Molecular Modelling of Structure Direction Phenomena

  • Alessandro Turrina
  • Paul A. CoxEmail author
Part of the Structure and Bonding book series (STRUCTURE, volume 175)


Organic structure-directing agents (OSDAs) are widely used in the synthesis of zeolitic materials. Molecular modelling methods are playing a key part in helping to establish the role of the OSDA in the synthesis process. Moreover, modelling is increasingly being used to design and screen new OSDAs for specific targets. This review aims to provide an overview of the methods used to investigate the relationship between OSDAs and their zeolitic products and to provide a series of examples to highlight the important contribution that modelling is making in this field.


De novo method High-throughput screening OSDA Template modelling Zeolite 


  1. 1.
    Grant GH, Richards WG (1998) Computational chemistry. Oxford University Press, OxfordGoogle Scholar
  2. 2.
    Leach AR (2001) Molecular modelling: principles and applications. Prentice Hall, DorchesterGoogle Scholar
  3. 3.
    Wells BA, Chaffee AL (2015) Ewald summation for molecular simulations. J Chem Theory Comput 11:3684–3695CrossRefGoogle Scholar
  4. 4.
    Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges. Tetrahedron 36:3219–3228CrossRefGoogle Scholar
  5. 5.
    Rappé AK, Goddard III WA (1991) Charge equilibration for molecular dynamics simulations. J Phys Chem 95:3358–3363CrossRefGoogle Scholar
  6. 6.
    Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT (1988) Structure and energetics of ligand binding to proteins. Proteins Struct Funct Genet 4:31–47CrossRefGoogle Scholar
  7. 7.
    Rappé AK, Casewit CJ, Colwell KS, Goddard III WA, Skiff WM (1992) UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc 114:10024–10035CrossRefGoogle Scholar
  8. 8.
    Sun H (1998) COMPASS: an ab initio force-field optimized for condensed-phase applications – overview with details on alkane and benzene compounds. J Phys Chem B 102:7338–7364CrossRefGoogle Scholar
  9. 9.
    Dassault Systèmes BIOVIA (2017) Materials studio version 2017 R2. San DiegoGoogle Scholar
  10. 10.
    Gale JD (1997) GULP: a computer program for the symmetry-adapted simulation of solids. J Chem Soc Faraday Trans 93:629–637CrossRefGoogle Scholar
  11. 11.
    Jensen F (2017) Introduction to computational chemistry. Wiley, ChichesterGoogle Scholar
  12. 12.
    Jackson RA, Catlow CRA (1988) Computer simulation studies of zeolite structure. Mol Simul 1:207–224CrossRefGoogle Scholar
  13. 13.
    Shannon MD, Casci JL, Cox PA, Andrews SJ (1991) Structure of the two-dimensional medium-pore high-silica zeolite NU-87. Nature 353:417–420CrossRefGoogle Scholar
  14. 14.
    Kiselev AV, Lopatkin AA, Shulga AA (1985) Molecular statistical calculation of gas adsorption by silicalite. Zeolites 5:261–267CrossRefGoogle Scholar
  15. 15.
    Oie T, Maggiora TM, Christoffersen RE, Duchamp DJ (1981) Development of a flexible intra- and intermolecular empirical potential function for large molecular systems. Int J Quantum Chem 20:1–47CrossRefGoogle Scholar
  16. 16.
    Tildesley DJ (1993) The molecular dynamics method. In: Allen MP, Tildesley DJ (eds) Computer simulation in chemical physics, NATO ASI series 397, pp 23–47Google Scholar
  17. 17.
    Stevens AP, Gorman AM, Freeman CM, Cox PA (1996) Prediction of template location via a combined monte-carlo simulated annealing approach. J Chem Soc Faraday Trans 92:2065–2073CrossRefGoogle Scholar
  18. 18.
    Ramachandran KI, Deepa G, Namboori K (2008) Computational chemistry and molecular modelling. Springer-Verlag, BerlinGoogle Scholar
  19. 19.
    Hasnip PJ, Refson K, Probert MIJ, Yates JR, Clark SJ, Pickard CJ (2014) Density functional theory in the solid state. Phil Trans R Soc A 372:20130270CrossRefGoogle Scholar
  20. 20.
    Thiel W (2014) Semiempirical quantum-chemical methods. WIREs Comput Mol Sci 4:145–157CrossRefGoogle Scholar
  21. 21.
    Andrews SJ, Casci JL, Cox PA, Shannon MD (1999) Determination of the location of the template molecules in zeolite EU-1 via a combined molecular modelling and X-ray diffraction approach. In: Treacy MMJ, Marcus BK, Bisher ME and Higgins JB (eds) Proceedings of the 12th international zeolite conference, Materials Research Society, Warrendale, pp 2355–2360Google Scholar
  22. 22.
    Guo P, Shin J, Greenaway AG, Min JG, Su J, Choi HJ, Liu LF, Cox PA, Hong SB, Wright PA, Zou XD (2015) A zeolite family with expanding structural complexity and embedded isoreticular structures. Nature 524:74–78CrossRefGoogle Scholar
  23. 23.
    Rollmann LD, Schlenker JL, Lawton SL, Kennedy CL, Kennedy GJ, Doren DJ (1999) On the role of small amines in zeolite synthesis. J Phys Chem B 103:7175–7183CrossRefGoogle Scholar
  24. 24.
    Wagner P, Nakagawa Y, Lee GS, Davis ME, Elomari S, Medrud RC, Zones SI (2000) Guest/host relationships in the synthesis of the novel cage-based zeolites SSZ-35, SSZ-36 and SSZ-39. J Am Chem Soc 122:263–273CrossRefGoogle Scholar
  25. 25.
    Lewis DW, Freeman CM, Catlow CRA (1995) Predicting the templating ability of organic additives for the synthesis of microporous materials. J Phys Chem 99:11194–11202CrossRefGoogle Scholar
  26. 26.
    Shen V, Bell AT (1996) Computer simulation of the interactions of tetraalkylammonium cations with ZSM-5 and ZSM-11. Microporous Mater 7:187–199CrossRefGoogle Scholar
  27. 27.
    Szyja BM, Vassilev P, Trinh TT, van Santen RA, Hensen EJM (2011) The relative stability of zeolite precursor tetraalkylammonium-silicate oligomer complexes. Microporous Mesoporous Mater 146:82–87CrossRefGoogle Scholar
  28. 28.
    Sánchez M, Diaz RD, Cordova T, Gonzalez G, Ruette F (2015) Study of template interactions in MFI and MEL zeolites using quantum methods. Microporous Mesoporous Mater 203:91–99CrossRefGoogle Scholar
  29. 29.
    Sastre G, Fornes V, Corma A (2002) On the preferential location of Al and proton siting in zeolites: a computational and infrared study. J Phys Chem B 106:701–708CrossRefGoogle Scholar
  30. 30.
    Gómez-Hortigüela L, Pinar AB, Cora F, Pérez-Pariente J (2010) Dopant-siting selectivity in nanoporous catalysts: control of proton accessibility in zeolite catalysts through the rational use of templates. Chem Commun 46:2073–2075CrossRefGoogle Scholar
  31. 31.
    Pinar AB, Gómez-Hortigüela L, McCusker LB, Pérez-Pariente J (2013) Controlling the aluminium distribution in the zeolite ferrierite via the organic structure directing agent. Chem Mater 25:3654–3661CrossRefGoogle Scholar
  32. 32.
    Sastre G, Pulido A, Castañeda R, Corma A (2004) Effect of the germanium incorporation in the synthesis of EU-1, ITQ-13, ITQ-22 and ITQ-24 zeolites. J Phys Chem B 108:8830–8835CrossRefGoogle Scholar
  33. 33.
    Pulido A, Moliner M, Corma A (2015) Rigid/flexible organic structure directing agents for directing the synthesis of multipore zeolites: a computational approach. J Phys Chem C 119:7711–7720CrossRefGoogle Scholar
  34. 34.
    Sastre G, Leiva S, Sabater MJ, Gimenez I, Rey F, Valencia S, Corma A (2003) Computational and experimental approach to the role of structure-directing agents in the synthesis of zeolites: the case of cyclohexyl alkyl pyrrolidinium salts in the synthesis of β, EU-1, ZSM-11 and ZSM-12 zeolites. J Phys Chem B 107:5432–5440CrossRefGoogle Scholar
  35. 35.
    Gómez-Hortigüela L, Pérez-Pariente J, Cora F (2009) Insights into structure direction of microporous aluminophosphates: competition between organic molecules and water. Chem Eur J 15:1478–1490CrossRefGoogle Scholar
  36. 36.
    Castro M, Garcia R, Warrender SJ, Slawin AMZ, Wright PA, Cox PA, Fecant A, Mellot-Fraznieks C, Bats N (2007) Co-templating and modelling in the rational synthesis of zeolitic solids. Chem Commun 33:3470–3472CrossRefGoogle Scholar
  37. 37.
    Almeida RKS, Gómez-Hortigüela L, Pinar AB, Pérez-Pariente J (2016) Synthesis of ferrierite by a new combination of co-structure-directing agents: 1,6-bis(N-methylpyrrolidinium)hexane and tetramethylammonium. Microporous Mesoporous Mater 232:218–226CrossRefGoogle Scholar
  38. 38.
    Turrina A, Garcia R, Cox PA, Casci JL, Wright PA (2016) A retrosynthetic co-templating method for the preparation of silicoaluminophosphate molecular sieves. Chem Mater 28:4998–5012CrossRefGoogle Scholar
  39. 39.
    Corma A, Rey F, Rius J, Sabater MJ, Valencia S (2004) Supramolecular self-assembled molecules as organic directing agent for the synthesis of zeolites. Nature 431:287–290CrossRefGoogle Scholar
  40. 40.
    Álvaro-Muñoz T, López-Arbeloa FL, Pérez-Pariente J, Gómez-Hortigüela L (2014) (1R,2S)-Ephedrine: a new self-assembling chiral template for the synthesis of aluminophosphate frameworks. J Phys Chem C 118:3069–3077CrossRefGoogle Scholar
  41. 41.
    Moliner M, Serna P, Cantin A, Sastre G, Díaz-Cabañas MJ, Corma A (2008) Synthesis of the Ti-Silicate form of BEC polymorph of β-Zeolite assisted by molecular modeling. J Phys Chem C 112:19547–19554CrossRefGoogle Scholar
  42. 42.
    Brand SK, Schmidt JE, Deem MW, Daeyaert F, Ma Y, Terasaki O, Orazov M, Davis ME (2017) Enantiomerically enriched, polycrystalline molecular sieves. Proc Natl Acad Sci 114:5101–5106CrossRefGoogle Scholar
  43. 43.
    Lewis RA (1990) Automated site-directed drug design. J Comput Aided Mol Des 4:205CrossRefGoogle Scholar
  44. 44.
    Douquet D, Munier-Lehmann H, Labesse G, Pochet S (2005) LEA3D: a computer-aided ligand design for structure-based drug design. J Med Chem 48:2457CrossRefGoogle Scholar
  45. 45.
    Pegg SCH, Haresco JJ, Kuntz ID (2001) A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des 15:911–933CrossRefGoogle Scholar
  46. 46.
    Lewis DW, Willock DJ, Catlow CRA, Thomas JM, Hutchings GJ (1996) De novo design of structure-directing agents for the synthesis of microporous solids. Nature 382:604–606CrossRefGoogle Scholar
  47. 47.
    Lewis DW, Sankar G, Wyles JK, Thomas JM, Catlow CRA, Willock DJ (1997) Synthesis of a small-pore microporous material using a computationally designed template. Angew Chem Int Ed Engl 36:2675–2677CrossRefGoogle Scholar
  48. 48.
    Barrett PA, Jones RH, Thomas JM, Sankar G, Shannon IJ, Catlow CRA (1996) Rational design of a solid acid catalyst for the conversion of methanol to light alkenes: synthesis, structure and performance of DAF-4. Chem Commun 17:2001–2002CrossRefGoogle Scholar
  49. 49.
    Pophale R, Daeyaert F, Deem MW (2013) Computational prediction of chemically synthesizable organic structure directing agents for zeolites. J Mater Chem A 1:6750–6760CrossRefGoogle Scholar
  50. 50.
    Schmidt JE, Deimund MA, Davis ME (2014) Facile preparation of aluminosilicate RTH across a wide composition range using a new organic structure-directing agent. Chem Mater 26:7099–7105CrossRefGoogle Scholar
  51. 51.
    Schmidt JE, Deem MW, Davis ME (2014) Synthesis of a specified, silica molecular sieve by using computationally predicted organic structure-directing agents. Angew Chem Int Ed 53:8372–8374CrossRefGoogle Scholar
  52. 52.
    Schmidt JE, Deem MW, Lew C, Davis TM (2015) Computationally-guided synthesis of the 8-ring zeolite AEI. Top Catal 58:410–415CrossRefGoogle Scholar
  53. 53.
    Davis TM, Liu AT, Lew CM, Xie D, Benin AI, Elomari S, Zones SI, Deem MW (2016) Computationally guided synthesis of SSZ-52: a zeolite for engine exhaust clean-up. Chem Mater 28:708–711CrossRefGoogle Scholar
  54. 54.
    Irwin JJ, Teague S, Mysinger MM, Bolstad ES, Coleman RG (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52:1757–1768CrossRefGoogle Scholar
  55. 55.
    Liang J, Edelsbrunner H, Woodward C (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 7:1884–1189CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Johnson Matthey Technology CentreBillinghamUK
  2. 2.School of Pharmacy and Biomedical SciencesUniversity of PortsmouthPortsmouthUK

Personalised recommendations