Binding of DNA Nucleobases and Nucleosides with Graphene

Interaction of two different samples of graphene with DNA nucleobases and nucleosides is investigated by isothermal titration calorimetry. The relative interaction energies of the nucleobases decrease in the order guanine (G) > adenine (A) > cytosine (C) > thy mine (T) in aqueous solutions, although the positions of C and T seem to be interchangeable. The same trend is found with the nucleosides. Interaction energies of the A-T and G-C pairs are somewhere between those of the constituent bases. Theoretical calculations including van der Wools interaction and solvation energies give the trend G > A similar to T > C. The magnitudes of the interaction energies of the nucleobases with graphene are similar to those found with single-walled carbon nonotubes.

Properties of the correlated electronic states of pyrene and hydrogenated pyrene

Approximate calculations are reported on pyrene within the PPP model Hamiltonian using a novel restricted CI scheme which employs both molecular orbital and valence bond techniques. Also reported are detailed full CI results of the PPP model on 2,7-dihydropyrene obtained using the valence bond method. Spectral studies, charge and spin density calculations in ground and excited states, and ring current calculations in the ground state of the molecules are presented. In pyrene, the calculated excitation energies are in good agreement with experiment. The closed structure pi-conjugated molecule pyrene appears to show smaller distortions from the ground state geometry compared with the open structure pi-conjugated molecule 2,7-dihydropyrene. The ground state equilibrium structure of 2,7-dihydropyrene can be viewed as two hexatriene molecules connected by a vinyl crosslink, as is evident from bond order and ring current calculations. This is consistent with the only Kekule resonant structure possible for this molecule.

Amidinato- and triazenido-bridged binuclear complexes of palladium and platinum

The reaction of [M2Cl2(mu-Cl)(2)(PR3)(2)] (M=Pd or Pt; PR3=PEt3, PBu3, PMe2Ph, PMePh2) with lithium amidinate or sodium triazenide gave binuclear complexes containing amidinato- or triazenido-bridges, [M2Cl2(mu-ArNENAr)(2)(PR3)(2)] (E=CH, CMe or N). These complexes were characterized by elemental analysis and NMR (H-1, P-31 or Pt-195) data. The structures of two complexes, [(PdCl2)-Cl-2(mu-PhNC(Me)NPh)(2)(PMe2Ph)(2)] (10) and [Pt2Cl2(mu-PhNNNPh)(2)(PEt3)(2)] (11) were established by single crystal X-ray structural analyses. The Pt-195 NMR data Show coupling between two metal centers in the cis triazenido-bridged complex. The corresponding amidinate bridged complex does not show coupling. The role of the bridging ligand in mediating interaction between the metal centers is probed through Extended Huckel Theory (EHT) calculations. It is suggested that M-M interactions are primarily affected by the bridging ligands

1H and 13C NMR spectra of some unsymmetric N,N-dipyridyl ureas: spectral assignments and molecular conformation

Abstract: The H-1 NMR spectra of N-(2-pyridyl), N'-(3-pyridyl)ureas and N-(2-pyridyl), N'-(4-pyridyl)ureas in CDCl3 and (CD3)(2)CO have been assigned with the aid of COSY and NOE experiments and chemical shift and coupling constant correlations, The C-13 NMR spectra in CDCl3 were analysed utilizing the HETCOR and proton coupled spectra, The H-1 NMR spectra, NOE effects and MINDO/3 calculations have been utilized to show that the molecular conformation of these compounds has the 2-pyridyl ring coplanar with the urea plane with the N-H group hydrogen bonded to the nitrogen of the 2-pyridyl group on the other urea nitrogen while the 3/4-pyridyl group rotates rapidly about the N-C-3/N-C-4 bond.

Structure of the benzene center dot center dot center dot ICI complex: A UVPES and ab initio molecular orbital study

UVPES studies and ab initio and DFT computations have been done on the benzene...ICl complex; electron spectral data and computed orbital energies show that donor orbitals are stabilized and acceptor orbitals are destabilized due to complexation. Calculations predict an oblique structure for the complex in which the interacting site is a C=C bond center in the donor and iodine atom in the acceptor, in full agreement with earlier experimental reports. BSSE-corrected binding energies closely match the enthalpy of complexation reported, and the NBO analysis clearly reveals the involvement of the pi orbital of benzene and the sigma* orbital of ICl in the complex.

Evolution of electronic structure with dimensionality in divalent nickelates

We investigate the evolution of electronic structure with dimensionality (d) of Ni-O-Ni connectivity in divalent nickelates, NiO (3-d), La2NiO4, Pr2NiO4 (2-d), Y2BaNiO5 (1-d) and Lu2BaNi5 (0-d), by analyzing the valence band and the Ni 2p core-level photoemission spectra in conjunction with detailed many-body calculations including full multiplet interactions. Experimental results exhibit a reduction in the intensity of correlation-induced satellite features with decreasing dimensionality. The calculations based on the cluster model, but evaluating both Ni 3d and O 2p related photoemission processes on the same footing, provide a consistent description of both valence-band and core-level spectra in terms of various interaction strengths. While the correlation-induced satellite features in NiO is dominated by poorly screened d(8) states as described in the existing literature, we find that the satellite features in the nickelates with lower dimensional Ni-O-Ni connectivity are in fact dominated by the over-screened d(10)L(2) states. It is found that the changing electronic structure with the dimensionality is primarily driven by two factors: (i) a suppression of the nonlocal contribution to screening; and (ii) a systematic decrease of the charge-transfer energy Delta driven by changes in the Madelung potential. [S0163-1829(99)09619-8].

Electronic structure of La1-xSrxCrO3

LaCrO3 is a wide-band-gap insulator which does not evolve to a metallic state even after hole doping. We report electronic structure of this compound and its Sr substituents investigated by photoemission and inverse photoemission spectroscopies in conjunction with various calculations. The results show that LaCrO 3 is close to the Mott-Hubbard insulating regime with a gap of about 2.8 eV. Analysis of Cr 2p core-level spectrum suggests that the intra-atomic Coulomb interaction strength and the charge-transfer energy to be 5.0 and 5.5 eV, respectively, We also estimate the intra-atomic exchange interaction strength and a crystal-field splitting of about 0.7 and 2.0 eV, respectively. Sr substitution leading to hole doping in this system decreases the charge-excitation gap, but never collapses it to give a metallic behavior. The changes in the occupied as well as unoccupied spectral features are discussed in terms of the formation of local Cr4+ configurations arising from strong electron-phonon interactions.

Unoccupied electronic states in NiS2-xSex across the metal-insulator transition

We investigate the evolution of the electronic structure across the insulator-metal transition in NiS2-xSex with changing composition, but in the absence of any structural or magnetic changes. A comparison of the inverse photoemission spectra with band-structure calculations establishes the importance of correlation effects in these systems. Systematic changes in the spectral distribution establish the persistence of the upper Hubbard band well into the metallic regime, with the insulator-to-metal transition being driven by a transfer of spectral weight from the Hubbard band to states close to the Fermi energy.

Electronic structure studies and photocatalytic properties of cubic Bi1.5ZnNb1.5O7

The photocatalytic ability of cubic Bi1.5ZnNb1.5O7 (BZN) pyrochlore for the decolorization of an acid orange 7 (AO7) azo dye in aqueous solution under ultraviolet (UV) irradiation has been investigated for the first time. BZN catalyst powders prepared using low temperature sol-gel and higher temperature solid-state methods have been evaluated and their reaction rates have been compared.The experimental band gap energy has been estimated from the optical absorption edge and has been used as reference for theoretical calculations. The electronic band structure of BZN has been investigated using first-principles density functional theory (DFT) calculations for random, completely and partially ordered solid solutions of Zn cations in both the A and B sites of the pyrochlore structure.The nature of the orbitals in the valence band (VB) and the conduction band (CB) has been identified and the theoretical band gap energy has been discussed in terms of the DFT model approximations.

Self-assembly of indole-2-carboxylic acid at graphite and gold surfaces

Model systems are critical to our understanding of self-assembly processes. As such, we have studied the surface self-assembly of a small and simple molecule, indole-2-carboxylic acid (I2CA). We combine density functional theory gas-phase (DFT) calculations with scanning tunneling microscopy to reveal details of I2CA assembly in two different solvents at the solution/solid interface, and on Au(111) in ultrahigh vacuum (UHV). In UHV and at the trichlorobenzene/highly oriented pyrolytic graphite (HOPG) interface, I2CA forms epitaxial lamellar structures based on cyclic OH⋯O carboxylic dimers. The structure formed at the heptanoic acid/HOPG interface is different and can be interpreted in a model where heptanoic acid molecules co-adsorb on the substrate with the I2CA, forming a bicomponent commensurate unit cell. DFT calculations of dimer energetics elucidate the basic building blocks of these structures, whereas calculations of periodic two-dimensional assemblies reveal the epitaxial effects introduced by the different substrates.

The equilibrium geometry and electronic structure of Bi nanolines on clean and hydrogenated Si(001) surfaces

The equilibrium geometry, electronic structure and energetic stability of Bi nanolines on clean and hydrogenated Si(001) surfaces have been examined by means of ab initio total energy calculations and scanning tunnelling microscopy. For the Bi nanolines on a clean Si surface the two most plausible structural models, the Miki or M model (Miki et al 1999 Phys. Rev. B 59 14868) and the Haiku or H model (Owen et al 2002 Phys. Rev. Lett. 88 226104), have been examined in detail. The results of the total energy calculations support the stability of the H model over the M model, in agreement with previous theoretical results. For Bi nanolines on the hydrogenated Si(001) surface, we find that an atomic configuration derived from the H model is also more stable than an atomic configuration derived from the M model. However, the energetically less stable (M) model exhibits better agreement with experimental measurements for equilibrium geometry. The electronic structures of the H and M models are very similar. Both models exhibit a semiconducting character, with the highest occupied Bi-derived bands lying at ~0.5 eV below the valence band maximum. Simulated and experimental STM images confirm that at a low negative bias the Bi lines exhibit an 'antiwire' property for both structural models.

The electronic origin of contrast reversal in bias-dependent STM images of nanolines

Self-organized Bi lines that are only 1.5 nm wide can be grown without kinks or breaks on Si(0 0 1) surfaces to lengths of up to 500 nm. Constant-current topographical images of the lines, obtained with the scanning tunneling microscope, have a striking bias dependence. Although the lines appear darker than the Si terraces at biases below ≈∣1.2∣ V, the contrast reverses at biases above ≈∣1.5∣ V. Between these two ranges the lines and terraces are of comparable brightness. It has been suggested that this bias dependence may be due to the presence of a semiconductor-like energy gap within the line. Using ab initio calculations it is demonstrated that the energy gap is too small to explain the experimentally observed bias dependence. Consequently, at this time, there is no compelling explanation for this phenomenon. An alternative explanation is proposed that arises naturally from calculations of the tunneling current, using the Tersoff–Hamann approximation, and an examination of the electronic structure of the line.

The geometry of Bi nanolines on Si(0 0 1)

A study of the Bi nanoline geometry on Si(0 0 1) has been performed using a combination of ab initio theoretical technique and scanning tunnelling microscopy (STM). Our calculations demonstrate decisively that the recently proposed Haiku geometry is a lower energy configuration than any of the previously proposed line geometries. Furthermore, we have made comparisons between STM constant-current topographs of the lines and Tersoff–Haman STM simulations. Although the Haiku and the Miki geometries both reproduce the main features of the constant-current topographs, the simulated STM images of the Miki geometry have a dark stripe between the dimer rows that does not correspond well with experiment.

The electronic properties of Si(001)–Bi(2 × n)

A Bi 2 × n surface net was grown on the Si(001) surface and studied with inverse photoemission, scanning tunnelling microscopy and ab initio and empirical pseudopotential calculations. The experiments demonstrated that Bi adsorption eliminates the dimer related π1* and π2* surface states, produced by correlated dimer buckling, leaving the bulk bandgap clear of unoccupied surface states. Ab initio calculations support this observation and demonstrate that the surface states derived from the formation of symmetric Bi dimers do not penetrate the fundamental bandgap of bulk Si. Since symmetric Bi dimers are an important structural component of the recently discovered Bi nanolines, that self-organize on Si(001) above the Bi desorption temperature, a connection will be made between our findings and the electronic structure of the nanolines.

Two-dimensional self-assembly of a symmetry-reduced tricarboxylic acid

Investigations of the self-assembly of simple molecules at the solution/solid interface can provide useful insight into the general principles governing supramolecular chemistry in two dimensions. Here, we report on the assembly of 3,4′,5-biphenyl tricarboxylic acid (H3BHTC), a small hydrogen bonding unit related to the much-studied 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), which we investigate using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. STM images show that H3BHTC assembles by itself into an offset zigzag chain structure that maximizes the surface molecular density in favor of maximizing the number density of strong cyclic hydrogen bonds between the carboxylic groups. The offset geometry creates “sticky” pores that promote solvent coadsorption. Adding coronene to the molecular solution produces a transformation to a high-symmetry host–guest lattice stabilized by a dimeric/trimeric hydrogen bonding motif similar to the TMA flower structure. Finally, we show that the H3BHTC lattice firmly immobilizes the guest coronene molecules, allowing for high-resolution imaging of the coronene structure.