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Effect of Pore Defects on Uniaxial Mechanical Properties of Bulk Hexagonal Hydroxyapatite: A Molecular Dynamics Study. Int J Mol Sci 2023; 24:ijms24021535. [PMID: 36675050 PMCID: PMC9862889 DOI: 10.3390/ijms24021535] [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: 11/30/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Hydroxyapatite (HAP) is a calcium apatite bioceramic used in various naturally-derived and synthetic forms for bone repair and regeneration. While useful for the regrowth of osseus tissue, the poor load-bearing capacity of this material relative to other biomaterials is worsened by the propensity for pore formation during the synthetic processing of scaffolds, blocks, and granules. Here we use molecular dynamics (MD) simulations to improve the current understanding of the defect-altered uniaxial mechanical response in hexagonal HAP single crystals relative to defect-free structures. The inclusion of a central spherical pore within a repeated lattice was found to reduce both the failure stress and failure strain in uniaxial tension and compression, with up to a 30% reduction in maximum stress at the point of failure compared to a perfect crystalline structure observed when a 30 Å diameter pore was included. The Z axis ([0 0 0 1] crystalline direction) was found to be the least susceptible to pore defects in tension but the most sensitive to pore inclusion in compression. The deformation mechanisms are discussed to explain the observed mechanical responses, for which charge imbalances and geometric stress concentration factor effects caused by pore inclusion play a significant role.
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2
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Nada H. Stable Binding Conformations of Polymaleic and Polyacrylic Acids at a Calcite Surface in the Presence of Countercations: A Metadynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7046-7057. [PMID: 35604639 DOI: 10.1021/acs.langmuir.2c00750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Elucidating the stable binding conformations of additives at the surface of CaCO3 crystals is essential to biomineralization, scale inhibition, and materials technology. However, accomplishing this by experimental means is rather difficult. In this study, molecular dynamics simulations based on a metadynamics approach were conducted to elucidate the stable binding conformations of a deprotonated polymaleic acid (PMA) additive and two deprotonated poly(acrylic acid) (PAA) additives with different polymerization degrees in the presence of various countercations at a hydrated calcite (104) surface. The simulated free-energy surfaces suggested the existence of several slightly different stable binding conformations for each additive. The appearance of these distinct binding conformations is speculated to originate from different balances of interactions between the additive, the calcite surface, and the countercations. The binding conformations and binding stabilities at the calcite surface were affected by the countercations, with Ca2+ ions producing a more pronounced effect than Na+ ions. Furthermore, the simulation results suggested that the binding stability at the calcite surface was higher for the PMA additive than for the PAA additives, and the PAA additive with a polymerization degree of 10 displayed a binding stability that was similar to or lower than that of the PAA additive with a polymerization degree of 5. The present simulation method provides a new strategy for analyzing the binding conformations of complex additives at material surfaces, developing additives that stably bind to these surfaces, and designing additives to control crystal growth.
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Affiliation(s)
- Hiroki Nada
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan
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3
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Snyder AD, Salehinia I. Study of nanoscale deformation mechanisms in bulk hexagonal hydroxyapatite under uniaxial loading using molecular dynamics. J Mech Behav Biomed Mater 2020; 110:103894. [PMID: 32957200 DOI: 10.1016/j.jmbbm.2020.103894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/19/2019] [Accepted: 05/29/2020] [Indexed: 01/05/2023]
Abstract
Hydroxyapatite (HAP) is a natural bioceramic which is currently used in scaffolds and coatings for the regrowth of osseous tissue but offers poor load-bearing capacity compared to other biomaterials. The deformation mechanisms responsible for the mechanical behavior of HAP are not well understood, although the advent of multiscale modeling offers the promise of improvements in many materials through computational materials science. This work utilizes molecular dynamics to study the nanoscale deformation mechanisms of HAP in uniaxial tension and compression. It was found that deformation mechanisms vary with loading direction in tension and compression leading to significant compression/tension asymmetry and crystal anisotropy. Bond orientation and geometry relative to the loading direction was found to be an indicator of whether a specific bond was involved in the deformation of HAP in each loading case. Tensile failure mechanisms were attributed to stretching and failure in loading case-specific ionic bond groups. The compressive failure mechanisms were attributed to coulombic repulsion in each case, although loading case-specific bond group rotation and displacement were found to affect specific failure modes. The elastic modulus was the highest for both tension and compression along the Z direction (i.e. normal to the basal plane), followed by Y and X.
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Affiliation(s)
- Alexander D Snyder
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Iman Salehinia
- Department of Mechanical Engineering, Northern Illinois University, DeKalb, IL, 60115, USA.
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4
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Alkyl-malonate-substituted thiacalix[4]arenes as ligands for bottom-up design of paramagnetic Gd(III)-containing colloids with low cytotoxicity. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2017.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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5
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Grasso G, Mercuri S, Danani A, Deriu MA. Biofunctionalization of Silica Nanoparticles with Cell-Penetrating Peptides: Adsorption Mechanism and Binding Energy Estimation. J Phys Chem B 2019; 123:10622-10630. [DOI: 10.1021/acs.jpcb.9b08106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Stefano Mercuri
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Marco A. Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
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6
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Barmpalexis P, Vardaka E, Moutafidis IM, Kachrimanis K. Amorphous agomelatine stabilization in the presence of pyrogenic silica: Molecular mobility and intermolecular interaction studies. Eur J Pharm Biopharm 2019; 139:291-300. [DOI: 10.1016/j.ejpb.2019.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/08/2019] [Accepted: 04/22/2019] [Indexed: 10/27/2022]
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7
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Aminpour M, Montemagno C, Tuszynski JA. An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications. Molecules 2019; 24:E1693. [PMID: 31052253 PMCID: PMC6539951 DOI: 10.3390/molecules24091693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/29/2023] Open
Abstract
In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.
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Affiliation(s)
- Maral Aminpour
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Carlo Montemagno
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Southern Illinois University, Carbondale, IL 62901, USA.
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
- Department of Mechanical Engineering and Aerospace Engineering (DIMEAS), Politecnico di Torino, 10129 Turin, Italy.
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8
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Buckle EL, Prakash A, Bonomi M, Sampath J, Pfaendtner J, Drobny GP. Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces. J Am Chem Soc 2019; 141:1998-2011. [PMID: 30618247 DOI: 10.1021/jacs.8b10990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Elucidation of the structure and interactions of proteins at native mineral interfaces is key to understanding how biological systems regulate the formation of hard tissue structures. In addition, understanding how these same proteins interact with non-native mineral surfaces has important implications for the design of medical and dental implants, chromatographic supports, diagnostic tools, and a host of other applications. Here, we combine solid-state NMR spectroscopy, isotherm measurements, and molecular dynamics simulations to study how SNa15, a peptide derived from the hydroxyapatite (HAP) recognition domain of the biomineralization protein statherin, interacts with HAP, silica (SiO2), and titania (TiO2) mineral surfaces. Adsorption isotherms are used to characterize the binding affinity of SNa15 to HAP, SiO2, and TiO2. We also apply 1D 13C CP MAS, 1D 15N CP MAS, and 2D 13C-13C DARR experiments to SNa15 samples with uniformly 13C- and 15N-enriched residues to determine backbone and side-chain chemical shifts. Different computational tools, namely TALOS-N and molecular dynamics simulations, are used to deduce secondary structure from backbone and side-chain chemical shift data. Our results show that SNa15 adopts an α-helical conformation when adsorbed to HAP and TiO2, but the helix largely unravels upon adsorption to SiO2. Interactions with HAP are mediated in general by acidic and some basic amino acids, although the specific amino acids involved in direct surface interaction vary with surface. The integrated experimental and computational approach used in this study is able to provide high-resolution insights into adsorption of proteins on interfaces.
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Affiliation(s)
- Erika L Buckle
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195 , United States
| | - Arushi Prakash
- Department of Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit , Institut Pasteur , CNRS UMR 3528, 75015 Paris , France
| | - Janani Sampath
- Department of Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Jim Pfaendtner
- Department of Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Gary P Drobny
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195 , United States
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9
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Rosa M, Di Felice R, Corni S. Adsorption Mechanisms of Nucleobases on the Hydrated Au(111) Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14749-14756. [PMID: 29723478 DOI: 10.1021/acs.langmuir.8b00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The solution environment is of fundamental importance in the adsorption of molecules on surfaces, a process that is strongly affected by the capability of the adsorbate to disrupt the hydration layer above the surface. Here we disclose how the presence of interface water influences the adsorption mechanism of DNA nucleobases on a gold surface. By means of metadynamics simulations, we describe the distinctive features of a complex free-energy landscape for each base, which manifests activation barriers for the adsorption process. We characterize the different pathways that allow each nucleobase to overcome the barriers and be adsorbed on the surface, discussing how they influence the kinetics of adsorption of single-stranded DNA oligomers with homogeneous sequences. Our findings offer a rationale as to why experimental data on the adsorption of single-stranded homo-oligonucleotides do not straightforwardly follow the thermodynamics affinity rank.
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Affiliation(s)
| | - Rosa Di Felice
- Center S3 , CNR Institute of Nanoscience , 41125 Modena , Italy
- Department of Physics and Astronomy , University of Southern California , Los Angeles , California 90089 , United States
| | - Stefano Corni
- Center S3 , CNR Institute of Nanoscience , 41125 Modena , Italy
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10
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Min K, Han J, Park B, Cho E. Characterization of Mechanical Degradation in Perfluoropolyether Film for Its Application to Antifingerprint Coatings. ACS APPLIED MATERIALS & INTERFACES 2018; 10:37498-37506. [PMID: 30298715 DOI: 10.1021/acsami.8b13159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Enhancing the mechanical durability of antifingerprint films is critical for its industrial application on touch-screen devices to withstand friction damage from repeated rubbing in daily usage. Using reactive molecular dynamics simulations, we herein implement adhesion, mechanical, and deposition tests to investigate two durability-determining factors: intrachain and interchain strength, which affect the structural stability of the antifingerprint film (perfluoropolyether) on silica. From the intrachain perspective, it is found that the Si-C bond in the polymer chain is the weakest, and therefore prone to dissociation and potentially forming a C-O bond. This behavior is demonstrated consistently, regardless of the cross-linking density between polymer chains. For the interchain interaction, increasing the chain length enhances the mechanical properties of the film. Furthermore, the chain deposition test, mimicking the experimental coating process, demonstrates that placing shorter chains first to the surface of silica and then depositing longer chains is an ideal way to improve the interchain interaction in the film structure. The current study reveals a clear pathway to optimize the configuration of the polymer chain as well as its film structure to prolong the product life of the coated antifingerprint film.
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11
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Nayebi N, Cetinel S, Omar SI, Tuszynski JA, Montemagno C. A computational method for selecting short peptide sequences for inorganic material binding. Proteins 2017; 85:2024-2035. [PMID: 28734030 DOI: 10.1002/prot.25356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 12/14/2022]
Abstract
Discovering or designing biofunctionalized materials with improved quality highly depends on the ability to manipulate and control the peptide-inorganic interaction. Various peptides can be used as assemblers, synthesizers, and linkers in the material syntheses. In another context, specific and selective material-binding peptides can be used as recognition blocks in mining applications. In this study, we propose a new in silico method to select short 4-mer peptides with high affinity and selectivity for a given target material. This method is illustrated with the calcite (104) surface as an example, which has been experimentally validated. A calcite binding peptide can play an important role in our understanding of biomineralization. A practical aspect of calcite is a need for it to be selectively depressed in mining sites.
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Affiliation(s)
- Niloofar Nayebi
- Ingenuity Lab, University of Alberta, Edmonton, Alberta, Canada.,Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Sibel Cetinel
- Ingenuity Lab, University of Alberta, Edmonton, Alberta, Canada.,Department of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Sara Ibrahim Omar
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.,Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Carlo Montemagno
- Ingenuity Lab, University of Alberta, Edmonton, Alberta, Canada.,Department of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta, Canada
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12
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Liu X, Lu X, Zhang Y, Zhang C, Wang R. Complexation of carboxylate on smectite surfaces. Phys Chem Chem Phys 2017; 19:18400-18406. [PMID: 28678224 DOI: 10.1039/c7cp03019c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a first principles molecular dynamics (FPMD) study of carboxylate complexation on clay surfaces. By taking acetate as a model carboxylate, we investigate its inner-sphere complexes adsorbed on clay edges (including (010) and (110) surfaces) and in interlayer space. Simulations show that acetate forms stable monodentate complexes on edge surfaces and a bidentate complex with Ca2+ in the interlayer region. The free energy calculations indicate that the complexation on edge surfaces is slightly more stable than in interlayer space. By integrating pKas and desorption free energies of Al coordinated water calculated previously (X. Liu, X. Lu, E. J. Meijer, R. Wang and H. Zhou, Geochim. Cosmochim. Acta, 2012, 81, 56-68; X. Liu, J. Cheng, M. Sprik, X. Lu and R. Wang, Geochim. Cosmochim. Acta, 2014, 140, 410-417), the pH dependence of acetate complexation has been revealed. It shows that acetate forms inner-sphere complexes on (110) in a very limited mildly acidic pH range while it can complex on (010) in the whole common pH range. The results presented in this study form a physical basis for understanding the geochemical processes involving clay-organics interactions.
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Affiliation(s)
- Xiandong Liu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210093, P. R. China.
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13
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Dharmawardhana CC, Kanhaiya K, Lin TJ, Garley A, Knecht MR, Zhou J, Miao J, Heinz H. Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1332414] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chamila C. Dharmawardhana
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - Krishan Kanhaiya
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - Tzu-Jen Lin
- Department of Chemical Engineering, Chung Yuan Christian University, Taoyuan City, Taiwan, ROC
| | - Amanda Garley
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - Marc R. Knecht
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Jihan Zhou
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, USA
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14
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Schäfer P, Lalitha A, Sebastian P, Meena SK, Feliu J, Sulpizi M, van der Veen MA, Domke KF. Trimesic acid on Cu in ethanol: Potential-dependent transition from 2-D adsorbate to 3-D metal-organic framework. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.01.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Atomistic Modelling of Confined Polypropylene Chains between Ferric Oxide Substrates at Melt Temperature. Polymers (Basel) 2016; 8:polym8100361. [PMID: 30974636 PMCID: PMC6431934 DOI: 10.3390/polym8100361] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022] Open
Abstract
The interactions and conformational characteristics of confined molten polypropylene (PP) chains between ferric oxide (Fe2O3) substrates were investigated by molecular dynamics (MD) simulations. A comparative analysis of the adsorbed amount shows strong adsorption of the chains on the high-energy surface of Fe2O3. Local structures formed in the polymer film were studied utilizing density profiles, orientation of bonds, and end-to-end distance of chains. At interfacial regions, the backbone carbon-carbon bonds of the chains preferably orient in the direction parallel to the surface while the carbon-carbon bonds with the side groups show a slight tendency to orient normal to the surface. Based on the conformation tensor data, the chains are compressed in the normal direction to the substrates in the interfacial regions while they tend to flatten in parallel planes with respect to the surfaces. The orientation of the bonds as well as the overall flattening of the chains in planes parallel to the solid surfaces are almost identical to that of the unconfined PP chains. Also, the local pressure tensor is anisotropic closer to the solid surfaces of Fe2O3 indicating the influence of the confinement on the buildup imbalance of normal and tangential pressures.
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16
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Dinjaski N, Ebrahimi D, Ling S, Shah S, Buehler MJ, Kaplan DL. Integrated Modeling and Experimental Approaches to Control Silica Modification of Design Silk-Based Biomaterials. ACS Biomater Sci Eng 2016; 3:2877-2888. [PMID: 33418709 DOI: 10.1021/acsbiomaterials.6b00236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mineralized polymeric biomaterials provide useful options toward mechanically robust systems for some tissue repairs. Silks as a mechanically robust protein-based material provide a starting point for biomaterial options, particularly when combined with silica toward organic-inorganic hybrid systems. To further understand the interplay between silk proteins and silica related to material properties, we systematically study the role of three key domains in bioengineered spider silk fusion proteins with respect to β-sheet formation and mineralization: (i) a core silk domain for materials assembly, (ii) a histidine tag for purification, and (iii) a silicification domain for mineralization. Computational simulations are used to identify the effect of each domain on the protein folding and accessibility of positively charged amino acids for silicification and predictions are then compared with experimental data. The results show that the addition of the silica and histidine domains reduces β-sheet structure in the materials, and increases solvent-accessible surface area to the positive charged amino acids, leading to higher levels of silica precipitation. Moreover, the simulations show that the location of the charged biomineralization domain has small effect on the protein folding and consequently surface exposure of charged amino acids. Those surfaces display correlation with the amount of silicification in experiments. The results demonstrate that the exposure of the positively charged amino acids impacts protein function related to mineralization. In addition, processing parameters (solvating agent, the method of β-sheet induction and temperature) affect protein secondary structure, folding and function. This integrated modeling and experimental approach provides insight into sequence-structure-function relationships for control of mineralized protein biomaterial structures.
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Affiliation(s)
- Nina Dinjaski
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Davoud Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shengjie Ling
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Suraj Shah
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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17
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Gierada M, Petit I, Handzlik J, Tielens F. Hydration in silica based mesoporous materials: a DFT model. Phys Chem Chem Phys 2016; 18:32962-32972. [DOI: 10.1039/c6cp05460a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, calculable and realistic DFT models of MCM-41 material that follow temperature dependence of silanol density were developed. They can be easily applied in further studies of adsorption or as a support for catalysts.
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Affiliation(s)
- Maciej Gierada
- Faculty of Chemical Engineering and Technology
- Cracow University of Technology
- 31-155 Kraków
- Poland
| | - Ivan Petit
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 7574
- Laboratoire Chimie de la Matière Condensée
- Collège de France
| | - Jarosław Handzlik
- Faculty of Chemical Engineering and Technology
- Cracow University of Technology
- 31-155 Kraków
- Poland
| | - Frederik Tielens
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 7574
- Laboratoire Chimie de la Matière Condensée
- Collège de France
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