Chemical Physics Letters (v.503, #4-6)
Editorial Board (IFC).
Ultrafast optical encoding of magnetic resonance by David Trease; Vikram S. Bajaj; Jeffrey Paulsen; Alexander Pines (187-190).
Display Omitted► Temporal resolution of MRI is limited by the time required to encode spins. ► We use the photoCIDNP effect to spatially encode NMR experiments with a laser. ► Optical encoding is three orders of magnitude faster than MRI gradient encoding.Temporal resolution in magnetic resonance imaging (MRI) is limited by the time required to encode the position of spins using time-varying (10–100 ms) magnetic field gradients. Here, we demonstrate spatial encoding of MRI images in a time that is three orders of magnitude shorter than what is possible by conventional gradient encoding techniques. Our method exploits the chemically induced dynamic nuclear polarization (CIDNP) effect and is an initial example of a set of approaches that seek to combine the favorable properties of optical spectroscopy with those of NMR for polarization, encoding, and detection.
13C chemical shifts of polyacetylene chains with charged conformational defects: A GIAO–DFT study by G. Colherinhas; T.L. Fonseca; M.A. Castro (191-196).
Display Omitted► In this study we investigate how the presence of a charged conformational defect affects the 13C chemical shifts of isolated polyacetylene chains. ► GIAO/B3LYP/pcS-2 results show that 13C chemical shift distributions reflect the detailed conformational changes of charged defect type. ► The results show that large variations of chemical shift could be detected in nuclear magnetic resonance experiments.The 13C chemical shifts of isolated polyacetylene chains bearing a singly or doubly charged defect have been studied using the GIAO approach through the B3LYP exchange–correlation functional with the pcS-2 basis set. Our results show that the distributions of chemical shift reflect the detailed structural distortions caused by the charged defects on the backbones of the polyenic chains. The results also show large variations of chemical shift between the corresponding charged chains with different charge states, which could be detected in nuclear magnetic resonance experiments.
Electronic spectrum of SnSi+: A MRDCI study by Susmita Chakrabarti; Kalyan Kumar Das (197-202).
Display Omitted► Multireference configuration interaction calculations have been carried out on the SnSi+ ion. ► Potential energy curves and spectroscopic constants of the ground and low-lying electronic states are computed for the ion. ► Effects of the spin–orbit coupling are studied. ► Radiative lifetimes of some dipole-allowed and spin-forbidden transitions are estimated.Multireference configuration interaction calculations are performed on the SnSi+ ion to study its electronic spectrum. Potential energy curves of the ground and low-lying states up to 35 000 cm−1 are constructed. Spectroscopic constants (T e, r e, ω e) of 18 bound states are calculated. The spin–orbit coupling is also included in the calculation to study its effect on the potential energy curves and spectroscopic properties of the ion. Transition dipole moments and hence radiative lifetimes of several dipole-allowed and spin-forbidden transitions are computed. Transitions such as 4 4 Σ - –X4Σ− and 4Π–X4Σ− are predicted to be highly probable, while the spin-forbidden transitions are weak.
Structure and hydrogen bond vibrations of the jet-cooled 1:1 complex between 7-azaindole and formamide: A laser-induced fluorescence spectroscopy study by Montu K. Hazra; Moitrayee Mukherjee; Debabrata Goswami; Tapas Chakraborty (203-209).
Display Omitted► Laser-induced fluorescence spectra of 7-azaindole ⋯ formamide complex are measured in a supersonic free jet expansion. ► Electronic structure calculation predicts a doubly hydrogen bonded cyclic geometry of the complex. ► Hydrogen-bond vibrations of the complex in the ground state are measured. ► The complex does not undergo excited state tautomerization, which is consistent with TDDFT and CIS calculations.Laser-induced fluorescence spectra of 7-azaindole ⋯ formamide complex are measured in a supersonic free jet expansion. Calculation at MP2/6-311++G∗∗ level predicts a cyclic doubly hydrogen-bonded structure for the complex is favoured most in the ground state. The complex emits only UV fluorescence from the locally excited state and tautomerization is inhibited under the jet-cooled environment. This photophysical behavior is consistent with the predictions of CIS/6-311++G∗∗ and TDDFT/6-311++G∗∗ calculations. The low-frequency bands in the fluorescence spectra are assigned to different hydrogen bond modes of the complex, and the spectra reveal signatures of mixing between inter- and intra-molecular vibrational modes in the excited state.
Direct ab initio dynamics study of the reaction of C2(A3Πu) radical with C2H6 by Na Li; Rui-Ping Huo; Xiang Zhang; Xu-Ri Huang; Ji-Lai Li; Chia-Chung Sun (210-214).
The variational effect is small and the nonclassical reflection effect is important to the H abstraction in high temperature region and the variational effect is negligible and the tunneling effect cooperating with the nonclassical reflection effect makes the rate constant temperature independence in low-temperature range.Display Omitted► Confirm the hydrogen abstraction mechanism theoretically and provide the electronic transfer information in detail. ► Give the theoretical rate constants over a wide temperature range for future investigation. ► Provide rational factors of rate constant under different temperature ranges. ► Give the temperature dependence of the reaction over different temperature ranges.The reaction of C2 (A3Πu) with C2H6 has been investigated at the BMC–CCSD//BB1K/6-311+G(2d, 2p) level. The classical barrier height for H-abstraction reaction is calculated to be 3.32 kcal/mol and the electron transfer behavior is also analyzed in detail. The rate constants are calculated by TST, CVT, and CVT/SCT over a wide temperature range 50–3000 K. The results indicate: (1) variational effect is small and nonclassical reflection effect is important to the H abstraction in high temperature region; and (2) variational effect is negligible and tunneling effect cooperating with the nonclassical reflection effect makes the rate constant temperature independence in low-temperature range. The CVT/SCT rate constants are in excellent agreement with experimental values.
Coupled-Cluster study of ‘no-pair’ bonding in the tetrahedral Cu4 cluster by Marco Verdicchio; Stefano Evangelisti; Thierry Leininger; José Sánchez-Marín; Antonio Monari (215-219).
Display Omitted► High level ab initio study of no pair bond in copper. ► CCSD(T) benchmark confirming the bonding nature of the state. ► Analysis of the basis set effect. ► Analysis of the core correlation effect. ► Analysis of the BSSE effect. ► Comparison with alkali metal no pair bond clusters. Ab initio Coupled-Cluster calculations with single and double excitations and perturbative correction to the triple, CCSD(T), have been carried out for the high-spin electronic state, ( 5 A 2 ) , of the copper cluster Cu 4 in its tetrahedral arrangement. Like alkali metals clusters, tetrahedral Cu 4 presents a bound quintet state, i.e., a situation where all the valence electrons are unpaired. This rather exotic wavefunction, also known as no-pair bonding state, is examined in detail. The influence of the basis set is also analyzed, as well as the importance of the core correlation and the effect of the basis-set superposition errors.
Experimental determination of thermal conductivity and interfacial energies of solid Pb solution in the Pb–Sb eutectic system by L. Karabulut; S. Aksöz; K. Keşlioğlu; N. Maraşlı; Y. Ocak (220-225).
Display Omitted► Thermal conductivities of different compositions in the Pb–Sb binary alloy have been measured. ► Solid–liquid and grain boundary energies have been determined for solid Pb solution in the Pb–Sb binary alloy. ► The Gibbs–Thomson coefficient for Pb solution have been determined.The equilibrated grain boundary groove shapes of solid Pb solution in equilibrium with the Pb–Sb eutectic liquid have been observed from quenched sample. The Gibbs–Thomson coefficient, solid–liquid interfacial energy and grain boundary energy of solid Pb solution have been determined. The thermal conductivity values for Pb–5.8 at.% Sb and Pb–17.5 at.% Sb and the thermal conductivity ratio of eutectic liquid phase to eutectic solid for Pb–17.5 at.% Sb alloy at the melting temperature have also been measured with a radial heat flow apparatus and Bridgman type growth apparatus, respectively.
Phase behavior of a simple model of ferrocolloidal fluid by I.A. Protsykevytch; Yu.V. Kalyuzhnyi; P.T. Cummings (226-230).
Display Omitted► Phase behavior is governed by the competition of magnetic and Coulomb interactions. ► Dipole–dipole interaction defines phase coexistence at low charge asymmetry. ► Charge–charge interaction defines phase coexistence at high charge asymmetry. ► For the intermediate charge asymmetry phase diagram possesses two critical points.We propose a simple model of ferrocolloidal fluid and study its phase behavior. The model consists of a two-component mixture of highly asymmetric charged hard spheres with the smaller hard spheres representing counterions, and the larger hard spheres, which represent the polyions, possessing both charge and a magnetic dipole moment. The liquid–gas phase behavior is studied at different values of the charge asymmetry using thermodynamic perturbation theory for associating fluids with central force associative potential. Upon increasing the counterion to polyion charge ratio the critical temperature and density exhibit nonmonotonic behavior, which is governed by the competition between dipole–dipole and charge–charge interactions.
Control of precipitation patterns in two-dimensions by pH field by Ferenc Molnár; László Roszol; András Volford; István Lagzi (231-234).
pH Field generated by acid and base reservoirs can control moving precipitation fronts.Display Omitted► Systematic deformation of a precipitation front into a 2D stationary profile can be achieved by a pH field generated by acidic and basic reservoirs. ► Numerical approaches, solving either time dependent reaction-diffusion equations or solving derived Laplace’s equation, provide a reasonable description of the system. ► Pattern formation can be described and discussed by a simple way taking only acid-base chemistry into account.Systematic deformation of a moving precipitation front into a 2D stationary profile by a pH field generated by acidic and basic reservoirs and its design procedure are discussed. Results indicate that in some pattern formation systems, where the pattern emerges by a precipitation reaction of metal and hydroxide ions, phenomena can be governed by a complex pH field. The pattern formation can be described and discussed by taking into account acid–base chemistry. Our approach, which relies on solving either time-dependent reaction–diffusion equations or derived Laplace’s equation, provides a reasonable description of the system.
NMR monitoring of nonequilibrium aggregation in ionic solutions by Vytautas Balevicius; Zofia Gdaniec; Vytautas Klimavicius; Arunas Masalka; Janez Plavec (235-238).
Display Omitted► The complex shaped 1H NMR signal of [C10mim][Br] has been observed after it was mixed with water. ► Mesoscopic nonequlibrium aggregates enhance Gauss contribution to the Voigt-shaped NMR signal. ► Nonequilibrium heterogeneities in the solution may be induced by temperature gradients. ► The hydrogen-bonded network of water appears to be completely equilibrated.The complex shaped 1H NMR signal of [C10mim][Br] has been observed after it was mixed with water. Within minutes the contour transformed into Voigt (V) profile with Gauss (G) contribution as dominant and started to evolve towards Lorentz-shaped (L) contour. Relative G/L contribution in V-profile was proposed as the measure of nonequilibrium aggregation in mesoscopic/supramolecular scale. The equilibration kinetics was monitored by time dependence of the half-widths G/L with waiting time up to 2–4 days. The ‘nonequilibrium’ covers only certain degrees of freedom of the guest (ionic liquid) molecules, whereas the matrix, i.e. the hydrogen-bonded network of water, is equilibrated.
Predicting metal-to-metal charge transfer in closed-shell transition metal oxides doped with Bi3+ or Pb2+ by Philippe Boutinaud; Enrico Cavalli (239-243).
Display Omitted► Incorporating Bi3+ or Pb2+ ions in d0 transition metal oxides generates MMCT transitions in the NUV. ► The MMCT transitions are predictable from the structural properties of the host lattices. ► The Eu3+ or Pr3+ luminescence can be sensitized by NUV excitation in the MMCT bands. ► Predicting MMCT transitions in Bi3+; Ln3+ codoped oxides allows the design of down-converters.An empirical model is proposed to predict the energy position of the metal-to-metal charge transfer (MMCT) bands in closed shell d0 transition metal complex oxides doped with Bi3+ or Pb2+ ions. The model is constructed on the basis of optical data compiled from the literature and from the investigation of the luminescence properties of a series of compounds (titanates, vanadates, niobates, tantalates, molybdates, and zirconates) prepared and characterized in this work.
On the superconductor mechanism of [bis(ethylenedithio)tetraselenafuvalene]2GaCl4 by Dage Sundholm (244-246).
Display Omitted► A quantum–mechanical transport mechanism for the supercurrent of the organic superconductor is proposed. ► For organic superconductors, open-shell singlet states are a prerequisite of accepting the superconducting Cooper pairs. ► The critical temperature for superconductivity is suggested to be determined by the energy difference between two electronic states with different spatial extent of the highest-occupied molecular orbital. ► The electron–phonon coupling is found to be unimportant for the quantum–mechanical transport of the supercurrent.The superconductivity of [BETS]2GaCl4, where BETS is bis(ethylenedithio)tetraselenafulvalene, is discussed in terms of electronic structure properties. The critical temperature, T c , for the organic superconductor is suggested to be determined by the energy splitting between two electronic states with different spatial extent of the orbitals at the Fermi level. The energetically lowest superconducting state has localized orbitals confined in the BETS moieties, whereas the conventionally conducting state has delocalized orbitals along the [BETS]2GaCl4 chains. The calculations suggest that the open-shell singlet state of [BETS]2GaCl4 pairs is the prerequisite of accepting the superconducting Cooper pairs.
Controlled growth of metal-free vertically aligned CNT arrays on SiC surfaces by Zhen Wang; Qiang Fu; Xuejun Xu; Hongbo Zhang; Wenliang Li; Min Gao; Dali Tan; Xinhe Bao (247-251).
Display Omitted► Metal-free CNT arrays can be obtained by high temperature decomposition of SiC(0 0 0 1 ¯ ) surface under oxygen-containing atmospheres, such as H2O. ► Formation of SiO nanoclusters at C/SiC interface via reaction between out-diffused Si nanoclusters and dissociated oxygen-containing species. ► The transient SiO nanoclusters are proposed to be the active sites for the continuous growth of CNTs on SiC surface.The growth of metal-free carbon nanotube (CNT) arrays on SiC surface was investigated systematically by using high temperature annealing of 6H–SiC(0 0 0 1 ¯ ) crystals under various atmospheres, including inert, hydrogen-containing, and oxygen-containing gaseous environments. Carbon nanowall structure consisting of graphene sheets standing vertically on the substrate forms under the inert and hydrogen-containing atmospheres, while vertically aligned CNT arrays can be obtained in oxygen-containing atmospheres, such as H2O. The comparative studies reveal that oxygen-containing species play a critical role in the formation of CNTs on SiC. Transient SiO nanoclusters formed at the C/SiC interface are proposed to be the active sites for CNT growth on SiC.
A numerical study upon the atomistic mechanisms of rapid diffusion in nanoclusters by Tomoaki Niiyama; Shin-ichi Sawada; Kensuke S. Ikeda; Yasushi Shimizu (252-255).
Display Omitted► The rapid diffusion in nanoparticles were reproduced by MD simulations. ► The atomistic diffusion mechanism in a metal cluster is Surface Peeling Mechanism. ► In contrast, the diffusion mechanism in an alkali halide cluster is Vacancy Mechanism. ► The vacancy formation energy of metal clusters increases as their size decreases, while that of alkali halides decreases. ► This opposite trend is a reason for the onset of the totally different mechanisms.An isoenergetic molecular dynamics simulation is done to investigate two fundamental atomistic mechanisms responsible for rapid diffusion in nanoclusters. Using a semi-empirical potential we successfully reproduce the so-called Spontaneous Alloying and Spontaneous Mixing phenomena, which have been found in experiments for bimetallic and ternary alkali halide clusters, respectively. We found that a novel mechanism, named here the Surface Peeling Mechanism, is of primary importance for Spontaneous Alloying, while the Vacancy Mechanism is dominant in Spontaneous Mixing. We also show that the dominant mechanism responsible for rapid diffusion is related to the size dependence of vacancy formation energy.
Fluorescence correlation spectroscopy near individual gold nanoparticle by Qingyan Wang; Guowei Lu; Lei Hou; Tianyue Zhang; Chunxiong Luo; Hong Yang; Grégory Barbillon; Franck H. Lei; Christophe A. Marquette; Pascal Perriat; Olivier Tillement; Stéphane Roux; Qi Ouyang; Qihuang Gong (256-261).
Display Omitted► Near-field effect near Au nanoparticle is investigated by fluorescence correlation spectroscopy. ► Single molecule diffusion dynamics within the near field of Au nanoparticle is observed clearly. ► Near-field volume is polarization dependent and dependent on the properties of Au nanoparticle. ► The diffusion kinetics of fluorophores is analyzed theoretically by a simple model.Dynamic behavior of fluorescent molecules near an individual gold nanoparticle is investigated experimentally by fluorescence correlation spectroscopy method. The gold particle that acts as an optical nano-antenna presents significant near-field volume reduction. The single molecule diffusion behavior is clearly observed within a reduced near-field volume due to a highly localized field enhancement. The near-field volume and fluorescence enhancement are polarization and concentration dependent and strongly depend on the properties of the gold nanoparticle. A simple approximated model is developed to fit the FCS autocorrelation curves. In principle, the single molecule analysis within the near-field volume of nanostructures could be applied to the analysis of biological membranes and intracellular processes.
Efficient photocatalytic hydrogen production over Ni@C/TiO2 nanocomposite under visible light irradiation by Peng Zeng; Xungao Zhang; Xiaohu Zhang; Bo Chai; Tianyou Peng (262-265).
Display Omitted► A novel visible-light-driven Ni@C/TiO2 nanocomposite is first prepared. ► Enhanced visible-light-driven photocatalytic H2 production efficiency with better durability. ► Beneficial for developing panchromatic respondent and low-cost photocatalysts.A novel visible-light-driven carbon-coated Ni (Ni@C)/TiO2 nanocomposite photocatalyst with enhanced photoactivity for hydrogen production was synthesized and characterized for the first time. The resultant Ni@C/TiO2 nanocomposites are composed of nanorods with an average diameter of ca. 10 nm and length in the range of 40–100 nm, and exhibit remarkable photostability in an aqueous suspension by using triethanolamine (TEOA) as a sacrificial reagent. Moreover, a hydrogen generation rate of up to 300 μmol h−1 over 5 wt% Ni@C/TiO2 without Pt-loading is achieved under visible light (λ ⩾ 420 nm) irradiation.
Investigation of 2D/3D defects in controlled-growth oxygen-deficient ZnO nanowires and their field emission by Jong Seok Jeong; Jeong Yong Lee; Hyung Koun Cho (266-271).
Display Omitted► Controlled growth of ZnO nanowires using ZnO seed films. ► Control of diameter, alignment, and density of ZnO nanowires. ► Defects analysis using transmission electron microscopy. ► Optical and field emission properties related to oxygen deficiency in ZnO nanowires.The controlled growth of oxygen-deficient ZnO nanowires on ZnO films in terms of diameter, alignment, and density is achieved by controlling the ZnO films, and the structural, optical, and field emission properties related to the oxygen-deficiency are discussed. Planar (2D) and nano-sized (3D) defects due to the large amount of oxygen deficiency are characterized using a high-resolution transmission electron microscopy with the aid of simulations. It is suggested that the two-stage linearity of the Fowler–Nordheim plot is attributable to the deep-level defects of the nonstoichiometric ZnO nanowires.
Molecular simulations on the chirality preference of single-walled carbon nanotubes upon ductile behavior under tensile stress at high temperature by Hirotoshi Deguchi; Yasutaka Yamaguchi; Kaori Hirahara; Yoshikazu Nakayama (272-276).
Display Omitted► We simulate superplastic elongation of single-walled carbon nanotubes using molecular dynamics method. ► We examine chirality changes for armchair nanotubes and found a systematic sequence of the chirality history different from a proposed model. ► We find that this difference is due to the torsional stress brought through the propagation of dislocation. ► We underpinned the fact through energy analysis.Molecular dynamics simulations were carried out on the ductile behavior of single-walled carbon nanotubes (SWNTs) under tensile stress by moving both ends at constant velocity at high temperature. The ( 10 , 10 ) armchair-SWNT resulted in plastic elongation through the sequential Stone–Wales (S–W) transformation, and the chirality changed keeping the two indices equal by alternately taking two dislocation directions with Burgers vectors b → = ( 1 , 0 ) and ( 0 , 1 ) instead of choosing only one of them toward zigzag-chirality with one index equal to zero. The comparison in the activation and formation energies for the two directions revealed that the torsional strain induced by the preceding S–W sequence was the main cause of this alternating choice.
Microphase separation in regular and random сopolymer melts by DPD simulations by Alexey A. Gavrilov; Yaroslav V. Kudryavtsev; Pavel G. Khalatur; Alexander V. Chertovich (277-282).
Display Omitted► Microphase separation appear upon increasing χ in random copolymer melts. ► At large mean block lengths, random multiblocks form a bicontinuous structure. ► The super-strong segregation regime was observed at very large values of χ. ► In a large simulation box, multidomain morphologies are observed.Phase separation in melts of regular and random multiblock AB copolymers of equimolar composition and various mean block length was modeled using parallel dissipative particle dynamics simulations. Regular copolymers form well-shaped lamellas, strong and super-strong segregation regimes being identified. Microstructure formation in random copolymers with short blocks takes place at higher χ values and results in rough lamellas, the period of which is larger in comparison with the regular multiblocks. For random copolymers, increasing the mean block length deteriorates lamellar morphology and finally results in the formation of a bicontinuous structure. In a large simulation box, multidomain morphologies are observed.
Diffusion activation energy of Ag in nanocomposite glasses determined by in situ monitoring of plasmon resonance evolution by J.A. Jiménez; M. Sendova (283-286).
Display Omitted► Plasmonic evolution in Ag nanocomposites by in situ optical microspectroscopy. ► Growth of glass-embedded Ag nanoparticles in real time. ► Ag nanoparticle growth mechanism. ► Activation energy for silver diffusion.We report an in situ non-destructive optical microspectroscopy method for measurement of the diffusion activation energy for silver in glass. The approach is based on a set of isothermal time-dependent characteristics of the surface plasmon resonance of Ag nanoparticles analyzed in the context of Mie extinction and crystal growth theories. The material studied in real time during thermal processing consisted of a melt-quenched phosphate-based glass system to which 4 mol% of Ag2O along with reducing agent SnO in the same amount were added. A diffusion activation energy of 5.2 eV was obtained and discussed in terms of glass composition. The mechanism of Ag nanoparticle growth was elucidated as well.
High reactivity of metal-free nitrogen-doped carbon nanotube for the C–H activation by Xingbang Hu; Zheng Zhou; Qiuxing Lin; Youting Wu; Zhibing Zhang (287-291).
Display Omitted► It was found that the N–C part of the nitrogen-doped carbon nanotube (NCNT) could be used as the active center in the methane C–H activation. ► The catalytic ability of the metal-free NCNT is comparable to these reported noble metal catalysts and enzyme. ► Both two O atoms of O2 can be effectively used as oxidant in the catalytic cycle of NCNT.Generally speaking, metal is necessary to serve as the active center in C–H activation. Herein, we found that the N–C part of the metal-free nitrogen-doped carbon nanotube (NCNT) can be used as the active center in methane C–H activation. The NCNT can activate O2 and further activate methane by the adsorbed oxygen atoms. The catalytic ability of this metal-free NCNT is comparable to these reported noble metal catalysts and enzymes. Another character being different from many previous catalysts is that both two O atoms of O2 can be effectively used as oxidant in the catalytic cycle of NCNT.
Bipolarons in homogeneous DNA duplexes by V.D. Lakhno; V.B. Sultanov (292-295).
► We have shown that the bipolaronic model can explain experiments on DNA superconductivity. ► The transition temperature depends on the parameter values of the model. ► We suggest that such experiments should be carried out for homogeneous Poly G/Poly C and Poly A/Poly T DNA duplexes.Numerical calculations using the Holstein–Hubbard model show that stable bipolarons can form in homogeneous DNA duplexes. Since matrix elements of the Hamiltonians are different, the phase diagram determining the bipolarons stability for a G/C duplex differs from that for an A/T duplex. It is shown that a bipolaron superconductivity with the transition temperature Tc = 6 – 20 K can take place in DNA, and the transition temperature depends on the parameter values of the model. The bipolaron model can serve as a basis for explaining experiments on DNA superconductivity.
Electronic structures of a [4Fe–4S] cluster, [Fe4S4(SCH3)3(CH3COO)], in dark-operative protochlorophyllide oxidoreductase (DPOR) by Yu Takano; Yasushige Yonezawa; Yuichi Fujita; Genji Kurisu; Haruki Nakamura (296-300).
Display Omitted► Redox potentials of the [4Fe–4S] clusters are sensitive to the terminal ligands. ► NB cluster can be a better electron-donor than conventional [4Fe–4S] clusters in DPOR. ► This redox character of the NB cluster can explain why Asp36 is essential in DPOR. ► The unknown ligand of the [4Fe–4S] cluster in the D36A mutant is a chloride ion.The electronic structure of a [4Fe–4S] cluster, so-called NB cluster [Fe4S4(SCH3)3(CH3COO)], found in dark-operative protochlorophyllide oxidoreductase (DPOR) has been studied using the density functional theory. The results show that this NB cluster can function as a better electron-donor than the conventional [4Fe–4S] cluster, [Fe4S4(SCH3)4], in the 2−/3− reduction in an environment with the dielectric constant higher than 10. This redox character of the NB cluster accounts for why Asp36 is essential in DPOR. It is also suggested that the unknown coordinating ligand of the [4Fe–4S] cluster in the D36A mutant of DPOR is a chloride ion.
The DF-LCCSD(T0) correction of the φ/ψ force field dihedral parameters significantly influences the free energy profile of the alanine dipeptide by Jiří Vymětal; Jiří Vondrášek (301-304).
Display Omitted► Quantum chemistry DF-LCCSD(T0) level is necessary to obtain correct torsion potentials of phi/psi dihedrals of peptide backbone. ► DF-LCCSD(T) corrected force field torsion parameters can be used to generate FES of alanine dipeptide. ► FES of alanine dipeptide obtained by metadynamics is in good agreement with experimental results.The conformational behavior of small peptides is mostly dictated by backbone rigidity, in which the φ/ψ torsions seem to play the most important role. We show that ab initio-based corrections of the torsion parameters in the FF-FOM force field determined by the DF-LCCSD(T0) method significantly influence the quality and minimum localization on the 2D free energy surface of the alanine dipeptide (AD) along the φ and ψ coordinates of the backbone torsion angles. The populations of the individual conformers are in good agreement with the experimental results published recently on the AD through an analysis of the amide III band and the Raman skeletal vibrations.
Reactivities of radicals of adenine and guanine towards reactive oxygen species and reactive nitrogen oxide species: OH • and NO2 • by Neha Agnihotri; P.C. Mishra (305-309).
Relative Gibbs free energies and binding energies of adducts of OH • and NO2 • at the C2, C5, C8 and other carbon sites of guanine and adenine radicals were obtained using different theoretical methods in gas phase and aqueous media.Display Omitted► Reactivities of all carbon sites of all the radicals of adenine and guanine studied for the first time. ► Theoretical results explain experimental observations establishing important general results. ► These results are important from the point of view of mutation and cancer caused by reactive species.Reactions of radicals of the DNA bases with reactive oxygen species and reactive nitrogen oxide species produce mutagenic products. We have studied reactivities of all the carbon sites of radicals of adenine A(-H) • and guanine G(-H) • obtained by removal of H-atoms from their nitrogen sites towards OH • and NO2 • . We studied stabilities of A(-H) • and G(-H) • and binding energies of their adducts with each of OH • and NO2 • using density functional theoretic and MP2 calculations employing the AUG-cc-pVDZ basis set. Solvation in aqueous media was treated using the polarization continuum model. The results obtained explain experimental observations.
Low-power homonuclear dipolar recoupling using supercycled symmetry-based and exponentially-modulated pulse sequences by Anders Bodholt Nielsen; Sheetal Kumar Jain; Niels Chr. Nielsen (310-315).
Display Omitted► Combined symmetry-based and exponentially-modulated field dipolar recoupling. ► Low-power pulse sequences for biological solid-state NMR spectroscopy. ► 13C–13C coherence transfer at high MAS spinning frequencies. ► 13C–13C coherence transfer with approximately 70% transfer efficiency. ► 2D 13C–13C correlation spectra of amyloid fibrils at 30.3 kHz spinning.Aimed at performing dipolar recoupling as part of biological solid-state NMR experiments without using excessively strong rf irradiation, we present a series of low-power supercycled symmetry-based and exponentially modulated pulse sequences facilitating efficient recoupling over specified chemical shift ranges even at high-speed spinning conditions. The experiments are designed through simple phase modulation of known ‘lower-quality’ symmetry-based pulse sequences or highly rf-demanding exponentially modulated recoupling experiments. The methods are described analytically and numerically and demonstrated experimentally by one- and two-dimensional correlation spectra of 2,3-13C2-L-alanine and the fibrillating-core decapeptide SNNFGAILSS of human Islet Amyloid Poly-Peptide (hIAPP, or amylin) uniformly 13C,15N-labeled at the FGAIL residues.
Analytical energy gradient of Gaussian and Fourier transform (GFT) method for periodic condensed systems by Tomomi Shimazaki; Momoji Kubo (316-321).
Display Omitted RHtriangle First-principles method with the periodic boundary conditions base on the Gaussian basis set. RHtriangle Analytical energy-gradient formalism for the Gaussian and Fourier transform (GFT) method. RHtriangle Fourier-transform-based DFT integration. RHtriangle First-principles molecular dynamics (MD) simulation of water.We have proposed the Gaussian and Fourier transform (GFT) method as an efficient calculation technique for the Hartree term under the periodic boundary condition (PBC), and discuss its analytical energy-gradient formalism in this Letter. We also discuss a Fourier transform technique to estimate the matrix element of the density functional theory (DFT) exchange correlation term. A first-principles molecular dynamics (MD) simulation of water at ambient conditions is executed using those methodologies.
Ab initio anharmonic calculations of vibrational frequencies of benzene by means of efficient construction of potential energy functions by Koichi Ohno; Satoshi Maeda (322-326).
Benzene undergoes strong vibronic interactions, which has been a cause of unbelievably difficult problems in assignment and prediction of in-plane vibrations including so called b2u Kekulé modes. Present ab initio anharmonic calculations excellently solved this problem to give an average frequency error of 3.5cm−1.Display Omitted►Ab initio anharmonic potentials for benzene were very efficiently created to the sixth order terms. ► Sampling directions for anharmonic corrections were effectively searched by the SHS method. ► Planar fundamental frequencies of benzene were reproduced with a RMS error of 3.5 cm−1. ► Various methods calculating vibrations of benzene were compared for vibronic characteristics. ► Techniques and criteria establishing well balanced anharmonic potentials were proposed.An efficient technique constructing anharmonic potential energy functions was applied to ab initio vibrational analysis of benzene. Anharmonic potentials including the 6-order terms, much higher than the full quartic force field, were automatically generated by a second-order algorithm using the scaled hypersphere search method, and vibrational calculations were performed at the level of VQDPT[1+2]. In comparison with previously reported anharmonic calculations, the present approach gave an excellent ab initio result for in-plane modes including the b2u so called Kekulé mode. Characteristic properties of various approaches were discussed in connection with the anharmonic effects and the strong vibronic effects.
Dielectric spectroscopy of water at low frequencies: The existence of an isopermitive point by A. Angulo-Sherman; H. Mercado-Uribe (327-330).
Display Omitted► Dielectric constant of water at low frequencies. ► It is found that there is a frequency where the dielectric constant does not change with temperature. ► We called this the isopermitive point. ► At this point, the effects of ions and dipoles in the dielectric response of water compensate each other.We have studied the relative permittivity of water from 100 Hz to 1 MHz. We have found that there is a frequency where this parameter is independent of temperature, and called this the isopermitive point. Below this point the relative permittivity increases with temperature, above, it decreases. To understand this behavior, we may consider water as a system of two species: ions and dipoles, the first giving rise to the so-called Maxwell–Wagner–Sillars effect, the second obeying the Maxwell–Boltzmann statistics. At the isopermitive point, the effects of both mechanisms in the dielectric response compensate each other.
Relativistic corrections for positronium–atom complexes by Shiro L. Saito (331-335).
Display Omitted► The Breit–Pauli Hamiltonian is extended to positron-and positronium-atom complexes. ► The energy differences between the high- and low-spin states of PsB-PsO, PsAl-PsS, PsGa-PsSe, and PsIn-PsTe are obtained. ► Relativistic corrections to the dissociation energies of PsB-PsF, PsAl-PsCl, PsGa-PsBr, and PsIn PsI are obtained. ► In some cases the relativistic corrections are capable of changing positive dissociation energies to negative values.The Breit–Pauli Hamiltonian for many-electronic positron- and positronium–atom complexes is considered and is applied to the neutral positronium–atom complexes PsB–PsF, PsAl–PsCl, PsGa–PsBr, and PsIn–PsI. For these complexes, energy differences between the high- and low-spin states which arise from different positronic spin coupling schemes are estimated, and relativistic corrections for the dissociation energies into a positronium and a neutral atom. The relativistic effects are obtained from first-order perturbation theory based on the Hartree–Fock description. The influence of correlation effects on the dissociation energies for positronium halides are also discussed.
On a class of distance-based molecular structure descriptors by Franka Miriam Brückler; Tomislav Došlić; Ante Graovac; Ivan Gutman (336-338).
Display Omitted► Q-indices aim at eliminating a general shortcomming of Wiener-type indices. ► Q-indices consist of contributions of vertex pairs that exponentially decrease with their distance. ► Q-indices are related to the Hosoya polynomial.A new class of distance-based molecular structure descriptors is put forward, aimed at eliminating a general shortcoming of the Wiener and Wiener-type indices, namely that the greatest contributions to their numerical values come from vertex pairs at greatest distance. The Q-indices, considered in this work, consist of contributions of vertex pairs that exponentially decrease with distance. It is shown that the Q-indices are equal to the Hosoya polynomial H(G,λ), evaluated at a pertinently selected value of the variable λ.
Author Index (339-344).