Performance of DFT/MPWB1K for stacking and H-bonding interactions

A newly developed exchange-correlation functional (MPWB1K) in density functional theory has been applied to describe stacking and hydrogen bonding interactions. The performance of this functional is assessed through the calculations of structural properties and binding energies of these interactions and their critical comparison with B3LYP and higher level ab initio calculations and available experimental data. Our results indicate, contrary to the previous DFT methods which are less reliable, MPWB1K performs better for the stacking interaction. Further, at the same time the new functional gives a good performance for hydrogen bonding.

[1]  Donald G Truhlar,et al.  How well can new-generation density functional methods describe stacking interactions in biological systems? , 2005, Physical chemistry chemical physics : PCCP.

[2]  Donald G Truhlar,et al.  Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory. , 2005, Journal of chemical theory and computation.

[3]  Pavel Hobza,et al.  Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. , 2002, Journal of the American Chemical Society.

[4]  Andreas Müller,et al.  Ab Initio Benchmark Study of (2-Pyridone)2, a Strongly Bound Doubly Hydrogen-Bonded Dimer , 2004 .

[5]  L. Adamowicz,et al.  Density Functional Theory Study of the Hydrogen-Bonded Pyridine−H2O Complex: A Comparison with RHF and MP2 Methods and with Experimental Data , 2000 .

[6]  J. SantaLucia,et al.  Thermodynamic parameters for DNA sequences with dangling ends. , 2000, Nucleic acids research.

[7]  Patricia Guadarrama,et al.  Local MP2-Based Method for Estimation of Intermolecular Interactions in Aromatic Molecules. Benzene, Naphthalene, and Pyrimidine Dimers. A Comparison with Canonical MP2 Method , 2003 .

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

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

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

[11]  Axel D. Becke,et al.  Density‐functional thermochemistry. IV. A new dynamical correlation functional and implications for exact‐exchange mixing , 1996 .

[12]  D. Pratt,et al.  Ammonia as a hydrogen bond donor and acceptor in the gas phase. Structures of 2-pyridone-NH3 and 2-pyridone-(NH3)2 in their S0 and S1 electronic states , 1993 .

[13]  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.

[14]  L. Adamowicz,et al.  DFT/B3-LYP study of the hydrogen-bonding cooperativity: application to (2-pyridone)(2), 2-pyridone-H2O, 2-pyridone-CH3OH and 2-pyridone-CH3OCH3 , 2000 .

[15]  J. D. Bene AB INITIO STUDY OF THE HYDROGEN-BONDED BRIDGING NH3:PYRIDONE COMPLEX , 1995 .

[16]  D. Pratt,et al.  Hydrogen bonding in the symmetry‐equivalent C2h dimer of 2‐pyridone in its S0 and S2 electronic states. Effect of deuterium substitution , 1992 .

[17]  Donald G. Truhlar,et al.  Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions , 2004 .

[18]  Jirí Cerný,et al.  The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking. , 2005, Physical chemistry chemical physics : PCCP.

[19]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[20]  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.

[21]  Christof M Niemeyer,et al.  Rational design of DNA nanoarchitectures. , 2006, Angewandte Chemie.

[22]  J. D. Bene An Ab Initio Study of Hydrogen-Bonded Complexes of Pyridone with Water , 1994 .

[23]  L. Adamowicz,et al.  Hybrid density functionals and ab initio studies of 2-pyridone–H2O and 2-pyridone–(H2O)2 , 2000 .