Abstract
Mapping of charge densities in molecular crystals has been contemplated ever since it was recognized that X-rays are scattered by the electron density in the crystal. The methodology both from the experimental and theoretical perspective was standardized and applied extensively only during the last few decades, as technological advances were a prerequisite in both data collection and computation. Multipole formalism developed for accurate X-ray diffraction data is routinely utilized in conjunction with the concept of atoms in molecules to obtain quantitative estimates of the topological properties in molecular crystals which allow the evaluation of both bonded and non-bonded contacts. Recently, with the advent of quantum crystallography, combining Hirshfeld atom refinement along with libraries of extremely localized molecular orbitals, HAR–ELMOs, has emerged as an alternate approach. Apart from the weak hydrogen bonds, other highly directional non-bonded contacts like halogen, pnicogen, chalcogen and carbon bonds have been subjected to charge density analysis to experimentally observe and quantify σ-holes using experimental high-resolution X-ray diffraction data. The recognition of lack of directional preferences in hydrophobic interactions is demonstrated experimentally which might have far reaching consequences in the areas of materials and biology.
Similar content being viewed by others
References
Desiraju GR, Vittal JJ, Ramanan A (2012) Crystal engineering: a textbook. World Scientific Publishing Company Incorporated, Singapore
Koritsanszky TS, Coppens P (2001) Chemical applications of X-ray charge-density analysis. Chem Rev 101(6):1583
McKinnon JJ, Spackman MA, Mitchell AS (2004) Novel tools for visualizing and exploring intermolecular interactions in molecular crystals. Acta Crystallogr Sect B 60:627
Krawczuk A, Macchi P (2014) Charge density analysis for crystal engineering. Chem Cent J 8(1):68
Hansen NK, Coppens P (1978) Testing aspherical atom refinements on small-molecule data sets. Acta Crystallogr Sect A 34:909
Koritsanszky T et al (2015) XD2015—a computer program package for multipole refinement, topological analysis of charge densities and evaluation of intermolecular energies from experimental and theoretical structure factors. University at Buffalo, State University of New York, NY, USA
Frisch M et al (2009) Gaussian 09, revision a. 02. Gaussian Inc., Wallingford, CT, p 200
Dovesi R et al (2017) CRYSTAL17 user’s manual. Università di Torino, Torino
Jayatilaka D, Grimwood DJ (2001) Wavefunctions derived from experiment. I. Motivation and theory. Acta Crystallogr Sect A 57(1):76
Capelli SC et al (2014) Hirshfeld atom refinement. IUCr J 1(5):361
Malaspina LA, Wieduwilt EK, Bergmann J, Kleemiss F, Meyer B, Ruiz-López MF, Pal R, Hupf E, Beckmann J, Piltz RO, Edwards AJ, Grabowsky S, Genoni A (2019) Fast and accurate quantum crystallography: from small to large, from light to heavy. J Phys Chem Lett 10:6973
Massa L, Huang L, Karle J (1995) Quantum crystallography and the use of kernel projector matrices. Int J Quantum Chem 56(S29):371
Clinton WL, Galli AJ, Massa LJ (1969) Direct determination of pure-state density matrices. II. construction of constrained idempotent one-body densities. Phys Rev 177(1):7
Tanaka K et al (2008) X-ray atomic orbital analysis. I. Quantum-mechanical and crystallographic framework of the method. Acta Crystallogr Sect A 64(4):437
Coppens P, Guru Row TN, Leung P, Stevens ED, Becker PJ, Yang YW (1979) Net atomic charges and molecular dipole moments from spherical-atom X-ray refinements, and the relation between atomic charge and shape. Acta Crystallogr Sect A 35:63
Bader RFW (1990) Atoms in molecules. Wiley, New York
Desiraju GR (1995) Supramolecular synthons in crystal engineering—a new organic synthesis. Angew Chem Int Ed Engl 34:2311
Desiraju GR (1997) Designer crystals: intermolecular interactions, network structures and supramolecular synthons. Chem Commun 16:1475
Nangia A, Desiraju GR (1998) Design of organic solids. In: Weber E (ed) Perspectives in supramolecular chemistry. Springer, Berlin, pp 57–95
Etter MC (1990) Encoding and decoding hydrogen-bond patterns of organic compounds. Acc Chem Res 23:120
Steiner T (2003) O hydrogen bonding in crystals. Cryst Rev 9(2–3):177
Koch U, Popelier PLA (1995) Characterization of C-H-O hydrogen bonds on the basis of the charge density. J Phys Chem 99:9747
Munshi P, Guru Row TN (2002) Electron density study of 2H-chromene-2-thione. Acta Crystallogr Sect B 58:1011
Mallinson PR, Smith GT, Wilson CC, Grech E, Wozniak KJ (2003) From weak interactions to covalent bonds: a continuum in the complexes of 1,8-Bis(dimethylamino)naphthalene. J Am Chem Soc 125:4259
Munshi P, Guru Row TN (2005) Exploring the lower limit in hydrogen bonds: analysis of weak C-H...O and C-H...pi interactions in substituted coumarins from charge density analysis. J Phys Chem A 109:659
Politzer P, Murray JS, Clark T (2013) Halogen bonding and other σ-hole interactions: a perspective. Phys Chem Chem Phys 15(27):11178
Desiraju GR et al (2013) Definition of the halogen bond (IUPAC Recommendations 2013). Pure Appl Chem 85(8):1711
Williams D, Hsu LY (1985) New analytical scattering-factor functions for free atoms and ions. Acta Crystallogr Sect A 41:296
Nyburg SC, Wong-Ng W (1979) Anisotropic atom–atom forces and the space group of solid chlorine. Proc R Soc Lond A 367:29
Desiraju GR, Parthasarathy R (1989) The nature of halogen.cntdot..cntdot..cntdot.halogen interactions: are short halogen contacts due to specific attractive forces or due to close packing of nonspherical atoms? J Am Chem Soc 111(23):8725
Rosenfield RE Jr, Parthasarathy R, Dunitz JDJ (1977) Directional preferences of nonbonded atomic contacts with divalent sulfur. 1. Electrophiles and nucleophiles. J Am Chem Soc 99(14):4860
Guru Row TN, Parthasarathy R (1981) Directional preferences of nonbonded atomic contacts with divalent sulfur in terms of its orbital orientations. 2. Sulfur.cntdot..cntdot..cntdot.sulfur interactions and nonspherical shape of sulfur in crystals. J Am Chem Soc 103(2):477
Mani D, Arunan E (2013) The X-CY (X = O/F, Y = O/S/F/Cl/Br/N/P)‘carbon bond’ and hydrophobic interactions. Phys Chem Chem Phys 15(34):14377
Desiraju G, Steiner T (1999) The weak hydrogen bond. In Structural Chemistry and Biology. Oxford University Press, Oxford
Volkov A, Koritsanszky 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 electron densities. Chem Phys Lett 391:170
Thomas SP, Pavan MS, Guru Row TN (2012) Experimental evidence for ‘carbon bonding’ in the solid state from charge density analysis. Cryst Growth Des 12:6083
Thalladi VR, Weiss H-C, Bläser D, Boese R, Nangia A, Desiraju GR (1998) C−H···F Interactions in the crystal structures of some fluorobenzenes. J Am Chem Soc 120:8702
Metrangolo P, Murray JS, Pilati T, Politzer P, Resnati G, Terraneo G (2011) Fluorine-centered halogen bonding: a factor in recognition phenomena and reactivity. Cryst Growth Des 11:4238
Hathwar VR, Guru Row T (2011) Charge density analysis of heterohalogen (Cl···F) and homohalogen (F···F) intermolecular interactions in molecular crystals: importance of the extent of polarizability. Cryst Growth Des 11:1338
Pavan MS, Prasad KD, Guru Row TN (2013) Halogen bonding in fluorine: experimental charge density study on intermolecular F⋯F and F⋯S donor–acceptor contacts. Chem Commun 49:7558
Thomas SP, Jayatilaka D, Guru Row TN (2015) S⋯O chalcogen bonding in sulfa drugs: insights from multipole charge density and X-ray wavefunction of acetazolamide. Phys Chem Chem Phys 17:25411
Sarkar S, Pavan MS, Guru Row TN (2015) Experimental validation of ‘pnicogen bonding’ in nitrogen by charge density analysis. Phys Chem Chem Phys 17:2330
Thomas SP, Nagarajan K, Guru Row TN (2012) Polymorphism and tautomeric preference in fenobam and the utility of NLO response to detect polymorphic impurities. Chem Commun 48:10559
Bundhun A, Ramasami P, Murray J, Politzer P (2013) Trends in σ-hole strengths and interactions of F3MX molecules (M = C, Si, Ge and X = F, Cl, Br, I). J Mol Model 19:2739
Thomas SP, Pavan MS, Guru Row TN (2014) Experimental evidence for ‘carbon bonding’ in the solid state from charge density analysis. Chem Commun 50:49
Sarkar S, Thomas SP, Lokeswara Rao P, Edwards AJ, Grosjean A, Ramanathan KV, Guru Row TN (2019) Experimental insights into the electronic nature, spectral features, and role of entropy in short CH3···CH3 hydrophobic interactions. J Phys Chem Lett 10(22):7224
Acknowledgements
The work reported in this review was mainly carried out by my students and post-doctoral associates in my group. I should specifically acknowledge the contributions from Drs. Parthapratim Munshi, Venkatesha Hathwar, Sajesh P. Thomas, Mysore S. Pavan, Sounak Sarkar who essentially contributed to the contents of this article. I would like to thank Indian Institute of Science and DST, India for the funding to procure the X-ray facility. I also acknowledge the funding provided under the J.C. Bose fellowship by DST, India.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Row, T.N.G. Unraveling the Nature of Weak Hydrogen Bonds and Intermolecular Interactions Involving Elements of Group 14–17 via Experimental Charge Density Analysis. J Indian Inst Sci 100, 203–220 (2020). https://doi.org/10.1007/s41745-019-00148-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s41745-019-00148-2