All 8 entries tagged Jenna
August 11, 2007
After last week’s work on optimising the parameters for the simulations, previous spectral simulations were redone to improve their quality.
At the end of last week my supervisor had asked me to prepare a talk for the next group meeting, which was to be held on the Friday morning. The majority of the week was thus spent creating the associated powerpoint slides, which I found to be a very useful exercise. The first thing I learnt was that you cannot include everything you’ve done into a talk; you have to pick out the sections that worked well and which link together in order to form a story. For this reason the talk omitted the simulations work, focusing only on relevant previous experimental work, my research and what they told about the possible structures of the samples.
I did a run through of the talk with a colleague, which was great for identifying flaws. After this the talk itself seemed to go fairly well :)
On Friday afternoon and the following Monday and Tuesday I started work on my poster.
Back in Devon now and enjoying the sunshine, but still with my poster to do. I’ll let you know when I finish!
Part of one day was spent looking again at the experimental spectral peaks we found and trying to come to some conclusions about whether it is what we expected.
Throughout the week we did absolutely loads of simulations work – some of which took quite a few goes to get:
a) atomic coordinates from molecule modelling programs and
b) input files written so that spectral peaks look as you would expect from experiment (there are several parameters that one can set)!
We tried a 2D simulation and did some 6-spin ones using coordinates from atoms that would be on adjacent molecules in a crystal.
When I started the project I was under the impression that simulations of our samples would have been completed by this stage. However I now realise that these things have to be done systematically and that you have to ensure that the basics are correct before moving onto the more complex.
We met Erwin Hahn! Who honourarily (?) graduated on Monday with the other physicists :) Go here to see him and the rest of us!
Work-wise I did more simulations using Spin Evolution, but this time using different pulse sequences. Amy did the equivalent using Simpson so we can compare.
Experimentally we had planned to run quite a few samples on the 600 MHz spectrometer but we had difficulty with various things so we didn’t get as much done as expected (research is seemingly a very slow process at times!).
On Thursday I did a 4-spin simulation using Spin Evolution. I chose atoms in the penicillin molecule to check that interatomic distances were represented on the spectum as expected. I also looked at the effect of changing the spinning speed and number of propagations.
Friday we ran a 2D experiment on sample B04. We got a lot of noise so left it running over the weekend.
July 22, 2007
This week brought more complex simulations in the form of Post C7 3-spin (3 atom) ones (after working out the problems of last week’s 2-spin ones). With more spins the Simpson simulation becomes a lot slower. I only managed one arrangement of the 3 spins (at different spinning speeds and number of pulse sequences) in one day, although this process had to be done accurately for suitable comparison with the equivalent setup using the Spin Evolution simulation.
Throughout the week I tried three more arrangements of three atoms, modelling them on the compound alanine and looking at both carbon and hydrogen spectral simulations. The amplitudes of each arragement’s spectra after different numbers of pulse sequences produced what is known as a build up curve. They should look fairly similar in shape…some did but some of the later ones didn’t…This is probably a problem with estimating the spectral peak amplitudes and I will try different methods at some point. If I do get good curves, it it a good indication of the simulations working correctly.
Amy put B05 in the spectrometer so now we have all six of the CP spectra!
July 09, 2007
To start the week I continued with reading but more concerning the physics behind simulation parameters than how the simulations work.
I tried two simulation programs and tried to get matching spectra on both – usually unsuccesfully! This is a minor setback and I’m sure that as I accumulate a greater understanding of the programs, my use of them will improve. I asked some of the others for help and have a few things to try for next time.
Using a previously found paper, which listed the chemical shifts of a very similar compound to those I am studying, I compared shifts in compounds. I found the expected similarities – indicating that the two samples have common molecular groups. I also found a large anomaly for one of the samples, suggesting that the sample isn’t of the structure we first assumed it to be.
July 02, 2007
This week mainly involved reading about NMR theory (in particular about expected locations of spectral peaks). The aim of this reading was to help me to identify which spectral peaks derived from which bonds in the molecule. To enable this to be done in a logical manner I have started to number the different bonds of each molecule, noting which bonds appear in more than one sample (which should be able to be identified from the spectra also). One spectra was collected and I observed a double quantum spectra, which provides information on distances between atoms.
On Thursday Amy went away for a week so I am left to run some simulations. During Thursday and Friday I read up on the background material and theory required for me to properly understand the workings of the simulations and how all of the parameters correspond to a real situation. I know I started a little on this reading last week, but after three years of not having to read much I find that it’s quite a slow process! It certainly is a change from labs when you’re more or less given all of the information you will need.
Thursday also meant Craft Day at WSAF during which I made a hat for the monkey that is perched over my desk:
I’ll take some proper science-related photos at some point.
June 23, 2007
Had a good second week (or second three days due to the Final Fling)! Ran another two guanosine spectra and felt a lot more confident with the use of the 300MHz spectrometer. One of our samples gave an abnormal spectrum initially, but after weighing it and noting that there was more of it than the previous samples the problem was proposed to be due to too much signal being given out. After decreasing the spectrometer gain and rerunning it, a better spectrum was obtained.
I practised using the Simpson simulation program for a good few hours by making notes on all of the parameters and then running and adapting example simulations to test whether I really knew what everything meant.
June 13, 2007
The aim of my project is to use NMR to determine the structure of six synthetic guanosine-based compounds. My supervisor and the PhD student I’ll be working with gave me an outline of the tasks I will be doing..
So far I have helped to pack one of the samples into a Bruker 4mm rotor which is then placed into a probe which fits into a 300MHz spectrometer.
Using the spectrometer requires a lot of setup, for example the probe has to be tuned and the system and settings calibrated (by comparing the spectra of an alanine sample to one made previously). After going through it all, Amy and I set the sample to run overnight, using the NMR pulse sequence known as Cross Polarisation. I hadn’t come across this sequence before so it’s likely that there’ll be a fair bit of reading involved before I can be confident that I understand the procedures!
We got results! The spectra was compared to the known spectra of guanosine so the extra peaks were identified as being those corresponding to the additional parts of the molecule. I learnt a bit about Double Quantum Coherence: a phenomenon which will be of great use in determining which atoms are adjacent to which in a molecule and their separation distances.
The second guanosine based sample was set to run overnight. I had a bigger part to play in the spectrometer set-up this time, which was quite a test of my 24 hour memory!
Learnt more about Double Quantum Coherence and the pulse sequence that is used to exploit it. We set histidine (another amino acid) spinning in the spectrometer and saw results which matched known information.
Also managed to prepare a plan! A lot of it presumes we can get spectrometer time though.
Drew lots of molecules using various software…was really fun! And they look so cool! Scoured databases to find molecules similar to the ones we are working on. When one was found we downloaded the structure and tried to see if the software used would allow us to add molecules in it to make our specimens. From there it will be possible to run computer simulations on it in order to obtain spectra without actually doing one experimentally.
Observed and assisted with the use of the 600MHz spectrometer and then read the instruction manual to try and remember key points about its use. I find it really hard to remember things I’m told so making notes and rereading manuals is a must for me! Started learning how to use the simulation program too.