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Produced by both nature and human activities, sulfur dioxide (SO2) is an important species in the earth's atmosphere. SO2 has also been found in the atmospheres of other planets and satellites in the solar system. The photoabsorption cross sections and photodissociation of SO2 have been studied for several decades. In this paper, we reported the experimental results for photodissociation dynamics of SO2 via the G̃1B1 state. By analyzing the images from the time-sliced velocity map ion imaging method, the vibrational state population distributions and anisotropy parameters were obtained for the O(1D2) + SO(X3Σ-, a1Δ, b1Σ+) and O(1S0) + SO(X3Σ-) channels, and the branching ratios for the channels O(1D2) + SO(X3Σ-), O(1D2) + SO(a1Δ), and O(1D2) + SO(b1Σ+) were determined to be ∼0.3, ∼0.6, and ∼0.1, respectively. The SO products were dominant in electronically and rovibrationally excited states, which may have yet unrecognized roles in the upper planetary atmosphere., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Molecular chirality has traditionally been viewed as a binary property where a molecule is classified as either chiral or achiral, yet in recent decades, mathematical methods for quantifying chirality have been explored. Here, we use toy molecular systems to systematically compare the performance of two state-of-the-art chirality measures: (1) the Continuous Chirality Measure (CCM) and (2) the Chirality Characteristic (χ). We find that both methods exhibit qualitatively similar behavior when applied to simple molecular systems such as a four-site molecule or the polymer double-helix, but we show that the CCM may be more suitable for evaluating the chirality of arbitrary molecules or abstract structures such as normal vibrational modes. We discuss a range of considerations for applying these methods to molecular systems in general, and we provide links to user-friendly codes for both methods. We aim for this paper to serve as a concise resource for scientists attempting to familiarize themselves with these chirality measures or attempting to implement chirality measures in their own work., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Chemical shakers are active particles with zero propulsion velocity whose activity derives from chemical reactions on portions of their surfaces. Although they do not move, except through Brownian motion, the nonequilibrium concentration and velocity fields that they generate endow them with properties that differ from their equilibrium counterparts. In particular, collections of such shakers can actively move, reorient, and self-assemble into various cluster states, which are the subject of this paper. Elongated chemical shakers constructed from linked catalytic and noncatalytic spheres are considered, and it is shown how hydrodynamic, chemotactic, and shape-dependent interactions give rise to various self-assembled shaker structures. The chemical forces responsible for cluster formation are described in terms of a model based on pair-wise additive contributions. The forms of the self-assembled structures can be varied by changing the chemostat concentrations that control the nonequilibrium state. The resulting structures and their manipulation through chemical means suggest ways to construct a class of active materials for applications., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This paper explores the unintentional contamination of Surface-Enhanced Raman Scattering (SERS) substrates by ambient hydrocarbon contaminants and their contribution to SERS spectra. Previous studies have identified amorphous carbon as a potential complicating factor in data analysis in SERS experiments, although its origin has been elusive. Our work showed that ambient hydrocarbon contamination and its decomposition products can be detected by SERS on a gold substrate. We propose that ambient air itself is a source of amorphous carbon contamination on SERS substrates. This understanding is crucial for the correct interpretation of SERS data and highlights the need for careful consideration of potential environmental contaminants in SERS analysis., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Packaging insulation materials with high thermal conductivity and excellent dielectric properties are favorable to meet the high demand and rapid development of third generation power semiconductors. In this study, we propose to improve the thermal conductivity of epoxy resin (EP) by incorporating a three-dimensional boron nitride thermally conductive network. Detailedly, polyurethane foam (PU) was used as a supporter, and boron nitride nanosheets (BNNSs) were loaded onto the PU supporter through chemical bonding (BNNS@PU). After immersing BNNS@PU into the EP resin, EP-based thermally conductive composites were prepared by vacuum-assisted impregnation. Fourier transform infrared spectrometer and scanning electron microscope were used to characterize the chemical bonding and morphological structure of BNNS@PU, respectively. The content of BNNS in BNNS@PU/EP composites was quantitatively analyzed by TGA. The results show that the thermal conductivity of the BNNS@PU/EP composites reaches 0.521 W/m K with an enhancement rate η of 30.89 at an ultra-low BNNS filler content (5.93 wt. %). Additionally, the BNNS@PU/EP composites have excellent dielectric properties with the frequency range from 101 to 106 Hz. This paper provides an interesting idea for developing high thermal conductivity insulating materials used for power semiconductor packaging., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Semiconductor nanocrystals (NCs) can function as efficient gain materials with chemical versatility because of their surface ligands. Because the properties of NCs in solution are sensitive to ligand-environment interactions, local chemical changes can result in changes in the optical response. However, amplification of the optical response is technically challenging because of colloidal instability at NC concentrations needed for sufficient gain to overcome losses. This paper demonstrates liquid lasing from plasmonic lattice cavities integrated with ligand-engineered CdZnS/ZnS NCs dispersed in toluene and water. By taking advantage of calcium ion-induced aggregation of NCs in aqueous solutions, we show how lasing threshold can be used as a transduction signal for ion detection. Our work highlights how NC solutions and plasmonic lattices with open cavity architectures can serve as a biosensing platform for lab-on-chip devices., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Ion channels are proteins that play a significant role in physiological processes, including neuronal excitability and signal transduction. However, the precise mechanisms by which these proteins facilitate ion diffusion through cell membranes are not well understood. This is because experimental techniques to characterize ion channel activity operate on a time scale too large to understand the role of the various protein conformations on diffusion. Meanwhile, computational approaches operate on a time scale too short to rationalize the observed behavior at the microscopic scale. In this paper, we present a continuous-time random walk model that aims to bridge the scales between the atomistic models of ion channels and the experimental measurement of their conductance. We show how diffusion slows down in complex systems by using 3D lattices that map out the pore geometry of two channels: Nav1.7 and gramicidin. We also introduce spatial and dynamic site disorder to account for system heterogeneity beyond the mean field approximation. Computed diffusion coefficients show that an increase in spatial disorder slows down diffusion kinetics, while dynamic disorder has the opposite effect. Our results imply that microscopic or phenomenological models based on the potential of mean force data overlook the functional importance of protein dynamics on ion diffusion through channels., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, the responses of assembled behaviors of block polyelectrolytes (PEs) to the strength of electrostatic interactions are studied through molecular dynamic simulations. The results show that the assembled structures closely depend on the electrostatic strength. It should be noted that PE coacervation can outweigh the nucleation of hydrophobic blocks and invert the micelle structures at strong electrostatic strengths, leading to the formation of inverted micelles of PE cores and hydrophobic coronas. In the poor solvent condition for neutral block, diverse anisotropic micelles are presented; candy-like conventional micelles of hydrophobic cores and PE patches coexist with inverted candy-like micelles of PE cores and hydrophobic patches and with Janus micelles of semi-neutral aggregate and semi-PE cluster in the presence of divalent and trivalent counterions. The formation of conventional or inverted micelle is largely determined by the type of micellar fusion, which results from the nucleation competition between electrostatic correlation and hydrophobic interaction. The merge of micelles mediated by hydrophobic attraction leads to conventional hydrophobic cores, and the fusion induced by electrostatic correlations results in PE cores micelles. At strong electrostatic strengths, the PE chains exhibit rich conformations at trivalent counterions, ranging from a fully collapsed state to a rod-like state, and parallel alignment of PE chains is found., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

To address the challenge of performance portability and facilitate the implementation of electronic structure solvers, we developed the basic matrix library (BML) and Parallel, Rapid O(N), and Graph-based Recursive Electronic Structure Solver (PROGRESS) library. The BML implements linear algebra operations necessary for electronic structure kernels using a unified user interface for various matrix formats (dense and sparse) and architectures (CPUs and GPUs). Focusing on density functional theory and tight-binding models, PROGRESS implements several solvers for computing the single-particle density matrix and relies on BML. In this paper, we describe the general strategies used for these implementations on various computer architectures, using OpenMP target functionalities on GPUs, in conjunction with third-party libraries to handle performance critical numerical kernels. We demonstrate the portability of this approach and its performance in benchmark problems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Within the context of fewest-switch surface hopping (FSSH) dynamics, one often wishes to remove the angular component of the derivative coupling between states J and K. In a previous set of papers, Shu et al. [J. Phys. Chem. Lett. 11, 1135-1140 (2020)] posited one approach for such a removal based on direct projection, while we isolated a second approach by constructing and differentiating a rotationally invariant basis. Unfortunately, neither approach was able to demonstrate a one-electron operatorÔ whose matrix element JÔK was the angular component of the derivative coupling. Here, we show that a one-electron operator can, in fact, be constructed efficiently in a semi-local fashion. The present results yield physical insight into designing new surface hopping algorithms and are of immediate use for FSSH calculations., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Conical intersection (CI) leads to fast electronic energy transfer. However, Hamm and Stock [Phys. Rev. Lett. 109, 173201 (2012)] showed the existence of a vibrational CI and its role in vibrational energy relaxation. In this paper, we further investigate the vibrational energy relaxation using an isolated model Hamiltonian system of four vibrational modes with two distinctively different timescales (two fast modes and two slow modes). We show that the excitation of the slow modes plays a crucial role in the energy relaxation mechanism. We also analyze the system from a mixed quantum-classical (surface hopping method) and a completely classical point of view. Notably, surface hopping and even classical simulations also capture fast energy relaxation, which is a signature of CI's existence., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Alchemical transformations showed that perturbation theory can be applied also to changes in the atomic nuclear charges of a molecule. The alchemical path that connects two different chemical species involves the conceptualization of a non-physical system in which an atom possess a non-integer nuclear charge. A correct quantum mechanical treatment of these systems is limited by the fact that finite size atomic basis sets do not define exponents and contraction coefficients for fractional charge atoms. This paper proposes a solution to this problem and shows that a smooth interpolation of the atomic orbital coefficients and exponents across the periodic table is a convenient way to produce accurate alchemical predictions, even using small size basis sets., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

This paper introduces a spin-free formulation of the supporting subspace factorization [C. Song and T. J. Martínez, J. Chem. Phys. 149, 044108 (2018)], enabling a reduction in the computational scaling of the extended multi-state complete active space second-order perturbation (XMS-CASPT2) method for arbitrary spins. Compared to the original formulation that is defined in the spin orbitals and is limited to singlet states, the spin-free formulation in this work treats different spin states equivalently, thus naturally generalizing the idea beyond singlet states. In addition, we will present a new way of deriving the supporting subspace factorization with the purpose of understanding its physical interpretation. In this new derivation, we separate the sources that make CASPT2 difficult into the "same-site interactions" and "inter-site interactions." We will first show how the Kronecker sum can be used to remove the same-site interactions in the absence of inter-site interactions, leading to MP2 energy in dressed orbitals. We will then show how the inter-site interactions can be exactly recovered using Löwdin partition, where the supporting subspace concept will naturally arise. The new spin-free formulation maintains the main advantage of the supporting subspace factorization, i.e., allowing XMS-CASPT2 energies to be computed using highly optimized MP2 energy codes and Fock build codes, thus reducing the scaling of XMS-CASPT2 to the same scaling as MP2. We will present and discuss results that benchmark the accuracy and performance of the new method. To demonstrate how the new method can be useful in studying real photochemical systems, the supporting subspace XMS-CASPT2 is applied to a photoreaction sensitive to magnetic field effects. The new spin-free formulation makes it possible to calculate the doublet and quartet states required in this particular photoreaction mechanism., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The diffusion of dilute molecular penetrants within polymers plays a crucial role in the advancement of material engineering for applications such as coatings and membrane separations. The potential of highly cross-linked polymer networks in these applications stems from their capacity to adjust the size and shape selectivity through subtle changes in network structures. In this paper, we use molecular dynamics simulation to understand the role of penetrant shape (aspect ratios) and its interaction with polymer networks on its diffusivity. We characterize both local penetrant hopping and the long-time diffusive motion for penetrants and consider different aspect ratios and penetrant-network interaction strengths at a variety of cross-link densities and temperatures. The shape affects the coupling of penetrant motion to the cross-link density- and temperature-dependent structural relaxation of networks and also affects the way a penetrant experiences the confinement from the network meshes. The attractive interaction between the penetrant and network primarily affects the former since only the system of dilute limit is of present interest. These results offer fundamental insights into the intricate interplay between penetrant characteristics and polymer network properties and also suggest future directions for manipulating polymer design to enhance the separation efficiency., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, we investigate the performance of different machine learning potentials (MLPs) in predicting key thermodynamic properties of water using RPBE + D3. Specifically, we scrutinize kernel-based regression and high-dimensional neural networks trained on a highly accurate dataset consisting of about 1500 structures, as well as a smaller dataset, about half the size, obtained using only on-the-fly learning. This study reveals that despite minor differences between the MLPs, their agreement on observables such as the diffusion constant and pair-correlation functions is excellent, especially for the large training dataset. Variations in the predicted density isobars, albeit somewhat larger, are also acceptable, particularly given the errors inherent to approximate density functional theory. Overall, this study emphasizes the relevance of the database over the fitting method. Finally, this study underscores the limitations of root mean square errors and the need for comprehensive testing, advocating the use of multiple MLPs for enhanced certainty, particularly when simulating complex thermodynamic properties that may not be fully captured by simpler tests., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

This article describes a method for calculating higher order or nonadiabatic corrections in Born-Oppenheimer theory and its interaction with the translational degrees of freedom. The method uses the Wigner-Weyl correspondence to map nuclear operators into functions on the classical phase space and the Moyal star product to represent operator multiplication on those functions. These are explained in the body of the paper. The result is a power series in κ2, where κ = (m/M)1/4 is the usual Born-Oppenheimer parameter. The lowest order term is the usual Born-Oppenheimer approximation, while higher order terms are nonadiabatic corrections. These are needed in calculations of electronic currents, momenta, and densities. The separation of nuclear and electronic degrees of freedom takes place in the context of the exact symmetries (for an isolated molecule) of translations and rotations, and these, especially translations, are explicitly incorporated into our discussion. This article presents an independent derivation of the Moyal expansion in molecular Born-Oppenheimer theory. We show how electronic currents and momenta can be calculated within the framework of Moyal perturbation theory; we derive the transformation laws of the electronic Hamiltonian, the electronic eigenstates, and the derivative couplings under translations; we discuss in detail the rectilinear motion of the molecular center of mass in the Born-Oppenheimer representation; and we show how the elimination of the translational components of the derivative couplings leads to a unitary transformation that has the effect of exactly separating the translational degrees of freedom., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, we develop and analyze a number of perturbation series that target the coupled cluster singles and doubles (CCSD) ground state energy. We show how classical Møller-Plesset perturbation theory series can be restructured to target the CCSD energy based on a reference CCS calculation and how the corresponding cluster perturbation series differs from the classical Møller-Plesset perturbation series. Subsequently, we reformulate these series using the coupled cluster Lagrangian framework to obtain series, where fourth and fifth order energies are determined only using parameters through second order. To test the methods, we perform a series of test calculations on molecular photoswitches of both total energies and reaction energies. We find that the fifth order reaction energies are of CCSD quality and that they are of comparable accuracy to state-of-the-art approximations to the CCSD energy based on local pair natural orbitals. The advantage of the present approach over local correlation methods is the absence of user defined threshold parameters for neglecting or approximating contributions to the correlation energy. Fixed threshold parameters lead to discontinuous energy surfaces, although this effect is often small enough to be ignored, but the present approach has a differentiable energy that will facilitate derivation and implementation of gradients and higher derivatives. A further advantage is that the calculation of the perturbation correction is non-iterative and can, therefore, be calculated in parallel, leading to a short time-to-solution., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

We introduce a generalized micro-macro Markov chain Monte Carlo (mM-MCMC) method with pseudo-marginal approximation to the free energy that is able to accelerate sampling of the microscopic Gibbs distributions when there is a time-scale separation between the macroscopic dynamics of a reaction coordinate and the remaining microscopic degrees of freedom. The mM-MCMC method attains this efficiency by iterating four steps: (i) propose a new value of the reaction coordinate, (ii) accept or reject the macroscopic sample, (iii) run a biased simulation that creates a microscopic molecular instance that lies close to the newly sampled macroscopic reaction coordinate value, and (iv) microscopic accept/reject step for the new microscopic sample. In the present paper, we eliminate the main computational bottleneck of earlier versions of this method: the necessity to have an accurate approximation of free energy. We show that the introduction of a pseudo-marginal approximation significantly reduces the computational cost of the microscopic accept/reject step while still providing unbiased samples. We illustrate the method's behavior on several molecular systems with low-dimensional reaction coordinates., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

In order to prepare highly heat-resistant packaging insulation materials, in this paper, bismaleimide/epoxy resin (BMI/EP55) composites with different contents of BMI were prepared by melt blending BMI into amino tetrafunctional and phenolic epoxy resin (at a ratio of 5:5). The microstructures and thermal and electrical properties of the composites were tested. The electrostatic potential distribution, energy level distribution, and molecular orbitals of BMI were calculated using Gaussian. The results showed that the carbonyl group in BMI is highly electronegative, implying that the carbonyl group has a strong electron trapping ability. The thermal decomposition temperature of the composites gradually increased with the increase of BMI content, and the 20% BMI/EP55 composites had the highest heat-resistance index, along with a glass transition temperature (Tg) of >250 °C. At different test temperatures, with increase in the BMI content, the conductivity of epoxy resin composites showed a tendency to first decrease and then increase, the breakdown field strength showed a tendency to first increase and then decrease, and the dielectric constant was gradually decreased. Two trap centers were present simultaneously in the composites, where the shallow trap energy level is the deepest in 20% BMI/EP composites and the deep trap energy level is the deepest in 10% BMI/EP55 composites. Correspondingly, the 10% BMI/EP55 composite had a slower charge decay rate, while the 20% BMI/EP55 had a faster charge decay rate. In summary, the BMI/EP55 composites with high heat resistance and insulating properties were prepared in this study, which provided ideas for preparing high-temperature packaging insulating materials., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, we report on the implementation of CC2 and CC3 in the context of molecules in finite magnetic fields. The methods are applied to the investigation of atoms and molecules through spectroscopic predictions and geometry optimizations for the study of the atmosphere of highly magnetized White Dwarf stars. We show that ground-state finite-field (ff) CC2 is a reasonable alternative to CCSD for energies and, in particular, for geometrical properties. For excited states, ff-CC2 is shown to perform well for states with predominant single-excitation character. Yet, for cases in which the excited state wavefunction has double-excitation character with respect to the reference, ff-CC2 can easily lead to completely unphysical results. Ff-CC3, however, is shown to reproduce the CCSDT behavior very well and enables the treatment of larger systems at a high accuracy., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C-O-N-O dihedral angle: cis-CH3ONO and trans-CH3ONO, with cis being more stable by ∼5 kJ/mol. The barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH3ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N2, Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance-contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH3ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N2:CH3ONO, Ar:CH3ONO, or Xe:CH3ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH3ONO more effectively than trans-CH3ONO, likely because cis-CH3ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Conical intersections are known to play a vital role in many photochemical processes. The breakdown of the Born-Oppenheimer approximation in the vicinity of a conical intersection causes exciting phenomena, such as the ultrafast radiationless decay of excited states. The passage of a molecule through a conical intersection creates a coherent superposition of electronic states via nonadiabatic couplings. Detecting this coherent superposition may serve as a direct probe of the conical intersection. In this paper, we theoretically demonstrate the use of coherent spontaneous emission in samples with long-range order for probing the occurrence of a conical intersection in a molecule. Our simulations show that the spectrum contains clear signatures of the created coherent superposition of electronic states. We investigate the bandwidth requirements for the x-ray probes, which influence the observation of coherent superposition generated by the conical intersection., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

The large discrepancy among the nucleation kinetics extracted from experimental measurements and computer simulations and the prediction of the classical nucleation theory (CNT) has stimulated intense arguments about its origin in the past decades, which is crucially relevant to the validity of the CNT. In this paper, we investigate the atomistic mechanism of the nucleation in liquid Al in contact with amorphous substrates with atomic-level smooth/rough surfaces, using molecular dynamics (MD) simulations. This study reveals that the slightly distorted local fcc/hcp structures in amorphous substrates with smooth surfaces can promote heterogeneous nucleation through a structural templating mechanism, and on the other hand, homogeneous nucleation will occur at a larger undercooling through a fluctuation mechanism if the surface is rough. Thus, some impurities, previously thought to be impotent, could be activated in the homogeneous nucleation experiments. We further find that the initial growth of the nucleus on smooth surfaces of amorphous substrates is one order of magnitude faster than that in homogeneous nucleation. Both these factors could significantly contribute to the discrepancy in the nucleation kinetics. This study is also supported by a recent study of the synthesis of high-entropy alloy nanoparticles assisted with the liquid metal Ga [Cao et al., Nature 619, 73 (2023)]. In this study, we established that the boundary existed between homogeneous and heterogeneous nucleation, i.e., the structural templating is a general mechanism for heterogeneous nucleation, and in its absence, homogeneous nucleation will occur through the fluctuation mechanism. This study provides an in-depth understanding of the nucleation theory and experiments., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

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., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca2+, Cd2+, Cu2+, Fe2+, Hg2+, Mg2+, Ni2+, Pb2+, and Zn2+, we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M(H2O)2]2+ aqua complexes to [M(H2O)9]2+, allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M(H2O)n]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion-water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

31P nuclear magnetic resonance (NMR) chemical shifts were shown to be very sensitive to the basis set used at the geometry optimization stage. Commonly used energy-optimized basis sets for a phosphorus atom containing only one polarization d-function were shown to be unable to provide correct equilibrium geometries for the calculations of phosphorus chemical shifts. The use of basis sets with at least two polarization d-functions on a phosphorus atom is strongly recommended. In this paper, an idea of creating the basis sets purposed for the geometry optimization that provide the least possible error coming from the geometry factor of accuracy in the resultant NMR shielding constants is proposed. The property-energy consisted algorithm with the target function in the form of the molecular energy gradient relative to P-P bond lengths was applied to create new geometry-oriented pecG-n (n = 1, 2) basis sets for a phosphorus atom. New basis sets have demonstrated by far superior performance as compared to the other commonly used energy-optimized basis sets in massive calculations of 31P NMR chemical shifts carried out at the gauge-including atomic orbital-coupled cluster singles and doubles/pecS-2 level of the theory by taking into account solvent, vibrational, and relativistic corrections., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

Chiral thin films showing electronic and plasmonic circular dichroism (CD) are intensively explored for optoelectronic applications. The most studied chiral organic films are the composites exhibiting a helical geometry, which often causes entanglement of circular optical properties with unwanted linear optical effects (linearly polarized absorption or refraction). This entanglement limits tunability and often translates to a complex optical response. This paper describes chiral films based on dark conglomerate, sponge-like, liquid crystal films, which go beyond the usual helical type geometry, waiving the problem of linear contributions to chiroptical electronic and plasmonic properties. First, we show that purely organic films exhibit high electronic CD and circular birefringence, as studied in detail using Mueller matrix polarimetry. Analogous linear properties are two orders of magnitude lower, highlighting the benefits of using the bi-isotropic dark conglomerate liquid crystal for chiroptical purposes. Next, we show that the liquid crystal can act as a template to guide the assembly of chemically compatible gold nanoparticles into 3D spiral-like assemblies. The Mueller matrix polarimetry measurements confirm that these composites exhibit both electronic and plasmonic circular dichroisms, while nanoparticle presence is not compromising the beneficial optical properties of the matrix., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the transition rates among states that appear in the Markov model when the monomer dynamics is diffusive can be determined by computing the relative entropy of states and their mean first passage times, quantities that are unchanged by the specification of the energies of the relevant states. In this paper, we verify the folding dynamics described by a diffusive linear chain model of the crambin protein in three distinct solvent systems, each differing in complexity: a hard-sphere solvent, a solvent undergoing multi-particle collision dynamics, and an implicit solvent model. The predicted transition rates among configurations agree quantitatively with those observed in explicit molecular dynamics simulations for all three solvent models. These results suggest that the local monomer-monomer interactions provide sufficient friction for the monomer dynamics to be diffusive on timescales relevant to changes in conformation. Factors such as structural ordering and dynamic hydrodynamic effects appear to have minimal influence on transition rates within the studied solvent densities., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This paper presents a general second-quantized form of a permutation operator interchanging n pairs of electrons between interacting subsystems in the framework of the symmetry-adapted perturbation theory (SAPT). We detail the procedure for constructing this operator through the consecutive multiplication of single-pair permutation operators. This generalized form of the permutation operator has enabled the derivation of universal formulas for S2n approximations of the exchange energies in the first and second order of the interaction operator. We present expressions for corrections of S4 approximations and assess its efficacy on a selection of systems anticipated to exhibit a slowly converging overlap expansion. Additionally, we outline a method to sum the overlap expansion series to infinity in second-quantization, up to the second order in V. This new approach offers an alternative to the existing formalism based on density-matrix formulations. When combined with a symbolic algebra program for automated derivations, it paves the way for advancements in SAPT theory, particularly for intricate wavefunction theories., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

The optical surface of extreme ultraviolet (EUV) lithography machines is highly vulnerable to contamination by hydrocarbons, resulting in the formation of carbon deposits that significantly degrade the quality and efficiency of lithography. The dynamic gas lock (DGL) has been proven as an effective approach to alleviate carbon deposition. However, the majority of existing studies on carbon deposition neglect the influence of the DGL. This paper is dedicated to investigating the phenomena of hydrocarbon adsorption, desorption, and cleavage with considering the effects of the DGL. A comprehensive mathematical model of the carbon deposition process is established, and the impact of radiation intensity, temperature, and hydrocarbon types on the depositing rate is considered. The results suggest that the primary cause of carbon deposition is the direct cracking of hydrocarbons induced by photons with a wavelength range between 12.5 and 14.5 nm. Additionally, it has been observed that the carbon deposition rate decreases exponentially as clean gas flow increases when EUV radiation intensity exceeds 50 mW/mm2. Conversely, at low EUV radiation intensity, clean gas flow has little effect on the carbon deposition rate. An effective approach to mitigate carbon deposition is to elevate the temperature of the optical surface and employ light hydrocarbon materials in the EUV process., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light-matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori-Nakajima-Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method's capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O(103) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Previous studies have shown that NaB6, KB6, and RbB6 adopting Pm3̄m are superconductors with a relatively high Tc under ambient conditions. In this paper, we conducted systematic structural and related properties research on CsB6 through a genetic evolution algorithm and total energy calculations based on density functional theory between 0 and 20 GPa. Our results reveal a cubic Pm3̄m CsB6, which is dynamically stable under the pressures we studied. We systematically calculated the formation enthalpies, electronic properties, and superconducting properties of Pm3̄m MB6 (M = Na, K, Rb, Cs). They all exhibit metallic features, and boron has high contributions to band structures, density of states, and electron-phonon coupling (EPC). The calculated results about the Helmholtz free energy difference of Pm3̄m CsB6 at 0, 10, and 20 GPa indicate that it is stable upon chemical decomposition (decomposition to simple substances Cs and B) from 0 to 400 K. The phonon density of states indicates that boron atoms occupy the high frequency area. The EPC results show that Pm3̄m CsB6 is a superconductor with Tc = 11.7 K at 0 GPa, close to NaB6 (13.1 K), KB6 (11.7 K), and RbB6 (11.3 K) at 0 GPa in our work, which indicates that boron atoms play an essential role in superconductivity: vibrations of B6 regular octagons lead to the high Tc of Pm3̄m MB6. Our work about Pm3̄m hexaborides provides a supplementary study on the borides of the group IA elements (without Fr and Li) and has an important guiding significance for the experimental synthesis of CsB6., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium "quench" process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The network structure within polymers significantly influences their mechanical properties, including their strength, toughness, and fatigue resistance. All-atom molecular dynamics (AAMD) simulations offer a method to investigate the energy dissipation mechanism within polymers during deformation and fracture; Such an approach is, however, computationally inefficient when used to analyze polymers with complex network structures, such as the common chemically double-networked hydrogels. Alternatively, coarse-grained molecular dynamics (CGMD) models, which reduce the computational degrees of freedom by concentrating a set of adjacent atoms into a coarse-grained bead, can be employed. In CGMD simulations, a coarse-grained force field (CGFF) is a critical factor affecting the simulation accuracy. In this paper, we proposed a data-based method for predicting the CGFF parameters to improve the simulation efficiency of complex cross-linked network in polymers. Here, we utilized a typical chemically double-networked hydrogel as an example. An artificial neural network was selected, and it was trained with the tensile stress-strain data from the CGMD simulations using different CGFF parameters. The CGMD simulations using the predicted CGFF parameters show good agreement with the AAMD simulations and are almost fifty times faster. The data-inspired CGMD model presented here broadens the applicability of molecular dynamics simulations to cross-linked polymers and has the potential to provide insights that will aid the design of polymers with desirable mechanical properties., (© 2024 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Stimulated Raman Adiabatic Passage (STIRAP) and its variants, such as M-type chainwise-STIRAP, allow for efficiently transferring the populations in a multilevel system and have widely been used to prepare molecules in their rovibrational ground state. However, their transfer efficiencies are generally imperfect. The main obstacle is the presence of losses and the requirement to make the dynamics adiabatic. To this end, in the present paper, a new theoretical method is proposed for the efficient and robust creation and detection of deeply bound molecules in three-level Λ-type and five-level M-type systems via "Invariant-based shortcut-to-adiabaticity." In the regime of large detunings, we first reduce the dynamics of three- and five-level molecular systems to those of effective two- and three-level counterparts. By doing so, the major molecular losses from the excited states can be well suppressed. Consequently, the effective two-level counterpart can be directly compatible with two different "Invariant-based Inverse Engineering" protocols; the results show that both protocols give a comparable performance and have a good experimental feasibility. For the effective three-level counterpart, by considering a relation among the four incident pulses, we show that this model can be further generalized to an effective Λ-type one with the simplest resonant coupling. This generalized model permits us to borrow the "Invariant-based Inverse Engineering" protocol from a standard three-level Λ-type system to a five-level M-type system. Numerical calculations show that the weakly bound molecules can be efficiently transferred to their deeply bound states without strong laser pulses, and the stability against parameter variations is well preserved. Finally, the detection of ultracold deeply bound molecules is discussed., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

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., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

A major limitation of amine-based post-combustion carbon capture technology is the necessity to regenerate amines at high temperatures, which dramatically increases operating costs. This paper concludes the effect of solvent choice as a possible route to modify the thermodynamics and kinetics characterizing the involved amine regeneration reactions and discusses whether these modifications can be economically beneficial. We report experimentally benchmarked computational chemistry calculations of monoethanolamine regeneration reactions employing aqueous and non-aqueous solvents with a wide range of dielectric constants. Unlike previous studies, our improved computational chemistry framework could accurately reproduce the right experimental activation energy of zwitterion formation. From the thermodynamics and kinetics of the predicted reactions, the use of non-aqueous solvents with small dielectric constants led to reductions in regeneration Gibbs free energies, activation barriers, and enthalpy changes. This can reduce energy consumption and give an opportunity to run desorption columns at relatively lower temperatures, thus offering the possibility of relying on low-grade waste heat as an energy input., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

Recent experiments by Brückner et al. [Science 380, 1357 (2023)] have observed an anomalous chain length dependence of the time of near approach of widely separated pairs of genomic elements on transcriptionally active chromosomal DNA. In this paper, I suggest that the anomaly may have its roots in internal friction between neighboring segments on the DNA backbone. The basis for this proposal is a model of chain dynamics formulated in terms of a continuum scaled Brownian walk (sBw) of polymerization index N. The sBw is an extension of the simple Brownian walk model widely used in path integral calculations of polymer properties, differing from it in containing an additional parameter H (the Hurst index) that can be tuned to produce varying degrees of correlation between adjacent monomers. A calculation using the sBw of the mean time τc for chain closure predicts-under the Wilemski-Fixman approximation for diffusion-controlled reactions-that at early times, τc varies as the 2/3 power of N, in close agreement with the findings of the Brückner et al. study. Other scaling relations of that study, including those related to the probability of loop formation and the mean square displacements of terminal monomers, are also satisfactorily accounted for by the model., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In a recent paper, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] presented a novel double hybrid density functional, "DH23," whose terms are based on good physics. Its 12 coefficients were trained on the GMTKN55 (general main-group thermochemistry, kinetics, and noncovalent interactions) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. The lowest GMTKN55 "WTMAD2" error to date for any hybrid or double hybrid density functional was obtained (1.76 kcal/mol). Here, we make some revisions to DH23 and test its efficacy on reference data beyond GMTKN55, namely, organometallic reaction energies and barrier heights. The results confirm that DH23 is robust outside its training set. In the process, a slightly smaller GMTKN55 WTMAD2 of 1.73 kcal/mol is achieved., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Modeling excited state processes in molecular crystals is relevant for several applications. A popular approach for studying excited state molecular crystals is to use cluster models embedded in point charges. In this paper, we compare the performance of several embedding models in predicting excited states and S1-S0 optical gaps for a set of crystals from the X23 molecular crystal database. The performance of atomic charges based on ground or excited states was examined for cluster models, Ewald embedding, and self-consistent approaches. We investigated the impact of various factors, such as the level of theory, basis sets, embedding models, and the level of localization of the excitation. We consider different levels of theory, including time-dependent density functional theory and Tamm-Dancoff approximation (TDA) (DFT functionals: ωB97X-D and PBE0), CC2, complete active space self-consistent field, and CASPT2. We also explore the impact of selection of the QM region, charge leakage, and level of theory for the description of different kinds of excited states. We implemented three schemes based on distance thresholds to overcome overpolarization and charge leakage in molecular crystals. Our findings are compared against experimental data, G0W0-BSE, periodic TDA, and optimally tuned screened range-separated functionals., (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

In this paper, we demonstrate that the weak temperature dependence of the structure factor of supercooled liquids, a defining feature of the glass transition, is a consequence of the averaging of the scattering intensity due to angular averaging. We show that the speckle at individual wavevectors, calculated from a simulated glass former, exhibits a Debye-Waller factor with a sufficiently large temperature dependence to represent a structural order parameter capable of distinguishing liquid from glass. We also extract from the speckle intensities a quantity proportional to the variance of the local restraint, i.e., a direct experimental measure of the amplitude of structural heterogeneity., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

As an optimal one-dimensional reaction coordinate, the committor function not only describes the probability of a trajectory initiated at a phase space point first reaching the product state before reaching the reactant state but also preserves the kinetics when utilized to run a reduced dynamics model. However, calculating the committor function in high-dimensional systems poses significant challenges. In this paper, within the framework of milestoning, exact expressions for committor functions at two levels of coarse graining are given, including committor functions of phase space point to point (CFPP) and milestone to milestone (CFMM). When combined with transition kernels obtained from trajectory analysis, these expressions can be utilized to accurately and efficiently compute the committor functions. Furthermore, based on the calculated committor functions, an adaptive algorithm is developed to gradually refine the transition state region. Finally, two model examples are employed to assess the accuracy of these different formulations of committor functions., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

In this paper, a global and full-dimensional potential energy surface at the 2A″ ground state for the Al + O2 → AlO + O reaction was constructed, for the first time, based on extensive electronic structure calculations using the doubly hybrid functional XYG3 and potential energy surface fittings by neural networks. Details of the reaction paths have been analyzed. It was found that both two intermediates, the cyclic-AlO2 and the linear-OAlO, were able to dissociate to the AlO + O products, and the isomerization process between these two intermediates was controlled by conical intersections between two 2A″ states. Ro-vibrational state resolved integral cross sections have also been calculated at collision energies from 1.0 to 10.0 kcal/mol. The results support the harpooning mechanism in this metal-oxidant-involved reaction., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Instanton-based rate theory is a powerful tool that is used to explore tunneling in many-dimensional systems. Yet, it diverges at the so-called "crossover temperature." Using the uniform semiclassical transmission probability of Kemble [Phys. Rev. 48, 549 (1935)], we showed recently that in one dimension, one might derive a uniform semiclassical instanton rate theory, which has no divergence. In this paper, we generalize this uniform theory to many-dimensional systems. The resulting theory uses the same input as in the previous instanton theory, yet does not suffer from the divergence. The application of the uniform theory to dissipative systems is considered and used to revise Wolynes' well-known analytical expression for the rate [P. G. Wolynes, Phys. Rev. Lett. 47, 968 (1981)] so that it does not diverge at the "crossover temperature.", (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

Polymer models describing the statistics of biomolecules under confinement have applications to a wide range of single-molecule experimental techniques and give insight into biologically relevant processes in vivo. In this paper, we determine the transverse position and bending correlation functions for a wormlike chain confined within slits and cylinders (with one and two confined dimensions, respectively) using a mean-field approach that enforces rigid constraints on average. We show the theoretical predictions accurately capture the statistics of a wormlike chain from Monte Carlo simulations in both confining geometries for both weak and strong confinement. We also show that the longitudinal correlation function is accurately computed for a chain confined to a slit and leverages the accuracy of the model to suggest an experimental technique to infer the (often unobservable) transverse statistics from the (directly observable) longitudinal end-to-end distance., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

TurboGenius is an open-source Python package designed to fully control ab initio quantum Monte Carlo (QMC) jobs using a Python script, which allows one to perform high-throughput calculations combined with TurboRVB [Nakano et al. J. Phys. Chem. 152, 204121 (2020)]. This paper provides an overview of the TurboGenius package and showcases several results obtained in a high-throughput mode. For the purpose of performing high-throughput calculations with TurboGenius, we implemented another open-source Python package, TurboWorkflows, that enables one to construct simple workflows using TurboGenius. We demonstrate its effectiveness by performing (1) validations of density functional theory (DFT) and QMC drivers as implemented in the TurboRVB package and (2) benchmarks of Diffusion Monte Carlo (DMC) calculations for several datasets. For (1), we checked inter-package consistencies between TurboRVB and other established quantum chemistry packages. By doing so, we confirmed that DFT energies obtained by PySCF are consistent with those obtained by TurboRVB within the local density approximation (LDA) and that Hartree-Fock (HF) energies obtained by PySCF and Quantum Package are consistent with variational Monte Carlo energies obtained by TurboRVB with the HF wavefunctions. These validation tests constitute a further reliability check of the TurboRVB package. For (2), we benchmarked the atomization energies of the Gaussian-2 set, the binding energies of the S22, A24, and SCAI sets, and the equilibrium lattice parameters of 12 cubic crystals using DMC calculations. We found that, for all compounds analyzed here, the DMC calculations with the LDA nodal surface give satisfactory results, i.e., consistent either with high-level computational or with experimental reference values., (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)