Name: analyzing the photo-oxidation of 2-propanol at indoor air level concentrations using field asymmetric ion mobility spectrometry
Uploaded: 2018-06-14T12:30:00.000+00:00
Duration: 8 min 23 s
Description: Watch this Scientific Journal Video about Analyzing the Photo-oxidation of 2-propanol at Indoor Air Level Concentrations Using Field Asymmetric Ion Mobility Spectrometry at JoVE.com

The authors are grateful for the financial support from the ERC, under grant number 259619 PHOTO EM and grant number 620298 PHOTO AIR (Proof of Concept).

1. Makeup of VOC permeation tubes, and determination of its diffusion rate
<ol>
	<li>Makeup of 2-propanol permeation tubes 
	Note: To avoid contamination, wear gloves during this process. 
	Caution: 2-propanol is flammable and an irritant. Carry out this procedure away from any open flames. Wear gloves when handling 2-propanol. Consult MSDS of 2-propanol for further information.
	<ol>
		<li>Measure out and cut a 14 cm length of PTFE tubing.</li>
		<li>Seal and crimp one end of the tube by inserting a 2 cm length of PTFE rod into the end of the PTFE tubing, and then covering with a 2 cm metallic crimp</li>
		<li>Place the PTFE tubing, rod and crimp into the crimping tool, and then place this into a vice. Turn the vice, tightening as much as possible to seal the PTFE tube with the crimp.</li>
		<li>Pipette into the open-end of the PTFE tube an amount of 2-propanol, such that the PTFE tubing is around 1/3 full (approximately 3 - 4 mL).</li>
		<li>Repeat 1.1.2 - 1.1.3 to seal and crimp the open end of the permeation tube; the permeation source is then complete.</li>
	</ol>
	</li>
	<li>Determination of diffusion rate of VOC in the permeation tube
	<ol>
		<li>Weigh the permeation tube, using a calibrated balance, to at least 4 decimal places, noting both the weight and time.</li>
		<li>From a compressed air supply (ideally medical grade compressed air or equivalent), connect tubing (PTFE tubing, diameter 1/8 in, internal diameter 0.063 in) to an in line pressure regulator. From the regulator, connect, using the same diameter PTFE tubing, to one of the ports of a GL45 4 port connector, screwed to a 250 mL GL45 glass bottle. Block off two of the ports, and connect a length of PTFE tubing to the final port and guide this outlet to a fume hood.</li>
		<li>Position the permeation tube into the GL45 glass bottle, and ensure there is a constant steam of compressed air at a flow rate of 2.5 L min-1. Alternatively, position the tube in the dilution chamber of the system as illustrated in Figure 1, and described in section 2.1.</li>
		<li>At specific time intervals (e.g. daily) repeat the weight measurement (1.2.1) and place back into the system (1.2.2). If the decrease in weight is undetectable using the balance, increase the time interval between weighing the permeation tube (e.g. weekly, bi-weekly). Note that this calibration process, depending on the diffusion rate, could take a time period of a few months.</li>
		<li>Graph the diffusion rate with time in minutes on the x axis and the mass loss in nanograms (ng) on the y axis. Draw a straight line between points; using the straight-line equation (y = mx + c), determine the slope (m) of the line. This is the permeation rate in ng min-1.</li>
	</ol>
	</li>
</ol>
2. Photo-oxidation Reaction
<ol>
	<li>Set-up of equipment for use in the blank and photo-oxidation reaction (Figure 1)
	<ol>
		<li>Connect tubing (PTFE tubing, diameter 1/8 in, internal diameter 0.063 in) from a compressed air supply to an in line pressure regulator. From this, connect a moisture trap, to ensure a consistent low level of moisture enters the setup. From here, connect the PTFE tubing to a scrubber to further clean the compressed air.</li>
		<li>From the moisture trap or scrubber, connect, using the same diameter PTFE tubing, to a glass bottle, which will be the dilution chamber that will be used to hold the permeation tubes (GL45, 500 mL). To ensure a gas tight connection, use a screw cap HPLC, GL45 4 port connector, complete with silicone seals: block off two of the ports, and connect the tubing from the scrubber or moister trap to one of the other two ports, ensuring the connection is tight. Screw HPLC GL 45 screw cap onto the 500 mL glass bottle.</li>
		<li>Connect PTFE tubing to the final port or the HPCL GL45 screw cap, and then connect this to a second HPLC GL45 4 port connector. As with 2.1.2, block off two of the ports. Screw this HPLC FG45 screw cap on to a glass bottle (GL 45, 250 mL), which will be used as the reaction chamber.</li>
		<li>Connect PTFE tubing to the final port on the HPLC GL45 screw cap, and from this, connect the tubing to the FAIMS gas analyzer, using Swagelok 1/8 gas tight fittings. Ensure the external port of the gas analyzer is guided to a fume hood to ensure no contamination enters the laboratory work area.</li>
		<li>Position the reaction chamber so that the center of the chamber is 15 cm from a UV lamp (e.g. a UV lamp, consisting of 2 x 8 W tube lamps, with a peak photon emission wavelength of 356 nm). 
		Caution: UV light is dangerous to eyes; ensure the lamp and reactor is surrounded by a metallic shield to avoid exposure to the light.</li>
	</ol>
	</li>
	<li>Photo-oxidation of 2-propanol
	<ol>
		<li>Place two 2-propanol permeation tubes assembled previously (1.1) in the dilution chamber of the setup described above. Place the catalyst (e.g., a titanium dioxide based felt, dimensions 55 mm x 25 mm x 1 mm) in the reaction chamber, and ensure the catalyst is facing the UV lamp. Turn on the flow of compressed air, and adjust so the flow is 2.5 L min-1, and the pressure is 1 bar.</li>
		<li>Turn on the FAIMS instrument, and set up the instrument so that the ion current of the 2-propanol can be seen. Using software configured for the FAIMS device, increase the RF waveform, so that distinct ion peaks can be seen on the spectrum being produced by the FAIMS instrument.</li>
		<li>Using the software configured for the FAIMS device, monitor and record the ion current that is emanating from the distinct ion peaks seen on the spectrum produced by the FAIMS for a period of time, with the catalyst in the dark. The peaks will be 2-propanol, and water. At a set point (e.g. after leaving overnight), turn on the UV lamp, and monitor the FAIMS spectrum for the 2-propanol and water ion currents, plus additional signals from intermediate VOCs such as acetone. Using system software, increase or decrease the RF waveform to determine new signals emanating from the intermediate ions. 
		Caution: Ensure both the UV light and reactor are covered with a metallic shield before the lamp is illuminated, and that the shield is present throughout the entire UV light reaction.</li>
		<li>At a set point (e.g. after 4 hours), turn off the UV lamp, and continue to monitor the FAIMS spectrum for 2-propanol and additional peaks.</li>
	</ol>
	</li>
</ol>

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	<li>Wang, S. B., Ang, H. M., Tade, M. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Volatile+organic+compounds+in+indoor+environment+and+photocatalytic+oxidation:+State+of+the+art.">Volatile organic compounds in indoor environment and photocatalytic oxidation: State of the art.</a> Environ. Int. 33 (5), 694-705 (2007).</li><li>Shah, J. J., Singh, H. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distribution+of+Volatile+Organic-Chemicals+in+Outdoor+and+Indoor+Air+-+a+National+Vocs+Data-Base.">Distribution of Volatile Organic-Chemicals in Outdoor and Indoor Air - a National Vocs Data-Base.</a> Environ. Sci. Technol. 22 (12), 1381-1388 (1988).</li><li>Jones, A. 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H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ion+mobility-mass+spectrometry.">Ion mobility-mass spectrometry.</a> J. Mass Spectrom. 43 (1), 1-22 (2008).</li><li>Ireland, C. P., Ducati, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigating+the+photo-oxidation+of+model+indoor+air+pollutants+using+field+asymmetric+ion+mobility+spectrometry.">Investigating the photo-oxidation of model indoor air pollutants using field asymmetric ion mobility spectrometry.</a> J. Photochem. Photobiol., A. 312, 1-7 (2015).</li><li>Vildozo, D., Ferronato, C., Sleiman, M., Chovelon, J. 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The authors Lauren Brown and Russell Paris are employees of Owlstone Nanotechnology, the company that manufactures the FAIMS analysis instrument that is used in this article.

The protocol describes an effective way of determining the effectiveness of the titanium oxide based catalyst, by determining its behavior in degrading a model VOC, 2-propanol, under UV illumination. Using FAIMS, the amount of 2-propanol can be monitored continuously throughout the reaction, in addition to any other VOC products that could be produced in the reaction, at concentrations comparable to indoor air. This continuous nature differs significantly from gas chromatography, traditionally used to monitor photocatalytic indoor air purification, which uses a batch process. An expensive, sensitive GC/MS system is generally required to determine the concentration of VOCs at such low concentrations, and detailed analysis of the photo-oxidation products generally requires further processing of the photo-oxidation products, such as adsorbing products onto activated carbon, and then desorbing them into the mass spectrometer. Whilst mass spectrometry is able to detect all products, a limitation of FAIMS is that only products with a high proton affinity can be detected. FAIMS is excellent at determining low concentration VOCs, but can be saturated at higher concentrations, which limits the system to indoor air level concentration applications. The advantages of FAIMS makes the system described here an effective, simple tool that can provide insights into photocatalytic reactions that gas chromatography is limited in achieving.
With the FAIMS system described here, medical grade air is used as the flow gas. With the FAIMS system being so sensitive, a high quality grade of air is critical in allowing the photo-oxidation to be analyzed. This ensures that any products detected are from the photo-oxidation process. Similarly, it is critical to ensure there is no leakage into the system, as laboratory air generally contains VOCs at concentrations the FAIMS is capable of detecting. The consumables listed for the setup of the system provide a reliable system, and continuous monitoring over a period of days has indicated no detectable VOCs when no catalyst or permeation tube is present.
Whilst the system is simple, it is also very flexible - alternative VOCs can be tested in this way, by simply making a permeation tub containing the alternative VOC, such as ethanol, acetone, or toluene, and following the protocol. Photocatalytic reactions are often affected by humidity. The system developed here operates under low humidity; however testing can be carried out at higher humidities buy introducing a humidifier into the system. Depending on the VOC used, it can result in the sensitivity of the FAIMS being reduced, but effective testing can be carried out.16
The continuous nature of FAIMS highlights an advantage over gas chromatography, which is traditionally used to determine the photocatalyst effectiveness in purifying air.16,17 Gas chromatography uses a batch process to collect and analyze air samples; FAIMS, with its continuous nature, allows a more detailed look at the kinetics of the photocatalytic reaction, which can be challenging to interpret with the batch gas chromatography technique. The simplicity of FAIMS is another advantage. In order to carry out the complex analysis of multiple VOCs FAIMS is capable of, the gas chromatograph will need to be linked to a mass spectrometer, which can be expensive and require additional processing. Additionally, to carry out long term reactions with a gas chromatograph, an expensive automated system would be required, or labor intensive sampling; this is not the case with FAIMS.
The continuous nature of FAIMS offers significant advantages over gas chromatography that can be utilized to gain a greater understanding of the photocatalysis process at these ppb concentrations. Moreover, the simple setup illustrated here is flexible, allowing alternative photocatalysts and VOCs to be tested under comparable conditions, further improving the understanding of the photocatalytic process.

The quality of indoor air has come to the forefront recently. Perhaps surprisingly, indoor air contains a greater number of volatile organic carbons (VOCs), and in higher concentrations than outdoor air.1 With people spending over 80% of their time indoors, in places such as residential homes, workplaces, and transport including cars, trains, and aircraft, air quality can be a real issue. Many of the VOCs common in indoor air are mutagenic or carcinogenic,2,3 and so the removal of these is a key priority, especially as the phenomena of &#39;sick building syndrome&#39; can lead to ill health and lost production through time off work.1 Air purification devices can include a photocatalyst, where a semiconductor, invariably titanium dioxide (TiO2), activated with UV light, degrades the VOC through a photo-oxidation process. Photocatalysis is a growing area of research, with applications in water splitting for hydrogen production and pollutant degradation4,5,6,7; air purification is a particularly active area due to the commercial viability of this application8. However, detecting VOCs at concentrations that are present in indoor air (typically ppb) is challenging. With the kinetics of the photocatalytic reaction following Langmuir Hinshelwood kinetics9, the effectiveness of the photocatalyst at degrading VOCs at high concentrations is not representative of its effectiveness at low concentrations. Here we describe a versatile system and protocol for determining the effectiveness of photocatalysts at degrading VOCs at such low concentrations using field asymmetric ion mobility spectroscopy (FAIMS), illustrating this with a TiO2 based photocatalyst, and the model VOC 2-propanol.
Ionizing a gas flow, FAIMS separates and identifies chemical ions based on their mobility under a varying electric field at atmospheric pressure10,11,12. Molecules with a high proton affinity, such as VOCs are well suited to be separated and detected by FAIMS, with parts per billion (ppb) resolution, and at ppb concentrations13. Capable of continuously monitoring multiple VOCs simultaneously, it is an ideal analysis to use in photocatalytic air purification testing, as in addition to monitoring the VOC used as pollutant. FAIMS can also detect intermediates or other VOC products with a high proton affinity from the photocatalytic reaction, a key requirement in proving that the photocatalyst is effective, as if the degradation is incomplete, some of the VOCs produced may be as toxic or more toxic than the VOC being degraded.
FAIMS has only recently been used for the first time in photocatalytic air purification applications14, and although not suggesting FAIMS is superior to gas chromatography, it clearly offers a versatile alternative, which has the potential to be a potent tool in studying air purification. Here we illustrate this technique with a protocol involving the photo-oxidation of 2-propanol with a titanium dioxide based photocatalyst. To generate 2-propanol at the indoor air level concentrations permeation tubes are used15. Consisting of a PTFE tube containing the liquid VOC, that is sealed and crimped at both ends, under a constant flow, the VOC contained within the sealed PTFE permeation tube diffuses out at a constant rate, at concentrations comparable to indoor air. This flow is then passed into a reaction chamber containing the felt, and then into the FAIMS analyzer, where the identity and quantification of the VOC can be determined. FAIMS allows the concentration of 2-propanol to be determined, and via a library of spectra of know VOCs, the identity of additional VOCs produced during the photo reaction such as acetone determined through comparison of their spectra with the library. A key advantage of this technique is its flexibility: by simply changing the permeation tube or catalyst, alternative VOCs and catalysts can be tested.

<table><tbody><tr><td>PTFE Tubing</td><td>Sigma-Aldrich</td><td>58699 SUPELCO&amp;nbsp;</td><td>L x OD x ID 50 ft x 1/8 in x 0063 in</td></tr><tr><td>In-line pressure regulator</td><td>Sigma-Aldrich</td><td>23882 SUPELCO</td><td>High purity version (outlet pressure 0-100 psi, 1/8 in stainless steel fittings</td></tr><tr><td>Moisture trap</td><td>Sigma-Aldrich</td><td>N9301193</td><td>70 ml 1/8 fittings</td></tr><tr><td>Screw Cap HPLC, GL 45</td><td>VWR</td><td>554-3002</td><td>4 ports complete with silicone seals</td></tr><tr><td>Duran GL 45 Glass Bottle</td><td>Scientific Laboratory Supplies</td><td>BOT5206</td><td>250 ml&amp;nbsp;</td></tr><tr><td>Duran GL 45 Glass Bottle</td><td>Scientific Laboratory Supplies</td><td>BOT5208</td><td>500 ml</td></tr><tr><td>Permeation tube making kit</td><td>Owlstone Nanotechnology</td><td></td><td></td></tr><tr><td>2-propanol</td><td>Fisher Scientific</td><td>10477070</td><td>&amp;nbsp;Isopropanol, extra pure, SLR</td></tr><tr><td>Quartzel PCO Felt</td><td>Saint Gobain</td><td></td><td></td></tr><tr><td>UVIlite&amp;nbsp; Lamp</td><td>UVItec Limited</td><td>LI-208BL</td><td></td></tr><tr><td>Swage Fittings</td><td>Swagelok</td><td>SS-202-1 / SS-200-SET</td><td></td></tr><tr><td>Lonestar Portable Analyzer</td><td>Owlstone Nanotechnology</td><td></td><td></td></tr></tbody></table>

analyzing the photo-oxidation of 2-propanol at indoor air level concentrations using field asymmetric ion mobility spectrometry

We demonstrate a versatile protocol to be used for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) volatile organic carbons (VOCs), illustrating this with a titanium dioxide based catalyst, and the VOC 2-propanol. The protocol takes advantage of field asymmetric ion mobility spectroscopy (FAIMS), an analysis tool that is capable of continuously identifying and monitoring the concentration of VOCs such as 2-propanol and acetone at the ppb level. The continuous nature of FAIMS allows detailed kinetic analysis, and long-term reactions, offering a significant advantage over gas chromatography, a batch process traditionally used in air purification characterization. The use of FAIMS in photocatalytic air purification has only recently been used for the first time, and with the protocol illustrated here, the flexibility in allowing alternative VOCs and photocatalysts to be tested using comparable protocols offers a unique system to elucidate photocatalytic air purification reactions at low concentrations.

The FAIMS gas analyzer continuously produces spectra of ion current vs. compensation voltage during the course of the photo oxidation reaction described in 2.2, utilizing two 2-propanol permeation tubes in the dilution chamber, and a titanium dioxide based felt photocatalyst in the reaction chamber. Spectra typically produced by the FAIMS analyzer when the felt is in the dark, and when the felt is illuminated are illustrated in Figure 2a. To obtain the spectra with the FAIMS instrument, the RF waveform on the instrument is set to 64% of the maximum. At this RF waveform value, hydronium ions (water clusters), acetone monomers, and 2-propanol monomers which can be formed from the FAIMS instrument ionization process reach the detector in the FAIMS at distinct compensation voltages (cv), and so are separated on the spectra. Flowing individual gasses exclusively through the FAIMS system can be used to determine the spectra and compensation values for each gas16. On the spectrum, the peak at a compensation voltage of -2.15 V is the hydronium ion, a water cluster ion formed when moisture in the air is ionized. The peak at a cv of -0.14 V is that of 2-propanol14. The ion current is directly proportional to that of the 2-propanol concentration, and so using the diffusion rate (1.2), the concentration of 2-propanol entering the FAIMS can be determined. Similarly with acetone, occurring at a cv of -1.44 V. Figure 2b shows the ion current measured at the specific peaks identified as 2-propanol and acetone in the spectra with the RF waveform at 64% of maximum, as a function of time throughout the photo-oxidation protocol described in section 2.2. As subtle changes in flow and humidity can have an effect of shifting the ion current peak cv value positively or negatively, the peak height at a CV value of &#177; 0.2 V is used.
The amount of 2-propanol entering the FAIMS analyzer, with the reaction chamber in the dark increases over time. As 2-propanol enters the dilution chamber, 2-propanol is adsorbed onto the surface of the catalyst, which accounts for the initial low amount of 2-propanol entering the FAIMS. As time continues a higher ion current is recorded, indicating that a higher amount of 2-propanol enters the FAIMS. This suggests that the surface of the felt is being covered with 2-propanol, hence adsorption onto the catalyst is decreasing.
When the reactor chamber is illuminated, there is an immediate increase in 2-propanol entering the FAIMS. This implies that an amount of 2-propanol desorbs from the surface of the felt, and enters the FAIMS analyzer. Concurrently, there is an increase in ion current from the peak at cv -1.44 V, which has previously been identified as acetone, indicating the felt under illumination has photo-oxidized 2-propanol to acetone. As time continues, the amount of 2-propanol decreases to a level significantly below the level at the initial point of illumination, and acetone continues to be detected, with both ion currents consistent over a period of around 3 hours. This implies that 2-propanol is consistently being photo-oxidized either to acetone, or to carbon dioxide and water. 2-propanol adsorbs onto the surface, is photo-oxidized, and the products desorb and enter the FAIMS, where acetone is recorded. After the light is turned off, the 2-propanol ion current increases, whilst the acetone ion current decreases implying the photo-oxidation has ceased.
The results are representative of the concentration of 2-propanol and acetone, continuously monitored at ppb concentrations. By comparing the steady state 2-propanol current under illumination with that of 2-propanol current entering the FAIMS before illumination, the effectiveness of the catalyst can be seen, with a greater decrease in 2-propanol entering the FAIMS indicative of a superior photocatalyst. The monitoring of additional VOCs also allows a better assessment of the effectiveness of the photocatalyst. In air purification applications, ideally the VOC should be degraded to carbon dioxide and water. Additional compounds detected demonstrate an ineffective catalyst or poor air purification strategy (flow rates, light intensity, humidity levels). FAIMS can monitor the photo-reaction, and so demonstrate the effectiveness of catalyst and air purification setup.
<img alt="Figure 1" src="/files/ftp_upload/54209/54209fig1.jpg" /> 
Figure 1. The Reactor Setup. Diagram illustrating the photocatalysis setup developed for use with the FAIMS gas analyzer (see 2.1). <a href="https://www.jove.com/files/ftp_upload/54209/54209fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/54209/54209fig2.jpg" /> 
Figure 2. Typical Results. (a) Typical spectra produced by the FAIMS when the RF waveform is 64% of maximum when the reaction containing the felt is in the dark (grey line) and when it is illuminated (green line). (b) Graph showing the ion current at peaks from the compensation voltage vs ion current spectra produced during the 2-propanol photo-oxidation reaction when the RF waveform is at 64% of maximum; 2-propanol (red line) and acetone (blue line) shown, with the illuminated reaction highlighted. <a href="https://www.jove.com/files/ftp_upload/54209/54209fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Analyzing the Photo-oxidation of 2-propanol at Indoor Air Level Concentrations Using Field Asymmetric Ion Mobility Spectrometry at JoVE.com

Analyzing the Photo-oxidation of 2-propanol at Indoor Air Level Concentrations Using Field Asymmetric Ion Mobility Spectrometry

A protocol for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) model volatile organic carbons such as 2-propanol is described.

We demonstrate a versatile protocol to be used for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) volatile ...

analyzing-photo-oxidation-2-propanol-at-indoor-air-level

Nanyang Technological University

Research

JoVE Journal

Chemistry

8.5K Views.  University of Cambridge. A protocol for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) model volatile organic carbons such as 2-propanol is described.

Video: Analyzing the Photo-oxidation of 2-propanol at Indoor Air Level Concentrations Using Field Asymmetric Ion Mobility Spectrometry

Monitoring the Reductive and Oxidative Half-Reactions of a Flavin-Dependent Monooxygenase using Stopped-Flow Spectrophotometry

Aspergillus fumigatus siderophore A (SidA) is an FAD-containing monooxygenase that catalyzes the hydroxylation of ornithine in the biosynthesis of hydroxamate siderophores that are essential for virulence (e.g. ferricrocin or N',N",N'''-triacetylfusarinine C)1. The reaction catalyzed by SidA can be divided into reductive and oxidative half-reactions (Scheme 1). In the reductive half-reaction, the oxidized FAD bound to Af SidA, is reduced by NADPH2,3. In the oxidative half-reaction, the reduced cofactor reacts with molecular oxygen to form a C4a-hydroperoxyflavin intermediate, which transfers an oxygen atom to ornithine. Here, we describe a procedure to measure the rates and detect the different spectral forms of SidA using a stopped-flow instrument installed in an anaerobic glove box. In the stopped-flow instrument, small volumes of reactants are rapidly mixed, and after the flow is stopped by the stop syringe (Figure 1), the spectral changes of the solution placed in the observation cell are recorded over time. In the first part of the experiment, we show how we can use the stopped-flow instrument in single mode, where the anaerobic reduction of the flavin in Af SidA by NADPH is directly measured. We then use double mixing settings where Af SidA is first anaerobically reduced by NADPH for a designated period of time in an aging loop, and then reacted with molecular oxygen in the observation cell (Figure 1). In order to perform this experiment, anaerobic buffers are necessary because when only the reductive half-reaction is monitored, any oxygen in the solutions will react with the reduced flavin cofactor and form a C4a-hydroperoxyflavin intermediate that will ultimately decay back into the oxidized flavin. This would not allow the user to accurately measure rates of reduction since there would be complete turnover of the enzyme. When the oxidative half-reaction is being studied the enzyme must be reduced in the absence of oxygen so that just the steps between reduction and oxidation are observed. One of the buffers used in this experiment is oxygen saturated so that we can study the oxidative half-reaction at higher concentrations of oxygen. These are often the procedures carried out when studying either the reductive or oxidative half-reactions with flavin-containing monooxygenases. The time scale of the pre-steady-state experiments performed with the stopped-flow is milliseconds to seconds, which allow the determination of intrinsic rate constants and the detection and identification of intermediates in the reaction4. The procedures described here can be applied to other flavin-dependent monooxygenases.5,6

We describe the use of a stopped-flow instrument to investigate both the reductive and oxidative half-reactions of Aspergillus fumigatus siderophore A (SidA), a flavin-dependent monooxygenase. We then show the spectra corresponding to the species in the reaction of SidA and we calculate the rate constants for their formation.

Aspergillus fumigatus siderophore A (SidA) is an FAD-containing monooxygenase that catalyzes the hydroxylation of ornithine in the biosynthesis of ...

Bioengineering

Production and Measurement of Organic Particulate Matter in a Flow Tube Reactor

Organic particulate matter (PM) is increasingly recognized as important to the Earth's climate system as well as public health in urban regions, and the production of synthetic PM for laboratory studies have become a widespread necessity. Herein, experimental protocols demonstrate approaches to produce aerosolized organic PM by &#945;-pinene ozonolysis in a flow tube reactor. Methods are described for measuring the size distributions and morphology of the aerosol particles. The video demonstrates basic operations of the flow tube reactor and related instrumentation. The first part of the video shows the procedure for preparing gas-phase reactants, ozonolysis, and production of organic PM. The second part of the video shows the procedures for determining the properties of the produced particle population. The particle number-diameter distributions show different stages of particle growth, namely condensation, coagulation, or a combination of both, depending on reaction conditions. The particle morphology is characterized by an aerosol particle mass analyzer (APM) and a scanning electron microscope (SEM). The results confirm the existence of non-spherical particles that have grown from coagulation for specific reaction conditions. The experimental results also indicate that the flow tube reactor can be used to study the physical and chemical properties of organic PM for relatively high concentrations and short time frames.

This paper describes the operation procedure for the flow tube reactor and related data collection. It shows the protocols for setting the experiments, recording data and generating the number-diameter distribution as well as the particle mass information, which gives useful information about chemical and physical properties of the organic aerosols.

Organic particulate matter (PM) is increasingly recognized as important to the Earth's climate system as well as public health in urban regions, and the ...

Environment

Production and Measurement of Organic Particulate Matter in the Harvard Environmental Chamber

The production and the evolution of atmospheric organic particulate matter (PM) are insufficiently understood for accurate simulations of atmospheric chemistry and climate. The complex production mechanisms and reaction pathways make this a challenging research topic. To address these issues, an environmental chamber, providing enough residence time and close-to-ambient concentrations of precursors for secondary organic materials, is needed. The Harvard Environmental Chamber (HEC) was built to serve this need, simulating the production of gas and particle phase species from volatile organic compounds (VOCs). The HEC has a volume of 4.7 m3 and a mean residence time of 3.4 h under typical operating conditions. It is operated as a completely mixed flow reactor (CMFR), providing the possibility of indefinite steady-state operation across days for sample collection and data analysis. The operation procedures are described in detail in this article. Several types of instrumentation are used to characterize the produced gas and particles. A High-Resolution Time-of-Fight Aerosol Mass Spectrometer (HR-ToF-AMS) is used to characterize particles. A Proton-Transfer-Reaction Mass Spectrometer (PTR-MS) is used for gaseous analysis. Example results are presented to show the use of the environmental chamber in a wide variety of applications related to the physicochemical properties and reaction mechanisms of organic atmospheric particulate matter.

This paper describes operation procedures for the Harvard Environmental Chamber (HEC) and related instrumentation for measuring gaseous and particle species. The environmental chamber is used to produce and study secondary organic species produced from the organic precursors, especially related to atmospheric organic particulate matter.

The production and the evolution of atmospheric organic particulate matter (PM) are insufficiently understood for accurate simulations of atmospheric ...

Original Experimental Approach for Assessing Transport Fuel Stability

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several technological changes to fulfill environmental and economic requirements. These developments have resulted in increasingly severe operating conditions whose suitability for conventional and alternative fuels needs to be addressed. For example, fatty acid methyl esters (FAMEs) introduced as biodiesel are more prone to oxidation and may lead to deposit formation. Although several methods exist to evaluate fuel stability (induction period, peroxides, acids, and insolubles), no technique allows one to monitor the real-time oxidation mechanism and to measure the formation of oxidation intermediates that may lead to deposit formation. In this article, we developed an advanced oxidation procedure (AOP) based on two existing reactors. This procedure allows the simulation of different oxidation conditions and the monitoring of the oxidation progress by the means of macroscopic parameters, such as total acid number (TAN) and advanced analytical methods like gas chromatography coupled to mass spectrometry (GC-MS) and Fourier Transform Infrared - Attenuated Total Reflection (FTIR-ATR). We successfully applied AOP to gain an in-depth understanding of the oxidation kinetics of a model molecule (methyl oleate) and commercial diesel and biodiesel fuels. These developments represent a key strategy for fuel quality monitoring during logistics and on-board utilization.

Oxidation stability of transport fuels has become a concern for future fuel development. This work presents an original methodology developed by IFP Energies Nouvelles for assessing fuel stability using two different reactors. This methodology was successfully applied to gain an in-depth understanding of the oxidation kinetics and pathways of model molecules and commercial fuels.

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several ...

Detection of 3-Nitrotyrosine in Atmospheric Environments via a High-performance Liquid Chromatography-electrochemical Detector System

3-nitrotyrosine (3-NT) is generated from the tyrosine residue in atmospheric bio-aerosol proteins via a reaction with ozone (O3) and nitrogen dioxide (NO2). Stable 3-NT is a specific marker for oxidative damage and is reported to have a promotive effect to elicit allergies. In the present study, we report the development of a highly sensitive assay to quantify 3-NT in air sampler filters to collect &#60; 2.5 &#181;m of particulate matter (PM2.5) from urban environmental air, including bio-aerosol. In this method, a 6 mm-diameter round hole was cut from the filters of air samplers and mixed with a nonspecific protease cocktail in order to hydrolyze proteins. Protein samples digested to the amino acid level were tested for 3-NT using a high-performance liquid chromatography-electrochemical detector (HPLC-ECD). The maximum 3-NT content was detected in a prefilter for PM of sizes from 4.5 to 7.3 &#956;m, with a detection limit of 1.13 pg/m3.

Detection of 3-Nitrotyrosine in Atmospheric Environments via a High-performance Liquid Chromatography-electrochemical Detector System

We present a method to detect 3-nitrotyrosine chemical modifications of atmospheric proteins with 6 mm-diameter rounds cut from air sampler prefilters using a high-performance liquid chromatography-electrochemical detector (HPLC-ECD).

3-nitrotyrosine (3-NT) is generated from the tyrosine residue in atmospheric bio-aerosol proteins via a reaction with ozone (O3) and nitrogen dioxide ...

Real-time Breath Analysis by Using Secondary Nanoelectrospray Ionization Coupled to High Resolution Mass Spectrometry

Exhaled volatile organic compounds (VOCs) have aroused considerable interest, since they can serve as biomarkers for disease diagnosis and environmental exposure in a non-invasive manner. In this work, we present a protocol to characterize the exhaled VOCs in real time by using secondary nanoelectrospray ionization coupled to high resolution mass spectrometry (Sec-nanoESI-HRMS). The homemade Sec-nanoESI source was readily set up based on a commercial nanoESI source. Hundreds of peaks were observed in the background-subtracted mass spectra of exhaled breath, and the mass accuracy values are -4.0-13.5 ppm and -20.3-1.3 ppm in the positive and negative ion detection modes, respectively. The peaks were assigned with accurate elemental composition according to the accurate mass and isotopic pattern. Less than 30 s is used for one exhalation measurement, and it takes approximately 7 min for six replicated measurements.

A protocol for characterizing chemical composition of exhaled breath in real time by using secondary nanoelectrospray ionization coupled to high resolution mass spectrometry is demonstrated.

Exhaled volatile organic compounds (VOCs) have aroused considerable interest, since they can serve as biomarkers for disease diagnosis and environmental ...

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This flexible tool offers a detailed observation of chemical gas-phase kinetics in reacting flows under well-controlled conditions. The vast range of operating conditions available in a laminar flow reactor enables access to extraordinary combustion applications that are typically not achievable by flame experiments. These include rich conditions at high temperatures relevant for gasification processes, the peroxy chemistry governing the low temperature oxidation regime or investigations of complex technical fuels. The presented setup allows measurements of quantitative speciation data for reaction model validation of combustion, gasification and pyrolysis processes, while enabling a systematic general understanding of the reaction chemistry. Validation of kinetic reaction models is generally performed by investigating combustion processes of pure compounds. The flow reactor has been enhanced to be suitable for technical fuels (e.g. multi-component mixtures like Jet A-1) to allow for phenomenological analysis of occurring combustion intermediates like soot precursors or pollutants. The controlled and comparable boundary conditions provided by the experimental design allow for predictions of pollutant formation tendencies. Cold reactants are fed premixed into the reactor that are highly diluted (in around 99 vol% in Ar) in order to suppress self-sustaining combustion reactions. The laminar flowing reactant mixture passes through a known temperature field, while the gas composition is determined at the reactors exhaust as a function of the oven temperature. The flow reactor is operated at atmospheric pressures with temperatures up to 1,800 K. The measurements themselves are performed by decreasing the temperature monotonically at a rate of -200 K/h. With the sensitive MBMS technique, detailed speciation data is acquired and quantified for almost all chemical species in the reactive process, including radical species.

An investigation of the oxidative combustion chemistry of novel biofuels, fuel components, or jet fuels by comparison of quantitative speciation data is presented. The data can be used for kinetic model validation and enables fuel assessment strategies.This manuscript describes the atmospheric high-temperature flow reactor and demonstrates its capabilities.

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This ...

Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization

We present a pump-probe method for preparing vibrational coherences in polyatomic radical cations and probing their ultrafast dynamics. By shifting the wavelength of the strong-field ionizing pump pulse from the commonly used 800 nm into the near-infrared (1200-1600 nm), the contribution of adiabatic electron tunneling to the ionization process increases relative to multiphoton absorption. Adiabatic ionization results in predominant population of the ground electronic state of the ion upon electron removal, which effectively prepares a coherent vibrational state (&#34;wave packet&#34;) amenable to subsequent excitation. In our experiments, the coherent vibrational dynamics are probed with a weak-field 800 nm pulse and the time-dependent yields of dissociation products measured in a time-of-flight mass spectrometer. We present the measurements on the molecule dimethyl methylphosphonate (DMMP) to illustrate how using 1500 nm pulses for excitation enhances the amplitude of coherent oscillations in ion yields by a factor of 10 as compared to 800 nm pulses. This protocol may be implemented in existing pump-probe setups through the incorporation of an optical parametric amplifier (OPA) for wavelength conversion.

We present a protocol for probing ultrafast vibrational coherences in polyatomic radical cations that result in molecular dissociation.

We present a pump-probe method for preparing vibrational coherences in polyatomic radical cations and probing their ultrafast dynamics. By shifting the ...

Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area of proteins. This technique relies on the reaction of amino acid side chains with hydroxyl radicals freely diffusing in solution. FPOP generates these radicals in situ by laser photolysis of hydrogen peroxide, creating a burst of hydroxyl radicals that is depleted on the order of a microsecond. When these hydroxyl radicals react with a solvent-accessible amino acid side chain, the reaction products exhibit a mass shift that can be measured and quantified by mass spectrometry. Since the rate of reaction of an amino acid depends in part on the average solvent accessible surface of that amino acid, measured changes in the amount of oxidation of a given region of a protein can be directly correlated to changes in the solvent accessibility of that region between different conformations (e.g., ligand-bound versus ligand-free, monomer vs. aggregate, etc.) FPOP has been applied in a number of problems in biology, including protein-protein interactions, protein conformational changes, and protein-ligand binding. As the available concentration of hydroxyl radicals varies based on many experimental conditions in the FPOP experiment, it is important to monitor the effective radical dose to which the protein analyte is exposed. This monitoring is efficiently achieved by incorporating an inline dosimeter to measure the signal from the FPOP reaction, with laser fluence adjusted in real-time to achieve the desired amount of oxidation. With this compensation, changes in protein topography reflecting conformational changes, ligand-binding surfaces, and/or protein-protein interaction interfaces can be determined in heterogeneous samples using relatively low sample amounts.

Fast photochemical oxidation of proteins is an emerging technique for the structural characterization of proteins. Different solvent additives and ligands have varied hydroxyl radical scavenging properties. To compare the protein structure in different conditions, real-time compensation of hydroxyl radicals generated in the reaction is required to normalize reaction conditions.

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area ...

Biochemistry

Detection of Nitric Oxide and Superoxide Radical Anion by Electron Paramagnetic Resonance Spectroscopy from Cells using Spin Traps

Reactive nitrogen/oxygen species (ROS/RNS) at low concentrations play an important role in regulating cell function, signaling, and immune response but in unregulated concentrations are detrimental to cell viability1, 2. While living systems have evolved with endogenous and dietary antioxidant defense mechanisms to regulate ROS generation, ROS are produced continuously as natural by-products of normal metabolism of oxygen and can cause oxidative damage to biomolecules resulting in loss of protein function, DNA cleavage, or lipid peroxidation3, and ultimately to oxidative stress leading to cell injury or death4. 
Superoxide radical anion (O2&bull;-) is the major precursor of some of the most highly oxidizing species known to exist in biological systems such as peroxynitrite and hydroxyl radical. The generation of O2&bull;- signals the first sign of oxidative burst, and therefore, its detection and/or sequestration in biological systems is important. In this demonstration, O2&bull;- was generated from polymorphonuclear neutrophils (PMNs). Through chemotactic stimulation with phorbol-12-myristate-13-acetate (PMA), PMN generates O2&bull;- via activation of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase5. 
Nitric oxide (NO) synthase which comes in three isoforms, as inducible-, neuronal- and endothelial-NOS, or iNOS, nNOS or eNOS, respectively, catalyzes the conversion of L- arginine to L-citrulline, using NADPH to produce NO6. Here, we generated NO from endothelial cells. Under oxidative stress conditions, eNOS for example can switch from producing NO to O2&bull;- in a process called uncoupling, which is believed to be caused by oxidation of heme7 or the co-factor, tetrahydrobiopterin (BH4)8.
There are only few reliable methods for the detection of free radicals in biological systems but are limited by specificity and sensitivity. Spin trapping is commonly used for the identification of free radicals and involves the addition reaction of a radical to a spin trap forming a persistent spin adduct which can be detected by electron paramagnetic resonance (EPR) spectroscopy. The various radical adducts exhibit distinctive spectrum which can be used to identify the radicals being generated and can provide a wealth of information about the nature and kinetics of radical production9.
The cyclic nitrones, 5,5-dimethyl-pyrroline-N-oxide, DMPO10, the phosphoryl-substituted DEPMPO11, and the ester-substituted, EMPO12 and BMPO13, have been widely employed as spin traps--the latter spin traps exhibiting longer half-lives for O2&bull;- adduct. Iron (II)-N-methyl-D-glucamine dithiocarbamate, Fe(MGD)2 is commonly used to trap NO due to high rate of adduct formation and the high stability of the spin adduct14.

Electron paramagnetic resonance (EPR) spectroscopy was employed to detect nitric oxide from bovine aortic endothelial cells and superoxide radical anion from human neutrophils using iron (II)-N-methyl-D-glucamine dithiocarbamate, Fe(MGD)2 and 5,5-dimethyl-1-pyroroline-N-oxide, DMPO, respectively.

Reactive nitrogen/oxygen species (ROS/RNS) at low concentrations play an important role in regulating cell function, signaling, and immune response but in ...

Analyzing the Photo-oxidation of 2-propanol at Indoor Air Level Concentrations Using Field Asymmetric Ion Mobility Spectrometry

Summary

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Chapters in this video

Monitoring the Reductive and Oxidative Half-Reactions of a Flavin-Dependent Monooxygenase using Stopped-Flow Spectrophotometry

Production and Measurement of Organic Particulate Matter in a Flow Tube Reactor

Production and Measurement of Organic Particulate Matter in the Harvard Environmental Chamber

Original Experimental Approach for Assessing Transport Fuel Stability

Detection of 3-Nitrotyrosine in Atmospheric Environments via a High-performance Liquid Chromatography-electrochemical Detector System

Real-time Breath Analysis by Using Secondary Nanoelectrospray Ionization Coupled to High Resolution Mass Spectrometry

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer

Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization

Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes

Detection of Nitric Oxide and Superoxide Radical Anion by Electron Paramagnetic Resonance Spectroscopy from Cells using Spin Traps