Organic Chemistry: Hydrocarbons and Nomenclature

• These notes cover organic chemistry topics, including definitions, nomenclature, hydrocarbons, isomers, stereochemistry, chirality, structural effects, and related concepts
• The study notes are prepared by Hajime Q. Nakaegawa, BS Biochemistry 2018, during the AY 2016-2017 under the Scholia Tutorial Club

Introduction to Organic Chemistry

• Organic chemistry centers on the study of carbon and its compounds
• Organic chemistry encompasses organic compounds, and hydrocarbon compounds with their derivatives
• An important building block in structural organic chemistry is the tetravalent carbon atom
• With limited exceptions, carbon compounds form four covalent bonds, irrespective of combination

Hydrocarbons

• Hydrocarbons consist solely of hydrogen and carbon
• Hydrocarbons are divided into aliphatic and aromatic compounds

Aliphatic Hydrocarbons

• Aliphatic hydrocarbons have an uncyclic or open structure
• Saturated aliphatic hydrocarbons contain single bonds and no pi bonds, like alkanes
• Unsaturated aliphatic hydrocarbons contain pi bonds, such as double or triple bonds, like alkenes and alkynes

Aromatic Hydrocarbons

• Aromatic hydrocarbons need to be cyclic by having a closed structure and lacking a terminal point
• They must be planar (2D)
• Must possess conjugated double bonds that alternate
• Must follow Huckel's Rule #pi e- = 4n + 2

Hydrocarbon Derivatives

• Hydrocarbon derivatives are formed through the substitution of a functional group at one or more positions
• IUPAC priority rules dictates the priority of functional groups

Nomenclature and IUPAC Naming

• Nomenclature focuses on naming organic compounds
• The International Union of Pure and Applied Chemistry (IUPAC) naming system aims to establish a clear, one-to-one relationship between a compound's name and its structure
• Distinct compounds should not share the same IUPAC name

Steps in IUPAC Naming

• Identify the longest continuous carbon chain that contains the highest-order functional group; this forms the parent chain
• Double or triple bonds between carbons must be part of the parent chain
• If a functional group provides a suffix, parent chain needs to contain and include the group within it
• The highest-priority functional group determines the suffix
• Number the carbon chain so that carbon 1 is closest to the highest-priority functional group
• If multiple functional groups have equal priority, number the chain to give the lowest possible numbers to substituted carbons
• Substituents are functional groups not part of the parent chain and named as prefixes
• Assign a number to each substituent to indicate its position on the parent chain
• Use di-, tri-, and tetra- prefixes for multiple identical substituents, along with carbon number designations
• Begin the name with substituents listed alphabetically, each with its number
• Ignore prefixes like di-, tri-, tetra-, n-, and tert- when alphabetizing, but include non-hyphenated roots
• Separate numbers with commas and numbers from words with hyphens
• Complete the name with the backbone chain's name, including the suffix for the highest priority functional group

Structural Formulas

• Kekule Formulas are Lewis structures showing covalent bonds as lines
• Kekule suggested a hexagonal structure with alternating single and double bonds arrangement for benzene
• Condensed formulas save space by not explicitly showing bonds but adhering to normal atomic valences
• 3D Structural Formulas show the three-dimensional arrangement of atoms
• Skeletal Formulas, or Line-Angle Formulas, represent structures in two dimensions, using lines to represent bonds and vertices for carbon atoms

Importance of Carbon

• Molecules containing carbon are classified as organic
• Molecules lacking carbon, such as carbon dioxide, are classified as inorganic

Key factors of Carbon

• Carbon is versatile and capable of forming up to four bonds in chains or rings
• Carbon bonds are high in energy
• Functional groups in organic molecules are less stable than carbon backbones, making them more likely to participate in chemical reactions
• Functional groups define characteristics and reactivity

Principles Affecting Electron Behavior

• Aufbau Principle: electrons occupy available orbitals in increasing energy levels; lowest energy fills first
• Hund's Rule of Multiplicity: Single electrons occupy degenerate orbitals before pairing occurs
• Pauli's Exclusion Principle: No two electrons in an atom can have identical quantum numbers; orbitals hold two electrons with opposite spins

Hybridization

• Hybridization is where atoms undergo to form equivalent orbitals
• The purpose is to form the equivalent orbitals (orbitals with the same shape)

Isomers and Stereochemistry

• Isomers are compounds sharing the same molecular formula but differing in atom arrangement and properties
• Isomers can differ in their arrangement of bonds as isomers with different connectivity of their atoms
• Configuration refers to permanent spatial positions, means configurational isomers can never be identical
• Conformation refers to temporary spatial positions, meaning two conformational isomers can be identical at one point

Types of Isomers

• Structural or Constitutional Isomers vary in their arrangement, including skeletal, positional, and functional isomers
• Stereoisomers vary in spatial position, including configurational and conformational isomers
• Configurational isomers can be optical (tetrahedral) like enantiomers and diastereomers or geometric (unsaturated/cyclic)
• Optical isomers: Enantiomers are mirror images, while diastereomers are not

Conformational Isomers

• Conformational isomers are the same molecule at different rotation points around single (σ) bonds
• Differ from configurational isomers, which interconvert only by breaking bonds
• Varying degrees of rotation around single bonds create different strain levels
• Newman projections visualize molecules along a carbon-carbon bond axis

Straight-Chain Conformations

• The ideal conformation for butane occurs when methyl groups are oriented away from each other
• Gauche conformations are where the groups are 60° apart
• Totally eclipsed conformations are the least favorable, with methyl groups directly overlapping

Cyclic Conformations

• Cycloalkanes can be fairly stable and fairly unstable, that depends on ring strain
• Ring strain arises from angle strain, torsional strain, and nonbonded steric strain
• Angle strain occurs when bond angles deviate from ideal values
• Torsional strain arises when cyclic molecules assume eclipsed or gauche conformations
• Nonbonded strain is when nonadjacent atoms compete for space; dominant in cyclohexane boat conformation

Cycloalkane Conformations

• Cycloalkanes alleviate strain by adopting nonplanar conformations
• Cyclobutane puckers into a "V" shape, while cyclopentane adopts an envelope conformation
• Cyclohexane exists mainly as chair, boat, and twist-boat forms
• The most stable conformation is the chair form

Axial-Equatorial Orientation

• Hydrogen atoms perpendicular to the ring plane are axial
• Hydrogen atoms parallel to the ring plane are equatorial
• Axial-equatorial orientations alternate around the ring such that the wedged bond on C-1 is axial, the dashed bond on C-2 will also be axial and the wedged bond on C-3 will also be axial
• Cyclohexane chair conformations undergo chair flips, interchanging axial and equatorial positions
• Bulky groups favor equatorial positions in substituted rings to minimize nonbonded steric strain

Cis/Trans Isomers

• In rings, cis means the listed groups are located on the same side and trans means the listed groups are located on opposite sides
• For simple compounds with one substituent on each side of an immovable bond, use cis/trans terms
• But for polysubstituted double bonds, (E)/(Z) nomenclature is used

Configurational Isomers

• Differ from conformational isomers through bond rotation
• Configurational isomers convert by breaking/reforming covalent bonds
• Enantiomers and diastereomers are in the two major types of configurational isomers
• Both enantiomers and diastereomers are optical isomers
• Optical isomers depends on the effects of the different spatial arrangement of the groups in the molecules and how it affects the rotation of plane-polarized light

Chirality

• An object is considered chiral if its mirror image cannot be superimposed on the original
• There is no internal symmetry with chirality

Enantiomers

• These are non-superimposable mirror images of each other

Diastereomers

• Non-mirror image configurational isomers
• Occur in molecules with two or more stereogenic centers but differ at not all of these centers
• This means that diastereomers need to have multiple chiral centers
• In any molecule with n chiral centers, there are 2^n possible steroisomers

Meso Compounds

• Molecules with optical activity must have no chiral centers and must lack a plane of symmetry
• If there is symmetry, the molecule is not optically active
• Plane of symmetry occurs at chiral or between chiral centers
• A molecule that has chiral centers with a plane of symmetry is a "meso compound" as it essentially is the molecular equivalent of a racemic mixture

Relative and Absolute Configuration

• Configuration is spatial arrangement of atoms or groups in a stereoisomer molecule
• Relative configuration relates configuration of a chiral molecule to another via interconversion
• Relative configuration is also determining if molecules are enantiomers, diastereomers, or identical
• Absolute configuration is the exact spatial arrangement of atoms, independent and not concerning any other molecules

(E) and (Z) Nomenclature

• Naming with (E) and (Z) is reserved for when classifying compounds with polysubstituted double bonds
• Priority based on the Cahn-Ingold-Prelog priority rules
• To name a compound, if the top two priorities are on the same side of the double bond, the compound is named "(Z)", meaning "together"
• If the top two priorities are on opposite sides, the compound is named "(E)", meaning "opposite"

The simple priority rules

• The higher number of atoms, the higher priority.
• If the number of atoms are equal, priority is determined by the next atoms outward with the higher number of atoms will lead in higher priority.
• If there is still a tie, the atoms in ths group are compared one by one in a declining number of atoms until the tie is broken
• for the sake of memorization Z = "z"ame side and E = "e"pposite side

Structural Effects

• Structural features influencing organic compound stability and reactivity

Types of Structural Effects

• Electron delocalization
• Inductive effect
• Steric effect
• Angle strain

Electron Delocalization

• Electrons in some molecules are not confined to specific bonds and atoms
• Delocalized electrons have no specific location, existing in molecular orbitals encompassing multiple atoms
• Delocalization enhances stability via resonance, impacting acidity and UV/visible light absorption
• Actual delocalized structure is a "resonance hybrid."

Molecular Orbital (MO) Theory

• Delocalization is explained by MO theory
• MO theory covers each atom's' structure
• It theorizes that electrons are in orbitals and spread throughout the molecule's entirety, rather that having lone pairs of electron in specific bonds
• Explains benzene and ozone with one Lewis and described as resonance hybrids because of delocalized electrons

Types of Electron Delocalization

• Pi electron delocalization is where delocalized electrons originate from a pi bond in a conjugated diene
• Sigma pi delocalization is where delocalized electrons derive from a sp3 hybridized carbon
• Lone pair delocalization is where delocalized electrons are from a lone pair, from nitrogen or oxygen atoms

Inductive Effect

• Inductive effect is the electronic effect that results from the polarization of sigma bonds within a particular molecule or ion
• Electronegativity differences between atoms at either ends of the bond cause the molecules to pull more of it's electrons within the bond towards itself, it creates a much higher bond polarity.
• The basis is polarity
• Electronegativity is what pulls
• Three considerations:
• Electronegativity
• Bonding order and charge
• Position within a structure

Inductive effects are determined by two factors

• Electron-attracting inductive effect happens when electrons are drawn towards atoms with excess positive charges, electronegative atoms, and an increased electronegativity due to more electrons because it shows a "negative inductive effect (-I)" example atoms with excess excess positive charge are more negative
• Electron-donating inductive effect happens when electrons are repelled and show a "positive inductive effect (+I)" example atoms with a less electronegative charge

Steric Effect

• Steric effect is electron instability due to closing in of electron dense atoms (because of repulsion between same types of charge)
• Atoms in molecules occupy space; close proximity causes electron cloud repulsion, creating steric strain that may affect the reactivity of the molecule

Angle Strain

Electric instability resulted because there are atoms closing in with small angles in cyclic compounds

• Atoms in cyclic molecules share a certain angle with each other, where the ideal is 109.5 degrees.
• When angle measurement are far or below, the effect of electrons on each other are all increased