Intermolecular interactions in the N≡C–C≡C–H dimer

Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

Crystallographic/Experimental Electron Density Characterizations and Reactions with Nucleophiles of β-Enaminonitriles Possessing a Pyrrolobenzazepine Core

In connection with a total synthesis of cephalotaxine (1a), we have examined the addition of various nucleophilic reagents to [ABC] subunits 2 and 7 possessing a pyrrolobenzazepine core. In fact, this reaction implicates invariably the carbonyl group of 2. Regarding the reaction of 7 with nucleophiles, the most striking aspect is the complete lack of reactivity of the enaminonitrile moiety. For instance, the condensation of 7 with methylmagnesium bromide involves exclusively the cleavage of the dioxole ring, yielding regioisomers 9 and 10. With the aim of understanding the unexpected reactivity of 2 and 7 toward nucleophiles, crystallographic studies of 2 and 7 and an experimental electron density determination of 7 were carried out. The marked reactivity of the carbonyl group of 2 was interpreted by invoking the weakness of the amide resonance, due to a pronounced delocalization of the N(9) lone pair over the enaminonitrile moiety. The electron density study of 7 reveals this electron delocalization along the enaminonitrile fragment, highlighted and quantified through the bond geometries, topological indicators, and atomic charges, a phenomenon that is responsible for the failure of the addition of nucleophilic species.

Ab initio inter-radical potential for p-phenylenediamine radical cation dimer

Ab initio molecular orbital calculations were carried out to investigate the inter-radical interaction of the paired p-phenylenediamine radical cations in the singlet state. After initial optimization of the dimer in the parallel sandwich (D2h) and parallel displaced (Cs) configurations at the B3LYP/6-31G* theoretical level, the MP2/6-31G* and B3LYP/6-31G* single energies of the dimer were calculated as a function of the inter-radical distance R. The depths of the potential minima near R = 3.2 A were estimated to be in the order of the hydrogen bonding energy, assuming that the electrostatic contribution between the cations is canceled out by the attractive contributions due to the counter anions on the aspect of a simple electrostatic model. This can be related to the indications of the cation dimer formation in solution in the presence of counter anions at a low temperature reported previously in the literature by resonance Raman and electronic absorption spectra. The inter-radical (Raman active) frequencies of the dimer were calculated, one of which corresponds to the reported value at 161 cm(-1) observed in the resonance Raman spectrum in ethanol at 200 K by Yokoyama and Maeda (Chem. Phys. Lett. 48 (1977) 59).