Implementation and performance of the artificial force induced reaction method in the GRRM17 program

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.

One-to-One Correspondence between Reaction Pathways and Reactive Orbitals

The one-to-one correspondence between reaction pathways in the potential energy theory and reactive orbitals in the electronic theory for reactions is presented. In this study, the reactive orbital energy method is applied to the intrinsic reaction coordinates of the global reaction route map generated by an automated reaction path search method. The reactive orbital energy method specifies the pairs of occupied and unoccupied reactive orbitals driving chemical reactions and determines whether the reactions are electron transfer-driven or dynamics-driven. Surprisingly, it is found that the reactive orbital pairs are determined one by one for the electron transfer-driven reaction pathways from an identical molecule. The reactive orbital energy method is also found to provide the sophisticated interpretations of reactions for the electronic motions. This one-to-one correspondence is expected to trigger the unification of the potential energy theory and the electronic theory for reactions that have been independently developed.

Visualization of reaction route map and dynamical trajectory in reduced dimension

In the quantum chemical approach, chemical reaction mechanisms are investigated based on a potential energy surface (PES). Automated reaction path search methods enable us to construct a global reaction route map containing multiple reaction paths corresponding to a series of elementary reaction processes. The on-the-fly molecular dynamics (MD) method provides a classical trajectory exploring the full-dimensional PES based on electronic structure calculations. We have developed two reaction analysis methods, the on-the-fly trajectory mapping method and the reaction space projector (ReSPer) method, by introducing a structural similarity to a pair of geometric structures and revealed dynamic aspects affecting chemical reaction mechanisms. In this review, we will present the details of these analysis methods and discuss the dynamics effects of reaction path curvature and reaction path bifurcation with applications to the CH₃OH + OH^- collision reaction and the Au₅ cluster branching and isomerization reactions.

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

Isolated nickel-doped aluminum oxide cations (NiO_m)(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.

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.

AutoMeKin2021: An open-source program for automated reaction discovery

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

The dioxasilepanyl group as a versatile organometallic unit: studies on stability, reactivity, and utility

Organic synthesis is performed based on precise choices of functional groups and reactions employed. In a multistep synthesis, an ideal functional group should be compatible with various reaction conditions and unaltered until it is subjected to a selective conversion. The current study was set out to search for a silicon functionality that meets these criteria. Here we have established a new silicon-based synthetic methodology centred on a bulky 7-membered dialkoxysilyl group (2,4,4,7,7-pentamethyl-1,3,2-dioxasilepan-2-yl) that uniquely has both stability and on-demand reactivity. The exceptional stability of this functional group was corroborated by both experimental and computational studies which demonstrated that key factors for its stability were a 7-membered structure and steric hindrance. In turn, the dioxasilepanyl group was found to become reactive and to be easily transformed in the presence of appropriate activators. Combined with the development of easy and robust methods to introduce the dioxasilepanyl group onto aryl rings, these findings have allowed a shorter and more efficient synthesis of a bioactive molecule, thus demonstrating the potential utility of the easily accessible dioxasilepanyl group in organic synthesis.

Non-Planar Perylene Bisimide Analogues with Inserted Carbonyl and Methylene Subunits

The synthesis and properties of dinaphthotropone bisimide (DNTrBI) and dinaphthocycloheptatriene bisimide (DNCHepBI) are described. Their molecular design is conceptually based on the insertion of a carbon atom into a perylene bisimide (PBI) core. These molecules adopt non-planar structures due to the presence of a seven-membered ring. The PBI derivative into which a carbonyl group was inserted (DNTrBI) immediately underwent nonradiative decay and/or intersystem crossing in its excited state. The PBI derivative into which a methylene group was inserted (DNCHepBI) was susceptible to deprotonation on account of the two electron-withdrawing naphthalene monoimide units. Subsequent aerobic oxidation resulted in the formation of a C-C bond at the central methylene unit, thus affording a σ-dimer. The formation of this C-C bond is dynamically redox-active, i.e., electron injection into the σ-dimer almost quantitatively regenerated the deprotonated DNCHepBI.

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

A three-component reaction (3CR) for the synthesis of difluoroglycine derivatives has been achieved by using amines, difluorocarbene (generated in situ), and the abundant, inexpensive, and nontoxic C₁ source CO₂ . Various tert-amines and pyridine, (iso)quinoline, imidazole, thiazole, and pyrazole derivatives were incorporated, and the corresponding products were isolated in solid form without purification by column chromatography on silica gel. Detailed reaction profiles of the 3CR were obtained from computational analysis using DFT calculations, and the results critically suggest that simple ammonia is not applicable to this reaction. In addition, as strongly supported by computational predictions, a new reagent that can generate difluorocarbene at 0 °C without any additives was discovered. Finally, radical substitution reactions of the obtained difluoroglycine derivatives under photoredox conditions, as well as a synthetic application as an N-heterocyclic carbene ligand are shown.

Observation of Borane-Olefin Proximity Interaction Governing the Structure and Reactivity of Boron-Containing Macrocycles

While attractive interactions between borane and olefin have been postulated to trigger various boron-mediated organic transformations, proximity structures of these functional groups, other than the formation of weak van der Waals complexes, have never been directly observed. Here we show that a close intramolecular borane-olefin interaction operates in macrocyclic systems containing borane and olefinic groups obtained by multi-step 1,2-carboboration between a strained alkyne and 9-borafluorene derivatives. Depending on Lewis acidity of the borane moiety and the size of the macrocycles, the magnitude of interaction changes, resulting in different reaction modes. The whole picture of the multi-step reactions has been revealed experimentally with theoretical supports. The present finding may not only provide a deeper understanding of the fundamental boron-mediated interaction but also lead to the development of new organic transformations involving molecular activation by boranes.

Application of Reaction Path Search Calculations to Potential Energy Surface Fits

There has been significant progress in recent years in the use of machine learning techniques to model high-dimensional reactive potential energy surfaces using large-scale data obtained from ab initio electronic structure calculations. In these methods, the strategy used to gather data becomes a key issue as the molecular size increases. In this work, we examine the applicability of the reaction path search algorithm implemented in the Global Reaction Route Mapping (GRRM) code as a data-gathering approach. The electronic energies and gradients sampled by using the GRRM calculation are directly used in potential energy surface fitting to a permutationally invariant polynomial function. This simple approach was applied to the HNS and HCNO reaction systems, and we found that the fitted potential energy surfaces reasonably reproduce the features of the electronic structure calculations used in the GRRM calculations. This suggests that the GRRM sampling scheme can be used to construct an initial potential energy surface.

Chiral Metal Salts as Ligands for Catalytic Asymmetric Mannich Reactions with Simple Amides

Catalytic asymmetric Mannich reactions of imines with weakly acidic simple amides were developed using a chiral potassium hexamethyldisilazide (KHMDS)-bis(oxazoline) potassium salt (K-Box) catalyst system. The desired reactions proceeded to afford the target compounds in high yields with high diastereo- and enantioselectivities. It was suggested that a K enolate interacted with K-Box to form a chiral K enolate that reacted with imines efficiently. In this system, K-Box (potassium salt of Box) worked as a chiral ligand of the active potassium species.

Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data

Presently, quantum chemical calculations are widely used to generate extensive data sets for machine learning applications; however, generally, these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surfaces provides important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulting from quantum chemical calculations. Our tool allows one to store, assemble, and analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for pathway analysis by graph algorithms. Original condensed graph of reaction technology is used to store any chemical reaction as a single graph.

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.

Pt(ii)-Chiral diene-catalyzed enantioselective formal [4 + 2] cycloaddition initiated by C–C bond cleavage and elucidation of a Pt(ii)/(iv) cycle by DFT calculations

A Pt(ii)-chiral diene complex demonstrates a high catalytic activity in the enantioselective formal [4 + 2] cycloaddition along with C–C bond cleavage of biphenylene at room temp. DFT calculations elucidated that the present catalysis involves a rare Pt(ii)/Pt(iv) cycle.

Mining hydroformylation in complex reaction network via graph theory

Data science is introduced to identify the reactant, product, and reaction path in the chemical reaction network. Cobalt catalyzed hydroformylation is investigated where the reaction network is built via first principles calculations. The closeness centrality and high frequency node are found to be the reactant cobalt tetracarbonyl hydride. In addition, betweenness centrality uncovers three reaction paths which have the products of aldehyde, CH₂O, and CO₂, respectively. The energy profile determines that the reaction path leading to aldehyde is energetically favored; thus, the reaction path for cobalt catalyzed hydroformylation is identified without kinetics. Hence, the proposed approach can act as a first step towards understanding the complex chemical reaction network and towards further kinetic understanding of the chemical reaction.

Data science is introduced to identify the reactant, product, and reaction path in the chemical reaction network.

Artificial intelligence and automation in computer aided synthesis planning

In this perspective we deal with questions pertaining to the development of synthesis planning technologies over the course of recent years.

Aggregation-Induced Emission in Tetrathia[8]circulene Octaoxides via Restriction of the Dynamic Motion of their Negatively Curved π-Frameworks

Curved polycyclic aromatic hydrocarbons exhibit intriguing properties, but their flexible and dynamic nature is often considered to be unfavorable for achieving excellent emission properties. In this study, we prepared tetrathia[8]circulene octaoxides that adopt a negatively curved conformation. We found that these molecules exhibit aggregation-induced emission (AIE) that originates from the restriction of the dynamic motion of their saddle-shaped π-frameworks in the solid and aggregated states.

Kinetic prediction of reverse intersystem crossing in organic donor-acceptor molecules

Reverse intersystem crossing (RISC), the uphill spin-flip process from a triplet to a singlet excited state, plays a key role in a wide range of photochemical applications. Understanding and predicting the kinetics of such processes in vastly different molecular structures would facilitate the rational material design. Here, we demonstrate a theoretical expression that successfully reproduces experimental RISC rate constants ranging over five orders of magnitude in twenty different molecules. We show that the spin flip occurs across the singlet–triplet crossing seam involving a higher-lying triplet excited state where the semi-classical Marcus parabola is no longer valid. The present model explains the counterintuitive substitution effects of bromine on the RISC rate constants of previously unknown molecules, providing a predictive tool for material design.

Understanding and predicting the kinetics of reverse intersystem crossing (RISC) facilitates the design of materials. Here, the authors demonstrate a theoretical expression that reproduces experimental RISC rate constants ranging over five orders of magnitude in selected molecules.

as-Indaceno[3,2,1,8,7,6-ghijklm]terrylene as a near-infrared absorbing C70-fragment

Carbon and hydrogen are fundamental components of organic molecules and a fascinating plethora of functions can be generated using these two elements. Yet, realizing attractive electronic structures only by using carbon and hydrogen remains challenging. Herein, we report the synthesis and properties of the C₇₀ fragment as-indaceno[3,2,1,8,7,6-ghijklm]terrylene, which exhibits near-infrared (NIR) absorption (up to ca. 1300 nm), even though this molecule consists of only 34 carbon and 14 hydrogen atoms. A remarkably small highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap is confirmed by electrochemical measurement and theoretical calculations. Furthermore, as-indacenoterrylene is stable despite the absence of peripheral substituents, which contrasts with the cases of other NIR-absorbing hydrocarbons such as diradicaloids and antiaromatic molecules. The results of this study thus offer fundamental insights into the design of hydrocarbons with a small band gap.

Global Search for Crystal Structures of Carbon under High Pressure

In this study, a systematic search for structures of carbon crystals under high pressure was performed by using the artificial force induced reaction method including periodic boundary conditions. To perform a search under an arbitrary pressure, an algorithm to take account of the pressure was implemented in the GRRM program. At 100 GPa, the search generated 710 unique structures automatically. These structures were compared with 982 structures obtained by the search under zero pressure. The structures at 100 GPa were much denser than those under zero pressure. Besides, new structures that were denser than diamond were obtained at 100 GPa.

Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.

Discovery of a synthesis method for a difluoroglycine derivative based on a path generated by quantum chemical calculations

The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced 'quantum chemistry aided retrosynthetic analysis' (QCaRA), which uses quantum chemical calculations to search systematically for the decomposition paths of a target product and proposes a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the most promising path chosen by an organic chemist among the predicted paths led to the discovery of a synthesis method for a difluoroglycine derivative. We emphasize that the purpose of this study is not to propose a fully automated workflow. Therefore, the extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.

The Exploration of Chemical Reaction Networks

Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.

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.

Catalytic Chemoselective O-Phosphorylation of Alcohols

Phosphorylation of alcohols is a fundamentally important reaction in both life science and physical science. Product phosphate monoesters play key roles in living organisms, natural products, pharmaceuticals, and organic materials. Most of the chemical methods to date for synthesizing phosphate monoesters, however, require multistep sequences or are limited to specific types of substrates possibly due to harsh conditions. An alternative way to enable the simple production of phosphate monoesters from highly functionalized precursor alcohols is, thus, highly desired. We report herein a catalytic phosphorylation of alcohols with high functional group tolerance using tetrabutylammonium hydrogen sulfate (TBAHS) and phosphoenolpyruvic acid monopotassium salt (PEP-K) as the catalyst and phosphoryl donor, respectively. This method enables the direct introduction of a nonprotected phosphate group to the hydroxy group of a diverse menu of alcohol substrates, including functionalized small molecules, carbohydrates, and unprotected peptides. Nuclear magnetic resonance, mass spectrometric, and density functional theory analyses suggest that an unprecedented mixed anhydride species, generated from PEP-K and TBAHS, acts as an active phosphoryl donor in this reaction. This operationally simple and chemoselective catalytic phosphorylation allows for the efficient production of densely functionalized O-phosphorylated compounds, which are useful in diverse fields including biology and medicine.

Comment on "Exploring Potential Energy Surface with External Forces"

Recently, a work (Wolinski, K., J. Chem. Theory Comput. 2018, 14, 6306, 10.1021/acs.jctc.8b00885 ) was published in which the SEGO method (standard and enforced geometry optimization) was proposed to find new minimums on potential energy surfaces. We study this important method from a theoretical point of view. Up to now, the understanding of the proposer does not take into account the barrier breakdown point on a SEGO path being usually half of the path, which is searched for. However, a better understanding of the method allows us to follow along the reaction pathway from a minimum to a saddle point or vice versa. We discuss the well-known two-dimensional MB test surface where we calculate full SEGO pathways. If one has special SEGO curves at hand, one can also detect some weaknesses of the ansatz.

AFIR explorations of transition states of extended unsaturated systems: automatic location of ambimodal transition states

Based on the artificial force induced reaction (AFIR) method, we proposed a procedure to systematically explore ambimodal transition states (TSs) that cause the dynamical bifurcation.

Computational searches for crystal structures of dioxides of group 14 elements (CO2, SiO2, GeO2) under ultrahigh pressure

In this study, we focused on the effect of pressure on the crystal structures of dioxides of group 14 elements, i.e. SiO₂, GeO₂, and CO₂.