Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

Rimola, Albert; Costa, Dominique; Sodupe, Mariona; Lambert, Jean-François; Ugliengo, Piero

doi:10.1021/cr3003054

Cited by 527 publications

(697 citation statements)

References 718 publications

(1,669 reference statements)

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“…It is known that the surface interaction between RSFs and SNSs leads to the coating of RSFs on the SNSs, rather than phase segregation. [37] No artificial crystallization step was included, which left a relatively large amount of amorphous RSF on the surface of SNS. The amorphous RSF was mainly removed by washing with water.…”

Section: Resultsmentioning

confidence: 99%

“…The high pH of the solution is believed to induce negative charges on the SNS surface, prompting formation of the b-sheet structure. [37,38] The thin b-sheet layers were then transformed into carbonaceous materials by heating to 800 8C in an inert gas atmosphere. Following the thermal treatment, the SNSs were removed using HF, yielding the UTH-CNs.…”

Section: Resultsmentioning

confidence: 99%

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Ultra‐Thin Hollow Carbon Nanospheres for Pseudocapacitive Sodium‐Ion Storage

et al. 2014

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Ultra‐thin hollow carbon nanospheres (UTH‐CNs) are fabricated for use as anodes of asymmetric sodium ion pseudocapacitors. The ∼3 nm thick amorphous carbon walls obtained from regenerated silk proteins as a template exhibit a well‐defined porous structure suitable for reversible sodium‐ion storage. The UTH‐CNs show remarkable electrochemical activity with sodium via a pseudocapacitive reaction, delivering a large reversible capacity as well as superior rate performance for more than 1000 cycles. The pseudocapacitors based on UTH‐CNs exhibit a capacitance of 186 F g−1, a specific energy of 43 Wh kg−1 and a power density of 10 kW kg−1. This represents the highest value yet reported for asymmetric sodium‐ion storage pseudocapacitors.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Ultra‐Thin Hollow Carbon Nanospheres for Pseudocapacitive Sodium‐Ion Storage

et al. 2014

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“…DFT calculations have also been used to elucidate amino acid adsorption on silica (Rimola et al 2013), hydroxyapatite (Jimenez-Izal et al 2012), alumina (Arrouvel et al 2007) and titania (Carravetta et al 2009;Koch et al 2011) surfaces where electrostatic interactions and hydrogen bonds are important, and where the formation of chemical bonds often implies complex reaction mechanisms. The interaction of quartz and aluminosilicate structures with phospholipids was also studied by DFT to understand why the enzyme phospholipase A2 digests phospholipids faster in the presence of quartz than aluminosilicates (Snyder & Madura, 2008).…”

Section: Morphologymentioning

confidence: 99%

“…A number of FFs have been developed for MD simulation of bulk silicon oxides and their interfaces with water due to the wide range of technological applications of silica-based materials (see reviews by Butenuth et al (2012) and by Rimola et al (2013)). There are, however, some challenges in building a FF for silicon oxide surfaces.…”

Section: Silicon Oxide Surfacesmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

181

193

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Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

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“…[3] Gly was among the products of the Miller experiment, which examined the production of amino acids under possible primitive Earth conditions, [9] and it has been considered a reference molecule in a large number of experimental and theoretical investigations regarding the adsorption of amino acids on mineral matter. [3,10,11] Titania was considered a model substrate in several studies that were primarily concerned with the adsorption of amino acids onto mineral oxides from both the aqueous and the gas phases. [3] Moreover, TiO 2 may have actually been present on prebiotic Earth.…”

mentioning

confidence: 99%

The Formation and Self‐Assembly of Long Prebiotic Oligomers Produced by the Condensation of Unactivated Amino Acids on Oxide Surfaces

Martra¹,

Deiana²,

Sakhno³

et al. 2014

Angewandte Chemie

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In situ IR and mass spectrometry evidence for the catalytic formation on SiO2 and TiO2 surfaces of glycine oligomers (poly‐Gly) up to 16 units long by successive feeding with monomers from the vapor phase is presented. Parallel experiments carried out on hydroxyapatite resulted in the unreactive adsorption of Gly, thus indicating that the oligomerization was specifically catalyzed by the surfaces of SiO2 and TiO2. Furthermore, the poly‐Gly moved on the surface when contacted with H2O vapor and formed self‐assembled aggregates containing both helical and β‐sheet‐like structural motifs. These results indicate that polypeptides formed by the condensation of amino acids adsorbed on a mineral surface can evolve into structured supramolecular assemblies.

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Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

Abstract: This is an author version of the contribution published on:Questa

Cited by 527 publications

References 718 publications

Ultra‐Thin Hollow Carbon Nanospheres for Pseudocapacitive Sodium‐Ion Storage

Ultra‐Thin Hollow Carbon Nanospheres for Pseudocapacitive Sodium‐Ion Storage

Modeling and simulation of protein–surface interactions: achievements and challenges

The Formation and Self‐Assembly of Long Prebiotic Oligomers Produced by the Condensation of Unactivated Amino Acids on Oxide Surfaces

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