Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration

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.

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“…The microiteration has already been implemented in GRRM14 . In GRRM17, it is also interfaced with the SC‐AFIR method.…”

Section: Interface With Oniommentioning

confidence: 99%

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

et al. 2017

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“…In contrast to optimization techniques that operate on a single state, reaction path optimization techniques operate on a "chain of states" that connect the reactant and product states. [2][3][4][14][15][16][17][18][19][20][21][22][23][24] This connection between the states in the path should be sufficient to accurately and robustly pinpoint the transition states using simple energy minimizations.…”

Section: Introductionmentioning

confidence: 99%

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization

Khavrutskii

Smith

Wallqvist

2013

The Journal of Chemical Physics

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Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM/molecular mechanical (QM/MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP/6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP/6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal/mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM/MM studies of reaction mechanisms.

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“…Although the lowest barrier was the same as for the manual exploration, C-H bond activation, a possible minor channel was identified where the superoxide instead attacks the sulfur coordinating to iron. [17,58] Atom-centered density matrix propagation has been used to facilitate the sampling of rare events in the dynamics of Soybean Lipoxygenase-1. Unlike the FEP studies described above, the QM part was here included in the dynamics.…”

Section: Exploring Reaction Pathwaysmentioning

confidence: 99%

Protein effects in non-heme iron enzyme catalysis: insights from multiscale models

Vedin

Lundberg

2016

J Biol Inorg Chem

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PostprintThis is the accepted version of a paper published in Journal of Biological Inorganic Chemistry. This paper has been peer-reviewed but does not include the final publisher proof-corrections or journal pagination. Citation for the original published paper (version of record):Vedin, N P., Lundberg, M. (2016) Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. from second-sphere residues. The long-range electrostatic effects on reaction barriers are small for many systems. In the systems where large electrostatic effects have been reported, these lead to higher barriers. There is thus no evidence of any significant long-range electrostatic effects contributing to the catalytic efficiency of non-heme iron enzymes. However, the correct evaluation of electrostatic contributions is challenging, and the correlation between calculated residue contributions and the effects of mutation experiments is not very strong. The largest benefits of QM/MM models are thus the improved active-site geometries, rather than the calculation of accurate energies. Reported differences in mechanistic predictions between QM and QM/MM models can be explained by differences in hydrogen bonding patterns in and around the active site. Correctly constructed cluster models can give results with similar accuracy as those from multiscale models, but the latter reduces the risk of drawing the wrong mechanistic conclusions based on incorrect geometries and are preferable for all types of modeling, even when using very large QM parts. Journal of Biological Inorganic

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Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration

Cited by 38 publications

References 73 publications

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

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

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization

Protein effects in non-heme iron enzyme catalysis: insights from multiscale models

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