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McCutchin C, Edgar KJ, Chen CL, Dove PM. Silica-Biomacromolecule Interactions: Toward a Mechanistic Understanding of Silicification. Biomacromolecules 2025; 26:43-84. [PMID: 39382567 PMCID: PMC11733937 DOI: 10.1021/acs.biomac.4c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 10/10/2024]
Abstract
Silica-organic composites are receiving renewed attention for their versatility and environmentally benign compositions. Of particular interest is how macromolecules interact with aqueous silica to produce functional materials that confer remarkable physical properties to living organisms. This Review first examines silicification in organisms and the biomacromolecule properties proposed to modulate these reactions. We then highlight findings from silicification studies organized by major classes of biomacromolecules. Most investigations are qualitative, using disparate experimental and analytical methods and minimally characterized materials. Many findings are contradictory and, altogether, demonstrate that a consistent picture of biomacromolecule-Si interactions has not emerged. However, the collective evidence shows that functional groups, rather than molecular classes, are key to understanding macromolecule controls on mineralization. With recent advances in biopolymer chemistry, there are new opportunities for hypothesis-based studies that use quantitative experimental methods to decipher how macromolecule functional group chemistry and configuration influence thermodynamic and kinetic barriers to silicification. Harnessing the principles of silica-macromolecule interactions holds promise for biocomposites with specialized applications from biomedical and clean energy industries to other material-dependent industries.
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Affiliation(s)
| | - Kevin J. Edgar
- Department
of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
- Macromolecules
Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chun-Long Chen
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Patricia M. Dove
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Macromolecules
Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Geosciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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2
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Doveiko D, Kubiak-Ossowska K, Chen Y. Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study. ACS OMEGA 2024; 9:4123-4136. [PMID: 38284092 PMCID: PMC10809255 DOI: 10.1021/acsomega.3c06657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/21/2023] [Accepted: 12/25/2023] [Indexed: 01/30/2024]
Abstract
Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.
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Affiliation(s)
- Daniel Doveiko
- Photophysics
Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, 107 Rottenrow, Glasgow G4 0NG, U.K.
| | - Karina Kubiak-Ossowska
- Chemical
Engineering, James Weir Building, University
of Strathclyde, Glasgow G1 1XJ, U.K.
| | - Yu Chen
- Photophysics
Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, 107 Rottenrow, Glasgow G4 0NG, U.K.
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Kaneda M, Dong D, Chen Y, Zhang X, Xue Y, Bryantsev VS, Elimelech M, Zhong M. Molecular Design of Functional Polymers for Silica Scale Inhibition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:871-882. [PMID: 38150403 DOI: 10.1021/acs.est.3c06504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.
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Affiliation(s)
- Masashi Kaneda
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Dengpan Dong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Yinan Chen
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Xiaowei Zhang
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Yazhen Xue
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Vyacheslav S Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Mingjiang Zhong
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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Jiang T, Hu XF, Guan YF, Chen JJ, Yu HQ. Molecular insights into complexation between protein and silica: Spectroscopic and simulation investigations. WATER RESEARCH 2023; 246:120681. [PMID: 37801982 DOI: 10.1016/j.watres.2023.120681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023]
Abstract
The synergistic effect of protein-silica complexation leads to exacerbated membrane fouling in the membrane desalination process, exceeding the individual impacts of silica scaling or protein fouling. However, the molecular-level dynamics of silica binding to proteins and the resulting structural changes in both proteins and silica remain poorly understood. This study investigates the complexation process between silica and proteins-negatively charged bovine serum albumin (BSA) and positively charged lysozyme (LYZ) at neutral pH-using infrared spectroscopy (IR), in situ attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), and multiple computational simulations. The findings reveal that both protein and silica structures undergo changes during the complexation process, with calcium ions in the solution significantly exacerbating these alterations. In particular, in situ ATR-FTIR combined with two-dimensional correlation spectroscopy analysis shows that BSA experiences more pronounced unfolding, providing additional binding sites for silica adsorption compared to LYZ. The adsorbed proteins promote silica polymerization from lower-polymerized to higher-polymerized species. Furthermore, molecular dynamics simulations demonstrate greater conformational variation in BSA through root-mean-square-deviation analysis and the bridging role of calcium ions via mean square displacement analysis. Molecular docking and density functional theory calculations identify the binding sites and energy of silica on proteins. In summary, this research offers a comprehensive understanding of the protein-silica complexation process, contributing to the knowledge of synergistic behaviors of inorganic scaling and organic fouling on membrane surfaces. The integrated approach used here may also be applicable for exploring other complex complexation processes in various environments.
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Affiliation(s)
- Ting Jiang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Xiao-Fan Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Yan-Fang Guan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China.
| | - Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China.
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Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration. Nat Commun 2023; 14:480. [PMID: 36717559 PMCID: PMC9886994 DOI: 10.1038/s41467-023-36112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Diatoms are unicellular algae characterized by silica cell walls. These silica elements are known to be formed intracellularly in membrane-bound silica deposition vesicles and exocytosed after completion. How diatoms maintain membrane homeostasis during the exocytosis of these large and rigid silica elements remains unknown. Here we study the membrane dynamics during cell wall formation and exocytosis in two model diatom species, using live-cell confocal microscopy, transmission electron microscopy and cryo-electron tomography. Our results show that during its formation, the mineral phase is in tight association with the silica deposition vesicle membranes, which form a precise mold of the delicate geometrical patterns. We find that during exocytosis, the distal silica deposition vesicle membrane and the plasma membrane gradually detach from the mineral and disintegrate in the extracellular space, without any noticeable endocytic retrieval or extracellular repurposing. We demonstrate that within the cell, the proximal silica deposition vesicle membrane becomes the new barrier between the cell and its environment, and assumes the role of a new plasma membrane. These results provide direct structural observations of diatom silica exocytosis, and point to an extraordinary mechanism in which membrane homeostasis is maintained by discarding, rather than recycling, significant membrane patches.
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Maddala SP, Liao WC, Joosten RRM, Soleimani M, Tuinier R, Friedrich H, van Benthem RATM. Chain length of bioinspired polyamines affects size and condensation of monodisperse silica particles. Commun Chem 2021; 4:160. [PMID: 36697574 PMCID: PMC9814531 DOI: 10.1038/s42004-021-00595-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/22/2021] [Indexed: 01/28/2023] Open
Abstract
Polyamines play a major role in biosilicification reactions in diatoms and sponges. While the effects of polyamines on silicic acid oligomerization and precipitation are well known, the impact of polyamines chain length on silica particle growth is unclear. We studied the effects of polyamine chain length on silica particle growth and condensation in a known, simple, and salt-free biphasic reaction system; with tetraethyl orthosilicate as organic phase and polyamine dissolved in the aqueous phase. The particles at various growth stages were characterized by Cryo- Transmission Electron Microscopy, Scanning Electron Microscopy, Thermogravimetric Analysis, Zeta Potential, and solid-state NMR analysis. Polyamines were found co-localized within silica particles and the particle diameter increased with an increase in polyamine chain length, whereas silica condensation showed the opposite trend. Particle growth is proposed to progress via a coacervate intermediate while the final particles have a core shell structure with an amine-rich core and silica-rich shell. The results presented in this paper would of interest for researchers working in the field of bioinspired materials.
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Affiliation(s)
- Sai Prakash Maddala
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Center for Multiscale Electron Microscopy, Eindhoven University of Technology, Groene Loper 5, 5612 AE, Eindhoven, The Netherlands
| | - Wei-Chih Liao
- DSM Materials Science Center, 6167 RD, Geleen, The Netherlands
| | - Rick R M Joosten
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Center for Multiscale Electron Microscopy, Eindhoven University of Technology, Groene Loper 5, 5612 AE, Eindhoven, The Netherlands
| | - Mohammad Soleimani
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Center for Multiscale Electron Microscopy, Eindhoven University of Technology, Groene Loper 5, 5612 AE, Eindhoven, The Netherlands
| | - Remco Tuinier
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Heiner Friedrich
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
- Center for Multiscale Electron Microscopy, Eindhoven University of Technology, Groene Loper 5, 5612 AE, Eindhoven, The Netherlands.
| | - Rolf A T M van Benthem
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
- DSM Materials Science Center, 6167 RD, Geleen, The Netherlands.
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Zhao P, Li X, Tong Y, Dong X, Qi M. Effect of the interface between magnetic particles and carrier liquids on magnetorheological properties and sedimentation of magnetorheological fluids: A molecular dynamics simulation and experimental insights. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Manning JH, Walkley B, Provis JL, Patwardhan SV. Mimicking Biosintering: The Identification of Highly Condensed Surfaces in Bioinspired Silica Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:561-568. [PMID: 33372796 PMCID: PMC7815198 DOI: 10.1021/acs.langmuir.0c03261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Interfacial interactions between inorganic surfaces and organic additives are vital to develop new complex nanomaterials. Learning from biosilica materials, composite nanostructures have been developed, which exploit the strength and directionality of specific polyamine additive-silica surface interactions. Previous interpretations of these interactions are almost universally based on interfacial charge matching and/or hydrogen bonding. In this study, we analyzed the surface chemistry of bioinspired silica (BIS) materials using solid-state nuclear magnetic resonance (NMR) spectroscopy as a function of the organic additive concentration. We found significant additional association between the additives and fully condensed (Q4) silicon species compared to industrial silica materials, leading to more overall Q4 concentration and higher hydrothermal stability, despite BIS having a shorter synthesis time. We posit that the polyfunctionality and catalytic activity of additives in the BIS synthesis lead to both of these surface phenomena, contrasting previous studies on monofunctional surfactants used in most other artificial templated silica syntheses. From this, we propose that additive polyfunctionality can be used to generate tailored artificial surfaces in situ and provide insights into the process of biosintering in biosilica systems, highlighting the need for more in-depth simulations on interfacial interactions at silica surfaces.
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Affiliation(s)
- Joseph
R. H. Manning
- Department
of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, U.K.
- Department
of Chemical Engineering, The University
of Bath, Bath BA2 7AY, U.K.
- Department
of Chemistry, University College London, London WC1E 6BT, U.K.
| | - Brant Walkley
- Department
of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, U.K.
- Department
of Materials Science and Engineering, The
University of Sheffield, Sheffield S1 3JD, U.K.
| | - John L. Provis
- Department
of Materials Science and Engineering, The
University of Sheffield, Sheffield S1 3JD, U.K.
| | - Siddharth V. Patwardhan
- Department
of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, U.K.
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