Office Hours: Dr. Kruse: Tue, 14:30-15:30 & Fri, 10:30-11:30 in ABB 142 (Chemistry Help Centre) TA's: tutorial time
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1 Chem 2P03 & ChemBio 2P03 Course Outline - Fall 2016 Applications of Physical Chemistry Prof. P. Kruse, ABB-263, x23480, pkruse@mcmaster.ca version 16 August 2016 Welcome to Applications of Physical Chemistry! This course outline summarizes the most important information about this course. Please also keep yourself current using the course website on Avenue to Learn. As the instructor of this course, I strive to provide you with all the necessary resources to start understanding physical chemistry and its applications. This course will introduce you to major concepts of thermodynamics and kinetics in order to predict the behavior of chemical, physical and biological systems. Your classmates will come from diverse backgrounds and be enrolled in programs such as Chemistry, Chemical Biology, Biology, Biochemistry, Life Sciences, Health Science. This course is a requirement for degrees in chemistry and chemical biology and an entrance requirement for pharmacy school. It is not a prerequisite for medical schools, but many pre-med students nevertheless take it. You will need basic mathematics, physics and chemistry skills (covered by prerequisites) to succeed in this course. If you would like to learn more about those concepts only briefly covered in this course, I encourage you to enroll in CHEM 2PC3, which will introduce you to the mathematical skills necessary to understand these topics in depth. Course Content: A. Thermodynamic States: preservation of energy state functions enthalpy ideal and real gases Carnot cycle entropy laws of thermodynamics B. Free Energy & Equilibria: free energy activity, standard states phase equilibria chemical equilibria C. Applied Equilibria & Molecular Motion: chemical, biochemical, electrochemical equilibria statistical thermodynamics binding of small molecules membranes transport phenomena D. Chemical Kinetics: rate laws, reaction orders and reaction mechanisms catalysis, autocatalysis, inhibition & competition oscillatory kinetics / pattern formation in living systems Textbook(s): Raymond Chang: Physical Chemistry for the Biosciences, 2005, University Science Books, ISBN-10: , ISBN-13: or Raymond Chang, John W. Thoman, Jr.: Physical Chemistry for the Chemical Sciences, 2014, University Science Books, ISBN: Office Hours: Dr. Kruse: Tue, 14:30-15:30 & Fri, 10:30-11:30 in ABB 142 (Chemistry Help Centre) TA's: tutorial time Evaluation: A2L Quizzes, 30 best of 32, each 2 questions covering one lecture = 30 x 2 x 0.4% = 24% iclicker Participation 0.1% per question = 40 x 0.1% = 4% Tutorials, 10 best of 12 (0% = fail, 0.6% = effort, 1.2% = pass) = 10 x 1.2% = 12% 3 Midterm Exams (during lecture time) = 3..0 x 15% \ Final Exam Part 1 ( 4 th midterm, non-cumulative) = 1 x 15% > = 60% Final Exam Part 2 (cumulative over 1 st 3 midterms) = 0..3 x 15% / Total = 100% Scheduled Midterms: Wed, 28 Sept, 26 Oct & 16 Nov 2015, 09:30 to 10:20, BSB-147 Course Outline Chem 2P03 / ChemBio 2P03 Fall 2016 Prof. Kruse page 1 of 5
2 In this course, you will be evaluated for participation (iclickers; tutorials), for understanding of important concepts (4 exams) and for your ability to apply the concepts to practical problems (A2L quizzes; tutorials). The marking scheme should have sufficient flexibility built in to accommodate most cases of potentially missed course work. The instructor will be reluctant to accommodate additional cases of missed course work, and will only do so if it is possible in a way that is fair to all students taking the course. There will be NO make-up midterms under any circumstances. Deferrals of final exams will be handled according to university regulations. All grades will be posted on Avenue to Learn. Every 'point' given or missed on an exam represents 1% of your final grade, with no intention to 'scale' or 'curve'. This way you always know where you are at and whether you need to work harder or can afford to take a break. 32 quizzes will be available on A2L throughout the course, each of which consists of 2 calculation questions that apply the concepts from one lecture. Each quiz is available from the start of the lecture until 48 hours after the end of the lecture. Detailed results for each student are only available after the end of the submission period. Each calculation question counts for 0.4%, making each quiz worth 0.8%. Only the 30 highest quiz marks will be counted towards the final grade, for a total of 24%. The entire course material is covered by a total of 4 non-cumulative exams (3 midterms and the first part of the final exam), for a total of 60% of the final grade. All of these are optional for passing the course and can be skipped, with a grade of ZERO assigned. The second part of the final exam will be cumulative over the material of the first 3 midterms, and the score on this part will be scaled appropriately and substituted for any of the 3 midterms that were skipped, or to replace a lower score. While it is thus possible to skip all 3 midterm exams and make up for it with the final exam, I would strongly advise against it, because participating in the midterm exams provides valuable practice and takes off a lot of pressure at the end. Practice exams will be provided in each case, which have an identical format and equivalent content to the real exams and are designed to aid your preparation for the exams. The course will use iclicker questions during lectures to test background knowledge and enhance understanding of lecture concepts during class. As a rule, 0.1% will added to the final grade for each iclicker question that a student participated in, up to 4% of the final grade (40 question participations). The total number of iclicker questions to be placed in the lectures is as of yet unknown but will safely exceed 50. Their distribution amongst lectures may not be entirely even, although an attempt will be made to have them cover the entire course. The purpose of these questions is to address common course concepts and to encourage pre-class preparation and in-class engagement. Your instructor will provide more information in class on the use of iclickers and how to register your iclicker. Please note: when registering your iclicker on iclicker.com please use your MACID (*not* your student number). Practice problem sets or practice exams will be posted before each weekly set of tutorials. Building on those questions, each tutorial will involve working on problems with several TAs present per section. Problem sets will be handed out to be solved during the tutorial, open book and with the opportunity to ask questions of the TAs and communicate with immediate neighbors. The TAs will collect these problem sets at the end of the tutorial and grade them according to the following scale: 0.0% for missing or insufficient effort; 0.6% for a good effort, but without the right results; 1.2% for more or less correct results, with a documented path leading to them (smaller errors and omissions will be forgiven). The best 10 out of 12 tutorial scores will be counted towards the final grade. If you have any suggestions of how I can help you learn better, please bring them to my attention and I will do my best to implement them, taking into account the limited resources and large number of students in the course. Course Outline Chem 2P03 / ChemBio 2P03 Fall 2016 Prof. Kruse page 2 of 5
3 Approximate Lecture Schedule (Fall 2016) # Date Contents Chapter (Chem) 1 Tue, 06 Sept 2016 Course Introduction; Review of Math, Physics, Chemistry PART A THERMODYNAMIC STATES Chapter (Bio) 2 Wed, 07 Sept 2016 A1: Heat & Work Fri, 09 Sept 2016 A2: Thermodynamic States & Pathways Tue, 13 Sept 2016 A3: Internal Energy & Temperature Wed, 14 Sept 2016 A4: Enthalpy & Heat Capacity Fri, 16 Sept 2016 A5: Real Gases Tue, 20 Sept 2016 A6: Adiabatic Processes Wed, 21 Sept 2016 A7: Carnot Cycle Fri, 23 Sept 2016 A8: Entropy Wed, 28 Sept 2016 *** 1 st Midterm *** PART B FREE ENERGY & EQUILIBRIA 10 Tue, 27 Sept 2016 B1: Free Energy Fri, 30 Sept 2016 B2: Properties of Free Energy Tue, 04 Oct 2016 B3: Chemical Potentials Wed, 05 Oct 2016 B4: Activities & Standard States 6, Fri, 07 Oct 2016 B5: One Component Phase Equilibria Tue, 18 Oct 2016 B6: Many Component Phase Equilibria Wed, 19 Oct 2016 B7: Reaction Equilibria in Gas Mixtures Fri, 21 Oct 2016 B8: Reaction Equilibria in Solutions Wed, 26 Sept 2016 *** 2 nd Midterm *** PART C APPLIED EQUILIBRIA & MOLECULAR MOTION 19 Tue, 25 Oct 2016 C1: Chemical & Biochemical Equilibria 8 6, 8 21 Fri, 28 Oct 2016 C2: Electrolytes & Electrochemistry 7, 9 5, 7 22 Tue, 01 Nov 2016 C3: Statistics of Molecular Motion Wed, 02 Nov 2016 C4: Applications of Statistical Thermodynamics 20, Fri, 04 Nov 2016 C5: Low-Dimensional Systems Tue, 08 Nov 2016 C6: Cell Membranes 19 5,7 26 Wed, 09 Nov 2016 C7: Diffusion & Viscosity Fri, 11 Nov 2016 C8: Sedimentation & Electrophoresis Wed, 16 Nov 2016 *** 3 rd Midterm *** PART D CHEMICAL KINETICS Course Outline Chem 2P03 / ChemBio 2P03 Fall 2016 Prof. Kruse page 3 of 5
4 # Date Contents Chapter (Chem) 28 Tue, 15 Nov 2016 D1: Kinetic Rate Laws & Order of a Reaction Fri, 18 Nov 2016 D2: Reaction Mechanisms & Complex Reactions 15 9 Chapter (Bio) 31 Tue, 22 Nov 2016 D3: Relaxation Kinetics & Photokinetics 15, 16 9, Wed, 23 Nov 2016 D4: Temperature Dependence & Transition States Fri, 25 Nov 2016 D5: Catalysts & Enzymes Tue, 29 Nov 2016 D6: Competition & Inhibition Wed, 30 Nov 2016 D7: Autocatalysis & Nonlinear Kinetics Fri, 02 Dec 2016 D8: Diffusion Controlled Reactions & Pattern Formation 15 9 SUMMARY & REVIEW 37 Tue, 06 Dec 2016 Summary & Review for Final Exam 38 Wed, 07 Dec 2016 Summary & Review for Final Exam Approximate Tutorial Schedule (Fall 2016) # Date Contents 1 Wed, 07 Sept Tue, 13 Sept 2016 Math Review: Units & Conversions; Integrals & Differentials 2 Wed, 14 Sept Tue, 20 Sept 2016 Thermodynamic Processes 3 Wed, 21 Sept Tue, 27 Sept 2016 Midterm Review 4 Wed, 28 Sept Tue, 04 Oct 2016 Entropy 5 Wed, 05 Oct Tue, 18 Oct 2016 Phase Equilibria (NO TUTORIALS DURING READING BREAK) 6 Wed, 19 Oct Tue, 25 Oct 2016 Midterm Review 7 Wed, 26 Oct Tue, 01 Oct 2016 Chemical Equilibria 8 Wed, 02 Nov Tue, 08 Nov 2016 Molecular Interactions 9 Wed, 09 Nov Tue, 15 Nov 2016 Midterm Review 10 Wed, 16 Nov Tue, 22 Nov 2016 Reaction Mechanisms 11 Wed, 23 Nov Tue, 29 Nov 2016 Enzyme Kinetics 12 Wed, 30 Nov Tue, 06 Dec 2016 Final Review Disclaimer: Changes to the course schedule and marking scheme may be made at the discretion of the instructor and announced to the students at any time during the course. An effort will be made to keep inconveniences from changes to a minimum. In this course we will be using Avenue to Learn. Students should be aware that, when they access the electronic components of this course, private information such as first and last names, user names for the McMaster accounts, and program affiliation may become apparent to all other students in the same course. The available information is dependent on the technology used. Continuation in this course will be deemed consent to this disclosure. If you have any questions or concerns about such disclosure please discuss this with the course instructor. Course Outline Chem 2P03 / ChemBio 2P03 Fall 2016 Prof. Kruse page 4 of 5
5 Copyright policy: In this course you will have access to material that is subject to copyright laws. This includes (but is not limited to) the textbook, solutions manual and all resources developed by the instructor such as lab manuals, demonstration videos, quizzes, assignments, tests, class notes and class slides. You are not allowed under any circumstances to share or redistribute this material in any printed or electronic form without the explicit written consent of the copyright holder. This includes posting any course material on Internet bulletin boards, course repositories, social networks, etc. Academic dishonesty: You are expected to exhibit honesty and use ethical behaviour in all aspects of the learning process. Academic credentials you earn are rooted in principles of honesty and academic integrity. Academic dishonesty is to knowingly act or fail to act in a way that results or could result in unearned academic credit or advantage. This behaviour can result in serious consequences, e.g. the grade of zero on an assignment, loss of credit with a notation on the transcript (notation reads: Grade of F assigned for academic dishonesty ), and/or suspension or expulsion from the university. It is your responsibility to understand what constitutes academic dishonesty. For information on the various types of academic dishonesty please refer to the Academic Integrity Policy, located at The following illustrates only three forms of academic dishonesty: 1. Plagiarism, e.g. the submission of work that is not one s own or for which other credit has been obtained. 2. Improper collaboration in group work. 3. Copying or using unauthorized aids in tests and examinations. Course Outline Chem 2P03 / ChemBio 2P03 Fall 2016 Prof. Kruse page 5 of 5
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