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  • Communication: The Al + CO2 → AlO + CO reaction: Experiment vs. theory
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-02
    Zhi Sun, Kevin B. MooreIII, Henry F. SchaeferIII

    Based on their highly sophisticated crossed-beam experimental studies of the Al + CO2 → AlO + CO reaction, Honma and Hirata have directly challenged the results of earlier theoretical studies of this system. We report high level theoretical studies of this system. It is shown that, consistent with Honma-Hirata experimental conclusions, the previous theoretical prediction of a substantial barrier height for this reaction was incorrect. However, for the structures of the possible intermediates, in agreement with the 1992 theoretical study of Sakai, we find striking disagreement with the experimental conclusion that the O–C–O moiety is nearly linear. The energies of the three entrance channel intermediates lie 14.4, 15.2, and 16.4 kcal mol−1 below separated Al + CO2.

    更新日期:2017-11-07
  • Performing SELEX experiments in silico
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-01
    J. A. J. Wondergem, H. Schiessel, M. Tompitak

    Due to the sequence-dependent nature of the elasticity of DNA, many protein-DNA complexes and other systems in which DNA molecules must be deformed have preferences for the type of DNA sequence they interact with. SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments and similar sequence selection experiments have been used extensively to examine the (indirect readout) sequence preferences of, e.g., nucleosomes (protein spools around which DNA is wound for compactification) and DNA rings. We show how recently developed computational and theoretical tools can be used to emulate such experiments in silico. Opening up this possibility comes with several benefits. First, it allows us a better understanding of our models and systems, specifically about the roles played by the simulation temperature and the selection pressure on the sequences. Second, it allows us to compare the predictions made by the model of choice with experimental results. We find agreement on important features between predictions of the rigid base-pair model and experimental results for DNA rings and interesting differences that point out open questions in the field. Finally, our simulations allow application of the SELEX methodology to systems that are experimentally difficult to realize because they come with high energetic costs and are therefore unlikely to form spontaneously, such as very short or overwound DNA rings.

    更新日期:2017-11-07
  • Theory of molecular nonadiabatic electron dynamics in condensed phases
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-01
    Kazuo Takatsuka

    In light of the rapid progress of ultrafast chemical dynamics driven by the pulse lasers having width as short as several tens of attoseconds, we herein develop a theory of nonadiabatic electron wavepacket dynamics in condensed phases, with which to directly track the dynamics of electronic-state mixing such as electron transfer in liquid solvents. Toward this goal, we combine a theory of path-branching representation for nonadiabatic electron wavepacket dynamics in vacuum {a mixed quantum-classical representation, Yonehara and Takatsuka [J. Chem. Phys. 129, 134109 (2008)]} and a theory of entropy functional to treat chemical dynamics in condensed phases {a mixed dynamical-statistical representation, Takatsuka and Matsumoto [Phys. Chem. Chem. Phys. 18, 1771 (2016)]}. Difficulty and complexity in the present theoretical procedure arise in embedding the Schrödinger equation into classically treated statistical environment. Nevertheless, the resultant equations of motion for electronic-state mixing due to the intrinsic nonadiabatic interactions and solute-solvent interactions, along with the force matrix that drives nuclear branching paths, both turn out to be clear enough to make it possible to comprehend the physical meanings behind. We also discuss briefly the nonvalidness of naive application of the notion of nonadiabatic transition dynamics among free energy surfaces.

    更新日期:2017-11-07
  • Benchmark CCSD-SAPT study of rare gas dimers with comparison to MP-SAPT and DFT-SAPT
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-02
    Leonid Shirkov, Vladimir Sladek

    Symmetry-adapted perturbation theory (SAPT) based on coupled cluster approach with single and double excitations (CCSD) treatment of intramonomer electron correlation effects was applied to study rare gas homodimers from He2 to Kr2. The obtained benchmark CCSD-SAPT energies, including cumulant contributions to first order exchange and second-order exchange-induction terms, were then compared to their counterparts found using other methods—Møller-Plesset-SAPT based on many-body Møller-Plesset perturbation theory and DFT-SAPT based on density functional theory. The SAPT terms up to the second-order were calculated with the basis sets close to the complete basis set at the large range of interatomic distances R. It was shown that overestimation of the binding energies De found with DFT-SAPT reported in the work of Shirkov and Makarewicz [J. Chem. Phys. 142, 064102 (2015)] for Ar2 and Kr2 is mostly due to underestimation of the exchange energy Eexch(1) when comparing to the CCSD-SAPT benchmark. The CCSD-SAPT potentials were found to give the following values of the dissociation energies D0: 0.0006 cm−1 for He2, 16.71 cm−1 for Ne2, 85.03 cm−1 for Ar2, and 129.81 cm−1 for Kr2, which agree well with the values found from previously reported highly accurate ab initio supermolecular potentials and experimental data. The long-range dispersion coefficients C2n up to n = 6 that give the dispersion energy asymptotically equivalent to its SAPT counterpart were calculated from dynamic multipole polarizabilities at different levels of theory.

    更新日期:2017-11-07
  • Similarity transformed equation of motion coupled-cluster theory based on an unrestricted Hartree-Fock reference for applications to high-spin open-shell systems
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-02
    Lee M. J. Huntington, Martin Krupička, Frank Neese, Róbert Izsák

    The similarity transformed equation of motion coupled-cluster approach is extended for applications to high-spin open-shell systems, within the unrestricted Hartree-Fock (UHF) formalism. An automatic active space selection scheme has also been implemented such that calculations can be performed in a black-box fashion. It is observed that both the canonical and automatic active space selecting similarity transformed equation of motion (STEOM) approaches perform about as well as the more expensive equation of motion coupled-cluster singles doubles (EOM-CCSD) method for the calculation of the excitation energies of doublet radicals. The automatic active space selecting UHF STEOM approach can therefore be employed as a viable, lower scaling alternative to UHF EOM-CCSD for the calculation of excited states in high-spin open-shell systems.

    更新日期:2017-11-07
  • Optimal updating magnitude in adaptive flat-distribution sampling
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-03
    Cheng Zhang, Justin A. Drake, Jianpeng Ma, B. Montgomery Pettitt

    We present a study on the optimization of the updating magnitude for a class of free energy methods based on flat-distribution sampling, including the Wang-Landau (WL) algorithm and metadynamics. These methods rely on adaptive construction of a bias potential that offsets the potential of mean force by histogram-based updates. The convergence of the bias potential can be improved by decreasing the updating magnitude with an optimal schedule. We show that while the asymptotically optimal schedule for the single-bin updating scheme (commonly used in the WL algorithm) is given by the known inverse-time formula, that for the Gaussian updating scheme (commonly used in metadynamics) is often more complex. We further show that the single-bin updating scheme is optimal for very long simulations, and it can be generalized to a class of bandpass updating schemes that are similarly optimal. These bandpass updating schemes target only a few long-range distribution modes and their optimal schedule is also given by the inverse-time formula. Constructed from orthogonal polynomials, the bandpass updating schemes generalize the WL and Langfeld-Lucini-Rago algorithms as an automatic parameter tuning scheme for umbrella sampling.

    更新日期:2017-11-07
  • Non-orthogonal internally contracted multi-configurational perturbation theory (NICPT): Dynamic electron correlation for large, compact active spaces
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-06
    Sven Kähler, Jeppe Olsen

    A computational method is presented for systems that require high-level treatments of static and dynamic electron correlation but cannot be treated using conventional complete active space self-consistent field-based methods due to the required size of the active space. Our method introduces an efficient algorithm for perturbative dynamic correlation corrections for compact non-orthogonal MCSCF calculations. In the algorithm, biorthonormal expansions of orbitals and CI-wave functions are used to reduce the scaling of the performance determining step from quadratic to linear in the number of configurations. We describe a hierarchy of configuration spaces that can be chosen for the active space. Potential curves for the nitrogen molecule and the chromium dimer are compared for different configuration spaces. Already the most compact spaces yield qualitatively correct potentials that with increasing size of configuration spaces systematically approach complete active space results.

    更新日期:2017-11-07
  • Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo featured
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-07
    T. McDaniel, E. F. D’Azevedo, Y. W. Li, K. Wong, P. R. C. Kent

    Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is, therefore, formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with an application of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. This procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo, where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi-core central processing units and graphical processing units.

    更新日期:2017-11-07
  • Relativistic effects on the NMR parameters of Si, Ge, Sn, and Pb alkynyl compounds: Scalar versus spin-orbit effects
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-01
    Taye B. Demissie

    The NMR chemical shifts and indirect spin-spin coupling constants of 12 molecules containing 29Si, 73Ge, 119Sn, and 207Pb [X(CCMe)4, Me2X(CCMe)2, and Me3XCCH] are presented. The results are obtained from non-relativistic as well as two- and four-component relativistic density functional theory (DFT) calculations. The scalar and spin–orbit relativistic contributions as well as the total relativistic corrections are determined. The main relativistic effect in these molecules is not due to spin–orbit coupling but rather to the scalar relativistic contraction of the s-shells. The correlation between the calculated and experimental indirect spin–spin coupling constants showed that the four-component relativistic density functional theory (DFT) approach using the Perdew’s hybrid scheme exchange-correlation functional (PBE0; using the Perdew-Burke-Ernzerhof exchange and correlation functionals) gives results in good agreement with experimental values. The indirect spin-spin coupling constants calculated using the spin-orbit zeroth order regular approximation together with the hybrid PBE0 functional and the specially designed J-coupling (JCPL) basis sets are in good agreement with the results obtained from the four-component relativistic calculations. For the coupling constants involving the heavy atoms, the relativistic corrections are of the same order of magnitude compared to the non-relativistically calculated results. Based on the comparisons of the calculated results with available experimental values, the best results for all the chemical shifts and non-existing indirect spin–spin coupling constants for all the molecules are reported, hoping that these accurate results will be used to benchmark future DFT calculations. The present study also demonstrates that the four-component relativistic DFT method has reached a level of maturity that makes it a convenient and accurate tool to calculate indirect spin–spin coupling constants of “large” molecular systems involving heavy atoms.

    更新日期:2017-11-07
  • Correlated electron dynamics in strong-field nonsequential double ionization of Mg
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-06
    Ning Li, Yueming Zhou, Xiaomeng Ma, Min Li, Cheng Huang, Peixiang Lu

    Using the classical ensemble model, we systematically investigate strong-field nonsequential double ionization (NSDI) of Mg by intense elliptically polarized laser pulses with different wavelengths. Different from the noble atoms, NSDI occurs for Mg driven by elliptically and circularly polarized laser fields. Our results show that in elliptically and circularly polarized laser fields, the NSDI yield is sharply suppressed as the wavelength increases. Interestingly, the correlated behavior in the electron momentum spectra depends sensitively on the wavelengths. The corresponding electron dynamics is revealed by back tracing the classical trajectory.

    更新日期:2017-11-07
  • A study on the plasticity of soda-lime silica glass via molecular dynamics simulations
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-02
    Shingo Urata, Yosuke Sato

    Molecular dynamics (MD) simulations were applied to construct a plasticity model, which enables one to simulate deformations of soda-lime silica glass (SLSG) by using continuum methods. To model the plasticity, stress induced by uniaxial and a variety of biaxial deformations was measured by MD simulations. We found that the surfaces of yield and maximum stresses, which are evaluated from the equivalent stress-strain curves, are reasonably represented by the Mohr-Coulomb ellipsoid. Comparing a finite element model using the constructed plasticity model to a large scale atomistic model on a nanoindentation simulation of SLSG reveals that the empirical method is accurate enough to evaluate the SLSG mechanical responses. Furthermore, the effect of ion-exchange on the SLSG plasticity was examined by using MD simulations. As a result, it was demonstrated that the effects of the initial compressive stress on the yield and maximum stresses are anisotropic contrary to our expectations.

    更新日期:2017-11-07
  • The accretion of the new ice layer on the surface of hexagonal ice crystal and the influence of the local electric field on this process
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-07
    Joanna Grabowska, Anna Kuffel, Jan Zielkiewicz

    The process of creation of a new layer of ice on the basal plane and on the prism plane of a hexagonal ice crystal is analyzed. It is demonstrated that the ordering of water molecules in the already existing crystal affects the freezing. On the basal plane, when the orientations of water molecules in the ice block are random, the arrangement of the new layer in a cubic manner is observed more frequently—approximately 1.7 times more often than in a hexagonal manner. When the water molecules in the ice block are more ordered, it results in the predominance of the oxygen atoms or the hydrogen atoms on the most outer part of the surface of the ice block. In this case, the hexagonal structure is formed more frequently when the supercooling of water exceeds 10 K. This phenomenon is explained by the influence of the oriented electric field, present as a consequence of the ordering of the dipoles of water molecules in the ice block. This field modifies the structure of solvation water (i.e., the layer of water in the immediate vicinity of the ice surface). We showed that the structure of solvation water predetermines the kind of the newly created layer of ice. This effect is temperature-dependent: when the temperature draws nearer to the melting point, the cubic structure becomes the prevailing form. The temperature at which the cubic and the hexagonal structures are formed with the same probabilities is equal to about 260 K. In the case of the prism plane, the new layer that is formed is always the hexagonal one, which is independent of the arrangement of water molecules in the ice block and is in agreement with previous literature data. For the basal plane, as well as for the prism plane, no evident dependence on the ordering of water molecules that constitute the ice block on the rate of crystallization can be observed.

    更新日期:2017-11-07
  • Going beyond the standard line tension: Size-dependent contact angles of water nanodroplets featured
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-01
    Matej Kanduč

    The dependence of the contact angle on the size of a nanoscopic droplet residing on a flat substrate is traditionally ascribed solely to line tension. Other contributions, stemming from the droplet geometry dependence of the surface tension and line tension, are typically ignored. Here, we perform molecular dynamics simulations of water droplets of cylindrical morphology on surfaces of a wide range of polarities. In the cylindrical geometry, where the line tension is not operative directly, we find significant contact angle dependence on the droplet size. The effect is most pronounced on hydrophilic surfaces, with the contact angle increase of up to 1 0 ° with a decreasing droplet size. On hydrophobic surfaces, the trend is reversed and considerably weaker. Our analysis suggests that these effects can be attributed to the Tolman correction due to the curved water–vapor interface and to a generalized line tension that possesses a contact angle dependence. The latter is operative also in the cylindrical geometry and yields a comparable contribution to the contact angle as the line tension itself in case of spherical droplets.

    更新日期:2017-11-07
  • Demixing of active particles in the presence of external fields
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-02
    Sunita Kumari, André S. Nunes, Nuno A. M. Araújo, Margarida M. Telo da Gama

    Self-propelled active particles are inherently out of equilibrium as they collect energy from their surroundings and transform it into directed motion. A recent theoretical study suggests that binary mixtures of active particles with distinct effective diffusion coefficients exhibit dynamical demixing when their diffusion coefficients differ by more than one order of magnitude. Here, we show that this difference may be reduced drastically in the presence of external fields even when the response to the field is the same for both species. We investigate this demixing as a function of the ratio of the diffusion coefficients and discuss the implications of the results for active systems.

    更新日期:2017-11-07
  • MnNiO3 revisited with modern theoretical and experimental methods
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-03
    Allison L. Dzubak, Chandrima Mitra, Michael Chance, Stephen Kuhn, Gerald E. JellisonJr., Athena S. Sefat, Jaron T. Krogel, Fernando A. Reboredo

    MnNiO3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å3, which compares well to the experimental value of 94.4 Å3. A bulk modulus of 217 GPa is predicted for MnNiO3. We rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO3.

    更新日期:2017-11-07
  • Retention of contaminants Cd and Hg adsorbed and intercalated in aluminosilicate clays: A first principles study
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-03
    F. D. Crasto de Lima, R. H. Miwa, Caetano R. Miranda

    Layered clay materials have been used to incorporate transition metal (TM) contaminants. Based on first-principles calculations, we have examined the energetic stability and the electronic properties due to the incorporation of Cd and Hg in layered clay materials, kaolinite (KAO) and pyrophyllite (PYR). The TM can be (i) adsorbed on the clay surface as well as (ii) intercalated between the clay layers. For the intercalated case, the contaminant incorporation rate can be optimized by controlling the interlayer spacing of the clay, namely, pillared clays. Our total energy results reveal that the incorporation of the TMs can be maximized through a suitable tuning of vertical distance between the clay layers. Based on the calculated TM/clay binding energies and the Langmuir absorption model, we estimate the concentrations of the TMs. Further kinetic properties have been examined by calculating the activation energies, where we found energy barriers of ∼20 and ∼130 meV for adsorbed and intercalated cases, respectively. The adsorption and intercalation of ionized TM adatoms were also considered within the deprotonated KAO surface. This also leads to an optimal interlayer distance which maximizes the TM incorporation rate. By mapping the total charge transfers at the TM/clay interface, we identify a net electronic charge transfer from the TM adatoms to the topmost clay surface layer. The effect of such a charge transfer on the electronic structure of the clay (host) has been examined through a set of X-ray absorption near edge structure (XANES) simulations, characterizing the changes of the XANES spectra upon the presence of the contaminants. Finally, for the pillared clays, we quantify the Cd and Hg K-edge energy shifts of the TMs as a function of the interlayer distance between the clay layers and the Al K-edge spectra for the pristine and pillared clays.

    更新日期:2017-11-07
  • Charge-regularized swelling kinetics of polyelectrolyte gels: Elasticity and diffusion
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-01
    Swati Sen, Arindam Kundagrami

    We apply a recently developed method [S. Sen and A. Kundagrami, J. Chem. Phys. 143, 224904 (2015)], using a phenomenological expression of osmotic stress, as a function of polymer and charge densities, hydrophobicity, and network elasticity for the swelling of spherical polyelectrolyte (PE) gels with fixed and variable charges in a salt-free solvent. This expression of stress is used in the equation of motion of swelling kinetics of spherical PE gels to numerically calculate the spatial profiles for the polymer and free ion densities at different time steps and the time evolution of the size of the gel. We compare the profiles of the same variables obtained from the classical linear theory of elasticity and quantitatively estimate the bulk modulus of the PE gel. Further, we obtain an analytical expression of the elastic modulus from the linearized expression of stress (in the small deformation limit). We find that the estimated bulk modulus of the PE gel decreases with the increase of its effective charge for a fixed degree of deformation during swelling. Finally, we match the gel-front locations with the experimental data, taken from the measurements of charged reversible addition-fragmentation chain transfer gels to show an increase in gel-size with charge and also match the same for PNIPAM (uncharged) and imidazolium-based (charged) minigels, which specifically confirms the decrease of the gel modulus value with the increase of the charge. The agreement between experimental and theoretical results confirms general diffusive behaviour for swelling of PE gels with a decreasing bulk modulus with increasing degree of ionization (charge). The new formalism captures large deformations as well with a significant variation of charge content of the gel. It is found that PE gels with large deformation but same initial size swell faster with a higher charge.

    更新日期:2017-11-07
  • A lattice model for the impact of volume fraction fluctuations upon percolation by cylinders
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-03
    Avik P. Chatterjee, Claudio Grimaldi

    A lattice model for continuum percolation by cylindrical rods is generalized to account for inhomogeneities in the volume fraction that are indicative of particle clustering or aggregation. The percolation threshold is evaluated from a formalism that uses two different categories of occupied sites (denoting particles) with different occupation probabilities that represent large and small local volume fractions. Our modeling framework enables independent variations in (i) the strength of the correlation that adjacent particles experience high (or low) effective volume fractions, (ii) the disparity between the macroscopically averaged volume fraction and (say) the volume fraction characterizing the regions with high effective particle concentrations, and (iii) the overall proportion of particles that are located in regions with either high or low volume fraction. Calculations performed for monodisperse cylinders show that enhancement in each of the above factors leads to reduction in the macroscopically averaged volume fraction at the percolation threshold.

    更新日期:2017-11-07
  • Non-constant link tension coefficient in the tumbling-snake model subjected to simple shear
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-06
    Pavlos S. Stephanou, Martin Kröger

    The authors of the present study have recently presented evidence that the tumbling-snake model for polymeric systems has the necessary capacity to predict the appearance of pronounced undershoots in the time-dependent shear viscosity as well as an absence of equally pronounced undershoots in the transient two normal stress coefficients. The undershoots were found to appear due to the tumbling behavior of the director u when a rotational Brownian diffusion term is considered within the equation of motion of polymer segments, and a theoretical basis concerning the use of a link tension coefficient given through the nematic order parameter had been provided. The current work elaborates on the quantitative predictions of the tumbling-snake model to demonstrate its capacity to predict undershoots in the time-dependent shear viscosity. These predictions are shown to compare favorably with experimental rheological data for both polymer melts and solutions, help us to clarify the microscopic origin of the observed phenomena, and demonstrate in detail why a constant link tension coefficient has to be abandoned.

    更新日期:2017-11-07
  • Note: MSM lag time cannot be used for variational model selection
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-11-03
    Brooke E. Husic, Vijay S. Pande

    The variational principle for conformational dynamics has enabled the systematic construction of Markov state models through the optimization of hyperparameters by approximating the transfer operator. In this note, we discuss why the lag time of the operator being approximated must be held constant in the variational approach.

    更新日期:2017-11-07
  • Preface: Special Topic: From Quantum Mechanics to Force Fields
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-24
    Jean-Philip Piquemal, Kenneth D. Jordan

    This Special Topic issue entitled “From Quantum Mechanics to Force Fields” is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

    更新日期:2017-11-01
  • Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-04-14
    Julien Steffen, Bernd Hartke

    Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

    更新日期:2017-11-01
  • Mapping the Drude polarizable force field onto a multipole and induced dipole model
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-06-05
    Jing Huang, Andrew C. Simmonett, Frank C. PickardIV, Alexander D. MacKerellJr., Bernard R. Brooks

    The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor self-consistent iterations. This opens up a wide range of new methodological opportunities for polarizable models.

    更新日期:2017-11-01
  • A comparison of sodium and hydrogen halides at the air-water interface
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-06-05
    Collin D. Wick

    New molecular models, parameterized to ab initio calculations, were developed to describe HBr and HI at the air-water interface. These were used to compare how the air-water interface influenced dissociation of NaX and HX, with X being Cl, Br, or I, and also their propensity for the interface. The polarizable multistate empirical valence bond method, which explicitly describes proton sharing, was used to model HX. Results showed that the air-water interface suppressed HX dissociation from a contact ion pair to a solvent separated to a greater degree than NaX dissociation. Furthermore, HX had a greater propensity for the interface than NaX, which was a consequence of the hydronium ion having a greatest interfacial activity of all species studied. As a consequence of this, the average configuration of dissociated HX, while in both contact ion and solvent separated ion pairs near the air-water interface, is with the dissociated hydrogen oriented more towards the air than the X atom.

    更新日期:2017-11-01
  • Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-06-13
    Anders S. Christensen, Jimmy C. Kromann, Jan H. Jensen, Qiang Cui

    To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy in solution is computed via a thermodynamic cycle that integrates dimer binding energy in the gas phase at the coupled cluster level and solute-solvent interaction with density functional theory; the estimated uncertainty of such calculated interaction energy is ±1.5 kcal/mol. The dataset is used to benchmark the performance of a set of semi-empirical quantum mechanical (SQM) methods that include DFTB3-D3, DFTB3/CPE-D3, OM2-D3, PM6-D3, PM6-D3H+, and PM7 as well as the HF-3c method. We find that while all tested SQM methods tend to underestimate binding energies in the gas phase with a root-mean-squared error (RMSE) of 2-5 kcal/mol, they overestimate binding energies in the solution phase with an RMSE of 3-4 kcal/mol, with the exception of DFTB3/CPE-D3 and OM2-D3, for which the systematic deviation is less pronounced. In addition, we find that HF-3c systematically overestimates binding energies in both gas and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need to be treated in a balanced fashion.

    更新日期:2017-11-01
  • Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-06-15
    Damien E. Coupry, Matthew A. Addicoat, Thomas Heine

    A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metal-organic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is now accessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations.

    更新日期:2017-11-01
  • Interpolation of intermolecular potentials using Gaussian processes
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-06-26
    Elena Uteva, Richard S. Graham, Richard D. Wilkinson, Richard J. Wheatley

    A procedure is proposed to produce intermolecular potential energy surfaces from limited data. The procedure involves generation of geometrical configurations using a Latin hypercube design, with a maximin criterion, based on inverse internuclear distances. Gaussian processes are used to interpolate the data, using over-specified inverse molecular distances as covariates, greatly improving the interpolation. Symmetric covariance functions are specified so that the interpolation surface obeys all relevant symmetries, reducing prediction errors. The interpolation scheme can be applied to many important molecular interactions with trivial modifications. Results are presented for three systems involving CO2, a system with a deep energy minimum (HF−HF), and a system with 48 symmetries (CH4−N2). In each case, the procedure accurately predicts an independent test set. Training this method with high-precision ab initio evaluations of the CO2−CO interaction enables a parameter-free, first-principles prediction of the CO2−CO cross virial coefficient that agrees very well with experiments.

    更新日期:2017-11-01
  • On the development of polarizable and Lennard-Jones force fields to study hydration structure and dynamics of actinide(III) ions based on effective ionic radii
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-05
    Riccardo Spezia, Valentina Migliorati, Paola D’Angelo

    In this contribution, we show how it is possible to develop polarizable and non-polarizable force fields to study hydration properties of a whole chemical series based on atomic properties such as ionic radii. In particular, we have addressed the actinide(III) ion series, from U3+ to Cf3+, for which X-ray absorption data and effective ionic radii are available. A polarizable force field has been re-parameterized improving the original one [M. Duvail et al., J. Chem. Phys. 135, 044503 (2011)] which was based on solid state ionic radii. The new force field does not depend on solid state properties but directly on the liquid phase ones, and it can be used to study these ions in liquid water without any ambiguity. Furthermore, we have shown that it is possible to parameterize also a non-polarizable potential using standard Lennard-Jones and Coulombic forces, which can be transferred to other systems in condensed phase. The structural and dynamical properties of these two force fields are compared to each other and with data available in the literature, providing a good agreement. Moreover, we show the comparison with experimental X-ray absorption data that are very well reproduced by both force fields.

    更新日期:2017-11-01
  • A general intermolecular force field based on tight-binding quantum chemical calculations featured
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-11
    Stefan Grimme, Christoph Bannwarth, Eike Caldeweyher, Jana Pisarek, Andreas Hansen

    A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

    更新日期:2017-11-01
  • Li+ solvation and kinetics of Li+–BF4/PF6 ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-19
    Tsun-Mei Chang, Liem X. Dang

    Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+–[BF4] and Li+–[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found that the residence times of EC around Li+ ions varied from 60 to 450 ps, depending on the correction method used. We found that the relaxation times changed significantly from Li+–[BF4] to Li+–[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influences the dissociation kinetics of ion pairing.

    更新日期:2017-11-01
  • Structure and polarization near the Li+ ion in ethylene and propylene carbonates
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-19
    Travis P. Pollard, Thomas L. Beck

    Research on fundamental interactions in Li-ion batteries is accelerating due to the importance of developing batteries with enhanced energy and power densities while maintaining safety. Improving electrode materials and controlling the formation of the solid electrolyte interphase during the first battery charge have been the main focus areas for research. Ion-solvent interactions in the electrolyte are also of great importance in tuning solvation and transport properties, however. Here we present ab initio density functional theory simulations of a Li+ ion in ethylene and propylene carbonates. The aim is to obtain a detailed analysis of local solvation structure and solvent polarization near the ion and in the bulk. The results indicate the significance of molecular polarization for developing accurate solvation models. The simulations illustrate the substantial differences between ion solvation in water and in organic materials.

    更新日期:2017-11-01
  • Structural study of Na2O–B2O3–SiO2 glasses from molecular simulations using a polarizable force field
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-19
    Fabien Pacaud, Jean-Marc Delaye, Thibault Charpentier, Laurent Cormier, Mathieu Salanne

    Sodium borosilicate glasses Na2O–B2O3–SiO2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO4 and BO4 (BIV) and triangular BO3 (BIII). One of the salient features of these compounds is the change of the BIII/BIV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of BIII/BIV with respect to the composition and the temperature.

    更新日期:2017-11-01
  • Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-21
    Oliver T. Unke, Mike Devereux, Markus Meuwly

    Most empirical force fields use atom-centered point charges (PCs) to represent the electrostatic potential (ESP) around molecules. While such PC models are computationally efficient, they are unable to capture anisotropic electronic features, such as σ holes or lone pairs. These features are better described using atomic multipole (MTP) moments, which significantly improve the quality of the resulting ESP. However, the improvement comes at the expense of a considerably increased computational complexity and cost for calculating the interaction energies and forces. In the present work, a novel minimal distributed charge model (MDCM) based on off-centered point charges is presented and the quality of the resulting ESP is compared to the performance of MTPs and atom-centered PC models for several test molecules. All three models are fitted using the same algorithm based on differential evolution, which is available as a Fortran90 program from the authors upon request. We show that the MDCM is capable of approximating the reference ab initio ESP with an accuracy as good as, or better than, MTPs without the need for computationally expensive higher order multipoles. Further it is demonstrated that the MDCM is numerically stable in molecular dynamics simulations and is able to reproduce electrostatic interaction energies and thermodynamic quantities with the same accuracy as MTPs at reduced computational cost.

    更新日期:2017-11-01
  • Combining configurational energies and forces for molecular force field optimization
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-21
    Lukas Vlcek, Weiwei Sun, Paul R. C. Kent

    While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. Here we propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information is used to optimize a molecular force field by minimizing the statistical distance similarity metric. We illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.

    更新日期:2017-11-01
  • Two-component, ab initio potential energy surface for CO2—H2O, extension to the hydrate clathrate, CO2@(H2O)20, and VSCF/VCI vibrational analyses of both
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-21
    Qingfeng (Kee) Wang, Joel M. Bowman

    We report an ab initio, full-dimensional, potential energy surface (PES) for CO2—H2O, in which two-body interaction energies are fit using a basis of permutationally invariant polynomials and combined with accurate potentials for the non-interacting monomers. This approach which we have termed “plug and play” is extended here to improve the precision of the 2-body fit in the long range. This is done by combining two separate fits. One is a fit to 47 593 2-body energies in the region of strong interaction and approaching the long range, and the second one is a fit to 6244 2-body energies in the long range. The two fits have a region of overlap which permits a smooth switch from one to the other. All energies are obtained at the CCSD(T)-F12b/aug-cc-pVTZ level of theory. Properties of the full PES, i.e., stationary points, harmonic frequencies of the global minimum, etc., are shown to be in excellent agreement with direct CCSD(T)-F12b/aug-cc-pVTZ results. Diffusion Monte Carlo calculations of the dimer zero-point energy (ZPE) are performed, and a dissociation energy, D0, of 787 cm−1 is obtained using that ZPE, De, and the rigorous ZPEs of the monomers. Using a benchmark De, D0 is 758 cm−1. Vibrational self-consistent field (VSCF)/virtual state configuration interaction (VCI) MULTIMODE calculations of intramolecular fundamentals are reported and are in good agreement with available experimental results. Finally, the full dimer PES is combined with an existing ab initio water potential to develop a potential for the CO2 hydrate clathrate CO2(H2O)20(512 water cage). A full normal-mode analysis of this hydrate clathrate is reported as are local-monomer VSCF/VCI calculations of the fundamentals of CO2.

    更新日期:2017-11-01
  • Toward chemical accuracy in the description of ion–water interactions through many-body representations. Alkali-water dimer potential energy surfaces featured
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-24
    Marc Riera, Narbe Mardirossian, Pushp Bajaj, Andreas W. Götz, Francesco Paesani

    This study presents the extension of the MB-nrg (Many-Body energy) theoretical/computational framework of transferable potential energy functions (PEFs) for molecular simulations of alkali metal ion-water systems. The MB-nrg PEFs are built upon the many-body expansion of the total energy and include the explicit treatment of one-body, two-body, and three-body interactions, with all higher-order contributions described by classical induction. This study focuses on the MB-nrg two-body terms describing the full-dimensional potential energy surfaces of the M+(H2O) dimers, where M+ = Li+, Na+, K+, Rb+, and Cs+. The MB-nrg PEFs are derived entirely from “first principles” calculations carried out at the explicitly correlated coupled-cluster level including single, double, and perturbative triple excitations [CCSD(T)-F12b] for Li+ and Na+ and at the CCSD(T) level for K+, Rb+, and Cs+. The accuracy of the MB-nrg PEFs is systematically assessed through an extensive analysis of interaction energies, structures, and harmonic frequencies for all five M+(H2O) dimers. In all cases, the MB-nrg PEFs are shown to be superior to both polarizable force fields and ab initio models based on density functional theory. As previously demonstrated for halide-water dimers, the MB-nrg PEFs achieve higher accuracy by correctly describing short-range quantum-mechanical effects associated with electron density overlap as well as long-range electrostatic many-body interactions.

    更新日期:2017-11-01
  • Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-26
    Timothy T. Duignan, Marcel D. Baer, Gregory K. Schenter, Chistopher J. Mundy

    Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

    更新日期:2017-11-01
  • Implementation of analytical gradients and of a mixed real and momentum space DVR method for excess electron systems described by a self-consistent polarization model
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-31
    Tae Hoon Choi, Tijo Vazhappilly, Kenneth D. Jordan

    This work presents two extensions of our self-consistent polarization model for treating non-valence excess electron systems. The first extension is the implementation of analytical gradients, and the second extension is the implementation of a mixed real space plus momentum space approach combined with fast Fourier transforms to reduce the computational time compared to a purely real space discrete variable representation approach. The performance of the new algorithms is assessed in calculations of the excess electron states of various size water clusters and of the non-valence correlation-bound anion of the C240 fullerene.

    更新日期:2017-11-01
  • Geometry-dependent atomic multipole models for the water molecule
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-07-31
    O. Loboda, C. Millot

    Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

    更新日期:2017-11-01
  • Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-08-01
    Chen Chen, Christopher Arntsen, Gregory A. Voth

    Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

    更新日期:2017-11-01
  • Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-08-18
    Céline Houriez, Valérie Vallet, Florent Réal, Michael Meot-Ner (Mautner), Michel Masella

    We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3COO−/CH3NH3+ solutions at the 0.2–0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO−/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO−/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

    更新日期:2017-11-01
  • Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-08-24
    Omar Demerdash, Yuezhi Mao, Tianyi Liu, Martin Head-Gordon, Teresa Head-Gordon

    In this work, we evaluate the accuracy of the classical AMOEBA model for representing many-body interactions, such as polarization, charge transfer, and Pauli repulsion and dispersion, through comparison against an energy decomposition method based on absolutely localized molecular orbitals (ALMO-EDA) for the water trimer and a variety of ion-water systems. When the 2- and 3-body contributions according to the many-body expansion are analyzed for the ion-water trimer systems examined here, the 3-body contributions to Pauli repulsion and dispersion are found to be negligible under ALMO-EDA, thereby supporting the validity of the pairwise-additive approximation in AMOEBA’s 14-7 van der Waals term. However AMOEBA shows imperfect cancellation of errors for the missing effects of charge transfer and incorrectness in the distance dependence for polarization when compared with the corresponding ALMO-EDA terms. We trace the larger 2-body followed by 3-body polarization errors to the Thole damping scheme used in AMOEBA, and although the width parameter in Thole damping can be changed to improve agreement with the ALMO-EDA polarization for points about equilibrium, the correct profile of polarization as a function of intermolecular distance cannot be reproduced. The results suggest that there is a need for re-examining the damping and polarization model used in the AMOEBA force field and provide further insights into the formulations of polarizable force fields in general.

    更新日期:2017-11-01
  • From dimers to the solid-state: Distributed intermolecular force-fields for pyridine
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-08-28
    Alexander A. Aina, Alston J. Misquitta, Sarah L. Price

    An anisotropic atom-atom force-field for pyridine, using distributed atomic multipoles, polarizabilities, and dispersion coefficients and an anisotropic atom-atom repulsion model derived from symmetry-adapted perturbation theory (density functional theory) dimer calculations, is used to model pyridine crystal structures. Here we show that this distributed intermolecular force-field (DIFF) models the experimental crystal structures as accurately as modelling all but the electrostatic term with an isotropic repulsion-dispersion potential that has been fitted to experimental crystal structures. In both cases, the differences are comparable to the changes in the crystal structure with temperature, pressure, or neglect of zero-point vibrational effects. A crystal structure prediction study has been carried out, and the observed polymorphs contrasted with hypothetical thermodynamically competitive crystal structures. The DIFF model was able to identify the structure of an unreported high pressure phase of pyridine, unlike the empirically fitted potential. The DIFF model approach therefore provides a model of the underlying pair potential energy surface that we have transferred to the crystalline phase with a considerable degree of success, though the treatment of the many-body terms needs improvement and the pair potential is slightly over-binding. Furthermore, this study of a system that exhibits isotopic polymorphism highlights that the use of an empirical potential has partially absorbed temperature and zero-point motion effects as well as the intermolecular forces not explicitly represented in the functional form. This study therefore highlights the complexity in modelling crystallization phenomena from a realistic pair potential energy surface.

    更新日期:2017-11-01
  • Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-08-29
    Chenchen Song, Todd J. Martínez

    Analytic energy gradients for tensor hyper-contraction (THC) are derived and implemented for second-order Møller-Plesset perturbation theory (MP2), with and without the scaled-opposite-spin (SOS)-MP2 approximation. By exploiting the THC factorization, the formal scaling of MP2 and SOS-MP2 gradient calculations with respect to system size is reduced to quartic and cubic, respectively. An efficient implementation has been developed that utilizes both graphics processing units and sparse tensor techniques exploiting spatial sparsity of the atomic orbitals. THC-MP2 has been applied to both geometry optimization and ab initio molecular dynamics (AIMD) simulations. The resulting energy conservation in micro-canonical AIMD demonstrates that the implementation provides accurate nuclear gradients with respect to the THC-MP2 potential energy surfaces.

    更新日期:2017-11-01
  • The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-08-29
    Félix Aviat, Louis Lagardère, Jean-Philip Piquemal

    In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180–190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered “non-iterative.” This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

    更新日期:2017-11-01
  • Improving the accuracy of Møller-Plesset perturbation theory with neural networks
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-06
    Robert T. McGibbon, Andrew G. Taube, Alexander G. Donchev, Karthik Siva, Felipe Hernández, Cory Hargus, Ka-Hei Law, John L. Klepeis, David E. Shaw

    Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol−1 (root-mean-square error 0.09 kcal mol−1), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

    更新日期:2017-11-01
  • Performing the Millikan experiment at the molecular scale: Determination of atomic Millikan-Thomson charges by computationally measuring atomic forces
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-07
    T. Ryan Rogers, Feng Wang

    An atomic version of the Millikan oil drop experiment is performed computationally. It is shown that for planar molecules, the atomic version of the Millikan experiment can be used to define an atomic partial charge that is free from charge flow contributions. We refer to this charge as the Millikan-Thomson (MT) charge. Since the MT charge is directly proportional to the atomic forces under a uniform electric field, it is the most relevant charge for force field developments. The MT charge shows good stability with respect to different choices of the basis set. In addition, the MT charge can be easily calculated even at post-Hartree-Fock levels of theory. With the MT charge, it is shown that for a planar water dimer, the charge transfer from the proton acceptor to the proton donor is about −0.052 e. While both planar hydrated cations and anions show signs of charge transfer, anions show a much more significant charge transfer to the hydration water than the corresponding cations. It might be important to explicitly model the ion charge transfer to water in a force field at least for the anions.

    更新日期:2017-11-01
  • The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-11
    Lori A. Burns, John C. Faver, Zheng Zheng, Michael S. Marshall, Daniel G. A. Smith, Kenno Vanommeslaeghe, Alexander D. MacKerellJr., Kenneth M. MerzJr., C. David Sherrill

    Accurate potential energy models are necessary for reliable atomistic simulations of chemical phenomena. In the realm of biomolecular modeling, large systems like proteins comprise very many noncovalent interactions (NCIs) that can contribute to the protein’s stability and structure. This work presents two high-quality chemical databases of common fragment interactions in biomolecular systems as extracted from high-resolution Protein DataBank crystal structures: 3380 sidechain-sidechain interactions and 100 backbone-backbone interactions that inaugurate the BioFragment Database (BFDb). Absolute interaction energies are generated with a computationally tractable explicitly correlated coupled cluster with perturbative triples [CCSD(T)-F12] “silver standard” (0.05 kcal/mol average error) for NCI that demands only a fraction of the cost of the conventional “gold standard,” CCSD(T) at the complete basis set limit. By sampling extensively from biological environments, BFDb spans the natural diversity of protein NCI motifs and orientations. In addition to supplying a thorough assessment for lower scaling force-field (2), semi-empirical (3), density functional (244), and wavefunction (45) methods (comprising >1M interaction energies), BFDb provides interactive tools for running and manipulating the resulting large datasets and offers a valuable resource for potential energy model development and validation.

    更新日期:2017-11-01
  • Quasi-chemical theory of F(aq): The “no split occupancies rule” revisited
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-12
    Mangesh I. Chaudhari, Susan B. Rempe, Lawrence R. Pratt

    We use ab initio molecular dynamics (AIMD) calculations and quasi-chemical theory (QCT) to study the inner-shell structure of F−(aq) and to evaluate that single-ion free energy under standard conditions. Following the “no split occupancies” rule, QCT calculations yield a free energy value of −101 kcal/mol under these conditions, in encouraging agreement with tabulated values (−111 kcal/mol). The AIMD calculations served only to guide the definition of an effective inner-shell constraint. QCT naturally includes quantum mechanical effects that can be concerning in more primitive calculations, including electronic polarizability and induction, electron density transfer, electron correlation, molecular/atomic cooperative interactions generally, molecular flexibility, and zero-point motion. No direct assessment of the contribution of dispersion contributions to the internal energies has been attempted here, however. We anticipate that other aqueous halide ions might be treated successfully with QCT, provided that the structure of the underlying statistical mechanical theory is absorbed, i.e., that the “no split occupancies” rule is recognized.

    更新日期:2017-11-01
  • Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-09-13
    Kuan-Yu Liu, John M. Herbert

    Papers I and II in this series [R. M. Richard et al., J. Chem. Phys. 141, 014108 (2014); K. U. Lao et al., ibid. 144, 164105 (2016)] have attempted to shed light on precision and accuracy issues affecting the many-body expansion (MBE), which only manifest in larger systems and thus have received scant attention in the literature. Many-body counterpoise (CP) corrections are shown to accelerate convergence of the MBE, which otherwise suffers from a mismatch between how basis-set superposition error affects subsystem versus supersystem calculations. In water clusters ranging in size up to (H2O)37, four-body terms prove necessary to achieve accurate results for both total interaction energies and relative isomer energies, but the sheer number of tetramers makes the use of cutoff schemes essential. To predict relative energies of (H2O)20 isomers, two approximations based on a lower level of theory are introduced and an ONIOM-type procedure is found to be very well converged with respect to the appropriate MBE benchmark, namely, a CP-corrected supersystem calculation at the same level of theory. Results using an energy-based cutoff scheme suggest that if reasonable approximations to the subsystem energies are available (based on classical multipoles, say), then the number of requisite subsystem calculations can be reduced even more dramatically than when distance-based thresholds are employed. The end result is several accurate four-body methods that do not require charge embedding, and which are stable in large basis sets such as aug-cc-pVTZ that have sometimes proven problematic for fragment-based quantum chemistry methods. Even with aggressive thresholding, however, the four-body approach at the self-consistent field level still requires roughly ten times more processors to outmatch the performance of the corresponding supersystem calculation, in test cases involving 1500–1800 basis functions.

    更新日期:2017-11-01
  • Links between the charge model and bonded parameter force constants in biomolecular force fields
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-04
    David S. Cerutti, Karl T. Debiec, David A. Case, Lillian T. Chong

    The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model. First, ff15ipq-Qsolv derives bonded parameters in the context of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq’s bonded parameters and runs simulations with the vacuum phase charge set used to derive those parameters. The IPolQ charge model and associated protocol for deriving bonded parameters are shown to be an incremental improvement over protocols that do not account for the material phases of each source of their fitting data. Both force fields incorporating the polarized charge set depict stable globular proteins and have varying degrees of success modeling the metastability of short (5–19 residues) peptides. In this particular case, ff15ipq-Qsolv increases stability in a number of α-helices, correctly obtaining 70% helical character in the K19 system at 275 K and showing appropriately diminishing content up to 325 K, but overestimating the helical fraction of AAQAA3 by 50% or more, forming long-lived α-helices in simulations of a β-hairpin, and increasing the likelihood that the disordered p53 N-terminal peptide will also form a helix. This may indicate a systematic bias imparted by the ff15ipq-Qsolv parameter development strategy, which has the hallmarks of strategies used to develop other popular force fields, and may explain some of the need for manual corrections in this force fields’ evolution. In contrast, ff15ipq-Vac incorrectly depicts globular protein unfolding in numerous systems tested, including Trp cage, villin, lysozyme, and GB3, and does not perform any better than ff15ipq or ff15ipq-Qsolv in tests on short peptides. We analyze the free energy surfaces of individual amino acid dipeptides and the electrostatic potential energy surfaces of each charge model to explain the differences.

    更新日期:2017-11-01
  • Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-04
    Hedieh Torabifard, Luke Reed, Matthew T. Berry, Jason E. Hein, Erik Menke, G. Andrés Cisneros

    The development of Li-ion batteries for energy storage has received significant attention. The synthesis and characterization of electrolytes in these batteries are an important component of this development. Ionic liquids (ILs) have been proposed as possible electrolytes in these devices. Thus, the accurate determination of thermophysical properties for these solvents becomes important for determining their applicability as electrolytes. In this contribution, we present the synthesis and experimental/computational characterization of thermodynamic and transport properties of a pyrrolidinium based ionic liquid as a first step to investigate the possible applicability of this class of ILs for Li-ion batteries. A quantum mechanical-based force field with many-body polarizable interactions has been developed for the simulation of spirocyclic pyrrolidinium, [sPyr+], with BF4− and Li+. Molecular dynamics calculations employing intra-molecular polarization predicted larger heat of vaporization and self-diffusion coefficients and smaller densities in comparison with the model without intra-molecular polarization, indicating that the inclusion of this term can significantly effect the inter-ionic interactions. The calculated properties are in good agreement with available experimental data for similar IL pairs and isothermal titration calorimetry data for [sPyr+][BF4−].

    更新日期:2017-11-01
  • Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-12
    Jingheng Wu, Lin Shen, Weitao Yang

    Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

    更新日期:2017-11-01
  • Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field featured
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-17
    Zhifeng Jing, Rui Qi, Chengwen Liu, Pengyu Ren

    The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

    更新日期:2017-11-01
  • Fast and reliable ab initio calculation of crystal field splittings in lanthanide complexes
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-23
    P. P. Hallmen, C. Köppl, G. Rauhut, H. Stoll, J. van Slageren

    Ab initio calculations of crystal field splittings and magnetic properties of lanthanide complexes are usually performed using state-averaged complete active space self-consistent field (CASSCF) calculations and a subsequent spin-orbit calculation mixing the CASSCF wave functions (CASSCF/state interaction with spin-orbit coupling). Because this approach becomes very time-consuming for large molecules, simplifications have been proposed in the literature to determine the state-averaged orbitals by configuration-averaged Hartree-Fock (CAHF) instead of CASSCF. We present an approach which is an extension of the CAHF method. We combine the techniques of local density fitting with CAHF and achieve a significant speedup compared to CASSCF without loss in accuracy. To assess the performance of our method, we apply it to three well-known molecules, namely, Er[N(SiMe3)2]3, Er(trensal), and the double-decker (NBu4)+ [Er(Pc)2]−.

    更新日期:2017-11-01
  • Fokker-Planck equation for the non-Markovian Brownian motion in the presence of a magnetic field
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-23
    Joydip Das, Shrabani Mondal, Bidhan Chandra Bag

    In the present study, we have proposed the Fokker-Planck equation in a simple way for a Langevin equation of motion having ordinary derivative (OD), the Gaussian random force and a generalized frictional memory kernel. The equation may be associated with or without conservative force field from harmonic potential. We extend this method for a charged Brownian particle in the presence of a magnetic field. Thus, the present method is applicable for a Langevin equation of motion with OD, the Gaussian colored thermal noise and any kind of linear force field that may be conservative or not. It is also simple to apply this method for the colored Gaussian noise that is not related to the damping strength.

    更新日期:2017-11-01
  • Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-23
    M. Núñez, T. Robie, D. G. Vlachos

    Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

    更新日期:2017-11-01
  • Mesh-free hierarchical clustering methods for fast evaluation of electrostatic interactions of point multipoles
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-23
    H. A. Boateng

    Electrostatic interactions involving point multipoles are being increasingly implemented to achieve higher accuracy in molecular simulations. A major drawback of multipolar electrostatics is the increased computational cost. Here we develop and compare two Cartesian tree algorithms which employ Taylor approximations and hierarchical clustering to speed up the evaluation of point multipole interactions. We present results from applying the algorithms to compute the free space Coulomb potential and forces of different sets of interacting point multipoles with different densities. The methods achieve high accuracy and speedup of more than an order of magnitude over direct sum calculations and scale well in parallel.

    更新日期:2017-11-01
  • Crossing conditions in coupled cluster theory
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-24
    Eirik F. Kjønstad, Rolf H. Myhre, Todd J. Martínez, Henrik Koch

    We derive the crossing conditions at conical intersections between electronic states in coupled cluster theory and show that if the coupled cluster Jacobian matrix is nondefective, two (three) independent conditions are correctly placed on the nuclear degrees of freedom for an inherently real (complex) Hamiltonian. Calculations using coupled cluster theory on a 21A′/31A′ conical intersection in hypofluorous acid illustrate the nonphysical artifacts associated with defects at accidental same-symmetry intersections. In particular, the observed intersection seam is folded about a space of the correct dimensionality, indicating that minor modifications to the theory are required for it to provide a correct description of conical intersections in general. We find that an accidental symmetry allowed 11A″/21A″ intersection in hydrogen sulfide is properly described, showing no artifacts as well as linearity of the energy gap to first order in the branching plane.

    更新日期:2017-11-01
  • Local-metrics error-based Shepard interpolation as surrogate for highly non-linear material models in high dimensions
    J. Chem. Phys. (IF 2.965) Pub Date : 2017-10-24
    Juan M. Lorenzi, Thomas Stecher, Karsten Reuter, Sebastian Matera

    Many problems in computational materials science and chemistry require the evaluation of expensive functions with locally rapid changes, such as the turn-over frequency of first principles kinetic Monte Carlo models for heterogeneous catalysis. Because of the high computational cost, it is often desirable to replace the original with a surrogate model, e.g., for use in coupled multiscale simulations. The construction of surrogates becomes particularly challenging in high-dimensions. Here, we present a novel version of the modified Shepard interpolation method which can overcome the curse of dimensionality for such functions to give faithful reconstructions even from very modest numbers of function evaluations. The introduction of local metrics allows us to take advantage of the fact that, on a local scale, rapid variation often occurs only across a small number of directions. Furthermore, we use local error estimates to weigh different local approximations, which helps avoid artificial oscillations. Finally, we test our approach on a number of challenging analytic functions as well as a realistic kinetic Monte Carlo model. Our method not only outperforms existing isotropic metric Shepard methods but also state-of-the-art Gaussian process regression.

    更新日期:2017-11-01
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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