Posts Tagged ‘ATAT duplex’

The thermodynamic energies of left and right handed DNA.

Saturday, March 5th, 2011
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In this earlier post, I noted some aspects of the calculated structures of both Z- and B-DNA duplexes. These calculations involved optimising the positions of around 250-254 atoms, for d(CGCG)2 and d(ATAT)2, an undertaking which has taken about two months of computer time! The geometries are finally optimised to the point where 2nd derivatives can be calculated, and which reveal up to 756 all-positive force constants and 6 translations and rotations which are close to zero! This now lets one compute the thermodynamic relative energies using ωB97XD/6-31G(d) (for 2nd derivatives) and 6-31G(d,p) (for dispersion terms). All geometries are optimized using a continuum solvent field (water), and are calculated, without a counterion, as hexa-anions. (more…)