Editor & viewer

Left: 2D editor (JSME). Middle: element palette. Right: 3D viewer (3Dmol.js).
🧬 Protein / PDB: or
2D editor
3D viewer
Formula
Atoms
Last measurement
Drag the 3D view to rotate · scroll to zoom · right-click drag to pan. Or draw on the left and click 2D → 3D.

2D skeletal structure

A clean PubChem-rendered drawing of the current preset.
Open on PubChem ↗

Reaction energy profiles

The shape of an energy profile tells you the kinetics (activation energy, catalysis) and the thermodynamics (ΔH, exo- vs endothermic).

Exothermic — energy released

Eₐ |ΔH| < 0 Reactants Products Transition state ‡ Reaction progress → Energy

Examples: combustion, neutralization (acid + base), thermite. Products are more stable than reactants — heat is released.

Endothermic — energy absorbed

Eₐ ΔH > 0 Reactants Products Transition state ‡ Reaction progress → Energy

Examples: photosynthesis, melting ice, dissolving NH₄NO₃ (cold pack). Products are less stable — heat is absorbed.

Catalyzed — lower Eₐ, same ΔH

Eₐ (no catalyst) Eₐ (cat.) Reactants Products No catalyst With catalyst Reaction progress → Energy

A catalyst provides an alternate pathway with lower Eₐ, so the reaction is faster. ΔH is unchanged — start and end energies are the same.

Multi-step — intermediates & rate-limiting step

TS₁ Intermediate TS₂ — rate-limiting Reactants Products Reaction progress → Energy

Multi-step reactions show intermediates (valleys between peaks). The slowest step (highest barrier, here TS₂) is rate-limiting.

Thermodynamics

ΔG = ΔH − TΔS

Spontaneous when ΔG < 0. Tells you if a reaction will go.

Kinetics

k = A·e−Eₐ/RT

The Arrhenius equation. Tells you how fast.

Equilibrium

ΔG° = −RT·ln K

Connects thermo to the equilibrium constant K.

Crystal unit cells in 3D

The repeating unit of a crystal lattice. Drag to rotate any of these — corner atoms are shared with adjacent unit cells, so each one only counts as ⅛ of an atom.

Simple cubic (SC)
8 corners · 1 atom/cell · α-Po
Body-centered (BCC)
8 corners + 1 center · 2 atoms/cell · Fe (α), Cr
Face-centered (FCC)
8 corners + 6 faces · 4 atoms/cell · Cu, Ag, Au, Al
Hexagonal close-packed (HCP)
12 vertices + 3 mid · 6 atoms/cell · Mg, Zn, Ti

Atomic orbitals

The shapes that hold electrons. Build atoms from these and you have the periodic table.

s
Spherical · holds 2 electrons
p (px, py, pz)
Dumbbell · 3 orientations · 6 e⁻ total
d (5 orientations)
Cloverleaf shapes · 10 e⁻ total
sp³ hybrid
Tetrahedral · 109.5°
sp²
Trigonal planar · 120° (e.g. C=C)
sp
Linear · 180° (e.g. C≡C, CO₂)
π (pi) bond
Side-by-side p overlap
σ (sigma) bond
Head-on overlap · strongest

Common molecular geometries (VSEPR)

Once you know how many bonded atoms and lone pairs surround the central atom, the shape is fixed.

Linear
180° · CO₂, BeCl₂
Trigonal planar
120° · BF₃, CO₃²⁻
Bent
~104.5° · H₂O, SO₂
Tetrahedral
109.5° · CH₄, NH₄⁺
Trigonal pyramidal
~107° · NH₃, PCl₃
Octahedral
90° · SF₆, [Fe(CN)₆]⁴⁻
Trigonal bipyramidal
90° & 120° · PCl₅, AsF₅
Bent (with 2 lone pairs)
<104° · H₂O variant

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