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interpret-ir-spectrum

pjt222
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About

This Claude Skill analyzes infrared spectra to identify functional groups by examining diagnostic and fingerprint regions. It detects hydrogen bonding effects and compiles a functional group inventory with confidence levels. Use it for initial compound screening or to confirm structural features in unknown samples.

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

Read IR absorption spectra. Identify functional groups. Check hydrogen bonding. Compile inventory of structural features in sample.

When Use

  • Identify functional groups in unknown compound as first screen
  • Confirm presence or absence of specific functional groups (e.g., verify reaction turned alcohol to ketone)
  • Monitor reaction progress by tracking appearance/disappearance of characteristic absorptions
  • Distinguish between similar compounds differing in functional group content
  • Complement NMR + mass spec data with vibrational info

Inputs

  • Required: IR spectrum data (absorption frequencies in cm-1 with intensities, as %Transmittance or Absorbance plot)
  • Required: Sample prep method (KBr pellet, ATR, Nujol mull, thin film, solution cell)
  • Optional: Molecular formula or expected compound class
  • Optional: Known structural fragments from other spectroscopic data
  • Optional: Instrument parameters (resolution, scan range, detector type)

Steps

Step 1: Check Spectrum Quality and Format

Verify spectrum suitable for interpretation before analyzing peaks:

  1. Check y-axis format: %Transmittance (%T, peaks point down) or Absorbance (A, peaks point up)? All analysis assumes consistent convention
  2. Verify wavenumber range: Covers at least 4000-400 cm-1 for standard mid-IR? Note any truncation
  3. Assess baseline: Good baseline relatively flat, near 100%T (or 0 Absorbance) in regions with no absorption. Sloping or noisy baselines cut reliability
  4. Check resolution: Adjacent peaks closer than instrumental resolution cannot be distinguished. Typical FTIR resolution = 4 cm-1
  5. Identify prep artifacts: KBr pellets may show broad O-H band from moisture (~3400 cm-1). Nujol mulls obscure C-H stretches. ATR spectra show intensity distortion at low wavenumbers. Note any artifacts limiting interpretation

Got: Spectrum confirmed suitable. Format, range, artifacts documented.

If fail: Severe baseline problems, saturation (flat-bottomed peaks from too-concentrated samples), or prep artifacts obscuring critical regions? Note limitation. Flag affected spectral regions unreliable.

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

Systematic analysis of high-frequency region where most functional groups make characteristic absorptions:

  1. O-H stretches (3200-3600 cm-1): Look for broad absorptions. Sharp peak near 3600 cm-1 = free O-H. Broad band centered at 3200-3400 cm-1 = hydrogen-bonded O-H (alcohols, carboxylic acids, water)
  2. N-H stretches (3300-3500 cm-1): Primary amines show two peaks (symmetric + asymmetric). Secondary amines show one. Typically sharper than O-H bands
  3. C-H stretches (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 region (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 region (1650-1800 cm-1) — most diagnostic single region in IR:
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 and C=N stretches (1600-1680 cm-1): Alkene C=C = 1620-1680 cm-1 (weak to medium). Aromatic C=C = multiple peaks near 1450-1600 cm-1. C=N (imine) = 1620-1660 cm-1

Got: All absorptions in diagnostic region identified, with functional group assignments and confidence levels (strong, tentative, absent).

If fail: Carbonyl region obscured (e.g., water absorption in KBr, atmospheric CO2)? Note gap. Expected functional group absorption absent? Confirm with second prep method before concluding truly absent.

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

Examine lower-frequency region for confirmatory and structural detail:

  1. C-O stretches (1000-1300 cm-1): Ethers, esters, alcohols, carboxylic acids make strong C-O stretching. Esters show characteristic strong band near 1000-1100 cm-1 in addition to carbonyl
  2. C-N stretches (1000-1250 cm-1): Amines and amides. Overlap with C-O makes assignment tentative without other evidence
  3. C-F, C-Cl, C-Br stretches:
Frequency (cm-1)Assignment
1000--1400C-F (strong)
600--800C-Cl
500--680C-Br
  1. Aromatic substitution pattern (700-900 cm-1): Out-of-plane C-H bending reveals substitution:
Frequency (cm-1)Pattern
730--770Mono-substituted (+ 690--710)
735--770Ortho-disubstituted
750--810, 860--900Meta-disubstituted
790--840Para-disubstituted
  1. Overall fingerprint compare: Fingerprint region unique to each compound. Reference spectrum available? Overlay and compare this region for identity confirmation

Got: Confirmatory assignments for functional groups from Step 2, plus additional structural detail (substitution patterns, C-O/C-N assignments).

If fail: Fingerprint region inherently complex and overlapping. Assignments ambiguous? Flag as tentative. Rely on diagnostic region and other spectroscopic data for final conclusions.

Step 4: Assess Hydrogen Bonding and Intermolecular Effects

Evaluate how sample state and intermolecular interactions affect spectrum:

  1. Hydrogen bonding broadening: Compare width and position of O-H and N-H bands. Free O-H sharp, near 3600 cm-1. Hydrogen-bonded O-H broad, shifted to 3200-3400 cm-1. Carboxylic acid dimers show very broad O-H from 2500-3300 cm-1
  2. Concentration and state effects: Solution spectra at different concentrations distinguish intramolecular (concentration-independent) from intermolecular (concentration-dependent) hydrogen bonds
  3. Fermi resonance: Two overlapping bands interact to split into doublet. Classic example: aldehyde C-H pair near 2720 and 2820 cm-1. Recognize Fermi resonance to avoid misassigning extra peaks as separate functional groups
  4. Solid-state effects: KBr pellets and Nujol mulls reflect solid-state packing. Broadens bands. Shifts frequencies 10-20 cm-1 relative to solution spectra. ATR spectra closest to neat liquid state

Got: Hydrogen bonding state characterized. Prep-method artifacts accounted for. Any anomalous band shapes explained.

If fail: Hydrogen bonding effects cannot be resolved (e.g., overlapping O-H and N-H bands)? Note ambiguity. D2O exchange experiment or variable-temperature study can help, but need additional data.

Step 5: Compile Functional Group Inventory

Assemble findings into structured report:

  1. List confirmed functional groups: Strong, unambiguous absorptions in diagnostic region (e.g., sharp C=O at 1715 cm-1 = ketone or aldehyde)
  2. List tentative assignments: Weaker evidence or overlapping absorptions that could be explained by more than one functional group
  3. List absent functional groups: Characteristic strong absorptions clearly missing (e.g., no broad O-H band = no free alcohol or carboxylic acid)
  4. Note discrepancies: Absorptions not fitting proposed functional group set, or expected absorptions missing
  5. Cross-reference: Compare IR-derived inventory with info from other techniques (NMR, MS, UV-Vis) if available

Got: Complete functional group inventory by confidence level, with specific frequencies and intensities cited as evidence for each assignment.

If fail: Inventory incomplete or contradictory? Identify which additional experiments (ATR vs. KBr compare, variable concentration, D2O exchange) would resolve ambiguities.

Checks

  • Spectrum quality assessed (baseline, resolution, artifacts, y-axis format)
  • Solvent, prep-method, atmospheric artifacts identified and excluded
  • All absorptions in diagnostic region (4000-1500 cm-1) assigned or flagged
  • Carbonyl region analyzed with specific sub-type assignment where possible
  • Fingerprint region examined for confirmatory evidence
  • Hydrogen bonding effects evaluated, influence on peak shape/position documented
  • Functional group inventory compiled with confidence levels
  • Absent functional groups explicitly noted (negative evidence informative)
  • Assignments cross-referenced with other available spectroscopic data

Pitfalls

  • Ignoring prep artifacts: KBr moisture (broad 3400 cm-1), Nujol C-H (2850-2950 cm-1), ATR intensity distortion at low wavenumbers all mimic or obscure real absorptions. Always consider prep method.
  • Over-interpret fingerprint region: Region below 1500 cm-1 complex and overlapping. Use for confirmation, not primary ID. Avoid assigning every peak.
  • Confuse atmospheric CO2 with sample peaks: Sharp doublet near 2350 cm-1 almost always atmospheric CO2, not sample absorption. Background subtraction should remove, but verify.
  • Neglect band intensity and width: Strong broad absorption differs from weak sharp peak at same frequency in diagnostic value. Report intensity (strong/medium/weak) and shape (sharp/broad) alongside frequency.
  • Single-peak assignments: Never identify functional group from single absorption alone. Carbonyl groups should be supported by additional bands (C-O for esters, N-H for amides, C-H for aldehydes).
  • Assume absence from weak absorption: Some functional groups make inherently weak IR absorptions (symmetric C=C, triple bonds in symmetric alkynes). Absence of peak does not always mean absence of group.

See Also

  • interpret-nmr-spectrum — determine detailed connectivity and hydrogen environments
  • interpret-mass-spectrum — establish molecular formula and fragmentation pattern
  • interpret-uv-vis-spectrum — characterize chromophores complementing IR functional group data
  • interpret-raman-spectrum — complementary vibrational data for IR-inactive modes
  • plan-spectroscopic-analysis — select and sequence spectroscopic techniques before data acquisition

GitHub Repository

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