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Substituent effects on the properties of the hemi-bonded complexes (XH2P···NH2Y)+ (X, Y=H, F, Cl, Br, NH2, CH3, OH)

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Abstract

Ab initio calculations have been performed to study the structures, binding energies, and bonding properties of the hemi-bonded binary complexes (XH2P···NH2Y)+ with the substituents X and Y being H, F, Cl, Br, NH2, CH3, and OH. The P···N interactions in these open-shelled systems have typical pnicogen bond characteristics but much stronger than the usual pnicogen bonds in closed-shell systems. This P···N bond can be strengthened by an electron-withdrawing substituent X or an electron-donating substituent Y, the bonding energy varies from 17 kcal mol-1 of (CH3H2P···NH2F)+ to 54 kcal mol-1 of (FH2P···NH2CH3)+. A nearly linear X-P···N arrangement is required by the pnicogen bond P···N and results in a strong hyperconjugation and charge transfer from the N lone pair to the X-P σ* antibond orbital for α spin, the P···N interaction is described as a single-electron σ bond of β spin. The AIM and NBO analyses revealed that the P···N bonds in the majority of the hemi-bonded complexes are partly covalent in nature.

The P···N interactions in the open-shelled systems (XH2P···NH2Y)+ (X, Y=H, F, Cl, Br, NH2, CH3, OH) with bonding energy of 17~54 kcal mol-1 have typical pnicogen bond characteristics but much stronger than the usual pnicogen bonds in closed-shell systems. This P···N bond can be strengthened by an electron-withdrawing substituent X or an electron-donating substituent Y

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References

  1. Hobza P, Zahradník R (1980) Weak intermolecular interactions in chemistry and biology, vol 200. Elsevier, Amsterdam

  2. Kaplan G (1986) Theory of molecular interactions. Elsevier, Amsterdam

    Google Scholar 

  3. Hobza P, Zahradnik R (1988) Intermolecular complexes. Elsevier, Amsterdam

    Google Scholar 

  4. Müller-Dethlefs K, Hobza P (2000) Noncovalent interactions: a challenge for experiment and theory. Chem Rev 100:143–168

    Article  Google Scholar 

  5. Stone AJ (2002) The theory of intermolecular forces. Oxford University Press, Oxford

    Google Scholar 

  6. Hobza P, Zahradník R, Müller-Dethlefs K (2006) The world of noncovalent interactions. Collect Czechoslov Chem Commun 71:443–531

    Article  CAS  Google Scholar 

  7. Hobza P, Müller-Dethlefs K (2010) Non-covalent interactions: theory and experiment. Royal Society of Chemistry, Cambridge

    Google Scholar 

  8. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment. J Am Chem Soc 122(17):4117–4128

    Article  CAS  Google Scholar 

  9. Li AY (2007) Chemical origin of blue-shifted and red-shifted H-bonds: intramolecular hyperconjugation and its coupling with intermolecular hyper-conjugation. J Chem Phys 126:154102–154111

    Article  Google Scholar 

  10. Li AY, Yan XH (2007) Electronic properties of multifurcated bent hydrogen bonds CH3···Y and CH2···Y. Phys Chem Chem Phys 9:6263–6271

    Article  CAS  Google Scholar 

  11. Arunan E, Desiraju GR, Klein RA, Sadlej J, Scheiner S, Alkorta I, Clary DC, Crabtree RH, Dannenberg JJ, Hobza P et al (2011) Definition of the hydrogen bond (IUPAC recommendations 2011). Pure Appl Chem 83:1637–1641

    CAS  Google Scholar 

  12. Metrangolo P, Resnati G (2008) Halogen bonding: fundamentals and applications. Structure and bonding, vol 126. Springer, Berlin

  13. Legon AC (2010) The halogen bond: an interim perspective. Phys Chem Chem Phys 12:7736–7747

    Article  CAS  Google Scholar 

  14. Desiraju GR, Ho PS, Kloo L, Legon AC et al (2013) Definition of the halogen bond (IUPAC recommendations 2013). Pure Appl Chem 85:1711–1713

    Article  CAS  Google Scholar 

  15. Politzer P, Murray JS (2013) Halogen bonding: an interim discussion. Chem Phys Chem 14:278–294

    CAS  Google Scholar 

  16. Nagao Y, Hirata T, Goto S, Sano S, Kakehi A, Iizuka K, Shiro M (1998) Intramolecular nonbonded S···O interaction recognized in (acylimino) thiadiazoline derivatives as angiotensin II receptor antagonists and related compounds. J Am Chem Soc 120:3104–3110

  17. Werz DB, Gleiter R, Rominger F (2002) Nanotube formation favored by chalcogen−chalcogen interactions. J Am Chem Soc 124:10638–10639

    Article  CAS  Google Scholar 

  18. Bleiholder C, Werz DB, Köppel H, Gleiter R (2006) Theoretical investigations on chalcogen−chalcogen interactions: what makes these nonbonded interactions bonding? J Am Chem Soc 128:2666–2674

    Article  CAS  Google Scholar 

  19. Murray JS, Lane P, Clark T, Politzer P (2007) σ-hole bonding: molecules containing group VI atoms. J Mol Model 13:1033–1038

    Article  CAS  Google Scholar 

  20. Adhikari U, Scheiner S (2012) Sensitivity of pnicogen, chalcogen, halogen and H-bonds to angular distortions. Chem Phys Lett 532:31–35

    Article  CAS  Google Scholar 

  21. Wang W, Ji B, Zhang Y (2009) Chalcogen bond: a sister noncovalent bond to halogen bond. J Phys Chem A 113:8132–8135

    Article  Google Scholar 

  22. Manna D, Mugesh G (2012) Regioselective deiodination of thyroxine by iodothyronine deiodinase mimics: an unusual mechanistic pathway involving cooperative chalcogen and halogen bonding. J Am Chem Soc 134:4269–4279

    Article  CAS  Google Scholar 

  23. Murray JS, Lane P, Politzer P (2007) A predicted new type of directional noncovalent interaction. Int J Quantum Chem 107:2286–2292

    Article  CAS  Google Scholar 

  24. Zahn S, Frank R, Hey-Hawkins E, Kirchner B (2011) Pnicogen bonds: a new molecular linker? Chem Eur J 17:6034–6038

    Article  CAS  Google Scholar 

  25. Scheiner S (2011) A new noncovalent force: comparison of P···N interaction with hydrogen and halogen bonds. J Chem Phys 134:094315–094324

    Article  Google Scholar 

  26. Scheiner S (2013) The pnicogen bond: its relation to hydrogen, halogen, and other noncovalent bonds. Acc Chem Res 46:280–288

    Article  CAS  Google Scholar 

  27. Scheiner S (2011) Effects of substituents upon the P···N noncovalent interaction: the limits of its strength. J Phys Chem A 115:11202–11209

    Article  CAS  Google Scholar 

  28. Del Bene JE, Alkorta I, Sanchez-Sanz G, Elguero J (2011) Structures, energies, bonding, and NMR properties of pnicogen complexes H2XP:NXH2 (X = H, CH3, NH2, OH, F, Cl). J Phys Chem A 115:13724–13731

    Article  Google Scholar 

  29. Del Bene JE, Alkorta I, Elguero J (2015) Substituent effects on the properties of pnicogen-bonded complexes H2XP:PYH2, for X, Y = F, Cl, OH, NC, CCH, CH3, CN, and H. J Phys Chem A 119:224–233

    Article  Google Scholar 

  30. Murray JS, Lane P, Politzer P (2009) Expansion of the σ-hole concept. J Mol Model 15:723–729

    Article  CAS  Google Scholar 

  31. Mani D, Arunan E (2013) The X−C···Y (X = O/F, Y = O/S/F/Cl/Br/N/P) ‘carbon bond’ and hydrophobic interactions. Phys Chem Chem Phys 15:14377–14383

    Article  CAS  Google Scholar 

  32. Mani D, Arunan E (2014) The X−C···π (X = F, Cl, Br, CN) carbon bond. J Phys Chem A 118:10081–10089

    Article  CAS  Google Scholar 

  33. Thomas SP, Pavan MS, Row TG (2014) Experimental evidence for ‘carbon bonding’ in the solid state from charge density analysis. Chem Commun (Cambridge, UK) 50:49–51

    Article  CAS  Google Scholar 

  34. Varadwaj PR, Varadwaj A, Jin B (2014) Significant evidence of C···O and C···C long-range contacts in several heterodimeric complexes of CO with CH3−X, should one refer to them as carbon and dicarbon bonds! Phys Chem Chem Phys 16:17238–17252

    Article  CAS  Google Scholar 

  35. Gill PMW, Radom L (1988) Structures and stabilities of singly charged three-electron hemibonded systems and their hydrogen bonded isomers. J Am Chem Soc 110:4931–4941

    Article  CAS  Google Scholar 

  36. Humbel S, Côte I, Hoffmann N, Bouquant J (1999) Three-electron binding between carbonyl-like compounds and ammonia radical cation. Comparison with the hydrogen bonded complex. J Am Chem Soc 121:5507–5512

    Article  CAS  Google Scholar 

  37. Grüning M, Gritsenko OV, van Gisbergen SJA, Baerends EJ (2001) The failure of generalized gradient approximations (GGAs) and meta-GGAs for the two-center three-electron bonds in He2 +, (H2O)2 +, and (NH3)2 +. J Phys Chem A 105(40):9211–9218

    Article  Google Scholar 

  38. Ghanty TK, Ghosh SK (2002) Simple density functional approach to polarizability, hardness, and covalent radius of atomic systems. J Phys Chem A 106(48):11815–11821

    Article  CAS  Google Scholar 

  39. Maity DK (2002) Sigma bonded radical cation complexes: a theoretical study. J Phys Chem A 106(23):5716–5721

    Article  CAS  Google Scholar 

  40. Ghanty TK, Ghosh SK (2002) Hardness and polarizability profiles for intramolecular proton transfer in water dimer radical cation. J Phys Chem A 106(16):4200–4204

    Article  CAS  Google Scholar 

  41. Joshi R, Ghanty TK, Naumov S, Mukherjee T (2007) Structural investigation of asymmetrical dimer radical cation system (H2O−H2S)+: proton-transferred or hemi-bonded? J Phys Chem A 111:2362–2367

    Article  CAS  Google Scholar 

  42. Joshi R, Ghanty TK, Naumov S, Mukherjee T (2007) Ionized state of hydroperoxy radical−water hydrogen-bonded complex: (HO2−H2O)+. J Phys Chem A 111(51):13590–13594

    Article  CAS  Google Scholar 

  43. Lee HM, Kim KS (2009) Water dimer cation: density functional theory vs Ab initio theory. J Chem Theory Comput 5(4):976–981

    Article  CAS  Google Scholar 

  44. Kim Hand Lee HM (2009) Ammonia−water cation and ammonia dimer cation. J Phys Chem A 113(25):6859–6864

    Article  Google Scholar 

  45. Pan PR, Lin YS, Tsai MK, Kuo JL, Chai JD (2012) Assessment of density functional approximations for the hemibonded structure of the water dimer radical cation. Phys Chem Chem Phys 14:10705–10712

    Article  CAS  Google Scholar 

  46. Joshi R, Ghanty TK, Mukherjee T, Naumov S (2012) Hydrogen bonding in neutral and cation dimers of H2Se with H2O, H2S, and H2Se. J Phys Chem A 116(48):11965–11972

    Article  CAS  Google Scholar 

  47. Do Hand Besley NA (2013) Proton transfer or hemibonding? The structure and stability of radical cation clusters. Phys Chem Chem Phys 15(38):16214–16219

    Article  Google Scholar 

  48. Tentscher PR, Arey JS (2013) On the nature of interactions of radicals with polar molecules. J Phys Chem A 117(47):12560–12568

    Article  CAS  Google Scholar 

  49. Ji LF, Li AY, Li ZZ (2015) Structures and stabilities of asymmetrical dimer radical cation systems (AH3–H2O)+ (A=N, P, As). Struct Chem 26:109–119

    Article  CAS  Google Scholar 

  50. Marín-Luna M, Alkorta I, Elguero J (2015) A computational study on [(PH2X)2]·+ homodimers involving intermolecular two-center three-electron bonds. Struct Chem. doi:10.1007/s11224-015-0617-5

    Google Scholar 

  51. Clark T, Hennemann M, Murray JS, Politzer P (2007) Halogen bonding: the σ-hole. J Mol Model 13:291–296

    Article  CAS  Google Scholar 

  52. Mohajeri A, Pakirai AH, Bagheri N (2009) Theoretical studies on the nature of bonding in σ-hole complexes. Chem Phys Lett 467:393–397

    Article  CAS  Google Scholar 

  53. Politzer P, Murray JS, Clark T (2013) Halogen bonding and other σ-hole interactions: a perspective. Phys Chem Chem Phys 15:11178–11189

    Article  CAS  Google Scholar 

  54. Ji LF, Li AY, Li ZZ (2015) Structures and stabilities of hemi-bonded vs proton-transferred isomers of dimer radical cation systems (XH3-YH3)+(X, Y = N, P, As). Chem Phys Lett 619:115–121

    Article  CAS  Google Scholar 

  55. Frisch MJ, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, CaricatoM, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, Jr., Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW,Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, revision A.02. Gaussian, Inc, Wallingford

  56. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566

    Article  CAS  Google Scholar 

  57. Weinhold F, Landis C (2005) Valency and bonding. A natural bond orbital donor–acceptor perspective. Cambridge University Press

  58. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88:899–926

    Article  CAS  Google Scholar 

  59. Glendening ED et al (2001) NBO 5.0. Theoretical Chemistry Institute, University of Wisconsin: Madison

  60. Reed AE, Weinstock RB, Weinhold F (1985) Natural population analysis. J Chem Phys 83:735–746

    Article  CAS  Google Scholar 

  61. Wiberg KB (1968) Tetrahedron 24:1083–1096

    Article  CAS  Google Scholar 

  62. Reed AE, Weinhold F (1985) Natural localized molecular orbitals. J Chem Phys 83:1736–1740

    Article  CAS  Google Scholar 

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

  64. Ziołkowski M, Grabowski SJ, Leszczynski J (2006) Cooperativity in hydrogen-bonded interactions: ab initio and “atoms in molecules” analyses. J Phys Chem A 110(20):6514–6521

    Article  Google Scholar 

  65. Cremer D, Kraka E (1984) Angew Chem Int Ed Engl 23:627–628

    Article  Google Scholar 

  66. Jenkins S, Morrison I (2000) The chemical character of the intermolecular bonds of seven phases of ice as revealed by ab initio calculation of electron densities. Chem Phys Lett 317:97–102

    Article  CAS  Google Scholar 

  67. Keith TA (2011) AIMAll (Versio Version 13.10.19). TK Gristmill software, Overland Park (aim.tkgristmill.com)

  68. Alkorta I, Barrios L, Rozas I, Elguero J (2000) Comparison of models to correlate electron density at the bond critical point and bond distance. J Mol Struct THEOCHEM 496:131–137

    Article  CAS  Google Scholar 

  69. Madzhidov TI, Chmutova GA (2013) The nature of the interaction of dimethylselenide with IIIA group element compounds. J Phys Chem A 117:4011–4024

    Article  CAS  Google Scholar 

  70. Politzer P, Murray JS, Clark T (2015) Mathematical modeling and physical reality in noncovalent interactions. J Mol Model 21:52

    Article  Google Scholar 

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Ji, L.F., Li, A.Y., Li, Z.Z. et al. Substituent effects on the properties of the hemi-bonded complexes (XH2P···NH2Y)+ (X, Y=H, F, Cl, Br, NH2, CH3, OH). J Mol Model 22, 1 (2016). https://doi.org/10.1007/s00894-015-2876-x

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