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Tavakol M, Liu J, Hoff SE, Zhu C, Heinz H. Osteocalcin: Promoter or Inhibitor of Hydroxyapatite Growth? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1747-1760. [PMID: 38181199 DOI: 10.1021/acs.langmuir.3c02948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Osteocalcin is the most abundant noncollagenous bone protein and the functions in bone remineralization as well as in inhibition of bone growth have remained unclear. In this contribution, we explain the dual role of osteocalcin in the nucleation of new calcium phosphate during bone remodeling and in the inhibition of hydroxyapatite crystal growth at the molecular scale. The mechanism was derived using pH-resolved all-atom models for the protein, phosphate species, and hydroxyapatite, along with molecular dynamics simulations and experimental and clinical observations. Osteocalcin binds to (hkl) hydroxyapatite surfaces through multiple residues, identified in this work, and the fingerprint of binding residues varies as a function of the (hkl) crystal facet and pH value. On balance, the affinity of osteocalcin to hydroxyapatite slows down crystal growth. The unique tricalcium γ-carboxylglutamic acid (Gla) domain hereby rarely adsorbs to hydroxyapatite surfaces and faces instead toward the solution. The Gla domain enables prenucleation of calcium phosphate for new bone formation at a slightly acidic pH of 5. The growth of prenucleation clusters of calcium phosphate continues upon increase in pH value from 5 to 7 and is much less favorable, or not observed, on the native osteocalcin structure at and above neutral pH values of 7. The results provide mechanistic insight into the early stages of bone remodeling from the molecular scale, help inform mutations of osteocalcin to modify binding to apatites, support drug design, and guide toward potential cures for osteoporosis and hyperosteogeny.
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Affiliation(s)
- Mahdi Tavakol
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
- Department of Mechanical Engineering, Sharif University of Technology, PO Box 11365-11155, Tehran, Iran
| | - Juan Liu
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
| | - Samuel E Hoff
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
- Materials Science and Engineering Program, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
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2
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Subhash B, Unocic RR, Lie WH, Gallington LC, Wright J, Cheong S, Tilley RD, Bedford NM. Resolving Atomic-Scale Structure and Chemical Coordination in High-Entropy Alloy Electrocatalysts for Structure-Function Relationship Elucidation. ACS NANO 2023; 17:22299-22312. [PMID: 37944052 DOI: 10.1021/acsnano.3c03884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The recent breakthrough in confining five or more atomic species in nanocatalysts, referred to as high-entropy alloy nanocatalysts (HEAs), has revealed the possibilities of multielemental interactions that can surpass the limitations of binary and ternary electrocatalysts. The wide range of potential surface configurations in HEAs, however, presents a significant challenge in resolving active structural motifs, preventing the establishment of structure-function relationships for rational catalyst design and optimization. We present a methodology for creating sub-5 nm HEAs using an aqueous-based peptide-directed route. Using a combination of pair distribution function and X-ray absorption spectroscopy, HEA structure models are constructed from reverse Monte Carlo modeling of experimental data sets and showcase a clear peptide-induced influence on atomic-structure and chemical miscibility. Coordination analysis of our structure models facilitated the construction of structure-function correlations applied to electrochemical methanol oxidation reactions, revealing the complex interplay between multiple metals that leads to improved catalytic properties. Our results showcase a viable strategy for elucidating structure-function relationships in HEAs, prospectively providing a pathway for future materials design.
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Affiliation(s)
- Bijil Subhash
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raymond R Unocic
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - William Hadinata Lie
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Leighanne C Gallington
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Joshua Wright
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Soshan Cheong
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Richard D Tilley
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicholas M Bedford
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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3
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Kanhaiya K, Nathanson M, In 't Veld PJ, Zhu C, Nikiforov I, Tadmor EB, Choi YK, Im W, Mishra RK, Heinz H. Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale. J Chem Theory Comput 2023; 19:8293-8322. [PMID: 37962992 DOI: 10.1021/acs.jctc.3c00750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed.
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Affiliation(s)
- Krishan Kanhaiya
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Michael Nathanson
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Pieter J In 't Veld
- BASF SE, Molecular Modeling & Drug Discovery, Carl Bosch Str. 38, 67056 Ludwigshafen, Germany
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Ilia Nikiforov
- Department of Aerospace Engineering and Mechanics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ellad B Tadmor
- Department of Aerospace Engineering and Mechanics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Ratan K Mishra
- BASF SE, Molecular Modeling & Drug Discovery, Carl Bosch Str. 38, 67056 Ludwigshafen, Germany
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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4
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Polasa A, Mosleh I, Losey J, Abbaspourrad A, Beitle R, Moradi M. Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesis. NANOSCALE ADVANCES 2022; 4:3161-3171. [PMID: 36132813 PMCID: PMC9417332 DOI: 10.1039/d2na00212d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/18/2022] [Indexed: 06/16/2023]
Abstract
The controlled formation of nanoparticles with optimum characteristics and functional aspects has proven successful via peptide-mediated nanoparticle synthesis. However, the effects of the peptide sequence and binding motif on surface features and physicochemical properties of nanoparticles are not well-understood. In this study, we investigate in a comparative manner how a specific peptide known as Pd4 and its two known variants may form nanoparticles both in an isolated state and when attached to a green fluorescent protein (GFPuv). More importantly, we introduce a novel computational approach to predict the trend of the size and activity of the peptide-directed nanoparticles by estimating the binding affinity of the peptide to a single ion. We used molecular dynamics (MD) simulations to explore the differential behavior of the isolated and GFP-fused peptides and their mutants. Our computed palladium (Pd) binding free energies match the typical nanoparticle sizes reported from transmission electron microscope pictures. Stille coupling and Suzuki-Miyaura reaction turnover frequencies (TOFs) also correspond with computationally predicted Pd binding affinities. The results show that while using Pd4 and its two known variants (A6 and A11) in isolation produces nanoparticles of varying sizes, fusing these peptides to the GFPuv protein produces nanoparticles of similar sizes and activity. In other words, GFPuv reduces the sensitivity of the nanoparticles to the peptide sequence. This study provides a computational framework for designing free and protein-attached peptides that helps in the synthesis of nanoparticles with well-regulated properties.
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Affiliation(s)
- Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas Fayetteville AR 72701 USA
| | - Imann Mosleh
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University Ithaca NY 14853 USA
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas Fayetteville AR 72701 USA
| | - James Losey
- Department of Chemistry and Biochemistry, University of Arkansas Fayetteville AR 72701 USA
| | - Alireza Abbaspourrad
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas Fayetteville AR 72701 USA
| | - Robert Beitle
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University Ithaca NY 14853 USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas Fayetteville AR 72701 USA
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5
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Kanhaiya K, Heinz H. Adsorption and Diffusion of Oxygen on Pure and Partially Oxidized Metal Surfaces in Ultrahigh Resolution. NANO LETTERS 2022; 22:5392-5400. [PMID: 35730668 DOI: 10.1021/acs.nanolett.2c00490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The interaction of gas molecules with metal and oxide surfaces plays a critical role in corrosion, catalysis, sensing, and heterogeneous materials. However, insights into the dynamics of O2 from picoseconds to microseconds have remained unavailable to date. We obtained 3D potential energy surfaces for adsorption of O2 on 11 common pristine and partially oxidized (hkl) surfaces of Ni and Al in picometer resolution and high accuracy of 0.1 kcal/mol, identified binding sites, and surface mobility from 25 to 300 °C. We explain relative oxidation rates and parameters for oxide growth. We employed over 150 000 molecular mechanics and molecular dynamics simulations with the interface force field (IFF) using structural data from X-ray diffraction (XRD) and low-energy electron diffraction (LEED). The methods reach 10 to 50 times higher accuracy than possible before and are suited to analyze gas interactions with metals up to the micrometer scale including defects and irregular nanostructures.
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Affiliation(s)
- Krishan Kanhaiya
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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6
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Qi X, Jin B, Cai B, Yan F, De Yoreo J, Chen CL, Pfaendtner J. Molecular Driving Force for Facet Selectivity of Sequence-Defined Amphiphilic Peptoids at Au-Water Interfaces. J Phys Chem B 2022; 126:5117-5126. [PMID: 35763341 DOI: 10.1021/acs.jpcb.2c02638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Shape-controlled colloidal nanocrystal syntheses often require facet-selective solution-phase chemical additives to regulate surface free energy, atom addition/migration fluxes, or particle attachment rates. Because of their highly tunable properties and robustness to a wide range of experimental conditions, peptoids represent a very promising class of next-generation functional additives for control over nanocrystal growth. However, understanding the origin of facet selectivity at the molecular level is critical to generalizing their design. Herein we employ molecular dynamics simulations and biased sampling methods and report stronger selectivity to Au(111) than to Au(100) for Nce3Ncp6, a peptoid that has been shown to assist the formation of 5-fold twinned Au nanostars. We find that facet selectivity is achieved through synergistic effects of both peptoid-surface and solvent-surface interactions. Moreover, the amphiphilic nature of Nce3Ncp6 together with the order of peptoid-peptoid and peptoid-surface binding energies, that is, peptoid-Au(100) < peptoid-peptoid < peptoid-Au(111), further amplifies its distinct collective behavior on different Au surfaces. Our studies provide a fundamental understanding of the molecular origin of facet-selective adsorption and highlight the possibility of future designs and uses of sequence-defined peptoids for predictive syntheses of nanocrystals with designed shapes and properties.
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Affiliation(s)
- Xin Qi
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Biao Jin
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bin Cai
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Feng Yan
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James De Yoreo
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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7
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8
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Liu J, Zeng J, Zhu C, Miao J, Huang Y, Heinz H. Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition. Chem Sci 2020; 11:8708-8722. [PMID: 34094188 PMCID: PMC8162032 DOI: 10.1039/d0sc01443e] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from -86 to -6 kcal mol-1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.
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Affiliation(s)
- Juan Liu
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Jin Zeng
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Jianwei Miao
- Department of Physics and Astronomy, University of California Los Angeles California 90095 USA
- California NanoSystems Institute, University of California, Los Angeles CA 90095 USA
| | - Yu Huang
- California NanoSystems Institute, University of California, Los Angeles CA 90095 USA
- Department of Materials Science and Engineering, University of California, Los Angeles 90095 USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
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9
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Mark LO, Zhu C, Medlin JW, Heinz H. Understanding the Surface Reactivity of Ligand-Protected Metal Nanoparticles for Biomass Upgrading. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04772] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesli O. Mark
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - J. Will Medlin
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
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10
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Adsorption behavior of β-cyclodextrin onto gold nanoparticles. J Mol Graph Model 2020; 94:107483. [DOI: 10.1016/j.jmgm.2019.107483] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/28/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022]
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11
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Exploring the intermolecular interaction of serine and threonine dipeptides with gold nanoclusters and nanoparticles of different shapes and sizes by quantum mechanics and molecular simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111903] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Slocik JM, Dennis PB, Govorov AO, Bedford NM, Ren Y, Naik RR. Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials. ACS Biomater Sci Eng 2019; 6:2612-2620. [PMID: 33463283 DOI: 10.1021/acsbiomaterials.9b00933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.
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Affiliation(s)
- Joseph M Slocik
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Lab, Wright Patterson Air Force Base, Ohio 45433-7750, United States
| | - Patrick B Dennis
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Lab, Wright Patterson Air Force Base, Ohio 45433-7750, United States
| | - Alexander O Govorov
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, United States
| | - Nicholas M Bedford
- School of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yang Ren
- X-Ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Lab, Wright Patterson Air Force Base, Ohio 45433-7750, United States
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13
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Kim JY, Yeom J, Zhao G, Calcaterra H, Munn J, Zhang P, Kotov N. Assembly of Gold Nanoparticles into Chiral Superstructures Driven by Circularly Polarized Light. J Am Chem Soc 2019; 141:11739-11744. [PMID: 31329438 PMCID: PMC7263784 DOI: 10.1021/jacs.9b00700] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Photon-to-matter chirality transfer offers both simplicity and universality to chiral synthesis, but its efficiency is typically low for organic compounds. Besides the fundamental importance of this process relevant for understanding the origin of homochirality on Earth, new pathways for imposing chiral bias during chemical process are essential for a variety of technologies from medicine to informatics. The strong optical activity of inorganic nanoparticles (NPs) affords photosynthetic routes to chiral superstructures using circularly polarized photons. Although plasmonic NPs are promising candidates for such synthetic routes due to the strong rotatory power of highly delocalized plasmonic states (Ma et al. Chem. Rev. 2017, 117 (12), 8041), realization of light-driven synthesis of chiral nanostructures has been more challenging for plasmonic NPs than for the semiconductor due to the short lifetime of the plasmonic states. Here we show that illumination of gold salt solutions with circularly polarized light induces the formation of NPs and their subsequent assembly into chiral nanostructures 10-15 nm in diameter. Despite their seemingly irregular shape, the resulting nanocolloids showed circular dichroism (CD) spectra with opposite polarity after exposure to photons with left and right circular polarization. The sign and spectral position of the CD peaks of illuminated dispersions matched those calculated for nanostructures with complex geometry identified from electron tomography images. Quantification of the complex shapes of NP assemblies using chirality measures revealed a direct correlation with the experimental spectra. The light-driven assembly of chiral nanostructures originates from the asymmetric displacement of NPs in dynamic assemblies by plasmonic fields followed by particle-to-particle attachment. The ability of gold NPs to "lock" the chirality of the incident photons in assembled nanostructures can be used to create a variety of chiral nanomaterials with plasmonic resonances.
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Affiliation(s)
| | | | - Gongpu Zhao
- Department of Structural Biology , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
- David Van Andel Advanced Cryo-Electron Microscopy Suite , Van Andel Research Institute , Grand Rapids , Michigan 49503 , United States
| | | | - Jiyoun Munn
- COMSOL, Inc. , Burlington , Massachusetts 01803 , United States
| | - Peijun Zhang
- Department of Structural Biology , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , U.K
- Electron Bio-Imaging Centre, Diamond Light Source , Harwell Science and Innovation Campus , Didcot OX11 0DE , U.K
| | - Nicholas Kotov
- Michigan Institute for Translational Nanotechnology , Ypsilanti , Michigan 48198 , United States
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14
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Jamil T, Gissinger JR, Garley A, Saikia N, Upadhyay AK, Heinz H. Dynamics of carbohydrate strands in water and interactions with clay minerals: influence of pH, surface chemistry, and electrolytes. NANOSCALE 2019; 11:11183-11194. [PMID: 31150033 DOI: 10.1039/c9nr01867k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Carbohydrate hydrogels are extensively used in pharmaceuticals and engineered biomaterials. Molecular conformations, assembly, and interactions of the carbohydrate strands with stabilizers such as clay minerals in aqueous solution are difficult to quantify in experiments and the hydrogel properties remain largely a result of trial-and-error studies. We analyzed the assembly of gellan gum in aqueous solution and interactions with dispersed clay minerals in all-atomic detail using molecular dynamics simulation, atomic force microscopy (AFM), and comparisons to earlier measurements. Gellan strands associate at low pH values of 2 and gradually disassemble to double strands with weak association of -0.4 kcal per mole carbohydrate ring as the pH values increases to 9. Ionization of the carbonic acid side groups in the backbone extends the chains and accelerates the conformational dynamics via rapidly changing intramolecular ion bridges. Gellan interactions with clay minerals depend on the strength of electric triple layers between clay, cations, and anionic polymer strands, as well as weaker hydrogen bonds along the edges, which are tunable as a function of the clay surface chemistry, local ionic strength, and pH values. Interaction energies range from -4 to +6 kcal per mol carbohydrate ring and were most favorable for electric triple layers with high charge mobility, which can be achieved for intermediate cation exchange capacity of the clay mineral and high pH values to increase ionization of the clay edges and of the polymer. The findings provide understanding and help control the dynamics and stabilization of carbohydrate hydrogels by clay minerals.
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Affiliation(s)
- Tariq Jamil
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA.
| | - Jacob R Gissinger
- Materials Science and Engineering Program, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Amanda Garley
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA.
| | - Nabanita Saikia
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA.
| | | | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA. and Materials Science and Engineering Program, University of Colorado at Boulder, Boulder, CO 80309, USA
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15
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Kyrychenko A, Blazhynska MM, Slavgorodska MV, Kalugin ON. Stimuli-responsive adsorption of poly(acrylic acid) onto silver nanoparticles: Role of polymer chain length and degree of ionization. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.130] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Nathanson M, Kanhaiya K, Pryor A, Miao J, Heinz H. Atomic-Scale Structure and Stress Release Mechanism in Core-Shell Nanoparticles. ACS NANO 2018; 12:12296-12304. [PMID: 30457827 DOI: 10.1021/acsnano.8b06118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Core-shell nanoparticles find applications in catalysts, sensors, and theranostics. The full internal 3D atomic structure, however, cannot be resolved by current imaging and diffraction techniques. We analyzed the atomic positions and stress-release mechanism in a cubic Au-Pd core-shell nanoparticle in approximately 1000 times higher resolution than current experimental techniques using large-scale molecular dynamics simulation to overcome these limitations. The core-shell nanocube of 73 nm size was modeled similarly to solution synthesis by random epitaxial deposition of a 4 nm thick shell of Pd atoms onto a Au core of 65 nm side length using reliable interatomic potentials. The internal structure reveals specific deformations and stress relaxation mechanisms that are caused by the +4.8% lattice mismatch of gold relative to palladium and differential confinement of extended particle facets, edges, and corners by one, two, or three Au-Pd interfaces, respectively. The three-dimensional lattice strain causes long-range, arc-like bending of atomic rows along the faces and edges of the particle, especially near the Au-Pd interface, a bulging deformation of the Pd shell, and stacking faults in the Pd shell at the corners of the particle. The strain pattern and mechanism of stress release were further characterized by profiles of the atomic layer spacing in the principal crystallographic directions. Accordingly, strain in the Pd shell is several times larger in the extended facets than near the edges and corners of the nanoparticle, which likely affects adsorption, optical, and electrochemical properties. The findings are consistent with available experimental data, including 3D reconstructions of the same cubic nanoparticle by coherent diffractive imaging (CDI) and may be verified by more powerful experimental techniques in the future. The stress release mechanisms are representative for cubic core-shell nanoparticles with fcc structure and can be explored for different shapes by the same methods.
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Affiliation(s)
- Michael Nathanson
- Department of Chemical and Biological Engineering , University of Colorado at Boulder , Boulder , Colorado 80309 , United States
| | - Krishan Kanhaiya
- Department of Chemical and Biological Engineering , University of Colorado at Boulder , Boulder , Colorado 80309 , United States
| | - Alan Pryor
- Department of Physics & Astronomy and California NanoSystems Institute , University of California , Los Angeles , California 90095 , United States
| | - Jianwei Miao
- Department of Physics & Astronomy and California NanoSystems Institute , University of California , Los Angeles , California 90095 , United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering , University of Colorado at Boulder , Boulder , Colorado 80309 , United States
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17
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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18
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Geada IL, Ramezani-Dakhel H, Jamil T, Sulpizi M, Heinz H. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential. Nat Commun 2018; 9:716. [PMID: 29459638 PMCID: PMC5818522 DOI: 10.1038/s41467-018-03137-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/22/2018] [Indexed: 12/11/2022] Open
Abstract
Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard–Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals. Molecular dynamics models for predicting the behavior of metallic nanostructures typically do not take into account polarization effects in metals. Here, the authors introduce a polarizable Lennard–Jones potential that provides quantitative insight into the role of induced charges at metal surfaces and related complex material interfaces.
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Affiliation(s)
- Isidro Lorenzo Geada
- Department of Physics, University of Mainz, Staudingerweg 7, D-55128, Mainz, Germany
| | - Hadi Ramezani-Dakhel
- Department of Polymer Engineering, University of Akron, 250S Forge St, Akron, OH, 44325, USA.,Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Tariq Jamil
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, 3415 Colorado Ave, Boulder, CO, 80309, USA
| | - Marialore Sulpizi
- Department of Physics, University of Mainz, Staudingerweg 7, D-55128, Mainz, Germany.
| | - Hendrik Heinz
- Department of Polymer Engineering, University of Akron, 250S Forge St, Akron, OH, 44325, USA. .,Department of Chemical and Biological Engineering, University of Colorado-Boulder, 3415 Colorado Ave, Boulder, CO, 80309, USA.
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Ding HM, Ma YQ. Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity. NANOSCALE HORIZONS 2018; 3:6-27. [PMID: 32254106 DOI: 10.1039/c7nh00138j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.
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Affiliation(s)
- Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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