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0141728274
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note
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The temperature was obtained as an average during the CPMD run. Instead of using a thermostat, another common method of adjusting the system to a desired temperature is to use, as the initial temperature for the CPMD simulation, a temperature which is approximately two times higher than the desired one. As time progresses, the system adjusts to the desired temperature and fluctuates around an average value, which in the present case equals 519 K.
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37
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0141616348
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note
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The system was adjusted to the particular constraint value within 1000 steps of the simulation. Therefore, the first ≈1000 steps were not taken into account for an estimation of the average force (average Lagrangian) acting on the system as a result of the constraint introduced in the system. After 1000 steps of the simulation, the average value of the Lagrangian fluctuates around a mean value that is taken for the estimation of the free energy through the integration scheme (for technical details, see refs. [20, 21]).
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38
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0141728271
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note
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1).
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39
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0141839556
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note
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Average temperatures of 521 K and 523 K as obtained during the CPMD trajectories.
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40
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0141504862
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note
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More specifically, this corresponds to a part of the translational energy that is associated with only one degree of freedom, namely the reaction coordinate. In case there are no other factors that might energetically facilitate a reaction (e.g. an entropy increase during a process or an exothermic reaction), only the thermal motion of the system in the direction of a reaction coordinate makes the reaction feasible.
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41
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0141839562
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note
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For details of the labeling code, see ref. [5]. A superscript in the labeling scheme points to one specific conformer although, in the case of the CPMD studies, because of the dynamical picture, we refrain from addressing a particular conformer. Therefore, labeled structures without a superscript represent a conformational subspace.
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42
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0141616346
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note
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A change in only one O-H distance is depicted in the inset in Figure 5. The distance between the other hydrogen atom attached to C4 and oxygen was also monitored resulting in a picture comparable to the that depicted in the inset of Figure 5.
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43
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0141839555
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note
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The short CPMD simulations for a particular value of the constrained parameter lasted for at least 0.9 ps. The system was adjusted to the particular constraint value within ≈3000 steps of the simulation. Therefore, the first 3000 steps were not taken into account for an estimation of the average force acting on the system as a result of the constraint introduced into the system.
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44
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0003651195
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