Chemistry and Biochemistry
Chemistry 410
Physical Chemistry
Syllabus
- Student Learning Objectives
- Prerequisites
- Course Material
- Grading Scheme
- Assignments
- Drills
- Quizzes
- Exams and Final
- ACS final exam in CHEM 410B
- Labs
- Lab Practical
- Missed Assignments
- DSS Accommodation
- Additional Hours
- Conduct of Class
Instructors:
- Andrew Cooksy (lecture and 410A Monday lab section 1)
- David Pullman (410A Wednesday lab section 2)
Materials:
- Book: spiral-bound lecture notes, printed by Montezuma. To keep your costs down, solutions to the end-of-chapter problem are not included, but are available on the course downloads page with the password to be given in class. Corrections to notes and solution sets will be posted to the CHEM 410A and CHEM 410B home pages, as well as other general announcements.
- There is no 410A lab manual. Short handouts will be distributed in lab. If any advance preparation is required for a particular lab, you will receive a handout in the preceding week's lab.
- Reserve materials: A few of the more recent Physical Chemistry texts are on reserve at Love Library, for those of you wishing to see an alternative presentation of the same material. Note that in most of these texts quantum will appear in the middle and thermodynamics at the beginning of the book, and statistical mechanics (Part IV in my notes) is usually not given so much attention.
- Blackboard will be used only to post grades for assignments. Please be aware that Blackboard does not know how to deal with certain aspects of our grading scheme, such as dropping the lowest scoring exam, so the point total evaluated by Blackboard is not what I use in my grading.
Student Learning Objectives:
In this course, encompassing Chem 410A and Chem 410B, we will examine in detail
the theoretical framework that justifies all chemical laws.
The student successfully completing the course will be able to:
- analyze diverse chemical systems and reduce them to their principal chemical and physical components and interactions for the purposes of mathematical description;
- calculate or estimate numerous physical properties of molecular structure and interaction using principles of quantum mechanics, statistical mechanics, chemical thermodynamics, and reaction kinetics;
- eventually build a meaningful intuition regarding chemical behavior based on this unified foundation of chemical theory;
- use Excel and Maple to carry out several basic operations for the analysis and visualization of scientific data (410A lab).
Prerequisites
Physical chemistry is a fairly demanding course, and we spend little time
reviewing material from the foundation courses that come earlier.
Enforcing the prerequisites allows us to better match the course to those
students who have at least partly established that foundation through their
prior coursework. We do not enforce the prerequisites at registration
because this would make it impossible for many qualified transfer students
to register. However, students who do not fulfill the course requirements
listed below will be dropped from the course by the
instructor:
- MATH 151, PHYS 196, and CHEM 231 and their prerequisites (MATH 150, PHYS 195, CHEM 200 and 201). To take CHEM 410A, a student must have already passed all of these courses. Concurrent enrollment is not sufficient. If you are missing only the PHYS 196 lab, you may enroll in CHEM 410A, but to register for CHEM 410B in the spring, you must either have completed or be enrolled in PHYS 196L by then.
- MATH 252 and CHEM 251. Although listed as prerequisites in the General Catalog, this term a student who has not taken one of these courses may take CHEM 410A, provided the student is (and remains) concurrently enrolled in the missing prerequisite course.
This is not a math class, and so I try to avoid unnecessarily lengthy mathematics in the problems. Usually. However, mathematics is our principal tool, and you need to be very comfortable with elementary algebra, geometry, and calculus (up to derivatives, simple integrals, and power series). The math is all manageable one step at a time, but there will sometimes be many steps.
This is pretty much a physics class, however. The first semester in particular we will call on results from mechanics and electromagnetism to justify some of our conclusions about atomic and molecular structure. You are probably familiar with the concepts if you've taken those courses, and we will introduce (but rarely prove) any equations from physics we need before using them.
There is an introductory chapter ("Chapter 0") to the course notes that summarizes the prerequisites we will rely on most often. (I will often make this available for download before the 410A semester begins. Please don't hesitate to ask.) Your texts for previous math and physics courses should help you if you're rusty in those areas.
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Course Material
In one sentence, the course covers principles of atomic and molecular structure,
molecular interactions, statistical mechanics, chemical thermodynamics,
chemical kinetics.
General
The 410A/B sequence covers the fundamental physics of chemical systems,
including structure, energetics, and interactions of molecules.
The material can be applied to inorganic, organic, and
biochemical molecules and reactions.
In fact, most of the important results in physical chemistry
will already be familiar to you from general chemistry.
If you find the details of our work in this class obscure the results,
you may want to go back and look at the relevant section
of a general chemistry text.
Topics and Organization
Physical chemistry examines chemical phenomena both on the
scale of individual atoms and molecules (the microscopic
limit) and on the scale of 10,000 gallon chemical reactors
(the bulk or macroscopic limit).
In this class, we build from the microscopic limit to the macroscopic:
- quantum mechanics of atoms
- quantum mechanics of molecules
- molecular interactions at microscopic scale
- statistical mechanics and extrapolation to the macroscopic limit
- thermodynamics and bulk properties of non-reactive systems
- bulk reaction thermodynamics and kinetics.
This differs from the organization of most textbooks in the field, which deal with quantum mechanics and statistical mechanics only after the more familiar topics of classical thermodynamics and kinetics. Although this can be a more easy-going way to start the class, that traditional organization makes thermodynamics and kinetics seem somewhat mysterious ("...and here's another equation which happens to be true...") and makes quantum mechanics seem irrelevant. Therefore, I am using my own lecture notes instead of a real textbook as your reference. Some real textbooks are on 3-day reserve at Love Library (see below).
One of the costs of using these notes is that they have not been as carefully proofread as a real textbook. Please let me know of any errors you locate in these notes, and any recommendations you have for improving them. A record of significant errors will be kept on the main course web pages.
The primary reference for the course is still the lectures themselves. No material is covered on the tests that has not been discussed in class, and occasional lecture topics may appear on the tests even if they are not included in the reading. But if you read ahead, you may find the lectures more useful, and your note-taking may be reduced to adding comments to the text rather than recording the entire lecture.
A more detailed breakdown of the course topics follows the chapters of the course reader in sequence:Chemistry 410A: Microscopic Systems | |
|---|---|
| chap | topic |
| Part I: Atomic Structure | |
| 1 | Introduction to quantum mechanics |
| 2 | One-electron atoms |
| 3 | Many-electron atoms |
| Part II: Molecular Structure | |
| 4 | Chemical bonds |
| 5 | Molecular symmetry |
| 6 | Electronic states |
| 7 | Vibrational states |
| 8 | Rotational states |
| Part III: Intermolecular Interactions | |
| 9 | Intermolecular forces in gases |
| 10 | Clusters and macromolecules |
| 11 | Structure of liquids |
| 12 | Structure of solids |
Chemistry 410B: Macroscopic Systems | |
| Part IV: Extrapolation to Macroscopic Systems | |
| 13 | Introduction to statistical mechanics |
| 14 | Statistical mechanics and gases |
| 15 | Stat mech and condensed phases |
| 16 | Transport processes |
| Part V: Non-reactive Macroscopic Systems | |
| 17 | Introduction to thermodynamics |
| 18 | Energy and enthalpy |
| 19 | Entropy |
| 20 | Phase transitions |
| 21 | Solutions |
| Part VI: Reactive Macroscopic Systems | |
| 22 | Chemical thermodynamics |
| 23 | Chemical kinetics: elementary reactions |
| 24 | Chemical kinetics: multistep reactions |
| 25 | Applications of physical chemistry |
For a tentative lecture schedule, please see the course calendar for CHEM 410A or CHEM 410B.
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Grading Scheme
Overall Grading Scheme
- quizzes 10%
- drills 10%
- 6 20-minute exams
- lowest score: 0%
- 5 highest scores: 10% each
- cumulative final: 30%
- drills 10%
| A | 80-100% |
| B | 60-79% |
| C | 40-59% |
Lab Grading Scheme (410A only)
The lab grade is based on several 10-point labs, with the lowest score dropped, and one 30-point lab practical, an in-lab exam based on the preceding lab material. The lab and lecture instructors (not always the same person) will determine the grading scale for the labs, and at the end of the semester the total lab scores will be normalized to the lecture grading scale below (so that for example a high B in lab is converted to a high B on the lecture grading scale). The final score will then be computed as 0.25(normalized lab score) + 0.75(lecture score). Go to top
Assignments
Drills
Three or four 10-minute quizzes on material that anybody
getting a passing grade in physical chemistry absolutely must know,
primarily calculations and techniques that should have been
covered in General Chemistry.
These are sometimes directly relevant to the lecture material,
and the dates on which they are given may be changed during the
semester to accommodate the variable lecture schedule.
Because it should not be necessary to spend a lot of time preparing for these,
three-day notice that a drill will be given is considered sufficient.
Drill material will not usually be reviewed in lecture.
- 410A drill topics may include:
- unit analysis and conversions,
- stoichiometry,
- reasonable values for physical quantities,
- basic integrals and derivatives,
- electron configurations for atoms,
- Lewis structures and VSEPR theory for molecules.
- 410B drill topics may include:
- more unit conversions and reasonable values,
- more basic calculus, including power series approximations,
- balancing chemical reactions,
- calculating enthalpies, energies, and entropies of reaction,
- elementary kinetics with rate laws.
Quizzes
One 10-minute quiz is given before each exam,
usually consisting of two problems, and
usually based on the more straightforward lecture material.
The primary goal of the quizzes is to get students preparing for the
exam a few days in advance.
They are not intended to reproduce problems
that will appear on the exams. Studying solutions to these
assignments alone will usually be of little benefit on the exams.
Exams and Final
There will be six 20-minute exams and one 2-hour final.
CHEM 410B has an additional ACS final exam.
For all exams and the final:
- Attempt all the questions.
- You are permitted to consult your own notes and our "textbook" during the exams, but additional textbooks are not allowed (because students would then not have equal access to the same information).
- All problems are equal credit but not equal difficulty. The prepared student will recognize the easier questions.
- The exams will begin with several short-answer problems, dealing with the most fundamental concepts in as straightforward a manner as I can manage. This section will count for 40% of the exam. Although there may be exceptions, in general do not expect partial credit to be available on these problems.
- There will be additional, harder problems, drawing from more specific topics. Partial credit is always available on these problems.
- For full credit, please put down your pen or pencil as soon as I say the exam is over.
Although the exams are all open-book, you must come to them prepared. You will have time only for very brief consultation of your notes. Attached to each 20-minute exam are what I deem all necessary tables, constants, and complicated equations. The final exam will offer you almost twice as much time per question, so will feel less rushed. But I find that the added time does not tend to greatly raise students' scores.
The 20-minute exam on which you get your lowest score will be dropped from calculation of the final grade. If you are unable to take an exam for any reason, that exam will become your dropped score. There are no make-up exams. Please beware of choosing an exam to drop; new course material is based on previous material throughout the two-semester sequence, and it doesn't pay to purposely neglect any section of the course.
The final exam will review all of the course material for the semester, and provides an opportunity to improve recorded scores on some problems from the short exams. Your exam scores are recorded question-by-question. After writing the final, I will match some of those questions to questions on the 20-minute exams which covered the same topic. If you score higher on one such question on the final than you did on the corresponding question on the 20-minute test, I will raise your grade on the 20-minute test. Beware of counting too much on this: because there are not nearly as many questions on the final as on the set of 20-minute tests, the final will not be able to correct substantially for routinely poor performance on the 20-minute tests. Also, the final is not capable of changing grades as much as one might think. The wide grade ranges of the grading scheme (with a 20% range for a B, for example) make it hard for any one assignment to shift the final total by a whole letter grade.
ACS final exam in CHEM 410B
Two final exams will be offered in CHEM 410B only:
- My own final exam, in the same format as the 20-minute exams, covering only the material from CHEM 410B and given on the last two days of class. This is the official final exam for the course, and attendance at this exam is mandatory.
- The ACS standardized, multiple choice examination in physical chemistry, covering material from CHEM 410A and CHEM 410B. This exam will be offered during the 2-hour slot scheduled for our final exam, to adhere to the testing procedures stipulated by the ACS. Attendance at this exam is optional, because it does cover material from 410A.
Labs (410A only)
The labs must normally be completed during the class period,
in the assigned classroom.
Exceptions require prior consent of the instructor.
If more than one lab section is being offered,
then changing sections for a particular lab to
accommodate a personal schedule conflict is allowable, provided
that consent is obtained from the instructor(s) for both sections
and that there are enough computers available.
Lab outline
- Introduction to Excel. Entering and evaluating formulas; naming cells.
- Numerical integration. Using the Newtonian integration scheme to evaluate integrals along one coordinate.
- Introduction to error analysis. Gaussian error distributions; calculating averages and standard deviations by formula and using the internal Excel functions.
- Introduction to error propagation. Estimating by the slope rule the errors of properties calculated from measured properties.
- More error propagation. Examples from spectroscopy.
- Introduction to linear least squares fitting (LINEST). Finding best-fit slope and intercept for a linear data set, and plotting trend lines.
- More linear least squares fitting. Linearizing non-linear equations, and resulting propagation of errors.
- Introduction to non-linear least squares fitting (Solver). Evaluation and minimization of chi squared.
- More non-linear least squares fitting.
- Introduction to symbolic math programs (Maple). Plotting wavefuntions, calculating basic physical properties from the wavefunction.
- Graphics in Maple. 3D plots, animated plots.
- Introduction to quantum chemistry computations (Gaussian 03).
Lab Practical (410A only)
A lab assignment consisting of numerical integration,
data and error analysis using EXCEL and/or MAPLE.
The material is based entirely on the methods of the preceding labs,
and is not intended to be longer or more difficult than any of those assignments.
The instructor will normally provide a summary of the lab assignments
for your use during the practical.
You are welcome to take notes on this handout while preparing for the practical,
but no other reference materials may be used during the practical.
Only your handout and the instructor may be consulted during the practical.
Missed Assignments
This course cannot always be your top priority, and in consideration of this,
the lowest scores of the 20-minute exams and of the regular labs are dropped.
If you cannot make one of these assignments for any reason, this becomes the
dropped assignment. Because it is not appropriate for me to weigh the magnitude
of one student's excuse against another's, there are no exceptions to this,
except when circumstances prevent a significant fraction of the class from
being able to make the assignment (as, for example, with the wildfires of
2003 and 2007).
Additional Hours
We have a lot of material to cover, and we will cover almost all of it.
Lectures are therefore rather fast-paced, and it is often not possible
to work through example problems during class time.
To make up for this, please take advantage of my office hours to go
over lecture material, sample problems, and to review quizzes and exams.
In addition to the regular office hours, a totally optional examples session is held each Monday evening (starting the second or third week of class). This allows us to go over additional problems, and at a more leisurely pace. New material for tests is never introduced at these sessions. You may arrive and leave anytime during the session, but please bring questions about the material or suggestions for problems to work through.
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Conduct of Class
Please ask questions. If we really are in too much of a hurry, or if I'm just stuck for a better explanation than I've given, we may need to postpone the discussion until office hours. However, classes in recent years have been exceptionally quiet, which only encourages me to keep talking.Please always disable any noisy electronic devices you have, such as cell phones and watch alarms, before you come into class so that they will not disturb us during lecture or lab. If you must use your phone during lab, please leave the room first.
The goal of the labs is for you to understand how to use the software to accomplish a specific task, and the assignment is there to keep your efforts focused. Please get assistance if you need it. In addition to asking the instructor questions, you are welcome to confer with each other during the regular labs, but only you and your instructor are permitted to edit your assignment. For example, other students should not type an expression into your Excel spreadsheet, or use your mouse to demonstrate how to change the appearance of your chart. Please also remember that the lab practical (worth 3 labs) is a non-trivial test of the skills introduced by the regular labs where you may not get assistance from your classmates, so you will want to know how to do your own work for these assignments.
I prefer not to invest class time in discussing the course administration, but of course you may ask me to justify any aspect of the syllabus. Please reserve those questions for office hours or email.
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