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Journal of Chemical Physics

Tamás Vörös, Győző György Lajgút, Gábor Magyarfalvi, György Tarczay
The [NH2, C, N, O] and the [NH2, C, N, S] molecular systems were investigated by computational and matrix-isolation spectroscopic methods. The determination of the equilibrium structures and relative energies by CCSD(T) method was followed by the computation of the harmonic and anharmonic vibrational wavenumbers, infrared intensities, relative Raman activities, and UV excitation energies. These computed data were used to assist the identification of products obtained by UV laser photolysis of 3,4-diaminofurazan and 3,4-diaminothiadiazole in low-temperature Ar and Kr matrices...
January 14, 2017: Journal of Chemical Physics
Ji-Xuan Hou
I present a refined version of the method for determining entanglement length through monomer mean-square displacement. By retrieving a prefactor π/2 that might be lost in previous derivation, the entanglement length of the standard bead-spring model estimated by this method coincides with the measurements of other methods.
January 14, 2017: Journal of Chemical Physics
D Vieira, R V Krems, T V Tscherbul
We use accurate quantum scattering calculations to elucidate the role of short-range molecule-field interactions in atom-molecule inelastic collisions and abstraction chemical reactions at low temperatures. We consider two examples: elastic and inelastic scattering of NH(Σ3) molecules with Mg(S1) atoms in a magnetic field; reactive scattering LiF + H → Li + HF in an electric field. Our calculations suggest that, for non-reactive collision systems and abstraction chemical reactions, the molecule-field interactions cannot generally be neglected at short range because the atom-molecule potential passes through zero at short range...
January 14, 2017: Journal of Chemical Physics
Liangxu Xie, Lin Shen, Zhe-Ning Chen, Mingjun Yang
Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling...
January 14, 2017: Journal of Chemical Physics
Kenichi Okutsu, Kenichiro Yamazaki, Keijiro Ohshimo, Fuminori Misaizu
We have observed fragment ion images produced by ultraviolet photodissociation of Mg(+)BrCH3 complex ions using a reflectron time-of-flight mass spectrometer combined with an imaging detector. The BrCH3(+) fragment ion was produced after the 266-nm excitation of Mg(+)BrCH3. In the image of the BrCH3(+) ions, a split distribution was observed parallel to the polarization direction of the photolysis laser. In calculated potential energy curves, we found a repulsive potential correlated with a dissociation limit of Mg + BrCH3(+): The calculation results indicate that the dissociation and the charge transfer occurred via non-adiabatic process after the 5(2)A' ← 1(2)A' photoexcitation...
January 14, 2017: Journal of Chemical Physics
Arthur C Reber, Vikas Chauhan, Shiv N Khanna
The removal of a single ligand from the magnetic Ni9Te6(L)8 (L = P(CH3)3, CO) clusters is found to quench the magnetic moment. The reduction in magnetic moment is caused by a geometric deformation of the Ni9Te6 core that breaks the octahedral symmetry of the cluster. This effect is observed in both the CO and phosphine based ligands. The octahedral symmetry bare cluster is also found to have a large magnetic moment. These results highlight the dilemma faced by magnetic ligand protected clusters whose symmetry has been broken: whether to break the spin symmetry as in Hund's rules or to break the spatial symmetry as in the Jahn-Teller effect...
January 14, 2017: Journal of Chemical Physics
R L Hudson, M J Loeffler, P A Gerakines
Infrared transmission spectra from 4000 to 400 cm(-1), and associated band strengths and absorption coefficients, are presented for the first time for both amorphous and crystalline N2O. Changes in the spectra as a function of ice thickness and ice temperature are shown. New measurements of density, refractive index, and specific refraction are reported for amorphous and crystalline N2O. Comparisons are made to published results, and the most-likely reason for some recent disagreements in the literature is discussed...
January 14, 2017: Journal of Chemical Physics
Dimitri Loutchko, Maximilian Eisbach, Alexander S Mikhailov
The enzyme tryptophan synthase is characterized by a complex pattern of allosteric interactions that regulate the catalytic activity of its two subunits and opening or closing of their ligand gates. As a single macromolecule, it implements 13 different reaction steps, with an intermediate product directly channeled from one subunit to another. Based on experimental data, a stochastic model for the operation of tryptophan synthase has been earlier constructed [D. Loutchko, D. Gonze, and A. S. Mikhailov, J. Phys...
January 14, 2017: Journal of Chemical Physics
Andrés Montoya-Castillo, David R Reichman
We derive a semi-analytical form for the Wigner transform for the canonical density operator of a discrete system coupled to a harmonic bath based on the path integral expansion of the Boltzmann factor. The introduction of this simple and controllable approach allows for the exact rendering of the canonical distribution and permits systematic convergence of static properties with respect to the number of path integral steps. In addition, the expressions derived here provide an exact and facile interface with quasi- and semi-classical dynamical methods, which enables the direct calculation of equilibrium time correlation functions within a wide array of approaches...
January 14, 2017: Journal of Chemical Physics
Oscar Mendoza, Said Houmadi, Jean-Pierre Aimé, Juan Elezgaray
Logic circuits based on DNA strand displacement reaction are the basic building blocks of future nanorobotic systems. The circuits tethered to DNA origami platforms present several advantages over solution-phase versions where couplings are always diffusion-limited. Here we consider a possible implementation of one of the basic operations needed in the design of these circuits, namely, signal replication. We show that with an appropriate preparation of the initial state, signal replication performs in a reproducible way...
January 14, 2017: Journal of Chemical Physics
M C Kirkegaard, J Langford, J Steill, B Anderson, A Miskowiec
Uranyl fluoride (UO2F2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R3¯m symmetry. The formally closed-shell electron structure of anhydrous UO2F2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies...
January 14, 2017: Journal of Chemical Physics
James Lim, David J Ing, Joachim Rosskopf, Jan Jeske, Jared H Cole, Susana F Huelga, Martin B Plenio
We investigate how correlated fluctuations affect oscillatory features in rephasing and non-rephasing two-dimensional (2D) electronic spectra of a model dimer system. Based on a beating map analysis, we show that non-secular environmental couplings induced by uncorrelated fluctuations lead to oscillations centered at both cross- and diagonal-peaks in rephasing spectra as well as in non-rephasing spectra. Using an analytical approach, we provide a quantitative description of the non-secular effects in terms of the Feynman diagrams and show that the environment-induced mixing of different inter-excitonic coherences leads to oscillations in the rephasing diagonal-peaks and non-rephasing cross-peaks...
January 14, 2017: Journal of Chemical Physics
R E Goetz, T A Isaev, B Nikoobakht, R Berger, C P Koch
Photoelectron circular dichroism refers to the forward/backward asymmetry in the photoelectron angular distribution with respect to the propagation axis of circularly polarized light. It has recently been demonstrated in femtosecond multi-photon photoionization experiments with randomly oriented camphor and fenchone molecules [C. Lux et al., Angew. Chem., Int. Ed. 51, 4755 (2012) and C. S. Lehmann et al., J. Chem. Phys. 139, 234307 (2013)]. A theoretical framework describing this process as (2+1) resonantly enhanced multi-photon ionization is constructed, which consists of two-photon photoselection from randomly oriented molecules and successive one-photon ionization of the photoselected molecules...
January 14, 2017: Journal of Chemical Physics
Yu-Qi Guo, Jun-Xing Pan, Min-Na Sun, Jin-Jun Zhang
We investigate the phase transition of a symmetric diblock copolymer induced by nanorods with different surface chemistry. The results demonstrate that the system occurs the phase transition from a disordered structure to ordered parallel lamellae and then to the tilted layered structure as the number of rods increases. The dynamic evolution of the domain size and the order parameter of the microstructure are also examined. Furthermore, the influence of rod property, rod-phase interaction, rod-rod interaction, rod length, and polymerization degree on the behavior of the polymer system is also investigated systematically...
January 14, 2017: Journal of Chemical Physics
L H Coudert
Terahertz pulses effects are investigated in an asymmetric top C2v molecule using numerical simulations. The average value of the direction cosine ΦZx is computed solving the time dependent Schrödinger equation for several types of pulses. The H2S molecule taken as a test case is first subject to two short terahertz pulses with a duration smaller than 5 ps, an identical maximum value of the electric field of 2 MV/cm, but a different shape. The thermal average ⟨⟨ΦZx⟩⟩ is calculated for several temperatures, and non-periodic time variations are found even for the lowest temperature...
January 14, 2017: Journal of Chemical Physics
Milan K Hazra, Biman Bagchi
Valuable dynamical and structural information about neat liquid DMSO at ambient conditions can be obtained through a study of low frequency vibrations in the far infrared (FIR), that is, terahertz regime. For DMSO, collective excitations as well as single molecule stretches and bends have been measured by different kinds of experiments such as OHD-RIKES and terahertz spectroscopy. In the present work, we investigate the intermolecular vibrational spectrum of DMSO through three different computational techniques namely (i) the far-infrared spectrum obtained through the Fourier transform of total dipole moment auto-time correlation function, (ii) from the Fourier transform of the translational and angular velocity time autocorrelation functions, and (iii) a quenched normal mode analysis of the parent liquid at 300 K...
January 14, 2017: Journal of Chemical Physics
Kikuko Hayamizu, Shiro Seki, Tomoyuki Haishi
Mobile lithium ions in a cubic garnet Li7La3Zr2O12 (Al-stabilized) were studied using (7)Li NMR spectroscopy for membrane and powder samples, the latter of which was ground from the membrane. Lithium diffusion in a micrometer space was measured using the pulsed-gradient spin-echo (7)Li NMR method between 70 and 130 °C. When the observation time (Δ) was shorter than 20 ms, the echo attenuation showed diffusive diffraction patterns, indicating that the Li(+) diffusing space is not free but restricted. For longer Δ, the values of apparent diffusion constant (Dapparent) became gradually smaller to approach an equilibrated value (close to a tracer diffusion constant)...
January 14, 2017: Journal of Chemical Physics
S V Novikov
Hopping charge transport in amorphous semiconductors having spatially correlated exponential density of states has been considered. Average carrier velocity is exactly calculated for the quasi-equilibrium (nondispersive) transport regime. We suggest also a heuristic approach for the consideration of the carrier velocity for the non-equilibrium dispersive regime.
January 14, 2017: Journal of Chemical Physics
Xiaojuan Dai, Di Song, Kunhui Liu, Hongmei Su
5-Iodouracil (5-IU) can be integrated into DNA and acts as a UV sensitive chromophore suitable for probing DNA structure and DNA-protein interactions based on the photochemical reactions of 5-IU. Here, we perform joint studies of time-resolved Fourier transform infrared (TR-FTIR) spectroscopy and ab initio calculations to examine the state-specific photochemical reaction mechanisms of the 5-IU. The fact that uracil (U) is observed in TR-FTIR spectra after 266 nm irradiation of 5-IU in acetonitrile and ascribed to the product of hydrogen abstraction by the uracil-5-yl radical (U·) provides experimental evidence for the C-I bond homolysis of 5-IU...
January 14, 2017: Journal of Chemical Physics
Gautham Dharuman, Liam G Stanton, James N Glosli, Michael S Murillo
Medium-range interactions occur in a wide range of systems, including charged-particle systems with varying screening lengths. We generalize the Ewald method to charged systems described by interactions involving an arbitrary dielectric response function ϵ(
January 14, 2017: Journal of Chemical Physics
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