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

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

A photovoltaic device fabricated with conventional zincblende materials can use the Type-II quantum well structure, which spatially separates electrons and holes, to reduce their recombination rate. In order to obtain higher power conversion efficiency, it is desirable to preserve more energetic carriers by engineering a phonon "bottleneck," a mismatch between the gaps in the well and barrier phonon structure. Such a mismatch leads to poor phonon transport and therefore prevents energy from leaving the system in the form of heat. In this paper, we perform a superlattice phonon calculation to verify the "bottleneck" effect and build on this a model to predict the steady state of the hot electrons under photoexcitation. We describe the electrons and phonons with a coupled Boltzmann equation system and numerically integrate it to get the steady state. We find that inhibited phonon relaxation does lead to a more out-of-equilibrium electron distribution and discuss how this might be enhanced. We examine the different behaviors obtained for various combinations of recombination and relaxation rates and their experimental signatures. [ABSTRACT FROM AUTHOR]

Simulations of exciton and charge hopping in amorphous organic materials involve numerous physical parameters. Each of these parameters must be computed from costly ab initio calculations before the simulation can commence, resulting in a significant computational overhead for studying exciton diffusion, especially in large and complex material datasets. While the idea of using machine learning to quickly predict these parameters has been explored previously, typical machine learning models require long training times, which ultimately contribute to simulation overheads. In this paper, we present a new machine learning architecture for building predictive models for intermolecular exciton coupling parameters. Our architecture is designed in such a way that the total training time is reduced compared to ordinary Gaussian process regression or kernel ridge regression models. Based on this architecture, we build a predictive model and use it to estimate the coupling parameters which enter into an exciton hopping simulation in amorphous pentacene. We show that this hopping simulation is able to achieve excellent predictions for exciton diffusion tensor elements and other properties as compared to a simulation using coupling parameters computed entirely from density functional theory. This result, along with the short training times afforded by our architecture, shows how machine learning can be used to reduce the high computational overheads associated with exciton and charge diffusion simulations in amorphous organic materials. [ABSTRACT FROM AUTHOR]

In this paper, we outline a physically motivated framework for describing spin-selective recombination processes in chiral systems, from which we derive spin-selective reaction operators for recombination reactions of donor–bridge–acceptor molecules, where the electron transfer is mediated by chirality and spin–orbit coupling. In general, the recombination process is selective only for spin-coherence between singlet and triplet states, and it is not, in general, selective for spin polarization. We find that spin polarization selectivity only arises in hopping-mediated electron transfer. We describe how this effective spin-polarization selectivity is a consequence of spin-polarization generated transiently in the intermediate state. The recombination process also augments the coherent spin dynamics of the charge separated state, which is found to have a significant effect on the recombination dynamics and to destroy any long-lived spin polarization. Although we only consider a simple donor–bridge–acceptor system, the framework we present here can be straightforwardly extended to describe spin-selective recombination processes in more complex systems. [ABSTRACT FROM AUTHOR]

The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided. [ABSTRACT FROM AUTHOR]

A large number of force fields have been proposed for describing the behavior of liquid water within classical atomistic simulations, particularly molecular dynamics. In the past two decades, models that incorporate molecular polarizability and even charge transfer have become more prevalent, in attempts to develop more accurate descriptions. These are frequently parameterized to reproduce the measured thermodynamics, phase behavior, and structure of water. On the other hand, the dynamics of water is rarely considered in the construction of these models, despite its importance in their ultimate applications. In this paper, we explore the structure and dynamics of polarizable and charge-transfer water models, with a focus on timescales that directly or indirectly relate to hydrogen bond (H-bond) making and breaking. Moreover, we use the recently developed fluctuation theory for dynamics to determine the temperature dependence of these properties to shed light on the driving forces. This approach provides key insight into the timescale activation energies through a rigorous decomposition into contributions from the different interactions, including polarization and charge transfer. The results show that charge transfer effects have a negligible effect on the activation energies. Furthermore, the same tension between electrostatic and van der Waals interactions that is found in fixed-charge water models also governs the behavior of polarizable models. The models are found to involve significant energy–entropy compensation, pointing to the importance of developing water models that accurately describe the temperature dependence of water structure and dynamics. [ABSTRACT FROM AUTHOR]

Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios. [ABSTRACT FROM AUTHOR]

In this paper, the solubility of carbon dioxide (CO2) in water along the isobar of 400 bar is determined by computer simulations using the well-known TIP4P/Ice force field for water and the TraPPE model for CO2. In particular, the solubility of CO2 in water when in contact with the CO2 liquid phase and the solubility of CO2 in water when in contact with the hydrate have been determined. The solubility of CO2 in a liquid–liquid system decreases as the temperature increases. The solubility of CO2 in a hydrate–liquid system increases with temperature. The two curves intersect at a certain temperature that determines the dissociation temperature of the hydrate at 400 bar (T3). We compare the predictions with T3 obtained using the direct coexistence technique in a previous work. The results of both methods agree, and we suggest 290(2) K as the value of T3 for this system using the same cutoff distance for dispersive interactions. We also propose a novel and alternative route to evaluate the change in chemical potential for the formation of hydrates along the isobar. The new approach is based on the use of the solubility curve of CO2 when the aqueous solution is in contact with the hydrate phase. It considers rigorously the non-ideality of the aqueous solution of CO2, providing reliable values for the driving force for nucleation of hydrates in good agreement with other thermodynamic routes used. It is shown that the driving force for hydrate nucleation at 400 bar is larger for the methane hydrate than for the carbon dioxide hydrate when compared at the same supercooling. We have also analyzed and discussed the effect of the cutoff distance of dispersive interactions and the occupancy of CO2 on the driving force for nucleation of the hydrate. [ABSTRACT FROM AUTHOR]

The development of multireference coupled cluster (MRCC) techniques has remained an open area of study in electronic structure theory for decades due to the inherent complexity of expressing a multiconfigurational wavefunction in the fundamentally single-reference coupled cluster framework. The recently developed multireference-coupled cluster Monte Carlo (mrCCMC) technique uses the formal simplicity of the Monte Carlo approach to Hilbert space quantum chemistry to avoid some of the complexities of conventional MRCC, but there is room for improvement in terms of accuracy and, particularly, computational cost. In this paper, we explore the potential of incorporating ideas from conventional MRCC—namely, the treatment of the strongly correlated space in a configuration interaction formalism—to the mrCCMC framework, leading to a series of methods with increasing relaxation of the reference space in the presence of external amplitudes. These techniques offer new balances of stability and cost against accuracy, as well as a means to better explore and better understand the structure of solutions to the mrCCMC equations. [ABSTRACT FROM AUTHOR]

In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo sampled and that the corresponding calculations achieve size-invariant [i.e., O (1) ] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method. [ABSTRACT FROM AUTHOR]

In this paper, we present a covariant approach that utilizes Noether's second theorem to derive a symmetric stress tensor from the grand thermodynamic potential functional. We focus on the practical case where the density of the grand thermodynamic potential is dependent on the first and second coordinate derivatives of the scalar order parameters. Our approach is applied to several models of inhomogeneous ionic liquids that consider electrostatic correlations of ions or short-range correlations related to packing effects. Specifically, we derive analytical expressions for the symmetric stress tensors of the Cahn–Hilliard-like model, Bazant–Storey–Kornyshev model, and Maggs–Podgornik–Blossey model. All of these expressions are found to be consistent with respective self-consistent field equations. [ABSTRACT FROM AUTHOR]

In this paper, we present a new module to predict the potential surface reconstruction configurations of given surface structures in the framework of our machine learning and graph theory assisted universal structure searcher. In addition to random structures generated with specific lattice symmetry, we made full use of bulk materials to obtain a better distribution of population energy, namely, randomly appending atoms to a surface cleaved from bulk structures or moving/removing some of the atoms on the surface, which is inspired by natural surface reconstruction processes. In addition, we borrowed ideas from cluster predictions to spread structures better between different compositions, considering that surface models of different atom numbers usually have some building blocks in common. To validate this newly developed module, we tested it with studies on the surface reconstructions of Si (100), Si (111), and 4H–SiC (1 1 ̄ 02) − c (2 × 2) , respectively. We successfully gave the known ground states, as well as a new SiC surface model, in an extremely Si-rich environment. [ABSTRACT FROM AUTHOR]

Semiflexible slender filaments are ubiquitous in nature and cell biology, including in the cytoskeleton, where reorganization of actin filaments allows the cell to move and divide. Most methods for simulating semiflexible inextensible fibers/polymers are based on discrete (bead-link or blob-link) models, which become prohibitively expensive in the slender limit when hydrodynamics is accounted for. In this paper, we develop a novel coarse-grained approach for simulating fluctuating slender filaments with hydrodynamic interactions. Our approach is tailored to relatively stiff fibers whose persistence length is comparable to or larger than their length and is based on three major contributions. First, we discretize the filament centerline using a coarse non-uniform Chebyshev grid, on which we formulate a discrete constrained Gibbs–Boltzmann (GB) equilibrium distribution and overdamped Langevin equation for the evolution of unit-length tangent vectors. Second, we define the hydrodynamic mobility at each point on the filament as an integral of the Rotne–Prager–Yamakawa kernel along the centerline and apply a spectrally accurate "slender-body" quadrature to accurately resolve the hydrodynamics. Third, we propose a novel midpoint temporal integrator, which can correctly capture the Ito drift terms that arise in the overdamped Langevin equation. For two separate examples, we verify that the equilibrium distribution for the Chebyshev grid is a good approximation of the blob-link one and that our temporal integrator for overdamped Langevin dynamics samples the equilibrium GB distribution for sufficiently small time step sizes. We also study the dynamics of relaxation of an initially straight filament and find that as few as 12 Chebyshev nodes provide a good approximation to the dynamics while allowing a time step size two orders of magnitude larger than a resolved blob-link simulation. We conclude by applying our approach to a suspension of cross-linked semiflexible fibers (neglecting hydrodynamic interactions between fibers), where we study how semiflexible fluctuations affect bundling dynamics. We find that semiflexible filaments bundle faster than rigid filaments even when the persistence length is large, but show that semiflexible bending fluctuations only further accelerate agglomeration when the persistence length and fiber length are of the same order. [ABSTRACT FROM AUTHOR]

Second-order N-electron valence state perturbation theory (NEVPT2) is an exactly size-consistent and intruder-state-free multi-reference theory. To accelerate the NEVPT2 computation, Guo and Neese combined it with the local pair-natural orbital (PNO) method using the projected atomic orbitals (PAOs) as the underlying local basis [Guo et al., J. Chem. Phys. 144, 094111 (2016)]. In this paper, we report the further development of the PNO-NEVPT2 method using the orthonormal and non-redundant localized virtual molecular orbitals (LVMOs) instead of PAOs. The LVMOs were previously considered to perform relatively poor compared to PAOs because the resulting orbital domains were unacceptably large. Our prior work, however, showed that this drawback can be remedied by re-forming the domain construction scheme using differential overlap integrals [Saitow et al., J. Chem. Phys. 157, 084101 (2022)]. In this work, we develop further refinements to enhance the feasibility of using LVMOs. We first developed a two-level semi-local approach for screening out so-called weak-pairs to select or truncate the pairs for PNO constructions more flexibly. As a refinement specific to the Pipek–Mezey localization for LVMOs, we introduced an iterative scheme to truncate the Givens rotations using varying thresholds. We assessed the LVMO-based PNO-NEVPT2 method through benchmark calculations for linear phenyl alkanes, which demonstrate that it performs comparably well relative to the PAO-based approach. In addition, we evaluated the Co–C bond dissociation energies for the cobalamin derivatives composed of 200 or more atoms, which confirms that the LVMO-based method can recover more than 99.85% of the canonical NEVPT2 correlation energy. [ABSTRACT FROM AUTHOR]

In two recent papers [A. D. Becke, J. Chem. Phys. 156, 214101 (2022) and A. D. Becke, J. Chem. Phys. 157, 234102 (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. The best error statistics reported to date for a hybrid functional on the general main-group thermochemistry, kinetics, and noncovalent interactions (GMTKN55) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)] were obtained. In the present work, additional second-order perturbation-theory terms are considered. The result is a 12-parameter double-hybrid density functional with the lowest GMTKN55 WTMAD2 "weighted total mean absolute deviation" error (1.76 kcal/mol) yet seen for any hybrid or double-hybrid density-functional approximation. We call it "DH23." [ABSTRACT FROM AUTHOR]

Metal oxide nanoparticle (NP) supports of both good conductivity and stability have the potential to enhance both the reaction activity and stability of the loaded electrocatalysts. In this paper, a facile two-step approach to disperse Pt nanoparticles on the surface of an IrO2 NP support (Pt/IrO2) was developed. Physical characterization by x-ray diffraction spectroscopy and transmission/scanning electron microscopy suggests a good dispersion of the Pt NPs. The temperature effect (from 293 to 353 K) of oxygen reduction reaction on Pt/IrO2 was studied by using a rotating ring disk electrode The results show that although the kinetic current density on Pt/IrO2 is close to that on commercial Pt/C at room temperature, the apparent activation energy (Ea,app) in the former case is much lower, suggesting a much higher activity at elevated temperatures. The superiority in Ea,app is attributed to the electron interaction between Pt and the IrO2 support, as supported by the change of surface chemical state given by x-ray photo-electron spectroscopy. [ABSTRACT FROM AUTHOR]

This paper aims at the theoretical study of the CO2 magnetic-dipole ν2 + ν3 rovibrational absorption band that was recently detected in the Martian atmosphere. Specific characteristics of the magnetic dipole operator are carefully examined. Our evaluation of the magnetic-dipole line intensities is based on the variational calculations and the use of molecular properties is determined through specially performed ab initio quantum chemical calculations. The comparison of our simulated magnetic-dipole spectrum with available laboratory taken data also requires the knowledge of line intensities in the quadrupole band, which partially overlaps with that magnetic-dipole. Quadrupole intensities, once reconsidered, are permitted to correct previously reported values of the integrated intensity as well as the intensity of selected branches. The sum of our calculated magnetic-dipole and quadrupole rovibrational lines is shown to be in good agreement with both sets of presently available data from FTIR and OFCEAS laboratory observations. [ABSTRACT FROM AUTHOR]

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

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

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

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

Exact nonadiabatic quantum evolution preserves many geometric properties of the molecular Hilbert space. In the first paper of this series ["Paper I," S. Choi and J. Vaníček, J. Chem. Phys. 150, 204112 (2019)], we presented numerical integrators of arbitrary-order of accuracy that preserve these geometric properties exactly even in the adiabatic representation, in which the molecular Hamiltonian is not separable into kinetic and potential terms. Here, we focus on the separable Hamiltonian in diabatic representation, where the split-operator algorithm provides a popular alternative because it is explicit and easy to implement, while preserving most geometric invariants. Whereas the standard version has only second-order accuracy, we implemented, in an automated fashion, its recursive symmetric compositions, using the same schemes as in Paper I, and obtained integrators of arbitrary even order that still preserve the geometric properties exactly. Because the automatically generated splitting coefficients are redundant, we reduce the computational cost by pruning these coefficients and lower memory requirements by identifying unique coefficients. The order of convergence and preservation of geometric properties are justified analytically and confirmed numerically on a one-dimensional two-surface model of NaI and a three-dimensional three-surface model of pyrazine. As for efficiency, we find that to reach a convergence error of 10−10, a 600-fold speedup in the case of NaI and a 900-fold speedup in the case of pyrazine are obtained with the higher-order compositions instead of the second-order split-operator algorithm. The pyrazine results suggest that the efficiency gain survives in higher dimensions. [ABSTRACT FROM AUTHOR]

In this paper, the Hessian matrix of valence bond (VB) self-consistent field (VBSCF) energy with respect to orbitals are evaluated by applying the nonorthogonal orbital based N-body reduced density matrices, which was presented in Paper I. To this end, an automatic formula/code generator (AFCG) is developed; with which the matrix elements between internally contracted excited configurations of VB wave function and the corresponding codes are generated automatically. Compared to the tedious manual formula deducing and implementing, AFCG is much more convenient and efficient, and enables us to avoid troublesome debugging. With the help of AFCG, the Hessian-based Newton-Raphson algorithm is implemented for the VBSCF orbital optimization. Test calculations indicate that the Newton-Raphson algorithm converges quadratically and has much better convergence behavior than the gradient-based LBFGS algorithms. Furthermore, a combined approach with LBFGS and Newton-Raphson algorithms is applied to reduce the total CPU time of the calculation. [ABSTRACT FROM AUTHOR]

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose web of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules. [ABSTRACT FROM AUTHOR]

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]

This paper makes an extensive comparison of a dynamical model for a mechanism of direct dissociation to the detailed molecular beam experiments of CH4 dissociation on a Ni(100) surface reported in the previous paper. When a PES incorporating an ‘‘exit channel’’ barrier is used in the model and steric (multidimensional) aspects are included approximately via a ‘‘hole’’ approximation, excellent agreement is achieved between the model and experiments. This strengthens the qualitative mechanistic conclusions of Holmblad, Wambach, and Chorkendorff [J. Chem. Phys. 102, 8255 (1995)]. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Two-dimensional (2D) Janus transition metal dichalcogenides MXY manifest novel physical properties owing to the breaking of out-of-plane mirror symmetry. Recently, the 2H phase of MoSH has been demonstrated to possess intrinsic superconductivity, whereas the 1T phase exhibits a charge density waves state. In this paper, we have systematically studied the stability and electron–phonon interaction characteristics of MoSLi. Our results have shown that both the 2H and 1T phases of MoSLi are stable, as indicated by the phonon spectrum and the ab initio molecular dynamics. However, the 1T phase exhibits an electron–phonon coupling constant that is twice as large as that of the 2H phase. In contrast to MoSH, the 1T phase of MoSLi exhibits intrinsic superconductivity. By employing the ab initio anisotropic Migdal-Eliashberg formalism, we have revealed the two-gap superconducting nature of 1T-MoSLi, with a transition temperature (Tc) of 14.8 K. The detailed analysis indicates that the superconductivity in 1T-MoSLi primarily originates from the interplay between the vibration of the phonon modes in the low-frequency region and the dz2 orbital. These findings provide a fresh perspective on superconductivity within Janus structures. [ABSTRACT FROM AUTHOR]

Endohedrally doped clusters form a large category of cage clusters, with unique structures, diverse elemental compositions, and highly tunable electronic structures and physisochemical properties. They have been widely achieved in laboratory and may serve as functional building blocks for assembling new supermolecular structures and devices. In this paper, for the first time, we disclosed the luminescence properties of endohedrally doped group-IV clusters by time-dependent density functional theory calculations. A total of 64 cage clusters have been explored in terms of stability, emission wavelength, and the energy difference between the first excited singlet and triplet states. The key geometric and electronic factors governing the photophysical properties of these cage clusters were unveiled, to provide crucial insights for crafting atomically precise nanoclusters for optical and optoelectronic applications. [ABSTRACT FROM AUTHOR]

It is significant to investigate the calcium carbonate (CaCO3) precipitation mechanism during the carbon capture process; nevertheless, CaCO3 precipitation is not clearly understood yet. Understanding the carbonation mechanism at the atomic level can contribute to the mineralization capture and utilization of carbon dioxide, as well as the development of new cementitious materials with high-performance. There are many factors, such as temperature and CO2 concentration, that can influence the carbonation reaction. In order to achieve better carbonation efficiency, the reaction conditions of carbonation should be fully verified. Therefore, based on molecular dynamics simulations, this paper investigates the atomic-scale mechanism of carbonation. We investigate the effect of carbonation factors, including temperature and concentration, on the kinetics of carbonation (polymerization rate and activation energy), the early nucleation of calcium carbonate, etc. Then, we analyze the local stresses of atoms to reveal the driving force of early stage carbonate nucleation and the reasons for the evolution of polymerization rate and activation energy. Results show that the higher the calcium concentration or temperature, the higher the polymerization rate of calcium carbonate. In addition, the activation energies of the carbonation reaction increase with the decrease in calcium concentrations. [ABSTRACT FROM AUTHOR]

Vibrational coherences in ultrafast pump–probe (PP) and 2D electronic spectroscopy (2DES) provide insights into the excited state dynamics of molecules. Femtosecond coherence spectra and 2D beat maps yield information about displacements of excited state surfaces for key vibrational modes. Half-broadband 2DES uses a PP configuration with a white light continuum probe to extend the detection range and resolve vibrational coherences in the excited state absorption (ESA). However, the interpretation of these spectra is difficult as they are strongly dependent on the spectrum of the pump laser and the relative displacement of the excited states along the vibrational coordinates. We demonstrate the impact of these convoluting factors for a model based upon cresyl violet. A careful consideration of the position of the pump spectrum can be a powerful tool in resolving the ESA coherences to gain insights into excited state displacements. This paper also highlights the need for caution in considering the spectral window of the pulse when interpreting these spectra. [ABSTRACT FROM AUTHOR]

This paper evaluates the accuracy of the Hermitian form of the downfolding procedure using the double unitary coupled cluster (DUCC) ansatz on the benchmark systems of linear chains of hydrogen atoms, H6 and H8. The computational infrastructure employs the occupation-number-representation codes to construct the matrix representation of arbitrary second-quantized operators, allowing for the exact representation of exponentials of various operators. The tests demonstrate that external amplitudes from standard single-reference coupled cluster methods that sufficiently describe external (out-of-active-space) correlations reliably parameterize the Hermitian downfolded effective Hamiltonians in the DUCC formalism. The results show that this approach can overcome the problems associated with losing the variational character of corresponding energies in the corresponding SR-CC theories. [ABSTRACT FROM AUTHOR]

Quantum Dot Cellular Automata (QCA) is an emerging trend in the field of nanoelectronics, and computing can be regarded as an alternative to the traditional complementary metal–oxide–semiconductor technology. The paper is devoted to the study of the key functional properties of the cells for molecular QCA based on mixed valence molecules. The theoretical results for the heat dissipation under the conditions of the fast nonadiabatic switching event and cell–cell response function are obtained in the framework of the quantum-mechanical vibronic approach. These results are parameterized using the previous reliable ab initio calculations performed for oxidized norbornadiene and its polycyclic derivatives with variable lengths of the bridge. The comparative analysis of the dimeric and bidimeric molecular cells composed of these compounds is given. It is underlined that the conditions of a strong non-linear response and a low heat release are contradictory. However, despite this problem, a parametric regime is proposed, which provides a low heat release in combination with a strong nonlinear response of the working cell to the electric field induced by the polarized driver cell. [ABSTRACT FROM AUTHOR]

In the previous paper [C. W. Kim and I. Franco, J. Chem. Phys. 160, 214111-1–214111-13 (2024)], we developed a theory called MQME-D, which allows us to decompose the overall energy dissipation process in open quantum system dynamics into contributions by individual components of the bath when the subsystem dynamics is governed by a Markovian quantum master equation (MQME). Here, we contrast the predictions of MQME-D against the numerically exact results obtained by combining hierarchical equations of motion (HEOM) with a recently reported protocol for monitoring the statistics of the bath. Overall, MQME-D accurately captures the contributions of specific bath components to the overall dissipation while greatly reducing the computational cost compared to exact computations using HEOM. The computations show that MQME-D exhibits errors originating from its inherent Markov approximation. We demonstrate that its accuracy can be significantly increased by incorporating non-Markovianity by exploiting time scale separations (TSS) in different components of the bath. Our work demonstrates that MQME-D combined with TSS can be reliably used to understand how energy is dissipated in realistic open quantum system dynamics. [ABSTRACT FROM AUTHOR]

The superadiabatic dynamical density functional theory (superadiabatic-DDFT) is a promising new method for the study of colloidal systems out-of-equilibrium. Within this approach, the viscous forces arising from interparticle interactions are accounted for in a natural way by explicitly treating the dynamics of the two-body correlations. For bulk systems subject to spatially homogeneous shear, we use the superadiabatic-DDFT framework to calculate the steady-state pair distribution function and the corresponding viscosity for low values of the shear-rate. We then consider a variant of the central approximation underlying this superadiabatic theory and obtain an inhomogeneous generalization of a rheological bulk theory due to Russel and Gast. This paper thus establishes for the first time a connection between DDFT approaches, formulated to treat inhomogeneous systems, and existing work addressing nonequilibrium microstructure and rheology in bulk colloidal suspensions. [ABSTRACT FROM AUTHOR]

We propose a new collocation multi-configuration time-dependent Hartree (MCTDH) method. It reduces point-set error by using more points than basis functions. Collocation makes it possible to use MCTDH with a general potential energy surface without computing any integrals. The collocation points are associated with a basis larger than the basis used to represent wavefunctions. Both bases are obtained from a direct product basis built from single-particle functions by imposing a pruning condition. The collocation points are those on a sparse grid. Heretofore, collocation MCTDH calculations with more points than basis functions have only been possible if both the collocation grid and the basis set are direct products. In this paper, we exploit a new pseudo-inverse to use both more points than basis functions and a pruned basis and grid. We demonstrate that, for a calculation of the lowest 50 vibrational states (energy levels and wavefunctions) of CH2NH, errors can be reduced by two orders of magnitude by increasing the number of points, without increasing the basis size. This is true also when unrefined time-independent points are used. [ABSTRACT FROM AUTHOR]

In this paper, we introduce the Floquet mean-field dynamics and Floquet surface hopping approaches to study the nonadiabatic dynamics in periodically driven solid systems. We demonstrate that these two approaches can be formulated in both real and reciprocal spaces. Using the two approaches, we are able to simulate the interaction between electronic carriers and phonons under periodic drivings, such as strong light–matter interactions. Employing the Holstein and Peierls models, we show that strong light–matter interactions can effectively modulate the dynamics of electronic population and mobility. Notably, our study demonstrates the feasibility and effectiveness of modeling low-momentum carriers' interactions with phonons using a truncated reciprocal space basis, an approach impractical in real space frameworks. Moreover, we reveal that even with a significant truncation, carrier populations derived from surface hopping maintain greater accuracy compared to those obtained via mean-field dynamics. These results underscore the potential of our proposed methods in advancing the understanding of carrier–phonon interactions in various periodically driven materials. [ABSTRACT FROM AUTHOR]

The application of first-principles calculations for predicting lattice thermal conductivity (LTC) in crystalline materials, in conjunction with the linearized phonon Boltzmann equation, has gained increasing popularity. In this calculation, the determination of force constants through first-principles calculations is critical for accurate LTC predictions. For material exploration, performing first-principles LTC calculations in a high-throughput manner is now expected, although it requires significant computational resources. To reduce computational demands, we integrated polynomial machine learning potentials on-the-fly during the first-principles LTC calculations. This paper presents a systematic approach to first-principles LTC calculations. We designed and optimized an efficient workflow that integrates multiple modular software packages. We applied this approach to calculate LTCs for 103 compounds of wurtzite, zinc blende, and rocksalt types to evaluate the performance of the polynomial machine learning potentials in LTC calculations. We demonstrate a significant reduction in the computational resources required for the LTC predictions. [ABSTRACT FROM AUTHOR]

In recent papers, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] and then Becke [J. Chem. Phys. 159, 241101 (2023)] have developed a novel double hybrid density functional, "DH23," whose terms are based on good local physics. Its 12 coefficients are 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 (1.73 kcal/mol for the revDH23 variant). Here, we simplify DH23 by introducing a dispersion damping scheme involving atomic numbers only and one global parameter. The resulting new functional, "DH24," performs as well as its predecessors. [ABSTRACT FROM AUTHOR]

In this paper, benchmark results are presented on the calculation of vertical electronic excitation energies using a long-range second-order polarization propagator approximation (SOPPA) description with a short-range density functional theory description based on the Perdew–Burke–Ernzerhof (PBE) functional. The excitation energies are investigated for 132 singlet states and 71 triplet states across 28 medium-sized organic molecules. The results show that overall SOPPA-srPBE always performs better than PBE and that SOPPA-srPBE performs better than SOPPA for singlet states, but slightly worse than SOPPA for triplet states when CC3 results are the reference values. [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]

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]

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]