Nucleotide bases, localization

Murray JS, Peralta-Inga Z, Politzer P, Ekanayake K, LeBreton P (2001) Computational characterization of nucleotide bases Molecular surfaceelectrostatic potentials and local ionization energies, and local polarization energies, Int. J. Quantum Chem. 83 245-254... 

We have applied this method first to formaldehyde and to l-oxy-3-aza-butadiene (see Figure 1). Both calculations have shown, in the MP2 and T2T2 approximation, that the method provides about 90% of the correlation energy, if one takes into account only excitations to the first neighbors as compared with the case where the orbitals are not localized and one takes into account all excitations.8,13 Since in the case of the larger nucleotide bases we could not perform a full T2T2 calculation, we could use the above described... 

As far as the evidence available is concerned there is no reason to suppose that histidine biosynthesis occurs in a different manner to that worked out for bacteria and fungi. However given the actual weight of evidence available this is not a very firm conclusion. Similarly the limited results obtained suggest that the pathway is feedback regulated by histidine at ATP-phosphoribosyltransferase. No information is available on any crosspathway regulation, neither with respect to other amino acids nor to nucleotide bases, or on the localization of the pathway within the plant cell. 

As a first step in this direction, an investigation of the localization properties of the filled and virtual (both a and n) orbitals of the four nucleotide bases has been performed. It has been found that the filled... 

As the next step in handling the correlation problem in larger molecules, the coupled-cluster doubles (CCD), also called coupled-pair many-electron theory (CPMET), introduced into the electronic correlation problem by Cizek, was first applied to smaller molecules and then to the nucleotide bases using localized orbitals. 

If a periodic polymer chain has a very narrow bandwidth [like the so-called narrow-band (widths of order 10" eV) periodic nucleotide base stacks or base pair stacks in Table 9.11) or a polymer consists of a nonperiodic sequence of different types of units, then the electronic states become localized molecular states and coherent Bloch-type conduction is no longer possible. 

It should be pointed out here that in the case of polymers with a larger molecule as unit cell (like TCNQ and TTF stacks, nucleotide base stacks or homopolypeptides with a larger amino acid residue as unit cell) it is necessary to localize further the WF s or Bloch orbitals into different parts of the molecule which is repeated in the periodic polymer. For that purpose one has to investigate how is possible to combine the Fourier transformation leading to WF s with the usual localization... 

The duplex with the normal HBB gene has one hydrogen-bonded base pair more than the duplex with the mutated HBB gene, and therefore the first duplex has more double-helical region. The single-nucleotide mismatch has a significant effect on the structure of the duplexes, which in turn strongly influences the local environment where the clusters could form. 

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