The Journal of Chemical Physics

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ISSN / EISSN : 0021-9606 / 1089-7690
Published by: AIP Publishing (10.1063)
Total articles ≅ 140,494
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Shengzhen Wang, Wensheng Ma, Wanfeng Yang, Qingguo Bai, Hui Gao, ,
Published: 22 October 2021
The Journal of Chemical Physics; https://doi.org/10.1063/5.0067237

Abstract:
Germanium (Ge) has become a promising anode material for lithium-ion batteries (LIBs) due to its high theoretical capacity and decent electron/ion conductivity, but exhibits inferior lifespan caused by dramatic volume variations during the (de)lithiation process. Herein, hierarchically nanoporous Ge (np-Ge) was fabricated by the combination of selective phase corrosion with chemical dealloying. As an anode for LIBs, the np-Ge electrode exhibits marvelous cycling stability with capacity retentions of 1060.0 mAh g-1 at 0.2 A g-1 and 767.1 mAh g-1 at 1 A g-1 after 100 cycles. Moreover, the electrode shows excellent rate capability with capacity retention of 844.2 mAh g-1 at 5 A g-1. Noticeably, the (de)lithiation mechanisms of np-Ge and porous Si-Ge (p-Si6Ge4) were unveiled by operando X-ray diffraction.
Elie Belorizky, Pascal H. Fries
Published: 21 October 2021
The Journal of Chemical Physics; https://doi.org/10.1063/5.0069362

Abstract:
We consider the longitudinal relaxation rate enhancement (QRE) of a 1H nucleus due to the time fluctuations of the local dipolar magnetic field created by a close quadrupole 14N nucleus, the electric-field gradient (EFG) Hamiltonian of which changes with time because of vibrations/distorsions of its chemical environment. The QRE is expressed analytically as a linear combination of the cosine Fourier transforms of the three quantum time auto-correlation functions GAA(t) of the 14N spin components along the principal axes A = X, Y, Z of the mean (time-averaged) EFG Hamiltonian. Denoting the three transition frequencies between the energy levels of this mean Hamiltonian by νA, the functions GAA(t) oscillate at frequencies νA + sA/(2π) with mono-exponential decays of relaxation time τA, where the frequency dynamic shifts sA and the relaxation times τA are closed expressions of the magnitude of the fluctuations of the instantaneous EFG Hamiltonian about its mean and of the characteristic fluctuation time. Thus, the theoretical QRE is the sum of three Lorentzian peaks centered at νA + sA/(2π) with full widths at half maxima 1/(π τA). The predicted peak widths are nearly equal. The predicted dynamic shifts of the peaks are much smaller than their widths and amazingly keep proportional to the transition frequencies νA for reasonably fast EFG fluctuations. The theory is further improved by correcting the transition frequencies by the Zeeman effects of second order. It is successfully applied to reinterpret the QRE pattern measured by Broche et al. in normal cartilage.
Published: 21 October 2021
The Journal of Chemical Physics; https://doi.org/10.1063/5.0062889

Abstract:
In this work, we developed a calculation method of local stress tensor applicable to non-equilibrium molecular dynamics (NEMD) systems, which evaluates the macroscopic momentum advection and the kinetic term of the stress in the framework of the Method of Plane (MoP), in a consistent way to guarantee the mass and momentum conservation. From the relation between the macroscopic velocity distribution function and the microscopic molecular passage across a fixed control plane, we derived a method to calculate the basic properties of the macroscopic momentum conservation law including the density, the velocity, the momentum flux, the interaction and kinetic terms of the stress tensor defined on a surface with a finite area. Any component of the streaming velocity can be obtained on a control surface, which enables the separation of the kinetic momentum flux into the advection and stress terms in the framework of MoP, and this enebles strict satisfaction of the the mass and momentum conservation for an arbitrary closed control volume (CV) set in NEMD systems. We validated the present method through the extraction of the density, velocity and stress distributions in a quasi-1D steady-state Couette flow system and in a quasi-2D steady-state NEMD system with a moving contact line. We showed that with the present MoP, in contrast to the volume average method (VA), the conservation law was satisfied even for a CV set around the moving contact line, which was located in a strongly inhomogeneous region.
Robin J. Shannon, Helen M. Deeks, Eleanor Burfoot, Edward Clark, Alex J. Jones, ,
Published: 21 October 2021
The Journal of Chemical Physics, Volume 155; https://doi.org/10.1063/5.0062517

Abstract:
The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR “game” was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and “molecular snapshots” from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.
Marco Cherubini, , Francesco Mauri
Published: 21 October 2021
The Journal of Chemical Physics; https://doi.org/10.1063/5.0062689

Abstract:
Water ice is a unique material presenting intriguing physical properties, like negative thermal expansion and anomalous volume isotope effect (VIE). They arise from the interplay between weak hydrogen bonds and nuclear quantum fluctuations, making theoretical calculations challenging. Here, we employ the stochastic self-consistent harmonic approximation (SSCHA) to investigate how thermal and quantum fluctuations affect the physical properties of ice XI with ab initio accuracy.Regarding the anomalous VIE, our work reveals that quantum effects on hydrogen are so strong to be in a nonlinear regime: when progressively increasing the mass of hydrogen from protium to infinity (classical limit), the volume firstly expands and then contracts, with a maximum slightly above the mass of tritium. We observe an anharmonic renormalization of about 10% in the bending and stretching phonon frequencies probed in IR and Raman experiments.For the first time, we report an accurate comparison of the low energy phonon dispersion with the experimental data, possible only thanks to high-level accuracy in the electronic correlation and nuclear quantum and thermal fluctuations, paving the way for the study of thermal transport in ice from first principles and the simulation of ice under pressure.
Yiheng Qiu,
Published: 21 October 2021
The Journal of Chemical Physics; https://doi.org/10.1063/5.0068887

Abstract:
We introduce hybrid gausslet/Gaussian basis sets, where a standard Gaussianbasis is added to a gausslet basis in order to increase accuracy near thenuclei while keeping the spacing of the grid of gausslets relatively large. TheGaussians are orthogonalized to the gausslets, which are already orthonormal,and approximations are introduced to maintain the diagonal property of the twoelectron part of the Hamiltonian, so that it continues to scale as the secondpower of the number of basis functions, rather than the fourth. We introduceseveral corrections to the Hamiltonian designed to enforce certain exactproperties, such as the values of certain two-electron integrals. We alsointroduce a simple universal energy correction which compensates for theincompleteness of the basis stemming from the electron-electron cusps, based onthe measured double occupancy of each basis function. We perform a number ofHartree Fock and full configuration interaction (full-CI) test calculations ontwo electron systems, and Hartree Fock on a ten-atom hydrogen chain, tobenchmark these techniques. The inclusion of the cusp correction allows us toobtain complete basis set full-CI results, for the two electron cases, at thelevel of several microHartrees, and we see similar apparent accuracy forHartree Fock on the ten-atom hydrogen chain.
Zheyao Hu, ,
Published: 21 October 2021
The Journal of Chemical Physics, Volume 155; https://doi.org/10.1063/5.0065163

Abstract:
The use of drugs derived from benzothiadiazine, which is a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension (treated with diuretics such as bendroflumethiazide or chlorothiazide), low blood sugar (treated with non-diuretic diazoxide) or the human immunodeficiency virus, among others. In this work we have investigated the interactions of benzothiadiazine with the basic components of cell membranes and solvents such as phospholipids, cholesterol, ions and water. The analysis of the mutual microscopic interactions is of central importance to elucidate the local structure of benzothiadiazine as well as the mechanisms responsible for the access of benzothiadiazine to the interior of the cell. We have performed molecular dynamics simulations of benzothiadiazine embedded in three different model zwitterionic bilayer membranes made by dimyristoilphosphatidylcholine, dioleoylphosphatidylcholine, 1,2- dioleoyl-sn-glycero-3-phosphoserine and cholesterol inside aqueous sodium-chloride solution in order to systematically examine microscopic interactions of benzothiadiazine with the cell membrane at liquid-crystalline phase conditions. From data obtained through radial distribution functions, hydrogen-bonding lengths and potentials of mean force based on reversible work calculations, we have observed that benzothiadiazine has a strong affinity to stay at the cell membrane interface although it can be fully solvated by water in short periods of time. Furthermore, benzothiadiazine is able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of different characteristic lengths.
Published: 21 October 2021
The Journal of Chemical Physics, Volume 155; https://doi.org/10.1063/5.0062497

Abstract:
We demonstrate that a program synthesis approach based on a linear code representation can be used to generate algorithms that approximate the ground-state solutions of one-dimensional time-independent Schrödinger equations constructed with bound polynomial potential energy surfaces (PESs). Here, an algorithm is constructed as a linear series of instructions operating on a set of input vectors, matrices, and constants that define the problem characteristics, such as the PES. Discrete optimization is performed using simulated annealing in order to identify sequences of code-lines, operating on the program inputs that can reproduce the expected ground-state wavefunctions ψ(x) for a set of target PESs. The outcome of this optimization is not simply a mathematical function approximating ψ(x) but is, instead, a complete algorithm that converts the input vectors describing the system into a ground-state solution of the Schrödinger equation. These initial results point the way toward an alternative route for developing novel algorithms for quantum chemistry applications.
, , Glenn H. Fredrickson
Published: 21 October 2021
The Journal of Chemical Physics, Volume 155; https://doi.org/10.1063/5.0065742

Abstract:
Polymer-mediated colloidal interactions control the stability and phase properties of colloid–polymer mixtures that are critical for a wide range of important applications. In this work, we develop a versatile self-consistent field theory (SCFT) approach to study this type of interaction based on a continuum confined polymer solution model with explicit solvent and confining walls. The model is formulated in the grand canonical ensemble, and the potential of mean force for the polymer-mediated interaction is computed from grand potentials. We focus on the case of non-adsorbing linear polymers and present a systematic investigation on depletion effects using SCFT. The properties of confined polymer solutions are probed, and mean-field profiles of induced interactions are shown across different physical regimes. We expose a detailed parametric dependence of the interaction, concerning both attractive and repulsive parts, on polymer concentration, chain length, and solvent quality and explore the effect of wall surface roughness, demonstrating the versatility of the proposed approach. Our findings show good agreement with previous numerical studies and experiments, yet extend prior work to new regimes. Moreover, the mechanisms of depletion attraction and repulsion, along with the influence of individual control factors, are further discussed. We anticipate that this study will provide useful insights into depletion forces and can be readily extended to examine more complex colloid–polymer mixtures.
Published: 21 October 2021
The Journal of Chemical Physics, Volume 155; https://doi.org/10.1063/5.0063173

Abstract:
Strong light–matter coupling to form exciton– and vibropolaritons is increasingly touted as a powerful tool to alter the fundamental properties of organic materials. It is proposed that these states and their facile tunability can be used to rewrite molecular potential energy landscapes and redirect photophysical pathways, with applications from catalysis to electronic devices. Crucial to their photophysical properties is the exchange of energy between coherent, bright polaritons and incoherent dark states. One of the most potent tools to explore this interplay is transient absorption/reflectance spectroscopy. Previous studies have revealed unexpectedly long lifetimes of the coherent polariton states, for which there is no theoretical explanation. Applying these transient methods to a series of strong-coupled organic microcavities, we recover similar long-lived spectral effects. Based on transfer-matrix modeling of the transient experiment, we find that virtually the entire photoresponse results from photoexcitation effects other than the generation of polariton states. Our results suggest that the complex optical properties of polaritonic systems make them especially prone to misleading optical signatures and that more challenging high-time-resolution measurements on high-quality microcavities are necessary to uniquely distinguish the coherent polariton dynamics.
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