The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

[1]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[2]  Pavel Hobza,et al.  Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations. , 2005 .

[3]  Jun Wang,et al.  SUCCESSFUL TEST OF A SEAMLESS VAN DER WAALS DENSITY FUNCTIONAL , 1999 .

[4]  Yingkai Zhang,et al.  Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional , 1997 .

[5]  Pavel Hobza,et al.  True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment. , 2003, Journal of the American Chemical Society.

[6]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[7]  G. Scuseria,et al.  Assessment of the Perdew–Burke–Ernzerhof exchange-correlation functional , 1999 .

[8]  Pavel Hobza,et al.  Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies , 2003 .

[9]  P Hobza,et al.  Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. , 1999, Chemical reviews.

[10]  V. Barone,et al.  From Classical Density Functionals to Adiabatic Connection Methods. the State of the Art. , 2000 .

[11]  W. Goddard,et al.  Accurate Energies and Structures for Large Water Clusters Using the X3LYP Hybrid Density Functional , 2004 .

[12]  Thomas Frauenheim,et al.  Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment , 2001 .

[13]  V. Barone,et al.  Toward reliable density functional methods without adjustable parameters: The PBE0 model , 1999 .

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

[15]  Vincenzo Barone,et al.  Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models , 1998 .

[16]  J. Šponer,et al.  Density functional theory and molecular clusters , 1995, Journal of Computational Chemistry.

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

[18]  Xin Xu,et al.  From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

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