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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]

We report further investigations to aid the development of a Laplace MP2 (second-order Møller Plesset) method with a range separated Coulomb potential partitioned into short- and long-range parts. The implementation of the method extensively uses sparse matrix algebra, density fitting techniques for the short-range part, and a Fourier transformation in spherical coordinates for the long-range part of the potential. Localized molecular orbitals are employed for the occupied space, whereas virtual space is described by orbital specific virtual orbitals (OSVs) associated with localized molecular orbitals. The Fourier transform is deficient for very large distances between localized occupied orbitals, and a multipole expansion for widely separated pairs is introduced for the direct MP2 contribution, which is applicable also to non-Coulombic potentials that do not satisfy the Laplace equation. For the exchange contribution, an efficient screening of contributing localized occupied pairs is employed, which is discussed more completely here. To mitigate errors due to the truncation of OSVs, a simple and efficient extrapolation procedure is used to obtain results close to MP2 for the full basis set of atomic orbitals Using a suitable set of default parameters, the accuracy of the approach is demonstrated. The current implementation of the approach is not very efficient, and the aim of this paper is to introduce and critically discuss ideas that can have more general applicability beyond MP2 calculations for large molecules. [ABSTRACT FROM AUTHOR]

The complexity of mathematical models in biology has rendered model reduction an essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described using the Chemical Master Equation, commonly used methods include time-scale separation, Linear Mapping Approximation, and state-space lumping. Despite the success of these techniques, they appear to be rather disparate, and at present, no general-purpose approach to model reduction for stochastic reaction networks is known. In this paper, we show that most common model reduction approaches for the Chemical Master Equation can be seen as minimizing a well-known information-theoretic quantity between the full model and its reduction, the Kullback–Leibler divergence defined on the space of trajectories. This allows us to recast the task of model reduction as a variational problem that can be tackled using standard numerical optimization approaches. In addition, we derive general expressions for propensities of a reduced system that generalize those found using classical methods. We show that the Kullback–Leibler divergence is a useful metric to assess model discrepancy and to compare different model reduction techniques using three examples from the literature: an autoregulatory feedback loop, the Michaelis–Menten enzyme system, and a genetic oscillator. [ABSTRACT FROM AUTHOR]

This paper concerns the representation of angular momentum operators in the Born–Oppenheimer theory of polyatomic molecules and the various forms of the associated conservation laws. Topics addressed include the question of whether these conservation laws are exactly equivalent or only to some order of the Born–Oppenheimer parameter κ = (m/M)1/4 and what the correlation is between angular momentum quantum numbers in the various representations. These questions are addressed in both problems involving a single potential energy surface and those with multiple, strongly coupled surfaces and in both the electrostatic model and those for which fine structure and electron spin are important. The analysis leads to an examination of the transformation laws under rotations of the electronic Hamiltonian; of the basis states, both adiabatic and diabatic, along with their phase conventions; of the potential energy matrix; and of the derivative couplings. These transformation laws are placed in the geometrical context of the structures in the nuclear configuration space that are induced by rotations, which include the rotational orbits or fibers, the surfaces upon which the orientation of the molecule changes but not its shape, and the section, an initial value surface that cuts transversally through the fibers. Finally, it is suggested that the usual Born–Oppenheimer approximation can be replaced by a dressing transformation, that is, a sequence of unitary transformations that block-diagonalize the Hamiltonian. When the dressing transformation is carried out, we find that the angular momentum operator does not change. This is a part of a system of exact equivalences among various representations of angular momentum operators in Born–Oppenheimer theory. Our analysis accommodates large-amplitude motions and is not dependent on small-amplitude expansions about an equilibrium position. Our analysis applies to noncollinear configurations of a polyatomic molecule; this covers all but a subset of measure zero (the collinear configurations) in the nuclear configuration space. [ABSTRACT FROM AUTHOR]

The interactions between molecules and electrode surfaces play a key role in electrochemical processes and are a subject of extensive research, both experimental and theoretical. In this paper, we address the water dissociation reaction on a Pd(111) electrode surface, modeled as a slab embedded in an external electric field. We aim at unraveling the relationship between surface charge and zero-point energy in aiding or hindering this reaction. We calculate the energy barriers with dispersion-corrected density-functional theory and an efficient parallel implementation of the nudged-elastic-band method. We show that the lowest dissociation barrier and consequently the highest reaction rate take place when the field reaches a strength where two different geometries of the water molecule in the reactant state are equally stable. The zero-point energy contributions to this reaction, on the other hand, remain nearly constant across a wide range of electric field strengths, despite significant changes in the reactant state. Interestingly, we show that the application of electric fields that induce a negative charge on the surface can make nuclear tunneling more significant for these reactions. [ABSTRACT FROM AUTHOR]

Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice–water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters. [ABSTRACT FROM AUTHOR]

Trapping diffusive particles at surfaces is a key step in many systems in chemical and biological physics. Trapping often occurs via reactive patches on the surface and/or the particle. The theory of boundary homogenization has been used in many prior works to estimate the effective trapping rate for such a system in the case that either (i) the surface is patchy and the particle is uniformly reactive or (ii) the particle is patchy and the surface is uniformly reactive. In this paper, we estimate the trapping rate for the case that the surface and the particle are both patchy. In particular, the particle diffuses translationally and rotationally and reacts with the surface when a patch on the particle contacts a patch on the surface. We first formulate a stochastic model and derive a five-dimensional partial differential equation describing the reaction time. We then use matched asymptotic analysis to derive the effective trapping rate, assuming that the patches are roughly evenly distributed and occupy a small fraction of the surface and the particle. This trapping rate involves the electrostatic capacitance of a four-dimensional duocylinder, which we compute using a kinetic Monte Carlo algorithm. We further use Brownian local time theory to derive a simple heuristic estimate of the trapping rate and show that it is remarkably close to the asymptotic estimate. Finally, we develop a kinetic Monte Carlo algorithm to simulate the full stochastic system and then use these simulations to confirm the accuracy of our trapping rate estimates and homogenization theory. [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]

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]

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]

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]

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

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

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

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

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

In this paper, the responses of assembled behaviors of block polyelectrolytes (PEs) to the strength of electrostatic interactions are studied through molecular dynamic simulations. The results show that the assembled structures closely depend on the electrostatic strength. It should be noted that PE coacervation can outweigh the nucleation of hydrophobic blocks and invert the micelle structures at strong electrostatic strengths, leading to the formation of inverted micelles of PE cores and hydrophobic coronas. In the poor solvent condition for neutral block, diverse anisotropic micelles are presented; candy-like conventional micelles of hydrophobic cores and PE patches coexist with inverted candy-like micelles of PE cores and hydrophobic patches and with Janus micelles of semi-neutral aggregate and semi-PE cluster in the presence of divalent and trivalent counterions. The formation of conventional or inverted micelle is largely determined by the type of micellar fusion, which results from the nucleation competition between electrostatic correlation and hydrophobic interaction. The merge of micelles mediated by hydrophobic attraction leads to conventional hydrophobic cores, and the fusion induced by electrostatic correlations results in PE cores micelles. At strong electrostatic strengths, the PE chains exhibit rich conformations at trivalent counterions, ranging from a fully collapsed state to a rod-like state, and parallel alignment of PE chains is found. [ABSTRACT FROM AUTHOR]

Ion channels are proteins that play a significant role in physiological processes, including neuronal excitability and signal transduction. However, the precise mechanisms by which these proteins facilitate ion diffusion through cell membranes are not well understood. This is because experimental techniques to characterize ion channel activity operate on a time scale too large to understand the role of the various protein conformations on diffusion. Meanwhile, computational approaches operate on a time scale too short to rationalize the observed behavior at the microscopic scale. In this paper, we present a continuous-time random walk model that aims to bridge the scales between the atomistic models of ion channels and the experimental measurement of their conductance. We show how diffusion slows down in complex systems by using 3D lattices that map out the pore geometry of two channels: Nav1.7 and gramicidin. We also introduce spatial and dynamic site disorder to account for system heterogeneity beyond the mean field approximation. Computed diffusion coefficients show that an increase in spatial disorder slows down diffusion kinetics, while dynamic disorder has the opposite effect. Our results imply that microscopic or phenomenological models based on the potential of mean force data overlook the functional importance of protein dynamics on ion diffusion through channels. [ABSTRACT FROM AUTHOR]