Biomolecular module
Protein & peptide IR
The amide backbone gives a small set of intense, structure-sensitive bands. They report secondary-structure composition and, with isotope editing, residue-resolved local structure — without crystals and in native-like environments.
The amide modes
| Mode | Position (cm⁻¹) | Composition | Use |
|---|---|---|---|
| Amide A | ~3300 | ν(N–H) | H-bonding / accessibility; amide B (~3100) is its Fermi partner. |
| Amide I | 1600–1700 | ~80% ν(C=O), +ν(C–N), δ(N–H) | Primary secondary-structure marker. Through-bond/space coupling sets band shape. |
| Amide II | 1510–1580 | δ(N–H) (~60%) + ν(C–N) | H/D exchange probe → amide II′ ~1450 on N-deuteration. |
| Amide III | 1200–1300 | ν(C–N) + δ(N–H), mixed | Weak but structure-sensitive; useful in Raman/IR combination. |
Why amide I works
Amide I is dominated by the carbonyl stretch, but the carbonyls are vibrationally coupled along the backbone (transition-dipole coupling + through-bond). The geometry of a given secondary structure fixes that coupling, so each fold produces a characteristic amide I sub-band. Bands overlap heavily, so resolution comes from Fourier self-deconvolution, second-derivative analysis, curve-fitting, and increasingly 2D-IR and isotope editing rather than the raw envelope.
Amide I secondary-structure band map
Representative component positions in H₂O. Positions shift in D₂O (typically −5 to −10 cm⁻¹) and with H-bond strength; ranges overlap, so treat single positions as indicative, not definitive.
| Component (cm⁻¹, H₂O) | Assignment | Notes |
|---|---|---|
| 1610–1628 | intermolecular β / aggregate | Strong low band ⇒ aggregation / amyloid cross-β. |
| 1623–1641 | β-sheet (intramolecular) | Main β component; antiparallel sheets add a weak high band. |
| 1642–1648 | random coil / disordered | Overlaps helix in H₂O — D₂O separates them (~1643). |
| 1648–1657 | α-helix | ~1654 typical; the canonical helix marker. |
| 1658–1666 | 3₁₀-helix | Higher than α-helix; common in short/terminal helices. |
| 1662–1685 | turns | β-turns and loops; several sub-types. |
| 1670–1695 | β-sheet (antiparallel, high-ν) | Weak partner of the ~1630 band; antiparallel diagnostic. |
🧬 Amide I component estimator
Enter an amide I sub-band position (1600–1700 cm⁻¹, H₂O) to get the most likely secondary-structure assignment.
cm⁻¹Techniques that add resolution
H/D exchange
Backbone N–H ⇄ N–D shifts amide II to ~1450 (amide II′). The exchange rate maps solvent accessibility and H-bond protection — a folding/dynamics readout.
¹³C / ¹³C=¹⁸O editing
Site-specifically labelling one carbonyl red-shifts its amide I by ~40 (¹³C) to ~65 cm⁻¹ (¹³C¹⁸O), lifting a single residue out of the congested band — residue-resolved structure.
2D-IR
Cross-peaks report vibrational coupling between labelled residues → distance/orientation constraints; waiting-time evolution gives picosecond dynamics and H-bond fluctuations.
Reaction-induced difference IR
Subtracting states (ligand bound/free, photo-triggered) isolates the few bands that change — used for enzyme mechanism, transport, and photoreceptors.
Honest limits
Amide I gives composition (fraction helix/sheet/turn/coil), not a residue-by-residue map — unless you isotope-edit specific sites. It does not yield primary sequence. Water absorbs strongly near amide I (δ(H–O–H) ~1640), so aqueous work needs short pathlengths, D₂O, or ATR. Quantitative composition from curve-fitting is model-dependent; report the deconvolution method.
Related: vibrational Stark probes for binding-pocket fields · the AI program on extracting structure from band shape · simulate amide-I band shapes on-site.
References
- Krimm, S. & Bandekar, J. Vibrational spectroscopy and conformation of peptides, Adv. Protein Chem. (1986).
- Byler, D. M. & Susi, H. Examination of the secondary structure of proteins by deconvolved FTIR spectra, Biopolymers (1986).
- Barth, A. Infrared spectroscopy of proteins, Biochim. Biophys. Acta (2007).
- Ganim, Z. et al. Amide I 2D-IR of proteins, Acc. Chem. Res. (2008).