Molecular docking's pioneering role in materials science. Metal ion site-preference in fluorapatite Scientific paper

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Marija Petković Benazzouz
https://orcid.org/0000-0003-3526-2054
Igor Radović
https://orcid.org/0000-0002-7047-9411
Dušan Milojkov
https://orcid.org/0000-0003-0746-4185
Goran Janjić
https://orcid.org/0000-0002-4138-2637

Abstract

Originally created for biological systems, molecular docking has proven to be useful to predict metal ion binding locations and affinities in materials. By using this novel approach, it was possible to estimate the binding energies of Ca2+, Sr2+, Mn2+, Cu2+, and Pr3+ ions for two different calcium sites in fluorapatite. The data obtained from the crystal structures of doped fluorapatites showed a good agreement with the docking research. The interpretation of docking results was made easier by combining results from DFT calculations with geometrical analysis of crystal structures of small molecules. Notably, this strategy is more favourable than previously used theoretical approaches due to the computational efficiency and the demonstrated reliability.

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How to Cite
[1]
M. Petković Benazzouz, I. Radović, D. Milojkov, and G. Janjić, “Molecular docking’s pioneering role in materials science. Metal ion site-preference in fluorapatite: Scientific paper”, J. Serb. Chem. Soc., vol. 90, no. 7-8, pp. 899–913, Sep. 2025.
Section
Theoretical Chemistry

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References

K. Pajor, L. Pajchel, J. Kolmas, Materials 12 (2019) 2683 (https://doi.org/10.3390/ma12172683)

N. Leroy, E. Bres, Eur. Cell Mater. 30 (2001) 36 (https://doi.org/10.22203/eCM.v002a05)

J. C. Elliott, Structure and chemistry of the apatites and other calcium orthophosphates. Studies in inorganic chemistry, Elsevier, Amsterdam London New-York Tokyo, 1994 (ISBN: 9780444815828)

E. R. Kreidler, F. A. Hummel, Am. Min. 55 (1970) 170.

D. V. Milojkov, V. Đ. Stanić, S. D. Dimović, D. R. Mutavdžić, V. Živković-Radovanović, G. V. Janjić, K. Radotić, Acta Phys. Pol. A. 136 (2019) 86 (https://dx.doi.org/10.12693/APhysPolA.136.86)

J. M. Hughes, M. Cameron, K. D. Crowley, Am. Min. 76 (1991) 1857 (http://www.minsocam.org/ammin/AM76/AM76_1857.pdf)

M. Miyake, K. Ishigaki, T. Suzuki, J. Solid State Chem. 61 (1986) 230 (https://doi.org/10.1016/0022-4596(86)90026-5)

D. V. Milojkov, M. D. Sokić, V. Živković‐Radovanović, V. D. Manojlović, D. R. Mutavdžić, G. V. Janjić, K. Radotić, Opt. Quantum Electron. 55 (2023) 84 (https://dx.doi.org/10.1007/s11082-022-04347-7)

M. E. Fleet, Y. Pan, Am. Min. 82 (1997) 870 (https://doi.org/10.2138/am-1997-9-1004)

P. E. Mackie, R. A. Young, J. Appl. Crystallogr. 6 (1973) 26 (https://doi.org/10.1107/S0021889873008009)

X. Li, J. Zhu, Z. Man, Y. Ao, H. Chen, Sci. Rep. 4446 (2014) 4446 (https://dx.doi.org/10.1038/srep04446)

C. R. Groom, I. J. Bruno, M. P. Lightfoot, S.C. Ward, Acta Crystallogr. B. 72 (2016) 171 (https://doi.org/10.1107/S2052520616003954)

J. M. Hughes, M. Cameron, K. D. Crowley, Am. Min.74 (1989) 870

G. M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson, J. Comput. Chem., 16 (2009) 2785 (https://doi.org/10.1002/jcc.21256)

D. Biovia, H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, T.J.T.J.o.C.P. Richmond, Dassault Systèmes BIOVIA, Discovery Studio Visualizer, v. 17.2.0.16349, San Diego: Dassault Systèmes, 2016, 10 (2000) 0021-9991

R. D. Shannon, Acta Crystallogr. A. 32 (1976) 751 https://doi.org/10.1107/S0567739476001551)

R. T. Downs, M. Hall-Wallace. Am. Min. 88 (2003) 247

D. V Milojkov, A. S Radosavljević-Mihajlović, V. Đ. Stanić, B. J Nastasijević, K. Radotić, I. Janković-Častvan, V. Živković-Radovanović, J. Photochem. Photobiol. B: Biology 239 (2023) 112649 (https://doi.org10.1016/j.jphotobiol.2023.112649)

R. Nikonam Mofrad, S. K. Sadrnezhaad, J. Vahdati Khaki, Scientia Iranica B 24 (2017) 2845 (https://doi.org/10.24200/sci.2017.4314)

V. Đ. Stanić, A. S. Radosavljević-Mihajlović, V. Živković-Radovanović, B. Nastasijević, M. Marinović-Cincović, J. P. Marković, M. D. Budimir, Appl. Surf. Sci, 337 (2015) 72 (https://doi.org/10.1016/j.apsusc.2015.02.065)

K. Tõnsuaadu, K. A. Gross, L. Plūduma, M. Veiderma, J. Therm. Anal. Calorim. 110 (2012) 647 (https://doi.org/10.1007/s10973-011-1877-y)

G. W. C. Silva, O. Hemmers, K. R. Czerwinski, D. W. Lindle, Inorg. Chem. 47 (2008) 7757 (https://doi.org/10.1021/ic800794x)

M. E. Fleet, Y. Pan, Am. Min. 80 (1995) 329 (https://doi.org/10.2138/am-1995-3-414)

D. V. Milojkov, O. F. Silvestre, V. Đ. Stanić, G. V. Janjić, D. R. Mutavdžić, M. Milanović, J. B. Nieder, J. Lumi. 217 (2020) 116757 (https://doi.org/10.1016/j.jlumin.2019.116757)

F. Keshavarz, B. Barbiellini, Comput. Mater. Sci. 226 (2023) 112257 (https://doi.org/10.1016/j.commatsci.2023.112257)

C. A. Anyama, H. Louis, B.E. Inah, T. E. Gber, J. O. Ogar, A. A. Ayi, J. Mol. Struct. 1277 (2023), 134825 (https://doi.org/10.1016/j.molstruc.2022.134825)

Q. Li, W. Zhang, O. Š. Miljanić, C.-H. Sue, Y.-L. Zhao, L. Liu, C. B. Knobler, J. F. Stoddart, O.M. Yaghi, Science 325 (2009) 855 (https://doi.org/10.1126/science.1175441)

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