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  • Transient absorption microscopy: Technological innovations and applications in materials science and life science
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Yifan Zhu, Ji-Xin Cheng

    Transient absorption (TA) spectroscopy has been extensively used in the study of excited state dynamics of various materials and molecules. The transition from TA spectroscopy to TA microscopy, which enables the space-resolved measurement of TA, is opening new investigations toward a more complete picture of excited state dynamics in functional materials, as well as the mapping of crucial biopigments for precision diagnosis. Here, we review the recent instrumental advancement that is pushing the limit of spatial resolution, detection sensitivity, and imaging speed. We further highlight the emerging application in materials science and life science.

    更新日期:2020-01-14
  • Near-unity photoluminescence quantum yield in inorganic perovskite nanocrystals by metal-ion doping
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Ghada H. Ahmed, Jun Yin, Osman M. Bakr, Omar F. Mohammed

    The luminescence and charge transport properties of inorganic CsPbX3 perovskite nanocrystals (NCs) make them attractive candidates for various optoelectronic applications, such as lasing, X-ray imaging, light communication, and light-emitting diodes (LEDs). However, to realize cutting-edge device performance, high-quality NCs with high photoluminescence quantum yields (PLQYs) are essential. Therefore, substantial efforts and progress have been made to attain superior design/engineering and optimization of the inorganic NCs with a focus on surface quality, reduced nonradiative charge carrier recombination centers, and improved colloidal stabilities. Metal-ion doping has been proven to have a robust influence on the electronic band structure, PL behavior, and charge carrier recombination dynamics. Thus, in this perspective, we summarize the recent progress of the significant impact of metal cation doping on the optical properties, including the PL enhancement of CsPbCl3, CsPbBr3, and CsPbI3 perovskite NCs. Moreover, we shed light on the mechanism behind such improved properties. We conclude by recommending possible aspects and strategies to be further explored and considered for better utilization of these doped NCs in thin-film optoelectronic and energy conversion devices.

    更新日期:2020-01-14
  • Ultrafast excited-state proton transfer dynamics in dihalogenated non-fluorescent and fluorescent GFP chromophores
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Cheng Chen, Liangdong Zhu, Sean A. Boulanger, Nadezhda S. Baleeva, Ivan N. Myasnyanko, Mikhail S. Baranov, Chong Fang

    Green fluorescent protein (GFP) has enabled a myriad of bioimaging advances due to its photophysical and photochemical properties. To deepen the mechanistic understanding of such light-induced processes, novel derivatives of GFP chromophore p-HBDI were engineered by fluorination or bromination of the phenolic moiety into superphotoacids, which efficiently undergo excited-state proton transfer (ESPT) in aqueous solution within the short lifetime of the excited state, as opposed to p-HBDI where efficient ESPT is not observed. In addition, we tuned the excited-state lifetime from picoseconds to nanoseconds by conformational locking of the p-HBDI backbone, essentially transforming the nonfluorescent chromophores into highly fluorescent ones. The unlocked superphotoacids undergo a barrierless ESPT without much solvent activity, whereas the locked counterparts exhibit two distinct solvent-involved ESPT pathways. Comparative analysis of femtosecond transient absorption spectra of these unlocked and locked superphotoacids reveals that the ESPT rates adopt an “inverted” kinetic behavior as the thermodynamic driving force increases upon locking the backbone. Further experimental and theoretical investigations are expected to shed more light on the interplay between the modified electronic structure (mainly by dihalogenation) and nuclear motions (by conformational locking) of the functionalized GFP derivatives (e.g., fluorescence on and off).

    更新日期:2020-01-14
  • Analytical classical density functionals from an equation learning network
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-14
    S.-C. Lin, G. Martius, M. Oettel

    We explore the feasibility of using machine learning methods to obtain an analytic form of the classical free energy functional for two model fluids, hard rods and Lennard–Jones, in one dimension. The equation learning network proposed by Martius and Lampert [e-print arXiv:1610.02995 (2016)] is suitably modified to construct free energy densities which are functions of a set of weighted densities and which are built from a small number of basis functions with flexible combination rules. This setup considerably enlarges the functional space used in the machine learning optimization as compared to the previous work [S.-C. Lin and M. Oettel, SciPost Phys. 6, 025 (2019)] where the functional is limited to a simple polynomial form. As a result, we find a good approximation for the exact hard rod functional and its direct correlation function. For the Lennard–Jones fluid, we let the network learn (i) the full excess free energy functional and (ii) the excess free energy functional related to interparticle attractions. Both functionals show a good agreement with simulated density profiles for thermodynamic parameters inside and outside the training region.

    更新日期:2020-01-14
  • Turing instability conditions in confined systems with an effective position-dependent diffusion coefficient
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    G. Chacón-Acosta, M. Núñez-López, I. Pineda

    We study a reaction-diffusion system within a long channel in the regime in which the projected Fick-Jacobs-Zwanzig operator for confined diffusion can be used. We found that under this approximation, Turing instability conditions can be modified due to the channel geometry. The dispersion relation, range of unstable modes where pattern formation occurs, and spatial structure of the patterns itself change as functions of the geometric parameters of the channel. This occurs for the three channels analyzed, for which the values of the projected operators can be found analytically. For the reaction term, we use the well-known Schnakenberg kinetics.

    更新日期:2020-01-14
  • Large-scale excited-state calculation using dynamical polarizability evaluated by divide-and-conquer based coupled cluster linear response method
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Takeshi Yoshikawa, Jyunya Yoshihara, Hiromi Nakai

    This study attempted to propose an efficient scheme at the coupled cluster linear response (CCLR) level to perform large-scale excited-state calculations of not only local excitations but also nonlocal ones such as charge transfers and transitions between delocalized orbitals. Although standard applications of fragmentation techniques to the excited-state calculations brought about the limitations that could only deal with local excitations, this study solved the problem by evaluating the excited states as the poles of dynamical polarizability. Because such an approach previously succeeded at the time-dependent density functional theory level [H. Nakai and T. Yoshikawa, J. Chem. Phys. 146, 124123 (2017)], this study was considered as an extension to the CCLR level. To evaluate the dynamical polarizability at the CCLR level, we revisited three equivalent formulas, namely, coupled-perturbed self-consistent field (CPSCF), random phase approximation (RPA), and Green’s function (GF). We further extended these formulas to the linear-scaling methods based on the divide-and-conquer (DC) technique. We implemented the CCLR with singles and doubles (CCSDLR) program for the six schemes, i.e., the standard and DC-type CPSCF, RPA, and GF. Illustrative applications of the present methods demonstrated the accuracy and efficiency. Although the standard three treatments could exactly reproduced the conventional frequency-domain CCSDLR results, their computational costs were commonly higher than that of the conventional ones due to large amount of computations for individual frequencies of the external electric field. The DC-type treatments, which approximately reproduced the conventional results, could achieve quasilinear scaling computational costs. Among them, DC-GF was found to exhibit the best performance.

    更新日期:2020-01-14
  • Adaptive Markov state model estimation using short reseeding trajectories
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Hongbin Wan, Vincent A. Voelz

    In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow time scales. A promising approach to enhanced sampling of MSMs is to use “adaptive” methods, in which new MD trajectories are “seeded” preferentially from previously identified states. Here, we investigate the performance of various MSM estimators applied to reseeding trajectory data, for both a simple 1D free energy landscape and mini-protein folding MSMs of WW domain and NTL9(1–39). Our results reveal the practical challenges of reseeding simulations and suggest a simple way to reweight seeding trajectory data to better estimate both thermodynamic and kinetic quantities.

    更新日期:2020-01-14
  • Dissipation and dynamics in ultrafast intersystem crossings
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Michel van Veenendaal

    The effects of dynamics and dissipation on ultrafast intersystem crossings are studied for a dissipative two-level system coupled to a local vibronic mode. A method of amplitude damping of the wave packet is presented that accounts better for the position of the wave packet and avoids spurious transitions between potential wells. It is demonstrated that Fermi’s golden rule, the typical semiquantitative approach to extract population transfer rates from potential landscapes, only holds under limited conditions. Generally, the effects of dynamics and dissipation lead to deviations from the expected exponential population transfer, strong changes in transfer times and total population transfer, and significant recurrence or “spill back” of the wave packet.

    更新日期:2020-01-14
  • Use of the complete basis set limit for computing highly accurateab initiodipole moments
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Eamon K. Conway, Iouli E. Gordon, Oleg L. Polyansky, Jonathan Tennyson

    Calculating dipole moments with high-order basis sets is generally only possible for the light molecules, such as water. A simple, yet highly effective strategy of obtaining high-order dipoles with small, computationally less expensive basis sets is described. Using the finite field method for computing dipoles, energies calculated with small basis sets can be extrapolated to produce dipoles that are comparable to those obtained in high order calculations. The method reduces computational resources by approximately 50% (allowing the calculation of reliable dipole moments for larger molecules) and simultaneously improves the agreement with experimentally measured infrared transition intensities. For atmospherically important molecules, which are typically too large to consider the use of large basis sets, this procedure will provide the necessary means of improving calculated spectral intensities by several percent.

    更新日期:2020-01-14
  • Quantum momentum distribution and quantum entanglement in the deep tunneling regime
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Yantao Wu, Roberto Car

    In this paper, we consider the momentum operator of a quantum particle directed along the displacement of two of its neighbors. A modified open-path path integral molecular dynamics is presented to sample the distribution of this directional momentum distribution, where we derive and use a new estimator for this distribution. Variationally enhanced sampling is used to obtain this distribution for an example molecule, malonaldehyde, in the very low temperature regime where deep tunneling happens. We find no secondary feature in the directional momentum distribution and that its absence is due to quantum entanglement through a further study of the reduced density matrix.

    更新日期:2020-01-14
  • Coarse-grained simulations of diffusion controlled release of drugs from neutral nanogels: Effect of excluded volume interactions
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    José Alberto Maroto-Centeno, Manuel Quesada-Pérez

    The primary goal of this work is to assess the effect of excluded volume interactions on the diffusion controlled release of drug molecules from a spherical, neutral, inert, and cross-linked device of nanometric size. To this end, coarse-grained simulations of the release process were performed. In this way, the inner structure and topology of the polymer network can be explicitly taken into account as well. Our in silico experiments reveal that the boundary condition of constant surface concentration is not appropriate for nanogels. In particular, the predictions based on the perfect sink condition clearly overestimate the fraction of drug released. In addition, these simulations provide values for the release exponent that depends on both the diameter of drug molecules and the number of drug molecules loaded in the matrix, which clearly contrasts with the classical prediction of a constant release exponent. Consequently, the widely used classification of drug release mechanisms based on this kinetic exponent must be extended to include new situations.

    更新日期:2020-01-14
  • Transforming high-dimensional potential energy surfaces into a canonical polyadic decomposition using Monte Carlo methods
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Markus Schröder

    A Monte Carlo method is proposed for transforming high-dimensional potential energy surfaces evaluated on discrete grid points into a sum-of-products form, more precisely into a Canonical Polyadic Decomposition form. To this end, a modified existing ansatz based on the alternating least squares method is used, in which numerically exact integrals are replaced with Monte Carlo integrals. This largely reduces the numerical cost by avoiding the evaluation of the potential on all grid points and allows the treatment of surfaces with many degrees of freedom. Calculations on the 15D potential of the protonated water dimer (Zundel cation) in a sum-of-products form are presented and compared to the results obtained in a previous work [M. Schröder and H.-D. Meyer, J. Chem. Phys. 147, 064105 (2017)], where a sum-of-products form of the potential was obtained in the Tucker format.

    更新日期:2020-01-14
  • Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Maria Pechlaner, Wilfred F. van Gunsteren

    Various algorithms to apply dihedral-angle constraints in molecular dynamics or stochastic dynamics simulations of molecular systems are presented, investigated, and tested. They use Cartesian coordinates and determine the Lagrangian multipliers necessary for maintaining the constraints iteratively. The most suitable algorithm to maintain a dihedral-angle constraint is numerically compared to the alternative to use distance constraints to this end. It can easily be used to obtain a potential of mean force along a dihedral-angle coordinate.

    更新日期:2020-01-14
  • Bayesian counting of photobleaching steps with physical priors
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Jon Garry, Yuchong Li, Brandon Shew, Claudiu C. Gradinaru, Andrew D. Rutenberg

    Counting fluorescence photobleaching steps is commonly used to infer the number n0 of monomeric units of individual oligomeric protein complexes or misfolded protein aggregates. We present a principled Bayesian approach for counting that incorporates the statistics of photobleaching. Our physics-based prior leads to a simple and efficient numerical scheme for maximum a posteriori probability (MAP) estimates of the initial fluorophore number n^0. Our focus here is on using a calibration to precisely estimate n^0, though our approach can also be used to calibrate the photophysics. Imaging noise increases with n^0, while bias is often introduced by temporal averaging. We examine the effects of fluorophore number n^0 of the oligomer or aggregate, lifetime photon yield μeff of an individual fluorophore, and exposure time Δt of each image frame in a time-lapse experiment. We find that, in comparison with standard ratiometric approaches or with a “change-point” step-counting algorithm, our MAP approach is both more precise and less biased.

    更新日期:2020-01-14
  • An accelerated linear method for optimizing non-linear wavefunctions in variational Monte Carlo
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Iliya Sabzevari, Ankit Mahajan, Sandeep Sharma

    Although the linear method is one of the most robust algorithms for optimizing nonlinearly parametrized wavefunctions in variational Monte Carlo, it suffers from a memory bottleneck due to the fact that at each optimization step, a generalized eigenvalue problem is solved in which the Hamiltonian and overlap matrices are stored in memory. Here, we demonstrate that by applying the Jacobi-Davidson algorithm, one can solve the generalized eigenvalue problem iteratively without having to build and store the matrices in question. The resulting direct linear method greatly lowers the cost and improves the scaling of the algorithm with respect to the number of parameters. To further improve the efficiency of optimization for wavefunctions with a large number of parameters, we use the first order method AMSGrad far from the minimum as it is very inexpensive and only switch to the direct linear method near the end of the optimization where methods such as AMSGrad have long convergence tails. We apply this improved optimizer to wavefunctions with real and orbital space Jastrow factors applied to a symmetry-projected generalized Hartree-Fock reference. Systems addressed include atomic systems such as beryllium and neon, molecular systems such as the carbon dimer and iron(ii) porphyrin, and model systems such as the Hubbard model and hydrogen chains.

    更新日期:2020-01-14
  • Compressed intramolecular dispersion interactions
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Cameron J. Mackie, Jérôme F. Gonthier, Martin Head-Gordon

    The feasibility of the compression of localized virtual orbitals is explored in the context of intramolecular long-range dispersion interactions. Singular value decomposition (SVD) of coupled cluster doubles amplitudes associated with the dispersion interactions is analyzed for a number of long-chain systems, including saturated and unsaturated hydrocarbons and a silane chain. Further decomposition of the most important amplitudes obtained from these SVDs allows for the analysis of the dispersion-specific virtual orbitals that are naturally localized. Consistent with previous work on intermolecular dispersion interactions in dimers, it is found that three important geminals arise and account for the majority of dispersion interactions at the long range, even in the many body intramolecular case. Furthermore, it is shown that as few as three localized virtual orbitals per occupied orbital can be enough to capture all pairwise long-range dispersion interactions within a molecule.

    更新日期:2020-01-14
  • Intermediate state representation approach to physical properties of molecular electron-detached states. I. Theory and implementation
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Adrian L. Dempwolff, Alexander C. Paul, Alexandra M. Belogolova, Alexander B. Trofimov, Andreas Dreuw

    The third-order non-Dyson algebraic-diagrammatic construction approach to the electron propagator [IP-ADC(3)] is extended using the intermediate state representation (ISR) formalism, allowing the wave functions and properties of molecular states with detached electron to be studied. The second-order ISR equations [ISR(2)] for the one-particle (transition) density matrix have been derived and implemented in the Q-CHEM program. The approach is completely general and enables evaluation of arbitrary one-particle operators and interpretation of electron detachment processes in terms of density-based quantities. The IP-ADC(3)/ISR(2) equations were implemented for Ŝz-adapted intermediate states, allowing open-shell molecules to be studied using unrestricted Hartree-Fock references. As a first test for computations of ground state properties, dipole moments of various closed- and open-shell molecules have been computed by means of electron detachment from the corresponding anions. The results are in good agreement with experimental data. The potential of IP-ADC(3)/ISR(2) for the interpretation of photoelectron spectra is demonstrated for the galvinoxyl free radical.

    更新日期:2020-01-14
  • Shadow Hamiltonian in classical NVE molecular dynamics simulations: A path to long time stability
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    K. D. Hammonds, D. M. Heyes

    The shadow energy, Es, is the conserved quantity in microcanonical ensemble (NVE) molecular dynamics simulations carried out with the position Verlet central-difference algorithm. A new methodology for calculating precise and accurate values of Es is presented. It is shown for the first time that Es rather than E is constant during structural changes occurring within a supercooled liquid. It is also explained how to prepare and conduct microsecond range bulk-phase NVE simulations with essentially zero energy drift without the need for thermostating. The drift is analyzed with block averaging and new drift functions of the shadow energy. With such minimal drift, extremely small and accurate standard errors in the mean for quantities like Es, E, and temperature, T, can be obtained. Values of the standard error for Es of ≈10−10 in molecule-based reduced units can be routinely achieved for simulations of 108 time steps. This corresponds to a simulation temperature drift of ≈10−6 K/μs, six orders of magnitude smaller than generally considered to be acceptable for protein simulations. We also show for the first time how these treatments can be extended with no loss of accuracy to polyatomic systems with both flexible degrees of freedom and arbitrary geometric constraints imposed via the SHAKE algorithm. As a bonus, estimates of simulation-average kinetic and total energies from high order velocity expressions can be obtained to a good approximation from 2nd order velocities and the average mean square force (for polyatomics, this refers to per site, including any constraint forces).

    更新日期:2020-01-14
  • Binuclear Mn oxo complex as a self-contained photocatalyst in water-splitting cycle: Role of additional Mn oxides as a buffer of electrons and protons
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Kentaro Yamamoto, Kazuo Takatsuka

    We theoretically propose a photoinduced water-splitting cycle catalyzed by a binuclear Mn oxo complex. In our “bottom-up approach” to this problem, we once proposed a working minimal model of water-splitting cycle in terms of a mononuclear Mn oxo complex as a catalyst along with water clusters [K. Yamamoto and K. Takatsuka, Phys. Chem. Chem. Phys. 20, 6708 (2018)]. However, this catalyst is not self-contained in that the cycle additionally needs buffering molecules for electrons and protons in order to reload the Mn complex with electrons and protons, which are lost by photoinduced charge separation processes. We here show that a binuclear Mn oxo complex works as a self-contained photocatalyst without further assistant of additional reagents and propose another catalytic cycle in terms of this photocatalyst. Besides charge separation and proton relay transfer, the proposed cycle consists of other fundamental chemical dynamics including electron–proton reloading, radical relay-transfer, and Mn reduction. The feasibility of the present water-splitting cycle is examined by means of full dimensional nonadiabatic electron–wavepacket dynamics based on multireference electronic wavefunctions and energy profiles estimated with rather accurate quantum chemical methods for all the metastable states appearing in the cycle.

    更新日期:2020-01-14
  • Linear scaling perturbative triples correction approximations for open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory [DLPNO-CCSD(T0/T)]
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Yang Guo, Christoph Riplinger, Dimitrios G. Liakos, Ute Becker, Masaaki Saitow, Frank Neese

    The coupled cluster method with single-, double-, and perturbative triple excitations [CCSD(T)] is considered to be one of the most reliable quantum chemistry theories. However, the steep scaling of CCSD(T) has limited its application to small or medium-sized systems for a long time. In our previous work, the linear scaling domain based local pair natural orbital CCSD variant (DLPNO-CCSD) has been developed for closed-shell and open-shell. However, it is known from extensive benchmark studies that triple-excitation contributions are important to reach chemical accuracy. In the present work, two linear scaling (T) approximations for open-shell DLPNO-CCSD are implemented and compared: (a) an algorithm based on the semicanonical approximation, in which off-diagonal Fock matrix elements in the occupied space are neglected [referred to as DLPNO-(T0)]; and (b) an improved algorithm in which the triples amplitudes are computed iteratively [referred to as DLPNO-(T)]. This work is based on the previous open-shell DLPNO-CCSD algorithm [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] as well as the iterative (T) correction for closed-shell systems [Y. Guo et al., J. Chem. Phys. 148, 011101 (2018)]. Our results show that the new open-shell perturbative corrections, DLPNO-(T0/T), can predict accurate absolute and relative correlation energies relative to the canonical reference calculations with the same basis set. The absolute energies from DLPNO-(T) are significantly more accurate than those of DLPNO-(T0). The additional computational effort of DLPNO-(T) relative to DLPNO-(T0) is a factor of 4 on average. We report calculations on systems with more than 4000 basis functions.

    更新日期:2020-01-14
  • Evaluation of the AMOEBA force field for simulating metal halide perovskites in the solid state and in solution
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    P. V. G. M. Rathnayake, Stefano Bernardi, Asaph Widmer-Cooper

    In this work, we compare the existing nonpolarizable force fields developed to study the solid or solution phases of hybrid organic-inorganic halide perovskites with the AMOEBA polarizable force field. The aim is to test whether more computationally expensive polarizable force fields like AMOEBA offer better transferability between solution and solid phases, with the ultimate goal being the study of crystal nucleation, growth, and other interfacial phenomena involving these ionic compounds. In the context of hybrid perovskites, AMOEBA force field parameters already exist for several elements in solution, and we decided to leave them unchanged and to only parameterize the missing ones (Pb2+ and CH3NH3+ ions) in order to maximize transferability and avoid overfitting to the specific examples studied here. Overall, we find that AMOEBA yields accurate hydration free energies (within 5%) for typical ionic species while showing the correct ordering of stability for the different crystal polymorphs of CsPbI3 and CH3NH3PbI3. Although the existing parameters do not accurately reproduce all transition temperatures and lattice parameters, AMOEBA offers better transferability between solution and solid states than existing nonpolarizable force fields.

    更新日期:2020-01-14
  • Orbital localization error of density functional theory in shear properties of vanadium and niobium
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Yi X. Wang, Hua Y. Geng, Q. Wu, Xiang R. Chen

    It is believed that the density functional theory (DFT) describes most elements with s, p, and d orbitals very well, except some materials that have strongly localized and correlated valence electrons. In this work, we find that the widely employed exchange-correlation (XC) functionals, including local-density approximation (LDA), generalized gradient approximation (GGA), and meta-GGA, underestimate the shear modulus and phase stability of V and Nb greatly. The advanced hybrid functional that is usually better for correlated systems, on the other hand, completely fails in these two simple metals. This striking failure is revealed due to the orbital localization error in GGA, which is further deteriorated by hybrid functionals. This observation is corroborated by a similar failure of DFT+U and van der Waals functionals when applied to V and Nb. To remedy this problem, a semiempirical approach of DFT+J is proposed, which can delocalize electrons by facilitating the on-site exchange. Furthermore, it is observed that including density derivatives slightly improves the performance of the semilocal functionals, with meta-GGA outperforms GGA, and the latter is better than LDA. This discovery indicates the possibility and necessity to include higher-order density derivatives beyond the Laplacian level for the purpose of removing the orbital localization error (mainly from d orbitals) and delocalization error (mainly from s and p orbitals) completely in V and Nb so that a better description of their electronic structures is achieved. The same strategy can be applied to the other d electron system and f electron system.

    更新日期:2020-01-14
  • Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Noriyuki Minezawa, Takahito Nakajima

    This paper presents the nonadiabatic molecular dynamics simulation in the solution phase using the spin-flip time-dependent density functional theory (SF-TDDFT). Despite the single-reference level of theory, the SF-TDDFT method can generate the correct topology of S0/S1 crossing points, thus providing a natural S1 → S0 nonadiabatic transition. We extend the gas-phase trajectory surface hopping simulation with the SF-TDDFT [N. Minezawa and T. Nakajima, J. Chem. Phys. 150, 204120 (2019)] to the hybrid quantum mechanical/molecular mechanics (QM/MM) scheme. To this end, we modify the code to evaluate the electrostatic interaction between the QM and MM atoms and to extract the classical MM energy and forces from the MM program package. We apply the proposed method to the photoisomerization reaction of aqueous E-azomethane and anionic green fluorescent protein chromophore in water and compare the results with those of the previous simulation studies based on the multireference methods.

    更新日期:2020-01-14
  • The nuclear Overhauser Effect (NOE) as a tool to study macromolecular confinement: Elucidation and disentangling of crowding and encapsulation effects
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Philipp Honegger, Othmar Steinhauser

    We propose a methodology to capture short-lived but biophysically important contacts of biomacromolecules using the biomolecule-water nuclear Overhauser effect as an indirect microscope. Thus, instead of probing the direct correlation with the foreign biomolecule, we detect its presence by the disturbance it causes in the surrounding water. In addition, this information obtained is spatially resolved and can thus be attributed to specific sites. We extend this approach to the influence of more than one change in chemical environment and show a methodological way of resolution. This is achieved by taking double differences of corresponding σNOE/σROE ratios of the systems studied and separating specific, unspecific, and intermediate influence. While applied to crowding and encapsulation in this study, this method is generally suitable for any combination of changes in chemical environment.

    更新日期:2020-01-14
  • Electrostatic interactions between spheroidal dielectric particles
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Ivan N. Derbenev, Anatoly V. Filippov, Anthony J. Stace, Elena Besley

    Theory is developed to address the significant problem of electrostatic interactions between charged polarizable dielectric spheroids. The electrostatic force is defined by particle dimensions and charge, dielectric constants of the interacting particles and medium, and the interparticle separation distance; and it is expressed in the form of an integral over the particle surface. The switching behavior between like charge repulsion and attraction is demonstrated as depending on the ratio of the major and minor axes of spheroids. When the major and minor axes are equal, the theory yields a solution equivalent to that obtained for spherical particles. Limiting cases are presented for nonpolarizable spheroids, which describe the electrostatic behavior of charged rods, discs, and point charges. The developed theory represents an important step toward comprehensive understanding of direct interactions and mechanisms of electrostatically driven self-assembly processes.

    更新日期:2020-01-14
  • Techniques for high-performance construction of Fock matrices
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Hua Huang, C. David Sherrill, Edmond Chow

    This paper presents techniques for Fock matrix construction that are designed for high performance on shared and distributed memory parallel computers when using Gaussian basis sets. Four main techniques are considered. (1) To calculate electron repulsion integrals, we demonstrate batching together the calculation of multiple shell quartets of the same angular momentum class so that the calculation of large sets of primitive integrals can be efficiently vectorized. (2) For multithreaded summation of entries into the Fock matrix, we investigate using a combination of atomic operations and thread-local copies of the Fock matrix. (3) For distributed memory parallel computers, we present a globally accessible matrix class for accessing distributed Fock and density matrices. The new matrix class introduces a batched mode for remote memory access that can reduce the synchronization cost. (4) For density fitting, we exploit both symmetry (of the Coulomb and exchange matrices) and sparsity (of 3-index tensors) and give a performance comparison of density fitting and the conventional direct calculation approach. The techniques are implemented in an open-source software library called GTFock.

    更新日期:2020-01-14
  • Timescale prediction of complex multi-barrier pathways using flux sampling molecular dynamics and 1D kinetic integration: Application to cellulose dehydration
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Pierre-Louis Valdenaire, Roland J. M. Pellenq, Franz J. Ulm, Adri C. T. van Duin, Jean-Marc Leyssale

    Reactive molecular dynamics (MD) simulations, especially those employing acceleration techniques, can provide useful insights on the mechanism underlying the transformation of buried organic matter, yet, so far, it remains extremely difficult to predict the time scales associated with these processes at moderate temperatures (i.e., when such time scales are considerably larger than those accessible to MD). We propose here an accelerated method based on flux sampling and kinetic integration along a 1D order parameter that can considerably extend the accessible time scales. We demonstrate the utility of this technique in an application to the dehydration of crystalline cellulose at temperatures ranging from 1900 K to 1500 K. The full decomposition is obtained at all temperatures apart from T = 1500 K, showing the same distribution of the main volatiles (H2O, CO, and CO2) as recently obtained using replica exchange molecular dynamics. The kinetics of the process is well fitted with an Arrhenius law with Ea = 93 kcal/mol and k0 = 9 × 1019 s−1, which are somehow larger than experimental reports. Unexpectedly, the process seems to considerably slow down at lower temperatures, severely departing from the Arrhenius regime, probably because of an inadequate choice of the order parameter. Nevertheless, we show that the proposed method allows considerable time sampling at low temperatures compared to conventional MD.

    更新日期:2020-01-14
  • Parameter-free coordination numbers for solutions and interfaces
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Ruben Staub, Stephan N. Steinmann

    Coordination numbers are among the central quantities to describe the local environment of atoms and are thus used in various applications such as structure analysis, fingerprints, and parameters. Yet, there is no consensus regarding a practical algorithm, and many proposed methods are designed for specific systems. In this work, we propose a scale-free and parameter-free algorithm for nearest neighbor identification. This algorithm extends the powerful Solid-Angle based Nearest-Neighbor (SANN) framework to explicitly include local anisotropy. As such, our Anisotropically corrected SANN (ASANN) algorithm provides with a fast, robust, and adaptive method for computing coordination numbers. The ASANN algorithm is applied to flat and corrugated metallic surfaces to demonstrate that the expected coordination numbers are retrieved without the need for any system-specific adjustments. The same applies to the description of the coordination numbers of metal atoms in AuCu nanoparticles, and we show that ASANN based coordination numbers are well adapted for automatically counting neighbors and the establishment of cluster expansions. Analysis of classical molecular dynamics simulations of an electrified graphite electrode reveals a strong link between the coordination number of Cs+ ions and their position within the double layer, a relation that is absent for Na+, which keeps its first solvation shell even close to the electrode.

    更新日期:2020-01-14
  • Intermediate state representation approach to physical properties of molecular electron-detached states. II. Benchmarking
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-14
    Adrian L. Dempwolff, Alexander C. Paul, Alexandra M. Belogolova, Alexander B. Trofimov, Andreas Dreuw

    The third-order algebraic-diagrammatic construction method for studies of electron detachment processes within the electron propagator framework [IP-ADC(3)] was extended to treat the properties of molecular states with a detached electron using the intermediate state representation (ISR) formalism. The second-order ISR(2) equations for the one-particle (transition) density matrix have been derived and implemented as an extension of the IP-(U)ADC(3) method available in the Q-CHEM program. As a first systematic test of the present IP-(U)ADC(3)/ISR(2) method, the dipole moments of various electronic states of closed- and open-shell molecules have been computed and compared to full configuration interaction (FCI) results. The present study employing FCI benchmarks also provides the first rigorous estimates for the accuracy of electron detachment energies obtained using the IP-ADC(3) method.

    更新日期:2020-01-14
  • Interpreting the chemical mechanism in SERS using a Raman bond model
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-14
    Ran Chen, Lasse Jensen

    We present a first-principles model that partitions Raman intensities to atomic and bond contributions. This framework allows us to interpret the chemical mechanism in surface-enhanced Raman scattering (SERS) as interatom charge flow modulations, which we define as Raman bonds. Hirshfeld partitioning and charge density localization are applied to express polarizability derivatives as charge flow modulations. Model systems consisting of pyridines, thiols, and carbenes interacting with metal clusters are studied using time-dependent density functional theory. We demonstrate that the mode-specific enhancements can be explained as Raman bonds conjugated across the molecule-metal interface. We also illustrate that the changes in Raman intensities induced by electric fields or chemical substitutions can generally be interpreted as changes of charge flows. The model is shown to work consistently for different types of molecule-metal bonds. Furthermore, our work shows that increasing the Raman bond conjugation across the interface leads to stronger chemical enhancements. The Raman bond model developed in this work provides a quantitative and intuitive interpretation of the chemical mechanism in SERS.

    更新日期:2020-01-14
  • Numerical assessment for accuracy and GPU acceleration of TD-DMRG time evolution schemes
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-14
    Weitang Li, Jiajun Ren, Zhigang Shuai

    The time dependent density matrix renormalization group (TD-DMRG) has become one of the cutting edge methods of quantum dynamics for complex systems. In this paper, we comparatively study the accuracy of three time evolution schemes in the TD-DMRG, the global propagation and compression method with the Runge-Kutta algorithm (P&C-RK), the time dependent variational principle based methods with the matrix unfolding algorithm (TDVP-MU), and with the projector-splitting algorithm (TDVP-PS), by performing benchmarks on the exciton dynamics of the Fenna-Matthews-Olson complex. We show that TDVP-MU and TDVP-PS yield the same result when the time step size is converged and they are more accurate than P&C-RK4, while TDVP-PS tolerates a larger time step size than TDVP-MU. We further adopt the graphical processing units to accelerate the heavy tensor contractions in the TD-DMRG, and it is able to speed up the TDVP-MU and TDVP-PS schemes by up to 73 times.

    更新日期:2020-01-14
  • Dissociative recombination of N2H+ions with electrons in the temperature range of 80–350 K
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Dmytro Shapko, Petr Dohnal, Miroslava Kassayová, Ábel Kálosi, Serhiy Rednyk, Štěpán Roučka, Radek Plašil, Lucie D. Augustovičová, Rainer Johnsen, Vladimír Špirko, Juraj Glosík

    Recombination of N2H+ ions with electrons was studied using a stationary afterglow with a cavity ring-down spectrometer. We probed in situ the time evolutions of number densities of different rotational and vibrational states of recombining N2H+ ions and determined the thermal recombination rate coefficients for N2H+ in the temperature range of 80–350 K. The newly calculated vibrational transition moments of N2H+ are used to explain the different values of recombination rate coefficients obtained in some of the previous studies. No statistically significant dependence of the measured recombination rate coefficient on the buffer gas number density was observed.

    更新日期:2020-01-14
  • Sulfurous and sulfonic acids: Predicting the infrared spectrum and setting the surface straight
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Jonathon P. Misiewicz, Kevin B. MooreIII, Peter R. Franke, W. James Morgan, Justin M. Turney, Gary E. Douberly, Henry F. SchaeferIII

    Sulfurous acid (H2SO3) is an infamously elusive molecule. Although some theoretical papers have supposed possible roles for it in more complicated systems, it has yet to be experimentally observed. To aid experiment in detecting this molecule, we have examined the H2O + SO2 potential energy surface at the CCSDT(Q)/CBS//CCSD(T)-F12b/cc-pVTZ-F12b level of theory to resolve standing discrepancies in previous reports and predict the gas-phase vibrational spectrum for H2SO3. We find that sulfurous acid has two potentially detectable rotamers, separated by 1.1 kcal mol−1 ΔH0K with a torsional barrier of 1.6 kcal mol−1. The sulfonic acid isomer is only 6.9 kcal mol−1 above the lowest enthalpy sulfurous acid rotamer, but the barrier to form it is 57.2 kcal mol−1. Error in previous reports can be attributed to misidentified stationary points, the use of density functionals that perform poorly for this system, and, most importantly, the basis set sensitivity of sulfur. Using VPT2+K, we determine that the intense S=O stretch fundamental of each species is separated from other intense peaks by at least 25 cm−1, providing a target for identification by infrared spectroscopy.

    更新日期:2020-01-14
  • O2activation by AuAg clusters on a defective (100)MgO surface
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    F. Buendía, A. T. Anzaldo, Carlos Vital, M. R. Beltrán

    In the present work, we discuss the electronic properties of supported dispersed bimetallic clusters with respect to their size, geometry, and Aun/Agm (n + m = 6) composition. We have studied with supercell-density functional theory calculations the role of the charge transfer from the MgO defective support toward the cluster in the activation of O2 by AunAgm clusters. We first considered gas-phase clusters with different atomic compositions; then, we deposited all of them on a pristine (100)MgO surface and finally on a more realistic (100)MgO F-center. We performed a global and unrestricted search of the (cluster + surface) geometry. The Mexican enhanced genetic algorithm has been used to exhaustively explore the potential energy surface. Our results show that O2 activation depends on the Aun/Agm ratio. It has been found that both metals involved play different and important roles toward (a) the actual O2 dissociation and (b) weakening of the oxygen-cluster bond, which, in turn, may promote the possibility of a catalytic process to take place, such as the oxidation process of CO and NOx among others.

    更新日期:2020-01-14
  • Measurement of sub-2 nm stable clusters during silane pyrolysis in a furnace aerosol reactor
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Miguel Vazquez-Pufleau, Yang Wang, Pratim Biswas, Elijah Thimsen

    The initial stages of particle formation are important in several industrial and environmental systems; however, the phenomenon is not completely understood due to the inability to measure cluster size distributions. A high resolution differential mobility analyzer with an electrometer was used to map out the early stages of Si particle formation from pyrolysis of SiH4 in a furnace aerosol reactor. We detected for the first time subnanometer stable clusters from silane pyrolysis, and the diameter was measured to be about 0.7 nm. This diameter is within the range of probable sizes that the reported families of critical silane clusters could have based on their actual molecular structure. The size distributions of negative clusters are also mapped out. In addition, gas chromatography mass spectrometry, and transmission electron microscopy characterizations of the clusters and primary particles are used to assess their mechanistic roles in aerosol dynamics of the initial stages of particle formation.

    更新日期:2020-01-14
  • Vibrational states of deuteratedtrans- andcis-formic acid: DCOOH, HCOOD, and DCOOD
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Antoine Aerts, P. Carbonnière, F. Richter, Alex Brown

    The vibrational eigenenergies of the deuterated forms of formic acid (DCOOD, HCOOD, and DCOOH) have been computed using the block-improved relaxation method, as implemented in the Heidelberg multiconfiguration time-dependent Hartree package on a previously published potential energy surface [F. Richter and P. Carbonnière, J. Chem. Phys. 148, 064303 (2018)] generated at the CCSD(T)-F12a/aug-cc-pVTZ-F12 level of theory. Fundamental, combination band, and overtone transition frequencies of the trans isomer were computed up to ∼3000 cm−1 with respect to the zero point energy, and assignments were determined by visualization of the reduced densities. Root mean square deviations of computed fundamental transition frequencies with experimentally available gas-phase measurements are 8, 7, and 3 cm−1 for trans-DCOOD, trans-HCOOD, and trans-DCOOH, respectively. The fundamental transition frequencies are provided for the cis isomer of all deuterated forms; experimental measurements of these frequencies for the deuterated cis isotopologues are not yet available, and the present work may guide their identification.

    更新日期:2020-01-14
  • On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Max F. Döpke, Othonas A. Moultos, Remco Hartkamp

    Countless molecular dynamics studies have relied on available ion and water force field parameters to model aqueous electrolyte solutions. The TIP4P/2005 model has proven itself to be among the best rigid water force fields, whereas many of the most successful ion parameters were optimized in combination with SPC/E, TIP3P, or TIP4P/Ew water. Many researchers have combined these ions with TIP4P/2005, hoping to leverage the strengths of both parameter sets. To assess if this widely used approach is justified and to provide a guide in selecting ion parameters, we investigated the transferability of various commonly used monovalent and multivalent ion parameters to the TIP4P/2005 water model. The transferability is evaluated in terms of ion hydration free energy, hydration radius, coordination number, and self-diffusion coefficient at infinite dilution. For selected ion parameters, we also investigated density, ion pairing, chemical potential, and mean ionic activity coefficients at finite concentrations. We found that not all ions are equally transferable to TIP4P/2005 without compromising their performance. In particular, ions optimized for TIP3P water were found to be poorly transferable to TIP4P/2005, whereas ions optimized for TIP4P/Ew water provided nearly perfect transferability. The latter ions also showed good overall agreement with experimental values. The one exception is that no combination of ion parameters and water model considered here was found to accurately reproduce experimental self-diffusion coefficients. Additionally, we found that cations optimized for SPC/E and TIP3P water displayed consistent underpredictions in the hydration free energy, whereas anions consistently overpredicted the hydration free energy.

    更新日期:2020-01-14
  • An analysis of radical diffusion in ionic liquids in terms of free volume theory
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Dalibor Merunka, Miroslav Peric

    The Heisenberg spin exchange–dipole-dipole separation method was used to measure the translational diffusion coefficients of the 14N-labeled perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (14N-pDTEMPONE) nitroxide spin probe as a function of temperature in two methylimidazolium ionic liquid series, one based on the tetrafluoroborate (BF4) anion and another one on the bis(trifluoromethane)sulfonimide (TFSI, Tf2N) anion. The obtained translational diffusion coefficients of 14N-pDTEMPONE were analyzed in terms of the Cohen–Turnbull free volume theory. It was found that the Cohen-Turnbull theory describes, exceptionally well, the translational diffusion of 14N-pDTEMPONE in all the ionic liquids in the measured temperature range. In addition, the Cohen-Turnbull theory was applied to the viscosity and self-diffusion coefficients of the cation and anion—taken from literature—in the same ionic liquids. The critical free volume for the self-diffusion of the cation and anion in a given ionic liquid is the same, which suggests that the diffusion of each ionic pair is coordinated. The critical free volumes for the 14N-pDTEMPONE diffusion, self-diffusion, and viscosity for a given cation were about 20% greater in the TFSI based ionic liquids than in the BF4 based ionic liquids. It appears that the ratio of the critical free volumes for a given cation between the two series correlates with the ratio of their densities.

    更新日期:2020-01-14
  • Comparison of time reversal symmetric and asymmetric nano-swimmers oriented with an electric field in soft matter
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    G. Rajonson, D. Poulet, M. Bruneau, V. Teboul

    Using molecular dynamics simulations, we compare the motion of a nanoswimmer based on Purcell’s suggested motor with a time asymmetrical cycle with the motion of the same molecular motor with a time symmetrical cycle. We show that Purcell’s theorem still holds at the nanoscale, despite the local structure and the medium’s fluctuations. Then, with the purpose of both orienting the swimmer’s displacement and increasing the breakdown of the theorem, we study the effect of an electric field on a polarized version of these swimmers. For small and large fields, the time asymmetrical swimmer is more efficient, as suggested by Purcell. However, we find a field range for which Purcell’s theorem is broken for the time symmetric motor. Results suggest that the breakdown of the theorem arises from the competition of the orientation field and Brownian forces, while for larger fields, the field destroys the effect of fluctuations restoring the theorem.

    更新日期:2020-01-14
  • How methane hydrate recovers at very high pressure the hexagonal ice structure
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    S. Schaack, Ph. Depondt, M. Moog, F. Pietrucci, F. Finocchi

    Methane hydrate was recently shown, both experimentally and through simulations, to be stable up to the remarkably high pressure of 150 GPa. A new methane hydrate high-pressure (MH-IV) phase, reminiscent of ice at ambient pressure, was described for pressures above approximately 40 GPa. We disentangle here the main contributions to the relative stability of the lower pressure, denoted MH-III, and the high-pressure MH-IV structures. Through several simulation techniques, including metadynamics and path integral molecular dynamics for nuclear quantum effects, we analyze the phase transition mechanism, which implies hydrogen bond breaking and reforming, as well as methane reordering. The transition pathway is far from trivial, and the quantum delocalization of the hydrogen nuclei plays a significant role.

    更新日期:2020-01-14
  • Non-monotonic response of a sheared magnetic liquid crystal to a continuously increasing external field
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-14
    Nima H. Siboni, Gaurav P. Shrivastav, Sabine H. L. Klapp

    Utilizing molecular dynamics simulations, we report a nonmonotonic dependence of the shear stress on the strength of a continuously increasing (i.e., time-varying) external magnetic field (H) in a liquid-crystalline mixture of magnetic and nonmagnetic anisotropic particles. We relate the origin of this nonmonotonicity of the transient dynamics to the competing effects of particle alignment along the shear-induced direction, on the one hand, and the magnetic field direction, on the other hand. To isolate the role of these competing effects, we consider a two-component mixture composed of particles with effectively identical steric interactions, where the orientations of a small fraction, i.e., the magnetic ones, are coupled to the external magnetic field. By increasing H from zero, the orientations of the magnetic particles show a Fréederickz-like transition and eventually start deviating from the shear-induced orientation, leading to an increase in shear stress. Upon further increase of H, a demixing of the magnetic particles from the nonmagnetic ones occurs, which leads to a drop in shear stress, hence creating a nonmonotonic response to H. Unlike the equilibrium demixing phenomena reported in previous studies, the demixing observed here is neither due to size-polydispersity nor due to a wall-induced nematic transition. Based on a simplified Onsager analysis, we rather argue that it occurs solely due to packing entropy of particles with different shear- or magnetic-field-induced orientations.

    更新日期:2020-01-14
  • Catalysis on oxidized ferroelectric surfaces—Epitaxially strained LaTiO2N and BaTiO3for photocatalytic water splitting
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Nathalie Vonrüti, Ulrich Aschauer

    Surface properties of ferroelectrics are promising for catalysis due to the spontaneous electric polarization that can be reversed by an applied electric field. While several theoretical studies show different catalytic activities for differently polarized ferroelectric surfaces at zero electric potential, little work was devoted to catalysis on ferroelectric surfaces at higher electric potentials. Under these conditions that are relevant for photocatalytic experiments and applications, surfaces are usually oxidized. Using density functional theory calculations, we show for LaTiO2N and BaTiO3 that this oxidation heavily impacts and even determines the electronic properties of the catalyst surface and therefore leads to similar reaction free energies for the catalytic steps of the oxygen evolution reaction, irrespective of the bulk polarization. This is opposed to experimental studies, which found different activities for differently polarized catalyst surface domains under oxidizing conditions. We therefore conclude that the experimentally observed activity difference does not originate from the surface polarization following the bulk polarization, but rather from different bulk polarization directions leading to different adsorbate coverages or even surface reconstructions.

    更新日期:2020-01-14
  • Sn-modification of Pt7/alumina model catalysts: Suppression of carbon deposition and enhanced thermal stability
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-08
    Guangjing Li, Borna Zandkarimi, Ashley C. Cass, Timothy J. Gorey, Bradley J. Allen, Anastassia N. Alexandrova, Scott L. Anderson

    An atomic layer deposition process is used to modify size-selected Pt7/alumina model catalysts by Sn addition, both before and after Pt7 cluster deposition. Surface science methods are used to probe the effects of Sn-modification on the electronic properties, reactivity, and morphology of the clusters. Sn addition, either before or after cluster deposition, is found to strongly affect the binding properties of a model alkene, ethylene, changing the number and type of binding sites, and suppressing decomposition leading to carbon deposition and poisoning of the catalyst. Density functional theory on a model system, Pt4Sn3/alumina, shows that the Sn and Pt atoms are mixed, forming alloy clusters with substantial electron transfer from Sn to Pt. The presence of Sn also makes all the thermally accessible structures closed shell, such that ethylene binds only by π-bonding to a single Pt atom. The Sn-modified catalysts are quite stable in repeated ethylene temperature programmed reaction experiments, suggesting that the presence of Sn also reduces the tendency of the sub-nano-clusters to undergo thermal sintering.

    更新日期:2020-01-14
  • Assessment of dynamic structural instabilities across 24 cubic inorganic halide perovskites
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    Ruo Xi Yang, Jonathan M. Skelton, Estelina L. da Silva, Jarvist M. Frost, Aron Walsh

    Metal halide perovskites are promising candidates for next-generation photovoltaic and optoelectronic applications. The flexible nature of the octahedral network introduces complexity when understanding their physical behavior. It has been shown that these materials are prone to decomposition and phase competition, and the local crystal structure often deviates from the average space group symmetry. To make stable phase-pure perovskites, understanding their structure–composition relations is of central importance. We demonstrate, from lattice dynamics calculations, that the 24 inorganic perovskites ABX3 (A = Cs, Rb; B = Ge, Sn, Pb; X = F, Cl, Br, I) exhibit instabilities in their cubic phase. These instabilities include cation displacements, octahedral tilting, and Jahn-Teller distortions. The magnitudes of the instabilities vary depending on the chemical identity and ionic radii of the composition. The tilting instabilities are energetically dominant and reduce as the tolerance factor increases, whereas cation displacements and Jahn-Teller type distortions depend on the interactions between the constituent ions. We further considered representative tetragonal, orthorhombic, and monoclinic perovskite phases to obtain phonon-stable structures for each composition. This work provides insights into the thermodynamic driving force of the instabilities and will help guide computer simulations and experimental synthesis in material screening.

    更新日期:2020-01-14
  • Filter function of graphene oxide: Trapping perfluorinated molecules
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-09
    David Barker, Angelica Fors, Emelie Lindgren, Axel Olesund, Elsebeth Schröder

    We need clean drinking water, but current water purification methods are not always sufficient. This study examines the binding and binding mechanisms when graphene oxide is used as a filter material for removing perfluorinated substances and trihalomethanes. We use density functional theory calculations to examine the binding of the harmful molecules on graphene oxide. Our results indicate that the binding energies between graphene oxide and the investigated molecules are in the range of 370–1450 meV per molecule, similar to the binding energies obtained in other studies, where adsorption of similar size molecules onto graphene oxide has been investigated. This indicates that graphene oxide has the potential to separate the molecules of interest from the water. Significant contribution to the binding energies comes from the van der Waals (dispersion) interaction between the molecule and graphene oxide, while the hydrogen bonding between the functional groups of graphene oxide and the hydrogen atoms in functional groups on the molecules also plays a role in the binding.

    更新日期:2020-01-14
  • Highly sensitive pressure and temperature induced SPP resonance shift at gold nanohole arrays
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Hiroki Ohnishi, Eyal Sabatani, Dung Vu Thi, Sotatsu Yanagimoto, Takumi Sannomiya

    Short range ordered (SRO) plasmonic nanohole arrays have a distinct surface plasmon polariton resonance in the visible region and exhibit an excellent sensing capability toward changes in the surrounding refractive index. While SRO and perfectly ordered plasmonic hole arrays have similar sensing properties, SRO arrays have clear advantages in fabrication, simplicity, and scalability. In this study, we use SRO gold nanoholes, which are subjected to pressure and temperature cycles, for vacuum and temperature sensing. The response of the transmission spectra to pressure changes in the range 10−3–105 Pa and temperature scans in the range 20–400 °C was recorded. Upon pressure cycling, a reversible response was observed. Upon initial temperature annealing, an irreversible blue shift in the resonance dip position was observed. Upon further temperature cycling, the resonance dip position shifts reversibly, with a notable red shift upon temperature increase. The results are discussed and interpreted based on possible molecular adsorption/desorption upon pressure cycling and in terms of the gold film’s recrystallization, thermal expansion, and free electron density variations.

    更新日期:2020-01-14
  • Improved description of hematite surfaces by the SCAN functional
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-10
    Yitao Si, Mingtao Li, Zhaohui Zhou, Maochang Liu, Oleg Prezhdo

    Controversies on the surface termination of α-Fe2O3 (0001) focus on its surface stoichiometry dependence on the oxygen chemical potential. Density functional theory (DFT) calculations applying the commonly accepted Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional to a strongly correlated system predict the best matching surface termination, but would produce a delocalization error, resulting in an inappropriate bandgap, and thus are not applicable for comprehensive hematite system studies. Besides, the widely applied PBE+U scheme cannot provide evidence for existence of some of the successfully synthesized stoichiometric α-Fe2O3 (0001) surfaces. Hence, a better scheme is needed for hematite DFT studies. This work investigates whether the strongly constrained and appropriately normed (SCAN) approximation reported by Perdew et al. could provide an improved result for the as-mentioned problem, and whether SCAN can be applied to hematite systems. By comparing the results calculated with the PBE, SCAN, PBE+U, and SCAN+U schemes, we find that SCAN and SCAN+U improves the description of the electronic structure of different stoichiometric α-Fe2O3 (0001) surfaces with respect to the PBE results, and that they give a consistent prediction of the surface terminations. Besides, the bulk lattice constants and the bulk density of states are also improved with the SCAN functional. This study provides a general characterization of the α-Fe2O3 (0001) surfaces and rationalizes how the SCAN approximation improves the results of hematite surface calculations.

    更新日期:2020-01-14
  • Chemical interface damping for propagating surface plasmon polaritons in gold nanostripes
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Brendan S. Brown, Gregory V. Hartland

    Leakage radiation microscopy has been used to examine chemical interface damping (CID) for the propagating surface plasmon polariton (PSPP) modes of Au nanostripes—nanofabricated structures with heights of 40 or 50 nm, widths between 2 and 4 µm, and 100 µm lengths. Real space imaging was used to determine the propagation lengths LSPP of the leaky PSPP modes, and back focal plane measurements generated ω vs k dispersion curves, which yield the PSPP group velocities vg. The combination of these two experiments was used to calculate the PSPP lifetime via T1 = LSPP/vg. The difference in T1 times between bare and thiol coated nanostripes was used to determine the dephasing rate due to CID ΓCID for the adsorbed thiol molecules. A variety of different thiol molecules were examined, as well as nanostripes with different dimensions. The values of ΓCID are similar for the different systems and are an order-of-magnitude smaller than the typical values observed for the localized surface plasmon resonances (LSPRs) of Au nanoparticles. Scaling the measured ΓCID values by the effective path length for electron-surface scattering shows that the CID effect for the PSPP modes of the nanostripes is similar to that for the LSPR modes of nanoparticles. This is somewhat surprising given that PSPPs and LSPRs have different properties: PSPPs have a well-defined momentum, whereas LSPRs do not. The magnitude of ΓCID for the nanostripes could be increased by reducing their dimensions, principally the height of the nanostructures. However, decreasing dimensions for the leaky PSPP mode increases radiation damping, which would make it challenging to accurately measure ΓCID.

    更新日期:2020-01-14
  • Water diffusion in rough carbon nanotubes
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-13
    Bruno H. S. Mendonça, Patricia Ternes, Evy Salcedo, Alan B. de Oliveira, Marcia C. Barbosa

    We use molecular dynamics simulations to study the diffusion of water inside deformed carbon nanotubes with different degrees of deformation at 300 K. We found that the number of hydrogen bonds that water forms depends on nanotube topology, leading to enhancement or suppression of water diffusion. The simulation results reveal that more realistic nanotubes should be considered to understand the confined water diffusion behavior, at least for the narrowest nanotubes, when the interaction between water molecules and carbon atoms is relevant.

    更新日期:2020-01-14
  • Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-02
    Bo Peng, Karol Kowalski, Ajay Panyala, Sriram Krishnamoorthy

    Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation and the exploration of the potential application of DNA strands in nanoelectronics. In this work, by employing our recently developed Green’s function coupled-cluster library on supercomputing facilities, we have studied the spectral functions of several guanine–cytosine (G–C) base pair structures ([G–C]n, n = 1–3) for the first time in a relatively broad near-valence regime ([−25.0, −5.0] eV) in the coupled-cluster with singles and doubles level. Our focus is to give a preliminary many-body coupled-cluster understanding and guideline of the vertical ionization energy (VIE), spectral profile, and ionization feature changes of these systems as the system size expands in this near-valence regime. The results show that, as the system size expands, even though the lowest VIEs keep decreasing, the changes of spectral function profile and the relative peak positions get unexpectedly smaller. Further analysis of the ionized states associated with the most intensive peak in the spectral functions reveals non-negligible |2h, 1p⟩’s in the ionized wave functions of the considered G–C base pair systems. The leading |2h, 1p⟩’s associated with the main ionizations from the cytosine part of the G–C base pairs feature a transition from the intra-base-pair cytosine π → π* excitation to the inter-base-pair electron excitation as the size of G–C base pairs expands, which also indicates the minimum quantum region in the many-body calculations of DNA systems.

    更新日期:2020-01-07
  • On the temperature dependence of liquid structure
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-07
    Zeke A. Piskulich, Ward H. Thompson

    We introduce a straightforward method for predicting an equilibrium distribution function over a wide range of temperatures from a single-temperature simulation. The approach is based on a simple application of fluctuation theory and requires only a standard equilibrium molecular dynamics (or Monte Carlo) simulation. In addition, it provides mechanistic insight into the origin of the temperature-dependent behavior. We illustrate the method by predicting the structure of liquid water, as represented by the O–O radial distribution function, for temperatures from 235 to 360 K from a room temperature molecular dynamics simulation.

    更新日期:2020-01-07
  • Capturing static and dynamic correlation withΔNO-MP2 andΔNO-CCSD
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-02
    Joshua W. Hollett, Pierre-François Loos

    The ΔNO method for static correlation is combined with second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster singles and doubles (CCSD) to account for dynamic correlation. The MP2 and CCSD expressions are adapted from finite-temperature CCSD, which includes orbital occupancies and vacancies, and expanded orbital summations. Correlation is partitioned with the aid of damping factors incorporated into the MP2 and CCSD residual equations. Potential energy curves for a selection of diatomics are in good agreement with extrapolated full configuration interaction results and on par with conventional multireference approaches.

    更新日期:2020-01-07
  • The vibronic absorption spectra and exciton dynamics of plasmon-exciton hybrid systems in the regimes ranged from Fano antiresonance to Rabi-like splitting
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-02
    Bin Zhang, WanZhen Liang

    The complex interplay between molecules and plasmonic metal nanoparticles (MNPs) presents a set of particular characteristics in absorption/scattering spectra such as excitonic splitting, asymmetric line shapes, plasmon-induced absorption enhancement and transparencies, etc. Although the MNP-molecule systems have been intensively investigated experimentally and theoretically, the construction of a theoretical framework which can produce all the disparate experimental observations and account for the electron-phonon (e-p) coupling is still in progress. Here, we present a theoretical approach which can account for both the plasmon-exciton coupling and the e-p interaction and produce all the spectral line shapes ranging from Fano antiresonance to Rabi splitting by simply tuning the coupling strength or plasmon damping rate. Additionally, we demonstrate the evolution of vibronic spectra and exciton dynamics with the coupling strength, plasmon damping rate, and detuning energy. It is found that the vibronic structures appearing in Rabi-like spectra are worse resolved, wider, and more largely shifted than those appearing in the Fano regime, attributed to the more significant deformation of the molecular vibrational wavepacket in the Rabi-like regime than that in the Fano regime as the molecular e-p interaction increases. The positive/negative value of detuning energy can induce different degrees of the vibrational wavepacket deformation and subsequently a different effect on the spectra in different coupling regimes.

    更新日期:2020-01-07
  • Ion pair free energy surface as a probe of ionic liquid structure
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-02
    Kalil Bernardino, Kateryna Goloviznina, Margarida Costa Gomes, Agílio A. H. Pádua, Mauro C. C. Ribeiro

    Numerous combinations of cations and anions are possible for the production of ionic liquids with fine-tuned properties once the correlation with the molecular structure is known. In this sense, computer simulations are useful tools to explain and even predict the properties of ionic liquids. However, quantum mechanical methods are usually restricted to either small clusters or short time scales so that parameterized force fields are required to study the bulk liquids. In this work, a method is proposed to enable a comparison between the quantum mechanical system and both polarizable and nonpolarizable force fields by means of the calculation of free energy surfaces for the translational motion of the anion around the cation in gas phase. This method was tested for imidazolium-based cations with 3 different anions, [BF4]−, [N(CN)2]−, and [NTf2]−. Better agreement was found with the density functional theory calculations when polarizability is introduced in the force field. In addition, the ion pair free energy surfaces reproduced the main structural patterns observed in the first coordination shell in molecular dynamics simulations of the bulk liquid, proving to be useful probes for the liquid phase structure that can be computed with higher level methods and the comparison with forcefields can indicate further improvements in their parameterization.

    更新日期:2020-01-07
  • Lead-free hybrid organic-inorganic perovskites for solar cell applications
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-03
    Vu Ngoc Tuoc, Tran Doan Huan

    Within materials informatics, a rapidly developing subfield of materials research, past (curated) data are mined and learned for either discovering new materials or identifying new functionalities of known materials. This paper provides an example of this process. Starting from a recently developed (very diverse) dataset which includes 1346 hybrid organic-inorganic perovskites (HOIPs), we downselect a subset of 350 three dimensional HOIPs to a final set of four lead-free HOIPs, including CH3NH3SnI3, HC(NH2)2SnI3, NH2NH3SnI3, and NH2(CH2)3SnI3, in which the first two were experimentally synthesized and the others remain hypothetical. Using first-principles based computational methods, we show that these HOIPs have preferable electronic band structures and carrier effective mass, good optical properties, and high spectroscopic limited maximum efficiency. Compared to the experimental data, we find that state-of-the-art numerical methods can predict the electronic and optical properties fairly well, while the current model for the spectroscopic limited maximum efficiency is inadequate for capturing the power conversion efficiency of a solar absorber. We suggest that the HOIP dataset should be expanded to include larger structures of HOIPs, thereby being more useful for future data-mining and machine-learning approaches.

    更新日期:2020-01-07
  • Calculation of the EPR g-tensor from auxiliary density functional theory
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-03
    Bernardo Zuniga-Gutierrez, Victor Medel-Juarez, Andres Varona, Henry Nicole González Ramírez, Roberto Flores-Moreno

    The working equations for the calculation of the electron paramagnetic resonance (EPR) g-tensor within the framework of the auxiliary density functional theory (ADFT) are presented. The scheme known as gauge including atomic orbitals (GIAOs) is employed to treat the gauge origin problem. This ADFT-GIAO formulation possesses an inherent high computational performance, allowing for the calculation of the EPR g-tensor of molecules containing some hundreds of atoms in reasonable computational time employing moderate computational resources. The effect of the use of a gauge independent auxiliary density on the quality of the g-tensor calculation for the evaluation of the exchange-correlation contribution is analyzed in this work. The best agreement with the experiment is obtained with the BLYP functional (Becke 1988 exchange and Lee-Yang-Parr correlation) in combination with a double-ζ basis set, in particular aug-cc-pVDZ. Furthermore, models of endohedral fullerenes [email protected]n, with n = {60, 70, 100, 180, 240}, were used for benchmarking its computational performance.

    更新日期:2020-01-07
  • The alchemical energy landscape for a pentameric cluster
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-03
    John W. R. Morgan, Sharon C. Glotzer

    We investigate the energy landscape of an alchemical system of point particles in which the parameters of the interparticle potential are treated as degrees of freedom. Using geometrical optimization, we locate minima and transition states on the landscape for pentamers. We show that it is easy to find the parameters that give the lowest energy minimum and that the distribution of minima on the alchemical landscape is concentrated in particular areas. In contrast to the usual changes to an energy landscape when adding more degrees of freedom, we find that introducing alchemical degrees of freedom can reduce the number of minima. Moreover, compared to landscapes of the same system with fixed parameters, these minima on the alchemical landscape are separated by high barriers. We classify transition states on the alchemical landscape by whether they become minima or remain transition states when the potential parameters are fixed at the stationary point value. We show that those that become minima have a significant alchemical component in the direction of the pathway, while those that remain as transition states can be characterized mainly in terms of atomic displacements.

    更新日期:2020-01-07
  • Implementation of harmonically mapped averaging in LAMMPS, and effect of potential truncation on anharmonic properties
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-06
    Apoorva Purohit, Andrew J. Schultz, David A. Kofke

    Implementation of the harmonically mapped averaging (HMA) framework in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is presented for on-the-fly computations of the energy, pressure, and heat capacity of crystalline systems during canonical molecular dynamics simulations. HMA has a low central processing unit and storage requirements and is straightforward to use. As a case study, the properties of the Lennard-Jones and embedded-atom model (parameterized for nickel) crystals are computed. The results demonstrate the higher efficiency of the new class compared to the inbuilt LAMMPS classes for calculating these properties. However, HMA loses its effectiveness in systems where diffusion occurs in the crystal, and an example is presented to allow this behavior to be recognized. In addition to its improved precision, HMA is less affected by small errors introduced by having a larger time step in molecular dynamics simulations. We also present an analysis of the effect of potential truncation on anharmonic properties, and show that artifacts of truncation on the HMA averages can be eliminated simply by shifting the potential energy to zero at the truncation radius. Full properties can be obtained by adding easily computed values for the lattice and harmonic properties using the untruncated potential.

    更新日期:2020-01-07
  • Flexible water molecule in C60: Intramolecular vibrational frequencies and translation-rotation eigenstates from fully coupled nine-dimensional quantum calculations with small basis sets
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-06
    Peter M. Felker, Zlatko Bačić

    We present a method for efficient calculation of intramolecular vibrational excitations of H2O inside C60, together with the low-energy intermolecular translation-rotation states within each intramolecular vibrational manifold. Apart from assuming rigid C60, this nine-dimensional (9D) quantum treatment is fully coupled. Following the recently introduced approach [P. M. Felker and Z. Bačić, J. Chem. Phys. 151, 024305 (2019)], the full 9D vibrational Hamiltonian of H2[email protected]60 is partitioned into two reduced-dimension Hamiltonians, a 6D one for the intermolecular vibrations and another in 3D for the intramolecular degrees of freedom, and a 9D remainder term. The two reduced-dimension Hamiltonians are diagonalized, and their eigenvectors are used to build up a product contracted basis in which the full vibrational Hamiltonian is diagonalized. The efficiency of this methodology derives from the insight of our earlier study referenced above that converged high-energy intramolecular vibrational excitations of weakly bound molecular complexes can be obtained from fully coupled quantum calculations where the full-dimensional product contracted basis includes only a small number of intermolecular vibrational eigenstates spanning the range of energies much below those of the intramolecular vibrational states of interest. In this study, the eigenstates included in the 6D intermolecular contacted basis extend to only 410 cm−1 above the ground state, which is much less than the H2O stretch and bend fundamentals, at ≈3700 and ≈1600 cm−1, respectively. The 9D calculations predict that the fundamentals of all three intramolecular modes, as well as the bend overtone, of the caged H2O are blueshifted relative to those of the gas-phase H2O, the two stretch modes much more so than the bend. Excitation of the bend mode affects the energies of the low-lying H2O rotational states significantly more than exciting either of the stretching modes. The center-of-mass translational fundamental is virtually unaffected by the excitation of any of the intramolecular vibrational modes. Further progress hinges on the experimental measurement of the vibrational frequency shifts in H2[email protected]60 and ab initio calculation of a high-quality 9D potential energy surface for this endohedral complex, neither of which is presently available.

    更新日期:2020-01-07
  • The combination of multipartitioning of the Hamiltonian with canonical Van Vleck perturbation theory leads to a Hermitian variant of quasidegenerate N-electron valence perturbation theory
    J. Chem. Phys. (IF 2.997) Pub Date : 2020-01-07
    Lucas Lang, Kantharuban Sivalingam, Frank Neese

    Many recent developments in the area of multistate multireference perturbation theories focused on methods that use a state-averaged 0th order Hamiltonian. We recently found that the dynamic correlation dressed complete active space method fails in describing ligand field and charge transfer states in a balanced way precisely because it uses a state-averaged 0th order Hamiltonian [L. Lang and F. Neese, J. Chem. Phys. 150, 104104 (2019)]. The multipartitioning idea allows the use of state-specific 0th order Hamiltonians in a multistate framework and could therefore alleviate the mentioned problem. However, the effective Hamiltonian is non-Hermitian in the traditional formulation of multipartitioning, which can lead to unphysical behavior, especially for nearly degenerate states. In order to achieve a more balanced treatment of states with different physical character and at the same time have a Hermitian effective Hamiltonian, we combine in this work multipartitioning with canonical Van Vleck perturbation theory. At the 2nd order, the result is a Hermitian variant of multipartitioning quasidegenerate N-electron valence state perturbation theory. The effect of model space noninvariance of the method is discussed and the benefit of a Hermitian formulation is highlighted with numerical examples. The method is shown to give good results for the calculation of electronic transitions of the [CuCl4]2−complex and for the calculation of electron paramagnetic resonance parameters, which are two examples where the balance between ligand field and charge transfer configurations is of utmost importance.

    更新日期:2020-01-07
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