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Zhu G, Huang Z, Zhao L, Tu Y. Unexpected spontaneous dynamic oxygen migration on carbon nanotubes. NANOSCALE 2021; 13:15231-15237. [PMID: 34553730 DOI: 10.1039/d1nr03251h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Combining density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations, we show that oxygen functional groups exhibit unexpected spontaneous dynamic behaviors on the interior surface of single-walled carbon nanotubes (SWCNTs). The hydroxyl and epoxy migrations are achieved by the C-O bond breaking/reforming reactions or the proton transfer reaction between the neighboring epoxy and hydroxyl groups. It is demonstrated that the spontaneous dynamic characteristic is attributed to the sharply reduced energy barrier less than or comparable to thermal fluctuations. We also observe a stable intermediate state with a dangling C-O bond, which permits the successive migration of the oxygen functional groups. However, on the exterior surface of SWCNTs, it is difficult for the oxygen groups to migrate spontaneously because there are relatively high energy barriers, and the dangling C-O bond prefers to transform into the more stable epoxy configuration. The spontaneous oxygen migration is further confirmed by the oxygen migration process using DFT calculations and AIMD simulations at room temperature. Our work provides a new understanding of the behavior of oxygen functional groups at interfaces and gives a potential route to design new carbon-based dynamic materials.
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Affiliation(s)
- Guangdong Zhu
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China.
| | - Zhijing Huang
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China.
| | - Liang Zhao
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China.
| | - Yusong Tu
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China.
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Wu L, Zhou X, Lu H, Liang Q, Kou J, Wu F, Fan J. A controllable water signal transistor. Phys Chem Chem Phys 2017; 19:9625-9629. [PMID: 28346547 DOI: 10.1039/c6cp08664k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We performed molecular dynamics simulations to study the regulating ability of water chains confined in a Y-shaped nanochannel. It was shown that a signal at the molecular level could be controlled by two other charge-induced signals when the water chains were confined in a Y-shaped nanochannel, demonstrating promising applications as water signal transistors in nanosignal systems. The mechanism of a water signal transistor is similar to a signal logic device. This remarkable ability to control the water signal is attributed to the strong dipole-ordering of the water chains in the nanochannel. The controllable water signal process of the Y-shaped nanochannel provides opportunities for future application in the design of molecular-scale signal devices.
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Affiliation(s)
- Lili Wu
- Xingzhi College, Institute of Condensed Matter Physics, and Zhejiang Province Key Laboratory of Solid State Optoelectronic Devices, Zhejiang Normal University, Jinhua 321004, China.
| | - Xiaoyan Zhou
- Xingzhi College, Institute of Condensed Matter Physics, and Zhejiang Province Key Laboratory of Solid State Optoelectronic Devices, Zhejiang Normal University, Jinhua 321004, China.
| | - Hangjun Lu
- Xingzhi College, Institute of Condensed Matter Physics, and Zhejiang Province Key Laboratory of Solid State Optoelectronic Devices, Zhejiang Normal University, Jinhua 321004, China.
| | - Qing Liang
- Xingzhi College, Institute of Condensed Matter Physics, and Zhejiang Province Key Laboratory of Solid State Optoelectronic Devices, Zhejiang Normal University, Jinhua 321004, China.
| | - Jianlong Kou
- Xingzhi College, Institute of Condensed Matter Physics, and Zhejiang Province Key Laboratory of Solid State Optoelectronic Devices, Zhejiang Normal University, Jinhua 321004, China.
| | - Fengmin Wu
- Xingzhi College, Institute of Condensed Matter Physics, and Zhejiang Province Key Laboratory of Solid State Optoelectronic Devices, Zhejiang Normal University, Jinhua 321004, China.
| | - Jintu Fan
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, NY 14853-4401, USA
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Garate JA, Perez-Acle T. From dimers to collective dipoles: Structure and dynamics of methanol/ethanol partition by narrow carbon nanotubes. J Chem Phys 2016; 144:064105. [PMID: 26874480 DOI: 10.1063/1.4941331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Alcohol partitioning by narrow single-walled carbon nanotubes (SWCNTs) holds the promise for the development of novel nanodevices for diverse applications. Consequently, in this work, the partition of small alcohols by narrow tubes was kinetically and structurally quantified via molecular dynamics simulations. Alcohol partitioning is a fast process in the order of 10 ns for diluted solutions but the axial-diffusivity within SWCNT is greatly diminished being two to three orders of magnitude lower with respect to bulk conditions. Structurally, alcohols form a single-file conformation under confinement and more interestingly, they exhibit a pore-width dependent transition from dipole dimers to a single collective dipole, for both methanol and ethanol. Energetic analyses demonstrate that this transition is the result of a detailed balance between dispersion and electrostatics interactions, with the latter being more pronounced for collective dipoles. This transition fully modifies the reorientational dynamics of the loaded particles, generating stable collective dipoles that could find usage in signal-amplification devices. Overall, the results herein have shown distinct physico-chemical features of confined alcohols and are a further step towards the understanding and development of novel nanofluidics within SWCNTs.
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Affiliation(s)
- Jose A Garate
- Computational Biology Laboratory, Fundación Ciencia and Vida, Santiago, Chile
| | - Tomas Perez-Acle
- Computational Biology Laboratory, Fundación Ciencia and Vida, Santiago, Chile
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Gu Z, Zhang Y, Luan B, Zhou R. DNA translocation through single-layer boron nitride nanopores. SOFT MATTER 2016; 12:817-23. [PMID: 26537824 DOI: 10.1039/c5sm02197a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ultra-thin nanopores have become promising biological sensors because of their outstanding signal-to-noise ratio and spatial resolution. Here, we show that boron nitride (BN), which is a new two-dimensional (2D) material similar to graphene, could be utilized for making a nanopore with an atomic thickness. Using an all-atom molecular dynamics simulation, we investigated the dynamics of DNA translocation through the BN nanopore. The results of our simulations demonstrated that it is possible to detect different double-stranded DNA (dsDNA) sequences from the recording of ionic currents through the pore during the DNA translocation. Surprisingly, opposite to results for a graphene nanopore, we found the calculated blockage current for poly(A-T)40 in a BN nanopore to be less than that for poly(G-C)40. Also in contrast with the case of graphene nanopores, dsDNA models moved smoothly and in an unimpeded manner through the BN nanopores in the simulations, suggesting a potential advantage for using BN nanopores to design stall-free sequencing devices. BN nanopores, which display several properties (such as being hydrophilic and non-metallic) that are superior to those of graphene, are thus expected to find applications in the next generation of high-speed and low-cost biological sensors.
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Affiliation(s)
- Zonglin Gu
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
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Bio-mimicking of proline-rich motif applied to carbon nanotube reveals unexpected subtleties underlying nanoparticle functionalization. Sci Rep 2014; 4:7229. [PMID: 25427563 PMCID: PMC4245522 DOI: 10.1038/srep07229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/11/2014] [Indexed: 11/09/2022] Open
Abstract
Here, we report computational studies of the SH3 protein domain interacting with various single-walled carbon nanotubes (SWCNT) either bare or functionalized by mimicking the proline-rich motif (PRM) ligand (PPPVPPRR) and compare it to the SH3-PRM complex binding. With prolines or a single arginine attached, the SWCNT gained slightly on specificity when compared with the bare control, whereas with multi-arginine systems the specificity dropped dramatically to our surprise. Although the electrostatic interaction provided by arginines is crucial in the recognition between PRM and SH3 domain, our results suggest that attaching multiple arginines to the SWCNT has a detrimental effect on the binding affinity. Detailed analysis of the MD trajectories found two main factors that modulate the specificity of the binding: the existence of competing acidic patches at the surface of SH3 that leads to "trapping and clamping" by the arginines, and the rigidity of the SWCNT introducing entropic penalties in the proper binding. Further investigation revealed that the same "clamping" phenomenon exits in the PRM-SH3 system, which has not been reported in previous literature. The competing effects between nanoparticle and its functionalization components revealed by our model system should be of value to current and future nanomedicine designs.
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Lv M, He B, Liu Z, Xiu P, Tu Y. Charge-signal multiplication mediated by urea wires inside Y-shaped carbon nanotubes. J Chem Phys 2014; 141:044707. [DOI: 10.1063/1.4890725] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Mei Lv
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
| | - Bing He
- School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China
| | - Zengrong Liu
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
| | - Peng Xiu
- Department of Engineering Mechanics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Yusong Tu
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
- College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China
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Tian X, Yang Z, Zhou B, Xiu P, Tu Y. Alcohol-induced drying of carbon nanotubes and its implications for alcohol/water separation: A molecular dynamics study. J Chem Phys 2013; 138:204711. [DOI: 10.1063/1.4807484] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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