Chemistry (9620) | Organic analysis

🔍 Organic Analysis: Being the Molecular Detective

Hello future Chemists! This chapter is all about becoming a molecular detective. When a chemist makes a new compound or tries to identify an unknown substance, they don't just guess; they use powerful analytical tools.

In "Organic Analysis," we bring together simple, classic test-tube reactions (AS level) with high-tech spectroscopic methods (AS/A2 level) to figure out exactly what an unknown organic molecule looks like. Mastering these techniques is crucial for structure determination in advanced chemistry!

1. Identifying Functional Groups using Test-Tube Reactions (AS)

These are the simplest, quickest tests. You mix a sample with a reagent and look for a visible change—like a colour change, a precipitate, or the formation of gas.

1.1 Test for Unsaturation (Alkenes)

The double bond in an alkene is a center of high electron density, making it very reactive.

Test: Add Bromine water (usually orange/brown) to the sample.
Result: If an alkene (or any unsaturated compound) is present, the orange/brown colour instantly disappears (decolorised). This is an addition reaction where bromine adds across the double bond.

1.2 Test for Carboxylic Acids

Carboxylic acids are weak acids, but they are strong enough to react with carbonates, producing carbon dioxide gas.

Test: Add aqueous sodium carbonate ($\text{Na}_2\text{CO}_3$) or sodium hydrogencarbonate ($\text{NaHCO}_3$) to the sample.
Result: Vigorous effervescence (fizzing) as $\text{CO}_2$ gas is produced.

1.3 Tests to Distinguish Aldehydes and Ketones

Aldehydes are easily oxidised to carboxylic acids, while ketones are resistant to mild oxidising agents. This difference allows us to use two key tests:

(a) Tollens’ Reagent (Silver Mirror Test)

Reagent: Ammoniacal silver nitrate solution.
Test: Heat the sample gently with Tollens’ reagent.
Result for Aldehyde: The $\text{Ag}^+$ ions are reduced to metallic silver, forming a distinctive silver mirror on the inside of the test tube.
Result for Ketone: No reaction, solution remains clear.

(b) Fehling’s Solution (or Benedict’s Solution)

Reagent: Alkaline solution containing copper(II) ions ($\text{Cu}^{2+}$), which are blue.
Test: Heat the sample gently with Fehling’s solution.
Result for Aldehyde: The $\text{Cu}^{2+}$ ions (blue) are reduced to copper(I) oxide ($\text{Cu}_2\text{O}$), which precipitates as a brick-red solid.
Result for Ketone: No reaction, solution remains blue.

2. Mass Spectrometry (MS) – Finding the Molecular Weight (AS/A2)

Mass spectrometry is used to determine the mass-to-charge ratio ($m/z$) of ions, giving us crucial information about the mass and identity of a molecule.

2.1 Determining Molecular Formula

The furthest peak to the right on a mass spectrum (the heaviest significant peak) corresponds to the Molecular Ion Peak, labeled $M^+$. This peak gives the relative molecular mass ($\text{M}_r$) of the compound.

To determine the *precise* molecular formula, we use precise atomic masses (e.g., C = 12.0000, O = 15.9949).

• If two compounds have the same nominal molecular mass (e.g., $\text{C}_2\text{H}_4\text{O}$ and $\text{N}_2$), they will have different precise molecular masses, allowing the mass spectrometer to tell them apart.

Did you know? This ability to distinguish compounds with the same nominal mass (like $\text{C}_2\text{H}_4\text{O}$ and $\text{N}_2$) is why high-resolution mass spec is so powerful. It confirms the exact combination of atoms present.

Key Takeaway: The $\text{M}^+$ peak gives the molecular mass. Use precise masses to figure out the exact elemental composition.

3. Infrared (IR) Spectroscopy – The Vibration Detective (AS)

IR spectroscopy works because chemical bonds vibrate (stretch and bend) at specific frequencies. If a bond absorbs infrared radiation that matches its natural vibrational frequency, it causes a dip (a peak) in the spectrum.

3.1 Principle of IR Absorption

Bonds in a molecule absorb infrared radiation at characteristic wavenumbers (measured in $\text{cm}^{-1}$). Wavenumber is proportional to energy.

• Every bond ($\text{C-H}$, $\text{C=O}$, $\text{O-H}$) has a specific region where it absorbs IR radiation.
• You must use the Chemistry data booklet to match the absorption peaks to known functional groups.

3.2 The Regions of the Spectrum

We divide the IR spectrum into two main areas:

1. Functional Group Region (4000 to $1500\,\text{cm}^{-1}$): This area contains absorptions corresponding to specific functional groups (like the sharp dip for $\text{C=O}$ or the broad trough for $\text{O-H}$). This is where you identify your main functional groups.
2. Fingerprint Region (Below $1500\,\text{cm}^{-1}$): This region is complex and unique to every single molecule (like a human fingerprint). It is used for identifying unknown compounds by comparing the spectrum to known samples.

Common IR Absorptions to Know:

• $\text{O-H}$ (Alcohol): Broad peak around $3200-3600\,\text{cm}^{-1}$.
• $\text{O-H}$ (Carboxylic Acid): Very broad peak around $2500-3300\,\text{cm}^{-1}$.
• $\text{C=O}$ (Carbonyl, Aldehydes/Ketones/Carboxylic acids/Esters): Strong, sharp peak around $1680-1750\,\text{cm}^{-1}$.
• $\text{C-H}$ (General Alkane): Strong peaks just below $3000\,\text{cm}^{-1}$.

3.3 IR and Global Warming

Absorption of IR radiation by bonds in certain atmospheric gases is linked to the greenhouse effect:

• Molecules like $\text{CO}_2$, methane ($\text{CH}_4$), and water vapour ($\text{H}_2\text{O}$) absorb IR radiation emitted by the Earth's surface.
• This absorbed energy is then re-radiated in all directions, warming the lower atmosphere.
• The specific vibrational frequencies of the bonds in these molecules mean they efficiently trap heat.

Key Takeaway: IR tells us which functional groups are present based on characteristic bond vibrations (wavenumbers). The fingerprint region confirms the exact identity.

4. Nuclear Magnetic Resonance (NMR) Spectroscopy (A2)

NMR is the most powerful technique for working out the *skeletal structure* of an organic molecule. It tells us about the environment of specific atoms, usually hydrogen ($^1\text{H}$) or carbon ($^{13}\text{C}$).

Don't worry if this seems tricky at first. It’s like learning a new language where peaks are letters, and patterns are words!

4.1 The Standard and Chemical Shift ($\delta$)

All NMR spectra are measured relative to a standard compound: Tetramethylsilane (TMS).

• TMS produces a single, sharp peak which is arbitrarily assigned a chemical shift ($\delta$) of $\mathbf{0\,ppm}$.
• Why use TMS? It is inert, non-toxic, has a low boiling point (easy to remove), and all 12 of its hydrogen atoms are in exactly the same environment, producing one strong reference peak.

The chemical shift ($\delta$) of a peak measures how much the environment of a nucleus differs from TMS.

• The more deshielded a proton or carbon atom is (i.e., closer to an electronegative atom like O or Cl), the higher its chemical shift ($\delta$).

4.2 Carbon-13 NMR ($^{13}\text{C}$ NMR)

$^{13}\text{C}$ NMR is simpler than $^1\text{H}$ NMR because the peaks are usually not split.

Key Information Provided:

• The number of peaks tells you the number of different carbon environments in the molecule.
• The chemical shift ($\delta$) tells you the type of carbon environment (e.g., whether it is an alkane C, a $\text{C=C}$ carbon, or a $\text{C=O}$ carbon). (Always refer to your data booklet for values).

4.3 Proton NMR ($^1\text{H}$ NMR)

$^1\text{H}$ NMR provides three main pieces of information:

(a) Number of Peaks (Chemical Shift $\delta$)

The number of peaks shows the number of different proton environments (sets of equivalent hydrogen atoms).

(b) Integration (Relative Number of Protons)

The area under each peak (the integration trace) is proportional to the number of protons in that specific environment.

Example: If peak A has an integration of 3 and peak B has an integration of 2, the ratio of protons in environment A to environment B is $3:2$.

(c) Splitting Pattern (The n+1 Rule)

The shape of a peak (the splitting pattern) is determined by the number of non-equivalent protons on the adjacent carbon atoms. This is called the $\mathbf{n+1}$ rule.

If a proton is adjacent to $n$ non-equivalent protons, its peak will be split into $(n+1)$ sub-peaks.

• $n=0$: 1 peak (Singlet)
• $n=1$: 2 peaks (Doublet)
• $n=2$: 3 peaks (Triplet)
• $n=3$: 4 peaks (Quartet)

This rule is limited to doublet, triplet, and quartet formation in aliphatic (chain) compounds. Protons attached to O or N (like $\text{O-H}$ or $\text{N-H}$) usually do not cause or show splitting because they exchange rapidly.

Key Takeaway: NMR maps the molecule. $^{13}\text{C}$ counts carbons. $^1\text{H}$ counts protons, tells you their neighbors ($n+1$ rule), and their relative quantities (integration).

5. Chromatography – Separation Techniques (A2)

Chromatography is essential for separating the components of a mixture before analysis, and often identifying them.

All chromatography relies on the distribution of components between two phases:

• Stationary Phase: A solid (or a solid coated with a liquid) that does not move.
• Mobile Phase: A solvent or gas that moves through the stationary phase.

Principle: Separation occurs because components have different solubilities in the mobile phase and different retention (sticking) onto the stationary phase. Components that spend more time in the mobile phase travel faster.

5.1 Types of Chromatography

• Thin-Layer Chromatography (TLC): Stationary phase is a coating on a plate (e.g., silica); mobile phase is a liquid solvent that moves up the plate by capillary action. Used for quick separation and purity checks.
• Column Chromatography (CC): Stationary phase is packed into a column; mobile phase (solvent) moves down the column. Used for separating larger amounts of product.
• Gas Chromatography (GC): Stationary phase is a solid or liquid-coated solid inside a long coiled column; mobile phase is an inert gas passed through the column under pressure at high temperature. Used for separating volatile mixtures.

5.2 Identification in Chromatography

(a) $R_f$ Values (TLC)

In TLC, substances are identified using the Retention Factor ($\mathbf{R}_f$) value. This is the ratio of the distance travelled by the spot to the distance travelled by the solvent front.

$$ R_f = \frac{\text{Distance travelled by spot}}{\text{Distance travelled by solvent front}} $$

The $R_f$ value is constant for a given substance under specific conditions (same solvent and stationary phase) and can be compared to standards for identification.

(b) Retention Times (GC)

In GC, substances are identified by their retention time—the time taken for the component to pass through the column to the detector.

The GC output can be coupled with a mass spectrometer (GC-MS), which analyzes each separated component as it leaves the column, giving a mass spectrum for precise identification.

Key Takeaway: Chromatography separates mixtures. TLC uses $R_f$ values. GC uses retention times and is often linked to MS for ultimate identification.