Spectra & Analysis
Exact Mass / Isotope Pattern
Calculate monoisotopic exact mass and an approximate M, M+1, M+2 isotope pattern from molecular formulas.
ChemistryAtlas Apps Hub
Spectra, chromatography, mass spectrometry, and analytical chemistry tools
Use ChemistryAtlas tools for exact mass, isotope patterns, NMR prediction, MS fragments, LC-MS or GC-MS helpers, chromatography planning, IR/Raman/UV-Vis interpretation, electrochemistry, and polymer analysis.
These tools help confirm structures, interpret analytical data, and translate raw or peak-list results into useful chemistry decisions.
Spectra and Analysis Tools
These tools help confirm structures, interpret analytical data, and translate raw or peak-list results into useful chemistry decisions.
What this hub covers
The Spectra and Analysis hub brings together confirmation workflows for synthetic, analytical, polymer, biomolecular, electrochemical, and chromatography work.
Common workflows
- Check exact mass, isotope envelope, likely adducts, fragments, and expected NMR or vibrational features.
- Plan TLC, flash, HPLC, GC, LC-MS, and GC-MS workups and interpret peak tables.
- Analyze electrochemistry, polymer molecular weights, peptide sequences, optical purity, and raw analytical files.
Related ChemistryAtlas pages
Featured tools in this workflow
Spectra & Analysis
1H / 13C NMR Predictor
Generate first-pass 1H and 13C NMR environment bins from RDKit structures.
Spectra & Analysis
MS Fragmentation Predictor
Generate exact-mass molecular ions and rule-based neutral-loss fragment hints.
Spectra & Analysis
Spectroscopy Predictor
Detect functional groups and report IR/Raman/UV-Vis quick-look features.
Spectra & Analysis
Chromatography Method / Retention Helper
Estimate C18/normal-phase retention behavior and practical TLC/HPLC adjustment guidance from RDKit descriptors.
Spectra & Analysis
Conformer Generator + 3D Viewer
Generate downloadable RDKit ETKDG/UFF conformers as SDF plus summary records.
Spectra & Analysis
Partial Charges / ESP Map
Calculate atom-level RDKit Gasteiger partial charges and charge-summary records.
Spectra & Analysis
QM Input Generator
Generate RDKit 3D geometries, Gaussian/ORCA/Psi4/xTB input files, command manifests, and geometry-opt workflow scripts.
Spectra & Analysis
Frontier Orbital + Reactivity Estimator
Estimate frontier/reactivity fields from RDKit charges and export xTB-ready inputs for real HOMO/LUMO/Fukui calculations.
Spectra & Analysis
Reaction Energetics / Thermo Setup
Check reaction balance, atom economy, delta-G equilibrium, and generate optional xTB thermo/TS-guess workflow manifests.
Spectra & Analysis
Analytical Calibration + Method Validation Suite
Fit calibration curves, compare forced/non-forced intercepts, calculate residuals, LOD/LOQ, and back-calculate unknown concentrations.
Spectra & Analysis
GC/HPLC Internal Standard Yield Calculator
Calculate assay amount, purity, and reaction yield from analyte/internal-standard peak areas, response factor, dilution, and reaction scale.
Spectra & Analysis
Chromatogram Peak Analyzer
Process chromatogram CSV traces into peak retention time, area, height, width, tailing, plates, and resolution metrics.
Spectra & Analysis
Ion Chromatography / HPLC Method Troubleshooter
Turn analyte, column, eluent, pH, retention, and peak-shape symptoms into method-development troubleshooting actions.
Spectra & Analysis
Unknown Ion / Qualitative Analysis Assistant
Rank possible ions from qualitative-test observations, colors, precipitates, solubility in ammonia/acid/base, and flame tests.
Spectra & Analysis
UV-Vis Quantification + Mixture Deconvolution
Run Beer-Lambert calibration, unknown concentration, or two-component UV-Vis mixture deconvolution from absorbance data.
Spectra & Analysis
Assay / Dose-Response Analysis
Estimate IC50/EC50, Hill slope, normalized response, Z-prime, and plate-map QC from dose-response CSV data.
Spectra & Analysis
NMR Data Processor
Process JCAMP-style text or peak lists into normalized integrals, coupling/assignment hints, and predicted-vs-observed context.
Spectra & Analysis
LC-MS / GC-MS Raw Data Helper
Parse peak lists or simple mzML-style text for peak picking, adduct matching, extracted-ion windows, and purity estimates.
Spectra & Analysis
CV / EIS Electrochemistry Analyzer
Analyze cyclic voltammetry peak metrics and EIS Nyquist summaries from potential/current or frequency/Z CSV data.
Spectra & Analysis
Peptide / Protein Calculator
Compute peptide/protein sequence mass, pI, net charge, extinction coefficient, and trypsin digestion fragments.
Spectra & Analysis
Optical Rotation / Chiral HPLC / ee Calculator
Calculate specific rotation, rotation-derived ee, chiral HPLC enantiomer ratio, and ee from peak areas.
AI Spectra + Virtual Screening
AI MS/MS Predictor
Predict MS/MS fragments using ms-pred/ICEBERG sidecar when available or deterministic exact-mass losses locally.
AI Spectra + Virtual Screening
Spectrum Similarity Scorer
Score experimental vs predicted/library spectra with cosine similarity and matched-peak diagnostics.
AI Spectra + Virtual Screening
Candidate Structure Ranker
Rank candidate structures against formula, exact mass, spectrum hits, fragments, and property filters.
AI Spectra + Virtual Screening
Formula + Spectrum Elucidation
Combine formula constraints and MS/MS similarity to produce structure-elucidation candidate reports.
AI Spectra + Virtual Screening
PyScreener Docking Workflow
Prepare a docking workflow and call PyScreener sidecar when configured; otherwise emit runnable docking manifests.
AI Spectra + Virtual Screening
MolPAL Active-Learning Virtual Screening
Plan or run MolPAL-style active-learning virtual screening from docking scores and candidate libraries.
AI Spectra + Virtual Screening
Protein/Ligand Prep Checklist
Generate a protein/ligand preparation checklist for docking, protonation, waters, cofactors, grid box, and controls.
AI Spectra + Virtual Screening
Docking Result Ranker
Rank docking results with score, ligand efficiency, strain, alerts, diversity, and interaction notes.
AI Spectra + Virtual Screening
Docking-to-Design Loop
Convert docking hits into next design ideas with R-group/scaffold suggestions and active-learning priorities.