1
|
Sikri G, Sawhney RS. Computational evaluation of transport parameters and logic circuit designing of L-Lysine amino acid stringed to Au, Ag, Cu, Pt, and Pd electrodes. J Mol Model 2023; 29:115. [PMID: 36973447 DOI: 10.1007/s00894-023-05471-1] [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: 07/29/2022] [Accepted: 02/09/2023] [Indexed: 03/29/2023]
Abstract
The integrants of proteins, i.e., amino acids, have grossed exceptional recognition for their applications towards designing imminent switching devices. Among 20 amino acids, L-Lysine (i.e., positively charged) has the highest number of CH2 chains, and such chains affect the rectification ratio in several biomolecules. Towards molecular rectification, we investigate the transport parameters of L-Lysine in conjunction with five different coinage metal electrodes, i.e., Au, Ag, Cu, Pt and Pd to form five distinct devices. We deputize the NEGF-DFT formulism for computing conductance, frontier molecular orbitals, current-voltage, and molecular projected self-Hamiltonian calculations using a self-consistent function. We focus on the most widely used electron exchange correlation combination, i.e., the PBE version of GGA with DZDP basis set. The molecular devices under inquisition exhibit phenomenal rectification ratios (RR) in conjunction with negative differential resistance (NDR) regimes. The nominated molecular device offers a substantial rectification ratio of 45.6 with platinum electrodes and a prominent peak to valley current ratio of 1.78 with copper electrodes. We deduce from these findings that L-Lysine based molecular devices would implicit in future bio-nanoelectronic devices. The OR and AND logic gates are also proposed hinged on highest rectification ratio of L-Lysine-based devices.
Collapse
Affiliation(s)
- Gaurav Sikri
- Department of Electronics Technology, Guru Nanak Dev University, Amritsar, India.
| | | |
Collapse
|
2
|
Molecular electronics behaviour of L-aspartic acid using symmetrical metal electrodes. J Mol Model 2021; 27:335. [PMID: 34718873 DOI: 10.1007/s00894-021-04936-5] [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: 05/21/2021] [Accepted: 09/22/2021] [Indexed: 10/19/2022]
Abstract
Protein-based electronics is one of the growing areas of bio-nanoelectronics, where novel electronic devices possessing distinctive properties are being fabricated using specific proteins. Furthermore, if the bio-molecule is analysed amidst different electrodes, intriguing properties are elucidated. This research article investigates the electron transport properties of L-aspartic acid (i.e. L-amino acid) bound to symmetrical electrodes of gold, silver, copper, platinum and palladium employing NEGF-DFT approach using self-consistent function. The theoretical work function of different electrodes is calculated using local density approximation and generalized gradient approximation approach. The calculated work function correlates well with the hole tunneling barrier and conductance of the molecular device, which further authenticate the coupling strength between molecule and electrode. Molecule under consideration also exhibits negative differential resistance region and rectification ratio with all the different electrodes, due to its asymmetrical structure. The molecular device using platinum electrodes exhibits the highest peak to valley ratio of 1.38 and rectification ratio of 3.20, at finite bias. The switching characteristics of different molecular device are justified with detailed transmission spectra and MPSH. These results indicate that L-aspartic acid and similar biomolecule can be vital to the growth of Proteotronics.
Collapse
|
3
|
Can One Define the Conductance of Amino Acids? Biomolecules 2019; 9:biom9100580. [PMID: 31591358 PMCID: PMC6843363 DOI: 10.3390/biom9100580] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/16/2019] [Accepted: 09/26/2019] [Indexed: 01/23/2023] Open
Abstract
We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering technique, we identified several conductance groups for each of the molecules considered. Ab initio calculations revealed that the observed broad conductance distribution stems from the possibility of various binding geometries which can be formed during stretching combined with a multitude of possible conformational changes. The results suggest that it would be helpful to explore different experimental techniques such as recognition tunneling and conditions to help identify the nature of amino-acid-based junctions even further, for example, with the goal to establish a firm platform for their unambiguous recognition by tunneling break-junction experiments.
Collapse
|
4
|
Schosser WM, Zotti LA, Cuevas JC, Pauly F. Doping hepta-alanine with tryptophan: A theoretical study of its effect on the electrical conductance of peptide-based single-molecule junctions. J Chem Phys 2019; 150:174705. [PMID: 31067872 DOI: 10.1063/1.5090457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Motivated by a recent experiment [C. Guo et al., Proc. Natl. Acad. Sci. U. S. A. 113, 10785 (2016)], we carry out a theoretical study of electron transport through peptide-based single-molecule junctions. We analyze the pristine hepta-alanine and its functionalizations with a single tryptophan unit, which is placed in three different locations along the backbone. Contrary to expectations from the experiment on self-assembled monolayers, we find that insertion of tryptophan does not raise the electrical conductance and that the resulting peptides instead remain insulating in the framework of a coherent transport picture. The poor performance of these molecules as conductors can be ascribed to the strongly off-resonant transport and low electrode-molecule coupling of the frontier orbitals. Although the introduction of tryptophan increases the energy of the highest occupied molecular orbital (HOMO) of the peptides in the gas phase, the new HOMO states are localized on the tryptophan unit and therefore essentially do not contribute to coherent charge transport.
Collapse
Affiliation(s)
- Werner M Schosser
- Department of Physics, University of Konstanz, 78457 Konstanz, Germany
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fabian Pauly
- Department of Physics, University of Konstanz, 78457 Konstanz, Germany
| |
Collapse
|
5
|
Zotti LA, Cuevas JC. Electron Transport Through Homopeptides: Are They Really Good Conductors? ACS OMEGA 2018; 3:3778-3785. [PMID: 31458620 PMCID: PMC6641635 DOI: 10.1021/acsomega.7b01917] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/26/2018] [Indexed: 06/10/2023]
Abstract
Motivated by recent experiments, we performed a theoretical study of electron transport through single-molecule junctions incorporating four kinds of homopeptides (based on alanine, glutamic acid, lysine, and tryptophan). Our results suggest that these molecules are rather insulating and operate in off-resonance tunneling as their main transport mechanism. We ascribe their poor performance as conductors to the high localization of their frontier orbitals. We found that binding scenarios in which side chains lie on the side of gold protuberances could give rise to an increase in conductance with respect to end-to-end binding configurations. These findings provide an insight into the conductance mechanism of the building blocks of proteins and identify key issues that need to be further investigated.
Collapse
Affiliation(s)
- Linda A. Zotti
- Departamento
de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Ciudad Universitaria
de Cantoblanco, E-28049 Madrid, Spain
| | - Juan Carlos Cuevas
- Departamento
de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Ciudad Universitaria
de Cantoblanco, E-28049 Madrid, Spain
| |
Collapse
|
6
|
Brisendine JM, Refaely-Abramson S, Liu ZF, Cui J, Ng F, Neaton JB, Koder RL, Venkataraman L. Probing Charge Transport through Peptide Bonds. J Phys Chem Lett 2018; 9:763-767. [PMID: 29376375 PMCID: PMC6420303 DOI: 10.1021/acs.jpclett.8b00176] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We measure the conductance of unmodified peptides at the single-molecule level using the scanning tunneling microscope-based break-junction method, utilizing the N-terminal amine group and the C-terminal carboxyl group as gold metal-binding linkers. Our conductance measurements of oligoglycine and oligoalanine backbones do not rely on peptide side-chain linkers. We compare our results with alkanes terminated asymmetrically with an amine group on one end and a carboxyl group on the other to show that peptide bonds decrease the conductance of an otherwise saturated carbon chain. Using a newly developed first-principles approach, we attribute the decrease in conductance to charge localization at the peptide bond, which reduces the energy of the frontier orbitals relative to the Fermi energy and the electronic coupling to the leads, lowering the tunneling probability. Crucially, this manifests as an increase in conductance decay of peptide backbones with increasing length when compared with alkanes.
Collapse
Affiliation(s)
- Joseph M Brisendine
- Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, and Department of Biochemistry, City College of New York , New York, New York 10031, United States
| | - Sivan Refaely-Abramson
- Department of Physics, University of California Berkeley , Berkeley, California 94720, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Zhen-Fei Liu
- Department of Physics, University of California Berkeley , Berkeley, California 94720, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Jing Cui
- Department of Physics, Columbia University , New York, New York 10027, United States
| | - Fay Ng
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Jeffrey B Neaton
- Department of Physics, University of California Berkeley , Berkeley, California 94720, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute at Berkeley , Berkeley, California 94720, United States
| | - Ronald L Koder
- Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, and Department of Biochemistry, City College of New York , New York, New York 10031, United States
- Department of Physics, City College of New York , New York, New York 10031, United States
| | - Latha Venkataraman
- Department of Chemistry, Columbia University , New York, New York 10027, United States
- Department of Applied Physics, Columbia University , New York, New York 10027, United States
| |
Collapse
|