Integration of models of several cellular processes into one computational description of a biological cell. In a model of Mycoplasma genitalium, coupling processes made their shared molecular resources and timing experimentally testable. Whole-cell describes intended coverage, not complete knowledge of every event.^[ref]

Computational integration of an organism’s interacting physiological and developmental processes at a stated resolution and for a stated range of conditions.

A point such that replacing every position $\mathbf{r}$ relative to it by $-\mathbf{r}$ leaves the structure unchanged. Molecular orbitals can then be classified as $g$ or $u$ according to their parity.

Invariance under a spatial reflection. A one-dimensional Quantum Hamiltonian invariant under $x\mapsto a-x$ admits energy eigenfunctions of definite even or odd midpoint parity. Even and odd functions are orthogonal on a reflection-symmetric interval.

A molecular association in which a host provides a binding site or cavity for a guest. Its equilibrium constant includes solvent and entropy contributions, not only direct host–guest attraction.

A noncovalent attraction between a cation and an electron-rich aromatic system, with electrostatic and polarization contributions. Its solution free energy depends strongly on solvation.

Restriction of a host or reactant towards a binding- or reaction-competent geometry before association. It can reduce a conformational penalty but may decrease adaptability to other guests.

A macrocycle containing triazole and other linking units. Appropriate inward-directed C–H donors can bind anions cooperatively; cavity size and molecular preorganization can produce strong halide selectivity.

Use of reversible covalent bond formation and exchange to let molecular connectivities reorganize. A template can shift the equilibrium library, provided exchange remains kinetically accessible.

Selective distribution of components among preferred assemblies from a mixture. Competition, concentration, solvent and protonation determine the distribution; a ranking of individual affinities does not imply perfectly pure species.

Assembly maintained or transiently created by consumption of a chemical fuel. A fuel-triggered state can decay as the fuel is irreversibly converted to waste, even though rapid binding equilibria hold within each instantaneous composition.

Reversible formation of covalent ligands and metal coordination bonds from simpler components in the same mixture. imine condensation around a metal template is a common example.

A reactant consumed irreversibly to drive a transient or maintained chemical state away from its unfuelled equilibrium.

A public archive of three-dimensional structures of biological macromolecules and associated experimental information. A deposited model describes coordinates and supporting evidence; its interpretation depends on resolution, uncertainty and the experimental preparation.^[ref]

A cis configuration places the specified substituents on the same side of a restricted structural element. A cis double bond in a fatty-acyl chain commonly disrupts close chain packing relative to the comparable trans arrangement.

A trans configuration places the specified substituents on opposite sides of a restricted structural element. For comparable fatty-acyl chains, trans unsaturation usually permits closer packing than cis unsaturation.

Sugar puckering describes the nonplanar conformation of a sugar ring. In nucleic acids, C2′-endo and C3′-endo conformations alter backbone geometry and help distinguish B-DNA from A-DNA.

A Newman projection views a molecule along a chosen bond, showing substituents on the front atom and rear atom. It makes relative torsions visible without assuming that the two centres lie in the plane of a skeletal drawing.

The Cahn-Ingold-Prelog priority rules rank substituent paths to assign stereochemical descriptors. Compare the next shell only after a tie; multiple bonds and aromatic paths require the prescribed duplicate-atom treatment. Spatial orientation and priority ranking are separate steps.

Diastereoselectivity is preferential formation or reaction of one diastereomer among competing possibilities. Unlike enantiomers, diastereomers can have different energies and physical properties even in an achiral environment.

For example, an addition reaction can favor one relative arrangement of two stereocenters, producing a $4:1$ diastereomeric ratio. This ratio describes product composition, while chemical yield describes how much product is obtained. Steric interactions, chelation, and conformational preferences can affect the competing transition-state energies, so the favored product depends on substrate and conditions.