Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following

Abstract

The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of reactions. It can make efficient use of parallel computing as the calculations of the discretization points, the so-called images, can be carried out simultaneously. In typical implementations, the images are distributed evenly along the path by connecting adjacent images with equally stiff springs. However, for systems with a high degree of flexibility, this can lead to poor resolution near the saddle point. By making the spring constants increase with energy, the resolution near the saddle point is improved. To assess the performance of this energy-weighted CI-NEB method, calculations are carried out for a benchmark set of 121 molecular reactions. The performance of the method is analyzed with respect to the input parameters. Energy-weighted springs are found to greatly improve performance and result in successful location of the saddle points in less than a thousand energy and force evaluations on average (about a hundred per image) using the same set of parameter values for all of the reactions. Even better performance is obtained by stopping the calculation before full convergence and complete the saddle point search using an eigenvector following method starting from the location of the climbing image. This combination of methods, referred to as NEB-TS, turns out to be robust and highly efficient as it reduces the average number of energy and force evaluations down to a third, to 305. An efficient and flexible implementation of these methods has been made available in the ORCA software.

On the Photostability of Cyanuric Acid and Its Candidature as a Prebiotic Nucleobase

“…To estimate the energy barrier to access the conical intersection calculated with LR-TD-DFT, optimizations along the O6C6N1C2 dihedral angle going from the S 1 minimum-geometry to the (S 1 /S 0 ) CI were performed. To estimate the energy barrier to access the conical intersection calculated with SF-TD-DFT, a minimum-energy path calculation between the S 1 minimum-geometry to the (S 1 /S 0 ) CI was performed at the TD-X3LYP/C-PCM/cc-pVDZ in water using the Nudged Elastic Band method as implemented in ORCA 5.0.0 [50]. The choice to use the minimum energy path calculation over optimizations along the O6C6N1C2 dihedral angle to get the energy barrier to access the (S 1 /S 0 ) CI was made because this calculation was less computationally expensive for the SF-TD-DFT approach.…”

HF Formation through Dissociative Electron Attachment—A Combined Experimental and Theoretical Study on Pentafluorothiophenol and 2-Fluorothiophenol

“…The minimum energy path for the HF formation and rearrangement mechanism was calculated using the Nudged Elastic Band method with transition state (TS) optimization (NEB-TS) [ 69 ] at the B3LYP D3BJ level, using the aug-cc-pVTZ basis set. For the reactants and products, we used the optimized geometry at the B3LYP D3BJ/aug-cc-pVTZ level of theory.…”

Theoretical Study of Light-Induced Crosslinking Reaction Between Pyrimidine DNA Bases and Aromatic Amino Acids

“…The RIJCOSX approximation ( Neese et al, 2009 ) designed to accelerate the Hartree–Fock and hybrid DFT calculations were considered together with the Def2/J ( Weigend, 2006 ) auxiliary basis set for the Coulomb fitting and def2-TZVPP/C ( Hellweg et al, 2007 ) auxiliary basis set for correlation fitting in the case of TDDFT calculations. The Nudged Elastic Band (NEB) method ( Henkelman and Jónsson, 2000 ; Ásgeirsson et al, 2021 ) is used to locate the transition state (TS) geometry and to find the minimum energy path (MEP) connecting the minims of different equilibrium geometries on the potential energy surface. The solvent environment of water was taken into account through the conductor-like polarizable continuum (CPCM) model ( Barone and Cossi, 1998 ) and explicitly included two water molecules close to the two carboxyl groups of the uracil molecule.…”