Author Archives: Gaohe Hu

Transition state search for CO reduction reaction

Abstract

In this post, the transition state search for a elementary reaction in carbon dioxide reduction on Cu(111) surface is performed using CASTEP, and the activation barrier for this reaction is calculated.

Introduction

Electrochemical reduction of CO_2 to valuable chemicals and fuels such as hydrocarbon and alcohols is of great interest. However, experimental results show that most metal electrodes except for copper could only reduce CO_2 mainly to CO. Previous computational work[1][2] showed that the transition state energy of reduction of CO is a good descriptor that could help us to understand the trends of catalytic activity of transition metal surfaces. To understand the process that adsorbed CO reduced to COH on Cu(111) surface, the transition state geometry and energy of *CO reduction to *COH on Cu(111) surface will be calculated and compared to reported results, here * signs are used to show the species are absorbed on the surface.

Method

In this work, plane-wave based DFT code CASTEP is used. The exchange-correlation functional is described by a GGA-PBE functional. As for pseudopotential,  “on the fly” generated ultrasoft pseudopotential for Cu is used with a core radius of 2.2 Bohr(1.16Å) and was generated with a 3d10 4s1 valence electronic configuration . The SCF tolerance is set to be 2e-6 eV per atom for all the optimization and single point energy calculations.

A 2×2 four-layer slab model is used to simulate Cu(111) surface structure with 10Å of vacuum. The optimized bulk with lattice parameter of 3.63Å is used to build the surface model. When the optimization and transition state search are performed, bottom two layers are kept fixed and remaining atoms are relaxed to simulate bulk behaviors. A optimized 5x5x1 k points grid and energy cutoff of 500 eV are kept consistent for all calculations.

Results

k points grid and energy cutoff optimization

With an energy cutoff of 500 eV, single point energies of 2×2 slab models are calculated. In figure 1, the energies of different k points gird relative to 8x8x1 k points grid is shown.

Figure 1. K points grid setting convergence optimization

The energy cutoff convergence optimization is carried out with a k point grid of 8x8x1. In figure 2 energies of different energy cutoff relative to 550 eV are shown.

Figure 2. Energy cutoff convergence optimization

According to those two convergence test results, a 5x5x1 k points grid with an energy cutoff of 500 eV is reasonable for calculation of a 2×2 slab model of Cu(111) surface. Thus these settings are kept consistent for subsequent optimization and search for transition state.

Cu(111) surface optimization

In order to build a reasonable model of reaction happens on Cu(111) surface, the optimization of surface structure is carried out first. A 2×2 Cu(111) surface slab model is used with bottom 2 layers fixed to represent bulk effects on metal surface. BFGS algorithm is used to perform the optimization with energy convergence of 2e-5 ev/atom and force convergence of 0.05 eV/A.

Transition state search

According to previous work[2],  co-adsorption of CO and H on Cu(111) surface will be neighboring hcp sites. In figure 3, co-adsorbed H and CO on neighboring Cu(111) surface is set as reactant geometry. In figure 4, adsorbed COH on Cu(111) hcp sites is set as product geometry. The structures of reactant and product are optimized using the same convergence setting for surface optimization as shown in figure 3 and 4.

Figure 3. Reactant structure of CO and H absorbed on Cu(111) surface.

Figure 4. Product structure of adsorbed COH on Cu(111) surface.

Figure 5. Transition state structure. The adsorbed species is no longer perpendicular to Cu(111) surface.

The transition state search is performed using a complete LST/QST method implemented in the CASTEP module of Material Studio. The RMS(Root Mean Square) convergence is set to 0.24 eV/A. Followed by a transition state confirmation of higher precision with energy convergence of 2.0e-5 eV/atom, maximum force of 0.1 eV/Å and maximum displacement of 0.005Å. In figure 5, the transition state geometry is shown. Although in both reactant and product structure, adsorbed species are perpendicular to Cu surface, the adsorbed species in transition state structure is rotated towards the initial position of adsorbed H atom.

Figure 6. Relative energy diagram for reaction *CO + H -> *COH

Figure 6 is the relative energy diagram. Here energy values are reported relative to that of initial reactant state. As shown in the figure, activation barrier  Consequently the activation energy from reactant is found to be 2.48 eV. Comparing to reported activation energy in [2-4], which is less than 1.0 eV, this activation energy is significantly larger. Since in their models, they include explicit water molecules to model what happens in solution. The structure of reactant and product used in this work actually modeled the reaction happens in gas phase. Meanwhile, they also argued that possible proton and electron transfer between adsorbed CO molecules and solvent molecules, which won’t induce surface atoms rearrangement as much as in gas phase.

Conclusion

The transition state geometry of *CO to *COH is found with a reaction barrier from reactant of 2.08 eV. Comparing to the reported electrode model, gas phase reduction of *CO to *COH is significantly more difficult. If given more computational time and resources, similar procedure could be used to address more complex surface reaction network starting from *CO and include explicit solvent molecules to model more realistic reaction conditions.

Reference

[1] Liu, X.; Xiao, J.; Peng, H.; Hong, X.; Chan, K.; Nørskov, J. K. Understanding Trends in Electrochemical Carbon Dioxide Reduction Rates. Nat. Commun. 2017, 8 (1), 15438. https://doi.org/10.1038/ncomms15438.

[2] Hussain, J.; Jónsson, H.; Skúlason, E. Calculations of Product Selectivity in Electrochemical CO2 Reduction. ACS Catal. 2018, 8 (6), 5240–5249. https://doi.org/10.1021/acscatal.7b03308.

[3] Nie, X.; Esopi, M. R.; Janik, M. J.; Asthagiri, A. Selectivity of CO2 Reduction on Copper Electrodes: The Role of the Kinetics of Elementary Steps. Angew. Chemie – Int. Ed. 2013, 52 (9), 2459–2462. https://doi.org/10.1002/anie.201208320.

[4] Nie, X.; Luo, W.; Janik, M. J.; Asthagiri, A. Reaction Mechanisms of CO2 Electrochemical Reduction on Cu(1 1 1) Determined with Density Functional Theory. J. Catal. 2014, 312, 108–122. https://doi.org/10.1016/j.jcat.2014.01.013.

Adsorption energy of CO on Rh(111) surface

Introduction

Adsorption of small molecules on transition metal surfaces is of great interest among chemists, since adsorption behavior could be essential to the catalytic process happening on transition metal surfaces. For adsorption on (111) surface of fcc metals, there are 4 different kinds of sites, as shown in figure 1. It is worth noticing that there are two different possible sites for threefold adsorption situations, which are called fcc and hcp site respectively. Since the bulk structure of Rh has been studied in previous work, in this work, the preference of adsorption of CO of low surface coverage on Rh (111) is assumed to be on-top site according former computational study[1]. Intuitively, CO adsorption on-top sites at low coverage is similar to the situation that CO bonds to central metal atom as a ligand, which should have a lower energy comparing to other adsorption sites.

Figure 1 (a) fcc site, (b) on-top site, (c) hcp site, (d) bridge site

Method

In this work, plane-wave based DFT code CASTEP is used. The exchange-correlation functional is described by a GGA-PBE functional, and pseudopotentials are kept default setting. As for pseudopotential, the “on the fly” generated ultrasoft pseudopotential for Rh is used with a core radius of 1.6 Bohr(0.847Å) and was generated with a 4d8 5s1 valence electronic configuration . The SCF tolerance is set to be 2e-6 eV per atom for all the optimization and single point energy calculations.

Optimized bulk structure of Rh is taken from previous work[2]. According to previous computational work[3], a 2×2 Rh(111) surface slab model of 4 layers of atoms is used to simulate the behavior of Rh surface. As for the optimization of surface slab model, energy cutoff is kept consistent with that for bulk calculation, while k points gird setting is set to 7x7x1. In order to get comparable energies for molecule and surfaces, the same setting is used for optimization of CO in vacuum. CO adsorption is modeled with single CO adsorbed on different sites of optimized surface model. The corresponding adsorption energy is calculated with the equation[4]

\begin{equation} E_{ads}=E_{Rh-CO}-E_{surface}-E_{CO} \end{equation}

Results

1. k points grid optimization

With an energy cutoff of 625 eV, single point energies of 1×1 slab models are calculated. In figure 2, the energies relative to 9x9x1 k points gird is shown. As a trade off of accuracy and efficiency, 7x7x1 k points grid is used to get valid results for surface calculations.

Figure 2 k points convergence test, energy relative to maximum k points grid is convergent for grid larger than 7x7x1 gird.

 

2. Surface optimization

Although 2×2 slab model will be used for adsorption of CO calculations in order to make sure a 1/4 ML coverage, here surface structure optimization is performed for 1×1 slab model. Due to the limitation of computation resources, 2×2 slab model optimization won’t converge in reasonable time, a 1×1 slab model is optimized instead. Since Rh surface slab model is periodic system, a 1×1 slab won’t introduce significant error to final results. Meanwhile, the energy of the supercell should be scalable, which makes it reasonable to get energy of 2×2 slab out of 1×1 slab. Only top two layers are relaxed while two layers at bottom are kept fixed to simulate bulk effect on surface atoms.

BFGS algorithm is used to perform the optimization with energy convergence of 2e-5 ev/atom and force convergence of 0.05 eV/A. The optimized structure has an energy of -12123.0410 eV.

3.Optimization of CO in vacuum

In order to obtain consistent value for molecular energy, CO configuration is optimized in the same lattice as the surface slab model. The optimized bond length is 1.138 A, with an energy of -596.123 eV.

4. Optimization of CO adsorption

A 2×2 slab model for Rh(111) surface is used to get a optimized structure of one single CO adsorption on- top site, which corresponds to a 1/4 ML coverage. Such systems would significantly increase the cost of computation if full optimization is performed. Thus, only the distance between CO molecule and Rh atom is allowed to relax to find the most stable configuration of CO adsorption on-top site. Such modelling of CO adsorption is based on the assumption that adsorption of CO with low coverage won’t induce significant surface structure reconstruction.

The optimization algorithm and convergence setting is consistent with those for surface structure optimization. The optimized distance between C and Rh atom is 1.843 A with a total energy of -49089.5603 eV. The CO adsorption energy for Rh on-top site is -1.273 eV. Meanwhile, C-O bond is stretched to 1.160 A, which suggests the weakening of bond strength between C and O.

Conclusion

The adsorption energy of CO on on-top site of Rh (111) surface is -1.273 eV with an optimized bond distance of 1.843 A, which is consistent with former computational results at 1/4 ML coverage, 1.83A [1] and 1.842 A[3], respectively. Since different levels of theory or different exchange-correlation functionals have been used, the bind energies are not comparable, it is reasonable to compare the bonding length between metal atoms and adsorbate to see if the optimized geometry is consistent with former study. Further work may focus on the influence of surface coverage on the adsorption energy and bond weakening of C-O bonds. On the other hand in order to get adsorption values comparable to experimental ones, a test for different exchange-correlation functionals and thermodynamic parameters are required.

Reference

[1] Mavrikakis, M., Rempel, J., Greeley, J., Hansen, L. B. & Nørskov, J. K. Atomic and molecular adsorption on Rh(111). J. Chem. Phys. 117, 6737–6744 (2002).

[2]Prediction of preferred structure and lattice parameters of Rh https://sites.psu.edu/dftap/2020/02/03/prediction-of-preferred-structure-and-lattice-parameters-of-rh/

[3] Krenn, G., Bako, I. & Schennach, R. CO adsorption and CO and O coadsorption on Rh(111) studied by reflection absorption infrared spectroscopy and density functional theory. J. Chem. Phys. 124, 144703 (2006).

[4] Sholl, D. & Steckel, J. A. Density functional theory: a practical introduction. (John Wiley & Sons, 2011).

Prediction of preferred structure and lattice parameters of Rh

Prediction of preferred structure and lattice parameters of Rh

By Gaohe Hu

Introduction

In this work, plane wave based DFT is used to determine the preferred structure of Rh and optimization method to calculate corresponding lattice constants. Experimentally, crystal structure of pure Rh is FCC with a lattice constant of 3.83A[1]. In this work, the stability of FCC and HCP structure is compared using DFT computation to find out the preferred structure of Rh crystal and corresponding lattice constants.

Method

In this work, plan-wave based DFT code CASTEP is used. The exchange-correlation functional is described by a GGA-PBE functional, and pseudopotentials are kept default setting. As for pseudopotential, the “on the fly” generated ultrasoft pseudopotential for Rh is used with a core radius of 1.6 Bohr(0.847Å) and was generated with a 4d8 5s1 valence electronic configuration . The SCF tolerance is set to be 2e-6 eV per atom.

First, experimental structure is used as an initial structure to find out convergence of k points and energy cutoff. The optimized energy cutoff and k points setting are 625eV and 7x7x6, respectively. Then the optimized k points and energy cutoff settings are used to calculate single point energies of FCC and HCP structure of different lattice constants around experimental lattice constant. Finally, the optimized lattice constant is determined by fitting the single point results into Birch-Murnaghan equation[2],

E_{tot}(a) = E_0 + \frac{9V_0B_0}{16}\{[(\frac{a_0}{a})^2-1]^3{B_0}'+[(\frac{a_0}{a})^2-1]^2[6-4(\frac{a_0}{a})^2]\}

where a_0 and a correspond to optimized lattice constant and lattice constant of current configuration. Thus a quadratic fit for optimized energy and latice constant is reasonable.

Results

1. Energy cutoff optimization

Energy cutoff/eV
Total Energy/eV
Time/s
Energy Difference/eV
500
-3030.852538
14.14
0.274603092
550
-3031.038616
13.97
0.088524243
575
-3031.075206
14.17
0.051934617
600
-3031.112203
14.28
0.014937231
625
-3031.121274
14.05
0.005866856
650
-3031.124957
14.44
0.002183397
675-3031.12642314.110.000717979
700
-3031.1269514.44
0.000190689
725
-3031.127141
14.59
0

Table 1 Energy cutoff optimization for FCC Rh

Figure 1 energy difference vs. energy cutoff

The energies relative to the value with an energy cutoff of 750 eV of different energy cutoff are shown in Figure 1. The total energy difference converges to less than 0.01eV when energy cutoff is larger than 625eV. As a compromise of time and numerical accuracy, an energy cutoff of 650eV is enough to generate comparable results.

2. K points optimization

FIgure 2 k points optimization

gridnum of kpointsEnergy/ eV
1x1x11-3036.4
2x2x12-3031.3
2x2x22-3031.7
3x3x34-3029.7
3x3x26-3030.9
4x4x410-3031.1
4x4x316-3030.8
5x5x324-3030.9
5x5x430-3030.9
6x6x554-3031.2
6x6x628-3031.1
7x7x684-3031.2
7x7x720-3031.2
8x8x7128-3031.1
9x9x7160-3031.1

Table 2 k point grid, number of k points and energy

The k points optimization was carried out as shown in Figure 2, the  total energy fluctuates as the k points grid grows larger. The detailed data can be seen in Table2. By increasing the grid of k points, the numerical accuracy just fluctuates, and doesn’t guarantee a better result with more time required. As a consequence,  a 7x7x6 k points grid is used with total k points number of 84 as the optimized k points setting. As for HCP structure,  the k point grid density is set to the similar magnitude(around 0.037 to 0.040 1/A).

3. FCC structure optimization

Taken from experimental results, an initial guess for FCC structure with the lattice constant of 3.83 A is used, and the step size is set to 0.002 A. A 7x7x6 k points grid and an energy cutoff of 625 eV is used.

According to Birch-Murnaghan equation,  a quadratic fit is valid around the equilibrium geometry. Optimization is carried out with respect to unit cell volume. Figure 3 shows the quadratic fit of total energy against volume, by minimizing the fitted equation, the optimized unit cell volume is found to be 55.90076 A^3 with a minimum of energy -3031.176001eV.

Figure 3 FCC geometry optimization

4.HCP structure optimization

Experimental results[3] of HCP structure is used, where a is 2.722 A and c is 4.386A. In order to keep k points grid consistent with that of FCC structure, a 11x11x7 k points grid is used. All the other parameters are set to be exactly the same. Final results and fitting curve are shown in figure 4.

 

Figure 4 HCP geometry optimization

The optimized structure has an energy of -3031.089268eV per atom, which is higher than that of FCC structure.

Conclusion

According to the computation above, the HCP structure of Rh has a minimized energy of -3031.089268eV, while FCC structure has a minimized energy of –3031.176001eV. Thus, FCC structure of Rh is energetically more favorable  than HCP structure, which is consistent with experimental results, with an optimized lattice constant of 3.824A.

Reference

1.  Entry 1011103, F m -3 m #225, Crystallography Open Database.

http://www.crystallography.net/cod/1534917.html

2. Sholl, D. & Steckel, J. A. Density functional theory: a practical introduction. (John Wiley & Sons, 2011).

3. Huang, J. L. et al. Formation of Hexagonal-Close Packed (HCP) Rhodium as a Size Effect. J. Am. Chem. Soc. 139, 575–578 (2017).