Using bonding to guide transition state optimization

Birkholz, Adam B.; Schlegel, H. Bernhard

doi:10.1002/jcc.23910

Cited by 18 publications

(30 citation statements)

References 45 publications

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“…The algorithms designed to locate TSs and RPs are usually classified as single‐ended or double‐ended . Single‐ended methods start from a single initial state and refine it systematically to locate a TS.…”

Section: Introductionmentioning

confidence: 99%

Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method

Jafari

Zimmerman

2017

J Comput Chem

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The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates. The double-ended and single-ended growing string methods are implemented using a hybrid coordinate system, then benchmarked for a test set of 43 elementary reactions occurring on surfaces. These results show that the growing string method is at least 45% faster than the widely used climbing image-nudged elastic band method, which also fails to converge in several of the test cases. Additionally, the surface growing string method has a unique single-ended search method which can move outward from an initial structure to find the intermediates, transition states, and reaction paths simultaneously. This powerful explorative feature of single ended-growing string method is demonstrated to uncover, for the first time, the mechanism for atomic layer deposition of TiN on Cu(111) surface. This reaction is found to proceed through multiple hydrogen-transfer and ligand-exchange events, while formation of H-bonds stabilizes intermediates of the reaction. Purging gaseous products out of the reaction environment is the driving force for these reactions. © 2017 Wiley Periodicals, Inc.

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Section: Introductionmentioning

confidence: 99%

Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method

Jafari

Zimmerman

2017

J Comput Chem

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“…From a set of benchmark reactions provided by Vaucher and Reiher, 21 adapted from Birkholz and Schlegel, 22 we took the 10 intermolecular reactions to demonstrate the results of applying our approach to a variety of different types of reaction classes. The structures for the original datasets were, in turn, obtained from a variety of sources; in some cases, product structures were obtained by geometry optimization of appropriately modified reactant structures using graphical user interface programs, 28 while other examples were obtained from previous benchmark sets, also used for TS optimization algorithms, 29 which were also generally constructed “by hand” from well‐known systems and well‐informed guesses to their TS structures.…”

Section: Resultsmentioning

confidence: 99%

“…Section 2 presents the algorithm, which optimizes a series of simple geometric functions depending on the translational and rotational degrees of freedom (DOF) of the reactive molecules. Section 3 highlights the result of each stage of our algorithm, demonstrating application of our approach to a set of 10 reactions from a benchmark set devised by Birkholz and Schlegel 21,22 . Finally, we quantify the degree of reliability of our algorithm by generating initial reactant/product configurations for a large test‐set of >3400 organic molecular reactions from the benchmark set devised by Grambow and coworkers 23 .…”

Section: Introductionmentioning

confidence: 99%

Simple position and orientation preconditioning scheme for minimum energy path calculations

Robertson

Habershon

2021

J Comput Chem

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Minimum‐energy path (MEP) calculations, such as those typified by the nudged elastic band method, require input of reactant and product molecular configurations at initialization. In the case of reactions involving more than one molecule, generating initial reactant and product configurations requires careful consideration of the relative position and orientations of the reactive molecules in order to ensure that the resulting MEP calculation proceeds without converging on an alternative reaction‐path, and without requiring excessive numbers of optimization iterations; as such, this initial system set‐up is most commonly performed “by hand,” with an expert user arranging reactive molecules in space to ensure that the following MEP calculation runs smoothly. In this Article, we introduce a simple preconditioning scheme which replaces this labor‐intensive, human‐knowledge‐based step with an automated deterministic computational scheme. In our approach, initial reactant and product configurations are generated such that steric hindrance between reactive molecules is minimized in the reactant and product configurations, while also simultaneously requiring minimal structural differences between the reactants and products. The method is demonstrated using a benchmark test‐set of >3400 organic molecular reactions, where comparison of the reactant/product configurations generated using our approach compare very well to initial configurations which were generated on an ad hoc basis.

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“…This approach can also be combined with the coupling constants used in the FVRC method in order to produce an initial path that minimizes S RIC and also travels through one or more particular geometries, such as known intermediates or guess transition state structures. In the case of bi-molecular reactions, it was previously demonstrated 22 that interpolation of the bond order for bonds being broken or formed is an effective approach for approximating the structure at the transition state, and the methods outlined in Section III can be modified to define the goal geometry only in terms of those bonds by setting n act = n cts , where n cts is the number of bonds being broken or formed, and defining the goal geometry only in terms of those bonds.…”

Section: Ric Arc Length Minimization Algorithmmentioning

confidence: 94%

“…where H is the potential energy Hessian and Tg is the product of the third derivative of the potential energy with the potential energy gradient. The Tg term was found to be unnecessary for good performance when using the focused VRC method, 22 so it is not included in the evaluation of η in this work. A positive definite shift matrix σ i µ jν is used to shift η so that it is positive definite while accounting for some of the curvilinear relationship between the LEC and the gradient…”

Section: Fvrc Methods Summarymentioning

confidence: 99%

Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation

Birkholz

Schlegel

2016

The Journal of Chemical Physics

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Reaction path optimization is being used more frequently as an alternative to the standard practice of locating a transition state and following the path downhill. The Variational Reaction Coordinate (VRC) method was proposed as an alternative to chain-of-states methods like nudged elastic band and string method. The VRC method represents the path using a linear expansion of continuous basis functions, allowing the path to be optimized variationally by updating the expansion coefficients to minimize the line integral of the potential energy gradient norm, referred to as the Variational Reaction Energy (VRE) of the path. When constraints are used to control the spacing of basis functions and to couple the minimization of the VRE with the optimization of one or more individual points along the path (representing transition states and intermediates), an approximate path as well as the converged geometries of transition states and intermediates along the path are determined in only a few iterations. This algorithmic efficiency comes at a high per-iteration cost due to numerical integration of the VRE derivatives. In the present work, methods for incorporating redundant internal coordinates and potential energy surface interpolation into the VRC method are described. With these methods, the per-iteration cost, in terms of the number of potential energy surface evaluations, of the VRC method is reduced while the high algorithmic efficiency is maintained.

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Using bonding to guide transition state optimization

Cited by 18 publications

References 45 publications

Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method

Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method

Simple position and orientation preconditioning scheme for minimum energy path calculations

Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation

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