General method for exact evaluation of parameters of the elementary steps of coupled reactions. Invariant analysis.
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ABSTRACT: A general method has been devised for the exact evaluation of the rate constants of the elementary steps of a system consisting of any number of coupled reactions. The method is independent of the structure of the network of coupled steps. The precision of the data evaluation is solely dependent on the quality of the detection unit. The application of the method is illustrated with data collected for the binding of the competitive inhibitor proflavine to chymotrypsin under such conditions that five states of the enzyme are required to interpret the results. In the absence of a substance possessing the binding specificity, the enzyme is present as an equilibrium between an active and an inactive conformer. The latter prevails. The binding of the specific inhibitor releases a slow proton transfer from the medium to the alpha-amino group of Ile-16. Subsequently, the enzyme-inhibitor (or enzyme-substrate) complex re-arranges to the catalytically active form, which is retained until the supply of specific substrate is exhausted. The control features described are general, but are particularly conspicuous under the special environmental conditions used here. A comparison between data for alpha- and delta-forms of chymotrypsin showed that the chain ends of the former impeded the substrate binding and that the activity controlling conformational change occurred in the interior of the enzyme molecule.
Project description:The electron-poor palladium(0) complex L3 Pd (L=tris[3,5-bis(trifluoromethyl)phenyl]phosphine) reacts with Grignard reagents RMgX and organolithium compounds RLi via transmetalation to furnish the anionic organopalladates [L2 PdR]- , as shown by negative-ion mode electrospray-ionization mass spectrometry. These palladates undergo oxidative additions of organyl halides R'X (or related SN 2-type reactions) followed by further transmetalation. Gas-phase fragmentation of the resulting heteroleptic palladate(II) complexes results in the reductive elimination of the cross-coupling products RR'. This reaction sequence corresponds to a catalytic cycle, in which the order of the elementary steps of transmetalation and oxidative addition is switched relative to that of palladium-catalyzed cross-coupling reactions proceeding via neutral intermediates. An attractive feature of the palladate-based catalytic system is its ability to mediate challenging alkyl-alkyl coupling reactions. However, the poor stability of the phosphine ligand L against decomposition reactions has so far prevented its successful use in practical applications.
Project description:A series of 3,5-disubstituted 1,4-dihydropyridine derivatives including the derivative with two chiral centers, 6H (R2 = CH3, CH2Ph), as a new type of organic hydride source were synthesized and characterized. The thermodynamic driving forces (defined as enthalpy changes or standard redox potentials) of the 6 elementary steps for the organic hydrides to release hydride ions in acetonitrile were measured by isothermal titration calorimetry and electrochemical methods. The impacts of the substituents and functional groups bearing the N1 and C3/C5 positions on the thermodynamic driving forces of the 6 elementary steps were examined and analyzed. Moreover, the results showed that the reaction mechanism between the chiral organic hydride and activated ketone (ethyl benzoylformate) was identified as the concerted hydride transfer pathway based on the thermodynamic analysis platform. These valuable and crucial thermodynamic parameters will provide a broadly beneficial impact on the applications of 3,5-disubstituted 1,4-dihydropyridine derivatives in organic synthesis and pharmaceutical chemistry.
Project description:An enhanced computational protocol has been devised for the accurate characterization of gas-phase barrier-less reactions in the framework of the reaction-path (RP) and variable reaction coordinate variational transition-state theory. In particular, the synergistic combination of density functional theory and Monte Carlo sampling to optimize reactive fluxes led to a reliable yet effective computational workflow. A black-box strategy has been developed for selecting the most suited density functional with reference to a high-level one-dimensional reference potential. At the same time, different descriptions of hindered rotations are automatically selected, depending on the corresponding harmonic frequencies along the RP. The performance of the new tool is investigated by means of two prototypical reactions involving different degrees of static and dynamic correlation, namely, H2S + Cl and CH3 + CH3. The remarkable agreement of the computed kinetic parameters with the available experimental data confirms the accuracy and robustness of the proposed approach. Together with their intrinsic interest, these results also pave the way toward systematic investigations of gas-phase reactions involving barrier-less elementary steps by a reliable, user-friendly tool, which can be confidently used also by nonspecialists.
Project description:We report on a class of gapped projected entangled pair states (PEPS) with non-trivial Euler topology motivated by recent progress in band geometry. In the non-interacting limit, these systems have optimal conditions relating to saturation of quantum geometrical bounds, allowing for parent Hamiltonians whose lowest bands are completely flat and which have the PEPS as unique ground states. Protected by crystalline symmetries, these states evade restrictions on capturing tenfold-way topological features with gapped PEPS. These PEPS thus form the first tensor network representative of a non-interacting, gapped two-dimensional topological phase, similar to the Kitaev chain in one dimension. Using unitary circuits, we then formulate interacting variants of these PEPS and corresponding gapped parent Hamiltonians. We reveal characteristic entanglement features shared between the free-fermionic and interacting states with Euler topology. Our results hence provide a rich platform of PEPS models that have, unexpectedly, a finite topological invariant, forming the basis for new spin liquids, quantum Hall physics, and quantum information pursuits.
Project description:Fermi level control by doping is established since decades in inorganic semiconductors and has been successfully introduced in organic semiconductors. Despite its commercial success in the multi-billion OLED display business, molecular doping is little understood, with its elementary steps controversially discussed and mostly-empirical-materials design. Particularly puzzling is the efficient carrier release, despite a presumably large Coulomb barrier. Here we quantitatively investigate doping as a two-step process, involving single-electron transfer from donor to acceptor molecules and subsequent dissociation of the ground-state integer-charge transfer complex (ICTC). We show that carrier release by ICTC dissociation has an activation energy of only a few tens of meV, despite a Coulomb binding of several 100 meV. We resolve this discrepancy by taking energetic disorder into account. The overall doping process is explained by an extended semiconductor model in which occupation of ICTCs causes the classically known reserve regime at device-relevant doping concentrations.
Project description:Most online chemical reaction databases are not publicly accessible or are fully downloadable. These databases tend to contain reactions in noncanonicalized formats and often lack comprehensive information regarding reaction pathways, intermediates, and byproducts. Within the few publicly available databases, reactions are typically stored in the form of unbalanced, overall transformations with minimal interpretability of the underlying chemistry. These limitations present significant obstacles to data-driven applications including the development of machine learning models. As an effort to overcome these challenges, we introduce PMechDB, a publicly accessible platform designed to curate, aggregate, and share polar chemical reaction data in the form of elementary reaction steps. Our initial version of PMechDB consists of over 100,000 such steps. In the PMechDB, all reactions are stored as canonicalized and balanced elementary steps, featuring accurate atom mapping and arrow-pushing mechanisms. As an online interactive database, PMechDB provides multiple interfaces that enable users to search, download, and upload chemical reactions. We anticipate that the public availability of PMechDB and its standardized data representation will prove beneficial for chemoinformatics research and education and the development of data-driven, interpretable models for predicting reactions and pathways. PMechDB platform is accessible online at https://deeprxn.ics.uci.edu/pmechdb.
Project description:We introduce RMechDB, an open-access platform for aggregating, curating, and distributing reliable data about elementary radical reaction steps for computational radical reaction modeling and prediction. RMechDB contains over 5,300 elementary radical reaction steps, each with a single transition state at or around room temperature. These elementary step reactions are manually curated plausible arrow-pushing steps for organic radical reactions. The steps were taken from a variety of sources. Over 2,000 mechanistic steps were extracted from textbooks and/or constructed from research publications. Another 3,000 were taken from gas-phase atmospheric reactions of isoprene and other organic molecules on the MCM (Master Chemical Mechanism) Web site. Reactions are encoded in the SMIRKS format with accurate atom mapping and annotations for arrow-pushing mechanisms. At its core, RMechDB consists of a database schema with an online interactive search interface and a request portal for downloading the raw form of elementary step reactions with their metadata. It also offers an interface for submitting new reactions to RMechDB and expanding the data set through community contributions. Although there are several applications for RMechDB, it is primarily designed as a central platform of radical elementary steps with a unified and structured representation. We believe that this open access to this data and platform enables the extension of data-driven models for chemical reaction predictions and other chemoinformatics predictive tasks.
Project description:The direct synthesis of complex chemicals from simple precursors (such as syngas) is one of the main objectives of current research in heterogeneous catalysis. To rationally design catalytic materials for this purpose, it is essential to identify the critical elementary reaction steps that ultimately determine a catalyst's activity and selectivity with respect to a desired product. Unfortunately, the number of potentially relevant elementary steps is in the thousands, even for relatively simple target species like ethanol. The challenge of identifying the critical steps is thus akin to finding the proverbial needle in a haystack. Recently, a model-reduction scheme has been proposed, which tackles this problem by prescreening the barriers of all potential reactions with computationally inexpensive approximations. Although this route appears highly promising, it raises the question of how the starting point of the model-reduction process can be determined. In this contribution, we present a systematic method for enumerating all intermediates and elementary reactions relevant to a chemical process of interest. Using this approach, we construct reaction networks for C,H,O-containing systems consisting of up to four non-hydrogen atoms (more than 1 million reactions). Importantly, the scheme goes beyond simple bond-breaking reactions and allows considering rearrangement and transfer reactions as well. The presented reaction networks thus cover the chemistry of syngas-based processes (and beyond) to an unprecedented scale.
Project description:The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.
Project description:Balancing kinetics, a crucial priority in catalysis, is frequently achieved by sacrificing activity of elementary steps to suppress side reactions and enhance catalyst stability. Dry reforming of methane (DRM), a process operated at high temperature, usually involves fast C-H activation but sluggish carbon removal, resulting in coke deposition and catalyst deactivation. Studies focused solely on catalyst innovation are insufficient in addressing coke formation efficiently. Herein, we develop coke-free catalysts that balance kinetics of elementary steps for overall thermodynamics optimization. Beginning from a highly active cobalt aluminum oxide (CoAl2O4) catalyst that is susceptible to severe coke formation, we substitute aluminum (Al) with gallium (Ga), reporting a CoAl0.5Ga1.5O4-R catalyst that performs DRM stably over 1000 hours without observable coke deposition. We find that Ga enhances DRM stability by suppressing C-H activation to balance carbon removal. A series of coke-free DRM catalysts are developed herein by partially substituting Al from CoAl2O4 with other metals.