Spectroscopy in
Organic Chemistry
Three complementary analytical tools — MS, IR, and NMR — together reveal the complete molecular identity of any organic compound: its mass, its functional groups, and its carbon–hydrogen framework. This resource provides structured lecture notes and interactive visualizers for each technique.
The Problem of Structure
Organic molecules cannot be seen directly — they are far too small for any optical microscope. For over a century, chemists had to infer structure from chemical reactions alone, a process that was slow, destructive, and often ambiguous. A synthesis yielding a white crystalline solid offered no rapid way to confirm whether the correct product had formed.
The development of physical spectroscopic methods in the mid-20th century transformed organic chemistry from an empirical art into a precise science. Today, a skilled chemist can determine the complete structure of a pure unknown compound within hours, using milligram quantities and leaving the sample largely intact.
The Complementarity Principle
No single technique provides a complete picture. MS gives the molecular mass and elemental formula but cannot alone distinguish structural isomers. IR reveals which functional groups are present but not how they are connected. NMR maps the carbon–hydrogen skeleton in detail but may require supporting mass data to confirm molecular formula.
The three techniques are designed to be used together. In practice, a chemist runs all three on a new compound and cross-validates the data: the M⁺ from MS, the C=O stretch from IR, and the splitting pattern from NMR collectively constrain the possible structures to a single answer.
Historical Context
The first practical infrared spectrometers appeared in the 1940s, initially for industrial process monitoring. Mass spectrometry, originally developed for isotope separation in the Manhattan Project era, was adapted for organic structure work by the 1950s. NMR spectroscopy, predicted theoretically and first demonstrated in 1945–46, became commercially available in the late 1950s and won its inventors the Nobel Prize in Physics (1952) and Chemistry (1991, 2002). The combination of all three, along with UV-Vis spectroscopy, defines the modern spectroscopic toolkit — taught in every university organic chemistry programme worldwide and used daily in pharmaceutical, materials, and chemical research.
A beam of high-energy electrons (70 eV in EI mode) strips one electron from each molecule, creating radical cations (M⁺•). These unstable ions fragment along characteristic bond cleavage pathways. The mass analyser separates all ions by their mass-to-charge ratio, producing a bar chart spectrum where each peak corresponds to a specific ionic fragment.
| › | M⁺ peak directly gives the molecular mass (nominal) |
| › | HRMS determines exact molecular formula to 4 d.p. |
| › | Halogen isotope patterns (Cl: 3:1, Br: 1:1) are diagnostic |
| › | Fragmentation reveals bond connectivity and functional groups |
| › | Nitrogen rule: odd M⁺ indicates odd number of N atoms |
Molecules absorb infrared radiation when the frequency of IR light matches a natural bond vibrational frequency and the vibration changes the molecular dipole moment. Different bond types vibrate at highly characteristic frequencies, making IR an effective "functional group scanner." The spectrum shows %Transmittance vs. wavenumber (cm⁻¹).
| › | O–H stretch: broad 3200–3550 cm⁻¹ (alcohol); 2500–3300 (acid) |
| › | C=O stretch: sharp, strong 1630–1800 cm⁻¹ (type-specific) |
| › | N–H: 1 peak (2° amine) or 2 peaks (1° amine) near 3300–3500 |
| › | Fingerprint region (400–1500 cm⁻¹): unique molecular signature |
| › | ATR-FTIR requires no sample preparation; direct surface analysis |
Nuclei with spin (¹H, ¹³C, ¹⁵N, ³¹P …) placed in a powerful magnetic field resonate at slightly different frequencies depending on their electronic environment. ¹H NMR reveals the number of distinct proton environments, their relative counts (integration), and their neighbours (J-coupling). ¹³C NMR maps the carbon skeleton directly.
| › | Chemical shift (δ, ppm) reports electronic environment of each nucleus |
| › | Integration gives relative ratio of proton counts per signal |
| › | n+1 rule: signal split into n+1 lines by n equivalent neighbours |
| › | DEPT-135: distinguishes CH, CH₂, CH₃ carbons from quaternary C |
| › | 2D NMR (COSY, HMBC) traces full connectivity in complex molecules |
| Property | MS | IR | NMR |
|---|---|---|---|
| Physical principle | Ionisation & mass separation | IR absorption by bond vibrations | Nuclear spin resonance in magnetic field |
| Primary output | Molecular mass; fragmentation pattern | Functional group identity | Carbon–hydrogen skeleton; connectivity |
| x-axis | m/z (mass-to-charge ratio) | Wavenumber (cm⁻¹), 4000→400 | Chemical shift δ (ppm) |
| y-axis | Relative intensity (%) | % Transmittance or Absorbance | Signal intensity (arbitrary) |
| Sample amount | ng–μg | μg–mg | 1–10 mg (¹H); 5–50 mg (¹³C) |
| Sample state | Gas, liquid, solid (via inlet) | Gas, liquid, solid, film, ATR | Solution (CDCl₃, D₂O, DMSO-d₆ …) |
| Destructive? | Yes (sample ionised) | No (ATR is fully non-destructive) | No (sample recovered) |
| Key diagnostic peaks | M⁺, base peak, isotope clusters | O–H, C=O, N–H, C≡N stretches | δ, integration, multiplicity, J-coupling |
| Cannot determine | Stereochemistry; regiochemistry alone | Molecular mass; exact structure | Molecular mass alone; heavy-atom-only frameworks |
| Typical cost & access | Moderate–high (GC-MS widely available) | Low (ATR-FTIR very common) | High (magnet cost); shared facility instruments |
Systematic Approach for an Unknown
| 01 | MS → Molecular mass. Identify M⁺ peak. Apply nitrogen rule. Calculate degree of unsaturation (DoU = (2C+2+N−H−X)/2). |
| 02 | MS → Formula (HRMS). If HRMS available, obtain exact molecular formula directly. Narrows possibilities dramatically. |
| 03 | IR → Functional groups. Scan 4000→1500 cm⁻¹. Note broad O–H, sharp C=O (position!), N–H doublet, C≡N/C≡C around 2100. |
| 04 | ¹H NMR → Proton count & environment. Count signals; integrate; note singlet/doublet/triplet/quartet patterns and aromatic vs. aliphatic region. |
| 05 | ¹³C NMR / DEPT → Carbon skeleton. Count carbons; identify carbonyl (δ 160–220), aromatic (δ 110–160), and aliphatic regions. |
| 06 | Propose & verify. Suggest structure consistent with all data. Confirm: every piece of data must be explicable. No unexplained peaks allowed. |
Key Decision Rules & Quick Tests
| — | Broad O–H (IR, 2500–3300) + C=O ~1710: Carboxylic acid |
| — | C=O ~1735 (IR) + two C–O bands: Ester; confirm with MS loss of OR• |
| — | Aldehyde: C=O ~1720 + IR Fermi doublet 2700–2850 + NMR δ ~9.5 (1H, s) |
| — | Cl present: M⁺ and M+2 in 3:1 ratio in MS; one Cl atom confirmed |
| — | Br present: M⁺ ≈ M+2 intensity (1:1 ratio) in MS |
| — | DoU = 4 + aromatic C–H (IR 3030, NMR δ 7–8): monosubstituted benzene ring |
| — | Odd M⁺ (MS): odd number of N atoms in molecule |
| — | NMR triplet + quartet (1:1 area ratio): ethyl group –CH₂CH₃ |
Each visualizer includes structured lecture notes and an interactive spectrum tool.
Explore m/z spectra for 20 compounds. Hover bars to reveal fragment identities. See isotope clusters for halogenated compounds.
| M⁺ peak | fragmentation | isotope patterns | Cl/Br clusters |
| Open MS Visualizer | → |
Drag the threshold line to reveal peak assignments. Compare simulated spectra with real SDBS spectra for 30+ compounds.
| functional groups | C=O region | real spectra | peak assignments |
| Open IR Visualizer | → |
Visualize ¹H and ¹³C NMR spectra. Explore chemical shifts, integration, and coupling patterns across multiple compound classes.
| chemical shift | splitting patterns | integration | ¹H & ¹³C |
| Open NMR Visualizer | → |