Combined local mode spectroscopy and ab initio modeling are used to demonstrate for the first time that oxygen atoms in thermal double donors (TDD) in Si are in close proximity. The observed vibrational modes in 16O, 18O, and mixed isotopic samples are consistent with a model involving [110] aligned oxygen chains made up of an insulating core lying between electrically active ends. The model also explains the minute spin density observed on oxygen in TDD+ as well as the piezospectroscopic tensors of the donors. The analogy between the thermal donors and quantum dots is emphasized.