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Frontiers of Chemical Science and Engineering

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ISSN 2095-0187(Online)

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Front. Chem. Sci. Eng.    2016, Vol. 10 Issue (2) : 203-212    https://doi.org/10.1007/s11705-016-1572-4
RESEARCH ARTICLE
Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions
Liaoran Cao1,Hong Ren2,Jing Miao1,Wei Guo1,Yan Li1,Guohui Li1,*()
1. Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
2. Department of Ophthalmology, Aerospace Center Hospital, Beijing 100049, China
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Abstract

Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.
Keywords nucleic acid      polarizable force field      AMOEBA     
Corresponding Author(s): Guohui Li   
Just Accepted Date: 25 April 2016   Online First Date: 11 May 2016    Issue Date: 19 May 2016
 Cite this article:   
Liaoran Cao,Hong Ren,Jing Miao, et al. Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions[J]. Front. Chem. Sci. Eng., 2016, 10(2): 203-212.
 URL:  
https://academic.hep.com.cn/fcse/EN/10.1007/s11705-016-1572-4
https://academic.hep.com.cn/fcse/EN/Y2016/V10/I2/203
Fig.1  Scheme 1A diagram of the nucleic acid molecules used in the following calculations
Acetic acid Benzene Methane Methanol Water
BSSE /(kcal·mol?1) 0.113 0.0677 0.422 0.098 0.147
Tab.1  BSSE of testing structures
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.914 0.969 0.0261 ?0.956 0.0507
AMBER 0.933 1.054 0.0248 ?0.913 0.0483
CHARMM 0.914 0.965 0.0259 ?0.871 0.0505
DNA AMOEBA 0.899 0.969 0.0257 0.787 0.0525
AMBER 0.893 1.004 0.0275 0.820 0.0562
CHARMM 0.893 0.964 0.0264 0.980 0.0540
Tab.2  Interaction energies between nucleic acids and acetic acid
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.895 1.109 0.0333 ?0.007 0.0413
AMBER 0.863 1.038 0.0363 ?0.101 0.0450
CHARMM 0.808 1.011 0.0433 ?0.825 0.0536
DNA AMOEBA 0.904 0.966 0.0254 ?0.331 0.0293
AMBER 0.897 0.963 0.0258 ?0.381 0.0297
CHARMM 0.898 0.966 0.0259 ?0.401 0.0298
Tab.3  Interaction energies between nucleic acids and benzene
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.878 1.020 0.0334 ?0.940 0.0207
AMBER 0.872 1.010 0.0340 ?0.853 0.0210
CHARMM 0.872 0.980 0.0330 ?0.144 0.0204
DNA AMOEBA 0.863 1.001 0.0315 ?0.318 0.0296
AMBER 0.845 0.933 0.0316 ?0.355 0.0296
CHARMM 0.856 0.983 0.0321 ?0.271 0.0201
Tab.4  Interaction energies between nucleic acids and methane
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.894 0.996 0.0301 ?0.167 0.0372
AMBER 0.907 0.997 0.0281 ?0.168 0.0347
CHARMM 0.905 1.023 0.0291 ?0.160 0.0360
DNA AMOEBA 0.895 0.979 0.0265 0.0997 0.0358
AMBER 0.899 1.003 0.0266 0.0861 0.0359
CHARMM 0.884 0.972 0.0278 0.0618 0.0376
Tab.5  Interaction energies between nucleic acids and methanol
Fig.2  Linear fit curve for the interaction energies between nucleic acid and acetic acid with various relative positions, data corresponding to Table 2. Top panel (a, b, c): interactions between RNA and acetic acid; Bottom panel (d, e, f): interactions between DNA and acetic acid. The results of different force fields are compared with the results from QM calculations. From left to right: AMOEBA (a and d), AMBER (b and e), CHARMM (c and f). This order is kept in Figs. 2 to 5
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.948 0.741 0.0109 0.0664 0.0229
AMBER 0.946 1.049 0.0157 0.363 0.0329
CHARMM 0.933 1.023 0.0172 0.351 0.0360
DNA AMOEBA 0.978 0.794 0.0074 0.104 0.0156
AMBER 0.948 1.017 0.0149 0.366 0.0314
CHARMM 0.921 0.994 0.0183 0.357 0.0383
Tab.6  Interaction energies between nucleic acids and water (3?5 Å)
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.742 0.792 0.0255 0.199 0.122
AMBER 0.872 0.963 0.0200 0.937 0.0962
CHARMM 0.853 0.853 0.0193 0.423 0.0932
DNA AMOEBA 0.927 0.958 0.0146 0.842 0.0698
AMBER 0.945 0.904 0.0112 0.627 0.0566
CHARMM 0.832 0.756 0.0108 0.123 0.0886
Tab.7  Interaction energies between nucleic acids and water (2.5?3 Å)
Fig.3  Linear fit curve for the interaction energies between nucleic acid and water within 3?5 Å, data corresponding to Table 6. The figures are in the same order as described in Fig. 1
Fig.4  Linear fit curve for the interaction energies between nucleic acid and water within 2.5?3 Å, data corresponding to Table 7. The figures are in the same order as described in Fig. 1
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.846 0.808 0.0215 ?5.419 1.065
AMBER 0.909 0.993 0.0197 5.722 0.974
CHARMM 0.856 0.929 0.0238 1.892 1.176
DNA AMOEBA 0.939 0.884 0.0141 ?1.074 0.708
AMBER 0.891 0.969 0.0212 5.630 1.064
CHARMM 0.837 0.906 0.0250 1.813 1.250
Tab.8  Interaction energies between nucleic acids and Na+
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.825 0.804 0.0231 ?6.500 1.126
AMBER 0.908 0.933 0.0185 3.136 0.901
CHARMM 0.886 0.906 0.0206 1.011 0.967
DNA AMOEBA 0.953 0.852 0.0666 ?3.509 0.324
AMBER 0.928 0.928 0.0642 2.660 0.061
CHARMM 0.905 0.869 0.0609 ?1.028 0.297
Tab.9  Interaction energies between nucleic acids and K+
Fig.5  Linear fit curve for the interaction energies between nucleic acid and sodium cation, data corresponding to Table 8. The figures are in the same order as described in Fig. 1
Fig.6  Linear fit curve for the interaction energies between nucleic acid and potassium cation, data corresponding to Table 9. The figures are in the same order as described in Fig. 1
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.816 0.849 0.0360 ?6.386 1.754
AMBER 0.938 1.006 0.0094 4.207 0.199
CHARMM 0.910 0.974 0.0440 1.931 1.689
DNA AMOEBA 0.954 0.906 0.0336 ?3.183 0.161
AMBER 0.953 0.999 0.0173 3.576 0.141
CHARMM 0.928 0.934 0.0850 ?0.216 0.170
Tab.10  Interaction energies between nucleic acids and K+ (RI-MP2)
Fig.7  Left: The absolute differences between QM calculation and AMOEBA FF results are plotted against the Phosphorus-Potassium distances in corresponding structures. Right: Representative conformations for the average distance and the largest distance
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