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interpret-ir-spectrum

pjt222
Updated 2 days ago
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About

This skill systematically interprets IR spectra to identify functional groups by analyzing diagnostic and fingerprint regions. It detects hydrogen bonding effects and creates a confidence-rated functional group inventory. Use it for initial compound screening, reaction monitoring, or confirming functional group presence/absence.

Quick Install

Claude Code

Recommended
Primary
npx skills add pjt222/agent-almanac -a claude-code
Plugin CommandAlternative
/plugin add https://github.com/pjt222/agent-almanac
Git CloneAlternative
git clone https://github.com/pjt222/agent-almanac.git ~/.claude/skills/interpret-ir-spectrum

Copy and paste this command in Claude Code to install this skill

Documentation

Interpret IR Spectrum

Analyze IR absorption → id functional groups, assess H-bonding, inventory structural features.

Use When

  • ID functional groups in unknown (first screen)
  • Confirm presence/absence (e.g., rxn converted OH → ketone?)
  • Monitor rxn progress → appear/disappear of absorptions
  • Distinguish similar compounds by functional group
  • Complement NMR + MS w/ vibrational info

In

  • Req: IR data (abs freq cm-1 + intensities, %T or Abs)
  • Req: Prep method (KBr, ATR, Nujol, thin film, soln cell)
  • Opt: Mol formula / expected class
  • Opt: Known frags from other spectra
  • Opt: Instrument params (res, range, detector)

Do

Step 1: Spectrum Quality + Format

Verify suitability before peak analysis:

  1. y-axis format: %T (peaks down) / Abs (peaks up). Keep consistent.
  2. Wavenumber range: ≥ 4000-400 cm-1 for mid-IR. Note truncation.
  3. Baseline: Flat + near 100%T (or 0 Abs) in no-abs regions. Slopes/noise → reduce reliability.
  4. Resolution: Adjacent peaks < instrumental res → can't distinguish. Typical FTIR: 4 cm-1.
  5. Prep artifacts: KBr → broad OH ~3400 cm-1 (moisture). Nujol obscures CH stretch. ATR distorts low wavenumbers. Note.

→ Spectrum suitable; format, range, artifacts documented.

If err: Severe baseline probs, saturation (flat-bottom peaks → too-conc sample), prep artifacts obscuring critical regions → note limitation + flag regions unreliable.

Step 2: Diagnostic Region (4000-1500 cm-1)

High-freq region → most functional groups:

  1. O-H (3200-3600 cm-1): Broad abs. Sharp ~3600 → free OH; broad 3200-3400 → H-bonded OH (alcohols, acids, water).
  2. N-H (3300-3500 cm-1): Primary amines → 2 peaks (sym+asym); secondary → 1. Sharper than OH.
  3. C-H (2800-3300 cm-1):
Frequency (cm-1)Assignment
3300sp C-H (alkyne, sharp)
3000--3100sp2 C-H (aromatic, vinyl)
2850--3000sp3 C-H (alkyl, multiple peaks)
2700--2850Aldehyde C-H (two peaks from Fermi resonance)
  1. Triple-bond (2000-2300 cm-1):
Frequency (cm-1)AssignmentNotes
2100--2260C triple-bond CWeak or absent if symmetric
2200--2260C triple-bond NMedium to strong
~2350CO2Atmospheric artifact, disregard
  1. Carbonyl (1650-1800 cm-1) — most diagnostic single region:
Frequency (cm-1)Assignment
1800--1830, 1740--1770Acid anhydride (two C=O stretches)
1770--1780Acid chloride
1735--1750Ester
1700--1725Carboxylic acid
1705--1720Aldehyde
1705--1720Ketone
1680--1700Conjugated ketone / alpha-beta unsaturated
1630--1690Amide (amide I band)
  1. C=C + C=N (1600-1680 cm-1): Alkene C=C → 1620-1680 (weak-med). Aromatic C=C → multiple 1450-1600. C=N (imine) → 1620-1660.

→ All abs in diagnostic ID'd w/ func group + confidence (strong/tentative/absent).

If err: Carbonyl obscured (water in KBr, atm CO2) → note gap. Expected group absent → confirm w/ 2nd prep before concluding absent.

Step 3: Fingerprint (1500-400 cm-1)

Low-freq region → confirmation + structural detail:

  1. C-O (1000-1300 cm-1): Ethers, esters, alcohols, acids → strong C-O. Esters → characteristic strong band 1000-1100 + carbonyl.
  2. C-N (1000-1250 cm-1): Amines + amides; overlap C-O → tentative w/o other evidence.
  3. C-F, C-Cl, C-Br:
Frequency (cm-1)Assignment
1000--1400C-F (strong)
600--800C-Cl
500--680C-Br
  1. Aromatic subst pattern (700-900 cm-1): OOP C-H bending → substitution:
Frequency (cm-1)Pattern
730--770Mono-substituted (+ 690--710)
735--770Ortho-disubstituted
750--810, 860--900Meta-disubstituted
790--840Para-disubstituted
  1. Fingerprint comparison: Region unique per compound. Ref spectrum avail → overlay + compare → identity confirm.

→ Confirmatory assignments for Step 2 groups + structural detail (subst patterns, C-O/C-N).

If err: Fingerprint inherently complex + overlapping. Ambiguous → flag tentative + rely on diagnostic + other spectra.

Step 4: H-bonding + Intermolecular Effects

Evaluate sample state + interactions:

  1. H-bonding broadening: Compare width+pos of OH, NH. Free OH sharp ~3600; H-bonded broad + shifted 3200-3400. Acid dimers → very broad OH 2500-3300.
  2. Conc + state effects: Soln spectra at diff conc → distinguish intramolecular (conc-indep) from intermolecular (conc-dep) H-bonds.
  3. Fermi resonance: 2 overlapping bands → doublet. Classic: aldehyde C-H pair ~2720 + 2820. Recognize → avoid mis-assign as separate groups.
  4. Solid-state effects: KBr + Nujol → solid packing → broadens bands + shifts 10-20 cm-1 vs soln. ATR closest to neat liquid.

→ H-bonding characterized, prep artifacts accounted, anomalous band shapes explained.

If err: H-bonding unresolved (overlap OH + NH) → note ambiguity. D2O exchange / var-temp → helps, requires add'l data.

Step 5: Compile Func Group Inventory

Assemble findings → structured report:

  1. Confirmed groups: Strong unambiguous abs in diagnostic (e.g., sharp C=O at 1715 = ketone/aldehyde).
  2. Tentative: Weaker evidence / overlap → >1 possible group.
  3. Absent: Characteristic strong abs clearly missing (no broad OH → no free alcohol/acid).
  4. Discrepancies: Abs not fitting proposed groups, or expected abs missing.
  5. Cross-ref: Compare IR inventory vs NMR, MS, UV-Vis if avail.

→ Complete inventory by confidence, specific freqs + intensities cited as evidence.

If err: Inventory incomplete/contradictory → ID which add'l exps (ATR vs KBr, var conc, D2O exchange) resolve ambiguity.

Check

  • Quality assessed (baseline, res, artifacts, y-axis)
  • Solvent, prep, atm artifacts ID'd + excluded
  • All abs in diagnostic (4000-1500) assigned / flagged
  • Carbonyl region → sub-type assignment where possible
  • Fingerprint examined for confirmation
  • H-bonding evaluated + peak shape/pos impact documented
  • Inventory compiled w/ confidence
  • Absent groups explicit (neg evidence informative)
  • Cross-ref vs other spectra

Traps

  • Ignore prep artifacts: KBr moisture (broad 3400), Nujol C-H (2850-2950), ATR distortion at low wavenumbers → mimic/obscure real. Always consider prep.
  • Over-interpret fingerprint: Region < 1500 complex+overlapping. Use for confirm not primary ID. Don't assign every peak.
  • Confuse atm CO2 w/ sample: Sharp doublet ~2350 = atm CO2 usually, not sample. BG subtraction removes, verify.
  • Neglect intensity+width: Strong broad ≠ weak sharp at same freq. Report intensity (str/med/weak) + shape (sharp/broad) + freq.
  • Single-peak assignment: Never ID func group from single abs. Carbonyls → supported by additional bands (C-O for esters, N-H for amides, C-H for aldehydes).
  • Absence from weak abs: Some groups → inherently weak IR (sym C=C, triple bonds sym alkynes). Absence ≠ always absence of group.

  • interpret-nmr-spectrum — detailed connectivity + H environments
  • interpret-mass-spectrum — mol formula + fragmentation
  • interpret-uv-vis-spectrum — chromophores complementing IR
  • interpret-raman-spectrum — complementary vibrational → IR-inactive modes
  • plan-spectroscopic-analysis — select + sequence techniques pre-acquisition

GitHub Repository

pjt222/agent-almanac
Path: i18n/caveman-ultra/skills/interpret-ir-spectrum
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