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Chemical Physics Letters (v.432, #1-3)
CRD and LIF spectra of the CaBr and CaI radicals by C. Bahrini; S. Douin; J. Rostas; G. Taieb (pp. 1-5).
The comparison of the absorption and the emission spectra of the two components of the C2Π–X2Σ+ of the CaI radical formed by reaction of Ca with CH2I2 in a Broida oven confirms the assumption already made that the C2Π3/2 component is pre-dissociated.The CRDS technique has been used to record CaBr and CaI absorption spectra at temperatures (about 350K) much lower than the spectra observed previously with the traditional techniques ( T=1300–2000K). For the CaBr A2Π–X2Σ+ transition, the bandhead intensity distributions of the CRD and LIF spectra are similar. In contrast, one observes a significant intensity weakening of the C2Π3/2–X2Σ+ heads in the LIF spectrum of CaI. This is further manifestation of a spin–orbit selective pre-dissociation of the Ω=3/2 component of the C2Πstate, confirming the recent observation of its anomalously short lifetime.
Theoretical studies on the reactions X+CHBrF2 (X=F, Br) by Hui Zhang; Gui-ling Zhang; Li Wang; Bo Liu; Xiao-yang Yu; Ze-sheng Li (pp. 6-10).
Theoretical investigations are carried out on the reactions F+CHBrF2→CBrF2+HF (R1) and Br+CHBrF2→CBrF2+HBr (R2) by means of direct dynamics method at the QCISD(T)/6-311+G(2df,2p)//BH&H-LYP/6-311G(d,p) level. The rate constants are calculated by CVT with SCT correction in the temperature range 200–3000K.Theoretical investigations are carried out on the reactions F+CHBrF2→CBrF2+HF (R1) and Br+CHBrF2→CBrF2+HBr (R2) by means of direct dynamics method. The minimum energy path (MEP) is obtained at the BH&H-LYP/6-311G(d,p) level, and energetic information is further refined at the QCISD(T)/6-311+G(2df,2p) (single-point) level. The rate constants for both reactions are calculated by canonical variational transition state theory (CVT) with the small-curvature tunneling (SCT) correction in a wide temperature range 200–3000K. The theoretical rate constant is in good agreement with the available experimental data. Furthermore, the rate constants of reaction Cl+CHBrF2→CBrF2+HCl (R3) calculated in the other paper are added to discuss the effects of halogen substitution on the rate constants of this class of hydrogen abstraction reactions.
Transition probabilities and spectroscopic properties of the low-lying states of GeC molecule by Leonardo T. Ueno; L.R. Marim; A. Dal Pino Jr.; Fernando R. Ornellas; Francisco B.C. Machado (pp. 11-16).
The low-lying electronic states of GeC are investigated using the CASSCF/MRSDCI approach, and the aug-cc-pVQZ basis set. Potential energy curves, spectroscopic properties, dipole moment and transition moment functions, transition probabilities and radiative lifetimes are calculated.The low-lying electronic states of GeC are investigated at a high level of correlation treatment using the CASSCF/MRSDCI approach, and the aug-cc-pVQZ basis set. Potential energy curves, spectroscopic properties, dipole moment and transition moment functions are given for all electronic singlet, triplet and quintet states that dissociate into the first channel. Transition probabilities and radiative lifetimes are also predicted using the Einstein coefficients.
Photoelectron spectroscopy of Ce(η-C5H5)3 – Accessing two ion states on 4f ionization by Marcello Coreno; Monica de Simone; Jennifer C. Green; Nikolas Kaltsoyannis; Naima Narband; Andrea Sella (pp. 17-21).
PE spectroscopy of Ce(η-C5H5)3 provides evidence that the ground state of the [Ce(η-C5H5)3]+ cation is described as a mixture of two configurations of1A1 symmetry, one with no 4f electron, Lf0and one with a single 4f electron interacting strongly with a hole of the same symmetry in the ligand shell, L−1f1.Valence PES have been measured for Ce(η-C5H5)3 in the gas phase with photon energies of 24–135eV. Two ion states arising from ionization of the single 4f electron are unambiguously characterized by the intensity behaviour of the associated bands. Assignment is made using a VBCI model where purely ionic components are allowed to mix under configuration interaction. Thus the ground state of the [Ce(η-C5H5)3]+ cation is described as a mixture of two configurations of1A1 symmetry, one with no 4f electron, Lf0 and one with a single 4f electron interacting strongly with a hole of the same symmetry in the ligand shell, L−1f1.
A B3LYP study of proton transfer path within a complex of benzene radical cation and water cluster by Moriyuki Shimizu; Emi Yamashita; Masaki Mitani; Yasunori Yoshioka (pp. 22-26).
We demonstrated the theoretical study of the proton transfer path from the complexC6H6+(H2O)4 to the complexC6H5+(H2O)4 with the planar cyclic geometry of (H2O)4H+. The proton transfer and redistribution from π to σ of theradical electron proceed separately not simultaneously.We made a theoretical study of the proton transfer path fromC6H6+(H2O)4 toC6H5(H2O)4H+ with a planar cyclic geometry of (H2O)4H+ by the hybrid density functional B3LYP method. The proton transfer proceeds in a three-step manner. In the first step, the proton inC6H6+(H2O)4, moves from the terminal H2O molecule in the (H2O)4 cluster to yield a (H2O)3H+ cluster. In the last third step, one H2O molecule leaves from C6H6(OH) in C6H6(OH)(H2O)3H+ to yield aC6H5(H2O)4H+ complex through the H-abstraction by the OH radical. It is found that the proton transfer and redistribution from π to σ of the radical electron proceed separately.
Theoretical survey of the potential energy surface of Ni++acetone reaction by Xiangfeng Chen; Wenyue Guo; Lianming Zhao; Qingtao Fu (pp. 27-32).
The C2H6 and CO loss in the Ni++acetone reaction leading respectively to Ni+(CO) and Ni+(C2H6) occurs through five elementary steps: encounter complexation, C–C activation, methyl migration, C–C coupling, and nonreactive dissociation, in which the third step is rate-determining. The alternative Ni+(CH3)2 yields is also possible.Density functional theory calculations have been carried out to explore the potential energy surface (PES) associated with the gas-phase reaction of Ni+ with acetone. The structures and energies of the different stationary points of this PES have been obtained at the B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2df,2pd) levels. The mechanism leading to the loss of C2H6 and CO is analyzed in terms of the topology of PES. Our calculations indicate the reaction of acetone with Ni+ takes place through five elementary steps: encounter complexation, C–C activation, methyl migration, C–C coupling, and nonreactive dissociation, in which the methyl migration process is rate-determining.
Can H…σ, π…H+…σ and σ…H+…σ interactions be classified as H-bonded? by Sławomir J. Grabowski; W. Andrzej Sokalski; Jerzy Leszczynski (pp. 33-39).
The following complexes are analyzed: FH…H2, C2H2…H+…H2 and H2…H+…H2 where specific interactions possessing characteristics which can be attributed to hydrogen bonds exist (X–H…σ, π…H+…σ and σ…H+…σ). The results indicate that these interactions possess some characteristics typical for classical hydrogen bonds.The following complexes are analyzed: FH…H2, C2H2…H+…H2 and H2…H+…H2 where specific interactions possessing characteristics which can be attributed to hydrogen bonds exist (X–H…σ, π…H+…σ and σ…H+…σ). High level calculations have been performed for these systems since MP2 method was applied and the following basis sets were used: 6-311++G(d,p), 6-311++G(2df,2pd), 6-311++G(3df,3pd) and the Dunning style aug-cc-pVXZ basis sets where the cardinal number X=2,3,4,5. Components of the interaction energy were calculated, and the QTAIM theory of Bader was applied in order to analyze in depth the physical nature of the stabilization of these complexes. The results indicate that these interactions possess some characteristics typical for classical hydrogen bonds.
Theoretical study on mechanism for NO3-initiated atmospheric oxidation of naphthalene by Xiaohui Qu; Qingzhu Zhang; Wenxing Wang (pp. 40-49).
In this Letter, we studied the mechanism for the NO3-initiated atmospheric oxidation reactions of naphthalene, using high-level molecular orbital theory. Geometries of the reactants, intermediates, transition states, and products have been optimized at the BB1K level with the 6-31+G(d,p) basis set. The single-point energy calculations have been carried out at the BB1K/6-311+G(3df,2p) level. The calculated results were compared with the available experimental observation. The possible secondary reactions were also studied. The formation mechanism of secondary pollutants from the OH-initiated reaction was also revealed.Polycyclic aromatic hydrocarbons (PAHs) are widespread and toxic pollutants. Naphthalene is the most abundant PAH found in polluted urban areas. In this Letter, we studied the mechanism for the NO3-initiated atmospheric oxidation reactions of naphthalene, using high-level molecular orbital theory. Geometries of the reactants, intermediates, transition states, and products have been optimized at the BB1K level with the 6-31+G(d,p) basis set. The single-point energy calculations have been carried out at the BB1K/6-311+G(3df,2p) level. Several energetically favorable reaction pathways were revealed for the first time. The calculated results were compared with the available experimental observation.
Electronic states and potential energy curves of InN2, In2N, and their ions by Zhiji Cao; Bingbing Suo; K. Balasubramanian (pp. 50-56).
Potential energy curves of low-lying electronic states of InN2, In2N, and their cations and anions are investigated by the complete active space multi-configuration self-consistent field followed by multi-reference singles + doubles configuration interaction computations.Potential energy curves of low-lying electronic states of InN2, In2N, and their cations and anions are investigated by the complete active space multi-configuration self-consistent field (CASSCF) followed by multi-reference singles + doubles configuration interaction (MRSDCI) computations. The neutral InN2 and In2N exhibit linear2Πand2Σu+ ground states, respectively. The InNN+ cation exhibits a linear C∞v ground state whereas In2N+ ion exhibits two nearly-degenerate singlet and triplet ground states. Whereas In2N− is strongly bound with an adiabatic electron affinity of 2.07eV, the electron affinity of InNN is only 0.2eV.
Kinetics of the gas phase reactions of chlorine atoms with a series of formates by T.J. Wallington; M.D. Hurley; A. Haryanto (pp. 57-61).
Relative rate methods were used to study the kinetics of the gas phase reactions of chlorine atoms with a series of formates. The rate constants measured are approximately 20–30% lower than the results from an absolute rate study of the reactivity of chlorine atoms towards esters. Likely explanations for the discrepancy are discussed.Relative rate techniques were used to study the reactivity of Cl atoms with a series of formates in 700Torr of N2 diluent at 296K. Rate constants were determined for the following compounds: methyl formate, (1.30±0.13)×10−12; ethyl formate, (9.57±1.27)×10−12; n-propyl formate, (4.65±0.47)×10−11; and n-butyl formate, (1.12±0.14)×10−10cm3molecule−1s−1. These results are consistent with previous relative rate studies but are approximately 20–30% lower than the results from an absolute rate study of the reactivity of chlorine atoms towards esters. Likely explanations for the discrepancy are discussed.
Energy of the quasi-free electron in xenon by Xianbo Shi; Luxi Li; C.M. Evans; G.L. Findley (pp. 62-67).
We report and analyze critical point effects in the xenon induced shift of the ionization energy of trimethylamine and N, N-dimethylaniline. The quasi-free electron energy (see figure) is accurately calculated within a local Wigner–Seitz model from low density up to the density of the triple point liquid.Field ionization of trimethylamine and of N, N-dimethylaniline doped into xenon is presented as a function of xenon number density up to the density of the triple point liquid, both at noncritical temperatures and along the critical isotherm. These data exhibit a decrease in the xenon induced shift of the dopant ionization energy near the xenon critical point. The energy of the quasi-free electron, arising from dopant field ionization, in xenon is calculated within a local Wigner–Seitz model to within ±0.3% of experiment at noncritical temperatures and for the critical isotherm.
Attosecond molecular Coulomb explosion by Tomoya Okino; Kaoru Yamanouchi; Toshihiko Shimizu; Kentaro Furusawa; Hirokazu Hasegawa; Yasuo Nabekawa; Katsumi Midorikawa (pp. 68-73).
(a) Autocorrelation trace of an attosecond pulse train synthesized by the time-of-flight mass spectra of N2 recorded as a function of the delay Δ t of one of the two separated harmonic beams. The delay Δ t is expressed in units of one cycle of fundamental laser light T0. (b) Ion signal intensities of the two side-peak areas marked as ‘S’ in the range specified by an arrow is plotted as a function of Δ t. (c) Ion signal intensities in the central-peak area ‘C’ in the range specified by an arrow is plotted as a function of Δ t. (d) Autocorrelation trace of the fundamental laser light measured by detecting the fragment ions N+ generated by exposing N2 only to the intense fundamental light field at 800nm.Molecular Coulomb explosion has been utilized as a precise temporal clock for probing ultrafast motion of nucleus and electrons during chemical reactions. With an intense attosecond pulse train in the extreme ultraviolet region, we were able to image attosecond molecular Coulomb explosion via two photon double ionization process. The present autocorrelation measurement, from which the duration of the attosecond pulse train was determined to be 300 as, serves as the first step toward a pump-and-probe measurement of molecular dynamics with attosecond temporal resolution.
Competition between the dissociation channels viaH∼�B∼2Σu+ andC∼2Σg+�B∼2Σu+ transitions forCS2+ ions by Xiujuan Zhuang; Limin Zhang; Jinting Wang; Yuchao Ma; Maoping Yang; Shuqin Yu; Xingxiao Ma (pp. 74-77).
To study the competition between the [1+1] and the [1+1′] dissociation channels forCS2+ ions, the dependence of the product branching ratios R(S+/CS+) on the intensity ratio RI( I2/ I1) of two dissociation lasers for theC∼2Σg+(100)�B∼2Σu+(100) andH∼�B∼2Σu+(100) transitions was shown with the experimental data and theoretical fitting curve.A model is provided to deal with the competition between the [1+1] dissociation channel viaH∼�B∼2Σu+(000,100)�X∼2Πg,3/2(000) transitions and the [1+1′] dissociation channel via theC∼2Σg+(000,100)�B∼2Σu+(000,100)�X∼2Πg,3/2(000)transitions forCS2+ ions. The dependence of the product branching ratios R=[S+]/[CS+] on the intensity ratios RI= I2/ I1 of two dissociation lasers was measured. By fitting the RI– R data with the theoretical formula the excitation cross section ratios of R σ(000)= σC(000)/ σH(000)=0.55±0.07 and R σ(100)= σC(100)/ σH(100)=0.43±0.04 have been obtained for the competitions betweenC∼(000)�B∼(000) andH∼�B∼(000) transitions, and betweenC∼(100)�B∼(100) andH∼�B∼(100) transitions, respectively.
Molecular dynamics study of diffusion of formaldehyde in ice by V. Ballenegger; S. Picaud; C. Toubin (pp. 78-83).
A formaldehyde molecule occupying a B site in a hexagonal ice cristal.We report a Molecular Dynamics simulation study of the diffusion process of formaldehyde (CH2O) in proton-disordered ice Ih at atmospheric pressure, in the temperature range 200–273K. CH2O molecules diffuse in ice predominantly by jumping between B sites (bond-breaking mechanism), but substitutional diffusion can also be observed. At 260K, the diffusion constant is predicted to be 4×10−7cm2/s with the TIP4P–Ew water model, and 3×10−7cm2/s with the TIP4P/Ice water model.
Cavity contact correlation function of water from scaled particle theory by Giuseppe Graziano (pp. 84-87).
The cavity contact correlation function G( Rc) of water can be reproduced in a satisfactory manner by classic scaled particle theory under reliable assumptions.The ratio of the number density of solvent molecules just outside a cavity of radius Rc to that in the bulk represents the cavity contact correlation function G( Rc). Experimental determination of G( Rc) for water by means of computer simulations has led to the claim that the shape of this function is a basic manifestation of the structural features of the H-bonded network of water [H.S. Ashbaugh, L.R. Pratt, Rev. Mod. Phys. 78 (2006) 159]. In this Letter, I would like to show that classic scaled particle theory is able to reproduce in a satisfactory manner the experimental G( Rc) values by taking into account two things: (a) the size of a water molecule depends on the interactions in which it is involved, so that the effective diameter of H-bonded molecules is 2.8â„«, whereas the van der Waals diameter of a water molecule is 3.2â„«; (b) at any time, liquid water contains both H-bonded molecules and molecules interacting by means of van der Waals forces.
3D-magnetic ordering of Co4+ dimers in a new Co3+,4+ oxychloride: Neutron diffraction analysis and DFT calculations by Matthieu Kauffmann; Olivier Mentré; Alexandre Legris; Nathalie Tancret; Francis Abraham; Pascal Roussel (pp. 88-93).
Magnetic and nuclear structure of the new mixed valence cobalt (III,IV) oxychloride Ba6Co6ClO16− x. The arrows indicate the spin orientation of the most stable structure as determined from neutron diffraction and DFT calculationsNeutron diffraction (ND) Rietveld refinements at 3K and ab initio density functional theory (DFT) calculations were performed on Ba6Co6ClO16− x, a new mixed valence cobalt oxychloride. The experimental data coincide with the theoretical ones to indicate that an antiferromagnetic ordering occurs. The refined magnetic structure displays antiferromagnetic Co2O7 tetrahedral dimers with a moment collinear to the c-axis, of 2.8μB/Co atom (ND), the DFT giving 2.3μB/Co. These results suggest that tetrahedral Co4+, in the intermediate spin configuration, are interconnected by tetrameric Co3+ octahedral units which are predicted by DFT to arrange ferromagnetically through delocalized electrons, in good agreement with ND.
Oxygen influence on the dissociative chemisorption of methane on nickel: A quantum chemical cluster model study by Morten B. Jensen; Unni Olsbye; Ole Swang (pp. 94-99).
A quantum chemical investigation of methane activation on reduced and partially oxidized Ni(100) surfaces has been performed. The activation energy of methane adsorption on a reduced Ni25 cluster was calculated at 108kJ/mol, while for various Ni25O clusters (modelling partially oxidized surfaces) the activation energies were significantly higher.A quantum chemical investigation of methane activation on reduced and partially oxidized Ni(100) surfaces has been performed. For all surfaces, methane activation has been assumed to proceed by dissociative adsorption at an on-top site. The activation energy of methane adsorption on a reduced Ni25 cluster was calculated at 108kJ/mol, while for various Ni25O clusters (modelling partially oxidized surfaces) the activation energies were significantly higher.
The effect of pressure on charge-enhanced C–H⋯O interactions in aqueous triethylamine hydrochloride probed by high pressure Raman spectroscopy by Hai-Chou Chang; Jyh-Chiang Jiang; Wei-Cheng Tsai; Guan-Ciao Chen; Chao-Yen Chang; Sheng Hsien Lin (pp. 100-105).
The high pressure study of the C–H bands for a dilute protonated triethylamine/D2O solution yielded an unusual nonmonotonic pressure dependence. This result indicated charge-enhanced C–H⋯O hydrogen-bond formation at high pressure. Electron density loss from the bridging hydrogen atom, the amount of charge transferred from the proton-acceptor molecule to the donor, and cooperativity were also discussed.The weak hydrogen bonding structures of protonated triethylamine in aqueous solution were investigated by Raman spectroscopy as a function of hydrostatic pressure. The formation of a weak hydrogen bond was directly evidenced by a low-frequency shift of the hydrogen-bonded C–H stretches in the protonated triethylamine moiety. For pure triethylamine, an increase in pressure leads to a blue frequency shift of the C–H bands. Nevertheless, the high pressure study of the C–H bands for a dilute protonated triethylamine/D2O solution yielded an unusual nonmonotonic pressure dependence. This result indicates charge-enhanced C–H⋯O hydrogen-bond formation at high pressure.
Femtosecond dynamics in ionic structures of a heart medicine by M. Gil; A. Douhal (pp. 106-109).
Femtosecond studies of ionic structures of milrinone – a medicine used to help the heart to recuperate its life- in water solutions show that the ICT reactions in the cation and in the anion happen in 550fs and ∼1.2ps, respectively. The transients also show a 2–3ps component, assigned to cooling and twisting motion in the produced states. The result might be used for a better understanding of other functional molecules.Femtosecond studies of ionic structures of milrinone – a medicine used to help the heart to recuperate its life – in acidic and alkaline water solutions show that the intramolecular charge transfer in the cation and in the anion happen in 550fs and ∼1.2ps, respectively. These times are longer than 100fs, observed in the keto (inotropic) form. The transients also show a 2–3ps component, assigned to cooling and twisting motion in the produced states. The result might be used for a better understanding of other functional molecules.
Evidence for electric field dependent dissociation of exciplexes in electron donor–acceptor organic solid films by J. Kalinowski; M. Cocchi; D. Virgili; V. Fattori; J.A.G. Williams (pp. 110-115).
Evidence for exciplex dissociation into electron–hole pair is presented based on electric field modulation of time-resolved luminescence from electron donor–acceptor organic solid films. The largest reduction of (up to 50%) of the lifetime has been observed for the exciplex phosphorescence (see figure).Electric field effect on time-resolved exciplex luminescence has been examined in electron donor–acceptor organic solid films of undoped and an organic phosphor PtL2Cl-doped (m-MTDATA:BPT:PC) blends. The applied field leads to a decrease of the initial amplitude and luminescence lifetimes for both singlet and triplet exciplex underlain emission. The largest reduction (up to 50%) of the lifetime has been observed for the triplet exciplex emission and the effect interpreted in terms of the exciplex dissociation into electron–hole pairs driven by hopping separation of such generated charge carriers.
Positron annihilation studies on the phase transition of benzene and reactivity of nitrobenzene in confined framework of ZSM-5 zeolite by D. Dutta; A. Sachdeva; P.K. Pujari (pp. 116-121).
We present new result on positron annihilation spectroscopic studies on phase transition and reactivity of liquids confined inside ZSM-5. Benzene inside mesopores and micropores of ZSM-5 shows two distinct freezing points. The reactivity of positronium towards nitrobenzene (known quencher of positronium) inside the pores of ZSM-5 is anomalously enhanced.We present a new result on positron annihilation spectroscopy on phase transition and reactivity (towards positronium) of confined liquids in the pores of ZSM-5 zeolite using Doppler broadened annihilation radiation measurement and lifetime spectroscopy. Benzene confined in intergranular spaces (mesopores) and micropores in ZSM-5 shows two distinct freezing points. While the freezing temperature of benzene in mesopore is close to the bulk value, a 5–6K depression is observed for benzene inside micropores (size ∼5Å). The reactivity of nitrobenzene towards positronium is studied in nitrobenzene–benzene mixture incorporated in ZSM-5 pores. An anomalous enhancement in the reactivity is observed as compared to measurements in the bulk liquid. The results are discussed.
Coupling between C–D and CO motions using dual-frequency 2D IR photon echo spectroscopy by Keshav Kumar; Louise E. Sinks; Jianping Wang; Yung Sam Kim; Robin M. Hochstrasser (pp. 122-127).
Coupling between C–D and CO vibrational modes of formamide has been characterized by dual-frequency 2D IR spectroscopy. The signals are consistent with those computed assuming an optically dense system at the CO frequency. The dephasing dynamics of the cross peak have been determined to characterize the coupling between modes.Coupling between C–D and CO vibrational modes of formamide has been characterized by dual-frequency 2D IR spectroscopy. The signals are consistent with those computed assuming an optically dense system at the CO frequency. A negative off-diagonal anharmonicity of ∼0.85±0.20cm−1 was obtained and the coupled modes have anticorrelated frequency distributions. Other features including relaxation times, diagonal anharmonicities for the individual CO and C–D modes and the dephasing dynamics of the cross peak have been determined to characterize the coupling between modes.
Luminescent properties of an Yb podate in sol–gel silica films, solution, and solid state by Steve Comby; Frédéric Gumy; Jean-Claude G. Bünzli; Tsialia Saraidarov; Renata Reisfeld (pp. 128-132).
An octadentate NIR-emitting ytterbium-containing podate has been doped into silica thin films and display interesting photophysical propertiesIn search of IR emitting materials a complex of YbIII with an octadentate ligand bearing four bidentate 8-hydroxyquinolinate subunits connected to a N, N, N′, N′-tetra-aminopropyl-1,2-ethylenediamine anchor [S. Comby, D. Imbert, A.S. Chauvin, J.C.G. Bünzli, Inorg. Chem. 45 (2006) 732.] has been incorporated into silica glasses obtained by a special two-step, catalyzed sol–gel method. Photophysical properties of the resulting thin films are investigated and compared to those of an aqueous solution 10−3M in HBS buffer (pH 7.4) and of a solid state sample, at room temperature and 10K. They point to the chelate withstanding the sol–gel process; moreover the lifetime and quantum yield are comparable and even slightly better than in aqueous solution.
Electronic excitations induced by surface reactions of H and D on gold by Beate Mildner; Eckart Hasselbrink; Detlef Diesing (pp. 133-138).
A metal-insulator-metal tunnel system has been used to study the extend of electronic substrate excitations caused by atomic hydrogen adsorption and recombinative desorption on a Au surface. Evidence is presented suggesting that a significant contribution arises from Langmuir–Hinshelwood type reactions. An isotope effect of 4.5 exists between H and D exposure.Chemically induced hot carriers are detected with a time resolution of 0.1s by measuring currents in Ta/TaO x/Au tunnel junctions while the Au top electrode is exposed to atomic hydrogen. Up to 3.5nAcm−2 are measured when exposing the Au surface to a flux of 0.4MLs−1. Comparison of the recorded current traces with modeled reaction kinetics indicates a large contribution from the Langmuir–Hinshelwood (LH) reaction. 4.5 times larger signals are observed for hydrogen than for deuterium exposure. A model using the concept of electronic friction provides first insights into the structure of the induced electronic excitations.
The influence of water on the dispersion of vanadia supported on silica SBA-15 by Christian Hess; Robert Schlögl (pp. 139-145).
X-ray photoelectron spectroscopy (XPS) is shown to be a sensitive tool to study the influence of water on the dispersion of silica SBA-15 supported vanadia model catalysts XPS characterization of the V 2p3/2 state reveals the presence of two V5+ states, which are assigned to vanadia with distinctly different cluster size. Upon dehydration a dramatic change in their intensity ratio is observed as a result of a substantial increase in the vanadia dispersion.The influence of water on the dispersion of silica SBA-15 supported vanadia model catalysts has been studied using X-ray photoelectron spectroscopy (XPS) as well as UV–VIS and Raman spectroscopy. XPS characterization of the V 2p3/2 state reveals the presence of two V5+ states, which are assigned to vanadia with distinctly different cluster size. Upon dehydration a dramatic change in their intensity ratio is observed as a result of a substantial increase in the vanadia dispersion. It is shown that the observed changes in vanadia dispersion are directly associated with the changes in the molecular structure of the surface vanadia species.
Ultrafast dynamics of vibrational N–H stretching excitations in the 7-azaindole dimer by Jason R. Dwyer; Jens Dreyer; Erik T.J. Nibbering; Thomas Elsaesser (pp. 146-151).
In the electronic ground state, the 7-azaindole dimer displays a ∼100fs population decay of N–H stretching excitations and coherent low-frequency motions of the intermolecular hydrogen bonds.The ultrafast vibrational response of hydrogen bonds in the 7-azaindole dimer, a model compound for DNA base pairing, is studied in infrared pump–probe experiments. We observe a ∼100fs relaxation of the v=1 state of the N–H stretching oscillators via anharmonically coupled over- and combination tones of fingerprint modes. In the monomer with a larger energy mismatch between the v=1 state and over-/combination tones, a much longer lifetime of 10ps is found. Femtosecond N–H stretching excitation induces coherent underdamped motions of the dimer, dominated by the anharmonically coupled 110cm−1 stretching mode of the hydrogen bonds.
27Al double rotation two-dimensional spin diffusion NMR: Complete unambiguous assignment of aluminium sites in 9Al2O3·2B2O3 by I. Hung; A.P. Howes; T. Anupõld; A. Samoson; D. Massiot; M.E. Smith; S.P. Brown; R. Dupree (pp. 152-156).
The two crystallographically distinct pentahedral Al sites of 9Al2O3·2B2O3 are distinguished by the presence or absence of correlation peaks with neighboring tetrahedral sites using 2D27Al double rotation spin diffusion NMR.High-resolution two-dimensional27Al spin diffusion NMR spectra of 9Al2O3·2B2O3 recorded under double rotation for different mixing times are presented. The two crystallographically distinct pentahedral Al sites are distinguished by the presence or absence of correlation peaks with neighboring tetrahedral sites.
First-principles calculations of the far-infrared absorption spectrum of 4′-dimethylamino- N-methyl-4-stilbazolium tosylate by Shigeki Saito; Talgat M. Inerbaev; Hiroshi Mizuseki; Nobuaki Igarashi; Ryunosuke Note; Yoshiyuki Kawazoe (pp. 157-162).
First-principles calculations of the phonon modes of 4′-dimethylamino- N-methyl-4-stilbazolium tosylate in the terahertz region were performed using periodic density functional calculations. The assignment of FIR-active modes provides fruitful ideas for the design and synthesis of promising derivatives.First-principles calculations of the phonon modes of 4′-dimethylamino- N-methyl-4-stilbazolium tosylate in the terahertz region were performed using periodic density functional calculations. The calculated far-infrared (FIR) spectrum estimated from the phonon modes of the crystal did not correspond to the sum of the calculated spectra of the constituent cation and anion. The intramolecular modes of the methyl and sulfone group torsions and of π-bridge bends were confirmed, including in-plane and out-of-plane intramolecular bending, with the intermolecular modes contributing to the FIR absorption of the collective peaks. The assignment of FIR-active modes provides fruitful ideas for the design and synthesis of promising derivatives.
Structures of undecagold clusters: Ligand effect by Kasi Spivey; Joseph I. Williams; Lichang Wang (pp. 163-166).
The structures of small gold clusters can be altered substantially in the presence of ligands. In the absence of ligands, the planar Au11 cluster (left) is more stable than the three-dimensional cluster (right). The relative stability is changed in the presence of ligands.The most stable structure of undecagold, or Au11, clusters was predicted from our DFT calculations to be planar [L. Xiao, L. Wang, Chem. Phys. Lett. 392 (2004) 452; L. Xiao, B. Tollberg, X. Hu, L. Wang, J. Chem. Phys. 124 (2005) 114309.]. The structures of ligand protected undecagold clusters were shown to be three-dimensional experimentally. In this work, we used DFT calculations to study the ligand effect on the structures of Au11 clusters. Our results show that the most stable structure of Au11 is in fact three-dimensional when SCH3 ligands are attached. This indicates that the structures of small gold clusters are altered substantially in the presence of ligands.
Molecular mechanics study of the influence of the alkyl substituents on the packing of the conjugated PEDOT chains by A. Dkhissi; P. Brocorens; R. Lazzaroni (pp. 167-171).
Our results show clearly that-interaction in the packing of C10-PEDOT is more important than in the packing of PEDOT. So the charge transport along the stacks should be better in the substituted PEDOT. Further, the regioregularity is a central parameter to control the organization of the conjugated PEDOT.The solid state packing of neutral chains of the conjugated polymers is studied by theoretical simulations. The conjugated systems considered here are the pol(3,4-ethylenedioxythiophene (PEDOT) and their substituted PEDOT derivatives PEDOT-C10H21. The molecular mechanics calculations indicate that the polymers tend to form stable π stacks and indicate that the alkyl side groups freeze the conjugated segments and allow a good organization of PEDOT-C10H21 chains. This explains the increase of conductivity in these systems compared to un-substituted PEDOT. Finally, the introduction of one defect in region-regularity causes a steric hindrance, resulting in less order and less compact π-stacking.
G band Raman features of DNA-wrapped single-wall carbon nanotubes in aqueous solution and air by H. Kawamoto; T. Uchida; K. Kojima; M. Tachibana (pp. 172-176).
It is found that E2 and lower-frequency modes in the G band Raman line for semiconducting single-wall carbon nanotubes (SWNTs), and the broad and asymmetric feature of the Breit–Wigner–Fano line for metallic SWNTs are drastically suppressed by the DNA-wrapping.G band Raman spectra for DNA-wrapped single-wall carbon nanotubes (SWNTs) in aqueous solution and air have been investigated. The lower-frequency mode in the G band associated with semiconducting SWNTs is drastically suppressed by DNA-wrapping. In addition, the broad and asymmetric feature of the Breit–Wiger–Fano (BWF) line in the G band associated with metallic SWNTs is vanished by DNA-wrapping in aqueous solution. The BWF feature strongly appears again after the DNA-wrapped SWNTs are dried in air. These changes in the G band are discussed in the light of the vibrations and electronic properties in the SWNTs wrapped by DNA.
Direct growth of carbon nanotube junctions by a two-step chemical vapor deposition by Zhong Jin; Xuemei Li; Weiwei Zhou; Zuoyan Han; Yan Zhang; Yan Li (pp. 177-183).
A simple two-step chemical vapor deposition (CVD) strategy was designed for the direct growth of all-carbon nanojunctions constituted by jointed carbon nanotubes. By changing temperature and switching carbon source gases in the CVD process, various nanojunctions composed of single-walled and multi-walled carbon nanotubes were prepared.A simple two-step chemical vapor deposition (CVD) strategy was designed for the direct growth of all-carbon nanojunctions constituted by jointed carbon nanotubes. In the process, Fe–Mo nanoparticles were used as the catalysts, while C2H2 and CH4 were used as the feeding gas in the first and second CVD steps, respectively. By changing temperature and switching carbon source gases in the CVD process, various nanojunctions composed of single-walled and multi-walled carbon nanotubes were prepared. These all-carbon nanojunctions are expected to show special mechanical and electrical properties for the potential applications as the field-emission probes, scanning probe microscope tips and field-effect transistors.
Destabilization of adsorbed CO on the Pd(111) surface by subsurface carbon: Density functional studies by Kok Hwa Lim; Konstantin M. Neyman; Notker Rösch (pp. 184-189).
Calculated destabilization of CO adsorption complexes at three-fold hollow sites0–6 of a Pd(111) surface due to subsurface atomic species Cint located below site0, as a function of the radial distance r(Cint–CO) between the C atoms of the impurity and the adsorbate.We employed periodic density functional slab model calculations and CO as probe molecule to examine the adsorption propensity of various sites of a Pd(111) substrate near subsurface carbon atoms. On all sites studied, CO adsorption is weakened compared to a clean Pd(111) surface. That destabilization, ∼50% at fcc sites directly above interstitial carbon and slowly decreasing at more distant hollow sites, is at variance with the conclusion recently derived from STM experiments, that subsurface impurities on Pd(111), tentatively assigned as interstitial atomic carbon species, are able to stabilize CO at nearby fcc adsorption sites.
Hydrogel-assisted synthesis of nanotubes and nanorods of CdS, ZnS and CuS, showing some evidence for oriented attachment by K.P. Kalyanikutty; M. Nikhila; Uday Maitra; C.N.R. Rao (pp. 190-194).
Nanotubes and nanorods of CdS, ZnS and CuS have been synthesized by a hydrogel-assisted method. Self-assembly of nanocrystals giving rise to chains of nanorods, a phenomenon similar to the growth of nanowires by oriented attachment has been observed.By carrying out the reaction of appropriate metal compounds with Na2S in the presence of a tripodal cholamide-based hydrogel, nanotubes and nanorods of CdS, ZnS and CuS have been obtained. The nanostructures have been characterized by transmission electron microscopy and spectroscopic techniques. Evidence is presented for the assembly of short nanorods to form one-dimensional chains.
Surface modification of gold nanotubules via microwave radiation, sonication and chemical etching by Yongquan Qu; Joshua D. Carter; Alex Sutherland; Ting Guo (pp. 195-199).
Gold nanotubules treated with microwave radiation for 5min and 10min. Smoother surfaces are achieved after approximately 10min of radiation. The scale bar is 100nm.We present here the results of smoothing the rough surface of as-prepared gold tubular nanoshells or nanotubules which were produced by reacting aged gold salts with tetrakis-hydroxymethyl-phosphonium chloride (THPC)-capped gold nanoparticles on amine terminated silica nanowires (SiNWs) or silica nanocoils (SiNCs). These as-prepared rough nanotubules exhibited metallic properties as determined by optical absorption spectroscopy. Microwave radiation, sonication, and chemical etching were used to effectively smooth the surface. Two parameters were used to define the surface smoothness on the nanoscale, and the outcomes of these three surface modification methods were compared.
Laser scanning confocal microscope (LSCM)-fluorescence spectral properties of Nile Red embedded in polystyrene film of different thickness by Hyong-Ha Kim; Nam Woong Song; Tae Sook Park; Minjoong Yoon (pp. 200-204).
The ensemble and single molecule fluorescence spectral properties of Nile Red embedded in polystyrene (PS) films on glasses were investigated. Two distinct environments exist in the thin PS films on glasses: a low polarity environment in PS bulk and a high polarity environment near the PS/glass interface.The ensemble and single molecule (SM) fluorescence properties of Nile Red embedded in polystyrene (PS) films on glasses were investigated. The ensemble spectra showed dual emission bands and SM spectra exhibited distribution with two emission maxima. These results indicate that two distinct environments exist in the thin PS film on a glass: a low polarity environment in the PS bulk and a high polarity environment near the PS/glass interface. It was also found that a PS film of ca. 10nm thick is sufficient to separate fluorophores from the charged species on glass surfaces.
An integrated route for purification, cutting and dispersion of single-walled carbon nanotubes by Yan Wang; Lian Gao; Jing Sun; Yangqiao Liu; Shan Zheng; Hisashi Kajiura; Yongming Li; Kazuhiro Noda (pp. 205-208).
SWNTs are purified, cut and dispersed using a novel dispersant of Pluronic P123. The finally obtained samples are of high purity about 98%, length-controlled, and effectively exfoliated with bundle diameters of 7–15nm. The dispersed SWNTs solution can exist stably for over two months.We have developed purification and cutting process of single-walled carbon nanotubes (SWNTs) by integrating (1) an acid reflux treatment to eliminate metal particles, (2) an ultrasonication in the H2SO4/HNO3 and H2SO4/H2O2 to cut and polish the SWNTs, respectively, and (3) an ammonia gas treatment to remove residual carbon impurities and to repair the sidewalls of SWNTs. The final products with a higher purity than 98% are well dispersed in aqueous solution using Pluronic P123 dispersant, which has been rarely used for the SWNTs dispersion. The dispersed SNWTs solution can exist stably for over two months.
High-yield synthesis of monodisperse polyhedral gold nanoparticles with controllable size and their surface-enhanced Raman scattering activity by Kihyun Kwon; Kang Yeol Lee; Minjung Kim; Young Wook Lee; Jinhwa Heo; Sang Jung Ahn; Sang Woo Han (pp. 209-212).
Monodisperse icosahedral gold nanoparticles with controllable size were prepared in high-yield by a seed-mediated growth approach.The aqueous-phase synthesis of polyhedral gold nanoparticles with remarkably narrow size distribution is reported. By using a seeding growth approach, icosahedral gold particles with controllable size can be synthesized in high-yield. Citrate-capped 3.5nm gold nanoparticles, prepared by the reduction of HAuCl4 with sodium borohydride, are used as seeds. The synthesized gold nanoparticles were characterized by transmission electron microscopy, scanning electron microscopy, and X-ray diffraction. The prepared gold nanoparticles show efficient surface-enhanced Raman scattering activities.
Electronic structures of Pt clusters adsorbed on (5,5) single wall carbon nanotube by Dam Hieu Chi; Nguyen Thanh Cuong; Nguyen Anh Tuan; Yong-Tae Kim; Ho Tu Bao; Tadaoki Mitani; Taisuke Ozaki; Hidemi Nagao (pp. 213-217).
A DFT calculation for the adsorption of Pt clusters on carbon nanotube was performed. The hybridization of electron states of the nanotube and the metal clusters, and the charge transfer from Pt clusters to the nanotube were occurred, enhancing the catalytic performance of Pt clusters.We present a DFT study for the adsorption of single Pt atom and Pt clusters on graphene surface and carbon nanotube. Adsorption of a Pt atom shows a heavy dependence of binding energy on the graphene curvature. The adsorbed Pt atoms tend to form clusters, than to disperse on the graphene surface. The Pt–Pt bond length and the charge transfer from Pt clusters to the nanotube vary as a function of cluster size. A simulation of oxygen adsorption suggests higher performance for catalytic activities of Pt clusters adsorbed on the nanotube, in comparison with free Pt clusters.
EPR theoretical investigation of substitution site and local lattice structure of tetragonal Cr2+ in cadmium thiogallate by Kuang Xiao-Yu; Tan Xiao-Ming; Zhou Kang-Wei (pp. 218-221).
By analyzing the experimental EPR zero-field-splitting (ZFS) parameters a, D and F, the substitution position and the local lattice structure of tetragonal Cr2+ center in cadmium thiogallate (CdGa2S4) crystal have been studied on the basis of the complete energy matrix for a d4 configuration in a tetragonal ligand-field within a strong-field-representation. Our results show that the Cd2+ site is the only substitutional position for Cr2+ in CdGa2S4 and the local structure around the Cr2+ is a compression distortion. From EPR calculations, the local lattice structure parameters R=2.44A and θ=57.74° are determined.By analyzing the experimental EPR zero-field-splitting (ZFS) parameters a, D and F, the substitution position and the local lattice structure of tetragonal Cr2+ center in cadmium thiogallate (CdGa2S4) crystal have been studied on the basis of the complete energy matrix for a d4 configuration in a tetragonal ligand-field within a strong-field-representation. Our results show that the Cd2+ site is the only substitutional position for Cr2+ in CdGa2S4 and the local structure around the Cr2+ is a compression distortion. From EPR calculations, the local lattice structure parameters R=2.44A and θ=57.74° are determined.
Fabrication of gold nanorod self-assemblies from rod and sphere mixtures via shape self-selective behavior by Zhi-Chuan Xu; Cheng-Min Shen; Cong-Wen Xiao; Tian-Zhong Yang; Shu-Tang Chen; Hu-Lin Li; Hong-Jun Gao (pp. 222-225).
The ordered gold nanorod self-assemblies on silicon wafer were fabricated from rod and sphere mixtures by shape induced self-selective behavior. The capillary force interaction between the surfaces of nanoparticles was proposed to explain the nanorods’ self-selective behavior.The ordered gold nanorod self-assemblies on silicon wafer were fabricated from rod and sphere mixtures by self-selective behavior. The as-prepared gold nanorod ordered packing structures show a remarkable shape dependence and prefer to pack together separately from spherical particles. This shape induced self-selective behavior was studied via a series of assemblies of nanorods with different aspect ratio. The capillary force interaction between the surfaces of nanoparticles was proposed to explain the nanorods’ self-selective behavior.
Deposition of thin films of a transition metal complex by spin coating by Björn Bräuer; Dietrich R.T. Zahn; Tobias Rüffer; Georgeta Salvan (pp. 226-229).
Spin coating is demonstrated to be a promising technique for depositing magnetically active transition metal complexes. The thin films show nano-crystalline formations with random orientations. The optical properties determined using spectroscopic ellipsometry compare well to those of single molecules in solution.Spin coating is demonstrated to be a promising technique for depositing magnetic transition metal complexes. The thin films show nano-crystalline formations with random orientations. The optical properties determined using spectroscopic ellipsometry compare well to those of single molecules in solution indicating the preservation of the molecular structure upon the deposition process.
Impurity driven clustering in a gas aggregation source by P. Feiden; J. Leygnier; Ph. Cahuzac; C. Bréchignac (pp. 230-234).
Gas phase Na n and Na n(NaOH)2 nanoparticles ( n=50–250) are produced in a gas aggregation source. Heterogeneous Na n(NaOH)2 clusters are shown to be produced by accretion of sodium atoms on nucleation centers initially formed by a chemical reaction between H2O and Na or Na2 molecules. Mass distributions are compared for Na n grown on an homogeneous nucleation center and for Na n(NaOH)2 developing on an heterogeneous seed in the same condensation source, allowing the comparison between homogeneous and heterogeneous clustering efficiency.Both gas phase Na n and Na n(NaOH)2 nanoparticle ensembles ( n=50–250) are produced in a gas aggregation source and studied by using laser-ionization time-of-flight mass spectrometry. Heterogeneous Na n(NaOH)2 clusters are shown to be produced by accretion of sodium atoms on nucleation centers initially formed by a chemical reaction between H2O and Na or Na2 molecules. Mass distributions are compared for Na n grown on an homogeneous nucleation center and for Na n(NaOH)2 developing on an heterogeneous seed in the same condensation source, allowing the comparison between homogeneous and heterogeneous clustering efficiency.
Photochemical window mechanism for controlled atom release in carborane endohedral boxes: Theoretical evidence by Luis Serrano-Andrés; Josep M. Oliva (pp. 235-239).
Guest atoms trapped in closed carborane boxes could be transported and selectively released in a photocontrolled process to be exploited for nanotechnological applications, as theoretical evidence suggests.On the basis of high-level quantum chemical calculations, closed-cage carboranes are shown to be prospective nanoscale mass selective conveyors via a photochemical switch. A mechanism is evidenced in which stable carborane boxes with lithium as endohedral atom, Li@CB11H12, can be photoinduced to sequentially evolve opening the cage, releasing the internal atom through a window in the box structure, and closing the cage toward either ionic or neutral channels where the charge or spin of the fragments may be controlled.
Formation of off-centered double-walled carbon nanotubes exhibiting wide interlayer spacing from bi-cables by Hiroyuki Muramatsu; Takuya Hayashi; Kim Yoong Ahm; Mauricio Terrones; Morinobu Endo (pp. 240-244).
Novel off-centered coaxial carbon nanotubes have been fabricated by coalescing adjacent double-walled carbon nanotubes using high temperature heat treatments. The eccentric nanotubes possess wide interlayer spacing, and arise by the merging of two narrow diameter (inner) tubes contained inside a large diameter tubes (also known as bi-cables).Novel off-centered coaxial carbon nanotubes have been fabricated by coalescing adjacent double-walled carbon nanotubes (DWNTs) using high temperature heat treatments. The eccentric nanotubes possess wide interlayer spacing, and arise by the merge of two narrow diameter (inner) tubes contained inside a large diameter tubes (also known as bi-cables). We propose a complete description of the coalescence process including the merge of two DWNTs, followed by the formation of bi-cables and the creation of off-centered DWNTs. We also performed molecular dynamics calculations that are in agreement with the experimental observations.
Chemical bonding and charge distribution at metallic nanocontacts by U. Schwingenschlögl; C. Schuster (pp. 245-247).
Partial Al 3 s and 3 p densities of states for the aluminium site at the neck of the nanocontact. Most of the occupied valence states are of 3 s type.We present results of electronic structure calculations for aluminium contacts of atomic size, based on density functional theory and the local density approximation. Addressing the atomic orbitals at the neck of the nanocontact, we find that the local band structure deviates strongly from bulk fcc aluminium. In particular, hybridization between Al 3 s and 3 p states is fully suppressed due to directed bonds at the contact. Moreover, a charge transfer of 0.6 electrons off the contact aluminium site is found. Both the suppressed hybridization and the violated charge neutrality are characteristic features of metallic nanocontacts. This fact has serious consequences for models aiming at a microscopic description of transport properties.
NMR investigation of the effect of caffeine on the hetero-association of an anticancer drug with a vitamin by M.P. Evstigneev; V.P. Evstigneev; D.B. Davies (pp. 248-251).
The complexation of anthracycline antibiotic Daunomycin and vitamin B2 derivative has been investigated by NMR in the presence of a third aromatic molecule, Caffeine. Quantitative analysis of the ternary mixture suggests that the in vivo efficacy of Drug–Vitamin interaction may be modified by the presence of caffeine.The complexation between an anti-cancer drug Daunomycin (DAU) and a Vitamin B2 derivative, flavin-mononucleotide (FMN), in the presence of a third type of aromatic molecule, caffeine (CAF), in aqueous solution has been studied by NMR spectroscopy. Ternary mixtures of the drug, vitamin and caffeine have been analysed quantitatively taking into account all possible complexation reactions between the aromatic molecules in solution. The results show that complexation between DAU and FMN decreases on addition of CAF which suggests that caffeine at physiological concentrations in vivo may affect the biological synergism of drug and vitamin.
On the color-tuning mechanism of Human-Blue visual pigment: SAC-CI and QM/MM study by Kazuhiro Fujimoto; Jun-ya Hasegawa; Shigehiko Hayashi; Hiroshi Nakatsuji (pp. 252-256).
Color-tuning mechanism of Human-Blue pigment, visual color-receptor in the cone cells of the eye, has been investigated. Based on the SAC-CI theoretical absorption energies, a decomposition analysis was performed and compared with the case of Bovine rhodopsin. The electrostatic effect from the opsin is primary important for the color-tuning.Color-tuning mechanism of Human-Blue pigment, visual color-receptor in the cone cells of the eye, has been investigated. Based on a previous Homology-modeling structure and experimental evidences, a working model was constructed, and the structure has been optimized by QM(B3LYP)/MM(AMBER) method. SAC-CI calculation was performed to obtain photo-absorption energy. The calculated absorption energy reasonably agrees with the experiment. A decomposition analysis was performed and compared with the case of Bovine rhodopsin. The electrostatic effect from the opsin is primarily important for the color-tuning. The electronic interaction (quantum effect) of the counter-residue is indispensable for quantitative calculation of the absorption energy.
Ultrafast charge transfer and solvation of DNA minor groove binder: Hoechst 33258 in restricted environments by Debapriya Banerjee; Samir Kumar Pal (pp. 257-262).
Picosecond resolved photophysical studies on a DNA minor groove binder, H33258 in bulk buffer and various restricted media including DNA reveal twisted intramolecular charge transfer as an important mode of excited state relaxation. A significantly longer component (8.5ns) in DNA-solvation dynamics associated with δ-relaxation of the DNA is identified.Picosecond resolved photophysical studies on a DNA minor groove binder, H33258 in bulk buffer and various restricted media including DNA reveal excited state charge transfer as an important mode of excited state relaxation. The charge transfer is found to be essentially associated with intramolecular twisting of the probe, being absent in SDS micellar environment and in DNA where twisting is hindered. Solvation and rotational dynamics of the probe in various restricted media including DNA are explored. A significantly longer component (8.5ns) in DNA-solvation dynamics, which is well known to be associated with δ-relaxation of the DNA, is identified.
Parity violation energy of biomolecules – III: RNA by Francesco Faglioni; Inmaculada GarcÃa Cuesta; Paolo Lazzeretti (pp. 263-268).
The energy of parity-violation associated with a typical RNA double helix is estimated with ab initio techniques. It is shown that weak nuclear interactions do not favour the formation of the double helices found in nature. Implications regarding the potential effect on biological homochirality are discussed.The energy of parity-violation associated with a typical RNA double helix is estimated with ab initio techniques. It is shown that weak nuclear interactions do not favour the formation of the double helices found in nature. Possible implications regarding the potential effect on the evolution of biological homochirality are discussed.
Theoretical study of the ionic hydrogen bond in the isolated proton-bound dimer of cytosine by Sang Yun Han; Han Bin Oh (pp. 269-274).
Theoretical study on the ionic hydrogen bond in the proton-bound homo-dimer of cytosine predicted a low energy pathway with a barrier of 1.6kcal/mol for the proton transfer in the ionic hydrogen bond, which may be supported by the stabilization in the transition state.We report a theoretical study of the ionic hydrogen bonding in the isolated proton-bound cytosine dimer, particularly in view of proton transfer. The theoretical study was carried out by B3LYP density functional and MP2 calculations. This study predicted 41.2kcal/mol for the dissociation energy of the proton-bound dimer. The calculation of the transition state revealed a low barrier of 1.6kcal/mol as well as a high rate constant of 5.9×1011s−1 for the proton transfer within the ionic hydrogen bond [B3LYP/6-311+G(2d,p)]. The stabilization in the transition state may provide the low energy pathway for the proton transfer.
On the energetics of protein folding in aqueous solution by Yuichi Harano; Roland Roth; Masahiro Kinoshita (pp. 275-280).
We argue that the structural stability of a protein in aqueous solution under physiological conditions is governed mainly by the entropy of water. We test 600 structures of protein G obtained as local-minimum states in water and find that the entropy of water is maximized for the native structure.We argue that upon the structural change of a protein, the gain or loss of the intramolecular energy is largely compensated by the loss or gain of the hydration energy, when the folding is considered under the isochoric condition. We introduce the sum of the intramolecular energy and the hydration free energy as the key function. The change in this function is governed by the change in the hydration entropy. A protein is designed to fold into the structure that maximizes the entropy of water under the requirement that sufficiently many intramolecular hydrogen bonds be formed to compensate the dehydration penalty.
Critical threshold of noise-induced Ca2+ signal in intracellular Ca2+ system by Ya Ping Li; Wei Liang Cao (pp. 281-285).
The detailed bifurcation diagram depending on fixed noise intensity ( β=0.01μM). Here: regions a and a′ represented the unexcitable regions, meaning that noise could not induce regular Ca2+ signal. Regions b and b′ represented the excitable regions, meaning that noise could induce regular Ca2+ signal. While region c represented the intrinsic Ca2+ signal of the system.Noise-induced Ca2+ signal (NICS) was explored in Ca2+ system. But how far from the bifurcation point, could one get the admissible region of NICS? We proposed and demonstrated numerically that there existed a critical threshold of NICS, and discussed the relationships of the noise intensity, the distance to the bifurcation point, and the critical threshold. Furthermore, the detailed bifurcation diagram for certain noise intensity was renewed. Finally, it was found that not all the NICS but partial NICS was optimized selectively with the assistance of noise.
Theoretical study of vibrational relaxation and internal conversion dynamics of chlorophyll-a in ethyl acetate solvent in femtosecond laser fields by Li-Qing Dong; Kai Niu; Shu-Lin Cong (pp. 286-290).
Seen from the caricature, the faster process of the FDS reflects the vibrational relaxation. The slower process describes the excited solvation effect of the Chl-a molecule in ethyl acetate solvent. The calculated FDS of Chl-a agrees well with the experimental result of Shi et al. [Shi et al., Chem. Phys. Lett. 410 (2005) 260].The density matrix and the transient linear susceptibility theories are used to calculate the fluorescence depletion spectrum and the internal conversion (IC) time of chlorophyll-a (Chl-a) in ethyl acetate solvent. The IC time and the vibrational relaxation time of Chl-a in the ethyl acetate solvent are 133fs and 1.5ps at room temperature, respectively. The calculated fluorescence depletion spectrum of Chl-a in the ethyl acetate solvent agrees well with the experimental result of Shi et al. [Shi et al.,Chem. Phys. Lett. 410 (2005) 260]. The effects of solvation and the IC time on the fluorescence depletion spectrum are also discussed.
Non-exponential decay of base-pair opening fluctuations in DNA by G. Kalosakas; K.Ø. Rasmussen; A.R. Bishop (pp. 291-295).
Time dependence of the local intra-base-pair displacement autocorrelation function for poly(dG)–poly(dC) DNA at various temperatures, showing the stretched exponential behavior (dashed lines) at picoseconds to nanoseconds time-scales.We report non-exponential decay of the time-dependent autocorrelation functions of base-pair opening dynamics in a model of DNA. Complex fluctuations occur in a wide temperature range, extending from below 200K up to the premelting transition regime above physiological temperatures. At least two distinct decay processes at different time scales are apparent. The observed decay in the picoseconds to nanoseconds range, attributed to vibrational hot-spots, is well described by a stretched exponential functional form. The temperature dependence of the corresponding rates and stretch exponents is presented and activation energies around 4–6kJ/mol are calculated.
Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach by Mei Hong; Tim Doherty (pp. 296-300).
The orientation of membrane proteins undergoing uniaxial rotational diffusion can be determined without macroscopic alignment. Theδ¯∥ frequency of the motionally averaged powder spectra equals the frequency of a sample aligned with the magnetic field. This allows the orientation determination of membrane-disruptive β-sheet peptides from13CO and15N powder spectra.The orientation of membrane proteins undergoing fast uniaxial rotation around the bilayer normal can be determined without macroscopic alignment. We show that the motionally averaged powder spectra exhibit their 0° frequency,δ¯∥, at the same position as the peak of an aligned sample with the alignment axis parallel to the magnetic field. This equivalence is exploited to determine the orientation of a β-sheet antimicrobial peptide not amenable to macroscopic alignment, using13CO and15N chemical shifts from powder spectra. This powder sample approach permits orientation determination of naturally membrane-disruptive proteins in diverse environments and under magic-angle spinning.
Theory of exciton–charge transfer state coupled systems by Tomáš ManÄ?al; Leonas Valkunas; Graham R. Fleming (pp. 301-305).
In this Letter we present a systematic theory of the system–bath interaction for the molecular systems with charge transfer states coupled to excitons. We provide analytical insight into the role of coherence transfer in inducing a temperature dependent absorbtion band shift in these systems.We present a systematic density matrix theory of excitons interacting with charge transfer states in molecular systems subject to influence of a semiclassical bath. An excitonic dimer interacting non-linearly with an overdamped Brownian oscillator bath is studied, and the effect of eigenstate renormalization by interaction with the bath is shown to be essential in a correct description of the unusual temperature dependence of the absorption spectrum of the exciton–charge transfer state system.
A multicanonical ab initio molecular dynamics method: Application to conformation sampling of alanine tripeptide by Ryota Jono; Kentaro Shimizu; Tohru Terada (pp. 306-312).
We propose a multicanonical ab initio molecular dynamics (AIMD) method for enhanced conformation sampling of biomolecules. This method was applied to a blocked alanine peptide, Ace-(Ala)2-NMe, and was proved to be more efficient in conformation sampling than a conventional AIMD method. This figure shows the free-energy landscape of the backbone ϕ– ψ dihedral angles of the first alanine in the canonical ensemble at 300K obtained from the simulation.We propose an ab initio molecular dynamics method combined with the multicanonical algorithm for enhanced conformation sampling of biomolecules. This method was applied to a system of a blocked alanine peptide, Ace-(Ala)2-NMe, in vacuo, and was proved to be more efficient in conformation sampling than a conventional ab initio molecular dynamics method. We calculated free-energy landscapes from the conformation ensemble and discussed their differences from classical simulations. In addition, we analyzed the fluctuations of atomic charges and demonstrated that there are significant correlations between atomic charges and the conformation of the peptide.
Unimolecular decomposition of aromatic bicyclic alkoxy radicals and their acyclic radicals by Inseon Suh; Jun Zhao; Renyi Zhang (pp. 313-320).
Theoretical calculations predict that the favorable decomposition pathways of the bicyclic alkoxy radicals correspond to the formation of dicarbonyl compounds along with glyoxal and methylglyoxal.The unimolecular decomposition of bicyclic alkoxy radicals and their subsequent ring-cleavage acyclic radicals from the OH-initiated reactions of toluene is investigated by means of theoretical quantum chemistry methods. The reaction and activation energies of ring-cleavage of the bicyclic alkoxy radicals are in the ranges of −45.9 to −54.5kcalmol−1 and 5.5–11.3kcalmol−1, respectively. The activation energies of C–C bond cleavage of the acyclic radicals are in the range of 2.5–27.0kcalmol−1. Kinetic calculations employing RRKM/ME formalism have been performed to assess the fate of chemically excited acyclic radicals for prompt decomposition or stabilization. The results indicate that the favorable decomposition pathways of the bicyclic alkoxy radicals correspond to the formation of dicarbonyl compounds along with glyoxal and methylglyoxal.
Structure and properties of multibranched isophorone-based materials for organic light-emitting diodes by Hai-Dong Ju; Xu-Tang Tao; Ying Wan; Jing-Hua Shi; Jia-Xiang Yang; Qian Xin; De-Chun Zou; Min-Hua Jiang (pp. 321-325).
A family of isophorone-based multi-branched compounds have been designed and synthesized. Because of they have the same electron donor and acceptor, branch number and steric structure have become as the important factors that differentiate their photo-physical characters. This Letter shows that the single-branched dye has better electroluminescent properties than the multi-branched in solid film.We designed and synthesized a three-branched isophorone-based compound, 4,4′,4′′-tri[2-(3-dicyanomethylene-5,5-dimethylcyclohex-1-enyl)vinyl]triphenylamine, as well as its one- and two-branched analogues. Their photophysical, electrochemical and electroluminescent characters showed a regular change with increasing branches. Density functional theory was employed to study their electron density distribution. Using the dyes as light-emitting layers without doping, organic light-emitting diodes showed appropriate red emission at λmax=647–670nm and a maximum brightness of 1801cdm−2. Moreover, the results shows that the device using the single-branched material as a pure emitting layer has higher efficiency and lower turn-on voltage than using multi-branched materials.
Contact angle determined by spontaneous dynamic capillary rises with hydrostatic effects: Experiment and theory by H.T. Xue; Z.N. Fang; Y. Yang; J.P. Huang; L.W. Zhou (pp. 326-330).
Curve (a) shows the experimental data. Curves (b) and (c) show the results obtained from our developed theory and Lucas–Washburn equation, in which the same parameters deduced from the data in curve (a) were adopted, respectively. Excellent agreement between our theory and experiment shows the validity of the proposed method.We investigate spontaneous dynamic capillary rises of liquids. While the liquid front rises spontaneously and vertically in a capillary, hydrostatic effects become more and more important. We theoretically derive new equations for capillary rises with hydrostatic effects, in order to describe the relation between the liquid front height and time, which enables us to experimentally measure contact angles of capillary tube surfaces directly. Excellent agreement between our theory and experiment shows the validity of the proposed method. Thus, it becomes possible to measure the wettability of small particles as well as porous materials.
A series of novel aromatic compounds with a planar N6 ring by Hong-Xia Duan; Qian-Shu Li (pp. 331-335).
Quantum chemistry calculations on a series of novel metal–N6 compounds at B3LYP/6-311+G∗ level demonstrate that the planarN64-ring in these metal–N6 molecules exhibits aromatic character and the incorporation of the metal atom remarkably increases their stability.A series of novel aromatic compoundsScN6-,VN6+, Ca2N6, and ScN6Cu, including a previously reported TiN6, are found to be local minima with C6v, C6v, D6h, and Cs symmetry, respectively, at the B3LYP/6-311+G∗ level of theory. These compounds may be regarded as 10π-electron complexes containing one or two metal cations and a planarN64- ring. They are predicted to have aromatic character. The nucleus-independent chemical shifts (NICS), the molecular orbitals, and the HOMO–LUMO gap analysis confirm that the planarN64- ring indeed exhibits aromaticity, which is remarkably enhanced by the incorporation of metal atom in these metal–N6 molecules.
Variational collapse of the optimized effective potential method with an orbital-dependent exchange-correlation functional based on second order perturbation theory by Daniel Rohr; Oleg Gritsenko; Evert Jan Baerends (pp. 336-342).
With a PT2 exchange-correlation functional, OEP potentials will take such a shape that HOMO and LUMO become degenerate and the energy collapses to minus infinity.It is well known, that second-order perturbation theory (PT2) breaks down when the gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied MO (LUMO) becomes too low. It is demonstrated that when the local Kohn–Sham (KS) potential vs is approximated by an expansion in a set of basis functions, exact HOMO–LUMO degeneracy occurs, if a finite orbital basis set is used. Numerical evidence is given for the He atom, which until now stood out as a ‘safe’ simple case. Variational collapse of the optimized effective potential (OEP) method with the PT2 functional in a finite orbital basis may be expected to be a common phenomenon. We also show variational breakdown with a non-perturbative functional when the HOMO–LUMO gap is used to regulate the contribution of virtual orbitals.
A general algorithm for calculation of Heisenberg exchange integrals J in multispin systems by M. Shoji; K. Koizumi; Y. Kitagawa; T. Kawakami; S. Yamanaka; M. Okumura; K. Yamaguchi (pp. 343-347).
We propose a practical algorithm for calculating Heisenberg exchange integrals J in multispin systems using broken-symmetry methods. Because the Heisenberg J values are critical to the low-lying energy levels and the magnetic properties, this generalized spin-projection (GP) method will be important to evaluate the J values from density-functional theory (DFT) calculations.We propose a practical algorithm for calculating Heisenberg exchange integrals, J, in multispin systems using broken-symmetry methods. Our generalized spin-projection (GP) method is an extended version of the approximate spin-projection (AP) method for two-spin systems. A notable feature of GP is its wide application for chemical bonds in magnetic materials, from covalent bonds to biradical bonds. The GP algorithm is applied to several transition metal complexes. The results show that this method effectively works for calculation of J values and is reliable in characterizing the detailed magnetic properties of multi-nuclear metal complexes.
Dependence of the length of the hydrogen bond on the covalent and cationic radii of hydrogen, and additivity of bonding distances by Raji Heyrovska (pp. 348-351).
Length of the hydrogen bond in ice (left) and liquid water (right): In ice, d(OH…O)=2.77Å and d(–H)= d( H)+ d( H+)+ d( H)=1.02Å. In liquid water, d(OH…O)=3Å and d(–H)= d( H)+ d ( H+)+2 d( H)=1.39ÅThe lengths of the hydrogen bond, d(–H) in inorganic and biochemical groups have been evaluated from the observed donor (X) to acceptor (Y) distances, d(XH…Y)obs using the covalent and ϕ-based ionic radii of X and Y, where ϕ is the Golden ratio. It is found that d(−H)= nd( H+)+ md( H), where d( H) and d( H+)=2 d(H)/ ϕ2=0.28Å are, respectively, the covalent and cationic radii, n=1 or 2 and m= mX+ mY=0, 1, 2 or 3. In all cases, d(XH…Y)obs= d(XH…Y)cal= d(X)+ d(H)+ d(–H)+ d(Y).
Co-doping effects and electrical transport in In–N doped zinc oxide by L.L. Chen; Z.Z. Ye; J.G. Lu; H.P. He; B.H. Zhao; L.P. Zhu; Paul K. Chu; L. Shao (pp. 352-355).
Dependence of electrical properties of In–N co-doped ZnO films on In concentrations.The influence of indium concentrations on electrical properties of In–N co-doped ZnO thin films has been studied. Based on Hall-effect measurements and analyses, impurity scattering is the dominant mechanism determining the diminished mobility in ZnO with higher In concentration. X-ray photoelectron spectroscopy reveals that the presence of In enhances the solubility of N with the formation of In–N and Zn–N bonds. The optimal properties, namely resistivity of 16.1Ωcm and Hall mobility of 1.13cm2V−1s−1, are obtained at an indium concentration of 0.14 at.%. The diffraction angle of co-doped ZnO is closest to that of un-doped ZnO.
Application of the linear/exponential hybrid force field scaling scheme to the bond length alternation modes of polyacetylene by Shujiang Yang; Miklos Kertesz (pp. 356-361).
The bond length alternation related backbone carbon–carbon stretching Raman active normal modes of polyacetylene are notoriously difficulty to predict theoretically. We apply our new linear/exponential scaled quantum mechanical force field scheme that adjust the decay of the coupling force constants between backbone stretching coordinates. The predictions with experiment are excellent.The two bond length alternation related backbone carbon–carbon stretching Raman active normal modes of polyacetylene are notoriously difficulty to predict theoretically. We apply our new linear/exponential scaled quantum mechanical force field scheme to tackle this problem by exponentially adjusting the decay of the coupling force constants between backbone stretchings based on their distance which extends over many neighbors. With transferable scaling parameters optimized by least squares fitting to the experimental vibrational frequencies of short oligoenes, the scaled frequencies of trans-polyacetylene and its isotopic analogs agree very well with experiments. The linear/exponential scaling scheme is also applicable to the cis-polyacetylene case.
Comparative measurements of aerosol droplet growth by Laura Mitchem; Rebecca J. Hopkins; Jariya Buajarern; Andrew D. Ward; Jonathan P. Reid (pp. 362-366).
We demonstrate the feasibility of a new strategy for examining interfacial processes in aerosols. Measurements of the simultaneous growth of two aerosol droplets during the accommodation of ethanol from the vapour phase allows the direct comparison of the a process on two different liquid surfaces.We present a novel approach for characterising the growth of aerosol droplets during the accommodation of a species from the gas phase. In particular, we illustrate that comparative growth measurements can be made on two aerosol droplets simultaneously, allowing the properties of different aerosols to be compared directly. A control droplet can provide a probe for monitoring the local gas phase composition with a fast time-response, while the variation in size and composition of the second droplet of interest can be investigated. We suggest that this strategy will allow accurate measurements of the thermodynamic and kinetic properties of aerosol droplets.
Cooperative quenching kinetics: Computer simulation and analytical solution by T.T. Basiev; K.K. Pukhov; I.T. Basieva (pp. 367-370).
The ensemble averaged donor fluorescence decay due to cooperative energy transfer from a donor ion to two-particle acceptors for different dimensions d, concentrations c, and multipolarity S corresponds to the asymptotic law I( t)∼exp[−( Wt) d/2 S− d] at the long-time stage. The cooperative quenching rate depends on the acceptor particle concentration as W∼ c2 S/ d.The cooperative energy transfer from a donor ion to two-particle acceptors is recently experimentally observed in many optically pumped rare-earth doped crystals and may appear in excitation quenching processes, as well as in down-conversion and sensitization energy transfer.Our theoretical study and computer simulation of cooperative three-body interaction for an ensemble of particles with different dimensions d, concentrations c, and multipolarity S have shown that donor fluorescence decay due to cooperative quenching corresponds to the asymptotic law I( t)∼exp[−( Wt) d/2 S− d] at the long-time stage. The power dependence of the cooperative quenching rate on the acceptor particle concentration was deduced to be W∼ c2 S/ d.
Correctly validating results from single molecule data: The case of stretched exponential decay in the catalytic activity of single lipase B molecules by Ophir Flomenbom; Johan Hofkens; Kelly Velonia; Frans C. de Schryver; Alan E. Rowan; Roeland J.M. Nolte; Joseph Klafter; Robert J. Silbey (pp. 371-374).
How to correctly validate results from single molecule data? This issue is addressed by using numerical and analytical tools. The results of this Letter validate the results in an earlier study of the activity of single lipase B molecules and disprove recent related critique.The question of how to validate and interpret correctly the waiting time probability density functions (WT-PDFs) from single molecule data is addressed. It is shown by simulation that when a stretched exponential WT-PDF,ϕoff(t)=ϕ0e-(t/τ)α, generates the off periods of a two-state trajectory, a reliable recovery of the input ϕoff( t) from the trajectory is obtained even when the bin size used to define the trajectory, d t, is much larger than the parameter τ. This holds true as long as the first moment of the WT-PDF is much larger than d t. Our results validate the results in an earlier study of the activity of single lipase B molecules and disprove recent related critique.
On the implementation of the Runge–Kutta–Fehlberg algorithm to integrate intrinsic reaction coordinate paths by Antoni Aguilar-Mogas; Xavier Giménez; Josep Maria Bofill (pp. 375-382).
The basic scheme drawing the relation between the steepest-descent curve-line with the theory of Hamilton–Jacobi equation, which is the ground of the proposed algorithm to integrate the intrinsic reaction coordinate path.A new algorithm for the integration of the intrinsic reaction coordinate path on a potential energy surface is proposed, based in solving the set of differential equations associated to the corresponding characteristic curve, rather than the differential equation of the curve itself. The integration of this set of differential equations is carried out by employing a Runge–Kutta–Fehlberg with τ-stage and p-algebraic order technique. In addition, an update Hessian matrix formula is reported for this specific algorithm. The examples show that the proposed algorithm is numerically stable, with no extra computational effort with respect to the standard algorithms.