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CM1121: BASIC ORGANIC CHEMISTRYDr. Lu Yixin Department of Chemistry National University of Singapore

CM1121, AY 2007-08 DR. LU YIXIN

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Course Outline (I) Lecture 1: Introduction; Lecture 2: Alkanes/ Cycloalkanes and their Conformations; Lecture 3: Reaction Mechanisms; Lecture 4: Alkenes and Electrophilic Additions; Lecture 5: Alkynes; Lecture 6: Stereochemistry and Chirality; Lecture 7: Alkyl Halides and Free Radical Reactions; Lecture 8: Alkyl Halides and Nucleophilic Substitution/ Eliminations;CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 2

Course Outline (II) Lecture 9: Aromaticity and Electrophilic Substitutions; Lecture 10: Alcohols and Phenols; Lecture 11: Ethers and Epoxides; Lecture 12: Carbonyl Compounds and Nucleophilic Additions; Lecture 13: Carbonyl Compounds and Nucleophilic Acyl Substitutions; Lecture 14: Carbonyl Compounds and Alpha Substitution Reactions; Lecture 15: Revision and a Brief Introduction to Multi-step synthesis.CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 3

Timetable (I)Week (Mon Fri) Week 1 (13/8-17/8) Week 2 (20/8-24/8) Week 3 (27/8-31/8) Week 4 (3/9-7/9) Week 5 (10/9-14/9) Week 6 (17/9-21/9) Recess (22/9-30/9) Week 7 (1/10-5/10)CM1121, AY 2007-08 DR. LU YIXIN

Mon (10am-12pm) Lecture 1 Lecture 2/3 Lecture 4 Tutorial Test 1 Lecture 8 Break Lecture 9LECTURE 1

Thurs (10am-12pm) Lecture 1/2 Lecture 3/ Tutorial Lecture 4/5 Lecture 6/ Tutorial Lecture 7/8 Tutorial Break Tutorial4

Timetable (II)Week (Mon Fri) Week 8 (8/10-12/10) Week 9 (15/10-19/10) Week 10 (22/10-26/10) Week 11 (29/10-2/11) Week 12 (5/11-9/11) Week 13 (12/11-16/11) Reading (17/11-23/11) Mon (10am-12pm) Thurs (10am-12pm) Lecture 10/11 Tutorial Tutorial Lecture 13 Lecture 14 Lecture 15/Tutorial Reading Lecture 10/11 Lecture 12 Test 2 Lecture 13/14 Holiday Tutorial Reading

Lecture notes will be uploaded to IVLE by noon of Sat & Wed. Final exam on 28 November, 2007, afternoon.CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 5

Grading MethodsPractical (20%)

EvaluationTest (20%) Final Closed -book Exam (60%)

CM1121, AY 2007-08 DR. LU YIXIN

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Aims To understand basic organic chemistry, the structure and reactivity of organic molecules; Be familiarized with reaction mechanisms; Be able to carry out simple synthesis.CM1121, AY 2007-08 DR. LU YIXIN

Learning Methods Do NOT just remember/memorize, try to understand, think and ask why! Understand the mechanism and use 3-D models; Practise & solve problems.7

LECTURE 1

Textbooks John McMurry, Organic Chemistry, 7th Edition (strongly recommended); Other useful books: John McMurry, Organic Chemistry: A Biological Approach, 2007 Edition; Bruice, Organic Chemistry, 5th Edition.

CM1121, AY 2007-08 DR. LU YIXIN

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Lecturer and Teaching Assistants Lecturer: Dr. Lu, Yixin; Office: S5-03-08; Consultation hours: Weds 2:00-3:00pm in my office; Teaching Assistants (Very Important Persons): Mr. Gunari, Parag; Mr. Zhang, Sheng; Mr. Soh Yong Bin Matthew. You are strongly encouraged to use Forum at IVLE for discussions, the top participants may be rewarded in the final grading.CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 9

Lecture 1:Introduction to Organic Chemistry

CM1121, AY 2007-08 DR. LU YIXIN

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Outline of Lecture 1 Organic chemistry and organic compounds; Atomic and molecular orbitals; Bonding theory; Resonance; Acids and bases; Non-covalent Interactions.CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 11

CM1121, AY 2007-08 DR. LU YIXIN

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Historical Foundations of organic chemistry can date back to mid-1700s; Organic until mid 1800s referred to compounds from living sources; Vitalism - It was originally thought organic compounds could be made only by living things by intervention of a vital force; Whler in 1828 showed that urea could be made from ammonium cyanate.

CM1121, AY 2007-08 DR. LU YIXIN

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Organic Chemistry Today, organic compounds organic chemistry Includes biological molecules (proteins, DNA), foods, medicines, solvents, dyes; Does not include metal salts (inorganic); Does not include materials of large repeating molecules without sequences (polymers).CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 14

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Periodic TableBe4

CHe5 6

2 7 8 9 10 18

H Li3 11 19 37 55 12 20 38 21 39 22 40 23 41 24 42 25 26 44

1S22S22P2V Cr Mn Fe Co Ni Cu Zn43 45 46 47 75 107 76 108 77 109 78 79 27 28 29 30 48

B13

C14 32 50 82

N

O15 16

F17

Ne

Na Mg K Ca Sc Ti Sr Y56 88 57 89

Al31 49

Si P33 51 83

S34 52 84

Cl Br35 53 85

Ar Kr Xe86 36 54

Ga Ge As Se In81

Rb Cs Fr

Zr72 104

Nb Mo Tc Ru Rh Pd Ag Cd73 74

Sn Sb Te I

Ba La Hf87

Ta105

W106

Re Os Ir

pt

Au Hg

80

Tl

Pb Bi Po At

Rn

Ra Ac Rf58 90

Db Sg61 93

Bh Hs Mt Uun63 95 64 65 66 67 99 68 100 69 101 70 102 71

110

59 91

60 92

Ce Pr Nd Th Pa U

Pm Sm Eu Gd Tb Dy Ho Np Pu Am Cm Bk94 96 97

62

Er Tm Yb Lu Fm Md No Lr103

Cf Es

98

CM1121, AY 2007-08 DR. LU YIXIN

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Why Carbon Atom? The second row of the periodic table; Carbon has four valence electrons (2s2 2p2) and can form 4 covalent bonds, Unique ability of carbon atoms to bond together, form long chains and rings; bond angle bond length Generate enormous diversity from methane to DNA, RNA, proteins etc.4 identical bonds?CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 16

Drawing Chemical Structures Chemists have various ways for writing structures: dot structure, dash formula, condensed formula and skeletal structure; Condensed structures: C-H and C-C and single bonds aren't shown but understood, vertical bonds are added for clarity.Lewis structure Each dash represents a pair of electrons

Lone pair electrons

CM1121, AY 2007-08 DR. LU YIXIN

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Skeletal Structures Minimum amount of information but unambiguous; Cs not shown, assumed to be at each intersection of two lines (bonds) and at end of each line; Hs bonded to Cs aren't shown whatever number is needed will be there; All atoms other than C and H are shown.

CM1121, AY 2007-08 DR. LU YIXIN

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3-D Structures & Molecular Models We often need to visualize the shape or connections of a molecule in 3-D; Molecular models are three dimensional objects that represent the aspects of interest of the molecules structure; Framework models/ball-and-stick are essential for seeing the relationships within and between molecules; Space-filling models are better for examining the crowding within a molecule; Drawings on paper and screens are limited!H H C C H H

H C C H

CM1121, AY 2007-08 DR. LU YIXIN

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Atomic Structure Structure of an atom: Positively charged nucleus (protons and neutrons, very dense and small (10-15 m)); Negatively charged electrons are in a cloud (10-10 m) around nucleus; Diameter is about 2 10-10 m (200 picometers (pm)) [the unit angstrom () is 10-10 m = 100 pm].

CM1121, AY 2007-08 DR. LU YIXIN

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Atomic Number and Atomic Mass The atomic number (Z) is the number of protons in the atom's nucleus; The mass number (A) is the number of protons plus neutrons; All the atoms of a given element have the same atomic number. Isotopes are atoms of the same element that have different numbers of neutrons and therefore different mass numbers; The atomic mass (atomic weight) of an element is the weighted average mass in atomic mass units (amu) of an elements naturally occurring isotopes; 1 amu (atomic mass unit) = 1/12 the mass of a C12 atom, or 1.661 x 10-24 g.CM1121, AY 2007-08 DR. LU YIXIN LECTURE 1 21

Atomic Structure: Orbitals Quantum mechanics: describes electron energies and locations by a wave equation- each wave function is an orbital,; Electron cloud has no specific boundary so the most probable area is shown; Four different kinds of orbitals denoted s, p, d, and f; s orbitals: spherical, nucleus at center; p orbitals: dumbbell-shaped, nucleus at middle.

CM1121, AY 2007-08 DR. LU YIXIN

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Orbitals and Shells Orbitals are grouped in shells of increasing size and energy; Different shells contain different numbers and kinds of orbitals; Each orbital can be occupied by two electrons; First shell contains one s orbital, denoted 1s, holds only two electrons; Second shell contains one s orbital (2s) and three p orbitals (2p), eight electrons; Third shell contains an s orbital (3s), three p orbitals (3p), and five d orbitals (3d), 18 electrons.

CM1121, AY 2007-08 DR. LU YIXIN

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p-Orbitals In each shell there are three perpendicular p orbitals, px, py, and pz of equal energy; Lobes of a p orbital are separated by region of zero electron density a node.

CM1121, AY 2007-08 DR. LU YIXIN

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Atomic Electron Configurations Ground-state electron configuration of an atom lists orbitals occupied by its electrons. Rules:1. Lowest-energy orbitals fill first: 1s 2s 2p 3s 3p 4s 3d (Aufbau (build-up) principle); 2. Electron spin can have only two orientations, up and down . Only two electrons can occupy an orbital, and they must be of opposite spin (Pauli exclusion principle) to have unique wave equations; 3. If two or more empty orbitals of equal energy are available, electrons occupy eac