1
|
Bro-Jørgensen W, Hamill JM, Mezei G, Lawson B, Rashid U, Halbritter A, Kamenetska M, Kaliginedi V, Solomon GC. Making the Most of Nothing: One-Class Classification for Single-Molecule Transport Studies. ACS NANOSCIENCE AU 2024; 4:250-262. [PMID: 39184833 PMCID: PMC11342344 DOI: 10.1021/acsnanoscienceau.4c00015] [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: 05/01/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 08/27/2024]
Abstract
Single-molecule experiments offer a unique means to probe molecular properties of individual molecules-yet they rest upon the successful control of background noise and irrelevant signals. In single-molecule transport studies, large amounts of data that probe a wide range of physical and chemical behaviors are often generated. However, due to the stochasticity of these experiments, a substantial fraction of the data may consist of blank traces where no molecular signal is evident. One-class (OC) classification is a machine learning technique to identify a specific class in a data set that potentially consists of a wide variety of classes. Here, we examine the utility of two different types of OC classification models on four diverse data sets from three different laboratories. Two of these data sets were measured at cryogenic temperatures and two at room temperature. By training the models solely on traces from a blank experiment, we demonstrate the efficacy of OC classification as a powerful and reliable method for filtering out blank traces from a molecular experiment in all four data sets. On a labeled 4,4'-bipyridine data set measured at 4.2 K, we achieve an accuracy of 96.9 ± 0.3 and an area under the receiver operating characteristic curve of 99.5 ± 0.3 as validated over a fivefold cross-validation. Given the wide range of physical and chemical properties that can be probed in single-molecule experiments, the successful application of OC classification to filter out blank traces is a major step forward in our ability to understand and manipulate molecular properties.
Collapse
Affiliation(s)
- William Bro-Jørgensen
- Department
of Chemistry and Nano-Science Center, University
of Copenhagen, Universitetsparken
5, Copenhagen Ø DK-2100, Denmark
| | - Joseph M. Hamill
- Department
of Chemistry and Nano-Science Center, University
of Copenhagen, Universitetsparken
5, Copenhagen Ø DK-2100, Denmark
| | - Gréta Mezei
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Műegyetem rkp. 3., Budapest H-1111, Hungary
- ELKH-BME
Condensed Matter Research Group, Műegyetem rkp. 3., Budapest H-1111, Hungary
| | - Brent Lawson
- Department
of Physics, Chemistry and Division of Material Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Umar Rashid
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
| | - András Halbritter
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Műegyetem rkp. 3., Budapest H-1111, Hungary
- ELKH-BME
Condensed Matter Research Group, Műegyetem rkp. 3., Budapest H-1111, Hungary
| | - Maria Kamenetska
- Department
of Physics, Chemistry and Division of Material Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Veerabhadrarao Kaliginedi
- Department
of Inorganic and Physical Chemistry, Indian
Institute of Science, Bangalore 560012, India
| | - Gemma C. Solomon
- Department
of Chemistry and Nano-Science Center, University
of Copenhagen, Universitetsparken
5, Copenhagen Ø DK-2100, Denmark
- NNF
Quantum
Computing Programme, Niels Bohr Institute, University of Copenhagen, Jagtvej 155 A, Copenhagen N DK-2200, Denmark
| |
Collapse
|
2
|
Hurtado-Gallego J, van der Poel S, Blaschke M, Gallego A, Hsu C, López-Nebreda R, Mayor M, Pauly F, Agraït N, van der Zant HSJ. Benchmarking break-junction techniques: electric and thermoelectric characterization of naphthalenophanes. NANOSCALE 2024; 16:10751-10759. [PMID: 38747099 PMCID: PMC11154865 DOI: 10.1039/d4nr00704b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/15/2024] [Indexed: 06/07/2024]
Abstract
Break-junction techniques provide the possibility to study electric and thermoelectric properties of single-molecule junctions in great detail. These techniques rely on the same principle of controllably breaking metallic contacts in order to create single-molecule junctions, whilst keeping track of the junction's conductance. Here, we compare results from mechanically controllable break junction (MCBJ) and scanning tunneling microscope (STM) methods, while characterizing conductance properties of the same novel mechanosensitive para- and meta-connected naphtalenophane compounds. In addition, thermopower measurements are carried out for both compounds using the STM break junction (STM-BJ) technique. For the conductance experiments, the same data processing using a clustering analysis is performed. We obtain to a large extent similar results for both methods, although values of conductance and stretching lengths for the STM-BJ technique are slightly larger in comparison with the MCBJ. STM-BJ thermopower experiments show similar Seebeck coefficients for both compounds. An increase in the Seebeck coefficient is revealed, whilst the conductance decreases, after which it saturates at around 10 μV K-1. This phenomenon is studied theoretically using a tight binding model. It shows that changes of molecule-electrode electronic couplings combined with shifts of the resonance energies explain the correlated behavior of conductance and Seebeck coefficient.
Collapse
Affiliation(s)
- Juan Hurtado-Gallego
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Sebastiaan van der Poel
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
| | - Matthias Blaschke
- Institute of Physics and Center for Advanced Analytics and Predictive Sciences, University of Augsburg, 86159 Augsburg, Germany.
| | - Almudena Gallego
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
| | - Chunwei Hsu
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
| | - Rubén López-Nebreda
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Marcel Mayor
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
- Institute for Nanotechnology, Karlsruhe Institute of Technology (KIT), P. O. Box 3640, 76021 Karlsruhe, Germany
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510274, P. R. China
| | - Fabian Pauly
- Institute of Physics and Center for Advanced Analytics and Predictive Sciences, University of Augsburg, 86159 Augsburg, Germany.
| | - Nicolás Agraït
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC) and Instituto Universitario de Ciencia de Materiales 'Nicolás Cabrera' (INC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Herre S J van der Zant
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
| |
Collapse
|
3
|
Hight MO, Wong JY, Pimentel AE, Su TA. Intramolecular London Dispersion Interactions in Single-Molecule Junctions. J Am Chem Soc 2024; 146:4716-4726. [PMID: 38325000 PMCID: PMC10885141 DOI: 10.1021/jacs.3c12183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
This work shows the first example of using intramolecular London dispersion interactions to control molecular geometry and quantum transport in single-molecule junctions. Flexible σ-bonded molecular junctions typically occupy straight-chain geometries due to steric effects. Here, we synthesize a series of thiomethyl-terminated oligo(dimethylsilmethylene)s that bear [CH2-Si(CH3)2]n repeat units, where all backbone dihedral states are sterically equivalent. Scanning tunneling microscopy break-junction (STM-BJ) measurements and theoretical calculations indicate that in the absence of a strong steric bias concerted intramolecular London dispersion interactions staple the carbosilane backbone into coiled conformations that remain intact even as the junction is stretched to its breakpoint. As these kinked conformations are highly resistive to electronic transport, we observe record-high conductance decay values on an experimental junction length basis (β = 1.86 ± 0.12 Å-1). These studies reveal the potential of using intramolecular London dispersion interactions to design single-molecule electronics.
Collapse
Affiliation(s)
- Matthew O Hight
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joshua Y Wong
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ashley E Pimentel
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Timothy A Su
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Materials Science & Engineering Program, University of California, Riverside, California 92521, United States
| |
Collapse
|
4
|
Marek Š, Korytár R. Widening of the fundamental gap in cluster GW for metal-molecular interfaces. Phys Chem Chem Phys 2024; 26:2127-2133. [PMID: 38131459 DOI: 10.1039/d3cp04082h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The GW approximation is very promising for an accurate first-principles description of charged excitations in single-molecule-metal interfaces. In the cluster approach for electronic transport across molecules, the infinite metal (with an adsorbed molecule) is replaced by a finite cluster whose volume should be incrementally increased to test the approach to the thermodynamic limit. Here we show that in GW, the approach to the thermodynamic limit will be much slower than in Kohn-Sham density-functional theory (DFT) because of the Coulomb interaction. To demonstrate this statement, we investigate spectral gaps in an ensemble of disordered sodium clusters in Kohn-Sham DFT, quasiparticle eigenvalue-self-consistent GW and Hartree-Fock. The fundamental gaps (i.e. difference between the lowest unoccupied and highest occupied level) in GW scale as N-1/3 on average, where N is the number of atoms. We demonstrate that this slow decrease artificially depletes the density of states at the Fermi level when the cluster is used to simulate a semi-infinite electrode. Therefore, the GW method cannot be taken as an out-of-the-box improvement of the DFT in cluster geometries, unless careful convergence checks are performed.
Collapse
Affiliation(s)
- Štěpán Marek
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Praha 2, 121 16, Czech Republic.
| | - Richard Korytár
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Praha 2, 121 16, Czech Republic.
| |
Collapse
|
5
|
Zhou P, Fu Y, Wang M, Qiu R, Wang Y, Stoddart JF, Wang Y, Chen H. Robust Single-Supermolecule Switches Operating in Response to Two Different Noncovalent Interactions. J Am Chem Soc 2023; 145:18800-18811. [PMID: 37590178 DOI: 10.1021/jacs.3c03282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.
Collapse
Affiliation(s)
- Ping Zhou
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Yanjun Fu
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Maolin Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Renhui Qiu
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Yuwei Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - J Fraser Stoddart
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yuping Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Hongliang Chen
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| |
Collapse
|