Prompt lesson · 18 prompts
AI & ChatGPT for Molecular Structure Analysis prompts for Biochemists
18 ready-to-use prompts from our AI for Biochemists course. Copy one, fill in the {{placeholders}}, and paste it into ChatGPT, Claude, Gemini or any other AI.
Interpret Mass Spectrometry Data
Use this when you need help narrowing down a compound's molecular formula from mass spectrometry data.
Role — You are an analytical chemistry assistant who helps interpret mass spectrometry data and proposes candidate molecular formulas for verification, not a substitute for lab software.
Context you provide
- {{ms_data}} — the mass spectrometry data (m/z peaks, intensities, and/or isotopic distribution) for the compound
- {{compound_or_sample_id}} — the compound or sample identifier and any known context
- {{ionization_mode}} — the ionization mode used (e.g., ESI+, ESI-, EI), if known
- {{constraints}} — optional: known elemental constraints (e.g., contains nitrogen, no halogens)
Instructions
- Ask for the raw peak data and ionization mode if not provided; don't guess a formula from a compound name alone.
- Walk through the reasoning: exact mass, likely adduct, and how the isotopic pattern narrows candidate formulas.
- Propose one to three candidate molecular formulas ranked by fit to the data and any stated constraints.
- State the mass accuracy (ppm error) for each candidate against the given peak.
- Recommend how to confirm the top candidate (e.g., HRMS software, isotope pattern matching, MS/MS fragmentation).
Output format — A short reasoning walkthrough, then a ranked table of candidate formulas with calculated mass, ppm error, and degree of unsaturation, ending with a one-line verification recommendation.
Guardrails
- Treat this as a hypothesis-generation aid, not a definitive result; recommend confirmation with dedicated MS software before relying on it.
- Do not fabricate peak values or isotopic ratios that weren't provided.
- Flag when the data given is too sparse to narrow down a formula confidently.
Example — {{ms_data}} = [M+H]+ at m/z 285.1234, M+1 isotope at 8.5% relative intensity; {{compound_or_sample_id}} = unknown metabolite from plasma extract; {{ionization_mode}} = ESI+; {{constraints}} = likely contains nitrogen.
Open this prompt Analysis · Advanced
Interpret Spectroscopic Data For Isomers
Use this when you have NMR, IR, or mass spectrometry data and need help identifying and comparing isomers.
Role — You are a spectroscopy analyst who helps chemists interpret NMR, IR, mass spectrometry, or UV-Vis data to distinguish between isomers.
Context you provide
- {{molecule_or_compound}} — the molecule or compound under investigation
- {{spectroscopic_data}} — the actual data, peak values, or spectrum description you paste in
- {{technique_used}} — which method the data comes from, such as NMR, IR, mass spec, or UV-Vis
- {{candidate_isomers}} — the specific isomers you suspect might be present, if known
Instructions
- Ask for {{spectroscopic_data}} and {{technique_used}} if not provided; do not proceed without actual data.
- Interpret the key peaks, shifts, or fragmentation patterns in {{spectroscopic_data}} relevant to identifying isomers.
- Explain how these features distinguish between {{candidate_isomers}}, or between plausible isomer types if none were named.
- State your confidence level and what additional data, if any, would confirm the identification.
- Note the structural or electronic reasoning behind the distinguishing features.
Output format — A short interpretation summary, then a table matching key data features to structural conclusions, ending with a confidence and next-steps note. Under 320 words.
Guardrails — Only interpret the data actually provided; do not invent peak values or spectral features. State uncertainty clearly rather than asserting a single definitive isomer without sufficient evidence. Recommend confirmatory techniques when the data is ambiguous.
Example — molecule_or_compound: a substituted cyclohexane derivative; spectroscopic_data: pasted NMR chemical shifts and coupling constants; technique_used: 1H NMR; candidate_isomers: cis and trans forms.
Open this prompt Analysis · Advanced
Interpret Spectroscopic Data For Stereochemistry
Use this when you have NMR or other spectroscopic data and need a reasoned interpretation of a molecule's stereochemistry.
Open this prompt Analysis · Advanced
Interpret Bond Angle And Length Data
Use this when you have crystallography measurements for a molecule and need help interpreting bond angles and lengths and what they imply structurally.
Open this prompt Analysis · Advanced
Interpret IR And NMR Peak Data
Use this when you have IR and NMR peak values and want a reasoned hypothesis on the functional groups they suggest.
Open this prompt Research · Advanced
Plan Molecular Modeling Analysis
Use this when you need to reason through a molecular modeling question and plan which computational method to run in dedicated software.
Open this prompt Research · Advanced
Protein Structure Prediction
Use this when you need to predict the 3D structure of a protein from its amino acid sequence.
Open this prompt Analysis · Advanced
Small Molecule Docking Studies
Use this when you need to analyze the interaction between small molecules and target proteins to understand binding affinity and mode of action.
Open this prompt Analysis · Advanced
Analyze Molecular Dynamics Simulation Results
Use this when you need to interpret molecular dynamics simulations to understand molecular behavior and interactions.
Open this prompt Analysis · Advanced
Analyze X-ray Crystallography Data
Use this when you need to process and interpret X-ray diffraction data to determine the 3D structure of a crystallized molecule.
Open this prompt Analysis · Advanced
NMR Spectroscopy Data Interpretation
Use this when you need to interpret NMR spectra to determine the structure and dynamics of molecules in solution.
Open this prompt Analysis · Advanced
Analyze Electron Microscopy Images for 3D Structures
Use this when you need to process and analyze electron microscopy images to determine macromolecular structures.
Open this prompt Analysis · Advanced
Predict Protein Structures via Comparative Genomics
Use this when you need to analyze protein sequences and predict structures using evolutionary relationships.
Open this prompt Analysis · Advanced
Design Drugs with Structure-Based Methods
Use this when you need to design or optimize drug candidates based on the molecular structure of a target protein.
Open this prompt Creating · Advanced
Protein-Ligand Interaction Analysis
Use this when you need to analyze protein-ligand interactions to understand binding affinity and specificity.
Open this prompt Analysis · Advanced
Compare Protein Structures
Use this when you need to analyze and compare protein structures to understand their function, evolution, or the impact of mutations.
Open this prompt Analysis · Advanced
Enzyme Engineering via Molecular Modeling
Use this when you need to design or engineer enzymes with improved catalytic properties using molecular modeling and mutation analysis.
Open this prompt Analysis · Advanced
Identify Drug Targets via Structural Genomics
Use this when you need to identify and prioritize potential drug targets from protein 3D structures using structural genomics data.
Open this prompt Analysis · Advanced