H2O mixtures. Koch and I think there could be some really interesting results/studies in the mixture range around the amount that is naturally occurring. So I want to do a broad study of different D2O amounts in DDW from 0 up to 100% so we can understand how the peaks shift from H2O bonds to DOH bonds to D2O bonds.
  3. FT-IR analysis of DDW time dependence. D-exchange is a real thing. It happens all the time and rapidly, but how long does it take for DDW to reach the levels of deuteration of naturally occuring water? This is something I’d like to know. And something we hope to find out.

So with all that said, I’ll be linking to Alex’s notebook with regards to these experiments in the future and add some minor notes myself here. In the meantime I will just twiddle my thumbs until those data sets get uploaded to figshare…

FTIR data on FigShare

I’ve uploaded the data to FigShare so that makes me cool!

The next phase of this experiment would be to setup some sort of equipment training for Alex and myself and to get room access. This way we could schedule ourselves to use the machine and not have to burden Stephen for his time.

Then I think I want to organize the experiment so that we take data perhaps once a week with a sample of DDW and a sample of D2O that are left out for several weeks. Then we can compare the samples over time to watch as the deuterium content adjusts to become similar to normal water.

I suppose I should also analyze a sample of tap water and compare that to the DI and DDW samples. Tap water would have more contaminants in it than either of those two samples and hopefully those would show up in the FTIR results. I do have to say that I’m surprised that the 3-month old DDW sample had the exact same profile as the DI water sample. That made me feel more certain that DDW is probably made from DI water first.

Anyways here is the open data:

FTIR study of differences between D2O, DDW, and DI water

Stephen Myers from the NSMS department graciously helped Alex and I out with the next phase of the FTIR experiment. He was able to get a hold of a couple of quartz cuvettes from Spectrocell. On top of that I had ordered one from Amazon.

The first part of the experiment required us to “blank” the samples so we put a Spectrocell cuvette into the FTIR machine and took a reading. For fun we then did the same thing with the Amazon cuvette and then compared the two curves.

Amazon cuvette overlayed on Spectrocell cuvette

While the two graphs look identical we noticed that the sample from Amazon had a weird periodic feature in the graph. Stephen said in other experiments he attributes this pattern to some kind of film, whether or not that is what is going on here is debatable. Regardless I decided to use the Spectrocells for the remaining experiments.

Before we began I thoroughly rinsed each cuvette with DI water and dried with nitrogen. This did not remove all the liquid water, but most of it. I attempted to air dry the remainder. This is important information for later. I used 3mL of each water type (DI, DDW, D2O, and a D2O/DDW mix) for analysis in the FTIR spectrometer. For the D2O sample and for the D2O/DDW mixture I used the second Spectrocell cuvette (which was not blanked) so that the high D2O content wouldn’t contaminate the DDW samples. I used the same cuvette for the DI, and two DDW samples (I’ll explain this in a second).

We took spec readings in this order: (first) DI water, D2O, DDW, D2O/DDW mix, (last) old DDW. I chose this really random order because we weren’t sure we would be able to get any interesting data so I wanted to see DI water vs D2O first. When that gave us obvious results we tried the first DDW sample (taken from a bottle that was opened 11/30/11). Then I wanted to compare all these results with a close to 50/50 mix of D2O and DDW (I didn’t pipette exactly 1.5mL of each nor can I report on how close to that number it is, I was merely trying to determine if there would be a difference between DI, D2O, and a mix of those two with a larger percentage of D2O). Finally we measured a sample of DDW that was taken from a bottle that was opened 9/6/11.

Here are those results.

Comparison of DI, D2O, 2 samples of DDW, and a D2O/DDW mix sample

Wowie zowie! The data display isn’t ideal (done in excel quickly) but you can see a difference between each of the samples. There is one exception that is actually remarkable. The sample of DDW from 9/6/11 matches really well with the sample of DI water. The newer sample of DDW (11/30/11) is more distinguishable from these two than it appears above. And the mixed sample and that of pure D2O are very distinguishable both from each other and from the other samples!

If you notice that just above 1.5um (wavelength) there are two tiny humps in the data. I have blown that up below.

Zoomed in portion of the graph above from 1.5um to 2um. Note the sample of D2O is not in this graph.

Here there isn’t much different between the DDW samples and DI sample, but there is a difference between those and the DDW/D2O mixed sample. I didn’t include the D2O sample because the transmission in this range was much larger than these samples.

Now for the best part: Stephen was totally shocked that we were able to notice these differences. He wasn’t expecting much and frankly neither was I (I had been expecting to not notice anything because most papers I had read focused on the MIR range for FTIR). I was super stoked about these results, and happily, Alex was as excited about these results as I was/am!

I uploaded the graphs to Google Docs and all the data can be accessed here. I’ll upload the data to FigShare and link to that later.

Update: I forgot to mention that we are using a Nicolet 6700 FTIR spectrometer from Thermo.

Update (12/25/11): Fixed link to data. Thanks Koch

FT-IR Preplanning Thread

I want to get some ft-ir studies off the ground. First experiment would be to just see if FT-IR spectroscopy reveals differences better natural water, DDW, and D2O. Comment for ideas…

1st Try at FT-IR Spectroscopy

I’ll explain the idea of these new experiments in more detail later, but I had this data from today and wanted to get the information in my notebook. There is an Ft-IR spectrometer at CHTM (actually 2) and we were granted permission to use it by Dr. Sanjay Krishna courtesy of Stephen Myers and my buddy John Montoya.

The purpose is to figure out a way to accurately measure the amounts of D2O in H2O or H2O in D2O. Today was just about seeing whether we could conduct these experiments with the equipment we have (plastic macro cuvettes). The answer is no, but the experiments are still worthwhile.

We ran 3 experiments: (1) nothing in the sample chamber but air, (2) an empty cuvette in the beam path, and (3) a cuvette with pure H2O (deuterium depleted water). The spectrometer has the capability of subtracting (dividing) out the background, sort of like blanking a solution when dealing with a nanodrop. So we used the empty chamber and the empty cuvette experiments as background readings to test the H2O. Here is the data:

The following graphs are % Transmittance (y) vs Wavenumber (x).

 This is the empty chamber sample.

This is the blank cuvette experiment.

This is the same experiment, except that in this graph the air background reading has been divided out.

This is the DDW sample with the cuvette reading divided out.

The data isn’t reliable because you can see in the last data set that there are transmittance numbers above 100%. Right now I can’t explain the how’s and why’s because I don’t know all that much about the equipment or the process, but in this range we were getting rather low transmittance anyway so I wouldn’t expect to get accurate results.