Blog
Chemistry workflows, cheminformatics insights, and updates from the ChemStitch team.
Buchwald–Hartwig Conditions: How to Choose Ligand, Base, and Solvent
How to choose Buchwald–Hartwig conditions: ligand, base, and solvent starting points by amine type, base sensitivity, and electrophile, and when to screen.
How to Check If a Retrosynthesis Route Has Literature Precedent
How to check if a retrosynthesis route has literature precedent: grade each step direct, analogous, or class-only using Reaxys, SciFinder, and patents.
What Goes Above and Below the Arrow in a Reaction Scheme
What goes above and below the arrow in a reaction scheme: reagents and equiv above, solvent and temperature below, yield under the product, one-pot rules.
Canonical vs Isomeric SMILES: Why They're Not Opposites
Canonical SMILES vs isomeric SMILES aren't opposites; they're independent axes. When to use each, and why canonical is only canonical per toolkit.
MOL File to SMILES: What Survives the Conversion and What Doesn't
Convert a MOL file to SMILES cleanly: what survives, what drops (coordinates, SDF fields, stereo), and how to verify the round-trip in RDKit.
MOL V2000 vs V3000: When the 999-Atom Limit Forces the Upgrade
The MOL V2000 vs V3000 difference, decided: the 999-atom limit, enhanced stereo, and R-groups, plus which format to export for each job.
The Dot in a SMILES: Writing Salts, Counterions, and Mixtures Correctly
Writing a SMILES for a salt with the dot: charge placement, stoichiometry by repeating fragments, hydrates, and canonical ordering for dedup.
Choosing the Limiting Reagent in Organic Synthesis: Cost, Scarcity, and Workup Trade-offs
Choosing the limiting reagent in organic synthesis: how cost, scarcity, workup burden, and kinetics decide which reactant to make limiting.
Get an InChIKey from a SMILES - and Use It to Search a Database
Get an InChIKey from a SMILES: generate the 27-character key, search PubChem with the full key or the 14-char connectivity block, avoid the one-way trap.
Calculating Reagent Volume from Density: Equivalents to Microliters in Organic Synthesis
Calculate reagent volume from density in organic synthesis: the equivalents-to-microliters formula, a worked triethylamine example, and where it breaks.
Salt-Form and Free-Base Correction in Stoichiometry: Why Your HCl Salt Needs More Mass
Salt-form and free-base correction in stoichiometry: weigh an HCl salt or hydrate against the right MW, with a worked example and the base gotcha.
SMILES to Structure Online: Paste a String, Edit It in Your Browser
Convert SMILES to a structure online, client-side and editable, with located parse errors. No install; your string never leaves the browser.
How to Interpret a logP Value (and the Estimator Trap)
How to interpret a logP value: the 1-3 oral sweet spot, the >1 log-unit estimator-disagreement trap, and the solubility-permeability tradeoff.
Lipinski Rule of Five Explained: A Worked Pass/Fail Walkthrough
Lipinski Rule of Five explained: the four thresholds, a worked aspirin and atorvastatin pass/fail, and when one violation is fine.
Predicting Ionization State at Physiological pH from pKa
Predicting ionization state at physiological pH from pKa: the Henderson-Hasselbalch fraction-ionized formula worked for an acid and a base at pH 7.4.
TPSA and Permeability: Reading the 140 and 90 Thresholds
What TPSA (topological polar surface area) is, how Ertl computes it from 2D, and reading the 140 oral and 90 CNS permeability thresholds.
Wedge and Dash Stereochemistry Drawing Conventions
Wedge and dash stereochemistry drawing conventions: where the narrow end goes, and how to make your 2D drawing agree with R/S and the SMILES descriptor.
Can AI Predict Reaction Products? What It Gets Right, and Where It Hallucinates
Can AI predict organic reaction products reliably? An honest breakdown of where it works, where it hallucinates, and a chemist's verification workflow.
Choosing the Strategic Disconnection: How to Choose a Disconnection in Retrosynthesis
How to choose disconnection in retrosynthesis: rank candidate bonds by skeleton simplification, reliable reactions, convergence, and availability.
Retrosynthesis Step by Step: Spotting Retrons and Choosing the Strategic Disconnection
How to do retrosynthesis step by step: map the target, spot retrons, cut the strategic bond, and turn synthons into real reagents.
Synthons vs Synthetic Equivalents: The Distinction That Makes a Route Executable
Synthon vs synthetic equivalent explained: a reference table mapping each idealized fragment to the real reagent you order, plus the translation procedure.
Umpolung: How to Recognize a 1,2- or 1,4-Target That Needs Polarity Inversion
Umpolung is polarity inversion in synthesis. Learn when to use it: recognize dissonant 1,2- and 1,4-targets and the acyl anion equivalents.
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 mistakes in drug discovery labs: notation ambiguity, DMSO non-additivity, pipetting limits, salt form corrections, and mixing failures.
Preparing pH Buffers: Henderson-Hasselbalch in Practice
How to make buffers with Henderson-Hasselbalch: a worked acetate example, choosing a buffer by pH, Tris and HEPES temperature corrections, and bench 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 with purity corrections, multi-step yield, and loss troubleshooting.
Limiting Reagent Calculations for Organic Synthesis: Scale-Up Without Wasted Material
How organic chemists calculate limiting reagents with equivalents: a worked amide coupling example, purity corrections, scale-up, and multi-step yield.
Serial Dilution for Assay Standards: Getting the Math Right Every Time
How to design serial dilutions for standard curves: choosing a dilution factor, a worked ELISA example, error propagation, mixing, and curve quality checks.
Molarity Calculations in the Lab: From Powder to Working Stock
Calculate molarity from molecular weight step by step: worked examples, salt form corrections, purity adjustments, and common bench mistakes to avoid.