Theoretical Chemistry Accounts

, 133:1575 | Cite as

Quantum molecular dynamics simulations of liquid benzene using orbital optimization

Regular Article
Part of the following topical collections:
  1. Ezra Festschrift Collection

Abstract

The structure of liquid benzene is investigated by quantum molecular dynamics simulations. Results using variationally optimized numerical pseudo-atomic orbitals are compared to those of generic optimized orbitals. The accuracy of the first-principle calculations is compared with recent experimental findings. Simulations using minimal basis sets with optimized orbitals are shown to successfully predict the local structure of liquid benzene, while simulations with non-optimized minimal basis sets have significant errors in the structure of the first solvation shell. The use of a minimal optimized basis set considerably speeds up simulations, while preserving much of the accuracy of a larger basis set formed by generic orbitals. The transferability of the optimized orbitals is also explored under different environmental conditions.

Keywords

Liquid benzene Ab initio simulations Orbital optimization Krylov Direct diagonalization 

References

  1. 1.
    Vallee R et al (2000) Nonlinear optical properties and crystalline orientation of 2-methyl-4-nitroaniline layers grown on nanostructured poly(tetrafluoroethylene) substrates. J Am Chem Soc 122(28):6701–6709CrossRefGoogle Scholar
  2. 2.
    Meyer EA, Castellano RK, Diederich F (2003) Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed 42(11):1210–1250CrossRefGoogle Scholar
  3. 3.
    Baker CM, Grant GH (2007) Role of aromatic amino acids in protein–nucleic acid recognition. Biopolymers 85(5–6):456–470CrossRefGoogle Scholar
  4. 4.
    Hunter CA (1993) Aromatic interactions in proteins, DNA and synthetic receptors. Philos Trans R Soc Mathe Phys Eng Sci 345(1674):77–85CrossRefGoogle Scholar
  5. 5.
    Cox EG, Smith JAS (1954) Crystal structure of benzene at-3-degrees-C. Nature 173(4393):75CrossRefGoogle Scholar
  6. 6.
    Cox EG, Cruickshank DWJ, Smith JAS (1955) Crystal structure of benzene—new type of systematic error in precision X-ray crystal analysis. Nature 175(4461):766CrossRefGoogle Scholar
  7. 7.
    Cox EG, Cruickshank DWJ, Smith JAS (1958) The crystal structure of benzene at-3-degrees-C. Proc R Soc Lond Ser Mathe Phys Sci 247(1248):1–21CrossRefGoogle Scholar
  8. 8.
    Janda KC et al (1975) Benzene dimer—polar molecule. J Chem Phys 63(4):1419–1421CrossRefGoogle Scholar
  9. 9.
    Steed JM, Dixon TA, Klemperer W (1979) Molecular-beam studies of benzene dimer, hexafluorobenzene dimer and benzene–hexafluorobenzene. J Chem Phys 70(11):4940–4946CrossRefGoogle Scholar
  10. 10.
    Hopkins JB, Powers DE, Smalley RE (1981) Mass-selective 2-color photo-ionization of benzene clusters. J Phys Chem 85(25):3739–3742CrossRefGoogle Scholar
  11. 11.
    Langridgesmith PRR et al (1981) Ultraviolet-spectra of benzene clusters. J Phys Chem 85(25):3742–3746CrossRefGoogle Scholar
  12. 12.
    Venturo VA, Felker PM (1993) Intermolecular Raman bands in the ground-state of benzene dimer. J Chem Phys 99(1):748–751CrossRefGoogle Scholar
  13. 13.
    Hobza P, Selzle HL, Schlag EW (1996) Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures: T-shaped and parallel-displaced. J Phys Chem 100(48):18790–18794CrossRefGoogle Scholar
  14. 14.
    Sato T, Tsuneda T, Hirao K (2005) A density-functional study on pi-aromatic interaction: benzene dimer and naphthalene dimer. J Chem Phys 123(10):104307CrossRefGoogle Scholar
  15. 15.
    Sinnokrot MO, Sherrill CD (2006) High-accuracy quantum mechanical studies of pi–pi interactions in benzene dimers. J Phys Chem A 110(37):10656–10668CrossRefGoogle Scholar
  16. 16.
    van der Avoird A et al (2010) Vibration–rotation–tunneling states of the benzene dimer: an ab initio study. Phys Chem Chem Phys 12(29):8219–8240CrossRefGoogle Scholar
  17. 17.
    Henson BF et al (1992) Raman-vibronic double-resonance spectroscopy of benzene dimer isotopomers. J Chem Phys 97(4):2189–2208CrossRefGoogle Scholar
  18. 18.
    Erlekam U et al (2006) An experimental value for the B-1u C–H stretch mode in benzene. J Chem Phys 124(17):171101CrossRefGoogle Scholar
  19. 19.
    Tsuzuki S et al (2005) Ab initio calculations of structures and interaction energies of toluene dimers including CCSD(T) level electron correlation correction. J Chem Phys 122(14):144323CrossRefGoogle Scholar
  20. 20.
    Lowden LJ, Chandler D (1974) Theory of intermolecular pair correlations for molecular liquids—applications to liquids carbon-tetrachloride, carbon-disulfide, carbon diselenide, and benzene. J Chem Phys 61(12):5228–5241CrossRefGoogle Scholar
  21. 21.
    Narten AH (1968) Diffraction pattern and structure of liquid benzene. J Chem Phys 48(4):1630–1634CrossRefGoogle Scholar
  22. 22.
    Narten AH (1977) X-ray-diffraction pattern and models of liquid benzene. J Chem Phys 67(5):2102–2108CrossRefGoogle Scholar
  23. 23.
    Katayama M et al (2010) Liquid structure of benzene and its derivatives as studied by means of X-ray scattering. Phys Chem Liq 48(6):797–809CrossRefGoogle Scholar
  24. 24.
    Bartsch E et al (1985) A neutron and X-ray-diffraction study of the binary-liquid aromatic system benzene-hexafluorobenzene.1. The pure components. Ber Bunsen Ges Phys Chem Chem Phys 89(2):147–156CrossRefGoogle Scholar
  25. 25.
    Headen TF et al (2010) Structure of pi–pi interactions in aromatic liquids. J Am Chem Soc 132(16):5735–5742CrossRefGoogle Scholar
  26. 26.
    Tassaing T et al (2000) The structure of liquid and supercritical benzene as studied by neutron diffraction and molecular dynamics. J Chem Phys 113(9):3757–3765CrossRefGoogle Scholar
  27. 27.
    Misawa M, Fukunaga T (1990) Structure of liquid benzene and naphthalene studied by pulsed neutron total scattering. J Chem Phys 93(5):3495–3502CrossRefGoogle Scholar
  28. 28.
    Fu C-F, Tian SX (2011) A comparative study for molecular dynamics simulations of liquid benzene. J Chem Theory Comput 7(7):2240–2252CrossRefGoogle Scholar
  29. 29.
    Bogdan TV (2006) Atom-atomic potentials and the correlation distribution functions for modeling liquid benzene by the molecular dynamics methods. Russ J Phys Chem 80:S14–S20CrossRefGoogle Scholar
  30. 30.
    Chelli R et al (2001) The fast dynamics of benzene in the liquid phase—Part II. A molecular dynamics simulation. Phys Chem Chem Phys 3(14):2803–2810CrossRefGoogle Scholar
  31. 31.
    Baker CM, Grant GH (2006) The structure of liquid benzene. J Chem Theory Comput 2(4):947–955CrossRefGoogle Scholar
  32. 32.
    Coutinho K, Canuto S, Zerner MC (1997) Calculation of the absorption spectrum of benzene in condensed phase. A study of the solvent effects. Int J Quantum Chem 65(5):885–891CrossRefGoogle Scholar
  33. 33.
    Jorgensen WL et al (1993) Monte-Carlo simulations of pure liquid substituted benzenes with OPLS potential functions. J Comput Chem 14(2):206–215CrossRefGoogle Scholar
  34. 34.
    Cabaco MI et al (1997) Neutron diffraction and molecular dynamics study of liquid benzene and its fluorinated derivatives as a function of temperature. J Phys Chem B 101(35):6977–6987CrossRefGoogle Scholar
  35. 35.
    Hunter CA, Sanders JKM (1990) The nature of pi–pi interactions. J Am Chem Soc 112(14):5525–5534CrossRefGoogle Scholar
  36. 36.
    Righini R (1993) Ultrafast optical kerr-effect in liquids and solids. Science 262(5138):1386–1390CrossRefGoogle Scholar
  37. 37.
    Zorkii PM, Lanshina LV, Bogdan TV (2008) Computer simulation and diffraction studies of the structure of liquid benzene. J Struct Chem 49(3):524–547CrossRefGoogle Scholar
  38. 38.
    Forsman J, Woodward CE, Trulsson M (2011) A classical density functional theory of ionic liquids. J Phys Chem B 115(16):4606–4612CrossRefGoogle Scholar
  39. 39.
    Song Z, Wang H, Xing L (2009) Density functional theory study of the ionic liquid [emim]OH and complexes [emim]OH(H2O) n (n = 1,2). J Solut Chem 38(9):1139–1154CrossRefGoogle Scholar
  40. 40.
    Umebayashi Y et al (2009) Raman spectroscopic study, DFT calculations and MD simulations on the conformational isomerism of N-Alkyl-N-methylpyrrolidinium Bis-(trifluoromethanesulfonyl) amide ionic liquids. J Phys Chem B 113(13):4338–4346CrossRefGoogle Scholar
  41. 41.
    Waller MP et al (2006) Hybrid density functional theory for pi-stacking interactions: application to benzenes, pyridines, and DNA bases. J Comput Chem 27(4):491–504CrossRefGoogle Scholar
  42. 42.
    Yan Z, Truhlar DG (2005) How well can new-generation density functional methods describe stacking interactions in biological systems? Phys Chem Chem Phys 7(14):2701–2705CrossRefGoogle Scholar
  43. 43.
    Tachikawa H (2013) Double pi-pi stacking dynamics of benzene trimer cation: direct ab initio molecular dynamics (AIMD) study. Theor Chem Acc 132(7):1374Google Scholar
  44. 44.
    Sherrill CD, Takatani T, Hohenstein EG (2009) An assessment of theoretical methods for nonbonded interactions: comparison to complete basis set limit coupled-cluster potential energy curves for the benzene dimer, the methane dimer, benzene-methane, and benzene-H2S. J Phys Chem A 113(38):10146–10159CrossRefGoogle Scholar
  45. 45.
    Pitonak M et al (2008) Benzene dimer: high-level wave function and density functional theory calculations. J Chem Theory Comput 4(11):1829–1834CrossRefGoogle Scholar
  46. 46.
    Wen X-D, Hoffmann R, Ashcroft NW (2011) Benzene under high pressure: a story of molecular crystals transforming to saturated networks, with a possible intermediate metallic phase. J Am Chem Soc 133(23):9023–9035CrossRefGoogle Scholar
  47. 47.
    Wang C, Zhang P (2010) The equation of state and nonmetal–metal transition of benzene under shock compression. J Appl Phys 107(8):083502CrossRefGoogle Scholar
  48. 48.
    Goldman N et al (2005) Bonding in the superionic phase of water. Phys Rev Lett 94(21):217801CrossRefGoogle Scholar
  49. 49.
    Schwegler E et al (2008) Melting of ice under pressure. Proc Natl Acad Sci U S A 105(39):14779–14783CrossRefGoogle Scholar
  50. 50.
    Ozaki T (2003) Variationally optimized atomic orbitals for large-scale electronic structures. Phys Rev B 67(15):155108CrossRefGoogle Scholar
  51. 51.
    Ozaki T, Kino H (2004) Numerical atomic basis orbitals from H to Kr. Phys Rev B 69(19):195113CrossRefGoogle Scholar
  52. 52.
    Junquera J et al (2001) Numerical atomic orbitals for linear-scaling calculations. Phys Rev B 64(23):235111CrossRefGoogle Scholar
  53. 53.
    Corsetti F et al (2013) Optimal finite-range atomic basis sets for liquid water and ice. J Phys: Condens Matter 25(43):435504Google Scholar
  54. 54.
    Ozaki T, Kino H (2004) Variationally optimized basis orbitals for biological molecules. J Chem Phys 121(22):10879–10888CrossRefGoogle Scholar
  55. 55.
    Ohwaki T et al (2012) Large-scale first-principles molecular dynamics for electrochemical systems with O(N) methods. J Chem Phys 136(13):134101CrossRefGoogle Scholar
  56. 56.
    Jorgensen WL, Tiradorives J (1988) The OPLS potential functions for proteins—energy minimizations for crystals of cyclic-peptides and crambin. J Am Chem Soc 110(6):1657–1666CrossRefGoogle Scholar
  57. 57.
    Jorgensen WL, Severance DL (1990) Aromatic aromatic interactions—free-energy profiles for the benzene dimer in water, chloroform, and liquid benzene. J Am Chem Soc 112(12):4768–4774CrossRefGoogle Scholar
  58. 58.
    Van der Spoel D et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701–1718CrossRefGoogle Scholar
  59. 59.
    Hess B (2009) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Abstracts of Papers of the American Chemical Society 237Google Scholar
  60. 60.
    NISTChemistryWebBook. http://webbook.nist.gov/chemistry
  61. 61.
    Nose S (1984) A molecular-dynamics method for simulations in the canonical ensemble. Mol Phys 52(2):255–268CrossRefGoogle Scholar
  62. 62.
    Hoover WG (1985) Canonical dynamics—equilibrium phase-space distributions. Phys Rev A 31(3):1695–1697CrossRefGoogle Scholar
  63. 63.
    Parrinello M, Rahman A (1981) Polymorphic transitions in single-crystals—a new molecular-dynamics method. J Appl Phys 52(12):7182–7190CrossRefGoogle Scholar
  64. 64.
    Nose S, Klein ML (1983) Constant pressure molecular-dynamics for molecular-systems. Mol Phys 50(5):1055–1076CrossRefGoogle Scholar
  65. 65.
    Hess B et al (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18(12):1463–1472CrossRefGoogle Scholar
  66. 66.
    Hess B (2008) P-LINCS: a parallel linear constraint solver for molecular simulation. J Chem Theory Comput 4(1):116–122CrossRefGoogle Scholar
  67. 67.
    Ozaki T, Kino H (2005) Efficient projector expansion for the ab initio LCAO method. Phys Rev B 72(4):045121CrossRefGoogle Scholar
  68. 68.
  69. 69.
    Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev B 136(3B):B864CrossRefGoogle Scholar
  70. 70.
    Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77(18):3865–3868CrossRefGoogle Scholar
  71. 71.
    Morrison I, Bylander DM, Kleinman L (1993) Nonlocal hermitian norm-conserving vanderbilt pseudopotential. Phys Rev B 47(11):6728–6731CrossRefGoogle Scholar
  72. 72.
    Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27(15):1787–1799CrossRefGoogle Scholar
  73. 73.
    Soler JM et al (2002) The SIESTA method for ab initio order-N materials simulation. J Phys: Condens Matter 14(11):2745–2779Google Scholar
  74. 74.
    Ozaki T (2006) O(N) Krylov-subspace method for large-scale ab initio electronic structure calculations. Physical Review B 74(24):245101CrossRefGoogle Scholar
  75. 75.
    Woodcock LV (1971) Isothermal molecular dynamics calculations for liquid salts. Chem Phys Lett 10(3):257–261CrossRefGoogle Scholar
  76. 76.
    Nose S (1984) A unified formulation of the constant temperature molecular-dynamics methods. J Chem Phys 81(1):511–519CrossRefGoogle Scholar
  77. 77.
    Takeuchi H (2012) Structural features of small benzene clusters (C6H6)(n) (n <= 30) as investigated with the All-Atom OPLS potential. J Phys Chem A 116(41):10172–10181CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2014

Authors and Affiliations

  1. 1.Physical and Life Sciences DirectorateLawrence Livermore National LaboratoryLivermoreUSA

Personalised recommendations