Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations

The binding orientation of a norindenoisoquinoline in the topoisomerase I-DNA cleavage complex is primarily governed by pi-pi stacking interactions

High level ab initio quantum chemical studies have shown that the binding orientations of topoisomerase I (top1) inhibitors such as camptothecins and indenoisoquinolines are primarily governed by pi-pi stacking. However, a recently discovered norindenoisoquinoline antitumor compound was observed by X-ray crystallography to adopt a "flipped" orientation (relative to indenoisoquinolines), which facilitates the formation of a characteristic hydrogen bond with the Arg364 of top1 in its binding with the top1-DNA complex. This observation raises the possibility that hydrogen bonding between the norindenoisoquinoline nitrogen and the Arg364 side chain of top1 might be responsible for the "flip". It also brings into question whether pi-pi stacking, as opposed to hydrogen bonding, is primarily responsible for the binding orientations of indenoisoquinolines and norindenoisoquinolines. In this study, the forces responsible for the binding orientation of a norindenoisoquinoline in the DNA cleavage site were systematically investigated using MP2 methods. The theoretical calculation of the preferred binding orientation based solely on pi-pi stacking was completely consistent with the actual orientation observed by X-ray crystallography, indicating that the binding of the norindenoisoquinoline in the top1-DNA complex is mainly governed by pi-pi stacking forces and that the "flip" can occur independently from hydrogen bonding.

The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water

Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementi's double zeta basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO(4)(-), to Na(+), and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zurich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO(4) (-) groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.

Dispersion interactions govern the strong thermal stability of a protein

Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an extremely thermostable protein, which makes it an attractive subject of protein folding and stability studies. A fundamental question arises as to what the reason for such extreme stability is and how it can be elucidated from a complex set of interatomic interactions. We addressed this issue first theoretically through a computational analysis of the hydrophobic core of the protein and its mutants, including the interactions taking place inside the core. Here we show that a single mutation of one of phenylalanine's residues inside the protein's hydrophobic core results in a dramatic decrease in its thermal stability. The calculated unfolding Gibbs energy as well as the stabilization energy differences between a few core residues follows the same trend as the melting temperature of protein variants determined experimentally by microcalorimetry measurements. NMR spectroscopy experiments have shown that the only part of the protein affected by mutation is the reasonably rearranged hydrophobic core. It is hence concluded that stabilization energies, which are dominated by London dispersion, represent the main source of stability of this protein.

Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic?

Autoionization of water which gives rise to its pH is one of the key properties of aqueous systems. Surfaces of water and aqueous electrolyte solutions are traditionally viewed as devoid of inorganic ions; however, recent molecular simulations and spectroscopic experiments show the presence of certain ions including hydronium in the topmost layer. This raises the question of what is the pH (defined using proton concentration in the topmost layer) of the surface of neat water. Microscopic simulations and measurements with atomistic resolution show that the water surface is acidic due to a strong propensity of hydronium (but not of hydroxide) for the surface. In contrast, macroscopic experiments, such as zeta potential and titration measurements, indicate a negatively charged water surface interpreted in terms of preferential adsorption of OH(-). Here we review recent simulations and experiments characterizing autoionization at the surface of liquid water and ice crystals in an attempt to present and discuss in detail, if not fully resolve, this controversy.

Non-covalent interactions in biomacromolecules

Non-covalent interactions play an important role in chemistry, physics and especially in biodisciplines. They determine the structure of biomacromolecules such as DNA and proteins and are responsible for the molecular recognition process. Theoretical evaluation of interaction energies is difficult; however, perturbation as well as variation (supermolecular) methods are briefly described. Accurate interaction energies can be obtained by complete basis set limit calculations providing a large portion of correlation energy is covered (e.g. by performing CCSD(T) calculations). The role of H-bonding and stacking interactions in the stabilisation of DNA, oligopeptides and proteins is described, and the importance of London dispersion energy is shown.

Water surface is acidic

Water autoionization reaction 2H2O --> H3O- + OH- is a textbook process of basic importance, resulting in pH = 7 for pure water. However, pH of pure water surface is shown to be significantly lower, the reduction being caused by proton stabilization at the surface. The evidence presented here includes ab initio and classical molecular dynamics simulations of water slabs with solvated H3O+ and OH- ions, density functional studies of (H2O)(48)H+ clusters, and spectroscopic isotopic-exchange data for D2O substitutional impurities at the surface and in the interior of ice nanocrystals. Because H3O+ does, but OH- does not, display preference for surface sites, the H2O surface is predicted to be acidic with pH < 4.8. For similar reasons, the strength of some weak acids, such as carbonic acid, is expected to increase at the surface. Enhanced surface acidity can have a significant impact on aqueous surface chemistry, e.g., in the atmosphere.

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared withab initioquantum mechanics calculations

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.

Quantum Chemical Prediction of Reaction Pathways and Rate Constants for Dissociative Adsorption of COx and NOx on the Graphite (0001) Surface

We present predictions of reaction rate constants for dissociative adsorption reactions of CO(x) (x = 1, 2) and NO(x) (x = 1, 2) molecules on the basal graphite (0001) surface based on potential energy surfaces (PES) obtained by the integrated ONIOM(B3LYP:DFTB-D) quantum chemical hybrid approach with dispersion-augmented density functional tight binding (DFTB-D) as low level method. Following an a priori methodology developed in a previous investigation of water dissociative adsorption reactions on graphite, we used a C(94)H(24) dicircumcoronene graphene slab as model system for the graphite surface in finite-size molecular structure investigations, and single adsorbate molecules reacting with the pristine graphene sheet. By employing the ONIOM PES information in RRKM theory we predict reaction rate constants in the temperature range between 1,000 and 5,000 K. We find that among CO(x) and NO(x) adsorbate species, the dissociative adsorption reactions of CO(2) and both radical species NO and NO(2) are likely candidates as a cause for high temperature oxidation and erosion of graphite (0001) surfaces, whereas reaction with CO is not likely to lead to long-lived surface defects. High temperature quantum chemical molecular dynamics simulations (QM/MD) at T = 5,000 K using on-the-fly DFTB-D energies and gradients confirm the results of our PES study.

How the Stabilization of INK4 Tumor Suppressor 3D Structure Evaluated by Quantum Chemical and Molecular Mechanics Calculations Corresponds Well with Experimental Results: Interplay of Association Enthalpy, Entropy, and Solvation Effects

The folding free energy of the INK4c tumor suppressor core, consisting of 10 helices, was determined as the sum of gas-phase interaction enthalpy, gas-phase interaction entropy, and dehydration and hydration free energy. The interaction energy and the hydration free energy were determined using the nonempirical density functional theory (DFT) method, augmented by a dispersion-energy correction term, the semiempirical density-functional tight-binding method covering the dispersion energy, and the density functional theory/conductor-like screening model (DFT/COSMO) procedure, whereas the interaction entropy was calculated with the empirical Cornell et al. force field. Alternatively, all contributions were evaluated consistently using empirical methods. All the values of the interaction energy of helix pairs are stabilizing, and the dominant stabilizing terms stem from the London dispersion energy and, in the case of charged systems, the electrostatic energy. The stabilization energy of the core, determined as the difference of the energy of the core and 10 separate helices, amounts to approximately 450 kcal/mol. Systematically, the difference in the hydration free energy of a helix pair and its separate components is smaller in magnitude than the interaction energy, and it is negative for some pairs while positive for others. The average total free energy of a core formation amounts to -29.6 kcal/mol (yielded by scaled quantum-chemical methods) and +13.9 kcal/mol (resulting from empirical methods). These values are considerably smaller than their single components, which are dominated by the interaction energy. The computationally predicted interval encloses the experimental value of the folding free energy (-2.8 kcal/mol).