Time-resolved Faradary rotation experiments have demonstrated coherent transfer of electron spin between CdSe colloidal quantum dots coupled by conjugated molecules. We employ here a Green's function approach, using semi-empirical tight-binding to treat the nanocrystal Hamiltonian and Extended Hückel theory to treat the linking molecule Hamiltonian, to obtain the coherent transfer probabilities from atomistic calculations, without the introduction of any new parameters. Calculations on 1,4-dithiolbenzene and 1,4-dithiolcyclohexane linked nanocrystals agree qualitatively with experiment and provide support for a previous transfer Hamiltonian model. We find a striking dependence on the transfer probabilities as a function of nanocrystal surface site attachment and linking molecule conformation. Additionally, we predict quantum interference effects in the coherent transfer probabilities for 2,7-dithiolnaphthalene and 2,6-dithiolnaphthalene linking molecules. We suggest possible experiments based on these results that would test the coherent, through-molecule transfer mechanism.