Chemical Physics Letters (v.578, #C)

Contents (iii-x).

Molecular applications of attosecond laser pulses by Franck Lépine; Giuseppe Sansone; Marc J.J. Vrakking (1-14).
We review the present state of the application of attosecond lasers in molecular physics. Following the first synthesis and characterization of attosecond laser pulses a little more than a decade ago, the first applications in molecular physics have been published only in the last few years. These have yielded new insight into the coupling of multiple electronic degrees of freedom and that of electronic and nuclear degrees of freedom on the attosecond to few-femtosecond timescale. We review these first experiments as well as theoretical work that was carried out during the same period, and sketch some future molecular applications of attosecond pump–probe spectroscopy.

Collision processes of liquid droplets were observed to study the dynamics of molecules in solution with an apparatus which allows us to observe the collision sequence stroboscopically with time resolution of ∼1 μs. The collision sequences of water–water and ethanol–water droplets were observed by production of droplets through piezo-driven nozzles. Formation of characteristic protrusion was traced in the collision of ethanol and water droplets. A model mechanism of protrusion in these systems is proposed based on the observed behavior indicating release deformation of surface tension that propagates as a capillary wave on the droplet surface.

Display OmittedWe present a quantum scattering calculation of initial-state-resolved reaction probabilities, integral cross section, initial state selected reaction rate constants and thermal rate constant for exchange and depletion channels of the H+ND reaction. The calculations are carried out using Coriolis coupling (CC) method on the modified NH2 A ̃ 2 A 1 potential energy surface(PES). The initial state selected reaction probabilities are calculated for 0.0–0.5 eV of collision energy range. The reaction probabilities for depletion channel shows some sharp and large resonances associated with long-lived collision complexes, as compared to exchange channel. Integral cross sections for both reactions depend strongly on initial rotational states. The calculated thermal reaction rate constant for the depletion channel is in a good agreement with the values previously obtained by the centrifugal sudden approximation, experimental and semiclassical results.

Display OmittedInfrared spectrum of the chloromethylene hydroperoxide cation, HC(Cl)OOH+ in solid argon is reported. The cation is produced by co-condensation of dichloromethane and dioxygen mixtures with high-frequency discharged argon at 4 K followed by visible light excitation. On the basis of isotopic substitutions as well as quantum chemical frequency calculations, absorptions at 3452.7, 3052.0, 1499.6, 976.9, 855.4 and 956.1 cm−1 are assigned to the O–H, C–H, C=O, C–Cl and O–O stretching and out-of-plane CH wagging vibrations of the chloromethylene hydroperoxy cation. The cation was predicted to have a singlet ground state with planar Cs symmetry.

Rate coefficients of the reactions of OH radicals and Cl atoms with 2,2,2 trifluoroethyl butyrate have been determined at 298 K and atmospheric pressure. The decay of the organics was followed using a gas chromatograph with a flame ionization detector (GC-FID) and the rate coefficients were determined using the relative rate method. This is the first kinetic study for these reactions under atmospheric pressure. The kinetic data are used to update the correlation k OH vs. k Cl for different fluoroesters, to develop reactivity trends in terms of halogen substitution and to estimate the tropospheric lifetime of 2,2,2 trifluoroethyl butyrate.

Influence of transition metal coordination on halogen bonding: CSD survey and theoretical study by Yanhua Wang; Weihong Wu; Yingtao Liu; Yunxiang Lu (38-42).
Display OmittedDensity functional theory calculations at the level of M06 have been carried out to investigate the influence of transition metal coordinate on halogen bonding. It was found that the introduction of coordination forces leads to much stronger halogen bonds. This effect has been analyzed in detail by the geometric, energetic, electrostatic potential, and AIM properties of the complexes. In addition, some crystal structures extracted from the Cambridge Structural Database were selected to provide experimental evidence of the combination of the two interactions.

We identified the H-bonded structure of the pyrrole–acetone 2-1 cluster by IR spectroscopy and quantum chemical calculations. The observed NH stretches at 3335 and 3406 cm−1 can be reproduced by the calculated ones of the cyclic structure formed by N–H⋯O=C and N–H⋯π H-bonds. We discuss the donor–acceptor interactions of the N–H⋯O=C H-bonds in cyclic clusters based on natural bond orbital analysis. The interaction makes a dominant contribution to the H-bond in the 2-1 cluster. This is in sharp contrast to the 1-2 cluster, in which the πσ interaction also plays a role in H-bond formation.

Display OmittedThe structures and local aromaticity of some conjugated polycyclic hydrocarbons (from the butadienoid, acene, and phenylene series) are studied using ab initio MO and density functional methods. The aromaticities of the molecules are estimated using three indices: the nucleus-independent chemical shift (NICS), the harmonic oscillator model of aromaticity (HOMA), and the index of deviation from aromaticity (IDA). Assessment of the relationships between the structures and the aromatic indices shows that the IDA values correspond best to the characteristics of the conjugated polycyclic hydrocarbon structures.

Electron attachment to the dipeptide alanyl-glycine by Janina Kopyra; Constanze König-Lehmann; Eugen Illenberger (54-58).
Dissociative electron attachment (DEA) to the simplest hetero dipeptide (alanyl-glycine) is studied by means of a beam experiment. The results are compared with those previously obtained from the single compounds alanine and glycine from which the dipeptide is formed. In addition to the resonances and DEA products formed from the single molecules, alanyl-glycine exhibits new resonant features right at threshold (≈0 eV energy) and additional fragments which arise from the cleavage of the peptide and N–Cα bond. A further strong reaction leads to the loss of a neutral water molecule. These results clearly demonstrate that the dipeptide is considerably more sensitive towards low energy electrons than its components, which is of particular relevance with respect of radiation damage of biomolecular systems.

The electronic properties of the substitutional 1B-group atoms in cubic SiC are analyzed by first-principles. One of the main effects of these substitutions is to generate bands in the energy band gap, which could have interesting optoelectronic properties. Nevertheless, because the intermediate bands widths are less than the semiconductor gap the correlation effects and a site deformation around the impurities could be very important. These bands could split into two sub-bands: a full one and an empty one. From our results, these effects or a combination of them split the bands in the energy band gap.

Quantum tunneling and low temperature delayed recombination in scintillating materials by E. Mihóková; L.S. Schulman; V. Jarý; Z. Dočekalová; M. Nikl (66-69).
Display OmittedWe study the origin of the low temperature contribution to delayed recombination decay in scintillating materials. This contribution represents the loss of fast scintillation light even at the lowest temperatures. The possible role of quantum effects, as previously suggested, is tested both experimentally and theoretically. The experiments were performed on Lu2Si2O7:Pr3+ crystals. The results suggest that quantum tunneling between the luminescence center and a nearby defect is a good candidate for explaining the observed phenomena.

Raman and fluorescence correlative microscopy in polarized light to probe local femtosecond laser-induced amorphization of the doped monoclinic crystal LYB:Eu by Nicolas Marquestaut; Marc Dussauze; Yannick Petit; Arnaud Royon; Véronique Jubera; Philippe Veber; Michel Couzi; Vincent Rodriguez; Thierry Cardinal; Lionel Canioni (70-75).
We report on Raman and fluorescence microscopy in polarized light in the oriented Eu3+-doped LYB monoclinic crystal after femtosecond laser irradiation. Differential spectra denote large bands typically centered on the pristine glass Raman and fluorescence lines, proving the crystal structure alteration and the significant existence of a laser-induced glassy environment of the Eu3+ ions inside the laser-induced modified zone. Such approach should be annotated for future control of direct laser writing onto biaxial crystals such as LYB:Eu. This is of tremendous interest to probe in situ local modifications, in order to develop new laser-induced optical properties in materials for further photonics applications.

We have studied BGO:Nd electronic structure in the energy region around the band gap, treating f electrons in two different ways, first as localized (using the open-core approximation), and second as delocalized. The aim is to investigate the changes in electronic properties of the BGO:Nd by analyzing the character and the position of the electronic states introduced by Nd. DFT was used within LAPW basis functions. The effects of exchange and correlation were simulated according to the GGA. Optical properties of BGO:Nd were also analyzed. The absorption spectrum is found to be similar for both treatments.

Pseudo Dirac dispersion in Mn-intercalated graphene on SiC by M. Upadhyay Kahaly; T.P. Kaloni; U. Schwingenschlögl (81-84).
Display OmittedThe atomic and electronic structures of bulk C6Mn, bulk C8Mn, and Mn-intercalated graphene on SiC(0 0 0 1) and SiC ( 0 0 0 1 ¯ ) are investigated by density functional theory. We find for both configurations of Mn-intercalated graphene a nonmagnetic state, in agreement with the experimental situation for SiC(0 0 0 1), and explain this property. The electronic structures around the Fermi energy are dominated by Dirac-like cones at energies consistent with data from angular resolved photoelectron spectroscopy [Gao et al., ACS Nano. 6 (2012) 6562]. However, our results demonstrate that the corresponding states trace back to hybridized Mn d orbitals, and not to the graphene.

Influence of activated carbon surface oxygen functionalities on SO2 physisorption – Simulation and experiment by Sylwester Furmaniak; Artur P. Terzyk; Piotr A. Gauden; Piotr Kowalczyk; Grzegorz S. Szymański (85-91).
The influence of the gradual oxidation of carbons on SO2 physisorption was studied, by comparison of experimental and simulated SO2 adsorption isotherms. The results confirmed a significant impact of surface groups on the SO2 adsorption. The simulations also revealed a similar, to that observed experimentally, effect of the increase in the percentage of the smallest micropores on adsorption isotherms. The isotherms were analysed using the CMMS model. The conclusion is that this model seems to be a good and sensitive tool for studying SO2 physisorption mechanism since a very good qualitative agreement between the experimental and simulated data was observed.

Scalable properties of metal clusters: A comparative DFT study of ionic-core treatments by Remi Marchal; Ilya V. Yudanov; Alexei V. Matveev; Notker Rösch (92-96).
To assess various ionic-core approximations we carried out density functional calculations on a series of octahedral palladium and gold model clusters M n with n  = 13–147. We compared results for average bond lengths, cohesive energies, vertical ionization potentials, and electron affinities to the corresponding all-electron scalar relativistic results. We used extrapolated bulk values to compare with experiments. The results of the projector-augmented wave method agree best with the all-electron results. When modeling palladium–gold nanoalloy particles, one should keep in mind that current ECP or PAW modeling of palladium moieties appears to be more accurate than modeling of gold species.

Transport properties of chemically functionalized graphene nanoribbon by C.Q. Qu; C.Y. Wang; L. Qiao; S.S. Yu; H.B. Li (97-101).
We perform a theoretical calculation in chemically functionalized zigzag graphene nanoribbons, which are terminated with different single atoms or groups, using density functional theory and nonequilibrium Green’s function techniques. The calculation results reveal that these different species of atoms and groups have a significant impact on the edge states near Fermi level as well as the spin-dependent electronic transport properties. The calculated IV curves exhibit negative differential resistance, which can be used for application in molecular spin electronic device.

Display OmittedBacteriochlorophyll(BChl)s-c were extracted, isolated and purified from cultured cells of a green photosynthetic bacterium, Chloroflexus (Cfl.) aurantiacus. Their self-aggregates were prepared from a hydrophobic hexane-based solution and the obtained self-aggregate solids were examined by electronic absorption and circular dichroism (CD) spectroscopy as well as atomic force microscopy (AFM). Visible/near-infrared absorption and CD spectra of the BChl-c self-aggregates were very similar to those in cells of Cfl. aurantiacus. AFM analysis indicated that some self-aggregates had rods with a 5-nm diameter and a 3.5-μm length at longest. The rod diameter was identical to that reported for natural chlorosomal rods of Cfl. aurantiacus. Rod self-aggregates of naturally occurring BChls-c with a 5-nm diameter were first reconstructed here in vitro.

We synthesized a new composite of poly sodium 4-styrenesulfonate intercalated graphene oxide for energy storage devices by controlling oxidation time in the synthesis of graphite oxide. Specific capacitance was improved from 20 F/g of the previous composites to 88 F/g of the new composite at the current density of 0.3 A/g. The capacitance retention was 94% after 3000 cycles, indicating that the new composites of high cyclic stability, prominent performance as electric double layer capacitor, and even low resistance could be an excellent carbon based electrode for further energy storage devices.

Methane hydrates and their HF doped analogues by Sukanta Mondal; Santanab Giri; Pratim Kumar Chattaraj (110-114).
Display OmittedA computational study is carried out to simulate methane hydrates as well as to know the effect of HF doping on their stability and structure. By using ab initio molecular dynamics simulation interaction of methane with HF doped clathrate hydrates is studied. The total energy profiles present insights into the stability and structure of methane hydrates. The HF doping increases the stability of the methane hydrates without any distortion of the cage when methane is encapsulated in 512 cages.

SANS study shows that for the equal ionic strength, interactions are largely modified by the tri-valent (Fe3+) and di-valent (Ni2+) ions and comparatively less by the mono-valent (Na+) ions.Bovine serum albumins, at physiological pH, shows a short-range attraction and in addition a long-range electrostatic repulsion among them. These interactions are modified in presence of different counterions. Small angle neutron scattering study shows that for the equal ionic strength, the interactions are largely modified by the tri-valent (Fe3+) and di-valent (Ni2+) ions and comparatively less by the mono-valent (Na+) ions. The effect is nearly similar for the di- and tri-valent ions in comparison with the mono-valent one. The strength of the attractive and repulsive interactions depends strongly on the type of the dissolved ions and salt concentrations.

π-Stacked polyphenolic dimers: A case study using dispersion-corrected methods by I. Bayach; J.C. Sancho-García; F. Di Meo; J.-F.F. Weber; P. Trouillas (120-125).
Display OmittedThe accuracy of dispersion-corrected calculations (DFT-D2, DFT-D3 and DFT-NL) is assessed here, with large basis sets (def2-QZVP) to avoid incompleteness effects, for the most stable structure of a real-world polyphenol dimer chosen as an appropriate model. Natural polyphenols form such complexes with π-stacking playing a key stabilizing role. Our benchmark calculations predict its existence favored by 22–24 kcal/mol with respect to the isolated monomers, mainly driven by both π–π and H-bonding interactions. The adequate comparison of lower-cost DFT-based methods allowed bracketing their expected accuracy. These results thus pave the way towards reliable studies of challenging aggregation processes of natural products.

We showed that biologically important planar Hyp·Hyp base pair (C s ) formed by the enol and keto tautomers of the hypoxanthine tautomerises via the synchronous concerted mechanism through the TS (C 2v ). The five key points were detected and completely investigated along the IRC of the Hyp·Hyp ↔ Hyp·Hyp tautomerisation via the DPT. It was found that intermolecular antiparallel О6Н…О6 and N1H…N1 H-bonds are cooperative and mutually reinforce each other. It was proved that the Hyp·Hyp/Hyp·Hyp base pair is dynamically stable structure with a lifetime 8.2 × 10−12 s and all its six low-frequency intermolecular vibrations are able to develop during this period of time.

Theoretical evidence of photo-induced charge transfer from DNA to intercalated ruthenium (II) organometallic complexes by Agisilaos Chantzis; Thibaut Very; Chantal Daniel; Antonio Monari; Xavier Assfeld (133-137).
Display OmittedThe absorption spectrum of two ruthenium (II) organometallic complexes intercalated into DNA is studied at the quantum mechanic/molecular mechanic level. The macromolecular environment is taken into account as to include geometric, electrostatic and polarization effects that can alter the excitation energy and oscillator strength. The inclusion of DNA base pairs into the quantum mechanic partition allows us for the first time to clearly evidence the presence of charge transfer excited states involving an electron withdraw from DNA base pairs to the organometallic complex.

Modelling the effect of osmolytes on peptide mechanical unfolding by Stefano Pieraccini; Simone Conti; Shilpi Chaurasia; Maurizio Sironi (138-143).
Osmolyte molecules can be classified in two different groups with respect to their effect on protein stability: osmoprotectants, which stabilize the protein or peptide folded state, and denaturants, which favor the denaturated state. Mechanical unfolding free energy of a model peptide has been obtained from umbrella sampling and weighted histogram analysis method, and the effect of four different osmolytes on the free energy difference between the folded and the denaturated state have been calculated. The observed trend mirrors the expected behavior of the studied osmolytes and unfolding pathways analysis allows an insight in the osmolyte action mechanism.

In HIV-1 infection, human antibody 2G12 is capable of recognizing the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. To investigate the ligand binding mechanisms of antibody 2G12 with glycans aiming for the contribution to the medications, we carried out classical molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the antibody 2G12 complex with its high-mannose ligand. We found that Mannose D1 of the ligand had the largest binding affinity with the antibody, which was well consistent with experimental reports. Furthermore, significant roles of Mannose 4 and 4′ in the ligand binding were theoretically indicated.

Theoretical investigation on the electronic and optical properties of diarylfluorene-based π-stacked molecules as supramolecular semiconductors by Chao-Peng Hu; Yu-Yu Liu; Ling-Hai Xie; Jie-Wei Li; Ya-Ru Li; Qiang Tai; Ming-Dong Yi; Wei Huang (150-155).
The structural substitution effects of different intramolecular π-stacking molecules at 9-position of diarylfluorenes were analyzed. Ground (excited-state) geometric conformations were optimized at B97-D/TZVP (TD-B97D/6-31+G) level and their intramolecular π–π interactions were investigated by non-covalent interactions (NCI) theory. UV–vis and photoluminescence (PL) spectra were obtained on the optimized structures at TD-B97D/TZVP level. The results show that the strong π–π interactions mainly focus on the middle area of substituent groups, whereas the outer is the weak π–π interactions. The π–π stacking interactions have different effect on the HOMOs and LUMOs in the diarylfluorenes and diaryldiazafluorenes, resulting in the distinct optical properties.

Optical and bowl-to-bowl inversion properties of sumanene substituted on its benzylic positions; a DFT/TD-DFT study by Stevan Armaković; Sanja J. Armaković; Jovan P. Šetrajčić; Igor J. Šetrajčić (156-161).
Sumanene has three sp3 hybridized carbon atoms at the benzylic positions. This specific structural property can allow the functionalization of a new bowl shaped structure. We investigated the effects of substitution of the benzylic carbon atoms of sumanene with boron and nitrogen atoms within the density functional theory and time-dependent density functional theory computations. The sumanene derivatives were subjected to the analysis of changes of the molecular electrostatic potential surfaces, optical properties (UV/Vis spectra) and bowl-to-bowl inversion barrier properties with solvent effects. The bowl shaped geometry and other properties were significantly affected by the introduction of hetero atoms.

The geometric configurations among phenylalanine derivatives (p-chlorophenylalanine, (p-CPA) thiophenylalanine (p-TPA), and p-nitrophenylalanine (p-NPA)) adsorbed on Ge(1 0 0) surfaces were investigated using density functional theory (DFT) calculations. We focused on describing the role of nucleophilic group (–Cl, –SH, and –NO2) being included in p-CPA, p-TPA, and p-NPA molecules, which can affect the stable adsorption structure energies and geometric configurations when they adsorb on the Ge(1 0 0) surface. We confirmed that geometric differences in the adsorption configurations indicated that their phenyl rings were tilted with respect to the Ge(1 0 0) surface by the effect of nucleophilicity and different sizes among –Cl, –SH and –NO2 groups.