Welcome on our blog page. Here you’ll find useful information on things we stumbled accross upon our research. Unfortunatly we need to restrict access to some content due to copyright regulations. If there is anything we can help you out with, feel free to contact us. The full content can be accessed by all members of the CRASY research group after log in!
Below, I posted a short video explaining how we observe rotation in the time domain. Please note that the video does not explain the quantum mechanical principles required to describe molecular rotation, but gives a pseudo-classical picture. This picture does not explain why molecular rotation is quantized or how we can relate rotational frequencies to molecular structure.
Here is a guide for CRASY data analysis, written for a UNIST lab course: PC_lab_course_CRASY_Schultz.pdf. You can find an installation guide for the data analysis software on page 6 and a guide for CRASY data analysis on the following pages. If you want to learn more about the CRASY experiment, navigate to the crasy.org landing page.
Required Software
You will require the following software:
(1) Python (I suggest to install the “Miniconda” package.)
(2) The crasyPlots program.
If you have trouble installing or running the software, watch the walk-through video below.
Data Analysis
The data is stored in compressed format (zip files). Here are a few data sets from 2020:
2-ns scan of carbon disulfide: 2020_CS2_Mar31_15.25_2ns
20-ns scan of pyridine: May25_17.31_20ns
100-ns scan of pyridine: 2020_pyridine_Mar26_16.00_100ns
500-ns scan of furan: 2020_furan_Jun02_10.45_500ns
Just follow the steps described in the guide. The pyridine (mass 79 u) and furan (mass 68 u) data also contains a small signal for CS2 (mass 76 u), which allows an easy calibration of the mass spectrum and also gives a nice frequency spectrum. If you have difficulties with the data analysis steps, you can watch the walk-through video below.
Our CRASY experiment measures rotational quantum waves of molecules. Usually we look at our data, but for the long traces we now measure this becomes a bit tedious and we really really have to zoom in to see anything. The example below is from a 17 nanosecond scan, but now we measure microsecond scans to get ever more precise data of our molecular structures.
How else could we explore our data?
Listen to it of course! So I slowed our data by a factor 50’000 to bring the Gigahertz frequencies into the audible range. Now you can hear our molecules rotate. The first example is our 300 nanosecond scan of the carbon disulfide rotational quantum-wave-packet. The molecule is linear and has a very simple harmonic spectrum.
So what do we actually hear? Like most things in the quantum world of atoms and molecules, the rotational motion is quantized and occurs only with discrete frequencies. We take snapshots of the molecular orientation at different points in time (in a mass spectrometer). Just like a rotating loudspeaker sounds louder when turned towards you, our signals are stronger when the molecules are oriented in a particular direction.
The hissing noise in the beginning is the signal from individual measurements. As we fill in more data points, the discrete molecular frequencies start to emerge. The spectrum is not quite harmonic because the molecules distort under the centripetal force of the rotation. This leads to the oscillating beating pattern at the end of the sound file.
To analyze the spectrum of frequencies, we can Fourier-transform the time-domain data and we get a spectrum as shown below. This data was published in PNAS.
Next, let’s listen to a 100 ns scan of 1,3-butadiene. This molecule is an asymmetric rotor and offers more complex harmonies. I’ll plot the corresponding frequency spectrum soon.
Finally the rather lengthy 1 microsecond scan of benzene. This molecule is a ‘symmetric rotor’ and has a much simpler spectrum than butadiene.
Below I plot some graphs from this 1 microsecond data-set. This scan was the longest time-domain measurement ever performed by us. The resolution is directly proportional to the scan length (Heisenberg’s time-energy uncertainty) and we obtained order-of-magnitude better resolution than any preceding Raman spectrum. The data is published in PCCP.
We actually observe our molecules in a mass spectrometer, so first we look at the mass spectrum to identify the molecules. Mass 78 is the mass of benzene, so in the second row we plot only this signal amplitude, but now as function of delay time. This second trace nicely illustrates the trick we use to get to large delays without too much effort: we skip most point and only measure data at a random subset of delays. This explain the grainy noise in the beginning of all the sound files: We don’t have enough information to piece together the waves from the few measured data points. The bottom graph shows the Fourier-transformed data from the middle graph. We can see the nice harmonic (evenly spaced) spectrum of benzene.
From the measured rotational frequencies, we determine the molecular shapes. But that story is better left for another post.
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The following are some resources that may help you with your scientific writing. Scientific writing can be a challenge even for native writers, so don’t despair. Practice makes perfect and you have to write to learn to write.
If you have to write a report, please use a template and submit your report with double line spacing for easier correction. I propose the template from JACS for MS Word or Latex.
To master structure and style, please refer to the relevant Style Guides. Here is a short 1-page cheat sheet to help you getting started: Writing_in_english_(1-page_for_koreans). Also look at the style guide of the American Institute of Physics for more extensive guidelines on the structure and style of scientific reports. You can find an excerpt from the AIP style guide at AIP_Style_4thed_extract or you can download the full guide from here. The ACS offers an exhaustive style guide at pubs.acs.org/styleguide.
Use dictionaries to find the right words (e.g.: www.merriam-webster.com (US-English), www.oxforddictionaries.com (British-English)). Use a spell checker to avoid unnecessary spelling mistakes.
If you are a non-native speaker, please make an extra effort to check your articles. Here is a very short primer about article placement in the English language:
E.g.: I teach in a University. (You didn’t know about it yet.) The University is new. (I talk about the same University, so you already know about it.) I like a University. (Now I talk about a different University that you don’t know about.) Universities are cool. (I make a general statement about all Universities.)
And finally, read English books or English newspapers to improve your English style and vocabulary. There are lots of exciting English texts out there and reading is the easiest way to learn!
Here is some specific feedback for the 2016 Lab course reports: report_feedback.
[1] SDBSWeb : http://sdbs.db.aist.go.jp (National Institute of Advanced Industrial Science and Technology, Aug. 9, 2016)
This is history! By fiddling around with the Klinger motion controller we brought over from the laboratory in Berlin, I figuered out that it is quite a challange to run and control it with our measurement computers. (more…)
Observing rotational coherences in time allows you to determine rotational constants of molecules with high accuracy. But what does high accuracy mean? Indeed, you can only be as accurate as the measurement you performed. If your measurement is sensitive to enviromental conditions, you have to also measure these conditions precisely. (more…)
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