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…)

## March 5, 2011

### The thermodynamic energies of left and right handed DNA.

## January 1, 2011

### A comparison of left and right handed DNA double-helix models.

When Watson and Crick (WC) constructed their famous 3D model for DNA, they had to decide whether to make the double helix left or right handed. They chose a right-handed turn, on the grounds that their attempts at left-handed models all “*violated permissible van der Waals contacts*“. No details of what these might have been were given in their original full article (or the particular base-pairs which led to the observation). This follow-up to my earlier post explores this aspect, using a computer model.