Electronegativity and polar bonds
Each bond is classed by the difference in Pauling electronegativity, Δχ: below 0.4 essentially nonpolar (C–H is 0.35), 0.4 to 1.7 polar covalent, above 1.7 largely ionic. A bond dipole arrow is drawn for every polar bond, pointing toward the atom that ends up with the more negative partial charge.
Partial charges
σ only uses the Gasteiger–Marsili method (partial equalization of orbital electronegativity): each atom's electronegativity depends on its element, hybridization and current charge, and charge flows along each bond from the less to the more electronegative atom in six damped steps. It captures inductive effects well but not resonance. σ + resonance adds the change in formal charge averaged over the resonance contributors found below, weighted by how good each contributor is: in full where charge is only shared between equivalent positions (carboxylate, nitro, allyl), and at half weight for charge-separated contributors, since the σ charges already include part of that polarization. That is why an amide N comes out less negative and its O more negative, and why both O atoms of a carboxylate match.
Dipole moment
μ = Σ q·r over all atoms, using the σ (Gasteiger) charges and 3D coordinates (drawings are first converted to 3D with the 3D Builder's geometry model) and reported in debye (1 e·Å = 4.80 D). Chemists draw the arrow from + to −, as here; physicists use the opposite direction. Values from partial charges are often 20–50% off measured ones (lone pairs and polarization are left out; they run low for water and ammonia and high for nitro compounds and acids), but polar and nonpolar molecules come out right, and symmetric molecules such as CO₂, CCl₄ and trans-1,2-dichloroethene cancel to zero. Ions have no origin-independent dipole, so none is given.
Electron density map
Colors show an electrostatic-potential–style map: the potential from the partial charges, Σ q/r, evaluated in the plane of the view inside a smooth envelope around the atoms (about 0.8 × their van der Waals radii). Red is electron-rich (negative potential, δ−), blue electron-poor (positive, δ+), yellow-green near neutral. The color scale adapts to each molecule; it is a picture of where density sits, not a quantum-chemical surface.
Functional groups
Groups are found from the connectivity: carbonyl families (aldehyde, ketone, acid, ester, amide, acyl halide, anhydride, carboxylate), alcohols, phenols, enols, ethers, amines (1°/2°/3°, aryl), nitriles, imines, nitro, thiols, sulfides, halides, alkenes, alkynes and aromatic rings.
Resonance
Atoms that can take part in delocalization (π bonds, lone pairs next to π bonds, empty p orbitals) are grouped into conjugated systems. Contributors are generated by electron pushing: a lone pair forms a π bond while an adjacent π bond moves onto the next atom; a π bond shifts toward a cation; a C=O or C=N π bond moves onto the electronegative atom; aromatic rings swap Kekulé structures. Each contributor is scored (charge separation, charge on the less suitable atom, incomplete octets) to estimate its weight.