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.     

A 3D network of helicates fully assembled by pi-stacking interactions

The neutral dinuclear dihelicate [Cu2(L)2] x 2CH3CN (1) forms a unique 3D network in the solid state due to pi-stacking interactions, which are responsible for intermolecular antiferromagnetic coupling between Cu(II) ions.     

Model chemistry calculations of thiophene dimer interactions: origin of pi-stacking

The intermolecular interaction energies of thiophene dimers have been calculated by using an aromatic intermolecular interaction (AIMI) model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium-size basis set. The calculated interaction energies of the parallel and perpendicular thiophene dimers are -1.71 and -3.12 kcal/mol, respectively. The substantial attractive interaction in the thiophene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge transfer but rather long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases the attraction significantly. The dispersion interaction is found to be the major source of attraction in the thiophene dimer. The calculated total interaction energy of the thiophene dimer is highly orientation dependent. Although electrostatic interaction is substantially weaker than dispersion interaction, it is highly orientation dependent, and therefore electrostatic interaction play an important role in the orientation dependence of the total interaction energy. The large attractive interaction in the perpendicular dimer is the cause of the preference for the herringbone structure in the crystals of nonsubstituted oligothiophenes (alpha-terthienyls), and the steric repulsion between the beta-substituents is the cause of the pi-stacked structure in the crystals of some beta-substituted oligothiophenes.     

Cation-induced pi-stacking

The design and synthesis of a new dipyridyl ligand with appended phenanthryl moieties is described. On addition of increments of silver(I) trifluoromethanesulfonate to a solution of the ligand, the phenanthryl protons shift upfield in the (1)H NMR spectrum, suggesting that the phenanthrenes pi-stack on coordination of silver(I). In accord with this, the oxidation potential decreased from 1.74 to 1.55 V on complexation of silver(I). The pi-stacking was confirmed with the single-crystal X-ray structure of a palladium(II) coordination complex.     

Cuprophilic and pi-stacking interactions in the formation of supramolecular stacks from dicoordinate organocopper complexes

The unsupported organocopper pyridine complexes C6F5Cu(py) (2) and [C6F5Cu]2(4,4'-bipy) (3) form supramolecular structures that are unprecedented in organocopper chemistry; one-dimensional chains of copper atoms with Cu...Cu distances of 2.8924(3) angstroms in the blue-luminescent complex are likely associated with cuprophilic interactions, whereas multiple perfluoroarene-arene interactions dominate in the supramolecular assembly of 3.     

Highly congested nondistorted diheteroarylnaphthalenes: model compounds for the investigation of intramolecular pi-stacking interactions

[structure: see text] The rigid, highly congested structure of 1,8-diacridylnaphthalenes has been studied in solution and in the solid state. The unique geometry of these compounds forces the acridyl rings to undergo face-to-face interactions while rendering T-shaped orientations and face-to-edge interactions impossible. Crystallographic analysis shows that splaying between the heteroaryl rings decreases while twisting between the cofacial rings increases as the acridyl nitrogens of the 1,8-diacridylnaphthalene framework are subsequently oxidized. The peri-acridyl rings are slightly splayed but remain perfectly planar in all cases. The significant decrease in splaying indicates enhanced pi-pi-attraction between the electron-rich acridyl N-oxide moieties, which is in agreement with recently reported symmetry-adapted perturbation theory calculations. The pi-stacking and the molecular geometry between the acridyl rings observed in the solid state have been confirmed through in-solution studies showing characteristic proton NMR upfield shifts and optical properties indicative of static intramolecular arene-arene interactions. Acridyl protons located directly above the adjacent aryl moiety as a consequence of twisting between the heteroaryl rings were identified by COSY NMR measurements and found to intrude into the pi-cloud and diamagnetic ring current of the neighboring acridine. Different shapes and strong red shifts of the fluorescence emission maxima of the diacridylnaphthalenes in comparison to parental acridyl monomers have been attributed to static excimer emission.     

Syntheses, pi-stacking interactions and base-pairings of uracil pyridinium salts and uracilyl betaines with nucleobases

Reaction of 6-chlorouracil with 4-(dimethylamino)pyridine, 4-methylpyridine, and pyridin-4-yl-morpholine yielded pyridinium-substituted uracils as chlorides which were converted into pyridinium uracilates by deprotonation. These heterocyclic mesomeric betaines are cross-conjugated and thus possess separate cationic (pyridinium) and anionic (uracilate) moieties. Calculations and X-ray single crystal analyses were performed in order to characterize these systems and to compare the salts with the betaines. (1)H NMR experiments in D(2)O proved pi-interactions between the uracilyl betaines and adenine, adenosine, as well as adeninium. No pi-stacking interactions were detected between the betaines and guanosine. The acidic N8-H group of the uracil pyridinium salts caused acid-base reactions which were observed in parallel to pi-stacking interactions. Self-complementarity of the modified uracils was detected by (1)H NMR experiments in DMSO-d(6) and electrospray ionisation mass spectrometry (ESIMS). Ab initio calculations predicted base-pairings of the modified uracils with adeninium, cytosine, and guanine. Several geometries of hydrogen-bonded associates were calculated. Hoogsteen pairings between the uracil-4-(dimethylamino)pyridinium salt and adeninium, as well as associates between the corresponding betaine plus cytosine, and the betaine plus guanine were calculated, and the most stable conformations were determined. In the ESI mass spectra, prominent peaks of associates between the modified uracils and adeninium, cytosine, cytidine, guanosine and d(CpGp) were detected.     

Design of a magnetic bistability molecular system constructed by H-bonding and pi...pi-stacking interactions

Crystal structures and magnetic properties were determined for two novel polymorphs of the complex [H2DABCO][Ni(mnt)2] [(H2DABCO)2+ = diprotonated 1,4-diazabicyclo[2.2.2]octane; mnt2- = maleonitriledithiolate]. For each polymorph, anions form a layered structure in which two kinds of dimers were observed. The adjacent anionic sheets are held together by cations via H-bonding interactions between protons of cations and CN groups of anions. Two polymorphs possess spin bistability; namely, upon cooling, a magnetic transition happens at around 120 K with about 1 K hysteresis on heating for the alpha phase and at 112 K with about 10 K hysteresis for the beta phase. Above the transition, the magnetic behaviors of two polymorphs can be approximately interpreted by a singlet-triplet model of an antiferromagnetically coupled S = 1/2 dimer, which is supported by the crystal structures and spin dimer analyses based on extended Hückel molecular orbital calculations.     

Completely regioselective, highly stereoselective syntheses of cis-Bisfullerene

cis-Bisfullerene[60] adducts of 6,13-disubstituted pentacenes (R = Ph, 4'-hydroxymethylphenyl) are synthesized in 75% to 85% isolated yields under kinetically controlled Diels-Alder conditions. The cycloadditions are completely regioselective and highly stereoselective, with only traces of the diastereomeric trans-bisfullerene[60] adducts forming.     

Effects of nucleobase metalation on frontier molecular orbitals: potential implications for pi-stacking interactions with tryptophan

Biochemical recognition processes mediated through pi-stacking interactions are a potential target for rational drug synthesis. A combination of electrostatic, hydrophobic, solvation, charge-transfer, induction, and dispersion interactions has been used to account for the three-dimensional arrangements observed in such motifs. A principal example involves the interaction of purine and pyrimidine rings of nucleic acids with aromatic amino-acid residues such as tryptophan, phenylalanine, and tyrosine. Protonation, alkylation, or coordination of a metal ion such as Pd(II) or Pt(II) to a nucleobase strengthens this interaction by lowering the energy of the lowest unoccupied molecular orbital (LUMO) of the modified nucleobase and improving overlap with the highest occupied molecular orbital (HOMO) in N-acetyl tryptophan. The relative energy difference between the frontier orbitals of isolated molecules, obtained using Density Functional Theory (DFT), is explored as a predictive tool for the strength of the pi-stacking interaction of the nucleobase/tryptophan pair. From the optimized structures of these species, evaluation of the donor-acceptor HOMO-LUMO gap (Deltaepsilon d-->a) suggests that this parameter is a promising predictor of pi-stacking strength for the donor-acceptor pairs presented in this study. The analysis correlates well with experimental association constants, measured by fluorescence spectroscopy, of metallated and alkylated nucleobases with tryptophan in comparison to free nucleobases.     

Hydrogen-bond-assisted pi-stacking of shape-persistent cyclophanes

The pi-stacking interaction between shape-persistent cyclophanes works cooperatively with multiple hydrogen bonding sites to form cyclophane dimers. These findings considerably broaden the applicability of pi-stacking interactions as a driving force in self-assembly chemistry. A gel formation effect was also noticed in one of the cyclophanes.     

Formation of dimers of inclusion cryptand/paraquat complexes driven by dipole-dipole and face-to-face pi-stacking interactions

Dimers of inclusion complexes were formed from a new cryptand and viologens (paraquats) driven by dipole-dipole and face-to-face pi-stacking interactions as shown by mass spectrometric characterization and X-ray analysis.     

Electron transport in a pi-stacking molecular chain

We have investigated the electronic structure and transport properties of a pi-stacking molecular chain which is covalently bonded to a H/Si(100) surface, using the first-principles density functional theory approach combined with Green's function method. The highest occupied molecular orbital (HOMO) dispersion is remarkably reduced, but remains noticeable ( approximately 0.1 eV), when a short pi-stacking styrene wire is cut from an infinitely long wire and sandwiched between metal electrodes. We find that the styrene chain's HOMO and lowest unoccupied molecular orbital (LUMO) states are not separated from Si, indicating that it does not work as a wire. By substituting -NO2 or -NH2 for the top -H of styrene, we are able to shift the position of the HOMO and LUMO with respect to the Fermi level. More importantly, we find that the HOMO of styrene-NH2 falls into the band gap of the substrate and is localized in the pi-stacking chain, which is what we need for a wire to be electrically separated from the substrate. The conductance of such an assembly is comparable to that of Au/benzene dithiolate/Au wire based on chemical bonding, and its tunability makes it a promising system for a molecular device.     

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.     

Dual-mode recognition of oxalate by protonated azacryptate hosts; conformational response of the guest maximizes pi-stacking interactions

Exceptionally large complexation constants for oxalate encapsulated within azacryptand hosts are partly explained by pi-stacking interactions between C=O and aromatic rings.     

Hybrid density functional theory for pi-stacking interactions: application to benzenes, pyridines, and DNA bases

The suitability of a hybrid density functional to qualitatively reproduce geometric and energetic details of parallel pi-stacked aromatic complexes is presented. The hybrid functional includes an ad hoc mixture of half the exact (HF) exchange with half of the uniform electron gas exchange, plus Lee, Yang, and Parr's expression for correlation energy. This functional, in combination with polarized, diffuse basis sets, gives a binding energy for the parallel-displaced benzene dimer in good agreement with the best available high-level calculations reported in the literature, and qualitatively reproduces the local MP2 potential energy surface of the parallel-displaced benzene dimer. This method was further critically compared to high-level calculations recently reported in the literature for a range of pi-stacked complexes, including monosubstituted benzene-benzene dimers, along with DNA and RNA bases, and generally agrees with MP2 and/or CCSD(T) results to within +/-2 kJ mol(-1). We also show that the resulting BH&H binding energy is closely related to the electron density in the intermolecular region. The net result is that the BH&H functional, presumably due to fortuitous cancellation of errors, provides a pragmatic, computationally efficient quantum mechanical tool for the study of large pi-stacked systems such as DNA.     

2D and 3D supramolecular structures via hydrogen bonds and pi-stacking interactions in arylsulfonates of nickel and cobalt

Five novel arylsulfonates of Ni and Co have been hydrothermally obtained and their structures determined by X-ray single-crystal diffraction. [Ni(Phen)(H2O)](1,5-NDS).2H2O (1) is a hydrogen-bonded supramolecular layered compound formed by self-assembly of tetraaqua-o-phenanthrolinenickel(II) cations and 1,5-naphthalenedisulfonate anions, [Ni(Phen)2(H2O)(1,5-NDS)] (2) and [Ni(Phen)2(H2O)(2,6-NDS)].2H2O (4) exhibit 2D structures via O-H...O and pi-pi (both perfect face-to-face and parallel-displaced) stacking interactions, [Co(Phen)2(H2O)(1,5-NDS)].2H2O (5) presents a 3D structure via O-H...O hydrogen-bond layers and pi-pi parallel-displaced stacking interactions, and [Co(Phen)2(1,5-NDS)] (3) is the first example of a covalently bonded polymeric cobalt sulfonate. Its 1D structure comprises chains formed through bitopic 1,5-NDS linkers. Rates and selectivities for oxidation of organic sulfides with H2O2 were measured with 2-5.     

Syntheses of soluble, pi-stacking tetracene derivatives

[reaction: see text] The syntheses of a series of fluorine- and alkyl/alkoxy-functionalized tetracenes are reported. These functional groups are found to improve the solubility in common organic solvents and tune molecular arrangement in solids. The crystal packing, electrochemical behavior, and UV-vis absorbance spectroscopy of these materials are discussed.     

Parametrization of an empirical correction term to density functional theory for an accurate description of pi-stacking interactions in nucleic acids

We present an accurate parametrization of density functional theory augmented with an empirical correction term to describe properly pi-stacking interactions in nucleic acids. The approach is based on the popular Perdew-Burke-Ernzerhof (PBE), Becke-Perdew (BP), and hybrid Becke-Lee-Yang-Parr (B3LYP) density functionals augmented by a classical London C(6)R(-6) dispersion term. The novelty of our implementation lies in the accurate tuning of the empirical parameters, included in the [formula: see text] damping function, to reproduce high-level post Hartree-Fock calculations. In particular, we present sets of parameters and the needed code to correct the PBE, BP, and B3LYP results from the Turbomole and ADF packages in connection with basis sets of double and triple zeta quality. The developed approach is validated by comparison with the JSCH-2005 benchmark and with best quality stacking energies reported in the literature for the stacking of H-bonded nucleic acids base pairs.     

Pyridinium CH...anion and pi-stacking interactions in modular tripodal anion binding hosts: ATP binding and solid-state chiral induction

The preparation of two new tripodal "pinwheel" type anion hosts based on a triethylbenzene core and bipyridinium or ethylnicotinium arms is reported. The new materials bind anions via CH...anion interactions. Complexes with Br(-) and PF(6)(-) have been characterised by X-ray crystallography as both solvates in a pure form. In the bipyridinium host CH...F interactions to PF(6)(-) induce a chiral C(3) symmetric conformation that is disrupted in the hydrate. The compound is also selective for ATP(2-) in aqueous acetonitrile.