Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration

被引:59
作者
Jambeck, Joakim P. M. [1 ]
Lyubartsev, Alexander P. [1 ]
机构
[1] Stockholm Univ, Div Phys Chem, Arrhenius Lab, SE-10691 Stockholm, Sweden
基金
瑞典研究理事会;
关键词
SOLVATION FREE-ENERGIES; SIDE-CHAIN ANALOGS; MOLECULAR-DYNAMICS SIMULATIONS; BINDING FREE-ENERGIES; PARTICLE MESH EWALD; WATER MODEL; PARTITION-COEFFICIENTS; COMPUTER-SIMULATIONS; EFFICIENT GENERATION; POTENTIAL FUNCTIONS;
D O I
10.1021/jp4111234
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
An approach to a straightforward reparametrization of the general AMBER force field (GAFF) for small organic solutes and druglike compounds is presented. The parametrization is based on specific pair interactions between the solvent and the solute, namely, the interactions between the constituting atoms of the solute and the oxygen of water were tuned in order to reproduce experimental hydration free energies for small model compounds. The key of the parametrization was to abandon the Lorentz-Berthelot combination rules for the van der Waals interactions. These parameters were then used for larger solutes in order to validate the newly derived pair interactions. In total close to 600 hydration free energies are computed, ranging from simple alkanes to multifunctional drug compounds, and compared to experimental data. The results show that the proposed parameters work well in describing the interactions between the solute and the solvent and that the agreement in absolute numbers is good. This modified version of GAFF is a good candidate for computing and predicting hydration free energies on a large scale, which has been a long-sought goal of computational chemists and can be used in rational drug design.
引用
收藏
页码:3793 / 3804
页数:12
相关论文
共 109 条
[1]   A general purpose model for the condensed phases of water: TIP4P/2005 [J].
Abascal, JLF ;
Vega, C .
JOURNAL OF CHEMICAL PHYSICS, 2005, 123 (23)
[2]  
[Anonymous], INTERMOLECULAR FORCE
[3]   Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field [J].
Baker, Christopher M. ;
Lopes, Pedro E. M. ;
Zhu, Xiao ;
Roux, Benoit ;
MacKerell, Alexander D., Jr. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (04) :1181-1198
[4]   Rational determination of transfer free energies of small drugs across the water-oil interface [J].
Bas, D ;
Dorison-Duval, D ;
Moreau, S ;
Bruneau, P ;
Chipot, C .
JOURNAL OF MEDICINAL CHEMISTRY, 2002, 45 (01) :151-159
[5]   DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652
[6]   A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy Calculations [J].
Beierlein, Frank R. ;
Michel, Julien ;
Essex, Jonathan W. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2011, 115 (17) :4911-4926
[7]   EFFICIENT ESTIMATION OF FREE-ENERGY DIFFERENCES FROM MONTE-CARLO DATA [J].
BENNETT, CH .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (02) :245-268
[8]   THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS [J].
BERENDSEN, HJC ;
GRIGERA, JR ;
STRAATSMA, TP .
JOURNAL OF PHYSICAL CHEMISTRY, 1987, 91 (24) :6269-6271
[9]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[10]   Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site [J].
Berka, Karel ;
Hendrychova, Tereza ;
Anzenbacher, Pavel ;
Otyepka, Michal .
JOURNAL OF PHYSICAL CHEMISTRY A, 2011, 115 (41) :11248-11255