Hydrogen-bonding-induced shifts of the excitation energies in nucleic acid bases: an interplay between electrostatic and electron density overlap effects

The theoretically calculated dimerization-induced shifts of the lowest excitation energies in two model systems, adenine-thymine and guanine-cytosine base pairs, are analyzed. The applied formalism is based on first principles and allows one to study the influence of the microscopic environment of a given molecule on its ground- [Wesolowski, T. A.; Warshel, A. J. Phys. Chem. 1993, 97, 8050] and excited-state [Casida, M. E.; Wesolowski, T. A. Int. J. Quantum Chem. 2004, 96, 577] properties. The assessment of the relative importance of such effects as (a) Coulomb interactions, (b) orbital interactions, (c) electronic polarization of the environment, and (d) electron density overlap effects is straightforward in this formalism. In the applied formalism, electron density overlap effects can be further decomposed into the exchange-correlation component which provides a small attractive contribution and the repulsive kinetic energy-dependent component. It is shown that the shifts can be attributed to the electrostatic interactions and the repulsive overlap-dependent term in the embedding potential. The electronic polarization of the environment plays a significant role (up to 30% of the total shift) only in transitions involving the orbitals localized on hydrogen bond donor groups. For all analyzed shifts, the contribution of the intermolecular orbital interactions is negligible. The analysis of this work provides strong evidence supporting the use of the widely applied embedding-molecule strategy in computational studies of chromophores in a condensed phase even in such cases where only one end of the hydrogen bond is included in the quantum mechanical part.     

On the classical behavior, coherent and incoherent contributions to scattering of atoms from a surface

In this work we calculate the coherent and incoherent contributions to the diffraction probability of atoms scattered by a surface. We are interested in exploring the relative importance of each of these contributions, and compare them with results obtained from molecular dynamics calculations. To achieve this goal, we employed a method developed by Heller that consists of writing the incident plane wave as a sum of Gaussian wave packets, propagating them independently by using the time dependent Schrödinger equation, and constructing the scattered wave function by adding coherently the scattered packets. For the system studied, the molecular dynamics results show the largest intensity in the specular region and also display a classical rainbow structure. On the other hand, the quantum results exhibit diffraction features, with the coherent contribution accounting for most of the total intensity probability.     

Surface-enhanced Raman scattering and surface-enhanced resonance Raman scattering excitation profiles of Ag-2,2'-bipyridine surface complexes and of [Ru(bpy)3]2+ on Ag colloidal surfaces: manifestations of the charge-transfer resonance contributions to the overall surface enhancement of Raman scattering

Excitation profiles of SERS (surface-enhanced Raman scattering) and/or SERRS (surface-enhanced resonance Raman scattering) spectral bands of two forms of a Ag-bpy (bpy = 2,2'-bipyridine) surface complex and of [Ru(bpy)3]2+ on Ag nanoparticle (hydrosol) surfaces were determined from the spectra excited in the 458-600 nm region and are reported together with the FT-SERS spectra of the Ag-bpy surface complex and FT Raman spectra of [Ru(bpy)3] Cl2. Seven of the observed 11 fundamentals as well as their first overtones and combination bands are selectively enhanced in SERS of the Ag-bpy surface complex formed in the Ag colloid/HCl/bpy system. The profiles of these bands show a common maximum at approximately 540 nm. The selectively enhanced bands of the Ag-bpy surface complex have nearly the same wavenumbers as those enhanced in the SERRS and resonance Raman spectra of [Ru(bpy)3]2+ upon excitation close to the 453 nm maximum of its MLCT absorption band. Moreover, the intensity patterns of the bpy vibrations of the two species match both in resonance (541 nm excitation for Ag-bpy, 458 nm for [Ru(bpy)3]2+) and in off-resonance (458 and 1064 nm for Ag-bpy, 1064 nm for [Ru(bpy)3]2+). The distinct band shapes of the excitation profiles of the selectively enhanced vibrational modes of the Ag-bpy surface complex, as well as the observation of overtones and combination bands in the SERS spectra upon excitation into this "band", are interpreted in terms of a charge-transfer resonance contribution to the overall SERS enhancement. In view of the near-coincidence of the vibrational modes coupled to the resonant electronic transition of Ag-bpy with those coupled to the MLCT transition of [Ru(bpy)3]2+, the resonant electronic transition is tentatively assigned to a Ag metal to bpy (pi*) CT transition.     

BPA-PC on a Ni111 surface: the interplay between adsorption energy and conformational entropy for different chain-end modifications

We extend a previous dual scale modeling approach for the behavior of polymers near a metal surface to a variety of end groups. Our approach combines a coarse-grained polymer model with ab initio DFT calculations. Such a procedure was applied to a melt of phenolic-like terminated Bisphenol A-polycarbonate (BPA-PC) interacting with a (111) nickel surface (Delle Site, L.; Abrams, C. F.; Alavi, A.; Kremer, K. Phys. Rev. Lett. 2002, 89, 156103. Abrams, C. F.; Delle Site, L.; Kremer, K. Phys. Rev. E 2003, 67, 021807). This work extends this study to different chain-end modifications of BPA-PC, p-tert-butylphenolic, p-tetramethylpropylphenolic, and p-cumylphenolic. We show how the interplay between adsorption energies and conformational entropy selects different morphologies for the various melts at the interface. Implications of these results for realistic technical materials are finally discussed.     

Statistical lattice model for the bimolecular reaction on the dynamically changing surface of a body-centered metal crystal

A statistical lattice model has been constructed for the surface of a body-centered cubic (bcc) crystal whose morphology varies under the action of external factors (temperature and adsorbate coverage). Monomolecular and dissociative bimolecular adsorption on the bcc crystal surface has been investigated. In this model, adsorption smoothens the originally rough surface owing to adsorbate molecules stabilizing their flat adsorption areas, as distinct from adsorption on the primitive cubic lattice. Our model differs from the models with invariable surface morphology in that the number of its accessible adsorption sites is variable and depends on external conditions. The kinetics of a catalytic reaction proceeding by the Langmuir-Hinshelwood mechanism have been studied for the (100) face of a bcc crystal whose morphology varies under the action of the reaction medium.     

Effect of polyethylene oxide on the viscosity of dispersions of charged silica particles: interplay between rheology, adsorption, and surface charge

In this study a systematic investigation on the adsorption of polyethylene oxide (PEO) onto the surface of silica particles and the viscosity behavior of concentrated dispersions of silica particles with adsorbed PEO has been performed. The variation of shear viscosity with the adsorbed layer density, concentration of free polymer in the solution (depletion forces), polymer molecular weight, and adsorbed layer thickness at different salt concentrations (range of the electrostatic repulsion between particles) is presented and discussed. Adsorption and rheological studies were performed on suspensions of silica particles dispersed in solutions of 10⁻² M and 10⁻⁴ M NaNO₃ containing PEO of molecular weights 7,500 and 18,500 of different concentrations. Adsorption measurements gave evidence of a primary plateau in the adsorption density of 7,500 MW PEO at an electrolyte concentration of 10⁻² M NaNO₃. Results indicate that the range of the electrostatic repulsion between the suspended particles affects both adsorption density of the polymer onto the surface of the particles and the viscosity behavior of the system. The adsorbed layer thickness was estimated from the values of zeta potential in the presence and absence of the polymer and was found to decrease with decreasing the range of the electrostatic repulsive forces between the particles. Experimental results show that even though there is a direct relation between the viscosity of the suspension and the adsorption density of the polymer onto the surface of the particles, variation of viscosity with adsorption density, equilibrium concentration of the polymer, and range of the electrostatic repulsion cannot be explained just in term of the effective volume fraction of the particles and needs to be further investigated. Received: 15 February 2000/Accepted: 26 June 2000     

The study of resonance Raman scattering spectrum on the surface of Cu nanoparticles with ultraviolet excitation and density functional theory

Cu colloid was prepared by oxidation-reduction; it was relatively steady in fixed conditions, with size about 10-30 nm. The Raman spectrum of p-hydroxybenzoic acid (PHBA) in Cu colloid solution with the ultraviolet (UV) excitation at 325 nm, was obtained, even it is usually difficult to obtain Raman signals in Ag or Au in the UV region. It was found that the Raman signal intensities result from the resonance enhanced of surface plasmon resonance of Cu nanoparticles excited at 325 nm. The adsorption behavior of PHBA on the Cu nanoparticles was studied by combining with density functional theory (DFT); it was found that the calculated Raman frequencies were in good agreement with experimental value. So one can conclude that the simplified model is probably reasonable to describe some resonance Raman experiments.     

Theoretical and experimental studies on the carbon-nanotube surface oxidation by nitric acid: interplay between functionalization and vacancy enlargement

The nitric acid oxidation of multiwalled carbon nanotubes leading to surface carboxylic groups has been investigated both experimentally and theoretically. The experimental results show that such a reaction involves the initial rapid formation of carbonyl groups, which are then transformed into phenol or carboxylic groups. At room temperature, this reaction takes place on the most reactive carbon atoms. At higher temperatures a different mechanism would operate, as evidenced by the difference in activation energies. Experimental data can be partially related to first-principles calculations, showing a multistep functionalization mechanism. The theoretical aspects of the present article have led us to propose the most efficient pathway leading to carboxylic acid functional groups on the surface. Starting from mono-vacancies, it ends up with the synergistic formation of dangling -COOH groups and the enlargement of the vacancies.     

Experimental study of the interplay between long-range electron transfer and redox probe permeation at self-assembled monolayers: evidence for potential-induced ion gating

Evidence for the competition between long-range electron transfer across self-assembled monolayers (SAMs) and incorporation of the redox probe into the film is reported for the electroreduction of Ru(NH(3)) at hydroxyl- and carboxylic-acid-terminated SAMs on a mercury electrode, by using electrochemical techniques that operate at distinct time scales. Two limiting voltammetric behaviors are observed, consistent with a diffusion control of the redox process at mercaptophenol-coated electrodes and a kinetically controlled electron transfer reaction in the presence of neutral HS-(CH(2))(10)-COOH and HS-(CH(2))(n)()-CH(2)OH (n = 3, 5, and 10) SAMs. The monolayer thickness dependence of the standard heterogeneous electron transfer rate constant shows that the electron transfer plane for the reduction of Ru(NH(3)) at hydroxyl-terminated SAMs is located outside the film | solution interface at short times. However, long time scale experiments provide evidence for the occurrence of potential-induced gating of the adsorbed structure in some of the monolayers studied, which takes the form of a chronoamperometric spike. Redox probe permeation is shown to be a kinetically slow process, whose activation strongly depends on redox probe concentration, applied potential, and chemical composition of the intervening medium. The obtained results reveal that self-assembled monolayers made of mercaptobutanol and mercaptophenol preserve their electronic barrier properties up to the reductive desorption potential of a fully grown SAM, whereas those of mercaptohexanol, mercaptoundecanol, and mercaptoundecanoic acid undergo an order/disorder transition below a critical potential, which facilitates the approach of the redox probe toward the electrode surface.     

Infrared study of adsorption of methanol,deuterated methanol and ethylene on the surface of ZSM-5 type zeolite

The surface species resulting in exposing of the ZSM-5 zeolite at elevated temperatures to methanol, deuterated methanol or ethylene have been studied by IR method.The three-step adsorption at 150°, 300°, 420° C or one-step adsorption at 420° C have been carried out in order to prepare the samples for IR. In all cases the most prominent band appeared in the range 1495–1515 cm^?1; besides two bands at about 1470 and 1370 cm^?1 have been observed. On the basis of Greenler's results and of the shift values of the bands in our spectrum of adsorbed deuterated methanol it was supposed that the band 1495–1515 cm^?1 is due to the OCO group from the surface species. Moreover these species would involve both oxygen atoms from the surface of zeolite but not from OH groups of methanol.     

A graphic model for calculating the properties of alkylsilanes, based on the additivity of energy contributions

A 18-constant additive scheme for calculating the physicochemical properties of alkylsilanes is obtained, based on the transferability of subgraphs in molecular graphs of the homologic SiC _n H_{2n + 4} series of alkylsilanes. The model considers multiple nonvalence interactions through no more than one atom and pair nonvalence interactions through no more than three skeletal atoms along a molecular chain. A linear dependence is established within the classification of the structural elements in a molecule. The enthalpies of formation Δ_f H° (g, 298 K) for alkylsilanes SiC _n H_{2n + 4} not studied experimentally were calculated numerically by considering different approximations.     

On the interplay between chemical reactions and phase transitions for molecules adsorbed on solid surfaces

We use Monte Carlo simulations to examine the manner in which reagent aggregation affects the reaction rate between molecules adsorbed on a solid surface. We discuss the temperature and concentration dependence of the rate of product formation.     

Calculation of the surface excitation parameter for Si and Ge from measured electron backscattered spectra by means of a Monte-Carlo simulation.

A new Monte Carlo method has been developed for simulating backscattered electron spectra, and this was applied for determining the surface excitation parameter (SEP). The simulation is based on direct tracking of electron trajectories in the solid, taking into account elastic and inelastic events. The elastic scattering cross sections are taken from literature, while inelastic cross section data are obtained by a fitting procedure. After some iterations, the program produces electron spectra fitting well to the experimental ones. Si and Ge electron spectra were simulated and SEP values were calculated. The SEP values are compared to other ones from literature.     

A study of electron scattering from benzene: excitation of the 1B1u, 3E2g, and 1E1u electronic states

We report results from measurements for differential and integral cross sections of the unresolved (1)B(1u) and (3)E(2g) electronic states and the (1)E(1u) electronic state in benzene. The energy range of this work was 10-200 eV, while the angular range of the differential cross sections was ～3°-130°. To the best of our knowledge there are no other corresponding theoretical or experimental data against which we can compare the present results. A generalized oscillator strength analysis was applied to our 100 and 200 eV differential cross section data, for both the (1)B(1u) and (1)E(1u) states, with optical oscillator strengths being derived in each case. The respective optical oscillator strengths were found to be consistent with many, but not all, of the earlier theoretical and experimental determinations. Finally, we present theoretical integral cross sections for both the (1)B(1u) and (1)E(1u) electronic states, as calculated within the BEf-scaling formalism, and compare them against relevant results from our measurements. From that comparison, an integral cross section for the optically forbidden (3)E(2g) state is also derived.     

Molecular hybrids of azobenzene polymer and liquid crystal molecule. A new approach for understanding the command surface system

Langmuir-Blodgett (LB) films consisting of the hybrid of a polymer having the azobenzene (Az) side chain and 4î-pentyl-4-cyanobiphenyl (5CB) are prepared. Microscopic observations and spectroscopic data both indicate that the Az side chain and 5CB are homogeneously mixed at a molecular level without phase separation in the layer. This provides a satisfactory model of the command surface system. Time course accumulation of spectroscopic data for multilayered hybrid films reveals the cooperative nature of the photo-motivated molecular motions.     

Laser illumination effects on the surface morphology,cyclic voltammetry,and surface-enhanced raman scattering of Ag electrodes

Scanning electron microscopy reveals that the structure of the Ag electrode is notably altered by laser illumination during electrochemical oxidation and reduction in 1 M KX (X = 1, Br, Cl, and F) electrolytes. Laser illumination also influences the voltammogram in 1 M Kl, the intensities of the SERS of adsorbed H₂O and pyridine, and the intensities of selected points in the featureless background of the SERS spectra.     

Semiempirical calculations on the interaction between dimethyltin(IV) and DNA model system

The interaction between a dinucleotide triphosphate duplex (DD), mimicking the DNA molecule, and the dimethyltin(IV) cation is studied by the semiempirical PM3 method. The results show that the interaction can occur involving the tin atom and the electron-donor centres of DD, requiring in some cases the presence of water molecules. In particular, the binding of the dimethyltin(IV) moiety with two adjacent phosphate oxygen atoms is allowed by the presence of water molecules coordinating to the tin atom. In this case the tin environment shows a geometry in agreement with ¹¹⁹Sn Mössbauer and X-ray data.     

Superoxide radical anions on the surface of zirconia and sulfated zirconia: formation mechanisms, properties and structure

In situ ESR spectroscopy has been used for direct comparison of different thermal and light-induced processes leading to generation of superoxide radical anions on the surface of various zirconia and sulfated zirconia materials. For materials of both types the magnetic resonance parameters of the radical anions were found to be practically independent of the generation method, except for oxygen coadsorption with NO that yields radicals with somewhat smaller gz values. The parameters appear to depend mostly on the state of the surface zirconia cations stabilizing the radical anions, so that the g tensor anisotropy is significantly smaller over sulfated zirconia. It is shown that light-induced formation of superoxide radical anions in the presence of coadsorbed hydrocarbons can be initiated with visible light. Original SIET reaction mechanisms are suggested for the formation of superoxide radical anions by coadsorption with hydrocarbons and illumination after such coadsorption to extend the previously known ones to account for the observed phenomena. Cluster model DFT calculations of magnetic resonance parameters of O2- radical anions stabilized on the surface of zirconium dioxide showed that the adsorption complexes have a -shape rather than linear structure. The magnetic resonance parameters obtained by calculations practically match experimental data and adequately describe their changes after the surface modification with sulfates.     

Basis set limit electronic excitation energies, ionization potentials, and electron affinities for the 3d transition metal atoms: Coupled cluster and multireference methods

Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s(2)3d(n-2)-4s(1)d(n-1) electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1 kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.     

加替沙星与人血浆及人血清蛋白作用机理的研究

利用荧光及紫外光谱法研究了水溶液中加替沙星(GFLX)与人血浆及人血清白蛋白(HSA)的相互作用机制.实验结果表明,GFLX对人血浆及HSA的荧光都有较强的猝灭作用,其类型主要为静态猝灭.在不同温度下求得了GFLX对人血浆及HSA的结合常数k,发现随反应温度上升k值下降.由热力学参数确定了GFLX对人血浆及HSA的结合作用主要为疏水作用力.根据F嵀rster理论,测得了GFLX对人血浆及HSA之间的能量转移效率,相互结合距离,阐述了猝灭机理是通过能量转移产生的,GFLX对人血浆及HSA作用行为基本相同.