Organic chemistry and instrumental analysis

Verification of structure

Experimental techniques in organic chemistry verify the chemical structure of a substance

Elemental microanalysis

Determines the masses of C, H, O, S, and N to find the empirical formula of an organic compound

Empirical formula

Shows the simplest ratio of elements in a molecule

Elemental microanalysis data

Can be determined from combustion product masses or percentage product by mass

Mass spectrometry

Determines accurate gram formula mass (GFM) and structural features of an organic compound

Mass spectrometry process

A sample is bombarded by high-energy electrons to form positively charged parent ions and fragments

Mass spectrum

A plot of relative abundance of ions vs. mass-to-charge (m/z) ratio

Parent ion m/z value

Used to determine the GFM and molecular formula from the empirical formula

Fragmentation data

Can be interpreted to gain structural information

Infrared (IR) spectroscopy

Identifies functional groups in organic compounds

IR absorption

Causes bonds in molecules to vibrate (stretch and bend)

IR absorption wavelength

Depends on type and strength of bond

IR spectroscopy process

Infrared radiation passes through the sample into a detector to measure absorbance

IR absorbance unit

Measured in wavenumbers (cm⁻¹)

IR characteristic absorptions

Given in the data booklet for identifying functional groups

¹H NMR spectroscopy

Gives information on the chemical environments of hydrogen atoms (¹H) and their quantities

¹H nuclei behaviour

Act as tiny magnets aligning with or against a magnetic field

¹H NMR radiation absorption

Radio frequency radiation flips ¹H nuclei to higher energy states

¹H NMR emission

Emitted radiation is detected as nuclei return to lower energy state

Chemical shift (δ)

Peak position in ¹H NMR related to hydrogen environment

¹H chemical shift values

Given in the data booklet

Peak area in ¹H NMR

Related to the number of hydrogen atoms in that environment

Integration curve

Represents relative number of ¹H atoms in each environment

Standard in ¹H NMR

Tetramethylsilane (TMS) assigned δ = 0 ppm

Low- and high-resolution ¹H NMR

Spectra can be obtained in either mode

High-resolution ¹H NMR

Uses higher frequencies and gives more detailed spectra

Multiplet splitting in ¹H NMR

Caused by interactions with ¹H on neighbouring carbon atoms

n+1 rule

Number of peaks in a multiplet = number of neighbouring ¹H atoms (n) + 1

Analysis of ¹H NMR spectra

Both low- and high-resolution spectra can be analysed

Sketching ¹H NMR

Low-resolution spectra can be drawn for given compounds

VSEPR limitation

VSEPR cannot explain bonding in all compounds, molecular orbital theory can explain more complex molecules

Molecular orbitals formation

Form when atomic orbitals combine

Number of molecular orbitals

Equals the number of atomic orbitals that combine

Bonding and antibonding orbitals

Form from the combination of two atomic orbitals

Bonding molecular orbital

Encompasses both nuclei and holds up to two electrons

Basis of bonding between atoms

Attraction between positively charged nuclei and negatively charged electrons in the bonding molecular orbital

Non-polar covalent bond

Bonding molecular orbital is symmetrical about the midpoint between two atoms

Polar covalent bond

Bonding molecular orbital is asymmetric with electrons shared unequally

Electronegativity effect

The atom with higher electronegativity has a greater share of bonding electrons

Ionic bonding and molecular orbitals

Bonding molecular orbital is almost entirely around one atom

Sigma (σ) molecular orbitals

Form by end-on overlap of atomic orbitals along the axis of the covalent bond

Pi (π) molecular orbitals

Form by side-on overlap of parallel atomic orbitals perpendicular to the axis of the covalent bond

Carbon bonding explanation

Requires hybridisation since isolated carbon atom configuration cannot explain bonding

Hybridisation

Mixing of atomic orbitals within an atom to form degenerate hybrid orbitals

Alkane hybridisation

Carbon’s 2s and three 2p orbitals form four degenerate sp³ hybrid orbitals in a tetrahedral arrangement

Alkane bonding

sp³ orbitals overlap end-on to form σ bonds

Alkene hybridisation

Carbon’s 2s and two 2p orbitals form three degenerate sp² hybrid orbitals in a trigonal planar arrangement

Alkene bonding

sp² orbitals form σ bonds and remaining unhybridised 2p orbitals overlap side-on to form π bonds

Benzene bonding

Six carbon atoms form σ bonds with sp² hybrid orbitals and π system formed from overlapping unhybridised p orbitals

Benzene π system

Extends across all six carbon atoms and electrons are delocalised

Alkyne hybridisation

Carbon’s 2s and one 2p orbital form two degenerate sp hybrid orbitals in a linear arrangement

Alkyne bonding

sp orbitals form σ bonds

two remaining unhybridised 2p orbitals form two π bonds via side-on overlap

Molecular orbital theory and colour

Explains colourlessness or colour of organic molecules by electron transitions between orbitals

HOMO

Highest Occupied Molecular Orbital containing electrons

LUMO

Lowest Unoccupied Molecular Orbital

Electron promotion

Absorption of electromagnetic energy promotes electrons from HOMO to LUMO

Colourless organic molecules

Have large energy gap between HOMO and LUMO

Chromophores

Groups of atoms responsible for absorption of visible light by promoting electrons from HOMO to LUMO

Conjugated system

System of adjacent unhybridised p orbitals overlapping side-on to form delocalised molecular orbitals

Examples of conjugated systems

Molecules with alternating single and double bonds

Conjugation and energy gap

More atoms in conjugated system = smaller HOMO–LUMO gap

Light absorbed in conjugated systems

Lower frequency (longer wavelength

Visible absorption and colour

If visible light is absorbed

Drugs

Substances that alter biochemical processes in the body

Medicines

Contain a drug and other ingredients such as fillers or sweeteners

Drug mechanism

Drugs generally work by binding to specific protein molecules

Drug target locations

Protein molecules may be receptors on cell surfaces or enzyme molecules within cells

Agonists

Drugs that mimic the natural compound and bind to receptors to produce a similar response

Antagonists

Drugs that prevent the natural compound from binding to the receptor and block the natural response

Enzyme inhibitors

Drugs that bind to the active site of an enzyme and block the normal catalysed reaction

Drug interaction design

A drug’s shape and size allow interaction with receptor binding sites or enzyme active sites

Drug interaction types

Interactions include van der Waals forces and/or ionic bonds

Structural fragment of a drug

Contains different functional groups correctly oriented to allow interaction with receptors or enzymes

Structure-activity comparison

Comparing structures of drugs with similar effects helps identify the active structural fragment

Isomers

Molecules that have the same molecular formula but different structural formulae

Structural isomers

Isomers where the atoms are bonded together in a different order in each isomer

Stereoisomers

Isomers where the order of bonding is the same but the spatial arrangement of atoms is different

Types of stereoisomers

Geometric and optical

Geometric isomers condition 1

Can occur when there is restricted rotation around a carbon-carbon double bond or a carbon-carbon single bond in a cyclic compound

Geometric isomers condition 2

Must have two different groups attached to each of the carbon atoms that make up the bond with restricted rotation

Geometric isomers labels

Can be labelled cis (same side) or trans (different sides) of the bond with restricted rotation

Geometric isomers physical properties

Can have differences in melting point and boiling point

Geometric isomers chemical properties

Can have differences in chemical properties

Optical isomers condition

Occur in compounds in which four different groups are arranged tetrahedrally around a central carbon atom (chiral centre)

Optical isomers symmetry

Are asymmetric

Optical isomers structure

Are non-superimposable mirror images of each other

Optical isomers name

Can be described as enantiomers

Optical isomers physical properties

Have identical physical properties except for their effect on plane-polarised light

Optical isomers chemical properties

Have identical chemical properties except in chiral environments (e.g. biological systems)

Optical activity of enantiomers

Rotate plane-polarised light by the same amount in opposite directions

Racemic mixture

A 1:1 mixture of enantiomers that is optically inactive because the rotational effects cancel out

Organic reaction

Bonds in reactants are broken and bonds in products are made.

Bond fission

The process of bond breaking in organic reactions.

Types of bond fission

Homolytic and heterolytic.

Homolytic fission

Results in two neutral radicals.

Homolytic fission mechanism

Each atom retains one electron from the σ bond. The bond breaks evenly.

When homolytic fission occurs

When non-polar covalent bonds are broken.

Homolytic fission in synthesis

Produces complex mixtures. Unsuitable for organic synthesis.

Heterolytic fission

Results in two oppositely charged ions.