1
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Cobeña-Reyes J, Ye T, Martini A. Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:147-156. [PMID: 37235190 PMCID: PMC10208375 DOI: 10.1021/cbmi.3c00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 05/28/2023]
Abstract
Achieving high-resolution images using dynamic atomic force microscopy (AFM) requires understanding how chemical and structural features of the surface affect image contrast. This understanding is particularly challenging when imaging samples in water. An initial step is to determine how well-characterized surface features interact with the AFM tip in wet environments. Here, we use molecular dynamics simulations of a model AFM tip apex oscillating in water above self-assembled monolayers (SAMs) with different chain lengths and functional groups. The amplitude response of the tip is characterized across a range of vertical distances and amplitude set points. Then relative image contrast is quantified as the difference of the amplitude response of the tip when it is positioned directly above a SAM functional group vs positioned between two functional groups. Differences in contrast between SAMs with different lengths and functional groups are explained in terms of the vertical deflection of the SAMs due to interactions with the tip and water during dynamic imaging. The knowledge gained from simulations of these simple model systems may ultimately be used to guide selection of imaging parameters for more complex surfaces.
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Affiliation(s)
- José Cobeña-Reyes
- Department
of Mechanical Engineering, University of
California Merced, Merced, California 95343, United States
| | - Tao Ye
- Department
of Chemistry & Biochemistry, University
of California Merced, Merced, California 95343, United States
| | - Ashlie Martini
- Department
of Mechanical Engineering, University of
California Merced, Merced, California 95343, United States
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2
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Zeng Y, Ananth R, Dill TJ, Rodarte A, Rozin MJ, Bradshaw N, Brown ER, Tao AR. Metasurface-Enhanced Raman Spectroscopy (mSERS) for Oriented Molecular Sensing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32598-32607. [PMID: 35816614 DOI: 10.1021/acsami.2c01656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is a widely used sensing technique for ultrasensitivity chemical sensing, biomedical detection, and environmental analysis. Because SERS signal is proportional to the fourth power of the local electric field, several SERS applications have focused on the design of plasmonic nanogaps to take advantage of the extremely strong near-field enhancement that results from plasmonic coupling, but few designs have focused on how SERS detection is affected by molecular orientation within these nanogaps. Here, we demonstrate a nanoparticle-on-metal metasurface designed for near-perfect optical absorption as a platform for Raman detection of highly oriented molecular analytes, including two-dimensional materials and aromatic molecules. This metasurface platform overcomes challenges in nanoparticle aggregation, which commonly leads to low or fluctuating Raman signals in other colloidal nanoparticle platforms. Our metasurface-enhanced Raman spectroscopy (mSERS) platform is based on a colloidal Langmuir-Schaefer deposition, with up to 32% surface coverage density of nanogaps across an entire sensor chip. In this work, we perform both simulations of the local electric field and experimental characterization of the mSERS signal obtained for oriented molecular layers. We then demonstrate this mSERS platform for the quantitative detection of the drinking-water toxin polybrominated diphenyl ether (BDE-15), with a limit of detection of 0.25 μM under 530 μW excitation. This detection limit is comparable to other SERS-based sensors operating at laser powers over 3 orders of magnitude higher, indicating the promise of our mSERS platform for nondestructive and low-level analyte detection.
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Affiliation(s)
- Yuan Zeng
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Riddhi Ananth
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Tyler J Dill
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
| | - Andrea Rodarte
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
| | - Matthew J Rozin
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nathan Bradshaw
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
| | - Eric R Brown
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
| | - Andrea R Tao
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive MC 0448, La Jolla, California 92093-0448, United States
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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3
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Ahmad K, Yang Q, Martini A. Simulations of Friction Anisotropy on Self-Assembled Monolayers in Water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6273-6280. [PMID: 35549237 DOI: 10.1021/acs.langmuir.1c03234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular dynamics simulations were performed to study nanoscale friction on hydrophilic and hydrophobic self-assembled monolayers (SAMs) immersed in water. Sliding was simulated in two different directions to capture anisotropy due to the direction of motion relative to the inherent tilted orientation of the molecules. It was shown that friction depends on both hydrophobicity and sliding direction, with the highest friction observed for sliding on hydrophobic SAM in the direction against the initial orientation of the molecules. The origins of the friction trends were analyzed by differentiating the tip-SAM and tip-water force contributions to friction. The tip-water force was higher on the hydrophilic SAM, and this was shown to be due to the presence of a dense layer of water adjacent to the surface and hydrogen bonding. In contrast, the tip-SAM force was higher on the hydrophobic SAM due to a water depletion layer, which enabled the tip to be closer to the SAM terminal group. The higher-friction cases all exhibited greater penetration of the tip below the surface of the SAM, accommodated by further tilting and reorientation of the SAM molecules.
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Affiliation(s)
- Khurshid Ahmad
- US-Pakistan Center for Advanced Studies in Energy, University of Engineering and Technology, Peshawar 25000, Pakistan
| | - Quanpeng Yang
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
| | - Ashlie Martini
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
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4
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Saha LC, Kikugawa G. Heat Conduction Performance over a Poly(ethylene glycol) Self-Assembled Monolayer/Water Interface: A Molecular Dynamics Study. J Phys Chem B 2021; 125:1896-1905. [PMID: 33569956 DOI: 10.1021/acs.jpcb.0c09385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This study examined the interfacial heat condition between a poly(ethylene glycol) (PEG) self-assembled monolayer (SAM) and water using molecular dynamics simulation. It was found that the PEG SAM has higher thermal boundary conductance (TBC) than the traditionally used alkane-based SAM. The TBC conditionally varied with the length of the PEG molecules, where interfacial thermal resistance was a key factor. Our results reveal that the TBC of the PEG SAM/water interface is greatly influenced by its structural properties rather than the matching of vibrational properties between the SAM terminal and water. The structural analysis shows that the water structure around the terminal oxygen atom of the SAM plays a vital role in controlling the TBC. In this study, the concept of free volume has also been exploited, and the result suggests that the reduction of the free volume fraction accommodates a higher TBC. The model was precisely validated against experimental data by calculating the tilt angle and dihedral angle of the PEG SAM, the persistence length of the PEG chain in the water medium, and the sulfur position of the PEG SAM headgroup on the gold surface using quantitative scanning transmission electron microscopy image simulation.
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Affiliation(s)
- Leton C Saha
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Gota Kikugawa
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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5
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Bhadra P, Siu SWI. Effect of Concentration, Chain Length, Hydrophobicity, and an External Electric Field on the Growth of Mixed Alkanethiol Self-Assembled Monolayers: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1913-1924. [PMID: 33503375 DOI: 10.1021/acs.langmuir.0c03414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Growing functionalized self-assembled monolayers (SAMs) with fewer defects and lower cost is the focus of ongoing investigations. In the present study, molecular dynamics simulations were performed to investigate the process of SAM formation on a gold substrate from mixed alkanethiolates in ethanol solution. Using the mixed-SAM system of 11-mercaptoundecanoic acid (MUA) with either 1-decanethiol (C9CH3) or 6-mercaptohexanol (C6OH) in a 3:7 ratio as the standard SAM model, we systematically investigated the effects of the concentration, chain length, functional group, and an external electric field on SAM growth. The results showed that the initial growth rate and surface coverage of the SAM are dependent on the ligand concentration. At a certain high concentration (about 1.2-1.5 times the minimum concentration), the final surface coverage is optimal. Reducing the chain length and increasing the proportion of hydrophobic diluting molecules are effective ways to improve the surface coverage, but the compositional ligands have to be changed, which may not be desirable for the functional requirements of SAMs. Furthermore, by investigating the behavior of the alkanethiolates and ethanol solvent under an applied external field, we find that a strong electric field with a proper field direction can facilitate the generation of defect-free monolayers. These findings will contribute to the understanding of mixed-SAM formation and provide insight into experimental design for efficient and effective SAM formation.
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Affiliation(s)
- Pratiti Bhadra
- Department of Computer and Information Science, University of Macau, Taipa, Macau
| | - Shirley W I Siu
- Department of Computer and Information Science, University of Macau, Taipa, Macau
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6
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Modulating catalytic activity of human topoisomerase II α enzyme by fluorescent gold nanoclusters. Int J Biol Macromol 2020; 170:523-531. [PMID: 33387542 DOI: 10.1016/j.ijbiomac.2020.12.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/22/2022]
Abstract
Precise monitoring of the enzyme activity by a suitable modulator is one of the very fundamental aspects of drug designing that provides the opportunity to overcome the challenges of several diseases. Herein, inhibition of human Topoisomerase IIα enzyme which serves as a potential target site for several anti-cancer drugs is demonstrated by using ultra-small size gold nanoclusters (Au NCs) with the dimension comparable with size of the active site of the enzyme. Molecular dynamics simulation results demonstrate that the Au NCs strongly interact with the human Topo IIα enzyme at its active site or allosteric site depending on forms of enzyme. Additionally, binding energy and interaction profile provides the molecular basis of understanding of interactions of ultra-small size Au NCs and human Topo IIα enzyme. Enthalpy change (ΔH) and binding constant (K) are measured based on a sequential binding model of the Au NCs with the enzyme as demonstrated by the ITC study. Moreover, the in-vitro inhibition study of the catalytic activity of the enzyme and gel electrophoresis indicates that the ultra-small size Au NCs may be used as a potent inhibitor of human Topo IIα enzyme.
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7
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Zhou G, Liu C, Bumm LA, Huang L. Force Field Parameter Development for the Thiolate/Defective Au(111) Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4098-4107. [PMID: 32200638 DOI: 10.1021/acs.langmuir.0c00530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A molecular-level understanding of the interplay between self-assembled monolayers (SAMs) of thiolates and gold surface is of great importance to a wide range of applications in surface science and nanotechnology. Despite theoretical research progress of the past decade, an atomistic model, capable of describing key features of SAMs at reconstructed gold surfaces, is still missing. In this work, periodic ab initio density functional theory (DFT) calculations were utilized to develop a new atomistic force field model for alkanethiolate (AT) SAMs on a reconstructed Au(111) surface. The new force field parameters were carefully trained to reproduce the key features, including vibrational spectra and torsion energy profiles of ethylthiolate (C2S) in the bridge or staple motif model on the Au(111) surface, wherein, the force constants of the bond and angle terms were trained by matching the vibrational spectra, while the torsion parameters of the dihedral angles were trained via fitting the torsion energy profiles from DFT calculations. To validate the developed force field parameters, we performed classical molecular dynamics (MD) simulations for both pristine and reconstructed Au-S interface models with a (2√3 × 3) unit cell, which includes four dodecanethiolate (C10S) molecules on the Au(111) surface. The simulation results showed that the geometrical features of the investigated Au-S interface models and structural properties of the C10S SAMs are in good agreement with the ab initio MD studies. The newly developed atomistic force field model provides new fundamental insights into AT SAMs on the reconstructed Au(111) surface and adds advancement to the existing interface research knowledge.
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Affiliation(s)
- Guobing Zhou
- School of Chemical, Biological and Materials Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Chang Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Lloyd A Bumm
- Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Liangliang Huang
- School of Chemical, Biological and Materials Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
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8
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Hu X, Yang Q, Ye T, Martini A. Simulation of Subnanometer Contrast in Dynamic Atomic Force Microscopy of Hydrophilic Alkanethiol Self-Assembled Monolayers in Water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2240-2246. [PMID: 32043893 DOI: 10.1021/acs.langmuir.9b03655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atomic resolution imaging of surfaces in liquid environments using atomic force microscopy (AFM) is challenging in terms of both reproducibility and measurement interpretation. To understand the origins of these challenges, we used molecular dynamics simulations of AFM on hydrophilic self-assembled monolayers (SAMs) in water. The force on the model AFM tip was calculated as a function of lateral and vertical position relative to the SAM surface. The contributions of the water and SAMs to the overall force were analyzed, and the former was correlated to the water density distribution. Then, dynamic AFM was modeled by oscillating the tip at a driving amplitude. It was found that the contrast between amplitudes at different lateral positions on the surface was dependent on the vertical position of the tip. Lastly, amplitude maps were produced for two vertical positions at constant height, and the ability to capture atomic resolution was related to the force on the tip. These results offer an explanation for the observed instability in atomic scale imaging using AFM and more generally provide insight into the contrast mechanisms of surface images obtained in liquid environments.
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Affiliation(s)
- Xiaoli Hu
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
| | - Quanpeng Yang
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
| | - Tao Ye
- Department of Chemistry and Chemical Biology, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
| | - Ashlie Martini
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
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9
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Latorre CA, Ewen JP, Gattinoni C, Dini D. Simulating Surfactant–Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics. J Phys Chem B 2019; 123:6870-6881. [DOI: 10.1021/acs.jpcb.9b02925] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - James P. Ewen
- Department of Mechanical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Chiara Gattinoni
- Department of Mechanical Engineering, Imperial College London, London SW7 2AZ, U.K
- Department of Materials, ETH Zürich, Zürich 8092, Switzerland
| | - Daniele Dini
- Department of Mechanical Engineering, Imperial College London, London SW7 2AZ, U.K
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10
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Merz SN, Farrell ZJ, Pearring J, Hoover E, Kester M, Egorov SA, Green DL, DuBay KH. Computational and Experimental Investigation of Janus-like Monolayers on Ultrasmall Noble Metal Nanoparticles. ACS NANO 2018; 12:11031-11040. [PMID: 30347139 DOI: 10.1021/acsnano.8b05188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Detection of monolayer morphology on nanoparticles smaller than 10 nm has proven difficult with traditional visualization techniques. Here matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is used in conjunction with atomistic simulations to detect the formation of Janus-like monolayers on noble metal nanoparticles. Silver metal nanoparticles were synthesized with a monolayer consisting of dodecanethiol (DDT) and mercaptoethanol (ME) at varying ratios. The nanoparticles were then analyzed using MALDI-MS, which gives information on the local ordering of ligands on the surface. The MALDI-MS analysis showed large deviations from random ordering, suggesting phase separation of the DDT/ME monolayers. Atomistic Monte Carlo (MC) calculations were then used to simulate the nanoscale morphology of the DDT/ME monolayers. In order to quantitatively compare the computational and experimental results, we developed a method for determining an expected MALDI-MS spectrum from the atomistic simulation. Experiments and simulations show quantitative agreement, and both indicate that the DDT/ME ligands undergo phase separation, resulting in Janus-like nanoparticle monolayers with large, patchy domains.
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Affiliation(s)
- Steven N Merz
- Department of Chemical Engineering , University of Virginia , 102 Engineers Way , Charlottesville , Virginia 22904 , United States
| | - Zachary J Farrell
- Department of Chemical Engineering , University of Virginia , 102 Engineers Way , Charlottesville , Virginia 22904 , United States
| | - Joseph Pearring
- Department of Chemical Engineering , University of Virginia , 102 Engineers Way , Charlottesville , Virginia 22904 , United States
| | - Elise Hoover
- Department of Biomedical Engineering , University of Virginia , Thornton Hall , P.O. Box 400259, Charlottesville , Virginia 22904 , United States
| | - Mark Kester
- School of Medicine , University of Virginia , 1215 Lee Street , Charlottesville , Virginia 22908 , United States
| | - Sergei A Egorov
- Department of Chemistry , University of Virginia , McCormick Road , PO Box 400319, Charlottesville , Virginia 22904 , United States
- Leibniz Institute for Polymer Research Dresden , Hohe Strasse 6 , D-01069 Dresden , Germany
| | - David L Green
- Department of Chemical Engineering , University of Virginia , 102 Engineers Way , Charlottesville , Virginia 22904 , United States
| | - Kateri H DuBay
- Department of Chemistry , University of Virginia , McCormick Road , PO Box 400319, Charlottesville , Virginia 22904 , United States
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11
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Hu X, Nanney W, Umeda K, Ye T, Martini A. Combined Experimental and Simulation Study of Amplitude Modulation Atomic Force Microscopy Measurements of Self-Assembled Monolayers in Water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9627-9633. [PMID: 30060661 DOI: 10.1021/acs.langmuir.8b01609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) can be used to measure surface properties at the nanoscale. However, interpretation of measurements from amplitude modulation AFM (AM-AFM) in liquid is not straightforward due to the interactions between the AFM tip, the surface being imaged, and the water. In this work, amplitude-distance measurements and molecular dynamics simulations of AM-AFM were employed to study the effect of surface chemistry on the amplitude of tip oscillation in water. The sample surfaces consisted of self-assembled monolayers where the hydrophilicity or hydrophobicity was determined by the terminal group of the alkanethiols. Analysis showed that surface chemical composition influences the hydration structure near the interface which affects the forces experienced by the tip and in turn changes the amplitude profile. This observation could aid our understanding of AM-AFM measurements of interfacial phenomena on various surfaces in water.
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Affiliation(s)
- Xiaoli Hu
- Department of Mechanical Engineering , University of California-Merced , 5200 N. Lake Road , Merced , California 95343 , United States
| | - Warren Nanney
- Chemistry and Chemical Biology , University of California-Merced , 5200 N. Lake Road , Merced , California 95343 , United States
| | - Kenichi Umeda
- Department of Advanced Material Science , the University of Tokyo , 5-1-5, Kashiwanoha , Kashiwa , Chiba 277-8561 , Japan
| | - Tao Ye
- Chemistry and Chemical Biology , University of California-Merced , 5200 N. Lake Road , Merced , California 95343 , United States
| | - Ashlie Martini
- Department of Mechanical Engineering , University of California-Merced , 5200 N. Lake Road , Merced , California 95343 , United States
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12
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Ouyang W, de Wijn AS, Urbakh M. Atomic-scale sliding friction on a contaminated surface. NANOSCALE 2018; 10:6375-6381. [PMID: 29560981 DOI: 10.1039/c7nr09530a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using non-equilibrium molecular dynamic simulations, we investigate the effect of adsorbates on nanoscopic friction. We find that the interplay between different channels of energy dissipation at the frictional interface may lead to non-monotonic dependence of the friction force on the adsorbate surface coverage and to strongly nonlinear variation of friction with normal load (non-Amontons' behavior). Our simulations suggest that the key parameter controlling the variation of friction force with the normal load, surface coverage and temperature is the time-averaged number of adsorbates confined between the tip and the substrate. Three different regimes of temperature dependence of friction in the presence of adsorbates are predicted. Our findings point on new ways to control friction on contaminated surfaces.
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Affiliation(s)
- Wengen Ouyang
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel. and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Astrid S de Wijn
- Department of Mechanical and Industrial Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway and Department of Physics, Stockholm University, 10691 Stockholm, Sweden
| | - Michael Urbakh
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel. and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
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13
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Ross-Naylor JA, Mijajlovic M, Zhang H, Biggs MJ. Characterizing the Switching Transitions of an Adsorbed Peptide by Mapping the Potential Energy Surface. J Phys Chem B 2017; 121:11455-11464. [DOI: 10.1021/acs.jpcb.7b10319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James A. Ross-Naylor
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Milan Mijajlovic
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Hu Zhang
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mark J. Biggs
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
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14
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Colangelo E, Chen Q, Davidson AM, Paramelle D, Sullivan MB, Volk M, Lévy R. Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:438-449. [PMID: 27982599 DOI: 10.1021/acs.langmuir.6b04383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The self-assembly and self-organization of small molecules on the surface of nanoparticles constitute a potential route toward the preparation of advanced proteinlike nanosystems. However, their structural characterization, critical to the design of bionanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles (GNPs) is developed using experimentally characterized Cys-Ala-Leu-Asn-Asn (CALNN)- and Cys-Phe-Gly-Ala-Ile-Leu-Ser-Ser (CFGAILSS)-capped GNPs as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated using both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on the peptide capping density and on the nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bionanomaterials.
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Affiliation(s)
- Elena Colangelo
- Institute of Integrative Biology, University of Liverpool , Crown Street, L69 7ZB Liverpool, U.K
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research) , 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Qiubo Chen
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Adam M Davidson
- Department of Chemistry, University of Liverpool , Liverpool L69 7ZD, U.K
| | - David Paramelle
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research) , 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634
| | - Michael B Sullivan
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Martin Volk
- Department of Chemistry, University of Liverpool , Liverpool L69 7ZD, U.K
- Department of Chemistry, Surface Science Research Centre, University of Liverpool , Abercromby Square, Liverpool L69 3BX, U.K
| | - Raphaël Lévy
- Institute of Integrative Biology, University of Liverpool , Crown Street, L69 7ZB Liverpool, U.K
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15
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Colangelo E, Comenge J, Paramelle D, Volk M, Chen Q, Lévy R. Characterizing Self-Assembled Monolayers on Gold Nanoparticles. Bioconjug Chem 2016; 28:11-22. [DOI: 10.1021/acs.bioconjchem.6b00587] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Elena Colangelo
- Institute
of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, United Kingdom
| | - Joan Comenge
- Institute
of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, United Kingdom
| | - David Paramelle
- Institute
of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634
| | - Martin Volk
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Surface
Science Research Centre, Department of Chemistry, Abercromby Square, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Qiubo Chen
- Institute
of High Performance Computing, A*STAR (Agency for Science, Technology and Research), 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Raphaël Lévy
- Institute
of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, United Kingdom
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16
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Majumdar S, Sierra-Suarez JA, Schiffres SN, Ong WL, Higgs CF, McGaughey AJH, Malen JA. Vibrational mismatch of metal leads controls thermal conductance of self-assembled monolayer junctions. NANO LETTERS 2015; 15:2985-2991. [PMID: 25884912 DOI: 10.1021/nl504844d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present measurements of the thermal conductance of self-assembled monolayer (SAM) junctions formed between metal leads (Au, Ag, Pt, and Pd) with mismatched phonon spectra. The thermal conductance obtained from frequency domain thermoreflectance experiments is 65 ± 7 MW/m(2) K for matched Au-alkanedithiol-Au junctions, while the mismatched Au-alkanedithiol-Pd junctions yield a thermal conductance of 36 ± 3 MW/m(2) K. The experimental observation that junction thermal conductance (per molecule) decreases as the mismatch between the lead vibrational spectra increases, paired with results from molecular dynamics (MD) simulations, suggest that phonons scatter elastically at the metal-SAM interfaces. Furthermore, we resolve a known discrepancy between measurements and MD predictions of SAM thermal conductance by using a contact mechanics model to predict 54 ± 15% areal contact in the Au-alkanedithiol-Au experimental junction. This incomplete contact obscures the actual junction thermal conductance of 115 ± 22 MW/m(2) K, which is comparable to that of metal-dielectric interfaces.
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Affiliation(s)
- Shubhaditya Majumdar
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
| | - Jonatan A Sierra-Suarez
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
| | - Scott N Schiffres
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
| | - Wee-Liat Ong
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
| | - C Fred Higgs
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
| | - Alan J H McGaughey
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
| | - Jonathan A Malen
- †Department of Mechanical Engineering, ‡Department of Electrical and Computer Engineering, and §Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh 15213, United States
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17
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Olmos-Asar JA, Ludueña M, Mariscal MM. Monolayer protected gold nanoparticles: the effect of the headgroup–Au interaction. Phys Chem Chem Phys 2014; 16:15979-87. [DOI: 10.1039/c4cp01963f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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18
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Rouhana LL, Moussallem MD, Schlenoff JB. Adsorption of Short-Chain Thiols and Disulfides onto Gold under Defined Mass Transport Conditions: Coverage, Kinetics, and Mechanism. J Am Chem Soc 2011; 133:16080-91. [DOI: 10.1021/ja2041833] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Layal L. Rouhana
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, United States
| | - Maroun D. Moussallem
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph B. Schlenoff
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, United States
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19
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Olmos-Asar JA, Rapallo A, Mariscal MM. Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles. Phys Chem Chem Phys 2011; 13:6500-6. [PMID: 21387045 DOI: 10.1039/c0cp02921a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.e. hollow, bridge, top, on-top Au adatom and the novel staple motif) for different crystalline facets, i.e. Au(111) and (100). Langevin dynamics simulations have been performed to study the capping effects of alkanethiolates molecules on Au nanoparticles in the range 1-4 nm. The simulation results reveal an enhancement of the coverage degree whilst the nanoparticles diameter decreases. A high surface disorder due to the strong S-Au bond was found, in very good agreement with very recent experimental findings [M. M. Mariscal, J. A. Olmos-Asar, C. Gutierrez-Wing, A. Mayoral and M. J. Yacaman, Phys. Chem. Chem. Phys., 2010, 12, 11785].
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Affiliation(s)
- Jimena A Olmos-Asar
- INFIQC/CONICET, Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (XUA5000), Córdoba, Argentina
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20
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Akimov A, Kolomeisky AB. DYNAMICS OF SINGLE-MOLECULE ROTATIONS ON SURFACES DEPEND ON SYMMETRY, INTERACTIONS AND MOLECULAR SIZES. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:125-131. [PMID: 21278909 PMCID: PMC3026388 DOI: 10.1021/jp108062p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Rotating surface-mounted molecules have attracted attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated that a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces, and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.
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21
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Mariscal MM, Olmos-Asar JA, Gutierrez-Wing C, Mayoral A, Yacaman MJ. On the atomic structure of thiol-protected gold nanoparticles: a combined experimental and theoretical study. Phys Chem Chem Phys 2010; 12:11785-90. [PMID: 20694260 DOI: 10.1039/c004229c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present work new findings on the structure of the S-Au interface are presented. Theoretical calculations using a new semiempirical potential, based on density functional theory and a bond-order Morse potential, are employed to simulate the adsorption process in a more realistic way. The simulation results reveal the formation of gold adatoms on the nanoparticle surface and high surface disorder due to the strong S-Au bond. Experimental data were acquired by aberration (Cs) corrected scanning transmission electron microscopy (STEM) using a high angle annular dark field detector (HAADF) that showed a great similarity with the theory predicted.
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Affiliation(s)
- M M Mariscal
- INFIQC-CONICET, Departamento de Matemática y Física, Fac. Cs. Químicas, Universidad Nacional de Córdoba, (5000) Cordoba, Argentina.
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22
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Zhang Y, Barnes GL, Yan T, Hase WL. Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer. Phys Chem Chem Phys 2010; 12:4435-45. [DOI: 10.1039/b923858c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Kim H, Saha LC, Saha JK, Jang J. Molecular simulation of the water meniscus in dip-pen nanolithography. SCANNING 2010; 32:2-8. [PMID: 19787663 DOI: 10.1002/sca.20157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report a molecular dynamics simulation of the nanometer water meniscus formed in dip-pen nanolithography (DPN). When an atomic force microscope tip is in contact with a surface, the meniscus is significantly asymmetric around the tip axis. The meniscus as a whole can move away from the tip axis due to surface diffusion. The structure of the meniscus fluctuates and its periphery has a finite thickness as large as 25% of its width. We simulated the transport of nonpolar hydrophobic molecules through a water meniscus. Molecules move on the surface of, not dissolving into the interior of, the meniscus. As a result, an annular pattern forms in DPN. Even if the meniscus is cylindrically symmetric, the molecular flow from the tip and the subsequent pattern growth on the surface are anisotropic at the nanosecond timescale.
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Affiliation(s)
- Hyojeong Kim
- Department of Nanomaterials Engineering, Pusan National University, Miryang, Republic of Korea
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24
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Iori F, Di Felice R, Molinari E, Corni S. GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water. J Comput Chem 2009; 30:1465-76. [DOI: 10.1002/jcc.21165] [Citation(s) in RCA: 211] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Maitani MM, Daniel TA, Cabarcos OM, Allara DL. Nascent Metal Atom Condensation in Self-Assembled Monolayer Matrices: Coverage-Driven Morphology Transitions from Buried Adlayers to Electrically Active Metal Atom Nanofilaments to Overlayer Clusters during Aluminum Atom Deposition on Alkanethiolate/Gold Monolayers. J Am Chem Soc 2009; 131:8016-29. [DOI: 10.1021/ja901376w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Masato M. Maitani
- Department of Materials Science and Engineering, The Materials Research Institute, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Thomas A. Daniel
- Department of Materials Science and Engineering, The Materials Research Institute, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Orlando M. Cabarcos
- Department of Materials Science and Engineering, The Materials Research Institute, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - David L. Allara
- Department of Materials Science and Engineering, The Materials Research Institute, and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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26
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Olmos Asar J, Leiva E, Mariscal M. The behavior of single-molecule junctions predicted by atomistic simulations. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2009.02.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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27
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Bubnis G, Cleary S, Mayne H. Self-assembly and structural behavior of a model rigid C60-terminated thiolate on Au(111). Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.01.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Biggs MJ, Mijajlovic M. Switching in of Ac-(Ala)10-NHMe at a solid surface. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2008; 4:262-265. [PMID: 18502185 DOI: 10.1016/j.nano.2008.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 03/23/2008] [Accepted: 03/31/2008] [Indexed: 05/26/2023]
Abstract
Using molecular simulation, we show how Ac-(Ala)(10)-NHMe adsorbed on a solid surface switches between three conformations at distinct surface energies. The first switch is from an alpha-helix to a 3.1(10)-helix. The second involves further stretching to a 2(7)-helix. This switching has several potential applications including memory in molecular computers to motility elements in nanotechnology, and could be relevant to biological activity of proteins near solid surfaces (e.g., nano and aerosol particles) and disease processes induced by such interactions.
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Affiliation(s)
- Mark J Biggs
- Institute for Materials and Processes, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
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29
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Henz BJ, Hawa T, Zachariah MR. Mechano-chemical stability of gold nanoparticles coated with alkanethiolate SAMs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:773-783. [PMID: 18189429 DOI: 10.1021/la7024473] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Molecular dynamics simulations are used to probe the structure and stability of alkanethiolate self-assembled monolayers (SAMs) on gold nanoparticles. We observed that the surface of gold nanoparticles becomes highly corrugated by the adsorption of the SAMs. Furthermore, as the temperature is increased, the SAMs dissolve into the gold nanoparticle, creating a liquid mixture at temperatures much lower than the melting temperature of the gold nanoparticle. By analyzing the mechanical and chemical properties of gold nanoparticles at temperatures below the melting point of gold, with different SAM chain lengths and surface coverage properties, we determined that the system is metastable. The model and computational results that provide support for this hypothesis are presented.
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Affiliation(s)
- Brian J Henz
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland, USA
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30
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Leng YS, Dyer PJ, Krstić PS, Harrison RJ, Cummings PT. Calibration of chemical bonding between benzenedithiolate and gold: the effects of geometry and size of gold clusters. Mol Phys 2007. [DOI: 10.1080/00268970601149298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Sung IH, Kim DE. Study on nanoscale abrasive interaction between nanoprobe and self-assembled molecular surface for probe-based nanolithography process. Ultramicroscopy 2007; 107:1-7. [PMID: 16762507 DOI: 10.1016/j.ultramic.2006.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2005] [Revised: 04/03/2006] [Accepted: 04/12/2006] [Indexed: 10/24/2022]
Abstract
Mechano-chemical scanning probe lithography (MC-SPL) is a nanofabrication technique that is based on the nanoscale abrasive interaction between a sharp nanoprobe and an ultrathin organic resist-coated surface. This work reviews the fundamental aspects of the MC-SPL process. The abrasive interaction at the tip-workpiece contact interface that occurs in the MC-SPL process was investigated by experimentally as well as by molecular dynamics simulation. Experimental results showed that severe wear of the tip that can generate just after coming into contact with the sample and the defects on the organic resists lead to the pattern broadening. In addition, the results from the simulation using the tips modeled with various shapes disclosed that the scribed pattern width was largely affected more by the shape of the tip rather than by the tip-surface contact area and thus the severe pattern broadening and large displacement of alkanethiol molecules around the tip could occur in the case of using the tip with large cone angle. It was found that these phenomena were due to the strong van der Waals interactions between the alkanethiol molecules.
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Affiliation(s)
- In-Ha Sung
- Department of Mechanical Engineering, Hannam University, 133 Ojeong-dong, Daedeok-gu, Daejeon 306-791, Korea
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32
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Lal M, Plummer M, Smith W. Solvent Density Effects on the Solvation Behavior and Configurational Structure of Bare and Passivated 38-Atom Gold Nanoparticle in Supercritical Ethane. J Phys Chem B 2006; 110:20879-88. [PMID: 17048902 DOI: 10.1021/jp0633650] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In exploring the effects of solvent density on the mode and the degree of solvation of the bare and passivated 38-atom gold particle in supercritical ethane, we have extended the molecular dynamics simulations of the system, reported previously,(34) to cover a range of isotherms in the T > T(c) regime, where T(c) is the critical temperature of the solvent. Consonant with our previous observations, the modes of solvation of the bare and the passivated particle, deduced from the radial distribution of the solvent about the metal core center of mass, are found to be vastly different from each other at all solvent densities: while the molecules solvating the bare particle form a well-defined, two-region layer around it, those solvating the passivated particle are loosely dispersed in the passivating layer. For the bare particle, the degree of solvation (vartheta) as a function of solvent density passes through a maximum occurring in the close vicinity of the critical point, consistent with our previous results and in agreement with Debenedetti's theoretical analysis,(22,23) which predicts a solvation enhancement effect in the critical region for systems where the unlike solvent/solute interaction is much stronger than the solvent/solvent interaction. Taking the degree of solvation (vartheta) as a measure of solvent quality, we have investigated how the solvent quality would vary along the solvent-density isotherms. In the solvent-density regime rho > rho(c), the solvent quality is found to be a decreasing function of the density as a result of progressive dominance of the excluded volume effect over the attractive particle/solvent interactions. The particle/solvent affinity is greatly reduced in the presence of the passivating layer, resulting in considerable shrinkage of the good-solvent-quality domain in the supercritical regime. The solvent environment and the presence of the passivating chains produce significant disorder in the equilibrium structure assumed by the nanoparticle core.
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Affiliation(s)
- Moti Lal
- Centre for Nanoscale Science, The Donnan and Robert Robinson Laboratories, University of Liverpool, Liverpool L69 7ZD, United Kingdom.
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33
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Zhao X, Leng Y, Cummings PT. Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:4116-24. [PMID: 16618153 DOI: 10.1021/la0532252] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.
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Affiliation(s)
- Xiongce Zhao
- Nanomaterials Theory Institute, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
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34
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Ahn Y, Hong S, Jang J. Growth Dynamics of Self-Assembled Monolayers in Dip-Pen Nanolithography. J Phys Chem B 2006; 110:4270-3. [PMID: 16509723 DOI: 10.1021/jp055778r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using molecular dynamics simulations, we studied the growth mechanism of self-assembled monolayers in dip-pen nanolithography. A molecule dropping from the tip kicks out a molecule sitting on the substrate, and the displaced molecule in turn kicks out a molecule next to it. This kicking propagates and finally stops when it hits the periphery of the monolayer. This monolayer growth is faster than predicted from the previous diffusion theory. Increasing the molecule-substrate binding strength enhances the molecular deposition rate and makes the monolayer well-ordered.
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Affiliation(s)
- Yoonho Ahn
- School of Nano Science & Technology, Pusan National University, Busan, Republic of Korea 609-735
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35
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Leng Y, Krstić PS, Wells JC, Cummings PT, Dean DJ. Interaction between benzenedithiolate and gold: Classical force field for chemical bonding. J Chem Phys 2005; 122:244721. [PMID: 16035807 DOI: 10.1063/1.1942468] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.
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Affiliation(s)
- Yongsheng Leng
- Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA.
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36
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A study of 1-decanethiol self-assembly on gold electrodes by computer simulation. J Electroanal Chem (Lausanne) 2005. [DOI: 10.1016/j.jelechem.2004.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Roper M, Skegg M, Fisher C, Lee J, Dhanak V, Woodruff D, Jones RG. Atop adsorption site of sulphur head groups in gold-thiolate self-assembled monolayers. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.02.109] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Lal M, Plummer M, Richmond NJ, Smith W. Solvation of Metal Nanoparticles in a Subcritical — Supercritical Fluid: A Computer Simulation Study. J Phys Chem B 2004. [DOI: 10.1021/jp036776e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Moti Lal
- Centre for Nanoscale Science, The Donnan and Robert Robinson Laboratories, University of Liverpool, Liverpool L69 7ZD, U.K., and Computational Science & Engineering Department, CCLRC Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, U.K
| | - Martin Plummer
- Centre for Nanoscale Science, The Donnan and Robert Robinson Laboratories, University of Liverpool, Liverpool L69 7ZD, U.K., and Computational Science & Engineering Department, CCLRC Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, U.K
| | - Nicola J. Richmond
- Centre for Nanoscale Science, The Donnan and Robert Robinson Laboratories, University of Liverpool, Liverpool L69 7ZD, U.K., and Computational Science & Engineering Department, CCLRC Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, U.K
| | - William Smith
- Centre for Nanoscale Science, The Donnan and Robert Robinson Laboratories, University of Liverpool, Liverpool L69 7ZD, U.K., and Computational Science & Engineering Department, CCLRC Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, U.K
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39
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Leng, Keffer DJ, Cummings PT. Structure and Dynamics of a Benzenedithiol Monolayer on a Au(111) Surface. J Phys Chem B 2003. [DOI: 10.1021/jp034405s] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leng
- Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, and Department of Chemical Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200
| | - David J. Keffer
- Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, and Department of Chemical Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200
| | - Peter T. Cummings
- Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, and Department of Chemical Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200
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Li B, Zeng C, Li Q, Wang B, Yuan L, Wang H, Yang J, Hou JG, Zhu Q. First-Principles Simulation of Scanning Tunneling Microscopy Images of Individual Molecules in Alkanethiol Self-Assembled Monolayers on Au(111). J Phys Chem B 2003. [DOI: 10.1021/jp0261861] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bin Li
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Changgan Zeng
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Qunxiang Li
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Bing Wang
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Lanfeng Yuan
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Haiqian Wang
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Jinlong Yang
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - J. G. Hou
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Qingshi Zhu
- Structure Research Laboratory and Open Laboratory of Bond Selective Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
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41
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Leng Y, Jiang S. Dynamic Simulations of Adhesion and Friction in Chemical Force Microscopy. J Am Chem Soc 2002; 124:11764-70. [PMID: 12296744 DOI: 10.1021/ja026274z] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A hybrid molecular simulation approach has been applied to investigate dynamic adhesion and friction between a chemical force microscope (CFM) tip and a substrate, both modified by self-assembled monolayers (SAMs) with hydrophobic methyl (CH(3)) or hydrophilic hydroxyl (OH) terminal groups. The method combines a dynamic model for the CFM tip-cantilever system and a molecular dynamics (MD) relaxation technique for SAMs on Au(111) at room temperature. The hybrid simulation method allows one to simulate force-distance curves (or adhesion) and friction loops (or friction coefficient) in the CFM on the experimental time scale for the first time. The simulation results also provide valuable molecular information at the interface that is not accessible in CFM experiments, such as the actual tip position with respect to the cantilever support position, molecular and hydrogen-bonding structures at the interface, and load distributions among different molecular chains (or single-molecule forces). Results show that the adhesion force and friction coefficient for the OH/OH contact pair are much larger than those for the CH(3)/CH(3) pair due to the formation of hydrogen bonds. During the retraction of a CFM tip from a surface, the CFM tip is away from the sample surface slightly while the spring undergoes dramatic elongation in the normal direction before rupture occurs. Single-molecule forces are distributed unevenly at the contact area. Surface energies calculated for functionalized surfaces compare well with those determined by experiments.
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Affiliation(s)
- Yongsheng Leng
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195-1750, USA
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42
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Jang J, Hong S, Schatz GC, Ratner MA. Self-assembly of ink molecules in dip-pen nanolithography: A diffusion model. J Chem Phys 2001. [DOI: 10.1063/1.1384550] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Dou Y, Zhigilei LV, Winograd N, Garrison BJ. Explosive Boiling of Water Films Adjacent to Heated Surfaces: A Microscopic Description. J Phys Chem A 2001. [DOI: 10.1021/jp003913o] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yusheng Dou
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Leonid V. Zhigilei
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Nicholas Winograd
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
| | - Barbara J. Garrison
- Department of Chemistry and Materials Research Institute, Penn State University, University Park, Pennsylvania 16802, and Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903
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44
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Liu KSS, Yong CW, Garrison BJ, Vickerman JC. Molecular Dynamics Simulations of Particle Bombardment Induced Desorption Processes: Alkanethiolates on Au(111). J Phys Chem B 1999. [DOI: 10.1021/jp984071k] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. S. S. Liu
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - C. W. Yong
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - B. J. Garrison
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. C. Vickerman
- Surface Analysis Research Centre, Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, U.K., School of Biological Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, U.K., and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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45
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Luedtke WD, Landman U. Structure and Thermodynamics of Self-Assembled Monolayers on Gold Nanocrystallites. J Phys Chem B 1998. [DOI: 10.1021/jp981745i] [Citation(s) in RCA: 211] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- W. D. Luedtke
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430
| | - Uzi Landman
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430
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46
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Beardmore KM, Kress JD, Grønbech-Jensen N, Bishop A. Determination of the headgroup-gold(111) potential surface for alkanethiol self-assembled monolayers by ab initio calculation. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(97)01361-4] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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