Chemical Physics Letters (v.507, #1-3)

Contents (iii-xiii).

Breaking bonds with electrons: Dissociative recombination of molecular ions by Viatcheslav Kokoouline; Nicolas Douguet; Chris H. Greene (1-10).
Display Omitted►Dissociative recombination is now described well for the simplest polyatomic ion. ► Applications can now treat more complex polyatomic targets in a simplified way. ► Applications to H 3 + , HCO+, LiH+ resolve discrepancies between theory and experiment. ► Three-body processes in a hydrogen discharge gas are now better understood.We discuss exciting recent progress in the theoretical description of molecular ion dissociative recombination, with further applications to related processes such as molecular photoionization and rovibrationally-inelastic electron collisions with molecular ions. The techniques are based on quantum defect theory, an efficient tool for characterizing electron–ion collision processes, and on a generalized adiabatic formulation. When needed, the approximation of adiabaticity in the dissociative coordinate is lifted by taking non-adiabatic couplings explicitly into account. We concentrate on a time-independent theoretical framework that has been applied to describe dissociative recombination in ions such as H 3 + , its isotopologues (H2D+, D2H+ and D 3 + ), and HCO+ (DCO+).

Probing the colloidal gold nanoparticle/aqueous interface with second harmonic generation by Louis H. Haber; Sheldon J.J. Kwok; Monica Semeraro; Kenneth B. Eisenthal (11-14).
Display Omitted► Freely adsorbing molecules at gold nanoparticle/water interface probed for first time. ► Second harmonic generation (SHG) from organic dye molecules located at interface. ► SHG signal at varying dye concentrations agrees with modified Langmuir model. ► The model fit provides the free energy and maximum site density of adsorption.The interface of 16 nm colloidal gold nanoparticles with the aqueous solution in which they are suspended is investigated using second harmonic generation. The population of malachite green freely adsorbing to the gold nanoparticle interface as a function of concentration is obtained. The experimental results are in good agreement with the modified Langmuir model, which includes depletion of the adsorbate bulk concentration. The free energy of adsorption is determined to be −15.4 ± 0.4 kcal/mol with 1.13 ± 0.04 × 103 sites per nanoparticle. These results provide the first direct measurement of the isotherm of molecules adsorbing to colloidal metallic nanoparticles.

Conformational energy gaps and scaling of conformer density in chain molecules by Peter L. Walters; Maxim B. Prigozhin; Tyler Y. Takeshita; Lu Xu; Felipe M. Olivarez; Martin Gruebele (15-18).
Display Omitted► Evolution selects ‘special conformers’ with extra low energy for biopolymers. ► Broken torsional symmetry provides such ‘special conformers’ for selection. ► A scaling law describes the energy spanned by conformational minima as a function of molecular size.We propose three reasons for the simplicity of vibrationally resolved electronic spectra of complex chain molecules: vibr(onic) state localization, insensitivity of chromophores to conformational changes outside the chromophore, and an ‘energy gap law’ for low-lying conformers. Here we use alkanals as simple models of chain molecules to study the third proposal. A disconnectivity tree and scaling analysis reveals an energy gap creating just two ‘special’ conformational minima in the torsional energy landscape of alkanals. We also derive a simple scaling formula to connect the energy spanned by all torsional minima in the alkanal energy landscape with molecular size.

Loss of octafluorocyclopentene versus CH3Cl (triangles) and CH3OCHO (circles) following exposure to Cl atoms.Display Omitted► Kinetics of the reactions of several fluorinated alkenes with OH radicals have been measured. ► Atmospheric lifetimes for several fluorinated alkenes have been estimated. ► Global warming potentials for several fluorinated alkenes have been estimated.The relative rate method was used to measure k(Cl + hexafluorocyclobutene) = (8.88 ± 0.69) × 10−13, k(Cl + octafluorocyclopentene) = (1.02 ± 0.11) × 10−12, k(Cl + hexafluoro-1,3-butadiene) = (7.28 ± 0.99) × 10−11, k(OH + hexafluorocyclobutene) = (8.6 ± 1.6) × 10−14, k(OH + octafluorocyclopentene) = (1.01 ± 0.16) × 10−13, and k(OH + hexafluoro-1,3-butadiene) = (9.64 ± 1.76) × 10−12  cm3  molecule−1  s−1 in 700 Torr N2, or air, diluent at 295 K. The atmospheric lifetimes of hexafluorocyclobutene, octafluorocyclopentene, and hexafluoro-1,3-butadiene were estimated to be 135, 104, and 1.1 days, respectively. The 100 year time horizon global warming potentials for hexafluorocyclobutene and octafluorocyclopentene are 42 and 28.

Display Omitted► We present a new global PES for the ground state reaction Ar + H 2 +  → ArH+  + H. ► The new PES coincides with the experiment results better than the earlier DIM PES. ► The cross-sections of QCT are in consistent with previous TSH results.An ab initio potential energy surface (PES) for the ground state (1 2 A ′ ) of the chemical reaction Ar + H 2 +    ArH+  + H has been constructed from a set of accurate ab initio data, which we have computed using the coupled-cluster theory including all single and double excitations plus perturbative corrections for the triples UCCSD(T) with a large orbital basis set of aug-cc-pV5Z. The new PES has a root-mean-square (rms) error of 0.5341 kcal/mol. The total integral reaction cross-sections have been calculated at three collision energies by means of the quasi-classical trajectory (QCT) calculation based on the new PES and compared with previous TSH results.

AIM and ELF analysis of the H-, Me-, and F-substituted FeIII–TAML complexes by Krzysztof Mierzwicki; Sławomir Berski; Zdzisław Latajka (29-36).
Display Omitted► Topological analysis of ρ and ELF function for the Fe–TAML activators was performed. ► The protonation sites on the terminal oxygen atoms were found. ► Intramolecular hydrogen bonds and weak interactions were found. ► Properties of F substituent do not fully explain observed H+-tolerance of Fe–TAML.Structure, bonding, and proton affinities of the H-, Me-, and F-substituted [FeIII–TAML] complexes and their protonated counterparts were investigated with the topological analysis of the electron density (AIM) and electron localization function (ELF) at the B3LYP/6-31 + G∗∗ level. Two protonation sites were found on each of the terminal oxygen atoms. The AIM analysis revealed existence of some weak interactions in the studied molecules. Changes induced by substitution of the tail Me groups by highly electronegative fluorine atoms are rather small (except for C25 atom) and do not fully explain experimentally observed high H+-tolerance of [FeIII–TAMLRF] molecule.

Display Omitted► The global minimum of Al2As belongs to the 2A′ state in the Cs structure. ► The 2A′ state correlates with the 2B2 state in the C2v structure. ► The stable minimum is found both for the 2A1 and 2B1 states. ► The Hartree–Fock instability occurs around the 2B2 state equilibrium. ► The photodetachments to the 2B2, 2A1, and 2B1 states can be observed.Recently the 2A′ ground state has been reported for Ga2P and Ga2As , however, there is no previous work on the Cs structure state of Al2As. This Letter reports the geometry optimisations and vibrational frequency calculations performed, using various approaches. In this study, the global minimum belongs to the 2A′ state, correlating with the 2B2 state. The 2A1 state is also reported for the first time. Difficulties in treating the 2B2 state are discussed in terms of the Hartree–Fock instability. Based on our calculations, we discuss the Al2As photoelectron spectrum.

Display Omitted► Krypton–neon diatom. ► Interaction-induced (hyper)polarizability. ► Collision-induced spectroscopy.We have obtained interaction-induced dipole moment, dipole polarizability and first hyperpolarizability curves for the KrNe rare gas heterodiatom using ab initio and DFT methods and a large, flexible atom-specific basis set. We have carefully examined the agreement between the two groups of theoretical methods. Although the experimentally deduced values for the dipole moment differ substantially, our best ab initio results are in very satisfactory agreement with the range suggested by the experimental estimates.

First-principles rotation–vibration spectrum of water above dissociation by Nikolay F. Zobov; Sergei V. Shirin; Lorenzo Lodi; Bruno C. Silva; Jonathan Tennyson; Attila G. Császár; Oleg L. Polyansky (48-51).
Display Omitted► A multi-photon above-dissociation spectrum of water is analyzed using first principles quantum mechanics for both the electronic structure and nuclear motion problems. ► The observed resonance structure is analyzed and assignments made. ► Both shape and Feshbach resonances are identified. ► A broad peak at dissociation is ascribed to direct photodissociation into the continuum.High-level ab initio electronic structure and variational nuclear motion computations are combined to simulate the spectrum of the water molecule at and above its first dissociation limit. Results of these computations are compared with the related state-selective multi-photon measurements of Grechko et al. [J. Chem. Phys. 138 (2010) 081 103]. Both measured and computed spectra show pronounced structures due to quasi-bound (resonance) states. Traditional resonance features associated with trapping of vibrational or rotational energy of the system are identified and assigned. A strong and broad feature observed slightly above dissociation is found to be associated with direct photodissociation into the continuum.

Measurement of vapor pressures using X-ray induced fluorescence by J.J. Curry; E.G. Estupiñán; A. Henins; W.P. Lapatovich; S.D. Shastri (52-56).
Display Omitted►A new method for measuring vapor pressures has been demonstrated. ► The method is based on high-energy X-ray induced fluorescence. ► It is applicable to pressures on the upper end of the Knudsen cell range and higher. ► Measurements of the total densities of Dy over DyI3 and Tm over TmI3, and their corresponding vapor pressures are reported.X-ray induced fluorescence is demonstrated as a novel and fast method for measuring vapor pressures at high temperatures and high pressures. As such, it is an excellent complement to the effusion method, which is limited to lower pressures. High-energy synchrotron radiation was used to measure the total densities of Dy in the equilibrium vapor over condensed DyI3 and Tm in the equilibrium vapor over condensed TmI3. Corresponding vapor pressures were determined with measured vapor cell temperatures across a range of vapor pressures of nearly three orders of magnitude, from less than 102  Pa to more than 104  Pa. Individual data points were obtained in time periods ranging from 10 to 30 s each.

Octahedral complexes of the series of actinides hexafluorides AnF6 by Andrea Pérez-Villa; Jorge David; Patricio Fuentealba; Albeiro Restrepo (57-62).
An approximate inverse Z dependency for the relativistic bonding energies is predicted.Display Omitted► Octahedral symmetry for AnF6. ► Non-relativistic vs relativistic: different energy trends. ► Bond length contraction up to 4%.Non-relativistic DFT (PW91, PBE, PB86) geometry optimizations followed by relativistic ZORA single point energy calculations on the neutral hexafluoride complexes of the series of actinides U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr in octahedral symmetry are presented. Bond lengths are in good agreement with available experimental data. Actinide bond length contraction as a function of the atomic number of the central metal atom of up to ≈ 4 % is observed. An approximate inverse relationship is predicted for the bonding energies as a function of the atomic number of the central cation at the two component ZORA//DFT level; pure DFT bonding energies do not exhibit the same pattern.

Display Omitted► Preferential population of optical rotamers was induced by molecular drag pumps. ► Enantiomeric excess was rationalized by macroscopic translation-rotational motions. ► Implications on the origin of the biomolecular homochirality were discussed.Four substituted simple alkanes – 1-bromo-2-chloroethane, 1-chloropropane, 1,1-dichloropropane, and 1,1,2-trichlorotrifluoroethane – can exist in gauche positive (G), gauche negative (G′), and trans (T) conformers. The G and G′ conformers are optical rotamers, while the T conformer is achiral. Here, the first observation of the preferential population of the optical rotamers in these alkanes induced by the molecular flow through molecular drag pumps is reported. The molecular mechanism of the observed enantiomeric excess of the studied alkanes is rationalized in the general framework of the molecular chirality generated through oriented collisions involving flowing molecules in macroscopic translation-rotational motions induced by a rotating surface.

Display Omitted► CH2Br2 in acetonitrile is a suitable precursor for radical species and their absorption bands. ► We record the UV absorption spectra of the CH2Br radical in acetonitrile and methylcyclohexane. ► The absorption of the CH3CN·Br charge-transfer complex is also recorded. ► Recording these spectra is made possible due to the ultrafast decay of the iso-CH2Br―Br product.Dibromomethane (CH2Br2) in acetonitrile is a suitable precursor to characterize the absorption signatures of the CH2Br radical and solvent Br charge-transfer complexes. Following irradiation of CH2Br2 at 255 nm, the iso-H2C―Br―Br isomer product rapidly converts back to the parent species, and transient absorption spectra reveal the bands of solvent-separated radical species, the CH2Br radical peaking at 235 nm, as well as the CH3CN·Br complex at 272 nm. The absorption of CH2Br exhibits minor solvatochromic shifts upon going from acetonitrile to cyclohexane, and the molecular decadic extinction coefficient of CH3CN·Br is estimated to be 1470 M−1  cm−1.

Display Omitted► Spectroscopic and calorimetric investigation of host-guest chemistry of AY with CB7. ► The mode of binding is confirmed by analyzing the 1H NMR data. ► Discrepancies in the findings of spectroscopy and calorimetry are rationalized.The study of binding of small molecules with supramolecular architecture comprises of one of the thriving areas of research today. In the present study, spectroscopic techniques have been used to decipher the interaction of Acridine Yellow with Cucurbit[7]uril and explore the consequence of host–guest interaction on the photophysical properties of the dye. Moreover, isothermal titration calorimetry has been used to unravel the thermodynamics of interaction. The probable causes of incongruity of the results obtained from spectroscopy and calorimetry have been rationalized. 1H NMR study and geometry optimization of the guest molecule confirm the actual mode of host–guest interaction.

Display Omitted► Very long molecular dynamics simulations of SPC/E water. ► Dielectric constant calculated as a function of system size and simulation length. ► No clear trend concerning system size dependence. ► Simulation length of at least 6 ns is required for proper convergence.The effect of the applied trajectory length on the convergence of the static dielectric constant was examined for the SPC/E water model with different system sizes. Very long simulation times of 6–8 ns were employed in order to track the convergence of this property. Temperature dependence and isotope effects were also investigated. A simulation for the polarizable SWM4-DP model was also carried out to compare the effect of different potential models. It is clearly shown that trajectories shorter than about 6 ns are not sufficient for a sufficiently accurate determination of the dielectric constant of these water models.

DFT simulations of CO2–HF mixture at extreme conditions: Thermodynamic and chemical properties by Jean-Bernard Maillet; Emeric Bourasseau; Gérald Jomard (84-88).
Display Omitted►Formation of new molecule at high temperature and pressure. ► Enhanced diffusivity of protons as a precursor of covalent bonding. ► Strong non-ideal behaviour of CO2–HF mixture due to chemistry. ► Comparison of the ABINIT and VASP ab initio codes on thermodynamical properties.We have conducted ab initio Molecular Dynamics simulations of CO2–HF fluid mixture on its T  = 3000 K isotherm in the pressure range 0–40 GPa. We predict the formation of new covalent bonds between carbon and fluorine atoms, and between oxygen and hydrogen atoms. As in the case of water (Maillet et al., J. Chem. Phys. 131 (2009) 084107), the dissociation of the HF molecule with pressure is seen as the precursor of this new chemistry at extreme environment. The CO2–HF mixture then exhibits a non-ideal behaviour as pressure increases. The appearance of new chemistry in the high pressure – high temperature regime could be a common feature in ionic liquids.

Hydration of NaHCO3, KHCO3, ( HCO 3 - )2, HCO 3 - and CO 3 2 - from molecular dynamics simulation and speed of sound measurements by Przemysław D. Dopieralski; Andrzej Burakowski; Zdzisław Latajka; Ivar Olovsson (89-95).
Display Omitted► The dimer formation of the bicarbonates is not important. ► HCO 3 - ion decreases the hydration number for sodium and potassium ions. ► The minor amount of dimeric structure of HCO 3 - cannot be definitely excluded.Car–Parrinello molecular dynamics and acoustic method have been applied to determine the hydration of HCO 3 - and CO 3 2 - ions in aqueous solution. From CPMD simulations the hydration numbers are 5.3 and 8.5 for the HCO 3 - and CO 3 2 - ions, respectively. From speed of sound and density measurements the hydration numbers for HCO 3 - and CO 3 2 - are 5.5 and 10.2, respectively. Our attempt to answer the old question concerning the status of HCO 3 - in solution quite well support the earlier spectroscopic results that no ( HCO 3 - )2 is present in the solution but the existence of the minor amount of dimers cannot be definitely excluded.

NMR study of a phasmid-like liquid crystal by Alberto Marini; Marco Geppi; Veena Prasad; Ronald Y. Dong (96-99).
Display Omitted► TDPABA is a semi-phasmidic liquid crystal giving nematic and columnar phases. ► We study orientational order properties of TDPABA by 13C NMR and DFT. ► TDPABA molecules form dimeric structures in solution and in the nematic phase. ► Order parameters in the nematic phase are quite high. ► Motion about column axes is frozen in the columnar phase.Carbon-13 NMR measurements of the chemical shifts are reported as a function of temperature for a semi-phasmidic molecule 4-(2,3,4-tridecyloxy-phenylazo)-benzoic acid (TDPABA). The data indicate a dimer structure in the solution and suggest a similar structure also in the nematic phase, which is consistent with it being a phasmid-like liquid crystal. The orientational order parameters are derived in the nematic phase based on the carbon shielding tensors calculated by Density Functional Theory. The nematic order parameter Szz is found to be (relatively) higher for TDPABA than that found in a typical calamitic liquid crystal, likely due to its underlying columnar phase.

Display Omitted► Cyclohexyl-imidazolium based ionic liquids. ► Physical properties of these species were compared with n-alkylimidazolium series. ► Cyclohexyl substituents lead lower fluidity in ionic liquids. ► Temperature dependence of NMR spectra is consistent with macroscopic observations.We have synthesized and characterized a series of cyclohexyl-imidazolium based ionic liquids incorporating a bis(trifluoromethanesulfonyl)amide anion. To reveal the characteristic features afforded by a flexible cyclohexyl substituent, the physicochemical properties including densities, shear viscosities, and thermal properties, were measured and compared with the respective n-alkyl-imidazolium ionic liquids. The cyclohexyl-imidazolium ionic liquids showed higher densities, higher shear viscosities, and higher glass transition temperatures than their acyclic counterparts. Using 1H and 13C nuclear magnetic resonance spectra, we also studied the conformational dynamics of these species.

In Situ Au L 3 and L 2 edge XANES spectral analysis during growth of thiol protected gold nanoparticles for the study on particle size dependent electronic properties by Junya Ohyama; Kentaro Teramura; Tetsuya Shishido; Yutaka Hitomi; Kazuo Kato; Hajime Tanida; Tomoya Uruga; Tsunehiro Tanaka (105-110).
Display Omitted► A u L edge XAS of thiol protected gold nanoparticles (AuNPs) were analyzed. ► The origin of the characteristic absorption band of the AuNPs was investigated. ► The band is due to Au--S scatterings and electronic transfer from Au to S. ► The electronic properties of the AuNPs with various sizes were evaluated. ► The electrons are increasingly transferred to S atoms as the size.The formation of gold nanoparticles in the presence of dodecanethiol was observed in situ by quick X-ray absorption fine structure spectroscopy with 100 ms time resolution at the Au L 3 and L 2 edges. The series of the X-ray absorption near edge structure spectra at both edges was analyzed to evaluate the dispersion and electronic properties of gold nanoparticles during their growth.

.Display Omitted► H2O either adsorbs or dissociates on ZnO nanoclusters. ► This depends on the stability of the clusters and the direction of approach. ► The band gap and excitation energies do not change significantly as a result of H2O adsorption. ► New IR frequency bands appear in the spectrum due to H2O adsorption.The interaction of a single H2O molecule on selected ZnO nanoclusters is investigated by carrying out calculations based on the density-functional theory at the hybrid-GGA (B97-2) level. These clusters have ring, drum, tube and bubble shapes and their physical properties like the binding energy and the band gap energy depend strongly on the shape and size of the cluster. Depending on the stability of the cluster, H2O show both chemisorption and dissociation on the surfaces of the clusters. We analyzed the effect of H2O adsorption on the properties of clusters of size n  = 12 via the density of state, HOMO–LUMO orbitals and the changes in the IR frequencies.

Confinement-induced changes in magnetic behavior of a Ti monolayer on Pt by Gustavo E. Ramírez-Caballero; Perla B. Balbuena (117-121).
Display Omitted► Confinement decreases magnetism of a Ti thin film. ► Electrons fill an ultrathin gap between surfaces changing surface magnetism. ► Thin film magnetism may be tuned by core composition.Density functional theory is used to examine the magnetic properties of a Ti monolayer over Pt when is brought in contact with a Pt surface, at distances of 4–12 Å. The average magnetic moment of the Ti film decreases sharply as the surface–surface separation decreases, coincident with migration of surface electrons towards the gap, surface d-band broadening, and decrease of the density of states at the Fermi level. The phenomenon is analyzed using the Stoner criterion that correlates the ferromagnetic behavior with exchange splitting and density of states at the Fermi level obtained from a paramagnetic calculation.

TEA acting as a surfactant form a diffuse layer around Zn+2 ions. The surface energies and growth rates of different crystallographic faces with the attachment of ethanolamine leads to spherical nanoparticles. In presence of surfactant as well as chelating agent leads to formation of spherical monodispersed ZnO nanoparticles without any agglomeration. But in the absence of chelating agent as-obtained nanoparticles forming bunches through agglomeration and larger in size.Display Omitted► Effect of surfactant and chelating agent on the formation of ZnO nanoparticles studied in detail. ► Synthesis of ZnO nanoparticles by low temperature reaction route via ultrasonication. ► Due to quantum confinement effects, the band gap of the ZnO nanoparticles is blue shifted compared with the bulk material. ► Band gap of the ZnO nanoparticles is blue shifted compared with the bulk material.A low temperature reaction route via ultrasonication has been demonstrated for the synthesis of ZnO nanoparticles. It is found that the morphology and photoluminescence has strong dependence on the surfactant, triethanolamine (TEA) and chelating agent, citric acid. Polyvinylpyrrolidine (PVP) is used as a capping agent. X-ray powder diffraction (XRD), transmission electron microscopy (TEM), FTIR, UV–Vis absorption and photoluminescence spectra are used to characterize the as-prepared ZnO nanoparticles.

Surface effects in chiral adsorption by Tatiana Popa; Irina Paci (128-133).
Display Omitted►Substrate effects on chiral adsorbed morphologies are examined for simple systems. ► Lennard–Jones attraction and surface layout show minor effects on adsorbed pattern. ► Suitable surface atom spacings can enhance chiral separation through commensuration. ► Significant enhancements of enantiomeric excess can be achieved.We report on Parallel Tempering Monte Carlo investigations of the influence of surface attraction and geometry on adsorption-induced chiral separation and phase behavior in two model systems. The two model molecules exhibited distinct chiral self-assembly outcomes in previous surface-free, two dimensional calculations. Here, by considering atomistic apolar rigid surfaces, we found that the adsorbed patterns and geometries were largely unaffected by surface attraction or layout. When the lattice spacing and/or atom size of the substrate were varied, however, several types of commensuration effects were observed, often leading to an enhancement of separation quality from the surface-free case.

Increased dispersion and solubility of carbon nanotubes noncovalently modified by the polysaccharide biopolymer, chitosan: MD simulations by Thanyada Rungrotmongkol; Uthumporn Arsawang; Chularat Iamsamai; Arthit Vongachariya; Stephan T. Dubas; Uracha Ruktanonchai; Apinan Soottitantawat; Supot Hannongbua (134-137).
Display Omitted► Models of increase in dispersion and solubility of chitosan-wrapped SWCNTs. ► MD simulations with three different chitosan concentrations were performed. ► Pristine CNT aggregates due to tube–tube hydrophobic and vdW interactions. ► At low concentration, chitosan on one tube bridges another to aggregate. ► Charge–charge repulsion leads to well dispersion of wrapped CNTs in solution.In order to explain the solubility of carbon nanotubes (CNT), including single walled CNTs, wrapped with chitosan of a 60% degree of deacetylation, MD simulations were applied to represent three chitosan concentrations, using two pristine CNTs (pCNT–pCNT), and one and two CNTs wrapped (pCNT–cwCNT and cwCNT–cwCNT). The CNT aggregation was observed in pCNT–pCNT and pCNT–cwCNT due to van der Waals interactions between tube–tube aromatic rings, and inter-CNT bridging by chitosan, respectively. At higher chitosan concentrations, such that most to all of CNTs were wrapped with chitosan, charge–charge repulsion was found to separate robustly the cwCNTs and lead to a well dispersed solution.

Display Omitted► We reported the different densely picked SAMs can selectivity adsorb organic molecules. ► A possible mechanism behind the selective deposition phenomenon was given in our work. ► This mechanism mentioned in our work may give a great contribution to the design of nanoscale devices.A series of MD simulations were conducted towards the selective deposition of organic luminescent molecules 3(5)-(9-anthryl) pyrazole (ANP) and perylene onto different densely packed organosilane self-assembled monolayers (SAMs). Our simulations indicated that the packing density of alkyl chains on SAM may directly control the site-selective deposition of organic molecules. Additionally we propose a possible mechanism for this phenomenon, which can also explain the experimental findings of the selective deposition of organic molecules onto template structures, made of l-α-dipalmitoyl-phosphatidylcholine (DPPC) in alternating liquid expanded (LE) and liquid condensed (LC) states.

Biotemplated synthesis of superconducting plate-like YBa2Cu3O7−δ using oligosaccharides by Simon R. Hall; Stuart C. Wimbush; Yosuke Shida; Wataru Ogasawara (144-150).
Display Omitted► Y123 superconductors as plate-like crystals. ► Improved critical current density through change in morphology. ► High purity biopolymers enables growth of sub-micron superconductors. ► Morphological control of complex oxide demonstrated in short-chained biomolecules.Crystallization of the high temperature superconductor YBa2Cu3O7−δ (Y123) in a plate-like morphology has been achieved through the use of the short-chained oligosaccharides. This is the first time that biotemplates with such a high degree of monodispersity have been used to synthesize superconducting oxides, with control over crystallization being effected through a single molecular species. We find that for all the oligosaccharides used, there is an increasing prevalence of thin, plate-like crystals as the oligosaccharide chain length increases. SQUID magnetometry revealed that there was an increase in critical current density (Jc ) concomitant with an increase in the plateyness of the crystallites.

Vibronic interactions in hole-transporting molecules: An interplay with electron–hole interactions by Tohru Sato; Katsuyuki Shizu; Keisuke Uegaito; Naoya Iwahara; Kazuyoshi Tanaka; Hironori Kaji (151-156).
Display Omitted►Vibronic couplings of TPD derivatives, CBP and TPF are studied. ► The TPF cation exhibits weak vibronic couplings. ► The effect of on-site Coulomb interaction on the vibronic couplings are investigated. ► The interaction causes the small electron-density difference on the fluorenyl group. ► This leads to the weak vibronic couplings of the TPF cation.Vibronic coupling constants of hole-transporting molecules, TPF and CBP, are estimated. Despite the planar structure of TPF, the calculated vibronic coupling constants are close to those of nonplanar TPD. The origin of the vibronic couplings in TPF is investigated employing the vibronic coupling density analysis. Based on a Hubbard Hamiltonian, electron–hole interactions are found to be crucial in the vibronic couplings. A large difference of on-site Coulomb interactions, or electron–hole interactions gives rise to a localization of the electron-density difference on a site which can lead to small vibronic couplings.

Molecular dynamics studies on the mutational structures of a nylon-6 byproduct-degrading enzyme by Takeshi Baba; Katsumasa Kamiya; Toru Matsui; Naoki Shibata; Yoshiki Higuchi; Tatsuya Kobayashi; Seiji Negoro; Yasuteru Shigeta (157-161).
Display Omitted► Wild-type and mutant structures of nylon-6 byproduct-degrading enzyme are determined. ► We sampled 25 000 data from 10–35 ns simulations to analyze MD trajectories. ► An importance of water exclusion environment around the catalytic site is proposed. ► A possibility that water behave as an inhibitor of the degradation is suggested.In order to understand roles of E168 and Y170 residues in loop-segment (N166–V177) of nylon-6 byproduct-degrading enzymes, we determined substrate-binding structures of E168Q and Y170F mutants using molecular dynamics simulation with in silico mutations. We found that movement of the loop-segment plays key roles not only in allowing the substrate to be bound by induced fit mechanism but also in forming water-exclusive environment. Fluctuations of the loop-segment in the mutant enzymes caused a room near the catalytic site, where water molecules can access. We propose that the water located exclusivity at the catalytic site is a major factor of its activity.

Display Omitted► Modulation of sensing efficiency of Acridine Orange to its maximum level toward Cu2+ sensor simply by altering its environment by the use of suitable surfactant at various pH has been reported. ► New mechanism and pH effect has been proposed towards photophysical chemistry of acridine orange in colloidal system.Photophysical properties and sensory capabilities of Acridine Orange (AO) have been studied in absence and presence of biomimicking anionic SDS (sodium dodecyl sulphate) micellar nanocage at various pH, where Cu2+ is introduced as sensing input. In pure aqueous system, AO fluorescence intensity quenched and enhanced by Cu2+ at pH ∼2 and pH ∼8, respectively. In presence of SDS micelle AO fluorescence intensity quenched by Cu2+ at both pH ∼2 and pH ∼8. Sensing [i.e. quenching] efficiency has been enhanced in presence of SDS micelle by ∼150 times at pH ∼2 and ∼250 times at pH ∼8, when compared with pure aqueous system.

A computational study of glutathione and its fragments: N-acetylcisteinylglycine and γ-glutamylmethylamide by Vanna Z.Y. Ding; Sean S.H. Dawson; Lewis W.Y. Lau; DongJin R. Lee; Natalie J. Galant; David H. Setiadi; Balázs Jójárt; Milán Szöri; Zoltán Mucsi; Béla Viskolcz; Svend J. Knak Jensen; Imre G. Csizmadia (168-173).
Glutathione in a “basket-like” conformation.Display Omitted► Molecular mechanics and DFT calculations yield comparable results for glutathione and fragments. ► Constructing stable structures from fragments require prior knowledge of structure of interest. ► Utilization of the advantages of each method is necessary to effectively model large molecules.This study reports first principle calculations and molecular mechanics calculations of glutathione and its fragments with the goal of determining whether the conformational nature of this tripeptide can be inferred based on the geometries of its constituents. Although the size of a molecule usually predetermines the applicable computational methodology (i.e., molecular mechanics or first principles), a combinatory approach that utilizes the advantages of both methods is useful to facilitate modelling of large molecular systems.

Modeling the diiron(II) ferroxidase complex in human H ferritin by Daniel E. Bacelo; R.C. Binning (174-177).
Display Omitted► A complete structure for the diiron(II) ferroxidase complex in human H ferritin has been obtained. ► The structure of the complex matches closely the experimental structure of its dizinc counterpart. ► The high-spin and broken symmetry spin coupling approximations yield similar structures. ► The structure of the diiron(II) complex advances research on the diiron(III) intermediate.Density functional theory calculations, in both the high-spin and broken symmetry approximations, have been conducted on models of the diiron(II) ferroxidase complex of human H ferritin. Initial configurations were chosen from previous experimental and theoretical structures of the dizinc complex. The diiron complexes show no significant deviation in ligand or metal positions from the corresponding dizinc complexes, even maintaining similar structures through an extensive reorganization, and thus the often-made assumption of homology between Fe(II) and Zn(II) is supported. Geometry differences between diiron complexes calculated in the high-spin and broken symmetry approximations are also found to be minor.

dhadhadhDisplay Omitted► Spin catalysis. ► Exchange-relaxation mechanism. ► Radical pairs. ► Green function. ► Bloch equations.An analytical formula for the description of exchange-relaxation mechanism of spin catalysis is derived. The formula is applied to describe the experiment on recombination of a radical pair obtained by diphenylpenthanon (DPP) photolysis on addition of spin catalyst. 2,2,6,6-Tetramethylpiperedin-1-oxyl (ТЕМPО) was used as a catalyst . Good agreement between theory and experiment is shown.

Display Omitted►Electrophilicity index and electron transfer parameter are often used inconsistently to each other due to two different definitions for absolute hardness. ► Work function is an appropriate measure of the electronegativity of bulk metal. ► Electron transfer from molecule to metal-surface is proportional to the difference between metal work function and molecular electronegativity.The electrophilicity index is often used in an inconsistent manner with other HSAB (Hard and Soft Acids and Bases) based parameters that depend on absolute hardness, such as, electron transfer (ΔN) and its associated change of energy (ΔE). We further comment on the use of ΔN parameter in the quantum chemical studies of corrosion inhibitors, where this parameter is used to discuss the interaction between an inhibitor molecule and metal surface. It is argued that the work function of metal surface is an appropriate measure of its electronegativity and should be used together with its vanishing absolute hardness to estimate the ΔN.

Display Omitted►Electron density topology in hydrogen bonded complexes perturbed by electric fields. ► External electric fields used for modeling the interaction environment. ► Hydrogen bond critical point properties proposed as estimators of interaction energy. ► Curvature along the hydrogen bond is the most suited estimator.The hydrogen bond interaction energy ( E HB ) of HF⋯HR (R = H, Li, Al, Cl, CCH) complexes under external electric fields is investigated in terms of the bonding distance and of several properties at the bond critical point. All these properties can be used for the estimation of E HB , being the positive curvature along the hydrogen bond path the most suited for the application to experimental electron densities.

Display Omitted►Using pulsed laser excitation, we measure the luminescence of the Nitrogen Vacancy Centre (NVC). ► Pulsed excitation allows us to easily calculate the NVC’s absorption cross-section. ► We find that the NVC’s absorption cross-section is 0.95 ± 0.25 × 10 - 16 cm 2 . ► We use the pulse-excitation method to estimate the number of NVCs in a crystal.In this report, we present a detection scheme that can be used to measure the absorption cross-section of the Nitrogen Vacancy (NV) centre, along with the results of an experimental implementation of this method. We also demonstrate how we quantify the number of NV centres in a crystal by calculating the collection efficiency of our apparatus. We find that the absorption cross-section for 532 nm excitation, averaged over the possible orientations of the transition dipole moments is ( 0.95 ± 0.25 ) × 10 - 16 cm 2 . This level of accuracy has not been achieved in previous investigations.

Display Omitted►Transient carrier transport in OFET with different traps condition is visualized. ► Trap condition can be intentionally controlled by applying gate voltage. ► The effective carrier mobility increased with the increase of filled-trap density. ► We quantitatively evaluated the trap density from saturation voltage of the mobility.By using time-resolved microscopic optical second-harmonic generation (TRM-SHG) imaging, we studied the trap-filling effect on transient carrier transport in pentacene field effect transistors (FETs). We showed that the transient carrier transport was strongly dependent on trap-filling condition at the pentacene and gate-insulator interface. The TRM-SHG imaging caught the transient electric field migration which was caused from traveling carriers along the channel. Results showed that the effective carrier mobility increased with increase of the filled-trap density, i,e., with decrease of empty trap-sites, and finally saturated after all trap-sites were filled. Saturation voltage of the mobility indicates the filled trap density of approximately 1.4 × 10 12 / cm 2 .

Display Omitted►A highly efficient cluster optimization method is proposed. ► The structures of silver clusters from Ag141 to Ag310 are systematically optimized. ► The previous global minima are improved for 19 clusters. ► The known global minima are reproduced for 22 clusters. ► For the other clusters under investigation, global minima are reported for the first time.The structures of silver clusters from Ag 141 to Ag 310 are systematically optimized with a modified version of the dynamic lattice searching method with constructed core (DLSc). The interaction between silver atoms is modeled by the Gupta potential. The optimized results indicate that the present method reproduces the known global minima for 22 clusters and improves the known global minima for 19 clusters. For the other clusters under investigation, putative global minima are first reported in this Letter. It is found that the definition of the energy of a single atom is a key factor affecting the efficiency of the dynamic lattice searching method.

Display Omitted► Transient optical and electrical response during laser-induced crystallization of Ge2Sb2Te5 thin film was compared. ► Much little time was needed to reach equilibrium state for electrical resistance than optical reflectivity. ► The dependence of crystallization time on laser pulse fluence was given. ► A 2-dimensional percolation model can be used to explain the difference between electrical and optical transients.The phase transition dynamics of Ge2Sb2Te5 thin films induced by single nanosecond laser pulses were studied by transient optical reflectivity and electrical resistance measurements with nanosecond resolution. It was found that the real-time responses of optical and electrical signals were different under the same pumping condition. It needs much little time to reach equilibrium state for electrical resistance than optical reflectivity. The dependence of crystallization time determined respectively by optical and electrical evolution curve on laser pulse fluence was compared and analyzed. A 2-dimensional percolation model was used to explain the differences between electrical and optical transient responses.