1
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Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
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Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
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2
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Antalicz B, Sengupta S, Vilangottunjalil A, Versluis J, Bakker HJ. Orientational Behavior and Vibrational Response of Glycine at Aqueous Interfaces. J Phys Chem Lett 2024; 15:2075-2081. [PMID: 38358315 PMCID: PMC10895693 DOI: 10.1021/acs.jpclett.3c02930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Aqueous glycine plays many different roles in living systems, from being a building block for proteins to being a neurotransmitter. To better understand its fundamental behavior, we study glycine's orientational behavior near model aqueous interfaces, in the absence and presence of electric fields and biorelevant ions. To this purpose, we use a surface-specific technique called heterodyne-detected vibrational sum-frequency generation spectroscopy (HD-VSFG). Using HD-VSFG, we directly probe the symmetric and antisymmetric stretching vibrations of the carboxylate group of zwitterionic glycine. From their relative amplitudes, we infer the zwitterion's orientation near surfactant-covered interfaces and find that it is governed by both electrostatic and surfactant-specific interactions. By introducing additional ions, we observe that the net orientation is altered by the enhanced ionic strength, indicating a change in the balance of the electrostatic and surfactant-specific interactions.
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Affiliation(s)
- Balázs Antalicz
- Ultrafast Spectroscopy, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Sanghamitra Sengupta
- Ultrafast Spectroscopy, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | - Jan Versluis
- Ultrafast Spectroscopy, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Huib J Bakker
- Ultrafast Spectroscopy, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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3
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Harold SE, Warf SL, Shields GC. Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water. Phys Chem Chem Phys 2023; 25:28517-28532. [PMID: 37847315 DOI: 10.1039/d3cp02915h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Insight into the origin of prebiotic molecules is key to our understanding of how living systems evolved into the complex network of biological processes on Earth. By modelling diglycine and triglycine peptide formation in the prebiotic atmosphere, we provide a plausible pathway for peptide growth. By examining different transition states (TSs), we conclude that the formation of diglycine and triglycine in atmospheric nanoclusters of water in the prebiotic atmosphere kinetically favors peptide growth by an N-to-C synthesis of glycines through a trans conformation. Addition of water stabilizes the TS structures and lowers the Gibbs free activation energies. At temperatures that model the prebiotic atmosphere, the free energies of activation with a six water nanocluster as part of the TS are predicted to be 16 kcal mol-1 relative to the prereactive complex. Examination of the trans vs. cis six water transition states reveals that a homodromic water network that maximizes the acceptor/donor nature of the six waters is responsible for enhanced kinetic favorability of the trans N-to-C pathway. Compared to the non-hydrated trans TS, the trans six-water TS accelerates the reaction of diglycine and glycine to form triglycine by 13 orders of magnitude at 217 K. Nature uses the trans N-to-C pathway to synthesize proteins in the ribosome, and we note the similarities in hydrogen bond stabilization between the transition state for peptide synthesis in the ribosome and the transition states formed in nanoclusters of water in the same pathway. These results support the hypothesis that small oligomers formed in the prebiotic atmosphere and rained onto earth's surface.
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Affiliation(s)
- Shannon E Harold
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - Skyler L Warf
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
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Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids. Proc Natl Acad Sci U S A 2022; 119:e2212642119. [PMID: 36191178 PMCID: PMC9586328 DOI: 10.1073/pnas.2212642119] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Amide bond formation, the essential condensation reaction underlying peptide synthesis, is hindered in aqueous systems by the thermodynamic constraints associated with dehydration. This represents a key difficulty for the widely held view that prebiotic chemical evolution leading to the formation of the first biomolecules occurred in an oceanic environment. Recent evidence for the acceleration of chemical reactions at droplet interfaces led us to explore aqueous amino acid droplet chemistry. We report the formation of dipeptide isomer ions from free glycine or L-alanine at the air-water interface of aqueous microdroplets emanating from a single spray source (with or without applied potential) during their flight toward the inlet of a mass spectrometer. The proposed isomeric dipeptide ion is an oxazolidinone that takes fully covalent and ion-neutral complex forms. This structure is consistent with observed fragmentation patterns and its conversion to authentic dipeptide ions upon gentle collisions and for its formation from authentic dipeptides at ultra-low concentrations. It also rationalizes the results of droplet fusion experiments that show that the dipeptide isomer facilitates additional amide bond formation events, yielding authentic tri- through hexapeptides. We propose that the interface of aqueous microdroplets serves as a drying surface that shifts the equilibrium between free amino acids in favor of dehydration via stabilization of the dipeptide isomers. These findings offer a possible solution to the water paradox of biopolymer synthesis in prebiotic chemistry.
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Abadian H, Cornette P, Costa D, Mezzetti A, Gervais C, Lambert JF. Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8038-8053. [PMID: 35737817 DOI: 10.1021/acs.langmuir.2c00841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO2 together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.
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Affiliation(s)
- Hagop Abadian
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Pauline Cornette
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Dominique Costa
- Institut de Recherche de Chimie Paris (IRCP, UMR8247 CNRS), 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alberto Mezzetti
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP, UMR 7574 CNRS), Case courrier 174, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface (LRS, UMR 7609 CNRS), Case courrier 178, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Giussani L, Tabacchi G, Coluccia S, Fois E. Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels. Int J Mol Sci 2019; 20:E2965. [PMID: 31216631 PMCID: PMC6627703 DOI: 10.3390/ijms20122965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 02/01/2023] Open
Abstract
Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.
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Affiliation(s)
- Lara Giussani
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Gloria Tabacchi
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Salvatore Coluccia
- Dipartimento di Chimica, Turin University, Via P. Giuria 7, I-10125 Turin, Italy.
| | - Ettore Fois
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
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7
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Trachta M, Bludský O, Rubeš M. The interaction of proteins with silica surfaces. Part II: Free energies of capped amino acids. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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9
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Shi B, Shin YK, Hassanali AA, Singer SJ. Biomolecules at the amorphous silica/water interface: Binding and fluorescence anisotropy of peptides. Colloids Surf B Biointerfaces 2017; 157:83-92. [DOI: 10.1016/j.colsurfb.2017.05.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/19/2023]
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10
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Sebben D, Pendleton P. Analysis of ionic strength effects on the adsorption of simple amino acids. J Colloid Interface Sci 2015; 443:153-61. [DOI: 10.1016/j.jcis.2014.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 11/29/2022]
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11
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Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation. Sci Rep 2014; 4:6594. [PMID: 25307449 PMCID: PMC4194432 DOI: 10.1038/srep06594] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/17/2014] [Indexed: 12/01/2022] Open
Abstract
Defects are often considered as the active sites for chemical reactions. Here a variety of defects in zeolites are used to stabilize zwitterionic glycine that is not self-stable in gas phase; in addition, effects of acidic strengths and zeolite channels on zwitterionic stabilization are demonstrated. Glycine zwitterions can be stabilized by all these defects and energetically prefer to canonical structures over Al and Ga Lewis acidic sites rather than Ti Lewis acidic site, silanol and titanol hydroxyls. For titanol (Ti-OH), glycine interacts with framework Ti and hydroxyl sites competitively, and the former with Lewis acidity predominates. The transformations from canonical to zwitterionic glycine are obviously more facile over Al and Ga Lewis acidic sites than over Ti Lewis acidic site, titanol and silanol hydroxyls. Charge transfers that generally increase with adsorption energies are found to largely decide the zwitterionic stabilization effects. Zeolite channels play a significant role during the stabilization process. In absence of zeolite channels, canonical structures predominate for all defects; glycine zwitterions remain stable over Al and Ga Lewis acidic sites and only with synergy of H-bonding interactions can exist over Ti Lewis acidic site, while automatically transform to canonical structures over silanol and titanol hydroxyls.
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12
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Gas-Phase and Microsolvated Glycine Interacting with Boron Nitride Nanotubes. A B3LYP-D2* Periodic Study. INORGANICS 2014. [DOI: 10.3390/inorganics2020334] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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13
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Heinz H. The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution--accurate computational models and experiment. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:244105. [PMID: 24863288 DOI: 10.1088/0953-8984/26/24/244105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a scale of 1-1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed.
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Affiliation(s)
- Hendrik Heinz
- Department of Polymer Engineering, University of Akron, Akron, OH 44325, USA
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Delle Piane M, Vaccari S, Corno M, Ugliengo P. Silica-Based Materials as Drug Adsorbents: First Principle Investigation on the Role of Water Microsolvation on Ibuprofen Adsorption. J Phys Chem A 2014; 118:5801-7. [DOI: 10.1021/jp411173k] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Massimo Delle Piane
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Stefano Vaccari
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Marta Corno
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Piero Ugliengo
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
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15
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Rimola A, Costa D, Sodupe M, Lambert JF, Ugliengo P. Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments. Chem Rev 2013; 113:4216-313. [PMID: 23289428 DOI: 10.1021/cr3003054] [Citation(s) in RCA: 328] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
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16
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De La Pierre M, Bruno M, Manfredotti C, Nestola F, Prencipe M, Manfredotti C. The (100), (111) and (110) surfaces of diamond: anab initioB3LYP study. Mol Phys 2013. [DOI: 10.1080/00268976.2013.829250] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Delle Piane M, Corno M, Ugliengo P. Does Dispersion Dominate over H-Bonds in Drug-Surface Interactions? The Case of Silica-Based Materials As Excipients and Drug-Delivery Agents. J Chem Theory Comput 2013; 9:2404-15. [PMID: 26583731 DOI: 10.1021/ct400073s] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Amorphous silica is widely employed in pharmaceutical formulations both as a tableting, anticaking agent and as a drug delivery system, whereas MCM-41 mesoporous silica has been recently proposed as an efficient support for the controlled release of drugs. Notwithstanding the relevance of this topic, the atomistic details about the specific interactions between the surfaces of the above materials and drugs and the energetic of adsorption are almost unknown. In this work, we resort to a computational ab initio approach, based on periodic Density Functional Theory (DFT), to study the adsorption behavior of two popular drugs (aspirin and ibuprofen) on two models of an amorphous silica surface characterized by different hydrophilic/hydrophobic properties due to different SiOH surface groups' density. Particular effort was devoted to understand the role of dispersive (vdW) interactions in the adsorption mechanism and their interplay with H-bond interactions. On the hydrophilic silica surface, the H-bond pattern of the Si-OH groups rearranges to comply with the formation of new H-bond interactions triggered by the adsorbed drug. The interaction energy of ibuprofen with the hydrophilic model of the silica surface is computed to be very close to the sublimation energy of the ibuprofen molecular crystal, accounting for the experimental evidence of ibuprofen crystal amorphization induced by the contact with the mesoporous silica material. For both surface models, dispersion interactions play a crucial role in dictating the features of the drug/silica system, and they become dominant for the hydrophobic surface. It was proved that a competition may exist between directional H-bonds and nonspecific dispersion driven interactions, with important structural and energetic consequences for the adsorption. The results of this work emphasize the inadequacy of plain DFT methods to model adsorption processes involving inorganic surfaces and drugs of moderate size, due to the missing term accounting for London dispersion interactions.
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Affiliation(s)
- Massimo Delle Piane
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, via P. Giuria 7, 10125 Torino, Italy
| | - Marta Corno
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, via P. Giuria 7, 10125 Torino, Italy
| | - Piero Ugliengo
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, via P. Giuria 7, 10125 Torino, Italy
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18
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Lambert JF, Jaber M, Georgelin T, Stievano L. A comparative study of the catalysis of peptide bond formation by oxide surfaces. Phys Chem Chem Phys 2013; 15:13371-80. [DOI: 10.1039/c3cp51282g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Wright LB, Walsh TR. First-principles molecular dynamics simulations of NH 4+ and CH3COO− adsorption at the aqueous quartz interface. J Chem Phys 2012; 137:224702. [DOI: 10.1063/1.4769727] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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20
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Costa D, Garrain PA, Baaden M. Understanding small biomolecule-biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces. J Biomed Mater Res A 2012; 101:1210-22. [DOI: 10.1002/jbm.a.34416] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 08/07/2012] [Accepted: 08/12/2012] [Indexed: 12/13/2022]
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21
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Patwardhan SV, Emami FS, Berry RJ, Jones SE, Naik RR, Deschaume O, Heinz H, Perry CC. Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption. J Am Chem Soc 2012; 134:6244-56. [PMID: 22435500 DOI: 10.1021/ja211307u] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15-450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion-dipole, dipole-dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide pI, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised.
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Affiliation(s)
- Siddharth V Patwardhan
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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22
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Costa D, Garrain PA, Diawara B, Marcus P. Biomolecule-biomaterial interaction: a DFT-D study of glycine adsorption and self-assembly on hydroxylated Cr2O3 surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2747-60. [PMID: 21338116 DOI: 10.1021/la104317j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The adsorption of glycine, the building block of amino acids, on hydroxylated (0001)-Cr2O3 model surfaces, representing the stainless steel passive film surface, was modeled by means of the GGA + U method. The roles of glycine coverage and surface termination (hydroxylated Cr- and O-terminated surfaces) on the adsorption mode and self-assembly properties were explored. The hydroxylated Cr-terminated Cr2O3 surface, which presents two types of (H)OH groups exhibiting different acidic character, is more reactive than the hydroxylated O-terminated surface, where one single type of OH group is present, for all adsorption modes and coverages considered. Outer sphere adsorption occurs in the zwitterion form, stabilized at low coverage through H-bond formation with coadsorbed water molecules, and at the monolayer coverage by glycine self-assembling. The OH substitution by glycinate is favored on the hydroxylated Cr-terminated surface and not on the O-terminated one. The inclusion of dispersion forces does not change the observed tendencies. An atomistic thermodynamics approach suggests that outer sphere adsorption is thermodynamically favored over inner sphere adsorption in the whole domain of glycine concentration. The obtained SAM's free energies of formation are rationalized in a model considering the balance between sublimation and solvation free energies, and extrapolated to other amino acids, to predict the SAMs formation above hydroxylated surfaces. It is found that hydrophobic AA tend to self-assemble at the surface, whereas hydrophilic ones do not.
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Affiliation(s)
- D Costa
- Laboratoire de Physico-Chimie des Surfaces, CNRS-ENSCP (UMR 7045) , Ecole Nationale Supérieure de Chimie de Paris, Chimie-Paristech, 11 rue Pierre et Marie Curie, 75005 France
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Understanding protein adsorption phenomena at solid surfaces. Adv Colloid Interface Sci 2011; 162:87-106. [PMID: 21295764 DOI: 10.1016/j.cis.2010.12.007] [Citation(s) in RCA: 986] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/21/2010] [Accepted: 12/28/2010] [Indexed: 11/21/2022]
Abstract
Protein adsorption at solid surfaces plays a key role in many natural processes and has therefore promoted a widespread interest in many research areas. Despite considerable progress in this field there are still widely differing and even contradictive opinions on how to explain the frequently observed phenomena such as structural rearrangements, cooperative adsorption, overshooting adsorption kinetics, or protein aggregation. In this review recent achievements and new perspectives on protein adsorption processes are comprehensively discussed. The main focus is put on commonly postulated mechanistic aspects and their translation into mathematical concepts and model descriptions. Relevant experimental and computational strategies to practically approach the field of protein adsorption mechanisms and their impact on current successes are outlined.
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Chashchikhin V, Rykova E, Bagaturyants A. Density functional theory modeling of the adsorption of small analyte and indicator dye 9-(diphenylamino)acridine molecules on the surface of amorphous silicananoparticles. Phys Chem Chem Phys 2011; 13:1440-7. [DOI: 10.1039/c0cp00821d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R, Walsh TR. Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics. Biomacromolecules 2010; 11:3266-74. [DOI: 10.1021/bm100646z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebecca Notman
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom, Genetically Engineered Materials Science and Engineering Center, and Departments of Materials Science and Engineering and Microbiology, University of Washington, Seattle, Washington, United States
| | - E. Emre Oren
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom, Genetically Engineered Materials Science and Engineering Center, and Departments of Materials Science and Engineering and Microbiology, University of Washington, Seattle, Washington, United States
| | - Candan Tamerler
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom, Genetically Engineered Materials Science and Engineering Center, and Departments of Materials Science and Engineering and Microbiology, University of Washington, Seattle, Washington, United States
| | - Mehmet Sarikaya
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom, Genetically Engineered Materials Science and Engineering Center, and Departments of Materials Science and Engineering and Microbiology, University of Washington, Seattle, Washington, United States
| | - Ram Samudrala
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom, Genetically Engineered Materials Science and Engineering Center, and Departments of Materials Science and Engineering and Microbiology, University of Washington, Seattle, Washington, United States
| | - Tiffany R. Walsh
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom, Genetically Engineered Materials Science and Engineering Center, and Departments of Materials Science and Engineering and Microbiology, University of Washington, Seattle, Washington, United States
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From biominerals to biomaterials: the role of biomolecule–mineral interactions. Biochem Soc Trans 2009; 37:687-91. [DOI: 10.1042/bst0370687] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Interactions between inorganic materials and biomolecules at the molecular level, although complex, are commonplace. Examples include biominerals, which are, in most cases, facilitated by and in contact with biomolecules; implantable biomaterials; and food and drug handling. The effectiveness of these functional materials is dependent on the interfacial properties, i.e. the extent of molecular level ‘association’ with biomolecules. The present article gives information on biomolecule–inorganic material interactions and illustrates our current understanding using selected examples. The examples include (i) mechanism of biointegration: the role of surface chemistry and protein adsorption, (ii) towards improved aluminium-containing materials, and (iii) understanding the bioinorganic interface: experiment and modelling. A wide range of experimental techniques (microscopic, spectroscopic, particle sizing, thermal methods and solution methods) are used by the research group to study interactions between (bio)molecules and molecular and colloidal species that are coupled with computational simulation studies to gain as much information as possible on the molecular-scale interactions. Our goal is to uncover the mechanisms underpinning any interactions and to identify ‘rules’ or ‘guiding principles’ that could be used to explain and hence predict behaviour for a wide range of (bio)molecule–mineral systems.
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Rimola A, Ugliengo P. The role of defective silica surfaces in exogenous delivery of prebiotic compounds: clues from first principles calculations. Phys Chem Chem Phys 2009; 11:2497-506. [DOI: 10.1039/b820577a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Rimola A, Corno M, Zicovich-Wilson CM, Ugliengo P. Ab initio modeling of protein/biomaterial interactions: competitive adsorption between glycine and water onto hydroxyapatite surfaces. Phys Chem Chem Phys 2009; 11:9005-7. [DOI: 10.1039/b913311a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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