Chemistry of the Atmosphere

METEO 532: Chemistry of the Atmosphere

Semester: Fall 2019 

Instructor: José D. Fuentes
Office: 508 Walker Building
Office hours: 1:30 – 5:00 PM Monday and 1:30 – 3:30 PM Wednesday, or by appointment
Telephone: 814 863 1585
Web page:

Class meeting time and location: M W F 11:15 AM - 12:05 PM in 109 Electrical Engineering West

Prerequisites: CHEM 110

Internet materials: CANVAS homepage – 

Course description

This course reviews the principles in gaseous and multiphase chemistry in the Earth’s atmosphere. It also covers elements, sources, effects, measurements, and meteorological conditions associated with air pollution. Temporal and spatial distribution of the most prevalent, reactive chemical species found in the atmosphere are reviewed and discussed.  Also, rates of trace gas emissions, transformation, transport, and deposition are studied. Meteorological conditions contributing to poor air quality are examined and discussed. The processes of pollutant transport and chemical transformation are also examined using numerical models. 


To develop a basic understanding of air chemistry phenomena such as photochemical smog, chemical formation of aerosols, and depletion of stratospheric ozone. 

To attain a working knowledge of numeric models to estimate formation, transport, and deposition of gaseous chemical species and aerosols 

To learn how science can guide the formulation of air quality policy in the United States. 

Books and reference materials

This class does not have a required textbook. However, the books listed below provide excellent background on chemistry of the atmosphere. Lecture notes will be derived from the books listed below. Also, lecture notes will be prepared based on journal manuscripts which will be distributed in advance of class discussions. Independent class preparation in advance for class discussions using the listed books is highly recommended. 

Reference books:

  • Atmospheric Chemistry and Physics: from Air Pollution to Climate Change by JH Seinfeld and SN Pandis, 1997. 
  • Chemistry of the Upper and Lower Atmosphere: Theory, Experiments, and Applications by BJ Finlayson-Pitts and JN Pitts, 1999. 
  • Atmospheric Chemistry and Global Change by Guy P. Brasseur, John J. Orlando, and Geoffrey S. Tyndall, 1997. 
  • Introduction to Atmospheric Chemistry by Daniel Jacob, 1999. 
  • The Mechanisms of Reactions Influencing Atmospheric Ozone by Jack G. Calvert, John J. Orlando, William R. Stockwell, Timothy J. Wallington, 2015. 
  • Modeling of Atmospheric Chemistry by Guy P. Brasseur and Daniel J. Jacob, 2017. 
  • Atmospheric Chemistry: From the Surface to the Stratosphere  by Grant Ritchie, 2017.

Relevant Journals:

Throughout the semester, several journal review articles will be studied and discussed. These articles come from the following journals, which can be access via the Web of Science (Penn State University library): 

  • Atmospheric Environment
  • Journal of Geophysical Research-Atmosphere
  • Environmental Science and Technology  
  • Journal of Atmospheric Chemistry
  • Atmospheric Chemistry and Physics

Course load and evaluation

This course consists of three 50-minute lectures or class discussions per week.  Class attendance and participation are critically essential to successfully achieve the course learning goals. For the course evaluation, problem sets and numerical modeling exercises will be given throughout the semester and considered in the final grade. There will be one mid-term exam to be scheduled during one of the regular class periods.  Also, students will be required to identify and complete one major research project.  This project will involve research to gather, analyze, and make interpretation of air chemistry data.  Ideally, it would be valuable to identify projects closely related to the student’s interests.  The project results will be included in a term paper, written following the format of peer-reviewed journals.  Also, the results will be per reviewed, following the procedures required by journal editors.  A final exam will be given at the end of the semester. Marks for the course will be allocated as follows: 

  • Assignments 10 % (Due dates will be announced in class)
  • Mid-term exam 20 % (18 October during class period)
  • Term Project report:
    • Project outline 10 % (21 October)
    • First project draft 10 % (18 November)
    • Final project draft 10 % (6 December)
    • Peer review 10 % (16 December)
  • Final exam  30 % (TBD) 

The final grade will be determined according to the following scale:

  • A: Above 90     
  • A-: 85-90
  • B+: 80-84               
  • B: 75-79           
  • B-: 70-74
  • C+: 65-69               
  • C: 60-64           
  • C-: 55-59
  • D+: 50-54               
  • D: 45-49           
  • D-: 40-44 


This course abides by the Penn State Class Attendance Policy 42-27:, Attendance Policy E-11:, and Conflict Exam Policy 44-35:  Please also see Illness Verification Policy, and Religious Observance Policy: Students who miss class for legitimate reasons will be given a reasonable opportunity to make up missed work, including exams and quizzes.  Students are not required to secure the signature of medical personnel in the case of illness or injury and should use their best judgment on whether they are well enough to attend class or not; the University Health Center will not provide medical verification for minor illnesses or injuries. Other legitimate reasons for missing class include religious observance, family emergencies, and regularly scheduled university-approved curricular or extracurricular activities.  Students who encounter serious family, health, or personal situations that result in extended absences should contact the Student Care and Advocacy for help:  Whenever possible, students participating in University-approved activities should submit to the instructor a Class Absence Form available from the Registrar's Office:, at least one week prior to the activity. 

Academic integrity

Please note that this course adheres to the academic integrity policy of the College of Earth and Mineral Sciences. The policy can be obtained from Students are expected to present their own work. Classmates may collaborate on assignments. However, each student must write up his or her answers separately.  Students who present other people's work as their own, as well as the students providing answers, will be in violation of the academic integrity policy. It is never acceptable to copy the work of another person. Students who present other people’s work as their own will not receive any credit on the impacted assignment and may receive a failure grade in the course. Plagiarism is also a serious academic misconduct. Whenever adopting materials from published results, the source of information needs to be properly cited or referenced. 

Accommodations for students with disabilities

Penn State welcomes students with disabilities into the University's educational programs. Every Penn State campus has an office for students with disabilities. The Office for Disability Services (ODS) Web site provides contact information for every Penn State campus: For further information, please visit the Office for Disability Services Web site: In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled, participate in an intake interview, and provide documentation: If the documentation supports your request for reasonable accommodations, your campus’s disability services office will provide you with an accommodation letter. 

Campus emergencies, including weather delays

Residence Instruction: Campus emergencies, including weather delays, are announced on Penn State News: and communicated to cellphones, email, the Penn State Facebook page, and Twitter via PSUAlert (Sign up at: 

Online Instruction: In case of weather-related delays at the University, this online course will proceed as planned. Your instructor will inform you if there are any extenuating circumstances regarding content or activity due dates in the course due to weather delays. If you are affected by a weather-related emergency, then please contact your instructor at the earliest possible time to make special arrangements.  

    1. Atmospheric chemistry is not just about chemistry
    2. Impacts of atmospheric chemistry
    3. The ideal gas law
    4. Units of concentration and molar mixing ratios
    5. Residence time and chemical lifetime
    6. Composition of the atmosphere
    7. Lifecycles of atmospheric constituents
    1. Regions of the world impacted by poor air quality
    2. Air quality guidelines
    3. Case study I: The United States
      1. Air quality criteria
      2. Ambient air quality standards
      3. Non-attainment areas
      4.  State implementation plan (SIP)
    4. Case study II: The Montreal protocol on chlorofluorocarbon emissions
    1. Global scale motions
    2. Synoptic motions
    3. Mesoscale motions
    4. Synoptic motions
    5. Local circulations
      1. Thermal structure of lower atmosphere
      2. Static and dynamic stability
      3. Convective and stable boundary layers
      4. Turbulent diffusion
      5. Role of clouds in mixing and transport of reactive gases and aerosols
    1. Actinic flux
    2. Spectroscopy
    3. Light absorptin
    4. Photophysical processes
    5. Photochemical reactions
      1. Cross section
      2. Quantum yields
      3. Photolysis
    6. Chemical kinetics
      1. Reactions
      2. Reaction energetics
      3. Rate equations
      4. Bimolecular reactions
      5. Termolecular reactions
      6. Equilibrium reactions
      7. Steady state
    1. Photochemistry of nitrogen oxides
      1. Photostationary state
      2. Reactive nitrogen chemical species
    2. Chemistry of the clean troposphere
    3. Atmospheric organic chemistry
      1. Alkanes
      2. Alkenes
      3. Aromatics
      4. Oxygenates
    4. Role of hydrocarbon and nitrogen oxides in ozone formation
      1. Generalized oxidation sequence
      2. Empirical Kinetic Modeling Approach (EKMA) diagram
      3. Nitrogen oxides or hydrocarbon sensitivity
    5. Halogen chemistry
    1. Atmospheric liquid water
    2. Chemical equlibria and Henry’s Law
    3. Sulfur chemistry and acid rain
    4. Nitrogen chemistry
    5. Organic acids
    6. Ecological and structural damage
    7. Successes and failures in reducing acid rain in the USA
    1. Physical properties and size distributions
    2. Particle formation and growth
    3. Particle chemical composition
    4. Semi-volatile organics
    5. Health and visibility effects
    1. Sources of stratospheric constituents
      1. Emissions
      2. Trends
    2. Sources, reservoir, and reactive species
    3. Ozone-destroying catalytic cycles
    4. The ‘ozone hole’
      1. Meteorological conditions
      2. Polar stratospheric clouds
      3. Heterogeneous chemistry
      4. Ozone-destroying catalytic cycles
    1. Gradient transport models 
    2. Gaussian diffusion models 
    3. Settling and deposition models
    1. Warming by greenhouse gases
      1. Long-lived species
      2. Tropospheric ozone
    2. Radiative forcing and climate sensitivity
    3. Direct effects of aerosols
    4. Indirect effects of aerosols
    5. Feedbacks between poor air quality and climate