Chemical Physics Letters (v.385, #5-6)

Kinetics of breaking a salt-bridge critical in protein unfolding by Andreea D. Gruia; Stefan Fischer; Jeremy C. Smith (337-340).
The rate of breaking an Arg–Glu salt bridge on the surface of a globular protein (Staphylococcal nuclease) is determined by using molecular dynamics simulations to derive the free energy activation barrier to dissociation and the pre-exponential rate factor for that reaction. The dissociation barrier obtained is 7 kcal/mol. The pre-exponential factor is derived using a novel method in which simulations are performed for the same system with the salt bridge weakened such that the rate can be observed directly. Combining the prefactor thus obtained (5×1011 s−1) with the above dissociation barrier height yields an estimated lifetime of the salt-bridge of 200 ns, suggesting that surface salt-bridges can cause significant kinetic barriers to protein folding or unfolding.

Recently it has been shown that maleic anhydride (MA) on Si(1 0 0) binds preferentially above the dimer troughs. This has been postulated to arise from the electrophilic nature of MA. We perform density-functional calculations at low and high coverage limit that indicate the importance of long-range substrate relaxations and explain the observed increasing preference for above-trough binding with increasing surface coverage. The electrophilic nature of MA gives rise only to small changes in the binding strength, but these may be large enough to explain the observed binding if kinetic rather than thermodynamic reaction control occurs.

Synthesis and bright luminescence of lanthanide (Eu(III), Tb(III)) complexes sensitized with a novel organic ligand by Bao-Li An; Meng-Lian Gong; Kok-Wai Cheah; Ji-Ming Zhang; King-Fai Li (345-350).
A novel organic ligand, 6-[(benzylamino) carbonyl]-2-pyridine carboxylic acid (HBAP), and the corresponding lanthanide complexes, tris(6-[(benzylamino) carbonyl]- 2-pyridine carboxylato) lanthanide(III) (Ln-BAP, Ln=Eu, Tb, Gd), have been designed and synthesized. The lanthanide (Eu(III), Tb(III)) complexes were efficiently sensitized by BAP ligand. The fluorescence quantum yields were investigated by comparison with a luminescence standard, and the yields were 15 ± 3%, 34 ± 3% for the solid europium and terbium complexes respectively. The lowest triplet level of HBAP ligand was calculated from the phosphorescence spectrum of Gd-BAP complex, and the energy transfer mechanisms in the lanthanide complexes were discussed.

Structural transitions and the melting behavior of crystalline, model poly(ethylene oxide), (CH2–CH2–O) n , (PEO) has been investigated using fully atomistic, constant pressure-constant temperature (NPT) molecular dynamics simulations. Melting of PEO proceeds in two stages; order parameters reveal the loss of interchain orientational correlations and of chain helicity in the first and second stages of melting, respectively. Sliding diffusion and anisotropic reorientational dynamics of the polymer backbone are observed in the solid state, in agreement with 1H NMR experiments.

Temperature dependence of solvation dynamics in a micelle. 4-Aminophthalimide in Triton X-100 by Pratik Sen; Saptarshi Mukherjee; Arnab Halder; Kankan Bhattacharyya (357-361).
Solvation dynamics of 4-aminophthalimide (4-AP) is studied in a Triton X-100 (TX) micelle at three different temperatures. The average solvation time 〈τ s〉 has been found to be 800, 400 and 110 ps at 283, 303 and 323 K, respectively. This corresponds to an activation energy of 9 ± 1 kcal mol−1. The observed temperature dependence is in qualitative agreement with recent computer simulations on the solvation dynamics in micelles.

An oligopeptide doubly labelled with an azulene chromophore and a TEMPO radical. Azulene triplet generation by enhanced ISC from S2 by Elena Sartori; Antonio Toffoletti; Carlo Corvaja; Luis Moroder; Fernando Formaggio; Claudio Toniolo (362-367).
Azulene and a nitroxyl radical have been incorporated in the same helical peptide template in order to study the excited state quenching of the chromophore by the radical. This process has been investigated by time resolved EPR by exciting the molecule with visible or UV laser pulses. Spin polarised radical EPR signals have been observed only by using UV light, hence only exciting azulene to its S2 excited state. When azulene and the nitroxyl radical are not linked together, no spin polarisation was observed. The results are accounted for by azulene triplet generation from the S2 state by enhanced intersystem crossing due to the close proximity of the free radical.

Structure and conformational equilibrium of new thiacalix[4]arene derivatives by A. Suwattanamala; A.L. Magalhães; J.A.N.F. Gomes (368-373).
Density functional theory was used to study the structure and conformational equilibrium of tetraaminothiacalix[4]arene (1) and tetramercaptothiacalix[4]arene (2), which are expected to open a new area of host–guest chemistry. All the calculations predict the cone as the most stable conformer for both compounds, which is in good agreement with an earlier theoretical study on the parent thiacalix[4]arene. It is shown that different substituents at the lower rim do not affect the stability ordering. The intramolecular bonding between hydrogen atoms and sulfur bridges seems to be a dominant factor in stabilizing all the conformers rather than hydrogen bonds between the groups of the lower rim.

Chemisorption of atomic oxygen on Pt(1 1 1) and Pt/Ni(1 1 1) surfaces by Timo Jacob; Boris V. Merinov; William A. Goddard (374-377).
Using density functional theory (B3LYP functional) we systematically studied Pt/Ni alloy clusters (⩽44 atoms) and found that the Pt/Ni(1 1 1) alloy surface prefers the bulk structure (Pt3Ni crystal), without showing surface segregation. This leads to an ordered surface with each Ni surrounded by 6 Pt atoms. We then examined the oxygen chemisorption at all surface sites and found strongest binding at a FCC site (2 Pt and 1 Ni atom, 3.50 eV). On pure Pt(1 1 1) oxygen is most stable (3.28 eV) at the FCC site formed by three Pt atoms. This finally leads to a channel-like mobility of oxygen on the alloy surface.

The librational and vibrational motions of water molecules in the first hydration shells of Na+ and K+ have been studied by combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, in which the ion and its first hydration sphere were treated at the Hartree–Fock level using LANL2DZ basis sets. The frequency shifts, together with the detailed analysis of water exchange processes and the mean residence times of the water molecules surrounding the ions, in comparison to those observed from a QM/MM simulation of pure water, provide a clear evidence for the background of the experimentally observed transition from structure-making to structure-breaking behavior from Na+ to K+.

Two-photon-induced excited-state intramolecular proton transfer (ESIPT) process of 1-hydroxyanthraquinone has been investigated by using a fluorescence up-conversion technique. The emission spectrum by two-photon excitation was identical with that by one-photon excitation. In temporal profiles, the fastest decay component shorter than 120 fs was interpreted to indicate the occurrence of ESIPT accompanied with the delocalization of excited-state wave function. The decay components of 2.5 and 18 ps were assigned to vibrational cooling and rotational diffusion processes, respectively. Time-zero anisotropy value was measured close to 0.53, which is accounted to be two-photon absorption process.

Prospects for a synthetic route towards well-defined stoichiometric silica nanoclusters: from siloxane to silica by Martijn A Zwijnenburg; Stefan T Bromley; Edwin Flikkema; Thomas Maschmeyer (389-393).
Based upon computational considerations, a novel synthetic route towards well-defined stoichiometric silica nanoclusters is proposed. Density-functional calculations demonstrate the viability of a route based upon siloxane cage thermolysis, while, molecular dynamics calculations were performed to test the stability of the cages formed. We predict for small siloxane cages defect-rich structures to be the main product, while, for larger siloxane cages fully coordinated silica nanoclusters iso-structural to their precursor to be formed. Overall, thermolysis of siloxane cages is expected to present a viable route towards specific types of metastable yet, well-defined silica nanoclusters, not obtainable by less targeted cluster generation methods.

The π-hydrogen bonded minimum on the standard and the counterpoise-corrected B3LYP, PBE1PBE/6-31++G(d,p) and MP2/6-31++G(d,p) potential energy hypersurfaces of the methanol–fluorobenzene dimer is studied. Anharmonic OH stretching frequency shift calculated at MP2 level is in excellent agreement with the experiment (20.5 vs. 20 cm−1), while all DFT values are too large, the B3LYP results being superior to the PBE1PBE ones, especially for the counterpoise-corrected PES. The OH stretching vibrational potentials are analyzed with the charge field perturbation methodology. Interaction and dissociation energy calculations, along with the NBO and AIM analyses of the MP2 and Kohn–Sham densities are carried out as well.

Oscillations in a B–Z system with oxalic acid (OA) + xylose (XY) as mixed organic substrates have been investigated. Neither of them acts as bromine scavenger and oscillations do not occur when either of them is used as organic substrate. Studies have been made for varying concentrations of OA but keeping XY fixed. Both single and dual frequency oscillations are observed. [Br2] and [Br] during oscillations were measured spectrophotometrically and electrochemically, respectively. Oscillations are quenched by addition of higher [Br] in the case of both type II oscillations and I. Experimental results support the mechanism for B–Z oscillations involving use of OA and fructose (F) and OA and glucose (G) as mixed substrates.

The title reaction is studied for the first time using a global double many-body expansion potential energy surface. The major differences between the calculated and experimental results are: (a) the calculated activation energy is larger than the experimental one; (b) the reaction is predicted to occur exclusively via oxygen abstraction from ozone while it has been suggested from experimental work that hydrogen abstraction accounts for 88–95% of the reactive encounters. This discrepancy in mechanism is tentatively attributed to scrambling reactions, with further theoretical and experimental work being required to clarify pending issues.

Magnetic field effects on the decay rates of triplet biradical photogenerated from intramolecular electron-transfer in a zinc-tetraphenylporphyrin-fullerene linked compound by Hiroaki Yonemura; Hideki Nobukuni; Shinya Moribe; Sunao Yamada; Yoshihisa Fujiwara; Yoshifumi Tanimoto (417-422).
Transient absorption spectra of a zinc-tetraphenylporphyrin(ZnP)-fullerene(C60) linked compound with flexible eight methylene groups indicated that intramolecular electron-transfer occurred in benzonitrile, while not in toluene. In benzonitrile, the decay rate constant of biradical decreases quickly in lower magnetic fields (<0.1 T), and then increases gradually and finally become almost constant in higher magnetic fields (0.1⩽H⩽1.2 T). The magnetic field effects (MFEs) verified that the triplet biradical was generated from the intramolecular electron-transfer of the triplet-excited states of ZnP and C60. The reverse phenomenon of the MFEs around 0.1 T is most likely ascribed to the properties of C60 moiety.

Cis-stilbene was excited by one photon at 270 nm in the gas phase and then probed by ionization at infrared wavelengths (810 and 2100 nm), recording the delay-time dependent mass spectra. We found not only a decay of 300 fs, previously assigned to departure from the fluorescent region, but also a second time constant (160 fs), probably representing departure from the ‘perpendicular minimum’ (excited state with twisted ethene part). In addition, two coherent oscillations (periods 140 and ≈600 fs) were found in the 300-fs window. We discuss their implications for the initial motion and point out the importance of vibronic interaction of excited states.

Atomic density radial functions from molecular densities by Tibor Koritsanszky; Anatoliy Volkov (431-434).
Stockholder atom densities are projected onto nucleus-centered spherical harmonics to derive radial basis functions that are applicable for modeling atoms in molecules. The method, providing an exact representation of the molecular density in terms of one-center contributions, can be used to predict electrostatic properties of large systems and to improve density fitting to X-ray diffraction data.

This Letter reports significant excitation of 13C homonuclear double-quantum coherence in a solid-state magic-angle-spinning NMR experiment, acquired without heteronuclear decoupling of abundant 1H spins. The heteronuclear decoupling efficiency of a group of existing homonuclear polarization transfer sequences are investigated and optimal schemes are identified. Since the approach permits the application of fast MAS and significantly reduces the total radio-frequency power used, it is particularly well suited to biomolecular applications at ultra-high magnetic fields.

Repeated heterogeneous nucleation of a single, unchanging aqueous sample of water in a container coated by a self-assembled monolayer (SAM) is studied using our automated lag-time apparatus showing that coating the walls of the sample container with the SAM decreases the average supercooled temperature (ΔT 50%) to colder temperatures, indicating that nucleation in an unmodified glass container takes place on the container walls in the absence of a substrate or impurities. Adding an AgI crystal increases ΔT 50% to the same warm temperature, whether the container is SAM-coated or not, suggesting that nucleation takes place on the surface of the added crystal.

Lifetime data concerning Cu+ fluorescence in RbCl by Leonardo Bosi; Francesco Leonardo Bosi; Carlo Sanipoli; Marco Zelada (446-448).
The fluorescence of Cu+ in RbCl was investigated in the temperature range of 20–300 K by performing accurate lifetime measurements. By growing high purity samples, the problem has been solved concerning the behaviour of the decay process: the lifetime data were found intrinsic and not affected either by different thermal treatments or by ageing. The Cu+ de-excitation mechanism has been simply interpreted in terms of the traditional Pedrini model. Moreover, the results are in agreement with the Bosi and Nimis model, where an off-centre configuration has been foreseen. Nevertheless, preliminary decay data concerning the fluorescence of Cu+ in RbI are unusual and limit the validity of the relationship adopted in the Pedrini model for the temperature dependence of the decay lifetime.

On the kinetic energy release distribution for C2 evaporation from fullerene ions by K Głuch; S Matt-Leubner; O Echt; R Deng; J.U Andersen; P Scheier; T.D Märk (449-455).
We present a critical evaluation of the kinetic energy released in the unimolecular dissociation of C60 +, C58 +, and C56 +. High-quality kinetic energy release distributions (KERD) have been recorded in a three-sector-field mass spectrometer that is equipped with two electric sectors. Systematic errors arising from assumptions about the shape of the KERD are explored by a combination of experiments and simulations; an alternative to the ‘model-free approach’ is suggested. For decay of C60 +, an average KER of 394 ± 14 meV is obtained. Surprisingly, the experimental KER distributions are virtually indistinguishable from the one expected for a pure Langevin-type interaction.

A full account of calculations of the electric dipole forbidden pure rotation and rotation–vibration transitions in the ground electronic state (1sσg) of D2 + is presented. The transitions have measurable intensity because of ortho–para mixing that arises from electronic g/u symmetry breaking caused by the Fermi contact hyperfine interaction. The transition moments for the most significant of these transitions (in the region 0.3…1000 cm−1) are determined to be between 5 × 10−3 and 7 × 10−6 ea0.

Raman band of matrix isolated Na M Se N clusters by C. Herwig; M. Schnell; J.A. Becker (462-466).
Selenium clusters are doped with sodium atoms in the reaction zone of a dual laser vaporization source. Product clusters Se N and Na2Se N with N=4–8 are deposited in a nitrogen matrix and investigated by Raman spectroscopy. Beside the Raman band of pure Se N clusters, a new intense band between 165 and 225 cm−1 is observed. Within a simple model of dynamical charge transfer the new band is attributed to certain vibrational modes with considerable changes of Na–Se bond lengths. The assignment is confirmed by density functional calculations. A bonding model for the Na2Se N clusters containing horseshoe shaped polyanionic selenium chains is developed.

Diffusion of nitrogen gas in ice Ih by Tomoko Ikeda-Fukazawa; Katsuyuki Kawamura; Takeo Hondoh (467-471).
Diffusion of N2 in ice crystal has been found from Raman scattering of the natural ice from the Antarctic ice sheet. In order to investigate the diffusion mechanism, we perform molecular dynamics simulations of diffusion of N2 in ice. The results show that the N2 molecule hops in the crystal by breaking hydrogen bonds in the ice lattice. The diffusion velocity with the mechanism is few orders larger than the estimate under the assumption of the interstitial mechanism. We conclude that the localized vibrational motion of N2 is the dominant factor governing the diffusion mechanism.

Template-engaged synthesis of RuSe2 and Pd17Se15 nanotubes by reacting precursor salts with selenium nanowires by Xuchuan Jiang; Brian Mayers; Yuliang Wang; Bryan Cattle; Younan Xia (472-476).
In the present work, nanowires of trigonal selenium (t-Se) were reacted with Ru(acac)3 and Pd(acac)2 (or PdCl2) to generate RuSe2 and Pd17Se15 on the surface of each t-Se nanowire as a uniform, conformal sheath. The unreacted cores of selenium could be evaporated by heating the as-synthesized Se@RuSe2 and Se@Pd17Se15 nanocables to yield selenide nanotubes with their typical wall-thickness around 6 nm. This template-engaged approach allowed for the production of both nanocables and nanotubes in a relatively large scale, and is believed to be able to get extended to synthesize other chalcogenides as tubular nanostructures.

Linear carbon allotrope – carbon atom wires prepared by pyrolysis of starch by Kuan-Hong Xue; Fei-Fei Tao; Wei Shen; Chun-Jian He; Qiao-Ling Chen; Li-Jun Wu; Yi-Mei Zhu (477-480).
A new method is reported to produce linear carbon allotrope from the pyrolysis of starch catalyzed by Fe. The pyrolytic product termed as carbon atom wires (CAW) is composed of winding lines with the diameter around 2.0 Å, indicated by magnified HRTEM images. The experimental results of UV and Raman spectra revealed a conjugated sequence of cumulated double bonds (CC) n presented in the hexane extract of CAW. Arguments about the sp hybridization bonding structure of CAW can also be supported by EELS and FT-IR measurements.

Light-emitting devices, using ruthenium(II)(4,7-diphenyl-1,10-phenanthroline)3 ([Ru(dphphen)3]2+) as dopant and emitting center have been investigated, in a structure of indium-tin-oxide glass (ITO)/poly(N-vinylcarbazole) (PVK):2-(4-biphenyl)-5-(4-ter-butylphenyl)-1,3,4-oxadiazole (PBD):[Ru(dphphen)3]2+/tris-(8-hydroxyquinoline) aluminum (Alq3)/Al. Instead of the long response time observed at high doping concentration, instantaneous light emission from [Ru(dphphen)3]2+ is obtained at a doping concentration at which the electronic coupling between the [Ru(dphphen)3]2+ molecules is eliminated by the host matrix. This is attributed to the direct exciton formation at [Ru(dphphen)3]2+ molecule by charge trapping from PVK and PBD. The emission is isolated to [Ru(dphphen)3]2+ by inserting a layer of 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (BCP) between PVK:PBD:[Ru(dphphen)3]2+ and Alq3 layers.

The new class of substitution reactions with oxygen molecule as an agent has been studied by combination of quantum chemistry calculation and transition state theory (TST). The ‘inversion substitution’ processes RH + O2  → RO2  + H (R=CH3 and SiH3) have been investigated. The energy for the stationary points (reagents, products and transition states) on the reaction coordinate has been calculated by G2M(CC,MP2) method and rate constants have been calculated within TST approach. The results show that in methane case the reaction considered (CH4  + O2  → CH3O2  + H) does not compete with generally accepted mechanism (CH4  + O2  → CH3  + HO2), but it does at elevated temperature in silane case.

The hydration of Fe2+ and Fe3+ ions in aqueous solution was studied by molecular dynamics simulation using ab initio pairwise interactions potential plus three-body correction terms. The simulations were performed at 298.16 K using the CF2 flexible water model. Radial distribution functions and their integration for Fe n+–O show that six water molecules reside in the first hydration shell for both Fe2+ and Fe3+ ions, with R FeO being 2.15 and 2.05 Å, respectively. The second hydration shell contains about 13 and 15 water molecules for Fe2+ and Fe3+ ions, respectively, forming hydrogen bonds to the water molecules in the first shell. Water exchange between the second shell and bulk occurs frequently. Librational and vibrational spectra of second shell water molecules are almost identical to those in the bulk, whereas for first shell ligands remarkable differences are observed.

An investigation of the 6ag inner valence orbital electron density of the antimicrobial agent diacetyl by binary (e,2e) spectroscopy by G.L. Su; X.G. Ren; S.F. Zhang; C.G. Ning; H. Zhou; B. Li; G.Q. Li; J.K. Deng; Y. Wang; Y. Zheng (498-501).
We report here the first measurements of the complete valence shell binding energy spectra and the 6ag inner valence orbital momentum profile of the antimicrobial agent diacetyl, also known as 2,3-butanedione (CH3COCOCH3), using a high-resolution binary (e,2e) electron momentum spectroscopy, at an impact energy of 1200 eV plus the binding energy, and using symmetric non-coplanar kinematics. The experimental momentum profile of the 6ag inner valence orbital is compared with Hartree–Fock (HF) and density functional theory (DFT) calculations. The experimental measurement is quite well described by the HF and DFT calculations.

The first study of the kinetics of B atoms with O2 at low and ultra-low temperatures is reported. Rate constants have been measured from 295 down to 24 K using the pulsed-laser photolysis-laser-induced fluorescence technique in a Cinétique de Réaction en Ecoulement Supersonique Uniforme apparatus. Rate constants were found to increase monotonically with decreasing temperature. The temperature dependence of the rate constant has also been calculated using a theoretical approach based on the adiabatic capture centrifugal sudden approximation method. In the limit of zero temperature, the reactivities of the two spin orbit states of the B atom towards the O2 molecule are also demonstrated to be different.

We developed a new experimental system (CLSM/AFM) and made the spectroscopic measurement in the contact area in liquid possible. We tried to measure the solvent properties between an AFM probe and hydrophilic or hydrophobic substrate surface. A microbead was attached to the AFM probe and fluorescent molecules were introduced to this probe to clarify the solvent property. As a result, when the probe was contacted, the fluorescence intensity changed according to these modified surfaces of substrates. This CLSM/AFM system could clarify the solvent property between an AFM probe and substrate surfaces directly.

We present a theoretical study on a novel series of Polycyclic Aromatic Hydrocarbons (PAHs) having hollow sites focusing particularly on electronic structures and spectroscopic aspects using molecular orbital and DFT levels of theory. We have found in the case of a new series of PAHs that the UV–Vis absorption spectra of some PAHs show blue shifts as the number of electrons increases in the π-system. Unusual behaviors of giant PAHs are discussed in connection with aromaticity.

Author index (520-528).