Search

This Editorial reports how the depletion force theory was originally developed by Sho Asakura and Fumio Oosawa and how their one-page paper was "rediscovered" about 20 years after the paper was published. The first part of this Editorial is mostly based on the lecture by Oosawa and his autobiographies, and the second part is written by one of two scientists who found the paper. The aim of this Editorial is to record the background of the discovery of the depletion force. We believe that this Editorial presents an interesting story showing how science develops. The story reminds us of the importance of basic education and continuous interests in unknown phenomena and interactions between people of different disciplines, although they are sometimes considered as separate elements of research. [ABSTRACT FROM AUTHOR]

The paper referred to in the title, in J. Chem. Phys. 84, 1788 (1986), presented results of computer simulations of non-Markovian barrier crossing dynamics, and compared these results with various theoretical predictions. One comment made here is that the observed limited applicability of the Grote–Hynes theory can be explained by singular perturbation theory. The other comment concerns the importance of a second constant of the motion when the non-Markovian friction has a very long relaxation time. [ABSTRACT FROM AUTHOR]

Several new variants of the locally-renormalized coupled-cluster (CC) approaches that account for the effect of triples (LR-CCSD(T)) have been formulated and implemented for arbitrary reference states using the TENSOR CONTRACTION ENGINE functionality, enabling the automatic generation of an efficient parallel code. Deeply rooted in the recently derived numerator–denominator-connected (NDC) expansion for the ground-state energy [K. Kowalski and P. Piecuch, J. Chem. Phys. 122, 074107 (2005)], LR-CCSD(T) approximations use, in analogy to the completely renormalized CCSD(T) (CR-CCSD(T)) approach, the three-body moments in constructing the noniterative corrections to the energies obtained in CC calculations with singles and doubles (CCSD). In contrast to the CR-CCSD(T) method, the LR-CCSD(T) approaches discussed in this paper employ local denominators, which assure the additive separability of the energies in the noninteracting system limit when the localized occupied spin-orbitals are employed in the CCSD and LR-CCSD(T) calculations. As clearly demonstrated on several challenging examples, including breaking the bonds of the F2, N2, and CN molecules, the LR-CCSD(T) approaches are capable of providing a highly accurate description of the entire potential-energy surface (PES), while maintaining the characteristic N7scaling of the ubiquitous CCSD(T) approach. Moreover, as illustrated numerically for the ozone molecule, the LR-CCSD(T) approaches yield highly competitive values for a number of equilibrium properties including bond lengths, angles, and harmonic frequencies. [ABSTRACT FROM AUTHOR]

We have analyzed the effects of the spreads in experimental parameters on the reliability of speeds and angular distributions extracted from a generic surface-scattering experiment based on planar laser-induced fluorescence detection. The numerical model assumes a pulsed beam of projectile molecules is directed at a surface. The spatial distribution of the scattered products is detected by imaging the laser-induced fluorescence excited by a thin, pulsed sheet of laser light. Monte Carlo sampling is used to select from realistic distributions of the experimental parameters. The key parameter is found to be the molecular-beam diameter, expressed as a ratio to the measurement distance from the point of impact. Measured angular distributions are negligibly distorted when this ratio is <∼10%. Measured most-probable speeds are more tolerant, being undistorted when it is <∼20%. In contrast, the spread of speeds or of corresponding arrival times in the incident molecular beam has only very minor systematic effects. The thickness of the laser sheet is also unimportant within realistic practical limits. These conclusions are broadly applicable to experiments of this general type. In addition, we have analyzed the specific set of parameters designed to match the experiments on OH scattering from a liquid perfluoropolyether (PFPE) surface in the Paper I [Roman et al., J. Chem. Phys. 158, 244704 (2023)]. This reveals that the detailed form of the molecular-beam profile is important, particularly on apparent angular distributions, for geometric reasons that we explain. Empirical factors have been derived to correct for these effects. [ABSTRACT FROM AUTHOR]

This is an I easier approach to implement into computer code i , because these equations [Eq. (95) of the paper] are simpler than the corresponding EOMs for { I i SB I n i sb , I i SB I n i sb }. CLARIFICATION ON THE NUMERICAL ALGORITHM USED TO PROPAGATE DYNAMICS We want to clarify the numerical algorithm we used to propagate the EOMs and generate all numerical results presented in the paper. In the above expressions, to compute HT ht , we use Eq. (C2) of the paper. [Extracted from the article]

Density-functional-theory-based chemical reactivity indicators are formulated for degenerate and near-degenerate ground states. For degenerate states, the functional derivatives of the energy with respect to the external potential do not exist, and must be replaced by the weaker concept of functional variation. The resultant reactivity indicators depend on the specific perturbation. Because it is sometimes impractical to compute reactivity indicators for a specific perturbation, we consider two special cases: point-charge perturbations and Dirac delta function perturbations. The Dirac delta function perturbations provide upper bounds on the chemical reactivity. Reactivity indicators using the common used 'average of degenerate states approximation' for degenerate states provide a lower bound on the chemical reactivity. Unfortunately, this lower bound is often extremely weak. Approximate formulas for the reactivity indicators within the frontier-molecular-orbital approximation and special cases (two or three degenerate spatial orbitals) are presented in the supplementary material. One remarkable feature that arises in the frontier molecular orbital approximation, and presumably also in the exact theory, is that removing electrons sometimes causes the electron density to increase at the location of a negative (attractive) Dirac delta function perturbation. That is, the energetic response to a reduction in the external potential can increase even when the number of electrons decreases. [ABSTRACT FROM AUTHOR]

This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in CG systems using a hard sphere mapping, the absence of rotational motions in single-site CG models introduces differences between FG and CG dynamics. In this third paper, our objective is to faithfully recover atomistic diffusion coefficients from CG dynamics by incorporating rotational dynamics. By extracting FG rotational diffusion, we unravel, for the first time reported to our knowledge, a universality in excess entropy scaling between the rotational and translational diffusion. Once the missing rotational dynamics are integrated into the CG translational dynamics, an effective translation-rotation coupling becomes essential. We propose two different approaches for estimating this coupling parameter: the rough hard sphere theory with acentric factor (temperature-independent) or the rough Lennard-Jones model with CG attractions (temperature-dependent). Altogether, we demonstrate that FG diffusion coefficients can be recovered from CG diffusion coefficients by (1) incorporating "entropy-free" rotational diffusion with translation-rotation coupling and (2) recapturing the missing entropy. Our findings shed light on the fundamental relationship between FG and CG dynamics in molecular fluids. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the role of electron correlation in predicting the S1–S0 and T1–S0 excitation energies and, hence, the singlet–triplet gap (ΔEST) in a set of cyclazines, which act as templates for potential candidates for fifth generation organic light emitting diode materials. This issue has recently garnered much interest with the focus being on the inversion of the ΔEST, although experiments have indicated near degenerate levels with both positive and negative being within the experimental error bar [J. Am. Chem. Soc. 102, 6068 (1980), J. Am. Chem. Soc. 108, 17(1986)]. We have carried out a systematic and exhaustive study of various excited state electronic structure methodologies and identified the strengths and shortcomings of the various approaches and approximations in view of this challenging case. We have found that near degeneracy can be achieved either with a proper balance of static and dynamic correlation in multireference theories or with state-specific orbital corrections, including its coupling with correlation. The role of spin contamination is also discussed. Eventually, this paper seeks to produce benchmark numbers for establishing cost-effective theories, which can then be used for screening derivatives of these templates with desirable optical and structural properties. Additionally, we would like to point out that the use of domain-based local pair natural orbital-similarity transformed EOM-coupled cluster singles and doubles as the benchmark for ΔEST [as used in J. Phys. Chem. A 126(8), 1378 (2022), Chem. Phys. Lett. 779, 138827 (2021)] is not a suitable benchmark for these classes of molecules. [ABSTRACT FROM AUTHOR]

Thermal energy storage and utilization has been widely concerned due to the intermittency, renewability, and economy of renewable energy. In this paper, the potential energy function of binary Na2CO3–K2CO3 salt was first constructed using the Deep Potential GENerator (DPGEN) enhanced sampling method. Deep potential molecular dynamics simulations were performed to calculate the thermal properties and structural evolution of binary carbonates. The results show that as the temperature increases from 1073 to 1273 K, the viscosity and thermal conductivity decrease from 5.011 mPa s and 0.502 W/(m K) to 2.526 mPa s and 0.481 W/(m K), respectively. The decrease in viscosity is related to the distance and interaction between the molten salt ions. In addition, the diffusion coefficients, energy barriers, ionic radius, angular distribution function, and coordination number of molten salt were calculated and analyzed. The CO32− exhibits a stable planar triangular structure. The ionic radius of Na+ is smaller than that of K+, which makes Na+ suffer less spatial hindrance during motion and has a higher diffusion coefficient. The energy barriers that Na+ needs to overcome to escape the Coulomb force is greater than that of K+ ions, so molten salt containing Na+ may possess greater heat storage potential. We believe that the potential function constructed with DPGEN enhanced sampling strategy can provide more convincing results for predicting the thermal properties of molten salts. This paper aims to provide a technical route to develop the novel complex molten salt phase change material for thermal energy storage. [ABSTRACT FROM AUTHOR]

Diffusion in complex heterogeneous media, such as biological tissues or porous materials, typically involves constrained displacements in tortuous structures and sticky environments. Therefore, diffusing particles experience both entropic (excluded-volume) forces and the presence of complex energy landscapes. In this situation, one may describe transport through an effective diffusion coefficient. In this paper, we examine comb structures with finite-length 1D and finite-area 2D fingers, which act as purely diffusive traps. We find that there exists a critical width of 2D fingers, above which the effective diffusion along the backbone is faster than for an equivalent arrangement of 1D fingers. Moreover, we show that the effective diffusion coefficient is described by a general analytical form for both 1D and 2D fingers, provided the correct scaling variable is identified as a function of the structural parameters. Interestingly, this formula corresponds to the well-known general situation of diffusion in a medium with fast reversible adsorption. Finally, we show that the same formula describes diffusion in the presence of dilute potential energy traps, e.g., through a landscape of square wells. While diffusion is ultimately always the result of microscopic interactions (with particles in the fluid, other solutes, and the environment), effective representations are often of great practical use. The results reported in this paper help clarify the microscopic origins and the applicability of global, integrated descriptions of diffusion in complex media. [ABSTRACT FROM AUTHOR]

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

This paper focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid–liquid separation of biomolecular condensates, which play a prominent role in cellular biophysics and for surfactant and polymer applications. Previous studies of simple models for multiblock chains have shown that, depending on the sequence pattern and chain length, such systems can fall into one of two categories: displaying either phase separation or aggregation into finite-size clusters. The key new result of this paper is that both formation of finite-size aggregates and phase separation can be observed for certain chain architectures at appropriate conditions of temperature and concentration. For such systems, a bulk dense liquid condenses from a dilute phase that already contains multi-chain finite-size aggregates. The computational approach used in this study involves several distinct steps using histogram-reweighting grand canonical Monte Carlo simulations, which are described in some level of detail. [ABSTRACT FROM AUTHOR]

In recent years there has been a rapid growth in the development and application of new stochastic methods in electronic structure. These methods are quite diverse, from many-body wave function techniques in real space or determinant space to being used to sum perturbative expansions. This growth has been spurred by the more favorable scaling with the number of electrons and often better parallelization over large numbers of central processing unit (CPU) cores or graphical processing units (GPUs) than for high-end non-stochastic wave function based methods. This special issue of the Journal of Chemical Physics includes 33 papers that describe recent developments and applications in this area. As seen from the articles in the issue, stochastic electronic structure methods are applicable to both molecules and solids and can accurately describe systems with strong electron correlation. This issue was motivated, in part, by the 2019 Telluride Science Research Center workshop on Stochastic Electronic Structure Methods that we organized. Below we briefly describe each of the papers in the special issue, dividing the papers into six subtopics. [ABSTRACT FROM AUTHOR]

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

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

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

A theoretical treatment of the vibrational–vibrational (VV) contribution to the vibrational energy relaxation time T1 of a solute normal mode in a molecular solvent, which extends a previous treatment [S. A. Adelman, R. H. Stote, and R. Muralidhar, J. Chem. Phys. 99, 1320 (1993), henceforth called Paper I] of the vibrational–translational–rotational (VTR) contribution to T1, is outlined and expressions for this VV contribution, valid for the infinitely dilute diatomic solution, are presented. The treatment is based on the formula T1=β-1(ωl), where β(ω) is the friction kernel of the relaxing solute mode and where ωl is its liquid phase frequency. β(ω) is evaluated as the cosine transform of the autocorrelation function 〈F(t)Fĩ〉0v of the fluctuating generalized force exerted by the vibrating solvent on the solute normal mode coordinate conditional that this coordinate is fixed at its equilibrium value. 〈F(t)F〉0v is expressed as a superposition of the rigid solvent autocorrelation function 〈F(t)F〉0 and a correction which accounts for solvent vibrational motion. For diatomic solvents one has 〈F(t)F〉0v= 〈F(t)F〉0+NSMD(t) cos ωDt F(ΩD), where NS=number of solvent molecules, MD(t) is the vibrational force gradient autocorrelation function, ωD and ΩD are solvent molecule liquid phase frequencies, and F(Ω)=1/2hΩ-1 coth[hΩ/2kBT].The Gaussian model is assumed for 〈F(t)F〉0 and MD(t) yielding β(ω) as a superposition of a Gaussian centered at ω=0 which mediates VTR processes and a Gaussian centered at ω=ωD which mediates VV processes. Vector integral expressions for MD(t), ωD, and ΩD are presented which are similar to the expressions for ωl and 〈F(t)F〉0 given in Paper I. These expressions permit the evaluation of the VV contribution to T1 from the atomic masses, bondlengths, vibrational frequencies, and site–site interaction... [ABSTRACT FROM AUTHOR]

Double Resonance is a powerful spectroscopic method that unambiguously assigns the rigorous quantum numbers of one state of a transition. However, there is often ambiguity as to the branch (ΔJ) of that transition. Spectroscopists have resolved this ambiguity by using the dependence of the double resonance intensity on the relative polarization directions of pump and probe radiation. However, published theoretical predictions for this ratio are based upon a weak (i.e., non-saturating) field approximation. This paper presents theoretical predictions for these intensity ratios for cases where the pump field is strongly saturating in the two limits of transitions dominated by homogeneous or of inhomogeneous broadening. Saturation reduces but does not eliminate the magnitude of the polarization effect (driving the intensity ratio closer to unity) even with strong pump saturation. For the case of an inhomogeneously broadened line, such as when Doppler broadened linewidth dominates over the power-broadened homogeneous line width, a large fraction of the low pump power polarization anisotropy remains. This paper reports predicted polarization ratios for both linear and circular pump and probe field polarizations. The present predictions are compared with experimental measurements on CH4 ground state → ν3 → 3ν3 transitions recently reported by de Oliveira et al.63 and these are in better agreement than with the weak field predictions. [ABSTRACT FROM AUTHOR]

This paper presents an exploration of a specific type of a generalized multicomponent solution model, which appears to be first given by Saulov in the current explicit form. The assumptions of the underlying theory and a brief derivation of the main equation have been provided preliminarily for completeness and notational consistency. The resulting formulae for the Gibbs free energy of mixing and the chemical potentials are multivariate polynomials with physically meaningful coefficients and the mole fractions of the components as variables. With one additional assumption about the relative magnitudes of the solvent–solute and solute–solute interaction exchange energies, combining rules were obtained that express the mixed coefficients of the polynomial in terms of its pure coefficients. This was done by exploiting the mathematical structure of the asymmetric form of the solvent chemical potential equation. The combining rules allow one to calculate the thermodynamic properties of the solvent with multiple solutes from binary mixture data only (i.e., each solute with the solvent), and hence, are of practical importance. Furthermore, a connection was established between the osmotic virial coefficients derived in this work and the original osmotic virial coefficients of Hill found by employing a different procedure, illustrating the equivalency of what appears to be two different theories. A validation of the combining rules derived here has been provided in a separate paper where they were successfully used to predict the freezing points of ternary salt solutions of water. [ABSTRACT FROM AUTHOR]

Solvation dynamics in ionic liquids show features that are often associated with supercooled liquids, including "stretched" nonexponential relaxation. To better understand the mechanism behind the stretching, the nonlinear mode-correlation methods proposed in Paper I [S. R. Hodge and M. A. Berg, J. Chem. Phys. 155, 024122 (2021)] are applied to a simulation of a prototypical ionic liquid. A full Green's function is recovered. In addition, specific tests for non-Gaussian dynamics are made. No deviations from Gaussian dynamics are found. This finding is incompatible with rate heterogeneity as a cause of the nonexponential relaxation and appears to be in conflict with an earlier multidimensional analysis of the same data. Although this conflict is not resolved here, this work does demonstrate the practicality of mode-correlation analysis in the face of finite datasets and calculations. [ABSTRACT FROM AUTHOR]

Our measurements of the relaxation times for the syn–anti isomerization of CH3ONO have been criticized by True et al. However, their recounting of the flaws in our procedure was based on distortions. Furthermore, the basic disagreement concerns the interpretation of the pressure dependence of the relaxation times they reported which differed insignificantly from our initial observations. The clear increase with decreasing pressure of the bimolecular rate constant (at low pressures) is not consistent with any RRKM model which has yet been proposed contrary to the claim by True. It is consistent with the limited phase space model proposed by Bauer and Lazaar. [ABSTRACT FROM AUTHOR]

Hydrodynamic effect on the relaxation modes for a system of charged particles is reexamined. This effect is shown to produce a decrease in the diffusion coefficient due to the cloud of particles surrounding each charge. [ABSTRACT FROM AUTHOR]

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

The theoretical treatment in Paper I [D. W. Miller and S. A. Adelman, J. Chem. Phys. 117, 2672, (2002), preceding paper] of the vibrational energy relaxation (VER) of low-frequency, large mass dihalogen solutes is extended to the VER of the high-frequency, small mass molecular hydrogen solutes H[sub 2] and D[sub 2] in a Lennard-Jones argon-like solvent. As in Paper I, values of the relaxation times T[sub 1] predicted by the theory are tested against molecular dynamics (MD) results and are found to be of semiquantitative accuracy. To start, it is noted that standard Lennard-Jones site-site potentials derived from macroscopic data can be very inaccurate in the steep repulsive slope region crucial for T[sub 1]. Thus, the H-Ar Lennard-Jones diameter σ[sub uv] is not taken from literature values but rather is chosen as σ[sub UV] = 1.39 Å, the value needed to make the theory reproduce the experimental H[sub 2]/Ar gas phase VER rate constant. Next, by MD simulation it is shown that the vibrational coordinate fluctuating force autocorrelation function 〈&Ftilde;(t)&Ftilde;〉[sub 0] of Paper I decays roughly an order of magnitude more rapidly for the molecular hydrogen solutions than for the dihalogen solutions. This result implies a relatively slow decay for the molecular hydrogen friction kernels β(ω) = (k[sub B]T)[sup -1] ∫[sup ∞, sub 0] 〈&Ftilde;(t)&Ftilde;〉[sub 0] cos ω tdt, yielding for the H[sub 2]/Ar and D[sub 2]/Ar systems at T= 150 K physical millisecond values for T[sub 1] =beta;[sup -1](ω) despite the high liquid phase vibrational frequencies ω[sub 1] of H[sub 2] and D[sub 2]. The rapid decay of 〈&Ftilde;(t)&Ftilde;&ran;[sub 0] is due to both the steepness of the repulsive slope of the H-Ar potential and the small masses of H and D. Thus, the small value chosen for σ[sub UV] is needed to avoid unphysically long T[sub 1]'s. Next, an analytical treatment of the H[sub 2]/D[sub... [ABSTRACT FROM AUTHOR]

This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem. Phys. 158, 244104 (2023)] in which a quantum-stochastic Liouville equation for the description of the quantum–classical dynamics of a molecule in a dissipative bath has been formulated in curvilinear internal coordinates. In such an approach, the coordinates of the system are separated into three subsets: the quantum coordinates, the classical relevant nuclear degrees of freedom, and the classical irrelevant (bath) coordinates. The equation has been derived in natural internal coordinates, which are bond lengths, bond angles, and dihedral angles. The resulting equation needs to be parameterized. In particular, one needs to compute the potential energy surfaces, the friction tensor, and the rate constants for the nonradiative jumps among the quantum states. While standard methods exist for the calculation of energy and dissipative properties, an efficient evaluation of the transition rates needs to be developed. In this paper, an approximated treatment is introduced, which leads to a simple explicit formula with a single adjustable parameter. Such an approximated expression is compared with the exact calculation of transition rates obtained via molecular dynamics simulations. To make such a comparison possible, a simple sandbox system has been used, with two quantum states and a single internal coordinate (together with its conjugate momentum). Results show that the adjustable parameter, which is an effective decoherence time, can be parameterized from the effective relaxation times of the autocorrelation functions of the conjugated momenta of the relevant nuclear coordinates. [ABSTRACT FROM AUTHOR]

In continuation with Paper I [S. R. Reddy et al., J. Chem. Phys. 151, 054303 (2019)], the vibronic structure and dynamics of the 1 Σ u + electronic state of C15, C17, C19, and C21 chains in the coupled manifold of 1 Σ u + –1Πg–1Πu– 1 Σ g + electronic states have been investigated in this paper. The model vibronic Hamiltonian developed through extensive ab initio quantum chemistry calculations in Paper I is employed, and first principles nuclear dynamics calculations are carried out to obtain the photoabsorption band of the 1 Σ u + electronic state. Both time-independent and time-dependent quantum mechanical calculations are carried out to precisely locate the vibrational levels, assign them with the progression of vibrational modes, and elucidate the impact of both Renner-Teller and pseudo-Renner-Teller couplings on them. The nonradiative decay of the 1 Σ u + electronic state is studied, and it is found that the decay rate is comparable with the prediction made for them to be qualified as a carrier of diffuse interstellar bands in the literature. The theoretical results are found to be in good accord with the available experimental results. [ABSTRACT FROM AUTHOR]

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

Comparing a discrete molecular spectrum to a continuous molecular spectrum in a quantitative manner is a challenging problem, for example, when attempting to fit a theoretical stick spectrum to a continuous spectrum. In this paper, the use of computational optimal transport is investigated for such a problem. In the optimal transport literature, the comparison of a discrete and a continuous spectrum is referred to as semi-discrete optimal transport and is a situation where a metric such as least-squares may be difficult to define except under special conditions. The merits of an optimal transport approach for this problem are investigated using the transport distance defined for the semi-discrete case. A tutorial on semi-discrete optimal transport for molecular spectra is included in this paper, and several well-chosen synthetic spectra are investigated to demonstrate the utility of computational optimal transport for the semi-discrete case. Among several types of investigations, we include calculations showing how the frequency resolution of the continuous spectrum affects the transport distance between a discrete and a continuous spectrum. We also use the transport distance to measure the distance between a continuous experimental electronic absorption spectrum of SO2 and a theoretical stick spectrum for the same system. The comparison of the theoretical and experimental SO2 spectra also allows us to suggest a theoretical value for the band origin that is closer to the observed band origin than previous theoretical values. [ABSTRACT FROM AUTHOR]

Lithium–ion batteries are key elements of electric vehicles and energy storage systems, and their accurate State of Charge (SOC) estimation is momentous for battery energy management, safe operation, and extended service life. In this paper, the Multi-Kernel Relevance Vector Machine (MKRVM) and Whale Optimization Algorithm (WOA) are used to estimate the SOC of lithium–ion batteries under different operating conditions. In order to better learn and estimate the battery SOC, MKRVM is used to establish a model to estimate lithium–ion battery SOC. WOA is used to automatically adjust and optimize weights and kernel parameters of MKRVM to improve estimation accuracy. The proposed model is validated with three lithium–ion batteries under different operating conditions. In contrast to other optimization algorithms, WOA has a better optimization effect and can estimate the SOC more accurately. In contrast to the single kernel function, the proposed multi-kernel function greatly improves the precision of the SOC estimation model. In contrast to the traditional method, the WOA-MKRVM has a higher precision of SOC estimation. [ABSTRACT FROM AUTHOR]

As in the preceding paper (Paper I) we study here a model of chains with excluded volume enclosed in a ‘‘box’’ on a square lattice. The system is simulated by the Metropolis Monte Carlo method and the entropy is extracted from the samples by using the ‘‘hypothetical scanning method.’’ With this method each system configuration is treated as if it has been generated step by step with the scanning method (studied in Paper I). The transition probabilities are reconstructed and three approximations of the entropy are obtained. Thus the pressure and the chemical potential are calculated directly from the results of the entropy as in Paper I using standard thermodynamic relations. These results are found to be in a very good agreement with those obtained in Paper I, which are considered to be exact within the statistical error. [ABSTRACT FROM AUTHOR]

In a recent paper [Aschi et al., ChemPhysChem 6, 53 (2005)], we characterized, by means of theoretical-computational procedures, the electronic excitation of water along the typical liquid state isochore (55.32 mol/l) for a large range of temperature. In that paper we were able to accurately reproduce the experimental absorption maximum at room temperature and to provide a detailed description of the temperature dependence of the excitation spectrum along the isochore. In a recent experimental work by Marin et al. [J. Chem. Phys. 125, 104314 (2006)], water electronic excitation energy was carefully analyzed in a broad range of density and temperature, finding a remarkable agreement of the temperature behavior of the experimental data with our theoretical results. Here, by means of the same theoretical-computational procedures (molecular dynamics simulations and the perturbed matrix method), we investigate water electronic absorption exactly in the same density-temperature range used in the experimental work, hence, now considering also the absorption density dependence. Our results point out that, (1) for all the densities and temperatures investigated, our calculated absorption spectra are in very good agreement with the experimental ones and (2) the gradual maxima redshift observed increasing the temperature or decreasing the density has to be ascribed to a real shift of the lowest X→A electronic transition, supporting the conclusions of Marin et al. [ABSTRACT FROM AUTHOR]

Jiang and co-workers use high resolution STM to investigate the reaction and self-assembly of (3,6-dibromo-9,10-phenanthrenequinone, or DBPQ) molecules on Ag (100) and Ag (110) surfaces in order to understand the mechanism of bottom-up assembly on surfaces.[31] They show that, through the inclusion of multiple functional groups within a precursor molecule, it becomes possible to fabricate new low-dimensional materials with unique chemical, physical, and electronic properties. Herbst and Fransson consider the core-valence separation approximation that is often used in the calculation of core-level spectra.[5] They show how to quantify the errors in this approximation, thereby opening the door to error-quantified predictions relevant to x-ray spectroscopy. 153(16), 164108 (2020).10.1063/5.0019557 5 M. F. Herbst and T. Fransson, "Quantifying the error of the core-valence separation approximation", J. Chem. Phys. Zhu and co-workers tackle this problem for a model system containing a 2D semiconductor heterojunction and show convincingly the efficient hot electron transfer from photoexcited MoTe SB 2 sb to WS SB 2 sb .[30] This finding provides important insight into the competition between hot electron cooling and transfer at 2D semiconductor interfaces and suggests an intriguing possibility for the exploration of hot electron devices. [Extracted from the article]

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

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

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

In this paper, we explore the molecular basis of combining photodynamic therapy (PDT), a light-triggered targeted anticancer therapy, with the traditional chemotherapeutic properties of the well-known cytotoxic agent gemcitabine. A photosensitizer prerequisite is significant absorption of biocompatible light in the visible/near IR range, ideally between 600 and 1000 nm. We use highly accurate multiconfigurational CASSCF/MS-CASPT2/MM and TD-DFT methodologies to determine the absorption properties of a series of gemcitabine derivatives with the goal of red-shifting the UV absorption band toward the visible region and facilitating triplet state population. The choice of the substitutions and, thus, the rational design is based on important biochemical criteria and on derivatives whose synthesis is reported in the literature. The modifications tackled in this paper consist of: (i) substitution of the oxygen atom at O2 position with heavier atoms (O → S and O → Se) to red shift the absorption band and increase the spin–orbit coupling, (ii) addition of a lipophilic chain at the N7 position to enhance transport into cancer cells and slow down gemcitabine metabolism, and (iii) attachment of aromatic systems at C5 position to enhance red shift further. Results indicate that the combination of these three chemical modifications markedly shifts the absorption spectrum toward the 500 nm region and beyond and drastically increases spin–orbit coupling values, two key PDT requirements. The obtained theoretical predictions encourage biological studies to further develop this anticancer approach. [ABSTRACT FROM AUTHOR]

Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium’s walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D0 is only slightly larger than the smallest dimension of a protein’s folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins’ misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature Tf on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media’s walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium. [ABSTRACT FROM AUTHOR]

Due to the ubiquity and importance of water, water dimer has been intensively studied. Computing the (ro-)vibrational spectrum of water dimer is challenging. The potential has eight wells separated by low barriers, which makes harmonic approximations of limited utility. A variational approach is imperative, but difficult because there are 12 coupled vibrational coordinates. In this paper, we use a product contracted basis whose functions are products of intramolecular and intermolecular functions computed using an iterative eigensolver. An intermediate matrix F facilitates calculating matrix elements. Using F, it is possible to do calculations on a general potential without storing the potential on the full quadrature grid. We find that surprisingly many intermolecular functions are required. This is due to the importance of coupling between inter- and intra-molecular coordinates. The full G16 symmetry of water dimer is exploited. We calculate, for the first time, monomer excited stretch states and compare P(1) transition frequencies with their experimental counterparts. We also compare with experimental vibrational shifts and tunneling splittings. Surprisingly, we find that the largest tunneling splitting, which does not involve the interchange of the two monomers, is smaller in the asymmetric stretch excited state than in the ground state. Differences between levels we compute and those obtained with a [6+6]D adiabatic approximation [Leforestier et al. J. Chem. Phys. 137 014305 (2012)] are ∼ 0.6 cm−1 for states without monomer excitation, ∼ 4 cm−1 for monomer excited bend states, and as large as ∼ 10 cm−1 for monomer excited stretch states. [ABSTRACT FROM AUTHOR]

Until quite recently, in almost all papers on crystal nucleation in glass-forming substances, it was assumed that nucleation proceeds in a completely relaxed supercooled liquid and, hence, at constant values of the critical parameters determining the nucleation rate for any given set of temperature, pressure, and composition. Here, we analyze the validity of this hypothesis for a model system by studying nucleation in a lithium silicate glass treated for very long times (up to 250 days) in deeply supercooled states, reaching 60 K below the laboratory glass transition temperature, Tg. At all temperatures in the considered range, T < Tg, we observed an enormous difference between the experimental number of nucleated crystals, N(t), and its theoretically expected value computed by assuming the metastable state of the relaxing glass has been reached. Analyzing the origin of this discrepancy, we confirmed that the key parameters determining the nucleation rates change with time as a result of the glass relaxation process. Finally, we demonstrate that, for temperatures below 683 K, this particular glass almost fully crystallizes prior to reaching the ultimate steady-state nucleation regime (e.g., at 663 K, it would take 176 years for the glass to reach 99% crystallization, while 2600 years would be needed for complete relaxation). This comprehensive study proves that structural relaxation strongly affects crystal nucleation in deeply supercooled states at temperatures well below Tg; hence, this phenomenon has to be accounted for in any crystal nucleation model. [ABSTRACT FROM AUTHOR]

The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids. [ABSTRACT FROM AUTHOR]

This paper reports the derivation and implementation of the electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability tensors at the density functional theory level with periodic boundary conditions (DFT-PBC). These tensors are combined to evaluate the Buckingham/Dunn tensor that describes the optical rotation (OR) in oriented chiral systems. We describe several aspects of the derivation of the equations and present test calculations that verify the correctness of the tensor formulation and their implementation. The results show that the full OR tensor is completely origin invariant as for molecules and that PBC calculations match molecular cluster calculations on 1D chains. A preliminary investigation on the choice of density functional, basis set, and gauge indicates a similar dependence as for molecules: the functional is the primary factor that determines the OR magnitude, followed by the basis set and to a much smaller extent the choice of gauge. However, diffuse functions may be problematic for PBC calculations even if they are necessary for the molecular case. A comparison with experimental data of OR for the tartaric acid crystal shows reasonable agreement given the level of theory employed. The development presented in this paper offers the opportunity to simulate the OR of chiral crystalline materials with general-purpose DFT-PBC methods, which, in turn, may help to understand the role of intermolecular interactions on this sensitive electronic property. [ABSTRACT FROM AUTHOR]