Advanced

Studies of pyridine in water clusters with synchrotron radiation and 3D momentum spectrometry

Bolling, Benjamin LU (2017) FYSK02 20171
Department of Physics
Synchrotron Radiation Research
Abstract
By using the site-selectivity enabled by synchrotron radiation, we can choose the ionization site on a molecule. Core-ionization can result in that the molecule dissociates into charged (and uncharged) ions. With mass spectroscopy, the dissociated fragments’ mass-over-charge can be identified in a time-of-flight spectrum. Pyridine dissociation was studied for pyridine and for pyridine mixed with protonated water clusters (a cluster is a larger molecular compound consisting of multiple molecules ‘clustered together’).

Fragments originating from different dissociation channels cannot be distinguished if they have the same mass-over-charge ratio in a time-of-flight spectrum, and therefore, by using momentum spectroscopy, the dissociation... (More)
By using the site-selectivity enabled by synchrotron radiation, we can choose the ionization site on a molecule. Core-ionization can result in that the molecule dissociates into charged (and uncharged) ions. With mass spectroscopy, the dissociated fragments’ mass-over-charge can be identified in a time-of-flight spectrum. Pyridine dissociation was studied for pyridine and for pyridine mixed with protonated water clusters (a cluster is a larger molecular compound consisting of multiple molecules ‘clustered together’).

Fragments originating from different dissociation channels cannot be distinguished if they have the same mass-over-charge ratio in a time-of-flight spectrum, and therefore, by using momentum spectroscopy, the dissociation channels were studied qualitatively with a radius vs. time spectra in order to distinguish fragments from different dissociation channels.

To correlate the different fragments (ions) with each other, an ion-ion coincidence map was used, which can be created from a 3D momentum spectrometer experiment to find out if it is a 2-body or 3-body dissociation, or neither (i.e., no or higher dissociation order).

The mass and momentum spectroscopy experiments provided much data with complex structures, which requires some advance data treatment methods. I have created a GUI (Graphical User Interface) based on a command-line interface developed by the research group with which my bachelor project was conducted. The command-line interface, and hence, also the GUI, is a systematic method for treating data from a 3D momentum spectrometer experiment.

I also developed an interactive tree structure within the GUI which allows for an interactive way of creating and combining filters recursively. The filters can then be used combined or individually while plotting the data, so that only data of interest is allowed through into the plot.

Using the GUI to treat the data from a 3D momentum spectrometer-based experiment, we performed a case study on pyridine with protonated water clusters. Pyridine was added to protonated water clusters. We investigated the mass spectra and observed the site-selectivity enabled by synchrotron radiation ‘in action’ for the protonated water clusters.

We also observed pyridinium (protonated pyridine), which means that proton transfer occurs from the protonated water to pyridine, and that high water molecules stabilize clusters with high pyridine concentration (more than 2 pyridine molecules in a single cluster). Thus, pyridine concentration determines how pyridine will interact with water. For high pyridine concentration, water molecules are more likely to be situated in the centre between the pyridine molecules to stabilize the cluster.

Further analysis showed indications that pyridine molecules seem to be embedded within larger clusters, as we did not observe pyridine fragments bond with water molecules. Thus, if this is the case, water molecules can be seen as an obstacle hindering the photons from reaching pyridine. (Less)
Popular Abstract
Global warming has increased because of the industrialization, and the release of various chemical compounds into the atmosphere can result in them becoming involved in chemical processes of the atmosphere, e.g. cloud formations. In order to understand how they behave in the atmosphere, we must first study how it arranges itself in conditions similar to those in which cloud formation takes place. This is achieved by doing the necessary preparations in the laboratory, incl. adjusting temperature and pressure.

In this work, pyridine - which is a flat, ring-structured molecule - is studied in microscopic water droplets referred to as water-clusters. Clusters can consist of anywhere between one to tens of thousands of molecules bond... (More)
Global warming has increased because of the industrialization, and the release of various chemical compounds into the atmosphere can result in them becoming involved in chemical processes of the atmosphere, e.g. cloud formations. In order to understand how they behave in the atmosphere, we must first study how it arranges itself in conditions similar to those in which cloud formation takes place. This is achieved by doing the necessary preparations in the laboratory, incl. adjusting temperature and pressure.

In this work, pyridine - which is a flat, ring-structured molecule - is studied in microscopic water droplets referred to as water-clusters. Clusters can consist of anywhere between one to tens of thousands of molecules bond together by non-covalent bonds (which, for water clusters, are hydrogen bonds). By understanding the interaction between pyridine and water in clusters, we can begin evaluating how pyridine water clusters react with their surroundings, or interferes with or even initiates other reactions in the atmosphere.

To study how molecules are structurally arranged with other molecules is, however, not an easy task. Therefore, the group with which this bachelor thesis was done has developed a computational method to study the light-matter interaction with cluster-molecules, such as pyridine in water clusters. The main principle is that light created in laboratory is released onto the sample. The light carries enough energy to dissociate the clusters into smaller clusters, or to dissociate the molecules into fragments. By studying the fragments’ energy, the conditions before the dissociation can be recreated by appropriate data treatment. The data treatment has, in this work, been carried out with the software that the research group has developed.

My task was to develop a graphical user interface (GUI) to enable data treatment to be carried out on multiple data files at the same time. This makes the data treatment procedure easier to learn and faster, resulting in that users will have more time to spend on the data analysis. With the GUI, I analysed the data coming from experiments with pyridine and pyridine in water clusters in order to check if the GUI works properly, while, at the same time, also trying to find new ways of increasing its user friendliness and analysing the data.

The data analysis showed that water molecules tend to stabilize clusters with three or four pyridine molecules. It also suggested that for pyridine and water clusters, the water-bond pyridine molecules do not dissociate, as pyridine fragments were not observed bond to water molecules. The most probable reason behind this is that free pyridine is dissociated, while water-bond pyridine molecules are ‘protected’ by water molecules from the lightsource. (Less)
Please use this url to cite or link to this publication:
author
Bolling, Benjamin LU
supervisor
organization
course
FYSK02 20171
year
type
M2 - Bachelor Degree
subject
language
English
id
8913482
date added to LUP
2017-06-12 11:52:01
date last changed
2017-06-12 11:52:01
@misc{8913482,
  abstract     = {By using the site-selectivity enabled by synchrotron radiation, we can choose the ionization site on a molecule. Core-ionization can result in that the molecule dissociates into charged (and uncharged) ions. With mass spectroscopy, the dissociated fragments’ mass-over-charge can be identified in a time-of-flight spectrum. Pyridine dissociation was studied for pyridine and for pyridine mixed with protonated water clusters (a cluster is a larger molecular compound consisting of multiple molecules ‘clustered together’). 

Fragments originating from different dissociation channels cannot be distinguished if they have the same mass-over-charge ratio in a time-of-flight spectrum, and therefore, by using momentum spectroscopy, the dissociation channels were studied qualitatively with a radius vs. time spectra in order to distinguish fragments from different dissociation channels.

To correlate the different fragments (ions) with each other, an ion-ion coincidence map was used, which can be created from a 3D momentum spectrometer experiment to find out if it is a 2-body or 3-body dissociation, or neither (i.e., no or higher dissociation order). 

The mass and momentum spectroscopy experiments provided much data with complex structures, which requires some advance data treatment methods. I have created a GUI (Graphical User Interface) based on a command-line interface developed by the research group with which my bachelor project was conducted. The command-line interface, and hence, also the GUI, is a systematic method for treating data from a 3D momentum spectrometer experiment. 

I also developed an interactive tree structure within the GUI which allows for an interactive way of creating and combining filters recursively. The filters can then be used combined or individually while plotting the data, so that only data of interest is allowed through into the plot.

Using the GUI to treat the data from a 3D momentum spectrometer-based experiment, we performed a case study on pyridine with protonated water clusters. Pyridine was added to protonated water clusters. We investigated the mass spectra and observed the site-selectivity enabled by synchrotron radiation ‘in action’ for the protonated water clusters.

We also observed pyridinium (protonated pyridine), which means that proton transfer occurs from the protonated water to pyridine, and that high water molecules stabilize clusters with high pyridine concentration (more than 2 pyridine molecules in a single cluster). Thus, pyridine concentration determines how pyridine will interact with water. For high pyridine concentration, water molecules are more likely to be situated in the centre between the pyridine molecules to stabilize the cluster. 

Further analysis showed indications that pyridine molecules seem to be embedded within larger clusters, as we did not observe pyridine fragments bond with water molecules. Thus, if this is the case, water molecules can be seen as an obstacle hindering the photons from reaching pyridine.},
  author       = {Bolling, Benjamin},
  language     = {eng},
  note         = {Student Paper},
  title        = {Studies of pyridine in water clusters with synchrotron radiation and 3D momentum spectrometry},
  year         = {2017},
}