SYLLABUS 2015 - CHEM 212 / ENCH 212: Principles of Chemical Reactivity Course instructor: Lab instructor: Dr. Jason Z. Vlahakis Chernoff Hall, Office Room 215 Phone: 613-533-6000 x 77769 E-mail: jason.vlahakis@chem.queensu.ca Office hours: TBA Dr Igor Kozin Chernoff Hall, Office Room 124 Phone : 613-533-6000 x 74665 E-mail: igor.kozin@chem.queensu.ca CHEM 212 uses Moodle this year. Lectures: Monday 11:30 am 12:20 pm Tuesday 1:30 pm 2:20 pm Thursday 12:30 pm 1:20 pm Lab Information Session (Administration, reports, etc.) is held on Thurs, Sept 17, 7:30 pm The full set of lecture notes will be compiled during class and then posted on the Moodle site. Aim and learning goals: (i) understanding the essence of the reactivity of organic molecules, (ii) being able to relate reactivity to kinetic studies and parameters; (iii) understanding solvent and electronic effects on reactivity. At the end of the course, students should be able to anticipate the reactivity of nearly any two reactive partners. Required textbooks: - Physical Chemistry, Peter Atkins and Julio de Paula, 10 th edition - Organic Chemistry, Jonathan Clayden, Nick Greeves, and Stuart Warren, 2 nd edition BOTH TEXTS CAN BE PURCHASED IN THE CAMPUS BOOK STORE Useful software: - free online testing and learning tools are available from the RSC website: http://www.rsc.org/learn-chemistry/resources/mechanism-inspector/ Several tutorials and exercises are mentioned in class as well as in the individual problem sets. Please take the time to study them: they are very useful. - free online reaction animations (as well as orbitals animations) are available at the following website: http://www.chemtube3d.com/ - data processing requires Microsoft Excel Problem sets: Practice problems and solutions will be posted on the CHEM212 Moodle site. These are not marked, but are recommended as they will help you prepare for the 1 st Exam, mid-term, and final exams. 1
CHEM 211 and CHEM 212 Help Desk: A help desk located in the 1 st floor atrium in Chernoff Hall where a TA will be available for your questions related to CHEM 211 and CHEM 212 course material. Help desk hours: Tues 10:30 11:30 am, Thurs 1:30 2:30 pm. There are also special help-desk hours prior to course exams (to be announced/confirmed by instructors). Special practice sessions: Although tutorials are not scheduled with this course, an attempt will be made by the instructor to organize special practice sessions, in addition to review sessions prior to the examinations. To be announced in class. Labs: All labs must be attended as scheduled. All students must attend the introductory lab (lab Group assignment, lab safety, lab quiz) in week 1 (~1 h). Regular 3 h labs will be held on alternate weeks, in room CHE210 on the 2 nd floor of Chernoff Hall. Lab Section 002 Tues 2:30 5:30 pm Lab Section 003 Mon 2:30 5:30 pm Lab Section 004 Thurs 2:30 5:30 pm Lab Section 005 Wed 2:30 5:30 pm In weeks 2-11 students will rotate between the following five experiments depending on Group: Experiment 1: Photo-isomerization Kinetics of 4-Hydroxyazobenzene Experiment 2: Kinetics of Nucleophilic Substitution Experiment 3: Enzyme Kinetics Enzyme Catalyzed Oxidation of DOPA Experiment 4: Stop-Flow Kinetics - Reaction of Fe 3+ and SCN - Ions Experiment 5: Gas Viscosity Determination of Collision Cross Sections for Gases Marking Scheme: there will be 3 exams: - 1 st exam (10%, 1 h) is tentatively scheduled on Friday, October 16 th, 2015, 6-7 pm Stirling Auditorium and Stirling C. (contact instructor early if you have a course conflict). - 2 nd Exam (Mid-term Exam) (25%, 2 h) is tentatively scheduled on Thursday, November 12 th, 2015, 6-8 pm Stirling Auditorium and Stirling C (contact instructor early if you have a course conflict). - Final Exam 40% (TBA, 3 h). - Labs: 25% (individual lab marking schemes are printed in the CHEM212 lab manual). IMPORTANT: 1) The lecture material is composed of the LECTURE NOTES; they take priority over the textbooks/online material. In the exams, you will be judged on your understanding of the LECTURE NOTES. They will be posted onto Moodle after each lecture. 2) The specific readings recommended in the lecture notes and/or syllabus are added to the materials you are responsible for learning. 3) Students must pass BOTH the lecture and the laboratory components to pass the course. If a student does not pass both the laboratory and lecture components of a course, he/she will fail the entire course and be allocated a mark of 47% or his/her actual mark, whichever is lower. Students who do not attend all lab sessions may be assigned a grade of incomplete (IN) and be required to attend and pass the missed lab(s) the following year before the IN is cleared from their transcript. 2
Course Outline 2015 Note: Text book references are to Physical Chemistry by Atkins 10 th Edition, and Organic Chemistry by Clayden 2 nd Edition. Atkins is used mainly in Section 1. Clayden is used mainly in Sections 2 and 3 as noted below. The order of topics is roughly as follows: Section 1: Physical views of reactivity (textbook is Atkins) CHEMICAL KINETICS [Atkins 20A]. The rates of chemical reactions. Rates, rate laws, reaction order, method of initial rates. Determining order. [Atkins 20B]. Integrated rate laws. Zero-, first-, and second-order. Half-lives. [Atkins 20C]. Reactions approaching equilibrium. [Atkins 20E]. Reactions mechanisms. Elementary reactions, consecutive elementary reactions, unstable intermediates, steady-state approximation (SSA), stable intermediates, pre-equilibria, pre-equilibrium assumption (PEA), kinetic and thermodynamic control of reactions, rate-determining step, mechanism examples such as S N 2 and S N 1. [Atkins 20H]. Enzymes. Michaelis Menten. [Atkins 20D]. The Arrhenius equation. Pre-exponential factor, activation energy, effect of catalyst on E a (see also [Clayden, page 254]). REACTION DYNAMICS [Atkins 21A]. Collision theory. [Atkins 21B]. Diffusion-controlled reactions. [Atkins 21C]. Transition-state theory. (see also [Clayden, pages 251 253]) Section 2: Chemical views of reactivity (textbook is Clayden) Structure of molecules. Atomic orbitals, molecular orbitals, bonding, antibonding, bond breaking, bond order, orbital interaction, hybridization, Chemical bonding (atoms, bonds, atomic and molecular orbitals). Assigned reading: [Clayden, Chapter 4, pages 80 106, read well in advance] The curved arrow notation. Assigned reading: [Clayden, Chater 5, pages 116 124]. Frontier molecular orbitals. HOMO, LUMO, radicals/somo, Types of Reactivity (Overview). Addition, substitution, elimination, rearrangement. Ionic reactions, radical reactions, concerted reactions. Classification of reactivity. Electrostatic control, orbital control, steric control. Reactive intermediates. Carbocations: structure, factors effecting stability. [Clayden pages 334 339]. Carbanions: structure, stability. Radicals: structure, stability. [Clayden, pages 977 979]. Energetics and kinetics of reactions. Kinetic vs thermodynamic control, Hammond s postulate, delocalization. [Clayden, Chapter 12] Acids and Bases. Lewis acids/bases, Bronsted acids/bases, K a, pk a, relative acidity, factors influencing basicity, hard and soft acid base theory, electrostatic/orbitals effects, inductive and resonance effects, hybridization, steric aspects, solvent effects [Clayden, Chapter 8] Nucleophiles and electrophiles. Nucleophilicity and factors influencing it, relation to pka/basicity, orbital effects, charge effects, solvent effects cation effects, steric effects [Clayden Chapt 5, pages 107 116]. 3
Section 3: Applications of chemical reactivity (Nucleophilic Substitution, Elimination, and Electrophilic Aromatic Substitution reactions) (textbook is Clayden) Overview of organic halides. Polarizablity, nucleophilic attack, electrophilic attack, induced acidity at β-carbon. Nucleophilic substitution. Nucleophiles, leaving groups. [Clayden, Chapter 15] S N 2. Kinetics, stereochemistry, energy profile, orbitals, interpretation, energy matching, orbital overlap, back vs front attack, stereoselectivity, stereospecificity, factors favoring S N 2 (R group in RX, nucleophile, leaving group, solvent) S N 1. Kinetics, stereochemistry, interpretation/mechanism, energy profile, factors favoring S N 1 (R group in RX, nucleophile, leaving group, solvent) Elimination. [Clayden, Chapter 17] E1. Kinetics, interpretation/mechanism, energy profile, compare to SN1, factors favoring E1 (R group in RX, leaving group, solvent), regioselectivity, stereoselectivity, carbocation intermediate stability, product distribution, cationic rearrangement. E2. Kinetics, interpretation/mechanism, energy profile, factors favoring E2 (R group in RX, leaving group, solvent), regioselectivity, stereoselectivity. Competition between Nucleophilic Substitution and Elimination. Factors influencing the competition. Electrophilic Aromatic Substitution. [Clayden, Chapter 21] Aromaticity. Assigned reading: [Clayden, pages 156 162] Monosubstitution of benzene. [Clayden, pages 473 478] Polysubstitution. [Clayden, pages 479 491] Please be reminded of Queen s University policies regarding academic integrity: Academic integrity is constituted by the five core fundamental values of honesty, trust, fairness, respect and responsibility (see www.academicintegrity.org). These values are central to the building, nurturing and sustaining of an academic community in which all members of the community will thrive. Adherence to the values expressed through academic integrity forms a foundation for the "freedom of inquiry and exchange of ideas" essential to the intellectual life of the University (see the following Senate Report on Principles and Priorities at http://www.queensu.ca/secretariat/policies/senate/report-principles-and-priorities). Students are responsible for familiarizing themselves with the regulations concerning academic integrity and for ensuring that their assignments conform to the principles of academic integrity. Information on academic integrity is available in the Arts and Science website (see http://www.queensu.ca/artsci/about/academic-integrity), and from the instructor of this course. Departures from academic integrity include plagiarism, use of unauthorized materials, facilitation, forgery and falsification, and are antithetical to the development of an academic community at Queen's. Given the seriousness of these matters, actions which contravene the regulation on academic integrity carry sanctions that can range from a warning or the loss of grades on an assignment to the failure of a course to a requirement to withdraw from the university. 4
Also, please be reminded of Queen s University policies regarding disability accommodations: Queen's University is committed to achieving full accessibility for persons with disabilities. Part of this commitment includes arranging academic accommodations for students with disabilities to ensure they have an equitable opportunity to participate in all of their academic activities. If you are a student with a disability and think you may need accommodations, you are strongly encouraged to contact the Disability Services Office (DSO) and register as early as possible. For more information, including important deadlines, please visit the DSO website at: http://www.queensu.ca/studentwellness/accessibility-services/ 5