Artificial Force Induced Reaction Research Articles

Chemography-guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst.

Visualization and analysis of large chemical reaction networks become rather challenging when conventional graph-based approaches are used. As an alternative, we propose to use the chemical cartography ("chemography") approach, describing the data distribution on a 2-dimensional map. Here, the Generative Topographic Mapping (GTM) algorithm - an advanced chemography approach - has been applied to visualize the reaction path network of a simplified Wilkinson's catalyst-catalyzed hydrogenation containing some 105 structures generated with the help of the Artificial Force Induced Reaction (AFIR) method using either Density Functional Theory or Neural Network Potential (NNP) for potential energy surface calculations. Using new atoms permutation invariant 3D descriptors for structure encoding, we've demonstrated that GTM possesses the abilities to cluster structures that share the same 2D representation, to visualize potential energy surface, to provide an insight on the reaction path exploration as a function of time and to compare reaction path networks obtained with different methods of energy assessment.

Low-Temperature Methane Combustion Using Ozone over Coβ Catalyst.

Catalytic methane (CH4) combustion is a promising approach to reducing the release of unburned methane in exhaust gas. Here, we report Co-exchanged β zeolite (Coβ) as an efficient catalyst for CH4 combustion using O3. A series of ion-exchanged β zeolites (Co, Ni, Mn, Fe, and Pd) are subjected to the catalytic test, and Coβ exhibits a superior performance in a low-temperature region (<100 °C). The results of X-ray absorption spectroscopy (XAS) and catalytic tests for Coβ with different Co loadings indicate the isolated Co species is the plausible active site. The reaction mechanism of CH4 combustion over the isolated Co2+ cation is theoretically investigated by the single-component artificial force-induced reaction (SC-AFIR) method to thoroughly search for possible reaction routes. The resulting path toward CO2 formation shows an activation energy of 73 kJ/mol for the rate-determining step and an exothermicity of 1025 kJ/mol, which supports the experimental results. During a long-term catalytic test for 160 h without external heating, the CH4 conversion gradually decreases from 80 to 40%, but the conversion fully recovers after dehydration at 500 °C (0.5 h). The copresence of H2O and CO exhibits a negative impact on the catalytic activity, while NO and SO2 do not markedly change the catalytic activity.

Tetraborylation of p-Benzynes Generated by the Masamune-Bergman Cyclization through Reaction Design Based on the Reaction Path Network.

Designing the reactant molecule of an initial reaction, based on quantum chemical pathway exploration, enabled us to access a new reaction, i.e., the tetraborylation reaction of p-benzynes generated from 1,2-diethynylbenzene derivatives, using bis(pinacolato)diborane(4) (B2pin2). Based on the reaction path network generated via the artificial-force-induced reaction (AFIR) method, desired and undesired paths were identified and used to modify the chemical structure of the reactant. After the in silico screening, the optimal structure of the reactant was determined to be a 1,2-diethynylbenzene derivative with a butylene linker. The reaction of the optimized reactant and its derivatives with an excess of B2pin2 gave the tetraborylated products in good yields (up to 58%). It is quite intriguing that the two carbons of p-benzyne behave formally as dicarbenes in this reaction.

Mechanochemical generation of aryl barium nucleophiles from unactivated barium metal.

Organobarium reagents are of interest as homologues of the Grignard reagents based on organomagnesium compounds due to their unique reactivity as well as regio- and stereoselectivity. However, reactions involving organobarium reagents are less developed in comparison to reactions involving Grignard reagents due to the lack of a simple and economical synthetic method and their high reactivity. To the best of our knowledge, there is no established method for the direct synthesis of organobarium compounds from commercially available bulk barium metal and organic halides. So far, the generation of organobarium compounds usually requires the use of activated barium (Rieke barium), which significantly reduces the practical utility of organobarium reagents and hinders the development of new organobarium-mediated transformations. Here, we present a mechanochemical strategy based on ball-milling that facilitates the direct generation of various aryl barium nucleophiles from commercially available unactivated barium metal and aryl halides without complicated pre-activation processes. Our simple mechanochemical protocol allows the rapid development of novel carbon-silicon-bond-forming reactions with hydrosilanes mediated by aryl barium nucleophiles; importantly, these reactions are difficult to achieve using other Grignard-type carbon nucleophiles. To the best of our knowledge, this is the first example of a nucleophilic substitution reaction involving an aryl barium species. Furthermore, this mechanochemical strategy established the first example of a nucleophilic addition to a carbonyl compound involving an aryl barium nucleophile. Preliminary theoretical calculations using the artificial force-induced reaction (AFIR) method to reveal the reaction mechanism of the hydrosilane arylation are also described.

Challenges for Kinetics Predictions via Neural Network Potentials: A Wilkinson's Catalyst Case.

Ab initio kinetic studies are important to understand and design novel chemical reactions. While the Artificial Force Induced Reaction (AFIR) method provides a convenient and efficient framework for kinetic studies, accurate explorations of reaction path networks incur high computational costs. In this article, we are investigating the applicability of Neural Network Potentials (NNP) to accelerate such studies. For this purpose, we are reporting a novel theoretical study of ethylene hydrogenation with a transition metal complex inspired by Wilkinson's catalyst, using the AFIR method. The resulting reaction path network was analyzed by the Generative Topographic Mapping method. The network's geometries were then used to train a state-of-the-art NNP model, to replace expensive ab initio calculations with fast NNP predictions during the search. This procedure was applied to run the first NNP-powered reaction path network exploration using the AFIR method. We discovered that such explorations are particularly challenging for general purpose NNP models, and we identified the underlying limitations. In addition, we are proposing to overcome these challenges by complementing NNP models with fast semiempirical predictions. The proposed solution offers a generally applicable framework, laying the foundations to further accelerate ab initio kinetic studies with Machine Learning Force Fields, and ultimately explore larger systems that are currently inaccessible.

Early-Stage Formation of the SIFSIX-3-Zn Metal-Organic Framework: An Automated Computational Study.

Metal-organic frameworks (MOFs) have attracted significant attention over the past 2 decades due to their wide applicability as functional materials. However, targeted synthesis of novel MOFs remains problematic as their formation mechanisms are poorly understood, which forces us to rely on serendipity in the synthesis of novel MOFs. Here, we demonstrate a workflow employing the artificial force induced reaction (AFIR) method to investigate the self-assembly process of the node of the SIFSIX-3-Zn MOF, [Zn(pyz)4(SiF6)2]2- (pyz = pyrazine), in an automated manner. The workflow encompassing AFIR calculations, generation of extensive reaction path networks, propagation simulations of intermediates, and further refinements of identified formation pathways showed that the nodal structure can form through multiple competing pathways involving interconvertible intermediates. This finding provides a plausible rationale for the stochastic multistage processes believed to be key in MOF formation. Furthermore, this work represents the first application of an automated reaction mechanism discovery method to a MOF system using a general workflow that is applicable to study the formation of other MOF motifs as well.

A systematic mechanistic survey on the reactions between OH radical and CH3OH on ice.

A systematic mechanistic survey was performed for the CH3OH + OH reaction on ice. ONIOM(ωB97X-D/Def2-TZVP:AMOEBA09) calculations suggested a range of binding energies for the CH2OH radical (0.29-0.69 eV) and CH3OH (0.15-0.72 eV) molecule on hexagonal water ice (Ih) and amorphous solid water (ASW). Computed average binding energies of CH2OH radical (0.49 eV) and CH3OH (0.41 eV) are relatively stronger compared to the CH3O radical binding energies (0.32 eV, Sameera et al., J. Phy. Chem. A, 2021, 125, 387-393). Thus, the CH3OH molecule, CH2OH and CH3O radicals can adsorb on ice, where the binding energies follow the order CH2OH > CH3OH > CH3O. The multi-component artificial force-induced reaction (MC-AFIR) method systematically determined the reaction mechanisms for the CH3OH + OH reaction on ice, where two reaction paths, giving rise to CH2OH and CH3O radicals, were confirmed. A range of reaction barriers, employing the ωB97X-D/Def2-TZVP level of theory, was found for each reaction (0.03-0.11 eV for CH2OH radical formation, and 0.03-0.44 eV for CH3O radical formation). Based on the lowest energy reaction paths, we suspect that both reactions operate on ice. The computed data in this study evidence that the nature of the binding site or the reaction site has a significant effect on the computed binding energies or reaction barriers. Thus, the outcomes of the present study will be very useful for the computational astrochemistry community to determine reliable binding energies and reaction barriers on ice.

Prediction of High-Yielding Single-Step or Cascade Pericyclic Reactions for the Synthesis of Complex Synthetic Targets.

Pericyclic reactions, which involve cyclic concerted transition states without ionic or radical intermediates, have been extensively studied since their definition in the 1960s, and the famous Woodward-Hoffmann rules predict their stereoselectivity and chemoselectivity. Here, we describe the application of a fully automated reaction-path search method, that is, the artificial force induced reaction (AFIR), to trace an input compound back to reasonable starting materials through thermally allowed pericyclic reactions via product-based quantum-chemistry-aided retrosynthetic analysis (QCaRA) without using any a priori experimental knowledge. All categories of pericyclic reactions, including cycloadditions, ene reactions, group-transfer, cheletropic, electrocyclic, and sigmatropic reactions, were successfully traced back via concerted reaction pathways, and starting materials were computationally obtained with the correct stereochemistry. Furthermore, AFIR was used to predict whether the identified reaction pathway can be expected to occur in good yield relative to other possible reactions of the identified starting material. In order to showcase its practical utility, this state-of-the-art technology was also applied to the retrosynthetic analysis of a natural product with a relatively high number of atoms (52 atoms: endiandric acid C methyl ester), which was first synthesized by Nicolaou in 1982 and provided the corresponding starting polyenes with the correct stereospecificity via three pericyclic reaction cascades (one Diels-Alder reaction as well as 6π and 8π electrocyclic reactions). Moreover, not only systems that obey the Woodward-Hoffmann rules but also systems that violate these rules, such as those recently calculated by Houk, can be retrosynthesized accurately.

A theory-driven synthesis of symmetric and unsymmetric 1,2-bis(diphenylphosphino)ethane analogues via radical difunctionalization of ethylene

1,2-Bis(diphenylphosphino)ethane (DPPE) and its synthetic analogues are important structural motifs in organic synthesis, particularly as diphosphine ligands with a C2-alkyl-linker chain. Since DPPE is known to bind to many metal centers in a bidentate fashion to stabilize the corresponding metal complex via the chelation effect originating from its entropic advantage over monodentate ligands, it is often used in transition-metal-catalyzed transformations. Symmetric DPPE derivatives (Ar12P−CH2−CH2−PAr12) are well-known and readily prepared, but electronically and sterically unsymmetric DPPE (Ar12P−CH2−CH2−PAr22; Ar1≠Ar2) ligands have been less explored, mostly due to the difficulties associated with their preparation. Here we report a synthetic method for both symmetric and unsymmetric DPPEs via radical difunctionalization of ethylene, a fundamental C2 unit, with two phosphine-centered radicals, which is guided by the computational analysis with the artificial force induced reaction (AFIR) method, a quantum chemical calculation-based automated reaction path search tool. The obtained unsymmetric DPPE ligands can coordinate to several transition-metal salts to form the corresponding complexes, one of which exhibits distinctly different characteristics than the corresponding symmetric DPPE–metal complex.

Five-Fold Symmetric Pentaindolo- and Pentakis(benzoindolo)Corannulenes: Unique Structural Dynamics Derived from the Combination of Helical and Bowl Inversions.

Peripherally π-extended corannulenes bearing quintuple azahelicene units, 10 and 11, were prepared and their dynamic behaviors were studied experimentally and theoretically. The fused corannulenes were synthesized from sym-pentabromocorannulene in three steps. X-Ray diffraction analysis for 10 displayed a conformer possessing a P(M) bowl chirality and a PPMPM (PMPMM) helical chirality, which was found to be the most stable conformer(s). Variable-temperature NMR measurements of 10 and 11 revealed that their structural isomers can be interconvertible in solution, depending on the steric congestion around the helical scaffolds. Automated search for conformers in the equilibrium and transition states by Artificial Force Induced Reaction (AFIR) method revealed their interconversion networks, including bowl-inversion and helical-inversion. This analysis indicated that the co-existing corannulene and azahelicene moieties influence the conformational dynamics, which leads to mitigation of the activation energy barriers for isomerization.

Five‐Fold Symmetric Pentaindolo‐ and Pentakis(benzoindolo)Corannulenes: Unique Structural Dynamics Derived from the Combination of Helical and Bowl Inversions

AbstractPeripherally π‐extended corannulenes bearing quintuple azahelicene units, 10 and 11, were prepared and their dynamic behaviors were studied experimentally and theoretically. The fused corannulenes were synthesized from sym‐pentabromocorannulene in three steps. X‐Ray diffraction analysis for 10 displayed a conformer possessing a P(M) bowl chirality and a PPMPM (PMPMM) helical chirality, which was found to be the most stable conformer(s). Variable‐temperature NMR measurements of 10 and 11 revealed that their structural isomers can be interconvertible in solution, depending on the steric congestion around the helical scaffolds. Automated search for conformers in the equilibrium and transition states by Artificial Force Induced Reaction (AFIR) method revealed their interconversion networks, including bowl‐inversion and helical‐inversion. This analysis indicated that the co‐existing corannulene and azahelicene moieties influence the conformational dynamics, which leads to mitigation of the activation energy barriers for isomerization.

Carboxylation of a Palladacycle Formed via C(sp3 )-H Activation: Theory-Driven Reaction Design.

Theory-driven organic synthesis is a powerful tool for developing new organic transformations. A palladacycle(II), generated from 8-methylquinoline via C(sp3 )-H activation, is frequently featured in the scientific literature, albeit that the reactivity toward CO2 , an abundant, inexpensive, and non-toxic chemical, remains elusive. We have theoretically discovered potential carboxylation pathways using the artificial force induced reaction (AFIR) method, a density-functional-theory (DFT)-based automated reaction path search method. The thus obtained results suggest that the reduction of Pd(II) to Pd(I) is key to promote the insertion of CO2 . Based on these computational findings, we employed various one-electron reductants, such as Cp*2 Co, a photoredox catalyst under blue LED irradiation, and reductive electrolysis ((+)Mg/(-)Pt), which afforded the desired carboxylated products in high yields. After screening phosphine ligands under photoredox conditions, we discovered that bidentate ligands such as dppe promoted this carboxylation efficiently, which was rationally interpreted in terms of the redox potential of the Pd(II)-dppe complex as well as on the grounds of DFT calculations. We are convinced that these results could serve as future guidelines for the development of Pd(II)-catalyzed C(sp3 )-H carboxylation reactions with CO2 .

Structural Characterization of Nickel-Doped Aluminum Oxide Cations by Cryogenic Ion Trap Vibrational Spectroscopy.

Isolated nickel-doped aluminum oxide cations (NiOm)(Al2O3)n(AlO)+ with m = 1-2 and n = 1-3 are investigated by infrared photodissociation (IRPD) spectroscopy in combination with density functional theory and the single-component artificial force-induced reaction method. IRPD spectra of the corresponding He-tagged cations are reported in the 400-1200 cm-1 spectral range and assigned based on a comparison to calculated harmonic IR spectra of low-energy isomers. Simulated spectra of the lowest energy structures generally match the experimental spectra, but multiple isomers may contribute to the spectra of the m = 2 series. The identified structures of the oxides (m = 1) correspond to inserting a Ni-O moiety into an Al-O bond of the corresponding (Al2O3)1-3(AlO)+ cluster, yielding either a doubly or triply coordinated Ni2+ center. The m = 2 clusters prefer similar structures in which the additional O atom either is incorporated into a peroxide unit, leaving the oxidation state of the Ni2+ atom unchanged, or forms a biradical comprising a terminal oxygen radical anion Al-O•- and a Ni3+ species. These clusters represent model systems for under-coordinated Ni sites in alumina-supported Ni catalysts and should prove helpful in disentangling the mechanism of selective oxidative dehydrogenation of alkanes by Ni-doped catalysts.

A reaction route network for methanol decomposition on a Pt(111) surface.

A reaction route network for the decomposition reaction of methanol on a Pt(111) surface was constructed by using the artificial force-induced reaction (AFIR) method, which can search for reaction paths automatically and systematically. Then, the network was kinetically analyzed by applying the rate constant matrix contraction (RCMC) method. Specifically, the time hierarchy of the network, the time evolution of the population initially given to CH3 OH to the other species on the network, and the most favorable route from CH3 OH to major and minor products were investigated by the RCMC method. Consistently to previous studies, the major product on the network was CO+4H, and the most favorable route proceeded through the following steps: CH3 OH → CH2 OH+H → HCOH+2H → HCO+3H → CO+4H. Furthermore, paths to byproducts found on the network and their kinetic importance were discussed. The present procedure combining AFIR and RCMC was thus successful in explaining the title reaction without using any information on its product or the reaction mechanism.

Synthesis of Difluoroglycine Derivatives from Amines, Difluorocarbene, and CO2 : Computational Design, Scope, and Applications.

Invited for the cover of this issue are Satoshi Maeda, Tsuyoshi Mita, and co-workers at ICReDD (Hokkaido University). The image depicts an Artificial Force Induced Reaction (AFIR) conducted on a supercomputer, which predicts a new chemical transformation and its application. Read the full text of the article at 10.1002/chem.202100812.

Front Cover: Synthesis of Difluoroglycine Derivatives from Amines, Difluorocarbene, and CO2: Computational Design, Scope, and Applications (Chem. Eur. J. 39/2021)

An Artificial Force Induced Reaction (AFIR) on a super computer has led to a new three-component reaction (3CR) of amines, difluorocarbene, and the inexpensive and non-toxic C1 source CO2. This reaction produces a broad range of α,α-difluoroglycine derivatives that are bioisosteres of natural glycine. The versatility of these products is very broad; i.e., they can be used as new difluorocarbene sources, substrates for radical substitution reactions, and precursors for new NHC ligands. More information can be found in the Full Paper by S. Maeda, T. Mita et al. (DOI: 10.1002/chem.202100812).

Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force

AbstractThis article provides an overview on an automated reaction path search method called artificial force induced reaction (AFIR). The AFIR method induces various chemical transformations by applying force between pairs of fragments in a system. By pushing fragments from their various mutual orientations or by applying force between various fragment pairs using the AFIR method, many reaction paths can be explored systematically. In this article, the basic ideas and several different implementations are introduced first. Then, its thoroughness in the automated reaction path search is discussed with its applications to two small molecules. In the later part, its versatility is shown with discussing some previous application examples to organic reaction, organometallic catalysis, photoreaction, surface reaction, phase transition, and enzyme reaction. In addition, an attempt of predicting an idea of new synthesis method from scratch on the basis of the concept quantum chemistry‐aided retrosynthetic analysis (QCaRA) is presented, where the AFIR method was used as a reaction path search engine in QCaRA. Finally, future outlook and a comment on the GRRM program in which the AFIR method is available are given.This article is categorized under: Structure and Mechanism &gt; Reaction Mechanisms and Catalysis Theoretical and Physical Chemistry &gt; Reaction Dynamics and Kinetics

Substitution effect on the nonradiative decay and trans → cis photoisomerization route: a guideline to develop efficient cinnamate-based sunscreens.

Cinnamate derivatives are very useful as UV protectors in nature and as sunscreen reagents in daily life. They convert harmful UV energy to thermal energy through effective nonradiative decay (NRD) including trans → cis photoisomerization. However, the mechanism is not simple because different photoisomeirzation routes have been observed for different substituted cinnamates. Here, we theoretically examined the substitution effects at the phenyl ring of methylcinnamate (MC), a non-substituted cinnamate, on the electronic structure and the NRD route involving trans → cis isomerization based on time-dependent density functional theory. A systematic reaction pathway search using the single-component artificial force-induced reaction method shows that the very efficient photoisomerization route of MC can be essentially described as "1ππ* (trans) → 1nπ* → T1 (3ππ*) → S0 (trans or cis)". We found that for efficient 1ππ* (trans) → 1nπ* internal conversion (IC), MC should have the substituent at the appropriate position of the phenyl ring to stabilize the highest occupied π orbital. Substitution at the para position of MC slightly lowers the 1ππ* state energy and photoisomerization occurs via a slightly less efficient "1ππ* (trans) → 3nπ* → T1 (3ππ*) → S0 (trans or cis)" pathway. Substitution at the meta or ortho positions of MC significantly lowers the 1ππ* state energy so that the energy barrier of IC (1ππ* → 1nπ*) becomes very high. This substitution leads to a much longer 1ππ* state lifetime than that of MC and para-substituted MC, and a change in the dominant photoisomerization route to "1ππ* (trans) → C[double bond, length as m-dash]C bond twisting on 1ππ* → S0 (trans or cis)". As a whole, the "1ππ* → 1nπ*" IC observed in MC is the most important initial step for the rapid change of UV energy to thermal energy. We also found that the stabilization of the π orbital (i) minimizes the energy gap between 1ππ* and 1nπ* at the 1ππ* minimum and (ii) makes the 0-0 level of 1ππ* higher than 1nπ* as observed in MC. These MC-like relationships between the 1ππ* and 1nπ* energies should be ideal to maximize the "1ππ* → 1nπ*" IC rate constant according to Marcus theory.

Some Mathematical Reasoning on the Artificial Force Induced Reaction Method.

There are works of the Maeda-Morokuma group, which propose the artificial force induced reaction (AFIR) method (Maeda et al., J. Comput. Chem. 2014, 35, 166 and 2018, 39, 233). We study this important method from a theoretical point of view. The understanding of the proposers does not use the barrier breakdown point of the AFIR parameter, which usually is half of the reaction path between the minimum and the transition state which is searched for. Based on a comparison with the theory of Newton trajectories, we could better understand the method. It allows us to follow along some reaction pathways from minimum to saddle point, or vice versa. We discuss some well-known two-dimensional test surfaces where we calculate full AFIR pathways. If one has special AFIR curves at hand, one can also study the behavior of the ansatz. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Exploration of Unimolecular and Bimolecular Pathways for Nitrile N‐Oxide Isomerization to Isocyanate Through Global Reaction Route Mapping Techniques

Mechanisms of the unimolecular and bimolecular isomerization of nitrile N‐oxide to isocyanate were investigated by quantum chemical calculations using the global reaction route mapping (GRRM) technique, which consists of the anharmonic downward distortion following (ADDF) and multi‐component artificial force induced reaction (AFIR) methods, which can exhaustively search reaction paths. In the unimolecular isomerization, isomerization paths of nitrile N‐oxide to isocyanate were exhaustively explored by the ADDF method. The energetically lowest path for 2,6‐dimethoxybenzonitrile oxide (Ar–CNO) isomerization was via oxazirine intermediate formation, which was the rate‐determining step with an activation free energy of 56.8 kcal mol–1. The high activation free energy indicates that the isomerization hardly proceeds as a thermal unimolecular reaction. Next, the bimolecular isomerization paths of Ar–CNO were explored for diradical addition, [3+2] and [3+3] cycloadditions, and self‐catalyzed isomerization through the AFIR method. The diradical addition was the energetically lowest path with an activation free energy of 55.4 kcal mol–1. Although the bimolecular isomerization was energetically favorable than the unimolecular isomerization, its activation free energy was still high for the reaction to proceed under thermal conditions. Exhaustive path searching for these unimolecular and bimolecular isomerizations suggest that these reactions are catalyzed by acid or base.