Reading: Chapter 1
Lucretius and atomic theory,
Read: Molecular Mechanics Tutorial, Introduction sections 1 and 3 (Force Fields and comparing structures)(also in our text Section 8.8): Reading Due date 09/14/2015.
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 09/14/2015.
Handin homework: Handin 1, : Due date 09/18/2015.
Homework (not to hand in): Ch. 1: 1-3,8,9,13,15,17,18,21,23,25,26
Pressure in mbars: Atlantic Hurricane Analysis,
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 09/23/2015.
Reading: Chapter 2.1-2.4
Calculus Review: Keyes 102 7:00 pm
For a good review of spontaneous or equilibrium processes: Brown, Lemay, Bursten, "Chemistry the Central Science," Section 19.1.
Lab report sheet: MOE Exercises Ch. 1-3 report (pdf), or MOE Exercises Ch. 1-3 report (docx), : Due date 09/23/2015.
Reading: Chapter 2
Lab for Monday: pKa of Methyl Red,
Handin homework: Handin 2, : Due date 09/25/2015.
Homework (important but not to hand in): Ch. 2: 2,3,4,6,8,9,11,13,14,18,19,21,22,23,24,29,30
Homework to hand in: Handin 3, Handin 3 Kinetics Simulation Introduction, : Due date 10/01/2015.
Reading: Chapter 3
Homework not to hand in: Ch. 3: 3,4,5,6,7,8,10,11,14,19,20,21,22,25,30,33,36
Home work to hand in: Handin 4, (note earlier due date) : Due date 10/07/2015.
Reading: Chapter 4
Home work (not to hand in): Ch. 4: 1-4,10,13,14,15,19,25,27,29,30,33(but,not for this test),35
Question and Answer session: 8:30 pm Keyes 102
Reading: Chapter 7 First Law of Thermodynamics
The formula sheet (1) that will be handed out at the test is on the Class Notes page: Class Notes,
The answers to the practice tests are on the Sample Exam Page, and also on Reserve in the Science Library
Test Chapters 1-4(pp. 125-143; 152-154)
Handin homework: Handin 5, : Due date 10/16/2015.
Home work, not to hand in: Ch. 7: 1,2,4,5,6,7,8,10,11,13,18,20,22,23,27
Home work to hand in: Handin 6, : Due date 10/23/2015.
Home work, not to hand in: Ch. 8: 3,5,7,9,12,13,17,22,26,27,31,33
Reading: Chapter 8
Home work to hand in: Handin 7, Problems 1, 2, and 4 (skip Problem 3) : Due date 10/30/2015.
Reading: Chapter 9
Home work (not to hand in): Ch. 8: 34,36 and Ch. 9: 1,3,4,5,8,12,14,15,16,18,21,26,28,30
Reading: Chapter 10
Reading for lab on Monday/Tuesday: Molecular Mechanics Introduction, , Section 4: Energy Minimization, Reading : Due date 11/02/2015.
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 11/02/2015.
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), : Due date 11/11/2015.
Home work to hand in: Handin 8, : Due date 11/06/2015.
Reading: Chapter 13
Home work not to hand in: Ch. 10: 1,2,3,5,7,10,12,13
File for today"s lab: MOE files,
Meet in Keyes 102
Meet in Keyes 102
For the practice test from 2009, problems 1, 9, and 11 are from Chapter 12. Skip these problems.
For the practice test from 2008, problem 2 is from Chapter 11. Skip this problem.
Home work not to hand in: Ch. 13: 2,8,9,10,13(1.00 mole),14,15,18,20,23,24
Read the Introduction, QSAR Introduction, History, and "Design and QSAR" sections in: Computer Aided Molecular Design Tutorial, (pp. 1-16). Reading : Due date 11/09/2015.
Print out "QSAR of Antitumor Activity in Aziridinyl Benzoquinones" and "Building a Receptor Model" in the CAMD Tutorial. Printing : Due date 11/09/2015.
Reading: Chapter 14
Home work not to hand in: Ch. 14: 1,2,3,4,7,8,10,11,12,14
Calculus review workshop: Partial Derivative Conversions 4:00 pm Keyes 102
Home work to hand in: Handin 9, (note the Wednesday afternoon due date- so I can get them graded in time to help study for the test.) : Due date 11/11/2015.
Lab assignment: Acetylcholine Esterase QSAR in Comptuer Aided Molecular Design Tutorial, pp. 21-28 [This assignment serves as the lab report for this week’s lab] : Due 11/18(Monday lab) or 11/19(Tuesday lab)
Review Session 7:30 pm Keyes 102
Test (pm): Chapters 7-10,13,14,15.1
Reading: Chapter 15
Home work to hand in: Handin 10, : Due date 11/20/2015.
Reading: Chapter 16
Homework (not to hand in): Ch. 15: 2,3,5,6,11,13,15,18,20,24,26,28,31
Homework (not to hand in): Ch. 16: 2,8,12,14,15,17,18,19,23,28,35,36,38
Homework (not to hand in): Ch. 17: 2,3,4,6,10,11,12,16,17,24
Reading: Chapt. 18
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 11/23 or 11/24/2015
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 11/23 or 11/24/2015
DelPhi continuum electrostatic solvation Barry Honig"s Lab at Columbia,
Electrostatic Surface for nicotinic agonist,
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.
Don"t forget to prepare your samples before class!
Home work to hand in: Handin 11, : Due date 12/04/2015.
Don"t forget to prepare your samples before 8:30 am.
Homework to hand in,
Homework to do, but not hand in.