Chemical Physics Letters (v.336, #5-6)

Enhanced chemi-mechanical transduction at nanostructured interfaces by Nickolay V. Lavrik; Christopher A. Tipple; Michael J. Sepaniak; Panos G. Datskos (371-376).
Interfacial molecular recognition processes can be converted into mechanical responses via modulation of surface stress. We demonstrate dramatic enhancement in this transduction when quasi 3-D interfaces with nano-size features are used. Microcantelever surfaces are modified with gold nanospheres or granular films and functionalized with macrocycle cavity and receptors. Deflections of these nanostructured cantilevers in response to vapor phase hydrocarbons are two orders of magnitude larger than with conventional smooth surfaces. Such a significant enhancements of surface stress changes resulting from intermolecular interactions at vapor- and liquid-solid interfaces offer an attractive means to develop novel nano-mechanical devices that respond directly and sensitively to chemical stimuli.

Interaction of sulfur with TiO2(1 1 0): photoemission and density-functional studies by José A. Rodriguez; Jan Hrbek; Joseph Dvorak; Tomas Jirsak; Amitesh Maiti (377-384).
Upon adsorption of S2 on TiO2(1 1 0) at 300 K, high-resolution photoemission shows the presence of at least three different types of sulfur species associated with SO x groups and S atoms bonded to the Ti rows or vacancies in the bridging oxygen rows. In addition, S n species are detected on the oxide surface after dosing sulfur at 100 K. The bonding of sulfur to TiO2(1 1 0) was examined using first-principles density-functional calculations and the periodic supercell approach. The density-functional calculations show important variations in the nature of the bonding depending on the sulfur coverage and the presence of O vacancies on the oxide surface.

The use of 1 H– 31 P cross-polarization (CP)-edited radio frequency dipolar recoupled (RFDR) two-dimensional (2D) NMR exchange experiments for the study of surface dissolution species in solution-aged metaphosphate glass is reported. It is demonstrated that use of CP allows the resonances of phosphate tetrahedral species within the hydrated dissolution surface to be selectively and cleanly edited from the bulk unaged phosphate species. Incorporating the CP-editing into a 2D RFDR exchange experiment also allows the local spatial connectivity between these surface dissolution phosphate species to be directly addressed.

Growth of carbon nanofibers array under magnetic force by chemical vapor deposition by L.F. Sun; Z.Q. Liu; X.C. Ma; D.S. Tang; W.Y. Zhou; X.P. Zou; Y.B. Li; J.Y. Lin; K.L. Tan; S.S. Xie (392-396).
In this Letter, we report the growth of carbon nanofibers arrays by chemical vapor deposition in the presence of magnetic force. We find that when a magnet is applied carbon nanofibers arrays are grown and when the magnet is absent carbon nanotubes arrays are grown at the same experimental conditions. The nanofibers are worse in alignment and less in graphitization than those of the nanotubes grown at the same conditions. What is interesting is that two or three nanofibers can be connected together through a catalyst nanoparticle. These connections might be useful, especially in the fabrication of nanoelectronic devices.

Electrical resistivity of graphitized ultra-disperse diamond and onion-like carbon by V.L. Kuznetsov; Yu.V. Butenko; A.L. Chuvilin; A.I. Romanenko; A.V. Okotrub (397-404).
Here we present the result of measurements of electrical resistivity of ultra-disperse diamonds (UDD) with different graphitization degrees and onion-like carbon (OLC) prepared by vacuum annealing of UDD samples at various fixed temperatures. Intermediate samples contain particles with a diamond core covered by closed curved graphitic shells. The temperature dependence of electrical resistivity ρ(T) of these structures is characteristic for the systems with localized electrons and variable hopping-length hopping conductivity (VHLHC). The data on sample resistance are discussed in terms of the variation of dimensionality of conductivity and changing the number of defects in the system.

Non-planar graphitic nanostructures have been generated by the reaction of atomic hydrogen with glassy carbon. The process allowed us to generate unconventional graphite-based tree-like deposits protruding from the tips of the etched glassy carbon surface. An individual tree-like deposit has dimensions ranging between 0.5 and 4 μm and is a porous aggregate of polyhedral nanoparticles and curled nanofilaments. Micro-Raman spectroscopy and electron diffraction have been used to monitor the structural modifications induced in the material. The Raman analysis of the bonding arrangement in the tree-like deposits indicates that exclusively sp2-coordinated C atoms form these unusual carbon structures.

Although proton detected heteronuclear Overhauser effect spectroscopy is known to be an efficient tool for probing molecular structure and dynamics, it is shown that, in practice, the method fails for observing weak 13C–1H heteronuclear Overhauser effect when the considered carbon-13 (in natural abundance) is not directly bonded to proton(s). Such a weak heteronuclear Overhauser effect has been successfully measured using a modified pulse sequence made of a selective TOCSY block followed by a classical (carbon-13 observation) one-dimensional HOESY sequence. The potentialities of this tool have been illustrated by the confirmation of the preferential conformation of uridine in water.

Collective effects in individual oligomers of the red fluorescent coral protein DsRed by Mircea Cotlet; Johan Hofkens; Fabian Köhn; Jan Michiels; Gunter Dirix; Maarten Van Guyse; Jos Vanderleyden; Frans C. De Schryver (415-423).
We report on single-molecule experiments that were performed on two biological systems, the recently cloned red fluorescent protein of a coral of the Discosoma genus (DsRed) and the enhanced green fluorescent protein, both of which were immobilized in polyvinylalcohol. Fluorescence intensity trajectories were recorded and compared to those of a reference compound, the organic dye hexaphenylbenzene perylenemonoimide. Evidence was found for the presence of DsRed as an oligomer even at subnanomolar concentrations. Both proteins show triplet blinking in the millisecond time range. Collective effects could be observed for the Dsred oligomers.

Transient absorption spectra of Pt-loaded TiO2 powder photocatalysts were measured by femtosecond diffuse reflectance spectroscopy and the dynamics of photogenerated electrons in TiO2 were investigated. The Pt-loaded TiO2 showed a new decay component of a few ps under 390 nm excitation in addition of normal charge recombination kinetics. This fast decay process can be interpreted as migration of electrons in TiO2 to Pt on the basis of detailed measurements changing experimental conditions such as Pt-loading, excitation wavelength and excitation fluence. These results clearly indicate that charge separation is responsible for the well-known enhancement of the catalytic reactivity of Pt-loaded TiO2.

Positive and negative ion emission from perfluorinated poly-ethers by J.M.C. Lourenço; R.T. Carrapa; O.M.N. Teodoro; A.M.C. Moutinho; M.A. Gleeson; J. Los; A.W. Kleyn (431-438).
Positive and negative ion ejection in the mass range below 200 Dalton is observed for perfluorinated poly-ether surfaces subjected to electron- and ion-beam irradiation. The exciting projectiles are Ar+ ions of 300 and 4000 eV and electrons of 3000 eV. The main positive ions found are fragments of CF3 + ions. Larger ions are found with lower probability. The main negative ion observed is F. The results show that the liquid–vacuum interface is formed by CF3 groups from the polymer.

Primary events in the photoactive yellow protein chromophore in solution by Pascale Changenet-Barret; Pascal Plaza; Monique M. Martin (439-444).
The photoinduced cis–trans isomerization of the photoactive yellow protein chromophore, the deprotonated trans-p-coumaric acid, is studied in solution by subpicosecond transient absorption and gain spectroscopy. A nonemissive photoproduct absorbing in the UV region, attributed to the cis isomer, is found to appear in 10 ps at the rate of the excited-state decay, demonstrating that there is no detectable intermediate in the relaxation pathway of the photoactive yellow protein chromophore in solution.

We study theoretically the influence of both diagonal and off-diagonal disorder on the absorption spectra of the light-harvesting antenna complex LH2 consisting of two circular aggregates, B850 and B800, of bacteriochlorophyll pigments in photosynthetic purple bacteria. Off-diagonal disorder, i.e., randomness in excitonic couplings between molecules, is introduced by a model of disorder in the position of each pigment molecule embedded in proteins. We demonstrate that a large contribution of positional disorder provides a natural explanation for the experimental fact that the excitonic B850 absorption peak is broader than that of monomeric B800 in spite of motional narrowing.

Polarizability of silicon clusters by Yuji Mochizuki; Hans Ågren (451-456).
The polarizability of hydrogen-terminated silicon clusters derived from the silicon diamond-lattice structure was evaluated by linear response calculations. The dependences on cluster size and basis set were systematically investigated. A convergence in calculated polarizability per silicon atom toward the bulk value was found. Frequency-dependent polarizabilities were also addressed.

About the evaluation of the local kinetic, potential and total energy densities in closed-shell interactions by E. Espinosa; I. Alkorta; I. Rozas; J. Elguero; E. Molins (457-461).
The local kinetic G( r ), potential V( r ) and total E( r ) energy densities, calculated at the critical points of 37 H⋯F closed-shell interactions by quantum mechanical methods, have been compared to their estimated values obtained by using an approximate evaluation of G( r ) and the local form of the virial theorem. The results presented here show very small differences between the corresponding quantities, and therefore support the validity of the estimations. Thus, the equations used in this procedure provide useful information for topological studies of experimental electron densities, permitting the evaluation of those energetic properties from the modelling of the topological properties of the electron density distribution.

The electronic factor (Δ) for photoinduced electron transfer (PET) in porphyrin–benzene–(bicyclo[2.2.2]octane) n –quinone (n=0,1,2) systems (P–B–Q) is calculated by using the CI–CNDO/S method. An artificial potential is employed in order to bring the systems to the avoided crossing region. The effects of Zn coordination on the porphyrin ring and peripheral substitution are studied. We found that, without Zn, methyl substitution on meso positions diminishes significantly the decay coefficient of Δ with P–Q distance (α). P-tolyl substituents, on positions (β,γ,δ), have a lower effect on α. Zn coordination is effective only in the case of methylated P ring, where α is lowered.

Total energy calculations of a neutral and charged Ni5 cluster and its isomers corresponding to different spin multiplicities have been carried out using density functional theory and generalized gradient approximation. It is demonstrated that its magnetic moment can be determined by comparing theoretical results with photo-detachment spectroscopy experiment. We find Ni5 to have two nearly degenerate isomers with magnetic moments of 0.8  μ B per atom and 1.2  μ B per atom.

Spin–spin coupling constants in C2H2 by Michał Jaszuński; Kenneth Ruud (473-478).
We present accurate ab initio calculations of the NMR indirect spin–spin coupling constants of acetylene. Very large basis sets have been used in order to ensure near basis-set limit results for the different coupling constants, and large CI expansions enable an accurate treatment of electron correlation effects. The calculated coupling constants are in good agreement with recent experimental estimates of the coupling constants in an isolated acetylene molecule, corrected for rovibrational effects.The results demonstrate that experiment and theory finally have reached almost the same values for all the spin–spin coupling constants of the isolated, rigid acetylene molecule.

Calculations on the unstable CO(X2 Π) anion by Edmond P.F. Lee; Jérôme Lozeille; Pavel Soldán; Timothy G. Wright (479-487).
It is demonstrated that CO(X2 Π) lies above CO(X1 Σ +) and hence is unstable with respect to autodetachment. This is in disagreement with an oft-cited experimental result, which concluded that CO has an electron affinity of +1.4 eV, but in agreement with electron scattering results. It might be concluded that the RCCSD(T) approach with aug-cc-pVQZ and aug-cc-pV5Z basis sets gives reliable electron affinities based upon comparison with identical calculations on N2; however, analysis of the electronic wave function indicates that this may be fortuitous. On the other hand, CASSCF + multireference configuration interaction (MRCI) calculations on CO seem to indicate a viable way forward, and spectroscopic constants are derived.

Extracting rates of vibrational energy relaxation from centroid molecular dynamics by Jens Poulsen; Søren R. Keiding; Peter J. Rossky (488-494).
We investigate the ability of centroid molecular dynamics (CMD) to determine quantum correlation functions pertinent to the bath force correlation function, appearing in the rate expression for vibrational energy relaxation. We consider a one-dimensional model consisting of two or three Helium atoms. As expected, it is found that CMD performs best when the dominant bath coupling is linear in the bath coordinates, but it also performs well in determining the high frequency components of the force correlation functions. It is suggested that CMD should be used instead of classical dynamics when studying vibrational energy relaxation in cases where quantum effects are expected to be significant.

Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms by Gennady M. Verkhivker; Paul A. Rejto; Djamal Bouzida; Sandra Arthurs; Anthony B. Colson; Stephan T. Freer; Daniel K. Gehlhaar; Veda Larson; Brock A. Luty; Tami Marrone; Peter W. Rose (495-503).
Thermodynamic and kinetic aspects of ligand–protein binding are studied for the methotrexate–dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand–protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Negative solubility coefficient of methylated cyclodextrins in water: A theoretical study by E.B Starikov; K Bräsicke; E.W Knapp; W Saenger (504-510).
Molecular dynamics and Monte Carlo simulations of β-cyclodextrin and its per-dimethylated derivative heptakis(2,6-di-O-methyl)-β-cyclodextrin have been carried out in water solutions at two temperatures, 25°C and 70°C. The structure of the hydration shells, as well as the solute–solvent and solvent–solvent correlations have been analyzed. The negative solubility coefficient of heptakis(2,6-di-O-methyl)-β-cyclodextrin is conditioned first of all by progressive destruction of the hydration shells around its methyl groups with temperature increase, whereas for β-cyclodextrin with positive temperature coefficient, solution is comparable at 25°C and 70°C.

Beam deviation of large polar molecules in static electric fields: theory and experiment by Philippe Dugourd; Isabelle Compagnon; Franck Lepine; Rodolphe Antoine; Driss Rayane; Michel Broyer (511-517).
A classical approach to calculate the energy and the orientation of symmetric top and linear molecules in high electric fields is proposed. This calculation is particularly well adapted to large molecules. It is used to simulate the deviation of a molecular beam in an inhomogeneous electric field. We give an example of experimental and calculated profiles of deviation for a transition metal-fullerene compound TiC60. This is the first direct measurement of the permanent dipole of a large rigid molecule in the gas phase.

On laser Coulomb explosion imaging of proton motion by André D. Bandrauk; Szczepan Chelkowski (518-522).
From exact non-Born–Oppenheimer simulations of the dissociative-ionization dynamics of H2 + in an intense (I>1015   W/cm 2), ultrashort (t p<5 fs) λ=800 nm laser pulse, one can measure the time evolution of the probability distribution |ψ(R,t)|2 of the initial proton wave packet. It is shown that best imaging is obtained for ultrashort pulses (t p<3 fs) at 4×1015   W/cm 2 or much shorter wavelengths, λ⩽30 nm. The relevance of this imaging criterion is discussed in relation to current laser Coulomb explosion imaging of proton transfer in large molecules.

Monte Carlo simulations are presented for the thermodynamic and structural properties of a size-asymmetric primitive model electrolyte with size ratio λ=d +/d =0.4. The results cover a wide range of temperatures and densities from gas to solid including the gas–liquid coexistence region. Comparison is made with hypernetted chain integral equation results.

Multireference Møller–Plesset perturbation theory using spin-dependent orbital energies by Yuka Kobayashi; Haruyuki Nakano; Kimihiko Hirao (529-535).
The use of spin-dependent orbital energies is proposed in the multireference Møller–Plesset perturbation theory. In this method a single canonical Fock orbital set is used for both alpha and beta electrons, while the orbital energies depend on the spin of the electron that occupies the orbital. The method is tested on the energy splitting between states of different spins in the CH2, CF2, CO, O2, N2 +, and o-benzyne molecules. The results agree well with available experimental data; the deviations are within 4 kcal/mol in all cases considered.

Author Index (537-544).