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Butt AS, Baig N, Khan M, Ul‐Hamid A, Sher M, Altaf M, Sohail M. HfO
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‐CoO nanoparticles for electrochemical dopamine sensing. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Abdul Samad Butt
- Department of Chemistry, School of Natural Sciences National University of Sciences and Technology Islamabad Pakistan
| | - Nadeem Baig
- Interdisciplinary Research Center for Membranes and Water Security King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia
| | - Munezza Khan
- School of Materials Sciences & Engineering Nanyang Technological University Singapore Singapore
| | - Anwar Ul‐Hamid
- Core Research Facilities King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia
| | - Muhammad Sher
- Department of Chemistry Allama Iqbal Open University Islamabad Pakistan
| | - Muhammad Altaf
- Department of Chemistry Government College University Lahore Pakistan
| | - Manzar Sohail
- Department of Chemistry, School of Natural Sciences National University of Sciences and Technology Islamabad Pakistan
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Miura T, Seki K. Effects of surface affinity on the ordering dynamics of self-assembled monolayers of chain molecules: Transition from a parallel to a perpendicular structure. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052604. [PMID: 26066191 DOI: 10.1103/physreve.91.052604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 06/04/2023]
Abstract
The effects of surface interactions on the ordering dynamics of self-assembled monolayers (SAM) of chain molecules were studied using molecular dynamics simulations. When the strength of surface-chain interactions was equal to or less than that of chain-chain interactions, domains of chain molecules adsorbed perpendicular to the surface ("upright" chains) formed on the surface. Although chain molecules adsorbed parallel to the surface ("lying" chains) were initially observed on the surface, they did not develop into two-dimensionally aligned structures. In contrast, when the strength of surface-chain interactions was at least twice that of chain-chain interactions, the proportion of upright chain molecules was initially small, and the reorientation of lying chains was observed shortly afterwards. In this case, the reorientation from lying to upright configuration developed slowly from the domain boundaries of two-dimensionally aligned structures late in the calculation period. Although the orientation processes of chain molecules on surfaces were strongly influenced by the strength of surface-chain interactions, the total adsorption rate on the surface was not. We also analyzed the maximum area of domains formed by lying chains. The development of two-dimensionally aligned domains required strong surface-chain interactions to prevent the spontaneous formation of nuclei of upright domains.
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Affiliation(s)
- Toshiaki Miura
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Central2, 1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuhiko Seki
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Central2, 1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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Artamonov M, Seideman T. Time-Dependent, Optically Controlled Dielectric Function. J Phys Chem Lett 2015; 6:320-325. [PMID: 26261940 DOI: 10.1021/jz502334z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We suggest optical modulation of the dielectric function of a molecular monolayer adsorbed on a metal surface as a potential means of controlling plasmon resonance phenomena. The dielectric function is altered using a laser pulse of moderate intensity and linear polarization to align the constituent molecules. After the pulse, the monolayer returns to its initial state. Time-dependent, optically controlled dielectric function is illustrated by molecular dynamics calculations.
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Affiliation(s)
- Maxim Artamonov
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Tamar Seideman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Babayco CB, Land DP, Parikh AN, Kiehl RA. Characterization of buried metal-molecule-metal junctions using Fourier transform infrared microspectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:094103. [PMID: 25273743 DOI: 10.1063/1.4896477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We have devised an infrared spectromicroscopy based experimental configuration to enable structural characterization of buried molecular junctions. Our design utilizes a small mercury drop at the focal point of an infrared microscope to act as a mirror in studying metal-molecule-metal (MmM) junctions. An organic molecular monolayer is formed either directly on the mercury drop or on a thin, infrared (IR) semi-transparent layer of Au deposited onto an IR transparent, undoped silicon substrate. Following the formation of the monolayer, films on either metal can be examined independently using specular reflection spectroscopy. Furthermore, by bringing together the two monolayers, a buried molecular bilayer within the MmM junction can be characterized. Independent examination of each half of the junction prior to junction formation also allows probing any structural and/or conformational changes that occur as a result of forming the bilayer. Because our approach allows assembling and disassembling microscopic junctions by forming and withdrawing Hg drops onto the monolayer covered metal, spatial mapping of junctions can be performed simply by translating the location of the derivatized silicon wafer. Finally, the applicability of this technique for the longer-term studies of changes in molecular structure in the presence of electrical bias is discussed.
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Affiliation(s)
- Christopher B Babayco
- Department of Chemistry, University of California, Davis, Davis, California 95616, USA
| | - Donald P Land
- Department of Chemistry, University of California, Davis, Davis, California 95616, USA
| | - Atul N Parikh
- Departments of Biomedical Engineering and of Chemical Engineering and Materials Science, University of California, Davis, Davis, California 95616, USA
| | - Richard A Kiehl
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, USA
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Hamzehloei A, Mousavi MF, Bathaie SZ. In Situ Synthesis of a Novel Quinone Imine Self-Assembled Monolayer and Consideration of Its Reactivity with L-Arginine. ELECTROANAL 2012. [DOI: 10.1002/elan.201200064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Miura T, Mikami M. Molecular dynamics study of the effects of chain properties on the order formation dynamics of self-assembled monolayers of long-chain molecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021801. [PMID: 20365584 DOI: 10.1103/physreve.81.021801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 11/27/2009] [Indexed: 05/29/2023]
Abstract
The order formation dynamics of self-assembled monolayers (SAM) of long-chain molecules were studied using coarse-grained molecular dynamics simulations. The primary kinetic processes of surface order formation from solution are adsorption to the surface and surface diffusion. For long-chain molecules, the degrees of freedom of the chain structure and motion add various complexities to the order formation dynamics. Specifically, the strength of the chain interaction, the chain flexibility and the chain length play a significant role, and this work focused on the effects of these chain properties on the order formation dynamics. The adsorption dynamics of SAM molecules can be explained by the same theoretical framework as the polymer brush. On the other hand, the evolution of highly ordered structure is specific to SAM systems. Simulation results revealed that the development of oriented domains can be grouped into three types, isolated island growth, packing growth, and growth suppression, which depend on temperature and chain flexibility. In packing growth, oriented domains are formed gradually due to the decrease in free volume as the surface density becomes high, while the tilt of the adsorbed chain molecules does not become upright gradually as a whole. Rather, inside the oriented domains, the adsorbed chains adopt "standing" states with tilt angles almost equal to the final values, which contributes to the gradual increase in the total tilt order. The effect of chain length was also studied. In the case of semirigid chain molecules, longer-chain systems showed slightly slower growth in adsorption but faster growth in oriented domains. These simulation results reveal how chain properties influence the dynamics of oriented structure formation on surfaces.
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Affiliation(s)
- Toshiaki Miura
- National Institute of Advanced Industrial Science and Technology, AIST Central 2, 1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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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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Dai J, Li Z, Jin J, Cheng J, Kong J, Bi S. Study of the solvent effect on the quality of dodecanethiol self-assembled monolayers on polycrystalline gold. J Electroanal Chem (Lausanne) 2008. [DOI: 10.1016/j.jelechem.2008.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zhou J, Chen S, Zhang L, Feng Y, Zhai H. Studies of protection of self-assembled films by 2-mercapto-5-methyl-1,3,4-thiadiazole on iron surface in 0.1M H2SO4 solutions. J Electroanal Chem (Lausanne) 2008. [DOI: 10.1016/j.jelechem.2007.10.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Molecular simulation study of 1,5-diphenylcarbazide self-assembled monolayers on a copper surface. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2007. [DOI: 10.2298/jsc0705475l] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this study, the adsorption process of 1,5- diphenylcarbazide (DPC) self-assembled monolayers on a copper surface was investigated by using molecular mechanics. The results indicated that the interaction of the ?-electrons in the -NH-NH- group and the ?-electrons in the phenyl ring could lead to strong adsorption of the highly symmetric DPC molecules on a copper surface. The synergy effect of the phenyl ring and the -NH-NH- group made the whole DPC molecule lay in parallel orientation on a copper surface when the coverage was low. However, at high coverage, the phenyl ring was slightly tilted because of the repulsion of the DPC molecules, while the -NH-NH- groups remained parallel to the copper surface.
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Whelan CM, Gatti F, Leigh DA, Rapino S, Zerbetto F, Rudolf P. Adsorption of Fumaramide [2]Rotaxane and Its Components on a Solid Substrate: A Coverage-Dependent Study. J Phys Chem B 2006; 110:17076-81. [PMID: 16928002 DOI: 10.1021/jp061836c] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration. In contrast, the thread shows no evidence of chemisorption or a preferential orientation. The introduction of the thread into the macrocycle partly disrupts the film order so that the resulting chemisorbed rotaxane shows intermediate behavior with a preferential orientation up to 0.5 ML coverage. A decrease in film order and the absence of a preferred molecular orientation is observed for all three molecules at multilayer coverages. The spectral differences are addressed by molecular dynamics simulations in terms of the mobility of the phenyls of the three molecules on Au(111).
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Affiliation(s)
- Caroline M Whelan
- Laboratoire Interdisciplinaire de Spectroscopie Electronique, Facultés Universitaires Notre-Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur, Belgium
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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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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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