Skip to main content
Log in

Miniature physical sphere-in-contact models of heterogeneous catalysts and metal nanoparticles

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Context

Physical molecular models have played a fundamental role in the understanding of chemical reactions on heterogeneous catalysts and on metal nanoparticles. To date, these physical models have been based on separate models of the metal nanoparticle (NP) or surface and of the substrate and the molecular structure of reactant and product adsorbates and their intermediates. In this paper, we try to provide a new miniature physical molecular model, the sphere-in-contact model of heterogeneous catalysts and metal nanoparticles that can build inexpensive, small and efficient molecular models that can be transported or shipped easily and that depict the chemical reaction as a whole, showing reactants, intermediates, products, the metal nanoparticle bound to the substrate which can give information about a reaction mechanism. These models reveal that there are certain rules with respect to the kind of sites you observe at the metal NP interface with the support by small movement of the nanoparticle.

Methods

We have used in this study physical molecular models using the sphere-in-contact model. This is the first time such physical models are built for heterogeneous catalytic reactions and metal nanoparticles, and they are constructed out of spheres that fuse together when exposed to water.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Data availability

The datasets generated during and/or analyzed during the current study are available from the author on reasonable request.

Code availability

No computational tools were used in this study.

References

  1. Kekulé A (1865) B Soc Chim Fr 3:98

    Google Scholar 

  2. Kekulé A (1866) Ann der Chem and Pharm 137:129

    Article  Google Scholar 

  3. Watson JD, Crick FH (1953) A structure for deoxyribose nucleic acid. Nature 171:737–738. https://doi.org/10.1038/171737a0

    Article  CAS  PubMed  Google Scholar 

  4. Pauling L, Corey RB, Branson HR (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205–211. https://doi.org/10.1073/pnas.37.4.205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Bragg SW (1925) Concerning the nature of things, six lectures delivered at the Royal Institution. G Bell and Sons Ltd, pp 1–232

  6. Corey RB, Pauling L (1953) Rev Sci Instr 24:621

    Article  CAS  Google Scholar 

  7. Koltun WL (1965) Space filling atomic units and connectors for molecular models. US Patent US3170246A

  8. Ollis WD (1972) Proc R Inst G B 45:1

    CAS  Google Scholar 

  9. Beevers CA, Ross ΜAS (1937) The crystal structure of “beta alumina” Na2O·11Al2O3. Zeitschrift für Kristallographie - Cryst Mater 97(1–6):59–66. https://doi.org/10.1524/zkri.1937.97.1.59

    Article  CAS  Google Scholar 

  10. Dreiding AS (1959) Einfache Molekularmodelle. Helv Chim Acta 42(4):1339–1344. https://doi.org/10.1002/hlca.19590420433

    Article  CAS  Google Scholar 

  11. Zeinalipour-Yazdi CD, Pullman DP, Catlow CRA (2016) The sphere-in-contact model of carbon materials. J Mol Model 22(1):40. https://doi.org/10.1007/s00894-015-2895-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Zeinalipour-Yazdi CD, Loizidou EZ (2017) Study of the cap structure of (3,3), (4,4) and (5,5)-SWCNTs: application of the sphere-in-contact model. Carbon 115:819–827

    Article  CAS  Google Scholar 

  13. Zeinalipour-Yazdi CD, Loizidou EZ (2019) Corrigendum to “study of the cap structure of (3,3), (4,4) and (5,5)-SWCNTs: application of the sphere-in-contact model” [Carbon 115 (2017) 819–827]. Carbon 146:369–370

    Article  CAS  Google Scholar 

  14. Melchor S, Dobado JA (2004) CoNTub: an algorithm for connecting two arbitrary carbon nanotubes. J Chem Inf Comput Sci 44:1639–1646

    Article  CAS  PubMed  Google Scholar 

  15. Zeinalipour-Yazdi CD, Pullman DP (2019) Study of a rhombohedral graphite X-ray filter using the sphere-in-contact model. Chem Phys Lett 734:136717. https://doi.org/10.1016/j.cplett.2019.136717

    Article  CAS  Google Scholar 

  16. Santen RAv (2017) Modern heterogeneous catalysis: an introduction. https://doi.org/10.1002/9783527810253

  17. van Santen R, Neurock M (2006) Molecular heterogeneous catalysis: a conceptual and computational approach. Wiley-VCH

    Book  Google Scholar 

  18. Sauer J (1989) Molecular models in ab initio studies of solids and surfaces: from ionic crystals and semiconductors to catalysts. Chem Rev 89(1):199–255. https://doi.org/10.1021/cr00091a006

    Article  CAS  Google Scholar 

  19. Mavrikakis M, Hammer B, Nørskov JK (1998) Effect of strain on the reactivity of metal surfaces. Phys Rev Lett 81(13):2819–2822. https://doi.org/10.1103/PhysRevLett.81.2819

    Article  Google Scholar 

  20. Car R, Parrinello M (1985) Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 55(22):2471–2474. https://doi.org/10.1103/PhysRevLett.55.2471

    Article  CAS  PubMed  Google Scholar 

  21. Water Fuse Beads Set, Model: 5mm-PD, CGBoom, Apex CE Specialists Limited, info@apex-ce.com (2023)

  22. Darling D (2018) "Cannonball problem" [online] Daviddarling.info. http://www.daviddarling.info/encyclopedia/C/Cannonball Problem.html [Accessed 26 Mar. 2018]. The internet encyclopedia of science Darling, D. (2018). Cannonball Problem.

  23. https://www.kickstarter.com/projects/veritasium/snatoms-the-magnetic-molecular-modeling-kit. Accessed 16 June 2023

  24. Meszaros L (1964) A magnetic molecular model. J Chem Educ 41(1):50. https://doi.org/10.1021/ed041p50

    Article  CAS  Google Scholar 

  25. Zeinalipour-Yazdi CD (January 2006) Doctoral thesis presentation "electronic structure and interlayer binding of graphite". https://doi.org/10.13140/RG.2.2.13745.56168.

  26. Zeinalipour-Yazdi CD (March 2006) Electronic structure and interlayer binding energy of graphite, PhD Advisor, David P Pullman. https://doi.org/10.13140/RG.2.2.18778.72646.

  27. Bohra M, Alman V, Showry A, Singh V, Diaz RE, Sowwan M, Grammatikopoulos P (2020) Aggregation vs surface segregation: antagonism over the magnetic behavior of NiCr nanoparticles. ACS Omega 5(51):32883–32889. https://doi.org/10.1021/acsomega.0c03056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Liu W, Ruiz VG, Zhang G-X, Santra B, Ren X, Scheffler M, Tkatchenko A (2013) Structure and energetics of benzene adsorbed on transition-metal surfaces: density-functional theory with van der Waals interactions including collective substrate response. New J Phys 15(5):053046. https://doi.org/10.1088/1367-2630/15/5/053046

    Article  CAS  Google Scholar 

  29. Zeinalipour-Yazdi CD (2022) Topology of active site geometries in HCP and FCC nanoparticles and surfaces. Chem Phys 559:111532. https://doi.org/10.1016/j.chemphys.2022.111532

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to acknowledge the companies that offer the beads and template with which these models were built and Sir Prof. Richard Catlow for useful discussions.

Author information

Authors and Affiliations

Authors

Contributions

This study was conceived, designed by Dr. Constantinos Zeinalipour-Yazdi. Both DPP and CDZ collected the data. did the analysis of the models, and wrote the paper.

Corresponding author

Correspondence to Constantinos D. Zeinalipour-Yazdi.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zeinalipour-Yazdi, C.D., Pullman, D.P. Miniature physical sphere-in-contact models of heterogeneous catalysts and metal nanoparticles. J Mol Model 29, 312 (2023). https://doi.org/10.1007/s00894-023-05721-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-023-05721-2

Keywords

Navigation