MolChart User's Manual

Everything in the editor, from first bond to export · open MolChart

MolChart is a chemical structure editor with two ways of working, and they mix freely:

• Describe it — type what you want into the AI assistant ("draw caffeine", "add a chlorine at position 4") and it draws, edits, and verifies the structure against PubChem.
• Draw it — a ChemDraw-style palette of bond, atom, ring, chain, arrow and text tools, with keyboard shortcuts for all of it.

This manual covers both, with the emphasis on hand drawing. Each section stands on its own.

Getting started

Open molchart.com. No install and no account are needed to draw and export.

• The left toolbar holds the drawing tools: selection, eraser, atoms, bonds, rings, chain, text, and arrows.
• The canvas is the drawing area in the middle. The editor opens with the single-bond tool armed, so your first click already draws.
• The assistant panel on the right takes plain-English requests. Close it with the × and reopen it from the toggle on its edge.
• The menu bar (File, Edit, Analyze, View, Help) holds document handling, imports/exports, analysis, and display options.
• The status bar at the bottom shows the live formula, molecular weight, atom and bond counts of the document, the zoom control, and the display toggles (atom indices, hydrogens, lone pairs, grid).

Your drawing is kept as you work: anonymous drawings persist in the browser, and signing in saves named documents to your account (Ctrl+S, File → Save Document As).

Drawing bonds and chains

The bond tools (single, double, triple, wedge, hash, wavy) draw and retype bonds. The editor starts with the single-bond tool armed.

• Click empty canvas — draws a complete bond: two carbons joined by the armed bond type.
• Click an existing atom — sprouts a new bond and atom from it, placed at a sensible ~120° angle and standard bond length. Keep clicking the new end atom to grow a zig-zag chain.
• Drag from an atom — draws the bond in the direction you drag, so you control the angle.
• Click an existing bond — retypes it to the armed tool (e.g. the double-bond tool makes it double). Clicking the same bond again cycles single → double → triple → single.
• Hover feedback — before you click, a ghost preview shows the bond a click would draw.
• Wedge (solid) and hash (dashed) bonds show stereochemistry: wedge points toward the viewer, hash away. The narrow end sits at the stereocentre. Wavy means undefined. Draw them from the stereocentre outward, or retype an existing bond with the wedge/hash tool. Analyze → Show Stereochemistry labels R/S and E/Z so you can check the result.
• Chain tool (zig-zag icon under DRAW) — press it and drag across the canvas to draw a whole alkyl chain in one gesture; the chain follows the drag with proper zig-zag geometry. Each new chain needs its own drag.
• Joining fragments — with the Select tool, drag an atom of one fragment onto an atom of another: the two fragments merge into one molecule joined by a single bond. There is no separate "join" tool.

Keyboard: 1 single bond, 2 double bond, T triple bond.

Atoms and elements

• Element hotkeys — press a key, then click the canvas to place that atom, or click an existing atom to change it: C carbon, N nitrogen, O oxygen, S sulfur, P phosphorus, F fluorine, L chlorine, I iodine, H hydrogen, K potassium, A sodium, R R-group, X halide placeholder. If an atom is already selected, pressing the key changes that atom immediately.
• B is benzene, not boron or bromine — see Rings. For bromine and every other element, use the periodic table or the label editor below.
• Atom palette — the ATOMS section of the toolbar has C, N, O, S, H one click away; the … button opens the full periodic table to pick any element.
• Placing vs changing — with an atom tool armed, clicking empty canvas drops one atom; clicking an existing atom changes its element. After dropping an atom the editor returns to the single-bond tool so you can keep drawing.
• Inline label editor — double-click any atom to open a small text box on it. Type an element symbol (Br, Si, Fe), or a group abbreviation, and press Enter. This is the quickest way to any element that has no hotkey.
• Group abbreviations — type a multi-letter abbreviation (in the label editor, or just on the keyboard with nothing selected) and it expands to the real group: Me, Et, Pr, iPr, Bu, tBu, Ph, Bn, Vinyl, Allyl, Cy, Tol, Mes, Boc, Cbz, Ac, Bz, Ts, Ms, TMS, OMe, OEt, OH, NH2, NO2, CN, CF3, COOH, CHO and many more. Edit → Change Element... does the same from the menu.

Hydrogens, charges, and lone pairs

Why a lone O shows as OH₂: MolChart fills every atom to its standard valence with implicit hydrogens, the way chemists draw skeletal structures — a bare oxygen atom therefore renders as OH₂, a nitrogen as NH₃, and a terminal carbon as CH₃/CH₄. Those hydrogens are implicit: they disappear as you draw real bonds to the atom.

• Pin the hydrogen count — select the atom (or the whole molecule) and press Ctrl+H to add a drawn hydrogen or Ctrl+Shift+H to remove one (Edit → Add Hydrogen / Remove Hydrogen). Removing down to 0 gives a truly bare atom — "just an O". The pinned count sticks: it survives bonding and exports as bracket SMILES ([O]). Nudging the count back to the normal valence value releases the pin, and the atom goes back to automatic hydrogens.
• Show or hide H atoms — the H toggle in the bottom status bar switches between condensed labels (OH, NH₂) and explicitly drawn H atoms with their bonds. This changes the display only, never the structure.
• Charges — select one or more atoms and press + or - (Edit → Increase Charge / Decrease Charge). Charges adjust the automatic hydrogen count the chemically correct way: O⁻ carries no H where OH would, N⁺ takes four bonds.
• Lone pairs — press Ctrl+. to add a lone pair to the selected atom and Ctrl+, to remove one (Edit → Add Lone Pair / Remove Lone Pair). The dots toggle (: in the status bar, or the assistant's Lewis-structure commands) shows computed lone pairs on every atom; the counts come from valence electrons, bonds and formal charges, and a manual edit overrides the computed number for that atom.

Rings

The RINGS toolbar section has cyclopropane through cyclooctane plus benzene, and the … button opens more templates: cyclopentadiene, pyridine, pyrrole, furan, thiophene, imidazole, pyrimidine, naphthalene, indole.

• Click empty canvas — drops the ring there.
• Click an existing bond — fuses the ring onto that bond (benzene onto benzene gives naphthalene), on the side with free space, keeping every bond at standard length.
• Click an existing atom — attaches the ring to that atom by a new bond.
• Hover shows a ghost of exactly what a click would add. After dropping a ring the editor returns to the single-bond tool.

Keyboard: 3 4 5 6 7 8 pick the 3- to 8-membered carbocycle, B picks benzene.

Selecting and editing

• Select tool (V, or Escape from any tool) — click an atom or bond to select it; drag a marquee over a region; drag a selected atom or molecule to move it.
• Select several — Shift+click each object to add it to (or remove it from) the selection, drag a marquee around them, or press Ctrl+A for everything. Align needs two or more selected objects; Distribute needs three.
• Lasso tool — draw a freehand loop; exactly the atoms inside it are selected, even across several molecules. A loop around a whole molecule selects the molecule.
• Delete (Del) removes the selection — only the selected atoms/bonds, not the whole molecule (unless the whole molecule is selected).
• Eraser (E) — click an atom to remove it with its bonds, or a bond to remove just the bond, leaving its atoms.
• Escape cancels the gesture in progress and returns to the Select tool.
• Undo / Redo — Ctrl+Z / Ctrl+Y, with a deep history.
• Cut / Copy / Paste — Ctrl+X / Ctrl+C / Ctrl+V work on the selection; Ctrl+A selects everything.
• Duplicate (Ctrl+D, Object → Duplicate) — copies the selection just down-right of the original and selects the copy: draw a reactant once, duplicate it, edit the copy into the product.
• Flip (Ctrl+Shift+F horizontal, Ctrl+Shift+U vertical; Object → Flip Horizontal / Flip Vertical) — mirrors the selection about its own centre. Several selected objects flip as one group, so a scheme keeps its footprint. Wedges and hashes swap on flip, so the drawing still shows the same enantiomer, not its mirror image. A lassoed group of atoms flips within its molecule.
• Align (Object → Align Left / Center / Right / Top / Middle / Bottom) — with two or more objects selected, lines them up on that edge or centre line. Alignment uses the drawn atoms, arrow ends and text boxes, so bond ends really meet the same line.
• Distribute (Object → Distribute Horizontally / Vertically) — with three or more objects selected, keeps the outer two where they are and makes the gaps between neighbours equal. Together with Align this is how to tidy a multi-step scheme: align the middles, then distribute horizontally.
• Nudge (arrow keys; Shift+arrows for 10 units) — moves the selection one canvas unit at a time for fine alignment. A held key repeats and counts as one undo step.
• Cleanup (bottom bar, or Object → Clean Up Structure, Ctrl+Shift+K) tidies bond lengths and angles after heavy editing; Align Reaction (Object menu, Ctrl+Shift+R) lays out reactants, arrow and products in a line; Check validates valences.

Keyboard shortcuts

Keys	Action
1 / 2 / T	Single / double / triple bond tool
3–8	3- to 8-membered ring
B	Benzene ring
C N O S P F L I H K A R X	Element (L = Cl, A = Na) — places an atom, or changes the selected one
Me, Et, Ph, tBu, … (typed)	Expand a group abbreviation
V	Select tool
G	Hand (pan) tool
E	Eraser
+ / -	Raise / lower formal charge on selection
Ctrl+H / Ctrl+Shift+H	Add / remove a drawn hydrogen (pins the count)
Ctrl+. / Ctrl+,	Add / remove a lone pair
Ctrl+Z / Ctrl+Y	Undo / redo
Ctrl+X / Ctrl+C / Ctrl+V	Cut / copy / paste
Ctrl+A	Select all
Shift+Click	Add / remove an object in the selection
Ctrl+D	Duplicate selection
Ctrl+Shift+F / Ctrl+Shift+U	Flip selection horizontally / vertically
Arrows / Shift+Arrows	Nudge selection by 1 / 10 units
Ctrl+Shift+C	Copy image for Word / Office
Del	Delete selection
Ctrl+N / Ctrl+O / Ctrl+S	New / open / save document
Ctrl++ / Ctrl+-	Zoom in / out
Escape	Cancel gesture, back to Select
Space or Shift + drag, middle drag	Pan the canvas from any tool (a Shift+click without dragging selects instead)
Wheel / Shift+Wheel	Pan up-down / left-right

Help → Keyboard Shortcuts shows this list inside the app.

View options

• Zoom — the − / + control in the status bar, Ctrl++ / Ctrl+- , or View → Zoom In / Zoom Out / Fit to Window / 100%.
• Panning — hold Space or Shift and drag, drag with the middle mouse button, use the mouse wheel (Shift+Wheel pans sideways), or arm the Hand tool with G and drag.
• Status-bar toggles — # atom indices, H explicit hydrogens, : lone-pair dots, Grid the background grid. All are display-only.
• 3D viewer — View → View 3D... (or ask the assistant) renders the current molecule in 3D: ball-and-stick, space-fill, or stick style, rotatable with the mouse.
• Protein and crystal structures — Analyze → Protein Structure (PDB)... loads any PDB entry; Analyze → Crystal Structure (COD)... loads crystallographic structures.

Arrows, text, and reactions

• Resize or re-aim an arrow — select it and drag the small square handle at either end; the other end stays put. Straight arrows snap to 15° steps like the drawing tool. The round corner handles rotate the arrow instead.
• Arrows — the ARROWS toolbar section has forward, equilibrium, resonance, retrosynthesis and no-go arrows, plus curved arrows and fishhook (single-electron) arrows for mechanisms. Pick one, then click (or drag) on the canvas. Select an arrow to recolour it or change its width.
• Text labels — the T tool (or Edit → Text Label) places free text; the TEXT section of the toolbar sets font, size and colour. Use text for annotations — put charges on atoms, not in labels.
• Reactions — lay out reactants and products left to right with a forward arrow between them (the assistant's "draw the reaction of X with Y" does the whole scheme in one go). Analyze → Interpret Reaction reads the scheme back; Show Reaction Roles labels reactants, reagents and products.

Import and export

All under the File menu:

• Import — Import SMILES..., Import MOL / SDF / CDX / CDXML... (ChemDraw files), Import by Name... (name → structure via PubChem).
• Export — PNG or SVG images (cropped to the drawing), MOL, SDF, CDXML or CDX files, and Copy as SMILES for the clipboard.
• Copy for Word / Office (Ctrl+Shift+C, Edit menu) — puts the selection (or the whole drawing when nothing is selected) on the clipboard as a high-resolution picture, ready to paste into Word, PowerPoint, Google Docs or LibreOffice. Word places it at page width; drag a corner to shrink it, and it stays sharp because the picture is 2000 pixels across. The picture is a bitmap, so it is not editable inside Word; to get an editable drawing back, keep the MolChart document or a CDX/CDXML export. On plain-http hosts and older browsers the image is downloaded as a PNG instead (Insert → Pictures in Word).
• PNG files remember their drawing — every PNG MolChart exports (Export as PNG, or the Copy-for-Word download) carries the structures inside it. File → Import MOL / SDF / CDX / CDXML... accepts such a PNG and restores the editable drawing; pasting the PNG file onto the canvas does the same. A PNG re-saved by another program usually loses that data.
• Structures with pinned hydrogen counts export faithfully: a bare oxygen is [O] in SMILES, and bracket-atom SMILES imports keep their hydrogen counts instead of refilling.

Analysis tools

Under the Analyze menu:

• Check Structure — valence and sanity check of everything on the canvas.
• Structure to Name — IUPAC/common name of the drawn molecule.
• Show Stereochemistry — assigns and labels R/S centres and E/Z double bonds from your wedges.
• Property Calculator... — molecular weight, formula, physicochemical properties and drug-likeness, plus tabs for tautomer enumeration, charge distribution, and substituent effects.
• Search by Structure... — look the drawn structure up in PubChem.

The AI assistant

The panel on the right takes plain English and can do nearly everything in this manual for you: draw from a name, SMILES or description; edit ("replace the OH with Cl", "make that bond a double bond"); build reaction schemes; toggle the display; open the 3D viewer; and check its own work — structures are verified against PubChem before it reports success.

Tips for good results:

• Name the thing: "draw ibuprofen" beats describing it atom by atom.
• Refer to atoms by their number (turn on # in the status bar) — "add a methyl at atom 3".
• It can teach: ask "how do I draw a wedge bond by hand?" and it answers from this manual.
• Free usage: 30 assistant prompts per day (100 total) without an account; a free account raises this to 100 per day / 200 per month; membership removes the limits. Drawing by hand is never limited.

Documents and accounts

• Anonymous — your canvas persists in the browser between visits. Signing up transfers the current drawing into your first saved documents automatically.
• Signed in — File → New / Open / Rename / Save Document As / Delete manage named documents stored in your account; Ctrl+S saves.
• Report Issue... under the Help menu sends a bug report straight to the developers.