1
|
Hamedian A, Vakili M, Brandán SA, Akbari M, Kanaani A, Darugar V. Theoretical study on the structure, spectroscopic, and current-voltage behavior of 11-Cis and Trans retinal isomers in rhodopsin. Sci Rep 2024; 14:12452. [PMID: 38816529 PMCID: PMC11140004 DOI: 10.1038/s41598-024-63249-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024] Open
Abstract
In this study, the electronic transport properties of 11-Cis and Trans retinal, components of rhodopsin, were investigated as optical molecular switches using the nonequilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT). These isomers, which can be reversibly converted into each other, were examined in detail. The structural and spectroscopic properties, including infrared (IR), Raman, nuclear magnetic resonance (NMR), and ultraviolet (UV) spectra, were analyzed using the hybrid B3LYP/6-311 + + G** level of theory. Complete vibrational assignments were performed for both forms utilizing the scaled quantum mechanical force field (SQMFF) methodology. To evaluate the conductivity of these molecules, we utilized current-voltage (I-V) characteristics, transmission spectra, molecular projected self-consistent Hamiltonian (MPSH), HOMO-LUMO gap, and second-order interaction energies (E2). The trendline extrapolation of the current-voltage plots confirmed our findings. We investigated the effect of different electrodes (Ag, Au, Pt) and various connection sites (hollow, top, bridge) on conductivity. The Ag electrode with the hollow site exhibited the highest efficiency. Our results indicate that the Cis form has higher conductivity than the Trans form.
Collapse
Affiliation(s)
- Amin Hamedian
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran
| | - Mohammad Vakili
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran.
| | - Silvia A Brandán
- Cátedra de Química General, Instituto de Química, Inorgánica Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, Tucumán, Argentina
| | - Mahmood Akbari
- UNESCO‑UNISA-ITL Africa Chair in Nanoscience and Nanotechnology (U2ACN2), College of Graduate Studies, University of South Africa (UNISA), Pretoria, South Africa
| | - Ayoub Kanaani
- School of Chemistry, Damghan University, Damghan, 36716-41167, Iran
| | - Vahidreza Darugar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran
| |
Collapse
|
2
|
Tada T. Quantum Chemical Studies on Possible Molecular Devices Based on Electric Field-Induced Intramolecular Charge Transfer. J Phys Chem A 2023; 127:7297-7308. [PMID: 37638599 DOI: 10.1021/acs.jpca.3c02195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
We report quantum chemical studies on possible molecular devices working based on electric field-induced intramolecular charge transfer (EFIMCT). In the case of donor-acceptor (DA)-type molecular systems, intramolecular charge transfer (IMCT) can be induced by applying the external electric field to molecular systems along the charge transport direction, providing a possible switching mechanism which does not depend upon the electron-phonon coupling effect and is different from the negative differential resistance mechanism observed in the well-known NO2-substituted phenylene ethynylene oligomers. When the EFIMCT proceeds, the molecular systems have strong static electron correlation effects, where the standard nonequilibrium Green's function-density functional theory (DFT) approach cannot be applied to the molecular junction. As a first step toward practical switching devices, we do quantum chemical studies on the EFIMCT in such molecular systems as an isolated molecule, instead of using the electrode-junction-electrode open quantum system model. A prototype molecule P1 is designed as a tentative candidate molecule where the EFIMCT can proceed. The complete active space self-consistent field (CASSCF) molecular orbital calculations on P1 indicate that the EFIMCT can proceed at the external electric field intensity of 0.003 au, corresponding to about 2.25 V bias voltage. This calculated result strongly suggests that the development of this type of switching devices working at practically low bias voltage is feasible if the molecular system is properly designed. Broken symmetry unrestricted Hartree-Fock and spin-polarized Kohn-Sham DFT calculations also qualitatively reproduce the CASSCF results on P1, to some extent, indicating that these approaches can be employed for rough estimations on the EFIMCT such as the first screening of a large quantity of candidate molecules for this type of molecular devices. The possibility of molecular memory devices based on the EFIMCT is also discussed by analyzing the ground and excited potential energy surface model. Remaining challenges to develop practical molecular devices are discussed.
Collapse
Affiliation(s)
- Tsukasa Tada
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-Ohsawa 1-1, Hachioji, Tokyo 192-0397, Japan
| |
Collapse
|
3
|
Bao L, Huang L, Guo H, Gao HJ. Construction and physical properties of low-dimensional structures for nanoscale electronic devices. Phys Chem Chem Phys 2022; 24:9082-9117. [PMID: 35383791 DOI: 10.1039/d1cp05981e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past decades, construction of nanoscale electronic devices with novel functionalities based on low-dimensional structures, such as single molecules and two-dimensional (2D) materials, has been rapidly developed. To investigate their intrinsic properties for versatile functionalities of nanoscale electronic devices, it is crucial to precisely control the structures and understand the physical properties of low-dimensional structures at the single atomic level. In this review, we provide a comprehensive overview of the construction of nanoelectronic devices based on single molecules and 2D materials and the investigation of their physical properties. For single molecules, we focus on the construction of single-molecule devices, such as molecular motors and molecular switches, by precisely controlling their self-assembled structures on metal substrates and charge transport properties. For 2D materials, we emphasize their spin-related electrical transport properties for spintronic device applications and the role that interfaces among 2D semiconductors, contact electrodes, and dielectric substrates play in the electrical performance of electronic, optoelectronic, and memory devices. Finally, we discuss the future research direction in this field, where we can expect a scientific breakthrough.
Collapse
Affiliation(s)
- Lihong Bao
- Institute of Physics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Li Huang
- Institute of Physics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Hui Guo
- Institute of Physics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Hong-Jun Gao
- Institute of Physics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| |
Collapse
|
4
|
Ramirez FF, Bustamente CM, González Lebrero MC, Scherlis DA. Transport and Spectroscopy in Conjugated Molecules: Two Properties and a Single Rationale. J Chem Theory Comput 2020; 16:2930-2940. [DOI: 10.1021/acs.jctc.9b01122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Francisco F. Ramirez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Carlos M. Bustamente
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| |
Collapse
|
5
|
Yamada A, Feng Q, Hoskins A, Fenk KD, Dunietz BD. Achieving Predictive Description of Molecular Conductance by Using a Range-Separated Hybrid Functional. NANO LETTERS 2016; 16:6092-6098. [PMID: 27636328 DOI: 10.1021/acs.nanolett.6b02241] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The conductance of molecular bridges tends to be overestimated by computational studies in comparison to measured values. While this well-established trend may be related to difficulties for achieving robust bridges, the employed computational scheme can also contribute to this tendency. In particular, caveats of the traditional functionals employed in first-principles-based calculations can lead to discrepancies reflected in exaggerated conductance. Here, we show that by employing a range-separated hybrid functional the calculated values are within the same order as the measured conductance for all four considered cases. On the other hand, with B3LYP, which is a widely used functional, the calculated values greatly overestimate the conductance (by about 1-2 orders of magnitude). The improved description of the conductance with a RSH functional builds on achieving a physically meaningful treatment of the quasi particles associated with the frontier orbitals.
Collapse
Affiliation(s)
- Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Austin Hoskins
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Kevin D Fenk
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| |
Collapse
|
6
|
Feng Q, Yamada A, Baer R, Dunietz BD. Deleterious Effects of Exact Exchange Functionals on Predictions of Molecular Conductance. J Chem Theory Comput 2016; 12:3431-5. [PMID: 27454778 DOI: 10.1021/acs.jctc.6b00493] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kohn-Sham (KS) density functional theory (DFT) describes well the atomistic structure of molecular junctions and their coupling to the semi-infinite metallic electrodes but severely overestimates conductance due to the spuriously large density of charge-carrier states of the KS system. Previous works show that inclusion of appropriate amounts of nonlocal exchange in the functional can fix the problem and provide realistic conductance estimates. Here however we discover that nonlocal exchange can also lead to deleterious effects which artificially overestimate transmittance even beyond the KS-DFT prediction. The effect is a result of exchange coupling between nonoverlapping states of diradical character. We prescribe a practical recipe for eliminating such artifacts.
Collapse
Affiliation(s)
- Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Roi Baer
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| |
Collapse
|
7
|
Pejov L, Petreska I, Kocarev L. Designing field-controllable graphene-dot-graphene single molecule switches: A quantum-theoretical proof-of-concept under realistic operating conditions. J Chem Phys 2015; 143:244704. [PMID: 26723699 DOI: 10.1063/1.4937411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical proof of the concept that a particularly designed graphene-based moletronics device, constituted by two semi-infinite graphene subunits, acting as source and drain electrodes, and a central benzenoid ring rotator (a "quantum dot"), could act as a field-controllable molecular switch is outlined and analyzed with the density functional theory approach. Besides the ideal (0 K) case, we also consider the operation of such a device under realistic operating (i.e., finite-temperature) conditions. An in-depth insight into the physics behind device controllability by an external field was gained by thorough analyses of the torsional potential of the dot under various conditions (absence or presence of an external gating field with varying strength), computing the torsional correlation time and transition probabilities within the Bloembergen-Purcell-Pound formalism. Both classical and quantum mechanical tunneling contributions to the intramolecular rotation were considered in the model. The main idea that we put forward in the present study is that intramolecular rotors can be controlled by the gating field even in cases when these groups do not possess a permanent dipole moment (as in cases considered previously by us [I. Petreska et al., J. Chem. Phys. 134, 014708-1-014708-12 (2011)] and also by other groups [P. E. Kornilovitch et al., Phys. Rev. B 66, 245413-1-245413-7 (2002)]). Consequently, one can control the molecular switching properties by an external electrostatic field utilizing even nonpolar intramolecular rotors (i.e., in a more general case than those considered so far). Molecular admittance of the currently considered graphene-based molecular switch under various conditions is analyzed employing non-equilibrium Green's function formalism, as well as by analysis of frontier molecular orbitals' behavior.
Collapse
Affiliation(s)
- Ljupčo Pejov
- Department of Physical Chemistry, Institute of Chemistry, SS. Cyril and Methodius University, Arhimedova 5, P.O. Box 162, 1001 Skopje, Republic of Macedonia
| | - Irina Petreska
- Institute of Physics, Faculty of Natural Sciences and Mathematics, SS. Cyril and Methodius University, P.O. Box 162, 1001 Skopje, Republic of Macedonia
| | - Ljupčo Kocarev
- Macedonian Academy of Sciences and Arts, Krste Misirkov 2, P.O. Box 428, 1000 Skopje, Republic of Macedonia
| |
Collapse
|
8
|
Pozner R, Lifshitz E, Peskin U. Negative Differential Resistance Probe for Interdot Interactions in a Double Quantum Dot Array. J Phys Chem Lett 2015; 6:1521-1528. [PMID: 26263306 DOI: 10.1021/acs.jpclett.5b00434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Colloidal quantum dots are free-standing nanostructures with chemically tunable electronic properties. In this work, we consider a new STM tip-double quantum dot (DQD)-surface setup with a unique connectivity, in which the tip is coupled to a single dot and the coupling to the surface is shared by both dots. Our theoretical analysis reveals a unique negative differential resistance (NDR) effect attributed to destructive interference during charge transfer from the DQD to the surface. This NDR can be used as a sensitive probe for interdot interactions in DQD arrays.
Collapse
Affiliation(s)
- Roni Pozner
- †Schulich Faculty of Chemistry, ‡Solid State Institute, ¶Russell Berrie Nanotechnology Institute, and ∥Lise Meitner Center for Computational Quantum Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Efrat Lifshitz
- †Schulich Faculty of Chemistry, ‡Solid State Institute, ¶Russell Berrie Nanotechnology Institute, and ∥Lise Meitner Center for Computational Quantum Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Uri Peskin
- †Schulich Faculty of Chemistry, ‡Solid State Institute, ¶Russell Berrie Nanotechnology Institute, and ∥Lise Meitner Center for Computational Quantum Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
9
|
Baratz A, White AJ, Galperin M, Baer R. Effects of Electromagnetic Coupling on Conductance Switching of a Gated Tunnel Junction. J Phys Chem Lett 2014; 5:3545-3550. [PMID: 26278607 DOI: 10.1021/jz501652y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Adva Baratz
- †Department of Environmental Physics, Israel Institute for Biological Research, P.O.B. 19, Ness-Ziona 74100, Israel
| | - Alexander J White
- ‡Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
- ∥Theoretical Division, Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Michael Galperin
- ‡Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Roi Baer
- §Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
10
|
Saraiva-Souza A, Smeu M, Zhang L, Souza Filho AG, Guo H, Ratner MA. Molecular Spintronics: Destructive Quantum Interference Controlled by a Gate. J Am Chem Soc 2014; 136:15065-71. [DOI: 10.1021/ja508537n] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Aldilene Saraiva-Souza
- Centre
for the Physics of Materials and Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Manuel Smeu
- Departamento
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Lei Zhang
- Centre
for the Physics of Materials and Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | | | - Hong Guo
- Centre
for the Physics of Materials and Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Mark A. Ratner
- Departamento
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
11
|
Fowler PW, Pickup BT, Todorova TZ, Borg M, Sciriha I. Omni-conducting and omni-insulating molecules. J Chem Phys 2014; 140:054115. [PMID: 24511930 DOI: 10.1063/1.4863559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The source and sink potential model is used to predict the existence of omni-conductors (and omni-insulators): molecular conjugated π systems that respectively support ballistic conduction or show insulation at the Fermi level, irrespective of the centres chosen as connections. Distinct, ipso, and strong omni-conductors/omni-insulators show Fermi-level conduction/insulation for all distinct pairs of connections, for all connections via a single centre, and for both, respectively. The class of conduction behaviour depends critically on the number of non-bonding orbitals (NBO) of the molecular system (corresponding to the nullity of the graph). Distinct omni-conductors have at most one NBO; distinct omni-insulators have at least two NBO; strong omni-insulators do not exist for any number of NBO. Distinct omni-conductors with a single NBO are all also strong and correspond exactly to the class of graphs known as nut graphs. Families of conjugated hydrocarbons corresponding to chemical graphs with predicted omni-conducting/insulating behaviour are identified. For example, most fullerenes are predicted to be strong omni-conductors.
Collapse
Affiliation(s)
- P W Fowler
- Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - B T Pickup
- Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - T Z Todorova
- Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Martha Borg
- Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Irene Sciriha
- Department of Mathematics, Faculty of Science, University of Malta, Msida MSD 2080, Malta
| |
Collapse
|