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In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by β-elimination. In addition, the polymerase activity of Polβ employs the "three-metal ion mechanism" instead of the long-standing "two-metal ion mechanism" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the "three-metal ion mechanism" vs the "two-metal ion mechanism" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ's catalytic mechanism provides valuable insights into DNA replication and damage repair. [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]

Chemical reaction networks can undergo nonequilibrium phase transitions upon variation in external control parameters, such as the chemical potential of a species. We investigate the flux in the associated chemostats that is proportional to the entropy production and its critical fluctuations within the Schlögl model. Numerical simulations show that the corresponding diffusion coefficient diverges at the critical point as a function of system size. In the vicinity of the critical point, the diffusion coefficient follows a scaling form. We develop an analytical approach based on the chemical Langevin equation and van Kampen's system size expansion that yields the corresponding exponents in the monostable regime. In the bistable regime, we rely on a two-state approximation in order to analytically describe the critical behavior. [ABSTRACT FROM AUTHOR]

Incorporating self-interaction corrections (SIC) significantly improves chemical reaction barrier height predictions made using density functional theory methods. We present a detailed orbital-by-orbital analysis of these corrections for three semi-local density functional approximations (DFAs) situated on the three lowest rungs of Jacob's ladder of approximations. The analysis is based on Fermi–Löwdin Orbital Self-Interaction Correction (FLOSIC) calculations performed at several steps along the reaction pathway from the reactants (R) to the transition state (TS) to the products (P) for four representative reactions selected from the BH76 benchmark set. For all three functionals, the major contribution to self-interaction corrections of the barrier heights can be traced to stretched bond orbitals that develop near the TS configuration. The magnitude of the ratio of the self-exchange–correlation energy to the self-Hartree energy (XC/H) for a given orbital is introduced as an indicator of one-electron self-interaction error. XC/H = 1.0 implies that an orbital's self-exchange–correlation energy exactly cancels its self-Hartree energy and that the orbital, therefore, makes no contribution to the SIC in the FLOSIC scheme. For the practical DFAs studied here, XC/H spans a range of values. The largest values are obtained for stretched or strongly lobed orbitals. We show that significant differences in XC/H for corresponding orbitals in the R, TS, and P configurations can be used to identify the major contributors to the SIC of barrier heights and reaction energies. Based on such comparisons, we suggest that barrier height predictions made using the strongly constrained and appropriately normed meta-generalized gradient approximation may have attained the best accuracy possible for a semi-local functional using the Perdew–Zunger SIC approach. [ABSTRACT FROM AUTHOR]

The electronic energies of molecules have been successfully evaluated on quantum computers. However, more attention is paid to the dynamics simulation of molecules in practical applications. Based on the variational quantum eigensolver (VQE) algorithm, Fedorov et al. proposed a correlated sampling (CS) method and demonstrated the vibrational dynamics of H2 molecules [J. Chem. Phys. 154, 164103 (2021)]. In this study, we have developed a quantum approach by extending the CS method based on the VQE algorithm (labeled eCS-VQE) for simulating chemical reaction dynamics. First, the CS method is extended to the three-dimensional cases for calculation of first-order energy gradients, and then, it is further generalized to calculate the second-order gradients of energies. By calculating atomic forces and vibrational frequencies for H2, LiH, H+ + H2, and Cl− + CH3Cl systems, we have seen that the approach has achieved the CCSD level of accuracy. Thus, we have simulated dynamics processes for two typical chemical reactions, hydrogen exchange and chlorine substitution, and obtained high-precision reaction dynamics trajectories consistent with the classical methods. Our eCS-VQE approach, as measurement expectations and ground-state wave functions can be reused, is less demanding in quantum computing resources and is, therefore, a feasible means for the dynamics simulation of chemical reactions on the current noisy intermediate-scale quantum-era quantum devices. [ABSTRACT FROM AUTHOR]

Chemical reactions can induce Marangoni flows by changing the surface tension of a solution open to the air, either by changing the composition and/or by modifying the temperature. We consider the case of a simple A + B → C reaction front propagating in a thin horizontal system open to air. The effect of the three chemical species on the surface tension of the aqueous solution is quantified by three solutal Marangoni numbers, while the effect of temperature changes is determined by the thermal Marangoni number. By integrating numerically the incompressible Navier–Stokes equations coupled to reaction-diffusion-convection equations for the chemical concentrations and temperature taking into account the Lewis number (ratio between heat and mass diffusivities), we emphasize the importance of thermal changes occurring due to the heat of reaction on the dynamics of chemically induced Marangoni convection. Based on the reaction-diffusion profiles of concentrations and temperature, asymptotic analytical solutions for the surface tension profiles are obtained and classified as a function of the Marangoni numbers and the Lewis number. This new classification allows for the prediction of the convective patterns in thermo-solutal Marangoni flows. The analytical predictions are further confirmed by numerical results and additional extrema in surface tension profiles induced by the thermal effects are found to affect the nonlinear dynamics. [ABSTRACT FROM AUTHOR]

The activation volume, which quantifies the response of the chemical reactions to the applied stress, plays a central role in controlling the mechanochemical reactions for applications including lubricity, wear, and the topographic fabrication of the surfaces under stress. However, the physical interpretations of the activation volume remain scientifically intriguing and largely unexplored. Here, density functional theory calculations are used to investigate the general rules of charge transfer underlying activation volume in controlling the typically mechanochemical reaction process. It is found that the activation volume could be decoupled into the electronic contributions from interface chemistry and bulk physical deformation, which are commonly linear dependent on the contact pressure. Therefore, the activation volume may, indeed, be derived from the stress-driven charge transfer underlying cooperative competition between interfacial chemistry and the bulk region. This competition is related to the stiffness change from the bulk to slab. The magnitude of the stiffness change represents the degree to which the interface atoms modify the bulk properties, which is directly related to the contribution of different regions to the activation volume. This work may open up the understanding of the activation volume from dynamic electron transfer to engineer mechanochemical reactions, different from the existing insights into the geometric dimensionality of the contact configuration. [ABSTRACT FROM AUTHOR]

We have investigated, using molecular dynamics, the surface chemistry of hydrogen incident on the amorphous and crystalline lithium oxide and lithium hydroxide surfaces upon being slowed down by a collision cascade and retained in the amorphous surface of either Li2O or LiOH. We looked for the bonding of H to the resident structures in the surface to understand a possible chain of chemical reactions that can lead to surface transformation upon H atom impact. Our findings, using Density-Functional Theory (DFT) trained ReaxFF force field/electronegativity equalization method potentials, stress the importance of inclusion of polarization in the dynamics of a Li–O–H system, which is also illustrated by DFT energy minimization and quantum–classical molecular dynamics using tight binding DFT. The resulting polar-covalent chemistry of the studied systems is complex and very sensitive to the instantaneous positions of all atoms as well as the ratio of concentrations of various resident atoms in the surface. [ABSTRACT FROM AUTHOR]

We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We characterize its scaling behavior in the macroscopic limit, its performances, and the impact of potential internal delays. We obtain analytical expressions for all quantities of interest: the generated reverse chemical current, the output power, the transduction efficiency, and correlation between the number of molecules. Due to a bound on the nonequilibrium response of its chemical reaction network, we find that, contrary to the electronic case, there is no way for the Maxwell demon to generate a finite output in the macroscopic limit. Finally, we analyze the information thermodynamics of the Maxwell demon from a bipartite perspective. In the limit of a fast demon, the information flow is obtained, its pattern in the state space is discussed, and the behavior of partial efficiencies related to the measurement and feedback processes is examined. [ABSTRACT FROM AUTHOR]

For an electronic system, given a mean field method and a distribution of orbital occupation numbers that are close to the natural occupations of the correlated system, we provide formal evidence and computational support to the hypothesis that the entropy (or more precisely −σS, where σ is a parameter and S is the entropy) of such a distribution is a good approximation to the correlation energy. Underpinning the formal evidence are mild assumptions: the correlation energy is strictly a functional of the occupation numbers, and the occupation numbers derive from an invertible distribution. Computational support centers around employing different mean field methods and occupation number distributions (Fermi–Dirac, Gaussian, and linear), for which our claims are verified for a series of pilot calculations involving bond breaking and chemical reactions. This work establishes a formal footing for those methods employing entropy as a measure of electronic correlation energy (e.g., i-DMFT [Wang and Baerends, Phys. Rev. Lett. 128, 013001 (2022)] and TAO-DFT [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)]) and sets the stage for the widespread use of entropy functionals for approximating the (static) electronic correlation. [ABSTRACT FROM AUTHOR]

Designing and predicting self-organized pattern formation in out-of-equilibrium chemical and biochemical reactions holds fundamental significance. External perturbations like light and electric fields exert a crucial influence on reaction-diffusion systems involving ionic species. While the separate impacts of light and electric fields have been extensively studied, comprehending their combined effects on spatiotemporal dynamics is paramount for designing versatile spatial orders. Here, we theoretically investigate the spatiotemporal dynamics of chlorine dioxide-iodine-malonic acid reaction-diffusion system under photo-illumination and circularly polarized electric field (CPEF). By applying CPEF at varying intensities and frequencies, we observe the predominant emergence of oscillating hexagonal spot-like patterns from homogeneous stable steady states. Furthermore, our study unveils a spectrum of intriguing spatiotemporal instabilities, encompassing stripe-like patterns, oscillating dumbbell-shaped patterns, spot-like instabilities with square-based symmetry, and irregular chaotic patterns. However, when we introduce periodic photo-illumination to the hexagonal spot-like instabilities induced by CPEF in homogeneous steady states, we observe periodic size fluctuations. Additionally, the stripe-like instabilities undergo alternating transitions between hexagonal spots and stripes. Notably, within the Turing region, the interplay between these two external influences leads to the emergence of distinct superlattice patterns characterized by hexagonal-and square-based symmetry. These patterns include parallel lines of spots, target-like formations, black-eye patterns, and other captivating structures. Remarkably, the simple perturbation of the system through the application of these two external fields offers a versatile tool for generating a wide range of pattern-forming instabilities, thereby opening up exciting possibilities for future experimental validation. [ABSTRACT FROM AUTHOR]

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic rates can in principle be obtained by different techniques after projecting the high-dimensional atomic dynamics on one (or a few) collective variable. Even though it is well-known that the projected dynamics approximately follows – in a statistical sense – the generalized, underdamped or overdamped Langevin equations (depending on the time resolution), to date it is nontrivial to parameterize such equations starting from a limited, practically accessible amount of non-ergodic trajectories. In this work we focus on Markovian, underdamped Langevin equations, that arise naturally when considering, e.g., numerous water-solution processes at sub-picosecond resolution. After contrasting the advantages and pitfalls of different numerical approaches, we present an efficient parametrization strategy based on a limited set of molecular dynamics data, including equilibrium trajectories confined to minima and few hundreds transition path sampling-like trajectories. Employing velocity autocorrelation or memory kernel information for learning the friction and likelihood maximization for learning the free-energy landscape, we demonstrate the possibility to reconstruct accurate barriers and rates both for a benchmark system and for the interaction of carbon nanoparticles in water. [ABSTRACT FROM AUTHOR]

The Meyer–Neldel compensation law, observed in a wide variety of chemical reactions and other thermally activated processes, provides a proportionality between the entropic and the enthalpic components of an energy barrier. By analyzing 31 different polymer systems, we show that such an intriguing behavior is encountered also in the slow Arrhenius process, a recently discovered microscopic relaxation mode, responsible for several equilibration mechanisms both in the liquid and the glassy state. We interpret this behavior in terms of the multiexcitation entropy model, indicating that overcoming large energy barriers can require a high number of low-energy local excitations, providing a multiphonon relaxation process. [ABSTRACT FROM AUTHOR]

Chemically driven fluids can demix to form condensed droplets that exhibit phase behaviors not observed at equilibrium. In particular, nonequilibrium interfacial properties can emerge when the chemical reactions are driven differentially between the interior and exterior of the phase-separated droplets. Here, we use a minimal model to study changes in the interfacial tension between coexisting phases away from equilibrium. Simulations of both droplet nucleation and interface roughness indicate that the nonequilibrium interfacial tension can either be increased or decreased relative to its equilibrium value, depending on whether the driven chemical reactions are accelerated or decelerated within the droplets. Finally, we show that these observations can be understood using a predictive theory based on an effective thermodynamic equilibrium. [ABSTRACT FROM AUTHOR]

We develop a semi-analytical model of self-diffusioosmotic transport in active pores, which includes advective transport and the inverse chemical reaction that consumes solute. In previous work [Antunes et al., Phys. Rev. Lett. 129, 188003 (2022)], we have demonstrated the existence of a spontaneous symmetry breaking in fore-aft symmetric pores that enables them to function as a micropump. We now show that this pumping transition is controlled by three timescales. Two timescales characterize advective and diffusive transport. The third timescale corresponds to how long a solute molecule resides in the pore before being consumed. Introducing asymmetry to the pore (either via the shape or the catalytic coating) reveals a second type of advection-enabled transition. In asymmetric pores, the flow rate exhibits discontinuous jumps and hysteresis loops upon tuning the parameters that control the asymmetry. This work demonstrates the interconnected roles of shape and catalytic patterning in the dynamics of active pores and shows how to design a pump for optimum performance. [ABSTRACT FROM AUTHOR]

Based on the relationship between average local ionization energy I ̄ (r) and average local electron affinity A ̄ (r) with the electronic Fukui functions, i.e., f−(r) and f+(r), respectively, in this paper, we establish a connection between nuclear and electronic Fukui functions beyond frontier molecular orbitals. As a consequence of this connection, we obtain expressions of average nuclear Fukui functions interpreted as a variation of average nucleophilicity or electrophilicity (weighted by the electronic orbital Fukui functions) with respect to nuclear displacements, which goes beyond the highest occupied molecular orbital/or lowest unoccupied molecular orbital consideration. Furthermore, from this connection and considering the frontier molecular orbital approximation, we derive expressions of nuclear Fukui functions in terms of the atom-condensed electronic Fukui functions, which imply a locality in the chemical reactivity and could be used to study the variation of local nucleophilicity or electrophilicity with respect to nuclear displacements. Finally, this new way to interpret the nuclear Fukui function could be useful in the future to study the chemical reactivity related to molecular vibrations, internal rotations, bond dissociation, chemical reaction along the model of reaction coordinate, and so on. [ABSTRACT FROM AUTHOR]

The use of oriented external electric fields (OEEFs) as a potential tool for catalyzing chemical reactions has gained traction in recent years. Electronic structure calculations using OEEFs are commonly done using methods based on density functional theory (DFT), but until now, the performance of DFT methods for calculating molecules in OEEFs had not been assessed in a more general scope. Looking at the accuracy of molecular geometries, electronic energies, and electric dipole moments compared to accurate coupled-cluster with perturbative triples data, we have investigated a wide variety of density functionals using different basis sets to determine how well the individual functionals perform on various types of chemical bonds. We found that most functionals accurately calculate geometries in OEEFs and that small basis sets are sufficient in many cases. Calculations of electronic energies show a significant error introduced by the OEEF, which the use of a larger basis set helps mitigate. Our findings show that DFT methods can be used for accurate calculations in OEEFs, allowing researchers to make full use of the advantages that they bring. [ABSTRACT FROM AUTHOR]

The recent demonstration of the existence of an intimate relationship between the chiral structure of some materials and the spin polarization of electrons transmitted through them, what has been called the chirality-induced spin selectivity (CISS) effect, is sparking interest in many related phenomena. One of the most notorious is the possibility of using magnetic materials to apply enantioselective interactions on chiral molecules and chemical reactions involving them. In this work, x-ray photoelectron spectroscopy has been used to characterize the adsorption and growth kinetics of enantiopure organic molecules on magnetic (Co) and non-magnetic (Cu) substrates. While on these latter, no significant enantiosensitive effects are found, on spin-polarized, in-plane magnetized Co surfaces, the two enantiomers have been found to deposit differently. The observed effects have been interpreted as the result of one of the enantiomers being adsorbed in a transient, weakly bound physisorbed-like state with higher mobility due to limited, spin-selective charge transfer between it and the substrate. The study of these phenomena can provide insight into the fundamental mechanisms responsible for the CISS effect. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations have become a powerful tool for investigating electrical double layers (EDLs), which play a crucial role in various electrochemical devices. In this Review, we provide a comprehensive overview of the techniques used in MD simulations for EDL studies, with a particular focus on methods for describing electrode polarization, and examine the principle behind these methods and their varying applicability. The applications of these approaches in supercapacitors, capacitive deionization, batteries, and electric double-layer transistors are explored, highlighting recent advancements and insights in each field. Finally, we emphasize the challenges and potential directions for future developments in MD simulations of EDLs, such as considering movable electrodes, improving electrode property representation, incorporating chemical reactions, and enhancing computational efficiency to deepen our understanding of complex electrochemical processes and contribute to the progress in the field involving EDLs. [ABSTRACT FROM AUTHOR]

This paper proposes a physics-based model based on possible chemical processes responsible for the resistive switching of sputter-deposited silicon oxide films. Diffusion–reaction differential equations are utilized to pursue physical and chemical origins of the switching phenomenon. Based on the theoretical model, the chemical reaction process is analytically and numerically solved, and an analytical model is proposed to elucidate the phenomenon. Theoretical simulation results are examined from the point of view of suitability of parameter values, and the analytical model is used to interpret the simulation results. Simulation results greatly assist in understanding the switching processes of silicon oxide films; that is, the diffusion processes of hydrogen and water molecules primarily rule the switching processes, and the displacement of oxygen atoms is assisted by those processes. The analytical model predicts that high-speed switching requires a large number of traps in the oxide, a relatively large binding energy, and a low leakage current; all of them can easily be satisfied for sputter-deposited oxide films. A combination of the theoretical simulation model and the analytical model gives a guideline of how the sputter-deposited silicon oxide films can be made suitable for high-speed resistive switching applications. [ABSTRACT FROM AUTHOR]

The control of electron spin, crucial to the stability of matter, offers new possibilities for manipulating the properties of molecules and materials with potential applications in spintronics and chemical reactions. Recent experiments have demonstrated that electron transmission through chiral molecules depends on the electron spin orientation, a phenomenon known as chiral-induced spin selectivity (CISS). In this study, we show that CISS can be observed in achiral systems driven by an external circularly polarized laser field in the framework of Floquet engineering. By using the Floquet theory for a time-periodically driven system to investigate spin-dependent electron transport in a two-terminal setup, we demonstrate that the spin polarization can approach unity if the light intensity is sufficiently strong, the rate of dephasing is sufficiently low, and the average chemical potential of the two leads is within an appropriate range of values, which is narrow because of the high frequency of the laser field. To obtain a broader range of energies for large spin polarization, a combination of chiral molecules and light–matter interactions is considered, and the spin polarization of electrons transported through a helical molecule driven by a laser field is evaluated. [ABSTRACT FROM AUTHOR]

"Gating" is a widely observed phenomenon in biochemistry that describes the transition between the activated (or open) and deactivated (or closed) states of an ion-channel, which makes transport through that channel highly selective. In general, gating is a mechanism that imposes an additional restriction on a transport, as the process ends only when the "gate" is open and continues otherwise. When diffusion occurs in the presence of a constant bias to a gated target, i.e., to a target that switches between an open and a closed state, the dynamics essentially slow down compared to ungated drift-diffusion, resulting in an increase in the mean completion time, ⟨TG⟩ > ⟨T⟩, where T denotes the random time of transport and G indicates gating. In this work, we utilize stochastic resetting as an external protocol to counterbalance the delay due to gating. We consider a particle in the positive semi-infinite space that undergoes drift-diffusion in the presence of a stochastically gated target at the origin and is moreover subjected to rate-limiting resetting dynamics. Calculating the minimal mean completion time ⟨ T r ⋆ G ⟩ rendered by an optimal resetting rate r⋆ for this exactly solvable system, we construct a phase diagram that owns three distinct phases: (i) where resetting can make gated drift-diffusion faster even compared to the original ungated process, ⟨ T r ⋆ G ⟩ < ⟨ T ⟩ < ⟨ T G ⟩ , (ii) where resetting still expedites gated drift-diffusion but not beyond the original ungated process, ⟨ T ⟩ ≤ ⟨ T r ⋆ G ⟩ < ⟨ T G ⟩ , and (iii) where resetting fails to expedite gated drift-diffusion, ⟨ T ⟩ < ⟨ T G ⟩ ≤ ⟨ T r ⋆ G ⟩. We also highlight various non-trivial behaviors of the completion time as the resetting rate, gating parameters, and geometry of the set-up are carefully ramified. Gated drift-diffusion aptly models various stochastic processes such as chemical reactions that exclusively take place in certain activated states of the reactants. Our work predicts the conditions under which stochastic resetting can act as a useful strategy to enhance the rate of such processes without compromising their selectivity. [ABSTRACT FROM AUTHOR]

Chemical reactions and energy transport phenomena have been experimentally reported to be significantly affected by strong light–matter interactions and vibrational polariton formation. These quasiparticles exhibit nontrivial transport phenomena due to the long-range correlations induced by the photonic system and elastic and inelastic scattering processes driven by matter disorder. In this article, we employ the Ioffe–Regel criterion to obtain vibrational polariton mobility edges and to identify distinct regimes of delocalization and transport under variable experimental conditions of light–matter detuning, disorder, and interaction strength. Correlations between the obtained trends and recent observations of polariton effects on reactivity are discussed, and essential differences between transport phenomena in organic electronic exciton and vibrational polaritons are highlighted. Our transport diagrams show the rich diversity of transport phenomena under vibrational strong coupling and indicate that macroscopic delocalization is favored at negative detuning and large light–matter interaction strength. We also find the surprising feature that, despite the presence of dephasing-induced inelastic scattering processes, macroscopic lower polariton delocalization and wave transport are expected to persist experimentally, even in modes with small photonic weight. [ABSTRACT FROM AUTHOR]

External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical reaction networks? Here, we analyze transitions giving rise to complex behavior in random reaction networks subject to external driving forces. In the absence of driving, we characterize the uniqueness of the steady state and identify the percolation of a giant connected component in these networks as the number of reactions increases. When subject to chemical driving (influx and outflux of chemical species), the steady state can undergo bifurcations, leading to multistability or oscillatory dynamics. By quantifying the prevalence of these bifurcations, we show how chemical driving and network sparsity tend to promote the emergence of these complex dynamics and increased rates of entropy production. We show that catalysis also plays an important role in the emergence of complexity, strongly correlating with the prevalence of bifurcations. Our results suggest that coupling a minimal number of chemical signatures with external driving can lead to features present in biochemical processes and abiogenesis. [ABSTRACT FROM AUTHOR]

Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted reaction currents, satisfies the law of mass-action and, hence, still describes a chemical process. We prove that the answer depends on the topological property of the underlying chemical reaction network known as deficiency. The answer is yes only for deficiency-zero networks. It is no for all other networks, implying that their steady-state currents cannot be inverted by controlling the kinetic constants of the reactions. Hence, the network deficiency imposes a form of non-invertibility to the chemical dynamics. We then ask whether catalytic chemical networks are deficiency-zero. We prove that the answer is no when they are driven out of equilibrium due to the exchange of some species with the environment. [ABSTRACT FROM AUTHOR]

Reactive materials (RMs) are special type of impact-initiated energetic materials that have been widely studied with broad military application prospects. However, simulating the ignition and reaction of RMs using current numerical methods is difficult due to their complex mechanism related to high dynamic loads. In this work, based on a theoretical model consisting of impact ignition criteria and chemical reaction rate of polymer-based RMs, a numerical method with a unified equation of state was proposed and compiled as an executable program. Experiments consisting of typical polytetrafluoroethylene /Al RM projectiles impacting double-spaced plates were conducted and simulated using the user-compiled program, and the results verified the effectiveness of the numerical method. The simulation also qualitatively analyzed the second-collision induced reaction enhancement mechanism. In addition, the results revealed that the kinetic-chemical combined effect is a crucial factor that determined the damage enhancement effect on the rear plates. [ABSTRACT FROM AUTHOR]

We study the response of chemical reaction networks driven far from equilibrium to logarithmic perturbations of reaction rates. The response of the mean number of a chemical species is observed to be quantitively limited by number fluctuations and the maximum thermodynamic driving force. We prove these trade-offs for linear chemical reaction networks and a class of nonlinear chemical reaction networks with a single chemical species. Numerical results for several model systems support the conclusion that these trade-offs continue to hold for a broad class of chemical reaction networks, though their precise form appears to sensitively depend on the deficiency of the network. [ABSTRACT FROM AUTHOR]

In this work, we investigate the physicochemical process of water photolysis to bridge physical and chemical processes by a newly developed first-principles calculation code. The deceleration, thermalization, delocalization, and initial hydration of the extremely low-energy electrons ejected by water photolysis are sequentially tracked in the condensed phase. We show herein the calculated results for these sequential phenomena during 300 fs. Our results indicate that the mechanisms heavily depend on the intermolecular vibration and rotation modes peculiar to water and the momentum transfer between the electrons and the water medium. We suggest that using our results for the delocalized electron distribution will reproduce successive chemical reactions measured by photolysis experiments using a chemical reaction code. We expect our approach to become a powerful technique for various scientific fields related to water photolysis and radiolysis. [ABSTRACT FROM AUTHOR]

The generalized Langevin mode analysis (GLMA) is applied to chemical reactions in biomolecules in solution. The theory sees a chemical reaction in solution as a barrier-crossing process, similar to the Marcus theory. The barrier is defined as the crossing point of two free-energy surfaces that are attributed to the reactant and product of the reaction. It is assumed that both free-energy surfaces are quadratic or harmonic. The assumption is based on the Kim-Hirata theory of structural fluctuation of protein, which proves that the fluctuation around an equilibrium structure is quadratic with respect to the structure or atomic coordinates. The quadratic surface is a composite of many harmonic functions with different modes or frequencies. The height of the activation barrier will be dependent on the mode or frequency—the less the frequency, the lower the barrier. Hence, it is essential to decouple the fluctuational modes into a hierarchical order. GLMA is impeccable for this purpose. It is essential for a theoretical study of chemical reactions to choose a reaction coordinate along which the reaction proceeds. We suppose that the mode whose center of coordinate and/or the frequency changes most before and after the reaction is the one relevant to the chemical reaction and choose the coordinate as the reaction coordinate. The rate of reaction along the reaction coordinate is k rate = ν ⁡ exp − Δ F (†) / k B T , which is similar to the Marcus expression for the electron transfer reaction. In the equation, ΔF(†) is the activation barrier defined by Δ F (†) ≡ F (r) Q † − F (r) ( Q e q (r) ) , where F (r) ( Q e q (r) ) and F (r) Q † denote the free energies at equilibrium Q e q (r) and the crossing point Q†, respectively, both on the free energy surface of the reactant. [ABSTRACT FROM AUTHOR]

The melting curve of H2O was investigated up to 54 GPa and ∼2000 K by Brillouin scattering spectroscopy in a diamond anvil cell. A CO2 laser was used for heating the H2O sample directly in order to reduce the risk of chemical reactions. The melting was identified based on the appearance of the Brillouin peaks derived from the liquid phase. The longitudinal wave velocity (Vp) of the liquid phase along the melting curve exhibits a smooth increase with pressure. The melting temperature of H2O shows no kink previously reported but a monotonic increase between 26 and 54 GPa. Present melting data suggest that the melting occurs from body-centered-cubic superionic phase in the pressure-temperature range investigated. [ABSTRACT FROM AUTHOR]

The practical description of disordered chemical reactions, where the reactions involve multiple species at multiple sites, is presently a challenge using correlated electronic structure methods due to their high computational cost and steep scaling. Here, we describe the gradient theory of multi-fragment density matrix embedding theory, which potentially provides a minimal computational framework to model such processes at the correlated electron level. We present the derivation and implementation of the gradient theory, its validation on model systems and chemical reactions using density matrix embedding, and its application to a molecular dynamics simulation of proton transport in a small water cluster, a simple example of multi-site reaction dynamics. [ABSTRACT FROM AUTHOR]

There are several industrial and biological applications for the study of squeezing flow, including cell squeeze technology, blood flow and food production. In particular, the load and thrust bearing qualities of human body joints and the compression molding processes of metals and polymers might be explained by this solution, which could also illustrate the classical lubrication problems. So, this work investigated the effects of cross-diffusion, an induced magnetic field and joule heating on an unsteady squeezing Casson fluid on a spinning disc. Using the proper similarity transformations, the systems of partial differential equations are drained into a system of ordinary differential equations, which are solved numerically using the finite difference method. This analysis accounts for the effects of biophysical parameters on velocity components, magnetic fields, heat and mass transfer profiles. Additionally, graphic representations are provided for the skin friction coefficient, Nusselt number and Sherwood number for various values of the governing parameters. The current investigation has been matched with published results in order to validate validity, and good agreements have been seen. The impacts of the problem parameters under consideration are also explained numerically and graphically. The top disc's rate of rotation is found to enhance the tangential fluid flow and temperature distribution, while it reduces velocity in the other directions and the induced magnetic field. [ABSTRACT FROM AUTHOR]

In this study, magnetohydrodynamic cross fluid model is used to formulate the 2D boundary layer equations of fluid moving on the parabolic surface. The surface is assumed to be in vertical shape due to the convection. The underlying effects of viscous dissipation and chemical reaction are modeled to observe the transportation of heat and mass rate. To understand fluid behavior, the thermophysical properties are considered as variable because they have huge influence in food processing, viscometers, lubricants and various industrial works. The assumed geometry of fluid flows is similar in shape of bullet, submarine, aircraft and car's bonnet, namely paraboloid surface. The modeled equations of cross fluid with mentioned effects are obtained in form of PDEs and then converted these equations in form of ODEs by assuming set of scaling transformations. For the sake of numerical and graphical outcomes, the resulting equations are solved numerically on Matlab software via BVP4c method. Results achieved across velocity indicate that the decay happens by numerous values of Weissenberg number, power law index, viscosity parameter and Hartmann number. The temperature and concentration fields attained increasing influence by thermal conductivity coefficient, Eckert number and thermal diffusivity parameter. [ABSTRACT FROM AUTHOR]

Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three‐dimensional extension (3D‐RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D‐RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D‐RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D‐RISM programs for single‐ and multi‐GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D‐RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io. [ABSTRACT FROM AUTHOR]

For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight‐binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one‐dimensional reaction coordinates in chemical reactions. [ABSTRACT FROM AUTHOR]

NO synthesis using plasma catalysis is analyzed in a parallel-plate atmospheric pressure RF plasma from N2/O2 admixed to helium exposed to Fe and Pt catalysts on a SiO2 support. The NO x species are measured by Fourier-transform infrared spectroscopy in a multi-pass cell. The trends in species densities can be well explained by air chemistry reactions, where NO's progressive oxidation occurs with increasing oxygen admixture and ozone generation. The sequence can be controlled by the state of the surface that preferentially quenches O3 and allows for an optimum NO production. The maximum production of NO is found at 70% N2/(N2+O2) mixture ratio at 120 ∘C using sandblasted glass, with a conversion rate of 0.085%. [ABSTRACT FROM AUTHOR]

The catalytic production of propylene via propane dehydrogenation (PDH) is a key reaction in the chemical industry. By combining operando transmission electron microscopy with density functional theory analysis, we show that the intercalation and ordering of carbon on Pt interstitials to form Pt−C solid solutions is relevant for increasing propylene production. More specifically, we found that at the point of enhanced propylene formation, the structure of platinum nanoparticles is transformed into a transient caesium chloride‐type Pt−C polymorph. At more elevated temperatures, the zincblende and rock salt polymorphs seemingly coexist. When propylene production was highest, multiple crystal structures consisting of Pt and carbon were occasionally found to coexist in one individual nanoparticle, distorting the Pt lattice. Catalyst coking was detected at all stages of the reaction, but did initially not affect all particles. These findings could lead to the development of novel synthesis strategies towards tailoring highly efficient PDH catalysts. [ABSTRACT FROM AUTHOR]

The purpose of this research is to discuss a two-dimensional (2D), laminar, continuous flow of Casson liquid through a stretched porous wedge in the presence of chemical reaction and buoyancy effects over wedge. This research is aimed at analyzing chemically reacting flow of Casson model over a heated porous wedge in order to understand the features of dynamic wedge. The governing equations and involved parameters are nondimensionalized using transformations. Bvp4c, a numerical tool in Matlab is employed to assess the solution. Significant findings of the major dimensionless parameters on state profiles of velocity, temperature and concentration are drawn graphically. The principal results indicate the impacts of Casson parameter, Eckert and Prandtl number, R stretching parameter, K 1 chemical parameter, Sc Schmidt number, C mass transfer parameter, m wedge angle parameter on concentration, velocity and temperature field. The Sherwood, Nusselt number and skin friction numerical values are presented in tabular form. Major findings show that drag force at wedge declines for greater K 1 . Nusselt number shrinks for larger behavior for K 1 . Sherwood number upsurges for greater performance for chemical reaction parameter K 1 . Moreover, K 1 upsurges the temperature slowly but the impacts of K 1 on concentration show a decreasing behavior. [ABSTRACT FROM AUTHOR]

In this research, the dynamics of MHD Casson fluid flow has been discussed in the presence of non-Darcy Forchheimer porous medium. The investigation is focused on how thermal radiation, Soret–Dufour, and chemical reactions affect the incompressible Casson flow in a non-Darcy Forchheimer porous medium, taking account of pressure force. The mathematical model of the system is solved using the finite difference scheme followed by the shooting technique with bvp4c tool in MATLAB. The effects of physical parameters on velocity and transport (heat and mass) profile are illustrated through graphs. From the results, it is observed that Soret effect reduces the thermal boundary layer thickness which leads to the asymptotic increase in heat dissipation. The findings of the study on MHD Casson fluid model considering the non-Darcy Forchheimer porous medium are useful in engineering and science areas such as chemical machinery systems, geophysics, etc. [ABSTRACT FROM AUTHOR]

The aim of this study is to investigate the effects of thermal radiation and chemical reactions on magnetohydrodynamic hyperbolic tangent liquid, which includes nanoparticles on a stretched surface while taking into account Brownian motion and thermophoresis. The nonlinear partial differential equations governing the system are converted into nonlinear ordinary differential equations through suitable similarity transformations. The focus of the study is to elucidate important engineering concepts such as skin friction, Sherwood number, and heat transfer, as well as to understand the effects of various expressions on the different profiles. The Keller-box approach, a sophisticated numerical tool, is used to get the numerical answers to the current enquiry. The generated findings are extensively tested for correctness and dependability. The findings of this study might have far-reaching ramifications for a variety of technical applications, including heat exchangers, chemical reactors, and thermal management systems.The results show that the rate of mass transfer rises with the increment in the factors of chemical reaction, thermal radiation, nanoparticles volume, and Brownian motion. [ABSTRACT FROM AUTHOR]

This paper considers the movement of an incompressible non-Newtonian Walters' B liquid within a rotating annulus. The flow lies within porous media and is magnetized by a uniform normal magnetic field. Mass transmission is included in the arrangements of homogeneous and heterogeneous chemical reactions (HHCR) with a thermal diffusion effect. Heat diffusion is exposed with a temperature- dependent heat source (THS) and an exponential radial-dependent heat source (ERHS), besides Joule heating and viscous dissipations. The mathematical construction is shown by momentum, energy and concentration of chemical materials equations along with time-periodic boundary conditions. The innovation of this study stems from considering mass transfer utilizing HHCR, with thermal diffusion effects in the flow within a rotating annulus, trying to understand the effect of these reactions on the flow and related applications. The principal regulating the structure of nonlinear partial differential equations is transferred by ordinary ones utilizing appropriate similarity analysis. These equations are analyzed by the homotopy perturbation method. Subsequently, the analytical solutions of the main profiles are obtained, and a graphical construction is established to clarify the effects of the relevant physical elements. It is observed that the velocity waves decrease with annulus width enlargement and increase with the wave phase amplitude. With an increase in all significant parameters, heat transmission gets better. Furthermore, as the strength of HHCR is increased, the concentration of molecules decreases. These outcomes are significant in several applications like cancer therapy, biochemical manufacturing purposes through reactors, where biochemical interactions can be regulated by accurate control of various parameters. [ABSTRACT FROM AUTHOR]

Framework and polymeric nanoreactors (NRs) have distinct advantages in improving chemical reaction efficiency in the tumor microenvironment (TME). Nanoreactor‐loaded oxidoreductase enzyme is activated by tumor acidity to produce H2O2 by increasing tumor oxidative stress. High levels of H2O2 induce self‐destruction of the vesicles by releasing quinone methide to deplete glutathione and suppress the antioxidant potential of cancer cells. Therefore, the synergistic effect of the enzyme‐loaded nanoreactors results in efficient tumor ablation via suppressing cancer‐cell metabolism. The main driving force would be to take advantage of the distinct metabolic properties of cancer cells along with the high peroxidase‐like activity of metalloenzyme/metalloprotein. A cascade strategy of dual enzymes such as glucose oxidase (GOx) and nitroreductase (NTR) wherein the former acts as an O2‐consuming agent such as overexpression of NTR and further amplified NTR‐catalyzed release for antitumor therapy. The design of cascade bioreductive hypoxia‐responsive drug delivery via GOx regulates NTR upregulation and NTR‐responsive nanoparticles. Herein, we discuss tumor hypoxia, reactive oxygen species (ROS) formation, and the effectiveness of these therapies. Nanoclusters in cascaded enzymes along with chemo‐radiotherapy with synergistic therapy are illustrated. Finally, we outline the role of the nanoreactor strategy of cascading enzymes along with self‐synergistic tumor therapy. [ABSTRACT FROM AUTHOR]

This document is a detailed description of a study on the oxidative chlorination of alkanes using visible light and HCl as the chlorine reagent. The researchers found that simple alkanes cannot be chlorinated effectively under the same reaction conditions, but functionalized alkanes with electron-withdrawing groups can undergo chlorination. The study includes experimental procedures, results, and characterization of the compounds using NMR analysis. The document also acknowledges the funding source and provides additional supporting information. [Extracted from the article]

Environmentally persistent free radicals are long-lived pollutants that maintain stability in air, soil, and water. They contribute to the production of reactive oxygen species in environmental media, leading to oxidative stress in biological organisms. This stress can provoke inflammation and damage to biological macromolecules, potentially resulting in cardiopulmonary dysfunction. In this review, we discuss the formation and classification of EPFRs. Typically, EPFRs form through electron transfer from organic compounds to transition metals during thermal processes. In metal-free environments, however, organic compounds can undergo bond cleavage, generating EPFRs under thermal conditions and light exposure. EPFRs are generally categorized into three types: oxygen-centered, carbon-centered, and those containing heteroatoms centered on either oxygen or carbon. We also provide a detailed summary of the fundamental characteristics of EPFRs in different environments such as air, soil, and water. Given their role as electron donors, EPFRs have potential applications in degrading organic pollutants in the environment. The review comprehensively addresses the deleterious impacts of EPFRs on organism health, highlighting risks to metabolic functions and cardiopulmonary health. Furthermore, it underscores the potential involvement of EPFRs as electron donors in atmospheric chemical reactions. The pivotal role of EPFRs in environmental pollutant transformation warrants more studies in future research endeavors. [ABSTRACT FROM AUTHOR]

This study examines the two-phase nanofluid magnetohydrodynamic (MHD) boundary layer flow model with heat absorption or generation and chemical reaction via porous media due to an exponential stretching sheet using the Haar wavelet collocation method (HWCM). First, the governing nonlinear partial differential equations (PDEs) are transformed into coupled, highly nonlinear, ordinary differential equations (ODEs) using similarity transformations. Then the coupled ODEs are translated from the infinite domain [0, ∞ ) to the finite domain [0, 1] via coordinate transformation because the wavelet plays a crucial role in [0, 1]. The obtained equations are solved using HWCM. The impacts of the physical parameters are discussed using tables and graphs. It was found that the Nusselt number R e x − 1 / 2 N u x is a decreasing function of the magnetic field, porous media parameter, heat generation or absorption parameter, and chemical reaction parameter. [ABSTRACT FROM AUTHOR]

Background: Doubtful reactions in patch testing are infrequently reported in the literature; however, recent reports have suggested they be assessed with the same scrutiny as stronger reactions. Objective: Assess the clinical relevance of doubtful reactions in patch testing. Methods: Retrospective study of 1514 patients comprehensively patch tested via the NACDG standard series and additional allergens based on history. The clinical relevance of each reaction was graded based on the NACDG scale: definite, probable, possible, past, unknown and irritant. Reactions were considered 'unique' if an additional mild‐to‐strong reaction to the same chemical at a different concentration was not observed. Results: 68.9% (1043) of patients demonstrated at least 1 doubtful reaction. Of 4453 total doubtful reactions, 92.2% (4106) were unique. Only 3.3% (137) and 12.2% (500) of these were determined to be of definite or probable clinical relevance respectively. 'Fragrance' was the most common allergen family present among the unique definite doubtful reactions (37). However, 24 (64.9%) of these also had a stronger reaction to another fragrance. Cocamidopropyl betaine was the second most frequent allergen demonstrating definite doubtful reactions (27) and unique in 85.2% (23) of cases. Methylchloroisothiazolinone/methylisothiazolinone (MCI/MI) was most prevalent (36) but less frequently unique (58.3%, 21). Conclusions: Doubtful reactions may not be as impactful to clinical decision making as theorised in the literature. Few demonstrate definite clinical significance, and many have related stronger reactions that capture them for clinical purposes. Identification of doubtful reactions to cocamidopropyl betaine and MCI/MI may be of greatest significance as they most frequently were not supported by stronger reactions. [ABSTRACT FROM AUTHOR]

1,4-Butanediol (1,4-BDO) is a valuable industrial chemical that is primarily produced via several energy-intensive petrochemical processes based on fossil-based raw materials, leading to issues related to: non-renewability, environmental contamination, and high production costs. 1,4-BDO is used in many chemical reactions to develop a variety of useful, valuable products, such as: polyurethane, Spandex intermediates, and polyvinyl pyrrolidone (PVP), a water-soluble polymer with numerous personal care and pharmaceutical uses. In recent years, to satisfy the growing need for 1,4-BDO, there has been a major shift in focus to sustainable bioproduction via microorganisms using: recombinant strains, metabolic engineering, synthetic biology, enzyme engineering, bioinformatics, and artificial intelligence-guided algorithms. This article discusses the current status of the development of: various chemical and biological production techniques for 1,4-BDO, advances in biological pathways for 1,4-BDO biosynthesis, prospects for future production strategies, and the difficulties associated with environmentally friendly and bio-based commercial production strategies. [ABSTRACT FROM AUTHOR]