Stacked Dimers Research Articles

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

In this work, DNA base monomers, 15 B-form stacking dimers and two G-quadruplex stacking dimers were studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal vibrational signatures for structural aspect of the base monomers and dimers. It was found that from isolated base monomers to stacking dimers, particularly those containing guanine, the interaction between the C=O stretching is very strong, as depicted by the significant changes of their vibrational frequencies and anharmonicities. Such changes can be manifested well in simulated 113 IR and 2D IR spectra. Delocalization degree of the C=O vibrational modes in stacking dimers, represented by the potential energy distribution and the contribution to the diagonal anharmonicity composition from the vibrators, was found to have significant variations in comparison with isolated bases, which resulted from the influences of the C=O stretching and the nearby vibrations of stacking bases.

Design of crystal packings of styrylheterocycles and [2+2] photocycloaddition reactions in their single crystals 7. Crystal structures of 4-styrylpyridine hydroperchlorates and solid-state [2+2] autophotocycloaddition reactions of these compounds

A series of 4-styrylpyridine hydroperchlorates were synthesized, and the [2+2] autophotocycloaddition (PCA) reaction in their polycrystalline films and single crystals resulting in the centrosymmetric rctt isomers of 1,2,3,4-tetrasubstituted cyclobutanes was investigated. Unlike neutral styrylpyridines, their protonated forms are better preorganized for the solid-state PCA reaction. According to the X-ray diffraction data, the cations of these compounds, like related styryl dyes, are mainly stacked in crystals in a head-to-head or head-to-tail fashion with equal probability. Only in the latter type of stacks, the PCA reaction is feasible as a single-crystal-to-single-crystal transformation. The crystal packing is stabilized by hydrogen bonds between organic cations and perchlorate anions, as well as by other weak directional interactions, for example, by S…S interactions, thus preventing the atomic displacements in the course of PCA. The completion of the PCA reaction in single crystals without their degradation was observed only for 15-crown-5-containing 4-styrylpyridine hydroperchlorate. The crystals of the latter compound are stabilized not by hydrogen bonds between the cations and anions but by N+-H…O(macrocycle) hydrogen bonds resulting in the formation of head-to-tail stacked dimers. In the crystals, these dimers are surrounded by a soft shell formed by rotationally and translationally mobile anions and benzene solvent molecules, as well as by conformationally flexible crown-ether moieties of adjacent dimer pairs. This leads to a decrease in the steric strain that occurs in the crystals in the course of PCA and prevents the degradation of single crystals. The PCA reaction is accompanied by the reduction in the crystal symmetry due to the doubling of the unit cell.

Weakly bonded cluster structures of N,N′-dimethylethyleneurea and water

Intermolecular interactions between a single water and two N,N′-dimethylethyleneurea (DMEU) molecules have been investigated using ab initio quantum chemistry method. The local and density-fitting approximations of the standard Møller–Plesset perturbation theory (DF-LMP2) have been employed together with the aug-cc-pVTZ basis set. Several trimeric systems were built where the water molecule, through the O–H⋯N hydrogen bond interactions, played the role of the bridge between the two DMEU molecules. The results show that the presence of the water molecule does not increase the stability of the trimeric systems. In the first three configurations the water molecule intercalates between two DMEU molecules, forming stable clusters. In the next three configurations, the water molecule is attached to a plane-parallel stacked DMEU dimer through the C=O⋯H–O hydrogen bond, and these structures are more stable than the first three. Small-angle neutron scattering data show clustering of DMEU molecules in their dilute aqueous solutions, and the ab initio results suggest that DMEU molecules could form contact pairs in dilute aqueous solutions.

Plasmon Hybridization in Stacked Double Crescents Arrays Fabricated by Colloidal Lithography

We apply colloidal lithography to construct stacked nanocrescent dimer structures with an exact vertical alignment and a separation distance of approximately 10 nm. Highly ordered, large arrays of these nanostructures are accessible using nonclose-packed colloidal monolayers as masks. Spatially separated nanocrescent dimers are obtained by application of spatially distributed colloids. The polarization dependent optical properties of the nanostructures are investigated in detail and compared to single crescents. The close proximity of the nanocrescents leads to a coupling process that gives rise to new optical resonances which can be described as linear superpositions of the individual crescents' plasmonic modes. We apply a plasmon hybridization model to explain the spectral differences of all polarization dependent resonances and use geometric arguments to explain the respective shifts of the resonances. Theoretical calculations are performed to support the hybridization model and extend it to higher order resonances not resolved experimentally.

Molecular and crystal structure of a sterically distorted complex of Pd(II) with 2,9-dimethyl-1,10-phenanthroline [Pd(2,9-Me2-phen)Cl2

A neutral complex of palladium(II) with 2,9-dimethyl-1,10-phenanthroline [Pd(2,9-Me2-phen)Cl2] (goldish orange colored) is examined by single crystal X-ray diffraction. The crystals of [Pd(2,9-Me2-phen)Cl2] are monoclinic and belong to the space group P21/n (a = 11.8670(7) A, b = 7.8195(5) A, c = 14.2418(9) A, β = 92.5450(10)°, Z = 4, V = 1320.25 A3, R = 0.0289). The complex [Pd(2,9-Me2-phen)Cl2] exhibits a strong distortion of the usual square-planar geometry with a deviation of the central Pd2+ ion and two chloride acido-ligands from the plane of coordinated 2,9-dimethyl-1,10-phenanthroline. The lengths of two Pd-N bonds are slightly different and are 2.058 A and 2.067 A, the lengths of the Pd-Cl bonds are equal and are 2.285 A. 2,9-Me2-phen itself also suffers some distortion of the planar geometry resulting in the boat conformation of the molecule. The crystal structure of the [Pd(2,9-Me2-phen)Cl2] complex is characterized by the presence of π-π stacked dimers arranged in infinite tilted stacks.

The excited electronic states of adenine-guanine stacked dimers in aqueous solution: a PCM/TD-DFT study

The excited-state behavior in the Franck-Condon (FC) region of the d(ApG) and d(GpA) dinucleoside monophosphate (A = adenine, G = guanine) is investigated in aqueous solution by means of time-dependent Density Functional Calculations, including solvent effects by the Polarizable Continuum Model and using three different functionals, i.e. PBE0, M052X, and CAM-B3LYP. Our analysis, focussed mainly on the two stacked dimers formed by 9-methyl-adenine and 9-methyl-guanine in the same arrangement as in the B structure of DNA (AG and GA), provides absorption and ECD spectra in very good agreement with their experimental counterparts. The sequence dependence of the dinucleoside excited-state properties is fully reproduced and it is explained on the grounds of the different interactions among the nucleobases' frontier orbitals existing in AG and GA. Our calculations predict that the 9Me-G --> 9Me-A charge transfer (CT) excited state is, at least, as stable as the lowest energy bright state of the dimers and that it is more stable than the intra-strand CT state in the (9Me-A)(2) stacked dimer. On the other hand, in AG and GA the 9Me-G --> 9Me-A CT state is significantly coupled to the dimer bright excited states and deviations from the decay rate predicted on the ground of the Marcus Theory are possible.

Crystallographic and Computational Analysis of the Supramolecular Structure of 2,5-Dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one

The structure of 5-dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one 1 has been determined by X-ray crystallography. The compound 1 crystallizes in the space group P−1 with two molecules in the asymmetric unit solvated with one molecule of the acetic acid The unit cell parameters are a = 8.796(1) A, b = 10.531(1) A, c = 10.680(1) A, α = 96.901(2)o, β = 98.135(2)o, γ = 107.248(2)o. In the crystal molecules A and B are linked into R 2 2 (9) hydrogen bonded rings and these rings form chains parallel to [101] Overall, the supramolecular structure 1 consists of two hydrogen bonded and two π–π stacking dimers. An energetic interplay between these dimers has been studied using B3LYP DFT calculations. In addition π–π interactions are analyzed using the Bader’s atoms in molecules’ (AIM) theory. The structure of 5-dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one 1 has been determined by X-ray crystallography. The compound 1 crystallizes in the space group P−1 with two molecules in the asymmetric unit solvated with one molecule of the acetic acid The unit cell parameters are a = 8.796(1) A, b = 10.531(1) A, c = 10.680(1) A, α = 96.901(2)o, β = 98.135(2)o, γ = 107.248(2)o. In the crystal molecules A and B are linked into R 2 2 (9) hydrogen bonded rings and these rings form chains parallel to [101] Overall, the supramolecular structure 1 consists of two hydrogen bonded and two π–π stacking dimers. An energetic interplay between these dimers has been studied using B3LYP DFT calculations. In addition π–π interactions are analyzed using the Bader’s atoms in molecules’ (AIM) theory.

Photoinduced transformations in single crystals of 1,2-bis(2-[(E)-3-oxo-3-phenylprop-1-enyl]phenoxy)ethane and 1,5-bis(2-[(E)-3-oxo-3-phenylprop-1-enyl]phenoxy)-3-oxapentane

Differences in the parameters of pre-organization of chalcone podands to intermolecular photoinduced [2+2] cycloaddition (PCA) in crystals were discovered. As a result of PCA, the chalcone podand with two oxyethylene units forms stereoregular cyclobutane-containing polymer chains over the whole volume of the single crystal. In the case of the chalcone podand with one oxyethylene unit, the PCA reaction in single crystal becomes impossible; however, its mechanical destruction results in the formation of surface layers with stacking dimers. In these layers, photodimerization occurs due to a decrease in topochemical control from the molecular lattice.

Coordination-induced sliding motion of a complementary porphyrin-phthalocyanine dimer: fluorescence-based molecular switch

The reversible control of dual (or multiple) states of molecules and supramolecules has attracted much attention for molecular switch, sensor, memory, logic gate, and molecular machine applications. In this paper, a ligand-induced sliding system using a complementary porphyrin-phthalocyanine dimer accompanied by a large fluorescence change is described. An imidazole-appended porphyrinatozinc-phthalocyaninatomagnesium complex 5 was synthesized by the palladium-catalyzed coupling reaction of the corresponding porphyrin and phthalocyanine moieties. The imidazole group of 5 coordinated to the magnesium ion of another 5 was formed spontaneously and dominantly to give a stacked dimer 5ST in non-coordinating solvents, such as chloroform, even at submicromolar concentration (< 10-6 M). When an appropriate amount of dimethyl sulfoxide (DMSO) was added to the 5ST solution, the stacked dimer was transformed almost quantitatively into the extended dimer 5Ex. This transformation was monitored by UV-vis and fluorescence spectroscopies. In the UV-vis spectra, the porphyrin's Soret band is split characteristically because of excitonic coupling between the two closely located porphyrins in 5Ex. At the same time, the fluorescence intensity of 5Ex at 700 nm (ex. 414 nm) increased by a factor of 28 compared with that of 5ST. Removal of the DMSO molecules by extraction with water from the system regenerated 5ST almost completely from 5Ex, and the fluorescence was quenched again. The reversible system can be repeated by cycles of addition and removal of DMSO. The present system can be classified as a coordination-induced sliding system accompanied by a large fluorescence change, and may be applied as a fluorescence-based molecular switch.

π-Stack Dimers of Small Polyaromatic Hydrocarbons: A Path to the Packing of Graphenes

MP2 calculations of the stacking energy are reported for the dimers of a set of polycyclic aromatic hydrocarbons. The interaction strengths and their dependence on the shape-dependent measures as well as the aromatic character of the monomer are studied. For small systems involving four to six rings, the noncovalent interactions seem to be independent of the shape of the monomers. The most preferred conformations for parallel stacked dimers are not aligned exactly but off-center with small shifts; however, these shifts are on the order of 1 A, and the energy necessary to keep them aligned is less than 0.5 kcal/mol per ring. Small-angle rotations within the molecular planes also do not require much energy, and in some cases they lead to stronger interactions.

Mo‐Catalyzed Cross‐Metathesis Reaction of Propynylferrocene (Eur. J. Inorg. Chem. 25/2008)

AbstractThe cover picture shows the reaction scheme for the cross‐metathesis of (prop‐1‐yn‐1‐yl)ferrocene with substituted propynes effected by catalysts generated from [Mo(CO)6] and halophenols, situated on a background full of typical ferrocene, autumn‐like colors. The metathesis reaction affords good yields of unsymmetric ferrocenyl alkynes, thus offering a new alternative approach toward their preparation. Also shown are the crystal structure of methyl 4‐[(ferrocenyl)ethynyl]benzoate and the orbital diagram of its solid‐state π···π stacked dimer as calculated by DFT methods. A survey of various substrates and catalysts, results of X‐ray structure analysis and DFT calculations as well as electrochemical data for a series of (phenylethynyl)ferrocenes substituted at the phenyl ring are discussed in the article by M. Kotora, P. Štěpnička et al. on p. 3911 ff.

Toward More Efficient CCSD(T) Calculations of Intermolecular Interactions in Model Hydrogen-Bonded and Stacked Dimers

Interaction energies of the model H-bonded complexes, the formamide and formamidine dimers, as well as the stacked formaldehyde and ethylene dimers are calculated by the coupled cluster CCSD(T) method. These systems serve as a model for H-bonded and stacking interactions, typical in molecules participating in biological systems. We use the optimized virtual orbital space (OVOS) technique, by which the dimension of the space of virtual orbitals in coupled cluster CCSD(T) calculations can be significantly reduced. We demonstrate that when the space of virtual orbitals is reduced to 50% of the full space, which means reducing computational demands by 1 order of magnitude, the interaction energies for both H-bonded and stacked dimers are affected by no more than 0.1 kcal/mol. This error is much smaller than the error when interaction energies are calculated using limited basis sets.

Ligand-Induced Interconversion of a Coordination-Organized Porphyrin Dimer: a Potential Fluorescence-Based Molecular Memory Monitor

A novel interconversion system between less-fluorescent stacked (S) dimer and fluorescent extended (E) dimer of the monoimidazolylbisporphyrinatozinc complex was investigated. The addition of pyridine induces transformation from the S to the E dimer, whereas the addition of acetic acid and subsequent heating reverses the transformation. The interconversion rate is controlled by ligand concentration and thermal treatment. The system can be applied to repeatedly readable molecular memory by highly sensitive fluorescence detection.

Intriguing relations of interaction energy components in stacked nucleic acids

Major components of the interaction energy that define several approximate levels starting from second order Möller-Plesset theory were studied for 58 stacked nucleic acid dimers. They included typical B-DNA and A-DNA structures, and selected published geometries. A survey of the various terms yields an unexpected correlation between the Pauli exchange and dispersion or correlation terms, which holds for each class of similar planar geometries and for various basis sets. The geometries that exhibit these correlations span a specific range of molecular overlaps when compared to a model benzene-pyridine stacked dimer. Also, the relationship between electrostatic interactions and MP2 stabilization energies reported earlier is confirmed and a prediction interval of practical relevance is estimated.

Optical Properties of the Phosphorescent Trinuclear Copper(I) Complexes of Pyrazolates: Insights from Theory

Theoretical investigations have been performed to explore the optical properties of {[3,5-(CF3)(2)Pz]Cu}3 in monomeric and dimeric forms using TD-DFT approaches. The emission of all complexes originates from the lowest triplet excited-states (T1), and the corresponding emissive states are assigned as the mixture of the metal-centered charge transfer and ligand-to-metal charge transfer. The features of the emission spectrum are clarified in detail. The bulk emission spectrum of complex is mainly determined by the stacked dimers rather than the individual monomers. The predicted maximum emission wavelength (lambda(em)) are in good agreement with experimental values, indicating that the phosphorescence bands can be assigned to two different conformations for the neighboring stacked dimers sharing the same monomer in the complex. Energy transfer from T1 of one stacked dimer to the neighboring one is responsible for the disappearance of the shoulder, leaving only the main peak upon heating. With the aim to reveal the conformational dependence for the triplet excited-state emission spectrum, the optical properties of various stacked dimers with different conformations are investigated by varying the relative arrangements through changing inter-monomer distance or rotational angles for the dimer which is responsible for the main peak emission. Calculation results suggest that the shortest intermolecular Cu...Cu distance plays an important role in the emission spectra of the vertical- and tilting-movement dimers, which is ascribed to the variation of the energy gap for the frontier molecular orbitals involved in the main emitting transition. The blue shift of lambda(em) in parallel-movement and rotational dimers can be traced back to the variation of the mutual spatial orientation. Therefore, the modulation of the extent of movement or rotational angles for stacked dimers by external perturbations creates new possibilities for the design of molecular light-emitting devices.

Electron and hole mobilities in polymorphs of benzene and naphthalene: Role of intermolecular interactions

The hole and electron mobilities of the polymorphs of benzene and naphthalene crystals are estimated through quantum chemical calculations. The reorganization energy (lambda) and the charge-transfer matrix elements (Hmn) calculated for the two molecules reveal that these crystals can be used for dual applications, for both hole and electron conductance. The electron mobilities are five to eight times more than the hole mobilities for benzene while for naphthalene, the hole mobilities are almost an order magnitude more than the electron mobilities. The transfer matrices for both hole and electron conductance decrease monotonically with increase in the intermolecular distances. Calculations for various unique stacked dimers as determined from the radial distribution functions in both the crystals for the two molecules show strong dependence on the orientations of the rings and for similar intermolecular separations; Hmnhole is larger than Hmnelectron. The crystal mobilities are calculated from the weighted average over all the unique pair of molecules. The overall preference in a crystal for hole or electron mobility depends on the mutual competition of lambdahole/lambdaelectron and Hmnhole/Hmnelectron. From our microscopic understanding of essential parameters, specific dimers are identified from the crystalline solids of the two polymorphs and experimental strategies are suggested to enrich such pairs in aggregates for enhancing mobilities for these organic solids.

A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine

The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.

Dodecin Sequesters FAD in Closed Conformation from the Aqueous Solution

Both extensive theoretical calculations and experimental data obtained during several decades leave little doubt that flavin adenine dinucleotide (FAD) exists in an open as well as in a closed conformation in aqueous solution. However, the knowledge about the intramolecularly stacked complex of FAD is constructed on indirect methods while direct structural evidence is lacking. Recently, dodecin was reported as an unspecific flavin binding protein which exhibits the unique binding mode of incorporating stacked dimers of flavins into a single binding pocket. Here, we show that FAD is not bound in this manner, but in monomers of intramolecularly stacked conformation. As resulting from the dodecin ligand binding characteristic, this FAD stacked conformation suggests to be directly sequestered from the aqueous solution and thus to be the first X-ray structural view on a FAD solution-stacked form. Moreover, in extraordinary FAD binding, dodecin serves as a model for studying bound monomeric (FAD) versus bound dimeric (e.g. riboflavin) flavin properties.

Topology Variation and Loop Structural Homology in Crystal and Simulated Structures of a Bimolecular DNA Quadruplex

The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K(+) ions between the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2(1) unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T(4) loops. A total of seven independent T(3) loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.

Computational Evaluation of Intermolecular Interactions of a Universal Base 3-Nitropyrrole in Stacked Dimers and DNA Duplexes

The stacking interactions between a universal base of 3-nitropyrrole (3NP) and four canonical nucleobases were studied by means of ab initio molecular orbital calculations. The stabilities of the complexes are comparable to those of the stacked dimers of canonical bases reported previously. The detailed analysis of the interaction energies revealed the importance of the dipole-dipole interaction included in the Hartree-Fock terms to determine the geometry dependence of the stacking energies. It was also clarified that the dispersion energies included in the electron-correlation terms were essential to obtain adequate stabilities. The contribution of the nitro group was evaluated by the comparative studies of pyrrole and 3NP. The increased molecular dipole moment and surface are expected to account for the enhancement of the stability of the stacked dimers containing 3NP. The force field parameters required for calculation of the molecular mechanics of 3NP were obtained for 3NP on the basis of these molecular orbital calculations. The energy-minimized structures obtained by the molecular mechanics calculations of 3NP accorded with those obtained by the molecular orbital calculations described above. A DNA duplex structure containing 3NP-A, 3NP-T, or 3NP-C was calculated by use of these force field parameters. In the case of 3NP-A, the computationally calculated structure was in good agreement with that previously determined by use of 1H-NMR except for the orientation of the nitro group.