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The Wigner phase space formulation of quantum mechanics is a complete framework for quantum dynamic calculations that elegantly highlights connections with classical dynamics. In this series of two articles, building upon previous efforts, we derive the full hierarchy of approximate semiclassical (SC) dynamic methods for adiabatic and non-adiabatic problems in Wigner phase space. In Paper I, focusing on adiabatic single surface processes, we derive the well-known double Herman–Kluk (DHK) approximation for real-time correlation functions in Wigner phase space and connect it to the linearized SC (LSC) approximation through a stationary phase approximation. We exploit this relationship to introduce a new hybrid SC method, termed Adiabatic Hybrid Wigner Dynamics (AHWD) that allows for a few important "system" degrees of freedom (dofs) to be treated at the DHK level, while treating the rest of the dofs (the "bath") at the LSC level. AHWD is shown to accurately capture quantum interference effects in models of coupled oscillators and the decoherence of vibrational probability density of a model I2 Morse oscillator coupled to an Ohmic thermal bath. We show that AHWD significantly mitigates the sign problem and employs reduced dimensional prefactors bringing calculations of complex system–bath problems within the reach of SC methods. Paper II focuses on extending this hybrid SC dynamics to nonadiabatic processes. [ABSTRACT FROM AUTHOR]

The Journal of Chemical Physics has released a special issue focused on software for atomistic machine learning. This issue aims to address the lack of journals dedicated to publishing scientific software papers. The collection of papers in this issue provides insight into the tools and goals of software implementations in the field of atomistic machine learning. The articles cover a range of topics, including machine-learning interatomic potentials, sampling, dataset repositories, workflows, and auxiliary tooling and analysis. The article concludes by emphasizing the importance of software implementations in the field and encourages further submissions on relevant topics. [Extracted from the article]

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence. [ABSTRACT FROM AUTHOR]

A preceding paper [M. Dhar, J. A. Dickinson, and M. A. Berg, J. Chem. Phys. 159, 054110 (2023)] shows how to remove additive noise from an experimental time series, allowing both the equilibrium distribution of the system and its Green's function to be recovered. The approach is based on nonlinear-correlation functions and is fully nonparametric: no initial model of the system or of the noise is needed. However, single-molecule spectroscopy often produces time series with either photon or photon-counting noise. Unlike additive noise, photon noise is signal-size correlated and quantized. Photon counting adds the potential for bias. This paper extends noise-corrected-correlation methods to these cases and tests them on synthetic datasets. Neither signal-size correlation nor quantization is a significant complication. Analysis of the sampling error yields guidelines for the data quality needed to recover the properties of a system with a given complexity. We show that bias in photon-counting data can be corrected, even at the high count rates needed to optimize the time resolution. Using all these results, we discuss the factors that limit the time resolution of single-molecule spectroscopy and the conditions that would be needed to push measurements into the submicrosecond region. [ABSTRACT FROM AUTHOR]

This article is a response to a comment made by Professor Liu regarding a previously published paper. The response addresses questions raised by Professor Liu and focuses on three key aspects of the validity of the paper. It explains the use of different contractions in the construction of the QED Hamiltonians and clarifies the commutation relations used in the calculations. The article also highlights that the formulation of the molecular orbital method described in the paper is independent of the ordering of the operators and can derive expressions for various perturbation theories. The response concludes by stating that alternative criteria for the QED Hamiltonians are not ruled out and could be explored in future research. [Extracted from the article]

This document is an erratum for a previous paper titled "Modified Fermi's golden rule rate expressions." The erratum corrects an error in equation (41) by adding a missing factor of 1/2. The correction does not change any major conclusions or implications of the paper, but it does require the correction of figures 1-4, which show results of model calculations. The corrected figures and their captions are provided in the erratum. [Extracted from the article]

Designing coatings and films that can protect surfaces is important in a wide variety of applications from corrosion prevention to anti-fouling. These systems are challenging from a modeling perspective because they are invariably multicomponent, which quickly leads to an expansive design space. At a minimum, the system has a substrate, a film (often composed of a polymeric material), a ubiquitous carrier solvent, which may be either a vapor or liquid phase, and one or more contaminants. Each component has an impact on the effectiveness of coating. This paper focuses on films that are used as a barrier to surface contamination, but the results also extend to surface coatings that are designed to extract a low density species from the fluid phase as in liquid chromatography. A coarse-grained model is developed using Yukawa potentials that encompasses both repulsive and attractive interactions among the species. Classical density functional theory calculations are presented to show how contaminant adsorption is controlled by the molecular forces in the system. Two specific vectors through the parameter space are considered to address likely experimental manipulations that change either the solvent or the polymer in a system. We find that all the adsorption results can be unified by considering an appropriate combination of molecular parameters. As a result, these calculations provide a link between molecular interactions and film performance and may serve to guide the rational design of films. [ABSTRACT FROM AUTHOR]

Heterojunction catalysts in the field of hydrogen evolution reaction (HER) from electrocatalytic water splitting have recently become a hot research topic. In this paper, we systematically calculated the HER catalytic performance of a MoS2/CoS2 heterojunction for the first time, considering the effect of edge sites regulation, strain and electric field. The results indicate that the MoS2/CoS2 heterojunction exhibits synergistic catalytic performance compared to MoS2 and CoS2, the HER catalytic activity of which can be improved by exposing more edge sites or regulating the S content on the edges, with an optimized ratio of 25%. Surprisingly, applying strain has a slight effect on the catalytic activity of the edge, however, an obvious effect on the basal plane. For example, applying 2% tensile strain on the MoS2/CoS2 heterojunction can improve the edge catalytic performance by 13%, and for the basal plane, this value can reach 92%. In this case, the catalytic performance of the basal plane is better than that of the edge with 2% and without strain. Since the basal plane accounts for the majority of the two-dimensional catalysts, the catalytic performance of the basal plane is generally much lower than that of the edge. This discovery is of great significance, which means by adjusting strain, the catalytic performance of the heterojunction catalyst is likely to be improved by orders of magnitude. Moreover, considering the actual experimental process, we also calculated the effect of the electric field and found that 0.7 V/Å electric field can enhance the HER catalytic activity of the MoS2/CoS2 heterojunction by 23%. [ABSTRACT FROM AUTHOR]

The calculation of molecular excited states is critically important to decipher a plethora of molecular properties. In this paper, we develop an equation of motion formalism on top of a bi-exponentially parameterized ground state wavefunction toward the determination of excited states. While the ground state bi-exponential parameterization ensures an accurate description of the wavefunction through the inclusion of high-rank correlation effects, the excited state is parameterized by a novel linear response operator with an effective excitation rank beyond two. To treat the ground and excited states in the same footings, in addition to the conventional one- and two-body response operators, we introduced certain two-body "generalized" response operators with an effective excitation rank of one. We introduce a projective formulation for determining the perturbed amplitudes for the set of "generalized" operators. Our formulation entails a significantly small number of unknown parameters and is shown to be highly accurate compared to allied methods for several difficult chemical systems. [ABSTRACT FROM AUTHOR]

Liquid–liquid phase transitions hold a unique and profound significance within condensed matter physics. These transitions, while conceptually intriguing, often pose formidable computational challenges. However, recent advances in neural network (NN) potentials offer a promising avenue to effectively address these challenges. In this paper, we delve into the structural transitions of liquid CdTe, CdS, and their alloy systems using molecular dynamics simulations, harnessing the power of an NN potential named LaspNN. Our investigations encompass both pressure and temperature effects. Through our simulations, we uncover three primary liquid structures around melting points that emerge as pressure increases: tetrahedral, rock salt, and close-packed structures, which greatly resemble those of solid states. In the high-temperature regime, we observe the formation of Te chains and S dimers, providing a deeper understanding of the liquid's atomic arrangements. When examining CdSxTe1−x alloys, our findings indicate that a small substitution of S by Te atoms for S-rich alloys (x > 0.5) exhibits a structural transition much different from CdS, while a large substitution of Te by S atoms for Te-rich alloys (x < 0.5) barely exhibits a structural transition similar to CdTe. We construct a schematic diagram for liquid alloys that considers both temperature and pressure, providing a comprehensive overview of the alloy system's behavior. The local aggregation of Te atoms demonstrates a linear relationship with alloy composition x, whereas that of S atoms exhibits a nonlinear one, shedding light on the composition-dependent structural changes. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the Feshbach resonances of high partial waves and the influence of spin–spin (S–S) interaction on ultracold scattering processes. Taking the N a 23 - R b 87 system as an example, we plot the variations of weakly bound state energy and elastic scattering cross section with magnetic field and with collision energy. We find that the number of splittings in high partial wave Feshbach resonances does not strictly conform to the expected l + 1 (l is rotational angular momentum), and the deviation is attributed to the influence of bound states in other channels coupled by S–S interaction. For different ml (the projection of l on the external magnetic field direction), the effects of S–S interaction lead to different scattering patterns in the incident channels. These results reveal the complex features of ultracold scattering processes in high partial waves caused by S–S interaction. [ABSTRACT FROM AUTHOR]

Strong light–matter coupling within an optical cavity leverages the collective interactions of molecules and confined electromagnetic fields, giving rise to the possibilities of modifying chemical reactivity and molecular properties. While collective optical responses, such as enhanced Rabi splitting, are often observed, the overall effect of the cavity on molecular systems remains ambiguous for a large number of molecules. In this paper, we investigate the non-adiabatic electron transfer process in electron donor–acceptor pairs influenced by collective excitation and local molecular dynamics. Using the timescale difference between reorganization and thermal fluctuations, we derive analytical formulas for the electron transfer rate constant and the polariton relaxation rate. These formulas apply to any number of molecules (N) and account for the collective effect as induced by cavity photon coupling. Our findings reveal a non-monotonic dependence of the rate constant on N, which can be understood by the interplay between electron transfer and polariton relaxation. As a result, the cavity-induced quantum yield increases linearly with N for small N (as predicted by a simple Dicke model) but shows a turnover and suppression for large N. We also interrelate the thermal bath frequency and the number of molecules, suggesting the optimal number for maximizing enhancement. The analysis provides an analytical insight for understanding the collective excitation of light and electron transfer, helping to predict the optimal condition for effective cavity-controlled chemical reactivity. [ABSTRACT FROM AUTHOR]

Understanding how external electric fields (EFs) impact the properties of aqueous molecules is crucial for various applications in chemistry, biology, and engineering. In this paper, we present a study utilizing molecular dynamics simulation to explore how direct-current (DC) and alternative-current (AC) EFs affect hydrophobic (n-triacontane) and hydrophilic (PEG-10) oligomer chains. Through a machine learning approach, we extract a 2-dimensional free energy (FE) landscape of these molecules, revealing that electric fields modulate the FE landscape to favor stretched configurations and enhance the alignment of the chain with the electric field. Our observations indicate that DC EFs have a more prominent impact on modulation compared to AC EFs and that EFs have a stronger effect on hydrophobic chains than on hydrophilic oligomers. We analyze the orientation of water dipole moments and hydrogen bonds, finding that EFs align water molecules and induce more directional hydrogen bond networks, forming 1D water structures. This favors the stretched configuration and alignment of the studied oligomers simultaneously, as it minimizes the disruption of 1D structures. This research deepens our understanding of the mechanisms by which electric fields modulate molecular properties and could guide the broader application of EFs to control other aqueous molecules, such as proteins or biomolecules. [ABSTRACT FROM AUTHOR]

This second paper in a series of two describes the chirped-pulse ice apparatus that permits the detection of buffer gas cooled molecules desorbed from an energetically processed ice using broadband mm-wave rotational spectroscopy. Here, we detail the lower ice stage developed to generate ices at 4 K, which can then undergo energetic processing via UV/VUV photons or high-energy electrons and which ultimately enter the gas phase via temperature-programmed desorption (TPD). Over the course of TPD, the lower ice stage is interfaced with a buffer gas cooling cell that allows for sensitive detection via chirped-pulse rotational spectroscopy in the 60–90 GHz regime. In addition to a detailed description of the ice component of this apparatus, we show proof-of-principle experiments demonstrating the detection of H2CO products formed through irradiation of neat methanol ices or 1:1 CO + CH4 mixed ices. [ABSTRACT FROM AUTHOR]

The high resolution Rydberg absorption spectrum of 2-butyne C4H6 recorded previously at the SOLEIL synchrotron facility has been interpreted using multichannel quantum defect theory (MQDT). The calculations are based on the continuum scattering calculations of Xu et al., J. Chem. Phys. 136, 154303 (2012) and of Jacovella et al., J. Phys. Chem. A 119, 12339 (2015) pertaining to the dipole-allowed excited state symmetries in absorption from the ground state. In contrast to the traditional approach of calculating low-lying electronic states first and then attempting to extend the calculations to ever higher energy, here the analysis proceeds through the extension of these detailed calculations of the electronic continuum scattering down into the discrete region of the spectrum. The continuum reaction matrices and dipole transition moments are adapted to the discrete Rydberg region via the use of an energy-modified formulation of MQDT theory and associated energy dependences of the quantum defects. The analysis reproduces more than 40 Rydberg states from n ≈ 10 down to the 3d and 4s levels with an rms error of better than 20 cm−1. These belong to five Rydberg series with three different molecular symmetries. While the approach predicts many additional series, most of these are calculated and observed to carry only little oscillator strength. The analysis shows that the Rydberg spectrum is dominated by the excitation of an e″ symmetry electron of fδ and gπ type, in line with what previous studies of the above-threshold shape resonance of 2-butyne have shown. The present study is intended to serve as an example showing how first principles continuum calculations may be useful for the interpretation of highly bound discrete states in a range that poses problems for the standard ab initio techniques. The quantitative treatment of the dipole absorption cross sections is deferred to a future paper. [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]

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]

The study and modeling of water exchange in complex media using different applications of diffusion and relaxation magnetic resonance (MR) have been of interest in recent years. Most models attempt to describe this process using a first order kinetics expression, which is appropriate to describe chemical exchange; however, it may not be suitable to describe diffusion-driven exchange since it has no direct relationship to diffusion dynamics of water molecules. In this paper, these limitations are addressed through a more general exchange expression that does consider such important properties. This exchange fraction expression features a multi-exponential recovery at short times and a mono-exponential decay at long times, both of which are not captured by the first order kinetics expression. Furthermore, simplified exchange expressions containing partial information of the analyzed system's diffusion and relaxation processes and geometry are proposed, which can potentially be employed in already established estimation protocols. Finally, exchange fractions estimated from simulated MR data and derived here were compared, showing qualitative similarities but quantitative differences, suggesting that the features of the derived exchange fraction in this paper can be partially recovered by employing an existing estimation framework. [ABSTRACT FROM AUTHOR]

Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586–599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head–tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes. [ABSTRACT FROM AUTHOR]

Despite the importance of rhodium complexes in catalysis, and the favorable 100% natural abundance of the spin-1/2 103Rh nucleus, there are few reports of 103Rh nuclear magnetic resonance (NMR) parameters in the literature. In part, this is the consequence of the very low gyromagnetic ratio of 103Rh and its dismal NMR sensitivity. In a previous paper [Harbor-Collins et al., J. Chem. Phys. 159, 104 307 (2023)], we demonstrated an NMR methodology for 1H-enhanced 103Rh NMR and demonstrated an application to the 103Rh NMR of the dirhodium formate paddlewheel complex. In this paper, we employ selective 18O labeling to break the magnetic equivalence of the 103Rh spin pair of dirhodium formate. This allows the estimation of the 103Rh–103Rh spin–spin coupling and provides access to the 103Rh singlet state. We present the first measurement of a 18O-induced 103Rh secondary isotope shift as well as the first instance of singlet order generated in a 103Rh spin pair. The field-dependence of 103Rh singlet relaxation is measured by field-cycling NMR experiments. [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]

It is significant to investigate the calcium carbonate (CaCO3) precipitation mechanism during the carbon capture process; nevertheless, CaCO3 precipitation is not clearly understood yet. Understanding the carbonation mechanism at the atomic level can contribute to the mineralization capture and utilization of carbon dioxide, as well as the development of new cementitious materials with high-performance. There are many factors, such as temperature and CO2 concentration, that can influence the carbonation reaction. In order to achieve better carbonation efficiency, the reaction conditions of carbonation should be fully verified. Therefore, based on molecular dynamics simulations, this paper investigates the atomic-scale mechanism of carbonation. We investigate the effect of carbonation factors, including temperature and concentration, on the kinetics of carbonation (polymerization rate and activation energy), the early nucleation of calcium carbonate, etc. Then, we analyze the local stresses of atoms to reveal the driving force of early stage carbonate nucleation and the reasons for the evolution of polymerization rate and activation energy. Results show that the higher the calcium concentration or temperature, the higher the polymerization rate of calcium carbonate. In addition, the activation energies of the carbonation reaction increase with the decrease in calcium concentrations. [ABSTRACT FROM AUTHOR]

Vibrational coherences in ultrafast pump–probe (PP) and 2D electronic spectroscopy (2DES) provide insights into the excited state dynamics of molecules. Femtosecond coherence spectra and 2D beat maps yield information about displacements of excited state surfaces for key vibrational modes. Half-broadband 2DES uses a PP configuration with a white light continuum probe to extend the detection range and resolve vibrational coherences in the excited state absorption (ESA). However, the interpretation of these spectra is difficult as they are strongly dependent on the spectrum of the pump laser and the relative displacement of the excited states along the vibrational coordinates. We demonstrate the impact of these convoluting factors for a model based upon cresyl violet. A careful consideration of the position of the pump spectrum can be a powerful tool in resolving the ESA coherences to gain insights into excited state displacements. This paper also highlights the need for caution in considering the spectral window of the pulse when interpreting these spectra. [ABSTRACT FROM AUTHOR]

This paper evaluates the accuracy of the Hermitian form of the downfolding procedure using the double unitary coupled cluster (DUCC) ansatz on the benchmark systems of linear chains of hydrogen atoms, H6 and H8. The computational infrastructure employs the occupation-number-representation codes to construct the matrix representation of arbitrary second-quantized operators, allowing for the exact representation of exponentials of various operators. The tests demonstrate that external amplitudes from standard single-reference coupled cluster methods that sufficiently describe external (out-of-active-space) correlations reliably parameterize the Hermitian downfolded effective Hamiltonians in the DUCC formalism. The results show that this approach can overcome the problems associated with losing the variational character of corresponding energies in the corresponding SR-CC theories. [ABSTRACT FROM AUTHOR]

Quantum Dot Cellular Automata (QCA) is an emerging trend in the field of nanoelectronics, and computing can be regarded as an alternative to the traditional complementary metal–oxide–semiconductor technology. The paper is devoted to the study of the key functional properties of the cells for molecular QCA based on mixed valence molecules. The theoretical results for the heat dissipation under the conditions of the fast nonadiabatic switching event and cell–cell response function are obtained in the framework of the quantum-mechanical vibronic approach. These results are parameterized using the previous reliable ab initio calculations performed for oxidized norbornadiene and its polycyclic derivatives with variable lengths of the bridge. The comparative analysis of the dimeric and bidimeric molecular cells composed of these compounds is given. It is underlined that the conditions of a strong non-linear response and a low heat release are contradictory. However, despite this problem, a parametric regime is proposed, which provides a low heat release in combination with a strong nonlinear response of the working cell to the electric field induced by the polarized driver cell. [ABSTRACT FROM AUTHOR]

In the previous paper [C. W. Kim and I. Franco, J. Chem. Phys. 160, 214111-1–214111-13 (2024)], we developed a theory called MQME-D, which allows us to decompose the overall energy dissipation process in open quantum system dynamics into contributions by individual components of the bath when the subsystem dynamics is governed by a Markovian quantum master equation (MQME). Here, we contrast the predictions of MQME-D against the numerically exact results obtained by combining hierarchical equations of motion (HEOM) with a recently reported protocol for monitoring the statistics of the bath. Overall, MQME-D accurately captures the contributions of specific bath components to the overall dissipation while greatly reducing the computational cost compared to exact computations using HEOM. The computations show that MQME-D exhibits errors originating from its inherent Markov approximation. We demonstrate that its accuracy can be significantly increased by incorporating non-Markovianity by exploiting time scale separations (TSS) in different components of the bath. Our work demonstrates that MQME-D combined with TSS can be reliably used to understand how energy is dissipated in realistic open quantum system dynamics. [ABSTRACT FROM AUTHOR]

The superadiabatic dynamical density functional theory (superadiabatic-DDFT) is a promising new method for the study of colloidal systems out-of-equilibrium. Within this approach, the viscous forces arising from interparticle interactions are accounted for in a natural way by explicitly treating the dynamics of the two-body correlations. For bulk systems subject to spatially homogeneous shear, we use the superadiabatic-DDFT framework to calculate the steady-state pair distribution function and the corresponding viscosity for low values of the shear-rate. We then consider a variant of the central approximation underlying this superadiabatic theory and obtain an inhomogeneous generalization of a rheological bulk theory due to Russel and Gast. This paper thus establishes for the first time a connection between DDFT approaches, formulated to treat inhomogeneous systems, and existing work addressing nonequilibrium microstructure and rheology in bulk colloidal suspensions. [ABSTRACT FROM AUTHOR]

We propose a new collocation multi-configuration time-dependent Hartree (MCTDH) method. It reduces point-set error by using more points than basis functions. Collocation makes it possible to use MCTDH with a general potential energy surface without computing any integrals. The collocation points are associated with a basis larger than the basis used to represent wavefunctions. Both bases are obtained from a direct product basis built from single-particle functions by imposing a pruning condition. The collocation points are those on a sparse grid. Heretofore, collocation MCTDH calculations with more points than basis functions have only been possible if both the collocation grid and the basis set are direct products. In this paper, we exploit a new pseudo-inverse to use both more points than basis functions and a pruned basis and grid. We demonstrate that, for a calculation of the lowest 50 vibrational states (energy levels and wavefunctions) of CH2NH, errors can be reduced by two orders of magnitude by increasing the number of points, without increasing the basis size. This is true also when unrefined time-independent points are used. [ABSTRACT FROM AUTHOR]