Download Syllabus 452 Aut`14 - University of Washington

SYLLABUS: CHEM 452-A, AUTUMN 2014, SLN 12248
• Canvas link for homework and handouts: https://canvas.uw.edu/courses/914041
• Do NOT use Canvas to send me messages or questions. I won’t check it; see other methods below.
• Discussion board for announcements, questions: https://catalyst.uw.edu/gopost/board/slkeller/37799/
• Address questions about subject matter to https://catalyst.uw.edu/gopost/board/slkeller/37799/
• Address questions about personal matters to:
[email protected] (please put “Chem 452” in the subject line)
(Questions relevant to all students will be bounced back for you to submit to the discussion board.)
• Lectures: MWF 11:20-12:20, Bagley 261. You may prefer Prof. Khalil’s teaching style; she teaches the same
course in Bagley 260 at the same time. The Department felt that you would enjoy smaller sections and a
choice of professors rather than a large section of 160 students in Bagley 131, so we invested the money
to split the class into two sections. Prof. Khalil and I agree that we want you to find the best learning
environment, so you are welcome to transfer between our sections if space is available or to visit the
other section’s lectures. Exam topics in the two sections will likely diverge as the course progresses.
• Homework and Study Sessions (All entirely optional!)
• Tuesdays 11:30-12:20, BAG 261, Sarah (Start your homework rough draft by this session.)
• Thursdays 11:30-12:20, CHB 239, Jonathan (Work on your homework final draft at this session.)
• Student-organized session: WHEN: _____________________ WHERE: _____________________
• Instructor: Prof. Sarah L. Keller
Office: Bagley 214, 543-9613, office hours are during Tues. study sessions and by the discussion board.
• TA: Jonathan Litz ([email protected]). If you need help outside of study sessions and GoPost,
e-mail him to schedule an appointment. He’ll let me know if I should cover for him to help you faster.
GRADING
There will be homework, two mid-terms and a final. The mid-term exams are expected to fall on
Monday, October 27 and Monday, November 24. Any date changes will be announced in class and on the
GoPost discussion board. I scheduled around BIOC440 exams to ensure no overlap. UW has scheduled your
final for Wednesday, December 10 from 2:30-4:20pm in Bagley 261 – I have no control over this date/time.
Note that there is an extra 25% in the total below:
Problem sets: 25% of the grade
Midterm 1:
25% of the grade
Midterm 2:
25% of the grade
Final:
50% of the grade
One part (25%) of your grade will automatically be dropped to maximize your grade. If your
worst grade is on the final, the final will count for only 25%. Don’t use the dropped score as an excuse to skip
homework. It is difficult to pass the class if you blow off the homework and also fail an exam. Since exams and
homeworks have different numbers of points possible, all scores will be recalibrated to the same mean score to
determine which grade is dropped. In other words, if I inadvertently write an unusually difficult exam, you will
be OK. I don’t have a formula to tell me mid-quarter what your projected grade is, so don’t ask. That said, if
you enjoy obsessing about grades, you can review details about how I calculate grades at:
http://faculty.washington.edu/slkeller/teaching.html. The mean final grade will usually correspond to a 2.9.
If you do an outstanding job as a class, you will be rewarded by a higher mean grade. This happens in about
half of my classes. Since there are two sections of this class, Prof. Khalil and I have decided to coordinate the
grades of our classes. This means that you should not expect a higher grade in my class vs. hers.
EXAM DETAILS
If you arrive after an exam has started, you may not stay late. If you often oversleep or miss buses, get a
friend to call you or search “free reminder call” online. There will be no make-up exams. If your absence
from a midterm is excused, your final exam grade will be counted as your missing midterm grade. To request
an excused absence, provide proof of your emergency (e.g. a doctor's note, an accident report, a memorial
folder) with a contact name and phone number. If you’d rather not have the flu during an exam, get a flu shot.
Absences due to participation in university-sponsored activities require prior approval (do this in week 1-2 of
the quarter). Departmental policy is to not offer make-up or alternate final exams. If you have completed work
at a passing grade through week 8 of the course, you may ask me to consider giving you an “incomplete”. To
remove an incomplete from your transcript, you must take the final exam for the same course in the next regular
academic quarter in which it is offered. If you are absent from the final and ineligible for an incomplete, a
course grade of 0.0 will be given.
1
I have already posted a short table of physical constants for water that I will provide on all exams. For
midterms, I will also supply a condensed list of all equations that I think you will need. A copy of last year’s
lists are already posted. On the final, I will not provide an equation list, but you can bring and use your own
sheet of notes throughout the exam. Your notes should be on an 8.5 x 11” sheet of paper, can fill both sides, and
must be turned in with the exam. To recap, on midterms I provide equations and you may not bring notes. On
the final, no equations are provided, but you may bring notes.
On exams I require you to use a scientific calculator that is non-graphing and does not do calculus.
You’ll want to practice doing your homework with this kind of calculator. Bring it to exams; learning how to
use a new calculator (e.g. one that somebody lends you) during an exam is stressful. All large-memory
calculators must have their memories zeroed during exams, with the penalty of a zero score on the exam.
I will post compendia of exam practice problems. For the midterm exams (but not the final), about half
of all points will come these posted practice problems. As a result, I will not give you the answers to the
practice problems (although you are welcome to compare answers with each other).
Midterm exams may be regraded, but final exams will not be regraded unless there is an egregious error
on our part. Disputed points for a regrade must be above a cutoff (typically 5%) unless there is simply an
addition error in totaling the points. Requests for regrades must be accompanied by a note detailing your reason
for a regrade. Regrade requests will be accepted only within one week after exams have been returned.
HOMEWORK DETAILS
Assignments and required coverpages will be posted on Canvas – please verify that you can access the
first set. Most homework occurs in three stages: (1) a rough draft with a cover sheet is due Thursdays at 10:59,
(2) answers are posted 2 minutes later, and (3) a final draft with a cover sheet is due Fridays at 4:59pm.
You will scan your handwritten homework into a single .pdf file with a cover page that is included with
the homework, and submit it via Canvas. You are welcome to use your own scanner, but not expected to have
one. There are free scanners for you all across campus, especially stand-alone scanning stations on the 2nd floor
of Odegaard. Ask at their help desk and see http://f2.washington.edu/fm/c2/printing-copying/dawg-prints-copylocations#scan. Do not wait to the last moment to learn how to scan. Late homework will not be accepted,
whether or not you experience scanning difficulties (to prepare you for future firm deadlines on job applications
and grant proposals deadlines). If you plan to be out of town, no problem, simply turn in your work early.
View all pages of your pdf before submitting it. Verify that (1) all pages are right side up, (2) all writing
is dark enough to read, and (3) all writing falls within the scanned area. If you need help adjusting scanner
settings, ask the Help Desk. The TA will grade the single, last file that you upload before the deadline. You are
welcome to upload new versions if you have corrections, but submissions after the deadline will be ignored.
Start your homework early. The homework can be challenging. I respect you intellectually, so I am not
going to give you busywork. You are encouraged to work together on homework (more on this later), but turn in
your own work. I want you to learn to think like a scientist, and to be able to apply what you’ve learned to real
problems that you have not seen before. I try to post the homework a full week before it is due, and if it is not
there, let me or the TA know because occasionally glitches happen, like the wrong file gets posted by mistake.
If the university’s server goes down the day before the due date or you get sick, homework is still due.
10 points total for the Thursday rough draft (before the answer key is posted)
You will receive 10 points for attempting some part of each problem, whether or not you finish, and half
for not attempting all. Your rough draft can be messy. Do not waste time making it look nice.
10 points total for the Friday final draft (after the answer key is posted)
8 points – Did you do all of the problems and include correct answers? 4 points for unfinished work.
1 point - Neatness. This point is easy to get. Are the questions all in order? Are the answers and the
question numbers boxed? Don’t expect full credit if the TA has difficulty finding your answers. Is
your name legible on the cover page? You do not get extra credit for condensing your whole
homework set on one page. Use space to show your work. If your rough draft was legible and
complete, don’t waste time rewriting your work for the final draft – minimize busywork.
1 point - Context. This point is much harder to get. Once you are done with a question, you should
reflect upon what your answer means (not just “this was hard”) and write it in a phrase or
sentence on the coversheet. Numbers are meaningless without a broader context.
2
Your lowest 20-point homework score will be dropped to account for the inevitable week when you
don’t turn in homework on time, or have an emergency/sickness. Homework will not be regraded except to
correct addition errors for your final score. Answer keys will be posted on Thursdays. Even if you receive a
perfect score on the homework, it is your responsibility to compare your (possibly incorrect) answers with the
key and make sure that you understand them.
Motivation: Back when we had funds to hire enough TAs to grade all homework content, we found that
high exam grades correlated with high-quality homework. Eventually working through problems on your own
(even if you did them with friends the first time) is very important since it is the only concrete way for you to
ensure that you understand material before exams. It behooves you to do and understand the homework since
many exam questions will be based on the homework. If you come across a concept in physical chemistry from
your research or reading that you’d like to see on a homework or exam, send me a reference and I may use it.
EXTRA CREDIT
1) If you find an error in my notes (in an equation or a concept, not just a typo or English mistake), you
will be rewarded with one extra credit point applied to your homework score (up to 3 total).
2) Based on data published in 2014 by Eddy et al. (CBE-Life Sciences Education), I will be instituting a
system of randomly calling on students to participate in class. My goal is to make equal educational
opportunities available to all. For every question you respond to (“I don’t know” is an acceptable answer), I will
apply one extra credit point to your homework score.
No other extra credit is offered. If you have time to do further extra credit, you will be better served by
preparing for the final exam.
TUTORIALS/STUDY SESSIONS
Tutorials are devoted for you to work in groups on homework. I will not lecture during tutorials and
there will be no quiz. Attendance is not required at tutorials, so if you wish to schedule another class during this
time, you may. Nevertheless, I very strongly encourage you to attend tutorials. Historically, large fractions of
students have attended tutorials, and the students attended tutorials have done better in the class than students
who did not. This is because you learn more by helping each other with problems and by checking your
answers than by listening to my lectures. Even the best students improve by explaining concepts to other
students in study sessions. Plus, attending the tutorials makes the class more enjoyable because you will
complete your homework faster and because you will form better study groups for exams.
LECTURE NOTES
My goal is to make it easy for you to learn, for me to teach, and for the T.A. to grade. I have spent a
great deal of time preparing lecture notes because I want you to spend class time listening, participating, and
jotting down key points rather than copying detailed notes. Each day’s notes will be posted at the webpage after
that lecture. (No, you may not have the notes beforehand. I want you to think in class when I ask a question.)
In return, you will have more personal responsibility for grading your homework and making sure that you
understand the answers.
TEXT
Atkins and dePaula, Physical Chemistry for the Life Sciences. ISBN: 1-4292-3114-9, 2nd Edition.
This summer, the Chem 452/453 faculty reviewed 12 textbooks because students disliked the text we used
previously. No perfect text meets all of our needs. We feel that the Atkins text is the most clearly written, with
the most biological examples. However, it does not treat the mathematical notation with the rigor we’d prefer.
Therefore, we will present that rigor in our lectures and hopefully you will find reading the book enjoyable.
A note about textbook prices: Assess your own learning style in order to decide whether to buy the
book. If you are a purely auditory learner and do not find that reading enhances your learning, then consider not
buying the textbook. We listed the book as required so that students who are on financial aid can get assistance
in purchasing it, but if you are willing to put in extra effort, you can find the same concepts described in
resources that cost less. We take the issue of textbook prices so seriously that Prof. Drobny agreed to try a free
online textbook for one term of Chem452. That book was “Themodynamics and Chemistry” by Howard DeVoe
and can be downloaded from www2.chem.umd.edu/thermobook. Prof. Stoll used it as a student and liked it; the
text contains the concepts you’ll use. However, it isn’t particularly enjoyable for biochemistry students to read;
Prof. Drobny’s students disliked it. Another option is E. Brian Smith’s “Basic Chemical Thermodynamics”
($31 from Oxford Press), which is dense, with no biological examples, but with good content. Some students
supplement with “Applied Mathematics for Physical Chemistry” by James R. Barrante. Other textbooks used in
similar courses are by Raymond Chang, by Tinoco, Sauer, Wang, and Puglisi, or by Engel and Reid.
3
LAPTOPS
I have received such negative feedback from students regarding laptop usage by other students that I’m
tempted to ban laptops altogether. Instead, here is my current policy:
a. Laptop computers may be used only for note-taking. Don’t even think of opening another window. Students
using computers and phones for activities not related to class distract other students. I know this because
(1) they’ve told me so, and (2) research has shown that a game or a picture on a laptop distracts not only the
student using the computer but also students nearby (Yamamoto 2007, Fried 2008).
b. Students using laptop computers to take notes or phones to check in on their e-mail must sit behind all other
students in order to not distract those who are trying to pay attention. Students who use laptops for non-class
activities will be asked to turn off their computers and may lose their computer privileges for the classroom.
My goal is to enable fair and equal access to education. If students in front of you are distracting you so that
you cannot pay attention in class, I hereby empower you to ask them to move.
COMMON COURTESY
I will not take attendance. If you don’t want to be in class to pay attention, don’t come. If your phone
rings, or if you are texting, checking e-mail, or reading a newspaper, I will ask you to leave. It is distracting and
annoying to other students. They tell me so. I will work very hard to start class on time and end on time. I
realize that, like me, you have many demands and obligations on your time. Nevertheless, you signed up for
this class at this time, and now I expect you to schedule around it. You may think that arriving late, packing up
early, or leaving early is simply a personal issue, that you can do these things without disturbing other students.
This is false. Ideally, arrive early enough to complete all noise-making activities (removing your coat, getting
out notes, zipping up your bag, turning off your phone) before class begins.
DISCUSSION BOARD
I’ve instituted a Go-Post discussion at the address on the first page. This will be particularly helpful to
anyone who cannot attend study sessions. It is a forum for you to give hints and help (rather than full answers)
to each other’s questions. It is also where the TAs and I will make announcements, offer hints to working
problems, and correct any typos. We are using the discussion board on Go-Post rather than on Canvas because
in response to strong recommendations by last year’s students in Chem452.
PREREQUISITES
This course requires calculus. Most students are rusty at calculus, and need to review derivatives and
integrals, especially those involving logs. Techniques common to linear algebra are helpful but not required.
FEEDBACK
There are two ways to give me feedback. The first is to fill out evaluations at the end of term. The
second (and preferred) method is to post a message on the discussion board or write me e–mail with “Chem
452” in the subject line. You can complain about something small (e.g. if my writing is too small) or something
big (e.g. you think I explained a concept incorrectly). If you feel too uncomfortable to contact me directly,
contact a T.A. and ask her/him to relay the message without your name attached. If you write with an issue that
affects the whole class, I will probably respond via the discussion board. I’m most likely to make major
changes to my class if there is good, hard data in the educational literature showing that the changes result in
better student learning or experiences, so please share any data you find.
TRANSITION TO DIFFERENT METHODS OF LEARNING
In your future careers you will need to learn things on the job. It is unlikely that there is a textbook
written for most of the topics you will encounter. My goal is to help you mature from learning only through
assigned textbooks to learning through a variety of sources. In this course you’ll be exposed to the text, lectures,
class notes, seminars, and journal articles. In your professional life you will never find a real problem to solve
in which exactly all of the right information is given to you, in the right units. You will always be faced with
either too much information or too little information and have to decide which parts are necessary. Being able
to tackle problems under these circumstances is an important skill and I will help prepare you in this course.
COLLOQUIA, SEMINARS
At this point in your college career, you are contemplating future jobs or graduate school. (By the way,
if you attend graduate school in chemistry you get paid >$25,000/yr to study.) The Chemistry advisors maintain
files on graduate schools. The Chemistry Dept. produces a weekly “Bagley Bulletin” listing jobs and seminars.
Ask the receptionist add you to the e-mail list for the bulletin. I strongly encourage you to attend seminars and
especially colloquia, which are more general talks. I have no idea how students can decide which field of
science to pursue without seeing what research is underway. Going to seminars is the easiest way I know of to
4
learn about current research. Most talks begin with a 5-minute introduction to the field. It is perfectly OK to sit
near a door and then very quietly slip out after the speaker’s introduction if you become bored.
How do you find out what seminars are on? There is unfortunately no central UW website that lists all
seminars on campus. Start at the “Campus Events Calendar” at www.washington.edu/calendar/ (unclick
everything except for “Lectures/Seminars” and select “all” under “Ongoing event”). Next, surf the websites of
your favorite departments, and look at flyers in the halls. In the Chem Department, seminar notices are posted
in the mailroom, on the web at: http://depts.washington.edu/chem/newsevents/eventsall.html, and in the hallway
between the front stairwells on the second floor of Bagley. I often post notices to seminars that look more
accessible to undergraduates on the class discussion board. Attendance at one seminar will be part of one of
your homework assignments. You may attend any seminar in science (broadly defined) on campus for this
assignment, not merely one that I recommend.
DISABILITY
To request academic accommodations due to a disability, contact Disabled Student Services, 448
Schmitz, 543-8924 (V/TTY). If you have a letter from DSS indicating you require accommodations, please
present the letter to me so we can discuss accommodations you might need for the class.
SCHEDULE OF ASSIGNMENTS – Double-check with Canvas to guard against any typos below
Friday, Sept 26, 4:59pm, Homework 1A (math refresher). There is no rough draft due this week.
(Note, if you have registered with UW Disability Resources for Students and are allowed 2X time on
“quick turnaround assignments”, then Homework 1A is due Oct 1 at 4:59pm. All other assignments
will be posted a week in advance, so do not require a DRS extension.)
Thurs, Oct 3, 10:59pm, Homework 1B rough draft
Friday, Oct 3, 4:59pm, Homework 1B final draft
Thurs, Oct 9, 10:59pm, Homework 2 rough draft
Friday, Oct 10, 4:59pm, Homework 2 final draft
Thurs, Oct 16, 10:59pm, Homework 3 rough draft
Friday, Oct 17, 4:59pm, Homework 3 final draft
Thurs, Oct 23, 10:59pm, Homework 4 rough draft
Friday, Oct 24, 4:59pm, Homework 4 final draft
Thurs, Oct 30, 10:59pm, Homework 5 rough draft. This is a half-homework set after your midterm.
Friday, Oct 31, 4:59pm, Homework 5 final draft
Thurs, Nov 6, 10:59pm, Homework 6 rough draft
Friday, Nov 7, 4:59pm, Homework 6 final draft
Thurs, Nov 13, 10:59pm, Homework 7 rough draft
Friday, Nov 14, 4:59pm, Homework 7 final draft
Thurs, Nov 20, 10:59pm, Homework 8 rough draft
Friday, Nov 21, 4:59pm, Homework 8 final draft
Thurs, Dec 4, 10:59pm, Homework 9 rough draft
Friday, Dec 5, 4:59pm, Homework 9 final draft
FREE TUTORS AT CLUE
Almost any graduate student in a physical chemistry track can help you with Chem452, so you can stop by the
Chemistry Study Center on the 3rd floor and ask when a P-Chem grad student will be on duty.
Not all CLUE tutors have taken Chem 452. Therefore, I specifically asked the CLUE lead chemistry tutor when
CLUE will be staffed with tutors who have already taken Chem452 and can offer good help to you. For
Autumn 2014, here are the times and places where CLUE says you can find tutors who are qualified to help you:
Mary Gates Hall:
McCarty (Rm 334):
Sunday (7pm-12), Monday (7pm-12), and Wednesday (7pm-12)
Tuesday (7-10pm)
5
ROUGH ORDER OF CHEM 452 TOPICS
- Definitions
- Energies associated with forces
- Gravity and springs (DNA as a spring, Bustamante data)
- Pressure/Volume for an ideal gas (Free expansion, constant volume, isothermal)
- Reversibility (Reversible cycles do the most work)
- Pressure/Volume for a Van der Waals gas
- Electrical field/Voltage/Current/Resistance (ion channels)
- Photons and Blackbody Radiation (Stefan-Boltzmann law)
- Heat
- 0th Law of Thermodynamics
- Heat capacity (Brief intro to degrees of freedom)
- 1st Law of Thermodynamics
- Fun with Calculus and State Functions
- State functions independent of path
- Order of differentiation doesn’t matter
- Summary of energies and state functions
- Enthalpy
- Cp and Cv for an ideal gas
- H is a function only of T for an ideal gas (Adiabatic expansion of an ideal gas)
- Phase Transitions
- Calorimetry
- Enthalpy of reaction, solution, vaporization and formation (Alternate paths)
- Bond energies
- Entropy
- Maximum number of states rather than simply “disorder”
- Carnot Cycle
- Entropy as a state function
- 2nd Law of Thermodynamics (Spontaneous Events)
- Efficiency
- Macroscopic vs. Microscopic and the statistical basis of the 2nd Law
- Entropy of Mixing
- 3rd Law of Thermodynamics
- Examples from charge neutralization, polar/nonpolar solvents,
degrees of freedom, multi-valent molecules, forming gases,
chemical reactions at different temperatures
(urea in solution, protein folding, lipids, DNA condensation)
- Gibbs Free energy
- Helmholtz and Gibbs
- Spontaneous reactions
- Entropic vs. enthalpic (MHC binding to peptides)
- Free energy of formation
- Pressure-dependence at constant temperature
- For liquids and solids (Formation of diamonds)
- For gases
- Temperature-dependence at constant pressure (supercooled water)
- Gibbs-Helmholtz Equation
- Clapeyron Equation
- Review of Equations using Gibbs Free Energy
- Review of state functions
- Maxwell Relations and practice
- Chemical Potential
- Equilibrium constants and their temperature dependence
- van’t Hoff
- Vapor
- Ideal solutions at equilibrium with vapor
- Raoult’s Law for a solvent of dilute solution (vapor pressure lowering)
- Henry’s Law for solutes of dilute solution
- Non-ideal solutions in equilibrium with vapor
- Chemical reactions at constant T and P
- Equilibrium constants of Unimolecular Rearrangements
6
- DNA supercoiling
- Ion-channels
- Change of solvent
- pH at a surface vs. in bulk
- Osmotic Pressure
- Weight of a Solute
- Freezing Point Depression, Boiling Point Elevation
- Electrochemistry
- Electrochemical Cell Potential
- Nernst Equation
- Half-Cell Potential
- Surface tension
- LaPlace pressure
- Capillary action
- The “hotdog” effect
- Coarsening (Lung surfactant, MEMS device problems)
- Effect on Vapor Pressure
7