A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems

被引:95
作者
Sumowski, Chris Vanessa [1 ]
Ochsenfeld, Christian [1 ]
机构
[1] Univ Tubingen, D-72076 Tubingen, Germany
关键词
ISOMERASE PHOSPHOGLYCOLOHYDROXAMATE COMPLEX; MOLECULAR-ORBITAL METHODS; TRIOSEPHOSPHATE ISOMERASE; BASIS-SETS; PROTON-TRANSFER; HARTREE-FOCK; QUANTUM; DYNAMICS; IMPLEMENTATION; MECHANICS;
D O I
10.1021/jp902876n
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
A systematic study of the convergence of QM/MM results with respect to the chosen size of the QM region is presented for two examples of peptidic systems. For this purpose, we increased the QM region to up to 1637 atoms at the HF/SVP and 383 atoms at the SOS-AO-MP2/6-31G** level. While the convergence behavior is almost independent of the chosen method and basis set, the study clearly shows that for the considered proton-transfer energy the QM/MM treatment leads to a significantly faster convergence than the pure QM treatment. This behavior can be rationalized by the fair description of the surrounding of the active center using MM methods, even though the MM description of the active center is not adequate in our present case. At the same time, the observed convergence is-quite insensitive to a variation of charge surroundings in the chosen model peptides. Although the QM/MM results do converge much quicker with the system size than the pure QM ones, the data show that even for the chosen simple model systems about 150-300 QM atoms are needed to achieve accuracies in the order of 10 kJ/mol and about 300-1000 atoms for an accuracy of 2 kJ/mol with respect to a convergence with the QM-region size.
引用
收藏
页码:11734 / 11741
页数:8
相关论文
共 72 条
[1]   Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes [J].
Altun, A ;
Thiel, W .
JOURNAL OF PHYSICAL CHEMISTRY B, 2005, 109 (03) :1268-1280
[2]   Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor [J].
Altun, Ahmet ;
Shaik, Sason ;
Thiel, Walter .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2006, 27 (12) :1324-1337
[3]   Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method [J].
Amara, P ;
Field, MJ .
THEORETICAL CHEMISTRY ACCOUNTS, 2003, 109 (01) :43-52
[4]  
[Anonymous], 1998, ACS S SERIES
[5]  
[Anonymous], 2006, ANGEW CHEM-GER EDIT, DOI 10.1002/ange.200602711
[6]   Adjusted connection atoms for combined quantum mechanical and molecular mechanical methods [J].
Antes, I ;
Thiel, W .
JOURNAL OF PHYSICAL CHEMISTRY A, 1999, 103 (46) :9290-9295
[7]   Theoretical study of environmental effects on proton transfer reaction through the peptide bond in a model system [J].
Asada, Toshio ;
Takahashi, Tadayoshi ;
Koseki, Shiro .
THEORETICAL CHEMISTRY ACCOUNTS, 2008, 120 (1-3) :263-271
[8]   Hybrid models for combined quantum mechanical and molecular mechanical approaches [J].
Bakowies, D ;
Thiel, W .
JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (25) :10580-10594
[9]   COMPUTER-SIMULATION AND ANALYSIS OF THE REACTION PATHWAY OF TRIOSEPHOSPHATE ISOMERASE [J].
BASH, PA ;
FIELD, MJ ;
DAVENPORT, RC ;
PETSKO, GA ;
RINGE, D ;
KARPLUS, M .
BIOCHEMISTRY, 1991, 30 (24) :5826-5832
[10]   SELF-CONSISTENT MOLECULAR-ORBITAL METHODS .21. SMALL SPLIT-VALENCE BASIS-SETS FOR 1ST-ROW ELEMENTS [J].
BINKLEY, JS ;
POPLE, JA ;
HEHRE, WJ .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1980, 102 (03) :939-947