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Physical Chemistry Chemical Physics: PCCP

Zhiqiang Zhao, Hang Yin, Kun Cai, Wanqi Zhou
The mechanical properties of black phosphorus (BP) are anisotropic. Correspondingly, the properties of the nanotubes formed by bending the same BP ribbon along different directions are different as well. When bending the ribbon along the [110] direction (i.e., stair direction), or along its perpendicular direction (i.e., ps-direction), s- or ps-BPNT can be obtained. The two types of BPNTs are investigated via molecular dynamics (MD) simulations on their thermal and mechanical properties. The results indicate that, for the thermal stability of the s-BPNTs with similar diameters, s-BPNT is weaker than a-BPNTs (armchair type) but stronger than ps-BPNT, and z-BPNT (zigzag type) is the weakest one...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
Maristella Alessio, Florian A Bischoff, Joachim Sauer
A hybrid QM:QM method that combines MP2 as high-level method on cluster models with density functional theory (PBE+D2) as low-level method on periodic models is applied to adsorption of methane and ethane on the MgO(001) surface for which reliable experimental desorption enthalpies are available. Two coverages are considered, monolayer (every second Mg2+ ion occupied) and one quarter coverage (one of eight Mg2+ ions occupied). Structure optimizations are performed at the hybrid MP2:(PBE+D2) level, with the MP2 energies and forces counterpoise corrected for basis set superposition error and extrapolated to the complete basis set limit...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
Shuangzhi Li, Lijun Liu, Qing Zhao, Chiyang He, Weikai Liu
Reducing Cr(vi) to Cr(iii) with formic acid is desirable for environmental protection, but the sluggish kinetics limits its practical application, which currently motivates the intensive study of efficient catalysts for this redox reaction. Here bimetallic PdCu nanoalloy (∼5 nm in size) supported by N-doped graphene was synthesized through a one-pot hydrothermal process. The catalytic activity of PdCu nanoalloy highly depends on the Pd/Cu atomic ratio and N-doped graphene support. The obtained Pd6Cu4/NG shows superior catalysis towards the Cr(vi) reduction by formic acid with a high kinetic constant (kn = 23...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
Diana Madsen, Ove Christiansen, Carolin König
We extend the fragmentation-based double incremental expansion in FALCON coordinates (DIF) and its linear-scaling analogue [C. König and O. Christiansen, J. Chem. Phys., 2016, 145, 064105] to dipole surfaces. Thereby, we enable the calculation of intensities in vibrational absorption spectra from these cost-efficient property surfaces. We validate the obtained potential energy and dipole surfaces by vibrational spectra calculations employing damped response theory for correlated vibrational coupled cluster wave functions...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
Prathitha Kar, Andrey G Cherstvy, Ralf Metzler
Proteins are capable of locating specific targets on DNA by employing a facilitated diffusion process with intermittent 1D and 3D search steps. Gene colocalisation and coregulation-i.e. the spatial proximity of two communicating genes-is one factor capable of accelerating the target search process along the DNA. We perform Monte Carlo computer simulations and demonstrate the benefits of gene colocalisation for minimising the search time in a model DNA-protein system. We use a simple diffusion model to mimic the search for targets by proteins, produced initially in bursts of multiple proteins and performing the first-passage search on the DNA chain...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
Andrzej Miniewicz, Hanna Orlikowska, Anna Sobolewska, Stanislaw Bartkiewicz
Single-component azobenzene-based phototropic liquid crystals (PtLC) are promising materials that have started to be explored for photonic applications. One of the essential factors determining the applicability of these materials is the rate of the thermally driven cis-trans isomerization. In this paper, the kinetics of the thermal back cis-to-trans reaction in a pure 4-hexyl-4'-methoxyazobenzene (6-AB-O1) compound in its isotropic liquid and nematic phases is studied (the undoped LC). The reaction rate constants, activation energies and thermal activation parameters were determined based on spectroscopic studies...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Miguel A Soler, Sara Fortuna, Ario de Marco, Alessandro Laio
Nanobodies offer a viable alternative to antibodies for engineering high affinity binders. Their small size has an additional advantage: it allows exploiting computational protocols for optimizing their biophysical features, such as the binding affinity. The efficient prediction of this quantity is still considered a daunting task especially for modelled complexes. We show how molecular dynamics can successfully assist in the binding affinity prediction of modelled nanobody-protein complexes. The approximate initial configurations obtained by in silico design must undergo large rearrangements before achieving a stable conformation, in which the binding affinity can be meaningfully estimated...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Pascal G Yot, Vibhav Yadav, Salem Ould Amara, Jean-Paul Itiè, Umit B Demirci, Guillaume Maurin
Crystalline B-N-H compounds of low molecular weight have been intensively investigated over the past two decades owing to their promises for chemical hydrogen storage. Hydrazine borane NH2-NH2-BH3 is one of the most recent examples of this family of materials. In the present work, we explored its structural behaviour under mechanical stimulus by synchrotron high pressure X-ray diffraction. It has been evidenced that hydrazine borane shows a gradual pressure-induced decrease of its unit cell dimension and the process is reversible when the applied pressure is released...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Eyad H Al-Samra, Nicholas J B Green
This study investigates the problem of diffusion kinetics in a three-body system, motivated by the theory of radiation chemical kinetics. The backward diffusion equation for the joint density of the distances is formulated, and an explicit formula for the infinitesimal covariance of two diffusing distances is derived. The Clifford-Green theorem is used to show how the infinitesimal covariance of two distances is linked to the covariance of the corresponding two squared distances as time evolves. In addition, computer simulations for the problem are presented, which indicate that hitting probabilities are also correlated...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
A Kharchenko, V Zholobenko, A Vicente, C Fernandez, H Vezin, V De Waele, S Mintova
The state of copper species stabilized in nanosized LTL zeolite subjected to various post-synthesis treatments was unveiled by a range of spectroscopic techniques. FTIR and UV-Vis studies demonstrated that the reduction process of copper in the LTL nanosized zeolite leads to the formation of different species including Cu2+, Cu+ and Cu nanoparticles (Cu NPs). The adsorption of probe molecules (NO and CO) was used to selectively monitor the copper species in the LTL nanosized zeolite upon oxidation and reduction post-synthesis treatments...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Xianghui Han, Sheng Chen, Xuguang Lv, Hang Luo, Dou Zhang, Chris R Bowen
Polymer nanocomposites based on conductive fillers for high performance dielectrics have attracted increasing attention in recent years. However, a number of physical issues are unclear, such as the effect of interfacial thickness on the dielectric properties of the polymer nanocomposites, which limits the enhancement of permittivity. In this research, two core-shell structured reduced graphene oxide (rGO)@rigid-fluoro-polymer conducting fillers with different shell thicknesses are prepared using a surface-initiated reversible-addition-fragmentation chain transfer polymerization method, which are denoted as rGO@PTFMS-1 with a thin shell and rGO@PTFMS-2 with a thick shell...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Takeshi Kai, Akinari Yokoya, Masatoshi Ukai, Kentaro Fujii, Tomohiro Toigawa, Ritsuko Watanabe
Although most of the radiation damage to genomic DNA could be rendered harmless using repair enzymes in a living cell, a certain fraction of the damage is persistent resulting in serious genetic effects, such as mutation induction. In order to understand the mechanisms of the deleterious DNA damage formation in terms of its earliest physical stage at the radiation track end, dynamics of low energy electrons and their thermalization processes around DNA molecules were investigated using a dynamic Monte Carlo code...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
A Cesaretti, B Carlotti, F Elisei, C G Fortuna, A Spalletti
The excited state dynamics of two quadrupolar polyaromatic N-methylpyridinium cations have been fully investigated in order to acquire detailed information on their photo-induced behavior. The two molecules are symmetric push-pull compounds having a D-π-A+-π-D motif, with the same electron-acceptor central unit (A = N-methylpyridinium) and two distinctive electron-donor polyaromatic side groups (D), namely naphthyl and pyrenyl substituents. Both molecules undergo charge transfer during the absorption, as revealed by a significant solvatochromism exhibited with solvent polarity, but the fate of their excited state was found to be markedly different...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Sung Gyu Han, Sang Youn Chae, Si Young Lee, Byoung Koun Min, Yun Jeong Hwang
Here, we successfully synthesized a Ta3N5 thin film using a simple metal-organic-precursor decomposition process followed by its conversion to nitride and studied its photoelectrochemical (PEC) properties to understand charge separation on the surface. Newly synthesized Ta3N5 photoanodes showed a significant difference in the PEC activity in relation to the annealing temperature under ammonia flow, although similar light absorption properties or electronic states were obtained. Charge separation related PEC properties were analyzed using intensity modulated photocurrent density spectroscopy (IMPS) and photocurrent measurements in the absence/presence of scavengers...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Tymofii Yu Nikolaienko, Leonid A Bulavin
A modification of the principal component regression model is proposed for obtaining a fixed set of atomic charges (referred to as dipole-derived charges) optimized for reproducing the dipole moment of a conformationally rich molecule, i.e., a molecule with multiple local minima on the potential energy surface. The method does not require any adjustable parameters and requires the geometries of conformers, their dipole moments and atomic polar tensor (APT) charges as the only input data. The fixed atomic charges generated by the method not only reproduce the molecular dipole moment in all the conformers accurately, but are also numerically close to the APT charges, thereby ensuring accurate reproduction of the dipole moment variations caused by small geometrical distortions (e...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
Luis Pérez-Mas, Alberto Martín-Molina, Manuel Quesada-Pérez, Arturo Moncho-Jordá
In this work the equilibrium absorption of nanometric cosolutes (which could represent drugs, reactants, small globular proteins and other kind of biomacromolecules) inside neutral hydrogels is studied. We specially focus on exploring, for different swelling states, the competition between the steric exclusion induced by the cross-linked polymer network constituting the hydrogel, and the solvent-induced short-range hydrophobic attraction between the polymer chains and the cosolute particle. For this purpose, the cosolute partition coefficient is calculated by means of coarse-grained grand canonical Monte Carlo simulations, and the results are compared to theoretical predictions based on the calculation of the excluded and binding volume around the polymer chains...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
Ryoji Kusaka, Masayuki Watanabe
Solvent extraction plays an integral part in the separation and purification of metals. Because extractants generally used as complexing agents for metal extractions, such as di-(2-ethylhexyl)phosphoric acid (HDEHP) for lanthanide extractions, are amphiphilic, they come to an organic/water interface, and the interface plays a crucial role as the site of the formation of metal complexes and the subsequent transfer reaction to an organic phase. Despite the importance of the interface for metal solvent extractions, its molecular-level structure is unclear because of the experimental difficulties...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
Petr Melichar, Drahomír Hnyk, Jindřich Fanfrlík
This paper presents a systematic study of multicenter and classical bonding on a broad series of experimentally known heteroboranes covering closo, nido, arachno and hypho types of cages with incorporated tetrel, pnictogen or chalcogen heterovertices up to the third-row elements. The nature of bonding is studied using a novel quantum-chemical tool, the intrinsic atomic/bond orbital (IAO/IBO) approach, which provides a direct connection between quantum chemistry and chemical concepts. We also discuss how the computed IBO properties are related to molecular observables such as interatomic distances, molecular electrostatic potential surfaces and dipole moments...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
P Polzin, I V Eliani, J Ströh, M Braun, N Ruser, N Heidenreich, P Rönfeldt, F Bertram, C Näther, S Wöhlbrandt, M Suta, H Terraschke
In situ monitoring of the formation of emissive complexes is essential to enable the development of rational synthesis protocols, to provide accurate control over the generation of structure-related properties (such as luminescence) and to facilitate the development of new compounds. In situ luminescence analysis of coordination sensors (ILACS) utilizes the sensitivity of the spectroscopic properties of lanthanide ions to their coordination environment to detect structural changes during crystallization processes...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
Irene Casademont-Reig, Tatiana Woller, Julia Contreras-García, Mercedes Alonso, Miquel Torrent-Sucarrat, Eduard Matito
The role of aromaticity in porphyrinoids is a current subject of debate due to the intricate structure of these macrocycles, which can adopt Hückel, Möbius and even figure-eight conformers. One of the main challenges in these large π-conjugated structures is identifying the most conjugated pathway because, among aromaticity descriptors, there are very few that can be applied coherently to this variety of conformers. In this paper, we have investigated the conjugated pathways in nine porphyrinoid compounds using several aromaticity descriptors, including BLA, BOA, FLU and HOMA, as well as the recently introduced AV1245 and AVmin indices...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
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