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Molecular dynamics (MD) is the method of choice for understanding the structure, function, and interactions of molecules. However, MD simulations are limited by the strong metastability of many molecules, which traps them in a single conformation basin for an extended amount of time. Enhanced sampling techniques, such as metadynamics and replica exchange, have been developed to overcome this limitation and accelerate the exploration of complex free energy landscapes. In this paper, we propose Vendi Sampling, a replica-based algorithm for increasing the efficiency and efficacy of the exploration of molecular conformation spaces. In Vendi sampling, replicas are simulated in parallel and coupled via a global statistical measure, the Vendi Score, to enhance diversity. Vendi sampling allows for the recovery of unbiased sampling statistics and dramatically improves sampling efficiency. We demonstrate the effectiveness of Vendi sampling in improving molecular dynamics simulations by showing significant improvements in coverage and mixing between metastable states and convergence of free energy estimates for four common benchmarks, including Alanine Dipeptide and Chignolin. [ABSTRACT FROM AUTHOR]

InP-based quantum dots (QDs) have Stokes shifts and photoluminescence (PL) line widths that are larger than in II–VI semiconductor QDs with comparable exciton energies. The mechanisms responsible for these spectral characteristics are investigated in this paper. Upon comparing different semiconductors, we find the Stokes shift decreases in the following order: InP > CdTe > CdSe. We also find that the Stokes shift decreases with core size and decreases upon deposition of a ZnSe shell. We suggest that the Stokes shift is largely due to different absorption and luminescent states in the angular momentum fine structure. The energy difference between the fine structure levels, and hence the Stokes shifts, are controlled by the electron–hole exchange interaction. Luminescence polarization results are reported and are consistent with this assignment. Spectral widths are controlled by the extent of homogeneous and inhomogeneous broadening. We report PL and PL excitation (PLE) spectra that facilitate assessing the roles of homogeneous and different inhomogeneous broadening mechanisms in the spectra of zinc-treated InP and InP/ZnSe/ZnS particles. There are two distinct types of inhomogeneous broadening: size inhomogeneity and core–shell interface inhomogeneity. The latter results in a distribution of core–shell band offsets and is caused by interfacial dipoles associated with In–Se or P–Zn bonding. Quantitative modeling of the spectra shows that the offset inhomogeneity is comparable to but somewhat smaller than the size inhomogeneity. The combination of these two types of inhomogeneity also explains several aspects of reversible hole trapping dynamics involving localized In3+/VZn2− impurity states in the ZnSe shells. [ABSTRACT FROM AUTHOR]

In this paper we present the Markovian Multiagent Monte-Carlo Second Order Self-Consistent Field Algorithm (M3-SOSCF). This algorithm provides a highly reliable methodology for converging SCF calculations in single-reference methods using a modified differential evolution approach. Additionally, M3 is embarrassingly parallel and modular in regards to Newton–Raphson subroutines. We show that M3 is able to surpass contemporary SOSCFs in reliability, which is illustrated by a benchmark employing poor initial guesses and a second benchmark with SCF calculations which face difficulties using standard SCF algorithms. Furthermore, we analyse inherent properties of M3 and show that in addition to its robustness and efficiency, it is more user-friendly than current SOSCFs. [ABSTRACT FROM AUTHOR]

Based on the relationship between average local ionization energy I ̄ (r) and average local electron affinity A ̄ (r) with the electronic Fukui functions, i.e., f−(r) and f+(r), respectively, in this paper, we establish a connection between nuclear and electronic Fukui functions beyond frontier molecular orbitals. As a consequence of this connection, we obtain expressions of average nuclear Fukui functions interpreted as a variation of average nucleophilicity or electrophilicity (weighted by the electronic orbital Fukui functions) with respect to nuclear displacements, which goes beyond the highest occupied molecular orbital/or lowest unoccupied molecular orbital consideration. Furthermore, from this connection and considering the frontier molecular orbital approximation, we derive expressions of nuclear Fukui functions in terms of the atom-condensed electronic Fukui functions, which imply a locality in the chemical reactivity and could be used to study the variation of local nucleophilicity or electrophilicity with respect to nuclear displacements. Finally, this new way to interpret the nuclear Fukui function could be useful in the future to study the chemical reactivity related to molecular vibrations, internal rotations, bond dissociation, chemical reaction along the model of reaction coordinate, and so on. [ABSTRACT FROM AUTHOR]

The Pauli kinetic energy functional and its functional derivative, termed Pauli potential, play a crucial role in the successful implementation of orbital-free density functional theory for electronic structure calculations. However, the exact forms of these two quantities are not known. Therefore, perforce, one employs the approximate forms for the Pauli functional or Pauli potential for performing orbital-free density functional calculations. In the present study, we developed a feed-forward neural network-based representation for the Pauli potential using a 1-dimensional (1-D) model system. We expanded density in terms of basis functions, and the coefficients of the expansion were used as input to a feed-forward neural network. Using the neural network-based representation of the Pauli potential, we calculated the ground-state densities of the 1-D model system by solving the Euler equation. We calculated the Pauli kinetic energy using the neural network-based Pauli potential employing the exact relation between the Pauli kinetic energy functional and the potential. The sum of the neural network-based Pauli kinetic energy and the von Weizsäcker kinetic energy resulted in an accurate estimation of the total kinetic energy. The approach presented in this paper can be employed for the calculation of Pauli potential and Pauli kinetic energy, obviating the need for a functional derivative. The present study is an important step in the advancement of application of machine learning-based techniques toward the orbital-free density functional theory-based methods. [ABSTRACT FROM AUTHOR]

Recent measurements of the third harmonic scattering responses of molecules have given a new impetus for computing molecular second hyperpolarizabilities (γ) and for deducing structure–property relationships. This paper has employed a variety of wavefunction and density functional theory methods to evaluate the second hyperpolarizability of the p-nitroaniline prototypical push-pull π-conjugated molecule, addressing also numerical aspects, such as the selection of an integration grid and the impact of the order of differentiation vs the achievable accuracy by using the Romberg quadrature. The reliability of the different methods has been assessed by comparison to reference Coupled-Cluster Singles and Doubles with perturbative treatment of the Triples results. On the one hand, among wavefunction methods, the MP2 scheme offers the best accuracy/cost ratio for computing the static γ. On the other hand, using density functional theory, γ remains a challenging property to compute because all conventional, global hybrid or range-separated hybrid, exchange–correlation functionals underestimate static γ values by at least 15%. Even tuning the range-separating parameter to minimize the delocalization errors does not enable to improve the γ values. Nevertheless, the original double-hybrid B2-PLYP functional, which benefits from 27% of PT2 correlation and 53% Hartree–Fock exchange, provides accurate estimates of static γ values. Unfortunately, the best performing exchange–correlation functionals for γ are not necessarily reliable for the first hyperpolarizability, β, and vice versa. In fact, the β of p-nitroaniline (pNA) could be predicted, with a good accuracy, with several hybrid exchange–correlation functionals (including by tuning the range-separating parameter), but these systematically underestimate γ. As for γ, the MP2 wavefunction method remains the best compromise to evaluate the first hyperpolarizability of pNA at low computational cost. [ABSTRACT FROM AUTHOR]

Interpreting high-dimensional data from molecular dynamics simulations is a persistent challenge. In this paper, we show that for a small peptide, deca-alanine, metastable states can be identified through a neural net based on structural information alone. While processing molecular dynamics data, dimensionality reduction is a necessary step that projects high-dimensional data onto a low-dimensional representation that, ideally, captures the conformational changes in the underlying data. Conventional methods make use of the temporal information contained in trajectories generated through integrating the equations of motion, which forgoes more efficient sampling schemes. We demonstrate that EncoderMap, an autoencoder architecture with an additional distance metric, can find a suitable low-dimensional representation to identify long-lived molecular conformations using exclusively structural information. For deca-alanine, which exhibits several helix-forming pathways, we show that this approach allows us to combine simulations with different biasing forces and yields representations comparable in quality to other established methods. Our results contribute to computational strategies for the rapid automatic exploration of the configuration space of peptides and proteins. [ABSTRACT FROM AUTHOR]

The analysis and modeling of high-resolution spectra of nonrigid molecules require a specific Hamiltonian and group-theoretical formulation that differs significantly from that of more familiar rigid systems. Within the framework of Hougen–Bunker–Johns (HBJ) theory, this paper is devoted to the construction of a nonrigid Hamiltonian based on a suitable combination of numerical calculations for the nonrigid part in conjunction with the irreducible tensor operator method for the rigid part. For the first time, a variational calculation from ab initio potential energy surfaces is performed using the HBJ kinetic energy operator built from vibrational, large-amplitude motion, and rotational tensor operators expressed in terms of curvilinear and normal coordinates. Group theory for nonrigid molecules plays a central role in the characterization of the overall tunneling splittings and is discussed in the present approach. The construction of the dipole moment operator is also examined. Validation tests consisting of a careful convergence study of the energy levels as well as a comparison of results obtained from independent computer codes are given for the nonrigid molecules CH2, CH3, NH3, and H2O2. This work paves the way for the modeling of high-resolution spectra of larger nonrigid systems. [ABSTRACT FROM AUTHOR]

In this paper, we apply a theoretical model for fluid state thermodynamics to investigate simulated water in supercooled conditions. This model, which we recently proposed and applied to sub- and super-critical fluid water [Zanetti-Polzi et al., J. Chem. Phys. 156(4), 44506 (2022)], is based on a combination of the moment-generating functions of the enthalpy and volume fluctuations as provided by two gamma distributions and provides the free energy of the system as well as other relevant thermodynamic quantities. The application we make here provides a thermodynamic description of supercooled water fully consistent with that expected by crossing the liquid–liquid Widom line, indicating the presence of two distinct liquid states. In particular, the present model accurately reproduces the Widom line temperatures estimated with other two-state models and well describes the heat capacity anomalies. Differently from previous models, according to our description, a cluster of molecules that extends beyond the first hydration shell is necessary to discriminate between the statistical fluctuation regimes typical of the two liquid states. [ABSTRACT FROM AUTHOR]

It is known that some non-dynamic effects of electron correlation can be included in coupled cluster theory using a tailoring technique that separates the effects of non-dynamic and dynamic correlations. Recently, the simple pCCD (pair coupled cluster doubles) wavefunction was shown to provide good results for some non-dynamic correlation problems, such as bond-breaking, in a spin-adapted way with no active space selection. In this paper, we report a study of excited states using "tailored coupled cluster singles and doubles," to attempt to use pCCD as a kernel for more complete coupled-cluster singles and doubles (CCSD) results for excited states. Several excited states are explored from those primarily due to single excitations to those dominated by doubly excited states and from singlet–triplet splittings for some diradical states. For the first two situations, tailored pCCD-TCCSD offers no improvement over equation of motion-CCSD. However, when we explore the singlet–triplet gap of diradical molecules that are manifestly multi-reference, a pCCD kernel provides improved results, particularly with generalized valence bond orbitals. [ABSTRACT FROM AUTHOR]

Ninety years ago, Wigner derived the leading order expansion term in ℏ2 for the tunneling rate through a symmetric barrier. His derivation included two contributions: one came from the parabolic barrier, but a second term involved the fourth-order derivative of the potential at the barrier top. He left us with a challenge, which is answered in this paper, to derive the same but for an asymmetric barrier. A crucial element of the derivation is obtaining the ℏ2 expansion term for the projection operator, which appears in the flux-side expression for the rate. It is also reassuring that an analytical calculation of semiclassical transition state theory (TST) reproduces the anharmonic corrections to the leading order of ℏ2. The efficacy of the resulting expression is demonstrated for an Eckart barrier, leading to the conclusion that especially when considering heavy atom tunneling, one should use the expansion derived in this paper, rather than the parabolic barrier approximation. The rate expression derived here reveals how the classical TST limit is approached as a function of ℏ and, thus, provides critical insights to understand the validity of popular approximate theories, such as the classical Wigner, centroid molecular dynamics, and ring polymer molecular dynamics methods. [ABSTRACT FROM AUTHOR]

The aging rate of glasses has traditionally been modeled as a function of temperature, T, and fictive temperature, while density, ρ, is not explicitly included as a parameter. However, this description does not naturally connect to the modern understanding of what governs the relaxation rate in equilibrium. In equilibrium, it is well known that the relaxation rate, γeq, depends on temperature and density. In addition, a large class of systems obeys density scaling, which means the rate specifically depends on the scaling parameter, Γ = e(ρ)/T, where e(ρ) is a system specific function. This paper presents a generalization of the fictive temperature concept in terms of a fictive scaling parameter, Γfic, and a density scaling conjecture for aging glasses in which the aging rate depends on Γ and Γfic. [ABSTRACT FROM AUTHOR]

The persistent problem posed by the glass transition is to develop a general atomic level description of amorphous solidification. The answer proposed in this paper is to measure a configuration's capacity to restrain the motion of the constituent atoms. Here, we show that the instantaneous normal modes can be used to define a measure of atomic restraint that accounts for the difference between fragile and strong liquids and the collective length scale of the supercooled liquid. These results represent a significant simplification of the description of amorphous solidification and provide a powerful systematic treatment of the influence of microscopic factors on the formation of an amorphous solid. [ABSTRACT FROM AUTHOR]

Erratum: "Physics-based, neural network force fields for reactive molecular dynamics: Investigation of carbene formation from [EMIM+][OAc-]" [J. Chem. Phys. We have recomputed the PMFs with AIMD, utilizing a consistent collective variable definition of Eq. (1). This was done using the plumed/ASE interface with a CP2K calculator.[[2], [5]] Corrected PMFs that employ the collective variable of Eq. (1) for all calculations are shown in the corrected Fig. [Extracted from the article]

A complete set of four polarization-dependent differential cross sections in the reactions of Cl + aligned-CHD3(v1 = 1, |jK) → DCl(v = 0) + CHD2(v1 = 1) is reported here for two different, rotationally polarized states with j = 1: specifically the |jK = |10 state prepared via the R(0) excitation and the |1 ± 1 state via Q(1). In stark contrast to the complicated situation of the HCl(v) + CD3(v = 0) channel reported in Paper-I, the stereo-requirement of this isotopic channel for both polarized reactants appears quite straightforward and consistent with a direct rebound mechanism. The extent of steric effects is moderate and relatively smaller than the alternative H-atom abstraction channel. All major findings reported here can qualitatively be understood by first noting that the present reaction invokes abstracting a D-atom, which is the spectator in the IR-excitation process. Next, it is recognized that the directional properties of two polarized states of CHD3(v1 = 1, |jK) should manifest primarily in the IR-excited C-H bond, leaving secondary imprints in the unexcited CD3-moiety. The stereo-specificity of the DCl + CHD2 product channel is further reduced by the fact that the abstraction can occur with any one of the three spatially distinct D-atoms. [ABSTRACT FROM AUTHOR]

In Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], we presented the ring-polymer instanton with explicit friction (RPI-EF) method and showed how it can be connected to the ab initio electronic friction formalism. This framework allows for the calculation of tunneling reaction rates that incorporate the quantum nature of the nuclei and certain types of non-adiabatic effects (NAEs) present in metals. In this paper, we analyze the performance of RPI-EF on model potentials and apply it to realistic systems. For a 1D double-well model, we benchmark the method against numerically exact results obtained from multi-layer multi-configuration time-dependent Hartree calculations. We demonstrate that RPI-EF is accurate for medium and high friction strengths and less accurate for extremely low friction values. We also show quantitatively how the inclusion of NAEs lowers the crossover temperature into the deep tunneling regime, reduces the tunneling rates, and, in certain regimes, steers the quantum dynamics by modifying the tunneling pathways. As a showcase of the efficiency of this method, we present a study of hydrogen and deuterium hopping between neighboring interstitial sites in selected bulk metals. The results show that multidimensional vibrational coupling and nuclear quantum effects have a larger impact than NAEs on the tunneling rates of diffusion in metals. Together with Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], these results advance the calculations of dissipative tunneling rates from first principles. [ABSTRACT FROM AUTHOR]

A Brownian bridge is a continuous random walk conditioned to end in a given region by adding an effective drift to guide paths toward the desired region of phase space. This idea has many applications in chemical science where one wants to control the endpoint of a stochastic process—e.g., polymer physics, chemical reaction pathways, heat/mass transfer, and Brownian dynamics simulations. Despite its broad applicability, the biggest limitation of the Brownian bridge technique is that it is often difficult to determine the effective drift as it comes from a solution of a Backward Fokker–Planck (BFP) equation that is infeasible to compute for complex or high-dimensional systems. This paper introduces a fast approximation method to generate a Brownian bridge process without solving the BFP equation explicitly. Specifically, this paper uses the asymptotic properties of the BFP equation to generate an approximate drift and determine ways to correct (i.e., re-weight) any errors incurred from this approximation. Because such a procedure avoids the solution of the BFP equation, we show that it drastically accelerates the generation of conditioned random walks. We also show that this approach offers reasonable improvement compared to other sampling approaches using simple bias potentials. [ABSTRACT FROM AUTHOR]

Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces—base stacking, counterion-induced backbone self-interactions, and base pairing—via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach. [ABSTRACT FROM AUTHOR]

The rotationally resolved infrared (IR) spectrum of the He– H 3 + complex has been measured in a cryogenic ion trap experiment at a nominal temperature of 4 K. Predissociation of the stored complex has been invoked by excitation of the degenerate ν2 mode of the H 3 + sub-unit using a pulsed optical parametric oscillator system. An assignment of the experimental spectrum became possible through one-to-one correlations with bands of the spectrum theoretically predicted in Paper I [Harding et al., J. Chem. Phys. 156, 144307 (2022)]. 19 bands have been assigned and analyzed, and the energy term diagram of the lower states of this floppy molecular complex has been derived from combination differences (CDs) in the experimental spectrum. Ground state combination differences (GSCDs) reveal a large part of the energy term diagram for the He– H 3 + complex in its vibrational ground state, v = 0. Experimental and theoretical term energies agree within experimental accuracy for the rotational fine structure associated with the total angular momentum quantum number J and the parity e/f as well as for the coarse spacing of the lowest K states of the complex. This favorable comparison shows that the potential energy surface (PES) calculated in Paper I is accurate. The barriers between the three equivalent global minima in this PES are relatively low and the He– H 3 + complex is extremely floppy, with nearly unhindered internal rotation of the H 3 + sub-unit. The resulting Coriolis interactions couple the internal and end-over-end rotation of the complex and contribute significantly to the energy terms. They are observed both in experiment and theory and are, e.g., the origin of different rotational constants for states of e and f parity. Also in this respect, experiment and theory agree very well. Despite the assignment and analysis of many bands of the extremely rich IR spectrum of He– H 3 + , higher levels of excitation, including the complex stretching mode, need further attention. [ABSTRACT FROM AUTHOR]

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute–solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies. [ABSTRACT FROM AUTHOR]

Biphasic interfaces are complex but fascinating regimes that display a number of properties distinct from those of the bulk. The CO2–H2O interface, in particular, has been the subject of a number of studies on account of its importance for the carbon life cycle as well as carbon capture and sequestration schemes. Despite this attention, there remain a number of open questions on the nature of the CO2–H2O interface, particularly concerning the interfacial tension and phase behavior of CO2 at the interface. In this paper, we seek to address these ambiguities using ab initio-quality simulations. Harnessing the benefits of machine-learned potentials and enhanced statistical sampling methods, we present an ab initio-level description of the CO2–H2O interface. Interfacial tensions are predicted from 1 to 500 bars and found to be in close agreement with experiment at pressures for which experimental data are available. Structural analyses indicate the buildup of an adsorbed, saturated CO2 film forming at a low pressure (20 bars) with properties similar to those of the bulk liquid, but preferential perpendicular alignment with respect to the interface. The CO2 monolayer buildup coincides with a reduced structuring of water molecules close to the interface. This study highlights the predictive nature of machine-learned potentials for complex macroscopic properties of biphasic interfaces, and the mechanistic insight obtained into carbon dioxide aggregation at the water interface is of high relevance for geoscience, climate research, and materials science. [ABSTRACT FROM AUTHOR]

In this paper, we explored the resistivity behavior of Sb7Se3 thin films on flexible mica. The films maintained their resistance characteristics through various thicknesses and bending cycles. With increasing bends, resistivity and phase transition temperature of both amorphous and crystalline states rose, while the resistance drift coefficient gradually increased. Raman and near infrared experiments confirmed the internal structural changes and bandgap enhancement after bending. Transmission electron microscopy showed enhanced crystallization and uniform element distribution after annealing. Atomic force microscopy observed cracks, explaining the property changes. Additionally, we developed a flexible Sb7Se3 thin-film resistive device with swift reversibility (∼10 ns) regardless of bending, opening new avenues for flexible information storage. [ABSTRACT FROM AUTHOR]

In the study of stochastic systems, the committor function describes the probability that a system starting from an initial configuration x will reach a set B before a set A. This paper introduces an efficient and interpretable algorithm for approximating the committor, called the "fast committor machine" (FCM). The FCM uses simulated trajectory data to build a kernel-based model of the committor. The kernel function is constructed to emphasize low-dimensional subspaces that optimally describe the A to B transitions. The coefficients in the kernel model are determined using randomized linear algebra, leading to a runtime that scales linearly with the number of data points. In numerical experiments involving a triple-well potential and alanine dipeptide, the FCM yields higher accuracy and trains more quickly than a neural network with the same number of parameters. The FCM is also more interpretable than the neural net. [ABSTRACT FROM AUTHOR]

Biphasic interfaces are complex but fascinating regimes that display a number of properties distinct from those of the bulk. The CO2–H2O interface, in particular, has been the subject of a number of studies on account of its importance for the carbon life cycle as well as carbon capture and sequestration schemes. Despite this attention, there remain a number of open questions on the nature of the CO2–H2O interface, particularly concerning the interfacial tension and phase behavior of CO2 at the interface. In this paper, we seek to address these ambiguities using ab initio-quality simulations. Harnessing the benefits of machine-learned potentials and enhanced statistical sampling methods, we present an ab initio-level description of the CO2–H2O interface. Interfacial tensions are predicted from 1 to 500 bars and found to be in close agreement with experiment at pressures for which experimental data are available. Structural analyses indicate the buildup of an adsorbed, saturated CO2 film forming at a low pressure (20 bars) with properties similar to those of the bulk liquid, but preferential perpendicular alignment with respect to the interface. The CO2 monolayer buildup coincides with a reduced structuring of water molecules close to the interface. This study highlights the predictive nature of machine-learned potentials for complex macroscopic properties of biphasic interfaces, and the mechanistic insight obtained into carbon dioxide aggregation at the water interface is of high relevance for geoscience, climate research, and materials science. [ABSTRACT FROM AUTHOR]

In this paper, an exact analytical solution is presented for achieving coherent population transfer and creating arbitrary coherent superposition states in a five-state chainwise system by a train of coincident pulses. We show that the solution of a five-state chainwise system can be reduced to an equivalent three-state Λ-type one with the simplest resonant coupling under the assumption of adiabatic elimination together with a requirement of the relation among the four coincident pulses. In this method, the four coincident pulses at each step all have the same time dependence, but with specific magnitudes. The results show that, by using a train of appropriately coincident pulses, this technique not only enables complete population transfer, but also creates any desired coherent superposition between the initial and final states, while the population in all intermediate states is effectively suppressed. Furthermore, this technique can also exhibit a one-way population transfer behavior. The results are of potential interest in applications where high-fidelity multi-state quantum control is essential, e.g., quantum information, atom optics, formation of ultracold molecules, cavity QED, nuclear coherent population transfer, and light transfer in waveguide arrays. [ABSTRACT FROM AUTHOR]

CuGBasis is a free and open-source CUDA®/Python library for efficient computation of scalar, vector, and matrix quantities crucial for the post-processing of electronic structure calculations. CuGBasis integrates high-performance Graphical Processing Unit (GPU) computing with the ease and flexibility of Python programming, making it compatible with a vast ecosystem of libraries. We showcase its utility as a Python library and demonstrate its seamless interoperability with existing Python software to gain chemical insight from quantum chemistry calculations. Leveraging GPU-accelerated code, cuGBasis exhibits remarkable performance, making it highly applicable to larger systems or large databases. Our benchmarks reveal a 100-fold performance gain compared to alternative software packages, including serial/multi-threaded Central Processing Unit and GPU implementations. This paper outlines various features and computational strategies that lead to cuGBasis's enhanced performance, guiding developers of GPU-accelerated code. [ABSTRACT FROM AUTHOR]

Motivated by the various applications of the trapping diffusion-influenced reaction theory in physics, chemistry, and biology, this paper deals with irreducible Cartesian tensor (ICT) technique within the scope of the generalized method of separation of variables (GMSV). We provide a survey from the basic concepts of the theory and highlight the distinctive features of our approach in contrast to similar techniques documented in the literature. The solution to the stationary diffusion equation under appropriate boundary conditions is represented as a series in terms of ICT. By means of proved translational addition theorem, we straightforwardly reduce the general boundary value diffusion problem for N spherical sinks to the corresponding resolving infinite set of linear algebraic equations with respect to the unknown tensor coefficients. These coefficients exhibit an explicit dependence on the arbitrary three-dimensional configurations of N sinks with different radii and surface reactivities. Our research contains all relevant mathematical details such as terminology, definitions, and geometrical structure, along with a step by step description of the GMSV algorithm with the ICT technique to solve the general diffusion boundary value problem within the scope of Smoluchowski's trapping model. [ABSTRACT FROM AUTHOR]

The description of quantum transport in the strong system–reservoir coupling regime poses a significant theoretical and computational challenge that demands specialized tools for accurate analysis. RealTimeTransport is a new open-source C++ library that enables the computation of both stationary and transient transport observables for generic quantum systems connected to metallic reservoirs. It computes the Nakajima–Zwanzig memory kernels for both dynamics and transport in real-time, going beyond traditional expansions in the bare system–reservoir couplings. Currently, several methods are available as follows: (i) A renormalized perturbation theory in leading and next-to-leading order, which avoids the low-temperature breakdown that limits the traditional theory. (ii) Starting from this well-behaved reference solution, a two- and three-loop, self-consistent renormalization-group transformation of the memory kernels is implemented. This allows refined quantitative predictions even in the presence of many body resonances, such as the Kondo enhancement of cotunneling. This paper provides an overview of the theory, the architecture of RealTimeTransport, and practical demonstrations of the currently implemented methods. In particular, we analyze the stationary transport through a serial double quantum dot and showcase for the T = 0 interacting Anderson model the complete time-development of single-electron tunneling (SET), cotunneling-assisted SET, and inelastic cotunneling resonances throughout the entire gate-bias stability diagram. We discuss the range of applicability of the implemented methods and benchmark them against other advanced approaches. [ABSTRACT FROM AUTHOR]

In this paper, we report a new algorithm for creating an adaptive basis set in the Multiconfigurational Ehrenfest (MCE) method, which is termed Full Cloning (FC), and test it together with the existing Multiple Cloning (MC) using the spin-boson model at zero-temperature as a benchmark. The zero-temperature spin-boson regime is a common hurdle in the development of methods that seek to model quantum dynamics. Two versions of MCE exist. We demonstrate that MC is vital for the convergence of MCE version 2 (MCEv2). The first version (MCEv1) converges much better than MCEv2, but FC improves its convergence in a few cases where it is hard to converge it with the help of a reasonably small size of the basis set. [ABSTRACT FROM AUTHOR]

Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software architecture, and examples of applications enabled by the methods it implements. [ABSTRACT FROM AUTHOR]

In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation. [ABSTRACT FROM AUTHOR]

In this paper, we consider the problem of numerical investigation of the counting statistics for a class of one-dimensional systems. Importance sampling, the cornerstone technique usually implemented for such problems, critically hinges on selecting an appropriate biased distribution. While an exponential tilt in the observable stands as the conventional choice for various problems, its efficiency in the context of counting statistics may be significantly hindered by the genuine discreteness of the observable. To address this challenge, we propose an alternative strategy, which we call importance sampling with the local tilt. We demonstrate the efficiency of the proposed approach through the analysis of three prototypical examples: a set of independent Gaussian random variables, Dyson gas, and symmetric simple exclusion process with a steplike initial condition. [ABSTRACT FROM AUTHOR]

Quantum dynamics simulation and computational spectroscopy serve as indispensable tools for the theoretical understanding of various fundamental physical and chemical processes, ranging from charge transfer to photochemical reactions. When simulating realistic systems, the primary challenge stems from the overwhelming number of degrees of freedom and the pronounced many-body correlations. Here, we present Kylin-V, an innovative quantum dynamics package designed for accurate and efficient simulations of dynamics and spectroscopic properties of vibronic Hamiltonians for molecular systems and their aggregates. Kylin-V supports various quantum dynamics and computational spectroscopy methods, such as time-dependent density matrix renormalization group and our recently proposed single-site and hierarchical mapping approaches, as well as vibrational heat-bath configuration interaction. In this paper, we introduce the methodologies implemented in Kylin-V and illustrate their performances through a diverse collection of numerical examples. [ABSTRACT FROM AUTHOR]

This paper explores the use of deoxyribonucleic acid (DNA) origami structures as nanorobot components. Investigating the functional properties of DNA origami structures can facilitate the fabrication of DNA origami-based nanorobots. The wireframe structure stands out as one of the most interesting DNA origami structures. Hence, the present study aims to employ these structures to create DNA origami nanoactuators. The research delves into the design of DNA origami structures with the aim of opening under specific temperature conditions. Short DNA strands (staples) are one of the crucial parts of DNA origami structures, and the appropriate design of these strands can lead to the creation of structures with different properties. Thus, the components of the DNA origami nanoactuator are tailored to enable intentional opening at specific temperatures while maintaining stability at lower temperatures. This structural modification showcases the functional property of the DNA origami structure. The engineered DNA origami nanoactuator holds potential applications in medicine. By carrying drugs under specific temperature conditions and releasing them under different temperature conditions, it can serve as a platform for smart drug delivery purposes. [ABSTRACT FROM AUTHOR]

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique "fingerprint" of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. We demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments. [ABSTRACT FROM AUTHOR]

Recently, Theophilou [J. Chem. Phys. 149, 074104 (2018)] proposed a peculiar version of the density functional theory by showing that the set of spherical averages of the density around the nuclei determines uniquely the external potential in atoms, molecules, and solids. Here, this novel theory is extended to individual excited states. The generalization is based on the method developed in the series of papers by Ayers, Levy, and Nagy [Phys. Rev. A 85, 042518 (2012)]. Generalized Hohenberg–Kohn theorems are proved to the set of spherically symmetric densities using constrained search. A universal variational functional for the sum of the kinetic and electron–electron repulsion energies is constructed. The functional is appropriate for the ground state and all bound excited states. Euler equations and Kohn–Sham equations for the set are derived. The Euler equations can be rewritten as Schrödinger-like equations for the square root of the radial densities, and the effective potentials in them can be expressed in terms of wave function expectation values. The Hartree plus exchange–correlation potentials can be given by the difference of the interacting and the non-interacting effective potentials. [ABSTRACT FROM AUTHOR]

In this paper, we use nested tensor-train contractions to compute vibrational and ro-vibrational energy levels of molecules with five and six atoms. At each step, we fully exploit symmetry by using symmetry adapted basis functions obtained from an irreducible tensor method. Contracted basis functions are determined by diagonalizing reduced dimensional Hamiltonian matrices. The size of matrices of eigenvectors, used to account for coupling between groups of coordinates, is reduced by discarding rows and columns. The size of the matrices that must be diagonalized is thus substantially reduced, making it possible to use direct eigensolvers, even for molecules with five and six atoms. The symmetry-adapted contracted vibrational basis functions have been used to compute J = 0 energy levels of the CH3CN (C3v) and J > 0 levels of CH4. [ABSTRACT FROM AUTHOR]

Neural network interatomic potentials (NNPs) have recently proven to be powerful tools to accurately model complex molecular systems while bypassing the high numerical cost of ab initio molecular dynamics simulations. In recent years, numerous advances in model architectures as well as the development of hybrid models combining machine-learning (ML) with more traditional, physically motivated, force-field interactions have considerably increased the design space of ML potentials. In this paper, we present FeNNol, a new library for building, training, and running force-field-enhanced neural network potentials. It provides a flexible and modular system for building hybrid models, allowing us to easily combine state-of-the-art embeddings with ML-parameterized physical interaction terms without the need for explicit programming. Furthermore, FeNNol leverages the automatic differentiation and just-in-time compilation features of the Jax Python library to enable fast evaluation of NNPs, shrinking the performance gap between ML potentials and standard force-fields. This is demonstrated with the popular ANI-2x model reaching simulation speeds nearly on par with the AMOEBA polarizable force-field on commodity GPUs (graphics processing units). We hope that FeNNol will facilitate the development and application of new hybrid NNP architectures for a wide range of molecular simulation problems. [ABSTRACT FROM AUTHOR]

Room temperature ionic liquids (RTILs) are molten salts consisting entirely of ions and have over the past decades gained increased interest due to their high potential in applications. These structurally complex systems often display multiple relaxation modes in the response functions at lower frequencies, hinting to complex underlying mechanisms. While the existence of these multimodal spectra in the shear mechanical, dielectric, and light scattering response of RTILs has been confirmed multiple times, controversy still surrounds the origin. This paper, therefore, aims to provide additional insights into the multimodal spectra seen in RTILs by presenting new shear mechanical results on seven different RTILs: Pyr1n-TFSI with n = 4, 6, and 8; Pyr18-TFSI mixed with Li-TFSI in two high concentrations; and Cn-mim-BF4 with n = 3 and 8. Dynamic depolarized light scattering was also measured on one of the Pyr18-TFSI Li-salt mixtures. These specific cases were analyzed in detail and put into a bigger perspective together with an overview of the literature. Recent literature offers two specific explanations for the origin of the multimodal shear mechanical spectra: (1) cation–anion time scale separation or (2) combined cation–anion relaxation in addition to a dynamic signal from mesoscale aggregates at lower frequencies. However, neither of these two pictures can consistently explain all the results on different ionic liquids. Instead, we conclude that the origin of the multimodal spectrum is system specific. This underlines the complexity of this class of liquids and shows that great care must be taken when making general conclusions based on specific cases. [ABSTRACT FROM AUTHOR]

The doping of CdS quantum dots (QDs) with Cu(I) disrupts electron–hole correlation due to hole trapping by the dopant ion, post-photoexcitation. The present paper examines the effect of such disruption on the rate of photoinduced electron transfer (PET) from the QDs to methyl viologen (MV2+), with implications in their photocatalytic activity. A significantly greater efficiency of PL quenching by MV2+ is observed for the doped QDs than for the undoped ones. Interestingly, the Stern–Volmer plots constructed using PL intensities exhibit an upward curvature for both the cases, while the PL lifetimes remain unaffected. This observation is rationalized by considering the adsorption of the quencher on the surface of the QDs and ultrafast PET post-photoexcitation. Ultrafast transient absorption experiments confirm a faster electron transfer for the doped QDs. It is also realized that the transient absorption experiment yields a more accurate estimate of the binding constant of the quencher with the QDs, than the PL experiment. [ABSTRACT FROM AUTHOR]

Fermi's golden rule (FGR) offers an empirical framework for understanding the dynamics of spin–lattice relaxation in magnetic molecules, encompassing mechanisms like direct (one-phonon) and Raman (two-phonon) processes. These principles effectively model experimental longitudinal relaxation rates, denoted as T 1 − 1 . However, under scenarios of increased coupling strength and nonlinear spin–lattice interactions, FGR's applicability may diminish. This paper numerically evaluates the exact spin–lattice relaxation rate kernels, employing the extended dissipaton equation of motion formalism. Our calculations reveal that when quadratic spin–lattice coupling is considered, the rate kernels exhibit a free induction decay-like feature, and the damping rates depend on the interaction strength. We observe that the temperature dependence predicted by FGR significantly deviates from the exact results since FGR ignores the higher order effects and the non-Markovian nature of spin–lattice relaxation. Our methods can be easily extended to study other systems with nonlinear spin–lattice interactions and provide valuable insights into the temperature dependence of T1 in molecular qubits when the coupling is strong. [ABSTRACT FROM AUTHOR]

The biochemical activity inside a cell has recently been suggested to act as a source of hydrodynamic fluctuations that can speed up or slow down enzyme catalysis [Tripathi et al., Commun. Phys. 5, 101 (2022).] The idea has been tested against and largely corroborated by simulations of activated barrier crossing in a simple fluid in the presence of thermal and athermal noise. The present paper attempts a wholly analytic solution to the same noise-driven barrier crossing problem but generalizes it to include viscoelastic memory effects of the kind likely to be present in cellular interiors. A calculation of the model's barrier crossing rate, using Kramers' flux-over-population formalism, reveals that in relation to the case where athermal noise is absent, athermal noise always accelerates barrier crossing, though the extent of enhancement depends on the duration τ0 over which the noise acts. More importantly, there exists a critical τ0—determined by the properties of the medium—at which Kramers' theory breaks down and, on approach to which, the rate grows significantly. The possibility of such a giant enhancement is potentially open to experimental validation using optically trapped nanoparticles in viscoelastic media that are acted on by externally imposed colored noise. [ABSTRACT FROM AUTHOR]

This paper presents the first implementation of a coupling between advanced wavefunction theories and molecular density functional theory (MDFT). This method enables the modeling of solvent effect into quantum mechanical (QM) calculations by incorporating an electrostatic potential generated by solvent charges into the electronic Hamiltonian. Solvent charges are deduced from the spatially and angularly dependent solvent particle density. Such a density is obtained through the minimization of the functional associated with the molecular mechanics (MM) Hamiltonian describing the interaction between the fluid particles. The introduced QM/MDFT framework belongs to QM/MM family of methods, but its originality lies in the use of MDFT as the MM solver, offering two main advantages. First, its functional formulation makes it competitive with respect to sampling-based molecular mechanics. Second, it preserves a molecular-level description lost in macroscopic continuum approaches. The excited state properties of water and formaldehyde molecules solvated into water have been computed at the selected configuration interaction (SCI) level. The excitation energies and dipole moments have been compared with experimental data and previous theoretical work. A key finding is that using the Hartree–Fock method to describe the solute allows for predicting the solvent charge around the ground state with sufficient precision for the subsequent SCI calculations of excited states. This significantly reduces the computational cost of the described procedure, paving the way for the study of more complex molecules. [ABSTRACT FROM AUTHOR]

Electron transfer reactions play an essential role in many chemical and biological processes. Fermi's golden rule (GR), which assumes that the coupling between electronic states is small, has formed the foundation of electron transfer rate theory; however, in short range electron/energy transfer reactions, this coupling can become very large, and, therefore, Fermi's GR fails to make even qualitatively accurate rate predictions. In this paper, I present a simple modified GR theory to describe electron transfer in the Marcus inverted regime at arbitrarily large electronic coupling strengths. This theory is based on an optimal global rotation of the diabatic states, which makes it compatible with existing methods for calculating GR rates that can account for nuclear quantum effects with anharmonic potentials. Furthermore, the optimal GR (OGR) theory can also be combined with analytic theories for non-adiabatic rates, such as Marcus theory and Marcus–Levich–Jortner theory, offering clear physical insights into strong electronic coupling effects in non-adiabatic processes. OGR theory is also tested on a large set of spin-boson models and an anharmonic model against exact quantum dynamics calculations, where it performs well, correctly predicting rate turnover at large coupling strengths. Finally, an example application to a boron-dipyrromethane–anthracene photosensitizer reveals that strong coupling effects inhibit excited state charge recombination in this system, reducing the rate of this process by a factor of 4. Overall, OGR theory offers a new approach to calculating electron transfer rates at strong couplings, offering new physical insights into a range of non-adiabatic processes. [ABSTRACT FROM AUTHOR]

Two-dimensional (2D) Janus transition metal dichalcogenides MXY manifest novel physical properties owing to the breaking of out-of-plane mirror symmetry. Recently, the 2H phase of MoSH has been demonstrated to possess intrinsic superconductivity, whereas the 1T phase exhibits a charge density waves state. In this paper, we have systematically studied the stability and electron–phonon interaction characteristics of MoSLi. Our results have shown that both the 2H and 1T phases of MoSLi are stable, as indicated by the phonon spectrum and the ab initio molecular dynamics. However, the 1T phase exhibits an electron–phonon coupling constant that is twice as large as that of the 2H phase. In contrast to MoSH, the 1T phase of MoSLi exhibits intrinsic superconductivity. By employing the ab initio anisotropic Migdal-Eliashberg formalism, we have revealed the two-gap superconducting nature of 1T-MoSLi, with a transition temperature (Tc) of 14.8 K. The detailed analysis indicates that the superconductivity in 1T-MoSLi primarily originates from the interplay between the vibration of the phonon modes in the low-frequency region and the dz2 orbital. These findings provide a fresh perspective on superconductivity within Janus structures. [ABSTRACT FROM AUTHOR]

Endohedrally doped clusters form a large category of cage clusters, with unique structures, diverse elemental compositions, and highly tunable electronic structures and physisochemical properties. They have been widely achieved in laboratory and may serve as functional building blocks for assembling new supermolecular structures and devices. In this paper, for the first time, we disclosed the luminescence properties of endohedrally doped group-IV clusters by time-dependent density functional theory calculations. A total of 64 cage clusters have been explored in terms of stability, emission wavelength, and the energy difference between the first excited singlet and triplet states. The key geometric and electronic factors governing the photophysical properties of these cage clusters were unveiled, to provide crucial insights for crafting atomically precise nanoclusters for optical and optoelectronic applications. [ABSTRACT FROM AUTHOR]