GRRM20 with Matlantis
Application Examples
Abstract
We introduce an application case provided by ENEOS Corporation as part of the joint development
among three companies of GRRM20 with Matlantis. To demonstrate the accelerated computational
speed of GRRM20 with Matlantis and its potential for large-scale systems, we conducted reaction
pathway searches in periodic boundary systems for the following reactions: 1) oxidation of carbon
monoxide on a platinum catalyst, 2) dehydrogenation of methylcyclohexane (MCH). For the former, we
obtained reaction pathways comparable with those found in the preceding study [1] using GRRM
calculations with DFT. For the latter, we successfully automated the search for the dehydrogenation
process of MCH, which is expected to be a hydrogen carrier in the CO2-free hydrogen supply chain
developed by ENEOS. We discovered reaction pathways, such as the simultaneous removal of twohydrogen atoms, which are difficult to examine using traditional Nudged Elastic Band (NEB) and String
methods, thereby demonstrating the usefulness of GRRM20 with Matlantis.

CO oxidation reaction
We have conducted reaction pathway searches using GRRM for the following two reactions on aplatinum (Pt) catalyst surface, both of which involve multi-step processes. These reactions are known
to be difficult to analyze using widely recognized reaction pathway search methods such as NEB andString methods.
1) Oxidation reaction of carbon monoxide (CO) (68-atoms system)2) Dehydrogenation of methylcyclohexane (MCH) (85-atoms system)

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Background
The oxidation of CO on a Pt catalyst is depicted in Fig. 1. Owing to the limited number of potential
reaction combinations involving CO and O2, which comprise four atoms in total, the search space isinherently constrained. This makes the calculation for reaction pathway search within this system
relatively straightforward. There is a preceding study [1] which has explored this system employing
GRRM and SIESTA.

Fig.1 Oxidation reaction of carbon monoxide (CO) on a platinum slab surface

In the preceding study[1], the computational method is as follows.
Calculation level: PBE/DZP
Vacuum layer thickness: 15 ÅGamma parameter for SC-AFIR : 250

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page 2 / 18Platinum slab modeling
The platinum slab model was created using the conditions outlined in Tab. 1, as illustrated in Fig. 2.

Tab.1 Conditions for creating a platinum slab model

Items

Details

Calculation system(Number of atoms)

Platinum slab (Pt 64 atoms)
1) CO+O2 (4 atoms)
2) MCH (21 atoms)

Platinum crystal structure

mp-126 (Materials Project [2])(Miller index 111)

Vacuum layer

20 Å

Calculation Conditions for
Structural Optimization

・Using ExpCellFilter
・LBFGS・fmax= 0.005

PFP version

v5.0.0PFP calculation mode1) CRYSTAL_U02) CRYSTAL_U0_PLUS_D3

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Fig. 2 Platinum slab model (Pt64)

Reaction pathway search
To perform a global search for reaction pathways, we applied kinetic navigation via the rate constantmatrix contraction (RCMC) method [3][4]. For the oxidation of CO, we performed SC-AFIR method(Single Component Artificial Force Induced Reaction) [5]. Subsequently, all reaction pathways
identified by SC-AFIR were relaxed through LUP (Locally Updated Planes) [6][7] using RePATH. The
initial structure is shown in Fig. 3. All slab atoms (Pt) and translation vectors (TV) were fixed during both
SC-AFIR and RePATH calculations.

Fig. 3 Initial structure in the reaction pathway search (CO oxidation reaction)

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Options in GRRM input fileTo preferentially search for reactions with molecules adsorbed on the slab surface, a weak force(Gamma=25) was set between four platinum atoms (Nos. 6, 10, 13, and 17, colored in light blue inFig. 4) and the reacting molecules (CO and O2) located at the center of the slab.
Four Pt atoms on the slab surface (No. 6, 9, 16, and 18 in Fig. 4) were set as AFIR targets (changedfrom the settings in the previous study where Nos. 6, 10, 13, and 17 were used) to facilitate finding
bond dissociation structures.
The AFIR threshold was set to Gamma=300.
The options in the GRRM input file are depicted in Fig. 5.

Fig.4 Numbering of slab Pt atoms (left) and reacting molecules (CO and O2) in the CO oxidation reaction

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page 5 / 18Fig. 5 Part of the GRRM input files for AC-AFIR (left) and RePATH (right) for the CO oxidation reaction ona platinum slab.

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Results
The number of structures identified through SC-AFIR and RePATH calculations is presented in Tab. 2.
The total number of discovered pathways corresponds to the sum of the path tops (PTs) and transition
states (TSs).

Tab.2 Equilibrium structures (EQs), path tops (PTs) and transition states (TSs) identified in thecalculation of CO oxidation on platinum slabs using SC-AFIR and RePATH.

CO oxidation reaction
SC-AFIR

RePATH

EQs

103

96

PTs

134

168

TSs

163

98

The equilibrium structures obtained with SC-AFIR were classified, and the most stable structures foreach composition were extracted. Tab. 3 compares these structures with those from the preceding
study, along with their relative energies with reference to CO2(g)+O* (see Tab. 3 (a)).







As shown in Fig. 6, the relative energy order of the structures identified in GRRM20 with Matlantis
consistent with the findings from the preceding study.
Although the OC-OO intermediate reported in the preceding study was not found in this study,
preventing a complete reproduction of the preceding results, the C* + 3O* intermediate not reported
in the preceding study was discovered (this intermediate was also confirmed in the reaction pathway
network depicted in Fig. 7).
There could be several reasons for discrepancies, including differences in calculation conditions
between this and the preceding study.
To confirm the C*+3O* intermediate as a novel reaction pathway, it is necessary to undertake more
extensive search of reaction pathways by lowering thresholds, thereby increasing the number ofpathways examined.
Additionally, a multi-step reaction CO* + O2* → CO2(g) + O* has been identified, as illustrated in Fig.
8.

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Tab. 3 Relative energies and structures of the CO oxidation reaction pathway on platinum slab model,
referenced to CO2(g) + O* compared to the preceding study [1]. The relative energies resulting fromGRRM20 with Matlantis are denoted on ΔGPFP, while the preceding study’s findings are represented as
ΔGDFT. Structures (a)~(e) and (g) are derived from GRRM 20 with Matlantis, while structure (f) is citedfrom the preceding study [1].

Fig. 6 Comparison of relative energies [kJ/mol] from GRRM20 with Matlantis (ΔGPFP) with those from thepreceding study (ΔGDFT), as presented in Table 3.

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Fig.7 Reaction pathway network (color coded according to relative energy ΔG, ranging from blue to red
representing 0 to 350 [kJ/mol])Fig. 8 Reaction pathway for CO* + O2* → CO2(g) + O*.

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MCH dehydrogenation reaction
Background
MCH (methylcyclohexane) is attracting attention as a hydrogen carrier for the efficient transport ofcarbon dioxide-free hydrogen produced from renewable energy sources. ENEOS is developing its
original technologies, Direct MCH® [8], among others. The dehydrogenation reaction of MCH is aprocess to extract hydrogen from MCH, and as illustrated in Fig. 9, it allows for the release of threehydrogen molecules (a total of six hydrogen atoms, denoted H*) in the conversion of MCH to toluene. Athorough understanding of the fundamental reactions is essential for investigating catalysts fordehydrogenation reactions.

Fig.9 Dehydrogenation reaction of methylcyclohexane (MCH)

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About Direct MCH


It is a proprietary technology owned by ENEOS for the production of MCH, which serves as ahydrogen carrier.
ENEOS is developing technologies to create a CO2-free hydrogen supply chain that employs MCH asa hydrogen carrier.

Fig.10 Conceptual diagram illustrating the CO2-free hydrogen supply chain utilizing MCH (Source:ENEOS Corporation)

Platinum slab modeling
The same platinum slab model was used for the MCH reaction as for the CO oxidation reaction.

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Reaction pathway search
To perform an extensive search for global reaction pathways, we employed kinetic navigation using
rate constant matrix contraction (RCMC) method [3][4]. Subsequently, we utilized SC-AFIR2 (SC-AFIRx[9] is a method designed for systematically searching transition states of higher energy) for the MCH
dehydrogenation reaction. Following this, RePATH was executed, and all resulting reaction pathways
were relaxed using LUP (locally updated planes) [6][7]. The initial structure is depicted in Fig. 11, withall slab atoms (Pt) and translation vectors (TV) being fixed during the SC-AFIR2 and RePATHcalculations.

Fig. 11 Initial structure in the reaction pathway search (MCH dehydrogenation reaction)

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Options settings in the GRRM input fileTo preferentially search for the reactions where the reactive molecule is adsorbed onto the slab
surface, we set a weak force (Gamma=15) between the nine central Pt atoms of the slab (atomsnumbered 22, 25, 29 to 33, 36, 37 in Fig. 12) and selected carbon (C) and hydrogen (H) atoms of thereactive molecule MCH (indicated in light blue in Fig. 12).
In order to improve the efficiency of the search for the dehydrogenation pathways, we targeted thesame atoms that are colored in light blue (associated with both the slab and MCH in Fig. 12) in ourreaction pathway search.
The settings for the options in the GRRM input file are presented in Fig. 13.

Fig.12 Numbering of platinum slab atoms (left) and MCH (right) for the MCH dehydrogenation reaction.

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Fig.13 Part of GRRM input files for SC-AFIR2 (left) and RePATH (right) in the MCH dehydrogenation
reaction on platinum slabs.

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Results
The number of structures identified by the SC-AFIR2 and RePATH calculations is presented in Tab. 4.
The number of reaction pathways discovered is given by the total number of path tops (PTs) andtransition states (TSs) structures.

Tab.4 Number of equilibrium structures (EQs), structures at energy maxima of reaction pathways (pathtops, PTs) and transition states (TSs) identified in SC-AFIR2 and RePATH calculations for thedehydrogenation of MCH on platinum slabs.

MCH dehydrogenation reaction
SC-AFIR

RePATH

EQs

414

1060

PTs

245

725

TSs

163

481

The equilibrium structures derived from SC-AFIR2 were classified, and the most stable structures foreach composition were identified. Due to the extraction of a total of 37 compositions, Tab. 5 selectively
presents the principal structures involving the release of hydrogen (H*), along with their relative
energies with reference to C7H7*+7H*.
・ As depicted in Tab. 5, reaction pathways encompassing the dissociation of one H* atom up to seven
H* atoms were determined.
・ The dehydrogenation pathway where six H* atoms are removed from MCH resulting in toluene(TOL) as demonstrated in Tab. 5 (g) was automatically searched.
・ Moreover, we uncovered pathways like C7H13* + H* → C7H11*+ 3H*, which involve the simultaneous
dissociation of two hydrogen atoms, which are difficult to explore using conventional approach such
as NEB calculations.

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page 15 / 18Tab.5 Key structures observed in the dehydrogenation pathway of MCH on platinum catalyst surfaces,with the dissociated hydrogen atoms (H*) highlighted in red, and their respective relative energies[kJ/mol] (with the structure having seven dissociated H* atoms (h) as the reference)

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Summary
We used GRRM20 with Matlantis to perform automated reaction pathway searches and relaxation
calculations (RePATH) using SC-AFIR and SC-AFIR2 method for 1) the CO oxidation reaction and 2) theMCH dehydrogenation reaction on a platinum slab.
●●●●When we compared our CO oxidation reaction pathways on the platinum catalyst surface to thosefrom the preceding study that used GRRM with SIESTA, we found that we could achieve similar
reaction pathways with comparable accuracy.
In our results, the previously reported OC-OO intermediate was not observed, indicating that ourreplication of the preceding study was not complete; however, we discovered an unreported C* +3O* intermediate.
Regarding the MCH dehydrogenation on a platinum catalyst surface, our pathway search identified
several processes for removing one to seven hydrogen atoms, including a significant reaction thatremoves six hydrogens from MCH to form toluene. This supports the use of MCH as a potential
hydrogen carrier and confirms the usefulness of GRRM20 with Matlantis as a tool for investigating
dehydrogenation catalysts.
Additionally, we identified complex reaction pathways involving the simultaneous removal of twohydrogen atoms, which are difficult to find using conventional method such as NEB and String
method.

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Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, and Kristin A. Persson[3] Y. Sumiya, Y. Nagahata, T. Komatsuzaki, T. Taketsugu, S. Maeda, J. Phys. Chem. A, 119,11641(2015)[4] Y. Sumiya, S. Maeda, Chem. Lett., 49, 553(2020)[5] S. Maeda, Y. Harabuchi, Comput. Mol. Sci., 11, e1538(2021)[6] C. Choi, R. Elber, J. Chem. Phys., 94, 751(1991)[7] P. Y. Ayala, H. B. Schlegel, J. Chem. Phys., 107, 375(1997)[8] https://www.eneos-rd.com/research/carbon-neutral/dmch.html[9] S. Maeda, T. Taketsugu, K. Morokuma, J. Comput. Chem. 35, 166 (2014)

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