The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions. The IRC gives a unique connection from a given transition structure to local minima of the reactant and product sides. This allows for easy understanding of complicated multistep mechanisms as a set of simple elementary reaction steps. In this article, three topics concerning the IRC approach are discussed. In the first topic, the first ab initio study of the IRC and a recent development of an IRC calculation algorithm for enzyme reactions are introduced. In the second topic, cases are presented in which dynamical trajectories bifurcate and corresponding IRC connections can be inaccurate. In the third topic, a recent development of an automated reaction path search method and its application to systematic construction of IRC networks are described. Finally, combining these three topics, future perspectives are discussed.

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.

A classical multidimensional scaling (CMDS) method is employed to visualize an intrinsic reaction coordinate (IRC) and a global reaction route map consisting of the equilibrium minima and transition state structures connected by the IRC network. As demonstrations, the method was applied to the IRCs of the intramolecular proton transfer in malonaldehyde and the S2 reaction of OH + CHF → CHOH + F, which are both well described by two principal coordinates. Next, the method was applied to the global reaction route map of the Au cluster; the resulting map shows appropriate positions of five minima and 14 transition states in a reduced 2- or 3-dimensional coordinate space successfully.

The formation of a Pd atomic chain in a hydrogen atmosphere was investigated by measurements of conductance and vibrational spectroscopy of a single molecular junction and the theoretical calculation. While atomic chains were not formed for clean 3d and 4d metals, in the case of Pd ͑a 4d metal͒ atomic chains could be formed in the presence of hydrogen. Stable atomic chains with two different atomic configurations were formed when the Pd atomic contact was stretched in a H 2 atmosphere: highly conductive short hydrogenadsorbed atomic chain and low conductive long hydrogen incorporated atomic chain.

The adsorption of Xe on graphene has been systematically investigated by ab initio MP2 calculations using Dunning's correlation-consistent basis sets. The polycyclic aromatic hydrocarbon (i.e., coronene) is employed to model the graphene surface. The adsorption energies at three high-symmetry sites on the surface are calculated at the MP2/cc-pVTZ/cc-pVDZ-PP level. Our results show that Xe preferentially occupies the hollow site on the graphene surface. The equilibrium distance of Xe at the hollow site is calculated as 3.56 Å, which is in excellent agreement with the available experimental value of 3.59 ( 0.05 Å. The corresponding binding energy at the hollow site is calculated as -142.9 meV, whereas the binding energies at the bridge and on-top sites are calculated as -130.8 and -127.4 meV, respectively. The adsorption of polar molecules, XeF and XeBeO, on graphene is also investigated to analyze the site preference.

A methodology to analyze a trajectory on-the-fly (TOF) based on a global reaction route map consisting of intrinsic reaction coordinate (IRC) pathways is proposed. By using the distance functions in the configurational space, the location of each point on the trajectories is detected, providing a dynamical picture that the molecular system goes over several minima and transition states in the reaction path network. In its application to structural transformations of an Au cluster, a variety of reaction routes are obtained, and the hopping from one IRC to another IRC (IRC-jump) is analyzed. The branching of trajectories over many minima on the potential energy surface via valley-ridge transition points is also discussed.

Articles you may be interested inA global reaction route map is generated for Au 5 by the anharmonic downward distortion following method in which 5 minima and 14 transition states (TSs) are located. Through vibrational analyses in the 3N − 7 (N = 5) dimensional space orthogonal to the intrinsic reaction coordinate (IRC), along all the IRCs, four IRCs are found to have valley-ridge transition (VRT) points on the way where a potential curvature changes its sign from positive to negative in a direction orthogonal to the IRC. The detailed mechanisms of bifurcations related to the VRTs are discussed by surveying a landscape of the global reaction route map, and the connectivity of VRT points and minima is clarified. Branching of the products through bifurcations is confirmed by ab initio molecular dynamics simulations starting from the TSs. A new feature of the reaction pathways, unification, is found and discussed. C 2015 AIP Publishing LLC. [http://dx

Following our recent work to reduce a dimension of a set of reference structures along the intrinsic reaction coordinate (IRC) by a classical multidimensional scaling (CMDS) approach (J. Chem. Theory Comput. 2018, 14, 4263−4270), we propose the method to project on-the-fly trajectories into a reduced-dimension subspace determined by the IRC network, using the out-of-sample extension of CMDS. The method was applied to the SN2 reaction, OH -+ CH3F, in which trajectories show a bifurcating nature around the highly-curved region of the IRC path, and to the structural transformation of Au5 cluster in which the global reaction path network consists of five equilibrium structures and 14 IRCs. It was demonstrated that the present analysis can visualize the dynamics effect by showing a dynamic reaction route on the basis of the static reaction paths.