Ch341

09/07/2016: Wednesday

Reading: Chapter 1
Lucretius and
atomic theory,

09/09/2016 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 09/12/2016.

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 09/12/2016.

Handin homework: Handin 1, : Due date 09/16/2016.

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,

09/12/2016: 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 09/21/2016.

For lab meet in Keyes 103: 1:00 PM

09/14/2016: Wednesday

Reading: Chapter 2.1-2.4

09/15/2016: Thursday

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 09/21/2016.


09/16/2016: Friday

Reading: Chapter 2
Lab for Monday:
pKa of Methyl Red,
Handin due

09/19/2016: Monday

Reading: Chapter 2.5-2.8 Flux-force relationships
Homework (not to hand in): Chapter 2: 2,3,4,6,8,9,11,13,14,18,19,21,22,23,24,29,30

09/20/2016: Tuesday

Homework to hand in:
Handin 2, : Due date 09/23/2016.

09/21/2016: Wednesday

Reading: Chapter 3.1-3.5 Reaction Kinetics
The OPTIONAL Quick-check
calculation sheet, is due on Friday if you want me to check your lab calculations : Due date 09/23/2016.

Error Analysis Lab assignment due (Monday Lab)

09/22/2016: Thurssday

Error Analysis Lab assignment due (Tuesday Lab)

09/23/2016: Friday

Reading: Chapter 3.6-3.7 Fast Reaction Kinetics
Homework (not to hand in): Chapter 3: 3,4,5,6,7,8,10,11,14,19,20,21,22,25,30,33,36
Crystal Violet Kinetics Data,
Handin due

09/27/2016: Tuesday

Homework to hand in:
Handin 3, : Due date 09/30/2016.

Homework to hand in: also Kinetics Simulation Handin 3, : Due date 09/30/2016.


09/28/2016: Wednesday

Reading: Ch. 4.1-4.3 Mechanisms, Steady state approximation

09/30/2016: Friday

Reading: Ch.4.5-4.6 Detailed Balance
Homework (not to hand in): Ch. 4: 1-4,10,13,14,19
Homework to hand in:
Handin 4 (Mechanisms), : Due date 10/07/2016.


10/06/2016: Thursday

Homework to hand in:
Handin 5, but just Problem 4 (we didn't get to the background for the first three problems in time)(Note the Wednesday date so that I can return your home work before the test) : Due date 10/12/2016.


10/07/2016: Friday

Reading: Ch. 7.1-7.8 First Law
Homework (not to hand in): Ch. 7: 1,2,4,5,6,7
Handin due

10/12/2016: Wednesday

Reading: Chapter 7.9-7.11 Non-PV work
Question and Answer session: Keyes 102, 7:00 PM
Homework (not to handin): Ch. 7: 8,10,11,13,18,20,22,23,27

10/14/2016: Friday

Test (pm): Ch. 1-4 (but skip 3.3 and 4.4), 7.1-7.5(p. 267)

10/18/2016: Tuesday

Homework to hand in:
Handin 5, question 3 only (Hint: see Eq. 7.6.29 and Problem 7.15 for something similar). : Due date 10/21/2016.


10/19/2016: Wednesday

Reading: Chapter 8.1-8.5 Thermochemistry

10/21/2016: Friday

Handin question 3 (only) due

10/25/2016: Tuesday

Homework to hand in:
Handin 6, : Due date 10/28/2016.


10/26/2016: Wednesday

Reading: Chapter 8.6-8.12; Chapter 9.1-9.6 Enthalpy
Homework (not to hand in): Ch. 8: 3,5,7,9,11,12,13,17,22,26,27,31,33,34,36

10/28/2016: Friday

Reading for lab on Monday/Tuesday:
Molecular Mechanics Introduction, Section 4: Energy Minimization, Reading : Due date 10/31/2016.

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 10/31/2016.

Remember to bring to lab the "Checklist for Molecular Mechanics Calculations" from the MOE Exercises Chapter 1.
Homework to hand in: Handin 7, : Due date 11/04/2016.


10/31/2016: Monday

Please use the following form to report your MOE results:
MOE Report Form (pdf), or MOE Report Form (doc), Due: Nov. 9 (Monday lab) or 10 (Tuesday lab)
Homework (not to hand in): Ch. 9: 1,3,4,5,8,12,14,15,16,18,21,26,28,30

11/02/2016: Wednesday

Reading: 9.7-9.10, 10.1, 11.1-11.4 Entropy
Homework (not to hand in): Ch. 10: 1,2,3,5,7,10,13,14; Ch. 11: 4,5,7,9,11

11/04/2016: Friday

Read the Introduction, QSAR Introduction, History, and "Design and QSAR" sections in:
Computer Aided Molecular Design Tutorial, , (pp. 1-16). Reading Due Nov 7 or 8
Print out and bring to lab "QSAR of Antitumor Activity in Aziridinyl Benzoquinones" and "Building a Receptor Model" in the CAMD Tutorial. Printing Due Date Nov 7 or Nov 8
Homework to hand in: Handin 8, : Due date 11/11/2016.


11/07/2016: Monday

Chapter 13 Entropy and Applications
Homework (not to hand in): Ch. 13: 2,8,9,10,13(1.00 mole),14,15,18,20,23,24
Chemical Abstract Services:
www.cas.org, 123 million compounds and counting
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 11/16(Monday lab) or 11/17(Tuesday lab)

11/08/2016: Tuesday

Calculus review workshop: Partial Derivative Conversions 8:00 pm Keyes 105

11/09/2016: Wednesday

Reading: Chapter 14 Chemical Reactivity (Chemical Potential)
Homework (not to hand in): Ch. 14: 1,2,3,4,7,8,10,11,12,14

11/11/2016: Friday

Reading: Chapter 15 Spontaneity, Free Energy
Homework (not to hand in) Ch. 15: 2,3,5,6,11 (save 13,15,18,20,24,26 for the final)
Homework to hand in:
Handin 9, (note the Wednesday due date so I can return your graded homework before the test) : Due date 11/16/2016.


11/13/2016: Sunday

For the Version 1 practice test from 2009, problems 1, 9, and 11 are from Chapter 12. Skip these problems.
For the Version 3 practice test from 2011, skip problems 4, 6, and 8. (Problem 4 is from Chapter 5 and Problem 8 is from Section 10.2.)

11/14/2016: Monday

Reading: Chapter 16.1-16.3 Thermodynamic forces
The formula sheet for test 2 is ready:
Formula Sheet 2, (the link is also on the lecture notes page)

11/16/2016: Wednesday

Handin due

11/18/2016: Friday

Test 2: (PM): Chapters 7-15.1, 15.2, 15.4 pp. 542-546, 15.5
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 11/21 or 11/22/2016
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 11/21 or 11/22/2016

11/21/2016: Monday

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 work alone). If you don"t get your samples in by 8:30 then you will need to stay later during the afternoon.
Reading: Chapter 16.4-16.9, Chapter 17.1

11/28/2016: Monday

Lab for 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. Lab normally is over early.
Homework to hand in: Handin 11, : Due date 12/02/2016.

Reading: Chapter 17 Phase transitions; Chapter 18.1-18.2 Partial Molar Quantitites

12/02/2016: Friday

Homework to hand in:
Handin 12, (skip Problem 3) : Due date 12/09/2016.

Homework (not to hand in): Ch. 17: 2,3,4,6,12,16,17,24; Ch. 18: 1,3,4,8,11,12

12/05/2016: Monday

Reading:Chapter 18: 18.3, 18.4, 18.6, 18.7; Chapter 19 Real Solutions

12/07/2016: Wednesday

Homework (not to hand in): Ch. 18: 18,21,26,27,30,31
Reading: Chapter 19 but skip sections 19.2, 19.3, and 19.6 that will not be covered on the final

12/09/2016: Friday

Reading: Chapter 20.1-20.3 Equilibrium
Home work (not to hand in): Ch. 20: 1-6,8,9,14,22,23,35
Handin(excluding problem 3) due

12/10/2016: Saturday

For the practice final version 2 from 2004: Skip Part I problems 7 and 11 (which are on electrochemistry) and Part II problem 2 (non-equilibrium)
For the practice final version 1 from 2005: Skip Part I problem 5 (which is on electrochemistry)

12/14/2016: Wednesday

Final: 6:00 pm, Keyes 102: 50% Emphasis on recent coverage: Chapters 15-20.3,20.7 (Skip sections:18.5,19.2,19.3,19.6,20.4-20.6)

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