Rigid rotor harmonic oscillator mode

In order to evaluate the thermodynamic functions of the process (5), it is necessary to know the interaction energy, equilibrium geometry and frequencies of the normal vibration modes of the bases and base pairs involved in equilibrium process. Interaction energies and geometries are evaluated using empirical potential or quantum chemically (see next section), and normal vibrational frequencies are determined by a Wilson FG analysis implemented in respective codes. Partition functions, computed from AMBER 4.1, HF/6-31G and MP2/6-31G (0.25) constants (see next section), are evaluated widiin the rigid rotor-harmonic oscillator-ideal gas approximations (RR-HO-IG). We have collected evidence [26] that the use of RR-HO-IG approximations yields reliable thermodynamic characteristics (comparable to experimental data) for ionic and moderately strong H-bonded complexes. We are, therefore,... 

In order to calculate the thermodynamic functions of the process described by Eq. (15), it is necessary to known the equilitHium geometry and tl frequencies of the normal vibrational modes of all species involved in the equilibrium process, as well as interaction energy, A . Partition functions, used for relatively strong vdW molecules, were evaluated using the rigid rotor-harmonic oscillator approximation. 

In the gas phase, it is usually sufhcient to calculate the partition functions and associated thermal corrections to the enthalpy and entropy using the standard textbook formulae [31] for an ideal gas under the harmonic oscillator-rigid rotor approximation, provided one then makes explicit corrections for low-frequency torsional modes. These modes can be treated instead as one-dimensional hindered internal rotations using the torsional eigenvalue summation procedure described in Ref. [32]. Rate and equilibrium constants can then be obtained from the following standard textbook formulae [31] ... 

The above treatment of hindered rotors assumes that a given mode can be approximated as a one-dimensional rigid rotor, and studies for small systems have shown that this is generally a reasonable assumption in those cases (82). However, for larger molecules, the various motions become increasingly coupled, and a (considerably more complex) multidimensional treatment may be needed in those cases. When coupling is significant, the use of a one-dimensional hindered rotor model may actually introduce more error than the (fully decoupled) harmonic oscillator treatment. Hence, in these cases, the one-dimensional hindered rotor model should be used cautiously. 

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