Organic Chemistry: Spectroscopy and Structure Determination

Structure determination sits at the center of organic chemistry. When you isolate a new natural product, check the purity of a synthesized intermediate, or confirm the identity of a reaction product, you are really asking the same question: what is this molecule, and how are its atoms connected?

Modern organic analysis answers that question by combining several spectroscopic techniques. No single method gives the whole structure in every case, but together NMR (¹H and ¹³C), IR spectroscopy, mass spectrometry, and UV-Vis provide a reliable, cross-checked pathway from an unknown sample to a defensible structure.

A practical workflow: from unknown to structure

In real laboratories, structure determination often follows a sequence that mirrors the type of information each technique provides.

1. Mass spectrometry (MS) establishes molecular weight and often molecular formula (especially with high-resolution MS), plus fragmentation clues.
2. IR spectroscopy quickly flags key functional groups (carbonyls, alcohols, amines, nitriles) and helps rule structures in or out.
3. NMR spectroscopy supplies the detailed connectivity map: how many distinct hydrogens and carbons exist, their electronic environments, and which atoms are neighbors.
4. UV-Vis spectroscopy supports conclusions about conjugation and aromatic systems, and it is especially useful for chromophoric compounds and purity checks.

The best determinations treat each dataset as a constraint. A proposed structure must satisfy all constraints simultaneously.

Mass spectrometry: mass, formula, and fragmentation logic

Mass spectrometry measures the mass-to-charge ratio $m/z$ of ionized molecules and fragments. The first critical datum is the molecular ion (often labeled $M^{+}$ in electron ionization). In softer ionization methods, you may instead see a protonated molecule $[M+H{]}^{+}$ or other adducts. The molecular ion region provides the molecular weight, which immediately narrows possible structures.

Molecular formula and isotopic patterns

With accurate mass (high-resolution MS), you can often infer a molecular formula. Once a formula is in hand, the degree of unsaturation (also called the double bond equivalent, DBE) indicates how many rings and π bonds the molecule contains. A common form is:

$$DBE=\frac{2C+2+N-H-X}{2}$$

where $C,H,N$ are counts of those atoms and $X$ is the number of halogens. Oxygen and sulfur do not change DBE directly.

Isotope patterns give additional clues:

• Chlorine produces a characteristic $M$ and $M+2$ pattern near a 3:1 ratio.
• Bromine produces $M$ and $M+2$ peaks near a 1:1 ratio.

Fragmentation as a structural hint

Fragment ions are not random. Carbonyl compounds often show acylium fragments; benzylic positions can fragment readily; and heteroatoms can direct cleavages. Fragmentation rarely solves a structure alone, but it can confirm substructures suggested by NMR and IR.

IR spectroscopy: functional group triage

IR spectroscopy reports bond vibrations. It is not usually a complete structure tool, but it is extremely efficient at identifying functional groups that have strong, diagnostic absorptions.

Common, high-value regions include:

• O-H stretch (alcohols, phenols): broad band in the 3200–3600 cm⁻¹ range.
• N-H stretch (amines, amides): typically sharper than O-H, often around 3300–3500 cm⁻¹.
• C=O stretch (carbonyls): strong absorption near 1650–1750 cm⁻¹, with the exact position influenced by conjugation and functional type (ester, ketone, aldehyde, amide).
• C≡N stretch (nitriles): sharp band around 2210–2260 cm⁻¹.
• C=C stretches (alkenes, aromatics): often 1600–1680 cm⁻¹, with aromatic rings also showing characteristic patterns in the fingerprint region.

IR’s real strength is speed and selectivity. If NMR suggests an aldehyde, the presence of a strong carbonyl and the aldehyde C-H stretches in the ~2700–2900 cm⁻¹ region supports that assignment. If IR shows no carbonyl band, any carbonyl-containing proposal becomes suspect.

¹H NMR spectroscopy: environments, integration, and coupling

Proton NMR is often the most information-dense spectrum in an organic characterization package. Three features carry most of the structural logic:

Chemical shift: where a proton sits electronically

Chemical shift reflects shielding and deshielding effects. Typical ranges (approximate, context-dependent) include:

• 0.8–2.0 ppm: alkyl protons
• 2.0–3.0 ppm: protons near π systems or carbonyls (allylic, benzylic, α to carbonyl)
• 3.0–4.5 ppm: protons on carbons bonded to electronegative atoms (C-O, C-N)
• 5.0–6.5 ppm: alkene protons
• 6.5–8.5 ppm: aromatic protons
• 9.0–10.5 ppm: aldehyde proton
• 10–13+ ppm: carboxylic acid and strongly hydrogen-bonded protons (often broad)

Integration: how many protons contribute

Signal areas correspond to relative proton counts. Integration is a direct check on whether a proposed fragment has the right number of hydrogens. It also helps detect symmetry: fewer signals than expected often means equivalent sets of protons.

Splitting patterns and coupling constants: who is neighboring whom

Spin-spin splitting reveals the number of adjacent, non-equivalent hydrogens (often introduced through the $n+1$ rule as a first approximation). Beyond multiplicity, coupling constants $J$ (in Hz) can identify geometries. For alkenes, larger $J$ values generally correspond to trans coupling compared with cis, helping distinguish stereochemistry in favorable cases.

In practice, ¹H NMR is a connectivity tool: it tells you which groups are adjacent and what electronic environments surround them.

¹³C NMR spectroscopy: the carbon skeleton

Carbon-13 NMR complements proton data by mapping distinct carbon environments. Because ¹³C signals are typically not integrated reliably in routine spectra, the key outputs are chemical shift positions and the number of unique carbons.

Useful shift ranges include:

• 0–50 ppm: sp³ carbons (alkyl)
• 50–90 ppm: sp³ carbons attached to heteroatoms (C-O, C-N) and some sp carbons
• 100–150 ppm: alkenes and aromatics
• 160–220 ppm: carbonyl carbons (esters and acids often 160–185 ppm; aldehydes and ketones often 190–220 ppm)

¹³C NMR is especially helpful for confirming carbonyl presence and counting aromatic or alkene carbons. It also exposes hidden symmetry: if a molecule has ten carbons but only five distinct ¹³C signals, equivalence is likely.

UV-Vis spectroscopy: conjugation and chromophores

UV-Vis spectroscopy measures electronic transitions, most commonly $\pi \to {\pi }^{\ast }$ and $n\to {\pi }^{\ast }$. For many saturated organic molecules, UV-Vis offers little. Its strength is in compounds with conjugated π systems, such as dienes, polyenes, aromatic rings, and many carbonyl-containing chromophores.

Practical uses include:

• Supporting the presence and extent of conjugation suggested by NMR and IR.
• Monitoring reaction progress and purity for chromophoric products.
• Identifying aromatic or highly conjugated systems when a spectrum shows strong absorption in the UV or visible range.

UV-Vis rarely proves a complete structure, but it can confirm that a proposed structure has the expected chromophore and conjugation length.

Putting the techniques together: consistency beats cleverness

The most reliable structural assignments are not built from a single “signature peak.” They come from checking whether all data agree.

A typical consistency check looks like this:

• MS gives a molecular weight and possibly a formula, from which DBE sets a minimum count of rings and π bonds.
• IR confirms whether key functionalities implied by DBE and NMR are present (for example, a carbonyl needed to explain deshielded signals).
• ¹H NMR accounts for all hydrogens implied by the formula and reveals neighbor relationships through splitting.
• ¹³C NMR confirms the count and types of carbons, including quaternary and carbonyl carbons that may not appear clearly in ¹H NMR.
• UV-Vis supports the presence of conjugation or aromaticity suggested by the other spectra.

If a proposed structure fits the mass but contradicts IR (no carbonyl band) or produces the wrong number of ¹³C environments, it is not correct. Structure determination is less about finding one perfect clue and more about satisfying a web of independent constraints.

Common pitfalls and good habits

• Don’t overinterpret IR fingerprint regions unless you have a direct comparison or strong experience. Focus on diagnostic functional group bands first.
• **Treat ¹H NMR integration as