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First-Principles Modeling of Non-covalent Interactions in Molecular Systems and Extended Materials

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Practical Aspects of Computational Chemistry V

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Abstract

The intermolecular non-covalent interactions through van der Waals or dispersion forces are pervasive in nature and play a fundamental role in regulating the structure and function of molecular systems ranging from solid state materials to biological systems. The atomistic modeling of non-covalent interactions is incredibly difficult, as they often require exact treatment of long-range electron correlation which in turn demand to go beyond second-order perturbation theory. As for example, the prediction of induction that stems from the response of a molecular system to a permanent multipole necessitate the precise evaluation of molecular polarizabilities. The computation of dispersion interaction also appears to be a formidable task as they involve Coulomb interaction between the instantaneous correlated fluctuations of electrons. Therefore, a systematic and unified theoretical framework for isolating non-covalent interactions is essentially required to reliably model the structure, energetics, and reactivities of realistic molecular systems. In this review, the fundamental theoretical principles and computational aspects for the estimation of strong and weak non-covalent interactions are discussed by emphasizing studies of classic examples such as hydrogen bonding and related properties of small water clusters, halide-water clusters, fatty acid dimers and their amides; several gas-phase and dihydrated cation-π complexes comprising benzene, p-methylphenol, and 3-methylindole as the π-donor systems and Mg2+, Ca2+, and NH4 + cations as the acceptor units; the π-π interactions between benzene and monosubstituted benzenes in parallel face-to-face stacking configuration, as well as the supramolecular complexes. A comprehensive picture of the accuracy of the most widely used first-principles approaches including dispersion-corrected density functional approximations, second order Møller-Plesset and symmetry-adapted perturbation theory, as well as non-canonical coupled cluster theory in predicting van der Waals and dispersion interactions has also been presented. The discussion culminates through the conceptual and mathematical ingredients required to establish structure-property relationships e.g., the correlation between hydrogen-boning and the vibrational modes, impact of electrostatic interactions on charge transfer to solvents, and the relation between Hammett substituent constants and the dispersion interactions in extended π-systems.

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References

  1. Pauling L (1931) The nature of the chemical bond. Application of results obtained from quantum mechanics and from theory of paramagnetic susceptibility to the structure of molecules. J Am Chem Soc 53:1367–1400

    Article  CAS  Google Scholar 

  2. Coulson CA (1953) Valence. Clarendon, Oxford

    Google Scholar 

  3. Szabo A, Ostlund NS (1989) Modern quantum chemistry, introduction to advanced electronic structure theory. Dover, New York

    Google Scholar 

  4. Roothaan CCJ (1951) New developments in the molecular orbital theory. Rev Mod Phys 23:69–89

    Article  CAS  Google Scholar 

  5. Møller C, Plesset MS (1934) Note on an approximation treatment for many-electron systems. Phys Rev 46:618–1622

    Article  Google Scholar 

  6. Foresman JB, Frisch AE (2015) Exploring chemistry with electronic structure methods.3rd edn. Gaussian, Wallingford, CT

    Google Scholar 

  7. Hehre WJ, Radom L, Schleyer PvR, Pople JA (1986) Ab initio molecular orbital theory. Wiley-Interscience, New York

    Google Scholar 

  8. Helgaker T, Jørgensen P, Olsen J (2000) Molecular electronic-structure theory. Wiley, Chichester

    Book  Google Scholar 

  9. Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136:B864–B871

    Article  Google Scholar 

  10. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133–A1138

    Article  Google Scholar 

  11. Stratmann RE, Scuseria GE, Frisch MJ (1998) An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. J Chem Phys 109:8218–8244

    Article  CAS  Google Scholar 

  12. Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with C-PCM solvation model. J Comput Chem 24:669–681

    Article  CAS  PubMed  Google Scholar 

  13. Kier LB, Aldrich HSA (1974) Theoretical study of receptor site models for trimethylammonium group interaction. J Theor Biol 46:529–541

    Article  CAS  PubMed  Google Scholar 

  14. Höltje H-D, Kier LB (1975) Nature of anionic or α-site of cholinesterase. J Pharm Sci 64:418–420

    Article  PubMed  Google Scholar 

  15. Dougherty DA (1996) Cation-p interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science 271:163–168

    Article  CAS  PubMed  Google Scholar 

  16. Ma JC, Dougherty DA (1997) The cation–π interactions. Chem Rev 97:1303–1324

    Article  CAS  PubMed  Google Scholar 

  17. Minuox H, Chipot C (1999) Cation-π interactions in proteins: can simple models provide an accurate description? J Am Chem Soc 121:10366–10372

    Article  CAS  Google Scholar 

  18. Kim KS, Tarakeswar P, Lee JY (2000) Molecular clusters of π-systems: theoretical studies of structures, spectra, and origin of interaction energies. Chem Rev 100:4145–4186

    Article  CAS  PubMed  Google Scholar 

  19. Dougherty DA, Stauffer DA (1990) Acetylcholine binding by a synthetic receptor: implications for biological recognition. Science 250:1558–1560

    Article  CAS  PubMed  Google Scholar 

  20. Kumpf RA, Dougherty DA (1993) A mechanism for ion selectivity in potassium channels: computational studies of cation–π interactions. Science 261:1708–1710

    Article  CAS  PubMed  Google Scholar 

  21. Gallivan JP, Dougherty DA (1999) Cation–π interactions in structural biology. Proc Natl Acad Sci USA 96:9459–9461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Xue Z, Suhm MA (2009) Probing the stiffness of the simplest double hydrogen bond: the symmetric hydrogen bond modes of jet-cooled formic acid dimer. J Chem Phys 131:054301-1–054301-4

    Google Scholar 

  23. Blandamer MJ, Fox MF (1970) Theory and applications of charge-transfer-to-solvent spectra. Chem Rev 70:59–93

    Article  CAS  Google Scholar 

  24. Wheeler SE, Houk KN (2008) Substituent effects in the benzene dimer are due to direct interactions of the substituents with the unsubstituted benzene. J Am Chem Soc 130:10854–10855

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chen X, Chen B (2015) Macroscopic and spectroscopic investigations of the adsorption of nitroaromatic compounds on graphene oxide, reduced graphene oxide, and graphene nanosheets. Environ Sci Technol 49:6181–6189

    Article  CAS  PubMed  Google Scholar 

  26. Zhao N, Yang M, Zhao Q, Gao W, Xie T, Bai H (2017) Superstretchable nacre-mimetic graphene/poly(vinyl alcohol) composite film based on interfacial architectural engineering. ACS Nano 11:4777–4748

    Article  CAS  PubMed  Google Scholar 

  27. Schöllkopf W, Toennies JP (1996) The nondestructive detection of the helium dimer and trimer. J Chem Phys R E 1155–1158

    Google Scholar 

  28. Grisenti RE, Schöllkopf W, Toennies JP (2000) Determination of the bond length and binding energy of the helium dimer by diffraction from a transmission grating. Phys Rev Lett 85:2284–2287

    Article  CAS  PubMed  Google Scholar 

  29. Roy D, Marionski M, Maitra NT, Dannenberg JJ (2012) Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error. J Chem Phys 137:134109-1–134109-12

    Google Scholar 

  30. Rigby M, Smith EB, Wakeham WA, Maitland GC (1986) The forces between molecules. Clarendon, Oxford

    Google Scholar 

  31. Standard JM, Certain PR (1985) Bounds to two- and three-body long-range interaction coefficients for S-state atoms. J Chem Phys 83:3002–3008

    Article  CAS  Google Scholar 

  32. Lennard-Jones JE (1924) On the determination of molecular fields. —II. From the equation of state of a gas. Proc R Soc Lond Ser A 106:463–477

    Article  Google Scholar 

  33. Hill TL (1948) Steric effects. I. Van der Waals potential energy curves. J Chem Phys 16:399–404

    Article  CAS  Google Scholar 

  34. Vedani A (1988) YETI: an interactive molecular mechanics program for small-molecule protein complexes. J Comp Chem 9:269–280

    Article  CAS  Google Scholar 

  35. Tang KT, Toennies JP (2003) The van der Waals potentials between all the rare gas atoms from He to Rn. J Chem Phys 118:4976

    Article  CAS  Google Scholar 

  36. Tang KT, Toennies JP (1984) An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients. J Chem Phys 80:3726–3741

    Article  CAS  Google Scholar 

  37. Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799

    Article  CAS  PubMed  Google Scholar 

  38. Grimme S, Antony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104-1–154104-18

    Google Scholar 

  39. Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456–1465

    Article  CAS  PubMed  Google Scholar 

  40. Xantheas SS (1994) Ab initio studies of cyclic water clusters (H2O)n, n=1-6. II. Analysis of many-body interactions. J Chem Phys 100:7523–7534

    Article  CAS  Google Scholar 

  41. Becke AD, Johnson ER (2005) A density-functional model of the dispersion interaction. J Chem Phys 122:154101-1–154101-9

    Google Scholar 

  42. Koide A (1976) A new expansion for dispersion forces and its application. J Phys B 9:3173–3183

    Article  CAS  Google Scholar 

  43. Gora RW, Barkowiak W, Roszak S, Leszczynski J (2002) A new theoretical insight into the nature of intermolecular interactions in the molecular crystal of urea. J Chem Phys 117:1031–1039

    Article  CAS  Google Scholar 

  44. Gora RW, Sokalski WA, Leszczynski J, Pett VB (2005) The nature of interactions in the ionic crystal of 3-pentenenitrile, 2-nitro-5-oxo, ion (−1) sodium. J Phys Chem B 109:2027–2033

    Article  CAS  PubMed  Google Scholar 

  45. Jeziorski B, Moszynski R, Szalewicz K (1994) Perturbation theory approach to intermolecular potential energy surfaces of van der Waals complexes. Chem Rev 94:1887–1930

    Article  CAS  Google Scholar 

  46. Heßelmann A (2018) DFT-SAPT intermolecular interaction energies employing exact-exchange Kohn–Sham response methods. J Chem Theor Comput 14:1943–1959

    Article  CAS  Google Scholar 

  47. Gutowski M, Piela L (1988) Interpretation of the Hartree-Fock interaction energy between closed-shell systems. Mol Phys 64:337–355

    Article  CAS  Google Scholar 

  48. Larson JW, McMahon TB (1984) Gas-phase bihalide and pseudobihalide ions. An ion cyclotron resonance determination of hydrogen bond energies in XHY- species (X, Y = F, Cl, Br, CN). Inorg Chem 23:2029–2033

    Google Scholar 

  49. Desiraju GR, Steiner T (1999) The weak hydrogen bond: In structural chemistry and biology. International Union of Crystallography, Monographs on crystallography, 9. Oxford University Press, Oxford and New York

    Google Scholar 

  50. Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1:337–341

    Article  CAS  PubMed  Google Scholar 

  51. Varadwaj PR, Varadwaj A, Marques HM, Yamashita K (2019) Significance of hydrogen bonding and other non-covalent interactions in determining octahedral tilting in the CH3NH3PbI3 hybrid organic-inorganic halide perovskite solar cell semiconductor. Sci Rep 9:1–29

    Google Scholar 

  52. Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010) Revealing non-covalent interactions. J Am Chem Soc 132:6498–6506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Kuo S-W (2018) Hydrogen bonding in polymer materials. Wiley-VCH, Weinheim

    Book  Google Scholar 

  54. Pugliano N, Saykally RJ (1992) Measurement of quantum tunneling between chiral isomers of the cyclic water trimer. Science 257:1937–1940

    Article  CAS  PubMed  Google Scholar 

  55. Cruzan JD, Braly LB, Liu K, Brown MG, Loeser JG, Saykally RJ (1996) Quantifying hydrogen bond cooperativity in water: VRT spectroscopy of the water tetramer. Science 271:59–62

    Article  CAS  PubMed  Google Scholar 

  56. Liu K, Brown MG, Cruzan JD, Saykally RJ (1996) Vibration-rotation tunneling spectra of the water pentamer: structure and dynamics. Science 271:62–64

    Article  CAS  Google Scholar 

  57. Liu K, Brown MG, Saykally RJ (1997) Terahertz laser vibration–rotation tunneling spectroscopy and dipole moment of a cage form of the water hexamer. J Phys Chem 101:8995–9010

    Article  CAS  Google Scholar 

  58. Vernon MF, Krajnovich DJ, Kwok HS, Lisy JM, Shen YR, Lee YT (1982) Infrared vibrational predissociation spectroscopy of water clusters by the crossed laser-molecular beam technique. J Chem Phys 77:47–57

    Article  CAS  Google Scholar 

  59. Gruenloh CJ, Carney JR, Arrington CA, Zwier TS, Fredricks SY, Jordan KD (1997) Infrared spectrum of a molecular ice cube: the S4 and D2d water octamers in benzene-(water)8. Science 276:1678–1681

    Article  CAS  Google Scholar 

  60. Buck U, Ettischer I, Melzer M, Buch V, Sadlej J (1998) Structure and spectra of three-dimensional (H2O)n clusters, n= 8, 9, 10. Phys Rev Lett 80:2578–2581

    Article  CAS  Google Scholar 

  61. Xantheas SS, Dunning Jr TH (1993) Ab initio studies of cyclic water clusters (H2O)n, n=1–6. I. Optimal structures and vibrational spectra. J Chem Phys 99:8774–8792

    Article  CAS  Google Scholar 

  62. Fowler JE, Schaefer III HF (1995) Detailed study of the water trimer potential energy surface. J Am Chem Soc 117:446–452

    Article  CAS  Google Scholar 

  63. Brudermann J, Melzer M, Buck U, Kazimirski JK, Sadlej J, Buch V (1999) The asymmetric cage structure of (H2O)7 from a combined spectroscopic and computational study. J Chem Phys 110:10649–10652

    Article  CAS  Google Scholar 

  64. Combariza JE, Kestner NR, Jortner J (1994) Energy-structure relationships for microscopic solvation of anions in water clusters. J Chem Phys 100:2851–2864

    Article  Google Scholar 

  65. Kim KS, Mhin BJ, Choi U-S, Lee K (1992) Ab initio studies of the water dimer using large basis sets: the structure and thermodynamic energies. J Chem Phys 97:6649–6662

    Article  CAS  Google Scholar 

  66. Kim J, Kim KS (1998) Structures, binding energies, and spectra of isoenergetic water hexamer clusters: extensive ab initio studies. J Chem Phys 109:5886–5895

    Article  CAS  Google Scholar 

  67. Kim J, Majumdar D, Lee HM, Kim KS (1999) Structures and energetics of the water heptamer: comparison with the water hexamer and octamer. J Chem Phys 110:9128–9134

    Article  CAS  Google Scholar 

  68. Temelso B, Archer KA, Shields GC (2011) Benchmark structures and binding energies of small water clusters with anharmonicity corrections. J Phys Chem A 115:12034–12046

    Article  CAS  PubMed  Google Scholar 

  69. Markovich G, Pollack S, Giniger R, Cheshnovsky O (1991) Photoelectron spectroscopy of iodine anion solvated in water clusters. J Chem Phys 95:9416–9419

    Article  CAS  Google Scholar 

  70. Markovich G, Pollack S, Giniger R, Cheshnovsky O (1994) Photoelectron spectroscopy of CI-, Br-, and 1- solvated in water clusters. J Chem Phys 101:9344–9353

    Article  CAS  Google Scholar 

  71. Combariza JE, Kestner NR, Jortner J (1993) Microscopic solvation of anions in water clusters. Chem Phys Lett 203:423–428

    Article  CAS  Google Scholar 

  72. Baik J, Kim J, Majumdar D, Kim KS (1999) Structures, energetics, and spectra of fluoride–water clusters F–(H2O)n , n=1–6: ab initio study. J Chem Phys 110:9116–9127

    Article  CAS  Google Scholar 

  73. Shi R, Wang P, Tang L, Huang X, Chen Y, Su Y, Zhao J (2018) Structures and spectroscopic properties of F−(H2O)n with n = 1–10 clusters from a global search based on density functional theory. J Phys Chem A 122:3413–3422

    Article  CAS  PubMed  Google Scholar 

  74. Arshadi M, Yamadgni R, Kebarle P (1970) Hydration of the halide negative ions in the gas phase. II. Comparison of hydration energies for the alkali positive and halide negative ions. J Phys Chem 74:1475–1482

    Article  CAS  Google Scholar 

  75. Hiraoka K, Mizuse S, Yamabe S (1988) Solvation of halide ions with H2O and CH3CN in the gas phase. J Phys Chem 92:3943–3952

    Article  CAS  Google Scholar 

  76. Fox MF, Hayon E (1977) Far ultraviolet solution spectroscopy of the iodide ion. J Chem Soc Faraday Trans 173:1003–1016

    Google Scholar 

  77. Serxner D, Dessent CEH, Johnson MA (1996) Precursor of the \( {I}_{aq}^{-} \) charge-transfer-to-solvent (CTTS) band in I–. (H2O)n clusters. J Chem Phys 105:7231–7234

    Google Scholar 

  78. Lehr L, Zanni MT, Frischkorn C, Weinkauf R, Neumark DM (1999) Electron solvation in finite systems: femtosecond dynamics of iodide·(water)n anion clusters. Science 284:635–638

    Article  CAS  PubMed  Google Scholar 

  79. Takahashi N, Sakai K, Tanida T, Watanabe I (1995) Vertical ionization potentials and CTTS energies for anions in water and acetonitrile. Chem Phys Lett 246:183–186

    Article  CAS  Google Scholar 

  80. Majumdar D, Kim J, Kim KS (2000) Charge transfer to solvent (CTTS) energies of small X–(H2O)n=1–4 (X=F, Cl, Br, I) clusters: ab initio study. J Chem Phys 112:101–105

    Article  CAS  Google Scholar 

  81. Kim J, Lee HM, Suh SB, Majumdar D, Kim KS (2000) Comparative ab initio study of the structures, energetics and spectra of X–(H2O)n=1–4 [F, Cl, Br, I] clusters. J Chem Phys 113:5259–5272

    Article  CAS  Google Scholar 

  82. Kim J, Suh SB, Kim KS (1999) Water dimer to pentamer with an excess electron: ab initio study. J Chem Phys 111:10077–10087

    Article  CAS  Google Scholar 

  83. Lee S, Kim J, Lee SJ, Kim KS (1997) Novel structures for the excess electron state of the water hexamer and the interaction forces governing the structures. Phys Rev Lett 79:2038–2041

    Article  CAS  Google Scholar 

  84. Olbert-Majkut A, Akhokas J, Lundell J, Petterson M (2011) Raman spectroscopy of acetic acid monomer and dimers isolated in solid argon. J Raman Spectrosc 42:1670–1681

    Article  CAS  Google Scholar 

  85. Cato Jr MA, Majumdar D, Roszak S, Leszczynski J (2013) Exploring relative thermodynamic stabilities of formic acid and formamide dimers—role of low-frequency hydrogen-bond vibration. J Chem Theory Comput 9:1016–1026

    Article  CAS  PubMed  Google Scholar 

  86. Copeland C, Menon O, Majumdar D, Roszak S, Leszczynski J (2017) Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers. Phys Chem Chem Phys 19:24866–24878

    Article  CAS  PubMed  Google Scholar 

  87. Tan TL, Goh KL, Ong PP, Teo HH (1999) Rovibrational constants for the ν6 and 2ν9 bands of HCOOD by Fourier transform infrared spectroscopy. J Mol Spectrosc 198:110–114

    Article  CAS  PubMed  Google Scholar 

  88. Bertie JE, Michaelian KH, Eysel HH, Hager D (1986) The Raman-active O–H and O–D stretching vibrations and Raman spectra of gaseous formic acid-d1 and -OD. J Chem Phys 85:4779–4789

    Article  CAS  Google Scholar 

  89. Pettersson M, Lundell J, Khriachtchev L, Räsänen M (1997) IR spectrum of the other rotamer of formic acid, cis-HCOOH. J Am Chem Soc 119:11715–11716

    Article  CAS  Google Scholar 

  90. Marushkevich K, Khriachtchev L, Lundell J, Domanskaya A, Räsänen M (2010) Matrix isolation and ab initio study of trans–trans and trans–cis dimers of formic acid. J Phys Chem A 114:3495–3502

    Article  CAS  PubMed  Google Scholar 

  91. Marushkevich K, Siltanen M, Räsänen M, Haloneu L, Khriachtchev L (2011) Identification of new dimers of formic acid: the use of a continuous-wave optical parametric oscillator in matrix isolation experiments. J Phys Chem Lett 2:695–699

    Article  CAS  Google Scholar 

  92. Marushkevich K, Khriachtchev L, Räsänen M, Melqvuori M, Londell J (2012) Dimers of the higher-energy conformer of formic acid: experimental observation. J Phys Chem A 116:2101–2108

    Article  CAS  PubMed  Google Scholar 

  93. Senent ML (2001) Ab initio determination of the torsional spectra of acetic acid. Mol Phys 99:1311–1321

    Article  CAS  Google Scholar 

  94. Maçôas EMS, Khriachtchev L, Pettersson M, Fausto R, Räsänen M (2003) Rotational isomerism in acetic acid: the first experimental observation of the high-energy conformer. J Am Chem Soc 125:16188–16189

    Article  PubMed  CAS  Google Scholar 

  95. Chocholoušová J, Vacek J, Hobza P (2003) Acetic acid dimer in the gas phase, nonpolar solvent, microhydrated environment, and dilute and concentrated acetic acid: ab initio quantum chemical and molecular dynamics simulations. J Phys Chem A 107:3086–3092

    Article  CAS  Google Scholar 

  96. Roszak S, Gee RH, Balasubramanian K, Fried LE (2005) New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid. J Chem Phys 123:144702-1–144702-10

    Google Scholar 

  97. Kollipost F, Larsen RW, Domanskaya AV, Nörenberg M, Shum MA (2012) Communication: the highest frequency hydrogen bond vibration and an experimental value for the dissociation energy of formic acid dimer. J Chem Phys 136:151101-1–151101-4

    Google Scholar 

  98. Goubet M, Soulard P, Pirali O, Asselin P, Réal F, Gruet S, Huet TR, Roy P, Georges R (2015) Standard free energy of the equilibrium between the trans-monomer and the cyclic-dimer of acetic acid in the gas phase from infrared spectroscopy. Phys Chem Chem Phys 17:7477–7488

    Article  CAS  PubMed  Google Scholar 

  99. Marrdyukov A, Sánchez-Garcia E, Rodziewicz P, Doltsinis NL, Sander W (2007) Formamide dimers: a computational and matrix isolation study. J Phys Chem A 111:10552–10561

    Article  CAS  Google Scholar 

  100. Albrecht M, Rice CA, Suhm MA (2008) Elementary peptide motifs in the gas phase: FTIR aggregation study of formamide, acetamide, N-methylformamide, and N-methylacetamide. J Phys Chem A 112:7530–7542

    Article  CAS  PubMed  Google Scholar 

  101. Nicholas JB, Hay BP, Dixon DA (1999) Ab initio molecular orbital study of cation–π binding between the alkali-metal cations and benzene. J Phys Chem A 103:1394–1400

    Article  CAS  Google Scholar 

  102. Sunner J, Nishizawa K, Kebarle P (1981) Ion-solvent molecule interactions in the gas phase. The potassium ion and benzene. J Phys Chem 85:1814–1820

    Article  CAS  Google Scholar 

  103. Kim KS, Lee JY, Lee SJ, Ha T-K, Kim DH (1994) On binding forces between aromatic ring and quaternary ammonium compound. J Am Chem Soc 116:7399–7400

    Article  CAS  Google Scholar 

  104. Kadlubanski P, Calderón-Mojica K, Rodriguez WA, Majumdar D, Roszak S, Leszczynski J (2013) Role of the multipolar Electrostatic interaction energy components in strong and weak cation–π interactions. J Phys Chem A 117(33):7989–8000

    Article  CAS  PubMed  Google Scholar 

  105. Meyer EA, Castellano RK, Diederich F (2003) Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed 42:1210–1250

    Google Scholar 

  106. Kryger G, Silman I, Sussman JL (1999) Structure of acetylcholinesterase complexed with E2020 (Aricept): implications for the design of new anti-Alzheimer drugs. Structure 7:297–307

    Article  CAS  PubMed  Google Scholar 

  107. Burley SK, Petsko GA (1985) Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 229:23–28

    Article  CAS  PubMed  Google Scholar 

  108. McGaughey GB, Gagne M, Rappe AK (1998) π-stacking interactions: alive and well in proteins. J Biol Chem 273:15458–15463

    Google Scholar 

  109. Gung BW, Xue X, Reich HJ (2005) The strength of parallel-displaced arene–arene interactions in chloroform. J Org Chem 70:3641–3644

    Article  CAS  PubMed  Google Scholar 

  110. Sinnokrot MO, Sherrill CD (2006) High-accuracy quantum mechanical studies of π–π interactions in benzene dimers. J Phys Chem A 110:10656–10668

    Article  CAS  PubMed  Google Scholar 

  111. Sinnokrot MO, Sherrill CD (2004) Substituent effects in π–π interactions: sandwich and T-shaped configurations. J Am Chem Soc 126:7690–7697

    Article  CAS  PubMed  Google Scholar 

  112. Sinnokrot MO, Valeev EF, Sherrill CD (2002) Estimates of the ab initio limit for π–π interactions: the benzene dimer. J Am Chem Soc 124:10887–10893

    Article  CAS  PubMed  Google Scholar 

  113. Tsuzuki S, Uchimaru T, Mikami M (2006) Intermolecular Interaction between hexafluorobenzene and benzene: ab initio calculations including CCSD(T) level electron correlation correction. J Phys Chem A 110:2027–2033

    Article  CAS  PubMed  Google Scholar 

  114. Tsuzuki S, Honda K, Uchimaru T, Mikami M (2005) Ab initio calculations of structures and interaction energies of toluene dimers including CCSD(T) level electron correlation correction. J Chem Phys 122:144323

    Article  PubMed  CAS  Google Scholar 

  115. Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K (2002) Origin of attraction and directionality of the π/π interaction: model chemistry calculations of benzene dimer interaction. J Am Chem Soc 124:104–112

    Article  CAS  PubMed  Google Scholar 

  116. Hunter CA, Sanders JKM (1990) The nature of π-π interactions. J Am Chem Soc 112:5525–5534

    Article  CAS  Google Scholar 

  117. Khan MH, Leszczynska D, Majumdar D, Roszak S, Leszczynski J (2018) Interactions of substituted nitroaromatics with model graphene systems: applicability of Hammett substituent constants to predict binding energies. ACS Omega 3:2773–2785

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. McManus JJ, Charbonneau P, Zaccarelli E, Asherie N (2016) The physics of protein self-assembly. Curr Opin Colloid Interface Sci 22:73–79

    Article  CAS  Google Scholar 

  119. Simon AJ, Zhou Y, Ramasubramani V, Glaser J, Pothukuchy A, Gollihar J, Gerberich JC, Leggere JC, Morrow BR, Jung C et al (2019) Supercharging enables organized assembly of synthetic biomolecules. Nat Chem 11:204–212

    Article  CAS  PubMed  Google Scholar 

  120. Ferrari S, Kahl G, Bianchi E (2018) Molecular dynamics simulations of inverse patchy colloids. Eur Phys J E Soft Matter Biol Phys 41:1–5

    Article  CAS  Google Scholar 

  121. Eom K (2019) Computer simulation of protein materials at multiple length scales: from single proteins to protein assemblies. Multiscale Sci Eng 1:1–25

    Article  Google Scholar 

  122. Zhang Z, Marson RL, Ge Z, Glotzer SC, Ma PX (2015) Simultaneous nano- and microscale control of nanofibrous microspheres self-assembled from star-shaped polymers. Adv Mater 27:3947–3952

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Elemans JAAW, Rowan AE, Nolte RJM (2003) Mastering molecular matter. Supramolecular architectures by hierarchical self-assembly. J Mater Chem 13:2661–2670

    Article  CAS  Google Scholar 

  124. Mandal D, Nasrolahi Shirazi A, Parang K (2014) Self-assembly of peptides to nanostructures. Org Biomol Chem 12:3544–3561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Eskandari S, Guerin T, Toth I, Stephenson RJ (2017) Recent advances in self-assembled peptides: implications for targeted drug delivery and vaccine engineering. Adv Drug Deliv Rev 110–111:169–187

    Article  PubMed  CAS  Google Scholar 

  126. Qiu F, Chen Y, Tang C, Zhao X (2018) Amphiphilic peptides as novel nanomaterials: design, self-assembly and application. Int J Nanomed 13:5003–5022

    Article  CAS  Google Scholar 

  127. Frederix PWJM, Patmanidis I, Marrink SJ (2018) Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 47:3470–3489

    Article  CAS  PubMed Central  Google Scholar 

  128. Tuttle T (2015) Computational approaches to understanding the self-assembly of peptide-based nanostructures. Isr J Chem 55:724–734

    Article  CAS  Google Scholar 

  129. Colombo G, Soto P, Gazit E (2007) Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology. Trends Biotechnol 25:211–218

    Article  CAS  PubMed  Google Scholar 

  130. Lee O-S, Stupp SI, Schatz GC (2011) Atomistic molecular dynamics simulations of peptide amphiphile self-assembly into cylindrical nanofibers. J Am Chem Soc 133:3677–3683

    Article  CAS  PubMed  Google Scholar 

  131. Filot IAW, Palmans ARA, Hilbers PAJ, van Santen RA, Pidko EA, de Greef TFA (2010) Understanding cooperativity in hydrogen-bond-induced supramolecular polymerization: a density functional theory study. J Phys Chem B 114:13667–13674

    Article  CAS  PubMed  Google Scholar 

  132. Kang M, Zhang P, Cui H, Loverde SM (2016) π–π stacking mediated chirality in functional supramolecular filaments. Macromolecules 49:994–1001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work has been supported by NSF-CREST (Award No. 154774) and EPSCOR R-II (Award No. OIA - 1632899). One of the authors (S.R.) acknowledges the financial support by the Faculty of Chemistry of Wroclaw University of Science and Technology.

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Authors and Affiliations

  1. Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA

    Pabitra Narayan Samanta, Devashis Majumdar & Jerzy Leszczynski

  2. Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland

    Szczepan Roszak

Authors
  1. Pabitra Narayan Samanta
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  2. Devashis Majumdar
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  3. Szczepan Roszak
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  4. Jerzy Leszczynski
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Corresponding authors

Correspondence to Devashis Majumdar or Jerzy Leszczynski .

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Editors and Affiliations

  1. Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA

    Jerzy Leszczynski

  2. US Army Engineer Research and Development Center, Vicksburg, MS, USA

    Manoj K. Shukla

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Samanta, P.N., Majumdar, D., Roszak, S., Leszczynski, J. (2022). First-Principles Modeling of Non-covalent Interactions in Molecular Systems and Extended Materials. In: Leszczynski, J., Shukla, M.K. (eds) Practical Aspects of Computational Chemistry V. Springer, Cham. https://doi.org/10.1007/978-3-030-83244-5_3

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