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Modern Charge-Density Analysis pp 553–572Cite as

Charge Densities and Crystal Engineering

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Abstract

This chapter discusses the ways in which the present techniques and tools of charge density analysis can contribute to the burgeoning field of crystal engineering. The principal focus is on use of theoretical and experimental charge densities, Hirshfeld surface analysis, as well as the calculation of energies of intermolecular interactions and their application to halogen bonded systems.

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References

  1. Desiraju GR (ed) (1989) Crystal engineering: the design of organic solids. Elsevier, Amsterdam

    Google Scholar 

  2. Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford University Press, Oxford

    Google Scholar 

  3. Matta CF, Boyd RJ (eds) (2007) The quantum theory of atoms in molecules. From solid state to DNA and drug design. Wiley-VCH, Weinheim

    Google Scholar 

  4. Gatti C (2007) Solid state applications of QTAIM and the source function: molecular crystals, surfaces, host-guest systems and molecular complexes. In: Matta CF, Boyd RJ (eds) The quantum theory of atoms in molecules. From solid state to DNA and drug design. Wiley-VCH, Weinheim, pp 165–206

    Google Scholar 

  5. Dunitz JD, Gavezzotti A (2005) Molecular recognition in organic crystals: directed intermolecular bonds or Nonlocalized bonding? Angew Chem Int Ed 44:1766–1787

    Article  CAS  Google Scholar 

  6. Seddon KR (1999) Crystal engineering. A case study. In: Seddon KR, Zaworotko M (eds) Crystal engineering. The design and application of functional solids. Kluwer, Amsterdam, pp 1–28

    Google Scholar 

  7. Koritsánszky T, Mallinson P, Macchi P, Volkov A, Gatti C, Richter T, Farrugia L (2007) XD2006. A computer program package for multipole refinement, topological analysis of charge densities and evaluation of intermolecular energies from experimental or theoretical structure factors. http://xd.chem.buffalo.edu/

  8. Dunitz JD, Gavezzotti A (2005) Toward a quantitative description of crystal packing in terms of molecular pairs: application to the hexamorphic crystal system, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile. Cryst Growth Des 5:2180–2189

    Article  CAS  Google Scholar 

  9. Gavezzotti A (2005) Calculation of lattice energies of organic crystals: the PIXEL integration method in comparison with more traditional methods. Z Kristallogr 220:499–510

    Article  CAS  Google Scholar 

  10. Novoa JJ, D’Oria E (2008) From bonds to packing: an energy-based crystal packing analysis for molecular crystals. In: Novoa JJ, Braga D, Addadi L (eds) Engineering of crystalline materials properties. State of the Art in modeling, design and applications. Springer, Dordrecht, pp 307–332

    Chapter  Google Scholar 

  11. Day GM, Cooper TG, Cruz-Cabeza AJ, Hejczyk KE, Ammon HL, Boerrigter SXM, Tan JS, Della Valle RG, Venuti E, Jose J, Gadre SR, Desiraju GR, Thakur TS, van Eijck BP, Facelli JC, Bazterra VE, Ferraro MB, Hofmann DWM, Neumann M, Leusen F, Kendrick J, Price SL, Misquitta AJ, Karamertzanis PG, Welch GWA, Scheraga HA, Arnautova YA, Schmidt MU, van de Streek J, Wolf AK, Schweizer B (2009) Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test. Acta Crystallogr B 65:107–125

    Article  Google Scholar 

  12. Neumann MA, Leusen FJJ, Kendrick J (2008) A major advance in crystal structure prediction. Angew Chem Int Ed 47:2427–2430

    Article  CAS  Google Scholar 

  13. Gavezzotti A (2002) Calculation of intermolecular interaction energies by direct numerical integration over electron densities. 1. Electrostatic and polarization energies in molecular crystals. J Phys Chem B 106:4145–4154

    Article  CAS  Google Scholar 

  14. Gavezzotti A (2003) Calculation of intermolecular interaction energies by direct numerical integration over electron densities. 2. An improved polarization model and the evaluation of dispersion and repulsion energies. J Phys Chem B 107:2344–2353

    Article  CAS  Google Scholar 

  15. Gavezzotti A (2003) Towards a realistic model for the quantitative evaluation of intermolecular potentials and for the rationalization of organic crystal structures. Part I. Philosophy. CrystEngComm 5:429–438

    Article  CAS  Google Scholar 

  16. Gavezzotti A (2003) Towards a realistic model for the quantitative evaluation of intermolecular potentials and for the rationalization of organic crystal structures. Part II. Crystal energy landscapes. CrystEngComm 5:439–446

    Article  CAS  Google Scholar 

  17. Volkov A, King HF, Coppens P (2006) Dependence of the intermolecular electrostatic interaction energy on the level of theory and the basis set. J Chem Theory Comput 2:81–89

    Article  CAS  Google Scholar 

  18. Berkovitch-Yellin Z, Leiserowitz L (1980) The role of coulomb forces in the crystal packing of amides. A study based on experimental electron densities. J Am Chem Soc 102:7677–7690

    Article  CAS  Google Scholar 

  19. Berkovitch-Yellin Z, Leiserowitz L (1982) Atom-atom potential analysis of the packing characteristics of carboxylic acids. A study based on experimental electron density distributions. J Am Chem Soc 104:4052–4064

    Article  CAS  Google Scholar 

  20. Spackman MA, Weber H-P, Craven BM (1988) Energies of molecular interactions from Bragg diffraction data. J Am Chem Soc 110:775–782

    Article  CAS  Google Scholar 

  21. Volkov A, Koritsansky T, Coppens P (2004) Combination of the exact potential and multipole methods (EP/MM) for evaluation of intermolecular electrostatic interaction energies with pseudoatom representation of molecular densities. Chem Phys Lett 391:170–175

    Article  CAS  Google Scholar 

  22. Barzaghi M (2006) PAMOC: properties of atoms in molecules and molecular crystals. http://www.istm.cnr.it/~barz/pamoc/

  23. Stewart RF, Spackman MA, Flensburg C (2000) VALRAY – User’s manual. 2.1 edn. Carnegie Mellon University & University of Copenhagen

    Google Scholar 

  24. Spackman MA (2006) The use of the promolecular charge density to approximate the penetration contribution to intermolecular electrostatic energies. Chem Phys Lett 418:158–162

    Article  CAS  Google Scholar 

  25. Spackman MA, Byrom PG (1997) A novel definition of a molecule in a crystal. Chem Phys Lett 267:215–220

    Article  CAS  Google Scholar 

  26. Whitten AE, Radford CJ, McKinnon JJ, Spackman MA (2006) Dipole and quadrupole moments of molecules in crystals: a novel approach based on integration over Hirshfeld surfaces. J Chem Phys 124:074106

    Article  Google Scholar 

  27. McKinnon JJ, Spackman MA, Mitchell AS (2004) Novel tools for visualizing and exploring intermolecular interactions in molecular crystals. Acta Crystallogr B 60:627–668

    Article  Google Scholar 

  28. Spackman MA, McKinnon JJ (2002) Fingerprinting intermolecular interactions in molecular crystals. CrystEngComm 4:378–392

    Article  CAS  Google Scholar 

  29. McKinnon JJ,~Jayatilaka D, Spackman MA (2007) Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chem Commun 3814–3816

    Google Scholar 

  30. Spackman MA, Jayatilaka D (2009) Hirshfeld surface analysis. CrystEngComm 11:19–32

    Article  CAS  Google Scholar 

  31. Wolff SK, Grimwood DJ, McKinnon JJ, Jayatilaka D, Spackman MA (2008) CrystalExplorer 2.1. http://hirshfeldsurface.net/CrystalExplorer

  32. Spackman MA, McKinnon JJ, Jayatilaka D (2008) Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm 10:377–388

    CAS  Google Scholar 

  33. Metrangolo P, Meyer F, Pilati T, Resnati G, Terraneo G (2008) Halogen bonding in supramolecular chemistry. Angew Chem Int Ed 47:6114–6127

    Article  CAS  Google Scholar 

  34. Metrangolo P, Neukirch H, Pilati T, Resnati G (2005) Halogen bonding based recognition processes: a world parallel to hydrogen bonding. Acc Chem Res 38:386–395

    Article  CAS  Google Scholar 

  35. Metrangolo P, Resnati G, Pilati T, Biella S (2008) Halogen bonding in crystal engineering. Struct Bond 126:105–136

    Article  CAS  Google Scholar 

  36. Bianchi R, Forni A, Pilati T (2003) The experimental electron density distribution in the complex of (E)-1,2-bis(4-pyridyl) ethylene with 1,4-diiodotetrafluorobenzene at 90 K. Chem Eur J 9:1631–1638

    Article  CAS  Google Scholar 

  37. Bianchi R, Forni A, Pilati T (2004) Experimental electron density study of the supramolecular aggregation between 4,4′-dipyridyl-N, N′-dioxide and 1,4-diiodotetrafluorobenzene at 90 K. Acta Crystallogr B 60:559–568

    Article  Google Scholar 

  38. Forni A (2009) Experimental and theoretical study of the Br···N halogen bond in complexes of 1, 4-dibromotetrafluorobenzene with dipyridyl derivatives. J Phys Chem A 113:3403–3412

    Article  CAS  Google Scholar 

  39. Bui TTT, Dahaoui S, Lecomte C, Desiraju GR, Espinosa E (2009) The nature of halogen…halogen interactions: a model derived from experimental charge-density analysis. Angew Chem Int Ed 48:3838–3841

    Article  CAS  Google Scholar 

  40. Bianchi R, Forni A (2005) VALTOPO: a program for the determination of atomic and molecular properties from experimental electron densities. J Appl Crystallogr 38:232–236

    Article  Google Scholar 

  41. Koritsanszky TS, Coppens P (2001) Chemical applications of X-ray charge-density analysis. Chem Rev 101:1583–1627

    Article  CAS  Google Scholar 

  42. Bader RFW, MacDougall PJ (1985) Toward a theory of chemical reactivity based on the charge density. J Am Chem Soc 107:6788–6795

    Article  CAS  Google Scholar 

  43. Sagar RP, Ku ACT, Smith VH, Simas AM (1988) The Laplacian of the charge density and its relationship to the shell structure of atoms and ions. J Chem Phys 88:4367–4374

    Article  CAS  Google Scholar 

  44. Shi Z, Boyd RJ (1988) The shell structure of atoms and the Laplacian of the charge density. J Chem Phys 88:4375–4377

    Article  CAS  Google Scholar 

  45. Espinosa E, Molins D, Lecomte C (1998) Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chem Phys Lett 285:170–173

    Article  CAS  Google Scholar 

  46. Espinosa E, Alkorta I, Elguero J, Molins E (2002) From weak to strong interactions: a comprehensive analysis of the topological and energetic properties of the electron density distribution involving X-H center dot center dot center dot F-Y systems. J Chem Phys 117:5529–5542

    Article  CAS  Google Scholar 

  47. Gatti C, May E, Destro R, Cargnoni F (2002) Fundamental properties and nature of CH··O interactions in crystals on the basis of experimental and theoretical charge densities. The case of 3,4-Bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) crystal. J Phys Chem A 106:2707–2720

    Article  CAS  Google Scholar 

  48. Gatti C (2005) Chemical bonding in crystals: new directions. Z Kristallogr 220:399–457

    Article  CAS  Google Scholar 

  49. Alkorta I, Blanco F, Solimannejad M, Elguero J (2008) Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases. J Phys Chem A 112:10856–10863

    Article  CAS  Google Scholar 

  50. Lu YX, Zou JW, Wang YH, Jiang YJ, Yu QS (2007) Ab initio investigation of the complexes between bromobenzene and several electron donors: some insights into the magnitude and nature of halogen bonding interactions. J Phys Chem A 111:10781–10788

    Article  CAS  Google Scholar 

  51. Gavezzotti A (2008) Non-conventional bonding between organic molecules. The ‘halogen bond’ in crystalline systems. Mol Phys 106:1473–1485

    Article  CAS  Google Scholar 

  52. Spackman MA (1999) Hydrogen bond energetics from topological analysis of experimental electron densities: recognising the importance of the promolecule. Chem Phys Lett 301:425–429

    Article  CAS  Google Scholar 

  53. Price SL, Stone AJ, Lucas J, Rowland RS, Thornley AE (1994) The nature of -Cl…Cl- intermolecular interactions. J Am Chem Soc 116:4910–4918

    Article  CAS  Google Scholar 

  54. Saha BK, Nangia A, Jaskólski M (2005) Crystal engineering with hydrogen bonds and halogen bonds. CrystEngComm 7:355–358

    Article  CAS  Google Scholar 

  55. Bujak M, Dziubek K, Katrusiak A (2007) Halogen…halogen interactions in pressure-frozen ortho- and meta-dichlorobenzene isomers. Acta Crystallogr B 63:124–131

    Article  Google Scholar 

  56. Dunitz JD, Gavezzotti A (2002) Electrostatic energies in the 1,4-dichlorobenzene polymorph crystals: the role of charge density overlap effects in crystal packing analysis. Helv Chim Acta 85:3949–3964

    Article  CAS  Google Scholar 

  57. Suponitsky KY, Tsirelson VG, Feil D (1999) Electron density based calculations of intermolecular energy: case of urea. Acta Crystallogr A 55:821–827

    Article  Google Scholar 

  58. Wood PA, Haynes DA, Lennie AR, Motherwell WDS, Parsons S, Pidcock E, Warren JE (2008) The anisotropic compression of the crystal structure of 3-aza-bicyclo(3.3.1)nonane-2,4-dione to 7.1 GPa. Cryst Growth Des 8:549–558

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. School of Biomedical, Biomolecular & Chemical Sciences, University of Western Australia, Crawley, WA, 6009, Australia

    Mark A. Spackman

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  1. Mark A. Spackman
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Correspondence to Mark A. Spackman .

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Editors and Affiliations

  1. Istit. di Scienze e Tecn. Molec. del CNR, c/o Dipt di Chim. Fis. ed Elettrochim., CNR-ISTM, Via Golgi 19, Milano, 20133, Italy

    Carlo Gatti

  2. , Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, 3012, Switzerland

    Piero Macchi

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Spackman, M.A. (2011). Charge Densities and Crystal Engineering. In: Gatti, C., Macchi, P. (eds) Modern Charge-Density Analysis. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3836-4_16

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