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ORGANIC CHEMISTRY Textbook: Hart et al., Organic Chemistry: A short Course, 12th edition, 2007. Chapter 1 Bonding and isomerism 1.1 electrons are arranged in atoms Atoms contain a small, dense nucles surrounded by electrons. The nucleus is positively charged and contains most of the mass of the atom. The nucleus consists of protons which are positively charged, and neutrons, which are neutral. The atomic number of an element is equal to the number of protons (and to the number of electrons around the nucleus in a neutral atom. Atomic weight is approximately equal to the sum of the number of protons and the number of neutrons in the nucleus. Electrons are very light. Electrons are concentrated in certains region of space around nucleus called orbitals. Each orbital can contain a maximum of two electrons. The orbitals, which differ in shape, are designated by the letters, s, p, d, and f. Outer electrons, or valence electrons, are mainly involved in chemical bonding.

1.2 ionic and covalent bonding Ionic bond (consider the “Electrogenativity”) The atom that gives up electrons becomes positively charged, a cation. The atom that receives electrons becomes negatively charged, an anion.

Sodium tend to give up (donate) electrons are said to be electropositive. Chlorine tends to accept electron are said to be electronegative. The reason of the electron moving is because of high

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electronegativity of chlorine. Question: Consider magnesium (Mg) and Fluorine atom (F) could form MgF2 Covalent bonding (similar electronegativity) Elements that are neither strongly electronegative nor strongly electropositive, or that have similar electronegativities, tend to form covalent bonds by sharing electron pairs rather than completely transferring electrons.

Two (or more) atoms joined by covalent bonds constitute a molecule. The energy to break it apart into atoms, we called bond energy. The distance between two nuclei is bond length. 1.3 Carbon and the covalent bond With four valence electrons, carbon usually forms covalent bonds with other atoms by sharing electrons. For examples, carbon combines with four hydrogen atoms by sharing four electron pairs. It is known as methane.

1.4 carbon-carbon single bond Carbon could share electrons with not only different elements but also carbon. In ethane, each carbon is connected to the other carbon and to three hydrogen atoms or three chlorine atoms.

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The C-C bond in ethane, like the H-H bond is a hydrogen molecule, is a purely covalent, with the electrons being shared equally between the two identical carbon atoms. Less heat is required to break the C-C bond in ethane than the H-H bond in a hydrogen molecule. The C-C-bond in ethane is 1.54 Å. The H-H bond in H2 molecule is 0.74 Å. The C-H is about 1.09 Å, close to the average of H-H bond and C-C bond. 1.5 Polar Covalent Bonds Two identical atoms share electrons to form covalents. However, two different atoms share electrons unequally to form polar covalent bond, such as H-Cl, C-Cl. H-O bonds. Hydrogen Chloride is an example of polar covalent bond.

The shared electron pair is attracted more toward chloride, which therefore is slightly negative with repect to the hydrogen. The bond polarization is indicated by an arrow whose head is hegative and whose tail is marked with a plus sign. Alternatively, a partial charge, written as + or (read delta plus or delta minus) Others polar covalent bonds are common is organic compounds.

1.6 Multiple covalent bonds

1.7 Valence The valence of an element is simply the number of bonds that an atom of the element can form. The number is normally equal to the number of electron needed to fill the valence shell.

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1.8 Isomerism and Writing Structural Formulas For the molecular formula C2H6O, there are two very different chemical substances are known. One is a liquid with the boilding point at 78 oC, the other is a gas at ordinary temperature (-23.6 oC)

Molecules that have the same kinds and numbers of atoms but different arrangements are called isomers. Structural (or constitutional) isomers are the compounds that have the same molecular formula but different structural formulas. Consider a formula of C5H12

C CH

HH

H

HC CH

H

H

HCH

HHC C C C C

C5H12continuous chain

C CH

HH

H

C

C CH

H

H

HH

HH

H

C C

C

C C

pentane

a branched chain

2-methylbutane

CC

CC C C

C

C

C C

HH H

H

HH H

H

H

HHH

2,2-dimethylpropane

1.10 Abbreviated structural Formulas

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Ultimate abbreviation of structures is the use of lines to represent the carbon framework. “C-C bond can be abbreviated to a line. C-H bond is omitted.” The atoms other than H and C should be presented, such as S, O, N, F, Br…etc.

n-pentane isopentane neopentane

3 lines at this posintthis carbon has 1 hydrogen attached to it

1 line at his point3 hydrogens attached to it

2 lines at this point2 hydrogens attached to it.

Consider these formulas

1.11 Formal Charge In some molecules may be charged, either positively or negatively. Because such charges usually

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affect chemical reactions. Therefore, it is very important to know how to tell the charge is located. Consider the formula for hydronium ion, H3O+, the product of the reaction of a water molecule with a proton.

Six of these eight electrons are used to from three O-H bonds, leaving one unshared electron pair on the oxygen. Entire hydronium ion carries a positive charge. Which atom bears the charge? To determine formal charge, we consider each atom to “own” all of its unshared electrons plus only half of its shared electrons

For H atom Formal charge = 1 – ( 0 + 1 ) = 0 For O atom Formal charge = 6 – (2 + 3) = 1 +1 1.12 Resonance Sometimes, an electron pair is involved with more than two atoms. Molecules and ions in which this occurs can not be adequately represented by a single electron-dot structure. Please consider the structure of the carbonate ion, CO3

2-

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Single bonded oxygen has a formal charge of -1, double bonded oxygen is neutral. When you wrote the electron-dot structure, there are in fact three exactly equivalent structures.

Physical measurement tell us that all three C-O bond length are identical: 1.31 Angstrom (Å) This distance is between the normal C=O (1.20 Å) and C-O (1.41 Å). We usually say the real carbonate ion has s structure that is resonance hydride of the three contributing resonance structures.

Sometimes we represent a resonance hydride with one formula by writing a solid line for each full bond and a dotted line for each partial bond. (the dots represent one third of a single bond)

1.13 Arrow Formalisn Arrow system is very important in Chemistry and has specific meaning. Curved arrows a pair of electron moving Fishhook arrows single electron moving Straight arrows point from reactants to products in chemical reaction equactions Straight arrow with half-heads used in pairs to indicate that the reaction is reversible. double-headed straight arrow between two structures indicates that they are resonance structure

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1.14 Bonding: the sigma bond Atomic orbitals. The s orbitals are spherical. The three orbitals are dumbbell shaped and mutually perpendicular, oriented along the three cooridinate axes, x, y, and z.

When atomic orbitals overlap to form a molecular orbital, electron occupy this molecular orbital. A bond is formed. Two s orbitals form a sigma bond.

Sigma bonds may also be formed by the overlap of an s and a p orbital or of two p orbitals.

1.15 Carbon sp3 hybrid orbitals In a carbon atom, the six electrons are arranged as shown below.

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The farther the electron is from the nucleus, the greater its potential energy, because it takes energy to keep the electron (negatively charged) and the nucleus (positively charged) apart. Like CH4 and CCl4, Carbon usually forms four single bonds, and often these bonds are all equivalent. It would like to mix or combine the four atomic orbitals of valence shell (one s and three p orbitals) to form four identical hydride orbitals, each containing ine valence electron. This model we call sp3 hydrid orbital, because each one has one part of s character and three part of p character.

Now, the carbon has four identical sp3 orbitals, the geometry is called tetrahedron. The angle between any two of the four bonds is approximately 109.5o. The angle made by lines drawn from the center the corners of a regular tetrahedron.

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1.6 Tetrahedral carbon; the bonding in methane With a molecular model

In methane, there are four sp3-s C-H sigma bonds, each directed from the carbon atom to one of the four corners of a regular tetrahedron. 1.17 classification according to molecular framework Acyclic Cyclic Heterocyclic 1.18 Classification according to functional group A list of main functional group

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structure class of compound example

functional groupcontaining nitrogen

C NH2 primary amine CH2CH2NH2

C N nitrile CH3CN

functional groupcontaining oxygenand nitrogen

CO

NH2primary amide CH

ONH2

functional groupcontaining halogen X

alkyl and aryl halide CH3I

functional groupcontaining sulfur

C SHthiol (mercaptan) CH3SH

C S C thioether (sulfide) SH3CH2C CH2CH3

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Chapter 2 Alkanes and cycloalkanes; conformational and geometric isomerism The main components of petroleum and natural gas, resource that now supply most of our fuel and energy, are hydrocarbon. 2.1 The structure of alkanes The simplest alkane is methane. It is a structure of tetrahedral. Name and formulas of unbranched alkanes.

All alkanes fit the general molecular formula CnH2n+2, where n is the number of carbon atoms. Unbranched alkane are claaed normal alkanes. Each member of this series differs from the next one by a -CH2 group (called methylele group. 2.2 Nomenclature of organic compounds Internationally recognized systems of nomenclature were devised by a commission of the International Union of Pure and Applied Chemistry; they are known as the IUPAC (pronounced ”eye-you-pack”.

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2.3 IUPAC rules for naming alkanes 1. The -ane ending is used for all saturated hydrocarbon. Other ending will be used for other

functional groups. 2. Alkanes without branches are named according to the number of carbon atoms. 3. For alkanes with branches, the root name is that of the longest continuous chain of carbon

atoms.

The longest continuous chain has five carbon atoms. The compound is therefore named as a substituted pentane, even through there are seven carbon atoms. 4. Groups attached to the main chain are called substituents. Saturated substituents that contain

only carbon and hydrogen are called alkyl groups. An alkyl group is named by taking the name of the alkane with the same number of carbon atoms and changing the -ane to -yl.

More in Section 2.4 5. The main chain is numbered in such a way that the first substitutents encountered along the

chain receives the lowest possible number. Then each substituent is then located by its name and by the number of the carbon atom to which it is attached. When two or more identical groups are attached to the main chain, prefixes such as di-,tri-, tetra- are used.

6. IF two or more different types of substituents are present, they are listed alphabetically, Except that prefixes such as di- and tri- are not considered when alphabetizing.

7. IUPAC names for hydrocarbon are written as one word. Numbers are separated from each other by commas (,) and are separated from letters by hyphens (-). There is no space between the last named substituent and the name of parent alkane.

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To easily let you understand these rule, we take the following steps to find an IUPAC name A. Loctae the longest continuous carbon chain. This gives the name of parent alkane.

pentane not butane

B. Number the longest chain beginning at the end of nearest the first branch point.

C. If there are two equally long continuous chains, select the one with the most branched.

D. If there is a branch equidistant from each end of the longest chain, begin numbering nearest to a third branch.

E. If there is no third brench, begin numbering nearest the substituent whose name has aliphabetic priority.

2.4 Alkyl and halogen substituents Alkyl substituents are named by changing the -ane ending of alkanes to -yl. Thus the two-carbon alkyl group is called the ethyl group, from ethane.

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Ethane ethyl Propane propyl isopropyl

Alkyl groups with up to four carbons are very common. The letter R is used as a general symbol for an alkyl group. Therefore, R-H represents alkanes. R-Cl stands for an alkyl chloride. Halogen substituents are named by changing the -ine ending of the elements to -o. F Fluoro- Cl Chloro- Br Bromo- I Iodo- 2.5 Use of the IUPAC rules Examples 2.7 Physical properties Alkanes are insoluble in water. That is because water molecules are polar, whereas alkanes are nopolar. (all C-C and C-H bonds are nearly purely covalent.) Alkanes have lower boiling points for a given molecular weight than most other organic compounds. The electrons in a nonpolar molecule can become unevenly distributed within the molecule, causing the molecule to have partially positive and partially negative end. The temporarily polarized molecules causes its neighbor molecules polarized as well. Such interaction are called Van der Waals attraction.

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The boiling points fo alkanes rise as the chain length increases and fall as the chains because brenched and more nearly spherical in shape.

Despite the same molecular weight, the rod-shaped pentane molecules have more surface area available for contact than the spherical 2,2-dimethylpropane. Therefore, van der Waals in the rod-shaped molecules is stronger than the spherical molecules. The boiling point of rod-shaped molecules is higher.

2.8 Conformation of alkanes. A simple molecule has an infinite number of shapes as a consequence of rotating one single bond. These arrangements are called conformations or conformers. Conformers are stereoisomers, isomers in which the atoms are connected in the same order but are arranged differently in space. Two possible conformers for ethane are staggered and eclipsed. Ethane as example:

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Projections Dash-wedge projection Sawhorse projection Newman projection

Conformers are just different forms of a single molecule that can be intervonverted by rotational motions about single bonds. 2.9 Cycloalkane nomenclature and conformation Cycloalkanes are saturated hydrocarbons.

cyclopropane cyclobutane cyclopetanecyclohexane

CH3

CH3

1,2-dimethylcyclopentane(not 1,5-di......)

CH3

CH2CH3

(1-ethyl-2-methylcyclopentane(not 2-ethyl-1-methyl....)

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The C-C-C bond angle of cyclopropane is only 60o, therefore it has a great ring strain. (Remember sp3-carbon is 109.5o)

Six-membered rings are so common in nature. It it has two common conformations, boat and chair conformation. (with molecular model)

In the chair conformatiom, the hydrogens in cyclohexane fall into two sets, called axial and equatorial. Three axial hydrogens lie above and three li below the average plane of the carbon atoms. The six equatorial hydrogens lie approximately in that plane.

Conformation of methylcyclohexane

Draw a chair conformation of -D-glucopyranose)

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2.10 Cis-Trans isomerization in cycloalkanes Stereoisomers deals with molecules that have the same order of attachment of atoms, but different arrangement of the atoms in space. Cis-trans isomers (sometimes called germetric isomers. Unlike conformers, stereoisomers are unique compounds. They are not interconverted by rotation around C-C bond.

2.11 Summary of isomerism

2.12 Reactions of alkanes 1) Oxidation and Combustion: alkanes as fuels CH4+2O2 CO2+ 2H2O + heat (212.8kcal/mol)

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2.13 The free-radical chain reaction of halogenations Halogenation of alkanes. Halogenation occurs via a free-radical chain of reactions. Initiation step

Propagation step

Termination steps