The overall aim of the following experiment is to explore the electronic structure of isolated gas phase molecules and clusters with molecular beams and synchrotron radiation. This is achieved by generating a supersonic expansion of a molecule seeded in a carrier gas in a molecular beam apparatus. As a second step, the resulting molecular beam is integrated with synchrotron radiation and mass spectrometry is performed.
Next, a photo ionization efficiency curve is generated in order to decipher and quantify the electronic properties of the studied system. Results are obtained that can be compared to theoretical calculations, and subsequently the electronic structure of molecules can be determined. The main advantage of this technique over others is that synchrotron radiation allows a very selective yet universal ionization method to probe molecules and clusters in the gas phase.
We hit upon this idea a few years ago since we wanted to get DNA molecules into the gas phase and measure the ionization energies. This method provides unprecedented access to electronic structures of molecules and clusters, particularly when one does photo ionization of DNA basis. To begin, remove the back flange and disassemble the three eighths of an inch stainless steel tube from the apparatus.
Make sure it is clean and the 100 micron orifice is clear by looking through it at a light source for cleaning. Fill the tube with approximately one milliliter of ethanol and scrub the inside using cotton tips. Then dry the tube with compress air.
To avoid blocking the orifice. Place a small aluminum foil ball or glass wall in front of the orifice. Then use a small clean spatula to place about 250 milligrams of sample in the front part of the nozzle.
Close to the foil ball or glass wool. Use a cotton tip to push the sample into the tube to ensure it is in the front 25 millimeters of the tube. This front part will comprise the heated zone.
Reattach the nozzle to the apparatus carefully to avoid moving the sample powder inside. Then attach the bird cage adapter heater block and thermocouple before closing the vacuum chamber. Measure the distance from the flange surface to the tip of the nozzle to be 22.5 inches.
This will allow 0.5 inches between the nozzle and the skimmer. When the vacuum chamber is closed, test the heater cartridge and thermocouple connections to make sure they're well connected to the feed through connectors. Make sure the carrier gas inlet valve is closed.
Close the venting valve. Slowly begin pumping the chamber using the roughing pumps. When the pressure in the chamber is less than one tour, start the turbomolecular pumps.
When the pressure in the chamber is less than 10 to the minus six tour, apply the voltages to the iron optics of the time of flight mass spectrometer. Next, open the shutter to allow the photon beam in the chamber. Open the carrier gas inlet valve and set the backing pressure regulator to four 60.
This is a vacuum regulator measuring in a negative scale from zero to minus 7 62. Hence, when set to four 60, it will regulate the pressure in the line to 300 tor. Under these conditions.
The pressure in the source and mass spectrometer chambers should be approximately one times 10 to the minus four tor and two times 10 to the minus six tor respectively. To acquire the mass spectrum first, start the fast card software on the computer and let it run in the background. Open the LabVIEW data acquisition program general interface.
fi using the a LS control tab In the LabVIEW software. Set the photon energy to the desired wavelength on the scaler tab. Set the number of time units to be been together.
Also set the range or number of bins and sweeps, which is the number of mass spectra added on top of each other to form the final mass spectrum. Then click accept so that these values will be stored and used. Next, click get data to begin the data acquisition.
When the acquisition is over, the mass spectrum will appear on the screen. Save the mass spectrum by clicking the save button. Using the a LS scan tab in the lab view software, it is possible to acquire data while tuning one of the beamline motors.
In this case, select the motor mono T three energy to tune over different photon energies. The undulating inside the synchrotron will move automatically to match the desired wavelength. Enter the start and stop energies in electron vaults as well as the step size.
Do not enter the number of sweeps as this will updated automatically by the value already entered. Click read current from K 4 86 to read the current measured by the photo diode. Next, click start to begin the scan.
The user is then prompted to choose a file name where the data will be stored at the end of the run. The first column in the data file contains the bin number and needs to be converted to mass units as described in the written protocol. Accompanying this video, save the data file with the first column converted to mass to plus A PIE curve.
A second LabVIEW program called ALS Energy Scan VI can be used, which is designed to analyze and plot the scan data. When starting the A ALS Energy Scan VI program, the user is prompted to select the file containing the data. This is the previously saved file and contains masses in the first column and ion counts at different photon energies in the next columns.
Note that the first and second row in the file indicate the photon energy and photo current of the data in that column respectively. In the top panel there is a 2D plot At the data. Moving the red horizontal marker selects a mass spectrum at a specific photon energy to be displayed in the lower panel.
The next step is to integrate the ion counts of a specific mass at each photon energy while subtracting the background signal. In the lower panel, the two vertical red markers should be set around the mass peak to be integrated. The two blue markers should be set around a nearby region with no data, which can serve as a background value.
The software will present the integrated data minus the background in the panel on the right. To present a true PIE curve, one must correct the ion counts to the varying photon flux at every step. This is done automatically by the software.
To skip this correction, click to turn off the current correction button to the right of the top panel. See the written protocol. If performing this step manually, click save spectrum in the lower right corner to save the corrected PIE curve.
Shown here is a typical mass spectrum of the supersonic expansion of one three dimethyl uracil vapors and the PIE curves of the three main features as extracted from A VUV scan between 8.0 electron volts and 10.0 electron volts. One three dimethyl is shown at mass overcharge 140 protonated one three dimethyl uracil at mass overcharge 141 and the one three dimethyl uracil dimer at mass overcharge 280. The gray shadow is the standard deviation from three consecutive scans Once mastered and performed properly.
These procedures take about one to eight hours if the synchrotron is behaving for you on that particular day. Following on, we use electronic structure calculations to visualize the photo animation dynamics of the molecules that we just put into the gas phase. After watching this video, I hope you have a good understanding of how one can use synchrotron radiation and molecular beams to probe the electronic structure of molecules and clusters in the gas phase.
