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Journal of Chemical Physics

Diego R Alcoba, Alicia Torre, Luis Lain, Gustavo E Massaccesi, Ofelia B Oña, Eduardo M Honoré, Ward Poelmans, Dimitri Van Neck, Patrick Bultinck, Stijn De Baerdemacker
This work proposes the variational determination of two-electron reduced density matrices corresponding to the ground state of N-electron systems within the doubly occupied-configuration-interaction methodology. The P, Q, and G two-index N-representability conditions have been extended to the T1 and T2 (T2') three-index ones and the resulting optimization problem has been addressed using a standard semidefinite program. We report results obtained from the doubly occupied-configuration-interaction method, from the two-index constraint variational procedure and from the two- and three-index constraint variational treatment...
January 14, 2018: Journal of Chemical Physics
S R Haqshenas, I J Ford, N Saffari
Effects of acoustic waves on a phase transformation in a metastable phase were investigated in our previous work [S. R. Haqshenas, I. J. Ford, and N. Saffari, "Modelling the effect of acoustic waves on nucleation," J. Chem. Phys. 145, 024315 (2016)]. We developed a non-equimolar dividing surface cluster model and employed it to determine the thermodynamics and kinetics of crystallisation induced by an acoustic field in a mass-conserved system. In the present work, we developed a master equation based on a hybrid Szilard-Fokker-Planck model, which accounts for mass transportation due to acoustic waves...
January 14, 2018: Journal of Chemical Physics
T Cunha, M Mendes, F Ferreira da Silva, S Eden, G García, P Limão-Vieira
This work demonstrates that selective excision of hydrogen atoms at a particular site of the DNA base adenine can be achieved in collisions with electronegative atoms by controlling the impact energy. The result is based on analysing the time-of-flight mass spectra yields of potassium collisions with a series of labeled adenine derivatives. The production of dehydrogenated parent anions is consistent with neutral H loss either from selective breaking of C-H or N-H bonds. These unprecedented results open up a new methodology in charge transfer collisions that can initiate selective reactivity as a key process in chemical reactions that are dominant in different areas of science and technology...
January 14, 2018: Journal of Chemical Physics
Lu Deng, Jincheng Du
Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties...
January 14, 2018: Journal of Chemical Physics
Dan Xu, Chun-Yan Ni, You-Liang Zhu, Zhong-Yuan Lu, Yao-Hong Xue, Hong Liu
Kinetic step-growth polymerization is studied by dissipative particle dynamics coupled with our previously developed reaction algorithm on a coarse-grained level. The simulation result proves that this step-growth polymerization obeys the second-order reaction kinetics. We apply this algorithm to study the step-growth polymerization using the subunits with different flexibilities or within confinement. Good agreement of the number fraction distributions with the Flory distribution is obtained, implying that this algorithm is reasonable to describe such a kind of step-growth polymerization...
January 14, 2018: Journal of Chemical Physics
Masoumeh Ozmaian, David Jasnow, Afshin Eskandari Nasrabad, Anton Zilman, Rob D Coalson
The effect of cohesive contacts or, equivalently, dynamical cross-linking on the equilibrium morphology of a polymer brush infiltrated by nanoparticles that are attracted to the polymer strands is studied for plane-grafted brushes using coarse-grained molecular dynamics and approximate statistical mechanical models. In particular, the Alexander-de Gennes (AdG) and Strong Stretching Theory (SST) mean-field theory (MFT) models are considered. It is found that for values of the MFT cross-link strength interaction parameter beyond a certain threshold, both AdG and SST models predict that the polymer brush will be in a compact state of nearly uniform density packed next to the grafting surface over a wide range of solution phase nanoparticle concentrations...
January 14, 2018: Journal of Chemical Physics
Esben L Kolsbjerg, Michael N Groves, Bjørk Hammer
No abstract text is available yet for this article.
January 14, 2018: Journal of Chemical Physics
Thomas-C Jagau
The impact of residual electron correlation beyond the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) approximation on positions and widths of electronic resonances is investigated. To establish a method that accomplishes this task in an economical manner, several approaches proposed for the approximate treatment of triple excitations are reviewed with respect to their performance in the electron attachment (EA) variant of EOM-CC theory. The recently introduced EOM-CCSD(T)(a)* method [D. A...
January 14, 2018: Journal of Chemical Physics
H H Katkar, M Muthukumar
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/NK, is longer than the relaxation time τ0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations...
January 14, 2018: Journal of Chemical Physics
Pei-Yang Chen, Mark E Tuckerman
Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions...
January 14, 2018: Journal of Chemical Physics
Danillo Valverde, Zélia Maria da Costa Ludwig, Célia Regina da Costa, Valdemir Ludwig, Herbert C Georg
At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach...
January 14, 2018: Journal of Chemical Physics
Jin Wang, Yu R Sun, Lei-Gang Tao, An-Wen Liu, Shui-Ming Hu
No abstract text is available yet for this article.
January 14, 2018: Journal of Chemical Physics
Aleksey Vishnyakov, Runfang Mao, Ming-Tsung Lee, Alexander V Neimark
We present a coarse-grained model of the acid form of Nafion membrane that explicitly includes proton transport. This model is based on a soft-core bead representation of the polymer implemented into the dissipative particle dynamics (DPD) simulation framework. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with water beads. Morse bond formation and breakup artificially mimics the Grotthuss hopping mechanism of proton transport. The proposed DPD model is parameterized to account for the specifics of the conformations and flexibility of the Nafion backbone and sidechains; it treats electrostatic interactions in the smeared charge approximation...
January 14, 2018: Journal of Chemical Physics
Ismail-Can Oğuz, Tzonka Mineva, Hazar Guesmi
The reactivity of various Pd ensembles on the Au-Pd(100) alloy catalyst toward CO oxidation was investigated by using density functional theory (DFT). This study was prompted by the search for efficient catalysts operating at low temperature for the CO oxidation reaction that is of primary environmental importance. To this aim, we considered Pd modified Au(100) surfaces including Pd monomers, Pd dimers, second neighboring Pd atoms, and Pd chains in a comparative study of the minimum energy reaction pathways...
January 14, 2018: Journal of Chemical Physics
Tony C Smith, Dennis J Clouthier
The SnH2 and SnD2 molecules have been detected for the first time in the gas phase by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the Ã1B1-X̃1A1 electronic transition. These reactive species were prepared in a pulsed electric discharge jet using (CH3)4Sn or SnH4/SnD4 precursors diluted in high pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state energy levels were measured from single rovibronic level emission spectra...
January 14, 2018: Journal of Chemical Physics
T J Zuehlsdorff, C M Isborn
The correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations...
January 14, 2018: Journal of Chemical Physics
Surajit Kayal, Khokan Roy, Siva Umapathy
Ultrafast torsional dynamics plays an important role in the photoinduced excited state dynamics. Tetraphenylethylene (TPE), a model system for the molecular motor, executes interesting torsional dynamics upon photoexcitation. The photoreaction of TPE involves ultrafast internal conversion via a nearly planar intermediate state (relaxed state) that further leads to a twisted zwitterionic state. Here, we report the photoinduced structural dynamics of excited TPE during the course of photoisomerization in the condensed phase by ultrafast Raman loss (URLS) and femtosecond transient absorption (TA) spectroscopy...
January 14, 2018: Journal of Chemical Physics
Fumio Hirata, Masatake Sugita, Masasuke Yoshida, Kazuyuki Akasaka
The thermodynamics hypothesis, casually referred to as "Anfinsen's dogma," is described theoretically in terms of a concept of the structural fluctuation of protein or the first moment (average structure) and the second moment (variance and covariance) of the structural distribution. The new theoretical concept views the unfolding and refolding processes of protein as a shift of the structural distribution induced by a thermodynamic perturbation, with the variance-covariance matrix varying. Based on the theoretical concept, a method to characterize the mechanism of folding (or unfolding) is proposed...
January 14, 2018: Journal of Chemical Physics
Derek Frydel, Yan Levin
In the present work, we investigate a gas-liquid transition in a two-component Gaussian core model, where particles of the same species repel and those of different species attract. Unlike a similar transition in a one-component system with particles having attractive interactions at long separations and repulsive interactions at short separations, a transition in the two-component system is not driven solely by interactions but by a specific feature of the interactions, the correlations. This leads to extremely low critical temperature, as correlations are dominant in the strong-coupling limit...
January 14, 2018: Journal of Chemical Physics
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