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Highly oxygenated molecules (HOM) are crucial in the processes of secondary organic aerosol (SOA). In this thesis, two studies on HOM are carried out. The first one applies a simplified HOM scheme to PyCHAM, a newly developed box mode, to simulate alpha-pinene ozonolysis experiments in the dark environment in two different chambers, and concludes the essential role of the second-generation autoxidation. The second study develops and tests a more mechanistic HOM scheme in PyCHAM to investigate the binary system containing alpha-pinene and isoprene in terms of SOA production. These two studies can contribute to a better understanding of HOM as the precursors of SOA production. A command-line tool that can co-operate with PyCHAM is developed and used in both studies.

Aerosols can substantially impact human health, atmospheric chemistry, and climate. The composition and photochemistry of a variety of anthropogenic and biogenic primary and secondary organic aerosols (POA and SOA) have yet to be fully characterized. The composition of organic aerosols is extremely complex - they contain a variety of highly oxidized, multifunctional, low vapor pressure organic compounds. The primary focus of this thesis is on the molecular characterization of organic aerosols that are not well understood or have not been studied before, such as primary emissions from electronic cigarettes, iron (III) mediated SOA, and photooxidized biodiesel and diesel fuel SOA. Another focus of this dissertation is the effect of direct photochemical aging on the composition of organic aerosol. Direct photolysis experiments were first applied to a system that is known to have a photolabile composition, alpha-pinene ozonolysis SOA, such that characterization of a photochemical effect would be possible to quantify. Photolysis of more complex SOA that have not been studied before, photooxidized biodiesel and diesel fuel SOA, were also investigated in this thesis. Advanced high resolution mass spectrometry techniques were used in the molecular characterization of organic aerosols, including nano-Desorption Electrospray Ionization Mass Spectrometry (nano-DESI) and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR). An additional suite of online instrumentation was used to measure gas-phase composition, particle-phase composition, particle size and concentration, and absorption properties: Proton Transfer Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS), Aerosol Mass Spectrometry (ToF-AMS), Scanning Mobility Particle Sizing (SMPS), and UV-vis spectroscopy. The molecular analysis of these aerosols provides valuable insight to the formation and photochemical behavior of unexpected, polymeric, light absorbing, and unique organosulfur species.