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note
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For some DNA-acrylamide fragment models, the solvated 2b state is slightly higher in energy than the solvated 2a state for the fully optimized structure because of a more open DNA structure. Nevertheless, the trend in the solvation properties is the same for all three DNA-acrylamide fragment models studied, and the biologically relevant DNA system is expected to have a more compact structure as a result of additional base pairs.
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41
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note
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In Figure 5, the product free energy surfaces are mixtures of the 2a and 2b VB states. Thus, the free energy differences between the lowest two product states in Figure 5 parts b and c are not the same as the values reported in Table 3 for the pure VB states.
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