A Computational Perspective on the Reactivity of π-spacers in Self-Immolative Elimination Reactions

The controlled release of chemicals, especially in drug delivery, is crucial, often employing "self-immolative" spacers to enhance reliability. These spacers separate the payload from the protecting group, ensuring a more controlled release. Over the years, design rules have been proposed to improve the elimination process's reaction rate by modifying spacers with electron-donating groups or reducing their aromaticity. The spacer design is critical for determining the range of functional groups released during this process. This study explores various strategies from the literature aimed at improving release rates, focusing on the electronic nature of the spacer, its aromaticity, the electronic nature of its substituents, and the leaving groups involved in the elimination reaction. Through computational analysis, I investigate activation free energies by identifying transition states for model reactions. My calculations align qualitatively with experimental results, demonstrating the feasibility and reliability of computationally pre-screening model self-immolative eliminations. This approach allows proposing optimal combinations of spacer and leaving group for achieving the highest possible release rate.

Substituent Dependence on the Reactions of Criegee Intermediates with Carbon Dioxide and Carbon Monoxide

Criegee intermediates (CIs), R1 R2 COO, are active molecules produced in the atmosphere from the ozonolysis of alkenes. Here, we systematically evaluated the reactivity of ten CIs with carbon monoxide and carbon dioxide using CCSD(T)-F12/cc-pVTZ-F12//B3LYP/6-311+G(2d,2p) energies and transition state theory. Many previous studies focused on alkyl substitution, but here we evaluated both alkyl and vinyl substitution toward the reactivity by studying five anti-type CIs: CH2 OO, anti-CH3 CHOO, anti-cis-C2 H5 CHOO, anti-trans-MACRO, anti-cis-MACRO; and five syn-type CIs: syn-CH3 CHOO, (CH3 )2 COO, syn-trans-C2 H5 CHOO, syn-trans-MVKO, and syn-cis-MVKO. Our study showed that reactions involving CO2 have a large substituent dependence varying nearly five orders of magnitude, while those involving CO have a much smaller two orders of magnitude difference. Analysis based on the strain interaction model showed that deformation of the CI is an important feature in determining the reactivity with CO2 . On the other hand, we used the OO and CO bond ratios to analyze the zwitterionic character of the CIs. We found that vinyl substitution with π-conjugation results in smaller zwitterionic character and lower reactivity with CO. Lastly, the reactivity of CIs with CO as well as CO2 were found to be not fast enough to be important in an atmospheric context.

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.

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.

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.

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.

Contiguous High-Mobility Interphase Surrounding Nano-Precipitates in Polymer Matrix Solid Electrolyte

We establish that an interfacial region develops around amorphous Li_1.3Al_0.3Ti_1.7(PO₄)₃ (LATP) nanoparticles in a poly(ethylene oxide) (PEO), which exhibits a 30 times higher Li⁺ mobility than the polymer matrix. To take advantage of this gain throughout the material, nanoparticles must be uniformly dispersed across the matrix, so that the interphase formation is minimally blocked by LATP particle agglomeration. This is achieved using a water-based in situ precipitation method, carefully controlling the temperature schedule during processing. A maximum conductivity of 3.80 × 10^-4 S cm^-1 at 20 °C for an ethylene oxide to Li ratio of 10 is observed at 25 wt % (12.5 vol %) particle loading, as predicted by our tri-phase model. Comparative infrared spectroscopy reveals softening and broadening of the C-O-C stretching modes, reflecting increased disorder in the polymer backbone that is consistent with opening passageways for cation migration. A transition state theory-based approach for analyzing the temperature dependence of the ionic conductivity reveals that thermally activated processes within the interphase benefit more from higher activation entropy than from the decrease in activation enthalpy. The lithium infusion from LATP particles is small, and the charge carriers tend to concentrate in a space-charge configuration near the particle/polymer interface.

Nucleation Rate Theory for Coordination Number: Elucidating Water-Mediated Formation of a Zigzag Na2SO4 Morphology

Predicting and controlling nanostructure formation during nucleation can pave the way to synthesizing novel energy materials via crystallization. However, such control over nucleation and crystallization remains challenging due to an inadequate understanding of critical factors that govern evolving atomistic structures and dynamics. Herein, we utilize coordination number as a reaction coordinate and rate theory to investigate how sodium sulfate, commonly known as a phase-change energy material, nucleates in a supersaturated aqueous solution. In conjunction with ab initio and force field-based molecular dynamics simulation, the rate theoretical analysis reveals that sodium sulfate from an initially dissolved metastable state transits to a heterogeneous mixture of prenucleated clusters and finally to a large cylindrical zigzag morphology. Measurements of Raman spectra and their ab initio modeling confirm that this nucleated morphology contains a few waters for every sulfate. Rate processes such as solvent exchange and desolvation exhibit high sensitivity to the evolving prenucleation/nucleation structures, providing a means to distinguish between critical nucleation precursors. Desolvation and forming the first-shell interionic coordination structure via monomer-by-monomer addition around sulfates are found to explain the formation of large nuclei. Thus, a detailed understanding of the step-by-step structure formation across scales has been achieved. This can be leveraged to predict nucleation-related structures and dynamics and potentially control the synthesis of novel phase-change materials for energy applications.

Understanding the Time-Lag Behavior of the Breakdown-Discharge Voltage

As the world enters the era of the Internet of Things (IoT), wireless devices and their networks become essential fundamental components. Recently, with the rapid development of the triboelectric nanogenerator (TENG), breakdown discharge has become an emerging hot topic in the field since it is the key limiting factor of the output performance, and it may also trigger new applications such as self-powered wireless sensing. However, understandings of the discharge behaviors in TENG are still limited. This study proposed a method to study the breakdown discharge with a large serial resistance and discovered the time-lag behavior of the breakdown discharge. A model based on the Eyring equation is demonstrated to explain this time-lag phenomenon. A convenient method to adjust the breakdown-discharge voltage is developed through this study. As an application, a wireless spark switch being modulated by a series-connected resistance is designed, which may be potentially utilized in wireless applications.

High Hydrogen Isotope Separation Efficiency: Graphene or Catalyst?

Single-layer graphene has been demonstrated to be a high-efficiency hydrogen isotope sieving membrane in the electrochemical hydrogen pumping system. In this work, we transferred this membrane to proton exchange membrane water electrolysis (PEMWE), which has wide industrial applications. Two membrane electrode assemblies with decorated Pt and ink-coated Pt were investigated. The graphene with the decorated Pt scheme acquired the reported highest proton-to-tritium separation factor of 19.50 in PEMWE. However, rather than graphene, the decorated catalyst was demonstrated to be responsible for this remarkable separation efficiency. Previous studies from Geim's group underestimated the enhanced separation efficiency of decorated Pt over ink-coated Pt, resulting in an exaggerated separation efficiency for graphene. The behavior of proton transfer with hydrogen isotope separation through graphene was interpreted by a serial-parallel circuit model, which suggested that hydrogen isotope separation occurs at defect sites. The limited separation efficiency for graphene was also well understood by a density functional theory (DFT) calculation using an SW 55-77 model and the transition state theory for the kinetic isotope effect. This research provides a thorough understanding of proton transfer with hydrogen isotope separation through graphene.

High-Performance Carbon Molecular Sieves for the Separation of Propylene and Propane

High-performance carbon molecular sieves (CMSs) for the separation of propylene (C₃H₆) and propane (C₃H₈) were synthesized in this study by chemical vapor deposition (CVD) of benzene on the pore entrances of activated carbon. The C₃H₆ and C₃H₈ separation characteristics of the CMSs were controlled by altering the amount of carbon deposited during CVD, and the resulting characteristic curve featuring the kinetic selectivity of C₃H₆ over C₃H₈ as a function of the adsorption rate constant of C₃H₆ is considered to be the upper bound of the C₃H₆-C₃H₈ separation factor for current CMSs because of the presence of previously reported CMS data under this curve. Additionally, CMS models were constructed using grand canonical molecular dynamics (GCMD) simulations mimicking the process of CVD, which revealed that the kinetic selectivity of C₃H₆ over C₃H₈ strongly depended on the size of the pore entrances at the level of 0.01 nm, and that strict control of the pore-entrance size was crucial for obtaining high-performance CMSs for C₃H₆-C₃H₈ separation. This was essentially achieved by controlling the duration of CVD, which led to the experimental realization of CMSs with a C₃H₆ selectivity over C₃H₈ of >2000 and a high uptake rate of C₃H₆. A design guideline for the development of high-performance CMSs for C₃H₆-C₃H₈ separation was proposed based on theoretical calculations performed using idealized carbon structures, which extracted the characteristics of the CMS models obtained from the GCMD simulations.

The Grotthuss mechanism for bifunctional proton transfer in poly(benzimidazole)

Poly(benzimidazole) (PBI) has received considerable attention as an effective high-temperature polymer electrolyte membrane for fuel cells. In this work, the Grotthuss mechanism for bifunctional proton transfer in PBI membranes was studied using density functional theory and transition state theory. This study focused on the reaction paths and kinetics for bifunctional proton transfer scenarios in neutral ([PBI]2), single (H+[PBI]2) and double-protonated (H2+[PBI]2) dimers. The theoretical results showed that the energy barriers and strength for H-bonds are sensitive to the local dielectric environment. For [PBI]2 with ε = 1, the uphill potential energy curve is attributed to extraordinarily strong ion-pair H-bonds in the transition structure, regarded as a 'dipolar energy trap'. For ε = 23, the ion-pair charges are partially neutralized, leading to a reduction in the electrostatic attraction in the transition structure. The dipolar energy trap appears to prohibit interconversion between the precursor, transition and proton-transferred structures, which rules out the possibility for [PBI]2 to be involved in the Grotthuss mechanism. For H+[PBI]2 and H2+[PBI]2 with ε = 1, the interconversion involves a low energy barrier, and the increase in the energy barrier for ε = 23 can be attributed to an increase in the strength of the protonated H-bonds in the transition structure: the local dielectric environment enhances the donor-acceptor interaction of the protonated H-bonds. Analysis of the rate constants confirmed that the quantum effect is not negligible for the N-H+ … N H-bond especially at low temperatures. Agreement between the theoretical and experimental data leads to the conclusion that the concerted bifunctional proton transfer in H2+[PBI]2 in a high local dielectric environment is 'the rate-determining scenario'. Therefore, a low local dielectric environment can be one of the required conditions for effective proton conduction in acid-doped PBI membranes. These theoretical results provide insights into the Grotthuss mechanism, which can be used as guidelines for understanding the fundamentals of proton transfers in other bifunctional H-bond systems.

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.

Reaction Mechanisms and Rate Constants of Auto-Catalytic Urethane Formation and Cleavage Reactions

The chemistry of urethanes plays a key role in important industrial processes. Although catalysts are often used, the study of the reactions without added catalysts provides the basis for a deeper understanding. For the non-catalytic urethane formation and cleavage reactions, the dominating reaction mechanism has long been debated. To our knowledge, the reaction kinetics have not been predicted quantitatively so far. Therefore, we report a new computational study of urethane formation and cleavage reactions. To analyze various potential reaction mechanisms and to predict the reaction rate constants quantum chemistry and transition state theory were employed. For validation, experimental data from literature and from own experiments were used. Quantitative agreement of experiments and predictions could be demonstrated. The calculations confirm earlier assumptions that urethane formation reactions proceed via mechanisms where alcohol molecules act as auto-catalysts. Our results show that it is essential to consider several transition states corresponding to different reaction orders to enable agreement with experimental observations. Urethane cleavage seems to be catalyzed by an isourethane, leading to an observed 2nd-order dependence of the reaction rate on the urethane concentration. The results of our study support a deeper understanding of the reactions as well as a better description of reaction kinetics and will therefore help in catalyst development and process optimization.

Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates

We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-adapted) enzymes show significantly different activation parameters (lower activation enthalpies and entropies) from their mesophilic counterparts. Furthermore, there is increasing evidence that the temperature dependence of many enzyme-catalyzed reactions is more complex than is widely believed. Many enzymes show curvature in plots of activity versus temperature that is not accounted for by denaturation or unfolding. This is explained by macromolecular rate theory: A negative activation heat capacity for the rate-limiting chemical step leads directly to predictions of temperature optima; both entropy and enthalpy are temperature dependent. Fluctuations in the transition state ensemble are reduced compared to the ground state. We show how investigations combining experiment with molecular simulation are revealing fundamental details of enzyme thermoadaptation that are relevant for understanding aspects of enzyme evolution. Simulations can calculate relevant thermodynamic properties (such as activation enthalpies, entropies, and heat capacities) and reveal the molecular mechanisms underlying experimentally observed behavior.

Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.

Chemical Kinetics of Hydrogen Atom Abstraction from Propargyl Sites by Hydrogen and Hydroxy Radicals

Hydrogen atom abstraction from propargyl C-H sites of alkynes plays a critical role in determining the reactivity of alkyne molecules and understanding the formation of soot precursors. This work reports a systematic theoretical study on the reaction mechanisms and rate constants for hydrogen abstraction reactions by hydrogen and hydroxy radicals from a series of alkyne molecules with different structural propargyl C-H atoms. Geometry optimizations and frequency calculations for all species are performed at M06-2X/cc-pVTZ level of theory and the hindered internal rotations are also treated at this level. The high-level W1BD and CCSD(T)/CBS theoretical calculations are used as a benchmark for a series of DFT calculations toward the selection of accurate DFT functionals for large reaction systems in this work. Based on the quantum chemistry calculations, rate constants are computed using the canonical transition state theory with tunneling correction and the treatment of internal rotations. The effects of the structure and reaction site on the energy barriers and rate constants are examined systematically. To the best of our knowledge, this work provides the first systematic study for one of the key initiation abstraction reactions for compounds containing propargyl hydrogen atoms.

Reaction Mechanisms and Kinetics of the Hydrogen Abstraction Reactions of C₄⁻C₆ Alkenes with Hydroxyl Radical: A Theoretical Exploration

The reaction of alkenes with hydroxyl (OH) radical is of great importance to atmospheric and combustion chemistry. This work used a combined ab initio/transition state theory (TST) method to study the reaction mechanisms and kinetics for hydrogen abstraction reactions by OH radical on C₄–C₆ alkenes. The elementary abstraction reactions involved were divided into 10 reaction classes depending upon the type of carbon atoms in the reaction center. Geometry optimization was performed by using DFT M06-2X functional with the 6-311+G(d,p) basis set. The energies were computed at the high-level CCSD(T)/CBS level of theory. Linear correlation for the computed reaction barriers and enthalpies between M06-2X/6-311+G(d,p) and CCSD(T)/CBS methods were found. It was shown that the C=C double bond in long alkenes not only affected the related allylic reaction site, but also exhibited a large influence on the reaction sites nearby the allylic site due to steric effects. TST in conjunction with tunneling effects were employed to determine high-pressure limit rate constants of these abstraction reactions and the computed overall rate constants were compared with the available literature data.

Temperature sensitivities of extracellular enzyme Vmax and Km across thermal environments

The magnitude and direction of carbon cycle feedbacks under climate warming remain uncertain due to insufficient knowledge about the temperature sensitivities of soil microbial processes. Enzymatic rates could increase at higher temperatures, but this response could change over time if soil microbes adapt to warming. We used the Arrhenius relationship, biochemical transition state theory, and thermal physiology theory to predict the responses of extracellular enzyme V_max and K_m to temperature. Based on these concepts, we hypothesized that V_max and K_m would correlate positively with each other and show positive temperature sensitivities. For enzymes from warmer environments, we expected to find lower V_max , K_m , and K_m temperature sensitivity but higher V_max temperature sensitivity. We tested these hypotheses with isolates of the filamentous fungus Neurospora discreta collected from around the globe and with decomposing leaf litter from a warming experiment in Alaskan boreal forest. For Neurospora extracellular enzymes, V_max Q₁₀ ranged from 1.48 to 2.25, and K_m Q₁₀ ranged from 0.71 to 2.80. In agreement with theory, V_max and K_m were positively correlated for some enzymes, and V_max declined under experimental warming in Alaskan litter. However, the temperature sensitivities of V_max and K_m did not vary as expected with warming. We also found no relationship between temperature sensitivity of V_max or K_m and mean annual temperature of the isolation site for Neurospora strains. Declining V_max in the Alaskan warming treatment implies a short-term negative feedback to climate change, but the Neurospora results suggest that climate-driven changes in plant inputs and soil properties are important controls on enzyme kinetics in the long term. Our empirical data on enzyme V_max , K_m , and temperature sensitivities should be useful for parameterizing existing biogeochemical models, but they reveal a need to develop new theory on thermal adaptation mechanisms.

Ultrahigh Storage and Fast Diffusion of Na and K in Blue Phosphorene Anodes

In the wake of blue phosphorene's (BP) computational discovery and experimental realization, it has emerged as a versatile material with interesting optical, electrical, and mechanical properties. In this study, using first principles density functional theory calculations, we have investigated the adsorption and diffusion of Na and K over monolayer BP to assess its suitability as Na-ion and K-ion battery anodes. The optimized adsorption energies were found to be -0.96 eV for Na and -1.54 eV for K, which are sufficiently large to ensure stability and safety during operation. In addition, BP could adsorb Na and K atoms up to a stoichiometric ratio of 1:1 which yields a high storage capacity of 865 mA h/g for both adatom species. Through examination of the electronic structure and projected density of states of BP as a function of Na/K concentration, we predict that the band gap of the system increasingly shrinks, and in the case of maximum K adsorption, the band gap diminishes completely. Additionally, the diffusion of Na and K over BP is observed to be ultrafast, especially for K, and anisotropic with modest energy barriers of 0.11 and 0.093 eV for Na and K, respectively. Building upon these findings, we employed vibrational analysis techniques with transition state theory to incorporate kinetic effects and predicted a diffusivity of 7.2 × 10^-5 cm²/s for Na and 8.58 × 10^-5 cm²/s for K on BP. Given these advantages, that is, ultrahigh capacity, electrical conductivity, and high Na/K diffusivity, we conclude that BP can be considered as an excellent candidate for anodes in Na- and K-ion batteries.

Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer

Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids. This review provides an overview of various temperature-dependent smFRET approaches from our laboratory and others, highlighting efforts in which such methods have been successfully applied to studies of single-molecule nucleic acid folding.

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.

Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis

Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc.

Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Mechanism of Kinetically Controlled Capillary Condensation in Nanopores: A Combined Experimental and Monte Carlo Approach

We find the rule of capillary condensation from the metastable state in nanoscale pores based on the transition state theory. The conventional thermodynamic theories cannot achieve it because the metastable capillary condensation inherently includes an activated process. We thus compute argon adsorption isotherms on cylindrical pore models and atomistic silica pore models mimicking the MCM-41 materials by the grand canonical Monte Carlo and the gauge cell Monte Carlo methods and evaluate the rate constant for the capillary condensation by the transition state theory. The results reveal that the rate drastically increases with a small increase in the chemical potential of the system, and the metastable capillary condensation occurs for any mesopores when the rate constant reaches a universal critical value. Furthermore, a careful comparison between experimental adsorption isotherms and the simulated ones on the atomistic silica pore models reveals that the rate constant of the real system also has a universal value. With this finding, we can successfully estimate the experimental capillary condensation pressure over a wide range of temperatures and pore sizes by simply applying the critical rate constant.

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.

Does Nonadiabatic Transition State Theory Make Sense Without Decoherence?

We analyze thermal rate constants as computed with surface hopping dynamics and resolve certain inconsistencies that have permeated the literature. On one hand, according to Landry and Subotnik (J. Chem. Phys. 2012, 137, 22A513), without decoherence, direct dynamics with surface hopping overestimates the rate of relaxation for the spin-boson Hamiltonian. On the other hand, according to Jain and Subotnik (J. Chem. Phys. 2015, 143, 134107), without decoherence, a transition state theory with surface hopping underestimates spin-boson rate constants. In this Letter, we resolve this apparent contradiction. We show that, without decoherence, direct dynamics and transition state theory should not agree; agreement is guaranteed only with decoherence. We also show that, even though the effects of decoherence may be hidden for isoenergetic reactions, these decoherence failures are exposed for exothermic reactions. We believe these lessons are essential when interpreting surface hopping papers published in the literature without any decoherence corrections.

Phase Space Structures Explain Hydrogen Atom Roaming in Formaldehyde Decomposition

We re-examine the prototypical roaming reaction--hydrogen atom roaming in formaldehyde decomposition--from a phase space perspective. Specifically, we address the question "why do trajectories roam, rather than dissociate through the radical channel?" We describe and compute the phase space structures that define and control all possible reactive events for this reaction, as well as provide a dynamically exact description of the roaming region in phase space. Using these phase space constructs, we show that in the roaming region, there is an unstable periodic orbit whose stable and unstable manifolds define a conduit that both encompasses all roaming trajectories exiting the formaldehyde well and shepherds them toward the H2···CO well.

Atmospheric Vinyl Alcohol to Acetaldehyde Tautomerization Revisited

The atmospheric oxidation of vinyl alcohol (VA) produced by photoisomerization of acetaldehyde (AA) is thought to be a source of formic acid (FA). Nevertheless, a recent theoretical study predicted a high rate coefficient k1(298 K) of ≈10(-14) cm(3) molecule(-1) s(-1) for the FA-catalyzed tautomerization reaction 1 of VA back into AA, which suggests that FA buffers its own production from VA. However, the unusually high frequency factor implied by that study prompted us to reinvestigate reaction 1 . On the basis of a high-level ab initio potential energy profile, we first established that transition state theory is applicable, and derived a k1(298 K) of only ≈2 × 10(-20) cm(3) molecule(-1) s(-1), concluding that the reaction is negligible. Instead, we propose and rationalize another important VA sink: its uptake by aqueous aerosol and cloud droplets followed by fast liquid-phase tautomerization to AA; global modeling puts the average lifetime by this sink at a few hours, similar to oxidation by OH.

Biochemistry students' ideas about how an enzyme interacts with a substrate

Enzyme-substrate interactions are a fundamental concept of biochemistry that is built upon throughout multiple biochemistry courses. Central to understanding enzyme-substrate interactions is specific knowledge of exactly how an enzyme and substrate interact. Within this narrower topic, students must understand the various binding sites on an enzyme and be able to reason from simplistic lock and key or induced fit models to the more complex energetics model of transition state theory. Learning to understand these many facets of enzyme-substrate interactions and reasoning from multiple models present challenges where students incorrectly make connections between concepts or make no connection at all. This study investigated biochemistry students' understanding of enzyme-substrate interactions through the use of clinical interviews and a national administration (N = 707) of the Enzyme-Substrate Interactions Concept Inventory. Findings include misconceptions regarding the nature of enzyme-substrate interactions, naïve ideas about the active site, a lack of energetically driven interactions, and an incomplete understanding of the specificity pocket.

A Signature of Roaming Dynamics in the Thermal Decomposition of Ethyl Nitrite: Chirped-Pulse Rotational Spectroscopy and Kinetic Modeling

Chirped-pulse (CP) Fourier transform rotational spectroscopy is uniquely suited for near-universal quantitative detection and structural characterization of mixtures that contain multiple molecular and radical species. In this work, we employ CP spectroscopy to measure product branching and extract information about the reaction mechanism, guided by kinetic modeling. Pyrolysis of ethyl nitrite, CH3CH2ONO, is studied in a Chen type flash pyrolysis reactor at temperatures of 1000-1800 K. The branching between HNO, CH2O, and CH3CHO products is measured and compared to the kinetic models generated by the Reaction Mechanism Generator software. We find that roaming CH3CH2ONO → CH3CHO + HNO plays an important role in the thermal decomposition of ethyl nitrite, with its rate, at 1000 K, comparable to that of the radical elimination channel CH3CH2ONO → CH3CH2O + NO. HNO is a signature of roaming in this system.

Unusual kinetics of thermal decay of dim-light photoreceptors in vertebrate vision

We present measurements of rate constants for thermal-induced reactions of the 11-cis retinyl chromophore in vertebrate visual pigment rhodopsin, a process that produces noise and limits the sensitivity of vision in dim light. At temperatures of 52.0-64.6 °C, the rate constants fit well to an Arrhenius straight line with, however, an unexpectedly large activation energy of 114 ± 8 kcal/mol, which is much larger than the 60-kcal/mol photoactivation energy at 500 nm. Moreover, we obtain an unprecedentedly large prefactor of 10(72±5) s(-1), which is roughly 60 orders of magnitude larger than typical frequencies of molecular motions! At lower temperatures, the measured Arrhenius parameters become more normal: Ea = 22 ± 2 kcal/mol and Apref = 10(9±1) s(-1) in the range of 37.0-44.5 °C. We present a theoretical framework and supporting calculations that attribute this unusual temperature-dependent kinetics of rhodopsin to a lowering of the reaction barrier at higher temperatures due to entropy-driven partial breakup of the rigid hydrogen-bonding network that hinders the reaction at lower temperatures.

Theoretical analysis on the kinetic isotope effects of bimolecular nucleophilic substitution (S(N)2) reactions and their temperature dependence

Factors affecting the kinetic isotope effects (KIEs) of the gas-phase S(N)2 reactions and their temperature dependence have been analyzed using the ion-molecule collision theory and the transition state theory (TST). The quantum-mechanical tunneling effects were also considered using the canonical variational theory with small curvature tunneling (CVT/SCT). We have benchmarked a few ab initio and density functional theory (DFT) methods for their performance in predicting the deuterium KIEs against eleven experimental values. The results showed that the MP2/aug-cc-pVDZ method gave the most accurate prediction overall. The slight inverse deuterium KIEs usually observed for the gas-phase S(N)2 reactions at room temperature were due to the balance of the normal rotational contribution and the significant inverse vibrational contribution. Since the vibrational contribution is a sensitive function of temperature while the rotation contribution is temperature independent, the KIEs are thus also temperature dependent. For S(N)2 reactions with appreciable barrier heights, the tunneling effects were predicted to contribute significantly both to the rate constants and to the carbon-13, and carbon-14 KIEs, which suggested important carbon atom tunneling at and below room temperature.

Mechanically unfolding proteins: the effect of unfolding history and the supramolecular scaffold

The mechanical resistance of a folded domain in a polyprotein of five mutant I27 domains (C47S, C63S I27)(5)is shown to depend on the unfolding history of the protein. This observation can be understood on the basis of competition between two effects, that of the changing number of domains attempting to unfold, and the progressive increase in the compliance of the polyprotein as domains unfold. We present Monte Carlo simulations that show the effect and experimental data that verify these observations. The results are confirmed using an analytical model based on transition state theory. The model and simulations also predict that the mechanical resistance of a domain depends on the stiffness of the surrounding scaffold that holds the domain in vivo, and on the length of the unfolded domain. Together, these additional factors that influence the mechanical resistance of proteins have important consequences for our understanding of natural proteins that have evolved to withstand force.