Blog
Chemistry workflows, cheminformatics insights, and updates from the ChemStitch team.
Reading SMILES Valence Errors: Which Atom Is Wrong and Why
A SMILES invalid valence error flags one overbonded atom. Read the message and fix the charge, bracket, or typo behind each common case.
From SMILES to InChI and InChIKey: Which Identifier to Use When
Convert SMILES to InChI and InChIKey, and know which to store: what each format preserves, the one-way hash, and the tautomer-normalization trap.
Why Your SMILES Won't Kekulize: Fixing the [nH] Nitrogen and Other Parse Errors
SMILES can't kekulize? Usually it's the [nH] aromatic nitrogen. A chemist's guide to the parse errors that stop a SMILES rendering, and how to fix each.
SMILES to Structure: Paste a String, Get an Editable Molecule
Paste a SMILES to structure and get a clean, editable molecule, then copy back a corrected SMILES, InChI, or InChIKey. A chemist's how-to round-trip.
Reagent Purity Corrections: When 95% Pure Means You Need More Mass
Purity correction for reagent stoichiometry: the formula, when to apply it (95% boronic acids, NaH dispersions, hydrates), three worked examples.
Reaction Concentration: Choosing Solvent Volume for an Organic Reaction
Choose reaction concentration for organic synthesis: typical range, the intramolecular vs intermolecular rule, and a path for unfamiliar reactions.
Scaling Up an Organic Synthesis: Where Linear Stoichiometry Stops Working
Scale up an organic synthesis without breaking it. What scales linearly, what does not (mixing, heat, concentration), and a Suzuki worked example.
Building a Reagent Table for Organic Synthesis: From Reaction Sketch to Bench-Ready List
Build a reagent table for organic synthesis: equiv, mmol, mass, volume columns. Worked Suzuki example. Spreadsheet vs ELN vs dedicated tool trade-offs.
From Milligrams to Millimoles: MW Conversions with Purity, Salt, and Hydrate Corrections
Convert mass to mmol from molecular weight with purity, salt-form, and hydrate corrections. Worked 4-bromobiphenyl example and precision-by-scale table.
How to Calculate Mol Percent Catalyst Loading: From Equivalents to Weighable Milligrams
Calculate mol percent catalyst loading from limiting reagent scale and catalyst MW. Worked Suzuki example, mol ppm regime, sub-2-mg weighing rule.
Retrosynthetic Analysis Tools: What Medicinal Chemists Are Using in 2026
Retrosynthesis software for med chem: decision tree by data sensitivity, chemistry scope, and ELN integration — with named tools and on-prem options.
InChI vs SMILES: When to Use Which Chemical Identifier Format
InChI vs SMILES: SMILES round-trips structures fast; InChIKey is the universal database key. Decision rules by workflow plus the stereo gotcha to avoid.
Atom Economy and E-Factor: Green Chemistry Metrics for Synthetic Routes
Atom economy and E-factor measure design separately from yield. Worked examples on Diels-Alder, Wittig, and route comparison for medicinal chemists.
SMILES Notation to Structure Converter: A Chemist's Reference for Reading and Debugging
SMILES syntax explained: graph traversal, brackets, ring closures, stereochemistry, plus tool comparison for SMILES-to-structure converters.
How to Balance a Chemical Equation for Synthesis: Half-Reactions and Cascade Balancing
Balancing equations for synthesis: oxidation states, half-reactions for redox, multi-step cascades. With worked examples for organic chemistry.
How to Draw Chemical Structures for Reports: Publication-Quality Software Compared
Drawing chemical structures for reports: ACS conventions, paste-and-edit workflow, tool comparison from ChemDraw to web-native editors.
Reaction Mode for Synthesis Planning: Tools That Think in Mechanisms, Not Just Structures
Synthesis-planning software covers three different jobs: retrosynthetic search, forward prediction, and reaction capture. Pick the right one.
Cumulative Yield in Multi-Step Synthesis: Where the Losses Come From
Calculating theoretical yield in multi-step synthesis is more than multiplying step yields. Where the losses actually come from, with a worked route.
Preparing 1 mM Stock Solutions from Solid Compound: Corrections That Matter
Preparing 1 mM stock solutions from solid compound: salt-form MW, purity, DMSO density, and weighing pitfalls with a full worked example.
Equivalents in Organic Chemistry: Calculating Reagent Ratios for Your Reaction
How to calculate equivalents in organic chemistry: reagent tables, density, salt-form fixes, theoretical yield, full worked amide coupling.
Dilution Factor Calculations: C1V1=C2V2 and When It Breaks Down
Five common dilution calculation mistakes in drug discovery labs: notation ambiguity, DMSO non-additivity, pipetting limits, salt form corrections, and mixing failures. Worked dose-response example included.
Preparing pH Buffers: Henderson-Hasselbalch in Practice
How to make buffer solutions using Henderson-Hasselbalch: worked acetate buffer example, buffer system selection by pH range, temperature corrections for Tris and HEPES, ionic strength effects, and common bench preparation mistakes.
Calculating Percent Yield: Why Your Reaction Gave Less Than Expected
How to calculate percent yield in organic synthesis: the formula, a worked amide coupling example with purity corrections, cumulative multi-step yield, loss troubleshooting, and reaction type benchmarks.
Limiting Reagent Calculations for Organic Synthesis: Scale-Up Without Wasted Material
How organic chemists calculate limiting reagents using equivalents: worked amide coupling example, purity corrections, scale-up considerations, and multi-step cumulative yield.
Serial Dilution for Assay Standards: Getting the Math Right Every Time
How to design and execute serial dilutions for standard curves: dilution factor selection, worked ELISA example, error propagation, mixing discipline, and curve quality checks.
Molarity Calculations in the Lab: From Powder to Working Stock
Step-by-step guide to calculating molarity from molecular weight, with worked examples, salt form corrections, purity adjustments, and common bench mistakes to avoid.