Structural-Dynamic Behavior of Histamine in Solution: the Role of Water Models
DOI:
https://doi.org/10.15407/ujpe71.11.867Keywords:
imidazole ligand, SPC/E water model, TIP3P water model, local solution structure, diffusion, histamineAbstract
A highly dilute aqueous solution of histamine at T = 300 K was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and hydrogen bonds and is practically independent of the choice of the water model. Dynamic analysis based on the mean square displacement functions revealed a significant dependence of the diffusion behavior of histamine on the water model. It was found that the TIP3P water model leads to overestimated values of the diffusion coefficients of water and histamine and a transition to diffusive motion. It was found that the SPC/E water model provides slower dynamics of the solution components, and the values of the diffusion coefficients are in better agreement with experimental data. It was shown that the dynamics of histamine is highly sensitive to the choice of the water model, and the SPC/E model is more suitable for the correct description of the dynamic properties of the "histamine-water" system under physiological conditions.
References
1. I. Bertini, H.B. Gray, E.I. Stiefel, J.S. Valentine. Biological Inorganic Chemistry: Structure and Reactivity (University Science Books, 2007) [ISBN: 1-891389-43-2].
2. Jan Reedijk, K.R. Poeppelmeier. Comprehensive Inorganic Chemistry II: From Elements to Applications (Elsevier Science, 2013) [ISBN: 9780080977744].
3. G. Pirc, J. Stare, J. Mavri, R. Vionello. Hydrogen bond dynamics of histamine monocation in aqueous solution: How geometric parameters influence the hydrogen bond strength. Croatica Chemica Acta 87, 397 (2014).
https://doi.org/10.5562/cca2512
4. M. Pekka, L. Nilsson. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J. Phys. Chem. A 105, 9954 (2001).
https://doi.org/10.1021/jp003020w
5. P. Florová, P. Sklenovsky, P. Banas, M. Otyepka. Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact. J. Chem. Theory and Comput. 6, 3569 (2010).
https://doi.org/10.1021/ct1003687
6. D. Braun, S. Boresch, O. Steinhauser. Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models. J. Chem. Phys. 140, 064107 (2014).
https://doi.org/10.1063/1.4864117
7. Manish Agarwal, Mohammad Parvez Alam, Charusita Chakravarty. Thermodynamic, diffusional, and structural anomalies in rigid-body water models. J. Phys. Chem. B 115, 6935 (2011).
https://doi.org/10.1021/jp110695t
8. W. Smith, T.R. Forester, I.T. Todorov, M. Leslie. The DL_POLY 2 User Manual, Version 2.16 (CCLRC, Daresbury Laboratory, 2006).
9. I. Rosbottom, C.W. Yong, D.L. Geatches, R.B. Hammond, I.T. Todorov, K.J. Roberts. The integrated DL_POLY/DL_FIELD/DL_ANALYSER software platform for molecular dynamics simulations for exploration of the synthonic interactions in saturated benzoic acid/hexane solutions. Molecular Simulation 47, 257 (2021).
https://doi.org/10.1080/08927022.2018.1560441
10. M.P. Allen, D.J. Tildesley. Computer Simulation of Liquids (Clarendon Press, 1986) [ISBN-13: 978-0198556459].
11. L. Hok, J. Mavri, R. Vianello. The effect of deuteration on the H2 receptor histamine binding profile: a computational insight into modified hydrogen bonding interactions. Molecules 25, 6017 (2020).
https://doi.org/10.3390/molecules25246017
12. Han Wang, Ch. Junghans, K. Kremer. Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? Europ. Phys. J. E 28, 221 (2009).
https://doi.org/10.1140/epje/i2008-10413-5
13. J. Stare, J. Mavri, J. Grdadolnik, J. Zidar, Z.B. Maksic, R. Vianello. Hydrogen bond dynamics of histamine monocation in aqueous solution: Car-Parrinello molecular dynamics and vibrational spectroscopy study. J. Phys. Chem. B 115, 5999 (2011).
https://doi.org/10.1021/jp111175e
14. José Guadalupe Rosas Jiménez, Balázs Fábián, Gerhard Hummer. Faster sampling in molecular dynamics simulations with TIP3P-F water. J. Chem. Theory and Comp. 20, 11068 (2024).
https://doi.org/10.1021/acs.jctc.4c00990
15. Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi. Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement. J. Chem. Phys. 150, 204502 (2019).
https://doi.org/10.1063/1.5095978
16. Suvendu Mandal, Th. Franosch, Th. Voigtmann. Glassy relaxation slows down by increasing mobility. Soft Matter 14, 9153 (2018).
https://doi.org/10.1039/C8SM01581C
17. K. Krynicki, Ch.D. Green, D.W. Sawyer. Pressure and temperature dependence of self-diffusion in water. Faraday Discuss. Chem. Soc. 66, 199 (1978).
https://doi.org/10.1039/dc9786600199
18. M. Spanner, F. Hofling, S.C. Kapfer, K.R. Mecke, G.E. Schroeder-Turk, Th. Franosch. Splitting of the universality class of anomalous transport in crowded media. Phys. Rev. Lett. 116, 060601 (2016).
https://doi.org/10.1103/PhysRevLett.116.060601
19. P. Gallo, et al. Water: A tale of two liquids. Chem. Rev. 116, 7463 (2016).
https://doi.org/10.1021/acs.chemrev.5b00750
20. N. Atamas, D. Gavryushenko, K.S. Yablochkova, M.M. Lazarenko, G. Taranyik. Temperature and temporal heterogeneities of water dynamics in the physiological temperature range. J. Mol. Liq. 340, 117201 (2021).
https://doi.org/10.1016/j.molliq.2021.117201
21. J. Frenkel. Kinetic Theory of Liquids (Dover Publications, 1955) [ISBN 13: 8166726261285].
22. N.A. Atamas, M.M. Lazarenko, K.S. Yablochkova, G. Taranyik. Strongly diluted dimethyl-imidazolium chloride-alcohol solutions: solvents are structurally different but dynamic heterogeneities are similar. RSC Advances 11, 37307 (2021).
https://doi.org/10.1039/D1RA05633F
23. V.V. Brazhkin, K. Trachenko. Collective excitations and thermodynamics of disordered state: new insights into an old problem. J. Phys. Chem. B 118, 11417 (2014).
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