  We present molecular mechanics {and spectroscopic} calculations on prototype
artificial light harvesting systems consisting of chromophores attached to a
tobacco mosaic virus (TMV) protein scaffold. These systems have been
synthesized and characterized spectroscopically, but information about the
microscopic configurations and geometry of these TMV-templated chromophore
assemblies is largely unknown. We use a Monte Carlo conformational search
algorithm to determine the preferred positions and orientations of two
chromophores, Coumarin 343 together with its linker, and Oregon Green 488, when
these are attached at two different sites (104 and 123) on the TMV protein. The
resulting geometric information shows that the extent of disorder and
aggregation properties, and therefore the optical properties of the
TMV-templated chromophore assembly, are highly dependent on the choice of
chromophores and protein site to which they are bound. We used the results of
the conformational search as geometric parameters together with an improved
tight-binding Hamiltonian to simulate the linear absorption spectra and compare
with experimental spectral measurements. The ideal dipole approximation to the
Hamiltonian is not valid since the distance between chromophores can be very
small. We found that using the geometries from the conformational search is
necessary to reproduce the features of the experimental spectral peaks.
