Chemical Physics Letters (v.625, #C)

Contents (iii-xii).

Free energy basin-hopping by K.H. Sutherland-Cash; D.J. Wales; D. Chakrabarti (1-4).
Display OmittedA global optimisation scheme is presented using basin-hopping with the acceptance criterion based on approximate free energy for the corresponding local minima of the potential energy. The method is illustrated for atomic and colloidal clusters and peptides to examine how the predicted global free energy minimum changes with temperature. Using estimates for the local free energies based on harmonic vibrational densities of states provides a computationally effective framework for predicting trends in structure at finite temperature. The resulting scheme represents a powerful tool for exploration of energy landscapes throughout molecular science.

The boron–carbon–nitrogen heterocyclic rings by Ambrish Kumar Srivastava; Neeraj Misra (5-9).
The heterocyclic rings containing B, C and N atoms, also known as azaborines, are systematically studied. The electronic properties of these BCN rings are explored by using second order perturbation theory and their aromaticity is discussed by the nucleus independent chemical shifts. These heterocyclic rings are found to be chemically more reactive than benzene and borazine, due to smaller HOMO–LUMO gap and non-zero dipole moment. However, the aromaticity of these BCN rings is less than benzene but two or three times that of borazine.

A new 2D NMR technique cited as CH-RES-TOCSY, for complete unraveling the spectra of enantiomers and for the measurement of structurally important C―H RDCs is reported. The spectral overlap and complexity of peaks were reduced by the blend of selective excitation and homo-decoupling. Differential values of C―H RDCs of enantiomers (R and S) are exploited to separate the enantiomeric peaks. The complete unraveling of the spectra of both the enantiomers is achieved by incorporating a TOCSY mixing block prior to signal acquisition. The additional application of the method is demonstrated for the assignment of symmetric isomers.

Enhanced spin thermoelectric effects in BN-embedded zigzag graphene nanoribbons by Y.S. Liu; W.Q. Zhou; J.F. Feng; X.F. Wang (14-19).
(a) Two-probe structure of the ZGNR embedded by four BN bonded pairs. (b) The corresponding transmission spectrum. (c) Charge current I C and (d) spin current I S as functions of ΔT at room temperature. At ΔT  = 171 K, I C is zero, while I S has a positive value.Display OmittedSpin thermoelectric effects in BN-embedded zigzag graphene nanoribbons (ZGNRs) are studied by a first-principles method. The multiple spin-up (spin-down) quasi-bound states below (above) the Fermi level can be introduced by the BN bonded pairs, leading to the dip structures in the transmission spectra. We further find that the spin thermoelectric effect at the Fermi level is obviously stronger than the corresponding charge thermoelectric effect. As the more BN bonded pairs are gradually doped from the edge to middle regions, the spin thermoelectric figure of merit (FOM) can be improved up to ten times than the charge thermoelectric FOM. A pure spin current can also be achieved in the BN-embedded ZGNRs under an external thermal bias.

Interaction energies (E int) were evaluated for n-alkanes dimers (C1–C10) using DFT-D, different functionals, and several basis sets. In addition, calculations were also carried out with DFTB-LD and MM3 and OPLS-AA force fields. Results show linear correlations of E int with respect to those obtained from literature at high levels of theory (MP2 and CCSD(T)). Relationships between E int and experimental heats of vaporization (ΔH v ) and critical temperatures (T c ) were obtained with MP2, DFT-D, MM and DFTB-LD. This leads to good extrapolations for hairpin-hexadecane using MM3 and DFTB-LD for ΔH v and T c , respectively. Dispersion in DFT is discussed.

Reaction kinetics of the CN radical with primary alcohols by Erik Janssen; John F. Hershberger (26-29).
The kinetics of the reactions of CN radicals with several small primary alcohol molecules were studied by transient infrared laser absorption spectroscopy. Direct time-resolved detection of CN was used to determine total rate constants. In addition, HCN and DCN products were detected in order to estimate the branching ratios of the CN + CH3OH reaction. We find that abstraction of an alkyl hydrogen atom dominates the CN + CH3OH reaction, but a small, ∼8% yield of hydroxyl hydrogen abstraction is also observed.

Antioxidant properties of xanthones extracted from the pericarp of Garcinia mangostana (Mangosteen): A theoretical study by Nguyen Minh Thong; Duong Tuan Quang; Ngoc Hoa Thi Bui; Duy Quang Dao; Pham Cam Nam (30-35).
A theoretical study on antioxidant properties of fourteen xanthones extracted from the pericarp of G. Mangostana has been performed. Three main reaction mechanisms are investigated: hydrogen atom transfer (HAT), single electron transfer–proton transfer (SETPT) and sequential proton loss electron transfer (SPLET). The O―H bond dissociation enthalpy (BDE), ionization energy (IE), proton affinity (PA) and electron transfer energy (ETE) parameters were computed in gas phase and water. The results show that HAT would be the most favorable mechanism for explaining antioxidant activity of xanthones in gas phase, whereas the SPLET mechanism is thermodynamically favored in water.

Reduction of graphene oxide film with poly (vinyl alcohol) by Sung Il Ahn; Kukjoo Kim; Ju Ra Jung; Keong Yeon Kang; Seon Min Lee; Ji Ye Han; Kyung Cheol Choi (36-40).
Graphene oxide (GO), products with various proportions of polyvinyl alcohol (PVA), was characterized to obtain verified patterns of reduced graphene oxide. FT-IR spectra indicated that PVA could lower the reduction temperature of GO by at around 70 °C. New peaks near D band and overlapped G band in the Raman spectra appear to indicate that some parts of PVA interact with GO. The sheet resistance of GO/PVA showed that the GO/PVA ratio was optimal between 1/0.25 and 1/2. Using GO/PVA, we printed a line on PET, and after annealing at 140 °C, it achieved a resistance of 23 kΩ/cm.

High-resolution nuclear magnetic resonance spectroscopy is widely used to analyze molecular structures and compositions. Here, we present a pulse sequence that simultaneously detects both intermolecular zero- (iZQC) and double-quantum coherence (iDQC) signals in inhomogeneous fields, offering high-resolution spectra in absolute-value mode after data processing. In comparison with pure iZQC or iDQC spectra, the proposed sequence can provide nearly doubled spectral resolutions and suppressions of strong coupling artifacts. It is the first time that iZQC and iDQC signals can be simultaneously obtained in one single measurement. This sequence may provide an alternative approach to studies of in situ inhomogeneous chemical systems.

Opening of an icosahedral boron framework: A combined infrared spectroscopic and computational study by Matias R. Fagiani; L. Liu Zeonjuk; Tim K. Esser; Detlef Gabel; Thomas Heine; Knut R. Asmis; Jonas Warneke (48-52).
The opening of an icosahderal boron cage in the periodinated closo-dodecaborate B12I12 2− upon deiodination is studied using cryogenic ion trap vibrational spectroscopy combined with electronic structure calculations. Comparison of simulated vibrational spectra to the infrared photodissociation spectra of messenger-tagged B12I12 2− and B12I n (n  = 7–9) formed by skimmer collision induced dissociation shows that the larger clusters absorb exclusively below 975 cm−1 and hence exhibit quasi-icosahedral B12-cage structures, while the higher energy absorptions in-between 1000 and 1300 cm−1 observed for n  = 7 can only be recovered by considering a breakup of the icosahedral cage upon deiodination from n  = 8 to n  = 7.

The Letter reports another approach to grow vertically aligned millimeter length multiwalled carbon nanotubes (MWCNT) using chemical vapor deposition technique. In this stack growth, the first grown MWCNT layer is observe to have been lift-off from the substrate surface by the newly grown underneath layer as a result of the diffusion of iron catalyst and carbon source through the first layer. The first grown layer acts as a permeable membrane allowing the catalyst vapor and carbon to reach the bottom layer and the top surface of the substrate, resulting in the growth of another layer of MWCNT underneath it.

Size dependent nonlinear optical absorption in BaTiO3 nanoparticles by Tesfakiros Woldu; B. Raneesh; P. Sreekanth; M.V. Ramana Reddy; Reji Philip; Nandakumar Kalarikkal (58-63).
We present nonlinear optical absorption properties of BaTiO3 nanoparticles of different sizes prepared by the modified polymer precursor method. Structural properties of the samples were characterized using XRD and TEM, and optical properties by UV–visible light absorption. Nonlinear optical properties of the samples were measured by the single-beam open aperture Z-scan technique using 5 ns laser pulses at 532 nm. Results show that all samples exhibit a size dependent nonlinear optical response. Optical limiting efficiency increases with grain size and has a strong dependence on the structural phase of the particles. Nonlinear optical absorption is found to be enhanced when the particles undergo a transition from the cubic to the tetragonal phase.

Electronic and optical properties of the five most stable C96 isomers by Ming Qian Wang; Xin Zhou; Wei Quan Tian; John D. Goddard (64-68).
Electronic spectra, and the nonlinear optical (NLO) properties of five isomers of C96 were investigated using density functional theory and semi-empirical methods. The simulated electronic spectra of C 2 :181, C 1 :144, C 1 :145, and C 2 :176 have strong absorptions above 500 nm. The electronic spectra of C 1 :144, C 1 :145, and C 2 :176 are similar. The third-order NLO properties of the isomers were analyzed under an external field. Small structural differences between C 1 :144 and C 1 :145 result in NLO responses that occur at different external fields. Entropy effects on the NLO properties are significant. The NLO responses of the five most stable isomers differ in the concentration averaged sample.

Strain in strain-free benzenoid hydrocarbons: The case of phenanthrene by Slavko Radenković; Ivan Gutman; Slađana Đorđević (69-72).
Display OmittedBenzenoid molecules possessing bays are traditionally considered as ‘strain-free’. Yet, repulsion between the two bay H-atoms affects the length of the near-lying carbon–carbon bonds. A method is developed to estimate the energy of this strain. In the case of phenanthrene its value was found to be about 7 kJ/mol.

Growth and mechanism of branched FeWO4@FeS core–shell nanostructures by Jingwen Qian; Zhijian Peng; Xiuli Fu (73-77).
Branched FeWO4@FeS core–shell nanostructures were synthesized on silicon substrates sputtered with approximately 5 nm of iron thin film via thermal evaporation of WO3 and S powder at 1050 °C in a tube furnace. Both the trunk and branch of the nanostructures are of uniform morphology and well-crystalline structure with diameters in the range of 100–400 nm and lengths up to tens of micrometers. It was proposed that the growth mechanism of the nanostructures was a combination of the classic vapor–liquid–solid and vapor–solid processes.

The strong solvent polarity dependence observed in the nonradiative decay rates of Bis[4-(dimethylamino)phenyl]squaraine (SQ-DMA) had previously been explained by the twisted intramolecular charge transfer mechanism. However, our recent theoretical study did not support this mechanism. We theoretically study the possibility of electron-driven proton transfer (EDPT) processes between an alcohol solvent molecule and the CO groups of SQ-DMA using a complex model. The results actually support the EDPT mechanism that proceeds via two nonadiabatic transitions: the first from the locally excited (π → π*) state of SQ-DMA to the charge transfer (CT) state, and the second from the CT to S0 states.

Plasmon-driven growth of various silver seed nanoparticles (spherical, flat and elongated) has been carried out in the solution containing silver cations and citrate. Although the growth of different seed nanoparticles has been carried out in the same conditions, the initial difference in the shape of seed nanoparticles leads to formation of different structures, which give significantly different surface-enhanced Raman scattering (SERS) spectra of adsorbed pyridine. Differences between measured SERS spectra are probably due to different efficiency of oxidation of various nanoparticles by ambient air. Light-induced transformation of silver sols may be also used to significantly increase their SERS activity.

Big data reduction by fitting mathematical functions by Anita Rágyanszki; Klára Z. Gerlei; Attila Surányi; András Kelemen; Svend J. Knak Jensen; Imre G. Csizmadia; Béla Viskolcz (91-97).
The potential energy surface associated with internal rotation of a pair of geminal functional groups was studied using electron structure calculations. The functional groups were attached to a methylene carbon and were chosen as saturated hydrocarbons, unsaturated hydrocarbons and heteroatom containing moieties like amide bonds in various orientations. For the majority of the studied compounds extended Fourier expansions, augmented with Gaussian functions were needed to achieve accuracy within a few kJ/mol. The present letter aims to take the first steps of a bottom up solution for protein folding by finding the functions of small peptide residues.

Applicability of Mulliken's formula for photoinduced and intramolecular charge-transfer energies by Ioannis D. Petsalakis; Giannoula Theodorakopoulos; Omri Buchman; Roi Baer (98-103).
The applicability of Mulliken's theory for photoinduced as well as intramolecular charge-transfer states is examined for several systems of interest by comparing its predictions to TDDFT excitation energies, obtained using functionals appropriate for charge-transfer (CT) states. The results show that it is possible to estimate the energy of the CT state of a donor–acceptor pair on the basis of information on the separate donor and acceptor moieties, along with structural data, within 0.3 eV of TDDFT values. The novelty and usefulness of the proposed method lies mainly in PET applications where the TDDFT determination of the CT state is challenging.

Thermal dissociation of gas phase iron oxide cluster ions, Fe n O m + (n  = 2–6), was observed by mass spectrometry. The dissociation processes were investigated by temperature-programmed desorption (TPD) measurements for different sized clusters. Oxygen molecules were found to be released from the cluster ions. The threshold energy required for dissociation, determined by analyzing TPD, was compared with the energies obtained by experiments of collision-induced dissociation and by calculations of density functional theory. The agreement of the energies indicates that the oxygen atoms bonded to the terminal site of clusters are more readily released into the gas phase than those in the bridge site.

Extraction of hydrofluoric acid (HF) from oils is a drastically important problem in petroleum industry, since HF causes quick corrosion of pipe lines and brings severe health problems to humanity. Some ionic liquids (ILs) constitute promising scavenger agents thanks to strong binding to polar compounds and tunability. PM7-MD simulations and hybrid density functional theory are employed here to consider HF capture ability of ILs. Discussing the effects and impacts of the cation and the anion separately and together, we evaluate performance of imidazolium acetate and outline systematic search guidelines for efficient adsorption and extraction of HF.

Display OmittedThe quantum mechanical charge-field molecular dynamics (QMCF-MD) simulation method was employed to study the hydration properties of gadolinium(III) and terbium(III). Slight differences of the solvation shells’ structural and dynamical properties were discovered. While the Ln―O radial distribution functions are in excellent agreement with recent experiments, average coordination numbers of 8.5 (Gd) and 8.4 (Tb) were found. Vivid ligand exchange dynamics along with rapid intrashell rearrangements were observed, underlined by mean residence times in the picosecond range, which is characteristic for trivalent lanthanoides according to quantum mechanical simulations. Vibrational analysis yielded ion-water force constants below 100 N m−1.

Display OmittedIn this Letter, non-equilibrium rates of Zeldovich reactions N2(i) + O ⇄ NO + N, O2(i) + N ⇄ NO + O in shock heated air flows are studied on the basis of state-to-state vibrational distributions. The comparison of reaction rate coefficients computed using state-to-state and thermally equilibrium vibrational distributions behind shock waves and different state-specific models for exchange reactions is presented. Reaction rates are calculated for various conditions before a shock front including a particular case of vibrationally excited free stream molecules. An essential influence of initial vibrational excitation of reactants on reaction rates behind a shock wave is shown.

Influence of charge state on catalytic properties of PtAu(CO) n in reduction of SO2 by CO by Guoping Gao; Shihao Wei; Xiangmei Duan; Xiaoyin Pan (128-131).
Display OmittedSearching excellent catalysts to remove both SO2 and CO of industrial exhaust simultaneously is of great significance to environment. The catalytic activities of clusters PtAu(CO) n (n  = 0–3) and their anion counterparts, to the reduction of SO2 by CO, are compared based on density-functional theory calculations. The d electrons of the anion catalysts are identified to be closed shell once CO pre-adsorbed, while the d electrons of the neutral clusters’ are open-shell configuration. The result is that the negatively charged [PtAu(CO) n ] clusters show less excellent catalytic properties than their corresponding neutral catalysts. The d-band center of the neutral PtAu(CO) n with uncoupled d electrons shift down relative to the Fermi level after sulfur dioxide adsorption, which therefore enhances the catalytic properties. Finding from this research will provide guard line to tune the catalytic properties of Pt/Au catalysts.

The potential energy surfaces of (H2O)7 and (H2O)8 clusters, as described by a one-electron model Hamiltonian, are thoroughly explored. The local minima and first-order saddle points are located and then used to construct disconnectivity graphs. The minimum energy pathways connecting the transition states and local minima are identified and discussed in the context of existing experimental observations reported in the literature.

The hydration structure and thermodynamics associated with the ion pairing between a halide anion and the tetramethyl ammonium cation in water are investigated by molecular dynamics simulations. Correlating the potential of mean force and different energy terms with the structure of the ion pair as a function of the interionic distance provides molecular level insight into recent experiments that shows increased affinity between a larger anion and the hydrophobic cation.

To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.

Irreversible temperature quenching and antiquenching of photoluminescence of ZnS/CdS:Mn/ZnS quantum well quantum dots by X. Ding; R.C. Dai; Z. Zhao; Z.P. Wang; Z.Q. Sun; Z.M. Zhang; Z.J. Ding (147-150).
An experimental observation on irreversible thermal quenching and antiquenching behavior is reported for photoluminescence of ZnS/CdS:Mn/ZnS quantum well quantum dots. The dual-color emissions, a blue emission centered at 430 nm and a Mn2+ 4 T 1  →  6 A 1 orange emission at 600 nm, were found to have different dependences of emission intensity on temperature in the range of 8–290 K. During temperature cooling/heating process, besides the usual thermal quenching, the orange emission shows stronger antiquenching behavior than that of blue emission in a certain temperature range.

Fluorenyl porphyrins for combined two-photon excited fluorescence and photosensitization by Olivier Mongin; Vincent Hugues; Mireille Blanchard-Desce; Areej Merhi; Samuel Drouet; Dandan Yao; Christine Paul-Roth (151-156).
The two-photon absorption (2PA), the luminescence and the photosensitization properties of porphyrin-cored fluorenyl dendrimers and meso-substituted fluorenylporphyrin monomer, dimer and trimer are described. In comparison with model tetraphenylporphyrin, these compounds combine enhanced (non-resonant) 2PA cross-sections in the near infrared and enhanced fluorescence quantum yields, together with maintained singlet oxygen generation quantum yields. ‘Semi-disconnection’ between fluorenyl groups and porphyrins (i.e. direct meso substitution) proved to be more efficient than non-conjugated systems (based on efficient FRET between fluorenyl antennae and porphyrins). These results are of interest for combined two-photon imaging and photodynamic therapy.

In this work, the multiple linear regression (MLR) method was applied for quantitative structure–property relationship (QSPR) modeling and predicting vertical detachment energy of superhalogen anions with descriptors calculated from the molecular structure for the first time. The square of the correlation coefficient (R 2  = 0.975), the cross-validated correlation coefficient ( Q CV 2 = 0.859 ), and the square of correlation coefficients of the test set ( Q EXT 2 = 0.960 ) demonstrated the reliability of the model. Since the developed QSPR model does not require 3-D structure generation and thus structure optimization with extensive quantum mechanical calculations it can be further used for relatively fast designing of new superhalogen anions.

Photodetachment velocity map imaging of the 1A′ ←  2A′ transition in the AuOH anion by Bradley R. Visser; Matthew A. Addicoat; Jason R. Gascooke; Xinxing Zhang; Kit Bowen; Warren D. Lawrance; Gregory F. Metha (164-167).
A velocity map imaging spectrometer was used to investigate the ( X ˜ 1 A ′ AuOH + e − ← X ˜ 2 A ′  AuOH − + h ν ) photodetachment transition at 560 nm. The extracted spectrum shows a well-defined vibrational progression, ω 3′, with a frequency of 567(5) cm−1. The adiabatic electron affinity is assigned to 1.695(5) eV and the presence of a vibrational hot band allows the determination of the corresponding anion frequency to 431(20) cm−1. This represents a re-assignment of the photoelectron spectrum previously reported by Zheng et al. [1]. A Franck–Condon simulation based on coupled cluster calculations is in excellent agreement with the observed vibronic progression.

The effect of the particle size reduction on ferromagnetic (FM) phase transition and magnetocaloric properties of the perovskite manganite La0.9Sr0.1MnO3 was studied. Indeed, it has been proven that the maximum of entropy change ( − Δ S M max ) and the relative cooling power (RCP) are strongly affected by the particle size. The measured entropy change (ΔS M) was analyzed using Landau theory. The obtained results have been explained in terms of core–shell model. Moreover, H12 (La0.9Sr0.1MnO3 annealed at 1200 °C) having large RCP and ΔS M values could be an interesting cooling material.

Semiclassical dynamics of electron attachment to guanine–cytosine base pair by Tomohiro Honda; Yusuke Minoshima; Yuki Yokoi; Toshiyuki Takayanagi; Motoyuki Shiga (174-178).
Electron attachment dynamics to the guanine–cytosine (G–C) base pair in the gas phase is studied using DFT and molecular dynamics. The potential energy surface of the G–C anion is constructed with the empirical-valence-bond method using force-field information obtained from long-range corrected DFT calculations. Ring-polymer molecular dynamics simulations predict that the initial dipole-bound anion readily converts into the valence-bound anion within 0.1 ps and proton-transfer occurs subsequently within 10 ps. The same process was found in classical simulations, but on a much slower time scale. This result suggests that nuclear quantum effects are important in understanding DNA damage by low-energy electrons.

Characterisation of the weak halogen bond in N2⋯ICF3 by pure rotational spectroscopy by Jonathan P. Anable; David E. Hird; Susanna L. Stephens; Daniel P. Zaleski; Nicholas R. Walker; Anthony C. Legon (179-185).
Rotational spectra of the symmetric-top complexes 14N2⋯ICF3 and 15N2⋯ICF3 were observed and analysed to give rotational constants B 0, centrifugal distortion constants D J and D JK , and nuclear quadrupole coupling constants χ aa (X). Significantly different values of χ aa (14Ni) and χ aa (14No) establish chemical inequivalence of the two 14N nuclei and an average zero-point oscillation angle of 19.8(5)° for the N2 subunit. A distance r N⋯I  = 3.443(1) Å only slightly shorter than the sum of the N and I van der Waals radii, a small intermolecular stretching force constant k σ  = 2.94 N m−1 and negligible charge redistribution on complex formation demonstrate the presence of a weak halogen bond.

Organic solvent simulations under non-periodic boundary conditions: A library of effective potentials for the GLOB model by Giordano Mancini; Giuseppe Brancato; Balasubramanian Chandramouli; Vincenzo Barone (186-192).
We extend the library of solvents that can be treated using the GLOB (general liquid optimized boundary) method, that allows to perform MD simulations under non-periodic boundary conditions (NPBC) optimizing effective potentials between explicit molecules and the boundary for four organic solvents: CHCl3, CCl4, CH3OH and CH3CN. We show that GLOB allows reducing the number of explicit solvent shells to be included, while yielding results comparable with PBC and significant advantages over simulations without explicit boundaries. Finally, we provide polynomial fittings for all available GLOB effective potentials (including SPC water) to simplify their implementation in NPBC MD simulations.

Theoretical analysis of a reaction–diffusion process involved in packed bed photobioreactor with immobilized-cell is presented. Good approximate analytical expressions for the non-linear reaction–diffusion equations for substrate and product concentrations are derived. Modified Adomian decomposition method is used to derive the dimensionless concentration under steady-state condition. To see the efficiency, our analytical results are compared with the numerical results. For all different concentrations, the analytical results matched well with the simulated results. The close matching of simulated and the analytical data shows that our proposed solution is able to simulate the dynamic performance of system using the parameters.