Global Reaction Route Mapping on Potential Energy Surfaces of Formaldehyde, Formic Acid, and Their Metal-Substituted Analogues

An integrated experimental and theoretical reaction path search: analyses of the multistage reaction of an ionized diethylether dimer involving isomerization, proton transfer, and dissociation

A multistage reaction involving isomerization, proton transfer, and dissociation of an ionized diethylether dimer is studied by combination of infrared spectroscopy, tandem mass spectrometry, and a theoretical reaction path search.

Pseudorotaxanes in the gas phase: structure and energetics of protonated dibenzylamine–crown ether complexes

Barrier in the “slippage” process with 24C8 and dBAMH⁺ is lower than the dissociation threshold in the gas phase.

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

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Photoassisted Homocoupling of Methyl Iodide Mediated by Atomic Gold in Low-Temperature Neon Matrix

Infrared spectroscopy and density functional theory calculations showed that the gold complexes [CH₃-Au-I] and [(CH₃)₂-Au-I₂], in which one and two CH₃I molecule(s), respectively, are oxidatively adsorbed on the Au atoms, are formed in a solid neon matrix via reactions between laser-ablated gold atoms and CH₃I. Global reaction route mapping calculations revealed that the heights of the activation barriers for the sequential oxidative additions to produce [CH₃-Au-I] and [(CH₃)₂-Au-I₂] are 0.53 and 1.00 eV, respectively, suggesting that the reactions proceed via electronically excited states. The reductive elimination of ethane (C₂H₆) from [(CH₃)₂-Au-I₂] leaving AuI₂ was hindered by an activation barrier as high as 1.22 eV but was induced by visible-light irradiation on [(CH₃)₂-Au-I₂]. These results demonstrate that photoassisted homocoupling of CH₃I is mediated by Au atoms via [(CH₃)₂-Au-I₂] as an intermediate.

Ethereal C-O Bond Cleavage Mediated by Ni(0)-Ate Complex: A DFT Study

Density functional theory calculations were performed to explore the mechanism of Ni-catalyzed cross-coupling reactions involving organo-lithium and -zinc reagents through ethereal C-O bond cleavage. Based on this work, together with our previous mechanistic study on etheric Kumada-Tamao reaction, we identify and characterize a novel catalytic cycle for cross-coupling mediated by Ni(0)-ate complex.

A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene

A novel DFT-based Reaction Kinetics (DFT-RK) simulation approach, employed in combination with real-time data from reaction monitoring instrumentation (like UV-vis, FTIR, Raman, and 2D NMR benchtop spectrometers), is shown to provide a detailed methodology for the analysis and design of complex synthetic chemistry schemes. As an example, it is applied to the opening of epoxides by titanocene in THF, a catalytic system with abundant experimental data available. Through a DFT-RK analysis of real-time IR data, we have developed a comprehensive mechanistic model that opens new perspectives to understand previous experiments. Although derived specifically from the opening of epoxides, the prediction capabilities of the model, built on elementary reactions, together with its practical side (reaction kinetics simulations of real experimental conditions) make it a useful simulation tool for the design of new experiments, as well as for the conception and development of improved versions of the reagents. From the perspective of the methodology employed, because both the computational (DFT-RK) and the experimental (spectroscopic data) components can follow the time evolution of several species simultaneously, it is expected to provide a helpful tool for the study of complex systems in synthetic chemistry.

Chemical pathways for poly-anionic isomerisation in the metastable anions of tetra-deprotonated naphthalene: an intra-molecular inter-ring proton-transfer

An intra-molecular proton-transfer between the two different aromatic rings of naphthalene in the metastable isomeric tetra-anionic species of naphthalene is revealed by this computational work.

Artificial Force Induced Reaction Method for Systematic Determination of Complex Reaction Mechanisms

Nowadays, computational studies are very important for the elucidation of reaction mechanisms and selectivity of complex reactions. However, traditional computational methods usually require an estimated reaction path, mainly driven by limited experimental implications, intuition, and assumptions of stationary points. However, the artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy can be used for unbiased and automatic reaction path searches for complex reactions. In this account, we highlight applications of the AFIR method to a variety of reactions (organic, organometallic, enzymatic, and photochemical) of complex molecular systems. In addition, the AFIR method has been successfully used to rationalise the origin of stereo- and regioselectivity. The AFIR method can be applied from small to large molecular systems, and will be a very useful tool for the study of complex molecular problems in many areas of chemistry, biology, and material sciences.

Study of Potential Energy Surfaces towards Global Reaction Route Mapping

The potential energy surface (PES) is just a theoretical construct based on the Born-Oppenheimer approximation, but it underlies various phenomena, including molecular vibrations, collisional ionizations, and chemical reactions. This account describes how a new idea for global reaction route mapping (GRRM), which had seemed to be impossible for chemical systems with more than three atoms, was born and has been developed during the course of the study of the PES. GRRM has pioneered new fields of chemistry. Furthermore, techniques for GRRM are still developing, and GRRM is further extending its application to various areas of chemistry and chemical physics.

Computational Catalysis Using the Artificial Force Induced Reaction Method

The artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy is an automatic approach to explore all important reaction paths of complex reactions. Most traditional methods in computational catalysis require guess reaction paths. On the other hand, the AFIR approach locates local minima (LMs) and transition states (TSs) of reaction paths without a guess, and therefore finds unanticipated as well as anticipated reaction paths. The AFIR method has been applied for multicomponent organic reactions, such as the aldol reaction, Passerini reaction, Biginelli reaction, and phase-transfer catalysis. In the presence of several reactants, many equilibrium structures are possible, leading to a number of reaction pathways. The AFIR method in the GRRM strategy determines all of the important equilibrium structures and subsequent reaction paths systematically. As the AFIR search is fully automatic, exhaustive trial-and-error and guess-and-check processes by the user can be eliminated. At the same time, the AFIR search is systematic, and therefore a more accurate and comprehensive description of the reaction mechanism can be determined. The AFIR method has been used for the study of full catalytic cycles and reaction steps in transition metal catalysis, such as cobalt-catalyzed hydroformylation and iron-catalyzed carbon-carbon bond formation reactions in aqueous media. Some AFIR applications have targeted the selectivity-determining step of transition-metal-catalyzed asymmetric reactions, including stereoselective water-tolerant lanthanide Lewis acid-catalyzed Mukaiyama aldol reactions. In terms of establishing the selectivity of a reaction, systematic sampling of the transition states is critical. In this direction, AFIR is very useful for performing a systematic and automatic determination of TSs. In the presence of a comprehensive description of the transition states, the selectivity of the reaction can be calculated more accurately. For relatively large molecular systems, the computational cost of AFIR searches can be reduced by using the ONIOM(QM:QM) or ONIOM(QM:MM) methods. In common practice, density functional theory (DFT) with a relatively small basis set is used for the high-level calculation, while a semiempirical approach or a force field description is used for the low-level calculation. After approximate LMs and TSs are determined, standard computational methods (e.g., DFT with a large basis set) are used for the full molecular system to determine the true LMs and TSs and to rationalize the reaction mechanism and selectivity of the catalytic reaction. The examples in this Account evidence that the AFIR method is a powerful approach for accurate prediction of the reaction mechanisms and selectivities of complex catalytic reactions. Therefore, the AFIR approach in the GRRM strategy is very useful for computational catalysis.

Exploring the role of a single water molecule in the tropospheric reaction of glycolaldehyde with an OH radical: a mechanistic and kinetics study

This work reveals that though a single-water molecule decelerates the atmospheric reaction between the glycolaldehyde and OH radical, however, it facilitates the cis–​trans interconversion along the hydrogen-abstraction pathways.

Theoretical insight into the wavelength-dependent photodissociation mechanism of nitric acid

The MS-CASPT2 method is used to study O(¹D) + HONO and OH + NO₂ photodissociation pathways of HNO₃ in the four lowest electronic singlet states.

The effect of Mg2+ incorporation on the structure of calcium carbonate clusters: investigation by the anharmonic downward distortion following method

A structure similar to calcite appears when only four CaCO₃ units aggregate into the cluster, and the addition of Mg changes its structure.

Exploration of Quenching Pathways of Multiluminescent Acenes Using the GRRM Method with the SF-TDDFT Method

The quenching pathways were investigated for three types of multiluminescent acene derivatives, which show environment-dependent fluorescence. Spin-flip time dependent density functional theory (SF-TDDFT) combined with the Global Reaction Route mapping (GRRM) strategy is employed to locate minimum-energy conical intersections (MECIs). The energies and geometries of the MECIs relative to the Franck-Condon (FC) state control the difference in fluorescence behavior among the three derivatives. For the molecule with a phenyamide moiety, a MECI with energy lower than the FC state with large geometrical change from V-type to flat structure provides an efficient internal conversion (quenching) pathway in solution. For the same molecule, in a solid, this large geometrical change is inhibited, and the second MECI, with an energy lower than FC but higher than the first MECI requiring only a small geometry change of CH out-of-plane bending, contributes to the quenching. The molecule with the napthaleneimide moiety has only one low-energy MECI that requires large geometrical change from the V-type to flat structure. Although this MECI provides the quenching pathway in solution, in the solid, this large motion is inhibited, and the molecule will stay in the excited state and emit. The molecule with an anthraceneimide moiety has no conical intersection lower than the FC state, and no quenching pathway is available in solution or solid. In addition, in this molecule, at the local minimum of the excited state, the dipole transition to the ground state is allowed, and this molecule prefers emission rather than internal conversion.

Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics

The thermodynamics and dynamics of a carbonaceous molecular bearing comprising a belt-persistent tubular molecule and a fullerene molecule have been investigated using density functional theory (DFT). Among ten representative methods, two DFT methods afforded an association energy that reasonably reproduced the experimental enthalpy of -12.5 kcal mol-1 at the unique curved π-interface. The dynamics of the molecular bearing, which was assembled solely with van der Waals interactions, exhibited small energy barriers with maximum values of 2-3 kcal mol-1 for the rolling motions. The dynamic motions responded sensitively to the steric environment and resulted in two distinct motions, precession and spin, which explained the unique NMR observations that were not clarified in previous experimental studies.