Molecular Manufacturing Glossary

Most of the following comes from Nanosystems, (c) Eric Drexler, 1992.

Terms in italics are also defined in this glossary.

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 or 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 substantian 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 no 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 aics in biology, both groups are bound to the same Carbon. 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 Drexler's usage, any programmable nanomechanical system able to perform a wide range of mechanosynthethic operations. See molecular manipulator, molecular mill.
Atomic force microscope - A type of scanning probe which uses a tip built on a cantilever to feel atomic interaction forces between the tip and the substrate in which it is used, and build a virtual map of the surface at the level of single atoms.
Barrier height - Roughly synonymous with activation energy.
Base - In the Brønsted definition, a base is a chemical species that can accept a proton from another species. In the Lewis definition, a base is a chemical species that can donate (and share) a pair of electrns with another species. See acid.
Bearing - A mechanical device that permits the motion of a component (ideally, with minimal resistance) in one or more degrees of freedom while resisting motion (ideally, with stiff restoring force) in all other degrees of freedom.
Binding energy - The reduction in the free energy of a system that occurs when a ligand binds to a receptor. Generally used to describe the total energy required to remove something, or to take a system apart into its constituent particles - for example, to separate two atoms from one another, or to separate an atom into electrons or nuclei.
Binding site - The active region of a receptor, any site at which a chemical species of interest tends to bind.
Binding - The process by which a molecule (or ligand) becomes bound, that is, confined in position (and often orientation) with respect to a receptor. Confinement occurs because structural features of the receptor create a potential well for the ligand, van der Walls and electrostatic interactions commonly contribute.
Bond - Two atoms are said to be bonded when the energy required to separate them is substantially larger than the van der Waals attraction energy. Ionic bonds result from the electrostatic attraction between ions; covalent and metallic bonds result from the sharing of electrons among atoms; hydrogen bonds are weaker and result from dipole interactions and limited electron sharing. When used without modification, bond usually refers to a covalent bond.
Brownian assembly - Brownian motion in a fluid brings molecules together in various positions and orientations. If molecules have suitable complementary surfaces, they can bind, assembling to form a specific structure. Brownian assembly is a less paradoxical nae for self-assembly (how can a structure assemble itself, or do anything, when it does not yet exist?).
Brownian motion - Motion of a particle in a fluid owing to thermal agitation, observed in 1827 by Robert Brown. (Originally thought to be caused by a vital force, Brownian motion in fact plays a vital role in the assembly and activity of the molecular structures of life.)
CAD - Computer-aided design.
Cam - A component that translates or rotates to move a contoured surface past a follower, the contours impose a sequence of motions (potentially complex) on the follower.
Carbene - A highly reactive chemical species containing an electrically neutral, divalent carbon tom with two non-bonding valence electrons; a prototype is <math>CH_2</math>.
Carbonyl - A chemical moiety consisting of Oxygen with a double bond to Carbon. If the Carbon is bonded to Nitrogen, the resulting structure is termed an amide; if it is bonded to Oxygen, it is termed a carboxylic acid or an ester linkage.
Carboxylic acid - A molecule that includes a Carbon having a double bond to Oxygen and a single bond to OH.
Catalyst - A chemical species or other structure that facilitates a chemical reaction without itself undergoing a permanent change.
Cation - A positively charged ion.
Classical mechanics - Classical mechanics describes a mechanical system as a set of particles (which in a limiting case can form continuous media) having a well-defined geometry at any given time, and undergoing motions determined by applied forces and by the initial positions and velocities of the particles. The forces themselves may have electromagnetic or quantum mechanical origins. Classical statistical mechanics uses the same physical model, by treats the geometry and velocities as uncertain, statistical quantities subject to random thermally-induced fluctuations. Classical mechanics and classical statistical mechanics give a good account of many mechanical properties and behaviors of molecules; but for describing the electronic properties and behaviors of molecules, they are often useless.
CMOS - An acronym for 'complementary metal-oxide-semiconductor', as in CMOS transistor or CMOS logic.
Col - In describing landforms, a pass between two valleys is sometimes termed a col. In describing molecular potential energy functions, this term is commonly used to describe analogous features of the PES; a col is the region around a saddle point having negative curvature along one axis and positive curvature along all orthogonal axes.
Configuration space - A mathematical space describing the three-dimensional coinfiguration of a system of particles (eg., atoms in a nanomechanical structure) as a single point; the configuration space for an N particle system has 3N dimensions.
Conjugated - A conjugated pi system is one in which pi bonds alternate with single bonds. The resulting electron distribution gives the intervening single bonds partial double-bond character, the pi electrons become delocalized, and the energy of the system is reduced.
Conservative - In design and analysis, a conservative model or a conservative assumption is one that departs from accuracy in such a way that it reduces the changes of a false-positive assessment of the feasibility of the system in question. Conservative assumptions overestimate problems and underestimate capabilities.
Covalent bond - A bond formed by sharing a pair of electrons between two atoms.
Covalent radius - Given a set of N elements that can form covalent single bonds in molecules, with N(N-1) possible elemental pairings, it has proved possible to define a covalent radius for each element such that the actual bond length between any two elements that form a covalent single bond is roughly equal to the sums of their covalent radii.
CPU - The central processing unit of a computer, responsible for executing instruction to process information.
Cyclic - A structure is termed cyclic if its covalent bonds form one or more rings.
Cycloaddition - A reaction in which two unsaturated molecules (or moieties within a molecule) join, forming a ring.
Diamondoid - Structures that have similar properties to that of diamond; such as a three-dimensional covalent-bonded cage-like structure, or material properties such as stiffness, chemical inertness, et cetera. Diamondoid is a superset of the fullerenes and contains, first and foremost, diamond and lonsdaleite, and also silicon carbide, boron nitride, adamantane (And any n-adamantane), iceane, cyclohexamantane, and even ionic ceramics such as sapphire that can be covalently bonded to purely covalent structures (Such as diamond).
Dissociation constant - For systems in which ligands of a particular kind bind to a receptor in a solvent there will be a characteristic frequency with which existing ligand-receptor complexes dissociate as a result of thermal excitation, and a characteristic frequency with which empty receptors bind ligands as a result of Brownian encounters, forming new complexes. The frequency of binding is proportional to the concentration of the ligand in solution. The dissociation constant is the magnitude of the ligand concentration at which the probability that the receptor will be found occupied is 1/2.
Dipolar bond - A covalent bond in which one atom supplies both bonding electrns, and the other atom supplies an empty orbital in which to share them. Also termed a dative bond.
Double bond - Two atoms sharing electrons as in a single bond (that is, a sigma bond) may also share electrons in an orbital with a node passing through the two atoms. This adds a second, weaker bonding interaction (a pi bond); the combination is termed a double bond. A twisting motion that forces the nodal plane at one atom to become perpendicular to the nodal plane on the other atom eliminates the (signed) overlap between the atomic orbitals, destroying the pi bond. The energy required to do this creates a large barrier to rotation about the bond (see triple bond).
Doublet - The electronic state of a molecule having one unpaired spin is termed a doublet (see radical). This term is derived from spectroscopy: an unpaired spin can be either up or down with respect to a magnetic field, and these states have different energy, resulting in field-dependent pairs, or doublets, of spectral lines. (See triplet, singlet.)
Elastic - An object behaves elastically if it returns to its original shape after a force is applied and then removed. (If an applied force causes a permanent deformation, the behavior is termed plastic.) In an elastic system, the internal potential energy is a function of shape alone, independent of past forces and deformations.
Electron density - The location of an electron is not fixed, but is instead described by a probability density function. The sum of the probability densities of all the electrons in a region is the electron density in that region.
Electronegativity - A measure of the tendency of an atom (or moiety) to withdraw electrons from structures to which it is bonded. In most circumstances, for example, sodium tends to donate electron density (it has a low electronegativity) and fluorine tends to withdraw electron density (it has a high electronegativity).
Electronic - Pertaining to the energies, distributions, and behaviors of electrons; see mechanical.
Endoergic - A transformation is termed endoergic if it absorbs energy; such a reaction increases molecular potential energy. (Sometimes wrongly equated to the narrower term endothermic.)
Endothermic - A transformation is termed endothermic if it absorbs energy in the form of heat. A typical endothermic reaction increases both entropy and molecular potential energy (and is thus analogous to a gas expanding while absorbing heat and compressing a spring).
Energy - A conserved quantity that can be interconverted among many forms, including kinetic energy, potential energy, and electromagnetic energy. Sometimes defined as "the capacity to do work, but in an environment at a uniform nonzero temperature, thermal energy does not provide this capacity. (Note, however, that all energy has mass, and thus can be used to do work by virtue of its gravitational potential energy; this caveat, however, is of no practical significance unless a really deep gravity well is available.) See free energy.
Enthalpy - The enthalpy of a system is its actual energy (termed the internal energy) plus the product of its volume and the external pressure. Though sometimes termed "heat content," the enthalpy in fact includes energy not contained in the system. Enthalpy proves convenient for describing processes in gases and liquids in laboratory environments, if one does not wish to account explicitly for energy stored in the atmosphere by work done when a system expands. It is of little use, however, in describing processes in nanomechanical systems, where work can take many forms: internal energy is then more convenient. Enthalpy is to energy what the Gibbs free energy is to the Helmholtz free energy.
Entropy - A measure of uncertainty regarding the state of a system: for example, a gas molecule at an unknown location in a large volume has a higher entropy than one known to be confined to a smaller volume. Free energy can be extracted in converting a low-entropy state to a high-entropy state: the (time-average) pressure exerted by a gas molecule can do useful work as a small volume is expanded to a larger volume. In the classical configuration space picture, any molecular system can be viewed as a single-particle gas in a high-dimensional space. In the quantum mechanical picture, entropy is described as a function of the probabilities of occupancy of different members of a set of alternative quantum states. Increased information regarding the state of a system reduces its entropy and thereby increases its free energy, as shown by the resulting ability to extract more work from it. An illustrative contradiction in the simple textbook view of entropy as a local property of a material (defining an entropy per mole, and so forth) can be shown as follows: The third law of thermodynamics states that a perfect crystal at absolute zero has zero entropy; this is true regardless of its size. A piece of disordered material, such as a glass, has some finite entropy G0 > 0 at absolute zero. In the local-property view, N pieces of glass, even (or especially) if all are atomically identical, must have an entropy of NG0. If these N pieces of glass are arranged in a regular three-dimensional lattice, however, the resulting structure constitutes a perfect crystal (with a large unit cell); at absolute zero, the third law states that this crystal has zero entropy, not NG0. To understand the informational perspective on entropy, it is a useful exercise to consider (1) what the actual entropy of such crystal is as a function of N, with and without information describing the structure of the unit cell, (2) how the third law can be phrased more precisely, and (3) what this more precise statement implies for the entropy of well-defined aperiodic structures. Note that any one unit cell in the crystal can be regarded as a description of all the rest.
Enzyme - A protein molecule that acts as a specific catalyst, binding to other molecules in a manner that facilitates a particular chemical reaction.
Equilibrium - A system is said to be at equilibrium (with respect to some set of feasible transformations) if it has minimal free energy. A system containing objects at different temperatures is in disequilibrium, because heat flow can reduce the free energy. Springs have equilibrium lengths, reactants and products in solution have equilibrium concentrations, thermally excited systems have equilibrium probabilities of occupying various states, and so forth.
Eutactic - Characterized by precise molecular order, like that of a perfect crystal, the interior of a protein molecule, or a machine-phase system; contrasted to the disorder of bulk materials, solution environments, or biological structures on a cellular scale. Borderline cases can be identified, but perfection is not necessary. As a crystal with sparse defects is best described as a crystal (rather than as amorphous), so a eutactic structure with sparse defects is best described as (imperfectly) eutactic, rather than as disordered.
Excluded volume - The presence of one molecule (or moiety) reduces the volume available for other molecules (or moieties); resulting reductions in their entropy are termed 'excluded volume effects'.
Exoergic - The opposite of endoergic; describes a transformation that releases energy.
Exothermic - The opposite of endothermic; describes an exoergic transformation in which energy is released as heat. Exoergic reactions in solution are commonly exothermic.
Follower - A component in a cam system that is driven through a pattern of displacements as it rests against a moving contoured surface.
Free energy - Free energy is a measure of the ability of a system to do work, such that a reduction in free energy could in principle yield an equivalent quantity of work. The Helmholtz free energy describes the free energy within a system; the Gibbs free energy does not.
Free radical - A radical.
Gate - In digital logic, a component that can switch the state of an output dependent on the states of one or more inputs.
Gibbs free energy - The Gibbs free energy is the Helmholtz free energy plus the product of the system volume and the external pressure. Changes in the Gibbs free energy at a constant pressure thus include work done against external pressure as a system undergoes volumetric changes. This proves convenient for describing equilibria in gases and liquids at a constant pressure (e.g., at one atmosphere), but is of little use in describing machine-phase chemical processes. Changes in the Gibbs free energy caused by a change in the applied pressure (at constant volume) have no direct physical significance. (See also enthalpy.)
Ground state - The lowest-energy state of a system. The electronic ground state of a system cannot reduce its energy by an electronic transition, but may contain vibrational energy (kinetic and potential energy associated with the motions and positions of its atoms); extended systems at ordinary temperatures are always vibrationally excited, and so "ground state" is often taken to mean "electronic ground state."
Group - A set of linked atoms in a molecule; a defined substructure. Typically, a set that is usefully regarded as a unit in chemical reactions of interest.
Group velocity - In wave propagation, the speed of the waveform (e.g., of a peak) can be different from the speed of a group of waves (e.g., of a set of ripples in water). The latter is the 'group velocity', and is the speed of propagation of information and wave energy. The waveform speed is the 'phase velocity'.
Harmonic oscillator - A system in which a mass is subject to a linear restoring force, like an ideal spring. A harmonic oscillator vibrates at a fixed frequency, independent of amplitude.
Heat - As defined in thermodynamics, heat is the energy that flows between two systems as a result of temperature differences (a system contains neither heat nor work, but can produce heat or do work). Heat thus differs from thermal energy.
Heat capacity - The ratio of the heat input to the temperature increase in a system. Note that this definition does not imply that a system contains heat, despite the name 'heat capacity'.
Helmholtz free energy - The internal energy of a system minus the product of its entropy and temperature; see free energy.
Hydrocarbon - A molecule consisting only of H and C.
Hydrogen bond - A hydrogen atom covalently bound to an electronegative atom (e.g., nitrogen, oxygen) has a significant positive charge and can form a weak bond to another electronegative atom; this is termed a hydrogen bond.
Hydrophobic force - Water molecules are linked by a network of hydrogen bonds. A nonpolar, nonwetting, surface (e.g., wax) cannot form hydrogen bonds. To form their full complement of hydrogen bonds, the nearby water molecules must form a more orderly (hence lower entropy) network. This both increases free energy and causes forces that tend to draw hydrophobic surfaces together across distances of several nanometers.
Intermolecular - Describes an interaction (e.g., a chemical reaction) between different molecules.
Internal energy - The sum of the kinetic and potential energies (including electromagnetic field energies) of the particles that make up a system.
Intramolecular - Describes an interaction (e.g., a chemical reaction) within a single molecule. Intramolecular interactions between widely separated parts of a molecule resemble intermolecular interactions in most respects.
Ion - An atom or molecule with a net charge.
Ionic bond - A chemical bond resulting chiefly from the electrostatic interaction between positive and negative ions.
Isoelectronic - Two molecules are described as isoelectronic if they have the same number of valence electrons in similar orbitals, although they may differ in their distribution of nuclear charges (e.g., H-C≡N⁺ and H-N+≡C^-. KineticPertaining to the rates of chemical reactions. A fast reaction is said to have fast kinetics; if the balance of products in a reaction is controlled by reaction rates rather than by thermodynamic equilibria, the reaction is said to be kinetically controlled.
Kinetic energy - Energy resulting from the motion of masses.
Ligand - In protein chemistry, a small molecule that is (or can be) bound by a larger molecule is termed a ligand. In organometallic chemistry, a moiety bonded to a central metal atom is also termed a ligand; the latter definition is more common in general chemistry.
Linear - Aside from its geometric meaning, linear describes systems in which an output is directly proportional to an input. In particular, a linear elastic system is one in which the internal displacements are (at equilibrium) directly proportional to applied forces.
London dispersion force - An attractive force caused by quantum-mechanical electron correlation. For example, a neutral spherical molecule (such as a single argon atom) has no charge and produces no external electric field, yet a pair of molecules has a distribution of electron configurations weighed towards those with lesser electron-electron repulsions; this creates a small net attraction.
Lone pair - Two valence electrons of an atom that share an orbital but do not participate in a bond.
Machine-phase chemistry - The chemistry of systems in which all potentially reactive moieties follow controlled trajectories (e.g., guided by molecular machines working in vacuum).
Machine Phase - A system where the position and velocity of every atom is known.
Mechanical - Pertaining to the positions and motions of atoms, as defined by the positions of their nuclei; see electronic. A purely mechanical device can be described in terms of atomic positions and motions without reference to electronic properties, save through their effect on the potential energy function
Mechanochemistry - In this volume, the chemistry of processes in which mechanical systems operating with atomic-scale precision either guide, drive, or are driven by chemical transformations. In general usage, the chemistry of processes in which energy is converted from mechanical to chemical form, or vice versa.
Mechanosynthesis - Chemical synthesis controlled by mechanical systems operating with atomic-scale precision, enabling direct positional selection of reaction sites; synthetic applications of mechanochemistry. Suitable mechanical systems include AFM mechanisms, molecular manipulators, and molecular mill systems. Processes that fall outside the intended scope of this definition include reactions guided by the incorporation of reactive moieties into a shared covalent framework (i.e., conventional intramolecular reactions), or by the binding of reagents to enzymes or enzymelike catalysts.
Metastable - A classical system is metastable if it is above its minimum-energy state, but requires an energy input before it can reach a lower-energy state; accordingly, a metastable system can act like a stable system, provided that energy inputs (e.g., thermal fluctuations) remain below some threshold. Systems with strong metastability are commonly described as stable. Quantum mechanical effects can permit metastable states to reach lower energies by tunneling, without an energy input; an associated, broader definition of 'metastable' embraces all systems that have a long lifetime (by some standard) in a state above the minimum-energy state.
Moiety - A portion of a molecular structure having some property of interest.
Mole - A number of instances of something (typically a molecular species) equaling 6.02214179( 30)x10²³
Molecular machine - A mechanical device that performs a useful function using components of nanometer scale and defined molecular structure; includes both artificial nanomachines and naturally occurring devices found in biological systems.
Molecular manipulator - A programmable device able to position molecular tools with high precision, for example, to direct a sequence of mechanosynthetic steps; a molecular assembler.
Molecular manufacturing - The production of complex structures via nonbiological mechanosynthesis (and subsequent assembly operations); the production of atomically-precise products (Even if the manufacturing system is not atom-by-atom or atomically-precise); a synonym for molecular nanotechnology.
Molecular mechanics models - Many of the properties of molecular systems are determined by the molecular potential energy function. Molecular mechanics models approximate this function as a sum of 2-atom, 3-atom, and 4-atom terms, each determined by the geometries and bonds of the component atoms. The 2-atom and 3-atom terms describing bonded interactions roughly correspond to linear springs.
Molecular mill - A mechanochemical processing system characterized by limited motions and repetitive operations without programmable flexibility (see molecular manipulator); a nanoscale 'assembly line' where machines perform limited operations from a small set to produce atomically-precise products.
Molecular nanotechnology - See nanotechnology.
Molecule - A set of atoms linked by covalent bonds. A macroscopic piece of diamond is technically a single molecule. (Sets of atoms linked by bonds of other kinds are sometimes also termed molecules.)
Nanomachine - An artificial eutactic mechanical device that relies on nanometer-scale components; see molecular machine.
Nanomechanical - Pertaining to nanomachines.
Nanoscale - On a scale of nanometers, from atomic dimensions to ~100 nm.
Nanosystem - A eutactic set of nanoscale components working together to serve a set of purposes; complex nanosystems can be of macroscopic size.
Nanotechnology - In recent general usage, any technology related to features of nanometer scale: thin films, fine particles, chemical synthesis, advanced microlithography, and so forth. As introduced by Drexler, a technology based on the ability to build structures to complex, atomic specifications by means of mechanosynthesis; this can be termed molecular nanotechnology.
NMOS - An acronym for 'n-channel metal-oxide-semiconductor', as in NMOS transistor and NMOS logic.
Nucleus - The positively charged core of an atom, an object of ~0.00001 atomic diameters containing >99.9% of the atomic mass. Nuclear positions define atomic positions.
Olefin - An alkene.
Omitted reaction - A chemical reaction that fails by not occurring (see misreaction).
Orbital - In the approximation that each electron in a molecule has a distinct, independent wave function, the spatial distribution of an electron wave function corresponds to a molecular orbital. These, in turn, can be approximated as sums of contributions from the orbitals characteristic of the isolated atoms. An electron added to a molecule — or, similarly, one excited to a higher-energy state within a molecule — would occupy a state with a different wave function from the rest; an unoccupied state of this kind corresponds to an unoccupied molecular orbital. Orbital-symmetry effects on reaction rates arise when a reaction requires overlap between two lobes of the orbitals on each of two reagents: if the algebraic signs of the wave functions in the facing lobes do not match, bond formation between those orbitals is prohibited.
Overlap - Orbitals lack sharply defined surfaces, declining in amplitude exponentially in their surface regions. When two orbitals are brought together, regions of substantial amplitude overlap. The resulting system can be described as two new orbitals, one formed by joining the two original orbitals without introducing a node in the wave function, and the other formed with a node between them. The nodeless joining reduces the energy of the electrons relative to the separate orbitals, resulting in a bonding interaction; joining with a node raises the energy, producing an antibonding interaction. If both new orbitals are occupied, antibonding forces dominate, resulting in overlap repulsion. Molecular mechanics models give an approximate description of overlap (and other) forces for a certain range of atoms and geometries.
Overlap repulsion - A repulsive force resulting from the nonbonding overlap of two atoms.
PDF - See probability density function.
Peptide - A short chain of amino acids; see protein.
PES - See potential energy surface.
Phase space - A classical system of N particles can be described by its 3N position and 3N momentum coordinates. The phase space associated with the system is the 6N dimensional space defined by these coordinates.
Phonon - A quantum of acoustic energy, analogous to the quantum of electromagnetic radiation, the photon. Thermal excitations in a crystal or in an elastic continuum can be described as a population of phonons (analogous to blackbody electromagnetic radiation). In highly inhomogeneous solids, a description in terms of phonons breaks down and localized vibrational modes become important.
Pi bond - A covalent bond formed by overlap between two p orbitals on different atoms (see sp). Pi bonds are superimposed on sigma bonds, forming double or triple bonds.
Polycyclic - A cyclic structure contains rings of bonds; a structure having many such rings is termed polycyclic. In the polycyclic structures of interest in this volume, a large fraction of the atoms are members of multiple small rings, resulting in considerable rigidity.
Potential energy - The energy associated with a configuration of particles, as distinct from their motions. In macroscopic experience, potential energy can be increased (for example) by stretching a spring or by lifting a mass against a gravitational force; in molecular systems, potential energy can be increased (for example) by stretching a bond or by separating molecules against a van der Waals attraction.
Potential energy surface - The potential energy of a ground-state molecular system containing N atoms is a function of its geometry, defined by 3N spatial coordinates (a configuration space). If the energy is imagined as corresponding to a height in a 3N + 1 dimensional space, the resulting landscape of hills, hollows, and valleys is the potential energy surface.
Potential well - In a potential energy surface, the region surrounding a local energy minimum. Typically taken to include at least those points in configuration space such that a path of steadily declining energy can be found that leads to the minimum in question, and such that no similar path can be found to any other minimum. If the PES were a landscape, this would be the region around the minimum that could be filled with water without any flowing down and away toward another minimum.
Probability density function - Consider an uncertain physical property and a corresponding space describing the range of values that the property can have (e.g., the configuration of a thermally excited N particle system and the corresponding 3N dimensional configuration space). The probability density function associated with a property is defined over the corresponding space; its value at a particular point is the probability per unit volume that the property has a value in an infinitesimal region around that point.
Protein - Living cells contain many molecules that consist of amino acid polymers folded to form more-or-less definite three-dimensional structures; these are termed proteins. Short polymers lacking definite three-dimensional structures are termed peptides. Many proteins incorporate structures other than amino acids, either as covalently attached side chains or as bound ligands. Molecular objects made of protein form much of the molecular machinery of living cells.
Quantum mechanics - Quantum mechanics describes a system of particles in terms of a wave function defined over the configuration space of the system. Although the concept of particles having distinct locations is implicit in the potential energy function that determines the wave function (e.g., of a ground-state system), the observable dynamics of the system cannot be described in terms of the motion of such particles from point to point. In describing the energies, distributions, and behaviors of electrons in nanometer-scale structures, quantum mechanical methods are necessary. Electron wave functions help determine the potential energy surface of a molecular system, which in turn is the basis for classical descriptions of molecular motion. Nanomechanical systems can almost always be described in terms of classical mechanics, with occasional quantum mechanical corrections applied within the framework of a classical model.
Radiation damage - Chemical changes (bond breakage, ionization) caused by high-energy radiation (e.g., x-rays, gamma rays, high-speed electrons, protons, etc.).
Radical - A structure with an unpaired electron (but excluding certain metal ions). In organic molecules, a radical is often associated with a highly reactive site of reduced valence (see doublet). The term radical is sometimes used to describe a substructure within a molecule; the term 'free radical' then describes a radical in this sense, viewed as the result of cleaving the bond linking the substructure to the rest of the molecule.
Reaction - A process that transforms one or more chemical species into others. Typical reactions make or break bonds; others change the state of ionization or other properties taken to distinguish chemical species.
Reagent - A chemical species that undergoes change as a result of a chemical reaction.
Reagent device - A large reagent structure (or a large structure that binds a smaller reagent) serving as a component of a mechanochemical system. A reagent device exists chiefly to hold, position, and manipulate the environment of a reagent moiety.
Reagent moiety - The portion of a reagent device that is intimately involved in a chemical reaction.
Receptor - A structure that can capture a molecule (often of a specific type in a specific orientation) owing to complementary surface shapes, charge distributions, and so forth, without forming a covalent bond. See dissociation constant.
Reconstruction - A crystal consists of a regular array of atoms, and the simplest model of a crystal surface would be generated by simply discarding all atoms to one side of a surface without changing the positions of the rest. In reality, however, the positions of the remaining atoms do change. A pattern of displacements that lowers the symmetry of the surface (relative to the ideally terminated crystal) is termed a surface reconstruction; some reconstructions alter the pattern of bonds.
Register - A temporary storage location for an array of bits within a digital logic system.
Relaxation time - A measure of the rate at which a disequilibrium distribution decays toward an equilibrium distribution. The electron relaxation time in a metal, for example, describes the time required for a disequilibrium distribution of electron momenta (e.g., in a flowing current) to decay toward equilibrium in the absence of an ongoing driving force and can be interpreted as the mean time between scattering events for a given electron.
Representative point - The point in a configuration space that represents the geometry of a system.
Rigid struture - As used in this volume, a covalent structure that is reasonably stiff. In a typical rigid structure, all modes of deformation encounter first-order restoring forces resulting from some combination of bond stretching and angle bending; such a structure cannot undergo deformation by bond torsion alone. Meeting this condition usually requires a polycyclic diamondoid structure.
Scanning tunneling microscope - A device in which a sharp conductive tip is moved across a conductive surface close enough to permit a substantial tunneling current (typically a nanometer or less). In a common mode of operation, the voltage is kept constant and the current is monitored and kept constant by controlling the height of the tip above the surface; the result, under favorable conditions, is an atomic-resolution map of the surface reflecting a combination of topography and electronic properties. The STM has been used to manipulate atoms and molecules on surfaces.
Self assembly - The process in which disorganized components arrange themselves into a larger structure without external guidance. In the case of molecular self-assembly, molecules are shuffled by Brownian motion until their complementary surfaces bind to each other, building a structure that is defined in the structure of the components and how they interact.
Shear - A shear deformation is one that displaces successive layers of a material transversely with respect to one another, like a crooked stack of cards. Shear is a dimensionless quantity measured by the ratio of the transverse displacement to the thickness over which it occurs.
Sigma bond - A covalent bond in which overlap between two atomic orbitals (e.g., of sp, sp2, or sp3 hybridization) produces a single bonding orbital in which the distribution of shared electrons has a roughly cylindrical symmetry about the axis linking the two atoms; see pi bond, single bond, double bond, triple bond. By themselves, sigma bonds present little barrier to rotation of one substructure with respect to another, although steric effects and cyclic structures may hinder or block rotation.
Single bond - A sigma bond having no associated pi bonds.
Singlet - An electronic state of a molecule in which all spins are paired; see doublet, triplet.
sp,sp²,sp³ - An isolated carbon atom has four valence orbitals: three mutually perpendicular p orbitals, each with a single nodal plane, and one spherically symmetric s orbital. A carbon atom in a typical molecule can be regarded as bonding with four orbitals consisting of weighted sums (termed hybrids) of these s and p orbitals. One common pattern has four equivalent orbitals, each formed by combining the three p orbitals with the s orbital; this is sp3 hybridization. An sp3 carbon atom forms four sigma bonds, usually in a roughly tetrahedral arrangement. Another common pattern has three equivalent orbitals formed by combining two p orbitals with the s orbital; this is termed sp2 hybridization. An sp2 carbon atom forms three roughly coplanar sigma bonds, usually separated by ~120 , and one pi bond (or several fractional pi bonds). If a single p orbital is combined with the s orbital, the result is sp hybridization, forming two sigma bonds and two pi bonds (usually in a straight line). Atoms of other kinds (e.g., N and O) can hybridize in an analogous manner.
Species - In chemistry, a distinct kind of molecule, ion, or other structure.
Stable - Strictly speaking, a system is termed stable if no rearrangement of its parts can form a system of lower free energy. In practice, the term is used with an implicit proviso regarding the transformations to be considered. Hydrogen is not considered unstable merely because it is subject to nuclear fusion at extreme temperatures. A system is usually regarded as stable (more precisely, as kinetically stable) if its rate of transformation to a state of lower free energy is negligible (by some standard) under the ambient conditions. In nanomechanical systems, a structure can commonly be regarded as stable if it has an extremely low rate of transformations when subjected to its intended operating conditions.
State - A physical system is said to be in a particular state when its physical properties fall within some particular range; the boundaries of the range defining a state depend on the problem under consideration. In a classical world, each point in phase space could be said to correspond to a distinct state. In the real world, time-invariant systems in quantum mechanics have a set of discrete states, particular superpositions of which constitute complete descriptions of the system. In practice, broader boundaries are usually drawn. A molecule is often said to be in a particular excited electronic state, regardless of its state of mechanical vibration. In nanomechanical systems, the PES often corresponds to a set of distinct potential wells, and all points in configuration space within a particular well can be regarded as one state. Definitions of state in the thermodynamics of bulk matter are analogous, but extremely coarse by these standards.
Steric - Pertaining to the spatial relationships of atoms in a molecular structure, and in particular, to the space-filling properties of a molecule. If molecules were rigid and had hard surfaces, steric properties would merely be an opaque way of saying "shape"; a flexible side-chain, however, has definite steric properties but no fixed shape. Nanomechanical systems make extensive use of the steric properties of relatively rigid molecules, for which the term "shape" has essentially its conventional meaning so long as one remembers that the surface interactions are soft on small length-scales.
Steric hindrance - Slowing of the rate of a chemical reaction owing to the presence of structures on the reagents that mechanically interfere with the motions associated with the reaction, typically by obstructing the reaction site.
Stiffness - The stiffness of a system with respect to a deformation (e.g., the stiffness of a spring with respect to stretching) is the second derivative of the energy with respect to the corresponding displacement; this measures the curvature of the potential energy surface along a particular direction. Positive stiffness is associated with stability, and a large stiffness can result in a small positional uncertainty in the presence of thermal excitation. Negative stiffnesses correspond to unstable locations on the potential energy surface. Alternative terms for stiffness include force gradient and rigidity.
STM - A scanning tunneling microscope.
Strain - In mechanical engineering, strain is a measure of the deformation resulting from stress (that is, force per unit area); the displacement of one point with respect to another, divided by their equilibrium separation in the absence of stress. In chemistry, a molecular fragment generally has some equilibrium geometry (bond lengths, interbond angles, etc.) when the rest of the molecular structure does not impose special constraints (e.g., bending bonds to form a small ring). Deviations from this equilibrium geometry are described as strain, and increase the energy of the molecule. Strain in the mechanical engineering sense causes strain in the chemical sense.
Stress - Force per unit area applied by one part of an object to another. Pressure is an isotropic compressive stress. Suspending a mass from a fiber places it in tensile stress. Gluing a layer of rubber between two plates and then sliding one over the other (while holding their separation constant) places the rubber in shear stress.
Structural volume - The interior of a diamondoid structure typically consists of a dense network of covalent bonds; a larger excluded volume, however, is determined by nonbonded repulsions at the surface. The structural volume corresponds to a region smaller than the excluded volume, chosen to make properties such as the strength and modulus nearly size independent by correcting for surface effects.
Synthesis - The production of a specific molecular structure by a series of chemical reactions.
System - In scientific usage, usually equivalent to "a collection of matter and energy being analyzed as a unit." In engineering usage, usually equivalent to "a set of components working together to serve a set of purposes."
Temperature - A system in which internal vibrational modes have equilibrated with one another can be said to have a particular temperature. Two systems A and B are said to be at different temperatures if, when brought into contact, heat flows from (say) A to B, increasing the thermal energy of B at the expense of the thermal energy of A.
Thermal energy - The internal energy present in a system as a result of the energy of thermally equilibrated vibrational modes and other motions (including both kinetic energy and molecular potential energy). The mean thermal energy of a classical harmonic oscillator is kT.
Thermal fluctuations - A receptor structure in which a bound ligand of a particular kind is confined on all sides by repulsive interactions (note that favorable binding energies are compatible with repulsive forces). A tight-receptor structure discriminates strongly against all molecules larger than the target.
Thermodynamics - A field of study embracing energy conversion among various forms, including heat, work, and potential and kinetic energy.
Thermoelastic - Both stress and temperature changes alter the dimensions of an object having a finite stiffness and a nonzero thermal expansion coefficient. Applying a stress then produces a temperature change; this can result in a heat flow which then changes the stress: these are thermoelastic effects, and result in losses of free energy.
Transition state - At the saddle point of a col linking two potential wells, the direction of maximum negative curvature defines the reaction coordinate; the transition state is a hypothetical system of reduced dimensionality, free to move only on a hypersurface perpendicular to the reaction coordinate at its point of maximum energy.
Transition state theory - Any of several theories that give approximate descriptions of chemical reaction rates based on the PES of the system, and in particular, on the properties of two potential wells and a transition state between them.
Triple bond - A double bond is formed when a pi bond is superimposed on a single bond; adding a second pi bond results in a triple bond. The two pi bonds have perpendicular nodal planes, and their sum has roughly cylindrical symmetry, permitting rotation in much the same manner as a single bond.
Triplet - An electronic state of a molecule in which two spins are aligned. This term is derived from spectroscopy: a system of two aligned spins has three possible orientations with respect to a magnetic field; each has a different energy, resulting in sets of three field-dependent spectral lines (see doublet, singlet.)
TST - Transition state theory.
Tunneling - A classical particle or system could not penetrate regions in which its energy would be negative, that is, barrier regions in which the potential energy is greater than the system energy. In the real world, however, a wave function of significant amplitude may extend into and beyond such a region. If the wave function extends into another region of positive energy, the barrier is crossed with some probability; this process is termed tunneling (since the barrier is penetrated rather than climbed).
Unimolecular - Occurring to or within a single molecule; like intramolecular, but can refer to fragmentation reactions.
Unsaturated - Possessing double or triple bonds.
Valence electrons - Electrons that can participate in bonds and in chemical reactions; lone-pair electrons are valence electrons, although not participating in a bond.
Valence - In covalent compounds, the valence of an atom is the number of bonds it forms to other atoms.
Van der Waals force - Any of several intermolecular attractive forces not resulting from ionic charges; in this volume, only London dispersion forces are described by this name. Descriptions of the potential energy of nonbonded interactions follow the convention of expressing van der Waals attractive forces and overlap repulsion forces as a single 'van der Waals potential'.
Wave function - In quantum mechanics, a complex function extending over the configuration space of a system; its complex conjugate yields the probability density function, and other mathematical operations yield other physical quantities.
Work - Energy transferred by applying a force over a distance; lifting a mass does work against gravity, and stores gravitational potential energy.
Young's Modulus - A modulus relating tensile (or compressive) stress to strain in a rod that is free to contract or expand transversely in accord with its Poisson's ratio. The relevant measure of strain is the elongation divided by the initial length.

Molecular Manufacturing Glossary

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