Chemical Physics Letters (v.535, #C)
Editorial Board (IFC).
Orienting polar molecules without hexapoles: Optical state selection with adiabatic orientation by Tim Schäfer; Nils Bartels; Nils Hocke; Xueming Yang; Alec M. Wodtke (1-11).
Display Omitted► Orienting highly vibrationally excited NO molecules using the Stark effect. ► Promising alternative to the commonly used hexapole filter technique. ► State-specific optical pumping followed by orientation in an electric field.A pedagogic review of technology used to orient polar molecules is presented to place in context the report of a new approach to this problem. Laboratory frame orientation of polar molecules is achieved by state-specific optical pumping in a region free of electric fields followed by adiabatic transport into a static electric field. This approach overcomes some of the limitations of the more common hexapole focusing method. In particular the method is nearly insensitive to the kinetic energy of the sample. We demonstrate production of oriented samples of NO (μel = 0.15 D) with translational energies above 1 eV in both high- and low-field seeking states. The method can be extended to many other classes of molecules, including near symmetric tops and ions.
Photoelectron spectra of solvated electrons in bulk water, methanol, and ethanol by Takuya Horio; Huan Shen; Shunsuke Adachi; Toshinori Suzuki (12-16).
Display Omitted► A linear TOF photoelectron spectroscopy with 100-kHz laser is demonstrated. ► High-resolution photoelectron spectra of solvated electrons were measured. ► Vertical binding energies of solvated electrons were determined for four solvents.Photoelectron spectra of solvated electrons in bulk liquids were obtained at energy-resolution of 60 meV using a linear time-of-flight photoelectron spectrometer and a 100 kHz ultraviolet femtosecond laser. Solvated electrons in H2O, D2O, methanol, and ethanol were generated by 226 nm excitation of the charge-transfer-to-solvent bands of I− in 0.1 M NaI solutions, and the photoelectron spectra were measured using 260 nm pulses with a time delay of 2 ns. The electron binding energies and band shapes are discussed.
The A 1 Σ + electronic state of KLi molecule by A. Grochola; J. Szczepkowski; W. Jastrzebski; P. Kowalczyk (17-20).
Display Omitted► The A 1 Σ + ← X 1 Σ + band system of KLi observed by polarisation labelling spectroscopy. ► The molecular constants and potential curve of the A 1 Σ + state determined. ► The result compared with the prediction of theoretical calculations.The A 1 Σ + ← X 1 Σ + band system in the 39K7Li molecule is investigated by the polarisation labelling spectroscopy technique. The excited state is characterised by a set of Dunham coefficients describing rovibrational levels v = 0 – 34 , J = 9 – 73 and the corresponding potential energy curve is constructed with the Rydberg–Klein–Rees method. The main equilibrium constants are T e = 12097.11 ( 3 ) cm - 1 , (with respect to the minimum of the electronic ground state), ω e = 137.0821 ( 131 ) cm - 1 , R e = 3.9466 ( 3 ) Å .
Laser spectroscopy of iridium monohydride and iridium monodeuteride by A.G. Adam; A.D. Granger; C. Linton; D.W. Tokaryk (21-25).
Display Omitted► IrH/IrD molecules produced using laser ablated Ir atoms and H2/D2 gas. ► First spectroscopic study of IrH/D. ► Eight vibronic bands observed for each isotopologue. ► Rotation and distortion constants determined for each band.Laser-induced fluorescence spectra of iridium monohydride (IrH) and monodeuteride (IrD) have been obtained at medium resolution. Eight red-degraded bands for each isotopologue were observed. The bands are assigned as Ω′ = 4 − Ω″ = 4 transitions with the ground state common to all bands in each isotopologue. The data are consistent with the ground state being the lowest component of a 3 Φi state. A global fit of all the rotationally resolved data yielded a set of rotation and distortion constants for each band. Ground state vibrational frequencies for IrH and IrD were determined to be 2216 and 1610 cm−1.
Determination of the rate constant of the reaction of NO3 with C2H5I using time-resolved cavity ring-down spectroscopy by Yukio Nakano; Yuichi Hosho; Kengo Sadamori; Takashi Ishiwata (26-29).
Display Omitted► The rate constant of the reaction of NO3 with C2H5I was reported for the first time. ► Time resolved cavity ring-down spectroscopy was applied to kinetic study. ► NO3 + C2H5I would play an important role in the iodine cycle at night.The reaction of NO3 with C2H5I was studied using time-resolved cavity ring-down spectroscopy. The rate constant of NO3 + C2H5I reaction was determined to be (2.4 ± 0.4) × 10−13 cm3 molecule−1 s−1 at 298 K and showed no pressure dependence in the range of 25–100 Torr of N2 diluent. The determined value of the rate constant suggests that the reaction of NO3 with C2H5I would play an important role in the iodine cycle at night.
Low-energy electron scattering from pyrimidine: Similarities and differences with benzene by D.B. Jones; S.M. Bellm; P. Limão-Vieira; M.J. Brunger (30-34).
Display Omitted► Electron impact excitation of pyrimidine. ► Absolute differential cross sections measured. ► Compared with measurements for benzene. ► Characterization of electron impact π–π∗ transitions in aromatic species.Differential cross sections for low-energy electron-impact excitation of the unresolved combinations of 23B2 + 21A1 and 31A1 + 21B2 electronic states of pyrimidine are reported. Comparisons are made with recent differential cross section measurements for the electron-impact excitation of the 1E1u and unresolved 1B1u + 3E2g electronic states of benzene [H. Kato, M. Hoshino, H. Tanaka, P. Limão-Vieira, O. Ingolfsson, L. Campbell, M.J. Brunger, J. Chem. Phys. 134 (2011) 134308.], in order to evaluate the nature of electron impact π–π∗ transitions in aromatic species.
Are the CF3 groups in 2,2-bis(trifluoromethyl)oxirane eclipsed or staggered? Insights from rotational spectroscopy and quantum chemical calculations by S.A. Cooke; A.J. Minei (35-39).
Display Omitted► We have recorded the chirped pulse Fourier transform microwave spectrum of 2,2-bis(trifluoromethyl)oxirane. ► We have calculated a portion of the potential energy surface pertaining to the conformation of the opposing CF3 groups. ► The opposing CF3 groups adopt an eclipsed conformation in the zero point but are staggered at the potential minimum.The pure rotational spectrum of 2,2-bis(trifluoromethyl)oxirane has been recorded using a chirped pulse Fourier transform microwave spectrometer. A total of 317 transitions have been recorded and spectroscopic constants have been determined for the first time. Quantum chemical calculations suggest that at equilibrium the two CF3-groups have a slightly staggered configuration with respect to one another. However, the barrier to an eclipsed configuration is calculated to be very low, ≈10 cm−1. Arguments are presented suggesting that the zero-point energy of the molecule is above the barrier to the CF3 eclipsed structure such that the zero-point geometry can reasonably be described as possessing eclipsed CF3-groups.
The pure rotational spectrum of platinum monocarbide, PtC by Chengbing Qin; Ruohan Zhang; Fang Wang; Timothy C. Steimle (40-43).
Display Omitted► Pure rotational spectrum of PtC. ► Assessment of proposed electronic state distribution. ► 195Pt hyperfine interaction. ► Comparison with PtSi.The J = 1 ← J = 0 and J = 2 ← J = 1 rotational transitions of platinum monocarbide, PtC, have been recorded using the separated field pump/probe microwave optical double resonance technique and analyzed to determine the fine and hyperfine parameters for the X 1Σ+(v = 0) state. The 195Pt (I = 1/2) nuclear spin–rotation interaction parameter, C I eff , was determined to be +0.138(6) MHz. A comparison with other Pt-containing molecules and a proposed molecular orbital correlation diagram is given.
Mechanism and electronic transition in the Cl + O 3 → ClO + O 2 reaction: On the fly dynamics simulations with multi-reference potentials by Jaroslaw Kalinowski; Markku Räsänen; Robert Benny Gerber (44-48).
Display Omitted► Detection of spin–flip transition in atmospherically relevant reaction. ► Estimation of detected spin–flip time scale using ab initio dynamics. ► Usage of high theory level multireference method for direct dynamics. ► Description of new parallelization algorithm.A mechanistic study of the reaction Cl + O 3 → ClO + O 2 at the high level of multi-reference DET-MRPT2 theory for both the static reaction path and the dynamics is presented. It is found that a spin–flip takes place along the computed dynamical path, a point neglected in previous studies. The time scale of the spin–flip is estimated from the dynamics. The algorithmic improvements that make possible the high-level multi-reference dynamics simulation are briefly discussed.
An analytical potential energy model for ammonia–H2 from first principle by John P. Sheppleman; Gregory W. Smizaski; E. Curotto; Massimo Mella (49-55).
Display Omitted► Analytical potential energy models for hydrogen–ammonia dimers. ► Fitted from ab initio at MP4 level. ► Dimers with para, ortho, and classical hydrogen and ammonia are compared.We construct a set of analytical potential energy models for the interaction of the para-H2–ammonia, ortho-H2–ammonia, and classical-H2–ammonia dimers by fitting a function to a number of ab initio energies. The minimum energy for the classical-H2–ammonia dimer is at −1.1164 mhartree. The classical-H2 molecule is the ‘hydrogen bond donor’ on the side of the lone pair on the nitrogen atom. The minimum energy obtained for the para-H2–ammonia is −0.289 mhartree, and for ortho-H2–ammonia is −0.281 mhartree. The ammonia molecule is the hydrogen bond donor in both dimers.
Study of packing of 4′-butyl-4-isothiocyanatotolane by X-ray diffraction and infrared spectra in polarized light by Paulina Majewska; Maria Rospenk; Rafał Petrus; Lucjan Sobczyk; Bogusława Czarnik-Matusewicz; Roman Dąbrowski (56-62).
Display Omitted► The flattened herringbone packing of 4TOLT in crystal – the X-ray results. ► Packing of 4TOLT in the crystal-like, smectic K and E phases – IR polarized results. ► Selection of modes involved in the Fermi resonance with the νas(NCS) vibration. ► Analysis of directions of the transition dipole moment vectors.The packing properties of 4′-butylo-4-isothiocyanatotolane in the solid state and the liquid crystalline phases were studied by X-ray diffraction and infrared spectroscopy. The crystal structure comprises a herringbone-like packing with an efficient π–π overlap. The factors that shape the unusual broad νas(NCS) band are discussed. Selection of modes involved in the Fermi resonance interaction with the νas(NCS) vibration is supported by directions of their transition dipole moments obtained at the DFT calculations. A specific rearrangement in the herringbone packing, accompanying transition from the solid state to the isotropic phase was confirmed by the dichroic ratio values.
Evidence of dual channel electron transfer induced negative magnetic field effect on exciplex emission at very high permittivity of medium by Amit Kumar Jana; Partha Roy; Deb Narayan Nath (63-68).
Kinetic model of the exciplex system at very high permittivity (ε ≈ 47). A-Py; D-DMA; [ ASD ] FC ∗ -accepter, donor and solvent molecule assembly undergoing super-exchange.Display Omitted► Dual channel electron transfer. ► Negative magnetic field effect. ► Relaxed and un-relaxed exciplex.Magnetic field induced change in the pyrene-N,N-dimethylaniline exciplex fluorescence has been studied in condensed phase with very high permittivity. In contrast to the commonly observed enhancement of exciplex fluorescence in presence of magnetic field (for 7 < ε < 33), the effect shows a complete reversal at low DMA concentration in DMSO which is observed only at the blue end of fluorescence. At high DMA concentration the negative MFE at blue end slowly reverts back to the normal. At the red end of the emission the MFE retains its normal character for all donor concentrations even at very high permittivity.
Ordered mesoporous ternary mixed oxide materials as potential adsorbent of biomolecules by Nabanita Pal; Asim Bhaumik (69-74).
Display Omitted► Synthesis of a new mesoporous ternary Co–Si–Al mixed oxide materials. ► Large mesopores and their nanoscale ordering using evaporation induced self-assembly (EISA) method. ► Adsorption of vitamin C, vitamin B6 and vitamin B3 over mesoporous materials. ► Selective adsorption of vitamin C (ascorbic acid).Designing a suitable mesoporous framework material for the selective adsorption or immobilization of biomolecules is a very challenging area of research. Mesoporous ternary Co–Si–Al oxide materials with large mesopore and their nanoscale ordering have been reported. The synthesis of these ternary oxides are accomplished through evaporation induced self-assembly (EISA) method using Pluronic non-ionic surfactant F127 under non-aqueous sol–gel route. N2 sorption study revealed high BET surface areas for these materials. These materials exhibited very efficient and selective adsorption for the essential biomolecules like vitamin C (ascorbic acid), vitamin B6 (pyridoxine) and vitamin B3 (nicotinic acid) from their respective aqueous solutions.
Electronic spin transitions in finite-size graphene by Buu Q. Pham; Thanh N. Truong (75-79).
Display Omitted► As graphene ribbon increases its length the band gap of the ground state decreases. ► When such a gap is below 1.13 eV, the ground state prefers a higher spin state. ► The results support co-existing of ferromagnetic and antiferromagnetic properties.Density Functional Theory study on graphene ribbons with various shapes and sizes shows that as ribbon increases in length and width, its orbital energy gap decreases and prefers a higher spin state. Such a transition occurs when the energy gap between the highest doubly occupied and the lowest unoccupied molecular orbitals of the ground state is about 1.13 eV. Our results suggest that high-spin states are stable, and graphene ribbons have ferromagnetic properties. The results are consistent with recent observations where bulk graphene possesses both ferromagnetic and antiferromagnetic properties as in phase-separated systems. The open-shell singlet state was suggested previously for the antiferromagnetic property of graphene ribbons.
Study of the interaction between copper and carbon nanotubes by Carla Bittencourt; Xiaoxing Ke; Gustaaf Van Tendeloo; Sebastian Thiess; Wolfgang Drube; Jacques Ghijsen; Chris P. Ewels (80-83).
Display Omitted► Cu atoms evaporated onto CNTs diffuse rapidly, forming crystalline particles. ► Cu has higher surface mobility on CNTs than Au, Ag, Pt, Pd, Rh, Ni, and Ti. ► Cu getters O from the basal plane but not from oxygenated vacancy sites. ► After exposure to air the nanoparticles restructure to Cu2O. ► O plasma pretreatment gives Cu2O/CNT composites with Cu2O nanoparticle size control.Copper deposited by thermal evaporation onto pristine and oxygen plasma treated carbon nanotubes (CNTs) diffuse over the CNT surface, coalescing and forming crystalline islands. The nucleation sites of the islands are preferentially defects, and more homogeneous island dispersion was observed at the CNT oxygen functionalized surface. The presence of weakly bound oxygen atoms at the CNT surface induces the formation of Cu–O bonds at the Cu/CNT interface, as described through density functional calculations. Exposure to air allows further oxidation to facetted crystalline Cu2O. Oxygen plasma pre-treatment represents a promising route for homogenous disperse Cu2O nanoparticle decoration of CNTs.
Tests of excess entropy scaling laws for diffusion of methane in silica nanopores by Peng He; Hui Liu; Jiqin Zhu; Yanfeng Li; Shiping Huang; Peng Wang; Huiping Tian (84-90).
The modified reduced self-diffusivity data (symbols) versus negative excess entropy per particle for CH4 diffusion in silica nanopore systems of different pore sizes from 1.0 to 5.8 nm using the (a) Rosenfeld and (b) Dzugutov scaling formalisms.Display Omitted► Extending two known scaling laws for describing diffusion of CH4 through pores. ► Ascertaining quantitative effects of pore confinement on molecular diffusion. ► Developing relationships for predicting diffusivity in nanopore systems.Molecular simulation was carried out to test the validity of two excess entropy scaling laws by Rosenfeld and Dzugutov, respectively, for their extended use in describing diffusion of CH4 molecules through silica nanopores of different sizes from 1.0 to 5.8 nm. The functional relationships between self-diffusivity and excess entropy formulated by the two laws are found to hold with the pre-exponential scaling parameters being peculiarly scale-dependent. Based on this, modified relations for the two scaling laws are proposed for predicting diffusivities of CH4 molecules in such pores over a wide range of concentration and temperature conditions.
Size-dependent absorption properties of CdX (X = S, Se, Te) quantum dots by C.C. Yang; Y.-W. Mai (91-93).
Display Omitted► Optical absorption properties of quantum dots were determined by a unified model. ► A new mechanism was proposed for tunable absorption properties of quantum dots. ► The model is beneficial for accurate determination of nanocrystal concentration.A unified nanothermodynamic model was developed to study the size effects on first absorption peak energy and molar extinction coefficient of semiconductor quantum dots (QDs) based on size-dependent cohesive energy and quantum confinement effect. It is found that: (1) the first absorption peak energy increases as QD size decreases; (2) the molar extinction coefficient decreases with decreasing QD size in strong confinement regime and (3) tunable absorption properties of semiconductor QDs are caused by size-induced cohesive energy variation owing to severe bond dangling. The accuracy of the developed model was verified with experimental data of CdS, CdSe and CdTe QDs.
Molecular arrangements in polymorphous monolayer structures of carbocyanine dye J-aggregates by Valery V. Prokhorov; Sergey I. Pozin; Dmitry A. Lypenko; Olga M. Perelygina; Eugene I. Mal’tsev; Anatoly V. Vannikov (94-99).
Display Omitted► We conducted subangstrom accuracy AFM height measurements of J-aggregate monolayers. ► J-aggregate polymorphism is caused by a coexistence of two molecular arrangements. ► Ladder rather than brickwork molecular arrangement is observed in J-aggregates. ► Carbocyanine dye molecules are antiparallelly stacked in J-aggregate monolayers. ► J-aggregate monolayers are labile.Subangstrom accuracy AFM height measurements and high-resolution visualization of crystallographic habits enabled us to give an insight into how stacked dye molecules are arranged in J-aggregate monolayers of 3,3′-di(γ-sulfopropyl)-4,4′,5,5′-dibenzo-9-ethylthiacarbocyanine betaine pyridinium. Ladder and staircase molecular arrangements were self-consistently proposed for the explanation of the stripe-like and leaf-like J-aggregate polymorphism correspondingly. It is inferred that a J-aggregate building unit constitutes a symmetric monolayer of ∼1.35 nm in a height that consists of all-trans monomers with anti-parallel up-down orientation and a slip angle of ∼15°. As it follows from AFM images of folded/overlapped J-aggregates, these species manifest themselves as mechanically very flexible structures.
Photovoltaic properties of dimeric methanofullerenes containing hydroxyl groups by Jing Ge; Juan Liu; Xia Guo; Yujun Qin; Hongxia Luo; Zhi-Xin Guo; Yongfang Li (100-105).
Display Omitted► New dimeric methanofullerene bearing hydroxyl groups was synthesized. ► The influence of covalent linkage of fullerene on the performance was investigated. ► The hydroxyl groups failed to improve the properties of the methanofullerenes. ► The solar cell based on the dimeric fullerene showed a PCE of 2.64%.Two new [C60]methanofullerenes containing hydroxyl groups, including a fullerene dimeric derivative and its analogue with one fullerene unit, are synthesized to investigate the influence of covalent linkage of fullerene and the hydroxyl groups on the photovoltaic properties of fullerene derivatives. It is found the hydroxyl groups cause poor compatibility between the methanofullerenes and the donor material P3HT, and both two new compounds show worse photovoltaic performance compared with PCBM. However, dimeric fullerene derivative demonstrates much better photovoltaic properties than mono-fullerene derivative, suggesting that the covalent aggregation of fullerene could significantly influence the performance of fullerene-based solar cells.
Synthesis and characterization of azo-containing organometallic thin films for all optical switching applications by R. Gatri; J.-L. Fillaut; J. Mysliwiec; A. Szukalski; S. Bartkiewicz; H. El-Ouazzani; I. Guezguez; F. Khammar; B. Sahraoui (106-110).
Display Omitted► Synthesis of organometallic containing azobenzene-based photochromic compounds. ► Fast all optical switching, with full reversibility and with neither saturation. ► The influence of ruthenium part on dynamics of molecular motions.Novel photoresponsive materials based on azo-containing bifunctional ruthenium-acetylides have been synthesized. All optical switching based on the Optical Kerr Effect in the organometallic thin films based on ruthenium(II) acetylides containing an azobenzene moiety as a photochromic unit in the main pi-conjugated system dispersed in a poly(methyl methacrylate) matrix has been observed. The excitation beam was delivered from a picosecond laser at wavelength 532 nm while dynamics of induced sample birefringence was probed by a non-absorbed linearly polarized beam of cw He–Ne laser (632.8 nm). The influence of ruthenium part on dynamics of molecular motions has been shown.
Transport spin polarization of magnetic C28 molecular junctions by Ke Xu; Jing Huang; Zhaoyong Guan; Qunxiang Li; Jinlong Yang (111-115).
Display Omitted► We explore the spin transport properties of C28 molecules. ► C28 molecular junctions exhibit robust transport spin polarization. ► Conductance of C28 is determined by the spin-down electrons. ► The TSP behavior can be effectively tuned by the gate. ► C28 molecule holds promise in molecular spintronics devices.We present a theoretical study of spin transport through a magnetic C28 molecule sandwiched between two Au (1 1 1) electrodes. The ab initio modeling is performed by spin density functional theory and nonequilibrium Green’s function technique. The results clearly show that the spin-resolved transmission spectra of C28 molecular junctions exhibit robust transport spin polarization (TSP) characteristics, which depends on the contact configuration. At the small bias voltage, the conductance of C28 is mainly determined by the spin-down electrons. The TSP behavior can be effectively tuned by the gate. Our results indicate that C28 molecule holds promise in future molecular spintronics applications.
Far-infrared spectroscopy investigation of sulfur–oxygen interactions in π-conjugated oligomers by P. Hermet; J.-L. Bantignies; J.-P. Lère-Porte; F. Serein-Spirau (116-119).
Display Omitted► Non-covalent S⋯O interactions are studied in oligo(thienylene-2,5-dialkoxyphenylene). ► They expected to lead to a better supramolecular order. ► Far-infrared measurements coupled to density functional theory are used. ► The most sensitive modes to the S⋯O interactions are located around 300 cm−1. ► They are assigned to in-plane shear of thiophene rings coupled to the methoxy groups.Two π-conjugated oligomer models which only differ from the methoxy groups on the phenyl ring, 1,4-bis(2-thienyl)benzene and 1,4-dimethoxy-2,5-bis(2-thienyl)benzene, have been considered to investigate the intramolecular non-covalent sulfur–oxygen interactions. For this purpose, we used far-infrared measurements coupled to density functional theory based calculations. We found that the most sensitive modes to the sulfur–oxygen interactions are located around 300 cm−1 and they are assigned to in-plane shear of thiophene rings coupled to the methoxy groups.
Effect of α-cyclodextrin on the optical and surface-morphological properties of pyrene–triazole azomethine oligomers by Aurica Farcas; Indrajit Ghosh; Werner M. Nau (120-125).
Display Omitted► The combined effects of oligomerization and rotaxane formation improve the optical properties. ► Oligomerization and rotaxane formation improves the morphological properties of the surface. ► Macrocyclic encapsulation by αCD of oligoazomethines enhances the solubility in polar solvents.In this study, we have investigated the effect of oligomerization and rotaxane formation on the optical and surface-morphological properties of pyrene–triazole azomethine based compounds. The combined effects of oligomerization and rotaxane formation improve the solubility, film forming ability, photophysical (increased fluorescence intensity and lifetime), and morphological properties of the azomethine oligomers. Upon rotaxane formation, the root-mean-square roughness of the films decreased from 3.5 to 1.0 nm (determined by AFM). On the contrary, no remarkable difference was found on the electrical conductivity of the iodine-doped rotaxane oligomer as compared to its un-doped form.
Is there a molecular signature of the LCST of single PNIPAM chains as measured by AFM force spectroscopy? by Edit Kutnyanszky; Anika Embrechts; Mark A. Hempenius; G. Julius Vancso (126-130).
Display Omitted► PNIPAM was grafted to AFM probe tips for single chain force spectroscopy. ► Solution temperature, and solvent (water–methanol, DMSO) were varied. ► Force chain extension curves show no variation of chain stiffness when crossing LCST.The molecular stretching behavior of temperature responsive poly(N-isopropylacrylamide) (PNIPAM) chains was studied by atomic force microscopy based single molecule force spectroscopy. Force–extension curves obtained in water below and above the lower critical solution temperature, in the co-nonsolvent water/methanol mixture, and in dimethyl sulfoxide (H-bond blocking) follow the same trajectory, independently whether the chain was pulled from a collapsed or from a solvated state. This result indicates that for a single PNIPAM chain the formation of intrachain H-bonds in the precipitated state does not cause measurable chain stiffening at the single chain level.
Density gradient ultracentrifugation and stability of SWNT–peptide conjugates by Holger Hartleb; Kristin Kröker; Tobias Hertel (131-135).
Display Omitted► Peptide functionalized biocompatible fluorescent carbon-nanotube conjugates. ► Density gradient ultracentrifugation isolates individual SWNTs from SWNT aggregates. ► Desorption of peptide from SWNTs limits their colloidal stability.Density gradient ultracentrifugation was used for preparation of biocompatible single-wall carbon nanotube (SWNT)–peptide conjugates. Aggregate size selected SWNT suspensions were analyzed by absorption and photoluminescence spectroscopy to determine stability and structure of conjugates. The results suggest that conjugates with densities over 1.19 g cm - 3 consist of SWNT aggregates. More buoyant fractions with ρ ≈ 1.18 g cm - 3 contain mostly individual SWNTs. Dilution experiments indicate that equilibration between SWNT-bound and free peptide in solution is approached within a few minutes making excess peptide in solution necessary to prevent peptide–SWNT conjugate aggregation. This has significant implications for the use of SWNT–peptide conjugates in biochemical applications.
Extending the applicability of the PBE0-DH double-hybrid model to weak interactions by J.C. Sancho-García (136-139).
Display Omitted► Extension to weak interactions (DFT framework). ► The (underlying) PBE0-DH double-hybrid model. ► Applications to databases and challenging systems.In the search of new cost-effective theoretical approximations, broadly applicable to a large variety of electronic structure problems, a new parameter-free double-hybrid (DH) density functional denominated PBE0-DH was recently launched. Previous successful applications to molecular properties have prompted us to further extend its range of applicability to weak interactions through the addition of a dispersion interaction term (–D). Calculations on some databases for weak interaction energies have confirmed the accuracy of the whole approach, thus giving support to the quality and reliability of the method, as already showed before for other double-hybrid density functionals.
Vibronic spectra of single dibenzoterrylene molecules in anthracene and 2,3-dimethylanthracene crystals by A. Makarewicz; I. Deperasińska; E. Karpiuk; J. Nowacki; B. Kozankiewicz (140-145).
Display Omitted► Single DBT molecules were studied in anthracene and 2,3-dimethylanthracene crystals. ► Vibronic spectra of single molecules depend on the local nano-environment. ► Dipolar disorder in the crystal leads to broad distribution of the (0, 0) frequencies. ► Calculated spectra of the free DBT isomers were compared with experimental results. ► DBT molecules can be considered as good probes of the shape of occupied cavity.The vibronic structure of fluorescence excitation spectra of single molecules of dibenzoterrylene (DBT) in anthracene (Ac) and in 2,3-dimethylanthracene (2,3-DMA) crystals were studied at 5 K. The vibronic patterns observed for different single molecules in the same crystal site were explained as fingerprints of the molecular geometry, which according to the ONIOM calculations are strongly dependent on the local insertion cavity. The ‘dipolar’ disorder encountered in the 2,3-DMA crystals led to a broad frequency distribution of the purely electronic lines of single molecules. The saturation curves for the (0, 0) and vibronic transitions were studied.
Surface-enhanced Raman scattering from small numbers of purified and oxidised single-walled carbon nanotubes by Nebras Al-Attar; Ilona Kopf; Eamonn Kennedy; Kevin Flavin; Silvia Giordani; James H. Rice (146-151).
Display Omitted► Surface-enhanced Raman scattering spectra of purified and oxidised single walled carbon nanotubes. ► Potential evidence for the presence of Stone–Thrower–Wales and heptagonal–pentagonal intramolecular junction defects. ► Effect of chemical introduction of carboxylic acid moieties to the surface of the nanotubes.Surface enhanced resonance Raman scattering (SERRS) has been applied to investigate defects in purified and carboxylated single-walled carbon nanotubes (SWCNTs). For both samples SERRS spectra with temporal fluctuating peak intensities and positions in the range of 1000–1350 cm−1 have been observed. A series of peaks in this window coincide with peak positions that have been assigned to arise from Stone–Thrower–Wales and heptagonal–pentagonal intramolecular junction defects on the nanotubes surface. The role of possible amorphous carbon impurities is also discussed.
Component analysis of the protein hydration entropy by Song-Ho Chong; Sihyun Ham (152-156).
Display Omitted► A novel method is developed for the component analysis of the solvation entropy. ► This method enables microscopic interpretation of macroscopic thermodynamic data. ► Solvation entropy increases upon misfolding of amyloid-beta protein in water. ► This increase is mainly attributed to the formation of non-local backbone contacts.We report the development of an atomic decomposition method of the protein solvation entropy in water, which allows us to understand global change in the solvation entropy in terms of local changes in protein conformation as well as in hydration structure. This method can be implemented via a combined approach based on molecular dynamics simulation and integral-equation theory of liquids. An illustrative application is made to 42-residue amyloid-beta protein in water. We demonstrate how this method enables one to elucidate the molecular origin for the hydration entropy change upon conformational transitions of protein.
Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage by Takayuki Tsukamoto; Yuji Mochizuki; Naoki Watanabe; Kaori Fukuzawa; Tatsuya Nakano (157-162).
Display Omitted► A partial geometry optimization was implemented at the FMO-MP2 level. ► TrpCage was employed as an illustrative test bed having dispersion type interactions. ► The optimized structure (red) agreed with the NMR structure (green) reasonably.The reliability of protein structure is a critical concern to grasp the insights with respect to residue–residue and residue–ligand interactions by computational methods. In such calculations, the molecular geometries are usually prepared by the optimization of experimental structure with empirical molecular mechanics (MM) parameters. As an alternative to MM methods, we have developed a partial geometry optimization with the fragment molecular orbital (FMO) scheme at the second-order Møller–Plesset perturbation (MP2) level. The TrpCage miniprotein was used as a demonstrative example. The geometries of the central region were partially optimized at the FMO-MP2 and Hartree–Fock (FMO-HF) levels, and the former with the correlation correction showed reasonable agreement with the experimental structure.
Aberrant structures of Parkinson’s disease-associated ubiquitin C-terminal hydrolase L1 predicted by molecular dynamics by Yuji Koseki; Tomohiro Kinjo; Masato Kuroki; Shunsuke Aoki (163-168).
Display Omitted► Aberrant structures of UCH-L1 were predicted by MD simulations. ► Significant differences between the secondary structures of WT and I93M were observed. ► This information could be useful for research into UCH-L1-associated PD.Ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) is a neuron-specific deubiquitinating enzyme. Single amino acid changes (S18Y and I93M) within UCH-L1 are associated with decreased and increased risk of Parkinson’s disease (PD), respectively. However, the molecular mechanism of pathogenesis in UCH-L1-associated PD remains to be elucidated. In this study, we performed molecular dynamics simulations of UCH-L1 variants. The simulation results show that I93M UCH-L1 is less stable than S18Y UCH-L1. In particular, the H7 and H8 α-helices in I93M UCH-L1 are partially denatured. Information regarding the aberrant UCH-L1 structures provides new insight into UCH-L1-associated PD.
Energy phase shift as mechanism for catalysis by Tamás Beke-Somfai; Bobo Feng; Bengt Nordén (169-172).
Display Omitted► By combining active sites, a catalyst can run without the input of energy. ► Phase shifting potentials leads to lower activation barriers. ► The energy barriers of ATP synthase are shown to exhibit this behavior.Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal ‘energy recycling’, bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex.
Forward–backward propagation in the mixed quantum–classical theory for the collisional energy transfer by Mikhail V. Ivanov; Dmitri Babikov (173-176).
Display Omitted► Recently developed mixed quantum–classical computational method is improved. ► Forward–backward propagation is incorporated into the theory. ► Unphysical quantum transitions without collision are excluded.A method of forward–backward propagation is incorporated into the mixed quantum–classical theory for calculations of the collisional energy transfer and ro-vibrational energy flow in a molecule + quencher encounter. This permits to avoid unphysical behavior of the energy transfer function in the range of large impact parameters. A case study is presented on stabilization of the metastable states of ozone in collisions with Ar bath gas.
Theoretical study on ultrafast intersystem crossing of chromium(III) acetylacetonate by Hideo Ando; Satoru Iuchi; Hirofumi Sato (177-181).
Display Omitted► Origin of ultrafast intersystem crossing in a chromium complex, CrIII (acac)3. ► Ab initio quantum chemistry and excited-state wavepacket dynamics. Potential energy surfaces of excited states and spin–orbit couplings. ► Duschinsky analysis of Jahn–Teller distortion. ► Potential crossings in the Franck–Condon region cause ultrafast intersystem crossing.In the relaxation process from the 4 T 2g state of chromium(III) acetylacetonate, Cr III ( acac ) 3 , ultrafast intersystem crossing (ISC) competes with vibrational relaxation (VR). This contradicts the conventional cascade model, where ISC rates are slower than VR ones. We hence investigate the relaxation process with quantum chemical calculations and excited-state wavepacket simulations to obtain clues about the origins of the ultrafast ISC. It is found that a potential energy curve of the 4 T 2g state crosses those of the 2 T 1g states near the Franck–Condon region and their spin–orbit couplings are strong. Consequently, ultrafast ISC between these states is observed in the wavepacket simulation.
Investigation of electron–hole correlation using explicitly correlated configuration interaction method by Jennifer M. Elward; Jacob Hoffman; Arindam Chakraborty (182-186).
Display Omitted► CI expansion is performed using explicitly correlated zeroth order reference wavefunction. ► Electron–hole cusp is described using Gaussian-type geminal function. ► The CI energy is the upper bound to the XCCI energy. ► Excited state energies are calculated from the explicitly correlated wavefunction. ► Excellent agreement between XCCI and R12-FCI energies.The explicitly correlated configuration interaction (XCCI) method is presented as a general technique for accurate description of electron–hole interaction. The XCCI method is a variational method where an R12-explicitly correlated wavefunction that depends on the electron–hole separation is used as the zeroth order reference wavefunction for performing the CI expansion. This is the main feature that differentiates the XCCI from the conventional CI method. Benchmark calculations on parabolic quantum dot using XCCI, FCI, and R12-FCI methods are presented and the results demonstrate that XCCI wavefunction is variationally superior to the FCI wavefunction for the ground and the excited states.
On the gradient for metallic systems with a local basis set by K. Doll (187-191).
Display Omitted► The theory of analytical gradients for metals is presented. ► Numerical and analytical gradients match well. ► Valid for one-, two-, three-dimensional periodicity, Hartree–Fock and DFT.The analytical gradient for periodic systems is presented, for the case of metallic systems. The total energy and the free energy are computed on the Hartree–Fock or density functional level, with the wave function being expanded in terms of Gaussian type orbitals. The expression for the gradient is similar to the case of insulating systems, when no thermal broadening is applied. When the occupation of the states is according to the Fermi function, then the gradient is consistent with the gradient of the free energy. By comparing with numerical derivatives, examples demonstrate that a reasonable accuracy is achieved.
Probing IR-Raman vibrationally excited molecules with X-ray spectroscopy by Selma Engin; Nicolas Sisourat; Patricia Selles; Richard Taïeb; Stéphane Carniato (192-195).
Display Omitted► We investigate infrared pump/X-ray probe spectroscopy. ► It is demonstrated to be a powerful tool for exploring molecular bond dissociation. ► With the example of HCl, we show that complete population transfer along the vibrational ladder can be achieved. ► X-ray photoelectron spectrum is a clear signature of the probed vibrational level.We present detailed calculations describing a new scheme for time control of bond dissociation. The scheme makes use of far-off-resonant Raman transitions and X-ray spectroscopy. We show how combining these techniques can be used to follow molecular systems climbing vibrational ladders through the change of core binding energy probed by X-ray interaction.
A diabatic state model for donor-hydrogen vibrational frequency shifts in hydrogen bonded complexes by Ross H. McKenzie (196-200).
Display Omitted► Two diabatic state Hamiltonian describes weak, low-barrier, and strong hydrogen bonds. ► Describes red (blue) shift of donor-hydrogen stretch (bend) with decreasing donor–acceptor distance. ► Describes correlation of D–H stretch frequency with difference between donor and acceptor proton affinity. ► Predicts UV photo-dissociation of strong H-bonded complexes via a ‘twin’ excited electronic state. ► Two parameter model quantitatively describes empirical correlations for wide range of H-bonded complexes.A simple diabatic two-state Hamiltonian is considered which describes hydrogen bonding and proton transfer between a donor (D) and an acceptor (A), including different classes of bonds (weak, low-barrier, and strong). The independent variables are the distance R and the difference in proton affinity ϵ between the donor and acceptor. With only two free parameters the model Hamiltonian gives a quantitative description of experimental data from a wide range of molecular complexes exhibiting correlations between R and ϵ and binding energies, D–H bond lengths, and the frequencies of D–H stretch and bend vibrations. The UV photo-dissociation of strong H-bonded complexes via an excited electronic state with an exalted vibrational frequency is predicted.
Kinetic models in spin chemistry. 1. The hyperfine interaction by Matin Mojaza; J. Boiden Pedersen (201-205).
Display Omitted► Connecting kinetic models and quantum descriptions in spin chemistry. ► The spin Hamiltonian determines the structure of the kinetic model. ► A kinetic description is exact for the hyperfine interaction. ► An exact expression for the phenomenological rate constant for quantum mixing.Kinetic models for quantum systems are quite popular due to their simplicity, although they are difficult to justify. We show that the transformation from quantum to kinetic description can be done exactly for the hyperfine interaction of one nuclei with arbitrary spin; more spins are described with a very good approximation. The crucial points are: to represents the quantum coherent oscillations by first order rate constants, and to determine the number of kinetic channels corresponding to a given interaction. We consider a radical pair system with spin selective reactions and calculate the spin induced enhancement of the reaction yield.