Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems

被引:25
作者
Kubar, Tomas [1 ]
Jurecka, Petr [1 ]
Cerny, Jiri [1 ]
Rezac, Jan [1 ]
Otyepka, Michal [1 ]
Valdes, Haydee [1 ]
Hobza, Pavel [1 ]
机构
[1] Acad Sci Czech Republ, Ctr Biomol & Complex Mol Syst, Inst Organ Chem & Biochem, CR-16610 Prague 6, Czech Republic
关键词
D O I
10.1021/jp068858j
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 ; 081704 ;
摘要
Recently, two computational approaches that supply a density-functional-based quantum-chemical method with an empirical term accounting for London dispersion were introduced and found use in the studies of biomolecular systems, namely, DFT-D and SCC-DFTB-D. Here, we examine the performance and usability of these combined techniques for dealing with several tasks typically occurring in the research of biomolecules. The interaction energy of small biomolecular complexes agrees very well with the reference data yielded by correlated ab initio quantum chemical methods. In real-life studies aimed at interaction energy, structure, and infrared spectra, the mentioned methods provide results in good agreement with each other and with experiment (where available). The very favorable time demands of these approaches are discussed, and for each of them, a suitable area of use is proposed on the basis of the results of our analysis.
引用
收藏
页码:5642 / 5647
页数:6
相关论文
共 36 条
[1]   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
[2]   INTERMOLECULAR FORCES IN SIMPLE SYSTEMS [J].
AHLRICHS, R ;
PENCO, R ;
SCOLES, G .
CHEMICAL PHYSICS, 1977, 19 (02) :119-130
[3]   DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652
[4]  
CASTLEMAN AW, 1988, CHEM REV, V88
[5]  
CASTLEMAN AW, CHEM REV, V94, P94
[6]   The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking [J].
Cerny, J ;
Hobza, P .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005, 7 (08) :1624-1626
[7]   Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D):: A promising tool for studying isolated small peptides [J].
Cerny, Jiri ;
Jurecka, Petr ;
Hobza, Pavel ;
Valdes, Haydee .
JOURNAL OF PHYSICAL CHEMISTRY A, 2007, 111 (06) :1146-1154
[8]   Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties [J].
Elstner, M ;
Porezag, D ;
Jungnickel, G ;
Elsner, J ;
Haugk, M ;
Frauenheim, T ;
Suhai, S ;
Seifert, G .
PHYSICAL REVIEW B, 1998, 58 (11) :7260-7268
[9]   Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment [J].
Elstner, M ;
Hobza, P ;
Frauenheim, T ;
Suhai, S ;
Kaxiras, E .
JOURNAL OF CHEMICAL PHYSICS, 2001, 114 (12) :5149-5155
[10]   Accurate description of van der Waals complexes by density functional theory including empirical corrections [J].
Grimme, S .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (12) :1463-1473