Parametrization of an empirical correction term to density functional theory for an accurate description of π-stacking interactions in nucleic acids

被引:39
作者
Ducere, Jean-Marie [1 ]
Cavallo, Luigi [1 ]
机构
[1] Univ Salerno, Dipartimento Chim, I-84084 Fisciano, SA, Italy
关键词
D O I
10.1021/jp072317s
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 [物理化学]; 081704 [应用化学];
摘要
We present an accurate parametrization of density functional theory augmented with an empirical correction term to describe properly a-stacking interactions in nucleic acids. The approach is based on the popular Perdew-Burke-Ernzerhof (PBE), Becke-Perdew (BP), and hybrid Becke-Lee-Yang-Parr (B3LYP) density functionals augmented by a classical London C6R-6 dispersion term. The novelty of our implementation lies in the accurate tuning of the empirical parameters, included in the f(a)(R) damping function, to reproduce high-level post Hartree-Fock calculations. In particular, we present sets of parameters and the needed code to correct the PBE, BP, and B3LYP results from the Turbomole and ADF packages in connection with basis sets of double and triple quality. The developed approach is validated by comparison with the JSCH-2005 benchmark and with best quality stacking energies reported in the literature for the stacking of H-bonded nucleic acids base pairs.
引用
收藏
页码:13124 / 13134
页数:11
相关论文
共 56 条
[1]
Efficient evaluation of three-center two-electron integrals over Gaussian functions [J].
Ahlrichs, R .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2004, 6 (22) :5119-5121
[2]
ELECTRONIC-STRUCTURE CALCULATIONS ON WORKSTATION COMPUTERS - THE PROGRAM SYSTEM TURBOMOLE [J].
AHLRICHS, R ;
BAR, M ;
HASER, M ;
HORN, H ;
KOLMEL, C .
CHEMICAL PHYSICS LETTERS, 1989, 162 (03) :165-169
[3]
INTERMOLECULAR FORCES IN SIMPLE SYSTEMS [J].
AHLRICHS, R ;
PENCO, R ;
SCOLES, G .
CHEMICAL PHYSICS, 1977, 19 (02) :119-130
[4]
Density functional theory including dispersion corrections for intermolecular interactions in a large benchmark set of biologically relevant molecules [J].
Antony, Jens ;
Grimme, Stefan .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2006, 8 (45) :5287-5293
[5]
DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652
[6]
DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT ASYMPTOTIC-BEHAVIOR [J].
BECKE, AD .
PHYSICAL REVIEW A, 1988, 38 (06) :3098-3100
[7]
VAN DER WAALS VOLUMES + RADII [J].
BONDI, A .
JOURNAL OF PHYSICAL CHEMISTRY, 1964, 68 (03) :441-+
[8]
CALCULATION OF SMALL MOLECULAR INTERACTIONS BY DIFFERENCES OF SEPARATE TOTAL ENERGIES - SOME PROCEDURES WITH REDUCED ERRORS [J].
BOYS, SF ;
BERNARDI, F .
MOLECULAR PHYSICS, 1970, 19 (04) :553-&
[9]
THEORETICAL-STUDIES OF VANDERWAALS MOLECULES AND INTERMOLECULAR FORCES [J].
BUCKINGHAM, AD ;
FOWLER, PW ;
HUTSON, JM .
CHEMICAL REVIEWS, 1988, 88 (06) :963-988
[10]
A combined QM/MM study of ligand substitution enthalpies in the L2Fe(CO)3, RuCpL2Cl, and RuCp*L2Cl systems [J].
Cavallo, L ;
Woo, TK ;
Ziegler, T .
CANADIAN JOURNAL OF CHEMISTRY-REVUE CANADIENNE DE CHIMIE, 1998, 76 (10) :1457-1466