Advanced Chemistry/ IB Chemistry II- Alkanes and Cycloalkanes

IB Curriculum: Topics 10.1, 20.1, & 20.6

I.  Defining Organic Molecules.

   Organic Chemistry-  The study of carbon-containing molecules.  Although CO₂ contains carbon, it isn't considered organic but 

    is assimilated into the millions of naturally occurring organic compounds via the carbon cycle.

    Stanley Miller and Harold Urey demonstrated that the simplest reduced form of carbon (methane: CH₄) can also be assimilated into  

   simple organic compounds needed to sustain life. See Miller-Urey Experiment.

        EXOBIOLOGY: An Interview with Stanley L. Miller

    A. Organic molecules are characterized by:

1.      Containing tetravalent carbon atoms: always forming 4 bonds. Due to sp³ hybridization. This was proposed by Friedrich Kekule

          - single covalent bonds possess rotational characteristics

          - in organic molecules, elements possess a well-defined valency (number of covalent bonds)

            > carbon is tetravalent, oxygen is divalent, hydrogen, fluorine and chlorine are commonly monovalent.

2.      All bonds between atoms are covalent bonds

-some intermolecular attractions occur but are less common due to nonpolar bonding between C-H

           Read about the Chemistry of Carbon Bonds.  Carbon has the ability to form long chains of carbon atoms through a process 

3.      Polar bonds occur when carbon is bonded to (N, O, F, & Cl)- due to the high differences in electronegativities

-other polar bonds are found with (H-O & H-N)

4.      Carbon can form multiple bonds by sharing more than 1 pair of electrons with other atoms

-based on the hybridization of carbon: double bond = sp²  and  triple bond  = sp

          -due to pi bonding, sp² and sp bonded carbons are NOT free to rotate.

5.      Organic molecules have specific three dimensional shapes

-due to # of electron dense regions- (bonded & lone pairs of electrons about central carbons)

-VSEPR- valence shell electron pair repulsion theory.

6.      Organic molecules commonly contain H, N, & O (also Cl, P, & S)

          Organic chemist's periodic table

II. Structures of Organic Molecules

Organic molecules are hydrocarbons that function as the skeletal framework of the molecule

    -hydrocarbon- compound containing carbon & hydrogen

Molecules differ by:

a.       structure of the parental hydrocarbon chain (skeletal framework)

b.      addition of functional groups: R represents any alkyl group (alkane group attached to another)

c.   geometric orientation of covalently bonded atoms

        >> Fischer projection models- a 2-D visual representation of a 3-D geometric structure. They are commonly used in biochemistry to view monosaccharides.

A. Isomerization

    Isomers- Compounds with the same molecular formula but having different structural formulas (molecular structures)

    - Homologous series- a group of organic compounds that possess the same general formula and functionality. Differences in properties are due to increases in mass

       due to the additional of a constant unit (e.g. -CH₂-)

    1. structural (constitutional) isomers- isomers that differ by the order of attachment of their atoms (connectivity) --

        -a large variance in chemical and physical properties occur within the homologous series (a group of isomers with common formulae)  

        a. skeletal (chain) isomers- molecules that differ by the composition of the hydrocarbon skeleton (chain of carbons)

            i. straight-chained- hydrocarbons where each carbon is bonded to a maximum of 2 other carbons. This produces primary and secondary carbons.

            ii. branched-chained- hydrocarbons where a carbon atom is bonded to 3 other carbons, producing tertiary and/or quaternary carbons.

                -parent chain- the longest continual chain of carbon atoms in the molecule

        b. positional isomers- molecules that differ by the position of substituents on the parent chain

            -substituent- a specific atom (or group of atoms) that is/are bonded to the parent chain

Isomers of C₁ to C₆ Alkanes -

        c. functional isomers- molecules that differ in the composition of specific substituents.

           -functional group- a substituent that consists of a specific set of elements, giving rise to differences in chemical and physical properties of the molecule

      -moiety- another term used to identify a functional group. Multiple moieties can be exist together to create a different functional group

        i. carbon numbering- the functional group is attached to the alpha (a) carbon in the chain.

            -The next carbon in the skeleton is the beta (b), followed by gamma (g), delta (d), etc.

        ii. functional groups by family

    2. Stereoisomers- molecules with the same molecular formula, same order of attachment (connectivity) but different geometric structures.

        a. enantiomers- molecules that are non-superposable mirror images

            -superposable- objects that are able to able to coincide in space with respect to composition and orientation

            -chirality- a characteristic of an object where the mirror-image creates a non-superposable structure

                >sp³-hybridized carbons with four different substituents (within the skeleton or not) are chiral carbons (stereocenter)

                > achiral is the lack of chirality. sp³-carbons with without 4 different substituents or sp² & sp hybridized carbons produce achiral molecules

                    -structure (a) possesses a plane of symmetry where structure (b) has no plane of symmetry

                > a stereocenter carbon (stereogenic) possesses 4 different substituents and by switching 2 substituents creates an enantiomeric pair

                > a racemic mixtures exists when two enantiomeric pairs exist at the same concentration.

            - Polarimeters are instruments used to identify the optical activity of substance by measuring the angle of rotation of the polarized light. 20.6.6

Resources: Polarimeters -- Polarization of light

        b. diastereomers- molecules that are non-superposable non-mirror images, common in alkenes, alkynes & cyclic structures.

            -These are commonly known as geometrical or "non-optical" isomers.

            i. cis/trans isomers- stereoisomers that differ by the position of substituents due to rotational restrictions

                cis- Latin for "on this side"

                trans- Latin for "across"

            ii. multiple stereocenters- molecules that possess two or more chiral carbons are diastereomers.

                mesomers (meso compounds)- molecules that have two (or more) chiral centers that are superposable

                - A plane of symmetry occurs within each molecule, thus making it achiral

            iii. conformations- 3-dimensional arrangement of atoms that result from free rotation about a single bond (sigma bond)

               -these are not really isomers because they have the same order of attachment and geometric structure.

        1.Staggered conformation- rotation occurs between 2 carbon atoms until atoms on adjacent carbons maximize their distances

        Newman projection- a molecular perspective that looks down the axis of a C -- C bond. The second carbon is