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Global Optimization of Adsorbate–Surface Structures While Preserving Molecular Identity

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Abstract

As the complexity of atomistic simulations in catalysis and surface science increases, the challenge of manually finding the lowest-energy adsorbate–surface geometries grows significantly. In the current work, a global optimization approach that preserves adsorbate identity is applied to enable the automated search for optimized binding geometries. This technique is based on the minima hopping method developed by Goedecker, but is modified to preserve the molecular identity of adsorbates by the application of a new class of Hookean constraints. These constraints are completely inactive when the adsorbate identity is preserved, but act to restore the adsorbate structure via a Hookean force when the bond length exceeds a threshold distance. Additionally, a related Hookean constraint has been developed to prevent adsorbates (particularly such adsorbates as CO and CH2O that have stable gas-phase forms) from volatilizing during the molecular dynamics portion of the minima hopping technique. This combination, referred to herein as the constrained minima hopping method, was tested for its suitability in finding the minimum-energy binding configuration for a set of 17 C x H y O z adsorbates on a stepped Cu fcc(211) surface and in all cases found the global minima in comparable or fewer steps than the previous brute force methodologies. It is expected that methods such as this will be crucial to finding low-energy states in more complex systems, such as those with high coverages of adsorbed species or in the presence of explicit solvent molecules.

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Notes

  1. Site 4–6 is a mirror image of site 4–7, and site 1–7 is a mirror image of site 2–7.

  2. http://wiki.fysik.dtu.dk/ase.

References

  1. Hammer B, Nørskov JK (1995) Electronic factors determining the reactivity of metal surfaces. Surf Sci 343:211

    Article  CAS  Google Scholar 

  2. Hammer B, Nørskov JK (1995) Why gold is the noblest of all the metals. Nature 376:238

    Article  CAS  Google Scholar 

  3. Gross A, Wilke S, Scheffler M (1995) Six-dimensional quantum dynamics of adsorption and desorption of H2 at Pd(100): steering and steric effects. Phys Rev Lett 75:2718

    Article  CAS  Google Scholar 

  4. Koper MT, van Santen RA (1999) Interaction of H, O and OH with metal surfaces. J Electroanal Chem 472:126

    Article  CAS  Google Scholar 

  5. Rostrup-Nielsen J, Nørskov J (2006) Step sites in syngas catalysis. Top Catal 40:45

    Article  CAS  Google Scholar 

  6. Iokibe K, Azumi K, Tachikawa H (2007) Surface diffusion of a Zn adatom on a Zn(001) surface: a DFT study. J Phys Chem C 111:13510

    Article  CAS  Google Scholar 

  7. Fajín JL, Cordeiro MND, Illas F, Gomes JR (2009) Influence of step sites in the molecular mechanism of the water gas shift reaction catalyzed by copper. J Catal 268:131

    Article  Google Scholar 

  8. Árnadóttir L, Stuve EM, Jónsson H (2010) Adsorption of water monomer and clusters on platinum(111) terrace and related steps and kinks: I. Configurations, energies, and hydrogen bonding. Surf Sci 604:1978

    Article  Google Scholar 

  9. Peterson AA, Dreher M, Wambach J, Nachtegaal M, Dahl S, Nørskov JK, Vogel F (2012) Evidence of scrambling over ruthenium-based catalysts in supercritical-water gasification. ChemCatChem 4:1185

    Article  CAS  Google Scholar 

  10. Zhu T, van Grootel PW, Filot IA, Sun S-G, van Santen RA, Hensen EJ (2013) Microkinetics of steam methane reforming on platinum and rhodium metal surfaces. J Catal 297:227

    Article  CAS  Google Scholar 

  11. Morin C, Eichler A, Hirschl R, Sautet P, Hafner J (2003) DFT study of adsorption and dissociation of thiophene molecules on Ni(110). Surf Sci 540:474

    Article  CAS  Google Scholar 

  12. Mudiyanselage K, Trenary M, Meyer RJ (2008) Formation of methyl isocyanide from dimethylamine on Pt(111). J Phys Chem C 112:3794

    Article  CAS  Google Scholar 

  13. Ferrin P, Simonetti D, Kandoi S, Kunkes E, Dumesic JA, Nørskov JK, Mavrikakis M (2009) Modeling ethanol decomposition on transition metals: a combined application of scaling and Brønsted–Evans–Polanyi relations. J Am Chem Soc 131:5809

    Article  CAS  Google Scholar 

  14. Blaylock DW, Ogura T, Green WH, Beran GJO (2009) Computational investigation of thermochemistry and kinetics of steam methane reforming on Ni(111) under realistic conditions. J Phys Chem C 113:4898

    Article  CAS  Google Scholar 

  15. Xu L, Mei D, Henkelman G (2009) Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100). J Chem Phys 131:244520

    Article  Google Scholar 

  16. Peterson AA, Abild-Pedersen F, Studt F, Rossmeisl J, Nørskov JK (2010) How copper catalyzes the electroreduction of carbon dioxide into hydrocarbon fuels. Energy Environ Sci 3:1311

    Article  CAS  Google Scholar 

  17. Molina LM, Lee S, Sell K, Barcaro G, Fortunelli A, Lee B, Seifert S, Winans RE, Elam JW, Pellin MJ, Barke I, von Oeynhausen V, Lei Y, Meyer RJ, Alonso JA, Rodrguez AF, Kleibert A, Giorgio S, Henry CR, Meiwes-Broer K-H, Vajda S (2011) Size-dependent selectivity and activity of silver nanoclusters in the partial oxidation of propylene to propylene oxide and acrolein: a joint experimental and theoretical study. Catal Today 160:116

    Article  CAS  Google Scholar 

  18. Liu W, Savara A, Ren X, Ludwig W, Dostert K-H, Schauermann S, Tkatchenko A, Freund H-J, Scheffler M (2012) Toward low-temperature dehydrogenation catalysis: isophorone adsorbed on Pd(111). J Phys Chem Lett 3:582

    Article  CAS  Google Scholar 

  19. Montemore MM, Medlin JW (2012) A density functional study of C1–C4 alkyl adsorption on Cu(111). J Chem Phys 136:204710

    Article  Google Scholar 

  20. Sinha NK, Neurock M (2012) A first principles analysis of the hydrogenation of C1–C4 aldehydes and ketones over Ru(0001). J Catal 295:31

    Article  CAS  Google Scholar 

  21. Goldsmith C (2012) Estimating the thermochemistry of adsorbates based upon gas-phase properties. Top Catal 55:366

    Article  CAS  Google Scholar 

  22. Tang H, Vander Ven A, Trout BL (2004) Phase diagram of oxygen adsorbed on platinum (111) by first-principles investigation. Phys Rev B 70:045420

    Article  Google Scholar 

  23. Miller SD, Kitchin JR (2009) Uncertainty and figure selection for DFT based cluster expansions for oxygen adsorption on Au and Pt (111) surfaces. Mol Simul 35:920

    Article  CAS  Google Scholar 

  24. Miller SD, Kitchin JR (2009) Relating the coverage dependence of oxygen adsorption on Au and Pt fcc(111) surfaces through adsorbate-induced surface electronic structure effects. Surf Sci 603:794

    Article  CAS  Google Scholar 

  25. Bromfield TC, Curulla Ferré D, Niemantsverdriet JW (2005) A DFT study of the adsorption and dissociation of CO on Fe(100): influence of surface coverage on the nature of accessible adsorption states. ChemPhysChem 6:254

    Article  CAS  Google Scholar 

  26. Orita H, Inada Y (2005) DFT investigation of CO adsorption on Pt(211) and Pt(311) surfaces from low to high coverage. J Phys Chem B 109:22469

    Article  CAS  Google Scholar 

  27. Ojifinni RA, Gong J, Froemming NS, Flaherty DW, Pan M, Henkelman G, Mullins CB (2008) Carbonate formation and decomposition on atomic oxygen precovered Au(111). J Am Chem Soc 130:11250

    Article  CAS  Google Scholar 

  28. Qi L, Li J (2012) Adsorbate interactions on surface lead to a flattened Sabatier volcano plot in reduction of oxygen. J Catal 295:59

    Article  CAS  Google Scholar 

  29. Seema P, Behler J, Marx D (2013) Adsorption of methanethiolate and atomic sulfur at the Cu(111) surface: a computational study. J Phys Chem C 117:337

    Article  CAS  Google Scholar 

  30. Zhuo M, Borgna A, Saeys M (2013) Effect of the CO coverage on the Fischer–Tropsch synthesis mechanism on cobalt catalysts. J Catal 297:217

    Article  CAS  Google Scholar 

  31. Laursen S, Linic S (2006) Oxidation catalysis by oxide-supported Au nanostructures: the role of supports and the effect of external conditions. Phys Rev Lett 97:026101

    Article  Google Scholar 

  32. Ammal SC, Heyden A (2010) Modeling the noble metal/TiO2 (110) interface with hybrid DFT functionals: a periodic electrostatic embedded cluster model study. J Chem Phys 133:164703

    Article  Google Scholar 

  33. Chen H-T, Chang J-G, Ju S-P, Chen H-L (2010) Ethylene epoxidation on a Au nanoparticle versus a Au(111) surface: a DFT study. J Phys Chem Lett 1:739

    Article  CAS  Google Scholar 

  34. Peterson AA, Grabow LC, Brennan TP, Shong B, Ooi C, Wu DM, Li CW, Kushwaha A, Medford AJ, Mbuga F, Li L, Nørskov JK (2012) Finite-size effects in O and CO adsorption for the late transition metals. Top Catal 55:1276

    Article  CAS  Google Scholar 

  35. Nieskens DLS, Curulla Ferré D, Niemantsverdriet JW (2005) The influence of promoters and poisons on carbon monoxide adsorption on Rh(100): a DFT study. ChemPhysChem 6:1293

    Article  CAS  Google Scholar 

  36. Rodríguez P, Koverga A, Koper M (2010) Carbon monoxide as a promoter for its own oxidation on a gold electrode. Angew Chem Int Ed 49:1241

    Article  Google Scholar 

  37. Dreher M, Johnson B, Peterson AA, Nachtegaal M, Wambach J, Vogel F (2013) Catalysis in supercritical water: pathway of the methanation reaction and sulfur poisoning over a Ru/C catalyst during the reforming of biomolecules. J Catal 301:38

    Article  CAS  Google Scholar 

  38. Filhol J-S, Neurock M (2006) Elucidation of the electrochemical activation of water over Pd by first principles. Angew Chem 118:416

    Article  Google Scholar 

  39. Schiros T, Ogasawara H, Näslund L-Å, Andersson KJ, Ren J, Meng S, Karlberg GS, Odelius M, Nilsson A, Pettersson LGM (2010) Cooperativity in surface bonding and hydrogen bonding of water and hydroxyl at metal surfaces. J Phys Chem C 114:10240

    Article  CAS  Google Scholar 

  40. Lew W, Crowe MC, Campbell CT, Carrasco J, Michaelides A (2011) The energy of hydroxyl coadsorbed with water on Pt(111). J Phys Chem C 115:23008

    Article  CAS  Google Scholar 

  41. Wang H-F, Liu Z-P (2009) Formic acid oxidation at Pt/H2O interface from periodic DFT calculations integrated with a continuum solvation model. J Phys Chem C 113:17502

    Article  CAS  Google Scholar 

  42. Li Y-F, Liu Z-P, Liu L, Gao W (2010) Mechanism and activity of photocatalytic oxygen evolution on titania anatase in aqueous surroundings. J Am Chem Soc 132:13008

    Article  CAS  Google Scholar 

  43. Goedecker S (2004) Minima hopping: an efficient search method for the global minimum of the potential energy surface of complex molecular systems. J Chem Phys 120:9911

    Article  CAS  Google Scholar 

  44. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671

    Article  CAS  Google Scholar 

  45. Pedersen A, Berthet J-C, Jónsson H (2012) Simulated annealing with coarse graining and distributed computing. In: Jónasson K (eds) Applied parallel and scientific computing, volume 7134 of Lecture Notes in Computer Science. Springer, Berlin, pp 34–44

    Google Scholar 

  46. Johnston RL (2003) Evolving better nanoparticles: genetic algorithms for optimising cluster geometries. Dalton Trans 0:4193

    Article  CAS  Google Scholar 

  47. Glass CW, Oganov AR, Hansen N (2006) USPEX—evolutionary crystal structure prediction. Comp Phys Commun 175:713

    Article  CAS  Google Scholar 

  48. Wales DJ, Doye JPK (1997) Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J Phys Chem A 101:5111

    Article  CAS  Google Scholar 

  49. Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci 99:12562

    Article  CAS  Google Scholar 

  50. Li Z, Scheraga HA (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci 84:6611

    Article  CAS  Google Scholar 

  51. Bulusu S, Yoo S, Apr E, Xantheas S, Zeng XC (2006) Lowest-energy structures of water clusters (H2O)11 and (H2O)13. J Phys Chem A 110:11781

    Article  CAS  Google Scholar 

  52. Hellmann W, Hennig RG, Goedecker S, Umrigar CJ, Delley B, Lenosky T (2007) Questioning the existence of a unique ground-state structure for Si clusters. Phys Rev B 75:085411

    Article  Google Scholar 

  53. Bao K, Goedecker S, Koga K, Lançion F, Neelov A (2009) Structure of large gold clusters obtained by global optimization using the minima hopping method. Phys Rev B 79:041405

    Article  Google Scholar 

  54. Kazachenko S, Thakkar AJ (2009) Improved minima-hopping. TIP4P water clusters, with n ≤ 37. Chem Phys Lett 476:120

    Article  CAS  Google Scholar 

  55. De S, Ghasemi SA, Willand A, Genovese L, Kanhere D, Goedecker S (2011) The effect of ionization on the global minima of small and medium sized silicon and magnesium clusters. J Chem Phys 134:124302

    Article  Google Scholar 

  56. Willand A, Gramzow M, Alireza Ghasemi S, Genovese L, Deutsch T, Reuter K, Goedecker S (2010) Structural metastability of endohedral silicon fullerenes. Phys Rev B 81:201405

    Article  Google Scholar 

  57. Gabriel MA, Genovese L, Krosnicki G, Lemaire O, Deutsch T, Franco AA (2010) Metallofullerenes as fuel cell electrocatalysts: a theoretical investigation of adsorbates on C5 9Pt. Phys Chem Chem Phys 12:9406

    Article  CAS  Google Scholar 

  58. De S, Willand A, Amsler M, Pochet P, Genovese L, Goedecker S (2011) Energy landscape of fullerene materials: a comparison of boron to boron nitride and carbon. Phys Rev Lett 106:225502

    Article  Google Scholar 

  59. Amsler M, Flores-Livas JA, Lehtovaara L, Balima F, Ghasemi SA, Machon D, Pailhès S, Willand A, Caliste D, Botti S, San Miguel A, Goedecker S, Marques MAL (2012) Crystal structure of cold compressed graphite. Phys Rev Lett 108:065501

    Article  Google Scholar 

  60. Roy S, Goedecker S, Field MJ, Penev E (2009) A minima hopping study of all-atom protein folding and structure prediction. J Phys Chem B 113:7315

    Article  CAS  Google Scholar 

  61. Amsler M, Goedecker S (2010) Crystal structure prediction using the minima hopping method. J Chem Phys 133:224104

    Article  Google Scholar 

  62. Amsler M, Flores-Livas JA, Huan TD, Botti S, Marques MAL, Goedecker S (2012) Novel structural motifs in low energy phases of LiAlH4. Phys Rev Lett 108:205505

    Article  Google Scholar 

  63. Flores-Livas JA, Amsler M, Lenosky TJ, Lehtovaara L, Botti S, Marques MAL, Goedecker S (2012) High-pressure structures of disilane and their superconducting properties. Phys Rev Lett 108:117004

    Article  Google Scholar 

  64. Roy S, Goedecker S, Hellmann V (2008) Bell–Evans–Polanyi principle for molecular dynamics trajectories and its implications for global optimization. Phys Rev E 77:056707

    Article  Google Scholar 

  65. Wang S, Petzold V, Tripkovic V, Kleis J, Howalt JG, Skúlason E, Fernández EM, Hvolbæk B, Jones G, Toftelund A, Falsig H, Björketun M, Studt F, Abild-Pedersen F, Rossmeisl J, Nørskov JK, Bligaard T (2011) Universal transition state scaling relations for (de)hydrogenation over transition metals. Phys Chem Chem Phys 13:20760

    Article  CAS  Google Scholar 

  66. Peterson AA, Nørskov JK (2012) Activity descriptors for CO2 electroreduction to methane on transition-metal catalysts. J Phys Chem Lett 3:251

    Article  CAS  Google Scholar 

  67. Besenbacher F, Nørskov JK (1993) Oxygen chemisorption on metal surfaces: general trends for Cu, Ni and Ag. Prog Surf Sci 44:5

    Article  CAS  Google Scholar 

  68. Bahn SR, Jacobsen KW (2002) An object-oriented scripting interface to a legacy electronic structure code. Comput Sci Eng 4:56

    Article  CAS  Google Scholar 

  69. Durand WJ, Peterson AA, Studt F, Abild-Pedersen F, Nørskov J. K (2011) Structure effects on the energetics of the electrochemical reduction of CO2 by copper surfaces. Surf Sci 605:1354

    Article  CAS  Google Scholar 

  70. Car R, Parrinello M (1985) Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 55:2471

    Article  CAS  Google Scholar 

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Acknowledgments

The author appreciates valuable technical discussions and feedback from Jens Nørskov (Stanford, SLAC), Lars Grabow (University of Houston), A.J. Medford (Stanford), and Sandip De (University of Basel); and wishes Professor Nørskov continued success as he celebrates his 60th birthday. The author thanks Yin-Jia Zhang (Brown University) for help in enumerating the possible binding configurations on an fcc(211) surface. This work was supported by the Young Investigator Award from the Office of Naval Research under award N00014-12-1-0851. High-performance computational resources were employed at the Center for Computation and Visualization, Brown University.

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    Andrew A. Peterson

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Peterson, A.A. Global Optimization of Adsorbate–Surface Structures While Preserving Molecular Identity. Top Catal 57, 40–53 (2014). https://doi.org/10.1007/s11244-013-0161-8

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