Glossary
Short answer: This glossary explains the chemistry and file terms used in MolDraw, from SMILES and InChI to wedge bonds, formal charge and Tanimoto similarity. Each term links to the docs page that shows how to use it.
Terms are in alphabetical order. Each row links to the page that covers the feature. For the chemistry behind a term, the MolDraw blog has longer guides, such as formal charge and hybridization, stereoisomers and arrow pushing.
| Term | Meaning | Docs page |
|---|---|---|
| Abbreviation | A short label, such as Ph, OMe or COOH, that stands for a whole group. MolDraw can expand known labels into full structures. | Read more |
| Aromatic ring | A flat ring with a closed loop of shared electrons, such as benzene. Aromatize shows it with an inner circle. Dearomatize brings back the double bonds. | Read more |
| Atom mapping | Numbers that link each atom in the reactants to the same atom in the products. Automap adds them for you. | Read more |
| Atomic orbital | A region where an electron is likely to be, drawn as s, p, d or hybrid lobes. | Read more |
| Ball and stick | A style that draws atoms as colored balls and bonds as sticks. MolDraw has it in 2D and in the 3D viewer. | Read more |
| Bond angle snap | The angle step new bonds snap to while you draw. 30 degrees suits ACS style and 15 degrees suits RSC style. | Read more |
| CAS number | A unique registry number for a substance, such as 50-78-2 for aspirin. Type it in the search box to draw the structure. | Read more |
| CDXML | The XML file format of ChemDraw. MolDraw opens and saves it, and also opens binary CDX files. | Read more |
| chemfig | A LaTeX package that draws structures from text code. MolDraw exports chemfig code for papers and theses. | Read more |
| CIP rules | The Cahn, Ingold and Prelog priority rules. They decide whether a stereocenter is R or S and a double bond is E or Z. | Read more |
| Clean up | An action that tidies a drawing: even bond lengths, standard angles and neat rings. | Read more |
| CML | Chemical Markup Language, an XML format for molecules. It is one of the download formats. | Read more |
| Command palette | A search box for every editor command. Press Ctrl+K or Cmd+K to open it. | Read more |
| Curved arrow | An arrow that shows a pair of electrons moving in a mechanism, from a lone pair or bond to an atom or bond. | Read more |
| Dative bond | A bond where both electrons come from one atom, common in metal complexes. It is drawn as an arrow from donor to acceptor. | Read more |
| E/Z | Labels for the geometry of a double bond. Z means the higher priority groups are on the same side. E means opposite sides. | Read more |
| Equilibrium arrow | A pair of half arrows pointing both ways. It shows a reaction that runs in both directions. | Read more |
| Exact mass | The mass of a molecule made of the most common isotope of each element. Mass spectrometry uses it. | Read more |
| Explicit hydrogen | A hydrogen drawn as its own atom with a bond. Add H adds them to the selected atoms. | Read more |
| Fishhook arrow | A curved arrow with a half head. It shows one electron moving, as in radical reactions. | Read more |
| Formal charge | The charge on one atom, found by comparing its valence electrons with the electrons it owns in the drawing. It shows as a plus or minus next to the atom. | Read more |
| Hash bond | A bond drawn as short lines that widen toward one end. It points away from the viewer, behind the page. | Read more |
| Implicit hydrogen | A hydrogen that is not drawn but is understood from the atom valence. Skeletal formulas leave C to H bonds implicit. | Read more |
| InChI | The IUPAC International Chemical Identifier, a text string that describes a structure in a standard way. | Read more |
| IUPAC name | The systematic name of a compound under IUPAC rules. Info looks it up for the selected structure. | Read more |
| Lewis structure | A drawing that shows every atom, every bond and every lone pair. Structure display can switch the canvas to it. | Read more |
| logP | The log of how a compound splits between octanol and water. Higher values mean the compound prefers fat over water. | Read more |
| Lone pair | Two valence electrons on one atom that are not in a bond. They are drawn as two dots or a short bar. | Read more |
| MEP | Molecular electrostatic potential. A colored surface shows where a molecule is electron rich (red) or electron poor (blue). | Read more |
| Microspecies | One protonation form of a molecule. Which forms exist depends on the pH. | Read more |
| MOL file | The MDL Molfile, a text format with atom coordinates and bonds. Most chemistry programs read it. | Read more |
| .moldraw file | The MolDraw design file. It keeps everything on the canvas, so you can open it and keep editing. | Read more |
| Molecular formula | The count of each element in a molecule, such as C9H8O4. It shows in Info and the status bar. | Read more |
| Molecular weight | The mass of one mole of a compound in g/mol, from average atomic masses. MW in the status bar. | Read more |
| PDB | The Protein Data Bank. It stores 3D structures of proteins and nucleic acids by a four character ID. | Read more |
| Point group | The set of symmetry operations a molecule has, such as C2v for water. | Read more |
| R group | A placeholder, such as R or R1, for any group at that position. It is used for general structures and series. | Read more |
| Radical | An atom with one unpaired electron, drawn as a single dot. | Read more |
| Repeat unit | The part of a polymer that repeats, drawn in brackets with n. | Read more |
| Resonance arrow | A double headed arrow between two drawings of the same molecule. It shows resonance forms, not a reaction. | Read more |
| Retrosynthetic arrow | An open arrow that points from a target back to simpler starting materials. | Read more |
| Ring fusion | Two rings that share a bond, as in naphthalene. Click a ring bond with a ring tool to fuse a new ring. | Read more |
| RXN file | The MDL reaction file. It stores reactants and products of one reaction. | Read more |
| SDF | Structure data file. It holds one or many molecules, each with optional data fields. | Read more |
| Skeletal formula | The usual organic drawing. Carbons sit at line ends and corners, and their hydrogens are not drawn. | Read more |
| SMARTS | A pattern language based on SMILES for searching substructures. It is one of the download formats. | Read more |
| SMILES | A one line text code for a structure, such as CCO for ethanol. Copy SMILES and Paste SMILES use it. | Read more |
| Stereocenter | An atom where swapping two groups gives a different stereoisomer. Most are carbons with four different groups. | Read more |
| Stoichiometry table | A table of equivalents, moles and masses for each reagent in a reaction. | Read more |
| Tanimoto similarity | A score from 0 to 1 that compares two molecules by their fingerprints. 1 means the fingerprints match. | Read more |
| Valence error | An atom with more bonds than it can have, such as a carbon with five bonds. Show errors marks it with an amber dot. | Read more |
| Wavy bond | A bond drawn as a wave. It means the stereochemistry at that position is unknown or mixed. | Read more |
| Wedge bond | A solid bond that widens toward one end. It points toward the viewer, out of the page. | Read more |
Tips#
- To try a term, open the editor and draw it. For example, draw a stereocenter and turn on R/S and E/Z labels in Settings.
- For SMILES rules, see the SMILES notation guide.
- For Tanimoto scores in more depth, read the similarity guide.
Questions and answers
What is the difference between SMILES and InChI?
Both are one line text codes for a structure. SMILES is short and easy to type. InChI is a standard identifier that gives one string per compound.
What is the difference between a wedge and a hash bond?
A wedge points toward you, out of the page. A hash points away from you, behind the page.
What is a skeletal formula?
A drawing where carbons sit at line ends and corners and their hydrogens are not drawn. It is the usual way to draw organic molecules.
What does an R group mean in a structure?
R is a placeholder for any group at that position. R1, R2 and so on mark different positions.
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