Ch341


09/03/2014: Wednesday

Reading: Chapter 1
Lucretius and
atomic theory,

09/05/2014: Friday

Read:
Molecular Mechanics Tutorial, Introduction sections 1 and 3 (Force Fields and comparing structures)(also in our text Section 8.8): Reading Due date 09/08/2014.

Print off and bring to lab Molecular Mechanics Exercises, Overview: HIV-Protease and Indinavir, Chapters 1: Building and Minimizing, 2: Conformational Preference of Methylcyclohexane, and 3: Geometry (You don"t need to read them in advance) : Printing Due date 09/08/2014.

Handin homework: Handin 1, : Due date 09/12/2014.

Homework (not to hand in): Ch. 1: 1-3,8,9,13,15,17,18,21,23,25,26

09/08/2014: Monday

Lab Assignments: error analysis homework, Least Squares Excel spreadsheet, MOE Exercises Questions for Chapt. 1.1,1.2,2.1,3.1-3.6 : Due date 09/17/2014.


09/10/2014: Wednesday

Reading: Chapter 2.1-2.4

09/11/2014: Thursday

Handin homework 1 hint: Look at back-of-the-chapter problem 26: (the answers are on reserve in the science library)

09/12/2014: Friday

Reading: Chapter 2.4-2.8 Flux-Force relationships
Homework (not to hand in): Ch. 2: 2,3,4,6,8,9,11,13,14,18,19,21,22,23,24,29,30

09/15/2014: Monday

Handin homework:
Handin 2, : Due date 09/19/2014.


09/17/2014: Wednesday

Reading: Chapter 3.1-3.3

09/19/2014: Friday

Crystal Violet Kinetics Data,
Handin homework: Handin 3 Kinetics, Handin 3 Kineitcs Simulation Introduction, : Due date 09/26/2014.


09/22/2014: Monday

Homework (not to hand in): Ch. 3: 3,4,5,6,7,8,10,11,14,19,20,21,22,25,30,36
Reading Ch 3.4-3.6

09/26/2014: Friday

Homework (not to hand in): Ch. 4: 1-4,10,13,14,15,25,27,28,30
Handin Homework:
Handin 4, (7:00 pm) : Due date 10/01/2014.

Reading Ch. 4.1-4.3, 4.5 up to page 154

10/01/2014: Wednesday

Review session: 7:00 pm Keyes 102

10/03/2014: Friday

Test pm Chapter 1 to 4.3, Section 4.5 to page 154

10/05/2014: Sunday

Sign up for a lab on the list on the door of Keyes 205 (P/Q Lab)

10/06/2014: Monday

Homework to hand in:
Handin 5, : Due date 10/10/2014.

Reading Chapter 7: First Law

10/10/2014: Friday

Homework (not to hand in): Ch. 7: 1,2,4,5,6,7,8,10,11,13,18,20,22,23,27
Reading Chapter 8: 8.1-8.5 Thermochemistry

10/13/2014: Monday

Homework to hand in:
Handin 6, (three quick thermochemistry problems) : Due date 10/17/2014.


10/17/2014: Friday

Homework (not to hand in): Ch. 8: 3,5,7,9,12,13,17,22,26,27,31,33,34,37
Reading: Ch 8.6-8.12 Molecular Mechanics, Normal Modes

10/20/2014: Monday

Homework to hand in: none for now, we haven"t gotten to Handin 7 material yet.

10/24/2014: Friday

Reading for lab on Monday/Tuesday:
Molecular Mechanics Introduction, Section 4: Energy Minimization, Reading : Due date 10/27/2014.

Print off and bring to lab: MOE Molecular Mechanics Exercises, Chapters 4, 6 (with Problems 6.1-6.3), 11, and 12. Printing : Due date 10/27/2014.

Reading: Chapter 9 Using the First Law

10/27/2014: Monday

Remember to bring to lab the "Checklist for Molecular Mechanics Calculations" from the MOE Exercises handout Chapter 1.
Please use the following form to report your MOE results:
MOE Report Form (pdf), MOE Report Form (doc),
MOE Guest Host files,
Homework to hand in: Homework 7, : Due date 10/31/2014.

Homework (not to hand in): Ch. 9: 1,3,4,5,8,12,14,15,16,18,21,26,28,30

10/29/2014: Wednesday

Reading: Chapter 10 and Section 13.1
Practice tests:
Version 1, Version 2, For version 1, questions 1, 9, and 11 are not covered this year. For version 2, questions 2 and 3 are not covered this year (we did Chapter 10 instead of Chapter 11 or 12)
Homework (not to hand in): Ch. 10: 1,2,5,7,10,12,13,14

10/31/2014: Friday

Chapter 13.2-13.8, Section 14.1
Homework to hand in:
Handin 8, Due 7:00 pm - Wednesday : Due date 11/5/2014.

Homework (not to hand in): Ch. 13: 2,8,9,10,13(1.00 mole),14,15,18,23,24
Read the Introduction, QSAR Introduction, History, and "Design and QSAR" sections in: Computer Aided Molecular Design Tutorial, , (pp. 1-16). Reading : Due date 11/03/2014.

Print out "QSAR of Antitumor Activity in Aziridinyl Benzoquinones" and "Building a Receptor Model" in the CAMD Tutorial. Printing : Due date 11/03/2014.


11/02/2014: Sunday

Calculus Methods Workshop and Review (optional): Keyes 102, Sunday 5:00-6:00 pm.

11/03/2014: Monday

Lab assignment: Acetylcholine Esterase QSAR in
Computer Aided Molecular Design Tutorial, pp. 21-28 [This assignment serves as the lab report for this week"s lab] : Due 11/12 or 13/2014

11/04/2014: Tuesday

For the MM3 calculation use Firefox or Safari on the Mac (don"t use Chrome) The Macs in Keyes 102, Keyes 103, and Arey 5 run the applet. PCs work well with Internet Explorer or Firefox.

11/05/2014: Wednesday

Question and Answer Session: Keyes 102 7:00 pm
Reading Chapter 14, 15.1-15.3

11/07/2014: Friday

Test 2:30-3:00 or 2:00-3:30 : Chapters 7-10, 13 but skip Section 8.11
For the lab read:
Molecular Mechanics Introduction Tutorial, Section 5 (Dynamics) and textbook Sec. 19.5 [the same material is also in the Molecular Mechanics Tutorial Section 8, Continuum Solvation]-- Reading Due 11/10 or 11/11/2014
For the lab: Read the Introductions to and bring to lab: MOE Molecular Mechanics Exercises, , Chapters 9 and 10: "Conformational Preference of Small Peptides" and "Dynamics in Small Peptides" and Chapter 13 "Henry"s Law and Gibbs Free Energy of Solvation,"--Reading and Printing Due 11/10 or 11/11/2014

11/10/2014: Monday

Homework to hand in:
Handin 10, : Due date 11/14/2014.

DelPhi continuum electrostaticsolvation Barry Honig"s Lab at Columbia,
Electrostatic Surface for nicotinic agonist,
Homework (not to hand in): Ch. 14: 1,2,3,4,7,8,10,11,12,14 -- Ch. 15: 2,3,5,6,11,13,15,18,20,24,26,28,31

11/12/2014: Wednesday

Reading Chapter 16
Homework (not to hand in): Ch. 16: 2,8,12,14,15,17,18,19,23,28,31

11/14/2014: Friday

Reading Chapter 17 Phase Transitions

11/19/2014: Wednesday

Homework to hand in:
Handin 11, : Due date 11/21/2014.


11/20/2014: Thursday

Reading Chapter 18 Ideal Solutions
Homework (not to hand in): Ch. 17: 2,3,4,6,10,11,12,16 Ch. 18: 1,3,4,8

11/21/2014: Friday

Lab for next Monday/Tuesday:
Solubility of AgBrO3, , You must prepare your samples before class on Monday or 8:30 on Tuesday (both partners must be present). If you don"t get your samples in by 8:30 then you will need to stay later during the afternoon.

11/24/2014: Monday

Lab for next Monday/Tuesday:
Solubility of AgBrO3, , You must prepare your samples before class on Monday or 8:30 on Tuesday (both partners must be present). If you don"t get your samples in by 8:30 then you will need to stay later during the afternoon.

12/01/2014: Monday

Homework to hand in:
Handin 12, : Due date 12/05/2014.

Reading SKIP sections 18.5, 19.2, and 19.3
Reading Chapter 19.1, 19.4-19.5, 19.7
Homework (not to hand in): Ch. 18: 1,3,4,8,11,12,18,21,26,27,30,31 Ch. 19: 1,2,4,5,7,11,12,13,14,15,16,17
Reading: we did not cover pp. 687-691, so that material will not be covered on the final (but please read, the material is generally important)

12/05/2014: Friday

Homework (not to hand in): Ch. 20: 1-6,8,9,14,22,35a,35b,35e,35f
Reading Chapter 20.1-20.3 Equilibrium

12/08/2014: Monday

Sample Finals, On the 2005 Final skip problem 5; On the 2004 final skip problems 7 and 11 (electrochemistry not covered this year)

Legend:
Homework to hand in, Homework to do, but not hand in.