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In-Depth Information
Among the processes of excitation energy transfer in quasi one-dimensional
molecular chains, collective processes, in particular, soliton mechanisms, are of
special importance. A soliton (also called solitary wave) is described as energy
excitation of the medium, propagating along the medium at long distances.
A fundamental role in studying these mechanisms in molecular systems and in
using them to explain a number of biological phenomena was played by the
prominent Soviet physicist A. S. Davydov and his school.
The concept of soliton switching, developed by Carter, is based on the
rearrangement of electronic structure initiated by collective processes of this type.
Below follows a brief description of these interesting molecular entities.
3.2.1 More Details: Molecular Structure—Spatial
Configuration of Molecular Nuclei
We use the term molecular structure to refer to the set of constants and functional
characteristics that describe the relative position and relative motion of the nuclei
and electrons of the molecule. Based on this premise, three main groups of
molecular characteristics are usually considered:
Parameters of the geometric configuration of the nuclei of the molecule (a full
set of internuclear distances and bond angles is often called the structure of the
molecule in a narrow sense)
Dynamic characteristics that determine the relative motion of the nuclei of the
molecule (energy levels, frequencies of oscillation, average displacements of
nuclei from their equilibrium positions, and so on)
Electronic characteristics (energy levels of the electrons of the molecule, the
electron density distribution and its further characteristics, such as electric
dipole and quadrupole moments of the molecule, etc.)
It is conventional to characterize the relative position of the nuclei of the
molecule by their equilibrium configuration corresponding to the minimum poten-
tial energy of the nuclei.
Among the vast number of molecules known today organic carbon compounds
display the largest variety. A unique feature of carbon is that its atoms are combined
into chains of repeating units of varying length. In this manner molecules are
formed that belong to various classes of organic compounds—saturated and unsat-
urated hydrocarbons, aromatic compounds, etc. The carbon atoms forming organic
compounds can exist in three structural states (Fig.
3.16
). The first one is the
tetrahedral state in which the carbon atom is at the center of a tetrahedron, and its
bonds with other atoms are directed to the vertices of the tetrahedron. In the second
state, which is called trigonal, the bonds of the carbon atom are directed from the
center of a plane triangle to its vertices. Finally, in the linear state, all three atoms—
