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=<b>Chemical Mechanisms and Kinetics in Atmospheric Chemistry</b>=
<b>Professor Mike Pilling - University of Leeds, United Kingdom,<br>
Department of Chemistry</b><br>
<b>Students are encouraged to write to Mike directly for questions regarding lecture notes and homework at M.J.Pilling@leeds.ac.uk</b><br>

[[File:Pilling.jpg]]<br>

==Dates and Time==
*<b>When: June 16th - 26th, 2009<br> 9:30 - 10:30 AM,<br> (Lecture 10 Will be from 10:40-11:40) </b>
*<b>Where: The lecture on Tuesday June 16 will be held in the JILA auditorium.<br> All of the following lectures will be held in the CIRES auditorium.</b>

==Directions==
<b>Directions to the JILA building can be found at the University of Colorado's [http://www.colorado.edu/Directories/WebMap/map.html?bldg=JILA Campus Map] <br>
Enter the JILA building from the North entrance, and the auditorium is immediately down the stairs to your right.</b><br><br>

[[File:Directions_to_cires_aud.jpg]]

==Abstracts==
===Lecture 1. Introduction to chemical mechanisms for tropospheric oxidation. Tuesday, June 16. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_one_6_16_09.pdf PDF of Lecture Slides]===
Volatile organic compounds (VOCs) are emitted into the atmosphere from a range of anthropogenic and biogenic sources. They are oxidized by a sequence of reactions that eventually, in the absence of heterogeneous processes, leads to the formation of CO2 and H2O. Along the way, a large number of partially oxidized compounds are formed. The reaction sequence is initiated by reaction of the VOC with OH, but reaction with NO3 or ozone, or photolysis can be important for specific species. The processes are photochemical, because OH is primarily formed in the atmosphere through reactions resulting from the photolysis of ozone. The chemistry depends also on the presence of NOx (NO + NO2), which is mainly emitted from combustion processes but is also formed in lightning and emitted by soils. Increases in  NOx concentration change the relative importance of some of the reactions and the nature of the chemistry. The principles of these reaction sequences, and the consequences of the interactions between them will be outlined.<br> 

This chemistry has an influence on a number of atmospheric processes, which will be discussed in this and in subsequent lectures:
*1.Ozone is formed and also removed by chemical reactions and is of importance at ground level because it causes respiratory problems in humans and also affects plant growth.  There are significant global, regional and local processes that affect the ozone concentration and hence human exposure.
*2.Ozone is also the third most important greenhouse gas. Its formation varies substantially throughout the troposphere. What are the factors that affect this variation?
*3.Methane is the second most important greenhouse gas and it is removed from the troposphere almost exclusively by reaction with OH. The concentration of OH is closely linked to the oxidation chemistry discussed above.
*4.This chemistry also influences the formation of secondary aerosol. 
<br><br>
===Lecture 2 Determinations of rate coefficients for elementary reactions Part - A. Wednesday, June 17. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_two_6_17_09.pdf PDF of Lecture Slides]===
1. Chemical mechanisms for atmospheric oxidation are made up of sequences of elementary, or single step reactions. The traditional approach is to investigate these reactions in the laboratory and measure their rate coefficients and the products formed experimentally. There are three main techniques that are used:
*Relative rate methods in which a reaction with a known rate coefficient is used  as a reference compound.
*Pulsed laser photolysis, in which a short lived species, such as OH, is generated with a laser pulse and its subsequent decay monitored using a variety of time-resolved techniques.
*Flow methods, in which a constant flow along a reactor is used to provide timescale for the reaction. The method is usually used in conjunction with an electric or microwave discharge that is used to generate the radical species.

2. Determining the products of the reaction can be difficult, especially when using time-resolved methods.<br> 

3. The determination of the temperature dependence of the reaction over the tropospheric range is essential for many reactions. In addition, some reactions of importance in the atmosphere, such as OH + NO2  HONO2, are pressure dependent. The rate coefficients must be parameterized (as functions of p and T) for inclusion in atmospheric models.<br> 

4. Understanding the p and T dependence has been greatly aided by the advent of relatively accurate electronic structure calculations. Some reactions proceed through several bound intermediates, and there is an interaction between reactive processes and energy transfer. Here master equation methods have proved useful. The techniques will be discussed and examples given.<br>

5. The field depends extensively on evaluation of rate data by experts. A further key topic is the generation of structure activity relations, which allow unkown rate coefficients to be estimated on the basis of known values.
<br><br>
===Lecture 3 Determinations of rate coefficients for elementary reactions Part - B. Thursday, June 18 [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_three_6_18_09.pdf PDF of Lecture Slides] [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/homework_one_6_18_09.pdf PDF of Homework One]===
This will be a continuation of the previous days lecture topic.
<br><br>
===Lecture 4 Chemical mechanisms and atmospheric models Part - A. Friday, June 19. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_four_6_19_09.pdf PDF of Lecture Slides]===
Chemical mechanisms for tropospheric chemistry are assemblies of the elementary reactions needed to describe the oxidation of a given organic compound and, for example, the formation of ozone. The mechanisms are used to help us understand the 
processes occurring in the atmosphere and the nature of the interactions between the elementary reactions. There main purpose, though, is for incorporation in atmospheric models that are used to predict the future behaviour of the atmosphere, e.g. from an air quality perspective or to develop policy. The chemistry is incorporated as a set of ordinary differential equations (odes), one for each species whose concentration varies. The models also incorporate atmospheric transport; in Eulerian models, it is necessary to solve the at a set of grid points that cover the space considered by the model – a region or the whole troposphere. Solving a large number of odes at each of these grid points carries a huge computational overhead and one approach has been to produce a ‘lumped’ chemical mechanism, in which the chemistry is described for representative species.<br>

An alternative approach is to use explicit mechanism, generated automatically by computer, or almost explicit mechanisms. These are directly linked to the lab chemistry discussed earlier. Such mechanism may be used directly in models, and they have been widely applied in interpreting field data. One such mechanism is the master chemical mechanism (MCM). The mechanism will be described and investigated via its website. One approach to lumping is via the MCM, where substantial recent progress has been made.<br>

An important issue is the accuracy of a chemical mechanism, which depends on a number of issues, but mainly its construction – has anything been omitted – and the uncertainty in its component rate parameters. Methods for assessing model uncertainty will be discussed. An important area of uncertainty is that of heterogeneous chemistry and some issues will be briefly examined
<br><br>
===Lecture 5. Chemical mechanisms and atmospheric models Part - B. Monday, June 23. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_five_6_22_09.pdf PDF of Lecture Slides]===
Note: slides 1-24 are the same as Lecture four.<br>
This will be a continuation of the previous days lecture topic.
<br><br>
===Lecture 6. Evaluation of chemical mechanisms using chamber experiments. Tuesday, June 23. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/Lecture_six_6_23_09.pdf PDF of Lecture Slides]===
There are many chemical reactions in the chemical mechanism for even modestly sized VOCs and there are significant uncertainties associated with the rate data and even uncertainties relating to which reactions should be included. It is important, therefore, to evaluate the mechanisms by comparing simulations based on them with experiments. The latter are generally based on chamber experiments, which provide a fairly realistic means of simulating the atmosphere.<br> 
	The use of large European outdoor chambers for this purpose will be discussed. The chambers at Valencia (EUPHORE) and Juelich (SAPHIR) are heavily instrumented and capable of measuring radicals and intermediates, such as oxygenates, as well as species such as O3 and NOxy. The chambers have been used to provide primary information, such as yields of key species. They have also been used to evaluate the MCM. Examples will be given.
<br><br>

===Lecture 7. Interactions between elementary reactions in a complex chemical mechanism. Wednesday, June 24. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/Lecture_seven_6_24_09.pdf PDF of Lecture Slides]===
Tropospheric oxidation can be thought of as a chain reaction, with initiation, propagation and termination reactions. It is therefore appropriate, and useful, to define, the chain length which is a measure of the ratio of the rate of propagation to the rate of initiation (or termination). There are complications, though, because, unlike the hydrogen + bromine chain reaction, there are multiple sites of initiation and termination, and the unique definition of the chain length is problematic; it should be defined, and stated, clearly. Examples will be given, including very clean environments, where the chain length is much less than unity, i.e. the rate of termination is faster than the rate of propagation, and highly polluted conditions, where the chain length can be much larger than unity.<br>

It is helpful, in understanding photochemical smog, to use the chain reaction concept. By assuming that the chain length is long, simple, general expressions can be obtained for the rate of ozone formation, that lead naturally to the idea of ozone isopleths, their dependence on the concentrations of NOx and VOCs, and the ideas of NOx and VOC control, that are important in developing policies for smog mitigation.<br>
 
The atmospheric lifetime of a given species is defined as the 1/e time of its loss and is equal to the reciprocal of the pseudo first order rate constant for this loss process. However, the interactions between the different reactions in which that species is involved lead to more complex behaviour in the atmosphere and the idea of the turnover time is useful. The turnover time and the lifetime can differ significantly. These ideas will be outlined, using methane and OH as examples.
<br><br>

===Lecture 8. Emissions Inventories. Thursday, June 25. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_eight_6_25_09.pdf PDF of Lecture Slides]===
It is necessary to provide estimates of emissions for modeling atmospheric processes. These estimates are provided in emissions inventories, which are spatially and temporally resolved, and include both anthropogenic and biogenic species.<br>

The lecture will include a brief review of global emissions of the major species (methane, CO, NOx, VOCs) and of global budgets. Some current issues associated with emissions inventories (primary emissions of NO2, future projections of NOx emissions, uncertainties in biogenic emissions) will be briefly outlined.<br>

A key problem is that of evaluating emissions inventories experimentally. Ground based measurements are generally made in discrete locations, and assessing distributed emissions and attributing sources is difficult. A key development is the use of satellite data, which provide spatially resolved data over large regions. Examples will be discussed, including measurements of NO2 and the use of HCHO to determine emissions of isoprene, for comparison with isoprene emissions models.
<br><br>
===Lecture 9 Current Issues Part - A. Friday, June 26. [http://www.colorado.edu/chemistry/volkamer/pilling_lectures/lecture_nine_6_26_09.pdf PDF of Lecture Slides] ===
The last two lectures will use the ideas developed in the earlier part of the course to examine some current issues in atmospheric chemistry:
*Ozone and ozone precursors can be transported over large distances and it is appropriate to consider that a component of ozone at any given location in hemispheric in nature. As a result, policies to control ozone cannot be developed just on a regional basis, e.g. in the United States, but require an international approach if the contribution from other continents is to be controlled. Measurements over the last two decades at Mace Head in W. Ireland, which, under westerly airflows provides a measure of the air arriving in Europe from other continents, show that the hemispheric contribution to ozone is increasing significantly, but not at a constant rate. The data will be examined and possible reasons for the increase discussed.
*Halogen chemistry influences the concentrations of a number of species in the atmosphere including ozone. The effects are particularly important in marine areas. The spatial extent of halogen chemistry is open to question – is it a purely coastal phenomenon, or are their contributions across the open oceans. The issue will be examined through recent studies at Mace Head and at an open ocean tropical site in the Cape Verde Islands in the eastern Atlantic. 
===Lecture 10 Current Issues Part - B. Friday, June 26.===
<b>Note: Lecture time is 10:40 - 11:40</b>
*The HOx (OH + HO2) budget has been examined in a number of recent field campaigns, e.g. in S. America and in S.E Asia. The results indicate that the current models omit a major source of OH. The evidence will be presented and possible sources examined.
*The rates of many chemical reactions depend on temperature. The question arises of the effect of climate change on tropospheric chemistry. Some aspects have been examined using global models and the likely effects of future changes in temperature on tropospheric ozone will be examined in the light of these calculations. 
===Podium discussion Friday, June 26===
*Both lectures on friday will be followed by a podium discussion from 11:45-12:30
*Confirmed speakers
**Mike Pilling (Leeds)
**Guy Brasseur (ESSL)
**TBD (CU)
**TBD (NOAA)

==Reference Material==
The aim of the course is to provide an overview of the influence of chemical kinetics and of chemical mechanisms on tropospheric chemistry. It will consist of 10 lectures and three written exercises /problems. The first 7.5 lectures will provide the basic material needed to understand the basic atmospheric chemistry and some aspects of its impact on air quality and climate change. The final 2.5 lectures will examine some current issues where there are uncertainties in our understanding and possible ways in which these issues may be resolved.<br>
The following text books are of value:
*R.P. Wayne "Chemistry of Atmospheres" (3rd Edition, OUP, 2000)
*D.J. Jacob, "Introduction to Atmospheric Chemistry", Princeton University Press, 1999. (available on his website)
*G.P. Brasseur, J.J. Orlando, and G.S. Tyndall, "Atmospheric Chemistry and Global Change" (OUP, 1999)
*J.H. Seinfeld and S.N. Pandis, "Atmospheric Chemistry and Physics: From Air Pollution to Climate Change", (Wiley, 1998)
*More detailed references to reviews and research publications will be given during the lecture course.
<br><br>