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Bassani CL, van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. Nanocrystal Assemblies: Current Advances and Open Problems. ACS NANO 2024; 18:14791-14840. [PMID: 38814908 DOI: 10.1021/acsnano.3c10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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Affiliation(s)
- Carlos L Bassani
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Greg van Anders
- Department of Physics, Engineering Physics, and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Uri Banin
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dmitry Baranov
- Division of Chemical Physics, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Qian Chen
- University of Illinois, Urbana, Illinois 61801, USA
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Michael S Dimitriyev
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Auckland 1142, New Zealand
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - G Ivan Guerrero-Garcia
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, 78295 San Luis Potosí, México
| | - Michael Gruenwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maria Ibáñez
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Matthias Karg
- Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Kraus
- INM - Leibniz-Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, Colloid and Interface Chemistry, 66123 Saarbrücken, Germany
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53717, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bortolo M Mognetti
- Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
| | - Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Oleg V Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sara Skrabalak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Ivan I Smalyukh
- Department of Physics and Chemical Physics Program, University of Colorado, Boulder, Colorado 80309, USA
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires 1428 Argentina
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David Vaknin
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xingchen Ye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Shan Zhou
- Department of Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701, USA
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Alex Travesset
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
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2
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Jiao S, Shell MS. Inverse design of pore wall chemistry and topology through active learning of surface group interactions. J Chem Phys 2024; 160:124705. [PMID: 38526115 DOI: 10.1063/5.0200900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Design of next-generation membranes requires a nanoscopic understanding of the effect of biologically inspired heterogeneous surface chemistries and topologies (roughness) on local water and solute behavior. In particular, the rejection of small, neutral solutes, such as boric acid, poses a heretofore unsolved challenge. In prior work, a computational inverse design technique using an evolutionary optimization successfully uncovered new surface design strategies for optimized transport of water over solutes in smooth, model pores consisting of two surface chemistries. However, extending such an approach to more complex (and realistic) scenarios involving many surface chemistries as well as surface roughness is challenging due to the expanded design space. In this work, we develop a new approach that uses active learning to optimize in a reduced feature space of surface group interactions, finding parameters that lead to their assembly into ordered, optimal patterns. This approach rapidly identifies novel surface functionalizations that maximize the difference in water and boric acid transport through the nanopore. Moreover, we find that the roughness of the nanopore wall, independent of its chemistry, can be leveraged to enhance transport selectivity: oscillations in the pore wall diameter optimally inhibit boric acid transport by creating energetic wells from which the solute must escape to transport down the pore. This proof-of-concept demonstrates the potential for active learning strategies, in concert with molecular simulations, to rapidly navigate complex design spaces of aqueous interfaces and is promising as a tool for engineering water-mediated surface interactions for a broad range of applications.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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3
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Jiao S, Robinson Brown DC, Shell MS. Relationships between Water's Structure and Solute Affinity at Polypeptoid Brush Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:761-771. [PMID: 38118078 DOI: 10.1021/acs.langmuir.3c02971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Excellent antifouling surfaces are generally thought to create a tightly bound layer of water that resists solute adsorption, and highly hydrophilic surfaces such as those with zwitterionic functionalities are of significant current interest as antifoulant strategies. However, despite significant proofs-of-concept, we still lack a fundamental understanding of how the nanoscopic structure of this hydration layer translates to reduced fouling, how surface chemistry can be tuned to achieve antifouling through hydration water, and why, in particular, zwitterionic surfaces seem so promising. Here, we use molecular dynamics simulations and free energy calculations to investigate the molecular relationships among surface chemistry, hydration water structure, and surface-solute affinity across a variety of surface-decorated chemistries. Specifically, we consider polypeptoid-decorated surfaces that display well-known experimental antifouling capabilities and that can be synthesized sequence specifically, with precise backbone positioning of, e.g., charged groups. Through simulations, we calculate the affinities of a range of small solutes to polypeptoid brush surfaces of varied side-chain chemistries. We then demonstrate that measures of the structure of surface hydration water in response to a particular surface chemistry signal solute-surface affinity; specifically, we find that zwitterionic chemistries produce solute-surface repulsion through highly coordinated hydration water while suppressing tetrahedral structuring around the solute, in contrast to uncharged surfaces that show solute-surface affinity. Based on the relationship of this structural perturbation to the affinity of small-molecule solutes, we propose a molecular mechanism by which zwitterionic surface chemistries enhance solute repulsion, with broader implications for the design of antifouling surfaces.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Dennis C Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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4
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Chen W, Sanders SE, Özdamar B, Louaas D, Brigiano FS, Pezzotti S, Petersen PB, Gaigeot MP. On the Trail of Molecular Hydrophilicity and Hydrophobicity at Aqueous Interfaces. J Phys Chem Lett 2023; 14:1301-1309. [PMID: 36724059 DOI: 10.1021/acs.jpclett.2c03300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Uncovering microscopic hydrophilicity and hydrophobicity at heterogeneous aqueous interfaces is essential as it dictates physico/chemical properties such as wetting, the electrical double layer, and reactivity. Several molecular and spectroscopic descriptors were proposed, but a major limitation is the lack of connections between them. Here, we combine density functional theory-based MD simulations (DFT-MD) and SFG spectroscopy to explore how interfacial water responds in contact with self-assembled monolayers (SAM) of tunable hydrophilicity. We introduce a microscopic metric to track the transition from hydrophobic to hydrophilic interfaces. This metric combines the H/V descriptor, a structural descriptor based on the preferential orientation within the water network in the topmost binding interfacial layer (BIL) and spectroscopic fingerprints of H-bonded and dangling OH groups of water carried by BIL-resolved SFG spectra. This metric builds a bridge between molecular descriptors of hydrophilicity/hydrophobicity and spectroscopically measured quantities and provides a recipe to quantitatively or qualitatively interpret experimental SFG signals.
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Affiliation(s)
- Wanlin Chen
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
| | - Stephanie E Sanders
- Department of Chemistry and Biochemistry, Ruhr University Bochum, 44801Bochum, Germany
| | - Burak Özdamar
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
| | - Dorian Louaas
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
| | - Flavio Siro Brigiano
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 4 Place Jussieu, 75005Paris, France
| | - Simone Pezzotti
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
- Department of Physical Chemistry II, Ruhr University Bochum, D-44801Bochum, Germany
| | - Poul B Petersen
- Department of Chemistry and Biochemistry, Ruhr University Bochum, 44801Bochum, Germany
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
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5
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Dallin BC, Kelkar AS, Van Lehn RC. Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces. Chem Sci 2023; 14:1308-1319. [PMID: 36756335 PMCID: PMC9891380 DOI: 10.1039/d2sc02856e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
The hydrophobicity of an interface determines the magnitude of hydrophobic interactions that drive numerous biological and industrial processes. Chemically heterogeneous interfaces are abundant in these contexts; examples include the surfaces of proteins, functionalized nanomaterials, and polymeric materials. While the hydrophobicity of nonpolar solutes can be predicted and related to the structure of interfacial water molecules, predicting the hydrophobicity of chemically heterogeneous interfaces remains a challenge because of the complex, non-additive contributions to hydrophobicity that depend on the chemical identity and nanoscale spatial arrangements of polar and nonpolar groups. In this work, we utilize atomistic molecular dynamics simulations in conjunction with enhanced sampling and data-centric analysis techniques to quantitatively relate changes in interfacial water structure to the hydration free energy (a thermodynamically well-defined descriptor of hydrophobicity) of chemically heterogeneous interfaces. We analyze a large data set of 58 self-assembled monolayers (SAMs) composed of ligands with nonpolar and polar end groups of different chemical identity (amine, amide, and hydroxyl) in five mole fractions, two spatial patterns, and with scaled partial charges. We find that only five features of interfacial water structure are required to accurately predict hydration free energies. Examination of these features reveals mechanistic insights into the interfacial hydrogen bonding behaviors that distinguish different surface compositions and patterns. This analysis also identifies the probability of highly coordinated water structures as a unique signature of hydrophobicity. These insights provide a physical basis to understand the hydrophobicity of chemically heterogeneous interfaces and connect hydrophobicity to experimentally accessible perturbations of interfacial water structure.
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Affiliation(s)
- Bradley C. Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison1415 Engineering DriveMadisonWI53706USA+1-608-263-9487
| | - Atharva S. Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison1415 Engineering DriveMadisonWI53706USA+1-608-263-9487
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison1415 Engineering DriveMadisonWI53706USA+1-608-263-9487
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6
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Hoff SE, Di Silvio D, Ziolo RF, Moya SE, Heinz H. Patterning of Self-Assembled Monolayers of Amphiphilic Multisegment Ligands on Nanoparticles and Design Parameters for Protein Interactions. ACS NANO 2022; 16:8766-8783. [PMID: 35603431 DOI: 10.1021/acsnano.1c08695] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Functionalization of nanoparticles with specific ligands is helpful to control specific diagnostic and therapeutic responses such as protein adsorption, cell targeting, and circulation. Precision delivery critically depends on a fundamental understanding of the interplay between surface chemistry, ligand dynamics, and interaction with the biochemical environment. Due to limited atomic-scale insights into the structure and dynamics of nanoparticle-bound ligands from experiments, relationships of grafting density and ligand chemistry to observable properties such as hydrophilicity and protein interactions remain largely unknown. In this work, we uncover how self-assembled monolayers (SAMs) composed of multisegment ligands such as thioalkyl-PEG-(N-alkyl)amides on gold nanoparticles can mimic mixed hydrophobic and hydrophilic ligand coatings, including control of patterns, hydrophilicity, and specific recognition properties. Our results are derived from molecular dynamics simulations with the INTERFACE-CHARMM36 force field at picometer resolution and comparisons to experiments. Small changes in ligand hydrophobicity, via adjusting the length of the N-terminal alkyl groups, tune water penetration by multiples and control superficial ordering of alkyl chains from 0 to 70% regularity. Further parameters include the grafting density of the ligands, curvature of the nanoparticle surfaces, type of solvent, and overall ligand length, which were examined in detail. We explain the thermodynamic origin of the formation of heterogeneous patterns of multisegment ligand SAMs and illustrate how different degrees of ligand order on the nanoparticle surface affect interactions with bovine serum albumin. The resulting design principles can be applied to a variety of ligand chemistries to customize the behavior of functionalized nanoparticles in biological media and enhance therapeutic efficiency.
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Affiliation(s)
- Samuel E Hoff
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303-0596, United States
| | - Desiré Di Silvio
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Paseo Miramon, 182, 20009 San Sebastian, Spain
| | - Ronald F Ziolo
- Centro de Investigación en Química Aplicada, Boulevard Enrique Reyna 140, 25294 Saltillo, Coahuila, México
| | - Sergio E Moya
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Paseo Miramon, 182, 20009 San Sebastian, Spain
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303-0596, United States
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7
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Jiao S, Rivera Mirabal DM, DeStefano AJ, Segalman RA, Han S, Shell MS. Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics. Biomacromolecules 2022; 23:1745-1756. [PMID: 35274944 DOI: 10.1021/acs.biomac.1c01687] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Daniela M Rivera Mirabal
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of Puerto Rico, Mayagüez, Puerto Rico 00681, United States
| | - Audra J DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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8
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Alencar WLM, da Silva Arouche T, Neto AFG, de Castro Ramalho T, de Carvalho Júnior RN, de Jesus Chaves Neto AM. Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics. Sci Rep 2022; 12:3316. [PMID: 35228662 PMCID: PMC8885651 DOI: 10.1038/s41598-022-07396-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values of - 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and - 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.
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Affiliation(s)
- Wilson Luna Machado Alencar
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
- Federal Institute of Pará (IFPA), C. P. BR 316, Km 61, Castanhal, PA, 68740-970, Brazil
| | - Tiago da Silva Arouche
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil
| | | | | | - Raul Nunes de Carvalho Júnior
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
- Pos-Graduation Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil
| | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil.
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil.
- Pos-Graduation Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil.
- National Professional Master's in Physics Teaching, Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil.
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9
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Kelkar AS, Dallin BC, Van Lehn RC. Identifying nonadditive contributions to the hydrophobicity of chemically heterogeneous surfaces via dual-loop active learning. J Chem Phys 2022; 156:024701. [PMID: 35032988 DOI: 10.1063/5.0072385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Hydrophobic interactions drive numerous biological and synthetic processes. The materials used in these processes often possess chemically heterogeneous surfaces that are characterized by diverse chemical groups positioned in close proximity at the nanoscale; examples include functionalized nanomaterials and biomolecules, such as proteins and peptides. Nonadditive contributions to the hydrophobicity of such surfaces depend on the chemical identities and spatial patterns of polar and nonpolar groups in ways that remain poorly understood. Here, we develop a dual-loop active learning framework that combines a fast reduced-accuracy method (a convolutional neural network) with a slow higher-accuracy method (molecular dynamics simulations with enhanced sampling) to efficiently predict the hydration free energy, a thermodynamic descriptor of hydrophobicity, for nearly 200 000 chemically heterogeneous self-assembled monolayers (SAMs). Analysis of this dataset reveals that SAMs with distinct polar groups exhibit substantial variations in hydrophobicity as a function of their composition and patterning, but the clustering of nonpolar groups is a common signature of highly hydrophobic patterns. Further molecular dynamics analysis relates such clustering to the perturbation of interfacial water structure. These results provide new insight into the influence of chemical heterogeneity on hydrophobicity via quantitative analysis of a large set of surfaces, enabled by the active learning approach.
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Affiliation(s)
- Atharva S Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
| | - Bradley C Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
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10
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Chew AK, Dallin BC, Van Lehn RC. The Interplay of Ligand Properties and Core Size Dictates the Hydrophobicity of Monolayer-Protected Gold Nanoparticles. ACS NANO 2021; 15:4534-4545. [PMID: 33621066 DOI: 10.1021/acsnano.0c08623] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The hydrophobicity of monolayer-protected gold nanoparticles is a crucial design parameter that influences self-assembly, preferential binding to proteins and membranes, and other nano-bio interactions. Predicting the effects of monolayer components on nanoparticle hydrophobicity is challenging due to the nonadditive, cooperative perturbations to interfacial water structure that dictate hydrophobicity at the nanoscale. In this work, we quantify nanoparticle hydrophobicity by using atomistic molecular dynamics simulations to calculate local hydration free energies at the nanoparticle-water interface. The simulations reveal that the hydrophobicity of large gold nanoparticles is determined primarily by ligand end group chemistry, as expected. However, for small gold nanoparticles, long alkanethiol ligands interact to form anisotropic bundles that lead to substantial spatial variations in hydrophobicity even for homogeneous monolayer compositions. We further show that nanoparticle hydrophobicity is modulated by changing the ligand structure, ligand chemistry, and gold core size, emphasizing that single-ligand properties alone are insufficient to characterize hydrophobicity. Finally, we illustrate that hydration free energy measurements correlate with the preferential binding of propane as a representative hydrophobic probe molecule. Together, these results show that both physical and chemical properties influence the hydrophobicity of small nanoparticles and must be considered together when predicting gold nanoparticle interactions with biomolecules.
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Affiliation(s)
- Alex K Chew
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Bradley C Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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11
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Xu P, Li X, Yu H. Thermodynamic Phase-like Transition Effect of Molecular Self-assembly. J Phys Chem Lett 2021; 12:126-131. [PMID: 33307700 DOI: 10.1021/acs.jpclett.0c03248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The technique of self-assembled monolayers (SAMs) is frequently applied for grafting functional groups or area-selective deposition of thin films on a material surface. The formation and quality of SAMs are fundamentally determined by thermodynamic data, which are difficult to measure with available experimental methods. This work quantitatively extracted thermodynamic parameters including ΔH°, ΔG°, and ΔS° during the SAMs construction process with an ultrasensitive resonant microcantilever as molecule-surface interactions real-time recording tool. By correlating the thermodynamic parameters with self-assembling temperatures, a new thermodynamic phase-like transition effect of molecular self-assembly has been first revealed. The sharp transition of the thermodynamic parameters defines the critical condition for SAMs formation. The thermodynamic data further provide optimized reaction conditions for constructing high-quality SAMs. The explored quantitative thermodynamic analysis method not only plays as criterion for SAM growth but also helps to fundamentally elucidate physicochemical mechanism of spontaneous self-assembly.
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Affiliation(s)
- Pengcheng Xu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinxin Li
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haitao Yu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China
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12
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Kelkar AS, Dallin BC, Van Lehn RC. Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks. J Phys Chem B 2020; 124:9103-9114. [DOI: 10.1021/acs.jpcb.0c05977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Atharva S. Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Bradley C. Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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13
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Marson D, Posel Z, Posocco P. Molecular Features for Probing Small Amphiphilic Molecules with Self-Assembled Monolayer-Protected Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5671-5679. [PMID: 32348150 PMCID: PMC8007095 DOI: 10.1021/acs.langmuir.9b03686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/21/2020] [Indexed: 06/11/2023]
Abstract
The sensing of small molecules poses the challenge of developing devices able to discriminate between compounds that may be structurally very similar. Here, attention has been paid to the use of self-assembled monolayer (SAM)-protected gold nanoparticles since they enable a modular approach to tune single-molecule affinity and selectivity simply by changing functional moieties (i.e., covering ligands), along with multivalent molecular recognition. To date, the discovery of monolayers suitable for a specific molecular target has relied on trial-and-error approaches, with ligand chemistry being the main criterion used to modulate selectivity and sensitivity. By using molecular dynamics, we showcase that either individual molecular characteristics and/or collective features such as ligand flexibility, monolayer organization, ligand local ordering, and interfacial solvent properties can also be exploited conveniently. The knowledge of the molecular mechanisms that drive the recognition of small molecules on SAM-covered nanoparticles will critically expand our ability to manipulate and control such supramolecular systems.
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Affiliation(s)
- Domenico Marson
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
| | - Zbyšek Posel
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
- Department
of Informatics, Jan Evangelista Purkyně
University, 40096 Ústí nad Labem, Czech Republic
| | - Paola Posocco
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
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14
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Yang A, Moore TC, Iacovella CR, Thompson M, Moore DJ, McCabe C. Examining Tail and Headgroup Effects on Binary and Ternary Gel-Phase Lipid Bilayer Structure. J Phys Chem B 2020; 124:3043-3053. [PMID: 32196346 DOI: 10.1021/acs.jpcb.0c00490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural properties of two- and three-component gel-phase bilayers were studied using molecular dynamics simulations. The bilayers contain distearoylphosphatidylcholine (DSPC) phospholipids mixed with alcohols and/or fatty acids of varying tail lengths, with carbon chain lengths of 12, 16, and 24 studied. Changes in both headgroup chemistry and tail length are found to affect the balance between steric repulsion and van der Waals attraction within the bilayers, manifesting in different bilayer structural properties. Lipid components are found to be located at different depths within the bilayer depending on both chain length and headgroup chemistry. The highest bilayer ordering and lowest area per tail are found in systems with medium-length tails. While longer tails can enhance van der Waals attractions, the increased tail-length asymmetry is found to induce disorder and reduce tail packing. Bulkier headgroups further increase steric repulsion, as reflected in increased component offsets and reduced tail packing. These findings help explain how bilayer composition affects the structure of gel-phase bilayers.
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Affiliation(s)
- Alexander Yang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Michael Thompson
- GlaxoSmithKline Consumer Health Care, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - David J Moore
- GlaxoSmithKline Consumer Health Care, 184 Liberty Corner Road, Suite 200, Warren, New Jersey 07059, United States
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States.,Multiscale Modeling and Simulation Center, Vanderbilt University, Nashville, Tennessee 37212, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
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15
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Fies WA, First JT, Dugger JW, Doucet M, Browning JF, Webb LJ. Quantifying the Extent of Hydration of a Surface-Bound Peptide Using Neutron Reflectometry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:637-649. [PMID: 31846580 DOI: 10.1021/acs.langmuir.9b02559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Establishing how water, or the absence of water, affects the structure, dynamics, and function of proteins in contact with inorganic surfaces is critical to developing successful protein immobilization strategies. In the present article, the quantity of water hydrating a monolayer of helical peptides covalently attached to self-assembled monolayers (SAMs) of alkyl thiols on Au was measured using neutron reflectometry (NR). The peptide sequence was composed of repeating LLKK units in which the leucines were aligned to face the SAM. When immersed in water, NR measured 2.7 ± 0.9 water molecules per thiol in the SAM layer and between 75 ± 13 and 111 ± 13 waters around each peptide. The quantity of water in the SAM was nearly twice that measured prior to peptide functionalization, suggesting that the peptide disrupted the structure of the SAM. To identify the location of water molecules around the peptide, we compared our NR data to previously published molecular dynamics simulations of the same peptide on a hydrophobic SAM in water, revealing that 49 ± 5 of 95 ± 8 total nearby water molecules were directly hydrogen-bound to the peptide. Finally, we show that immersing the peptide in water compressed its structure into the SAM surface. Together, these results demonstrate that there is sufficient water to fully hydrate a surface-bound peptide even at hydrophobic interfaces. Given the critical role that water plays in biomolecular structure and function, these results are expected to be informative for a broad array of applications involving proteins at the bio/abio interface.
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Affiliation(s)
- Whitney A Fies
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 2506 Speedway STOP A5300 , Austin , Texas 78712 , United States
| | - Jeremy T First
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 2506 Speedway STOP A5300 , Austin , Texas 78712 , United States
| | - Jason W Dugger
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 , United States
| | - Mathieu Doucet
- Neutron Scattering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - James F Browning
- Neutron Scattering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Lauren J Webb
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 2506 Speedway STOP A5300 , Austin , Texas 78712 , United States
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