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The synergistic effect of electron lone pairs and aromaticity on the binding affinity towards metal surfaces. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2023.131127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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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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Fallaque JG, Rodríguez-González S, Díaz C, Martín F. A simple model to engineer single-molecule conductance of acenes by chemical disubstitution. NANOSCALE 2022; 14:464-472. [PMID: 34908088 DOI: 10.1039/d1nr06687k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding and controlling electrical conductivity at the single-molecule level is of fundamental importance for the development of new molecular electronic devices. This ideally requires considering the many different options offered by the molecular structure, the nature of the electrodes, and all possible molecule-electrode anchoring configurations, which is experimentally tedious and theoretically very expensive. Here we present a systematic theoretical study of the conductance of di-amino, di-methylthio and di-(4-methylthio)phenyl acenes, from benzene to pentacene, and for all possible distributions of two identical linkers symmetrically placed on opposite sides of the same ring. We show that, for all investigated compounds, the relative variation of the conductance is well explained by the variations of the HOMO energies as predicted by a simple extended-Hückel approach, i.e., without the need for further input from more elaborate calculations. The model predicts quite nicely that diamino acenes are better conductors than their corresponding dimethylthio analogues, and both much better than the di-(4-methylthio)phenyl counterparts, irrespective of the linkers' relative positions. It also predicts, for a given pair of linkers, the variations in the conductance resulting from changing the acene size and/or the relative position of the linkers. These variations can be as large as an order of magnitude, and therefore can be used to engineer molecular conductance. Finally, we show that a similar approach should be useful to predict trends in the relative conductance of a large variety of disubstituted acene isomers, including various linkers.
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Affiliation(s)
- Joel G Fallaque
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nano), Campus de Cantoblanco, 28049 Madrid, Spain.
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sandra Rodríguez-González
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Departamento de Química Física, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Cristina Díaz
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Fernando Martín
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nano), Campus de Cantoblanco, 28049 Madrid, Spain.
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Chiang KR, Tang YH. Effect of Contact Geometry on Spin Transport in Amine-Ended Single-Molecule Magnetic Junctions. ACS OMEGA 2021; 6:19386-19391. [PMID: 34368525 PMCID: PMC8340092 DOI: 10.1021/acsomega.1c00930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
We employ the first-principles calculation with non-equilibrium Green's function method to comprehensively investigate the crucial role of interfacial geometry in spin transport properties of Co/1,4-benzenediamine (BDA)/Co single-molecule magnetic junctions (SMMJs). Two bonding mechanisms are proposed for the hard-hard Co-N coupling: (1) the covalent bonding between the H-dissociated amine linker and spin-polarized Co apex atoms and (2) the dative interaction between the H-non-dissociated (denoted by +H) amine linker and Co apex atoms. The former covalent contact dominates the π-resonance interfacial spin selection that can be well preserved in H-dissociated cases regardless of the choice of top, bridge, and hollow contact sites. From our detailed analyses of spin-polarized transmission spectra, local density of states, and molecular density of states, the underlying mechanism is that the strong hybridization between Co-d, N-p y , and the π-orbital of the phenyl ring in dissociated cases renders the 2-fold HOMO (4-fold LUMO) of the central molecule closer to the Fermi energy. In contrast, the enlarged Co-N bond length of the latter dative contact in the H-non-dissociated case not only destroys the spinterface coupling but also blocks the spin injection. This theoretical work may provide vital and practical insights to illustrate the spin transport property in real amine-ended SMMJs since the contact geometries and interfacial bond mechanisms remain unclear during the breaking junction technique.
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Affiliation(s)
- Kuan-Rong Chiang
- Department of Physics, National
Central University, Jung-Li 32001, Taiwan
| | - Yu-Hui Tang
- Department of Physics, National
Central University, Jung-Li 32001, Taiwan
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Ryu HJ, Lee WK, Kim YH, Lee JS. Interfacial interactions of SERS-active noble metal nanostructures with functional ligands for diagnostic analysis of protein cancer markers. Mikrochim Acta 2021; 188:164. [PMID: 33844071 DOI: 10.1007/s00604-021-04807-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/22/2021] [Indexed: 12/27/2022]
Abstract
Noble metal nanostructures with designed hot spots have been widely investigated as surface-enhanced Raman spectroscopy (SERS)-active substrates, particularly for selective and sensitive detection of protein cancer markers. For specific target recognition and efficient signal amplification, SERS probe design requires a choice of SERS-active nanostructures as well as their controlled functionalization with Raman dyes and target recognition entities such as antibodies. However, the chemical conjugation of antibodies and Raman dyes to SERS substrates has rarely been discussed to date, despite their substantial roles in detection schemes. The interfacial interactions of metal nanostructures with functional ligands during conjugation are known to be strongly influenced by the various chemical and physical properties of the ligands, such as size, molecular weight, surface charge, 3-dimensional structures, and hydrophilicity/hydrophobicity. In this review, we discuss recent developments in the design of SERS probes over the last 4 years, focusing on their conjugation chemistry for functionalization. A strong preference for covalent bonding is observed with Raman dyes having simpler molecular structures, whereas more complicated ones are non-covalently adsorbed. Antibodies are both covalently and non-covalently bonded to nanostructures, depending on their activity in the SERS probes. Considering that ligand conjugation is highly important for chemical stability, biocompatibility, and functionality of SERS probes, this review is expected to expand the understanding of their interfacial design, leading to SERS as one of the most promising spectroscopic analytical tools for the early detection of protein cancer markers.
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Affiliation(s)
- Han-Jung Ryu
- Department of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Won Kyu Lee
- Department of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Yoon Hyuck Kim
- Department of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jae-Seung Lee
- Department of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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Taninaka A, Yoshida S, Sugita Y, Takeuchi O, Shigekawa H. Evolution of local conductance pathways in a single-molecule junction studied using the three-dimensional dynamic probe method. NANOSCALE 2019; 11:5951-5959. [PMID: 30869706 DOI: 10.1039/c9nr00717b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding of the dynamics of the bonding states of molecules with electrodes while the molecular conformation is changed is particularly important for elucidating the details of electrochemical devices as well as molecular devices in which the reaction dynamics of the electrodes and molecules plays an important role, such as in fuel cells, catalysis and bioelectrochemical devices. However, it has been difficult to make measurements when the distance between counter electrodes is short, namely, the molecule is raised from a lying form, almost parallel and close to the electrodes, toward a standing form and vice versa. We previously have developed a method called the three-dimensional (3D) dynamic probe method, which enables conductance measurement while the conformation of a single-molecule junction is precisely controlled by scanning tunneling microscopy (STM) techniques. Here, by combining this method with density functional theory (DFT) calculations, it has become possible to simultaneously consider the effects of the dynamics of molecular structures and the bonding states at the electrodes on the local transmission pathways, local-bond contributions to conductance. Here, by performing an analysis on 1,4-benzenediamine (BDA) and 1,4-benzenedithiol (BDT) single molecule junctions, we have observed, for the first time, the effect of a change in the molecular conformations and bonding states on the local transmission pathways for a short Au electrode distance condition.
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Affiliation(s)
- Atsushi Taninaka
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Shoji Yoshida
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Yoshihiro Sugita
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Osamu Takeuchi
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Hidemi Shigekawa
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
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