Journal ArticleDOI
Intrinsic reaction coordinate: Calculation, bifurcation, and automated search
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TLDR
The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions as mentioned in this paper, which gives a unique connection from a given transition structure to local minima of the reactant and product sides.Abstract:
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. © 2014 Wiley Periodicals, Inc.read more
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Automated exploration of the low-energy chemical space with fast quantum chemical methods
TL;DR: An efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm is proposed and discussed, opening many possible applications in modern computational chemistry and drug discovery.
Journal ArticleDOI
TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations
Sree Ganesh Balasubramani,Guo P. Chen,Sonia Coriani,Michael Diedenhofen,Marius S. Frank,Yannick J. Franzke,Filipp Furche,Robin Grotjahn,Michael E. Harding,Christof Hättig,Arnim Hellweg,Benjamin Helmich-Paris,Christof Holzer,Uwe Huniar,Martin Kaupp,Alireza Marefat Khah,Sarah Karbalaei Khani,Thomas Müller,Fabian Mack,Brian Nguyen,Shane M. Parker,Eva Perlt,Dmitrij Rappoport,Kevin Reiter,Saswata Roy,Matthias Rückert,Gunnar Schmitz,Marek Sierka,Enrico Tapavicza,David P. Tew,Christoph van Wüllen,Vamsee K. Voora,Florian Weigend,Artur Wodyński,Jason M. Yu +34 more
TL;DR: This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems.
Journal ArticleDOI
Methods for exploring reaction space in molecular systems
TL;DR: Several of these approaches, which are categorized based on their overarching TS finding strategies, have been described in this paper, and future advances are discussed that may revolutionize the ability of simulation to fully predict not just the reaction mechanism but reaction outcomes.
Journal ArticleDOI
Implementation and performance of the artificial force induced reaction method in the GRRM17 program
Satoshi Maeda,Yu Harabuchi,Yu Harabuchi,Makito Takagi,Kenichiro Saita,Kimichi Suzuki,Kimichi Suzuki,Tomoya Ichino,Yosuke Sumiya,Kanami Sugiyama,Yuriko Ono +10 more
TL;DR: Investigation 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.
Journal ArticleDOI
Post-transition state bifurcations gain momentum – current state of the field
TL;DR: In this article, the existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurlcations have been occurring at a much higher rate.
References
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Journal ArticleDOI
Use of an eigenmode method to locate the stationary points on the potential energy surfaces of selected argon and water clusters
TL;DR: In this article, the eigenmode method for locating stationary points (both minima and first-order saddle points) is illustrated for a two-dimensional model potential and is applied to the (Ar) n, n=7-13, and (H 2 O) m, m=2-5, clusters.
Journal ArticleDOI
A semiclassical tunneling model for use in classical trajectory simulations
Nancy Makri,William H. Miller +1 more
TL;DR: In this paper, a semiclassical model for tunneling from one classically allowed region on a potential energy surface to another is described, which can be implemented in a straightforward way within the framework of a standard classical trajectory simulation.
Journal ArticleDOI
Energy landscapes: calculating pathways and rates
TL;DR: In this article, a discrete path sampling approach is used to obtain phenomenological two-state rate for a set of local minima with a particular structural motif. But the authors do not consider the transition states that link individual local minimima, and evaluate rate constants for the corresponding elementary rearrangements.
Journal ArticleDOI
Potential energy and free energy landscapes.
David J. Wales,Tetyana V. Bogdan +1 more
TL;DR: Stepping between the local minima of V provides powerful methods for locating the global potential energy minimum, and for calculating global thermodynamic properties, and when the transition states that link local minata are also sampled the authors can exploit statistical rate theory to obtain insight into global dynamics and rare events.
Journal ArticleDOI
Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation.
Brianna R. Heazlewood,Meredith J. T. Jordan,Scott H. Kable,Talitha M. Selby,David L. Osborn,Benjamin C. Shepler,Bastiaan J. Braams,Joel M. Bowman +7 more
TL;DR: It is shown that roaming pathways are important in the 308-nm photodissociation of CH3CHO to CH4 + CO, where the CH4 product is found to have extreme vibrational excitation, with the vibrational distribution peaked at ≈95% of the total available energy.
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