The 100 most-cited articles in The Journal of Chemical Physics, 2019

The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are precomputed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole as well as dipole-quadrupole…

The ab initio computational treatment of electrochemical systems requires an appropriate treatment of the solid/liquid interfaces. A fully quantum mechanical treatment of the interface is computationally demanding due to the large number of degrees of freedom involved. In this work, we develop a computationally efficient model where the electrode part of the interface is described at the density-functional theory (DFT) level, and the electrolyte part is represented through an implicit solvation model based on the Poisson-Boltzmann equation. We describe the implementation of the linearized Poisson-Boltzmann equation into the Vienna Ab initio Simulation Package, a widely used DFT code, followed by validation and benchmarking of the method. To demonstrate the utility of the implicit electrolyte model, we apply it to study the surface energy of Cu crystal facets in an aqueous electrolyte as a function of applied electric potential. We show that the applied potential enables the control of the shape of nanocrystals from an octahedral to a truncated octahedral morphology with increasing…

Electrocatalysis is central to the production of renewable fuels and high-value commodity chemicals. The electrolyte and the electrode together determine the catalytic properties of the liquid/solid interface. In particular, the cations of the electrolyte can greatly change the rates and reaction selectivity of many electrocatalytic processes. For this reason, the careful choice of the cation is an essential step in the design of catalytic interfaces with high selectivity for desired high-value products. To make such a judicious choice, it is critical to understand where in the electric double layer the cations reside and the various distinct mechanistic impacts they can have on the electrocatalytic process of interest. In this perspective, we review recent advances in the understanding of the electric double layer with a particular focus on the interfacial distribution of cations and the cations' hydration states in the vicinity of the electrode under various experimental conditions. Furthermore, we summarize the different ways in which cations can alter the rates and selectivity…

Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling.

. These ions were selected as they appear in the composition of seawater, and they are also found in biological systems. The force field proposed (denoted as Madrid-2019) is nonpolarizable, and both water molecules and sulfate anions are rigid. For water, we use the TIP4P/2005 model. The main idea behind this work is to further explore the possibility of using scaled charges for describing ionic solutions. Monovalent and divalent ions are modeled using charges of 0.85 and 1.7, respectively (in electron units). The model allows a very accurate description of the densities of the solutions up to high concentrations. It also gives good predictions of viscosities up to 3 m concentrations. Calculated structural properties are also in reasonable agreement with the experiment. We have checked that no crystallization occurred in the simulations at concentrations similar to the solubility limit. A test for ternary mixtures shows that the force field provides excellent performance at an affordable computer cost. In summary, the use of scaled charges, which could be regarded as an effective…

We propose modifications to the functional form of the Strongly Constrained and Appropriately Normed (SCAN) density functional to eliminate numerical instabilities. This is necessary to allow reliable, automatic generation of pseudopotentials (including projector augmented-wave potentials). The regularized SCAN is designed to match the original form very closely, and we show that its performance remains comparable.

Nonequilibrium molecular dynamics (NEMD) has been extensively used to study thermal transport at various length scales in many materials. In this method, two local thermostats at different temperatures are used to generate a nonequilibrium steady state with a constant heat flux. Conventionally, the thermal conductivity of a finite system is calculated as the ratio between the heat flux and the temperature gradient extracted from the linear part of the temperature profile away from the local thermostats. Here, we show that, with a proper choice of the thermostat, the nonlinear part of the temperature profile should actually not be excluded in thermal transport calculations. We compare NEMD results against those from the atomistic Green's function method in the ballistic regime and those from the homogeneous nonequilibrium molecular dynamics method in the ballistic-to-diffusive regime. These comparisons suggest that in all the transport regimes, one should directly calculate the thermal conductance from the temperature difference between the heat source and sink and, if needed,…

A formal analysis is conducted on the exactness of various forms of unitary coupled cluster (UCC) theory based on particle-hole excitation and de-excitation operators. Both the conventional single exponential UCC parameterization and a factorized (referred to here as "disentangled") version are considered. We formulate a differential cluster analysis to determine the UCC amplitudes corresponding to a general quantum state. The exactness of conventional UCC (ability to represent any state) is explored numerically, and it is formally shown to be determined by the structure of the critical points of the UCC exponential mapping. A family of disentangled UCC wave functions is proven to exactly parameterize any state, thus showing how to construct Trotter-error-free parameterizations of UCC for applications in quantum computing. From these results, we construct an exact disentangled UCC parameterization that employs an infinite sequence of particle-hole or general one- and two-body substitution operators.

The most successful and popular machine learning models of atomic-scale properties derive their transferability from a locality ansatz. The properties of a large molecule or a bulk material are written as a sum over contributions that depend on the configurations within finite atom-centered environments. The obvious downside of this approach is that it cannot capture nonlocal, nonadditive effects such as those arising due to long-range electrostatics or quantum interference. We propose a solution to this problem by introducing nonlocal representations of the system, which are remapped as feature vectors that are defined locally and are equivariant in O(3). We consider, in particular, one form that has the same asymptotic behavior as the electrostatic potential. We demonstrate that this framework can capture nonlocal, long-range physics by building a model for the electrostatic energy of randomly distributed point-charges, for the unrelaxed binding curves of charged organic molecular dimers, and for the electronic dielectric response of liquid water. By combining a representation of…

Water's phase diagram displays enormous complexity with currently 17 experimentally confirmed polymorphs of ice and several more predicted computationally. For almost 120 years, it has been a stomping ground for scientific discovery, and ice research has often been a trailblazer for investigations into a wide range of materials-related phenomena. Here, the experimental progress of the last couple of years is reviewed, and open questions as well as future challenges are discussed. The specific topics include (i) the polytypism and stacking disorder of ice I, (ii) the mechanism of the pressure amorphization of ice I, (iii) the emptying of gas-filled clathrate hydrates to give new low-density ice polymorphs, (iv) the effects of acid/base doping on hydrogen-ordering phase transitions as well as (v) the formation of solid solutions between salts and the ice polymorphs, and the effect this has on the appearance of the phase diagram. In addition to continuing efforts to push the boundaries in terms of the extremes of pressure and temperature, the exploration of the "chemical" dimensions of…

We discuss grand canonical simulations based on density-functional theory to study the thermodynamic properties of electrochemical interfaces of metallic electrodes in aqueous environments. Water is represented using implicit solvation, here via the self-consistent continuum solvation (SCCS) model, providing a charge-density dependent dielectric boundary. The electrochemical double layer is accounted for in terms of a phenomenological continuum description. It is shown that the experimental potentials of zero charge and interfacial capacitances can be reproduced for an optimized SCCS parameter set [ρmin = 0.0013, ρmax = 0.010 25]. By performing a detailed derivation and analysis of the interface energetics for selected electrochemical systems, we are able to relate the widely used approach of the computational hydrogen electrode (CHE) to a general grand canonical description of electrified interfaces. In particular, charge-neutral CHE results are shown to be an upper-boundary estimate for the grand canonical interfacial free energies. In order to demonstrate the differences between…

The applications of machine learning techniques to chemistry and materials science become more numerous by the day. The main challenge is to devise representations of atomic systems that are at the same time complete and concise, so as to reduce the number of reference calculations that are needed to predict the properties of different types of materials reliably. This has led to a proliferation of alternative ways to convert an atomic structure into an input for a machine-learning model. We introduce an abstract definition of chemical environments that is based on a smoothed atomic density, using a bra-ket notation to emphasize basis set independence and to highlight the connections with some popular choices of representations for describing atomic systems. The correlations between the spatial distribution of atoms and their chemical identities are computed as inner products between these feature kets, which can be given an explicit representation in terms of the expansion of the atom density on orthogonal basis functions, that is equivalent to the smooth overlap of atomic…

Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the final quantity of interest. Methods such as clustering and dimensionality reduction have been used to provide a simplified, coarse-grained representation of the structure and dynamics of complex systems from proteins to nanoparticles. In recent years, the rise of machine learning has led to an even more widespread use of these algorithms in atomistic modeling and to consider different classification and inference techniques as part of a coherent toolbox of data-driven approaches. This perspective briefly reviews some of the unsupervised machine-learning methods-that are geared toward classification and coarse-graining of molecular simulations-seen in relation to the fundamental mathematical concepts that underlie all machine-learning techniques. It discusses the importance of using concise yet complete representations of atomic structures as the…

The theoretical exploration of the phase diagrams of binary hydrides under pressure using ab initio crystal structure prediction techniques coupled with first principles calculations has led to the in silico discovery of numerous novel superconducting materials. This Perspective focuses on the alkaline earth and rare earth polyhydrides whose superconducting critical temperature, Tc, was predicted to be above the boiling point of liquid nitrogen. After providing a brief overview of the computational protocol used to predict the structures of stable and metastable hydrides under pressure, we outline the equations that can be employed to estimate Tc. The systems with a high Tc can be classified according to the motifs found in their hydrogenic lattices. The highest Tcs are found for cages that are reminiscent of clathrates and the lowest for systems that contain atomic and molecular hydrogen. A wide variety of hydrogenic motifs including 1- and 2-dimensional lattices, as well as H10δ− molecular units comprising fused H5δ− pentagons, are present in phases with intermediate Tcs. Some of…

Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to…

A new improved implementation of the second-order multiconfiguration self-consistent field optimization method of Werner and Knowles [J. Chem. Phys. 82, 5053 (1985)] is presented. It differs from the original method by more stable and efficient algorithms for minimizing the second-order energy approximation in the so-called microiterations. Conventionally, this proceeds by alternating optimizations of the orbitals and configuration (CI) coefficients and is linearly convergent. The most difficult part is the orbital optimization, which requires solving a system of nonlinear equations that are often strongly coupled. We present a much improved algorithm for solving this problem, using an iterative subspace method that includes part of the orbital Hessian explicitly, and discuss different strategies for performing the uncoupled optimization in a most efficient manner. Second, we present a new solver in which the orbital-CI coupling is treated explicitly. This leads to quadratic convergence of the microiterations but requires many additional evaluations of reduced (transition) density…

Abstract The inner workings of a biological cell or a chemical reaction can be rationalized by the network of reactions, whose structure reveals the most important functional mechanisms. For complex systems, these reaction networks are not known a priori and cannot be efficiently computed with ab initio methods, therefore an important approach goal is to estimate effective reaction networks from observations, such as time series of the main species. Reaction networks estimated with standard machine learning techniques such as least-squares regression may fit the observations, but will typically contain spurious reactions. Here we extend the sparse identification of nonlinear dynamics (SINDy) method to vector-valued ansatz functions, each describing a particular reaction process. The resulting sparse tensor regression method “reactive SINDy” is able to estimate a parsimonious reaction network. We illustrate that a gene regulation network can be correctly estimated from observed time series.

The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow collective motions governing the long-time conformational dynamics of a system. It is challenging to intuit these slow CVs for all but the simplest molecular systems, and their data-driven discovery directly from molecular simulation trajectories has been a central focus of the molecular simulation community to both unveil the important physical mechanisms and drive enhanced sampling. In this work, we introduce state-free reversible VAMPnets (SRV) as a deep learning architecture that learns nonlinear CV approximants to the leading slow eigenfunctions of the spectral decomposition of the transfer operator that evolves equilibrium-scaled probability distributions through time. Orthogonality of the learned CVs is naturally imposed within network training without added regularization. The CVs are inherently explicit and differentiable functions of the input coordinates making them well-suited to use in enhanced…

Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data, machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based neural network architectures have emerged in recent years as the most successful approach for predictions based on molecular structure and have consistently achieved the best performance on benchmark quantum chemical datasets. However, these models have typically required optimized 3D structural information for the molecule to achieve the highest accuracy. These 3D geometries are costly to compute for high levels of theory, limiting the applicability and practicality of machine learning methods in high-throughput screening applications. In this study, we present a new database of candidate molecules for organic photovoltaic applications, comprising approximately 91 000 unique chemical structures. Compared to existing datasets, this dataset contains substantially larger molecules (up to 200 atoms) as well as extrapolated properties for long polymer…

Despite the diversity of materials designated as active matter, virtually all active systems undergo a form of dynamic arrest when crowding and activity compete, reminiscent of the dynamic arrest observed in colloidal and molecular fluids undergoing a glass transition. We present a short perspective on recent and ongoing efforts to understand how activity competes with other physical interactions in dense systems. We review recent experimental work on active materials that uncovered both classic signatures of glassy dynamics and intriguing novel phenomena at large density. We discuss a minimal model of self-propelled particles where the competition between interparticle interactions, crowding, and self-propulsion can be studied in great detail. We present more complex models that include some additional, material-specific ingredients. We provide some general perspectives on dense active materials, suggesting directions for future research, in particular, for theoretical work.

The nature of alterations to dynamics and vitrification in the nanoscale vicinity of interfaces—commonly referred to as “nanoconfinement” effects on the glass transition—has been an open question for a quarter century. We first analyze experimental and simulation results over the last decade to construct an overall phenomenological picture. Key features include the following: after a metrology- and chemistry-dependent onset, near-interface relaxation times obey a fractional power law decoupling relation with bulk relaxation; relaxation times vary in a double-exponential manner with distance from the interface, with an intrinsic dynamical length scale appearing to saturate at low temperatures; the activation barrier and vitrification temperature Tg approach bulk behavior in a spatially exponential manner; and all these behaviors depend quantitatively on the nature of the interface. We demonstrate that the thickness dependence of film-averaged Tg for individual systems provides a poor basis for discrimination between different theories, and thus we assess their merits based on the…

The development of high throughput reaction discovery methods such as the ab initio nanoreactor demands massive numbers of reaction rate calculations through the optimization of minimum energy reaction paths. These are often generated from interpolations between the reactant and product endpoint geometries. Unfortunately, straightforward interpolation in Cartesian coordinates often leads to poor approximations that lead to slow convergence. In this work, we reformulate the problem of interpolation between endpoint geometries as a search for the geodesic curve on a Riemannian manifold. We show that the perceived performance difference of interpolation methods in different coordinates is the result of an implicit metric change. Accounting for the metric explicitly allows us to obtain good results in Cartesian coordinates, bypassing the difficulties caused by redundant coordinates. Using only geometric information, we are able to generate paths from reactants to products which are remarkably close to the true minimum energy path. We show that these geodesic paths are excellent starting…

The role of response operators is well established in quantum mechanics. We investigate their use for universal quantum machine learning models of response properties in molecules. After introducing a theoretical basis, we present and discuss numerical evidence based on measuring the potential energy's response with respect to atomic displacement and to electric fields. Prediction errors for corresponding properties, atomic forces, and dipole moments improve in a systematic fashion with training set size and reach high accuracy for small training sets. Prediction of normal modes and infrared-spectra of some small molecules demonstrates the usefulness of this approach for chemistry.

Machine learning (ML) methods have the potential to revolutionize materials design, due to their ability to screen materials efficiently. Unlike other popular applications such as image recognition or language processing, large volumes of data are not available for materials design applications. Here, we first show that a standard learning approach using generic descriptors does not work for small data, unless it is guided by insights from physical equations. We then propose a novel method for transferring such physical insights onto more generic descriptors, allowing us to screen billions of unknown compositions for Li-ion conductivity, a scale which was previously unfeasible. This is accomplished by using the accurate model trained with physical insights to create a large database, on which we train a new ML model using the generic descriptors. Unlike previous applications of ML, this approach allows us to screen materials which have not necessarily been tested before (i.e., not on ICSD or Materials Project). Our method can be applied to any materials design application where a…

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles…

The fast increase in available computation power allowed us to decrease the cooling rate in molecular dynamics (MD) simulation of vitrification by several orders of magnitude. While the reliability of the MD simulation should obviously benefit from this increase in the computational power, in some cases, it led to unexpected results. In particular, Ryltsev et al. [J. Chem. Phys. 149, 164502 (2018)] found that the most popular potentials for the Cu-Zr and Cu-Zr-Al alloys from Mendelev et al. [Philos. Mag. 89, 967 (2009)] and Cheng et al. [Phys. Rev. Lett. 102, 245501 (2009)] do not actually describe good glass forming systems but in contradiction with experiment predict rather fast crystallization of the Cu64.5Zr35.5 alloy which is the well-known example of bulk metallic glasses. In this paper, we present a new Cu-Zr semiempirical potential suitable to simulate vitrification. No crystal nucleation was observed in MD simulation using this potential in the concentration range from 75% to 5% of Zr. Since the new potential leads to about the same liquid structure and viscosity as the…

The viability of next generation lithium and beyond-lithium battery technologies hinges on the development of electrolytes with improved performance. Comparing electrolytes is not straightforward as multiple electrochemical parameters affect the performance of an electrolyte. Additional complications arise due to the formation of concentration gradients in response to dc potentials. We propose a modified version of Ohm’s law to analyze current through binary electrolytes driven by a small dc potential. We show that the proportionality constant in Ohm’s law is given by the product of the ionic conductivity, κ, and the ratio of currents in the presence (iss) and absence (iΩ) of concentration gradients, ρ+. The importance of ρ+ was recognized by Evans et al. [Polymer 28, 2324 (1987)]. The product κρ+ is used to rank order a collection of electrolytes. Ideally, both κ and ρ+ should be maximized, but we observe a trade-off between these two parameters, resulting in an upper bound. This trade-off is analogous to the famous Robeson upper bound for permeability and selectivity in gas…

Sequential infiltration synthesis (SIS) is an emerging materials growth method by which inorganic metal oxides are nucleated and grown within the free volume of polymers in association with chemical functional groups in the polymer. SIS enables the growth of novel polymer-inorganic hybrid materials, porous inorganic materials, and spatially templated nanoscale devices of relevance to a host of technological applications. Although SIS borrows from the precursors and equipment of atomic layer deposition (ALD), the chemistry and physics of SIS differ in important ways. These differences arise from the permeable three-dimensional distribution of functional groups in polymers in SIS, which contrast to the typically impermeable two-dimensional distribution of active sites on solid surfaces in ALD. In SIS, metal-organic vapor-phase precursors dissolve and diffuse into polymers and interact with these functional groups through reversible complex formation and/or irreversible chemical reactions. In this perspective, we describe the thermodynamics and kinetics of SIS and attempt to…

The configurational entropy is one of the most important thermodynamic quantities characterizing supercooled liquids approaching the glass transition. Despite decades of experimental, theoretical, and computational investigation, a widely accepted definition of the configurational entropy is missing, its quantitative characterization remains fraught with difficulties, misconceptions, and paradoxes, and its physical relevance is vividly debated. Motivated by recent computational progress, we offer a pedagogical perspective on the configurational entropy in glass-forming liquids. We first explain why the configurational entropy has become a key quantity to describe glassy materials, from early empirical observations to modern theoretical treatments. We explain why practical measurements necessarily require approximations that make its physical interpretation delicate. We then demonstrate that computer simulations have become an invaluable tool to obtain precise, nonambiguous, and experimentally relevant measurements of the configurational entropy. We describe a panel of available…

Thanks to a constant energy input, active matter can self-assemble into phases with complex architectures and functionalities such as living clusters that dynamically form, reshape, and break-up, which are forbidden in equilibrium materials by the entropy maximization (or free energy minimization) principle. The challenge to control this active self-assembly has evoked widespread efforts typically hinging on engineering of the properties of individual motile constituents. Here, we provide a different route, where activity occurs as an emergent phenomenon only when individual building blocks bind together in a way that we control by laser light. Using experiments and simulations of two species of immotile microspheres, we exemplify this route by creating active molecules featuring a complex array of behaviors, becoming migrators, spinners, and rotators. The possibility to control the dynamics of active self-assembly via light-controllable nonreciprocal interactions will inspire new approaches to understand living matter and to design active materials.

We report that a recent active space model of the nitrogenase FeMo cofactor, proposed in the context of simulations on quantum computers, is not representative of the electronic structure of the FeMo cofactor ground-state. A more representative model does not affect much certain resource estimates for a quantum computer such as the cost of a Trotter step, while strongly affecting others such as the cost of adiabatic state preparation. Thus, conclusions should not be drawn from the complexity of quantum or classical simulations of the electronic structure of this system in this active space. We provide a different model active space for the FeMo cofactor that contains the basic open-shell qualitative character, which may be useful as a benchmark system for making resource estimates for classical and quantum computers.

We present the construction of molecular force fields for small molecules (less than 25 atoms) using the recently developed symmetrized gradient-domain machine learning (sGDML) approach [Chmiela et al., Nat. Commun. 9, 3887 (2018) and Chmiela et al., Sci. Adv. 3, e1603015 (2017)]. This approach is able to accurately reconstruct complex high-dimensional potential-energy surfaces from just a few 100s of molecular conformations extracted from ab initio molecular dynamics trajectories. The data efficiency of the sGDML approach implies that atomic forces for these conformations can be computed with high-level wavefunction-based approaches, such as the “gold standard” coupled-cluster theory with single, double and perturbative triple excitations [CCSD(T)]. We demonstrate that the flexible nature of the sGDML model recovers local and non-local electronic interactions (e.g., H-bonding, proton transfer, lone pairs, changes in hybridization states, steric repulsion, and n → π* interactions) without imposing any restriction on the nature of interatomic potentials. The analysis of sGDML…

The change in refractive index around plasmonic nanoparticles upon binding to biomolecules is routinely used in localized surface plasmon resonance (LSPR)-based biosensors and in biosensing platforms. In this study, the plasmon sensitivity of hollow gold (Au) nanoshells is studied using theoretical modeling where the influence of shape, size, shell thickness, and aspect ratio is addressed. Different shapes of hollow Au nanoshells are studied that include sphere, disk, triangular prism, rod, ellipsoid, and rectangular block. Multilayered Mie theory and discrete dipole approximation were used to determine the LSPR peak position and LSPR sensitivity as a function of size, shell thickness, shape, and aspect ratio. The change in LSPR peak wavelength per unit refractive index is defined as the sensitivity, and interesting results were obtained from the analysis. The rectangular block and rod-shaped Au nanoshells have shown maximum LSPR sensitivity when compared to other shaped Au nanoshells. In addition, increased sensitivity was observed for higher aspect ratio as well as for smaller…

We address the degree to which machine learning (ML) can be used to accurately and transferably predict post-Hartree-Fock correlation energies. Refined strategies for feature design and selection are presented, and the molecular-orbital-based machine learning (MOB-ML) method is applied to several test systems. Strikingly, for the second-order Møller-Plessett perturbation theory, coupled cluster with singles and doubles (CCSD), and CCSD with perturbative triples levels of theory, it is shown that the thermally accessible (350 K) potential energy surface for a single water molecule can be described to within 1 mhartree using a model that is trained from only a single reference calculation at a randomized geometry. To explore the breadth of chemical diversity that can be described, MOB-ML is also applied to a new dataset of thermalized (350 K) geometries of 7211 organic models with up to seven heavy atoms. In comparison with the previously reported Δ-ML method, MOB-ML is shown to reach chemical accuracy with threefold fewer training geometries. Finally, a transferability test in which…

This perspective describes the advantages of infrared colloidal quantum dots (CQDs) for photodetection beyond silicon and provides a brief review of the development of CQD photodetection. The standard specifications for photodetectors are listed with particular emphasis on the detectivity. High gain improves the responsivity but does not improve the detectivity, while nonradiative losses do not prevent high responsivity but limit the detectivity. Performances of CQD detectors and HgTe CQDs, in particular, are compared with the maximum possible detectivity based on detailed balance from the device temperature and nonradiative losses.

As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application…

We propose a trajectory-based method for simulating nonadiabatic dynamics in molecular systems with two coupled electronic states. Employing a quantum-mechanically exact mapping of the two-level problem to a spin-12 coherent state, we use the Stratonovich-Weyl transform to construct a classical phase space of a spin vector constrained to a spherical surface whose radius is consistent with the quantum magnitude of the spin. In contrast with the singly excited harmonic oscillator basis used in Meyer-Miller-Stock-Thoss (MMST) mapping, the theory requires no additional projection operators onto the space of physical states. When treated under a quasiclassical approximation, we show that the resulting dynamics are equivalent to those generated by the MMST Hamiltonian. What differs is the value of the zero-point energy parameter as well as the initial distribution and the measurement operators used in constructing correlation functions. For various spin-boson models, the results of the method are seen to be a significant improvement compared to both standard Ehrenfest dynamics and…

We present diffusion coefficient and shear viscosity data for the Lennard-Jones fluid along nine isochores above the critical density, each involving a temperature variation of roughly two orders of magnitude. The data are analyzed with respect to the Stokes-Einstein (SE) relation, which breaks down gradually at high temperatures. This is rationalized in terms of the fact that the reduced diffusion coefficient D̃ and the reduced viscosity η̃ are both constant along the system’s lines of constant excess entropy (the isomorphs). As a consequence, D̃η̃ is a function of T/TRef(ρ) in which T is the temperature, ρ is the density, and TRef(ρ) is the temperature as a function of the density along a reference isomorph. This allows one to successfully predict the viscosity from the diffusion coefficient in the studied region of the thermodynamic phase diagram.

We present an analysis of quantum confinement of carriers and excitons, and exciton fine structure, in metal halide perovskite (MHP) nanocrystals (NCs). Starting with coupled-band k · P theory, we derive a nonparabolic effective mass model for the exciton energies in MHP NCs valid for the full size range from the strong to the weak confinement limits. We illustrate the application of the model to CsPbBr3 NCs and compare the theory against published absorption data, finding excellent agreement. We then apply the theory of electron-hole exchange, including both short- and long-range exchange interactions, to develop a model for the exciton fine structure. We develop an analytical quasicubic model for the effect of tetragonal and orthorhombic lattice distortions on the exchange-related exciton fine structure in CsPbBr3, as well as some hybrid organic MHPs of recent interest, including formamidinium lead bromide (FAPbBr3) and methylammonium lead iodide (MAPbI3). Testing the predictions of the quasicubic model using hybrid density functional theory (DFT) calculations, we find qualitative…

The interaction between molecular (atomic) electron(s) and the vacuum field of a reflective cavity generates significant interest, thanks to the rapid developments in nanophotonics. Such interaction which lies within the realm of cavity quantum electrodynamic can substantially affect the transport properties of molecular systems. In this work, we consider a nonadiabatic electron transfer process in the presence of a cavity mode. We present a generalized framework for the interaction between a charged molecular system and a quantized electromagnetic field of a cavity and apply it to the problem of electron transfer between a donor and an acceptor placed in a confined vacuum electromagnetic field. The effective system Hamiltonian corresponds to a unified Rabi and spin-boson model which includes a self-dipole energy term. Two limiting cases are considered: one where the electron is assumed much faster than the cavity mode and another in which the electron tunneling time is significantly larger than the mode period. In both cases, a significant rate enhancement can be produced by…

We introduce a simple, fast, and easy to implement unsupervised learning algorithm for detecting different local environments on a single-particle level in colloidal systems. In this algorithm, we use a vector of standard bond-orientational order parameters to describe the local environment of each particle. We then use a neural-network-based autoencoder combined with Gaussian mixture models in order to autonomously group together similar environments. We test the performance of the method on snapshots of a wide variety of colloidal systems obtained via computer simulations, ranging from simple isotropically interacting systems to binary mixtures, and even anisotropic hard cubes. Additionally, we look at a variety of common self-assembled situations such as fluid-crystal and crystal-crystal coexistences, grain boundaries, and nucleation. In all cases, we are able to identify the relevant local environments to a similar precision as "standard," manually tuned, and system-specific, order parameters. In addition to classifying such environments, we also use the trained autoencoder in…

In this communication, we present a new and simple route to derive range-separated exchange (RSX) hybrid and double hybrid density functionals in a nonempirical fashion. In line with our previous developments [Brémond et al., J. Chem. Theory Comput. 14, 4052 (2018)], we show that by imposing an additional physical constraint to the exchange-correlation energy, i.e., by enforcing to reproduce the total energy of the hydrogen atom, we are able to generalize the nonempirical determination of the range-separation parameter to a family of RSX hybrid density functionals. The success of the resulting models is illustrated by an accurate modeling of several molecular systems and properties, like ionization potentials, particularly prone to the one- and many-electron self-interaction errors.

A number of economical modifications to the high-accuracy extrapolated ab initio thermochemistry (HEAT) model chemistry are evaluated. The two resulting schemes, designated as mHEAT and mHEAT+, are designed for efficient and pragmatic evaluation of molecular energies in systems somewhat larger than can be practically studied by the unapproximated HEAT scheme. It is found that mHEAT+ produces heats of formation with nearly subchemical (±1 kJ/mol) accuracy at a substantially reduced cost relative to the full scheme. Total atomization energies calculated using the new thermochemical recipes are compared to the results of the HEAT-345(Q) model chemistry, and enthalpies of formation for the three protocols are also compared to Active Thermochemical Tables. Finally, a small selection of transition states is studied using mHEAT and mHEAT+, which illuminates some interesting features of reaction barriers and serves as an initial benchmark of the performance of these model chemistries for chemical kinetics applications.

Analytic energy gradients of individual singlet and triplet states with respect to nuclear coordinates are derived and implemented for the collinear mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT), which eliminates the problematic spin-contamination of SF-TDDFT. Dimensional-transformation matrices for the singlet and triplet response spaces are introduced, simplifying the subsequent derivations. These matrices enable the general forms of MRSF-TDDFT equations to be similar to those of SF-TDDFT, suggesting that the computational overhead of singlet or triplet states for MRSF-TDDFT is nearly identical to that of SF-TDDFT. In test calculations, the new MRSF-TDDFT yields quite different optimized structures and energies as compared to SF-TDDFT. These differences turned out to mainly come from the spin-contamination of SF-TDDFT, which are largely cured by MRSF-TDDFT. In addition, it was demonstrated that the clear separation of singlet states from triplets dramatically simplifies the location of minimum energy conical intersection. As a result, it is clear…

The study of matter at extreme densities and temperatures as they occur in astrophysical objects and state-of-the-art experiments with high-intensity lasers is of high current interest for many applications. While no overarching theory for this regime exists, accurate data for the density response of correlated electrons to an external perturbation are of paramount importance. In this context, the key quantity is given by the local field correction (LFC), which provides a wave-vector resolved description of exchange-correlation effects. In this work, we present extensive new path integral Monte Carlo (PIMC) results for the static LFC of the uniform electron gas, which are subsequently used to train a fully connected deep neural network. This allows us to present a representation of the LFC with respect to continuous wave-vectors, densities, and temperatures covering the entire warm dense matter regime. Both the PIMC data and neural-net results are available online. Moreover, we expect the presented combination of ab initio calculations with machine-learning methods to be a promising…

Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic time scale separation; the Franck-Condon method, which includes dynamical effects but generally only at the harmonic level; and the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap…

In this paper, we discuss the extension of the recently introduced subsystem embedding subalgebra coupled cluster (SES-CC) formalism to unitary CC formalisms. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induced complete active space (CAS) effective Hamiltonian. In contrast to the standard single-reference SES-CC theory, the unitary CC approach results in a Hermitian form of the effective Hamiltonian. Additionally, for the double unitary CC (DUCC) formalism, the corresponding CAS eigenvalue problem provides a rigorous separation of external cluster amplitudes that describe dynamical correlation effects—used to define the effective Hamiltonian—from those corresponding to the internal (inside the active space) excitations that define the components of eigenvectors associated with the energy of the entire system. The proposed formalism can be viewed as an efficient way of downfolding many-electron Hamiltonian to the low-energy model represented by a…

Pauli repulsion is a key component of any theory of intermolecular interactions. Although Pauli or exchange repulsion has its origin in the quantum mechanical nature of electrons, it is possible to describe the resulting energetic effects via a classical model in terms of the overlap of electron densities. In fact, closed shell intermolecular repulsion can be explained as a diminution of election density in the internuclear region resulting in decreased screening of nuclear charges and increased nuclear-nuclear repulsion. We provide a concise anisotropic repulsion formulation using the atomic multipoles from the Atomic Multipole Optimized Energetics for Biomolecular Applications force field to describe the electron density at each atom in a larger system. Mathematically, the proposed model consists of damped pairwise exponential multipolar repulsion interactions truncated at short range, which are suitable for use in compute-intensive biomolecular force fields and molecular dynamics simulations. Parameters for 26 atom classes encompassing most organic molecules are derived from a…

A comprehensive approach to modeling open quantum systems consistent with thermodynamics is presented. The theory of open quantum systems is employed to define system bath partitions. The Markovian master equation defines an isothermal partition between the system and bath. Two methods to derive the quantum master equation are described: the weak coupling limit and the repeated collision model. The role of the eigenoperators of the free system dynamics is highlighted, in particular, for driven systems. The thermodynamical relations are pointed out. Models that lead to loss of coherence, i.e., dephasing are described. The implication of the laws of thermodynamics to simulating transport and spectroscopy is described. The indications for self-averaging in large quantum systems and thus its importance in modeling are described. Basic modeling by the surrogate Hamiltonian is described, as well as thermal boundary conditions using the repeated collision model and their use in the stochastic surrogate Hamiltonian. The problem of modeling with explicitly time dependent driving is analyzed.…

In this work, we use large-scale molecular dynamics simulations coupled to free energy calculations to identify for the first time a limit of stability (spinodal) and a change in the nucleation mechanism in aqueous NaCl solutions. This is a system of considerable atmospheric, geological, and technical significance. We find that the supersaturated metastable NaCl solution reaches its limit of stability at sufficiently high salt concentrations, as indicated by the composition dependence of the salt chemical potential, indicating the transition to a phase separation by spinodal decomposition. However, the metastability limit of the NaCl solution does not correspond to spinodal decomposition with respect to crystallization. We find that beyond this spinodal, a liquid/amorphous separation occurs in the aqueous solution, whereby the ions first form disordered clusters. We term these clusters as "amorphous salt." We also identify a transition from one- to two-step crystallization mechanism driven by a spinodal. In particular, crystallization from aqueous NaCl solution beyond the spinodal…

The NL-eEDM collaboration is building an experimental setup to search for the permanent electric dipole moment of the electron in a slow beam of cold barium fluoride molecules [NL-eEDM Collaboration, Eur. Phys. J. D 72, 197 (2018)]. Knowledge of the molecular properties of BaF is thus needed to plan the measurements and, in particular, to determine the optimal laser-cooling scheme. Accurate and reliable theoretical predictions of these properties require the incorporation of both high-order correlation and relativistic effects in the calculations. In this work, theoretical investigations of the ground and lowest excited states of BaF and its lighter homologs, CaF and SrF, are carried out in the framework of the relativistic Fock-space coupled cluster and multireference configuration interaction methods. Using the calculated molecular properties, we determine the Franck-Condon factors (FCFs) for the A2Π1/2→X2Σ1/2+ transition, which was successfully used for cooling CaF and SrF and is now considered for BaF. For all three species, the FCFs are found to be highly diagonal. Calculations…

Understanding chemical mechanisms requires estimating dynamical statistics such as expected hitting times, reaction rates, and committors. Here, we present a general framework for calculating these dynamical quantities by approximating boundary value problems using dynamical operators with a Galerkin expansion. A specific choice of basis set in the expansion corresponds to the estimation of dynamical quantities using a Markov state model. More generally, the boundary conditions impose restrictions on the choice of basis sets. We demonstrate how an alternative basis can be constructed using ideas from diffusion maps. In our numerical experiments, this basis gives results of comparable or better accuracy to Markov state models. Additionally, we show that delay embedding can reduce the information lost when projecting the system's dynamics for model construction; this improves estimates of dynamical statistics considerably over the standard practice of increasing the lag time.

The ionization potential (IP) of a molecule quantifies the energy required to remove an electron from the system. As such, it is a fundamental quantity in the context of redox chemistry, charge transfer, and molecular electronics. The accurate theoretical prediction of this property is therefore highly desirable for virtual materials design. Furthermore, vertical IPs are of interest in the development of many-body Green's function methods like the GW formalism, as well as density functionals and semiempirical methods. In this contribution, we report over 1468 vertical valence IPs calculated with the IP variant of equation-of-motion coupled cluster theory with singles and doubles (IP-EOM-CCSD) covering 155 molecules. The purpose of this is two-fold: First, the quality of the predicted IPs is compared with respect to experiments and higher-order coupled cluster theory. This confirms the overall high accuracy and robustness of this method, with some outliers which are discussed in detail. Second, a large set of consistent theoretical reference values for vertical valence IPs are…

local minima lying within 5 kcal/mol from the putative minima for water clusters of sizes n = 3-25 using an improved version of the Monte Carlo temperature basin paving (MCTBP) global optimization procedure in conjunction with the ab initio based, flexible, polarizable Thole-Type Model (TTM2.1-F, version 2.1) interaction potential for water. Several of the low-lying structures, as well as low-lying penta-coordinated water networks obtained with the TTM2.1-F potential, were further refined at the Møller-Plesset second order perturbation (MP2)/aug-cc-pVTZ level of theory. In total, we have identified 3 138 303 networks corresponding to local minima of the clusters n = 3-25, whose Cartesian coordinates and relative energies can be obtained from the webpage https://sites.uw.edu/wdbase/. Networks containing penta-coordinated water molecules start to appear at n = 11 and, quite surprisingly, are energetically close (within 1-3 kcal/mol) to the putative minima, a fact that has been confirmed from the MP2 calculations. This large database of water cluster minima spanning quite dissimilar…

We study a system of non-interacting active particles, propelled by colored noises, characterized by an activity time τ, and confined by a double-well potential. A straightforward application of this system is the problem of barrier crossing of active particles, which has been studied only in the limit of small activity. When τ is sufficiently large, equilibrium-like approximations break down in the barrier crossing region. In the model under investigation, it emerges as a sort of “negative temperature” region, and numerical simulations confirm the presence of non-convex local velocity distributions. We propose, in the limit of large τ, approximate equations for the typical trajectories which successfully predict many aspects of the numerical results. The local breakdown of detailed balance and its relation with a recent definition of non-equilibrium heat exchange is also discussed.

Heat transfer between a silver nanoparticle and surrounding water has been studied using molecular dynamics (MD) simulations. The thermal conductance (Kapitza conductance) at the interface between a nanoparticle and surrounding water has been calculated using four different approaches: transient with/without temperature gradient (internal thermal resistance) in the nanoparticle, steady-state non-equilibrium, and finally equilibrium simulations. The results of steady-state non-equilibrium and equilibrium are in agreement but differ from the transient approach results. MD simulation results also reveal that in the quenching process of a hot silver nanoparticle, heat dissipates into the solvent over a length-scale of ∼2 nm and over a time scale of less than 5 ps. By introducing a continuum solid-like model and considering a heat conduction mechanism in water, it is observed that the results of the temperature distribution for water shells around the nanoparticle agree well with the MD results. It is also found that the local water thermal conductivity around the nanoparticle is greater…

The Journal of Chemical Physics (JCP) article collection on Markov Models of Molecular Kinetics (MMMK) features recent advances developing and using Markov State Models (MSMs) in atomistic molecular simulations and related applications. This editorial provides a brief overview of the state of the art in the field and relates it to the articles in this JCP collection.

Understanding the origins of enhanced reactivity of supported, subnanometer in size, metal oxide clusters is challenging due to the scarcity of methods capable to extract atomic-level information from the experimental data. Due to both the sensitivity of X-ray absorption near edge structure (XANES) spectroscopy to the local geometry around metal ions and reliability of theoretical spectroscopy codes for modeling XANES spectra, supervised machine learning approach has become a powerful tool for extracting structural information from the experimental spectra. Here, we present the application of this method to grazing incidence XANES spectra of size-selective Cu oxide clusters on flat support, measured in operando conditions of the methanation reaction. We demonstrate that the convolution neural network can be trained on theoretical spectra and utilized to “invert” experimental XANES data to obtain structural descriptors—the Cu–Cu coordination numbers. As a result, we were able to distinguish between different structural motifs (Cu2O-like and CuO-like) of Cu oxide clusters,…

The committor function is a central object of study in understanding transitions between metastable states in complex systems. However, computing the committor function for realistic systems at low temperatures is a challenging task due to the curse of dimensionality and the scarcity of transition data. In this paper, we introduce a computational approach that overcomes these issues and achieves good performance on complex benchmark problems with rough energy landscapes or in high dimensions. The new approach combines deep learning, data sampling, and feature engineering techniques. This establishes an alternative practical method for studying rare transition events between metastable states in complex, high dimensional systems.

Recent advances in theoretical characterization of reaction dynamics on metal surfaces are reviewed. It is shown that the widely available density functional theory of metals and their interactions with molecules have enabled first principles theoretical models for treating surface reaction dynamics. The new theoretical tools include methods to construct high-dimensional adiabatic potential energy surfaces, to characterize nonadiabatic processes within the electronic friction models, and to describe dynamics both quantum mechanically and classically. Three prototypical surface reactions, namely, dissociative chemisorption, Eley-Rideal reactions, and recombinative desorption, are surveyed with a focus on some representative examples. While principles governing gas phase reaction dynamics may still be applicable, the presence of the surface introduces a higher level of complexity due to strong interaction between the molecular species and metal substrate. Furthermore, most of these reactive processes are impacted by energy exchange with surface phonons and/or electron-hole pair…

We provide a spin-adapted formulation of the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) algorithm, based on the Graphical Unitary Group Approach (GUGA), which enables the exploitation of SU(2) symmetry within this stochastic framework. Random excitation generation and matrix element calculation on the Shavitt graph of GUGA can be efficiently implemented via a biasing procedure on the branching diagram. The use of a spin-pure basis explicitly resolves the different spin-sectors and ensures that the stochastically sampled wavefunction is an eigenfunction of the total spin operator S^2. The method allows for the calculation of states with low or intermediate spin in systems dominated by Hund’s first rule, which are otherwise generally inaccessible. Furthermore, in systems with small spin gaps, the new methodology enables much more rapid convergence with respect to walker number and simulation time. Some illustrative applications of the GUGA-FCIQMC method are provided: computation of the 2F − 4F spin gap of the cobalt atom in large basis sets, achieving chemical…

Non-photochemical laser-induced nucleation (NPLIN) is the formation of a new phase from a metastable phase by the action of light on matter. Using millijoule, nanosecond laser pulses at visible and near-infrared wavelengths, it is possible to form the new phase localized in the volume of the beam. In the case of nucleating molecular solids, the laser polarization may have an effect on the particular polymorph that is formed. Despite the huge potential for applications of NPLIN, there is uncertainty regarding the molecular-scale mechanism, and various possible scenarios may well be relevant to nucleation in general and not just NPLIN. In this Perspective, the discovery and phenomenology of NPLIN are described, putative mechanisms are outlined, and some observations on the broader class of nucleation phenomena are given.

We have applied a two-structure approach to the description of the thermodynamic properties of supercooled and stretched water, metastable toward vapor, ice, or both, by incorporating the stability limit of liquid with respect to vapor at negative pressures. In addition to the properties of water considered in previous studies, we include new data recently obtained in deeply supercooled and stretched regions. Our model reproduces the experimentally observed anomalies in metastable water up to 400 MPa and down to -140 MPa, and can provide a physically based extrapolation in regions where no measurements are available yet. Moreover, we are able to elucidate the thermodynamic nature of the alternative "states" of liquid water, namely, high-temperature denser water (state A) and "mother-of-ice" lighter water (state B). Based on the internal consistency of the described anomalies and new data on the isothermal compressibility, we exclude the critical-point-free scenario in which the first-order liquid-liquid transition line would continue into the stretched liquid state (doubly…

This work describes a domain-based local pair natural orbital (DLPNO) implementation of the equation of motion coupled cluster method for the computation of electron affinities (EAs) including single and double excitations. Similar to our earlier work on ionization potentials (IPs), the method reported in this study uses the ground state DLPNO framework and extends it to the electron attachment problem. While full linear scaling could not be achieved as in the IP case, leaving the Fock/Koopmans' contributions in the canonical basis and using a tighter threshold for singles PNOs allows us to compute accurate EAs and retain most of the efficiency of the DLPNO technique. Thus as in the IP case, the ground state truncation parameters are sufficient to control the accuracy of the computed EA values, although a new set of integrals for singles PNOs must be generated at the DLPNO integral transformation step. Using standard settings, our method reproduces the canonical results with a maximum absolute deviation of 49 meV for bound states of a test set of 24 molecules. Using the same…

Despite mounting evidence that the same gradients, which active colloids use for swimming, induce important cross-interactions (phoretic interactions), they are still ignored in most many-body descriptions, perhaps to avoid complexity and a zoo of unknown parameters. Here we derive a simple model, which reduces phoretic far-field interactions to a pair-interaction whose strength is mainly controlled by one genuine parameter (swimming speed). The model suggests that phoretic interactions are generically important for autophoretic colloids (unless effective screening of the phoretic fields is strong) and should dominate over hydrodynamic interactions for the typical case of half-coating and moderately nonuniform surface mobilities. Unlike standard minimal models, but in accordance with canonical experiments, our model generically predicts dynamic clustering in active colloids at a low density. This suggests that dynamic clustering can emerge from the interplay of screened phoretic attractions and active diffusion.

We propose a cavity QED approach to describe light-matter interaction of an infrared cavity field with an anharmonic vibration of a single nonpolar molecule. Starting from a generic Morse oscillator potential with quantized nuclear motion, we derive a multilevel quantum Rabi model to study vibrational polaritons beyond the rotating-wave approximation. We analyze the spectrum of vibrational polaritons in detail and compare it with available experiments. For high excitation energies, the system exhibits a dense manifold of polariton level crossings and avoided crossings as the light-matter coupling strength and cavity frequency are tuned. We also analyze polariton eigenstates in nuclear coordinate space. We show that the bond length of a vibrational polariton at a given energy is never greater than the bond length of a Morse oscillator with the same energy. This type of polariton bond strengthening occurs at the expense of the creation of virtual infrared cavity photons and may have implications in chemical reactivity of polariton states.

Three-wave mixing spectroscopy of chiral molecules, which exist in left-handed and right-handed conformations, allows for enantioselective population transfer despite random orientation of the molecules. This is based on constructive interference of the three-photon pathways for one enantiomer and the destructive one for the other. We prove here that three mutually orthogonal polarization directions are required to this end. Two different dynamical regimes exist to realize enantioselective population transfer, and we show that they correspond to different phase conditions in the three-wave mixing. We find the excitation scheme used in current rotational three-wave mixing experiments of chiral molecules with C1 symmetry to be close to optimal and discuss the prospects for rovibrational three-wave mixing experiments of axially chiral molecules. Our comprehensive study allows us to clarify earlier misconceptions in the literature.

Self-interaction (SI) error, which results when exchange-correlation contributions to the total energy are approximated, limits the reliability of many density functional approximations. The Perdew-Zunger SI correction (PZSIC), when applied in conjunction with the local spin density approximation (LSDA), improves the description of many properties, but overall, this improvement is limited. Here, we propose a modification to PZSIC that uses an iso-orbital indicator to identify regions where local SICs should be applied. Using this local-scaling SIC (LSIC) approach with LSDA, we analyze predictions for a wide range of properties including, for atoms, total energies, ionization potentials, and electron affinities and, for molecules, atomization energies, dissociation energy curves, reaction energies, and reaction barrier heights. LSIC preserves the results of PZSIC-LSDA for properties where it is successful and provides dramatic improvements for many of the other properties studied. Atomization energies calculated using LSIC are better than those of the Perdew, Burke, and Ernzerhof…

Approximating the electron repulsion integrals using inner projections is a well-established approach to reduce the computational demands of electronic structure calculations. Here, we present a two-step Cholesky decomposition algorithm where only the elements of the Cholesky basis (the pivots) are determined in the pivoting procedure. This allows for improved screening, significantly reducing memory usage and computational cost. After the pivots have been determined, the Cholesky vectors are constructed using the inner projection formulation. We also propose a partitioned decomposition approach where the Cholesky basis is chosen from a reduced set generated by decomposing diagonal blocks of the matrix. The algorithm extends the application range of the methodology and is well suited for multilevel methods. We apply the algorithm to systems with up to 80 000 atomic orbitals. The accuracy of the integral approximations is demonstrated for a formaldehyde-water system using a new Cholesky-based CCSD implementation.

A systematic study of interfacial properties of binary mixtures of simple fluids was carried out by molecular dynamics (MD) simulation and density gradient theory (DGT). The fluids are described by the Lennard-Jones truncated and shifted (LJTS) potential with truncation radius of 2.5 diameters. The following interfacial properties were studied: surface tension, relative adsorption, enrichment, and interfacial thickness. A recently developed equation of state for the LJTS fluid, the Perturbed Lennard-Jones truncated and shifted equation of state (PeTS EOS) was used as the basis for DGT. Six binary mixtures (components 1 + 2) were studied at a constant temperature, which was chosen such that the high-boiling component 1 is subcritical, while the low-boiling component 2 is either subcritical or supercritical. Furthermore, a parameter ξ in the combination rule for the unlike dispersive interaction was varied such that the resulting mixtures showed three types of behavior: high-boiling azeotrope, ideal, and low-boiling azeotrope. The parameters of the LJTS potential, including ξ, were…

Individual chemically active drops suspended in a surfactant solution were observed to self-propel spontaneously with straight, helical, or chaotic trajectories. To elucidate how these drops can exhibit such strikingly different dynamics and "decide" what to do, we propose a minimal axisymmetric model of a spherical active drop, and show that simple and linear interface properties can lead to both steady self-propulsion of the droplet as well as chaotic behavior. The model includes two different mobility mechanisms, namely, diffusiophoresis and the Marangoni effect, which convert self-generated gradients of surfactant concentration into the flow at the droplet surface. In turn, surface-driven flow initiates surfactant advection that is the only nonlinear mechanism and, thus, the only source of dynamical complexity in our model. Numerical investigation of the fully coupled hydrodynamic and advection-diffusion problems reveals that strong advection (e.g., large droplet size) may destabilize a steadily self-propelling drop; once destabilized, the droplet spontaneously stops and a…

Instant machine learning predictions of molecular properties are desirable for materials design, but the predictive power of the methodology is mainly tested on well-known benchmark datasets. Here, we investigate the performance of machine learning with kernel ridge regression (KRR) for the prediction of molecular orbital energies on three large datasets: the standard QM9 small organic molecules set, amino acid and dipeptide conformers, and organic crystal-forming molecules extracted from the Cambridge Structural Database. We focus on the prediction of highest occupied molecular orbital (HOMO) energies, computed at the density-functional level of theory. Two different representations that encode the molecular structure are compared: the Coulomb matrix (CM) and the many-body tensor representation (MBTR). We find that KRR performance depends significantly on the chemistry of the underlying dataset and that the MBTR is superior to the CM, predicting HOMO energies with a mean absolute error as low as 0.09 eV. To demonstrate the power of our machine learning method, we apply our model to…

In this work, we revisited the idea of using the coupled-cluster (CC) ground state formalism to target excited states. Our main focus was targeting doubly excited states and double core hole states. Typical equation-of-motion (EOM) approaches for obtaining these states struggle without higher-order excitations than doubles. We showed that by using a non-Aufbau determinant optimized via the maximum overlap method, the CC ground state solver can target higher energy states. Furthermore, just with singles and doubles (i.e., CCSD), we demonstrated that the accuracy of ΔCCSD and ΔCCSD(T) (triples) far surpasses that of EOM-CCSD for doubly excited states. The accuracy of ΔCCSD(T) is nearly exact for doubly excited states considered in this work. For double core hole states, we used an improved ansatz for greater numerical stability by freezing core hole orbitals. The improved methods, core valence separation (CVS)-ΔCCSD and CVS-ΔCCSD(T), were applied to the calculation of the double ionization potential of small molecules. Even without relativistic corrections, we observed qualitatively…

We present how to compute vibrational eigenstates with tree tensor network states (TTNSs), the underlying ansatz behind the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method. The eigenstates are computed with an algorithm that is based on the density matrix renormalization group (DMRG). We apply this to compute the vibrational spectrum of acetonitrile (CH3CN) to high accuracy and compare TTNSs with matrix product states (MPSs), the ansatz behind the DMRG. The presented optimization scheme converges much faster than ML-MCTDH-based optimization. For this particular system, we found no major advantage of the more general TTNS over MPS. We highlight that for both TTNS and MPS, the usage of an adaptive bond dimension significantly reduces the amount of required parameters. We furthermore propose a procedure to find good trees.

The formulation of the time-dependent Schrödinger equation in terms of coupled-cluster theory is outlined, with emphasis on the bivariational framework and its classical Hamiltonian structure. An indefinite inner product is introduced, inducing physical interpretation of coupled-cluster states in the form of transition probabilities, autocorrelation functions, and explicitly real values for observables, solving interpretation issues which are present in time-dependent coupled-cluster theory and in ground-state calculations of molecular systems under the influence of external magnetic fields. The problem of the numerical integration of the equations of motion is considered, and a critical evaluation of the standard fourth-order Runge-Kutta scheme and the symplectic Gauss integrator of variable order are given, including several illustrative numerical experiments. While the Gauss integrator is stable even for laser pulses well above the perturbation limit, our experiments indicate that a system-dependent upper limit exists for the external field strengths. Above this limit,…

We have implemented and applied the GW method and the static screened Bethe–Salpeter equation (BSE) for calculating linear-response properties for quasirelativistic molecular systems. Our ansatz is based on a two-component (2c) scheme that includes spin–orbit coupling as well as scalar relativistic effects. Efficient, state-of-the-art approaches including the analytic continuation (employing Padé approximants, scaling as N 4 with system size N ) and contour deformation schemes are presented to obtain the required 2c quasirelativistic GW quasiparticle energies. Screened exchange contributions are computed within the resolution-of-the-identity approximation, and working equations for the 2c GW/BSE method are given. The performance of the 2c GW/BSE method is assessed, and results are compared to other methods and experimental data. A robust iterative scheme for solving the eigenvalue problems occurring in the 2c GW/BSE and hybrid time-dependent density functional theories is presented.

We propose a compression of the opposite-spin coupled cluster doubles amplitudes of the form τijab≡UiaVTVWUjbW, where UiaV are the nV-highest magnitude eigenvectors of the MP2 or MP3 doubles amplitudes. Together with a corresponding parameterization of the opposite-spin coupled cluster Lagrange multipliers of the form λabij≡UiaVLVWUjbW, this yields a fully self-consistent parameterization of reduced-rank coupled cluster equations in terms of the Lagrangian L0TVW,LVW. Making this Lagrangian stationary with respect to the LVW parameters yields a perfectly determined set of equations for the TVW equations and coupled cluster energy. These equations can be solved using a Lyapunov equation for the first-order amplitude updates. We test this “rank-reduced coupled cluster” method for coupled cluster singles and doubles in medium sized molecules and find that substantial compression of the T^2 amplitudes is possible with acceptable accuracy.

We apply a recently developed optimization scheme to obtain effective potentials for alkali and alkaline-earth aluminosilicate glasses that contain lithium, sodium, potassium, or calcium as modifiers. As input data for the optimization, we used the radial distribution functions of the liquid at high temperature generated by means of ab initio molecular dynamics simulations and density and elastic modulus of glass at room temperature from experiments. The new interaction potentials are able to reproduce reliably the structure and various mechanical and vibrational properties over a wide range of compositions for binary silicates. We have tested these potentials for various ternary systems and find that they are transferable and can be mixed, thus allowing us to reproduce and predict the structure and properties of multicomponent glasses.

We investigate the microscopic origin of water's anomalies by inspecting the hydrogen bond network (HBN) and the spatial organization of low-density-liquid (LDL) like and high-density-liquid (HDL) like environments. Specifically, we simulate-via classical molecular dynamics simulations-the isobaric cooling of a sample composed of 512 water molecules from ambient to deeply undercooled conditions at three pressures, namely, 1 bar, 400 bars, and 1000 bars. In correspondence with the Widom line (WL), (i) the HDL-like dominating cluster undergoes fragmentation caused by the percolation of LDL-like aggregates following a spinodal-like kinetics; (ii) such fragmentation always occurs at a "critical" concentration of ∼20%-30% in LDL; (iii) the HBN within LDL-like environments is characterized by an equal number of pentagonal and hexagonal rings that create a state of maximal frustration between a configuration that promotes crystallization (hexagonal ring) and a configuration that hinders it (pentagonal ring); (iv) the spatial organization of HDL-like environments shows a marked variation.…

We identify and rectify a crucial source of bias in the initiator full configuration interaction quantum Monte Carlo algorithm. Noninitiator determinants (i.e., determinants whose population is below the initiator threshold) are subject to a systematic undersampling bias, which in large systems leads to a bias in the energy when an insufficient number of walkers are used. We show that the acceptance probability (pacc), that a noninitiator determinant has its spawns accepted, can be used to unbias the initiator bias, in a simple and accurate manner, by reducing the applied shift to the noninitiator proportionately to pacc. This modification preserves the property that in the large walker limit, when pacc → 1, the unbiasing procedure disappears, and the initiator approximation becomes exact. We demonstrate that this algorithm shows rapid convergence to the FCI limit with respect to the walker number and, furthermore, largely removes the dependence of the algorithm on the initiator threshold, enabling highly accurate results to be obtained even with large values of the threshold. This…

Electronic and/or vibronic coherence has been found by recent ultrafast spectroscopy experiments in many chemical, biological, and material systems. This indicates that there are strong and complicated interactions between electronic states and vibration modes in realistic chemical systems. Therefore, simulations of quantum dynamics with a large number of electronic and vibrational degrees of freedom are highly desirable. Due to the efficient compression and localized representation of quantum states in the matrix-product state (MPS) formulation, time-evolution methods based on the MPS framework, which we summarily refer to as tDMRG (time-dependent density-matrix renormalization group) methods, are considered to be promising candidates to study the quantum dynamics of realistic chemical systems. In this work, we benchmark the performances of four different tDMRG methods, including global Taylor, global Krylov, and local one-site and two-site time-dependent variational principles (1TDVP and 2TDVP), with a comparison to multiconfiguration time-dependent Hartree and experimental…

We explore the electroluminescence efficiency for a quantum mechanical model of a large number of molecular emitters embedded in an optical microcavity. We characterize the circumstances under which a microcavity enhances harvesting of triplet excitons via reverse intersystem-crossing (R-ISC) into singlet populations that can emit light. For that end, we develop a time-local master equation in a variationally optimized frame, which allows for the exploration of the population dynamics of chemically relevant species in different regimes of emitter coupling to the condensed phase vibrational bath and to the microcavity photonic mode. For a vibrational bath that equilibrates faster than R-ISC (in emitters with weak singlet-triplet mixing), our results reveal that significant improvements in efficiencies with respect to the cavity-free counterpart can be obtained for strong coupling of the singlet exciton to a photonic mode, as long as the singlet to triplet exciton transition is within the inverted Marcus regime; under these circumstances, the activation energy barrier from the triplet…

The twin-formulation of quantum statistical mechanics is employed to describe a new methodology for the solution of the equations of motion of the reduced density matrix in their hierarchical formulation. It is shown that the introduction of tilde operators and of their algebra in the dual space greatly simplifies the application of numerical techniques for the propagation of the density matrix. The application of tensor-train representation of a vector to solve complex quantum dynamical problems within the framework of the twin-formulation is discussed. Next, applications of the hierarchical equations of motion to a dissipative polaron model are presented showing the validity and accuracy of the new approach.

The hierarchical equations of motion (HEOM) provide a numerically exact approach for computing the reduced dynamics of a quantum system linearly coupled to a bath. We have found that HEOM contains temperature-dependent instabilities that grow exponentially in time. In the case of continuous-bath models, these instabilities may be delayed to later times by increasing the hierarchy dimension; however, for systems coupled to discrete, nondispersive modes, increasing the hierarchy dimension does little to alleviate the problem. We show that these instabilities can also be removed completely at a potentially much lower cost via projection onto the space of stable eigenmodes; furthermore, we find that for discrete-bath models at zero temperature, the remaining projected dynamics computed with few hierarchy levels are essentially identical to the exact dynamics that otherwise might require an intractably large number of hierarchy levels for convergence. Recognizing that computation of the eigenmodes might be prohibitive, e.g., for large or strongly coupled models, we present a Prony…

Trajectory surface hopping (TSH) methods have been widely used to study photoinduced nonadiabatic processes. In the present study, nonadiabatic dynamics simulations with the widely used Tully’s fewest switches surface hopping (FSSH) algorithm and a Landau-Zener-type TSH (LZSH) algorithm have been performed for the internal conversion dynamics of pyrazine. The accuracy of the two TSH algorithms has been critically evaluated by a direct comparison with exact quantum dynamics calculations for a model of pyrazine. The model comprises the three lowest excited electronic states (B3u(nπ*), A1u(nπ*), and B2u(ππ*)) and the nine most relevant vibrational degrees of freedom. Considering photoexcitation to the diabatic B2u(ππ*) state, we examined the time-dependent diabatic and adiabatic electronic population dynamics. It is found that the diabatic populations obtained with both TSH methods are in good agreement with the exact quantum results. Fast population oscillations between the B3u(nπ*) and A1u(nπ*) states, which reflect nonadiabatic electronic transitions driven by coherent dynamics in…

= 0 triplets); however, matrix elements for all components are necessary for deriving spin-dependent experimental observables. Wigner-Eckart's theorem allows one to circumvent explicit calculations of all multiplet components. We generate all other spin-orbit matrix elements by applying Wigner-Eckart's theorem to a reduced one-particle transition density matrix computed for a single multiplet component. In addition to computational efficiency, this approach also resolves the phase issue arising within Born-Oppenheimer's separation of nuclear and electronic degrees of freedom. A general formalism and its application to the calculation of spin-orbit couplings using equation-of-motion coupled-cluster wave functions are presented. The two-electron contributions are included via the mean-field spin-orbit treatment. Intrinsic issues of constructing spin-orbit mean-field operators for open-shell references are discussed, and a resolution is proposed. The method is benchmarked by using several radicals and diradicals. The merits of the approach are illustrated by a calculation of the…

The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins. The potentials of mean force corresponding to backbone-local and backbone-correlation energy terms were calculated from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline, and the respective analytical expressions, derived by using the scale-consistent formalism, were fitted to them. The parameters of all these potentials depend on single-residue types, thus reducing their number and preventing over-fitting. The UNRES force field with the revised backbone-local and backbone-correlation terms was calibrated with a set of four small proteins with basic folds: tryptophan cage variant (TRP1; α), Full Sequence Design (FSD; α + β), villin headpiece (villin; α), and a truncated FBP-28 WW-domain variant (2MWD; β) (the NEWCT-4P force field) and, subsequently, with an enhanced set of 9 proteins composed of TRP1, FSD,…

Non-equilibrium molecular dynamics simulations were conducted for solid-liquid-solid systems with nanometer scale grooved surfaces and an induced heat flux for a wide range of topology and solid-liquid interaction conditions to investigate the mechanism of solid-liquid heat transfer, which is the first work of such extensive detail done about the nanoscale roughness effect on heat transfer properties. Single-atom molecules were used for liquid, and the solid-liquid interaction was varied from superhydrophobic to superhydrophilic, while the groove scale was varied from single atom to several nanometers, while keeping the surface area twice that of a flat surface. Both Wenzel and Cassie wetting regimes with a clear transition point were observed due to the capillary effect inside larger grooves that were more than 5 liquid molecule diameters, while such transition was not observed at smaller scales. At the hydrophobic state, large scale grooves had lower interfacial thermal conductance (ITC) due to the Cassie regime, i.e., having unfilled grooves, while at the hydrophilic state,…

Simulating the nonadiabatic dynamics of condensed-phase systems continues to pose a significant challenge for quantum dynamics methods. Approaches based on sampling classical trajectories within the mapping formalism, such as the linearized semiclassical initial value representation (LSC-IVR), can be used to approximate quantum correlation functions in dissipative environments. Such semiclassical methods however commonly fail in quantitatively predicting the electronic-state populations in the long-time limit. Here we present a suggestion to minimize this difficulty by splitting the problem into two parts, one of which involves the identity and treating this operator by quantum-mechanical principles rather than with classical approximations. This strategy is applied to numerical simulations of spin-boson model systems, showing its potential to drastically improve the performance of LSC-IVR and related methods with no change in the equations of motion or the algorithm in general, but rather by simply using different functional forms of the observables.

In the previous work of Cotton and Miller [J. Chem. Phys. 145, 144108 (2016)], an improved symmetrical quasi-classical (SQC) windowing model for the molecular dynamics treatment of electronically non-adiabatic processes was developed in order to extend the original SQC approach to the regime of weak-coupling between the electronic states. The improved SQC model-based on triangular-shaped window functions-handled the weak-coupling limit as intended and, as a bonus, was shown to be universally superior to the original square/histogram SQC windowing model over all coupling regimes, but only for treating systems of two electronic states, as no higher-dimensional generalization was evident. This paper, therefore, provides a generalized version for treating an arbitrary number of electronic states. By construction, the benefits of the two-state triangle model-seamless treatment of weak-coupling and improved accuracy in all coupling regimes-carry over to the generalized version. Far more significant, however, is that the new model provides vastly improved windowing statistics in higher…

Milestoning on a one-dimensional potential starts by choosing a set of points, called milestones, and initiating short trajectories from each milestone, which are terminated when they reach an adjacent milestone for the first time. From the average duration of these trajectories and the probabilities of where they terminate, a rate matrix can be constructed and then used to calculate the mean first-passage time (MFPT) between any two milestones. All these MFPT's turn out to be exact. Here we adopt a point of view from which this remarkable result is not unexpected. In addition, we clarify the nature of the "states" whose interconversion is described by the rate matrix constructed using information obtained from short trajectories and provide a microscopic expression for the "equilibrium population" of these states in terms of equilibrium averages of the committors.

We report the electrocatalysis of the chlorine evolution reaction (CER) on well-defined RuO2(110) and IrO2(110) surfaces. RuO2 and IrO2 are known for their capabilities to catalyze the CER. Until now, the CER measurements have only been reported on well-defined RuO2 surfaces and only at high Cl− concentrations. We present the CER measurement and the role of Cl− at lower concentration on single-orientation RuO2(110) and IrO2(110) films. We find that RuO2(110) is two orders of magnitude more active than IrO2(110). Moreover, we observe the correlation between the CER activity and the Oad formation potential on RuO2 and IrO2, supporting the prior suggestion that the Oad is the active site for the CER. We further use the reaction order analysis to support the Volmer-Heyrovsky mechanism of the CER, which was previously suggested from the Tafel slope analysis. Our finding highlights the importance of the surface Oad species on oxides for the CER electrocatalysis and suggests the electrochemical formation of Clad on Oad (for example, Cl− + Oad ↔ OClad + e−) as the crucial step in the CER…

A prime example of a non-equilibrium or active environment is a biological cell. In order to understand in vivo functioning of biomolecules such as proteins and chromatins, a description beyond equilibrium is absolutely necessary. In this context, biomolecules have been modeled as Rouse chains in a Gaussian active bath. However, these non-equilibrium fluctuations in biological cells are non-Gaussian. This motivates us to take a Rouse chain subjected to a series of pulses of force with a finite duration, mimicking the run and tumble motion of a class of microorganisms. Thus by construction, this active force is non-Gaussian. Our analytical calculations show that the mean square displacement (MSD) of the center of mass grows faster and even shows superdiffusive behavior at higher activity. The MSD of a tagged monomer in an active bath also shows superdiffusion at an intermediate time unlike a monomer of a Rouse chain. In the case of a short chain length, reconfiguration is slower and the reconfiguration time of a chain with N monomers scales as Nσ, with σ ≈ 1.6 − 2. In addition, the…

High-accuracy noncovalent interaction energies are indispensable as data points for potential energy surfaces and as benchmark values for improving and testing more approximate approaches. The preferred algorithm (the gold standard) for computing these energies has been the coupled-cluster method with singles, doubles, and perturbative triples [CCSD(T)] converged to the complete basis set (CBS) limit. However, gold-standard calculations are expensive as correlated interaction energies converge slowly with the basis set size, and establishing the CBS limit to better than 0.05 kcal/mol typically requires a CCSD(T) calculation in a basis set of at least triple-zeta quality. If an even higher accuracy is required (for example, for the assignment of complicated high-resolution spectra), establishing a superior platinum standard requires both a precisely converged CCSD(T)/CBS limit and the corrections for the core correlation, relativistic effects, and higher-order coupled-cluster terms at least through the perturbative quadruple excitations. On the other hand, if a triple-zeta CCSD(T)…

One of the most remarkable predictions to emerge out of the exact infinite-dimensional solution of the glass problem is the Gardner transition. Although this transition was first theoretically proposed a generation ago for certain mean-field spin glass models, its materials relevance was only realized when a systematic effort to relate glass formation and jamming was undertaken. A number of nontrivial physical signatures associated with the Gardner transition have since been considered in various areas, from models of structural glasses to constraint satisfaction problems. This perspective surveys these recent advances and discusses the novel research opportunities that arise from them.

The ability of night-migratory songbirds to sense the direction of the Earth’s magnetic field is increasingly attributed to a photochemical mechanism in which the magnetic field acts on transient radical pairs in cryptochrome flavoproteins located in the birds’ eyes. The magnetically sensitive species is commonly assumed to be [FAD•− TrpH•+], formed by sequential light-induced intraprotein electron transfers from a chain of tryptophan residues to the flavin adenine dinucleotide chromophore. However, some evidence points to superoxide, O2•−, as an alternative partner for the flavin radical. The absence of hyperfine interactions in O2•− could lead to a more sensitive magnetic compass, but only if the electron spin relaxation of the O2•− radical is much slower than normally expected for a small mobile radical with an orbitally degenerate electronic ground state. In this study we use spin dynamics simulations to model the sensitivity of a flavin-superoxide radical pair to the direction of a 50 μT magnetic field. By varying parameters that characterize the local environment and molecular…

Quantitative colloidal ligand exchange on lead-halide perovskite nanocrystals (NCs) has remained a challenge due to the dynamic passivation of amines and carboxylic acids and the instability of core lead-halide perovskite systems. Here, we present a facile colloidal ligand exchange process using cinnamate acid ligands to quantitatively displace native oleate ligands on CsPbBr3 NCs. The short cinnamate ligands lead to a 23-fold enhancement of the electron-donating ability of the CsPbBr3 NCs when benzoquinone is used as an electron acceptor. A significantly increased photoredox activity is also observed in a complete photocatalytic reaction: the α-alkylation of aldehydes. Our results provide a new strategy to tune the photoredox activity of halide perovskite NCs as well as the exploration of NC-ligand interactions.

-bonded carbon is of overwhelming interest. However, these systems are notoriously challenging to model, even for electronic structure methods such as density functional theory (DFT), because of the crucial role played by London dispersion forces and noncovalent interactions, in general. Recent efforts have established reference quality interactions of several carbon nanostructures interacting with water. Here, we compile a new benchmark set (dubbed WaC18), which includes a single water molecule interacting with a broad range of carbon structures and various bulk (3D) and two-dimensional (2D) ice polymorphs. The performance of 28 approaches, including semilocal exchange-correlation functionals, nonlocal (Fock) exchange contributions, and long-range van der Waals (vdW) treatments, is tested by computing the deviations from the reference interaction energies. The calculated mean absolute deviations on the WaC18 set depend crucially on the DFT approach, ranging from 135 meV for local density approximation (LDA) to 12 meV for PBE0-D4. We find that modern vdW corrections to DFT…

We perform stringent tests of thermodynamic theories of the glass transition over the experimentally relevant temperature regime for several simulated glass-formers. The swap Monte Carlo algorithm is used to estimate the configurational entropy and static point-to-set lengthscale, and careful extrapolations are used for the relaxation times. We first quantify the relation between configurational entropy and the point-to-set lengthscale in two and three dimensions. We then show that the Adam-Gibbs relation is generally violated in simulated models for the experimentally relevant time window. Collecting experimental data for several supercooled molecular liquids, we show that the same trends are observed experimentally. Deviations from the Adam-Gibbs relation remain compatible with random first order transition theory and may account for the reported discrepancies between Kauzmann and Vogel-Fulcher-Tammann temperatures. Alternatively, they may also indicate that even near Tg thermodynamics is not the only driving force for slow dynamics.

The Fano spectrum decomposition (FSD) scheme is proposed as an efficient and accurate sum-over-poles expansion of Fermi and Bose functions at cryogenic temperatures. The new method practically overcomes the discontinuity of Fermi and Bose functions near zero temperature, which causes slow convergence in conventional schemes such as the state-of-the-art Padé spectrum decomposition (PSD). The FSD scheme fragments Fermi or Bose function into a high-temperature reference and a low-temperature correction. While the former is efficiently decomposed via the standard PSD, the latter can be accurately described by several modified Fano functions. The resulting FSD scheme is found to converge overwhelmingly faster than the standard PSD method. Remarkably, the low-temperature correction supports further a recursive and scalable extension to access the near-zero temperature regime. Thus, the proposed FSD scheme, which obeys rather simple recursive relations, has a great value in efficient numerical evaluations of Fermi or Bose function-involved integrals for various low-temperature condensed…