Chapter 15: Organic Compounds and the Atomic Properties of Carbon

The Special Nature of Carbon and Organic Molecular Characteristics

• Covalent Bonding of Carbon:

  • Carbon forms covalent bonds in all of its elemental forms and compounds.

  • Electron Configuration: The ground state electron configuration of Carbon (C) is $1s^2 2s^2 2p^2$. Because it is midway through the second period, the formation of carbon ions is energetically unfavorable; instead, it prefers to share electrons.

  • Electronegativity: Carbon has an electronegativity of $2.5$, which is situated midway between the values of most metals and nonmetals.

  • Catenation: This is the unique ability of carbon to bond to itself to form stable chains, rings, and branched compounds.

  • Atom Size and Bond Strength: The small size of the C atom allows it to form short, strong bonds. These short bonds facilitate the formation of $\pi$ bonds, which significantly increases the variety and complexity of possible carbon compounds.

• Comparison of Carbon and Silicon:

  • Atomic size increases as one moves down Group 14. Consequently, bonds between identical atoms become longer and weaker.

  • A $C-C$ bond is much stronger than a $Si-Si$ bond.

  • Bond Energy Comparison: In carbon, the energies of a $C-C$ bond, a $C-O$ bond, and a $C-Cl$ bond are very similar.

  • Carbon compounds can undergo diverse reactions while remaining stable, whereas Silicon (Si) compounds often cannot.

• Diversity and Reactivity of Organic Molecules:

  • Heteroatoms: Many organic compounds contain atoms other than C and H, such as Oxygen (O), Nitrogen (N), and Halogens.

  • Reaction Sites: Chemical reactions typically involve the interaction between an electron-rich area in one molecule and an electron-poor site in another.

  • Bond Reactivity: $C-C$ and $C-H$ bonds tend to be relatively unreactive. Conversely, bonds between Carbon and a heteroatom are usually polar, creating an imbalance in electron density that provides a site for chemical reactions.

  • Functional Groups: A functional group is a specific combination of bonded atoms that reacts in a characteristic manner regardless of the molecule in which it occurs.

Structure and Classes of Hydrocarbons

• Carbon Skeletons:

  • Each carbon atom can form a maximum of four bonds.

  • Bonding Permutations: This includes four single bonds, one double and two single bonds, or one triple and one single bond.

  • Rotation: Single ($\sigma$) bonds can rotate relatively freely, meaning several equivalent arrangements of the same skeleton exist. A branch pointing up is equivalent to one pointing down.

  • Restricted Rotation: Double bonds restrict rotation, leading to different spatial arrangements of groups.

  • Skeletal Types: Skeletons can be straight-chain, branched-chain, or cyclic (rings).

• The "H-atom Skin" Rules:

  • A C atom single-bonded to one other atom requires three H atoms.

  • A C atom single-bonded to two other atoms requires two H atoms.

  • A C atom single-bonded to three other atoms requires one H atom.

  • A C atom single-bonded to four other atoms requires zero H atoms.

  • A double-bonded C atom is treated as if it were bonded to two other atoms (it needs H atoms accordingly to reach four total bonds).

  • A triple-bonded C atom or a C atom with one double and one single bond is treated as if bonded to three atoms.

• Alkanes (Saturated Hydrocarbons):

  • Contain only single bonds and are considered "saturated" with hydrogen.

  • General Formula: $C_nH_{2n+2}$, where $n$ is a positive integer.

  • Homologous Series: A group of compounds where each member differs from the next by a $-CH_2-$ unit.

  • Hybridization: Each carbon in an alkane is $sp^3$ hybridized with bond angles of approximately $109.5^\circ$.

  • Physical Properties: Alkanes are nonpolar and exhibit only dispersion forces. These forces increase in strength as the molar mass increases, affecting boiling and melting points.

• IUPAC Naming Rules for Alkanes:

  • The name consists of a Prefix (positions/identity of branches) + Root (longest chain length) + Suffix (family type).

  • Numerical Roots:

    • 1: meth-

    • 2: eth-

    • 3: prop-

    • 4: but-

    • 5: pent-

    • 6: hex-

    • 7: hept-

    • 8: oct-

    • 9: non-

    • 10: dec-

  • Step-by-Step Naming:

    1. Find the longest continuous chain to determine the root.

    2. Add the suffix "-ane" for alkanes.

    3. Identify branches (alkyl groups). Change the root of the branch to end in "-yl" (e.g., methyl, ethyl).

    4. Number the main chain starting from the end closest to the first branch to give the lowest possible numbers.

    5. Alphabetize different branches. Use multipliers (di-, tri-, tetra-) if the same branch appears multiple times.

  • Cycloalkanes: For rings, precede the root with "cyclo-". The general formula is $C_nH_{2n}$.

Isomerism and Chirality

• Constitutional (Structural) Isomers:

  • Molecules with the same molecular formula but different arrangements of bonded atoms.

  • They have different physical and chemical properties. For example, butane ($n-butane$) boils at $-0.5^\circ \text{C}$, while 2-methylpropane ($isobutane$) boils at $-11.6^\circ \text{C}$.

• Stereoisomers:

  • Molecules with the same atom-to-atom connectivity but different orientations of groups in space.

• Optical Isomers (Enantiomers) and Chirality:

  • Chirality: A molecule that is asymmetric and cannot be superimposed on its mirror image is termed chiral.

  • Chiral Center: Typically, a carbon atom bonded to four different groups.

  • Optical Activity: Chiral compounds rotate the plane of polarized light.

    • Dextrorotatory: Rotates light clockwise.

    • Levorotatory: Rotates light counterclockwise.

  • Enzymes and Drugs: Biological systems provide chiral environments. Often, only one optical isomer of a drug fits into an enzyme's binding site, while its mirror image is inactive or harmful.

• Geometric (Cis-Trans) Isomers:

  • Occur in alkenes due to restricted rotation around the double bond.

  • Cis Isomer: Larger groups are on the same side of the double bond.

  • Trans Isomer: Larger groups are on opposite sides of the double bond.

  • These isomers have distinct physical properties (e.g., cis-2-butene density is $0.621 \text{ g/mL}$, while trans-2-butene is $0.604 \text{ g/mL}$).

Alkenes, Alkynes, and Aromatics

• Alkenes:

  • Contain at least one $C=C$ double bond and are unsaturated.

  • General Formula: $C_nH_{2n}$.

  • Bonding: Double-bonded carbons are $sp^2$ hybridized with trigonal planar geometry ($120^\circ$ angles).

  • Naming: Use suffix "-ene". Number the chain to give the double bond the lowest possible number.

• Alkynes:

  • Contain at least one $C \equiv C$ triple bond.

  • General Formula: $C_nH_{2n-2}$.

  • Bonding: Triple-bonded carbons are $sp$ hybridized with linear geometry ($180^\circ$ angles).

  • Naming: Use suffix "-yne".

• Aromatic Hydrocarbons:

  • Contain one or more rings with extensive delocalization of $\pi$ electrons.

  • Benzene ($C_6H_6$): Represented as a resonance hybrid of two structures with alternating single and double bonds.

  • Stability: Benzene is unusually stable due to electron delocalization. Despite having double-bond character, it prefers substitution reactions over addition reactions to maintain its aromatic system.

Analytical Techniques: NMR and MRI

• Nuclear Magnetic Resonance (NMR) Spectroscopy:

  • Utilizes the magnetic properties of atomic nuclei (often $^1H$).

  • In a magnetic field ($B_0$), nuclear spins align parallel or antiparallel to the field, creating an energy difference ($\Delta E$).

  • Absorption of radio-frequency radiation cause a "spin flip."

  • Spectrum Interpretation: Peaks indicate different environments for Hydrogen nuclei. For example, acetone ($CH_3COCH_3$) shows one peak for its six equivalent H nuclei, while dimethoxymethane shows two distinct peaks.

• Magnetic Resonance Imaging (MRI):

  • An application of NMR used in medicine to visualize soft tissues and detect abnormalities like tumors.

Types of Organic Reactions

• Addition Reactions:

  • An unsaturated reactant becomes a saturated product.

  • The $\pi$ bond of a double or triple bond breaks, leaving the $\sigma$ bond intact to form new single bonds.

  • Example: Ethene + $HCl \rightarrow$ Chloroethane.

  • Hydrogenation: Addition of $H_2$ to $C=C$ or $C \equiv C$ bonds.

• Elimination Reactions:

  • A saturated reactant becomes an unsaturated product (the reverse of addition).

  • C atoms are bonded to fewer atoms in the product.

  • Commonly involves removing H and a halogen ($HX$) or H and an $-OH$ group ($H_2O$).

• Substitution Reactions:

  • An atom or group replaces another atom or group on a carbon atom.

  • The number of atoms bonded to carbon remains the same.

  • Example: Ethanol metabolism or formation of banana oil.

• Redox Processes in Organic Chemistry:

  • Oxidation: A Carbon atom forms more bonds to O or fewer bonds to H.

  • Reduction: A Carbon atom forms fewer bonds to O or more bonds to H.

Survey of Key Functional Groups

• Alcohols ($R-OH$):

  • Suffix: "-ol".

  • Properties: High boiling points due to hydrogen bonding.

  • Reactions:

    1. Dehydration: Elimination of H and OH to form an alkene (requires acid catalyst).

    2. Oxidation: Elimination of two H atoms to form a carbonyl group ($C=O$).

• Haloalkanes ($R-X$, where X = halogen):

  • Prefix: halo- (e.g., chloro-, bromo-).

  • Reactions:

    1. Substitution with base ($OH^-$) to form alcohols.

    2. Elimination of $HX$ with strong base to form alkenes.

• Amines ($R-NH_2, R_2NH, R_3N$):

  • Suffix: "-amine".

  • Classification: Primary ($1^\text{o}$), Secondary ($2^\text{o}$), or Tertiary ($3^\text{o}$) based on the number of non-H groups attached to Nitrogen.

  • Properties: $1^\text{o}$ and $2^\text{o}$ amines can H-bond. Low molar mass amines are fishy-smelling and weakly basic.

• Aldehydes and Ketones (Carbonyl Group $C=O$):

  • Aldehydes ($R-CHO$): Suffix "-al"; always at the end of a chain.

  • Ketones ($R-CO-R'$): Suffix "-one"; carbonyl is within the chain.

  • Reactions:

    1. Reduction to alcohols.

    2. Addition of organometallic compounds (metal covalently bonded to C) to the electron-poor carbonyl carbon.

• Carboxylic Acids ($R-COOH$):

  • Suffix: "-oic acid".

  • Properties: Weak acids in water; react with strong bases to form salts.

• Esters ($R-COOR'$):

  • Suffix: "-oate".

  • Formed by reaction of an alcohol and a carboxylic acid (esterification).

  • Saponification: Base-promoted hydrolysis of esters, used to make soap from lipids.

• Amides ($R-CONH_2, R-CONHR, R-CONR_2$):

  • Suffix: "-amide".

  • Contains a Carbonyl group bonded to a Nitrogen.

  • Peptide bonds in proteins are amide bonds.

Synthetic Macromolecules (Polymers)

• Addition Polymers (Chain-Growth):

  • Monomers (usually alkenes) add to each other until a long chain forms.

  • Free-Radical Polymerization: Involves an initiator that creates a species with an unpaired electron.

  • Examples: Polyethylene (bags), Polypropylene (carpeting), PVC (plumbing), Polystyrene (insulation), Teflon (non-stick pans).

• Condensation Polymers (Step-Growth):

  • Monomers link via a dehydration-condensation reaction, losing a small molecule like $H_2O$.

  • Monomers must be bifunctional.

  • Nylon-66: Formed by reacting a diacid with a diamine to create a polyamide.

Biological Macromolecules

• Sugars and Polysaccharides:

  • Monosaccharides: Simple sugars like glucose (polyhydroxy aldehydes or ketones).

  • Disaccharides: Two monosaccharides linked by condensation.

  • Polysaccharides: Long chains like cellulose (structure), starch (plant energy), and glycogen (animal energy).

• Amino Acids and Proteins:

  • Amino Acids: Contain an amine group, a carboxyl group, and a variable R group.

  • Peptide Bond: Amide linkage formed between amino acids.

  • Protein Structure Hierarchy:

    1. Primary ($1^\text{o}$): Linear sequence of amino acids.

    2. Secondary ($2^\text{o}$): Local folding ($\alpha$-helix or $\beta$-pleated sheet).

    3. Tertiary ($3^\text{o}$): Overall 3D shape of a single polypeptide.

    4. Quaternary ($4^\text{o}$): Aggregation of multiple polypeptide subunits.

• Nucleotides and Nucleic Acids:

  • Monomer: Mononucleotide (Sugar + Nitrogenous Base + Phosphate group).

  • RNA vs. DNA: RNA contains ribose; DNA contains deoxyribose.

  • Nitrogenous Bases: Pyrimidines (C, T, U) and Purines (A, G).

  • Structure: DNA exists as a double helix held together by base pairing (A with T, G with C).

• Genetic Processes:

  • Transcription: DNA is used as a template to make mRNA.

  • Translation: mRNA sequence is decoded at the ribosome by tRNA to synthesize proteins.

  • Replication: DNA polymerase unzips the double helix and synthesizes new strands from mononucleoside triphosphates.

• Biotechnology Applications:

  • Sanger Method: DNA sequencing using dideoxyribonucleoside triphosphates (ddNTPs) to terminate chain growth.

  • STR Analysis: Short Tandem Repeat analysis used in forensic DNA fingerprinting.