Cytosine stack

The MCF method applied to generate an effective potential of the water environment surrounding polynucleotide chains is presented in Chapter 7. The respective positions of the water molecules and ions were taken from the results of extensive Monte Carlo simulations performed by dementi s group. The first results as to how this effective potential caused by the environment affects the band structure of a cytosine stack are also reviewed in this chapter. 

Correlation Energy and Quasi-Particle Gap in a Cytosine Stack... 

Inspection of the five water clusters (see Figure 7.1) around a cytidine unit shows, however, that most of the water molecules are situated in the immediate neighborhood of the cytosine molecules (forming the larger part of their first hydration shell) while only some of the water molecules are further apart than in the case of a cytosine stack. Therefore, the error is less than one would expect without looking at the details. When the motivation of this model calculation is understood in the sense discussed above, it can be regarded as the next step after the work of Clementi, who calculated the band structure of polyethylene in the field of periodic point charges situated around it in different ways. 

TABLE 7.1. Conduction and Valence Bands of a Cytosine Stack Calculated without and with Hydration ... 

In a subsequent calculation the intermediate exciton theory with correlation was applied to a cytosine stack, the superimposed cytosine molecules possessing the same relative geometry as in the in vivo stable DNA B. In this calculation, only a double-C basis was applied (no polarization functions) owing to the rather large size of the unit cell (a cytosine molecule). ... 

Table 8.2 presents the calculated exciton energies and intensities of the first two exciton bands of a cytosine stack. ... 

Since the unit cells in homopolynucleotides and homopolypeptides are in most cases fairly large, calculations performed until now are mostly only minimal basis ab initio band structure calculations. There are a few cases when aperiodicity in DNA and proteins were treated and a pilot calculation has been performed to treat the effect of the surrounding water on a cytosine stack /3/. 

For a cytosine stack model calculations have been performed to investigate the effect of water molecules on its electronic structure (16). In this first approach the water structure of a cytidine unit in aperiodic B-DNA obtained with the help of Monte Carlo computer experiments (17) has been used. This choice of the water structure, of course, does not give a realistic description for cytosine,but we get in a relatively simple model calculation an order of magnitude estimate of the effects. The bound water molecules act on the electronic system of the stacked nucleotide bases as an external field. By a proper representation of the electron distribution of the water molecules through point charges one can easily calculate the matrix elements of this perturbing field in terms of the Bloch functions of the finite polymer and include in this way its effect on the band structure. 

Until now the effect of the water molecules and the ions on the energy band structures of the periodic homopolynucleotides has not been investigated. Therefore, in this Section only a short review will be given of the method to determine the point charge representation of the hydration shell, as it has been used in the study of the effect of hydration on the electronic structure of a cytosine stack (see Section 2.1). 

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