I. Course Title: Introduction to Organic Chemistry with Instrumental Methods of Analysis II. Course Description: This introduction to Organic Chemistry and Instrumental Analysis course is designed for those students who plan to pursue careers in chemical sciences or related engineering disciplines. Students with interests in other sciences gain valuable experiences in dealing with sophisticated topics. The course is also designed to aid students in the development and generation of ideas for Senior Research. Topics include nomenclature, characterization, reactions, synthesis, and selected topics in biochemistry. The students will also be exposed to the theory, operation and data interpretation of chemical instrumentation such as infrared spectroscopy, UV-Vis spectroscopy, fluorescence, gas chromatography, refractometry, mass spectroscopy, nuclear magnetic resonance spectroscopy. Laboratory experiments are also offered so students gain hands-on experience related to organic chemistry lab topics. *NOTE: This course is also a pre- or co-requisite for Chemical Analysis Research. Priority for Seniors will be for those also enrolled in Chemical Analysis Research Grade Level(s): 11-12 Unit of Credit: 0.5 Prerequisite: Advanced Placement Chemistry (Priority for students in grade 12 will be for those also enrolled in Chemical Analysis Research)
III. Performance Indicators Standard 1 - Essential Experimental and Laboratory Investigations. The student will investigate and perform laboratory experiments involving Organic Chemistry and common instrumental methods of analysis. Key concepts include: a) designated laboratory techniques (advanced methods beyond AP Chemistry); b) safe use of chemicals and equipment, and proper response to emergency situations. c) designated laboratory experiments related to Organic Chemistry and Instrumental Analysis. (note: these are designed to be at an AP Chemistry level with a focus on Organic Chemistry) Standard 1 ORGO.1 a-e a) Techniques for experimentation involve the identification and the proper use of chemicals, the description of equipment, and the recommended statewide framework for high school laboratory safety. b) Measurements of physical properties of organic molecules, including melting point, boiling point, refractive index, solubility. c) Determine organic structure and functional groups from infrared spectral (IR) data, MS data, and/or NMR data. d) Perform laboratory experiments to synthesize, isolate, and characterize organic compounds (e.g., aspirin, esters, or similar appropriate for standard high school chemistry lab). Examples provided below. e) Write formal laboratory reports according to ACS journal article submission guidelines. Benchmark ORGO.1.a Essential The student will investigate and understand designated, advanced lab techniques beyond AP Chemistry level. Techniques for experimentation involve the identification and the proper use of chemicals, the description of equipment, and the recommended statewide framework for high school laboratory safety. Indicator ORGO.1.a. Understand Material Safety Data Sheet (MSDS) warnings, including handling chemicals, lethal dose (LD), hazards, disposal, and chemical spill cleanup. Demonstrate safe laboratory practices, procedures, and techniques. Identify, locate, and know how to use laboratory safety equipment, including aprons, goggles, gloves, fire extinguishers, fire blanket, safety shower, eye wash, broken glass container, and fume hood. Benchmark ORGO.1.b Essential Students will perform laboratory experiments to include measurements of physical properties of organic molecules, including melting point, boiling point, refractive index, solubility. Indicator ORGO.1.b Organic Chemistry Page 1
Typed formal lab reports adhering to ACS style guide for publications. Benchmark ORGO.1.c Essential Students will determine organic structure and functional groups from infrared spectral (IR) data, MS data, and/or NMR data. (Note, this does not include/require use of instrumentation, only data interpretation). Indicator ORGO.1.c Characterization of organic molecular structure from data (IR, NMR, MS). Benchmark ORGO.1.d. Perform laboratory experiments to synthesize, isolate, and characterize organic compounds (e.g., aspirin, esters, or similar appropriate for standard high school chemistry lab). Examples to include: i) Experiment 1: Introduction to chemical analysis of organic molecules physical properties 1) Part 1 - Determination of melting points (MelTemp apparatus). 2) Part 2 - Refractive index (Abbe 3L Refractometer) 3) Part 3 Introduction to spectral interpretation of organic molecules: Fourier Transform- Infrared (FT-IR) Spectroscopy (data analysis only) ii) Experiment 2: Microscale Synthesis of Acetylsalicylic Acid Indicators ORGO.1.d. Demonstrate the following advanced lab techniques: determine mp of solids, performing simple distillations, organic extractions, organic synthesis and characterization. Make the following measurements, using the specified equipment: - MelTemp melting point apparatus - mass: electronic balance - Volume using standard labware and micro-pipets - Use Abbe Refractometer to determine refractive index of liquids - Interpret IR spectral data (instrument use not part this Standard) - Determine percent error - Identification of unknowns (qualitative and quantitative) based on student generated data (IR data provided as needed from, e.g., SDBS of Japan). Benchmark ORGO.1.e. Write formal laboratory reports according to ACS journal article submission guidelines. Indicator ORGO.1.e. Write formal lab reports using formats similar to American Chemical Society (ACS) publications with numerical in-text references and appropriate bibliographies. Maintain a lab journal according to ACS guidelines. Perform literatures searches to analyze and compare experimental data to published or literature values. Use manuals and books such as the CRC Handbook, Aldrich Catalog, or similar, to evaluate literature values for comparison to experimental values. Organic Chemistry Page 2
Standard ORGO.2 Essential Introduction to Organic Chemistry and Molecules The student will investigate and understand the Structure and Properties of Organic Molecules with relation to bonding, resonance, and formation of molecular structure. Standard ORGO.2 a- d a. Overview of carbon as central to organic chemistry b. Atomic structure and relations to bonding in organic molecules c. Resonance, formal charges, and stability during reactions d. Molecular structure Benchmarks ORGO.2.a.Essential Overview of carbon as central to organic chemistry Organic chemistry is the chemistry of Carbon and its compounds. Indicators ORGO. 2.a. Students will be able to understand applications of chemical concepts to include central focus on organic molecules. Benchmarks ORGO.2.b.Essential Atomic structure and relations to bonding in organic molecules Structure of the Atom, Electronic Structure of the Atom, and Atomic Orbitals, and Electronic Configuration of Atoms. The Pauli Exclusion Principle, Aufbau Principle, Hund s Rule. Bonding and Multiple Bonds (single vs. double. vs. triple); Bond Polarity- A covalent bond, where the electrons are shared equally is called a nonpolar bond. Indicators ORGO.2.b. Students will be able to understand atomic structure and relations to bonding in organic molecules Benchmarks ORGO.2.c.Essential Resonance, formal charges, and stability during reactions Formal Charges and Partial charges. Lewis Structures, to include non bonding pairs of electrons ( lone pairs.) Ionic Structures- Some organic compounds do contain ionic bonds. Resonance Structures, Charge delocalization, resonance stabilized. (Major and Minor contributors). Indicators ORGO.2.c. Students will be able to understand resonance, formal charges, and stability during reactions. Organic Chemistry Page 3
Benchmarks ORGO 2.d.Essential Molecular structure Structural Formulas: Lewis, Condensed Structural, Line Angle Formula (Stick Figures) Acids and Bases; ph values; three different definitions: Arrhenius, Bronsted-Lowry, Lewis Conjugate Acids and Bases and Acid Strength vs. Base Strength Structural Effects on Acidity Factors that influence stability of conjugate bases (anions) Lewis Acids and Bases nucleophile vs. electrophile. Indicators ORGO.2.d. Students will be able to understand molecular structure and how it relates to drawing molecules, acid/base properties, and factors that influence structure. Standard ORGO.3 Essential Structure and Properties of Organic Molecules The student will investigate and understand the Structure and Properties of Organic Molecules with relation to bonding, resonance, and formation of molecular structure with relations to include hybridization and isomers. Standard ORGO.3.a - d The student will investigate and understand that the phases of matter are explained by kinetic theory and forces of attraction between particles. Key concepts include a. Structure and Properties of Organic Molecules b. Bonding c. Hybridization d. Isomers Benchmarks ORGO.3.a.Essential Structure and Properties of Organic Molecules Students will develop an essential understanding of the key topics indicated below: Structure and Properties of Organic Molecules Benchmarks ORGO.3.b.Essential Bonding Students will develop an essential understanding of the key topics indicated below: Linear Combinations of Atomic Orbitals (LCAO) Molecular Orbitals (bonding and antibonding MO s) Constructive Interference vs Destructive Interference to form orbitals Sigma bonds are the most common bonds in organic chemistry. Pi (Π) Bonding, Single, Double and Triple Bonds (versus CCB s in metal:ligand complexes) Organic Chemistry Page 4
Benchmarks ORGO.3.c.Essential Hybridization; Structure, Geometry and Conformations Students will develop an essential understanding of the key topics indicated below: Hybrid orbitals (Hybridization) Valence Shell Electron Pair Repulsion Theory VSEPR theory. Structure and Geometry conformations and three dimensional structures Benchmarks ORGO.3.d.Essential Isomers Students will develop an essential understanding of the key topics indicated below: Isomers Stereoisomers, cis/trans isomers, and structural. Indicators ORGO.3.d. Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. Standard ORGO.4: IUPAC Nomenclature for Organic Molecules The student will name and draw organic molecules according to IUPAC conventions. The student will be able to neatly draw and name organic molecules. Standard ORGO.4.a - c The student will be able to name and draw organic molecules according to IUPAC conventions. a) converting structure to name b) converting name to structure; and c) using correct IUPAC nomenclature conventions for all classes of organic molecules, as follows: o Alkanes, Alkenes, Alkenes (and cyclic analogs) o Alkyl Halides and Alcohols o Ethers, Epoxides, and Sulfides o Aromatic Compounds o Ketones and Aldehydes o Amines and Nitriles o Carboxylic Acids and Carboxylic Acid Derivatives o Carbohydrates and Nucleic Acids o Amino Acids, Peptides, Proteins, and Lipids Benchmarks ORGO.4.a c Students will be able to name and draw organic structures. Organic Chemistry Page 5
Indicators ORGO.4.a - c Students can name and draw organic molecular structure for all classes of IUPAC naming for organic molecules. These will also be correlated with spectroscopic determination of molecular structure (Standard 7). Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. The final exam will be comprehensive and cover topics to include IUPAC Nomenclature (from Standard 4).and spectral problems (from Standard 7). Final exam to count as 20% of final course grade. Standard ORGO.5 Essential Structure and Stereochemistry of Organic Molecules The student will investigate and understand the Structure and Stereochemistry of Organic Molecules, to include simple alkanes, alkenes, alkynes, and cycloalkanes. Standard ORGO.5.a c a. Nomenclature, properties, reactivity, structure and conformation of alkanes b. Nomenclature, properties, reactivity, structure and conformation of cycloalkanes c. Stereochemistry of alkanes, alkenes, alkynes and cyclic alkanes. Benchmarks ORGO.5.a - c Students will develop an essential understanding of the key topics to include: Alkanes are the simplest organic molecules, they only contain C and hydrogen, and only contain single bonds. General Formula: C n H 2n+2 Properties, Reactivity, and Structure and Conformation of Alkanes Drawing Conformations - three common ways of drawing conformations: o Wedges (ORGO Stnd 3 and 4), Newman Projections, and Sawhorse Structures Conformations of Organic Molecules - conformational analysis. o Important conformations: Totally Eclipsed, Gauche, Eclipsed, Anti Cycloalkanes, Nomenclature, Geometric Isomerism In Cycloalkanes Ring Strain in Cycloalkanes and Calculation of Ring Strain o Cyclopropane, cyclobutane, cyclopentane, cyclohexane Boat and Chair Conformations, Axial And Equatorial Positions Conformations of Monosubstituted Cyclohexanes and Disubstituted Cyclohexanes Substituents of Different Sizes and Extremely Bulky groups Bicyclic Alkanes - Fused, Bridged, Spirocyclic; Nomenclature of Bicyclic Alkenes Indicators ORGO.5.a - c Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. Organic Chemistry Page 6
Standard ORGO.6 The Study of Chemical Reactions The student will understand the nature of chemical reactions in organic chemistry. Standard ORGO.6.a c a. Students will understand the concepts of organic chemical reactions. b. Students will understand how to evaluate and determine the mechanism, thermodynamics, and kinetics associated with organic chemical reactions. c. Students will understand the Hammond Postulate and energy diagrams for organic reactions. Benchmarks ORGO.6.a - c Students will develop an essential understanding of the key topics to include: Mechanisms, Thermodynamics, and Kinetics for Organic Reactions The Free Radical Chain Reaction- three different steps: Initiation, Propagation, Termination Equilibrium Constants, Free Energy, Enthalpy and Entropy Bond Dissociation Energies (BDE s) Homolytic Cleavage (gives free radicals) versus Heterolytic (Ionic) Cleavage (gives ions) Kinetics and the Rate Equation (Activation Energy (Ea) and Temperature Dependence of Rates) Reaction Energy Profiles, Transition States, Rates of Multistep Reactions, Rate Determining Step Isotope Effects and Halogenation of Higher Alkanes The Hammond Postulate - compare the energy profile diagrams for the Cl and Br of propane Reactive Intermediates, Free Radicals, Carbocations, Carbanions, and Carbenes Indicators ORGO.6.a - c Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. Organic Chemistry Page 7
Standard ORGO.7 Essential Spectroscopic determination of molecular structure organic chemistry The student will be able to explain the theory and operation of instrumentation used by organic chemists, and will also be able to interpret data for determining chemical structure, using Infrared Spectroscopy, Mass Spectroscopy, and Nuclear Magnetic Resonance Spectroscopy, 1 H and 13 C. (2-D and 3-D). **Note: Use of the above instruments is not included in the course. Data analysis is based on provided spectra for all problems. Sample spectral data bases include the Spectral Data Base System of Japan, or the Aldrich Spectral Libraries ORGO 7.a - b a) Evaluate the theory, operation, and data analysis for organic spectral analysis in order to determine molecular structure using the following instrumental methods: 1. Infrared Spectroscopy 2. Mass Spectrometry 3. Nuclear Magnetic Resonance Spectroscopy ( 1 H and 13 C). b) Spectroscopic analysis for structure determination and nomenclature for all classes of organic molecules, as follows: 1. Alkanes, Alkenes, Alkenes (and cyclic analogs) 2. Alkyl Halides and Alcohols 3. Ethers, Epoxides, and Sulfides 4. Aromatic Compounds 5. Ketones and Aldehydes 6. Amines and Nitriles 7. Carboxylic Acids and Carboxylic Acid Derivatives 8. Carbohydrates and Nucleic Acids 9. Amino Acids, Peptides, Proteins, and Lipids Benchmarks ORGO.7.a - b a) Students will be able to understand interpret data based on the theory, operation, and data analysis for organic spectral analysis in order to determine molecular structure. Instrumental methods, to include IR, MS, H 1 -NMR and C 13 -NMR in theoretical applications, to enable students to be able to perform data analysis for structure determination. Standard does not include or rely upon actual use of such instruments. b) Students will be able to determine molecular structure for the classes of molecules indicated above. [ Associated with Standard 4, students will also be able to provide IUPAC names.] Indicators ORGO.7.a - b Students can name/draw organic molecular structure for all classes of IUPAC naming for organic molecules (Standard 4). Students can evaluate data for spectroscopic determination of molecular structure (Standard 7). Organic Chemistry Page 8
Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. The final exam will be comprehensive and cover topics to include IUPAC Nomenclature (from Standard 4) and spectral problems (from Standard 7). Counts as 20% of course grade. Standard ORGO.8 Essential (potentially TJ Extension) Stereochemistry ORGO 8.a - b a) Chirality b) (R) and (S) Nomenclature of Asymmetric Carbon Atoms c) Optical Activity d) Racemic Mixtures e) Enantiomeric Excess and Optical Purity f) Chirality of Conformationally Mobile Systems g) Chiral Compounds without Asymmetric Atoms h) Fischer Projections i) Diastereomers j) Stereochemistry of Molecules with Two or More Asymmetric Carbons Benchmarks ORGO.8.a - j Students will develop an essential understanding of the key topics indicated above. a) Draw all of the stereoisomers of a given structure, and identify the relationships between the stereoisomers b) Classify molecules as chiral or achiral, and draw their mirror images. Identify and draw any mirror plane of symmetry. c) Identify asymmetric carbon atoms, and name them using the (R) and (S) nomenclature. d) Use Fischer projections to represent the stereochemistry of compounds with one or more asymmetric carbon atoms. Indicators ORGO.8.a - j Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. Organic Chemistry Page 9
Standard ORGO.9 Essential (potentially TJ Extension) Alkyl Halides: Nucleophilic Substitution and Elimination ORGO 9.a b a) Physical Properties of Alkyl Halides b) Preparation of Alkyl Halides c) Reactions of Alkyl Halides: Substitution and Elimination d) Second-Order Nucleophilic Substitution: The SN2 Reaction e) Generality of the SN2 Reaction f) Factors Affecting SN2 Reactions: Strength of the Nucleophile g) Reactivity of the Substrate in SN2 Reactions h) Stereochemistry of the SN2 Reaction i) First-Order Nucleophilic Substitution: the SN1 Reaction j) Stereochemistry of the SN1 Reaction k) Rearrangements in SN1 Reactions l) Comparison of SN1 and SN2 Reactions m) First-Order Elimination: The E1 Reaction n) Positional Orientation of Elimination: Zaitsev's Rule o) Second-Order Elimination: The E2 Reaction p) Stereochemistry of the E2 Reaction q) Comparison of E1 and E2 Elimination Mechanisms Benchmarks ORGO.9.a - j Students will develop an essential understanding of the key topics indicated above, to include: a) Correctly name alkyl halides, summarize their physical properties, and identify them as 1, 2, or 3. b) Show how free-radical halogenation might be used for the synthesis of some alkyl halides, especially for making allylic and benzylic alkyl halides. c) Predict the products of SN1, SN2, E1, and E2 reactions, including stereochemistry. Use Zaitsev s rule to predict the major and minor products of eliminations. d) Draw the mechanisms and energy profiles of SN1, SN2, E1, and E2 reactions. e) Predict and explain the stability and rearrangement of cations in first-order reactions. f) Predict which substitutions or eliminations will be faster, based on differences in substrate, base or nucleophile, leaving group, and solvent. g) Predict whether a reaction will be first-order or second-order. h) When possible, predict whether substitution or elimination will predominate. i) Given a set of reaction conditions, identify the possible mechanisms, and predict which mechanism(s) and product(s) are most likely. j) Show how substitutions and eliminations of alkyl halides might be used to synthesize other types of compounds. Indicators ORGO.9.a - q Assessments including problem sets, quizzes and formal exams will be used to determine student s level of understanding and comprehension. Organic Chemistry Page 10
Standard ORGO.10 Essential Instrumental Methods for Chemical Analysis A primary component of this course involves learning about Instrumental Methods for Chemical Analysis. The goal of this Standard is to address Instrumental Methods for Chemical Analysis through project-based learning format and student discussion format using the Socratic Method. Students must prepare presentations and/or prepare in advance of presentations to be actively engaged in the learning process. Standard ORGO.10.a- f a. Understand how chemical analysis can be performed using technology and instrumentation, see list below. b. Evaluate literature and textbooks to develop a formal description of theory, operation, use and data analysis for instrumentation. c. Perform library searches to locate and then evaluate and write article reviews for primary sources of peer-reviewed research articles. Articles to be selected from ACS journal including ACS Nano, Anal. Chem., and Env. Sci, & Tech. (not JCE ) d. Use extant body of knowledge, literature, and internet sources to develop a research report integrating all aspects of the instrumentation theory and use, and the current applications of such instrumentation. e. Propose potential research projects utilizing instrumentation topic, to be included within formal report. f. Use the Socratic Method with a Powerpoint presentation for providing a class-engaging discussion about the instrumental methods of analysis, associated applications/current trends and student-proposed research ideas. Benchmark ORGO.10.a - Essential Students will be able to understand how chemical analysis can be performed using technology and instrumentation from the following list of Instrumental Methods to Investigate: 1. Fluorescence Spectroscopy 2. Raman Spectroscopy and Surface Enhanced Raman Spectroscopy (SERS) 3. Inductively coupled plasma mass spectrometry - (ICP-MS) 4. Atomic Absorption and X-ray spectrometry 5. Gas Chromatography 6. Liquid Chromatography 7. Capillary Electrophoresis 8. UV/Vis Spectroscopy 9. Others with approval. Indicators ORGO.10.a Report to include Title, Introduction, Theory of Operation and Use, Applications and Current Research, Summarize this current research area that uses the instrument and how the instrument is beneficial to the research goals (from article reviews). Also to provide at least one research project idea to explore if we had this instrument; summarize the idea and Organic Chemistry Page 11
elaborate upon what would be your research goals. References to be included in ACS format. Benchmark ORGO.10.b - Essential Evaluate literature and textbooks to develop a formal description of theory, operation, use, and data analysis for instrumentation. Indicators ORGO.10.b Provide thorough, clear description of assigned instrumentation and learn about other methods during presentations. Benchmark ORGO.10.c Essential Students to perform online literature searches and write article reviews for primary sources of peer-reviewed research articles. Articles to be selected from ACS journal including ACS Nano, Anal. Chem., and Env. Sci, & Tech. (not JCE ) Indicators ORGO.10.c Written article reviews of two articles related to assigned instrument. Discussion of current literature related to instrumentation use within formal report. Benchmark ORGO.10d Essential Students, in teams of two to three, to write a research report integrating all aspects of the instrumentation theory and use, and the current applications of such instrumentation. Indicators ORGO.10.d Final, formal written report adhering to ACS style guides for publications. Benchmark ORGO.10.e Essential Students, within the research report, are to propose and write a research proposal that utilizes the instrument they are investigating. Indicators ORGO.10.e Research ideas are proposed within the formal report. Research ideas are discussed coherently during presentation. Benchmark ORGO.10.f.1. Essential Students must use the Socratic Method with a Powerpoint presentation for discussing the instrumental methods of analysis and associated applications and research. Benchmark ORGO.10.f.2. Essential Organic Chemistry Page 12
Students must engage the class to educate them all aspects of their instrumental method, the current events, and their research ideas. Indicators ORGO.10.f.1-2 Formal presentation to present, discuss, and educate classmates on assigned instrumental method of chemical analysis. Extensions ORGO.10.f.1-2 Students design and complete experimentation proposed in Instrumentation Project. This document is intended for internal use only within TJHSST only by TJHSST staff for the only purpose of vertical integration of learning objectives for students. Permission is NOT given for electronic or hardcopy distribution, electronic posting to websites, or other purposes. Doing so is a violation of U.S. Copyright laws and regulations. Organic Chemistry Page 13