Three 1,4-disubstituted anthraquinone dyes with bis(4-n-butylphenyl) substituents connected via amine or amide linking groups have been studied as guest molecules dissolved in the nematic host E7. UV-visible absorption spectroscopy has shown each of the dyes to exhibit multiple absorption bands in the visible region, and dichroic order parameters obtained from polarised spectra of aligned guest–host samples were shown to differ significantly between the bands for each dye, and between the dyes. Time-dependent density functional theory calculations indicated that each dye exhibits several transitions, giving transition dipole moment vectors with a range of orientations, and fully atomistic molecular dynamics simulations of the guest–host mixtures showed differences in the calculated molecular alignments of the dyes. Combining the results from these two sets of calculations enabled a comparison of molecular alignment models based on the moments of inertia and the surface tensors of the dyes. The match between calculated and experimental values was improved significantly when using the surface tensor rather than the moment of inertia model, indicating that the shapes of the molecular surfaces of these dyes are crucial to their alignment. A novel method of calculating polarised UV-visible absorption spectra of dyes in liquid crystal hosts is also presented.