DEPT. OF EARTH & ENVIRONMENTAL SCIENCES, UNIVERSITY OF ROCHESTER

EES 218 Atmospheric Chemistry

Pollution plume at sunset over Western New York viewed from Space Shuttle Discovery, Oct. 21, 2000.

Spring 2019Syllabus

Last Updated: January 16, 2019

EES 218 Spring 2019 Atmospheric Chemistry pg. 2 of 13

CONTENTS

1 Overview 31.1 Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.2 Pre-requisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.3 Main Learning Goals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2 Readings 42.1 Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42.2 Supplemental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3 Schedule 63.1 Recitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

4 Grading 114.1 Exams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

4.1.1 Midterm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.1.2 Final . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

4.2 Quizzes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.3 Participation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.4 Short Presentations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

5 Homework Policy 12

6 Classroom Policies 126.1 Diversity and Disabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126.2 Electronic Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

7 Academic Honesty 13

8 Initial Meeting 13

9 Feedback 13

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1 OVERVIEW

Course Location: Harkness 210Course Time: M/W 12:30 PM-1:45 PM

Recitation Location: LeChase Hall 148Recitation Time: F 12:30-1:30 PM

Instructor: Prof. Lee T. MurrayE-mail: lee.murray@rochester.eduPhone: +1 585-275-2077 (better to e-mail)Office Location: Hutchison Hall 479Office Hours: after class, or by appointment

Teaching Assistant: Xin TieE-mail: xtie@ur.rochester.eduOffice Hours: TBDOffice Location: Hutchison Hall 117

1.1 DESCRIPTION

The atmosphere helps to maintain habitable temperatures on our planet’s surface, shields life fromdestructive cosmic and ultraviolet radiation and contains gases such as oxygen and carbon dioxide,which are essential for life. In this course we will work toward an understanding of several importantquestions. What is in the Earth’s atmosphere? What are the sources and sinks of the most importantgases in the atmosphere? How does the atmosphere affect the Earth’s surface climate? What is the roleof photochemistry in atmospheric composition? How does the atmosphere interact with the land andoceans? How has human activity affected the atmosphere?

1.2 PRE-REQUISITES

Required, unless granted permission by instructor:

• EES 101 (Intro. to Geology), EES 103 (Intro. to Environmental Sci.), or EES 105 (Intro. to ClimateChange) or equivalent

• CHM 131 (Intro. College Chemistry I) or equivalent

• MTH 141-142 (Calculus I and II) or equivalent

Recommended, but not required:

• CHM 132 (Intro. College Chemistry II) or equivalent

Permission of instructor is required for majors other than GEO, EVS and ESP.

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1.3 MAIN LEARNING GOALS

By the end of the course, students will understand:

• The composition of the modern atmosphere• The basics of atmospheric structure and circulation• The concepts of sink, source, and lifetime, and be able to make and use simple box models to

describe changes in atmospheric composition• The atmospheric budgets of the most important trace gases• The dominant processes and chemical reactions in the stratosphere• The dominant processes and chemical reactions of both nighttime and daytime tropospheric

chemistry• The stratospheric ozone loss problem• Major surface air-quality issues and their associated control strategies• Earth’s radiative energy budget and how the greenhouse effect works• The sources and sinks of aerosols and how they affect climate• The coupling between air quality and climate change

In addition, students will gain practice giving an effective short presentation

2 READINGS

2.1 REQUIRED

BOOK

Jacob, D. J. (1999), Introduction to Atmospheric Chemistry, 1st ed., Princeton University Press, Prince-ton, NJ, http://acmg.seas.harvard.edu/publications/jacobbook/index.html.

ARTICLES AND EXCERPTS

Gruber, N., and J. N. Galloway (2008), An Earth-system perspective of the global nitrogen cycle, Nature,451(7176), 293–296, doi:10.1038/nature06592.

Jacob, D. J., and D. A. Winner (2009), Effect of climate change on air quality, Atmos Environ, 43(1),51–63, doi:10.1016/j.atmosenv.2008.09.051.

Kuklinska, K., L. Wolska, and J. Namiesnik (2015), Air quality policy in the U.S. and the EU – a review,Atmos Poll Res, 6(1), 129–137, doi:10.5094/APR.2015.015.

MJ Bradley & Associates (2005), Best Available Technology for Air Pollution Control: Analysis Guid-ance and Case Studies for North America , Tech. rep., Manchester, NH, http://www3.cec.org/islandora/en/item/2195-best-available-technology-air-pollution-control/.

Myhre, G., D. T. Shindell, F.-M. Bréon, W. Collins, and J. S. Fuglestvedt (2013), Anthropogenic andNatural Radiative Forcing, in Climate Change 2013 - The Physical Science Basis, Cambridge Uni-versity Press, Cambridge, UK, https://www.ipcc.ch/site/assets/uploads/2018/02/WG1AR5_Chapter08_FINAL.pdf.

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Parrella, J. P., et al. (2012), Tropospheric bromine chemistry: implications for present and pre-industrialozone and mercury, Atmos Chem Phys, 12(15), 6723–6740, doi:10.5194/acp-12-6723-2012.

Selin, N. E. (2009), Global Biogeochemical Cycling of Mercury: A Review, Annu Rev Env Resour, 34(1),43–63, doi:10.1146/annurev.environ.051308.084314.

Sherwen, T., et al. (2016), Global impacts of tropospheric halogens (Cl, Br, I) on oxidants and composi-tion in GEOS-Chem, Atmos Chem Phys, 16(18), 12,239–12,271, doi:10.5194/acp-16-12239-2016.

Tham, K. W. (2016), Indoor air quality and its effects on humans—A review of challenges and develop-ments in the last 30 years, Energy and Buildings, 130, 637–650, doi:10.1016/j.enbuild.2016.08.071.

Wania, F., and D. Mackay (1996), Tracking the distribution of persistent organic pollutants, Environ SciTechnol, 30(9), A390–A396, doi:10.1021/es962399q.

2.2 SUPPLEMENTAL

BOOKS

Seinfeld, J. H., and S. N. Pandis (2016), Atmospheric Chemistry and Physics: From Air Pollutionto Climate Change, 1152 pp., Wiley, Hoboken, NJ, https://ebookcentral.proquest.com/lib/rochester/detail.action?docID=4462549.

ARTICLES

Burkholder, J. B., et al. (2015), Chemical Kinetics and Photochemical Data for Use in Atmospheric Stud-ies: Evaluation Number 18, Tech. Rep. JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena,CA, https://jpldataeval.jpl.nasa.gov/pdf/JPL_Publication_15-10.pdf.

Davidson, C. I., R. F. Phalen, and P. A. Solomon (2007), Airborne Particulate Matter and Human Health:A Review, Aerosol Science and Technology, 39(8), 737–749, doi:10.1080/02786820500191348.

Lyons, T. W., C. T. Reinhard, and N. J. Planavsky (2014), The rise of oxygen in Earth’s early ocean andatmosphere, Nature, 506(7488), 307–315, doi:10.1038/nature13068.

Seinfeld, J. H., and S. N. Pandis (2016), Atmospheric Chemistry and Physics: From Air Pollutionto Climate Change, 1152 pp., Wiley, Hoboken, NJ, https://ebookcentral.proquest.com/lib/rochester/detail.action?docID=4462549.

Sillman, S. (2002), Chapter 12 The relation between ozone, NOx and hydrocarbons in urban andpolluted rural environments, in Air Pollution Science for the 21st Century, pp. 339–385, Elsevier,doi:10.1016/S1474-8177(02)80015-8.

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3 SCHEDULE

Below is the tentative class schedule, with topics for each class, associated readings, and problem setdue dates. Schedule subject to change pending course progress.

Required reading assignments in bold. Supplemental or alternative readings in italics.

MONDAY WEDNESDAY

Jan 14th 16th 1

Introduction and OverviewKey Topics

1. History and evolution of Earth’satmospheric composition

Reading• Syllabus• Jacob (1999) Ch. 6.2• Seinfeld and Pandis (2016) Ch. 1.1

21st

Martin Luther King Day

23rd 2

Fundamentals: Pressure and TemperatureKey Topics

1. Atmospheric pressure and density2. Equation of state (Ideal Gas Law)3. Changes of pressure with altitude

(Barometric Law)4. Temperature structure

Reading• Jacob (1999) Ch. 2• Seinfeld and Pandis (2016) Ch. 1.1-1.5

28th 3

Fundamentals: CompositionKey Topics

1. Measures of abundance: mixing ratio,number density, and partial pressure

2. Composition of the present-dayatmosphere

Reading• Jacob (1999) Ch. 1• Seinfeld and Pandis (2016) Ch. 1.6-1.8

30th 4

Fundamentals: Mathematical ModelsKey Topics

1. Simple box models, budgets, and lifetime2. Steady-state assumptions3. Solution to the first-order loss problem4. Continuity equation5. Multi-box models

Reading• Jacob (1999) Ch. 3

PS1 Out

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MONDAY WEDNESDAY

Feb 4th 5

Fundamentals: Chemical KineticsKey Topics

1. Photodissociation2. Bi- and termolecular reaction rates3. Equilibrium4. Chemical families5. Isotope fractionation

Reading• Jacob (1999) Ch. 9• Seinfeld and Pandis (2016) Ch. 3.1-3.6, 4.5• Burkholder et al. (2015) Sect. 1.1, 2.1-2.6,

3.1-3.2, 4.1-4.2

6th 6

Biogeochemical Cycles: Oxygen and NitrogenKey Topics

1. Global oxygen budget2. Global nitrogen budget

Reading• Jacob (1999) Ch. 6.1-6.4• Seinfeld and Pandis (2016) Ch. 2.3• Lyons et al. (2014)

PS1 Due at Class Start; PS2 Out

11th 7

Biogeochemical Cycles: Carbon: Part IKey Topics

1. Global carbon budget2. Carbon uptake by ocean3. Carbonate chemistry

Reading• Jacob (1999) Ch. 6.5• Seinfeld and Pandis (2016) Ch. 22.2

13th 8

Biogeochemical Cycles: Carbon: Part IIKey Topics

1. Carbonate chemistry, ctd.2. Carbon uptake by terrestrial biosphere

Reading• Jacob (1999) Ch. 6.5• Seinfeld and Pandis (2016) Ch. 22.2

PS2 Due at Class Start; PS3 OutSign up for Short Presentations

18th 9

Stratospheric Chemistry: ChapmanMechanismKey Topics

1. Stratospheric ozone formationReading

• Jacob (1999) Ch. 10.1• Seinfeld and Pandis (2016) Ch. 5.1

20th 10

Stratospheric Chemistry: Catalytic Loss CyclesKey Topics

1. HOx cycles2. NOx cycles3. Halogen cycles4. Stratospheric ozone depletion

Reading• Jacob (1999) Ch. 10.2• Seinfeld and Pandis (2016) Ch. 5.2, 5.3,

5.4.1PS3 Due at Class Start; PS4 Out

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MONDAY WEDNESDAY

25th 11

Stratospheric Chemistry: HeterogeneousProcessesKey Topics

1. Polar stratospheric clouds (PSCs)2. Antarctic ozone hole3. Volcanic aerosols and geoengineering

Reading• Jacob (1999) Ch. 10.3-10.4• Seinfeld and Pandis (2016) Ch. 5.6-5.8

27th 12

Tropospheric Chemistry: BackgroundPhotochemistryKey Topics

1. Photostationary state (NO, NO2, O3)2. OH production and budget3. HOx and NOx in the troposphere4. CO oxidation and production of ozone5. Tropospheric ozone budget

Reading• Jacob (1999) Ch. 11.1, 11.3-11.3.2,

11.4-11.5• Seinfeld and Pandis (2016) Ch. 6.1-6.3, 6.6

PS4 Due at Class Start

Mar 4th 13

Tropospheric Chemistry: Oxidized NitrogenKey Topics

1. NOx budget: sources, sinks, and trends2. Daytime NOx chemistry3. Nighttime NOx chemistry4. Reservoir species (NOy )

Reading• Jacob (1999) Ch. 11.4• Seinfeld and Pandis (2016) Ch. 6.5,

6.10-6.11

6th

MidtermIn ClassPS5 Out

11th

Spring Break

13th

Spring Break

18th 14

Tropospheric Chemistry: Reduced CarbonKey Topics

1. CO budget: sources, sinks, and trends2. CH4 budget: sources, sinks, and trends3. Non-methane VOCs (isoprene,

monoterpenes)Reading

• Jacob (1999) Ch. 11.2, 11.3.3• Seinfeld and Pandis (2016) Ch. 6.4,

6.10-6.11

20th 15

Air Pollution: Photochemical SmogKey Topics

1. Surface ozone pollution: impacts2. Urban O3 pollution chemistry3. NOx- vs. VOC-limited regimes

Reading• Jacob (1999) Ch. 12• Seinfeld and Pandis (2016) Ch. 6.4,

6.10-6.11• Sillman (2002)

PS5 Due at Class Start; PS6 Out

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MONDAY WEDNESDAY

25th 16

Air Pollution: Acid and Nutrient DepositionKey Topics

1. Acid rain impacts, chemistry, and physics2. Atmospheric fertilization: eutrophication

and stressesReading

• Jacob (1999) Ch. 13• Gruber and Galloway (2008)• Seinfeld and Pandis (2016) Ch. 20.5-20.6

27th 17

Air Pollution: Heavy Metals and PersistentsKey Topics

1. Lead: Impacts and global budget2. Mercury: Impacts, budget and chemistry3. Persistent organic pollutants (POPs)

Readings• Selin (2009)• Wania and Mackay (1996)• Seinfeld and Pandis (2016) Ch. 6.15

PS6 Due at Class Start; PS7 Out

Apr 1st 18

Air Pollution: Particulate Matter (PM)1. Particle composition, size distributions

and morphology2. Sulfate-nitrate-ammonium aerosol

sources and sinks3. Primary and secondary organic aerosol4. Black carbon

Reading• Jacob (1999) Ch. 8• Davidson et al. (2007)• Seinfeld and Pandis (2016) Summaries of

Ch. 8-14

3rd 19

Air Pollution: Indoor1. Photochemical pollutants2. Carbon monoxide3. Radon4. Asbestos

Reading• Tham (2016)

PS7 Due at Class Start; PS8 Out

8th 20

Effects of Meteorology on Air PollutionKey Topics

1. Forces, winds and global circulation2. Vertical pollutant transport3. Horizontal pollutant transport

Reading• Jacob (1999) Ch. 4• Seinfeld and Pandis (2016) Ch. 16, 21

10th 21

Tropospheric Chemistry: Halogens1. Bromine sources and chemistry2. Iodine sources and chemistry3. Flourine sources and chemistry

Reading• Parrella et al. (2012)• Sherwen et al. (2016)

PS8 Due at Class Start; PS9 OutOptional lecture to be given at rescheduledtime

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MONDAY WEDNESDAY

15th 22

Air Pollution and Radiation: ShortwaveKey Topics

1. Solar radiation spectrum2. Atmospheric scattering of radiation3. Visibility4. Colors in the atmosphere

Reading• Jacob (1999) Ch. 8.2• Seinfeld and Pandis (2016) Ch. 24

17th 23

Air Pollution and Radiation: LongwaveKey Topics

1. Atmospheric absorption of radiation2. Black body radiation (Planck’s Law)3. Earth’s radiative balance and effective

temperature4. The greenhouse effect

Reading• Jacob (1999) Ch. 7.1-7.3• Seinfeld and Pandis (2016) Ch. 23

PS9 Due at Class Start; PS10 Out

22nd 24

Chemical Forcing of ClimateKey Topics

1. Radiative forcing2. Global warming potential (GWP)3. Global temperature potential (GTP)4. Climate feedbacks5. Forcing agents

Reading• Jacob (1999) Ch. 7.4-7.6• Myhre et al. (2013) Sect. 8.1-8.7

24th 25

Climate Forcing of ChemistryKey Topics

1. Anticipated future emissions2. Changing chemical regimes and

air-quality “climate penalties”3. Mitigation strategies4. The future of air pollution

Reading• Jacob and Winner (2009)• Seinfeld and Pandis (2016) Ch. 23.10

PS10 Due at Class Start; PS11 Out

29th 26

Air Quality Policy: RegulationsKey Topics

1. Regulation in the United States (Clean AirAct and Amendments)

2. Regulation and pollution trendselsewhere in the world

3. International treatiesReading

• Kuklinska et al. (2015)

May 1st 27

Air Quality Policy: TechnologyKey Topics

1. Pollution control technologies2. Clean, low-risk, sustainable energy

systemsReading

• MJ Bradley & Associates (2005)PS11 Due at Class Start

6th

Exam PeriodFinal ExamTues. May 7 @ 8:30 AM

8th

Exam Period

3.1 RECITATION

This course follows the College credit hour policy for four-credit courses. This course meets twiceweekly for three academic hours per week. The course also includes a recitation for one academichour per week.In the 1-hr recitation session, the TA will go over example problems similar to the homework and ex-

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ams, and answer any questions from the class.

4 GRADING

Your final grade will be calculated with the following breakdown

Problem Sets: 40 %Midterm: 20 %

Final Exam: 25 %Short Presentation: 5 %

Quizzes: 5 %Participation: 5 %

Total: 100 %

4.1 EXAMS

All exams will be comprised of a multiple-choice section, a short-answer section, and a longer quanti-tative problem section.

4.1.1 MIDTERM

There will be one midterm exam administered in class, which will test qualitative content from Lectures1-13 and quantitative questions derived from Problem Sets 1-4.

4.1.2 FINAL

There will be one comprehensive final exam. The final will contain content from throughout thecourse, with a greater emphasis on the second half. Quantitative questions will be derived from theProblem Sets.

4.2 QUIZZES

At the end of each class, there will be a short quiz on the main concepts covered by the reading and/orlecture. Please bring calculators to class to use for in-class problems. Unexcused absences will resultin a zero on that day’s quiz. Quizzes on days of an excused absence (see below) will have zero weight infinal quiz grade.

4.3 PARTICIPATION

The participation score will reflect the following activities:

1. Attendance to class as reflected by quiz participation, and attendance to recitation. I must beinformed via e-mail of any absences ahead of time. Illness or other educational/research experi-ences are examples of excusable absences.

2. General participation: e.g., by asking or answering questions during class, and/or by asking ques-tions during office hours.

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4.4 SHORT PRESENTATIONS

Each student will be required to prepare and present one 5-minute slide presentation to the class forcredit during the recitation. In week four, a sign-up list of available topics and associated dates (begin-ning with lecture 12) will be made available in class. Sample topics might include:

• Health effects of ground-level ozone

• The effect of the record 1991 Mt. Pinatubo eruption on atmospheric chemistry

• Geoengineering: iron fertilization of the ocean: technique and feasibility

Each student will meet with me in advance of the lecture to receive feedback on their slides and pre-sentation.

5 HOMEWORK POLICY

The aim of the problem sets is to help you learn the course concepts. Working together with your class-mates is thus encouraged, although problem sets should always be solved and written up individually.If you collaborate, write who you worked with on your submission.

Show all work, explaining in sufficient detail how you arrived at the answer. Describe the rational be-hind each step using language like “Convert from kg to molecules” or “Apply the hypsometric equationto determine layer thickness.” Partial credit for ultimately wrong answers will be assigned based onwork shown. A correct answer with no work shown earns no credit. A numerical answer withoutunits is incorrect.

Problem sets are due at the beginning of class on the day indicated. After that, 10% is deducted off thepossible total score for each day late. No credit is given after one week late.

Your lowest problem set score will be dropped from your final grade calculation. You may use this atyour discretion as a free pass for a busy week or to try to maximize your mean problem set grade.

No exceptions to the late policy will be accepted, except with a medical note or request via the disabil-ities office.

6 CLASSROOM POLICIES

6.1 DIVERSITY AND DISABILITIES

This classroom is an inclusive and welcoming learning environment for all students regardless of back-ground or ability, consistent with both University policy and state and federal laws. Students must re-spect the different experiences, identities, beliefs and values expressed by their peers, and refrain fromderogatory comments about other individuals, cultures, groups, or viewpoints. Please let me know ifyou have any preferred nicknames, pronouns, etc., that you would like me to use.

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I encourage you to meet with me about any concern or situation that affects your ability to completeyour academic work successfully. Students requiring accommodations should contact one of the Ac-cess Coordinators at the Center for Excellence in Teaching & Learning (office: 1-154 Dewey Hall; e-mail:cetl@rochester.edu; phone: x5-9049 internal / 585-275-9049 external).

6.2 ELECTRONIC DEVICES

Cell phones must be silenced. You may use a laptop or tablet to take notes. Mobile devices and laptopsmay also be used for prepared active learning activities. However, they should not be used for anythingelse during class. If a peer tells me your actions on your laptop are distracting during a lecture, you willlose the privilege.

7 ACADEMIC HONESTY

All assignments and activities associated with this course must be performed in accordance with theUniversity of Rochester’s Academic Honesty Policy. A comprehensive description of the University ofRochester’s Academic Honesty Policy is available at: http://www.rochester.edu/college/honesty.For this course, all exams and reports need to be completed individually, but I encourage collaborationon the problem sets.

8 INITIAL MEETING

I would like to learn about your background and goals, both for this course and for the future, to helptailor the semester to those interests. You are encouraged to schedule (via e-mail) a quick 5-minutemeeting early in the semester. The meeting is entirely optional and will not impact your participationgrade.

9 FEEDBACK

I want you to get the most out of this class. Students are encouraged to offer feedback at any time aboutthe course and my instruction to me in person, through e-mail to lee.murray@rochester.edu, or via ananonymous note placed in my departmental mailbox located in Hutchison Hall 227. At the end of thecourse, I would greatly appreciate if you were to fill out the course review.