plan-spectroscopic-analysis

name: plan-spectroscopic-analysis locale: caveman-ultra source_locale: en source_commit: 82c77053 translator: "Julius Brussee homage — caveman" translation_date: "2026-04-26" description: > Plan spectroscopic analysis campaign: define analytical question, assess sample, pick techniques via decision matrix, plan prep per technique, sequence non-destructive → destructive, define success criteria w/ cross-validation strategy. license: MIT allowed-tools: Read Grep Glob WebFetch WebSearch metadata: author: Philipp Thoss version: "1.0" domain: spectroscopy complexity: intermediate language: natural tags: spectroscopy, analytical-planning, technique-selection, sample-preparation

Plan Spectroscopic Analysis

Design spectroscopic campaign: pick right techniques, sequence efficiently, define success criteria → answer specific analytical question.

Use When

• Investigate unknown compound → which spectroscopic techniques?
• Optimize analysis sequence → preserve sample for destructive methods
• Plan sample prep before instrument time
• Cross-validate complementary techniques
• Budget instrument time + prioritize when resources limited
• Train new analysts in systematic planning

In

• Required: Analytical question (structure ID, quantitation, purity, functional group screen, reaction monitoring)
• Required: Sample desc (physical state, qty, known/suspected class)
• Optional: Available instruments + capabilities
• Optional: Budget + time constraints
• Optional: Safety data (toxicity, reactivity, volatility, light)
• Optional: Prior data (if any)

Do

Step 1: Define Analytical Question

Clarify info needed before picking technique.

1. Classify question:

   • Structure ID: Full molecular structure of unknown. Broadest set.
   • Structure confirm: Known compound matches expected. Few, focused on diagnostics.
   • Quantitative: Concentration of known analyte. Calibration + good linearity (UV-Vis, NMR w/ internal std).
   • Purity: Impurities present? Identify? High sensitivity + separation.
   • Functional group screen: Which groups present, no full structure. IR often enough.
   • Reaction monitor: Track reaction over time. Speed + compatibility w/ conditions (in situ IR, Raman, UV-Vis).

2. Success criteria: Explicit. Structure ID → "single proposal consistent w/ all data". Quantitation → "concentration w/ <5% rel error".

3. Existing knowledge: Compile (elemental analysis, reaction scheme, expected product, lit precedent). Constrains problem, fewer techniques needed.

→ Clear analytical question w/ success criteria + existing knowledge summary.

If err: question vague ("characterize this") → narrow w/ requestor. Vague → unfocused → wasted instrument time.

Step 2: Assess Sample Characteristics

Eval sample → which techniques feasible.

1. Physical state: Solid (crystalline, amorphous, powder), liquid, solution, gas, thin film, biological tissue. Each constrains prep + technique.
2. Quantity: Total mass/vol. NMR needs mg, MS µg, SERS ng.
3. Solubility: Test/estimate in common solvents (water, methanol, DMSO, chloroform, hexane). NMR → deuterated solvent. UV-Vis → transparent.
4. Stability: Thermal (GC-MS needs volatilization), photo (Raman uses laser), air/moisture (KBr pellet), solution (time-dependent).
5. Safety: Toxicity, flammability, reactivity, radioactivity. Affects handling, may exclude techniques (volatile toxics → no open-atmosphere Raman w/o containment).
6. MW range: Small (<1000 Da) vs polymers/biomolecules (>1000 Da) → different MS ionization + NMR strategies.

→ Sample characterization summary: state, qty, solubility, stability, hazards, MW range.

If err: can't characterize adequately (qty too small to test solubility) → conservative: start non-destructive minimal-sample (Raman, ATR-IR), reassess after.

Step 3: Select Techniques via Decision Matrix

Pick most informative techniques based on question + sample.

*IR with KBr is non-destructive to the molecule but the sample cannot be easily recovered from the pellet.

1. Match question to technique: Structure ID → NMR + MS + IR min. Functional group → IR only. Quantitation → UV-Vis or NMR best.
2. Feasibility: Cross-ref candidates w/ Step 2 sample. Eliminate incompatible (GC-MS for non-volatile, NMR for paramagnetic).
3. Prioritize by info density: Rank by info per question.
4. Cost + availability: If equal info, prefer faster, cheaper, more available.

→ Ranked list of techniques w/ justification + excluded ones w/ reasons.

If err: no single sufficient (common for structure ID) → plan complementary techniques together. None suitable → note limitation, recommend alts (derivatization → GC-MS).

Step 4: Plan Sample Prep per Technique

Prep reqs per selected technique.

1. NMR prep: Dissolve 1-50 mg in 0.5-0.7 mL deuterated solvent. Solvent by solubility + spectral window:

2. IR prep: Method by sample state:

   • ATR: Solid/liquid direct on crystal. Fastest, minimal prep.
   • KBr pellet: Grind 1-2 mg w/ 100-200 mg dry KBr, press into transparent disk.
   • Solution cell: Dissolve in IR-transparent solvent (CCl4, CS2). Limited transparency windows.
   • Thin film: Cast from solution onto NaCl/KBr window. Polymers + oils.

3. MS prep: Match ionization to sample:

   • EI (GC-MS): Sample volatile. Volatile solvent (DCM, hexane).
   • ESI (LC-MS): ESI-compatible solvent (methanol/water, acetonitrile/water w/ 0.1% formic acid).
   • MALDI: Mix w/ matrix (DHB, CHCA, sinapinic acid), dry on target.

4. UV-Vis prep: UV-transparent solvent. Conc → absorbance at lambda-max 0.1-1.0. Matched cuvettes for sample + ref.

5. Raman prep: Minimal. Solids neat. Liquids in glass vials (weak Raman). Avoid fluorescent containers. Aqueous solutions OK (water = weak Raman scatterer).

→ Prep protocol per technique: solvents, qtys, special handling.

If err: qty insufficient for all → prioritize by Step 3 hierarchy. Insoluble in all suitable → solid-state techniques (ATR-IR, Raman, solid-state NMR, MALDI-MS).

Step 5: Sequence + Cross-Validation Strategy

Order analyses → preserve sample, max info flow.

1. Sequence by destructiveness: Non-destructive first, destructive last.

   • Tier 1 (non-destructive, no prep): Raman, ATR-IR
   • Tier 2 (non-destructive, requires prep): UV-Vis, NMR (sample often recoverable by evaporation)
   • Tier 3 (destructive or consumes sample): MS (ESI, EI/GC-MS, MALDI)

2. Info flow: Early results refine later:

   • IR/Raman functional groups → choose NMR experiments (no carbonyl in IR → skip carbonyl-focused 13C).
   • MW from MS → interpret NMR (integration ratios, peak count).
   • NMR connectivity → interpret MS fragmentation.

3. Cross-validation points: Where techniques must agree:

   • Molecular formula: MS (mol ion) = NMR (H + C count) = elemental analysis.
   • Functional groups: IR assignments consistent w/ NMR shifts + MS fragmentation.
   • Degree of unsaturation: From formula (MS) = observed rings + double bonds (NMR, UV-Vis).

4. Contingencies: What if ambiguous:

   • NMR unexpected complexity → run 2D (COSY, HSQC, HMBC).
   • MS mol ion ambiguous → different ionization or HRMS.
   • IR dominated by one group → Raman for complementary.

5. Document plan: Written plan w/ sequence, prep, turnaround, decision points.

→ Complete ordered plan w/ prep, cross-validation, contingencies doc'd.

If err: plan can't complete due to sample/instrument → doc limitations, propose best achievable subset.

Check

• Analytical question clear w/ explicit success criteria
• Sample characteristics assessed (state, qty, solubility, stability, hazards)
• Techniques selected via decision matrix w/ justifications
• Infeasible techniques excluded w/ reasons
• Sample prep planned per technique
• Analysis sequence non-destructive → destructive
• Cross-validation points defined
• Contingency experiments ID'd for ambiguous
• Total sample consumption estimated vs available qty

Traps

• Skip planning: Jumping to nearest instrument → wastes sample + time. 15 min planning saves hours of re-analysis.
• Pick by habit not need: Not every analysis needs NMR. Functional group confirm → only IR. Match technique to question.
• Underestimate sample reqs: Running out mid-sequence avoidable. Calc total upfront + 20% reserve.
• Destructive methods first: GC-MS before NMR → NMR needs separate aliquot. Non-destructive first → max info per mg.
• Neglect solvent compat: Sample in DMSO-d6 (NMR) → not easy for GC-MS (non-volatile). Plan solvents across all.
• No cross-validation strategy: No checkpoints → contradictory results unnoticed until final interp.

→

• interpret-nmr-spectrum — interpret NMR per this plan
• interpret-ir-spectrum — interpret IR per this plan
• interpret-mass-spectrum — interpret MS per this plan
• interpret-uv-vis-spectrum — interpret UV-Vis per this plan
• interpret-raman-spectrum — interpret Raman per this plan
• validate-analytical-method — validate quantitative methods from this plan