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]

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]

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]

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]

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]

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]

This paper proposes the first linear scaling implementation for the domain decomposition approach of the polarizable continuum model (ddPCM) for the computation of the solvation energy and forces. The ddPCM-equation consists of a (non-local) integral equation on the van der Waals or solvent accessible surface of the solute's cavity resulting in a dense solution matrix, and, in turn, one matrix–vector multiplication has a quadratic arithmetic complexity with respect to the number of atoms of the solute molecule. The use of spherical harmonics as basis functions makes it natural to employ the fast multipole method (FMM) in order to provide an asymptotically linear scaling method. In this paper, we employ the FMM in a non-uniform manner with a clusterization based on a recursive inertial bisection. We present some numerical tests illustrating the accuracy and scaling of our implementation. [ABSTRACT FROM AUTHOR]

In Paper I, the performances of pre-screening (PS), extended PS (EPS), and cumulant (CU) approximations to the fourth-order density matrix were examined in the context of second-order N-electron valence state perturbation theory (NEVPT2). It has been found that the CU, PS, and even EPS approximations with loose thresholds may introduce intruder states. In the present work, the origin of these "false intruder" states introduced by approximated density matrices is discussed. Canonical NEVPT2 implementations employ a rank reduction trick. By analyzing its residual error, we find that the omission of the rank reduction leads to a more stable multireference perturbation theory for incomplete active space reference wave functions. Such a full rank (FR)-NEVPT2 formulation is equivalent to the conventional NEVPT2 method for the complete active space self-consistent field/complete active space configuration interaction reference wave function. A major drawback of the FR-NEVPT2 formulation is the necessity of the fifth-order density matrix. To avoid the construction of the high-order density matrices, the combination of the FR-NEVPT2 with the CU approximation is studied. However, we find that the CU approximation remains problematic as it still introduces intruder states. The question of how to robustly and efficiently perform internally contracted multireference perturbation theories with approximate densities remains a challenging field of investigation. [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]

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]

Experimental demonstrations of polarization-selection two-dimensional Vibrational-Electronic (2D VE) and 2D Electronic-Vibrational (2D EV) spectroscopies aim to map the magnitudes and spatial orientations of coupled electronic and vibrational coordinates in complex systems. The realization of that goal depends on our ability to connect spectroscopic observables with molecular structural parameters. In this paper, we use a model Hamiltonian consisting of two anharmonically coupled vibrational modes in electronic ground and excited states with linear and bilinear vibronic coupling terms to simulate polarization-selective 2D EV and 2D VE spectra. We discuss the relationships between the linear vibronic coupling and two-dimensional Huang–Rhys parameters and between the bilinear vibronic coupling term and Duschinsky mixing. We develop a description of the vibronic transition dipoles and explore how the Hamiltonian parameters and non-Condon effects impact their amplitudes and orientations. Using simulated polarization-selective 2D EV and 2D VE spectra, we show how 2D peak positions, amplitudes, and anisotropy can be used to measure parameters of the vibronic Hamiltonian and non-Condon effects. This paper, along with the first in the series, provides the reader with a detailed description of reading, simulating, and analyzing multimode, polarization-selective 2D EV and 2D VE spectra with an emphasis on extracting vibronic coupling parameters from complex spectra. [ABSTRACT FROM AUTHOR]

Two-dimensional Electronic–Vibrational (2D EV) spectroscopy and two-dimensional Vibrational–Electronic (2D VE) spectroscopy are among the newest additions to the coherent multidimensional spectroscopy toolbox, and they are directly sensitive to vibronic couplings. In this first of two papers, the complete orientational response functions are developed for a model system consisting of two coupled anharmonic oscillators and two electronic states in order to simulate polarization-selective 2D EV and 2D VE spectra with arbitrary combinations of linearly polarized electric fields. Here, we propose analytical methods to isolate desired signals within complicated spectra and to extract the relative orientation between vibrational and vibronic dipole moments of the model system using combinations of polarization-selective 2D EV and 2D VE spectral features. Time-dependent peak amplitudes of coherence peaks are also discussed as means for isolating desired signals within the time-domain. This paper serves as a field guide for using polarization-selective 2D EV and 2D VE spectroscopies to map coupled vibronic coordinates on the molecular frame. [ABSTRACT FROM AUTHOR]

The objective of this paper is to describe a new data-driven framework for computational screening and discovery of a class of materials termed "metavalent" solids. "Metavalent" solids possess characteristics that are nominally associated with metallic and covalent bonding (in terms of conductivity and coordination numbers) but are distinctly different from both because they show anomalously large response properties and a unique bond-breaking mechanism that is not observed in either covalent or metallic solids. The paper introduces the use of Hirshfeld surface analysis to provide quantum level descriptors that can be used for rapid screening of crystallographic data to identify potentially new "metavalent" solids with novel and emergent properties. [ABSTRACT FROM AUTHOR]

Stable crystalline structures of confined water can be different from bulk ice. In Paper I [T. Yagasaki et al., J. Chem. Phys. 151, 064702 (2019)] of this study, it was shown, using molecular dynamics (MD) simulations, that a zeolite-like ice structure forms in nanobrushes consisting of (6,6) carbon nanotubes (CNTs) when the CNTs are located in a triangle arrangement. The melting temperature of the zeolite-like ice structure is much higher than the melting temperature of ice Ih when the distance between the surfaces of CNTs is ∼0.94 nm, which is the best spacing for the bilayer structure of water. In this paper, we perform MD simulations of nanobrushes of CNTs that are different from (6,6) CNTs in radius. Several new porous ice structures form spontaneously in the MD simulations. A stable porous ice forms when the radius of its cavities matches the radius of the CNTs well. All cylindrical porous ice structures found in this study can be decomposed into a small number of structural blocks. We provide a new protocol to classify cylindrical porous ice crystals on the basis of this decomposition. [ABSTRACT FROM AUTHOR]

Ninety years ago, Wigner derived the leading order expansion term in ℏ2 for the tunneling rate through a symmetric barrier. His derivation included two contributions: one came from the parabolic barrier, but a second term involved the fourth-order derivative of the potential at the barrier top. He left us with a challenge, which is answered in this paper, to derive the same but for an asymmetric barrier. A crucial element of the derivation is obtaining the ℏ2 expansion term for the projection operator, which appears in the flux-side expression for the rate. It is also reassuring that an analytical calculation of semiclassical transition state theory (TST) reproduces the anharmonic corrections to the leading order of ℏ2. The efficacy of the resulting expression is demonstrated for an Eckart barrier, leading to the conclusion that especially when considering heavy atom tunneling, one should use the expansion derived in this paper, rather than the parabolic barrier approximation. The rate expression derived here reveals how the classical TST limit is approached as a function of ℏ and, thus, provides critical insights to understand the validity of popular approximate theories, such as the classical Wigner, centroid molecular dynamics, and ring polymer molecular dynamics methods. [ABSTRACT FROM AUTHOR]

The aging rate of glasses has traditionally been modeled as a function of temperature, T, and fictive temperature, while density, ρ, is not explicitly included as a parameter. However, this description does not naturally connect to the modern understanding of what governs the relaxation rate in equilibrium. In equilibrium, it is well known that the relaxation rate, γeq, depends on temperature and density. In addition, a large class of systems obeys density scaling, which means the rate specifically depends on the scaling parameter, Γ = e(ρ)/T, where e(ρ) is a system specific function. This paper presents a generalization of the fictive temperature concept in terms of a fictive scaling parameter, Γfic, and a density scaling conjecture for aging glasses in which the aging rate depends on Γ and Γfic. [ABSTRACT FROM AUTHOR]

The persistent problem posed by the glass transition is to develop a general atomic level description of amorphous solidification. The answer proposed in this paper is to measure a configuration's capacity to restrain the motion of the constituent atoms. Here, we show that the instantaneous normal modes can be used to define a measure of atomic restraint that accounts for the difference between fragile and strong liquids and the collective length scale of the supercooled liquid. These results represent a significant simplification of the description of amorphous solidification and provide a powerful systematic treatment of the influence of microscopic factors on the formation of an amorphous solid. [ABSTRACT FROM AUTHOR]

This paper reports on the effects of shear rate and interface modeling parameters on the hydrodynamic slip length (LS) for water–graphite interfaces calculated using non-equilibrium molecular dynamics. Five distinct non-bonded solid–liquid interaction parameters were considered to assess their impact on LS. The interfacial force field derivations included sophisticated electronic structure calculation-informed and empirically determined parameters. All interface models exhibited a similar and bimodal LS response when varying the applied shear rate. LS in the low shear rate regime (LSR) is in good agreement with previous calculations obtained through equilibrium molecular dynamics. As the shear rate increases, LS sharply increases and asymptotes to a constant value in the high shear regime (HSR). It is noteworthy that LS in both the LSR and HSR can be characterized by the density depletion length, whereas solid–liquid adhesion metrics failed to do so. For all interface models, LHSR calculations were, on average, ∼28% greater than LLSR, and this slip jump was confirmed using the SPC/E and TIP4P/2005 water models. To address the LS transition from the LSR to the HSR, the viscosity of water and the interfacial friction coefficient were investigated. It was observed that in the LSR, the viscosity and friction coefficient decreased at a similar rate, while in the LSR-to-HSR transition, the friction coefficient decreased at a faster rate than the shear viscosity until they reached a new equilibrium, hence explaining the LS-bimodal behavior. This study provides valuable insights into the interplay between interface modeling parameters, shear rate, and rheological properties in understanding hydrodynamic slip behavior. [ABSTRACT FROM AUTHOR]

In this paper, we present a combined experimental and theoretical study that explored the initial sticking of water on cooled surfaces. Specifically, these ultra-high vacuum gas–surface scattering experiments utilized supersonic molecular beam techniques in conjunction with a cryogenically cooled highly oriented pyrolytic graphite crystal, giving control over incident kinematic conditions. The D2O translational energy spanning 300–750 meV, the relative D2O flux, and the incident angle could all be varied independently. Three different experimental measurements were made. One involved measuring the total amount of D2O scattering as a function of surface temperature to determine the onset of sticking under non-equilibrium gas–surface collision conditions. Another measurement used He specular scattering to assess structural and coverage information for the interface during D2O adsorption. Finally, we used time-of-flight (TOF) measurements of the scattered D2O to determine how energy is exchanged with the graphite surface at surface temperatures above and near the conditions needed for gaseous condensation. For comparison and elaboration of the roles that internal degrees of freedom play in this process, we also did similar TOF measurements using another mass 20 incident particle, atomic neon. Enriching this study are precise molecular dynamics simulations that elaborate on gas–surface energy transfer and the roles of molecular degrees of freedom in gas–surface collisional energy exchange processes. This study furthers our fundamental understanding of energy exchange and the onset of sticking and ultimately gaseous condensation for gas–surface encounters occurring under high-velocity flows. [ABSTRACT FROM AUTHOR]

The combination of vibrational perturbation theory with the replacement of the harmonic oscillator quantization condition along the reaction coordinate with an imaginary action to be used in the uniform semiclassical approximation for the transmission probability has been shown in recent years to be a practical method for obtaining thermal reaction rates. To date, this theory has been developed systematically only up to second order in perturbation theory. Although it gives the correct leading order term in an ℏ2 expansion, its accuracy at lower temperatures, where tunneling becomes important, is not clear. In this paper, we develop the theory to fourth order in the action. This demands developing the quantum perturbation theory up to sixth order. Remarkably, we find that the fourth order theory gives the correct ℏ4 term in the expansion of the exact thermal rate. The relative magnitude of the fourth order correction as compared to the second order term objectively indicates the accuracy of the second order theory. We also extend the previous modified second order theory to the fourth order case, creating an ℏ2 modified potential for this purpose. The resulting theory is tested on the standard examples—symmetric and asymmetric Eckart potentials and a Gaussian potential. The modified fourth order theory is remarkably accurate for the asymmetric Eckart potential. [ABSTRACT FROM AUTHOR]

Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a number of limitations. In this paper, we address these challenges by introducing a new path-like collective variable called the "deep-locally non-linear-embedding," which is inspired by principles of the locally linear embedding technique and is trained on a reactive trajectory. The variable mimics the ideal reaction coordinate by automatically generating a non-linear combination of features through a differentiable generalized autoencoder that combines a neural network with a continuous k-nearest neighbor selection. Among the key advantages of this method is its capability to automatically choose the metric for searching neighbors and to learn the path from state A to state B without the need to handpick landmarks a priori. We demonstrate the effectiveness of DeepLNE by showing that the progression along the path variable closely approximates the ideal reaction coordinate in toy models, such as the Müller-Brown potential and alanine dipeptide. Then, we use it in the molecular dynamics simulations of an RNA tetraloop, where we highlight its capability to accelerate transitions and estimate the free energy of folding. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) molecular models greatly reduce the computational cost of simulations allowing for longer and larger simulations, but come with an artificially increased acceleration of the dynamics when compared to the parent atomistic (AA) simulation. This impedes their use for the quantitative study of dynamical properties. During coarse-graining, grouping several atoms into one CG bead not only reduces the number of degrees of freedom but also reduces the roughness on the molecular surfaces, leading to the acceleration of dynamics. The RoughMob approach [M. K. Meinel and F. Müller-Plathe, J. Phys. Chem. B 126(20), 3737–3747 (2022)] quantifies this change in geometry and correlates it to the acceleration by making use of four so-called roughness volumes. This method was developed using simple one-bead CG models of a set of hydrocarbon liquids. Potentials for pure components are derived by the structure-based iterative Boltzmann inversion. In this paper, we find that, for binary mixtures of simple hydrocarbons, it is sufficient to use simple averaging rules to calculate the roughness volumes in mixtures from the roughness volumes of pure components and add a correction term quadratic in the concentration without the need to perform any calculation on AA or CG trajectories of the mixtures themselves. The acceleration factors of binary diffusion coefficients and both self-diffusion coefficients show a large dependence on the overall acceleration of the system and can be predicted a priori without the need for any AA simulations within a percentage error margin, which is comparable to routine measurement accuracies. Only if a qualitatively accurate description of the concentration dependence of the binary diffusion coefficient is desired, very few additional simulations of the pure components and the equimolar mixture are required. [ABSTRACT FROM AUTHOR]

In nonequilibrium statistical physics, quantifying the nearest (and higher-order) neighbors and free volumes of particles in many-body systems is crucial to elucidating the origin of macroscopic collective phenomena, such as glass/granular jamming transitions and various aspects of the behavior of active matter. However, conventional techniques (based on a fixed-distance cutoff or the Voronoi construction) have mainly been applied to equilibrated, homogeneous, and monodisperse particle systems. In this paper, we implement simple and efficient methods for local structure analysis in nonequilibrium, inhomogeneous, and polydisperse hard disk systems. We show how these novel methods can overcome the difficulties encountered by conventional techniques as well as demonstrate some applications. [ABSTRACT FROM AUTHOR]

Produced by both nature and human activities, sulfur dioxide (SO2) is an important species in the earth's atmosphere. SO2 has also been found in the atmospheres of other planets and satellites in the solar system. The photoabsorption cross sections and photodissociation of SO2 have been studied for several decades. In this paper, we reported the experimental results for photodissociation dynamics of SO2 via the G ̃ 1B1 state. By analyzing the images from the time-sliced velocity map ion imaging method, the vibrational state population distributions and anisotropy parameters were obtained for the O(1D2) + SO(X3Σ−, a1Δ, b1Σ+) and O(1S0) + SO(X3Σ−) channels, and the branching ratios for the channels O(1D2) + SO(X3Σ−), O(1D2) + SO(a1Δ), and O(1D2) + SO(b1Σ+) were determined to be ∼0.3, ∼0.6, and ∼0.1, respectively. The SO products were dominant in electronically and rovibrationally excited states, which may have yet unrecognized roles in the upper planetary atmosphere. [ABSTRACT FROM AUTHOR]

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

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

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

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

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