The 100 most-cited articles in The Journal of Chemical Physics, 2017

A new model, termed D4, for the efficient computation of molecular dipole-dipole dispersion coefficients is presented. As in the related, well established D3 scheme, these are obtained as a sum of atom-in-molecule dispersion coefficients over atom pairs. Both models make use of dynamic polarizabilities obtained from first-principles time-dependent density functional theory calculations for atoms in different chemical environments employing fractional atomic coordination numbers for interpolation. Different from the D3 model, the coefficients are obtained on-the-fly by numerical Casimir-Polder integration of the dynamic, atomic polarizabilities α(iω). Most importantly, electronic density information is now incorporated via atomic partial charges computed at a semi-empirical quantum mechanical tight-binding level, which is used to scale the polarizabilities. Extended statistical measures show that errors for dispersion coefficients with the proposed D4 method are significantly lower than with D3 and other, computationally more involved schemes. Alongside, accurate isotropic charge and…

Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field. We summarize some recent advances and suggest avenues for future developments.

) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few…

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solve the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth…

This article describes recent progress in understanding highly stable glasses prepared by physical vapor deposition and provides perspective on further research directions for the field. For a given molecule, vapor-deposited glasses can have higher density and lower enthalpy than any glass that can be prepared by the more traditional route of cooling a liquid, and such glasses also exhibit greatly enhanced kinetic stability. Because vapor-deposited glasses can approach the bottom of the amorphous part of the potential energy landscape, they provide insights into the properties expected for the "ideal glass." Connections between vapor-deposited glasses, liquid-cooled glasses, and deeply supercooled liquids are explored. The generality of stable glass formation for organic molecules is discussed along with the prospects for stable glasses of other types of materials.

New correlation consistent basis sets based on pseudopotential (PP) Hamiltonians have been developed from double- to quintuple-zeta quality for the late alkali (K-Fr) and alkaline earth (Ca-Ra) metals. These are accompanied by new all-electron basis sets of double- to quadruple-zeta quality that have been contracted for use with both Douglas-Kroll-Hess (DKH) and eXact 2-Component (X2C) scalar relativistic Hamiltonians. Sets for valence correlation (ms), cc-pVnZ-PP and cc-pVnZ-(DK,DK3/X2C), in addition to outer-core correlation [valence + (m-1)sp], cc-p(w)CVnZ-PP and cc-pwCVnZ-(DK,DK3/X2C), are reported. The -PP sets have been developed for use with small-core PPs [I. S. Lim et al., J. Chem. Phys. 122, 104103 (2005) and I. S. Lim et al., J. Chem. Phys. 124, 034107 (2006)], while the all-electron sets utilized second-order DKH Hamiltonians for 4s and 5s elements and third-order DKH for 6s and 7s. The accuracy of the basis sets is assessed through benchmark calculations at the coupled-cluster level of theory for both atomic and molecular properties. Not surprisingly, it is found that…

The Berendsen barostat from molecular dynamics simulation is applied in both standard dissipative particle dynamics (DPD) and many-body dissipative particle dynamics (MDPD) simulations. The original Berendsen barostat works well in (M)DPD simulation of a single-component system under constant pressure condition and in nonequilibrium dynamic processes. The partial Berendsen barostat is proposed for multi-component system simulation with (M)DPD. The displacement rescaling process of the Berendsen barostat is only applied on the particles outside the center region, acting as a pressure "boundary condition." The center part forms the free zone, in which the interface shape and nonequilibrium dynamic behavior between different phases can be captured properly. An immiscible bubble in the second fluid under constant pressure condition is studied, and the oscillation of the bubble radius and fluctuation of systempressure can be obtained by the current barostat. Preliminary models for bubble growing and collapsing under square pressure wave and bubble oscillation under harmonic pressure wave…

This topical review discusses the theoretical progress made in the field of polymer nanocomposites, i.e., hybrid materials created by mixing (typically inorganic) nanoparticles (NPs) with organic polymers. It primarily focuses on the outstanding issues in this field and is structured around five separate topics: (i) the synthesis of functionalized nanoparticles; (ii) their phase behavior when mixed with a homopolymer matrix and their assembly into well-defined superstructures; (iii) the role of processing on the structures realized by these hybrid materials and the role of the mobilities of the different constituents; (iv) the role of external fields (electric, magnetic) in the active assembly of the NPs; and (v) the engineering properties that result and the factors that control them. While the most is known about topic (ii), we believe that significant progress needs to be made in the other four topics before the practical promise offered by these materials can be realized. This review delineates the most pressing issues on these topics and poses specific questions that we believe…

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals for the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. The chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.

We introduce a new fingerprint that allows distinguishing between liquid-like and solid-like atomic environments. This fingerprint is based on an approximate expression for the entropy projected on individual atoms. When combined with local enthalpy, this fingerprint acquires an even finer resolution and it is capable of discriminating between different crystal structures.

In this work, we present a linear scaling formulation of the coupled-cluster singles and doubles with perturbative inclusion of triples (CCSD(T)) and explicitly correlated geminals. The linear scaling implementation of all post-mean-field steps utilizes the SparseMaps formalism [P. Pinski et al., J. Chem. Phys. 143, 034108 (2015)]. Even for conservative truncation levels, the method rapidly reaches near-linear complexity in realistic basis sets, e.g., an effective scaling exponent of 1.49 was obtained for n-alkanes with up to 200 carbon atoms in a def2-TZVP basis set. The robustness of the method is benchmarked against the massively parallel implementation of the conventional explicitly correlated coupled-cluster for a 20-water cluster; the total dissociation energy of the cluster (∼186 kcal/mol) is affected by the reduced scaling approximations by only ∼0.4 kcal/mol. The reduced scaling explicitly correlated CCSD(T) method is used to examine the binding energies of several systems in the L7 benchmark data set of noncovalent interactions.

With the advent of molecular electronics, tremendous attention has been paid towards understanding the structure-function relationship of molecular junctions. Understanding how heat is transported, dissipated, and converted into electricity in molecular junctions is of great importance for designing thermally robust molecular circuits and high-performance energy conversion devices. Further, the study of thermal and thermoelectric phenomena in molecular junctions provides novel insights into the limits of applicability of classical laws. Here, we present a review of the computational and experimental progress made in probing thermoelectric effects, thermal conduction, heat dissipation, and local heating/cooling in self-assembled monolayer and single molecule junctions. We also discuss some outstanding challenges and potential future directions.

The complexation of mixtures of cationic and anionic polymers to produce complex-coacervate phases is a subject of fundamental importance to colloid and polymer science as well as to applications including drug delivery, sensing technologies, and bio-inspired adhesives. Unfortunately the theoretical underpinnings of complex coacervation are widely misunderstood and conceptual mistakes have propagated in the literature. Here, a simple symmetric polyelectrolyte mixture model in the absence of salt is used to discuss the salient features of the phase diagram, including the location of the critical point, binodals, and spinodals. It is argued that charge compensation by dimerization in the dilute region renders the phase diagram of an oppositely charged polyelectrolyte mixture qualitatively and quantitatively similar to that of a single-component symmetric diblock polyampholyte solution, a system capable of "self-coacervation." The theoretical predictions are verified using fully fluctuating field-theoretic simulations for corresponding polyelectrolyte and diblock polyampholyte models.…

Photoelectron photoion coincidence (PEPICO) spectroscopy could become a powerful tool for the time-resolved study of multi-channel gas phase chemical reactions. Toward this goal, we have designed and tested electron and ion optics that form the core of a new PEPICO spectrometer, utilizing simultaneous velocity map imaging for both cations and electrons, while also achieving good cation mass resolution through space focusing. These optics are combined with a side-sampled, slow-flow chemical reactor for photolytic initiation of gas-phase chemical reactions. Together with a recent advance that dramatically increases the dynamic range in PEPICO spectroscopy [D. L. Osborn et al., J. Chem. Phys. 145, 164202 (2016)], the design described here demonstrates a complete prototype spectrometer and reactor interface to carry out time-resolved experiments. Combining dual velocity map imaging with cation space focusing yields tightly focused photoion images for translationally cold neutrals, while offering good mass resolution for thermal samples as well. The flexible optics design incorporates…

In recent years it has become clear that the interfacial layer formed around nanoparticles in polymer nanocomposites (PNCs) is critical for controlling their macroscopic properties. The interfacial layer occupies a significant volume fraction of the polymer matrix in PNCs and creates strong intrinsic heterogeneity in their structure and dynamics. Here, we focus on analysis of the structure and dynamics of the interfacial region in model PNCs with well-dispersed, spherical nanoparticles with attractive interactions. First, we discuss several experimental techniques that provide structural and dynamic information on the interfacial region in PNCs. Then, we discuss the role of various microscopic parameters in controlling structure and dynamics of the interfacial layer. The analysis presented emphasizes the importance of the polymer-nanoparticle interactions for the slowing down dynamics in the interfacial region, while the thickness of the interfacial layer appears to be dependent on chain rigidity, and has been shown to increase with cooling upon approaching the glass transition.…

One of the most promising frameworks for understanding the anomalies of cold and supercooled water postulates the existence of two competing, interconvertible local structures. If the non-ideality in the Gibbs energy of mixing overcomes the ideal entropy of mixing of these two structures, a liquid-liquid phase transition, terminated at a liquid-liquid critical point, is predicted. Various versions of the "two-structure equation of state" (TSEOS) based on this concept have shown remarkable agreement with both experimental data for metastable, deeply supercooled water and simulations of molecular water models. However, existing TSEOSs were not designed to describe the negative pressure region and do not account for the stability limit of the liquid state with respect to the vapor. While experimental data on supercooled water at negative pressures may shed additional light on the source of the anomalies of water, such data are very limited. To fill this gap, we have analyzed simulation results for TIP4P/2005, one of the most accurate classical water models available. We have used…

Although molecular dynamics (MD) simulations are commonly used to predict the structure and properties of glasses, they are intrinsically limited to short time scales, necessitating the use of fast cooling rates. It is therefore challenging to compare results from MD simulations to experimental results for glasses cooled on typical laboratory time scales. Based on MD simulations of a sodium silicate glass with varying cooling rate (from 0.01 to 100 K/ps), here we show that thermal history primarily affects the medium-range order structure, while the short-range order is largely unaffected over the range of cooling rates simulated. This results in a decoupling between the enthalpy and volume relaxation functions, where the enthalpy quickly plateaus as the cooling rate decreases, whereas density exhibits a slower relaxation. Finally, we show that, using the proper extrapolation method, the outcomes of MD simulations can be meaningfully compared to experimental values when extrapolated to slower cooling rates.

We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level ab initio PES of methyl chloride with 44 819 points. The ML model is trained on sets of different sizes and then used to predict the energies for tens of thousands of nuclear configurations…

To clarify atomic diffusion in amorphous materials, which is important in novel information and energy devices, theoretical methods having both reliability and computational speed are eagerly anticipated. In the present study, we applied neural network (NN) potentials, a recently developed machine learning technique, to the study of atom diffusion in amorphous materials, using Li3PO4 as a benchmark material. The NN potential was used together with the nudged elastic band, kinetic Monte Carlo, and molecular dynamics methods to characterize Li vacancy diffusion behavior in the amorphous Li3PO4 model. By comparing these results with corresponding DFT calculations, we found that the average error of the NN potential is 0.048 eV in calculating energy barriers of diffusion paths, and 0.041 eV in diffusion activation energy. Moreover, the diffusion coefficients obtained from molecular dynamics are always consistent with those from ab initio molecular dynamics simulation, while the computation speed of the NN potential is 3–4 orders of magnitude faster than DFT. Lastly, the structure of…

We extend our recently developed heat-bath configuration interaction (HCI) algorithm, and our semistochastic algorithm for performing multireference perturbation theory, to calculate excited-state wavefunctions and energies. We employ time-reversal symmetry, which reduces the memory requirements by more than a factor of two. An extrapolation technique is introduced to reliably extrapolate HCI energies to the full CI limit. The resulting algorithm is used to compute fourteen low-lying potential energy surfaces of the carbon dimer using the cc-pV5Z basis set, with an estimated error in energy of 30-50 μHa compared to full CI. The excitation energies obtained using our algorithm have a mean absolute deviation of 0.02 eV compared to experimental values.

A hybrid stochastic-deterministic approach for computing the second-order perturbative contribution E(2) within multireference perturbation theory (MRPT) is presented. The idea at the heart of our hybrid scheme—based on a reformulation of E(2) as a sum of elementary contributions associated with each determinant of the MR wave function—is to split E(2) into a stochastic and a deterministic part. During the simulation, the stochastic part is gradually reduced by dynamically increasing the deterministic part until one reaches the desired accuracy. In sharp contrast with a purely stochastic Monte Carlo scheme where the error decreases indefinitely as t−1/2 (where t is the computational time), the statistical error in our hybrid algorithm displays a polynomial decay ∼t−n with n = 3–4 in the examples considered here. If desired, the calculation can be carried on until the stochastic part entirely vanishes. In that case, the exact result is obtained with no error bar and no noticeable computational overhead compared to the fully deterministic calculation. The method is illustrated on the…

Multicomponent density functional theory (DFT) enables the consistent quantum mechanical treatment of both electrons and protons. A major challenge has been the design of electron-proton correlation (epc) functionals that produce even qualitatively accurate proton densities. Herein an electron-proton correlation functional, epc17, is derived analogously to the Colle-Salvetti formalism for electron correlation and is implemented within the nuclear-electronic orbital (NEO) framework. The NEO-DFT/epc17 method produces accurate proton densities efficiently and is promising for diverse applications.

Poly(N-isopropylacrylamide) (PNIPAm) is a smart polymer that presents a lower critical transition temperature (LCST) of 305 K. Interestingly, this transition point falls within the range of the human body temperature, making PNIPAm a highly suitable candidate for bio-medical applications. However, it is sometimes desirable to have a rather flexible tuning of the LCST of these polymers to further increase their range of applications. In this work, we use all-atom molecular dynamics simulations to study the LCST of PNIPAm-based (co-)polymers. We study different molecular architectures where the polymer sequences are tuned either by modifying its stereochemistry or by the co-polymerization of PNIPAm with acrylamide (Am) units. Our analysis connects global polymer conformations with the microscopic intermolecular interactions. These findings suggest that the collapse of a PNIPAm chain upon heating is dependent on the hydration structure around the monomers, which is strongly dependent on the tacticity and the presence of more hydrophilic acrylamide monomers. Our results are found to be…

Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where an initial path is iteratively shifted to the nearest minimum energy path. The computational effort can be large, especially when ab initio or electron density functional calculations are used to evaluate the energy and atomic forces. Here, we show how the number of such evaluations can be reduced by an order of magnitude using a Gaussian process regression approach where an approximate energy surface is generated and refined in each iteration. When the goal is to evaluate the transition rate within harmonic transition state theory, the evaluation of the Hessian matrix at the initial and final state minima can be carried out beforehand and used as input in the minimum energy path calculation, thereby improving stability and reducing the number of iterations needed for convergence. A Gaussian process model also provides an uncertainty estimate for…

Organic-inorganic halide perovskites present a number of challenges for first-principles atomistic materials modeling. Such "plastic crystals" feature dynamic processes across multiple length and time scales. These include the following: (i) transport of slow ions and fast electrons; (ii) highly anharmonic lattice dynamics with short phonon lifetimes; (iii) local symmetry breaking of the average crystallographic space group; (iv) strong relativistic (spin-orbit coupling) effects on the electronic band structure; and (v) thermodynamic metastability and rapid chemical breakdown. These issues, which affect the operation of solar cells, are outlined in this perspective. We also discuss general guidelines for performing quantitative and predictive simulations of these materials, which are relevant to metal-organic frameworks and other hybrid semiconducting, dielectric and ferroelectric compounds.

Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters. While it is known how to estimate MSMs from trajectories whose starting points are not sampled from an equilibrium ensemble, this has not yet been the case for TICA and the VAC. Previous estimates from short trajectories have been strongly biased and thus not variationally optimal. Here, we employ the Koopman operator theory and the ideas from dynamic mode decomposition to extend the VAC and TICA to non-equilibrium data. The main insight is that the VAC and TICA provide a coefficient matrix…

We extent the recently developed Multi-Layer Multi-Configuration Time-Dependent Hartree method for Bosons for simulating the correlated quantum dynamics of bosonic mixtures to the fermionic sector and establish a unifying approach for the investigation of the correlated quantum dynamics of a mixture of indistinguishable particles, be it fermions or bosons. Relying on a multi-layer wave-function expansion, the resulting Multi-Layer Multi-Configuration Time-Dependent Hartree method for Mixtures (ML-MCTDHX) can be adapted to efficiently resolve system-specific intra- and inter-species correlations. The versatility and efficiency of ML-MCTDHX are demonstrated by applying it to the problem of colliding few-atom mixtures of both Bose-Fermi and Fermi-Fermi types. Thereby, we elucidate the role of correlations in the transmission and reflection properties of the collisional events. In particular, we present examples where the reflection (transmission) at the other atomic species is a correlation-dominated effect, i.e., it is suppressed in the mean-field approximation.

A combination of theory, X-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) are used to probe the hydration structure of aqueous Na+. The high spatial resolution of the XRD measurements corresponds to Qmax = 24 Å−1 while the first-reported Na K-edge EXAFS measurements have a spatial resolution corresponding to 2k = Qmax = 16 Å−1. Both provide an accurate measure of the shape and position of the first peak in the Na–O pair distribution function, gNaO(r). The measured Na–O distances of 2.384 ± 0.003 Å (XRD) and 2.37 ± 0.024 Å (EXAFS) are in excellent agreement. These measurements show a much shorter Na–O distance than generally reported in the experimental literature (Na–Oavg ∼ 2.44 Å) although the current measurements are in agreement with recent neutron diffraction measurements. The measured Na–O coordination number from XRD is 5.5 ± 0.3. The measured structure is compared with both classical and first-principles density functional theory (DFT) simulations. Both of the DFT-based methods, revPBE and BLYP, predict a Na–O distance that is too long by about…

Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of…

In this paper, we combine two powerful computational techniques, well-tempered metadynamics and time-lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy landscapes. Metadynamics is a well-established and widely used enhanced sampling method whose efficiency depends on an appropriate choice of collective variables. Often the initial choice is not optimal leading to slow convergence. However by analyzing the dynamics generated in one such run with a time-lagged independent component analysis and the techniques recently developed in the area of conformational dynamics, we obtain much more efficient collective variables that are also better capable of illuminating the physics of the system. We demonstrate the power of this approach in two paradigmatic examples.

We outline ideas on desired properties for a new generation of effective core potentials (ECPs) that will allow valence-only calculations to reach the full potential offered by recent advances in many-body wave function methods. The key improvements include consistent use of correlated methods throughout ECP constructions and improved transferability as required for an accurate description of molecular systems over a range of geometries. The guiding principle is the isospectrality of all-electron and ECP Hamiltonians for a subset of valence states. We illustrate these concepts on a few first- and second-row atoms (B, C, N, O, S), and we obtain higher accuracy in transferability than previous constructions while using semi-local ECPs with a small number of parameters. In addition, the constructed ECPs enable many-body calculations of valence properties with higher (or same) accuracy than their all-electron counterparts with uncorrelated cores. This implies that the ECPs include also some of the impacts of core-core and core-valence correlations on valence properties. The results open…

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…

The structure of liquid water as a function of temperature is investigated through the modeling of infrared and Raman spectra along with structural order parameters calculated from classical and quantum molecular dynamics simulations with the MB-pol many-body potential energy function. The magnitude of nuclear quantum effects is also monitored by comparing the vibrational spectra obtained from classical and centroid molecular dynamics, both in intensities and peak positions. The observed changes in spectral activities are shown to reflect changes in the underlying structure of the hydrogen-bond network and are found to be particularly sensitive to many-body effects in the representation of the electrostatic interactions. Overall, good agreement is found with the experimental spectra, which provides further evidence for the accuracy of MB-pol in predicting the properties of water.

An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The new algorithm is an order of magnitude faster than our previous one and removes the bottleneck related to the calculation of the (T) contribution. First, a numerical Laplace transformed expression for the (T) fragment energy is introduced, which requires on average 3 to 4 times fewer floating point operations with negligible compromise in accuracy eliminating the redundancy among the evaluated triples amplitudes. Second, an additional speedup factor of 3 is achieved by the optimization of our canonical (T) algorithm, which is also executed in the local case. These developments can also be integrated into canonical as well as alternative fragmentation-based local CCSD(T) approaches with minor modifications. As it is demonstrated by our benchmark calculations, the evaluation of the new Laplace transformed (T) correction can…

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the…

In this perspective, I review methods for computing (ro-)vibrational energy levels and wavefunctions of molecules with more than four atoms. I identify three problems one confronts (1) reducing the size of the basis; (2) computing hundreds of eigenvalues and eigenvectors of a large matrix; (3) calculating matrix elements of the potential, and present ideas that mitigate them. Most modern methods use a combination of these ideas. I divide popular methods into groups based on the strategies used to deal with the three problems.

Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of calculations required for chemical accuracy is still prohibitively expensive for the ab initio MBE to compete with force field approximations for applications beyond single-point energies. Alongside the MBE, empirical models of ab initio potential energy surfaces have improved, especially non-linear models based on neural networks (NNs) which can reproduce ab initio potential energy surfaces rapidly and accurately. Although they are fast, NNs suffer from their own curse of dimensionality; they must be trained on a representative sample of chemical space. In this paper we examine the synergy of the MBE and NN’s and explore their complementarity. The MBE offers a systematic way to treat systems of arbitrary size while reducing the scaling problem of large systems. NN’s reduce, by a factor in excess of 106, the computational overhead of the MBE and reproduce the accuracy of ab initio…

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interactionentropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interactionentropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method…

An exhaustive study by molecular dynamics has been performed to analyze the factors that enhance the precision of the technique of direct coexistence for a system of ice and liquid water. The factors analyzed are the stochastic nature of the method, the finite size effects, and the influence of the initial ice configuration used. The results obtained show that the precision of estimates obtained through the technique of direct coexistence is markedly affected by the effects of finite size, requiring systems with a large number of molecules to reduce the error bar of the melting point. This increase in size causes an increase in the simulation time, but the estimate of the melting point with a great accuracy is important, for example, in studies on the ice surface. We also verified that the choice of the initial ice Ih configuration with different proton arrangements does not significantly affect the estimate of the melting point. Importantly this study leads us to estimate the melting point at ambient pressure of two of the most popular models of water, TIP4P/2005 and TIP4P/Ice,…

Despite considerable efforts over more than two decades, our knowledge of the interactions in electrolyte solutions is not yet satisfactory. Not even one of the most simple and important aqueous solutions, NaCl(aq), escapes this assertion. A requisite for the development of a force field for any water solution is the availability of a good model for water. Despite the fact that TIP4P/2005 seems to fulfill the requirement, little work has been devoted to build a force field based on TIP4P/2005. In this work, we try to fill this gap for NaCl(aq). After unsuccessful attempts to produce accurate predictions for a wide range of properties using unity ionic charges, we decided to follow recent suggestions indicating that the charges should be scaled in the ionic solution. In this way, we have been able to develop a satisfactory non-polarizable force field for NaCl(aq). We evaluate a number of thermodynamic properties of the solution (equation of state, maximum in density, enthalpies of solution, activity coefficients, radial distribution functions, solubility, surface tension, diffusion…

The solubility of a crystalline substance in the solution can be estimated from its absolute solid free energy and excess solvation free energy. Here, we present a numerical method, which enables convenient solubility estimation of general molecular crystals at arbitrary thermodynamic conditions where solid and solution can coexist. The methodology is based on standard alchemical free energy methods, such as thermodynamic integration and free energy perturbation, and consists of two parts: (1) systematic extension of the Einstein crystal method to calculate the absolute solid free energies of molecular crystals at arbitrary temperatures and pressures and (2) a flexible cavity method that can yield accurate estimates of the excess solvation free energies. As an illustration, via classical Molecular Dynamic simulations, we show that our approach can predict the solubility of OPLS-AA-based (Optimized Potentials for Liquid Simulations All Atomic) naphthalene in SPC (Simple Point Charge) water in good agreement with experimental data at various temperatures and pressures. Because the…

Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory…

Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their accuracy. Here, using charging curves for an electrode in the presence of an inert aqueous electrolyte, we demonstrate that most continuum models, which are parameterized and benchmarked for molecules, anions, and cations in solution, undersolvate metal surfaces, and underestimate the surface charge as a function of applied potential. We examine features of the electrolyte and interface that are captured by these models and identify improvements necessary for realistic electrochemical calculations of metal surfaces. Finally, we reparameterize popular solvation models using the surface charge of Ag(100) as a function of voltage to find improved accuracy for metal surfaces without significant change in utility for molecular and ionic solvation.

We present a new method for sampling stochastic displacements in Brownian Dynamics (BD) simulations of colloidal scale particles. The method relies on a new formulation for Ewald summation of the Rotne-Prager-Yamakawa (RPY) tensor, which guarantees that the real-space and wave-space contributions to the tensor are independently symmetric and positive-definite for all possible particle configurations. Brownian displacements are drawn from a superposition of two independent samples: a wave-space (far-field or long-ranged) contribution, computed using techniques from fluctuating hydrodynamics and non-uniform fast Fourier transforms; and a real-space (near-field or short-ranged) correction, computed using a Krylov subspace method. The combined computational complexity of drawing these two independent samples scales linearly with the number of particles. The proposed method circumvents the super-linear scaling exhibited by all known iterative sampling methods applied directly to the RPY tensor that results from the power law growth of the condition number of tensor with the number of…

The accurate prediction of singlet and triplet excitation energies is an area of intense research of significant fundamental interest and critical for many applications. Most calculations of singlet and triplet energies use time-dependent density functional theory (TDDFT) in conjunction with an approximate exchange-correlation functional. In this work, we examine and critically assess an alternative method for predicting low-lying neutral excitations with similar computational cost, the ab initio Bethe-Salpeter equation (BSE) approach, and compare results against high-accuracy wavefunction-based methods. We consider singlet and triplet excitations of 27 prototypical organic molecules, including members of Thiel's set, the acene series, and several aromatic hydrocarbons exhibiting charge-transfer-like excitations. Analogous to its impact in TDDFT, we find that the Tamm-Dancoff approximation (TDA) overcomes triplet instabilities in the BSE approach, improving both triplet and singlet energetics relative to higher level theories. Finally, we find that BSE-TDA calculations built on…

The incremental expansion provides a polynomial scaling method for computing electronic correlation energies. This article details a new algorithm and implementation for the incremental expansion of full configuration interaction (FCI), called iFCI. By dividing the problem into n-body interaction terms, accurate correlation energies can be recovered at low n in a highly parallel computation. Additionally, relatively low-cost approximations are possible in iFCI by solving for each incremental energy to within a specified threshold. Herein, systematic tests show that FCI-quality energies can be asymptotically reached for cases where dynamic correlation is dominant as well as where static correlation is vital. To further reduce computational costs and allow iFCI to reach larger systems, a select-CI approach (heat-bath CI) requiring two parameters is incorporated. Finally, iFCI provides the first estimate of FCI energies for hexatriene with a polarized double zeta basis set, which has 32 electrons correlated in 118 orbitals, corresponding to a FCI dimension of over 1038.

We present the implementation and performance of the strongly constrained and appropriately normed, SCAN, meta-GGA exchange-correlation (XC) approximation in the planewave-pseudopotential (PW-PP) formalism using the Troullier-Martins pseudopotential scheme. We studied its performance by applying the PW-PP implementation to several practical applications of interest in condensed matter sciences: (a) crystalline silicon and germanium, (b) martensitic phase transition energetics of phosphorene, and (c) a single water molecule physisorption on a graphene sheet. Given the much-improved accuracy over the GGA functionals and its relatively low computational cost compared to hybrid XC functionals, the SCAN functional is highly promising for various practical applications of density functional theory calculations for condensed matter systems. At same time, the SCAN meta-GGA functional appears to require more careful attention to numerical details. The meta-GGA functional shows more significant dependence on the fast Fourier transform grid, which is used for evaluating the XC potential in…

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…

A novel reduced-order method is presented for modeling reacting flows characterized by strong non-equilibrium of the internal energy level distribution of chemical species in the gas. The approach seeks for a reduced-order representation of the distribution function by grouping individual energy states into macroscopic bins, and then reconstructing state population using the maximum entropy principle. This work introduces an adaptive grouping methodology to identify and lump together groups of states that are likely to equilibrate faster with respect to each other. To this aim, two algorithms have been considered: the modified island algorithm and the spectral clustering method. Both methods require a measure of dissimilarity between internal energy states. This is achieved by defining “metrics” based on the strength of the elementary rate coefficients included in the state-specific kinetic mechanism. Penalty terms are used to avoid grouping together states characterized by distinctively different energies. The two methods are used to investigate excitation and dissociation of N2…

We present global potential energy surfaces for nine adiabatic electronic states of O3, namely, 1 1A′, 2 1A′, 1 1A″, 1 3A′, 2 3A′, 1 3A″, 1 5A′, 2 5A′, and 1 5A″. These are the states of O3 that are accessed in electronically adiabatic collisions of a ground-state triplet O2 molecule with a ground-state triplet O atom. The surfaces are based on XMS-CASPT2 electronic structure calculations with dynamically scaled external correlation. The active space has 12 active electrons distributed in the nine 2p orbitals. The adiabatic surfaces are fitted to analytic functions using a many-body expansion where the pairwise additive term is fitted to an accurate diatomic potential including a damped dispersion term, and the many-body part, without disconnected terms, is fitted with permutationally invariant polynomials in mixed exponential-Gaussians to the electronic structure data points. The selection and weighting of points for the fits are designed to produce surfaces suitable for describing energy transfer and dissociation in high-energy collisions.

The shear thinning of a lubricant significantly affects lubrication film generation at high shear rates. The critical shear rate, defined at the onset of shear thinning, marks the transition of lubricant behaviors. It is challenging to capture the entire shear-thinning curve by means of molecular dynamics (MD) simulations owing to the low signal-to-noise ratio or long calculation time at comparatively low shear rates (104–106 s−1), which is likely coincident with the shear rates of interest for lubrication applications. This paper proposes an approach that correlates the shear-thinning phenomenon with the change in the molecular conformation characterized by the radius of gyration of the molecule. Such a correlation should be feasible to capture the major mechanism of shear thinning for small- to moderate-sized non-spherical molecules, which is shear-induced molecular alignment. The idea is demonstrated by analyzing the critical shear rate for squalane (C30H62) and 1-decene trimer (C30H62); it is then implemented to study the behaviors of different molecular weight poly-α-olefin…

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th–U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac–Lr have been calculated using the Feller-Peterson-Dixon (FPD)…

Increasing emissions of carbon dioxide and the depletion of finite fossil fuels have led to many concerns about global warming and energy crises. Consequently, a sustainable and alternative method, photocatalytic CO2 reduction to chemical fuels has received considerable attention. This perspective highlights recent knowledge and the main challenges in CO2 photoreduction primarily from the theoretical field. The fundamental understanding of CO2 adsorption and reaction mechanism at an atomic level is fully addressed, and the relevant effects dominating the process of CO2 photoreduction are also elucidated. Moreover, recent development of photocatalysts including structural modification is presented, which greatly affects the efficiency and selectivity of CO2 conversion. Finally, the possibilities and challenges in this field are discussed.

The depth to which the local glass transition temperature Tg and alpha-relaxations are perturbed near a boundary is believed to be related to the characteristic length scales associated with cooperative dynamics in dynamically heterogeneous glasses. Following our recent work [R. R. Baglay and C. R. Roth, J. Chem. Phys. 143, 111101 (2015)] that measured a very broad 350-400 nm local Tg(z) profile across a glassy-rubbery interface of polystyrene (PS)/poly(n-butyl methacrylate) (PnBMA), we compare here how the Tg(z) profile in PS varies when changing the neighboring polymer from a lower Tg material to a higher Tg material. Here we report local Tg(z) profiles for PS when in contact with polysulfone (PSF), poly(methyl methacrylate) (PMMA), and poly(isobutyl methacrylate) (PiBMA). We find that the distance from the interface before bulk Tg of PS (Tgbulk=101 °C) is recovered depends on whether PS forms the high-Tg glassy component experiencing so-called soft confinement, z ≈ 225-250 nm for PS next to PiBMA (Tgbulk=62 °C) and PnBMA (Tgbulk=21 °C), or PS forms the low-Tg rubbery component…

In this review, we give an overview on the spin crossover of Fe(phen)2(NCS)2 complexes adsorbed on Cu(100), Cu2N/Cu(100), Cu(111), Co/Cu(111), Co(100), Au(100), and Au(111) surfaces. Depending on the strength of the interaction of the molecules with the substrates, the spin crossover behavior can be drastically changed. Molecules in direct contact with non-magnetic metallic surfaces coexist in both the high- and low-spin states but cannot be switched between the two. Our analysis shows that this is due to a strong interaction with the substrate in the form of a chemisorption that dictates the spin state of the molecules through its adsorption geometry. Upon reducing the interaction to the surface either by adding a second molecular layer or inserting an insulating thin film of Cu2N, the spin crossover behavior is restored and molecules can be switched between the two states with the help of scanning tunneling microscopy. Especially on Cu2N, the two states of single molecules are stable at low temperature and thus allow the realization of a molecular memory. Similarly, the molecules…

We introduce a mixed density fitting scheme that uses both a Gaussian and a plane-wave fitting basis to accurately evaluate electron repulsion integrals in crystalline systems. We use this scheme to enable efficient all-electron Gaussian based periodic density functional and Hartree-Fock calculations.

The intramolecular dynamics of flexible and semiflexible polymers in response to active noise is studied theoretically. The active noise may either originate from interactions of a passive polymer with a bath of active Brownian particles or the polymer itself is comprised of active Brownian particles. We describe the polymer by the continuous Gaussian semiflexible-polymer model, taking into account the finite polymer extensibility. Our analytical calculations predict a strong dependence of the polymer dynamics on the activity. In particular, active semiflexible polymers exhibit a crossover from a bending elasticity-dominated dynamics at weak activity to that of flexible polymers at strong activity. The end-to-end vector correlation function decays exponentially for times longer than the longest polymer relaxation time. Thereby, the polymer relaxation determines the decay of the correlation function for long and flexible polymers. For shorter and stiffer polymers, the relaxation behavior of individual active Brownian particles dominates the decay above a certain activity. The…

We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i.e., hexane). Finally, we illustrate the transferability of a subset of the determined parameters by calculating the critical micelle concentrations and mean aggregation numbers of selected alkyl ethoxylate surfactants, in good agreement with reported experimental values.

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.…

We address the effects of chain connectivity on electrostaticfluctuations in polyelectrolyte solutions using a field-theoretic, renormalizedGaussian fluctuation (RGF) theory. As in simple electrolyte solutions [Z.-G. Wang,Phys. Rev. E 81, 021501 (2010)], the RGF provides a unified theory forelectrostatic fluctuations, accounting for both dielectric and charge correlationeffects in terms of the self-energy. Unlike simple ions, the polyelectrolyte self energydepends intimately on the chain conformation, and our theory naturally provides aself-consistent determination of the response of intramolecular chain structure topolyelectrolyte and salt concentrations. The effects of the chain-conformation on theself-energy and thermodynamics are especially pronounced for flexiblepolyelectrolytes at low polymer and salt concentrations, where application of thewrong chain structure can lead to a drastic misestimation of the electrostaticcorrelations. By capturing the expected scaling behavior of chain size from dilute tosemi-dilute regimes, our theory provides improved estimates of the self…

We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N2O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H2O illustrates the case of a non-linear molecule with comparably simple…

We present a refined version of the polarizable Martini water model - coined refPOL - designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water force field when particle mesh Ewald electrostatics are employed. Our study reveals that the model remains applicable with various commonly used settings for the non-bonded interactions, including reaction field electrostatics. The oil/water partitioning behavior of uncharged Martini bead types is thoroughly investigated: Lennard-Jones interactions between the refPOL model and the remaining Martini beads are adjusted to reproduce the hydration free energies obtained with the original polarizable water model, while free energies of solvation in apolar media remain unchanged. The cross-interactions with charged bead types are parameterized to agree with the experimentally observed area per lipid of a fully solvated dipalmitoylphosphatidylcholine…

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…

Recent time-resolved spectroscopic experiments have indicated that vibronic coupling plays a vital role in facilitating the process of singlet fission. In this work, which forms the first article of a series, we set out to unravel the mechanisms underlying singlet fission through a vibronic exciton theory. We formulate a model in which both electronic and vibrational degrees of freedom are treated microscopically and non-perturbatively. Using pentacene as a prototypical material for singlet fission, we subject our theory to comparison with measurements on polarization-resolved absorption of single crystals, and employ our model to characterize the excited states underlying the absorption band. Special attention is given to the convergence of photophysical observables with respect to the basis size employed, through which we determine the optimal basis for more expensive calculations to be presented in subsequent work. We furthermore evaluate the energetic separation between the optically prepared singlet excited state and the correlated triplet pair state, as well as provide a…

This paper describes an interface between the density matrix renormalization group (DMRG) method and the complete active-space self-consistent field (CASSCF) method and its analytical gradient, as well as an extension to the second-order perturbation theory (CASPT2) method. This interfacing allows large active-space multi-reference computations to be easily performed. The interface and its extension are both implemented in terms of reduced density matrices (RDMs) which can be efficiently computed via the DMRG sweep algorithm. We also present benchmark results showing that, in practice, the DMRG-CASSCF calculations scale with active-space size in a polynomial manner in the case of quasi-1D systems. Geometry optimization of a binuclear iron-sulfur cluster using the DMRG-CASSCF analytical gradient is demonstrated, indicating that the inclusion of the valence p-orbitals of sulfur and double-shell d-orbitals of iron lead to non-negligible changes in the geometry compared to the results of small active-space calculations. With the exception of the selection of M values, many computational…

Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems, as a maximally predictive one-dimensional projection. We then show that this criterion is uniquely satisfied by a dominant eigenfunction of an integral operator associated with the ensemble dynamics. We present a new sparse estimator for these eigenfunctions which can search through a large candidate pool of structural order parameters and build simple, interpretable approximations that employ only a small number of these order parameters. Example applications with a small molecule's rotational dynamics and simulations of protein conformational change and folding show that this approach can filter through statistical noise to identify simple reaction coordinates from complex dynamics.

Monolayer Mo2C is a new member of two-dimensional materials. Here the electronic structure and lattice dynamics of monolayer Mo2C are calculated. According to the electron-phonon interaction, it is predicted that monolayer Mo2C could be a quasi-two-dimensional superconductor and the effects of functional-groups are crucially important considering its unsaturated surface. Despite the suppressed superconductivity by chalcogen adsorption, our most interesting prediction is that the electron-phonon interaction of monolayer Mo2C can be greatly enhanced by bromine absorption, suggesting that Mo2CBr2 as a good candidate for a nanoscale superconductor.

Although the importance of temperature control in nonequilibrium molecular dynamics simulations is widely accepted, the consequences of the thermostatting approach in the case of strongly confined fluids are underappreciated. We show the strong influence of the thermostatting method on the water transport in carbon nanotubes (CNTs) by considering simulations in which the system temperature is controlled via the walls or via the fluid. Streaming velocities and mass flow rates are found to depend on the tube flexibility and on the thermostatting algorithm, with flow rates up to 20% larger when the walls are flexible. The larger flow rates in flexible CNTs are explained by a lower friction coefficient between water and the wall. Despite the lower friction, a larger solid-fluid interaction energy is found for flexible CNTs than for rigid ones. Furthermore, a comparison of thermostat schemes has shown that the Berendsen and Nosé-Hoover thermostats result in very similar transport rates, while lower flow rates are found under the influence of the Langevin thermostat. These findings…

Modification of the water hydrogen bond network imposed by disaccharides is known to serve as a bioprotective agent in living organisms, though its comprehensive understanding is still yet to be reached. In this study, aiming to characterize the dynamical slowing down and destructuring effect of disaccharides, we performed broadband dielectric spectroscopy, ranging from 0.5 GHz to 12 THz, of sucrose and trehalose aqueous solutions. The destructuring effect was examined in two ways (the hydrogen bond fragmentation and disordering) and our result showed that both sucrose and trehalose exhibit an obvious destructuring effect with a similar strength, by fragmenting hydrogen bonds and distorting the tetrahedral-like structure of water. This observation strongly supports a chaotropic (structure-breaking) aspect of disaccharides on the water structure. At the same time, hydration water was found to exhibit slower dynamics and a greater reorientational cooperativity than bulk water because of the strengthened hydrogen bonds. These results lead to the conclusion that strong…

A simple model has been developed to describe the symmetry-breaking of the electronic distribution of AL–D–AR type molecules in the excited state, where D is an electron donor and AL and AR are identical acceptors. The origin of this process is usually associated with the interaction between the molecule and the solvent polarization that stabilizes an asymmetric and dipolar state, with a larger charge transfer on one side than on the other. An additional symmetry-breaking mechanism involving the direct Coulomb interaction of the charges on the acceptors is proposed. At the same time, the electronic coupling between the two degenerate states, which correspond to the transferred charge being localised either on AL or AR, favours a quadrupolar excited state with equal amount of charge-transfer on both sides. Because of these counteracting effects, symmetry breaking is only feasible when the electronic coupling remains below a threshold value, which depends on the solvation energy and the Coulomb repulsion energy between the charges located on AL and AR. This model allows reproducing…

The Meyer-Miller (MM) classical vibronic (electronic + nuclear) Hamiltonian for electronically non-adiabatic dynamics-as used, for example, with the recently developed symmetrical quasiclassical (SQC) windowing model-can be written in either a diabatic or an adiabatic representation of the electronic degrees of freedom, the two being a canonical transformation of each other, thus giving the same dynamics. Although most recent applications of this SQC/MM approach have been carried out in the diabatic representation-because most of the benchmark model problems that have exact quantum results available for comparison are typically defined in a diabatic representation-it will typically be much more convenient to work in the adiabatic representation, e.g., when using Born-Oppenheimer potential energy surfaces (PESs) and derivative couplings that come from electronic structure calculations. The canonical equations of motion (EOMs) (i.e., Hamilton's equations) that come from the adiabatic MM Hamiltonian, however, in addition to the common first-derivative couplings, also involve…

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

We show a unified second-order scheme for constructing simple, robust, and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB algorithm that has been recently investigated. We show that the scheme is also useful for other types of thermostats, such as the Andersen thermostat and Nosé-Hoover chain, regardless of whether the thermostat is deterministic or stochastic. In addition to analytical analysis, two 1-dimensional models and three typical real molecular systems that range from the gas phase, clusters, to the condensed phase are used in numerical examples for demonstration. Accuracy may be increased by an order of magnitude for estimating coordinate-dependent properties in molecular dynamics (when the same time interval is used), irrespective of which type of thermostat is applied. The scheme is especially useful for path integral molecular dynamics because it consistently improves the efficiency for evaluating all thermodynamic properties for any type of thermostat.

We study a tensor hypercontraction decomposition of the Coulomb integrals of periodic systems where the integrals are factorized into a contraction of six matrices of which only two are distinct. We find that the Coulomb integrals can be well approximated in this form already with small matrices compared to the number of real space grid points. The cost of computing the matrices scales as O(N4) using a regularized form of the alternating least squares algorithm. The studied factorization of the Coulomb integrals can be exploited to reduce the scaling of the computational cost of expensive tensor contractions appearing in the amplitude equations of coupled cluster methods with respect to system size. We apply the developed methodologies to calculate the adsorption energy of a single water molecule on a hexagonal boron nitride monolayer in a plane wave basis set and periodic boundary conditions.

We present an analytical theory to compute conformations of heteropolymers-applicable to describe disordered proteins-as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence-while maintaining the same charge composition-can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar…

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We…

A novel method to calculate the solid-liquid contact angle is introduced in this study. Using the 3D configuration of a liquid droplet on a solid surface, this method calculates the contact angle along the contact line and provides an angular distribution. Although this method uses the 3D configuration of liquid droplets, it does not require the calculation of the 3D density profile to identify the boundaries of the droplet. This decreases the computational cost of the contact angle calculation greatly. Moreover, no presumption about the shape of the liquid droplet is needed when using the method introduced in this study. Using this method, the relationship between the size and the contact angle of water nano-droplets on a graphite substrate was studied. It is shown that the contact angle generally decreases by increasing the size of the nano-droplet. The microscopic contact angle of 83.0° was obtained for water on graphite which is in a good agreement with previous experimental and numerical studies. Neglecting other nanoscale effects which may influence the contact angle, the line…

When a three-phase contact line moves along a solid surface, the contact angle no longer corresponds to the static equilibrium angle but is larger when the liquid is advancing and smaller when the liquid is receding. The difference between the advancing and receding contact angles, i.e., the contact angle hysteresis, is of paramount importance in wetting and capillarity. For example, it determines the magnitude of the external force that is required to make a drop slide on a solid surface. Until now, fundamental origin of the contact angle hysteresis has been controversial. Here, this origin is revealed and a quantitative theory is derived. The theory is corroborated by the available experimental data for a large number of solid-liquid combinations. The theory is applied in modelling the contact angle hysteresis on a textured surface, and these results are also in quantitative agreement with the experimental data.

A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties. The agreement with the best available experimental data for the investigated properties is excellent; the new potential function is superior not only to previous ab initio potentials but also to the most popular empirical ones.

We present global ground-state potential energy surfaces for the quintet and singlet spin states of the O4 system that are suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation in electronically adiabatic, spin-conserving O2–O2 collisions. The surfaces are based on MS-CASPT2/maug-cc-pVTZ electronic structure calculations with scaled external correlation. The active space has 16 electrons in 12 orbitals. The calculations cover nine kinds of geometrical arrangements corresponding to dissociative diatom-diatom collisions of O2, geometries corresponding to O3–O, geometries identified by running trajectories, and geometries along linear synchronous transit paths. The global ground-state potential energy surfaces were obtained by a many-body approach with an accurate O–O pairwise interaction and a fit of the many-body interaction to 12 684 electronic structure data points for the singlet and 10 543 electronic structure data points for the quintet. The many-body fit is based on permutationally invariant polynomials in terms of…

Highly oxidized multifunctional organic molecules, which span a wide range of low volatilities, are capable of driving particle formation as well as the initial growth of particles in the atmosphere. However, their participant mechanism in new particle formation still remains largely ambiguous. Here we present an investigation of the potentially participant mechanism of the simplest hydroxyl acid, glycolic acid (GA) on clusters formation by sulfuric acid (SA) and ammonia (A). Density functional theory calculations at the M062X/6-311++G(3df,3pd) level of theory combining with atmospheric cluster dynamics code simulations of (𝐒𝐀)x⋅𝐀y⋅(𝐆𝐀)z cluster (y≤x + z ≤ 3) systems at different temperatures (298, 278, 258, 238, and 218 K) give direct evidence of the enhancement effect of GA on the formation rates of SA-A-based clusters at high concentration of GA and T = 238 K and 218 K. Moreover, within GA’s enhancement concentrations, the enhancement strength R of GA presents a positive dependence on its atmospheric concentrations and a negative dependence on temperature. A competitive…

Nanoparticle (NP) diffusion was measured in polyacrylamide gels (PAGs) with a mesh size comparable to the NP size, 21 nm. The confinement ratio (CR), NP diameter/mesh size, increased from 0.4 to 3.8 by increasing crosslinker density and from 0.4 to 2.1 by adding acetone, which collapsed the PAGs. In all gels, NPs either became localized, moving less than 200 nm, diffused microns, or exhibited a combination of these behaviors, as measured by single particle tracking. Mean squared displacements (MSDs) of mobile NPs decreased as CR increased. In collapsed gels, the localized NP population increased and MSD of mobile NPs decreased compared to crosslinked PAGs. For all CRs, van Hove distributions exhibited non-Gaussian displacements, consistent with intermittent localization of NPs. The non-Gaussian parameter increased from a maximum of 1.5 for crosslinked PAG to 5 for collapsed PAG, consistent with greater network heterogeneity in these gels. Diffusion coefficients decreased exponentially as CR increased for crosslinked gels; however, in collapsed gels, the diffusion coefficients…

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

In this paper, we provide a detailed description of the inchworm Monte Carlo formalism for the exact study of real-time non-adiabatic dynamics. This method optimally recycles Monte Carlo information from earlier times to greatly suppress the dynamical sign problem. Using the example of the spin-boson model, we formulate the inchworm expansion in two distinct ways: The first with respect to an expansion in the system-bath coupling and the second as an expansion in the diabatic coupling. The latter approach motivates the development of a cumulant version of the inchworm Monte Carlo method, which has the benefit of improved scaling. This paper deals completely with methodology, while Paper II provides a comprehensive comparison of the performance of the inchworm Monte Carlo algorithms to other exact methodologies as well as a discussion of the relative advantages and disadvantages of each.

A new analytical expression for the size-dependent bandgap of colloidal semiconductor nanocrystals is proposed within the framework of the finite-depth square-well effective mass approximation in order to provide a quantitative description of the quantum confinement effect. This allows one to convert optical spectroscopic data (photoluminescence spectrum and absorbance edge) into accurate estimates for the particle size distributions of colloidal systems even if the traditional effective mass model is expected to fail, which occurs typically for very small particles belonging to the so-called strong confinement limit. By applying the reported theoretical methodologies to CdTe nanocrystals synthesized through wet chemical routes, size distributions are inferred and compared directly to those obtained from atomic force microscopy and transmission electron microscopy. This analysis can be used as a complementary tool for the characterization of nanocrystal samples of many other systems such as the II-VI and III-V semiconductor materials.

Liquid water’s rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H2O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H2O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm−1 to beyond 1900 cm−1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm−1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest…

A thorough analytical and numerical characterization of the whole perturbation series of one-particle many-body Green's function (MBGF) theory is presented in a pedagogical manner. Three distinct but equivalent algebraic (first-quantized) recursive definitions of the perturbation series of the Green's function are derived, which can be combined with the well-known recursion for the self-energy. Six general-order algorithms of MBGF are developed, each implementing one of the three recursions, the ΔMPn method (where n is the perturbation order) [S. Hirata et al., J. Chem. Theory Comput. 11, 1595 (2015)], the automatic generation and interpretation of diagrams, or the numerical differentiation of the exact Green's function with a perturbation-scaled Hamiltonian. They all display the identical, nondivergent perturbation series except ΔMPn, which agrees with MBGF in the diagonal and frequency-independent approximations at 1≤n≤3 but converges at the full-configuration-interaction (FCI) limit at n=∞ (unless it diverges). Numerical data of the perturbation series are presented for Koopmans…

The mean-field solutions of electronic excited states are much less accessible than ground state (e.g., Hartree-Fock) solutions. Energy-based optimization methods for excited states, like Δ-SCF (self-consistent field), tend to fall into the lowest solution consistent with a given symmetry—a problem known as “variational collapse.” In this work, we combine the ideas of direct energy-targeting and variance-based optimization in order to describe excited states at the mean-field level. The resulting method, σ-SCF, has several advantages. First, it allows one to target any desired excited state by specifying a single parameter: a guess of the energy of that state. It can therefore, in principle, find all excited states. Second, it avoids variational collapse by using a variance-based, unconstrained local minimization. As a consequence, all states—ground or excited—are treated on an equal footing. Third, it provides an alternate approach to locate Δ-SCF solutions that are otherwise hardly accessible by the usual non-aufbau configuration initial guess. We present results for this new…

Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. We develop quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, and show that these analytical results accurately predict the behavior of strongly anharmonic systems. We also show that it is possible to correct, to a significant extent, the effects of the GLE term onto the corresponding microcanonical dynamics, which puts on more solid grounds the use of non-equilibrium Langevin dynamics to approximate quantum nuclear effects and could help improve the prediction of dynamical quantities from techniques that use a Langevin term to stabilize dynamics. Finally we address the use of thermostats in the context of approximate path-integral-based models of quantum nuclear dynamics. We demonstrate…

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 10° 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…

Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of…

Coupled cluster theory is the method of choice for weakly correlated systems. But in the strongly correlated regime, it faces a symmetry dilemma, where it either completely fails to describe the system or has to artificially break certain symmetries. On the other hand, projected Hartree-Fock theory captures the essential physics of many kinds of strong correlations via symmetry breaking and restoration. In this work, we combine and try to retain the merits of these two methods by applying symmetry projection to broken symmetry coupled cluster wave functions. The non-orthogonal nature of states resulting from the application of symmetry projection operators furnishes particle-hole excitations to all orders, thus creating an obstacle for the exact evaluation of overlaps. Here we provide a solution via a disentanglement framework theory that can be approximated rigorously and systematically. Results of projected coupled cluster theory are presented for molecules and the Hubbard model, showing that spin projection significantly improves unrestricted coupled cluster theory while…

Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as “hard” (irreversibly bound to the surface), “soft” (with reduced mobility but orientation freedom near the surface), or “bulk.” The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.

First-principles screening studies aimed at predicting the catalytic activity of transition metal (TM) catalysts have traditionally been based on mean-field (MF) microkinetic models, which neglect the effect of spatial correlations in the adsorbate layer. Here we critically assess the accuracy of such models for the specific case of CO methanation over stepped metals by comparing to spatially resolved kinetic Monte Carlo (kMC) simulations. We find that the typical low diffusion barriers offered by metal surfaces can be significantly increased at step sites, which results in persisting correlations in the adsorbate layer. As a consequence, MF models may overestimate the catalytic activity of TM catalysts by several orders of magnitude. The potential higher accuracy of kMC models comes at a higher computational cost, which can be especially challenging for surface reactions on metals due to a large disparity in the time scales of different processes. In order to overcome this issue, we implement and test a recently developed algorithm for achieving temporal acceleration of kMC…

A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller-Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices. After removing the NOs of low occupation number, natural auxiliary functions (NAFs) are constructed [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], and the NAF basis is also truncated. Our results show that, for a triple-zeta basis set, about 60% of the virtual MOs can be dropped, while the size of the fitting basis can be reduced by a factor of five. This results in a dramatic reduction of the computational costs of the solution of the CC2 equations, which are in our approach about as expensive as…

The explicitly correlated approach is one of the most important breakthroughs in ab initio electronic structure theory, providing arguably the most compact, accurate, and efficient ansatz for describing the correlated motion of electrons. Since Hylleraas first used an explicitly correlated wave function for the He atom in 1929, numerous attempts have been made to tackle the significant challenges involved in constructing practical explicitly correlated methods that are applicable to larger systems. These include identifying suitable mathematical forms of a correlated wave function and an efficient evaluation of many-electron integrals. R12 theory, which employs the resolution of the identity approximation, emerged in 1985, followed by the introduction of novel correlation factors and wave function ansätze, leading to the establishment of F12 theory in the 2000s. Rapid progress in recent years has significantly extended the application range of explicitly correlated theory, offering the potential of an accurate wave-function treatment of complex systems such as photosystems and…

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au147), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au147, and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au147 is performed, and it is concluded that Au147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Nanoparticle and polymer dynamics in nanocomposites containing spherical nanoparticles were investigated by means of molecular dynamics simulations. We show that the polymer diffusivity decreases with nanoparticle loading due to an increase of the interfacial area created by nanoparticles, in the polymer matrix. We show that small sized nanoparticles can diffuse much faster than that predicted from the Stokes-Einstein relation in the dilute regime. We show that the nanoparticle diffusivity decreases at higher nanoparticle loading due to nanoparticle-polymer interface. Increase of the nanoparticle radius slows the nanoparticle diffusion.

We have developed a new basis set family, denoted as aug-cc-pVnZ-F12 (or aVnZ-F12 for short), for explicitly correlated calculations. The sets included in this family were constructed by supplementing the corresponding cc-pVnZ-F12 sets with additional diffuse functions on the higher angular momenta (i.e., additional d-h functions on non-hydrogen atoms and p-g on hydrogen atoms), optimized for the MP2-F12 energy of the relevant atomic anions. The new basis sets have been benchmarked against electron affinities of the first- and second-row atoms, the W4-17 dataset of total atomization energies, the S66 dataset of noncovalent interactions, the Benchmark Energy and Geometry Data Base water cluster subset, and the WATER23 subset of the GMTKN24 and GMTKN30 benchmark suites. The aVnZ-F12 basis sets displayed excellent performance, not just for electron affinities but also for noncovalent interaction energies of neutral and anionic species. Appropriate CABSs (complementary auxiliary basis sets) were explored for the S66 noncovalent interaction benchmark: between similar-sized basis sets,…

localizations per second to be calculated on a standard multi-core central processing unit with localization accuracies in line with the most accurate algorithms currently available. Our algorithm converts the region of interest around a point spread function to two phase vectors (phasors) by calculating the first Fourier coefficients in both the x- and y-direction. The angles of these phasors are used to localize the center of the single fluorescent emitter, and the ratio of the magnitudes of the two phasors is a measure for astigmatism, which can be used to obtain depth information (z-direction). Our approach can be used both as a stand-alone algorithm for maximizing localization speed and as a first estimator for more time consuming iterative algorithms.