The making and breaking of σ bonds is an integral part of almost all photochemical reactions. Yet, the electronic states of σ electrons are not nearly as well understood as the states of π-electron systems. Efforts in our laboratory to enhance the current state of their understanding are described, using the specific example of oligosilanes. We address the intrinsically cyclic nature of σ delocalization and its dependence on chain length and conformation, both in terms of theory and spectroscopic experiments, from the simplest disilane chromophore to the spectral properties of the individual conformers of permethylated heptasilane. We also describe a new low-energy luminescence from certain conformers of permethylated oligosilanes.
The TD B3LYP/6-311G(d,p) method slightly overestimates the excitation energies of the first UV absorption band of the all-transoid conformers of SinMe2n + 2 (n = 2-8, 10), deduced from temperature-dependent measurements on conformer mixtures in hydrocarbon solvents, by a nearly constant amount (approximately 2000 cm-1). The TD B3LYP/6-31G(d) results are less satisfactory. The first band is calculated to be due to a sigma pi * excitation in Si2Me6 and to a superposition of overlapping sigma sigma * and sigma pi * excitations in the longer oligosilanes. The sigma pi * excitation is calculated to lie a little below the sigma sigma * excitation up to Si4Me10, the two transitions are nearly degenerate in Si5Me12, and the sigma sigma * excitation drops increasingly below the sigma pi * as the chain length is extended. The dipole strength of the sigma sigma * excitation grows by 4.8 D2 (D = debye) per added SiSi bond (more slowly up to n = 5) and the calculation overestimates it by a factor of about three. The sigma pi * excitation is computed to carry no or almost no oscillator strength, but as noted earlier by others, its presence is critical for the interpretation of the observed thermochromism. Upon cooling below room temperature, the first absorption maximum is blue-shifted in short chains and red-shifted in long chains. Unlike the prior investigators, we attribute the blue shift to the disappearance of hot bands built on the sigma pi * origin using intensity borrowing sigma-pi mixing vibrations (b1 in Si3Me8). As usual, the red shift is attributed to the disappearance of twisted conformers, which have higher calculated sigma sigma * excitation energies.
The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.
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