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Salt bridge An ionic bond between charged groups that are part of larger covalent structures; salt bridges occur in many proteins.
Saturated An organic molecule is described as saturated if it is a closed shell species lacking double or triple bonds; forming a new bond to a saturated molecule requires the cleavage of an existing bond.
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.
Shear modulus Shear stress divided by shear strain; has the units of force per unit area.
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.
Statistical mechanics Statistical mechanics treats the detailed state of a system (its quantum state or, in classical models, its position in phase space) as unknown and subject to statistical uncertainties; entropy is a measure of this uncertainty. Statistical mechanics describes the distribution of states in an equilibrium system at a given temperature (describing either the distribution of probabilities of quantum states or the probability density function in phase space), and can be used to derive thermodynamic properties from properties at the molecular level. These equilibrium results are useful in nanomechanical design.
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."


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