Stress-dependent activation entropy in thermally activated cross-slip of dislocations.

Cross-slip of screw dislocations in crystalline solids is a stress-driven thermally activated process essential to many phenomena during plastic deformation, including dislocation pattern formation, strain hardening, and dynamic recovery. Molecular dynamics (MD) simulation has played an important role in determining the microscopic mechanisms of cross-slip. However, due to its limited timescale, MD can only predict cross-slip rates in high-stress or high-temperature conditions. The transition state theory can predict the cross-slip rate over a broad range of stress and temperature conditions, but its predictions have been found to be several orders of magnitude too low in comparison to MD results. This discrepancy can be expressed as an anomalously large activation entropy whose physical origin remains unclear. Here, we resolve this discrepancy by showing that the large activation entropy results from anharmonic effects, including thermal softening, thermal expansion, and soft vibrational modes of the dislocation. We expect these anharmonic effects to be significant in a wide range of stress-driven thermally activated processes in solids.

The Hidden Role of the Dielectric Effect in Nanofiltration: A Novel Perspective to Unravel New Ion Separation Mechanisms.

Nanofiltration (NF) membranes play a critical role in separation processes, necessitating an in-depth understanding of their selective mechanisms. Existing NF models predominantly include steric and Donnan mechanisms as primary mechanisms. However, these models often fail in elucidating the NF selectivity between ions of similar dimensions and the same valence. To address this gap, an innovative methodology was proposed to unravel new selective mechanisms by quantifying the nominal dielectric effect isolated from steric and Donnan exclusion through fitted pore dielectric constants by regression analysis. We demonstrated that the nominal dielectric effect encompassed unidentified selective mechanisms of significant relevance by establishing the correlation between the fitted pore dielectric constants and these hindrance factors. Our findings revealed that dehydration-induced ion-membrane interaction, rather than ion dehydration, played a pivotal role in ion partitioning within NF membranes. This interaction was closely linked to the nondeformable fraction of hydrated ions. Further delineation of the dielectric effect showed that favorable interactions between ions and membrane functional groups contributed to entropy-driven selectivity, which is a key factor in explaining ion selectivity differences between ions sharing the same size and valence. This study deepens our understanding of NF selectivity and sheds light on the design of highly selective membranes for water and wastewater treatment.

Efficient photocatalysis activation for reactive red 195 degradation by magnetic MIL-53(Fe)/Fe3O4@TiO2 hybrid nanocomposite.

The study investigated the performance of a novel magnetic hybrid MIL-53(Fe)/Fe3O4@TiO2 composite for removing reactive red 195 (RR195) dye from water using UVc light. Various analytical techniques were used to characterize the nanocomposite materials. X-ray diffraction analysis confirmed the presence of MIL-53(Fe) and TiO2 in the composite. FT-IR analysis identified carboxyl and Ti-O-Ti groups in the photocatalyst structure. The study evaluated the effects of pH, dye concentration, photocatalyst dosage, and temperature on RR195 photodegradation. The Langmuir-Hinshelwood kinetic model provided the best fit for the reaction rate. Optimal conditions for an 84 % dye degradation were found at a photocatalyst dose of 15 mg/100 mL, pH 3, dye concentration of 100 mg/L, and 35 °C after 120 minutes of UVc light exposure. Thermodynamic analysis indicated an endothermic reaction with positive values for Δ#H and negative values for Δ#S. The MIL-53(Fe)/Fe3O4@TiO2 composite demonstrated excellent stability and achieved over 90 % dye degradation after five cycles. Overall, the composite shows promise for treating wastewater with dyes.

Reaction Rate Rules of Intramolecular H-Migration Reaction Class for RIORIIOO·Radicals in Ether Combustion.

The intramolecular H-migration reaction of RIORIIOO· radicals constitute a key class of reactions in the low-temperature combustion mechanism of ethers. Despite this, there is a dearth of direct computations regarding the potential energy surface and rate constants specific to ethers, especially when considering large molecular systems and intricate branched-chain structures. Furthermore, combustion kinetic models for large molecular ethers generally utilize rate constants derived from those of structurally similar alcohols or alkane fuels. Consequently, chemical kinetic studies involve the calculation of energy barriers and rate rules for the intramolecular H-migration reaction class of RIORIIOO· radicals, which are systematically conducted using the isodesmic reaction method (IRM). The geometries of the species participating in these reactions are optimized, and frequency calculations are executed using the M06-X method in tandem with the 6-31+G(d,p) basis set by the Gaussian 16 program. Moreover, the M06-2X/6-31+G(d,p) method acts as the low-level ab initio method, while the CBS-QB3 method is utilized as the high-level ab initio method for calculating single-point energies. Rate constants at the high-pressure-limit are computed based on the reaction class transition state theory (RC-TST) by ChemRate program, incorporating asymmetric Eckart tunneling corrections for intramolecular H-migration reactions across a temperature range of 500 to 2000 K. It was found that the isodesmic reaction method gives accurate energy barriers and rate constants, and the rate constants of the H-migration reaction for RIORIIOO· radicals diverge from those of comparable reactions in alkanes and alcohol fuels. There are significant disparities in energy barriers and rate constants across the entire reaction classes of the H-migration reaction for RIORIIOO· radicals, necessitating the subdivision of the H-migration reaction into subclasses. Rate rules are established by averaging the rate constants of representative reactions for each subclass, which is pivotal for the advancement of accurate low-temperature combustion reaction mechanisms for ethers.

Simultaneous Manipulation of Membrane Enthalpy and Entropy Barriers towards Superior Ion Separations.

Sub-nanoporous membranes with ion selective transport functions are important for energy utilization, environmental remediation, and fundamental bioinspired engineering. Although mono/multivalent ions can be separated by monovalent ion selective membranes (MISMs), the current theory fails to inspire rapid advances in MISMs. Here, we apply transition state theory (TST) by regulating the enthalpy barrier (ΔH) and entropy barrier (ΔS) for designing next-generation monovalent cation exchange membranes (MCEMs) with great improvement in ion selective separation. Using a molecule-absorbed porous material as an interlayer to construct a denser selective layer can achieve a greater absolute value of ΔS for Li+ and Mg2+ transport, greater ΔH for Mg2+ transport and lower ΔH for Li+ transport. This recorded performance with a Li+/Mg2+ perm-selectivity of 25.50 and a Li+ flux of 1.86 mol ⋅ m-2 ⋅ h-1 surpasses the contemporary "upper bound" plot for Li+/Mg2+ separations. Most importantly, our synthesized MCEM also demonstrates excellent operational stability during the selective electrodialysis (S-ED) processes for realizing scalability in practical applications.

Recent Developments in Kramers' Theory of Reaction Rates.

In this short review, we provide an update of recent developments in Kramers' theory of reaction rates. After a brief introduction stressing the importance of this theory initially developed for chemical reactions, we briefly present the main theoretical formalism starting from the generalized Langevin equation and continue by showing the main points of the modern Pollak, Grabert and Hänggi theory. Kramers' theory is then sketched for quantum and classical surface diffusion. As an illustration the surface diffusion of Na atoms on a Cu(110) surface is discussed showing escape rates, jump distributions and diffusion coefficients as a function of reduced friction. Finally, some very recent applications of turnover theory to different fields such as nanoparticle levitation, microcavity polariton dynamics and simulation of reaction in liquids are presented. We end with several open problems and future challenges faced up by Kramers turnover theory.

Computational Studies on the Reactivity of Polycyclic Aromatic Hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) are widely present in the environment as toxic pollutants. In this study, quantum chemistry methods are used to study reactions of PAHs in both particle and gas phases. Seven theoretical methods are exploited to predict the reactive sites of 15 PAHs in the particle phase. Among these methods, the performance of the condensed Fukui function (CFF) is optimum. The gas-phase reactions of eight PAHs are also investigated. Except for fluorene, CFF predicts correctly the gas-phase mono-nitro products for seven systems. The products of fluorene predicted by CFF are 1-nitrofluorene and 3-nitrofluorene, which is however inconsistent with the experimental results. Transition state theory is then used to investigate the reaction mechanism of fluorene. Calculated rate constants for 3-nitrofluorene and 2-nitrofluorene formation are much bigger than that for 1-nitrofluorene formation, which is in agreement with the experimental results.

A Multiconformational Transition State Theory Approach to OH Tropospheric Degradation of Fluorotelomer Aldehydes.

Experimental work on the OH-initiated oxidation reactions of fluorotelomer aldehydes (FTALs) strongly suggests that the respective rate coefficients do not depend on the size of the Cx F2x+1 fluoroalkyl chain. FTALs hence represent a challenging test to our multiconformer transition state theory (MC-TST) protocol based on constrained transition state randomization (CTSR), since the calculated rate coefficients should not show significant variations with increasing values of x ${x}$ . In this work we apply the MC-TST/CTSR protocol to the x = 2 , 3 ${x={\rm 2,3}}$ cases and calculate both rate coefficients at 298.15 K with a value of k = ( 2 . 4 ± 1 . 4 ) × 10 - 12 ${k=(2.4\pm 1.4)\times {10}^{-12}}$  cm3  molecule-1 s-1 , practically coincident with the recommended experimental value of kexp = ( 2 . 8 ± 1 . 4 ) × 10 - 12 ${(2.8\pm 1.4)\times {10}^{-12}}$  cm3  molecule-1 s-1 . We also show that the use of tunneling corrections based on improved semiclassical TST is critical in obtaining Arrhenius-Kooij curves with a correct behavior at lower temperatures.

Theoretical Kinetics studies of isoprene peroxy radical chemistry: The fate of Z-δ-(4-OH, 1-OO)-ISOPOO radical.

The OH radical recycling mechanism in isoprene oxidation is one of the most exciting topics in atmospheric chemistry, and the corresponding studies expand our understanding of oxidation mechanisms of volatile organic compounds in the troposphere and provide reliable evidence to improve and develop conventional atmospheric models. In this work, we performed a detailed theoretical kinetics study on the Z-δ-(4-OH, 1-OO)-ISOPOO radical chemistry, which is proposed as the heart of OH recycling in isoprene oxidation. With the full consideration of its accumulation and consumption channels, we studied and discussed the fate of Z-δ-(4-OH, 1-OO)-ISOPOO radical by solving the energy-resolved master equation over a broad range of conditions, including not only room temperatures but also high temperatures of a forest fire or low temperatures and pressures of the upper troposphere. We found non-negligible pressure dependence of its fate at combustion temperatures (up to two orders of magnitude) and demonstrated the significance of both the multi-structural torsional anharmonicity and tunneling for accurately calculating kinetics of the studied system. More interestingly, the tunneling effect on the phenomenological rate constants of the H-shift reaction channel is also found to be pressure-dependent due to the competition with the O2 loss reaction. In addition, our time evolution calculations revealed a two-stage behavior of critical species in this reaction system and estimated the shortest half-lives for the Z-δ-(4-OH, 1-OO)-ISOPOO radical at various temperatures, pressures and altitudes. This detailed kinetics study of Z-δ-(4-OH, 1-OO)-ISOPOO radical chemistry offers a typical example to deeply understand the core mechanism of OH recycling pathways in isoprene oxidation, and provides valuable insights for promoting the development of relevant atmospheric models.

The Nature of the Enthalpy-Entropy Compensation and "Exotic" Arrhenius Parameters in the Denaturation Kinetics of Proteins.

Protein unfolding is a ubiquitous process responsible for the loss of protein functionality (denaturation), which, in turn, can be accompanied by the death of cells and organisms. The nature of enthalpy-entropy compensation (EEC) in the kinetics of protein unfolding is a subject of debate. In order to investigate the nature of EEC, the "completely loose" transition state (TS) model has been applied to calculate the Arrhenius parameters for the unfolding of polyglycine dimers as a model process. The calculated Arrhenius parameters increase with increasing dimer length and demonstrate enthalpy-entropy compensation. It is shown that EEC results from the linear correlations of enthalpy and entropy of activation with dimer length, which are derived directly from the properties of the transition state. It is shown that EEC in solvated (hydrated, etc.) proteins is a direct consequence of EEC in proteins themselves. The suggested model allows us also to reproduce and explain "exotic" very high values of the pre-exponential factor measured for the proteins unfolding, which are drastically higher than those known for unimolecular reactions of organic molecules. A similar approach can be applied to analyzing the nature of EEC phenomena observed in other areas of chemistry.

Ionization of 2- and 4(5)-Nitroimidazoles Radiosensitizers: A "Kinetic Competition" Between NO2 and NO Losses.

Nitroimidazoles are a class of chemicals with a remarkable broad spectrum of applications from the production of explosives to the use as radiosensitizers in radiotherapy. The understanding of thedynamics of their fragmentation induced by ionizing sources is of fundamental interest. The goal of this work is to theoretically investigate the kinetic competition between the two most important decomposition channels of 2, 4 and 5-Nitroimidazole cations: the NO and NO2 losses. The calculated rate constants of the two processes are in very good agreement with the experimental Photoelectron-Photoion Coincidence (PEPICO) branching ratio. This study solves the intriguing and theoretically unexplained experimental observation that 2-Nitroimidazole, at variance with the other two regio-isomers is a source for only NO at low energies (<12.76 eV). This is a key point for biomedical application of the nitroimidazoles, because NO is the vasodilator that favors the reoxigenation of hypoxic tumor tissues.

Enthalpic and Entropic Selectivity of Water and Small Ions in Polyamide Membranes.

While polyamide reverse osmosis and nanofiltration membranes have been extensively utilized in water purification and desalination processes, the molecular details governing water and solute permeation in these membranes are not fully understood. In this study, we apply transition-state theory for transmembrane permeation to systematically break down the intrinsic permeabilities of water and small ions in loose and tight polyamide nanofiltration membranes into enthalpic and entropic components using an Eyring-type equation. We analyze trends in these components to elucidate molecular phenomena that induce water-salt, monovalent-divalent, and monovalent-monovalent selectivity at different pH values. Our results suggest that in pores that are either too small or contain an electrostatically repelling mouth, the thermal activation of ions in the form of ion dehydration is less likely, promoting entropically driven selectivity with steric exclusion of hydrated ions. Instead, larger uncharged pores enable ion dehydration, inducing enthalpic selectivity that is driven by differences in the ion hydration properties. We also demonstrate that electrostatic interactions between cations and intrapore carboxyl groups hinder salt permeability, increasing the enthalpic barrier of the transport. Last, permeation tests of monovalent cations in the loose and tight polyamide membranes expose opposite rejection trends that further support the phenomenon of ion dehydration in large subnanopores.

ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments.

The determination of the temperature dependence of enzyme catalysis has traditionally been a labourious undertaking. We have developed a new approach to the classical Arrhenius parameter estimation by fitting the change in velocity under a gradual change in temperature. The evaluation with a simulated dataset shows that the approach is valid. The approach is demonstrated as a useful tool by characterizing the Bacillus pumilus LipA enzyme. Our results for the lipase show that the enzyme is psychrotolerant, with an activation energy of 15.3 kcal/mol for the chromogenic substrate para-nitrophenyl butyrate. Our results demonstrate that this can produce equivalent curves to the traditional approach while requiring significantly less sample, labour and time. Our method is further validated by characterizing three α-amylases from different species and habitats. The experiments with the α-amylases show that the approach works over a wide range of temperatures and clearly differentiates between psychrophilic, mesophilic and thermophilic enzymes. The methodology is released as an open-source implementation in Python, available online or used locally. This method of determining the activation parameters can make studies of the temperature dependence of enzyme catalysis more widely adapted to understand how enzymes have evolved to function in extreme environments. Moreover, the thermodynamic parameters that are estimated serve as functional validations of the empirical valence bond calculations of enzyme catalysis.

Variational transition state theory rate constants and H/D kinetic isotope effects for CH3 + CH3 OCOH reactions.

The rate constants and H/D kinetic isotope effect for hydrogen abstraction reactions involving isotopomers of methyl formate by methyl radical are computed employing methods of the variational transition state theory (VTST) with multidimensional tunneling corrections. The energy paths were built with a dual-level method using the moller plesset second-order perturbation theory (MP2) method as the low-level and complete basis set (CBS) extrapolation as the high-level energy method. Benchmark calculations with the CBSD-T approach give an enthalpy of reaction at 0 K for R1 (-4.5 kcal/mol) and R2 (-4.2 kcal/mol) which are in good agreement with the experiment, that is, -4.0 and - 4.8 kcal/mol. For the reactional paths involving the isotopomers CH3 + CH3 OCOH → CH4 + CH3 OCO and CH3 + CH3 OCOD → CH3 D + CH3 OCO, the value of kH /kD (T = 455 K) using the canonical VTST/small-curvature tunneling approximation method is 6.7 in close agreement with experimental value (6.2). © 2019 Wiley Periodicals, Inc.

Kinetics of Drug Binding and Residence Time.

The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). There are many experimental and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time. We first introduce the theoretical background of drug binding kinetics from a physicochemical standpoint. We then analyze the recent literature in the field, starting from the experimental methodologies and applications thereof and moving to theoretical and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of molecular dynamics and related methods, which comprise a great number of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.

Quantifying the limits of transition state theory in enzymatic catalysis.

While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis.

Heavy-Atom Tunneling Through Crossing Potential Energy Surfaces: Cyclization of a Triplet 2-Formylarylnitrene to a Singlet 2,1-Benzisoxazole.

Not long ago, the occurrence of quantum mechanical tunneling (QMT) chemistry involving atoms heavier than hydrogen was considered unreasonable. Contributing to the shift of this paradigm, we present here the discovery of a new and distinct heavy-atom QMT reaction. Triplet syn-2-formyl-3-fluorophenylnitrene, generated in argon matrices by UV-irradiation of an azide precursor, was found to spontaneously cyclize to singlet 4-fluoro-2,1-benzisoxazole. Monitoring the transformation by IR spectroscopy, temperature-independent rate constants (k≈1.4×10-3  s-1 ; half-life of ≈8 min) were measured from 10 to 20 K. Computational estimated rate constants are in fair agreement with experimental values, providing evidence for a mechanism involving heavy-atom QMT through crossing triplet to singlet potential energy surfaces. Moreover, the heavy-atom QMT takes place with considerable displacement of the oxygen atom, which establishes a new limit for the heavier atom involved in a QMT reaction in cryogenic matrices.

KoBra: A rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings.

We present a new method for calculating the diffusion tensor for the systems of sorbates inside nanoporous materials at different loadings by just using transition rate constants. In addition, a user-friendly program with graphical user interface has been developed and is freely provided to be used (https://sourceforge.net/projects/kobra/). It needs from the user just to provide the values of the unit cell lengths and angles, the transition rate constants for each sorbate, and any spatial constraint between these sorbates. This program is shown to be about 30 times faster than kinetic Monte Carlo method. Application of the method to the problem of diffusion of aromatics in silicalite-1 at different loadings is presented too. © 2019 Wiley Periodicals, Inc.

Electron transfer across a thermal gradient.

Charge transfer is a fundamental process that underlies a multitude of phenomena in chemistry and biology. Recent advances in observing and manipulating charge and heat transport at the nanoscale, and recently developed techniques for monitoring temperature at high temporal and spatial resolution, imply the need for considering electron transfer across thermal gradients. Here, a theory is developed for the rate of electron transfer and the associated heat transport between donor-acceptor pairs located at sites of different temperatures. To this end, through application of a generalized multidimensional transition state theory, the traditional Arrhenius picture of activation energy as a single point on a free energy surface is replaced with a bithermal property that is derived from statistical weighting over all configurations where the reactant and product states are equienergetic. The flow of energy associated with the electron transfer process is also examined, leading to relations between the rate of heat exchange among the donor and acceptor sites as functions of the temperature difference and the electronic driving bias. In particular, we find that an open electron transfer channel contributes to enhanced heat transport between sites even when they are in electronic equilibrium. The presented results provide a unified theory for charge transport and the associated heat conduction between sites at different temperatures.

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C2F4), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.