Search

Introducing nanorods into a polymeric matrix can enhance the physical and mechanical properties of the resulting material. In this paper, we focus on understanding the dispersion and orientation patterns of nanorods in an unentangled polymer melt, particularly as a function of nanorod concentration, using molecular dynamics simulations. The system is comprised of flexible polymer chains and multi-thread nanorods that are equilibrated in the NPT ensemble. All interactions are purely repulsive except for those between polymers and rods. Results with attractive vs repulsive polymer–rod interactions are compared and contrasted. The concentration of rods has a direct impact on the phase behavior of the system. At lower concentrations, rods phase separate into nematic clusters, whereas at higher concentrations more isotropic and less structured rod configurations are observed. A detailed examination of the conformation of the polymer chains near the rod surface shows extension of the chains along the director of the rods (especially within clusters). The dispersion and orientation of the nanorods are a result of the competition between depletion entropic forces responsible for the formation of rod clusters, the enthalpic effects that improve mixing of rods and polymer, and entropic losses of polymers interpenetrating rod clusters. [ABSTRACT FROM AUTHOR]

Electrochemical impedance spectroscopy (EIS) is a powerful characterization technique for the in-depth investigation of kinetic/transport parameters detection, reaction mechanism understanding, and degradation effects exploration in lithium-ion battery (LIB) systems. However, due to the lack of standardized criterion/paradigm, severe misinterpretations occur frequently during an EIS measurement. In this paper, the significance of instrumental accuracy is described and the character/principle of selection on the simulation model is illuminated/proposed, showing that an adequate precision device and an appropriate fitting model are a prerequisite for a correct EIS analysis. Moreover, the drawbacks of conventional two-electrode EIS experiments for typical coin-type cells are rigorously pointed out by comparison with the ideal three-electrode configuration, where the real impedance information of the cathode would be masked by the sum of both the anode film resistance response and the unavoidable inductive loop signal. The three-electrode case enables efficient accurate observations on individual electrodes, thus facilitating abundant and useful information acquisition. Consequently, devices with a sufficient accuracy, rational simulation models, and advanced three-electrode cells are distinctly illustrated as standardized criterion/paradigm for EIS characterizations, which are essentially important for electrode and interface modifications in LIBs. [ABSTRACT FROM AUTHOR]

Fewest-switches surface hopping (FSSH) has emerged as one of the leading methods for modeling the quantum dynamics of molecular systems. While its original formulation was limited to adiabatic populations, the growing interest in the application of FSSH to coherent phenomena prompts the question of how one should construct a complete density matrix based on FSSH trajectories. A straightforward solution is to define adiabatic coherences based on wavefunction coefficients. In this paper, we demonstrate that inconsistencies introduced in the density matrix through such treatment may lead to a violation of positivity. We furthermore show that a recently proposed coherent generalization of FSSH results in density matrices that satisfy positivity while yielding improved accuracy throughout much (but not all) of parameter space. [ABSTRACT FROM AUTHOR]

The transport of particles through channels is of paramount importance in physics, chemistry, and surface science due to its broad real world applications. Much insight can be gained by observing the transition paths of a particle through a channel and collecting statistics on the lifetimes in the channel or the escape probabilities from the channel. In this paper, we consider the diffusive transport through a narrow conical channel of a Brownian particle subject to intermittent dynamics, namely, stochastic resetting. As such, resetting brings the particle back to a desired location from where it resumes its diffusive phase. To this end, we extend the Fick–Jacobs theory of channel-facilitated diffusive transport to resetting-induced transport. Exact expressions for the conditional mean first passage times, escape probabilities, and the total average lifetime in the channel are obtained, and their behavior as a function of the resetting rate is highlighted. It is shown that resetting can expedite the transport through the channel—rigorous constraints for such conditions are then illustrated. Furthermore, we observe that a carefully chosen resetting rate can render the average lifetime of the particle inside the channel minimal. Interestingly, the optimal rate undergoes continuous and discontinuous transitions as some relevant system parameters are varied. The validity of our one-dimensional analysis and the corresponding theoretical predictions is supported by three-dimensional Brownian dynamics simulations. We thus believe that resetting can be useful to facilitate particle transport across biological membranes—a phenomenon that can spearhead further theoretical and experimental studies. [ABSTRACT FROM AUTHOR]

Using an approach based on the diffusion analog of the Cattaneo–Vernotte differential model, we find the exact analytical solution to the corresponding time-dependent linear hyperbolic initial boundary value problem, describing irreversible diffusion-controlled reactions under Smoluchowski's boundary condition on a spherical sink. By means of this solution, we extend exact analytical calculations for the time-dependent classical Smoluchowski rate coefficient to the case that includes the so-called inertial effects, occurring in the host media with finite relaxation times. We also present a brief survey of Smoluchowski's theory and its various subsequent refinements, including works devoted to the description of the short-time behavior of Brownian particles. In this paper, we managed to show that a known Rice's formula, commonly recognized earlier as an exact reaction rate coefficient for the case of hyperbolic diffusion, turned out to be only its approximation being a uniform upper bound of the exact value. Here, the obtained formula seems to be of great significance for bridging a known gap between an analytically estimated rate coefficient on the one hand and molecular dynamics simulations together with experimentally observed results for the short times regime on the other hand. A particular emphasis has been placed on the rigorous mathematical treatment and important properties of the relevant initial boundary value problems in parabolic and hyperbolic diffusion theories. [ABSTRACT FROM AUTHOR]

In this paper, we investigate prenucleation and heterogeneous nucleation in the liquid Pb/solid Al system as an example of systems with large lattice misfit using molecular dynamics simulation. Solid Pb and Al have a large positive lattice misfit (f) of 18.2% along the densely packed [110] direction. This study reveals that prenucleation occurs at 600 K (an undercooling of 15 K), and a 2-dimensional (2D) ordered structure forms at the interface with a coincidence site lattice (CSL) between the first Pb and first Al layers. The CSL accommodates the major part of the f, and only a small residual lattice misfit (fr) of 1.9% remains. The formation of the CSL transforms the original substrate into a considerably potent nucleant, where the first Pb layer becomes the new surface layer of the substrate. At an undercooling of about 22 K, nucleation proceeds by merging 2D ordered structure through structural templating: the second Pb layer is epitaxial to the CSL Pb layer, the third Pb layer largely accommodates the fr, and the fourth Pb layer is a nearly perfect crystalline plane. Further analysis indicates that the interface with the CSL has a lower interfacial energy than with a cube-to-cube orientation relationship. For the first time, we established that the CSL was an effective mechanism to accommodate the f for systems with a large positive misfits. Heterogeneous nucleation is governed not by a single mechanism (misfit dislocations in Turnbull's model), but instead by various mechanisms depending on f. This study sheds new light on the atomistic mechanism of heterogeneous nucleation. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural properties, assessing dynamic properties in CG modeling is often unfeasible due to the accelerated dynamics of the CG models, which allows for more efficient structural sampling. Therefore, the ultimate goal of the present series of articles is to establish a better correspondence between the FG and CG dynamics. To assess and compare dynamical properties in the FG and the corresponding CG models, we utilize the excess entropy scaling relationship. For Paper I of this series, we provide evidence that the FG and the corresponding CG counterpart follow the same universal scaling relationship. By carefully reviewing and examining the literature, we develop a new theory to calculate excess entropies for the FG and CG systems while accounting for entropy representability. We demonstrate that the excess entropy scaling idea can be readily applied to liquid water and methanol systems at both the FG and CG resolutions. For both liquids, we reveal that the scaling exponents remain unchanged from the coarse-graining process, indicating that the scaling behavior is universal for the same underlying molecular systems. Combining this finding with the concept of mapping entropy in CG models, we show that the missing entropy plays an important role in accelerating the CG dynamics. [ABSTRACT FROM AUTHOR]

For many laser-based methods of material characterization and analysis, a tensor formulation of theory is necessary, especially in techniques that exploit nonlinear or chiral optics. The fundamental interactions that underpin such methods offer various levels of approach to theory, but the most rigorous often lead to equations of considerable complexity. To compute the values for individual material parameters frequently demands making assumptions of extreme simplicity, overly dependent on calculational method, yet still providing unsatisfactory results. A pragmatic and entirely rigorous symmetry-based approach to the irreducible tensorial structures circumvents many of these problems, securing reliable results and guiding the pathway to applications. Instead of focusing on individual tensor components, such an approach can rapidly determine the number of linearly independent quantities—and hence the number of operationally different setups necessary for full characterization. By such means, one can directly ascertain how variations of optical polarization and beam geometry can reliably capture the response of any material system. The use of an irreducible tensor method operates independently of any means that might be chosen to calculate material properties. It removes the need for common simplifying assumptions, such as the approximation of tensorial structure by a scalar representation, adoption of a two-state model, or disregarding near-resonance damping. It also obviates any dependence on a choice of simulation package or quantum-calculational software. In this paper, the principles are set down and illustrated by application to experiments of varying degrees of complexity, including interactions of growing significance in the realm of chiral nonlinear optics. Limitations of this approach are also critically assessed. [ABSTRACT FROM AUTHOR]

Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Qy transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory's accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies. [ABSTRACT FROM AUTHOR]

Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the simulation of electronic dynamics, which plays an essential role in chemical reactions, non-equilibrium dynamics, and material design. These systems are time-dependent, which requires that the corresponding simulation algorithm can be successfully concatenated with itself over different time intervals to reproduce the overall coherent quantum dynamics of the system. In this paper, we quantify such simulation algorithms by the property of being fully-coherent: the algorithm succeeds with arbitrarily high success probability 1 − δ while only requiring a single copy of the initial state. We subsequently develop fully-coherent simulation algorithms based on quantum signal processing (QSP), including a novel algorithm that circumvents the use of amplitude amplification while also achieving a query complexity additive in time t, ln(1/δ), and ln(1/ϵ) for error tolerance ϵ: Θ ‖ H ‖ | t | + ln (1 / ϵ) + ln (1 / δ) . Furthermore, we numerically analyze these algorithms by applying them to the simulation of the spin dynamics of the Heisenberg model and the correlated electronic dynamics of an H2 molecule. Since any electronic Hamiltonian can be mapped to a spin Hamiltonian, our algorithm can efficiently simulate time-dependent ab initio electronic dynamics in the circuit model of quantum computation. Accordingly, it is also our hope that the present work serves as a bridge between QSP-based quantum algorithms and chemical dynamics, stimulating a cross-fertilization between these exciting fields. [ABSTRACT FROM AUTHOR]

Lyotropic liquid crystal phases (LCPs) are widely studied for diverse applications, including protein crystallization and drug delivery. The structure and properties of LCPs vary widely depending on the composition, concentration, temperature, pH, and pressure. High-throughput structural characterization approaches, such as small-angle x-ray scattering (SAXS), are important to cover meaningfully large compositional spaces. However, high-throughput LCP phase analysis for SAXS data is currently lacking, particularly for patterns of multiphase mixtures. In this paper, we develop semi-automated software for high throughput LCP phase identification from SAXS data. We validate the accuracy and time-savings of this software on a total of 668 SAXS patterns for the LCPs of the amphiphile hexadecyltrimethylammonium bromide (CTAB) in 53 acidic or basic ionic liquid derived solvents, within a temperature range of 25–75 °C. The solvents were derived from stoichiometric ethylammonium nitrate (EAN) or ethanolammonium nitrate (EtAN) by adding water to vary the ionicity, and adding precursor ions of ethylamine, ethanolamine, and nitric acid to vary the pH. The thermal stability ranges and lattice parameters for CTAB-based LCPs obtained from the semi-automated analysis showed equivalent accuracy to manual analysis, the results of which were previously published. A time comparison of 40 CTAB systems demonstrated that the automated phase identification procedure was more than 20 times faster than manual analysis. Moreover, the high throughput identification procedure was also applied to 300 unpublished scattering patterns of sodium dodecyl-sulfate in the same EAN and EtAN based solvents in this study, to construct phase diagrams that exhibit phase transitions from micellar, to hexagonal, cubic, and lamellar LCPs. The accuracy and significantly low analysis time of the high throughput identification procedure validates a new, rapid, unrestricted analytical method for the determination of LCPs. [ABSTRACT FROM AUTHOR]

This paper presents a theoretical investigation of the design of a new actuator type made of anisotropic colloidal particles grafted with stimuli-responsive polymer chains. These artificial muscles combine the osmotic actuation principle of stimuli-responsive hydrogels with the structural alignment of colloidal liquid crystals to achieve directional motion. The solubility of the stimuli-responsive polymer in the neutral state, its degree of polymerization, the salt concentration, and the grafting density of the polymer chains on the surface of the colloidal particles are investigated and identified as important for actuator performance and tunability. The computational results suggest that the proposed mechanically active material matches or exceeds the performances of natural muscles and provide the guidelines for the realization of artificial muscles with predetermined actuation properties. [ABSTRACT FROM AUTHOR]

Light-induced orientation of gas phase molecules is a long-pursued goal in physics and chemistry. Here, we experimentally demonstrate a six-fold increase in the terahertz-induced orientation of iodomethane (CH3I) molecules at room temperature, provided by rotational pre-excitation with a moderately intense near-IR pulse. The paper highlights the underlying interference of multiple coherent transition pathways within the rotational coherence manifold and is analyzed accordingly. Our experimental and theoretical results provide desirable and practical means for all-optical experiments on oriented molecular ensembles. [ABSTRACT FROM AUTHOR]

This paper presents a state-averaged complete active space self-consistent field (SA-CASSCF) in the atomic multipole optimized energetics for biomolecular application (AMOEBA) polarizable water model, which enables rigorous simulation of non-adiabatic molecular dynamics with nonequilibrium solvation effects. The molecular orbital and configuration interaction coefficients of the solute wavefunction, and the induced dipoles on solvent atoms, are solved by minimizing the state averaged energy variationally. In particular, by formulating AMOEBA water models and the polarizable continuum model (PCM) in a unified way, the algorithms developed for computing SA-CASSCF/PCM energies, analytical gradients, and non-adiabatic couplings in our previous work can be generalized to SA-CASSCF/AMOEBA by properly substituting a specific list of variables. Implementation of this method will be discussed with the emphasis on how the calculations of different terms are partitioned between the quantum chemistry and molecular mechanics codes. We will present and discuss results that demonstrate the accuracy and performance of the implementation. Next, we will discuss results that compare three solvent models that work with SA-CASSCF, i.e., PCM, fixed-charge force fields, and the newly implemented AMOEBA. Finally, the new SA-CASSCF/AMOEBA method has been interfaced with the ab initio multiple spawning method to carry out non-adiabatic molecular dynamics simulations. This method is demonstrated by simulating the photodynamics of the model retinal protonated Schiff base molecule in water. [ABSTRACT FROM AUTHOR]

Quantum mechanics has a deterministic Schrödinger equation for the wave function. The Göttingen–Copenhagen statistical interpretation is based on the Born Rule that interprets the wave function as a "probability amplitude." A precept of this interpretation is the lack of determinism in quantum mechanics. The Bohm interpretation is that the wave function is a source of a field experienced by the electrons, thereby attributing determinism to quantum theory. In this paper, we present a new perspective on such determinism. The ideas are based on the equations of motion or "Quantal Newtonian" Laws obeyed by each electron. These Laws, derived from the temporal and stationary-state Schrödinger equation, are interpreted in terms of "classical" fields whose sources are quantal expectations of Hermitian operators taken with respect to the wave function. According to the Second Law, each electron experiences an external field—the quantal Coulomb-Lorentz law. It also experiences an internal field representative of properties of the system: correlations due to Coulomb repulsion and Pauli principle; the density; kinetic effects; and an internal magnetic field component. There is a response field. The First Law states that the sum of the external and internal fields experienced by each electron vanishes. These fields are akin to those of classical physics: They pervade all space; their structure is descriptive of the quantum system; the energy of the system is stored in these fields. It is in the classical behavior of these fields, which arise from quantal sources that one may then speak of determinism in quantum mechanics. [ABSTRACT FROM AUTHOR]

Ambient pressure x-ray photoelectron spectroscopy (APXPS) can provide a compelling platform for studying an analyte's oxidation and reduction reactions in solutions. This paper presents proof-of-principle operando measurements of a model organometallic complex, iron hexacyanide, in an aqueous solution using the dip-and-pull technique. The data demonstrates that the electrochemically active liquid meniscuses on the working electrodes can undergo controlled redox reactions which were observed using APXPS. A detailed discussion of several critical experimental considerations is included as guidance for anyone undertaking comparable experiments. [ABSTRACT FROM AUTHOR]

Spiky coatings (also known as nanoforests or Fakir-like surfaces) have found many applications in chemical physics, material sciences, and biotechnology, such as superhydrophobic materials, filtration and sensing systems, and selective protein separation, to name but a few. In this paper, we provide a systematic study of steady-state diffusion toward a periodic array of absorbing cylindrical pillars protruding from a flat base. We approximate a periodic cell of this system by a circular tube containing a single pillar, derive an exact solution of the underlying Laplace equation, and deduce a simple yet exact representation for the total flux of particles onto the pillar. The dependence of this flux on the geometric parameters of the model is thoroughly analyzed. In particular, we investigate several asymptotic regimes, such as a thin pillar limit, a disk-like pillar, and an infinitely long pillar. Our study sheds light onto the trapping efficiency of spiky coatings and reveals the roles of pillar anisotropy and diffusional screening. [ABSTRACT FROM AUTHOR]

Some diarylethene molecular switches have a low quantum yield for cycloreversion when excited by a single photon, but react more efficiently following sequential two-photon excitation. The increase in reaction efficiency depends on both the relative time delay and the wavelength of the second photon. This paper examines the wavelength-dependent mechanism for sequential excitation using excited-state resonance Raman spectroscopy to probe the ultrafast (sub-30 fs) dynamics on the upper electronic state following secondary excitation. The approach uses femtosecond stimulated Raman scattering (FSRS) to measure the time-gated, excited-state resonance Raman spectrum in resonance with two different excited-state absorption bands. The relative intensities of the Raman bands reveal the initial dynamics in the higher-lying states, Sn, by providing information on the relative gradients of the potential energy surfaces that are accessed via secondary excitation. The excited-state resonance Raman spectra reveal specific modes that become enhanced depending on the Raman excitation wavelength, 750 or 400 nm. Many of the modes that become enhanced in the 750 nm FSRS spectrum are assigned as vibrational motions localized on the central cyclohexadiene ring. Many of the modes that become enhanced in the 400 nm FSRS spectrum are assigned as motions along the conjugated backbone and peripheral phenyl rings. These observations are consistent with earlier measurements that showed higher efficiency following secondary excitation into the lower excited-state absorption band and illustrate a powerful new way to probe the ultrafast dynamics of higher-lying excited states immediately following sequential two-photon excitation. [ABSTRACT FROM AUTHOR]

In this study, based on the theory developed in Paper I, we explore the combined effects of molecular fluorescence and excitation energy transfer in a minimal model—a pair of single-vibration-mode chromophores coupled to surface plasmon polaritons. For the chromophores with zero Huang–Rhys factors and strong couplings to surface plasmon polaritons, we find that the frequencies of Rabi oscillations (the strengths of strong light–matter couplings) are associated with the initial excitation conditions. On the other hand, for the chromophores weakly coupled to surface plasmon polaritons, our numerical calculations together with analytical analysis elaborate on the conditions for the superradiant and subradiant decay behaviors. Moreover, we show that the modified decay rate constants can be explicitly expressed in terms of generalized spectral densities (or dyadic Green's functions), revealing a relationship between photonic environments and the collective effects such as superradiance and subradiance. For the chromophores with nonzero Huang–Rhys factors and strong coupling to surface plasmon polaritons, the effects of molecular vibrations emerge. We demonstrate that the low-frequency vibrational modes do not affect the excited state population dynamics, while the high-frequency vibrational modes can modify either the period of Rabi oscillation (Franck–Condon Rabi oscillation) or the amplitude of excited state population. Our study shows that the collective effects, including superradiance and subradiance, can be controlled via dielectric environments and initial excitation conditions, providing new insights into polariton chemistry and the design of quantum optical devices. [ABSTRACT FROM AUTHOR]

In a recent paper [A. D. Becke, J. Chem. Phys. 156, 214101 (2022)], we compared two Kohn–Sham density functionals based on physical modeling and theory with the best density-functional power series fits in the literature. With only a handful of physically motivated pre-factors, our functionals matched, and even slightly exceeded, the performance of the best power-series functionals on the general main group thermochemistry, kinetics, and noncovalent interactions (GMTKN55) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. This begs the question: how much can their performance be improved by adding power-series terms of our own? We address this question in the present work. First, we describe a series expansion variable that we believe contains more local physics than any other variable considered to date. Then we undertake modest, one-dimensional fits to the GMTKN55 data with our theory-based functional corrected by power-series exchange and dynamical correlation terms. We settle on 12 power-series terms (plus six parent terms) and achieve the lowest GMTKN55 "WTMAD2" error yet reported, by a substantial margin, for a hybrid Kohn–Sham density functional. The new functional is called "B22plus." [ABSTRACT FROM AUTHOR]

The formalism of the generalized quantum master equation (GQME) is an effective tool to simultaneously increase the accuracy and the efficiency of quasiclassical trajectory methods in the simulation of nonadiabatic quantum dynamics. The GQME expresses correlation functions in terms of a non-Markovian equation of motion, involving memory kernels that are typically fast-decaying and can therefore be computed by short-time quasiclassical trajectories. In this paper, we study the approximate solution of the GQME, obtained by calculating the kernels with two methods: Ehrenfest mean-field theory and spin-mapping. We test the approaches on a range of spin–boson models with increasing energy bias between the two electronic levels and place a particular focus on the long-time limits of the populations. We find that the accuracy of the predictions of the GQME depends strongly on the specific technique used to calculate the kernels. In particular, spin-mapping outperforms Ehrenfest for all the systems studied. The problem of unphysical negative electronic populations affecting spin-mapping is resolved by coupling the method with the master equation. Conversely, Ehrenfest in conjunction with the GQME can predict negative populations, despite the fact that the populations calculated from direct dynamics are positive definite. [ABSTRACT FROM AUTHOR]

In this paper, we report an open system consisting of three self-replicating peptides, in which peptide 1 inhibits the duplex template of peptide 2, peptide 2 inhibits duplex 3, and peptide 3 inhibits duplex 1 to complete the negative feedback loop. This interacting chemical network yields oscillations in the concentrations of all species over time and establishes a possible mechanism for pre-biotic chemical systems organization. The first focus of our analysis is the effect of altering rates of duplex formation and inhibition on oscillations. We then examine the autocatalytic rate constant in the symmetric and asymmetric cases. [ABSTRACT FROM AUTHOR]

Recent experiments of chemical reactions in optical cavities have shown great promise to alter and steer chemical reactions, but still remain poorly understood theoretically. In particular, the origin of resonant effects between the cavity and certain vibrational modes in the collective limit is still subject to active research. In this paper, we study the unimolecular dissociation reactions of many molecules, collectively interacting with an infrared cavity mode, through their vibrational dipole moment. We find that the reaction rate can slow down by increasing the number of aligned molecules, if the cavity mode is resonant with a vibrational mode of the molecules. We also discover a simple scaling relation that scales with the collective Rabi splitting, to estimate the onset of reaction rate modification by collective vibrational strong coupling and numerically demonstrate these effects for up to 104 molecules. [ABSTRACT FROM AUTHOR]

This paper provides results of dielectric relaxation (DR) spectroscopy of aqueous solutions of tris(hydroxymethyl)aminomethane (Tris) covering frequencies of 0.05 ≤ ν/GHz ≤ 89. The DR spectra can be well fit by a sum of Cole–Cole relaxation, assigned to the solute, and 2 Debye modes already observed for neat water. Analysis of the amplitudes reveals that Tris is hydrated by 7 H2Os up to its solubility limit. However, the rather high effective solute dipole moment of ≈12 D suggests that H2O dipoles in contact with Tris should reorient independently from it. Accordingly, an alternative description of the DR spectra with a superposition of 4 Debyerelaxations was attempted. In this model, the slowest mode at ∼4 GHz arises from solute reorientation and that at ∼8 GHz was assigned to dynamically retarded hydration water, whereas relaxations at ∼18 and ∼500 GHz are again those of (rather unperturbed) bulk water. Analysis of the solvent-related modes shows that Tris indeed slows down 7–8 H2O molecules. However, the solute–solvent interaction strength is rather weak, excluding the rotation of an alleged Tris-(7–8) H2O cluster as an entity. The now derived effective dipole moment of (6.3 ± 0.5) D for the bare Tris molecule allows speculations on its conformation. With the help of computational methods, we suggest that Tris dissolved in water most likely possesses an intramolecular H-bond between the nitrogen and hydrogen atoms of amino and hydroxyl groups, respectively. In addition, computational results indicate that the seven hydration H2Os found by DR bind directly to the Tris OH groups. [ABSTRACT FROM AUTHOR]

Dilute magnetic semiconductors (DMSs) with both charge and spin degrees of freedom have emerged as promising candidates in the spintronic industry. However, the Curie temperature below room temperature and uncertainty about the origin of ferromagnetism hinder the application of DMSs. To address these issues, we explored a better SnO2-based co-doped method (Fe, V + VSn) using ab initio calculations. The calculation results show that the Sn13FeVO32 (Fe, V + VSn) has a high Curie temperature (716 K), good ferromagnetic properties, stronger covalency of bonds, and better optical transparency in the visible light range. In addition, the holes or electrons generated by the complexes in the (Fe, V + VO/VSn) co-doped system cause a spin-polarized double exchange effect in the Fe-3d, V-3d, and O-2p orbitals, which leads to magnetism of the co-doped systems. The static dielectric constant ɛ1(0) of the system increases after doping. Among them, Sn14FeVO31 (Fe, V + VO) has the largest ɛ1(0), indicating that Sn14FeVO31 has the strongest polarization ability and better photocatalytic properties. In Sn14FeVO31, the imaginary part of the dielectric function and the absorption spectrum all have new peaks in the low-energy region, which are caused by the jump of electrons from the guide band of the spin-polarized impurity energy level. This paper proposes a new method for preparing dilute magnetic semiconductors in spin electronic devices with high room temperature ferromagnetic properties and excellent optical properties through the (Fe, V + VO/VSn) co-doped SnO2. [ABSTRACT FROM AUTHOR]

Seniority-zero geminal wavefunctions are known to capture bond-breaking correlation. Among this class of wavefunctions, Richardson–Gaudin states stand out as they are eigenvectors of a model Hamiltonian. This provides a clear physical picture, clean expressions for reduced density matrix (RDM) elements, and systematic improvement (with a complete set of eigenvectors). Known expressions for the RDM elements require the computation of rapidities, which are obtained by first solving for the so-called eigenvalue based variables (EBV) and then root-finding a Lagrange interpolation polynomial. In this paper, we obtain expressions for the RDM elements directly in terms of the EBV. The final expressions can be computed at the same cost as the rapidity expressions. Therefore, except, in particular, circumstances, it is entirely unnecessary to compute rapidities at all. The RDM elements require numerically inverting a matrix, and while this is usually undesirable, we demonstrate that it is stable, except when there is degeneracy in the single-particle energies. In such cases, a different construction would be required. [ABSTRACT FROM AUTHOR]

Both the reweighting factor and the modified T-move algorithm proposed in this work contribute to reducing the time-step errors. Both the reweighting factor and the modified T-move algorithm proposed in this work contribute to reducing the time-step errors. We discovered a programming error and an error in some of the input files, which led us to recommend a reweighting factor that gives a positive and far from optimal time-step error. [Extracted from the article]

In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction. [ABSTRACT FROM AUTHOR]

This paper presents further development of the new semi-classical trajectory-based formalism described in Paper I [Chistikov et al., J. Chem. Phys. 151, 194106 (2019)]. We report the results of simulation and analysis of the low-frequency collision-induced absorption (CIA) in CO2–Ar, including its true dimer component. Our consideration relies on the use of ab initio intermolecular potential energy and induced dipole surfaces for CO2–Ar calculated in an assumption of a rigid CO2 structure using the CCSD(T) method. The theory, the details of which are reported in Paper I [Chistikov et al., J. Chem. Phys. 151, 194106 (2019)], permits taking into account the effect of unbound and quasi-bound classical trajectories on the CIA in the range of a rototranslational band. This theory is largely extended by trajectory-based simulation of the true bound dimer absorption in the present paper. The spectra are obtained from a statistical average over a vast ensemble of classical trajectories restricted by properly chosen domains in the phase space. Rigorous classical theory is developed for two low-order spectral moments interpreted as the Boltzmann-weighted average of the respective dipole functions. These spectral moments were then used to check the accuracy of our trajectory-based spectra, for which both spectral moments can be evaluated independently in terms of specific integrals over the trajectory-based calculated spectral profiles. Good agreement between the spectral moments calculated as integrals over the frequency domain or the phase space largely supports the reliability of our simulated CIA spectra, which conform with the available microwave and far-infrared observations. [ABSTRACT FROM AUTHOR]

Often, a single correlation function is used to measure the kinetics of a complex system. In contrast, a large set of k-vector modes and their correlation functions are commonly defined for motion in free space. This set can be transformed to the van Hove correlation function, which is the Green's function for molecular diffusion. Here, these ideas are generalized to other observables. A set of correlation functions of nonlinear functions of an observable is used to extract the corresponding Green's function. Although this paper focuses on nonlinear correlation functions of an equilibrium time series, the results are directly connected to other types of nonlinear kinetics, including perturbation–response experiments with strong fields. Generalized modes are defined as the orthogonal polynomials associated with the equilibrium distribution. A matrix of mode-correlation functions can be transformed to the complete, single-time-interval (1D) Green's function. Diagonalizing this matrix finds the eigendecays. To understand the advantages and limitation of this approach, Green's functions are calculated for a number of models of complex dynamics within a Gaussian probability distribution. Examples of non-diffusive motion, rate heterogeneity, and range heterogeneity are examined. General arguments are made that a full set of nonlinear 1D measurements is necessary to extract all the information available in a time series. However, when a process is neither dynamically Gaussian nor Markovian, they are not sufficient. In those cases, additional multidimensional measurements are needed. [ABSTRACT FROM AUTHOR]

Allowing triplet components of individual geminals, spin-contaminated strongly orthogonal geminal wave functions may emerge, which can be ameliorated by spin-projection techniques. Of the latter, half-projection was previously shown to be useful, offering a compromise between the amount of remaining spin-contamination and the violation of size consistency generated by projection. This paper investigates how a half-projected spin-contaminated geminal wave function can be improved by multi-configuration perturbation theory to incorporate dynamical correlation effects. [ABSTRACT FROM AUTHOR]

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

Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca 2 + , Cd 2 + , Cu 2 + , Fe 2 + , Hg 2 + , Mg 2 + , Ni 2 + , Pb 2 + , and Zn 2 + , we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M( H 2 O)2]2+ aqua complexes to [M( H 2 O) 9]2+, allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M( H 2 O) n]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion–water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data. [ABSTRACT FROM AUTHOR]

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

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

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

Previous studies have shown that NaB6, KB6, and RbB6 adopting Pm 3 ̄ m are superconductors with a relatively high Tc under ambient conditions. In this paper, we conducted systematic structural and related properties research on CsB6 through a genetic evolution algorithm and total energy calculations based on density functional theory between 0 and 20 GPa. Our results reveal a cubic Pm 3 ̄ m CsB6, which is dynamically stable under the pressures we studied. We systematically calculated the formation enthalpies, electronic properties, and superconducting properties of Pm 3 ̄ m MB6 (M = Na, K, Rb, Cs). They all exhibit metallic features, and boron has high contributions to band structures, density of states, and electron–phonon coupling (EPC). The calculated results about the Helmholtz free energy difference of Pm 3 ̄ m CsB6 at 0, 10, and 20 GPa indicate that it is stable upon chemical decomposition (decomposition to simple substances Cs and B) from 0 to 400 K. The phonon density of states indicates that boron atoms occupy the high frequency area. The EPC results show that Pm 3 ̄ m CsB6 is a superconductor with Tc = 11.7 K at 0 GPa, close to NaB6 (13.1 K), KB6 (11.7 K), and RbB6 (11.3 K) at 0 GPa in our work, which indicates that boron atoms play an essential role in superconductivity: vibrations of B6 regular octagons lead to the high Tc of Pm 3 ̄ m MB6. Our work about Pm 3 ̄ m hexaborides provides a supplementary study on the borides of the group IA elements (without Fr and Li) and has an important guiding significance for the experimental synthesis of CsB6. [ABSTRACT FROM AUTHOR]

This paper presents a general second-quantized form of a permutation operator interchanging n pairs of electrons between interacting subsystems in the framework of the symmetry-adapted perturbation theory (SAPT). We detail the procedure for constructing this operator through the consecutive multiplication of single-pair permutation operators. This generalized form of the permutation operator has enabled the derivation of universal formulas for S2n approximations of the exchange energies in the first and second order of the interaction operator. We present expressions for corrections of S4 approximations and assess its efficacy on a selection of systems anticipated to exhibit a slowly converging overlap expansion. Additionally, we outline a method to sum the overlap expansion series to infinity in second-quantization, up to the second order in V. This new approach offers an alternative to the existing formalism based on density-matrix formulations. When combined with a symbolic algebra program for automated derivations, it paves the way for advancements in SAPT theory, particularly for intricate wavefunction theories. [ABSTRACT FROM AUTHOR]

Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light–matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori–Nakajima–Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method's capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O (1 0 3 ) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies. [ABSTRACT FROM AUTHOR]

This paper reports the energies and charge and spin distributions of the low-lying excited states in singlet and triplet N2V defects in diamond from direct Δ-SCF calculations based on Gaussian orbitals within the B3LYP, PBE0, and HSE06 functionals. They assign the observed absorption at 2.463 eV, first reported by Davies et al. [Proc. R. Soc. London 351, 245 (1976)], to the excitation of a N(sp3) lone-pair electron in the singlet and triplet states, respectively, with estimates of ∼1.1 eV for that of the unpaired electrons, C(sp3). In both cases, the excited states are predicted to be highly local and strongly excitonic with 81% of the C(sp3) and 87% of the N(sp3) excited charges localized at the three C atoms nearest neighbor (nn) to the excitation sites. Also reported are the higher excited gap states of both the N lone pair and C unpaired electron. Calculated excitation energies of the bonding sp3 hybrids of the C atoms nn to the four inner atoms are close to that of the bulk, which indicates that the N2V defect is largely a local defect. The present results are in broad agreement with those reported by Udvarhelyi et al. [Phys. Rev. B 96, 155211 (2017)] from plane wave HSE06 calculations, notably for the N lone pair excitation energy, for which both predict an energy of ∼2.7 eV but with a difference of ∼0.5 eV for the excitation of the unpaired electron. [ABSTRACT FROM AUTHOR]

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

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

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

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

A major limitation of amine-based post-combustion carbon capture technology is the necessity to regenerate amines at high temperatures, which dramatically increases operating costs. This paper concludes the effect of solvent choice as a possible route to modify the thermodynamics and kinetics characterizing the involved amine regeneration reactions and discusses whether these modifications can be economically beneficial. We report experimentally benchmarked computational chemistry calculations of monoethanolamine regeneration reactions employing aqueous and non-aqueous solvents with a wide range of dielectric constants. Unlike previous studies, our improved computational chemistry framework could accurately reproduce the right experimental activation energy of zwitterion formation. From the thermodynamics and kinetics of the predicted reactions, the use of non-aqueous solvents with small dielectric constants led to reductions in regeneration Gibbs free energies, activation barriers, and enthalpy changes. This can reduce energy consumption and give an opportunity to run desorption columns at relatively lower temperatures, thus offering the possibility of relying on low-grade waste heat as an energy input. [ABSTRACT FROM AUTHOR]

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

In this paper, we demonstrate that the weak temperature dependence of the structure factor of supercooled liquids, a defining feature of the glass transition, is a consequence of the averaging of the scattering intensity due to angular averaging. We show that the speckle at individual wavevectors, calculated from a simulated glass former, exhibits a Debye–Waller factor with a sufficiently large temperature dependence to represent a structural order parameter capable of distinguishing liquid from glass. We also extract from the speckle intensities a quantity proportional to the variance of the local restraint, i.e., a direct experimental measure of the amplitude of structural heterogeneity. [ABSTRACT FROM AUTHOR]

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

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

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