CHMI-2426E Fall-2011

Gerardo Ulbarri, PhD S-410 Manager of the NMR Facility Medicinal Chemistry Research EcoHealth Research
-West Nile virus mosquito control -Bioremediation using Medicinal Plants -Complexation of Metals with cyclic peptides
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CHMI-2426E Fall-2011

5% Assistance

10% Quizzes

30% Mid-term

15% Lab.

40% Final

Tutorials; Alison Ralph, PhD Student (BMS) Monday/Lundi 05:30PM - 06:50PM, Arts Building, Room A-226 Thursday/Jeudi 04:00PM - 05:20PM, Classroom Building, Room C-309
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CHMI-2426E Fall-2011
You must pass the Laboratory (>7.5/15) to pass the course If you already passed the lab. and are retaking the course, come to see me after class You must pass the course (>51/100) to pass the course

Tutorial Monday/Lundi 05:30PM - 06:50PM, Arts Building, Room A-226 Tutorial Thursday/Jeudi 04:00PM - 05:20PM, Classroom Building, Room C-309
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CHMI-2426E Fall-2011

http://ebooks.bfwpub.com/organic6e.php

Manuals-Bookstore

Labs.

Manager: Berni Shami

Behaviour before the lab. -READ THE EXPERIMENT BEFORE YOU START -Be on time, or before the lab. starts -No playing/noise outside the lab. -backpacks/coats/loads must stay outside the lab, properly placed! -You are responsible for your valuables Behavior while in the lab. -Must wear safety glasses/no contact lenses -Must wear a clean labcoat -No eating/drinking while in the lab. -No jokes/horse playing in the lab.

Course syllabus
Chap.1.-Structure and Bonding in Organic Molecules Chap.2.-Structure And Reactivity: Acids and Bases, Polar and Nonpolar Molecules Chap.3.-Reactions of Alkanes: Bond-Dissociation Energies, Radical Halogenation, and Relative Reactivity Chap.4.-Cycloalkanes Chap.5.-Stereoisomers Chap.6.-Properties and Reactions of Haloalkanes: Bimolecular Nucleophilic Substitution Chap.7.-Further Reactions of Haloalkanes: Unimolecular Substitution and Pathways of Elimination Chap.8.-Hydroxy Functional Group: Alcohols. Properties, Preparation, and Strategy of Synthesis
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Chapter 1.-Structure and Bonding in Organic Molecules We begin with the alkanes: chemical compounds with only carbon and hydrogen atoms (hydrocarbons) connected by bonds made with shared electrons. They lack any functional groups (handles) and as such constitute the basic scaffold of organic molecules.

Coulomb Forces: A Simplified View of Bonding The bonds between atoms hold a molecule together. But what causes bonding? Two atoms form a bond only if their interaction is energetically favorable; that is, if energyheat, for exampleis released when the bond is formed. Conversely, breaking that bond requires the input of the same amount of energy. The two main causes of the energy release associated with bonding are based on Coulombs law of electric charge: Opposite charges attract each other (electrons are attracted to protons). Like charges repel each other (electrons spread out in space).

Coulomb Forces: A Simplified View of Bonding

Each atom consists of a nucleus containing electrically neutral particles, or neutrons and positively charged protons.

Surrounding the nucleus are negatively charged electrons, equal in number to the protons so that the net charge is zero. As two atoms approach each other, the positively charged nucleus of the first atom attracts the electrons of the second atom; similarly, the nucleus of the second atom attracts the electrons of the first atom.

The Chemistry of magnetic attractions

Coulomb Forces: A Simplified View of Bonding When the atoms reach a certain closeness, no more energy is released. The distance between the two nuclei at this point is called the bond length.

Bringing the atoms closer together than this distance results in a sharp increase in energy though electronic repulsion.

A covalent bond is formed by the sharing of electrons

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An alternative to this type of bonding results from the complete transfer of an electron from one atom to the other. The result is two charged ions: one positively charged, a cation, and one negatively charged, an anion.

An ionic bond is based on the electrostatic attraction of two ions with opposite charges
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For those who remember CHMI-1006/1007

Carbon has 6 electrons, 4 in the outer shell: 1S2, 2S2, 2P2

The first two electrons go into the 1S orbital. Then the next two go into the 2S orbital, and six go into the 2P orbital, since P has the Px, Py, and Pz orbitals12

Ionic and Covalent Bonds: The Octet Rule

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Once the shells are filled, the electrons are inaccessible for bonding=noble gas configuration Carbon=1s2, 2s2, 2p2
Valence Electrons: Electrons in the outermost shell (principal quantum level) of an atom. Core Electrons: Electrons in the inner closed shells.

Can accept 4 eor can donate 4 e14

Once the shells are filled, the electrons are inaccessible for bonding=noble gas configuration Nitrogen=1s2, 2s2, 2p3 Can accept 3 eor can donate 5 e15

Once the shells are filled, the electrons are inaccessible for bonding=noble gas configuration Oxygen=1s2, 2s2, 2p4 Can accept 2 eor can donate 6 e16

Once the shells are filled, the electrons are inaccessible for bonding=noble gas configuration Halogens=1s2, 2s2, 2p5 Can accept 1 eor can donate 7 e17

An ionic bond is based on the electrostatic attraction of two ions with opposite charges. In pure ionic bonds, electron octets are formed by transfer of electrons

One has to think in two rules: the octet rule and the charge rule

It takes energy to remove an electron from an atom. This energy is the ionization potential (IP) of the atom. Conversely, energy may be released when an electron attaches itself to an atom, this energy is called its electron affinity (EA)
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Na. + Cl.

Na-Cl

The overall ionization requires energy However, at the most favorable interatomic distance (2.8 ) (magnets:positive/negative charges) the ionic attraction (neutralization of charges) releases about 120 kcal mol1(502 kJ mol1). [+36 120 = 84 kcal mol1 (351 kJ mol1)]
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The elements share electrons so that each atom attains a noble-gas configuration.

The drawings above, with pairs of electron dots representing bonds, are also called Lewis structures. 20

Formation of ionic bonds require a lot of energy! Molecules prefer to share their orbital electrons

By sharing their lone electron, they can form a covalent bond, keep their own electrons and fulfill the octet rule!
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RULE 1. Draw the (given or desired) molecular skeleton.

CH4

RULE 2. Count the number of available valence electrons. Add up all the valence electrons of the component atoms.
Special care has to be taken with charged structures (anions or cations), in which case the appropriate number of electrons has to be added or subtracted to account for extra charges.

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RULE 3. (The octet rule) Depict all covalent bonds by two shared electrons, giving as many atoms as possible a surrounding electron octet, except for H, which requires a duet.
Make sure that the number of electrons used is exactly the number counted according to rule 2. Elements at the right in the periodic table may contain pairs of valence electrons not used for bonding, called lone electron pairs or just lone pairs.

C2H4

C2H2

CH2O

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RULE 4. Assign ( formal) charges to atoms in the molecule.

Each lone pair contributes two electrons to the valence electron count of an atom in a molecule, and each bonding (shared) pair contributes one. An atom is charged if this total is different from the outer-shell electron count in the free, nonbonded atom. Thus we have the formula

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The octet rule does not always hold

EXCEPTION 1. The correct Lewis structures contain an even number of electrons distributed as bonding or lone pairs. This distribution is not possible in species having an odd number of electrons, such as nitrogen oxide (NO) and neutral methyl (methyl radical, CH3)

EXCEPTION 2. Some compounds of the early second-row elements, such as BeH2 and BH3, have a deficiency of valence electrons.

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EXCEPTION 3. Beyond the second row, the simple Lewis model is not strictly applied, and elements may be surrounded by more than eight valence electrons, a feature referred to as valence shell expansion.

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Once the shells are filled, the electrons are inaccessible for bonding=noble gas configuration
Atom Hydrogen Sodium Carbon Nitrogen Oxygen Halogens # e- s 1 1 4 5 6 7 Take 2 1 Give away 1 1 Share 1 4 3 2 1 Ionic form H+ Na+ O-2 x27

Carbon=1s2, 2s2, 2p2

Coulombs law of electric charge: Opposite charges attract each other (electrons are attracted to protons). Like charges repel each other (electrons spread out in space).
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Carbon=1s2, 2s2, 2p2

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Carbon=1s2, 2s2, 2p2 hybridization

4 sp3 hybrid orbitals Overlap these orbitals (with one electron each) with up to 4 orbitals (with one electron each) to form covalente bonds!
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Carbon=1s2, 2s2, 2p2

Tetrahedral configuration

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Carbon=1s2, 2s2, 2p2

3 sp2 hybrid orbitals + one p orbital 2 sp hybrid orbitals + two p orbital

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