The molecular dynamics of silica acids in aqueous solution: Qualitative and quantitative characteristics of oligomers
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The molecular dynamics of silica acids in aqueous solution: Qualitative and quantitative characteristics of oligomers

E.D. Izotova∗ , M.A. Rudakova∗∗ , N.I. Akberova∗∗∗

Kazan Federal University, Kazan, 420008 Russia

E-mail: ∗izotova.e.d@gmail.com, ∗∗maychonka@gmail.com, ∗∗∗nakberov@mail.com

Received January 17, 2020

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DOI: 10.26907/2541-7746.2020.1.5-26 

For citation: Izotova E.D., Rudakova M.A., Akberova N.I. The molecular dynamics of silica acids in aqueous solution: Qualitative and quantitative characteristics of oligomers. Uchenye Zapiski Kazanskogo Universiteta. Seriya Fiziko-Matematicheskie Nauki, 2020, vol. 162, no. 1, pp. 5–26. doi: 10.26907/2541-7746.2020.1.5-26. (In Russian)

 

Abstract

In this work, we studied the diversity of silicic acid oligomers with Sin=(3−8) obtained during molecular dynamics in a reaction Feston–Garofalini force field that describes the process of oligomerization of silicic acids in an aqueous solution at the atomic level. Two systems with different concentrations of silicic acids, including 576 and 729 monomers Si(OH)4 , were studied. According to the calculation results, the highest frequency isomers were represented by linear and branched forms. Throughout the simulation, a high level of dimers was constantly observed. The silicic acids oligomers size increased over time up to 27 Si atoms. The distribution of oligomers by the frequency of permeability for Si n=(3−5) was almost completely comparable with the NMR 29Si and quantum-chemical calculations. A previously undescribed new low-frequency isomer presented in both studied systems was identified among the pentamers. For oligomers with Si n=(6−8) , a wide variety of spatial isomers were observed; some of them have been partially or completely detected experimentally. Analysis of the Si average coordination number during MD simulation showed that 98% of Si atoms have a degree of coordination IV.

Keywords: silicic acids, oligomerization, spatial isomers, molecular dynamics, reaction force field

Figure Captions

Fig. 1. Dynamics of changes in the proportion of silicic acid oligomers with a chain length from Si n=1−8 during 3 ns: a) Si n=1−4 for system45; b) Si n=4−8 for system45; c) Si n=1−4 for system56; d) Si n=4−8 for system56.

Fig. 2. Quantitative distribution of silicon oligomers with chain length Si n=2−27 , during 3 ns MD: a) Si n=2−10 , b) Si n=11−27 . Black color – system45, gray color – system56.

Fig. 3. The twenty most high-frequency graph isomers of silicic acids, for system45 (a) and system56 (b). The proportion of the linear trimmer is taken as 1.

Fig. 4. Trimers of Si n=3 silicic acids: a) the distribution of molecular graphs of silicic acids, b) a stepwise mechanism of a cyclic trimer formation.

Fig. 5. Tetramers of Si n=4 silicic acids: a) the distribution of molecular graphs of silicic acids, b) a stepwise mechanism of a bicyclic tetramer.

Fig. 6. Pentamers of Si n=5 silicic acids: a) the distribution of molecular graphs of silicic acids, b) a stepwise mechanism of formation of Q 1 Q 2 Q 4 (9/10).

Fig. 7. Distribution of molecular graphs of silicic acids hexamers (Si n=6 ): a) system45, b) system56.

Fig. 8. Distribution of molecular graphs of silicic acids heptamers (Si n=7 ): a) system45, b) system56, c) additional structures containing fragments detected by experimental methods [2, 5, 27, 30, 34].

Fig. 9. Distribution of molecular graphs of silicic acids octamers (Si n=8 ): a) system45, b) system56, c) some low-frequency oligomers, fragments of which were detected by the 29Si NMR method [2, 27, 34].

Fig. 10. The coordination number of Si in Si–O compounds and some silicic acid oligomers containing V-coordinated Si.

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