Mathematical Challenges from Theoretical/Computational Chemistry (1995) / Chapter Skim
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Glossary
Pages 123-131
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Even without reading the main text, a perusal of this Glossary may convey a sense of the linguistic barriers that occasionally inhibit effective collaboration. Ab intro method Usually, quantum chemical computation procedures that explicitly include all electrons and utilize their full Hamiltonian operator; occasionally used to describe pseudopotential methods or other approaches with minimal semiempirical input.
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From page 124... ...
Biological assay An experimental procedure to test molecules for their ability to elicit a biochemical or pharmacological response. Born-Oppenhenner approximation, potential surface Approximate separation of variables in atomic and molecular quantum mechanics justified by the large ratio of nuclear to electron masses; also the potential energy surface resulting therefrom, as a function of nuclear positions.
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Density matrix Hermitian matrix composed as the direct product of a wavefunction and its complex conjugate. "Reduced density matrices" are obtained by integrating over some of the variables in the full density matrix.
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From page 126... ...
Hessian matrix Symmetric matrix of second partial derivatives, often used in optimization routines for many types of objective functions. A frequently encountered application involves searching for extremes on potential energy surfaces.
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Molecular dynamics Wide Computer simulation technique for many-body systems that relies on numerical solution of classical equations of motion for atoms or molecules and evaluates thermodynamic, kinetic, and structural properties as time averages. Molecular mechanics The field encompassing molecular statics, or the construction of appropriate force fields for representing molecular systems and the associated potential energy minimizations.
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From page 128... ...
Phanmacophore The chemical identity and geometrical arrangement of key substituents in a molecule that confer biochemical or pharmacological effects. Phase in quantum mechanics, the phase angle of a complex wavefunction or order parameter; in statistical mechanics, the state of aggregation of matter (e.g., crystal, liquid, vapor, quasicrystal, liquid crystal)
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From page 129... ...
Quasicrystals Solids exhibiting long-range orientational coherence of local atomic coordination geometry but no crystallographic periodicity or unit cell. Quasi-ergodic Property of a dynamical system that it eventually visits a well-defined neighborhood of any Cinematically accessible point in its phase space.
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From page 130... ...
The basic principles of this discipline were laid down in the nineteenth century by Ludwig Boltzmann, James Clerk Maxwell, and Josiah Willard Gibbs. Stereoisomers Molecules that differ only by mirror inversion of bonds at chiral centers (usually carbon atoms)
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From page 131... ...
phase Phase factor appearing in a nuclear wavefunction that arises from, and varies continuously around, a conical intersection of two electronic potential surfaces. Transition state Saddle point on a potential energy surface separating chemical reactants from products.
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