Tutorials
Everyday chemistry tasks, step by step, on Mac and Windows.
How to draw a chemical structure from SMILES
Turn a SMILES string into a clean 2-D structure drawing, with correct wedges for stereocentres, and copy canonical SMILES back from any drawing. Mac and Windows.
How to get the InChI and InChIKey of a molecule
Generate the standard IUPAC InChI and InChIKey of a drawn molecule, including stereo layers, and use them to look the compound up in PubChem. Mac and Windows.
How to draw wedge and hash bonds and check R/S
Draw solid wedge, hashed wedge and wavy bonds at a stereocentre, flip them, and check that the (R)/(S) assignment, SMILES and InChI match your drawing.
How to convert an IUPAC name to a structure, and a structure to a name
Draw a structure from its IUPAC name and generate the IUPAC name of a drawing, including (R)/(S) descriptors. Covers alcohols, amines, acids, esters, ethers, ketones, rings and substituted benzenes.
How to draw a reaction scheme with reagents and conditions
Draw a reaction scheme: reactants, products, plus signs and a reaction arrow with reagents above and solvent and temperature below. Equilibrium, retrosynthesis and curved mechanism arrows too.
How to calculate the limiting reagent and percentage yield
Work out moles, equivalents, the limiting reagent, theoretical yield and percentage yield straight from a drawn reaction scheme. Worked example: Fischer esterification of acetic acid.
How to calculate molecular weight, exact mass, TPSA and logP
Get the molecular formula, molecular weight, monoisotopic mass, TPSA, logP, H-bond donors and acceptors, pKa estimates and predicted NMR shifts of a drawn molecule.
How to simulate the isotope pattern of a molecule (mass spectrum)
Simulate the isotopic distribution of a molecule's molecular ion and read off M, M+1 and M+2 peaks. Worked example: the Br/Cl pattern of 1-bromo-4-chlorobenzene.
How to put chemical structures into Word, PowerPoint, Pages and Keynote
Copy crisp chemical structures into Word, PowerPoint, Pages and Keynote, or export vector PDF and SVG and 300–600 dpi PNG for papers, posters and slides.
How to view a molecule in 3-D from an SDF or MOL file
Open a 3-D SDF or MOL file, for example a PubChem conformer, and turn the molecule in an interactive ball-and-stick viewer.
Try it yourself. ChemPencil runs on macOS 12 and later and on Windows 10 and 11.