Chemical Physics Letters (v.395, #1-3)

Solvation thermodynamics of protein studied by the 3D-RISM theory by Takashi Imai; Andriy Kovalenko; Fumio Hirata (1-6).
The partial molar volume and the solvation free energy of five globular proteins in aqueous solutions are calculated by the three-dimensional reference interaction site model theory, a modern integral equation theory of molecular liquids. The partial molar volume calculated by the theory shows quantitative agreement with the corresponding experimental data. Concerning the solvation free energy, the theoretical results are compared with estimations by an empirical method which uses the accessible surface area of atoms, because the corresponding experimental data are not available. Possible applications of the method to problems related to the solvation thermodynamics of protein are discussed.

Recent experiments indicate wide variation of the quality of metal–nanotube contacts with the choice of metal. With Au, Pt and Pd as examples, we present DFT results for the interaction of a metal atom, monolayer, multilayer and cluster with a graphene surface, a representative of wide-diameter carbon nanotubes. We also study nanotubes placed on flat metal surfaces. We discover interesting effects including, strong variations of binding energy as a function of metal configuration, and cross-section-deformation of nanotubes placed on Pt and Pd surfaces driven by sp2  → sp3 transition of metal-adjacent C-atoms. The results provide an explanation for poorer Pt-contacts as compared to Pd.

Coupled cluster theory and Dunning’s correlation consistent basis sets have been employed to determine the Δ H f , 298 0 of some halogen oxides XO, XOO and OXO X = F, Cl, Br. The estimated Δ H f , 298 0 of the XO radicals, OClO and OBrO are within ±1 kcal/mol of the experimental results available. However those of ClOO and BrOO exhibit large errors when they are estimated with the atomization reaction. Our revisited Δ H f , 298 0 ( FOO ) including scalar relativistic effects and spin–orbit splitting is Δ H f , 298 0 ( FOO ) = 7.5 kcal / mol , 1–2 kcal/mol larger than the experimental results. For all the molecules considered CCSDT increased the binding energies, improving the agreement with the experimental estimations, except five molecules HSO, OClO, OBrO, BN 1Σ+ and O3. The correction of the CCSD(T) geometries for the missing triple excitations elongates the equilibrium bond lengths, improving the agreement with the experimental determinations for the XO radicals and both states of BN (1Σ+ and 3Π). The present results confirms that for some particular systems, such us the XO, XOO radicals, and hypervalent molecules like OFO, the CCSDT method is preferred over CCSD(T) to predict their thermochemistry and structural parameters.

Investigation of probe–solvent interactions: color effects in optical line widths by Christoph Hecht; Markus Stübner; Josef Friedrich; Ta-Chau Chang (21-26).
We have measured the optical hole width as a function of wave number across the inhomogeneous lines for two aromatic probe molecules, namely thionin and BODIPY. Upon tuning the laser to the red edge of the inhomogeneous band the hole width of thionin decreases, whereas the hole width of BODIPY increases. The color effect is correlated with the solvent shift in the former case and anti-correlated in the latter case. We suggest possible scenarios to explain these observations and back up our reasoning by site dependent Stark-effect experiments.

The hydrogen bond interaction in [AH3–H3O]+• radical cations for A = C, Si, Ge, Sn and Pb is studied at the CCSD(T)/6-311G++(3df,2pd)//MP2/6-31G++(d,p) level of theory. Two unusual hydrogen bond structures are found to be stable: the single-electron (SEHB) and the proton-hydride (PHHB) ones. The latter structures have been found to easily evolve to a [AH2H2O]+• –H2 complex, from which H2 can be eliminated.

A DFT study of hydrogen and carbon monoxide chemisorption onto small gold clusters by Noko S. Phala; Günter Klatt; Eric van Steen (33-37).
DFT calculations have been performed to study the interaction of small gold clusters, Au1–Au13, with H and CO. An odd–even oscillation of the H chemisorption energy was observed, with H adsorption onto odd-numbered clusters being more favourable. This correlates with the smaller HOMO–LUMO gaps for these clusters. For CO chemisorption, the overlap between CO orbitals and cluster frontier orbitals is important. As a result, there is no simple relationship between CO chemisorption energy and the frontier orbital energies of Au n clusters.

The reaction of Ga2 with H2 to form the most stable singlet Ga(μ-H)2Ga isomer 1 observed to occur spontaneously in solid noble gas matrices by Downs has been investigated theoretically with single- and multi-reference ab initio and DFT methods. Early on the reaction coordinate, a spin crossing is expected to move the process from the reactant ground-state triplet surface onto the singlet surface of the product. The singlet direct C2v path involves the most favourable TSPH-H activation transition state lying, at CCSD(T), 2.7 kcal/mol above Ga 2 ( 1 Σ g + ) + H 2 .

The influence of carbon nanotube (CNT) contents on electrical and rheological properties of CNTs-reinforced polypropylene (PP) composites was studied. As a result, the volume resistivity of the composites was decreased with increasing the CNT content and the electrical percolation threshold was formed between 1 and 2 wt% CNTs, which were caused by the formation of conductive chains in the composites. And the viscosity of the composites was increased with the addition of CNTs, which was accompanied by an increase in elastic melt properties (G′). This could be explained by the higher aspect ratio of the CNTs. And the composites containing more than 2 wt% CNTs exhibited non-Newtonian curves at low frequency.

Stabilization of an anionic guest adsorbed on sodium faujasites through enhanced Coulombic interaction by José Raul Herance; Jordi Marquet; José Luis Bourdelande; Hermenegildo Garcı́a (49-52).
The negatively charged adduct formed by reaction of 2,4-dinitroaniline with NaBH4 (Meisenheimer complex) has been successfully incorporated inside faujasites. The internal location of the anionic Meisenheimer guest was confirmed by XPS. This anionic reaction intermediate becomes largely stabilized by the inclusion in zeolite as the result of an increase of the association constant with alkali metal ions inside the zeolite cavities.

A pulsed, low-temperature beam of supersonically cooled free radical OH molecules by H.J. Lewandowski; Eric R. Hudson; J.R. Bochinski; Jun Ye (53-57).
An improved system for creating a pulsed, low-temperature molecular beam of hydroxyl radical (OH) radicals has been developed. We use a pulsed discharge to create OH from H2O seeded in Xe during a supersonic expansion, where the high-voltage pulse duration is significantly shorter than the width of the gas pulse. The pulsed discharge allows for control of the mean speed of the molecular packet as well as maintains a low temperature supersonic expansion. A hot filament is placed in the source chamber to initiate the discharge for shorter durations and at lower voltages, resulting in a translationally and rotationally colder packet of OH molecules.

Hydration dynamics of a protein in the presence of urea and sodium dodecyl sulfate by Pratik Sen; Durba Roy; Kalyanasis Sahu; Sudip Kumar Mondal; Kankan Bhattacharyya (58-63).
The antagonistic effects of unfolding of a protein (lysozyme) by urea and refolding by sodium dodecyl sulfate (SDS), have been studied by solvation dynamics and circular dichroism. Efficient fluorescence resonance energy transfer from tryptophan to coumarin 153 (C153) indicates that the solvation probe, C153 is located near tryptophan 62 and 108 of lysozyme. The average solvation time of C153 bound to lysozyme in 7 M urea and 3 mM SDS is quite close to that in the native state of lysozyme while in 28 mM SDS and 7 M urea the average solvation time is nearly three times slower.

The effect of preadsorbed potassium on the pattern forming NO + H2 reaction on Rh(1 1 0) has been studied in the 10−7 mbar range using photoelectron emission microscopy (PEEM) and scanning photoelectron microscopy (SPEM) as spatially resolving methods. Domain patterns of travelling wave fragments develop with pulses in adjacent domains moving in opposite directions parallel to the [1  1 ̄  0] direction. 2D-elemental maps from in situ SPEM measurements show that potassium is concentrated in the oxygen covered part of the pattern whereas the nitrogen covered parts are largely free of potassium.

Preparation of mesoporous silica films using sol–gel process and argon plasma treatment by Alagappan Palaniappan; Jian Zhang; Xiaodi Su; Francis E.H. Tay (70-74).
This Letter demonstrates the first attempt of using sol–gel technique in combination with argon plasma calcination for the preparation of mesoporous silica films. CTAB is used as an organic template to generate the porous structure upon removal by the argon plasma treatment. Field emission scanning electron microscope, Fourier transform infrared spectroscopy, small angle X-ray scattering, N2-sorption experiment and nanoindentation technique are used for characterization. Results show that the obtained films have identical chemical structure and comparable mechanical properties with those prepared using thermal calcination. The plasma parameters have distinct influences on the thickness and mesoporous property of the films.

Magnetic study of the polymeric chain in Cu(II) (1,4-C4H4N2)(C4O4)(H2O)4 by M. Belaı¨che; M. Benhammou; M. Drillon; A. Derory; M. Soufiaoui (75-77).
The magnetic properties of the one dimensional Cu(II)(1,4-C4H4N2)(C4O4)(H2O)4 have been studied. This compound is a typical linear chain. Susceptibility measurements show strong antiferromagnetic intrachain exchange of the order of −8.72 K with poor interchain exchange coupling.

Electronic properties for the C2v and Cs isomers of Pr@C82 studied by Raman, resistivity and scanning tunneling microscopy/spectroscopy by Tomoko Hosokawa; Satoshi Fujiki; Eiji Kuwahara; Yoshihiro Kubozono; Hiroshi Kitagawa; Akihiko Fujiwara; Taishi Takenobu; Yoshihiro Iwasa (78-81).
Electronic properties of the major and minor isomers of Pr@C82, I (C2v) and II (Cs), are studied by Raman scattering, resistivity measurement, scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). The valences of the Pr atom in both isomers are determined to be +3 based on the Raman shift in the Pr–C82 stretching mode. The transport properties showed that both isomers are normal semiconductors with a small energy gap (E g). STM of isomer I shows internal structures dependent on bias voltage V s, and STS shows that this isomer is a semiconductor with E g  = 0.7 eV.

Aggregation and photophysical properties of water-soluble sapphyrins by P. Kubát; K. Lang; Z. Zelinger; V. Král (82-86).
Aggregation and photophysical properties of three sapphyrins were studied by UV/Vis, emission, resonance light scattering and laser kinetic spectroscopies. The relative abundance of various types of aggregates depends mainly on the structure of sapphyrin, solvent and temperature. The formation of H-dimers is related to negative entropy and enthalpy changes and it is controlled mainly by electrostatic interactions between the positively charged sapphyrin unit and negative substituents. Excitation of the H-dimers leads to the formation of the triplet states of the sapphyrin monomers. The quantum yields of the singlet oxygen in methanol vary between 0.30–0.33 and are independent of substitution.

Photophysical properties of boron-dipyrrin appended porphyrins with heteroatom cores by D. Kumaresan; Anindya Datta; M. Ravikanth (87-91).
The photophysical properties of porphyrins with N3S and N3O cores appended with two boron-dipyrrin units and porphyrins with N2S2 and N4 cores appended with four boron-dipyrrin units are described. The steady-state fluorescence measurements indicate that the energy transfer from boron-dipyrrin units to the porphyrin unit is efficient with N4 and N3O porphyrin cores and less efficient with N3S and N2S2 cores. The energy transfer rates calculated from lifetime measurements are also in support with these observations.

The optical absorption of ordered and disordered π-conjugated molecules is described on the same microscopic footing. This gives a concise picture of the length dependence of the optical absorption of π-conjugated systems.

Novel long-lifetime photoluminescence of nanosized ZnO included in the mesoporous MCM-41 by Guo-Qing Tang; Ying Xiong; Lei Z. Zhang; Gui-Lan Zhang (97-102).
The photoluminescence behavior of ZnO is largely dependent on its defect properties that are resulted from different preparation conditions. In this Letter, several kinds of nanosized ZnO are successfully encapsulated in the mesopores of the MCM-41 with different starting materials and at various calcination atmospheres. A novel long-lifetime photoluminescence of the nanostructured ZnO is observed for the first time and is attributed to the donor–acceptor pair (DAP) luminescence. The time-delayed spectra and decay kinetics of the DAP luminescence are also presented. An energy-state model depicting the luminescence is proposed finally, which would be useful for our understanding the mechanism of the blue or green emission of ZnO.

The effects of ionic and nonionic micelles on the excited state proton transfer processes of 2-hydroxy 1-naphthaldehyde (HNL) have been reported in this Letter. Deprotonation of HNL is considerably retarded in neutral and anionic micelles than that in cationic type as evinced from the increased neutral emission. Increased anion emission of HNL in cationic micelle is more due to the abundance of hydroxyl ions in the environment as well as less nonradiative deactivation. Anion emission is found to decrease in anionic micelle due to less formation of the conformer along with increase in nonradiative decay. The nonradiative processes from neutral to ionic form and ionic to ground state are less affected in neutral micelle as compared to HNL in ionic micelles.

Fission of doubly ionized calcium clusters by Estela Blaisten-Barojas; Chang-Hong Chien; Mark R. Pederson; Jeff W. Mirick (109-113).
Cluster ions, Ca N + and Ca N 2 + , containing up to N  = 8 atoms are studied within density functional theory. Ground and first excited states, and ionization energies are reported for all sizes. At zero temperature Ca 3 2 + and Ca 4 2 + are linear, whereas Ca 5 2 + through Ca 7 2 + undergo structural transitions from 3D-configurations into linear ions below 600 K. As a consequence, fission that occurs above 600 K starts from linear configurations. Ca 8 2 + has an hexagonal bipyramidal structure. The preferred fission channels are Ca N 2 + → Ca + + Ca N - 1 + with fission barriers smaller than the evaporation energy up to Ca 7 2 + . However, Ca 8 2 + presents a large fission barrier and would rather evaporate one atom than undergo fission.

Sub-5-fs two-dimensional spectroscopy of pseudoisocyanine J-aggregates by Kumiko Nishimura; Eiji Tokunaga; Takayoshi Kobayashi (114-119).
The oscillations of the absorbance change due to molecular vibrations in pseudoisocyanine bromide J-aggregates were real-time resolved with sub-5-fs laser pulses. In spite of weak exciton–phonon coupling in the Frenkel exciton system, it was possible to observe the modulation of difference absorbance because of the enhanced transition moment. The non-Condon-type exciton–phonon coupling was invoked to explain the oscillatory signals and the transition dipole modulations were evaluated. The band at 38 cm−1 was assigned to optical phonon mode, and the band at 152 cm−1, which had never been detected in Raman scattering, was also real-time resolved.

Vibrational averaging and solvent effects on the isotropic hyperfine coupling constants of dimethyl nitroxide have been investigated by an integrated computational tool including Car–Parrinello molecular dynamics and discrete-continuum solvent models. The results allow an unbiased judgement of the role of different effects in determining the observed EPR parameters.

Little is known about the microscopic mechanism of solvation dynamics in room-temperature ionic liquids, but experimental studies have found that the solvent response has both sub-picosecond and nanosecond timescale components. We present the results of molecular dynamics calculations of the time-resolved fluorescence response of a chromophore in an ionic liquid, and analyze the solute–solvent interactions responsible for the observed signal. We find evidence for collective cation–anion motion on sub-picosecond timescales, contradicting earlier work suggesting the sub-picosecond response is purely anionic. We present an alternative hypothesis to explain our results and the widely disparate timescales for solvation response.

The theory of dipole polarization as used in molecular mechanics energy functions is analyzed, and the difference in induction energy between an iterative (self-consistent) and non-iterative (one-step) scheme is derived. It is concluded that this difference is bound to be small in most cases, so that a non-iterative polarization model can be expected to give a satisfactory representation of the induction energy. This is demonstrated with examples of configurations of water molecules. The advantages of a one-step procedure are discussed.

Laser ablation of diamond nanoparticles suspended in solvent: synthesis of polyynes by Hiroshi Tabata; Minoru Fujii; Shinji Hayashi (138-142).
Laser ablation of diamond nanoparticles suspended in ethanol has been performed by using the second harmonic of a Nd:YAG laser (532 nm). UV–Vis absorption spectra revealed the formation of polyynes (C n H2: n  = 8, 10, 12, 14, and 16). The same experiment was performed for graphitic nanoparticles suspended in ethanol. It was found that ablation of diamond nanoparticles results in larger amounts of long polyynes.

Self-consistent reaction field study was performed to rationalize the selective formation of 3,7-dimethyloctanal by hydrogenation of citral (3,7-dimethyl 2,6-octadienal) exclusively in supercritical carbon dioxide medium. We have used density functional theory (DFT) to calculate and compare the reactivity of the atoms present in the reactant molecule for a range of solvent with variable dielectric constant. Solvent with low dielectric constant was found to be reducing the electrophilicity of the sites present and hence enhances the selectivity of an isolated and conjugated C=C bond-breaking phenomenon. In contrast to that, solvents with high dielectric constant prefer to hydrogenate the conjugated C=C. The geometric and electronic aspects were compared to propose a plausible explanation for the unprecedented selectivity observed in supercritical carbon dioxide medium.

The reaction path is an important concept of theoretical chemistry. We employ the definitions of the Newton trajectory (NT) and of the gradient extremal (GE). An NT follows a curve where the gradient is always a pointer to a fixed direction. A GE is a curve where the gradient of the potential energy surfaces (PES) is eigenvector of the Hessian. Examples are given with the Müller–Brown potential and further model PESs. An induced tangent opens the possibility to follow the curve by a predictor–corrector method. We show that the two kinds of curves can be treated as curves with induced tangent, however, the gradient descent, or intrinsic reaction coordinate not.

EPR study of radical reactions of C60 dimer connected by a silicon bridge and single bond (C60SiPh2C60) by B.L. Tumanskii; O.G. Kalina; V.I. Sokolov; A.L. Chistyakov; I.V. Stankevich; A. Han; Y. Murata; K. Komatsu (157-160).
Radical reactions of C60 dimer connected by a silicon bridge and single bond (C60SiPh2C60) were studied by EPR-spectroscopy. Attack of phosphoryl radicals or 2,2,6,6-tetramethylpiperidine-N-oxyl on the silicon atom leads to radical substitution of the fullerene and formation of a new fullerenyl radical, the structure of the former being confirmed by quantum-chemical calculations (DFT). The formation of only one type of spin-adduct on addition of phosphoryl radicals to the fullerene core is associated with small distortion of the fullerene cage in C60SiPh2C60. Geometry of fullerene core in dimer differs only slightly from C60 owing probably to flexibility of Si–C and C–C bonds which share a five-membered ring.

Surface structure of thin ice films by D. Nordlund; H. Ogasawara; Ph. Wernet; M. Nyberg; M. Odelius; L.G.M. Pettersson; A. Nilsson (161-165).
An angular dependent X-ray absorption spectroscopy study of the surface of thin ice films grown on Pt(1 1 1) is presented. Using different probing depths together with spectral calculations based on density functional theory, the spectra are interpreted in terms of the structure of surface, subsurface and bulk regions. It is shown that the crystalline ice is terminated with a large abundance of isotropically distributed free O–H groups and a distorted subsurface.

We report the electronic structure of [(Re6S8)Cl6]3− using theoretical calculations. Since the lowest 2Au and 2Ag states were energetically very close to each other, we employed single and double excitation configuration interaction method and coupled pair approximation to specify the ground state. It was settled to the 2Au state. Wavefunctions of many lower excited states were obtained by the Tamm–Dankoff type CI. Calculated oscillator strength distribution was in good agreement with observed absorption intensity curve. Those excited states lower than 2.3 eV were described mainly as intra ligands transition and those higher than 2.3 eV were charge transfer transition from ligands to metals.

A LEED and STM study of H(D) adsorption on C(0 0 0 1) surfaces by A. Güttler; Th. Zecho; J. Küppers (171-176).
Adsorption of H (D) atoms on natural graphite (NG) single crystal and highly oriented pyrolytic graphite (HOPG) surfaces was studied with low-energy electron diffraction (LEED) and scanning tunnelling microscopy (STM). No superstructure was observed in LEED, which suggests random adsorption of H on C(0001). Loss of diffraction at increasing H(D) coverage indicates loss of translational symmetry on the surface. STM data suggest that on D covered surfaces randomly distributed C atoms exist which pucker out of the basal plane. Puckered atoms are those which contribute to the STM profile of clean HOPG, i.e., which have no neighbour in the plane below.