S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

被引:837
作者
Rezac, Jan [1 ,2 ]
Riley, Kevin E. [1 ,2 ]
Hobza, Pavel [1 ,2 ,3 ]
机构
[1] Acad Sci Czech Republ, Inst Organ Chem & Biochem, CR-16610 Prague, Czech Republic
[2] Ctr Biomol & Complex Mol Syst, Prague 16610, Czech Republic
[3] Palacky Univ, Reg Ctr Adv Technol & Mat, Dept Phys Chem, Olomouc 77146, Czech Republic
关键词
GAUSSIAN-BASIS SETS; INTERMOLECULAR INTERACTION ENERGIES; CORRELATED MOLECULAR CALCULATIONS; NONCOVALENT INTERACTION ENERGIES; PLESSET PERTURBATION-THEORY; KOHN-SHAM ORBITALS; DENSITY FUNCTIONALS; ACCURATE CCSD(T); BASE-PAIRS; STACKING;
D O I
10.1021/ct2002946
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
With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set.
引用
收藏
页码:2427 / 2438
页数:12
相关论文
共 56 条
[1]   DFTB+, a sparse matrix-based implementation of the DFTB method [J].
Aradi, B. ;
Hourahine, B. ;
Frauenheim, Th. .
JOURNAL OF PHYSICAL CHEMISTRY A, 2007, 111 (26) :5678-5684
[2]   Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures [J].
Berka, Karel ;
Laskowski, Roman ;
Riley, Kevin E. ;
Hobza, Pavel ;
Vondrasek, Jiri .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5 (04) :982-992
[3]   On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level [J].
Dabkowska, I ;
Jurecka, P ;
Hobza, P .
JOURNAL OF CHEMICAL PHYSICS, 2005, 122 (20)
[4]   Optimized spin-component scaled second-order Moller-Plesset perturbation theory for intermolecular interaction energies [J].
Distasio, Robert A., Jr. ;
Head-Gordon, Martin .
MOLECULAR PHYSICS, 2007, 105 (08) :1073-1083
[6]   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
[7]   Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-Ligand Complexes [J].
Faver, John C. ;
Benson, Mark L. ;
He, Xiao ;
Roberts, Benjamin P. ;
Wang, Bing ;
Marshall, Michael S. ;
Kennedy, Matthew R. ;
Sherrill, C. David ;
Merz, Kenneth M., Jr. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (03) :790-797
[8]   Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals-Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions [J].
Goerigk, Lars ;
Grimme, Stefan .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (02) :291-309
[9]   A General Database for Main Group Thermochemistry, Kinetics, and Noncovalent Interactions - Assessment of Common and Reparameterized (meta-)GGA Density Functionals [J].
Goerigk, Lars ;
Grimme, Stefan .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (01) :107-126
[10]   Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set [J].
Grafova, Lucie ;
Pitonak, Michal ;
Rezac, Jan ;
Hobza, Pavel .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (08) :2365-2376