Physisorption of nucleobases on graphene: a comparative van der Waals study

The physisorption of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) on graphene is studied using several variants of the density functional theory (DFT): the generalized gradient approximation with the inclusion of van der Waals interaction (vdW) based on the TS approach (Tkatchenko and Scheffer 2009 Phys. Rev. Lett. 102 073005) and our simplified version of this approach (here called sTS), the van der Waals density functional vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401) and vdW-DF2 (Lee et al 2010 Phys. Rev. B 82 081101), and DFT-D2 (Grimme 2006 J. Comput. Chem. 27 1787) and DFT-D3 (Grimme et al 2010 J. Chem. Phys. 132 154104) methods. The binding energies of nucleobases on graphene are found to be in the following order: G > A > T > C > U within TS, sTS, vdW-DF, and DFT-D2, and in the following order: G > A > T ~ C > U within DFT-D3 and vdW-DF2. The binding separations are found to be different within different methods and in the following order: DFT-D2 < TS < DFT-D3 ~ vdW-DF2 < vdW-DF. We also comment on the efficiency of combining the DFT-D approach and vdW-DF to study systems with van der Waals interactions.

[1]  Pier Luigi Silvestrelli,et al.  Van der Waals interactions in DFT made easy by Wannier functions. , 2007, Physical review letters.

[2]  A. Becke,et al.  Exchange-hole dipole moment and the dispersion interaction. , 2005, The Journal of chemical physics.

[3]  Stefan Grimme,et al.  Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..

[4]  A. Tkatchenko,et al.  Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. , 2009, Physical review letters.

[5]  K. Jacobsen,et al.  Real-space grid implementation of the projector augmented wave method , 2004, cond-mat/0411218.

[6]  J. Perdew,et al.  Accurate and simple density functional for the electronic exchange energy: Generalized gradient approximation. , 1986, Physical review. B, Condensed matter.

[7]  T. Kaneko,et al.  Electrically triggered insertion of single-stranded DNA into single-walled carbon nanotubes , 2006 .

[8]  Weitao Yang,et al.  Challenges for density functional theory. , 2012, Chemical reviews.

[9]  G. Kresse,et al.  Ab initio molecular dynamics for liquid metals. , 1993 .

[10]  J. Soler,et al.  Efficient implementation of a van der Waals density functional: application to double-wall carbon nanotubes. , 2008, Physical review letters.

[11]  R. Ahuja,et al.  Physisorption of nucleobases on graphene : Density-functional calculations , 2007, 0704.1316.

[12]  Kresse,et al.  Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. , 1996, Physical review. B, Condensed matter.

[13]  A. Becke,et al.  A post-Hartree-Fock model of intermolecular interactions. , 2005, The Journal of chemical physics.

[14]  Z. Shi,et al.  Monolayer Guanine and Adenine on Graphite in NaCl Solution: A Comparative STM and AFM Study , 1994 .

[15]  E. Tu,et al.  Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Jirí Cerný,et al.  Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. , 2006, Physical chemistry chemical physics : PCCP.

[17]  K. Berland,et al.  Benchmarking van der Waals density functionals with experimental data: potential-energy curves for H2 molecules on Cu(111), (100) and (110) surfaces , 2012, Journal of physics. Condensed matter : an Institute of Physics journal.

[18]  Alan Gelperin,et al.  DNA-decorated carbon nanotubes for chemical sensing. , 2005 .

[19]  S. Grimme,et al.  Structures and interaction energies of stacked graphene-nucleobase complexes. , 2008, Physical chemistry chemical physics : PCCP.

[20]  M. Dresselhaus,et al.  Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly , 2003, Science.

[21]  Hiromi Nakai,et al.  Density functional method including weak interactions: Dispersion coefficients based on the local response approximation. , 2009, The Journal of chemical physics.

[22]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[23]  F. Bechstedt,et al.  Attracted by long-range electron correlation: adenine on graphite. , 2005, Physical review letters.

[24]  Kyuho Lee,et al.  Higher-accuracy van der Waals density functional , 2010, 1003.5255.

[25]  P. Hyldgaard,et al.  Van der Waals density functional: Self-consistent potential and the nature of the van der Waals bond , 2007, cond-mat/0703442.

[26]  Yingkai Zhang,et al.  Comment on “Generalized Gradient Approximation Made Simple” , 1998 .

[27]  A. Dalgarno,et al.  Linear response time-dependent density functional theory for van der Waals coefficients. , 2004, The Journal of chemical physics.

[28]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[29]  Michael S. Strano,et al.  Optical Detection of DNA Conformational Polymorphism on Single-Walled Carbon Nanotubes , 2006, Science.

[30]  Michael S Strano,et al.  Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes. , 2006, Nano letters.

[31]  M. Dion,et al.  van der Waals density functional for general geometries. , 2004, Physical review letters.

[32]  Qin Wu,et al.  Empirical correction to density functional theory for van der Waals interactions , 2002 .

[33]  Stefan Grimme,et al.  Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..

[34]  Huixin He,et al.  DNA and carbon nanotubes as medicine. , 2010, Advanced drug delivery reviews.

[35]  Jorge Kohanoff,et al.  Electronic Structure Calculations for Solids and Molecules: Theory and Computational Methods , 2006 .

[36]  M. Dion,et al.  Erratum: Van der Waals Density Functional for General Geometries [Phys. Rev. Lett. 92, 246401 (2004)] , 2005 .

[37]  Marco Cecchini,et al.  Adsorption of Aromatic and Anti-Aromatic Systems on Graphene through π−π Stacking , 2010 .

[38]  Friedhelm Bechstedt,et al.  Semiempirical van der Waals correction to the density functional description of solids and molecular structures , 2006 .

[39]  G. Kresse,et al.  From ultrasoft pseudopotentials to the projector augmented-wave method , 1999 .

[40]  M. Zheng,et al.  DNA-assisted dispersion and separation of carbon nanotubes , 2003, Nature materials.

[41]  Blöchl,et al.  Projector augmented-wave method. , 1994, Physical review. B, Condensed matter.

[42]  A. Becke,et al.  A density-functional model of the dispersion interaction. , 2005, The Journal of chemical physics.

[43]  A. Govindaraj,et al.  Binding of DNA nucleobases and nucleosides with graphene. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.