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This glossary is intended to offer help in crossing disciplinary boundaries, especially for those beginning to explore the terminology-rich field of chemistry. The entries are neither exhaustive in scope nor definitional in quality. A small fraction of the entries define terms introduced in the present work. Cross-references are marked as links (for example, abstraction reaction); an alphabetical search will occasionally yield a different form of the indicated word. Some words in the main text are marked in the same way.
Abstraction reaction A reaction that removes an atom from a structure.
Acid In the Brønsted definition, an acid is a chemical species that can donate a proton to another species (a base). In the Lewis definition, an acid is a chemical species that can accept (and share) a pair of electrons from another species. Hydrochloric acid is a Brønsted acid; the proton it donates is a Lewis acid. A neutral Lewis acid and a neutral Lewis base can commonly form a dipolar bond.
Activation energy Distinct states correspond to minima of a potential energy surface in a configuration space. In this classical picture, the activation energy for transforming state A into state B is the maximum increase in energy (relative to the ground state of A) encountered on a minimum-energy path from A to B. Energy here refers to potential energy; an analogous definition based on free energy can be constructed. When tunneling is considered, lower energy paths become possible, but an activation energy can be associated with the reaction (at a given temperature) via the relationship between temperature and reaction rate.
Acyclic Not cyclic.
Affinity constant The reciprocal of the dissociation constant; a measure of the binding energy of a ligand in a receptor.
AFM An atomic force microscope.
Alkane A saturated, acyclic hydrocarbon structure; usually quite inert.
Alkene A hydrocarbon containing a double bond; often rather reactive.
Alkyne A hydrocarbon containing a triple bond; often rather reactive.
Amide A molecule containing an amine bonded to a carboxyl group; the resulting bond has substantial double-bond character. Also termed a peptide; amide bonds link amino acids in proteins.
Amine A molecule containing N with a single bond to C and two other single bonds to H or C (but not an amide); the amine group or moiety.
Amino acid A molecule containing both an amine and a carboxylic acid group; in the 20 genetically encoded amino acids in biology, both groups are bound to the same C. Amino acids joined by amide bonds form peptides and proteins; these do not contain amino acids as such, and are instead said to contain amino acid residues.
Anion A negatively charged ion.
Aromatic A term used to describe cyclic pi-bonded structures of special stability.
Assembler In recent popular usage, any nanomachine, usually assumed to offer magical, universal capabilities in an atom-sized package. In the author's usage, any programmable nanomechanical system able to perform a wide range of mechanosynthetic operations. See molecular manipulator, molecular mill.
Atomic force microscope A device in which the deflection of a sharp stylus mounted on a soft spring is monitored as the stylus is moved across a surface. If the deflection is kept constant by moving the surface up and down by measured increments, the result (under favorable conditions) is an atomic-resolution topographic map of the surface. Also termed a scanning force microscope.


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