The relative energies of radical cation states on nucleobases in DNA are considerably affected by the local distribution of water molecules and counterions. In fact, fluctuations of ΔG are large enough to render electron‐hole transfer from G+ to A energetically feasible, thus allowing a changeover from the generally accepted G‐hopping mechanism to A‐hopping (see picture).

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The solvent reorganization energy λs can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)−acceptor (A) distance R DA. To estimate λs and the resulting effective contribution β s to the falloff parameter β for the overall transfer rate constant, the Poisson equation was solved numerically for several systems representing DNA duplexes, 5‘-GGGT n GGG-3‘, in a realistically structured heterogeneous dielectric, as determined by molecular dynamics (MD) simulations. The charge transfer was modeled primarily for holes localized on single guanine bases. Effects of thermal fluctuations on λs were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of λs were found to be rather insensitive to thermal fluctuations of the DNA fragments but depended in crucial fashion on details of the dielectric model (shape and dielectric constants of various zones) that was used to describe the polarization response of the DNA and its environment to the charge transfer. λs was calculated to increase rapidly at small R DA values (<15 Å), and accordingly the falloff parameter β s (defined as a local function of R DA) decreases appreciably with increasing R DA (from 1.0 Å-1 with only one intermediate base pair between D and A to 0.15 Å-1 for systems with five intervening pairs). Calculated λs values were accurately fitted (standard deviation of ∼0.5 kcal/mol) to a linear function of 1/R DA, including all cases except contact (R DA = 3.4 Å), where some overlap of D and A sites may occur. A linear fit to an exponential (of form exp(−βs R DA)) gave comparable accuracy for the entire R DA range. λs based on D and A holes delocalized over two adjacent guanine bases was uniformly ∼12 kcal/mol smaller than the corresponding results for holes localized on single guanines, almost independent of R DA. The internal reorganization energy for hole transfer between GC pairs was calculated at 16.6 kcal/mol at the B3LYP/6-31G* level.

In the present work we present a comprehensive study of the magneto-structural correlations of a series of ferromagnetic triply heterobridged Cu(II) dinuclear compounds containing [Cu(2)(mu-O(2)CR)(mu-OH)(mu-X)(L)(2)](2+) ions (where X = OH(2), Cl(-), OMe(-) and L = bpy, phen, dpyam) which have the particularity of being all ferromagnetic. The present theoretical study, based on hybrid density functional theory (DFT) calculations, leads to strong conclusions about the role of the pentacoordination geometry of the Cu(II) ions (square base pyramidal (SP) or trigonal bipyramidal (TBP) coordination) and the nature of the third bridging ligand in determining the final value of the magnetic coupling constants in this series of compounds. These investigations point toward the existence of a maximum value for the ferromagnetic interaction and may offer some useful information to synthetic chemists aiming at obtaining new compounds with enhanced ferromagnetism.

During the last two decades, electron transfer (ET) through DNA and its artificial analogues has been an area of extensive experimental and theoretical studies. This process plays an important role in biology (damage and repair of DNA in living cells) and is of potential interest in material sciences. Because structural dynamics of the π stack and its environment affect essentially the electron transport, some significant details of excess charge migration cannot be derived from experiments. Computer simulations of the ET process provide microscopic insights into mechanisms of this process. In the paper, we consider computational methods used to describe the propagation of excess charges through π stacks of DNA and related systems. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

Five new triply bridged dinuclear Cu(II) compounds have been synthesized, and their magnetic properties have been measured and characterized. The magnetic coupling constants (J) of these compounds plus a previously structurally characterized compound of the same type have been derived by appropriate fitting of the experimentally measured molar susceptibility variation with the temperature. Two of the compounds are ferromagnetically coupled, and three are antiferromagnetically coupled with J values in the [+150, -40] cm(-1) range. The validity of the structural aggregate Addison's parameter as a qualitative magneto-structural correlation is confirmed. The origin of the magnetic interactions and the magnitude of the magnetic coupling have been analyzed by means of density functional theory-based calculations using a variety of state of the art exchange-correlation potentials. It is shown that the long-range separated LC-ωPBE provides the overall best agreement with experiment for this family as well as for a set of previously reported hetero triply bridged dinuclear Cu(II) compounds, especially for ferromagnetic systems.

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Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studies of DNA hairpins. Because the capping groups in the hairpins can remarkably influence the structure and flexibility of the pi stack, and therefore, the charge transfer rate, the question arises of whether the HT parameters obtained for hairpins may be transferred to DNA oligomers. On the basis of large-time scale QM/MD simulations, we compare structural and electronic parameters of AT stacks in hairpins and DNA oligomers. We find that even in short hairpins, Sa-AA-Sd and Sa-AAA-Sd, the effects of the capping chromophores on the structure of the pi stack and the HT couplings properly averaged over MD trajectories are relatively small, and therefore, the hairpins are good models to study hole transfer through DNA. By contrast, the calculations of the electronic couplings based on the average structures of the systems lead to essential errors in the HT rate and the misleading statement that the charge transfer properties of DNA domains within hairpins are quite different from those of normal sequences.