MoleBench

Guided tutorials

A hands‑on walkthrough of every MoleBench feature, grouped from basics to molecular orbitals. Each card opens the right molecule in the Studio — do the steps there, then come back for the next. No prior software experience needed.

Getting started

Build & visualize

Your first molecule

  1. Open the Studio and type ethane (or the SMILES CC) in the build bar; press Build molecule.
  2. On the 3D tab, drag to rotate, scroll to zoom. Try the style chips: ball & stick, stick, sphere, line, surface.
  3. Switch to the 2D tab to see the flat structure. Toggle ◌ spin on the 3D tab.
You should see: a 3‑D ethane (2 C, 6 H) and the Properties panel filling in MW ≈ 30 g/mol.
Open ethane → …or benzene

Draw your own

Sketch a structure + pick elements

  1. Click ✏️ Draw to open the sketcher. Use the bond/ring tools to draw a skeleton (all carbons).
  2. In the periodic table below the canvas, click an element (e.g. N or O), then click an atom in your sketch to change it.
  3. Press Use this structure → to send it to the Studio.
You should see: your drawn molecule build in 3D. The picked element recolors the atom (e.g. ethanol from a 2‑carbon chain + an O).
Open the sketcher →

Measure geometry

Bond lengths, angles & dihedrals

  1. Build water. Click the 📏 measure chip above the viewer.
  2. Click the two H atoms, then the O — clicking 3 atoms reports the H–O–H angle (~104°).
  3. Build butane and click the four carbons in a row for the C–C–C–C dihedral.
You should see: a water angle near 104°, an O–H bond near 0.96 Å if you pick two atoms.
Open water → Butane

Functional groups & library

Recognise groups & browse presets

  1. Build aspirin. Below the viewer, use the Highlight group chips to mark the ester and carboxyl groups on the 2D structure.
  2. Open the Molecule library panel and click a category (Everyday, Drugs & medicine, Aromatics…), then a molecule to load it.
You should see: aspirin's carbonyl/hydroxyl groups highlighted, and one‑click loading from the library.
Open aspirin →

Properties

Drug‑likeness

logP, TPSA & the rule of five

  1. Build ibuprofen. In the Properties panel read MW, cLogP, TPSA, H‑bond donors/acceptors, rotatable bonds.
  2. Check the Lipinski and Veber pass/fail flags.
  3. Compare with caffeine and aspirin.
You should see: ibuprofen passing the rule of five, computed instantly in your browser (RDKit).
Open ibuprofen → Caffeine

Quantum calculations

Optimize & energy

A real geometry optimization

  1. Build methanol (CO). In panel 2 · Quantum calculation, press Optimize & compute.
  2. The 3D view snaps to the GFN2‑xTB optimized geometry.
  3. Read the total energy, HOMO–LUMO gap and dipole.
You should see: a dipole ≈ 1.7 D for methanol. Try benzene (~0 D, nonpolar) for contrast.
Open methanol →

DFT & reactivity

B3LYP energies + reactivity indices

  1. Build acetone. In panel 2 press DFT (B3LYP) for a real density‑functional single point and note the dipole.
  2. Now set solvent = water (the picker next to "charge") and press DFT again — the dipole grows (the solvent reaction field polarises the molecule) and the result is labelled "water (implicit)".
  3. Below, read the Reactivity indices: electronegativity χ, hardness η, chemical potential μ, electrophilicity ω.
You should see: a B3LYP gas dipole ≈ 2.8 D rising to ≈ 3.3 D in water (PCM implicit solvation), plus conceptual‑DFT reactivity numbers.
Open acetone →

Advanced

Choose your own level of theory

  1. Build water. In panel 2 open ⚙️ Advanced.
  2. Pick a method (GFN2‑xTB / HF / B3LYP / PBE0 / M06‑2X), a basis set (STO‑3G … def2‑TZVP) and a task (energy / optimize), then Run.
  3. Compare the total energy as you change method & basis.
You should see: the energy shift as you climb the ladder of theory — a hands‑on feel for why level of theory matters.
Open water →

Implicit solvation

Put your molecule in a solvent

  1. Build acetone. In panel 2, with solvent = gas phase, press DFT (B3LYP) and note the dipole.
  2. Change the solvent picker (next to "charge") to water and press DFT again — the result is labelled "water (implicit)" and the dipole grows as the solvent's reaction field polarises the molecule.
  3. Solvation applies to Optimize, DFT, IR and the reactions panel too (xtb ALPB / Psi4 PCM, 9 solvents). Try water vs DMSO vs gas.
You should see: acetone's dipole rise from ≈ 2.8 D (gas) to ≈ 3.3 D (water) — the molecule is more polarised in solution.
Open acetone →

Spectra

IR & thermochemistry

A vibrational spectrum + free energy

  1. Build formaldehyde (C=O). Open panel 3 · Spectra & thermochemistry and press Compute IR + thermo.
  2. Read the IR stick spectrum — the tall peak ~1700–1800 cm⁻¹ is the C=O stretch. Click any peak to animate that vibration in the 3D viewer (watch the C=O stretch, the bends, the C–H stretches).
  3. Below it, read the ZPE, enthalpy, entropy, Gibbs free energy at 298 K.
  4. Try setting a solvent (panel 2, e.g. water) and re-running — the bands shift slightly in solution.
You should see: a strong carbonyl band, a clickable/animated normal mode, and a thermochemistry table (water gives entropy ≈ 45 cal/mol·K — the textbook value).
Open formaldehyde →

Animate a vibration

Watch a bond actually move

  1. Build water and press Compute IR + thermo (panel 3).
  2. Click each of the three peaks in turn. The 3D viewer animates that normal mode — you'll see the symmetric stretch, the asymmetric stretch, and the scissoring bend.
  3. Try a bigger molecule (e.g. ethanol) and hunt for the O–H stretch, the C–H stretches and the bends by watching which atoms move.
You should see: each IR peak map to a specific atomic motion — the abstract "1539 cm⁻¹ band" becomes a bond you can watch flexing.
Open water →

UV‑Vis

Excited states & absorption

  1. Build formaldehyde. In panel 3 press UV‑Vis (TD‑DFT).
  2. Read the absorption stick spectrum (wavelength vs oscillator strength) and the transition table.
  3. Note the orbital assignment for each band (HOMO→LUMO, etc.).
You should see: the dark n→π* band ~320 nm (HOMO→LUMO, f≈0) and a bright π→π* at shorter wavelength.
Open formaldehyde →

NMR

Predict a ¹H / ¹³C spectrum

  1. Build ethanol (CCO). In panel 3 press NMR → Quick run (~30 s–2 min — it runs a real GIAO DFT calculation).
  2. Read the two predicted stick spectra. Equivalent nuclei are grouped and the stick height shows the integration (how many H's).
  3. Match the peaks to the structure: the CH₂ (~3.7 ppm, 2H), the CH₃ (~1.2 ppm, 3H), and on the ¹³C the two carbons near 59 and 18 ppm.
You should see: ¹H peaks at roughly 3.7 (2H) and 1.2 (3H) and the O–H, and ¹³C around 59 and ~20 ppm. Shifts are empirically scaled to experiment — ¹H good to ~0.2 ppm, ¹³C to ~8 ppm (benzene comes out 128.7 vs the real 128.4).
Open ethanol →

Molecular orbitals

Orbital energy diagram

View any molecular orbital

  1. Build benzene. Open panel 4 · Orbitals and press Compute orbitals.
  2. You get an interactive energy‑level diagram — occupied levels with ↑↓ electrons, virtual levels dashed, the HOMO–LUMO gap shaded.
  3. Click a level to render that MO (HOMO‑2 … LUMO+2). Try HOMO‑1 and LUMO.
You should see: benzene's degenerate frontier orbitals (HOMO/HOMO‑1 at the same energy), each rendered as red/blue π lobes.
Open benzene →

Density & ESP

Electron density & electrostatic potential

  1. Build water and Compute orbitals (panel 4).
  2. Click Density for the electron‑density surface, then ESP map.
  3. On the ESP map find the red region (electron‑rich, the lone pairs) and the blue (the H's).
You should see: water's ESP map red over the oxygen lone‑pair side, blue over the hydrogens.
Open water →

Reactivity maps

HOMO / LUMO & ionization maps

  1. Build formaldehyde and Compute orbitals.
  2. Click LUMO map — the LUMO painted on the density shows the electrophilic site (the carbonyl carbon).
  3. Click Ionization map — red marks where electrons are loosely held (electron‑rich, nucleophilic sites). Try HOMO map too.
You should see: the LUMO map highlighting the carbon; the ionization map (a short extra calc) marking the reactive regions.
Open formaldehyde → Ammonia

Localized orbitals

See the bonds & lone pairs

  1. Build water and Compute orbitals.
  2. Click Localized (bonds) — the delocalized MOs are localized (Pipek‑Mezey) into bonds, lone pairs and cores, each labelled.
  3. Click the chips: the two O–H bonds and the two oxygen lone pairs.
You should see: water's textbook picture — 1 core + 2 lone pairs + 2 O–H bonds, each a clickable labelled orbital.
Open water →

Spin density

Where the unpaired electron lives

  1. Build ammonia (N) and Compute orbitals.
  2. In the Open‑shell row set charge = 1, mult = 2 (the radical cation), then press Spin density.
  3. The blue isosurface shows the excess α spin — the unpaired electron.
You should see: the NH₃⁺ spin density (blue) localized on nitrogen. (Use ions of closed‑shell molecules — set charge ±1.)
Open ammonia →

Method & isovalue

Pick the level & tune the surface

  1. Build water. In panel 4 set Method = B3LYP and Basis = 6‑31G*, then Compute orbitals.
  2. View the HOMO, then drag the Isovalue slider to make the surface tighter/looser.
  3. Compare HOMO energies between HF/3‑21G and B3LYP/6‑31G*.
You should see: B3LYP/6‑31G* gives a more realistic HOMO (≈ −7.9 eV) than HF/3‑21G, and the isosurface resizing live.
Open water →

Conformations

Conformer search

The preferred shape of a flexible molecule

  1. Build butane. Open panel 5 · Conformers & dihedral scan and press Search conformers.
  2. Read the table of relative energies and Boltzmann populations at 298 K.
  3. The 3D view loads the lowest‑energy conformer.
You should see: butane's anti conformer lowest (~79%) and the gauche ~0.8 kcal/mol higher (~21%).
Open butane → Ethylene glycol

Dihedral scan

Set your own rotation

  1. Build butane and Optimize it (panel 2) so the structure is clean.
  2. In panel 5 under Dihedral scan, use …or choose bond to pick the central C–C bond (it highlights gold), or ① Pick 4 atoms manually.
  3. Set Start 0 · Stop 360 and a Step (e.g. 30°), then ② Run scan. Click points on the energy plot, and download the CSV/structures.
You should see: butane's torsion curve — minima at anti (180°) and gauche, a ~4.8 kcal/mol eclipsed barrier — clickable and downloadable.
Open butane →

2D conformational map

A whole energy surface at once

  1. Build pentane (CCCCC). In panel 5 under 2D conformational map the two central C–C–C–C torsions are pre-selected as bond X and bond Y.
  2. Press Run 2D map — it computes the full energy surface over both dihedrals (a Ramachandran-style heatmap).
  3. Click any cell to load that conformer in 3D. Find the deep-blue anti–anti minimum and the red high-energy corners.
You should see: a coloured grid with low-energy basins where both dihedrals are ~180° (anti–anti) and high-energy clashes near eclipsed/syn-pentane geometries.
Open pentane →

Reactions & transition states

Watch a reaction happen

Reaction path & transition state

  1. Open panel 6 · Reactions & transition states. Pick a reaction — SN2, E2, Menshutkin, Diels-Alder, or the electrocyclic ring-opening — and press Run reaction (~30–90 s).
  2. Read the activation barrier ‡ and reaction energy ΔE, then press Jump to transition state ‡.
  3. Drag the slider back and forth to step the geometry from reactants → TS → products and watch the bonds break and form. Download the energy CSV or the path as an XYZ trajectory.
  4. Press ✓ Refine TS (Psi4) (optionally choose HF/3-21G or HF/6-31G*) to rigorously optimize the saddle point and confirm it has exactly one imaginary frequency, then Animate the reaction mode to watch the atoms vibrate along the reaction coordinate.
  5. Make your own: choose ✎ Custom in the reaction list, build a molecule, then click two atoms to mark a bond to form and/or break — MoleBench drives that coordinate and finds the TS (best for intramolecular reactions, e.g. a ring-opening or cyclization).
You should see: an energy-vs-reaction-coordinate curve with the TS marked, a scrubbable 3D animation (SN2 inverts like an umbrella; Diels-Alder forms two C–C bonds at once), a barrier of a few–~12 kcal/mol, and — after refining — a confirmed single imaginary frequency animated as the reaction mode.
Open the reactions panel →

Beyond the studio

Export & share

Take your molecule with you

  1. Build aspirin. In the Export panel click Copy SMILES and 🔗 Share link (a URL that rebuilds the exact molecule).
  2. Click Download .sdf (3D) and Download 2D .png.
You should see: the SMILES on your clipboard, a shareable link, and downloaded structure/image files.
Open aspirin →

Proteins

From small molecules to whole proteins

  1. Go to the Proteins page. Type the PDB ID 1CRN (crambin) and load it.
  2. Switch styles: cartoon (the fold), surface (the shape), stick (every atom).
  3. Try 4HHB (hemoglobin) or 1BNA (B‑DNA).
You should see: crambin's α‑helix and β‑sheet in cartoon view — the same viewer, scaled to biology.
Open the protein viewer →

Calculators

The everyday chemistry math

  1. Scroll to the Calculators on the Studio page (or the nav link).
  2. Balance C3H8 + O2 → CO2 + H2O (propane combustion); find the molar mass of CuSO4·5H2O.
  3. In Reaction thermodynamics, click methane combustion to get ΔH, ΔS, ΔG and K; then change the temperature and watch ΔG and K update (try limestone decomp. to find the temperature where it turns spontaneous).
  4. Use C₁V₁=C₂V₂ for a dilution and compute a pH — leave one box blank and it solves.
You should see: the balanced equation C3H8 + 5O2 → 3CO2 + 4H2O, methane combustion at ΔH = −890.5 kJ/mol (spontaneous, K ≈ 10¹⁴³), a molar mass of 249.7 g/mol, and instant solves.
Open the calculators →

Open the Studio   Read the full manual →