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Mejía L, Cossio P, Franco I. Microscopic theory, analysis, and interpretation of conductance histograms in molecular junctions. Nat Commun 2023; 14:7646. [PMID: 37996422 PMCID: PMC10667247 DOI: 10.1038/s41467-023-43169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
Molecular electronics break-junction experiments are widely used to investigate fundamental physics and chemistry at the nanoscale. Reproducibility in these experiments relies on measuring conductance on thousands of freshly formed molecular junctions, yielding a broad histogram of conductance events. Experiments typically focus on the most probable conductance, while the information content of the conductance histogram has remained unclear. Here we develop a microscopic theory for the conductance histogram by merging the theory of force-spectroscopy with molecular conductance. The procedure yields analytical equations that accurately fit the conductance histogram of a wide range of molecular junctions and augments the information content that can be extracted from them. Our formulation captures contributions to the conductance dispersion due to conductance changes during the mechanical elongation inherent to the experiments. In turn, the histogram shape is determined by the non-equilibrium stochastic features of junction rupture and formation. The microscopic parameters in the theory capture the junction's electromechanical properties and can be isolated from separate conductance and rupture force (or junction-lifetime) measurements. The predicted behavior can be used to test the range of validity of the theory, understand the conductance histograms, design molecular junction experiments with enhanced resolution and molecular devices with more reproducible conductance properties.
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Affiliation(s)
- Leopoldo Mejía
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA.
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Pilar Cossio
- Center for Computational Mathematics, Flatiron Institute, New York City, NY, 10010, USA
- Center for Computational Biology, Flatiron Institute, New York City, NY, 10010, USA
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia, 050010, Medellín, Colombia
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA.
- Department of Physics, University of Rochester, Rochester, NY, 14627, USA.
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Pan X, Matthews K, Lawson B, Kamenetska M. Single-Molecule Conductance of Intramolecular Hydrogen Bonding in Histamine on Gold. J Phys Chem Lett 2023; 14:8327-8333. [PMID: 37695735 DOI: 10.1021/acs.jpclett.3c02172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
We perform single-molecule conductance measurements and DFT calculations on histamine, a biogenic amine that contains a flexible aliphatic linker and several nitrogen moieties with a potential for hydrogen bonding. Our study determines that junctions containing the free-base form of histamine can bridge through a molecular structure containing an intramolecular hydrogen bond. Conductance of this structure is higher than that through the saturated aliphatic linker. Flicker noise analysis of junction conductance confirms that transport occurs through the hydrogen bond and establishes a benchmark for noise measurements in hydrogen-bonded junctions. Overall, our work provides insights into the formation and conduction of intramolecular hydrogen bonding in single-molecule conductance measurements and into the conformations of the neurotransmitter histamine on noble metal surfaces.
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Affiliation(s)
- Xiaoyun Pan
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Katherine Matthews
- Department of Physics and Astronomy, Haverford College, Haverford, Pennsylvania 1904, United States
| | - Brent Lawson
- Department of Physics, Boston University, Boston, Massachusetts 02215, United States
| | - Maria Kamenetska
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, Boston, Massachusetts 02215, United States
- Divistion of Material Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
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Mejía L, Kleinekathöfer U, Franco I. Coherent and incoherent contributions to molecular electron transport. J Chem Phys 2022; 156:094302. [DOI: 10.1063/5.0079708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We numerically isolate the limits of validity of the Landauer approximation to describe charge transport along molecular junctions in condensed phase environments. To do so, we contrast Landauer with exact time-dependent non-equilibrium Green’s function quantum transport computations in a two-site molecular junction subject to exponentially correlated noise. Under resonant transport conditions, we find Landauer accuracy to critically depend on intramolecular interactions. By contrast, under nonresonant conditions, the emergence of incoherent transport routes that go beyond Landauer depends on charging and discharging processes at the electrode–molecule interface. In both cases, decreasing the rate of charge exchange between the electrodes and molecule and increasing the interaction strength with the thermal environment cause Landauer to become less accurate. The results are interpreted from a time-dependent perspective where the noise prevents the junction from achieving steady-state and from a fully quantum perspective where the environment introduces dephasing in the dynamics. Using these results, we analyze why the Landauer approach is so useful to understand experiments, isolate regimes where it fails, and propose schemes to chemically manipulate the degree of transport coherence.
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Affiliation(s)
- Leopoldo Mejía
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
- Department of Physics, University of Rochester, Rochester, New York 14627-0216, USA
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Zhu Y, Tan Z, Hong W. Simultaneous Electrical and Mechanical Characterization of Single-Molecule Junctions Using AFM-BJ Technique. ACS OMEGA 2021; 6:30873-30888. [PMID: 34841131 PMCID: PMC8613807 DOI: 10.1021/acsomega.1c04785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The fabrication and characterization of single-molecule junctions provide a unique platform to study the physical phenomena of a single molecule, and the electrical characterization enables us to understand the electrical transport properties of a single molecule and guide the fabrication of molecular electronic devices. However, the electrical characterization of single-molecule junctions is sometimes insufficient to extract the structural information on single-molecule junctions, and an alternate method to address this problem is to characterize the mechanical properties of single-molecule junctions. Simultaneous measurement of mechanical and electrical properties can provide complementary information on single molecules to analyze the correlations of their electrical and mechanical properties in the evolution of single-molecule junctions. In this mini-review, we summarize the progress on the simultaneous characterizations of mechanical and electrical properties for single-molecule junctions, and discuss the challenges and perspectives of this research area.
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Guan S, Cai Z, Liu J, Pang R, Wu D, Ulstrup J, Tian Z. Adsorption, Stretching, and Breaking Processes in Single‐Molecule Conductance of
para
‐Benzenedimethanethiol in Gold Nanogaps: A DFT‐NEGF Theoretical Study**. ChemElectroChem 2021. [DOI: 10.1002/celc.202100184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Si‐Yuan Guan
- State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China
| | - Zhuan‐Yun Cai
- State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China
| | - Ran Pang
- State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China
| | - De‐Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China
| | - Jens Ulstrup
- Department of Chemistry Technical University of Denmark 2800 Kongens Lyngby Denmark
| | - Zhong‐Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surface Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 P. R. China
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Zhuang X, Wu Q, Zhang A, Liao L, Fang B. Single-molecule biotechnology for protein researches. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Camarasa-Gómez M, Hernangómez-Pérez D, Inkpen MS, Lovat G, Fung ED, Roy X, Venkataraman L, Evers F. Mechanically Tunable Quantum Interference in Ferrocene-Based Single-Molecule Junctions. NANO LETTERS 2020; 20:6381-6386. [PMID: 32787164 DOI: 10.1021/acs.nanolett.0c01956] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ferrocenes are ubiquitous organometallic building blocks that comprise a Fe atom sandwiched between two cyclopentadienyl (Cp) rings that rotate freely at room temperature. Of widespread interest in fundamental studies and real-world applications, they have also attracted some interest as functional elements of molecular-scale devices. Here we investigate the impact of the configurational degrees of freedom of a ferrocene derivative on its single-molecule junction conductance. Measurements indicate that the conductance of the ferrocene derivative, which is suppressed by 2 orders of magnitude as compared to a fully conjugated analogue, can be modulated by altering the junction configuration. Ab initio transport calculations show that the low conductance is a consequence of destructive quantum interference effects of the Fano type that arise from the hybridization of localized metal-based d-orbitals and the delocalized ligand-based π-system. By rotation of the Cp rings, the hybridization, and thus the quantum interference, can be mechanically controlled, resulting in a conductance modulation that is seen experimentally.
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Affiliation(s)
- María Camarasa-Gómez
- Institute of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
| | - Daniel Hernangómez-Pérez
- Institute of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Michael S Inkpen
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Giacomo Lovat
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - E-Dean Fung
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Xavier Roy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Latha Venkataraman
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Ferdinand Evers
- Institute of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
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Mejía L, Franco I. Force-conductance spectroscopy of a single-molecule reaction. Chem Sci 2019; 10:3249-3256. [PMID: 30996909 PMCID: PMC6429593 DOI: 10.1039/c8sc04830d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/24/2019] [Indexed: 01/23/2023] Open
Abstract
We demonstrate how simultaneous measurements of conductance and force can be used to monitor the step-by-step progress of a mechanically-activated cis-to-trans isomerization single-molecule reaction, including events that cannot be distinguished using force or conductance alone. To do so, we simulated the force-conductance profile of cyclopropane oligomers connected to graphene nanoribbon electrodes that undergo a cis-to-trans isomerization during mechanical elongation. This was done using a combination of classical molecular dynamics simulation of the pulling using a reactive force field, and Landauer transport computations of the conductance with nonequilibrium Green's function methods. The isomerization events can be distinguished in both force and conductance profiles. However, the conductance profile during the mechanical elongation distinguishes between reaction intermediates that cannot be resolved using force. In turn, the force signals non-reactive deformations in the molecular backbone which are not visible in the conductance profile. These observations are shown to be robust to the choice of electrode and Hamiltonian model. The computations exemplify the potential of the integration of covalent mechanochemistry with molecular conductance to investigate chemical reactivity at the single-entity limit.
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Affiliation(s)
- Leopoldo Mejía
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , USA .
| | - Ignacio Franco
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , USA .
- Department of Physics , University of Rochester , Rochester , New York 14627-0216 , USA
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Stefani D, Perrin M, Gutiérrez‐Cerón C, Aragonès AC, Labra‐Muñoz J, Carrasco RDC, Matsushita Y, Futera Z, Labuta J, Ngo TH, Ariga K, Díez‐Pérez I, van der Zant HSJ, Dulić D, Hill JP. Mechanical Tuning of Through‐Molecule Conductance in a Conjugated Calix[4]pyrrole. ChemistrySelect 2018. [DOI: 10.1002/slct.201801076] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Davide Stefani
- Kavli Institute of NanoscienceDelft University of Technology Lorentzweg 1 2628 CJ Delft The Netherlands
| | - Mickael Perrin
- Kavli Institute of NanoscienceDelft University of Technology Lorentzweg 1 2628 CJ Delft The Netherlands
| | - Cristian Gutiérrez‐Cerón
- Physics DepartmentFaculty of Physical and Mathematical SciencesUniversity of Chile, Av. Blanco Encalada 2008 Santiago Chile
| | - Albert C. Aragonès
- Department of ChemistryFaculty of Natural & Mathematical SciencesKing's College London, Brittania House, 7 Trinity Street London SE1 1DB United Kingdom
| | - Jacqueline Labra‐Muñoz
- Physics DepartmentFaculty of Physical and Mathematical SciencesUniversity of Chile, Av. Blanco Encalada 2008 Santiago Chile
| | - Rodrigo D. C. Carrasco
- Physics DepartmentFaculty of Physical and Mathematical SciencesUniversity of Chile, Av. Blanco Encalada 2008 Santiago Chile
| | - Yoshitaka Matsushita
- Research Network and Facilities DivisionNational Institute for Materials Science, Sengen 1-2-1, Tsukuba Ibaraki 305-0047 Japan
| | - Zdenek Futera
- School of Chemical & Bioprocess EngineeringUniversity College Dublin, Belfield Dublin 4 Ireland
| | - Jan Labuta
- WPI Center for Materials NanoarchitectonicsNational Institute for Materials Science, Namiki 1–1, Tsukuba Ibaraki 305-0044 Japan
| | - Thien H. Ngo
- WPI Center for Materials NanoarchitectonicsNational Institute for Materials Science, Namiki 1–1, Tsukuba Ibaraki 305-0044 Japan
| | - Katsuhiko Ariga
- WPI Center for Materials NanoarchitectonicsNational Institute for Materials Science, Namiki 1–1, Tsukuba Ibaraki 305-0044 Japan
| | - Ismael Díez‐Pérez
- Department of ChemistryFaculty of Natural & Mathematical SciencesKing's College London, Brittania House, 7 Trinity Street London SE1 1DB United Kingdom
| | - Herre S. J. van der Zant
- Kavli Institute of NanoscienceDelft University of Technology Lorentzweg 1 2628 CJ Delft The Netherlands
| | - Diana Dulić
- Physics DepartmentFaculty of Physical and Mathematical SciencesUniversity of Chile, Av. Blanco Encalada 2008 Santiago Chile
| | - Jonathan P. Hill
- WPI Center for Materials NanoarchitectonicsNational Institute for Materials Science, Namiki 1–1, Tsukuba Ibaraki 305-0044 Japan
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Mejía L, Renaud N, Franco I. Signatures of Conformational Dynamics and Electrode-Molecule Interactions in the Conductance Profile During Pulling of Single-Molecule Junctions. J Phys Chem Lett 2018; 9:745-750. [PMID: 29369638 DOI: 10.1021/acs.jpclett.7b03323] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We demonstrate that conductance can act as a sensitive probe of conformational dynamics and electrode-molecule interactions during the equilibrium and nonequilibrium pulling of molecular junctions. To do so, we use a combination of classical molecular dynamics simulations and Landauer electron transport computations to investigate the conductance of a family of Au-alkanedithiol-Au junctions as they are mechanically elongated. The simulations show an overall decay of the conductance during pulling that is due to a decrease in the through-space electrode-molecule interactions, and that sensitivity depends on the electrode geometry. In addition, characteristic kinks induced by level alignment shifts (and to a lesser extent by quantum destructive interference) were also observed superimposed to the overall decay during pulling simulations. The latter effect depends on the variation of the molecular dihedral angles during pulling and therefore offers an efficient solution to experimentally monitor conformational dynamics at the single-molecule limit.
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Affiliation(s)
- Leopoldo Mejía
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Nicolas Renaud
- Netherlands eScience Center , Science Park 140 1098 XG Amsterdam, The Netherlands
| | - Ignacio Franco
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
- Department of Physics, University of Rochester , Rochester, New York 14627-0216, United States
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Pirrotta A, Solomon GC, Franco I, Troisi A. Excitonic Coupling Modulated by Mechanical Stimuli. J Phys Chem Lett 2017; 8:4326-4332. [PMID: 28837767 DOI: 10.1021/acs.jpclett.7b01828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding energy transfer is of vital importance in a diverse range of applications from biological systems to photovoltaics. The ability to tune excitonic coupling in any of these systems, however, is generally limited. In this work, we have simulated a new class of single-molecule spectroscopy in which force microscopy is used to control the excitonic coupling between chromophores. Here we demonstrate that the excitonic coupling can be controlled by mechanical manipulation of the molecule (perylenediimide dimers and terrylenediimide-perylenediimide heterodimers) and can be tuned over a broad range of values (0.02-0.15 eV) that correspond to different regimes of exciton dynamics going from the folded to the elongated structure of the dimer. In all of the systems considered here, the switching from high to low coupling takes place simultaneously with the mechanical deformation detected by a strong increase and subsequent decay of the force. These simulations suggest that single-molecule force spectroscopy can be used to understand and eventually aid the design of excitonic devices.
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Affiliation(s)
- Alessandro Pirrotta
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Gemma C Solomon
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Ignacio Franco
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool , L69 7DZ Liverpool, United Kingdom
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Carey R, Chen L, Gu B, Franco I. When can time-dependent currents be reproduced by the Landauer steady-state approximation? J Chem Phys 2017; 146:174101. [DOI: 10.1063/1.4981915] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Evers F, Venkataraman L. Preface: Special Topic on Frontiers in Molecular Scale Electronics. J Chem Phys 2017. [DOI: 10.1063/1.4977469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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