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Part of the book series: Structure and Bonding ((STRUCTURE,volume 175))

Abstract

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.

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References

  1. Grant GH, Richards WG (1998) Computational chemistry. Oxford University Press, Oxford

    Google Scholar 

  2. Leach AR (2001) Molecular modelling: principles and applications. Prentice Hall, Dorchester

    Google Scholar 

  3. Wells BA, Chaffee AL (2015) Ewald summation for molecular simulations. J Chem Theory Comput 11:3684–3695

    Article  CAS  Google Scholar 

  4. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges. Tetrahedron 36:3219–3228

    Article  CAS  Google Scholar 

  5. Rappé AK, Goddard III WA (1991) Charge equilibration for molecular dynamics simulations. J Phys Chem 95:3358–3363

    Article  Google Scholar 

  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 4:31–47

    Article  CAS  Google Scholar 

  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 114:10024–10035

    Article  Google Scholar 

  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 102:7338–7364

    Article  CAS  Google Scholar 

  9. Dassault Systèmes BIOVIA (2017) Materials studio version 2017 R2. San Diego

    Google Scholar 

  10. Gale JD (1997) GULP: a computer program for the symmetry-adapted simulation of solids. J Chem Soc Faraday Trans 93:629–637

    Article  CAS  Google Scholar 

  11. Jensen F (2017) Introduction to computational chemistry. Wiley, Chichester

    Google Scholar 

  12. Jackson RA, Catlow CRA (1988) Computer simulation studies of zeolite structure. Mol Simul 1:207–224

    Article  Google Scholar 

  13. Shannon MD, Casci JL, Cox PA, Andrews SJ (1991) Structure of the two-dimensional medium-pore high-silica zeolite NU-87. Nature 353:417–420

    Article  CAS  Google Scholar 

  14. Kiselev AV, Lopatkin AA, Shulga AA (1985) Molecular statistical calculation of gas adsorption by silicalite. Zeolites 5:261–267

    Article  CAS  Google Scholar 

  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 20:1–47

    Article  Google Scholar 

  16. Tildesley DJ (1993) The molecular dynamics method. In: Allen MP, Tildesley DJ (eds) Computer simulation in chemical physics, NATO ASI series 397, pp 23–47

    Google Scholar 

  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 92:2065–2073

    Article  CAS  Google Scholar 

  18. Ramachandran KI, Deepa G, Namboori K (2008) Computational chemistry and molecular modelling. Springer-Verlag, Berlin

    Google Scholar 

  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 372:20130270

    Article  Google Scholar 

  20. Thiel W (2014) Semiempirical quantum-chemical methods. WIREs Comput Mol Sci 4:145–157

    Article  CAS  Google Scholar 

  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 2355–2360

    Google Scholar 

  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 524:74–78

    Article  CAS  Google Scholar 

  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 103:7175–7183

    Article  CAS  Google Scholar 

  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 122:263–273

    Article  CAS  Google Scholar 

  25. Lewis DW, Freeman CM, Catlow CRA (1995) Predicting the templating ability of organic additives for the synthesis of microporous materials. J Phys Chem 99:11194–11202

    Article  CAS  Google Scholar 

  26. Shen V, Bell AT (1996) Computer simulation of the interactions of tetraalkylammonium cations with ZSM-5 and ZSM-11. Microporous Mater 7:187–199

    Article  CAS  Google Scholar 

  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 146:82–87

    Article  CAS  Google Scholar 

  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 203:91–99

    Article  Google Scholar 

  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 106:701–708

    Article  CAS  Google Scholar 

  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 46:2073–2075

    Article  Google Scholar 

  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 25:3654–3661

    Article  CAS  Google Scholar 

  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 108:8830–8835

    Article  CAS  Google Scholar 

  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 119:7711–7720

    Article  CAS  Google Scholar 

  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 107:5432–5440

    Article  CAS  Google Scholar 

  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 15:1478–1490

    Article  Google Scholar 

  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 33:3470–3472

    Article  Google Scholar 

  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 232:218–226

    Article  CAS  Google Scholar 

  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 28:4998–5012

    Article  CAS  Google Scholar 

  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 431:287–290

    Article  CAS  Google Scholar 

  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 118:3069–3077

    Article  Google Scholar 

  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 112:19547–19554

    Article  CAS  Google Scholar 

  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 114:5101–5106

    Article  CAS  Google Scholar 

  43. Lewis RA (1990) Automated site-directed drug design. J Comput Aided Mol Des 4:205

    Article  CAS  Google Scholar 

  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 48:2457

    Article  Google Scholar 

  45. Pegg SCH, Haresco JJ, Kuntz ID (2001) A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des 15:911–933

    Article  CAS  Google Scholar 

  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 382:604–606

    Article  CAS  Google Scholar 

  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 36:2675–2677

    Article  CAS  Google Scholar 

  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 17:2001–2002

    Article  Google Scholar 

  49. Pophale R, Daeyaert F, Deem MW (2013) Computational prediction of chemically synthesizable organic structure directing agents for zeolites. J Mater Chem A 1:6750–6760

    Article  CAS  Google Scholar 

  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 26:7099–7105

    Article  CAS  Google Scholar 

  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 53:8372–8374

    Article  CAS  Google Scholar 

  52. Schmidt JE, Deem MW, Lew C, Davis TM (2015) Computationally-guided synthesis of the 8-ring zeolite AEI. Top Catal 58:410–415

    Article  CAS  Google Scholar 

  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 28:708–711

    Article  CAS  Google Scholar 

  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 52:1757–1768

    Article  CAS  Google Scholar 

  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 7:1884–1189

    Article  CAS  Google Scholar 

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Correspondence to Paul A. Cox .

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Turrina, A., Cox, P.A. (2017). Molecular Modelling of Structure Direction Phenomena. In: Gómez-Hortigüela, L. (eds) Insights into the Chemistry of Organic Structure-Directing Agents in the Synthesis of Zeolitic Materials. Structure and Bonding, vol 175. Springer, Cham. https://doi.org/10.1007/430_2017_16

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