journal article·2017-06-15

Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton

Haiyang Zhang, Yang Jiang, Hai Yan, Chunhua Yin, Tianwei Tan, David van der Spoel

Publisher page

Abstract

Computational free-energy correction strategies and the choice of experimental proton hydration free energy, Δ G s * (H + ), are analyzed to investigate the apparent controversy in experimental thermodynamics of ionic hydration. Without corrections, the hydration free-energy (Δ G hyd ) calculations match experiments with Δ G s * (H + ) = −1064 kJ/mol as reference. Using the Galvani surface potential the resulting (real) Δ G hyd are consistent with Δ G s * (H + ) = −1098 kJ/mol. When applying, in an ad hoc manner, the discrete solvent correction, Δ G hyd matching the “consensus” Δ G s * (H + ) of −1112 kJ/mol are obtained. This analysis rationalizes reports on Δ G hyd calculations for ions using different experimental references. For neutral amino acid side chains Δ G hyd are independent of the water model, whereas there are large differences in Δ G hyd due to the water model for charged species, suggesting that long-range ordering of water around ions yields an important contribution to the Δ G hyd . These differences are reduced significantly when applying consistent corrections, but to obtain the most accurate results it is recommended to use the water model belonging to the force field.
Source: openalex_inverted_index · Quality: baseline

Research context

OpenAlex topics: Spectroscopy and Quantum Chemical Studies · Protein Structure and Dynamics · Advanced Chemical Physics Studies

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China

Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China

Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden

Funding

Vetenskapsr?det · Ministry of Education of the People's Republic of China · Ministry of Science and Technology of the People's Republic of China · Natural Science Foundation of Beijing Municipality · China Postdoctoral Science Foundation · National Natural Science Foundation of China

References (64)

Show source-provided references
1. 10.1038/351761a010.1038/351761a0 ↗
2. 10.1073/pnas.05252079910.1073/pnas.052520799 ↗
3. 10.1002/prot.2288610.1002/prot.22886 ↗
4. 10.1093/nar/gks37510.1093/nar/gks375 ↗
5. 10.1021/acs.chemrev.6b0044010.1021/acs.chemrev.6b00440 ↗
6. Hünenberger P. · 2011
7. 10.1039/FT991870299510.1039/FT9918702995 ↗
8. 10.1039/tf956520157310.1039/tf9565201573 ↗
9. 10.1021/ja00863a00210.1021/ja00863a002 ↗
10. 10.1021/cr60236a00410.1021/cr60236a004 ↗
11. 10.1063/1.356702210.1063/1.3567022 ↗
12. 10.1021/ct300156h10.1021/ct300156h ↗
13. 10.1021/jp982638r10.1021/jp982638r ↗
14. 10.1021/jp054088k10.1021/jp054088k ↗
15. 10.1021/jp063552y10.1021/jp063552y ↗
16. Marenich A. V. · 2012
17. 10.1021/ct400751u10.1021/ct400751u ↗
18. 10.1021/ct400146w10.1021/ct400146w ↗
19. 10.1021/ct500918t10.1021/ct500918t ↗
20. 10.1021/jp505875v10.1021/jp505875v ↗
21. 10.1021/acs.jpclett.5b0112210.1021/acs.jpclett.5b01122 ↗
22. 10.1021/jp501737x10.1021/jp501737x ↗
23. 10.1021/acs.jctc.6b0022310.1021/acs.jctc.6b00223 ↗
24. 10.1021/acs.jcim.5b0028610.1021/acs.jcim.5b00286 ↗
25. 10.1021/bi00507a03010.1021/bi00507a030 ↗
26. 10.1021/j100058a04310.1021/j100058a043 ↗
27. 10.1063/1.55601810.1063/1.556018 ↗
28. 10.1021/je000236i10.1021/je000236i ↗
29. 10.1063/1.158711910.1063/1.1587119 ↗
30. 10.1063/1.482626110.1063/1.4826261 ↗
31. 10.1063/1.220169810.1063/1.2201698 ↗
32. Case D. A. · 2010
33. 10.1021/acs.jpca.6b1269110.1021/acs.jpca.6b12691 ↗
34. 10.1021/acs.jpcb.5b1080910.1021/acs.jpcb.5b10809 ↗
35. 10.1021/jp056043p10.1021/jp056043p ↗
36. 10.1515/umcschem-2015-001310.1515/umcschem-2015-0013 ↗
37. 10.1063/1.217259310.1063/1.2172593 ↗
38. 10.1093/bioinformatics/btt05510.1093/bioinformatics/btt055 ↗
39. 10.1021/ct700301q10.1021/ct700301q ↗
40. 10.1002/jcc.2029110.1002/jcc.20291 ↗
41. Atomic charges of His+and Lys0residues for AMBER 03 and of Hid0and Hie0for OPLS-AA/L in GROMACS 4.4.5 have been corrected and updated in the latest version of GROMACS 5.1.4, and these updates have been used in this work.
42. 10.1016/0167-4838(83)90276-510.1016/0167-4838(83)90276-5 ↗
43. 10.1093/protein/4.1.5710.1093/protein/4.1.57 ↗
44. 10.1139/o77-08310.1139/o77-083 ↗
45. 10.1021/ct200196m10.1021/ct200196m ↗
46. 10.1002/jcc.2009010.1002/jcc.20090 ↗
47. 10.1021/ct050225610.1021/ct0502256 ↗
48. 10.1063/1.168307510.1063/1.1683075 ↗
49. 10.1021/ct050164b10.1021/ct050164b ↗
50. 10.1039/f1987830298510.1039/f19878302985 ↗
51. 10.1039/a907160a10.1039/a907160a ↗
52. 10.1063/1.158712210.1063/1.1587122 ↗
53. 10.1021/ja037005r10.1021/ja037005r ↗
54. 10.1021/jp000041h10.1021/jp000041h ↗
55. 10.1016/j.cocis.2016.06.01510.1016/j.cocis.2016.06.015 ↗
56. 10.1021/jp408632e10.1021/jp408632e ↗
57. 10.1063/1.47709610.1063/1.477096 ↗
58. 10.1021/jp012536s10.1021/jp012536s ↗
59. 10.1016/j.cplett.2013.01.00810.1016/j.cplett.2013.01.008 ↗
60. 10.1002/prot.2112310.1002/prot.21123 ↗
61. 10.1002/jcc.1034910.1002/jcc.10349 ↗
62. 10.1021/jp000784310.1021/jp0007843 ↗
63. 10.1021/jp003919d10.1021/jp003919d ↗
64. Lopes P. E. M. · 2015 · 4710.1007/978-1-4939-1465-4_3 ↗