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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]

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]

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]

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 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]

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]

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]

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]

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]

Two-dimensional transition metal dichalcogenides and semiconductor metal oxides have shown great potential in photocatalysis. However, their stability and efficiency need to be further improved. In this paper, porous ZnO nanorods with high specific surface area were prepared from metal-organic framework ZIF-8 by a simple hydrothermal method. A MoS2/ZnO composite was constructed by loading MoS2 onto the surface of porous ZnO nanorods. Compared with ZnO materials prepared by other methods, MoS2/ZnO prepared in this paper exhibits superior photocatalytic performance. The enhanced photocatalytic activity of the MoS2/ZnO composite can be attributed to the formation of heterojunctions and strong interaction between them, which greatly facilitate the separation of electrons and holes at the contact interface. In addition, due to the wide absorption region of the visible spectrum, MoS2 can greatly broaden the light absorption range of the material after the formation of the composite material, increase the utilization rate of visible light, and reduce the combination of electrons and holes. This study provides a new way to prepare cheap and efficient photocatalysts. [ABSTRACT FROM AUTHOR]

Developing fluorescence-encoded infrared (FEIR) vibrational spectroscopy for single-molecule applications requires a detailed understanding of how the molecular response and external experimental parameters manifest in the detected signals. In Paper I [L. Whaley-Mayda, A. Guha, and A. Tokmakoff, J. Chem. Phys. 159, 194201 (2023)] we introduced a nonlinear response function theory to describe vibrational dynamics, vibronic coupling, and transition dipole orientation in FEIR experiments with ultrashort pulses. In this second paper, we apply the theory to investigate the role of intermode vibrational coherence, the orientation of vibrational and electronic transition dipoles, and the effects of finite pulse durations in experimental measurements. We focus on measurements at early encoding delays—where signal sizes are largest and therefore of most value for single-molecule experiments, but where many of these phenomena are most pronounced and can complicate the appearance of data. We compare experiments on coumarin dyes with finite-pulse response function simulations to explain the time-dependent behavior of FEIR spectra. The role of the orientational response is explored by analyzing polarization-dependent experiments and their ability to resolve relative dipole angles in the molecular frame. This work serves to demonstrate the molecular information content of FEIR experiments, and develop insight and guidelines for their interpretation. [ABSTRACT FROM AUTHOR]

Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck–Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design. [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]