We know the kinematic equation in terms of quaternion is the following:
$$\dot{q}(t) = \frac{1}{2}\Omega(t)q(t)$$ where $q(t)$ is the unit quaternion. Now if I want to differentiate the above equation w.r.t "$t$" again:
$$\ddot{q}(t) = \frac{1}{2}\dot\Omega(t)q(t)+\frac{1}{2}\Omega(t)\dot q(t)$$ where $$\dot\Omega(t) = \begin{bmatrix} 0 & \omega_3(t) & -\omega_2(t) & \omega_1(t) \\ -\omega_3(t) & 0 & \omega_1(t) & \omega_2(t) \\ \omega_2(t) & -\omega_1(t) & 0 & \omega_3(t) \\ -\omega_1(t) & -\omega_2(t) & -\omega_3(t) & 0\end{bmatrix}'\\ = \begin{bmatrix} 0 & \alpha_3(t) & -\alpha_2(t) & \alpha_1(t) \\ -\alpha_3(t) & 0 & \alpha_1(t) & \alpha_2(t) \\ \alpha_2(t) & -\alpha_1(t) & 0 & \alpha_3(t) \\ -\alpha_1(t) & -\alpha_2(t) & -\alpha_3(t) & 0\end{bmatrix}$$
where $\alpha(t)$ denotes the angular acceleration.
The derivation of the above is one step of my research, just sincerely make sure that if the above makes sense (mathematical and physical). I search a few papers, just by the title of my question; however, I have not seen "one step" of these papers related to the above.
References:
http://www.tu-berlin.de/fileadmin/fg169/miscellaneous/Quaternions.pdf
http://www.euclideanspace.com/physics/kinematics/angularvelocity/QuaternionDifferentiation2.pdf
http://ieeexplore.ieee.org/document/127239/
https://arxiv.org/abs/1510.02224
Actually I am reading a paper related to the soft-landing problem:
http://web.mit.edu/larsb/www/iee_tcst13.pdf
And focus on the state space representation of a system with the state $x = [q \ \ \dot q ]$. And include this to a optimization problem.
Hope this will gain a bit physical point of view.