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Fig. 5. Electron densities at the N₄ nucleotide positions of the outside (continuous) and inside (crossing) strands that complement the N₇ nucleotide forming hydrogen bonds (H-bonds) or halogen bonds (X-bonds) in the H₂J junction. The 2F_o - F_c electron density maps calculated at 1s and 3s levels are shown in blue and red, respectively, and the F_o F_c difference map calculated at 2s and 3s levels shown in yellow and green, respectively. (Left) N₄ nucleotide base of the outside strand of the asymmetric unit modeled as an adenine, with the N₇ nucleotide base of the complementary strand modeled as a uracil. The 2F_o - F_c map extends away from the C2 carbon toward the minor groove of the purine base, whereas the F_o - F_c map shows a strong, spherical difference density located in the minor groove at a distance equivalent to a C-N covalent bond from the C2 carbon (arrow). Together, the two sets of electron densities indicate the presence of an extracyclic N2 amino nitrogen, consistent with this base being a guanine and its complement at nucleotide N₇ being a cytosine. (Right) The base for the same position of the inside stand also modeled as an adenine. In this case, the calculated electron densities show no evidence for an N2 amino group, indicating that it is properly modeled as an adenine.

Fig. 6. Estimating the bromine occupancy at the N₇ nucleotide on the outside strand (H-isomer) of Br₁J (labeled as U17, black triangles). The amount of bromine located at the N₇ position of the Br₁J construct was quantified by adding increments of bromine (in 1%, 2%, 3%, 4%, and 5% increments for five separate studies, closed triangles) and monitoring the effect on the crystallographic R_free parameter. These data were fit to a second-order polynomial equation (R of fit = 0.91). The minimum for the curve and the average data falls at ~0.08 Br. As controls, increments of bromine atoms were added to pyrimidine bases that should have no bromines in either isomer form [C₂ of the inside strand (open squares) and C18 of the outside strand (gray circles)] and are on the same helical arm as U17.

Fig. 7. Electrostatic potentials from ab initio calculations of the bromine halogen bonds in Br₂J and Br₁J show the characteristic anisotropic distribution of charges on the bromine atoms. Charge potentials were rendered by using SPARTAN (Wavefunction, Inc., Irvine, CA), with negative electrostatic charges shown in red, positive charges in blue, and neutral charges in yellow. The energies of the phosphate and uracil base components have been subtracted from the overall energies to calculate the interaction energy of each model system The geometry of the X-bond in the Br₂J geometry is estimated to be ~3 kcal/mol more stable than that in Br₁J.