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Vázquez H. Toward Density-Functional Theory-Based Structure-Conductance Relationships in Single Molecule Junctions. J Phys Chem Lett 2022; 13:9326-9331. [PMID: 36178209 DOI: 10.1021/acs.jpclett.2c02349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A method is presented that allows for the calculation using density functional theory (DFT) of the tunneling conductance of single molecule junctions for thousands of junction structures. With a single scaling parameter, conductance is evaluated from clusters consisting of the molecule bonded to one Au atom at each end. Junction geometries are obtained without any constraints from ab initio molecular dynamics simulations at room temperature. This method accurately reproduces standard DFT-based conductance values for several molecular and electrode structures while reducing the computational cost by a factor of ∼400×, allowing for the conductance of tens of thousands of geometries to be computed. When applied to a pair of conjugated molecules, these large data sets quantify the effect on conductance of molecular structure or quantum chemical properties. This methodology enables reliable DFT-based conductance calculations at a negligible computational cost and opens the way to quantitative structure-conductance relationships.
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Affiliation(s)
- Héctor Vázquez
- Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10, PragueCZ-162 00, Czech Republic
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2
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Arasu NP, Vázquez H. Development of Classical Force Fields for Interfaces between Single Molecules and Au. J Phys Chem A 2022; 126:5031-5039. [PMID: 35880700 DOI: 10.1021/acs.jpca.2c02514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interfaces between metals and organic materials play an essential role in molecular surface science, photovoltaics, or molecular electronics. Modeling the evolution of interface geometry over sufficiently long timescales requires an accurate parameterization of the relevant metal-molecule interactions. Here, we describe a method for calculating interface parameters from reference density functional theory calculations of small metal-molecule complexes. We apply this method to develop a parameter set for a series of metal-molecule-metal junctions. We study the dynamics of short oligophenyls with amine, methyl-sulfide, or direct Au-C links, which are bonded to Au(111) via small adatom structures. Nanosecond classical molecular dynamics simulations using the generated parameter set reveal insight into molecular degrees of freedom not accessible from ab initio molecular dynamics simulations.
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Affiliation(s)
- Narendra P Arasu
- Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10, 162 00 Prague, Czech Republic.,Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague, Czech Republic
| | - Héctor Vázquez
- Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10, 162 00 Prague, Czech Republic
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Chen X, Yeoh YQ, He Y, Zhou C, Horsley JR, Abell AD, Yu J, Guo X. Unravelling Structural Dynamics within a Photoswitchable Single Peptide: A Step Towards Multimodal Bioinspired Nanodevices. Angew Chem Int Ed Engl 2020; 59:22554-22562. [PMID: 32851761 DOI: 10.1002/anie.202004701] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/15/2020] [Indexed: 12/13/2022]
Abstract
The majority of the protein structures have been elucidated under equilibrium conditions. The aim herein is to provide a better understanding of the dynamic behavior inherent to proteins by fabricating a label-free nanodevice comprising a single-peptide junction to measure real-time conductance, from which their structural dynamic behavior can be inferred. This device contains an azobenzene photoswitch for interconversion between a well-defined cis, and disordered trans isomer. Real-time conductance measurements revealed three distinct states for each isomer, with molecular dynamics simulations showing each state corresponds to a specific range of hydrogen bond lengths within the cis isomer, and specific dihedral angles in the trans isomer. These insights into the structural dynamic behavior of peptides may rationally extend to proteins. Also demonstrated is the capacity to modulate conductance which advances the design and development of bioinspired electronic nanodevices.
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Affiliation(s)
- Xinjiani Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
| | - Yuan Qi Yeoh
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Yanbin He
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.,Pharmaceutical Department, Changzhi Medical College, Changzhi, 046000, P. R. China
| | - Chenguang Zhou
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - John R Horsley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), School of Physical Sciences, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Xuefeng Guo
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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Chen X, Yeoh YQ, He Y, Zhou C, Horsley JR, Abell AD, Yu J, Guo X. Unravelling Structural Dynamics within a Photoswitchable Single Peptide: A Step Towards Multimodal Bioinspired Nanodevices. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xinjiani Chen
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 P. R. China
| | - Yuan Qi Yeoh
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Yanbin He
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
- Pharmaceutical Department Changzhi Medical College Changzhi 046000 P. R. China
| | - Chenguang Zhou
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - John R. Horsley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Andrew D. Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) Institute of Photonics and Advanced Sensing (IPAS) School of Physical Sciences The University of Adelaide North Terrace Adelaide SA 5005 Australia
| | - Xuefeng Guo
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 P. R. China
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
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Ismael AK, Al-Jobory A, Grace I, Lambert CJ. Discriminating single-molecule sensing by crown-ether-based molecular junctions. J Chem Phys 2017; 146:064704. [PMID: 28201900 DOI: 10.1063/1.4975771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Crown-ether molecules are well known to selectively bind alkali atoms, so by incorporating these within wires, any change in electrical conductance of the wire upon binding leads to discriminating sensing. Using a density functional theory-based approach to quantum transport, we investigate the potential sensing capabilities of single-molecule junctions formed from crown ethers attached to anthraquinone units, which are in turn attached to gold electrodes via alkyl chains. We calculate the change in electrical conductance for binding of three different alkali ions (lithium, sodium, and potassium). Depending on the nature of the ionic analyte, the conductance is enhanced by different amounts. This change in electrical conductance is due to charge transfer from the ion to molecular wire causing the molecular resonances to shift closer to the electrode Fermi energy.
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Affiliation(s)
- Ali K Ismael
- Department of Physics, Lancaster University, Lancaster, United Kingdom
| | - Alaa Al-Jobory
- Department of Physics, Lancaster University, Lancaster, United Kingdom
| | - Iain Grace
- Department of Physics, Lancaster University, Lancaster, United Kingdom
| | - Colin J Lambert
- Department of Physics, Lancaster University, Lancaster, United Kingdom
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Liu L, Zhang Q, Tao S, Zhao C, Almutib E, Al-Galiby Q, Bailey SWD, Grace I, Lambert CJ, Du J, Yang L. Charge transport through dicarboxylic-acid-terminated alkanes bound to graphene-gold nanogap electrodes. NANOSCALE 2016; 8:14507-14513. [PMID: 27412865 DOI: 10.1039/c6nr03807g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Graphene-based electrodes are attractive for single-molecule electronics due to their high stability and conductivity and reduced screening compared with metals. In this paper, we use the STM-based matrix isolation I(s) method to measure the performance of graphene in single-molecule junctions with one graphene electrode and one gold electrode. By measuring the length dependence of the electrical conductance of dicarboxylic-acid-terminated alkanes, we find that the transport is consistent with phase-coherent tunneling, but with an attenuation factor of βN = 0.69 per methyl unit, which is lower than the value measured for Au-molecule-Au junctions. Comparison with density-functional-theory calculations of electron transport through graphene-molecule-Au junctions and Au-molecule-Au junctions reveals that this difference is due to the difference in Fermi energies of the two types of junction, relative to the frontier orbitals of the molecules. For most molecules, their electrical conductance in graphene-molecule-Au junctions is higher than that in Au-molecule-Au junctions, which suggests that graphene offers superior electrode performance, when utilizing carboxylic acid anchor groups.
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Affiliation(s)
- Longlong Liu
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, Jiangsu 215123, China.
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Quantum interference effect of single-molecule conductance influenced by insertion of different alkyl length. Electrochem commun 2016. [DOI: 10.1016/j.elecom.2016.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Manrique DZ, Al-Galiby Q, Hong W, Lambert CJ. A New Approach to Materials Discovery for Electronic and Thermoelectric Properties of Single-Molecule Junctions. NANO LETTERS 2016; 16:1308-1316. [PMID: 26784577 DOI: 10.1021/acs.nanolett.5b04715] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We have investigated a large set of symmetric and asymmetric molecules to demonstrate a general rule for molecular-scale quantum transport, which provides a new route to materials design and discovery. The rule states "the conductance GXBY of an asymmetric molecule is the geometric mean of the conductance of the two symmetric molecules derived from it and the thermopower SXBY of the asymmetric molecule is the algebraic mean of their thermopowers". The studied molecules have a structure X-B-Y, where B is the backbone of the molecule, while X and Y are anchor groups, which bind the molecule to metallic electrodes. When applied to experimentally measured histograms of conductance and thermopower, the rules apply to the statistically most probable values. We investigated molecules with anchors chosen from the following family: cyano, pyridl, dihydrobenzothiol, amine and thiol. For the backbones B, we tested 14 different structures. We found that the formulas (GXBY)(2) = GXBX*GYBY and SXBY = (SXBX + SYBY)/2 were satisfied in the large majority of the cases, provided the Fermi energy is located within the HOMO-LUMO gap of the molecules. The circuit rules imply that if measurements are performed on molecules with nA different anchors and nB different backbones, then properties of nA(nA + 1)nB/2 molecules can be predicted. So for example, in the case of 20 backbones and 10 anchors, 30 measurements (or reliable calculations) can provide a near quantitative estimate for 1070 measurements of other molecules, at no extra cost.
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Affiliation(s)
| | - Qusiy Al-Galiby
- Department of Physics, Lancaster University , Lancaster LA1 4YB, United Kingdom
| | - Wenjing Hong
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Colin J Lambert
- Department of Physics, Lancaster University , Lancaster LA1 4YB, United Kingdom
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Souza AM, Rungger I, Schwingenschlögl U, Sanvito S. The image charge effect and vibron-assisted processes in Coulomb blockade transport: a first principles approach. NANOSCALE 2015; 7:19231-19240. [PMID: 26525140 DOI: 10.1039/c5nr04245c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a combination of density functional theory and of both non-equilibrium Green's function formalism and a Master equation approach to accurately describe quantum transport in molecular junctions in the Coulomb blockade regime. We apply this effective first-principles approach to reproduce the experimental results of Perrin et al., [Nat. Nanotechnol., 2013, 8, 282] for the transport properties of a Au-(Zn)porphyrin-Au molecular junction. We demonstrate that energy level renormalization due to the image charge effect is crucial to the prediction of the current onset in the current-voltage, I-V, curves as a function of electrode separation. Furthermore, we show that for voltages beyond that setting the current onset, the slope of the I-V characteristics is determined by the interaction of the charge carriers with molecular vibrations. This corresponds to current-induced local heating, which may also lead to an effective reduced electronic coupling. Overall our scheme provides a fully ab initio description of quantum transport in the Coulomb blockade regime in the presence of electron-vibron coupling.
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Affiliation(s)
- A M Souza
- School of Physics, CRANN and AMBER, Trinity College, Dublin 2, Ireland.
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Li Y, Baghernejad M, Qusiy AG, Zsolt Manrique D, Zhang G, Hamill J, Fu Y, Broekmann P, Hong W, Wandlowski T, Zhang D, Lambert C. Three-State Single-Molecule Naphthalenediimide Switch: Integration of a Pendant Redox Unit for Conductance Tuning. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Li Y, Baghernejad M, Qusiy AG, Zsolt Manrique D, Zhang G, Hamill J, Fu Y, Broekmann P, Hong W, Wandlowski T, Zhang D, Lambert C. Three-State Single-Molecule Naphthalenediimide Switch: Integration of a Pendant Redox Unit for Conductance Tuning. Angew Chem Int Ed Engl 2015; 54:13586-9. [DOI: 10.1002/anie.201506458] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 11/07/2022]
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