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COURSE TITLE: Advanced Organic Chemistry
CREDIT WEIGHT AND WEEKLY TIME DISTRIBUTION: credits 3 (hrs lect 3 - hrs sem 0 - hrs lab 3)
COURSE DESCRIPTION: The correlation between structure and reactivity of complex organic molecules is studied through reaction mechanisms. Concepts important to theoretical organic chemistry are introduced and applied. Laboratories focus on synthetic organic chemistry and physical organic techniques. Microscale organic techniques are utilized in the laboratory, as well as computer modelling of organic structures.

Prerequisites: CHEM 351
  • Felix Carroll; Perspectives on Structure and Mechanism in Organic Chemistry, 2nd  Edition, USA: John Wiley & Sons,  2010  (REQUIRED)
  • Zubrick, J. W. The Organic Chem Lab Survival Guide, 9th edition, USA: John Wiley & Sons, 2012. (RECOMMENDED)
  • Beyond Benign. A Green Chemistry Resource Guide for the Organic Chemistry Laboratory Course, (REQUIRED, accessed Sept 2017)
  • Dicks, A.; Hent, A. Green Chemistry Metrics: A Guide to Determining and Evaluating Product Greenness, Springer, 2015. (Available in library)
  • Wavefunction, Inc. Spartan Student V6 Molecular Modeling Software (Site license available in all campus computer labs)
  • Wavefunction, Inc. Odyssey 4.1 Molecular Dynamics Software (Site license available in all campus computer labs)
  • Supplementary readings will be required from the primary and review literature in chemistry.  Also required are safety glasses, two laboratory data notebooks and a set of molecular models.
  • Access to Moodle:
Mid-term Exam25%
Final Exam25%
Special Topic15%
Assignments, Participation, Quizzes15%
  • A. Depth and Breadth of Knowledge
    • To develop deeper understanding and appreciation for the importance of organic chemistry and the ubiquitous nature of carbon compounds in everyday life.
    • To probe at an advanced level the complex relationships between molecular structure and chemical reactivity.
    • To provide an in-depth focus on models of molecular structure and bonding, including molecular orbital descriptions, and a clear understanding of the strengths and limitations of different models.
    • To understand and use the tools that allow investigation of reaction mechanisms in chemistry, including the study of reaction products, reactive intermediates, isotopic labeling, isotope effects, stereochemical studies, kinetics, substituent effects, linear free energy relationships, and solvent effects.
  • B. Knowledge of Methodologies
    • To gain expertise in the use of computer models of molecular structure and integrate the use of models with experimental measurements in the laboratory to solve problems. 
    • To gain expertise in the hands-on use of modern spectroscopic tools for determination of molecular structure, including NMR, IR, and GC-MS.
    • Engage with the primary and review literature to compare data, develop experimental procedures, and analyze and interpret data.
    • To develop experience with microscale techniques in the organic laboratory.
    • To explore fundamental concepts, principles, and metrics of green chemistry  
  • C. Application of Knowledge
    • To develop a greater ability to design and implement an experiment to answer a specific chemical question
    • To use the results of molecular modeling calculations to inform the interpretation of laboratory experiments.
    • To interpret experimental data and determine what conclusions can and cannot be made based on experimental design and assessment of the results.
    • To apply basic concepts and principles of green chemistry, and green chemistry metrics to an advanced integrated laboratory experiment, and to organic chemistry relevant to addressing climate change. 
  • D. Communication Skills
    • To develop increased self-confidence in orally presenting results of individual and group problem solving activities to peers and self-confidence in clearly presenting and defending explanations. 
    • To communicate clearly in individual and group oral assessments, and to constructively critique the explanations given by peers in class and assessment contexts.
    • To gain further experience in presenting clear and organized written reports of laboratory results.
    • To participate in and contribute to sharing knowledge of green chemistry through a contemporary science communication network 
  • E. Awareness of the Limits of Knowledge
    • To be aware of the historical contexts, developments, and philosophical presuppositions that have given rise to modern organic chemistry.
    • To re-evaluate models that were used at introductory levels to explain empirical observations and assess the extent to which they are “good enough” to provide explanations for new and more complex data.
    • To be aware of the professional responsibility of chemists for the materials they make, and to make conscious ethical choices about their potential uses and abuses.
  • F. Maturity and Professional Capacity
    • To nurture a positive, constructive, and supportive learning community among students and between students and instructors.
    • To engage in problem solving group activities and conduct experiments with other students, developing good interpersonal skills to accomplish course and laboratory tasks
  • G. Respect and Appreciation for the Discipline
    • To develop a sense of the power, elegance, and beauty of reaction mechanisms that explain experimental evidence and inform molecular-level understanding of organic reactions.  
    • Understand that the development of ideas, models, and theories has taken place over long periods of time and greatly contributed to our understanding of the molecular world.
  • Introduction to course and to Green Chemistry
  • Concepts and Models in Organic Chemistry
  • Stereochemistry and Stereotopicity
  • Green Chemistry Concepts, Principles and Metrics
  • Conformational Analysis and Molecular Mechanics
  • Applications of MO and Valence Bond Theory
  • Pericyclic Reactions
  • Methods of Studying Organic Reactions
  • Introduction to Microscale, Fractional distillation w spinning band column, analysis of purity
  • Group project: Green chemistry principles and metrics
  • Using your metrics: Greening a laboratory experiment
  • Computational Chemistry: Molecular mechanics, semiempirical and ab initio methods and applications, molecular dynamics calculations
  • Computational Chemistry QSAR, Spartan/Gaussian Lab
  • An Alkylation Puzzle: Fe(III) chloride catalyzed rxn of m-xylene and t-butyl chloride:  IR analysis and molecular mechanics

Required texts, assignments, and grade distributions may vary from one offering of this course to the next. Please consult the course instructor for up to date details.

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