Chemistry and Biochemistry

Jaron C. Hansen

Jaron Hansen

Office: C307 BNSN
Office Phone: 801-422-4066
Lab Room: C394 BNSN
Lab Phone: 801-422-8980
Office Hours


BS, Utah State University (1997)

Ph.D., Purdue University (2002)

Postdoctoral Scholar, California Institute of Technology/Jet Propulsion Laboratory (2002-2005)


Hansen Lab Group

Atmospheric and Environmental Chemistry

Our group utilizes both computational and experimental tools to investigate a variety of environmental and atmospheric chemistry issues. We couple together high level ab initio computational studies with experimental studies designed to investigate the kinetics and spectroscopy of important atmospheric species and reactions.  Our laboratory studies are complemented by in situ air sampling campaigns designed to investigate source apportionment and general air quality issues.  We utilize a human subject exposure chamber/environmental chamber to aid in the interpretation of our air sampling campaign studies.   We also have an active research element in our group that studies the conversion of biomass into energy.  These elements are described in more detail in the following links: 

Kinetics and Spectroscopy of Earth’s Atmosphere

The research objective of this element in our group’s efforts is to improve the understanding of atmospheric chemical processes through focused laboratory and computational studies. Our current research involves the study of organic peroxy radicals (RO2) and the influence of water vapor on their reactivity. We employ both computational and experimental tools to address this issue.

Organic peroxy radicals (RO2) play an important role in the atmospheric oxidation and in the combustion of hydrocarbons and are important precursors in the formation of smog. They are formed as a result of the addition of molecular oxygen to alkyl radicals. In polluted environments, the most important loss mechanism for RO2 radicals is by reaction with NO.

RO2 + NO → RO + NO2                                                (1)
→ RONO (2)

The dominate product pathway oxidizes NO to NOand consequently produces an alkoxy radical (RO). For larger alkyperoxy radicals a substantial fraction of the product yield is stable alkyl nitrate species (RONO2). The mechanism for production of an alkyl nitrate has been postulated by Darnall et al. to proceed through a vibrationally excited ROONO* intermediate.

RO2 + NO → ROONO*                                      (3)
ROONO* → RONO2* (4)
RONO2* + M → RONO+ M (5)

As a consequence of the formation of a vibrationally excited intermediate during the reaction mechanism, one would expect that the production of an alkyl nitrate would depend on the size of the peroxy radical and demonstrate both a pressure and negative temperature dependence. For larger radicals (i.e. carbon chains > 4), the formation of a stable alkyl nitrate can represent 35% of the product yield. It has been postulated that the formation of various alkyl nitrates from Reaction 4 at 1 atm may be a significant source of missing NOy species [NOy = NOx + sum of all other NO(NO and NO2) containing species]. This is important because organic nitrates are relatively inert and can provide a mechanism for long-range transport of pollution from one region to another. Close to source regions, the formation of organic nitrates, which serve as nitrogen oxide reservoirs, determines the extent to which nitrogen oxide emissions contribute to local ozone production and secondary organic aerosol formation. 

The simplest peroxy radical and the one found in the largest concentrations in the atmosphere (peak concentrations between 108-109 molecules cm-3) is the hydroperoxy radical, HO2. These radicals behave in a fashion similar to organic peroxy radicals in that its most important loss mechanism in polluted environments is reaction with NO.

HO+ NO → NO2 + OH                                 (6a)
→ HNO3 (6b)

The dominant path is the formation of NO2. A second association/isomerization branch forms nitric acid (6b). A third minor channel has been shown to produce HOONO. The pressure dependence on the branching ratio (k6a/k6b) has been reported by a number of investigators. Included in these investigations have been studies aimed at understanding the water vapor dependence on the kinetics and branching ratio of Reaction 6. Butkovskaya et al., probing the effects of temperature and water vapor on Reaction 6, have shown that the yield of HNO3 increases by 90% in the presence of modest amounts of water vapor (~ 3 Torr). The increased HNO3 production as a function of increasing water vapor was explained as occurring because of the formation of a HO2-H2O complex during the reaction mechanism. 

HO2 + H2O ƒH2O-HO2                                                   (7)
HO2-H2O + NO → H2O-HOONO (8)
H2O-HOONO → HNO3 + H2O (9)

The water in the complex serves as an efficient energy dump which favors the formation of the association product, nitric acid. Increased production of nitric acid was shown by Butkovskaya et al. to have important ramifications for atmospheric chemistry models as well as for measurement techniques commonly used to measure HO2 radical in the atmosphere.

Our group has proposed the idea that other RO2 radicals in the presence of water may form similar complexes. In a recent high level ab initio study, Clark et al. reported on the optimized geometries, binding energies, and equilibrium constants for a series of organic peroxy radical-water complexes. Our work showed that for species with strong binding energies (~ 5-7 kcal mol-1) a significant fraction (10-25 %) of the RO2 radicals can exist as a RO2-H2O complex in the atmosphere. It was shown that the binding energy of the complexes is largest when the R-group in the peroxy radical includes a carbonyl (C=O) or alcohol (-OH) moiety.

Our group has investigated the water vapor dependence on a variety of radical-radical reactions using the experimental technique of laser flash photolysis/UV time-resolved absorption spectroscopy/NIR diode laser spectroscopy and laser induced fluorescence. A diagram of our instrument is given in Figure 1.

Pictures of this instrument are given in Figure 2.

A high-powered laser fires a pulse of 351 nm light through a 2 meter long Pyrex reaction cell and is used to initiate the formation of the peroxy radical of interest.  UV light from a D2 lamp is directed through the cell and is used to measure the concentration of both the reactants and products as a function of time using either a PMT or intensified and gated CCD as the detector. Simultaneously, light from a tunable diode laser operating in the NIR is directed into the reaction cell and is used to measure the concentration of HO2 or H2O. A laser induced fluorescence detection system is currently being tested that ultimately will be integrated into our kinetics apparatus (Figure 2) and will measure the concentration of NO2 in the reaction cell. This detection system will be used to measure the water vapor dependence on the product branching ratio for RO2 + NO reactions to form either RO + NO2 or RONO2.   A schematic of this system is given Figure 3.

This instrument allows us to simultaneously measure the concentration of reactants and products in short time intervals over a range of reaction times. This information is used in conjunction with kinetic models to measure reaction rate coefficients. This information is then incorporated into photochemistry models to predict the influence of a reaction on the composition of the atmosphere.

Air Sampling Campaigns and Human Exposure Chamber/Environmental Chamber

The most frequent cause of death among adults in the United States is disease of the heart (principally heart attacks), followed by cancer, and cerebrovascular diseases (stroke). Two of the three main causes are related to the function of the cardiovascular system. Long term exposure to elevated levels of particulate matter (PM) pollution have been implicated in the increased risk of the onset of ischemic heart disease and sub-clinical chronic inflammatory lung injury and atherosclerosis. A proposed mechanism for the effects of PM exposure on the cardiovascular system is via an inflammatory response of the endothelium. The exposure of heritable hyperlipidemic rabbits and mice to elevated, environmentally relevant PM concentrations has been shown to accelerate the progression of atherosclerotic plaques and vascular inflammation. Short term exposure to elevated and acute levels of PM was found to cause an increase in fibrogen and inflammatory markers in pulmonary and respiratory system of humans.

The connection of short term PM exposure and the onset of myocardial infarction has been observed in general population studies. Additionally, a cross-over study of 12,865 patients living in Utah showed that short-term exposure to high PM levels contributed to acute coronary disease, especially among the individuals predisposed or with current coronary condition. Acute vasoconstriction was observed in healthy adults after short term exposure to levels of fine particulate pollution and ozone common in urban areas.  Although the effects of exposure to ambient pollution in humans have been studied, and the effects of exposure of experimental animals to concentrated ambient particulate material, CAPS, has been reported in several studies, a study of the endothelial function effects of direct, short-term exposure of humans to PM in laboratory conditions have not yet been performed.

Several designs for controlled human exposure have been developed. These include full-body exposure chambers, hoods and masks. Particulate matter generation in these systems employs either on-board production of pollution via previously obtained powder samples (wheat flour, dust, etc.) or the use of the particulate pollution directly extracted and concentrated from ambient atmospheric conditions. Our group has designed and characterizes the performance of a two-stage PM exposure chamber/environmental chamber for human subjects developed to study the effects of short-term PM exposure as well as serve as an environmental chamber. The design of this chamber allows for the measurement of: 1) the concentrations of non-volatile and semi-volatile PM using semi-continuous monitors, 2) time-dependant size distribution, and 3) the concentrations of environmentally relevant gases, including CO, CO2, NOx, and O3. Additionally, the current design allows for the pretreatment (photochemically aging) of PM or atmospheric gases mixtures. The system allows us to investigate the influence of various conditions on ozone and PM production. A diagram of our human exposure chamber/environmental chamber design is given in Figure 4.

a) ~40 m3Teflon bag; b) human exposure chamber; c) internal air circulation pump; d) bag-chamber transfer pump; e) bag-to-chamber transfer line; f) bag purge line; g) clean air filling line; h) combustion emissions intake line and catalyst; i) chamber-to-bag transfer line; j) bag sampling manifold; UV lights not shown ;k) particle control transfer values ;l) chamber sampling manifold. The sampling manifolds are also used in conjunction with item e.

A picture of the human exposure chamber system is given in Figure 5.

Our group uses this exposure/environmental chamber to test and validate new semi-continuous instruments designed to measure PM and its components. These instruments are ultimately placed into the field where they are used in air sampling campaigns designed to investigate source apportionment. Our group operates a sampling site in Lindon, Utah (Figure 6) as well as a trailer outfitted with a suite of air sampling instruments. We collaborate closely with the Utah Department of Air Quality and Southern California Edison to conduct air quality sampling campaigns.

Biofuel/Alternative Energy

Figure 7.jpgLignocellulose is the structural material that makes up much of the structural matter of   plants. Approximately 33% of all plant matter is cellulose. Cellulose hemicellulose and lignin are the principle components of lignocellulose. Cellulose forms linear polymer chains in which individual monomer units are connected to one another through beta 1‐4 glycosidic bonds (β(1→4). (See Figure 7)

The inherit stability of β(1→4) glycosidic bonds makes it difficult for most organisms to break down cellulose. Our group investigates pretreatment methods that disrupt the long‐chain polymer linkages of cellulose and of lignin-cellulose.   The result is the formation of monomer glucose and smaller chained cellulose polymer chains that are susceptible to further breakdown by anaerobic bacteria. This pretreated substrate is then introduced into an anaerobic induced blanket reactor (IBR) to digest the cellulose and consequently convert it into methane gas.   The gas that is produced from the digestion of cellulose and lignocellulose is typically composed of 75 % CH4, 25% CO2, 1000-2000 ppm H2S and saturated in water vapor. The second research objective of our group in biofuel/alternative energy is to purify the biogas stream liberated by the anaerobic digestion process. Our group to date has filed 3 patents (patent pending) technologies. This technology has been licensed from Brigham Young University to a start-up company called Anaerobic Digestion Technology (AD Tech). Our technology has been successfully used to pretreat and digest algae, green waste (leaves and grass clippings), and sawdust.

Research Group


  1. Hansen, Jaron C.; Li, Yumin; Francisco, Joseph S.; Li, Zhuangjie, “On the Mechanism of the BrO + CH2O Reaction” Journal of Physical Chemistry, A, 1999,103, 8543-8546.
  2. Good, David A.; Hansen, Jaron; Francisco, Joseph S.; Li, Zhuangjie; Jeong, Gill-Ran, “Kinetics and Reaction Mechanism of Hydroxyl Radical Reaction with Methyl Formate,” Journal of Physical Chemistry, A, 1999, 103, 10893-10898.
  3. Hansen, Jaron C.; Li, Yumin; Li, Zhuangjie; Francisco, Joseph S., “On the Mechanism of the BrO + HBr Reaction,” Chemical Physical Letters, 1999, 314, 341-346.
  4. Good, David A.; Hansen, Jaron; Kamboures, Mike; Santiono, Randy; Francisco, Joseph S., “An Experimental and Computational Study of the Kinetics and Mechanism of the Reaction of Methyl Formate with Cl Atoms,” Journal of Physical Chemistry, A, 2000, 104,1505-1511.
  5. Li, Zhuangjie; Tao, Ahining; Naik, Vaishali; Good, David A.; Hansen, Jaron C.; Jeong, Gill-Ran; Francisco, Joseph S.; Atul K.; Wuebbles, Donald J., “Global Warming Potential Assessment for CF3OCF=CF2,” Journal of Geophysical Research, 2000, 105, 4019-4029.
  6. Hansen, Jaron C.; Li, Yumin; Francisco, Joseph S.; Szente, Joseph J.; Maricq, M. Matti, “An Experimental and Computational Study of the Methyl Formate Radical Ultraviolet Spectrum,” Journal of Chemical Physics, 2000, 113, 6465-6468.
  7. Li,Z.; Jeong, G.-R.; Hansen, J.C.; Good, D.A.; Francisco, J.S., “Rate constant for the reactions of CF3OCHFCF3 with OH and Cl.” Chemical Physics Letters, 2000, 320, 70-76.
  8. Jain, Atul K.; Li, Zhuangjie; Naik, Vaishali; Wuebbles, Donald J.; Good, David A.; Hansen, Jaron C.; Francisco, Joseph S., “Evaluation of the Atmospheric Lifetime and Radiative Forcing on Climate for 1,2,2,2-Tetrafluoroethyl Trifluoromethyl Ether (CF3CHFOCF3),” Journal of Geophysical Research, 2001, 106, 12615-12618.
  9. Kamboures, Mike; Hansen, Jaron C.; Francisco, Joseph S., “A Study of the Kinetics and Mechanism Involved in the Atmospheric Degradation of Bromoform by Atomic Chlorine,” Chemical Physics Letters, 2002, 353, 335-344.
  10. Hansen, Jaron C.;Francisco, J.S.; Szente, Joseph J.; Maricq, M. Matti, “An Experimental Study of the Mechanism and Branching Ratio for the Reaction between Methyl Formate and Chlorine Atoms,” Chemical Physics Letters, 2002, 365, 267-278.
  11. Xu, Dadong; Huang, Jianhua; Francisco, Joseph S.; Hansen, Jaron C.; Jackson, William M., "Photodissociation of carbonic dibromide at 267nm: observation of three-body dissociation and molecular elimination of Br2," Journal of Chemical Physics, 2002, 117, 7483-7490.
  12. Hansen, Jaron C. and Francisco, Joseph S., “Radical-molecule complexes: changing our perspective on the molecular mechanisms of radical-molecule reactions and their impact on atmospheric chemistry,” ChemPhysChem, 2002, 3, 833-840.
  13. Hansen, Jaron C.; Li, Yumin; Rosado-Reyes, Claudette M.; Francisco, Joseph S.; Szente, Joseph J.; Maricq, M. Matti, “Theoretical and Experimental Investigation of the UV Cross Section and Kinetics of the Methyl Formate Peroxy Radical,” Journal of Physical Chemistry, 2003, 107, 5306-5316.
  14. Christensen, Lance E.; Okumura, Mitchio; Hansen, Jaron C.; Sander, Stanley P.; Francisco, Joseph S., “Experimental and ab Initio Study of the HO2-CH3OH Complex: Thermodynamics and Kinetics of Formation,” Journal of Physical Chemistry A, 2006,110,6948-6959.
  15. Hansen, Jaron C.; Flowers, Bradley A.; Stanton, John F., “Computational study of the vibrational and electronic spectroscopy of a HO2-H2O2 complex,” Journal of Molecular Structure: THEOCHEM, 2006, 768, 111-118.
  16. Pope, Francis D.; Hansen, Jaron C.; Bayes, Kyle D.; Friedl, Randall R.; Sander, Stanley P.” Ultraviolet Absorption Spectrum of Chlorine Peroxide, ClOOCl,” Journal of Physical Chemistry A., 2007,111,4322-4332.
  17. Clark, Jared; English, Alecia M.; Francisco, Joseph S.; Hansen, Jaron C. “Computational Study of the Existence of Organic Peroxy Radical-Water Complexes (RO2-H2O),“ Journal of Physical Chemistry A, 2008,112,1587-1595.
  18. English, Alecia J.; Szente, Joseph J.; Maricq, Matti M.; Hansen, Jaron C., “The Effects of Water Vapor on the CH3O2 Self-Reaction and Reaction with HO2,“ Journal of Physical Chemistry A., 2008,112,9220-9228.
  19. Hansen, Jaron C.; Friedl, Randall R.; Sander, Stanley P. “Kinetics of the OH + ClOOCl and OH + Cl2O Reactions: Experiment and Theory,” Journal of Physical Chemistry A, 2008, 112,9229-9237.
  20. Hansen, Jaron C.; Woolwine III, Woods R.; Bates, Brittney L.; Clark, Jared M.; Kuprov, Roman Y.; Mukherjee, Puspak; Murray, Jacolin A.; Simmons, Michael A.; Waite, Mark F.; Eatough, Norman L.; Eatough, Delbert J.; Long, Russell; Grove, Brett D. “Semi-Continuous PM2.5 and PM10 Mass and Composition Measurements in Lindon, Utah During Winter 2007,“ Journal of the Air and Waste Management Association, 2010,60,346-355.
  21. Kuprov, Roman; Eatough, Delbert J.; Cruickshank, Tyler; Olson, Neal; Hansen, Jaron C. “Composition and Secondary Formation of Fine Particulate Material in the Salt Lake Valley: Winter 2009,” in review, Journal of the Air and Waste Management Association, 2010.
  22. Clark, Jared; Call, Seth T.; Austin, Daniel; Hansen, Jaron C. “Computational Study of Isoprene Hydroxyalkyl Peroxy Radical-Water Complexes (C5H8(OH)O2-H2O),” Journal of Physical Chemistry A, 2010, 114,6534-6541.
  23. Hansen, Clifford W.; Hansen, Lee D.; Nicholson, Allen D.; Thomas, Nathan; Clark, Jared; Chilton, Marie C.; Hansen, Jaron C.; “Correction for Instrument Time Constant in Determination of Reaction Kinetics” International Journal of Chemical Kinetics, Oct. 20, 2010.
  24. Cline, Taylor; Thomas, Nathan; Shumway, Logan; Yeung, Irene; Hansen, Conly L.; Hansen, Lee D.; Hansen, Jaron C. “ Method for Evaluating Anaerobic Digester Performance,” Bioresource Technology, 2010, 101,8623-8626
  25. Riffault, Veronique; Hansen, Jaron C.; Clark, Jared; Ravishankara, A.R.; Burkholder, James B. “ Temperature-Dependent Rate Coefficients and Theoretical Calculations for the OH + Cl2O Reaction” ChemPhysChem, 2010,11,4060-4068.
  26. Kuprov, Roman; Buck, David; Eatough, Delbert J.; Hansen, Jaron C.; “Design and Characterization of a Two-stage Human Subject Exposure Chamber,” Journal of the Air and Waste Management Association, August 23, 2011.
  27. Mayo, MacKenzie H.; Nicholson, Allen D.; Hansen, Lee D.; Hansen, Jaron C. “Chemical Treatment of Algae to Facilitate Biogas Production by Anaerobic Digestion,” American Society of Agricultural and Biological Engineers, 2011, 54(4),1547-1550.
  28. Pope, Arden C. III; Hansen, Jaron C.; Kuprov, Roman; Sanders, Matthew D.; Anderson, Michael N.; Eatough, Delbert J. “ Vascular Function and Short-Term Exposure to Fine Particulate Air Pollution”, Journal of the Air and Waste Management Association, August 23, 2011.
  29. Burrell, Emily; Clark, Jared M.; Snow, Mathew; Dumais, Heidi; Lee, Seong-Cheol; Nielson, Brad J.; Osborne, Derek; Cardona-Salamanca, Lucia; Zemp, Logan; DaBell, Ryan S.; Hansen, Jaron C. “Computational Study of Hexanal Peroxy Radical-Water Complexes” International Journal of Quantum Chemistry, August 29, 2011.
  30. Clark, Jared; Kumbhani, Sambhav; Francisco, Joseph S.; Hansen, Jaron C. “HNO3-NHx, H2SO4-NHx, CH(O)OH-NHx, and CH3C(O)OH-NHx complexes and their role in the formation of condensation nuclei”, The Journal of Chemical Physics, 2011, 135, 244305.
  31. L. D. Hansen, A. Nogales, B. Arnholdt-Schmitt, L. G. Neven, N. Barros, “Biocalorimetry of plants, insects, and soil microorganisms,” Enthalpy and Internal Energy: Liquids, Solutions, and Vapours, 2017, Royal Society of Chemistry, pp. 336-363.


  1. Hansen, J.C., Hansen, L.D. Method for Pretreatment of Cellulosic and Lignocellulosic Materials for Conversion into Bioenergy, Utility Patent Filed July 6, 2010.
  2. Hansen, J.C., Hansen, L.D. Device for Effective Heat Management for Biogas/Sour Gas Conditioning, Utility Patent Filed August 21, 2010.
  3. Hansen, J.C., Hansen, L.D. Self-contained Portable System for Treatment of Human Waste and Energy Production, Patent Filed April 13, 2012