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

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

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

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

In this paper, we improve the collocation method for computing vibrational spectra that was presented in the work of Avila and Carrington, Jr. [J. Chem. Phys. 143, 214108 (2015)]. Known quadrature and collocation methods using a Smolyak grid require storing intermediate vectors with more elements than points on the Smolyak grid. This is due to the fact that grid labels are constrained among themselves and basis labels are constrained among themselves. We show that by using the so-called hierarchical basis functions, one can significantly reduce the memory required. In this paper, the intermediate vectors have only as many elements as the Smolyak grid. The ideas are tested by computing energy levels of CH2NH. [ABSTRACT FROM AUTHOR]

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat1/3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve. [ABSTRACT FROM AUTHOR]

In this paper, we perform the exact diagonalization of a light–matter strongly coupled system taking into account arbitrary losses via both energy dissipation in the optically active material and photon escape out of the resonator. This allows us to naturally treat the cases of couplings with structured reservoirs, which can strongly impact the polaritonic response via frequency-dependent losses or discrete-to-continuum strong coupling. We discuss the emergent gauge freedom of the resulting theory and provide analytical expressions for all the gauge-invariant observables in both the Power–Zienau–Woolley and the Coulomb representations. In order to exemplify the results, the theory is finally specialized to two specific cases. In the first one, both light and matter resonances are characterized by Lorentzian linewidths, and in the second one, a fixed absorption band is also present. The analytical expressions derived in this paper can be used to predict, fit, and interpret results from polaritonic experiments with arbitrary values of the light–matter coupling and with losses of arbitrary intensity and spectral shape in both the light and matter channels. A Matlab code implementing our results is provided. [ABSTRACT FROM AUTHOR]

Transient absorption (TA) and time-resolved photoluminescence (PL) spectroscopies have been used to elucidate the hole tunneling and Auger dynamics in biexcitons and negative trions in high-quality InP/ZnSe/ZnS quantum dots (QDs). In a previous paper [Nguyen et al., J. Phys. Chem. C 125, 15405–15414 (2021)], we showed that under high-intensity photoexcitation, two types of biexcitons are formed: those having two conduction band electrons and two valence band holes (designated as an XX state) and those having two conduction band electrons, one valence band hole, and an additional trapped hole (designated as an XT state). In the present paper, we show that both types of biexcitons can undergo Auger processes, with those of the XT state being a factor of four to five slower than those of the XX state. In addition, the trapped holes can undergo tunneling into the valence band, converting an XT state to an XX state. The relative amplitudes of the fast (XX) and slow (XT) components are different in the TA and PL kinetics, and these differences can be quantitatively understood in terms of oscillator strengths and electron–hole overlap integrals of each state. XT to XX hole tunneling rates are obtained from the comparison of the XT state lifetimes with those of the negative trions. This comparison shows that the tunneling times decrease with decreasing core size and shell thickness. These times are about 2 ns for the thinnest shell red-emitting QDs and decrease to 330 ps for QDs that luminesce in the yellow. [ABSTRACT FROM AUTHOR]

This paper reports the energies and charge and spin distributions of both the vertically excited and fully relaxed GR1 states of the neutral singlet vacancy in diamond obtained from direct Δ-SCF calculations used previously to describe the low-lying excited states in AFII NiO and α-Al2O3. The calculations are based on the B3LYP functional in its standard form, with a C basis set that is identical to that which was used previously in numerous calculations of the ground state properties of defective diamond. Both the vertically excited and thermally relaxed GR1 states are predicted to be excitonic and insulating, with extensive re-distribution of charge and spin density and back-donation to the donor site. The present calculations suggest that the triplet state makes no contribution to the GR1 excitation. The predicted energy of the zero phonon line (1.57 eV) compares with the observed value of 1.67 eV, which also suggests that the GR1 state is neutral. The bandgaps lead to an estimate of the next higher (GR2) excited state energy, which is close to that found in the observed spectra. Similar calculations are used to predict the energies of the higher gap states at (5.0–5.5) eV, including the bulk value of 7.3 eV, which compares with the experimental value of (7.3–7.4) eV. An explanation is suggested as to why only the GR1 luminescence is observed. This paper also suggests an alternative channel for the recovery of the ground state in photoluminescence studies. [ABSTRACT FROM AUTHOR]

It is well-known experimentally that the positively charged muon and the muonium atom may bind to molecules and solids, and through muon's magnetic interaction with unpaired electrons, valuable information on the local environment surrounding the muon is deduced. Theoretical understanding of the structure and properties of resulting muonic species requires accurate and efficient quantum mechanical computational methodologies. In this paper, the two-component density functional theory (TC-DFT), as a first principles method, which treats electrons and the positive muon on an equal footing as quantum particles, is introduced and implemented computationally. The main ingredient of this theory, apart from the electronic exchange–correlation functional, is the electron–positive muon correlation functional that is foreign to the purely electronic DFT. A Wigner-type local electron–positive muon correlation functional, termed eμc-1, is proposed in this paper and its capability is demonstrated through its computational application to a benchmark set of muonic organic molecules. The TC-DFT equations containing eμc-1 are not only capable of predicting the muon's binding site correctly, but they also reproduce muon's zero-point vibrational energies and the muonic densities much more accurately than the TC-DFT equations lacking eμc-1. Thus, this study sets the stage for developing accurate electron–positive muon functionals, which can be used within the context of the TC-DFT to elucidate the intricate interaction of the positive muon with complex molecular systems. [ABSTRACT FROM AUTHOR]

We obtain the phase diagram of the hard core lattice gas with third nearest neighbor exclusion on the triangular lattice using Monte Carlo simulations that are based on a rejection-free flat histogram algorithm. In a recent paper [Darjani et al., J. Chem. Phys. 151, 104702 (2019)], it was claimed that the lattice gas with third nearest neighbor exclusion undergoes two phase transitions with increasing density with the phase at intermediate densities exhibiting hexatic order with continuously varying exponents. Although a hexatic phase is expected when the exclusion range is large, it has not been seen earlier in hard core lattice gases with short range exclusion. In this paper, by numerically determining the entropies for all densities, we show that there is only a single phase transition in the system between a low-density fluid phase and a high density ordered sublattice phase and that a hexatic phase is absent. The transition is shown to be first order in nature, and the critical parameters are determined accurately. [ABSTRACT FROM AUTHOR]

In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)]. [ABSTRACT FROM AUTHOR]

In this paper, we study the permeation of polyatomic gas molecules through 2D graphene membranes. Using equilibrium molecular dynamics simulations, we investigate the permeation of pure gas compounds (CH4, CO2, O2, N2, and H2) through nanoporous graphene membranes with varying pore sizes and geometries. Our simulations consider the recrossing mechanism, often neglected in previous studies, which has a significant effect on permeation for intermediate pore size to molecular diameter ratios. We find that the permeation process can be decoupled into two steps: the crossing process of gas molecules through the pore plane and the escaping process from the pore region to a neighboring adsorption site, which prevents recrossing. To account for these mechanisms, we use a permeance model expressed as the product of the permeance for the crossing process and the probability of molecule escape. This phenomenological model is extended to account for small polyatomic gas molecules and to describe permeation regimes ranging from molecular sieving to effusion. The proposed model captures the temperature dependence and provides insights into the key parameters of the gas/membrane interaction controlling the permeance of the system. This work lays the foundation for predicting gas permeance and exploring membrane separation factors in 2D materials such as graphene. [ABSTRACT FROM AUTHOR]

Nowadays, academic research relies not only on sharing with the academic community the scientific results obtained by research groups while studying certain phenomena but also on sharing computer codes developed within the community. In the field of atomistic modeling, these were software packages for classical atomistic modeling, and later for quantum-mechanical modeling; currently, with the fast growth of the field of machine-learning potentials, the packages implement such potentials. In this paper, we present the MLIP-3 package for constructing moment tensor potentials and performing their active training. This package builds on the MLIP-2 package [Novikov et al., "The MLIP package: moment tensor potentials with MPI and active learning," Mach. Learn.: Sci. Technol., 2(2), 025002 (2020)], however, with a number of improvements, including active learning on atomic neighborhoods of a possibly large atomistic simulation. [ABSTRACT FROM AUTHOR]

This paper presents the molecular dynamics simulation of 1 mol kg−1 LiPF6 in a binary solvent of ethylene carbonate (EC) and dimethylcarbonate, which is a representative electrolyte solution for lithium-ion batteries. The simulation successfully reproduced the diffusion coefficient, ionic conductivity, and shear viscosity as functions of EC content at 300 K, which had been experimentally determined in our previous study. The Yukawa potential was adopted to model intercharge interactions to reduce computational costs, which consequently allowed us to precisely calculate the conductivity and viscosity by directly integrating time-correlation functions without explicitly modeling the molecular polarization. Breaking down microscopic current correlation functions into components revealed that, whereas the cation–anion attractive interaction dominantly impedes the conduction when the EC content is low, it is the cation–cation and anion–anion repulsive interactions that reduce the conductivity at a high EC content. An analysis of the pressure correlations revealed that all components positively contribute to the viscosity in the binary solvent without the electrolyte. On the other hand, negative terms are observed in five out of six cross correlations in the presence of the electrolyte, implying that these correlations negatively contribute to the shear stress and entropy production, both of which are net positive. [ABSTRACT FROM AUTHOR]

Electron transport through a variety of helical structures has been shown to exhibit high-efficiency spin filtering, which is called chirality-induced spin selectivity (CISS). In this paper, we consider a helical chain of atomic p orbitals, which has been employed as a model in exploring the mechanism of CISS in previous theories, and show that the interatomic hopping along the helical chain induces an effective magnetic field (EMF) acting on the atomic orbital angular momentum (OAM). In chains where the curvature and torsion of the helix are small, we find that the EMF on the binormal component of the atomic OAM is created by the curvature, while that on the tangential component is produced by the torsion. We show that such coupling of the atomic OAM and the interatomic hopping leads to current-induced orbital and spin polarizations. We expect that the present coupling, which is expressed locally, can be used to estimate orbital and spin polarizations locally induced in molecules and solids. [ABSTRACT FROM AUTHOR]

This paper presents a comprehensive study of the theory of entangled two-photon emission/absorption (E2P-EA) between a many-level cascade donor and a many-level acceptor (which could be quantum dots or molecules) using second-order perturbation theory and where the donor–acceptor pair is in a homogeneous but dispersive medium. To understand the mechanism of E2P-EA, we analyze how dipole orientation, radiative lifetime, energy detuning between intermediate states, separation distance, and entanglement time impact the E2P-EA rate. Our study shows that there are quantum interference effects in the E2P-EA rate expression that lead to oscillations in the rate as a function of entanglement time. Furthermore, we find that the E2P-EA rate for a representative system consisting of two quantum dots can be comparable to one-photon emission/absorption (OP-EA) when donor and acceptor are within a few nm. However, the E2P-EA rate falls off much more quickly with separation distance than does OP-EA. [ABSTRACT FROM AUTHOR]

Many state-of-the art machine learning (ML) interatomic potentials are based on a local or semi-local (message-passing) representation of chemical environments. They, therefore, lack a description of long-range electrostatic interactions and non-local charge transfer. In this context, there has been much interest in developing ML-based charge equilibration models, which allow the rigorous calculation of long-range electrostatic interactions and the energetic response of molecules and materials to external fields. The recently reported kQEq method achieves this by predicting local atomic electronegativities using Kernel ML. This paper describes the q-pac Python package, which implements several algorithmic and methodological advances to kQEq and provides an extendable framework for the development of ML charge equilibration models. [ABSTRACT FROM AUTHOR]

As biomolecules vibrate and rotate in the terahertz band, the biological effects of terahertz electromagnetic fields have drawn considerable attention from the physiological and medical communities. Ion channels are the basis of biological electrical signals, so studying the effect of terahertz electromagnetic fields on ion channels is significant. In this paper, the effect of a terahertz electromagnetic field with three different frequencies, 6, 15, and 25 THz, on the Kv1.2 potassium ion channel was investigated by molecular dynamics simulations. The results show that an electromagnetic field with a 15 THz frequency can significantly enhance the permeability of the Kv1.2 potassium ion channel, which is 1.7 times higher than without an applied electric field. By analyzing the behavior of water molecules, it is found that the electromagnetic field with the 15 THz frequency shortens the duration of frozen and relaxation processes when potassium ions pass through the channel, increases the proportion of the direct knock-on mode, and, thus, enhances the permeability of the Kv1.2 potassium ion channel. [ABSTRACT FROM AUTHOR]

The collective coupling of an ensemble of molecules to a light field is commonly described by the Tavis–Cummings model. This model includes numerous eigenstates that are optically decoupled from the optically bright polariton states. Accessing these dark states requires breaking the symmetry in the corresponding Hamiltonian. In this paper, we investigate the influence of non-unitary processes on the dark state dynamics in the molecular Tavis–Cummings model. The system is modeled with a Lindblad equation that includes pure dephasing, as it would be caused by weak interactions with an environment, and photon decay. Our simulations show that the rate of pure dephasing, as well as the number of two-level systems, has a significant influence on the dark state population. [ABSTRACT FROM AUTHOR]

The MACE architecture represents the state of the art in the field of machine learning force fields for a variety of in-domain, extrapolation, and low-data regime tasks. In this paper, we further evaluate MACE by fitting models for published benchmark datasets. We show that MACE generally outperforms alternatives for a wide range of systems, from amorphous carbon, universal materials modeling, and general small molecule organic chemistry to large molecules and liquid water. We demonstrate the capabilities of the model on tasks ranging from constrained geometry optimization to molecular dynamics simulations and find excellent performance across all tested domains. We show that MACE is very data efficient and can reproduce experimental molecular vibrational spectra when trained on as few as 50 randomly selected reference configurations. We further demonstrate that the strictly local atom-centered model is sufficient for such tasks even in the case of large molecules and weakly interacting molecular assemblies. [ABSTRACT FROM AUTHOR]

Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree–Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency. [ABSTRACT FROM AUTHOR]

Inferring transient molecular structural dynamics from diffraction data is an ambiguous task that often requires different approximation methods. In this paper, we present an attempt to tackle this problem using machine learning. Although most recent applications of machine learning for the analysis of diffraction images apply only a single neural network to an experimental dataset and train it on the task of prediction, our approach utilizes an additional generator network trained on both synthetic and experimental data. Our network converts experimental data into idealized diffraction patterns from which information is extracted via a convolutional neural network trained on synthetic data only. We validate this approach on ultrafast electron diffraction data of bismuth samples undergoing thermalization upon excitation via 800 nm laser pulses. The network was able to predict transient temperatures with a deviation of less than 6% from analytically estimated values. Notably, this performance was achieved on a dataset of 408 images only. We believe that employing this network in experimental settings where high volumes of visual data are collected, such as beam lines, could provide insights into the structural dynamics of different samples. [ABSTRACT FROM AUTHOR]

Salt solubility is generally determined under isotropic stress conditions. Yet, in the context of salt weathering of porous media, mechanical constraints on the in-pore growth of salt crystals are likely to be orientation-dependent, resulting in an anisotropic stress state on the crystal. In this paper, we determine by molecular simulation the solubility of NaCl in water when the crystal is subjected to anisotropic stress. Such anisotropy causes the chemical potential of the crystal to be orientation-dependent, and proper thermodynamic formulation requires describing the chemical potential as a tensor. The solute and crystal chemical potentials are computed from free energy calculations using Hamiltonian thermodynamic integration, and the usual condition of solubility is reformulated to account for the tensorial nature of the crystal chemical potential. We investigate in detail how the uniaxial compression of the crystal affects its solubility. The molecular simulation results led to revisiting the Correns law under anisotropic stress. Regarding the solute, the non-ideal behavior of the liquid phase is captured using Pitzer's ion interaction approach up to high concentrations of interest for in-pore crystallization and beyond the concentrations addressed in the existing literature. Regarding NaCl crystals, the validity of the generalized Gibbs–Duhem equation for a tensorial chemical potential is carefully verified, and it is found that crystallization progresses almost orthogonally to the crystal surface even under high shear stresses. Comparing uniaxial and isotropic compression highlights the major differences in solubility caused by stress anisotropy, and the revisited Correns law offers an appropriate framework to capture this phenomenon. [ABSTRACT FROM AUTHOR]

The present paper reformulates and improves a previously proposed determinant-based second-order multi-reference perturbative formalism. Through a rather simple modification of the energy denominators, this formalism takes into account the interactions between the model space determinants, which are repeated in outer space. The method has been shown to be size-consistent when the model space is a complete active space, which is a severe limit. It is shown here that the completeness of the model space is not necessary to keep this property, provided that the zero-order function satisfies some conditions. For instance, size consistency may be obtained from truncated complete active spaces. It may even be satisfied from Singles and Doubles Configuration Interactions, provided that a coupled electron pair approximation is used in the definition of the model space wave function. The physical content of the method is illustrated by a series of model problems, showing its robustness. A major benefit of the fact that the perturbers are single determinants is the possibility to revise with full flexibility the model-space component of the wave function, i.e., to treat the feedback effect of the dynamic correlation on the valence component of the wave function. [ABSTRACT FROM AUTHOR]

Tensor algebra operations such as contractions in computational chemistry consume a significant fraction of the computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. TAMM decouples the specification of the computation from the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM, whereas high-performance computing developers can direct their attention to various optimizations on the underlying constructs, such as efficient data distribution, optimized scheduling algorithms, and efficient use of intra-node resources (e.g., graphics processing units). The modular structure of TAMM allows it to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to the sustainable development of scalable ground- and excited-state electronic structure methods. We present case studies highlighting the ease of use, including the performance and productivity gains compared to other frameworks. [ABSTRACT FROM AUTHOR]

In this paper, we present a continuation of our research on modeling electrolyte solutions within charged pores. We make use of the model developed by Blossey et al. [Phys. Rev. E 95, 060602 (2017)], which takes into account the structural interactions between ions through a bilinear form over the gradients of local ionic concentrations in the grand thermodynamic potential, as well as their steric interactions through the lattice gas model. The structural interactions may describe the effects of the molecular structure of ions at a phenomenological level. For example, these effects include steric effects due to non-spherical shapes of ions, their conformational lability, and solvent effects. In addition, we explore their specific interactions with the pore walls by incorporating external attractive potentials. Our primary focus is on observing the behavior of ionic concentration profiles and the disjoining pressure as the pore width changes. By starting with the local mechanical equilibrium condition, we derive a general expression for the disjoining pressure. Our findings indicate that considering the structural interactions of ions leads to a pronounced minimum on the disjoining pressure profiles at small pore widths. We attribute this minimum to the formation of electric double layers on the electrified surfaces of the pore. In addition, our results demonstrate that the inclusion of the attractive interactions of ions with the pore walls enhances this minimum and shifts it to smaller pore thicknesses. Our theoretical discoveries may be useful for those involved in supercapacitor electrochemical engineering, particularly when working with porous electrodes that have been infused with concentrated electrolyte solutions. [ABSTRACT FROM AUTHOR]

In this paper, we present an extended dissipaton equation of motion for studying the dynamics of electronic impurity systems. Compared with the original theoretical formalism, the quadratic couplings are introduced into the Hamiltonian accounting for the interaction between the impurity and its surrounding environment. By exploiting the quadratic fermionic dissipaton algebra, the proposed extended dissipaton equation of motion offers a powerful tool for studying the dynamical behaviors of electronic impurity systems, particularly in situations where nonequilibrium and strongly correlated effects play significant roles. Numerical demonstrations are carried out to investigate the temperature dependence of the Kondo resonance in the Kondo impurity model. [ABSTRACT FROM AUTHOR]

The dual exponential coupled cluster theory proposed by Tribedi et al.[J. Chem. Theory Comput. 16, 10, 6317–6328 (2020)] performs significantly better for a wide range of weakly correlated systems than the coupled cluster theory with singles and doubles excitations due to the implicit inclusion of high-rank excitations. The high-rank excitations are included through the action of a set of vacuum annihilating scattering operators that act non-trivially on certain correlated wavefunctions and are determined via a set of local denominators involving the energy difference between certain excited states. This often leads the theory to be prone to instabilities. In this paper, we show that restricting the correlated wavefunction, on which the scattering operators act, to be spanned by only the singlet-paired determinants can avoid catastrophic breakdown. For the first time, we present two nonequivalent approaches to arrive at the working equations, viz., the projective approach with sufficiency conditions and the amplitude form with many-body expansion. Although the effect of the triple excitation is quite small around molecular equilibrium geometry, this scheme leads to a better qualitative description of the energetics in the regions of strong correlation. With many pilot numerical applications, we have demonstrated the performance of the dual-exponential scheme with both the proposed solution strategies while restricting the excitation subspaces coupled to the corresponding lowest spin channels. [ABSTRACT FROM AUTHOR]

We investigate, in this paper, the Gaussian (G) function with odd powers of r, rxaybzc exp(−αr2), called the r-Gaussian or simply the rG function. The reason we investigate this function here is that it is generated as the elements of the complement functions (cf's) when we apply the free complement (FC) theory for solving the Schrödinger equation to the initial functions composed of the Gaussian functions. This means that without the rG functions, the Gaussian set of functions cannot produce the exact solutions of the Schrödinger equation, showing the absolute importance of the rG functions in quantum chemistry. Actually, the rG functions drastically improve the wave function near the cusp region. This was shown by the applications of the present theory to the hydrogen and helium atoms. When we use the FC-sij theory, in which the inter-electron function rij is replaced with its square s i j = r i j 2 that is integrable, we need only one- and two-electron integrals for the G and rG functions. The one-center one- and two-electron integrals of the rG functions are always available in a closed form. To calculate the integrals of the multi-centered rG functions, we proposed the rG-NG expansion method, in which an rG function is expanded by a linear combination of the G functions. The optimal exponents and coefficients of this expansion were given for N = 2, 3, 4, 5, 6, and 9. To show the accuracy and the usefulness of the rG-NG method, we applied the FC-sij theory to the hydrogen molecule. [ABSTRACT FROM AUTHOR]

The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these applications because dramatic differences in molecular diffusion can result from subtle changes in the network structure. In this paper, we use molecular simulation to understand the role that cross-linked network polymers have in governing the molecular motion of penetrants. By considering the local, activated alpha relaxation time of the penetrant and its long-time diffusive dynamics, we can determine the relative importance of activated glassy dynamics on penetrants at the segmental scale vs entropic mesh confinement on penetrant diffusion. We vary several parameters, such as the cross-linking density, temperature, and penetrant size, to show that cross-links primarily affect molecular diffusion through the modification of the matrix glass transition, with local penetrant hopping at least partially coupled to the segmental relaxation of the polymer network. This coupling is very sensitive to the local activated segmental dynamics of the surrounding matrix, and we also show that penetrant transport is affected by dynamic heterogeneity at low temperatures. To contrast, only at high temperatures and for large penetrants or when the dynamic heterogeneity effect is weak, does the effect of mesh confinement become significant, even though penetrant diffusion more broadly empirically follows similar trends as established models of mesh confinement-based transport. [ABSTRACT FROM AUTHOR]

In this paper, a broadband metamaterial absorber consisting of the doped silicon substrate and the square array of doped silicon covered by a SU-8 layer is presented. The target structure achieves an average absorption of 94.42% in the studied frequency range (0.5–8 THz). In particular, the structure exceeds 90% absorption in the frequency range of 1.44–8 THz, which is a significant increase in bandwidth relative to reported devices of the same type. Next, the near-perfect absorption of the target structure is verified by the impedance matching principle. Furthermore, through the analysis of the electric field distribution inside the structure, the physical mechanism of its broadband absorption is investigated and explained. Finally, the impact of fluctuations in the incident angle, polarization angle, and structural parameters on the absorption efficiency is examined at length. The analysis shows that the structure has characteristics, such as polarization insensitivity, wide-angle absorption, and good process tolerance. The proposed structure is advantageous for applications in THz shielding, cloaking, sensing, and energy harvesting. [ABSTRACT FROM AUTHOR]

Cation exchange is a versatile post-synthetic method to explore a wide range of nanoparticle compositions, phases, and morphologies. Recently, several studies have expanded the scope of cation exchange to magic-size clusters (MSCs). Mechanistic studies indicated that MSC cation exchange undergoes a two-stage reaction pathway instead of the continuous diffusion-controlled mechanism found in nanoparticle cation exchange reactions. The cation exchange intermediate, however, has not been well-identified despite it being the key to understanding the reaction mechanism. Only indirect evidence, such as exciton peak shifts and powder x-ray diffraction, has been used to indicate the formation of the cation exchange intermediate. In this paper, we investigate the unusual nature of cation exchange in nanoclusters using our previously reported CdS MSC. High-resolution mass spectra reveal two cation exchanged reaction intermediates [Ag2Cd32S33(L) and AgCd33S33(L), L: oleic acid] as well as the fully exchanged Ag2S cluster. Crystal and electronic structure characterizations also confirm the two-stage reaction mechanism. Additionally, we investigate the Cu/CdS MSC cation exchange reaction and find a similar two-stage reaction mechanism. Our study shows that the formation of dilutely exchanged intermediate clusters can be generally found in the first stage of the MSC cation exchange reaction. By exchanging different cations, these intermediate clusters can access varying properties compared to their unexchanged counterparts. [ABSTRACT FROM AUTHOR]

A novel chiroptical sensing technique was recently introduced that utilized the helical phase of the structured light as a chiral reagent instead of polarization of light to differentiate enantiopure chiral liquids. The unique advantage of this non-resonant, nonlinear technique is that the chiral signal can be scaled and tuned. In this paper, we extend this technique to enantiopure powders of alanine and camphor by dissolving them in solvents of varying concentrations. We show the differential absorbance of helical light to be an order of magnitude higher relative to conventional resonant linear techniques and is comparable to nonlinear techniques that use circularly polarized light. The origin of helicity dependent absorption is discussed in terms of induced multipole moments in nonlinear light–matter interaction. These results opens up new opportunities in using helical light as a primary chiral reagent in nonlinear spectroscopic techniques. [ABSTRACT FROM AUTHOR]

In this paper, we announce the public release of a massively parallel, graphics processing unit (GPU)-accelerated software, which is the first to combine both coarse-grained particle simulations and field-theoretic simulations in one simulation package. MATILDA.FT (Mesoscale, Accelerated, Theoretically Informed, Langevin, Dissipative particle dynamics, and Field Theory) was designed from the ground-up to run on CUDA-enabled GPUs with Thrust library acceleration, enabling it to harness the possibility of massive parallelism to efficiently simulate systems on a mesoscopic scale. It has been used to model a variety of systems, from polymer solutions and nanoparticle-polymer interfaces to coarse-grained peptide models and liquid crystals. MATILDA.FT is written in CUDA/C++ and is object oriented, making its source-code easy to understand and extend. Here, we present an overview of the currently available features, and the logic of parallel algorithms and methods. We provide the necessary theoretical background and present examples of systems simulated using MATILDA.FT as the simulation engine. The source code, along with the documentation, additional tools, and examples, can be found on the GitHub MATILDA.FT repository. [ABSTRACT FROM AUTHOR]

Inelastic collisions of OH with an inert liquid perfluoropolyether (PFPE) surface have been studied experimentally. A pulsed molecular beam of OH with a kinetic energy distribution peaking at 35 kJ mol−1 was directed at a continually refreshed PFPE surface. OH molecules were detected state-selectively with spatial and temporal resolution by pulsed, planar laser-induced fluorescence. The scattered speed distributions were confirmed to be strongly superthermal, regardless of the incidence angle (0° or 45°). Angular scattering distributions were measured for the first time; their reliability was confirmed through extensive Monte Carlo simulations of experimental averaging effects, described in Paper II [A. G. Knight et al., J. Chem. Phys. 158, 244705 (2023)]. The distributions depend markedly on the incidence angle and are correlated with scattered OH speed, consistent with predominantly impulsive scattering. For 45° incidence, the angular distributions are distinctly asymmetric to the specular side but peak at sub-specular angles. This, along with the breadth of the distributions, is incompatible with scattering from a surface that is flat on a molecular scale. New molecular dynamics simulations corroborate the roughness of the PFPE surface. A subtle but unexpected systematic dependence of the angular distribution on the OH rotational state was found, which may be dynamical in origin. The OH angular distributions are similar to those for kinematically similar Ne scattering from PFPE and hence not strongly perturbed by OH being a linear rotor. The results here are broadly compatible with prior predictions from independent quasiclassical trajectory simulations of OH scattering from a model-fluorinated self-assembled monolayer surface. [ABSTRACT FROM AUTHOR]

The research presented in the paper concerns the elastic properties of struvite. The article combines theoretical and experimental research. Experimental studies were carried out on struvite single crystals grown in sodium metasilicate gel by single diffusion. This unique method leads to obtaining crystals of sufficiently large size to conduct, for the first time, experimental measurement of elastic properties of monocrystalline struvite. Using the nanoindentation method, the Ez = 29.1 ± 0.7 GPa value of the component of Young's modulus was determined for a struvite single crystal. In addition, the elastic constants C11, C22, and C33 were determined using micro-Brillouin spectroscopy. Theoretical calculations of the abovementioned properties have been carried out by employing density functional theory methods. Scaling of the theoretical elastic constants leads to obtaining good agreement with the experimental values. Values of the Ex and Ey components of the Young's modulus, not available from the experimental nanoindentation technique, have been determined theoretically as 23 GPa and 27 GPa, respectively. Differences in the values of elastic components and Young's modulus components are related to the layered crystal structure of struvite and directional character of the hydrogen-bonding pattern. [ABSTRACT FROM AUTHOR]

With increasing demand and environmental concerns, researchers are exploring new materials that can perform as well or better than traditional materials while reducing environmental impact. The BAMline, a real-life sample materials research beamline, provides unique insights into materials' electronic and chemical structure at different time and length scales. The beamline specializes in x-ray absorption spectroscopy, x-ray fluorescence spectroscopy, and tomography experiments. This enables real-time optimization of material properties and performance for various applications, such as energy transfer, energy storage, catalysis, and corrosion resistance. This paper gives an overview of the analytical methods and sample environments of the BAMline, which cover non-destructive testing experiments in materials science, chemistry, biology, medicine, and cultural heritage. We also present our own synthesis methods, processes, and equipment developed specifically for the BAMline, and we give examples of synthesized materials and their potential applications. Finally, this article discusses the future perspectives of the BAMline and its potential for further advances in sustainable materials research. [ABSTRACT FROM AUTHOR]

We present the computational methodology, which for the first time allows rigorous twelve-dimensional (12D) quantum calculations of the coupled intramolecular and intermolecular vibrational states of hydrogen-bonded trimers of flexible diatomic molecules. Its starting point is the approach that we introduced recently for fully coupled 9D quantum calculations of the intermolecular vibrational states of noncovalently bound trimers comprised of diatomics treated as rigid. In this paper, it is extended to include the intramolecular stretching coordinates of the three diatomic monomers. The cornerstone of our 12D methodology is the partitioning of the full vibrational Hamiltonian of the trimer into two reduced-dimension Hamiltonians, one in 9D for the intermolecular degrees of freedom (DOFs) and another in 3D for the intramolecular vibrations of the trimer, and a remainder term. These two Hamiltonians are diagonalized separately, and a fraction of their respective 9D and 3D eigenstates is included in the 12D product contracted basis for both the intra- and intermolecular DOFs, in which the matrix of the full 12D vibrational Hamiltonian of the trimer is diagonalized. This methodology is implemented in the 12D quantum calculations of the coupled intra- and intermolecular vibrational states of the hydrogen-bonded HF trimer on an ab initio calculated potential energy surface (PES). The calculations encompass the one- and two-quanta intramolecular HF-stretch excited vibrational states of the trimer and low-energy intermolecular vibrational states in the intramolecular vibrational manifolds of interest. They reveal several interesting manifestations of significant coupling between the intra- and intermolecular vibrational modes of (HF)3. The 12D calculations also show that the frequencies of the v = 1, 2 HF stretching states of the HF trimer are strongly redshifted in comparison to those of the isolated HF monomer. Moreover, the magnitudes of these trimer redshifts are much larger than that of the redshift for the stretching fundamental of the donor-HF moiety in (HF)2, most likely due to the cooperative hydrogen bonding in (HF)3. The agreement between the 12D results and the limited spectroscopic data for the HF trimer, while satisfactory, leaves room for improvement and points to the need for a more accurate PES. [ABSTRACT FROM AUTHOR]

This paper reports the release of PathSum, a new software suite of state-of-the-art path integral methods for studying the dynamics of single or extended systems coupled to harmonic environments. The package includes two modules, suitable for system–bath problems and extended systems comprising many coupled system–bath units, and is offered in C++ and Fortran implementations. The system–bath module offers the recently developed small matrix path integral (SMatPI) and the well-established iterative quasi-adiabatic propagator path integral (i-QuAPI) method for iteration of the reduced density matrix of the system. In the SMatPI module, the dynamics within the entanglement interval can be computed using QuAPI, the blip sum, time evolving matrix product operators, or the quantum–classical path integral method. These methods have distinct convergence characteristics and their combination allows a user to access a variety of regimes. The extended system module provides the user with two algorithms of the modular path integral method, applicable to quantum spin chains or excitonic molecular aggregates. An overview of the methods and code structure is provided, along with guidance on method selection and representative examples. [ABSTRACT FROM AUTHOR]

With the development of modern industry, the discharge of dye wastewater is increasing year by year, and the damage caused by this wastewater to the ecosystem is often irreversible. Therefore, the research on the harmless treatment of dyes has attracted much attention in recent years. In this paper, commercial titanium dioxide (anatase nanometer titanium dioxide) was heat treated with anhydrous ethanol to synthesize titanium carbide (C/TiO2). Its maximum adsorption capacity for cationic dyes methylene blue (MB) and Rhodamine B is 27.3 and 124.6 mg g−1, respectively, which is much higher than that of pure TiO2. The adsorption kinetics and isotherm model of C/TiO2 were studied and characterized by Brunauer–Emmett–Teller, x-ray photoelectron spectroscopy, x-ray diffraction, Fourier transform infrared spectroscopy, and other methods. The results show that the carbon layer on the surface of C/TiO2 promotes the increase in surface hydroxyl groups, which is the main reason for the increase in MB adsorption. Compared with other adsorbents, C/TiO2 showed excellent reusability. The experimental results of adsorbent regeneration showed that the adsorption rate R% of MB was almost unchanged after three cycles. During the recovery of C/TiO2, the dyes adsorbed on its surface are removed, which solves the problem that the adsorbent cannot degrade dyes simply by adsorption. Additionally, C/TiO2 has a stable adsorption effect, is insensitive to the pH value, has a simple preparation process, and has relatively low raw material prices, making it suitable for large-scale operation. Therefore, it has good commercial prospects in the organic dye industry wastewater treatment. [ABSTRACT FROM AUTHOR]

Some chemical reactions proceed on multiple potential energy surfaces and are often accompanied by a change in spin multiplicity, being called spin-forbidden reactions, where the spin–orbit coupling (SOC) effects play a crucial role. In order to efficiently investigate spin-forbidden reactions with two spin states, Yang et al. [Phys. Chem. Chem. Phys. 20, 4129–4136 (2018)] proposed a two-state spin-mixing (TSSM) model, where the SOC effects between the two spin states are simulated by a geometry-independent constant. Inspired by the TSSM model, we suggest a multiple-state spin-mixing (MSSM) model in this paper for the general case with any number of spin states, and its analytic first and second derivatives have been developed for locating stationary points on the mixed-spin potential energy surface and estimating thermochemical energies. To demonstrate the performance of the MSSM model, some spin-forbidden reactions involving 5d transition elements are calculated using the density functional theory (DFT), and the results are compared with the two-component relativistic ones. It is found that MSSM DFT and two-component DFT calculations may provide very similar stationary-point information on the lowest mixed-spin/spinor energy surface, including structures, vibrational frequencies, and zero-point energies. For the reactions containing saturated 5d elements, the reaction energies by MSSM DFT and two-component DFT agree very well within 3 kcal/mol. As for the two reactions OsO+ + CH4 → OOs(CH2)+ + H2 and W + CH4 → WCH2 + H2 involving unsaturated 5d elements, MSSM DFT may also yield good reaction energies of similar accuracy but with some counterexamples. Nevertheless, the energies may be remarkably improved by a posteriori single point energy calculations using two-component DFT at the MSSM DFT optimized geometries, and the maximum error of about 1 kcal/mol is almost independent of the SOC constant used. The MSSM method as well as the developed computer program provides an effective utility for studying spin-forbidden reactions. [ABSTRACT FROM AUTHOR]

In modern electronics and power systems, good-performance dielectric capacitors have an essential function. Polymer-based dielectrics are widely used in the field of dielectric capacitors because of their large dielectric constant, flexibility, low density, and ease of processing. At present, ferroelectric polymers suffer from low breakdown field strength and high dielectric losses. How to improve the performance of dielectric materials in capacitors is still a promising research. This paper chooses the ferroelectric polymer poly(vinylidene fluoride) (PVDF) that worked as the matrix, and the linear polymers polyimide, cyanoethyl pullulan (CR-S), polyethersulfone, and cyanoethylated cellulose served as fillers. This all-organic dielectric composite produced as films working in electrostatic energy storage devices is prepared by using a casting method. Analyzing the test results, the composite film exhibited excellent electrical properties when the CR-S doping content was 5 wt. %. The organic composite dielectric based on CR-S/PVDF has a breakdown field strength of 450 MV/m, a discharge energy storage density (Ue) of 10.3 J/cm3, a high dielectric constant of 10.9, and a low dielectric loss of 0.004 at 1 kHz, which is a significant improvement compared with other dielectric composites. This all-organic dielectric composite strategy offers a new approach to achieve better-performance dielectric energy storage materials. [ABSTRACT FROM AUTHOR]

Observations of a high spin selectivity in various helical structures, which is called the chirality-induced spin selectivity, suggest a common mechanism originating from the helical geometry. In this paper, we consider a helical chain of atomic p± orbitals having the tangential angular momentum l = ±1. We show in this model that the coupling of l and the spin gives rise to spin-velocity locking, i.e., directions of spin and group velocity are parallel or antiparallel depending on the chirality of the helix, and consequently, an almost perfect spin selectivity in a specific energy region in a wide range of the curvature and the torsion of the helix. We find that the present spin-velocity locking originates from the helical symmetry in which the Hamiltonian is invariant with respect to a combined operation of the rotation around the helix axis and the translation along the helix axis. Therefore, we expect that spin-velocity locking occurs in a wide variety of helical structures. [ABSTRACT FROM AUTHOR]

Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. Despite their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to the overall motion of the particles they bind to. This limits numerical and theoretical approaches that need to resolve these diverse timescales with high accuracy. Many models, therefore, resort to effective, yet ad hoc, dynamics, where linker motion is only accounted for when bound. This paper provides a mathematical justification for such coarse-grained dynamics that preserves detailed balance at equilibrium. Our derivation is based on multiscale averaging techniques and is broadly applicable. We verify our results with simulations on a minimal model of fast linker binding to a slow particle. We show how our framework can be applied to various systems, including those with multiple linkers, stiffening linkers upon binding, or slip bonds with force-dependent unbinding. Importantly, the preservation of detailed balance only sets the ratio of the binding to the unbinding rates, but it does not constrain the detailed expression of binding kinetics. We conclude by discussing how various choices of binding kinetics may affect macroscopic dynamics. [ABSTRACT FROM AUTHOR]

In this paper, we use the previously introduced Canonical Polyadic (CP)-Multiple Shift Block Inverse Iteration (MSBII) eigensolver [S. D. Kallullathil and T. Carrington, J. Chem. Phys. 155, 234105 (2021)] in conjunction with a contraction tree to compute vibrational spectra. The CP-MSBII eigensolver uses the CP format. The memory cost scales linearly with the number of coordinates. A tensor in CP format represents a wavefunction constrained to be a sum of products (SOP). An SOP wavefunction can be made more accurate by increasing the number of terms, the rank. When the required rank is large, the runtime of a calculation in CP format is long, although the memory cost is small. To make the method more efficient, we break the full problem into pieces using a contraction tree. The required rank for each of the sub-problems is small. To demonstrate the effectiveness of the ideas, we computed vibrational energy levels of acetonitrile (12-D) and ethylene oxide (15-D). [ABSTRACT FROM AUTHOR]

In Paper I [J. R. Elliott, A. J. Schultz, and D. A. Kofke, J. Chem. Phys. 143, 114110 (2015)] of this series, a methodology was presented for computing the coefficients of a power series of the Helmholtz energy in reciprocal temperature, β, through density series based on cluster integral expansions. Previously, power series in β were evaluated by thermodynamic perturbation theory (TPT) using molecular simulation of a reference fluid. The present methodology uses cluster integrals to evaluate coefficients of the density expansion at each individual order of temperature. While Paper I [J. R. Elliott, A. J. Schultz, and D. A. Kofke, J. Chem. Phys. 143, 114110 (2015)] developed this methodology for square well (SW) spheres, the present work extends the methodology to Lennard-Jones (LJ) spheres, where the reference fluid is the Weeks-Chandler-Andersen potential. Comparisons of TPT coefficients computed from cluster integrals to those from molecular simulation show good agreement through third order in β when coefficients are expressed with effective approximants. Notably, the agreement for LJ spheres is much better than for SW spheres although fewer coefficients of the density series (B2–B5) are available than for SW spheres (B2–B6). The coefficients for Bi(β) of the reference fluid are shown to follow a simple relationship to the virial coefficients of hard sphere fluids, corrected for the temperature dependency of the equivalent hard sphere diameter. This lays the foundation for a correlation of the second virial coefficient of LJ spheres B2(β) that extrapolates to infinite order in temperature. This correlation of B2(β) provides a basis for estimating the low density limit of TPT coefficients at all orders in temperature, facilitating a recursive extrapolation formula to estimate TPT coefficients of fourth order and higher over the entire density range. The applicability of the resulting equation of state is demonstrated by computing the thermodynamic properties for LJ spheres and comparing to standard simulation results. [ABSTRACT FROM AUTHOR]

The present paper is the second part of a series of papers aimed at assessing the accuracy of alchemical computational approaches based on nonequilibrium techniques for solvation free energy of organic molecules in the context of molecular dynamics simulations. In Paper I [Procacci, J. Chem. Phys. 151, 144113 (2019)], we dealt with bidirectional estimates of solvation free energies using nonequilibrium approaches. Here, we assess accuracy and precision of unidirectional estimates with the focus on the Gaussian and Jarzynski estimators. We present a very simple methodology to increase the statistics in the work distribution, hence boosting the accuracy and precision of the Jarzynski unidirectional estimates at no extra cost, exploiting the observed decorrelation between the random variables represented by the Lennard-Jones solute-solvent recoupling or decoupling work and by the electrostatic work due to the charging/discharging of the solute in the solvent. [ABSTRACT FROM AUTHOR]

The polymeric Langmuir theory, developed in Paper I [J. Dudowicz et al., J. Chem. Phys. 151, 124706 (2019)], is employed to investigate the influence of van der Waals interactions and chain rigidity on the thermodynamics of the reversible molecular binding to interfaces in one component polymer fluids (polymer melts). Both van der Waals interactions and chain stiffness are found to influence the temperature variation of the surface coverage Θ, the binding transition itself, and the cooperativity of molecular binding. Re-entrancy of the surface coverage Θ(T) is found to arise when the intermolecular interactions are sufficiently attractive to cause a liquid-vapor like phase separation in the interfacial region, a phenomenon that can occur in the binding of both small molecules and polymer chains to surfaces. [ABSTRACT FROM AUTHOR]

We report the vacuum-ultraviolet threshold-photoelectron spectrum of HC5N recorded over a wide spectral range, from 84 000 to 120 000 cm−1, with a 120 cm−1 spectral resolution, better than what was achieved in previous photoelectron studies, and with mass selectivity. The adiabatic ionization potential of cyanobutadiyne is measured at 85 366 (±40) cm−1. Assignment of the vibrational bands of the four lowest electronic states X+2Π, A+2Π, B+2Σ+, and C+2Π are performed, supported by high level ab initio calculations which are fully detailed in Paper II [B. Gans et al., J. Chem. Phys. 150, 244303 (2019)] and by Franck-Condon simulations. Only vibrational stretching modes are observed in the threshold-photoelectron spectra. The ground state of HC5N+ exhibits a vibrational progression in the ν2 stretching mode involving mainly the elongation of the C≡C triple bonds, whereas the A+ and C+ excited electronic states show a progression in the stretching mode mainly associated with the elongation of the C≡N bond, i.e., ν4 and ν3, respectively. The B+ state appears almost as a vibrationless structure in close vicinity to the A+ state. [ABSTRACT FROM AUTHOR]