We present a detailed low-temperature investigation of the statics and dynamics of the anions and methyl groups in the organic conductors (TMTSF)$_2$PF$_6$ and (TMTSF)$_2$AsF$_6$ (TMTSF : tetramethyl-tetraselenafulvalene). The 4 K neutron scattering structure refinement of the fully deuterated (TMTSF)$_2$PF$_6$-D12 salt allows locating precisely the methyl groups at 4 K. This structure is compared to the one of the fully hydrogenated (TMTSF)$_2$PF$_6$-H12 salt previously determined at the same temperature. Surprisingly it is found that deuteration corresponds to the application of a negative pressure of 5 x 10$^2$ MPa to the H12 salt. Accurate measurements of the Bragg intensity show anomalous thermal variations at low temperature both in the deuterated PF$_6$ and AsF$_6$ salts. Two different thermal behaviors have been distinguished. Low-Bragg-angle measurements reflect the presence of low-frequency modes at characteristic energies {theta}$_E$ = 8.3 K and {theta}$_E$ = 6.7 K for the PF$_6$-D12 and AsF$_6$-D12 salts, respectively. These modes correspond to the low-temperature methyl group motion. Large-Bragg-angle measurements evidence an unexpected structural change around 55 K which probably corresponds to the linkage of the anions to the methyl groups via the formation of F...D-CD2 bonds observed in the 4 K structural refinement. Finally we show that the thermal expansion coefficient of (TMTSF)$_2$PF$_6$ is dominated by the librational motion of the PF$_6$ units. We quantitatively analyze the low-temperature variation of the lattice expansion via the contribution of Einstein oscillators, which allows us to determine for the first time the characteristic frequency of the PF6 librations: {theta}$_E$ = 50 K and {theta}$_E$ = 76 K for the PF$_6$-D12 and PF$_6$-H12 salts, respectively.
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