On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions
Abstract
:1. Introduction
2. Results
2.1. The Energy Minima
2.2. The Molecular Size Dependence of
2.3. The Conformational Dependence of
3. Discussion
4. Materials and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Li, T.; Bandari, V.K.; Schmid, O.G. Molecular Electronics: Creating and Bridging Molecular Junctions and Promoting Its Commercialization. Adv. Mater. 2023, 35, 2209088. [Google Scholar] [CrossRef]
- Li, X.; Ge, W.; Guo, S.; Bai, J.; Hong, W. Characterization and Application of Supramolecular Junctions. Angew. Chem. 2023, 62, 202216819. [Google Scholar] [CrossRef]
- Ayinla, R.T.; Shiri, M.; Song, B.; Gangishetty, M.; Wang, K. The pivotal role of non-covalent interactions in single-molecule charge transport. Mater. Chem. Front. 2023, 7, 3524–3542. [Google Scholar] [CrossRef]
- Zhang, C.; Cheng, J.; Wu, Q.; Hou, S.; Feng, S.; Jiang, B.; Lambert, C.J.; Gao, X.; Li, Y.; Li, J. Enhanced π–π Stacking between Dipole-Bearing Single Molecules Revealed by Conductance Measurement. J. Am. Chem. Soc. 2023, 145, 1617–1630. [Google Scholar] [CrossRef]
- Homma, K.; Kaneko, S.; Tsukagoshi, K.; Nishino, T. Intermolecular and Electrode-Molecule Bonding in a Single Dimer Junction of Naphthalenethiol as Revealed by Surface-Enhanced Raman Scattering Combined with Transport Measurements. J. Am. Chem. Soc. 2023, 145, 15788–15795. [Google Scholar] [CrossRef]
- Li, R.; Zhou, Y.; Ge, W.; Zheng, J.; Zhu, Y.; Bai, J.; Li, X.; Lin, L.; Duan, H.; Shi, J.; et al. Strain of Supramolecular Interactions in Single-Stacking Junctions. Angew. Chem. 2022, 61, e202200191. [Google Scholar] [CrossRef]
- Hihath, J.; Arroyo, C.R.; Rubio-Bollinger, G.; Tao, N.; Agraït, N. Study of Electron—Phonon Interactions in a Single Molecule Covalently Connected to Two Electrodes. Nano Lett. 2008, 8, 1673–1678. [Google Scholar] [CrossRef]
- Li, X.; Wu, Q.; Bai, J.; Hou, S.; Jiang, W.; Tang, C.; Song, H.; Huang, X.; Zheng, J.; Yang, Y.; et al. Structure-Independent Conductance of Thiophene-Based Single-Stacking Junctions. Angew. Chem. 2020, 8, 3280–3286. [Google Scholar] [CrossRef]
- Xiang, L.; Hines, T.; Palma, J.L.; Lu, X.; Mujica, V.; Ratner, M.A.; Zhou, G.; Tao, N. Non-exponential Length Dependence of Conductance in Iodide-Terminated Oligothiophene Single-Molecule Tunneling Junctions. J. Am. Chem. Soc. 2016, 138, 679–687. [Google Scholar] [CrossRef]
- Chen, H.; Stoddart, J.F. From molecular to supramolecular electronics. Nat. Rev. Mater. 2021, 6, 804–828. [Google Scholar] [CrossRef]
- Patkowski, K. Recent developments in symmetry-adapted perturbation theory. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2020, 10, e1452. [Google Scholar] [CrossRef]
- Xie, X.; Li, P.; Xu, Y.; Zhou, L.; Yan, Y.; Xie, L.; Jia, C.; Guo, X. Single-Molecule Junction: A Reliable Platform for Monitoring Molecular Physical and Chemical Processes. ACS Nano 2022, 16, 3476–3505. [Google Scholar] [CrossRef]
- Tang, Y.; Zhou, Y.; Zhou, D.; Chen, Y.; Xiao, Z.; Shi, J.; Liu, J.; Hong, W. Electric Field-Induced Assembly in Single-Stacking Terphenyl Junctions. J. Am. Chem. Soc. 2020, 142, 19101–19109. [Google Scholar] [CrossRef]
- Bootsma, A.N.; Doney, A.C.; Wheeler, S.E. Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chains. J. Am. Chem. Soc. 2019, 141, 11027–11035. [Google Scholar] [CrossRef]
- Czernek, J.; Brus, J.; Czerneková, V. A Cost Effective Scheme for the Highly Accurate Description of Intermolecular Binding in Large Complexes. Int. J. Mol. Sci. 2022, 23, 15773. [Google Scholar] [CrossRef]
- Sedlak, R.; Janowski, T.; Pitoňák, M.; Řezáč, J.; Pulay, P.; Hobza, P. Accuracy of Quantum Chemical Methods for Large Noncovalent Complexes. J. Chem. Theory Comput. 2013, 9, 3364–3374. [Google Scholar] [CrossRef]
- Czernek, J.; Brus, J.; Czerneková, V.; Kobera, L. Quantifying the Intrinsic Strength of C–H⋯O Intermolecular Interactions. Molecules 2023, 28, 4478. [Google Scholar] [CrossRef]
- Řezáč, J.; Hobza, P. Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications. Chem. Rev. 2016, 116, 5038–5071. [Google Scholar] [CrossRef]
- Řezáč, J.; Riley, K.E.; Hobza, P. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures. J. Chem. Theory Comput. 2011, 7, 2427–2438. [Google Scholar] [CrossRef]
- Li, Z.; Mejía, L.; Marrs, J.; Jeong, H.; Hihath, J.; Franco, I. Understanding. the Conductance Dispersion of Single-Molecule Junctions. J. Phys. Chem. C 2021, 125, 3406–3414. [Google Scholar] [CrossRef]
- Mejía, L.; Kleinekathöfer, U.; Franco, I. Coherent and incoherent contributions to molecular electron transport. J. Chem. Phys. 2022, 156, 094302. [Google Scholar] [CrossRef]
- von Lilienfeld, O.A.; Tkatchenko, A. Two- and three-body interatomic dispersion energy contributions to binding in mole-cules and solids. J. Chem. Phys. 2010, 132, 234109. [Google Scholar] [CrossRef] [PubMed]
- Al-Hamdani, Y.S.; Nagy, P.R.; Zen, A.; Barton, D.; Kállay, M.; Bradenburg, J.G.; Tchatkenko, A. Interactions between large molecules pose a puzzle for reference quantum mechanical methods. Nat. Commun. 2021, 12, 3927. [Google Scholar] [CrossRef] [PubMed]
- 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. [Google Scholar] [CrossRef] [PubMed]
- Wu, C.; Bates, D.; Sangtarash, S.; Ferri, N.; Thomas, A.; Higgins, S.J.; Robertson, C.M.; Nichols, R.J.; Sadeghi, H.; Vezzoli, A. Folding a Single-Molecule Junction. Nano Lett. 2020, 20, 7980–7986. [Google Scholar] [CrossRef]
- Zhu, Y.; Zhou, Y.; Ren, L.; Ye, J.; Wang, H.; Liu, X.; Huang, R.; Liu, H.; Liu, J.; Shi, J.; et al. Switching Quantum Interference in Single-Molecule Junctions by Mechanical Tuning. Angew. Chem. 2023, 62, e202302693. [Google Scholar] [CrossRef]
- Magyarkuti, A.; Adak, O.; Halbritter, A.; Venkataraman, L. Electronic and mechanical characteristics of stacked dimer molecular junctions. Nanoscale 2018, 10, 3562–3568. [Google Scholar] [CrossRef]
- Irikura, K.K.; National Institute of Standards and Technology. Using the Output File from a Gaussian Frequency Calculation to Compute Ideal-Gas Thermodynamic Functions. Available online: https://www.nist.gov/mml/csd/chemical-informatics-research-group/products-and-services/program-computing-ideal-gas/ (accessed on 12 August 2023).
- Frish, M.J.; Trucks, J.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Petersson, G.A.; Nakatsuji, H.; et al. Gaussian 16; Revision C.01; Gaussian, Inc.: Wallingford, CT, USA, 2019. [Google Scholar]
- Becke, A. Density-Functional Thermochemistry. V. Systematic Optimization of Exchange-Correlation Functionals. J. Chem. Phys. 1997, 107, 8554–8560. [Google Scholar] [CrossRef]
- Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 2006, 27, 1787–1799. [Google Scholar] [CrossRef]
- Weigend, F.; Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297–3305. [Google Scholar] [CrossRef]
- Grimme, S. Semiempirical hybrid density functional with perturbative second-order correlation. J. Chem. Phys. 2006, 124, 034108. [Google Scholar] [CrossRef] [PubMed]
- Goerigk, L.; Hansen, A.; Bauer, C.; Ehrlich, S.; Najibi, A.; Grimme, S. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys. Chem. Chem. Phys. 2017, 19, 32184–32215. [Google Scholar] [CrossRef] [PubMed]
- Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 154104. [Google Scholar] [CrossRef]
- Rappoport, D.; Furche, F. Property-optimized Gaussian basis sets for molecular response calculations. J. Chem. Phys. 2010, 133, 134105. [Google Scholar] [CrossRef]
- Brémond, É.; Savarese, M.; Su, N.Q.; Pérez-Jiménez, Á.J.; Xu, X.; Sancho-García, J.C.; Adamo, C. Benchmarking Density Functionals on Structural Parameters of Small-/Medium-Sized Organic Molecules. J. Chem. Theory Comput. 2016, 12, 459–465. [Google Scholar] [CrossRef]
- Dunning, T.H., Jr. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 1989, 90, 1007. [Google Scholar] [CrossRef]
- Kendall, R.A.; Dunning, T.H., Jr. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 1992, 96, 6796. [Google Scholar] [CrossRef]
- Weigend, F.; Häser, M. RI-MP2: First derivatives and global consistency. Theor. Chem. Acc. 1997, 97, 331–340. [Google Scholar] [CrossRef]
- Weigend, F.; Häser, M.; Patzelt, H.; Ahlrichs, R. RI-MP2: Optimized auxiliary basis sets and demonstration of efficiency. Chem. Phys. Lett. 1998, 294, 143–152. [Google Scholar] [CrossRef]
- Balasubramani, S.G.; Chen, G.P.; Coriani, S.; Diedenhofen, M.; Frank, M.S.; Franzke, Y.J.; Furche, F.; Grotjahn, R.; Harding, M.E.; Hättig, C.; et al. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simula-tions. J. Chem. Phys. 2020, 152, 184107. [Google Scholar] [CrossRef]
- Werner, H.J.; Knowles, P.J.; Manby, F.R.; Black, J.A.; Doll, K.; Hesselmann, A.; Kats, D.; Kohn, A.; Korona, T.; Kreplin, D.A.; et al. The Molpro quantum chemistry package. J. Chem. Phys. 2020, 152, 144107. [Google Scholar] [CrossRef] [PubMed]
- Czernek, J.; Brus, J.; Czerneková, V. A computational inspection of the dissociation energy of mid-sized organic dimers. J. Chem. Phys. 2022, 156, 204303. [Google Scholar] [CrossRef] [PubMed]
- Heßelmann, A.; Jansen, G. First-order intermolecular interaction energies from Kohn—Sham orbitals. Chem. Phys. Lett. 2002, 357, 464–470. [Google Scholar] [CrossRef]
- Heßelmann, A.; Jansen, G. Intermolecular dispersion energies from time-dependent density functional theory. Chem. Phys. Lett. 2003, 367, 778–784. [Google Scholar] [CrossRef]
- Heßelmann, A.; Jansen, G. Intermolecular induction and exchange-induction energies from coupled-perturbed Kohn—Sham density functional theory. Chem. Phys. Lett. 2002, 362, 319–325. [Google Scholar] [CrossRef]
- Moszynski, R.; Heijmen, T.G.A.; Jeziorski, B. Symmetry-adapted perturbation theory for the calculation of Hartree—Fock interaction energies. Mol. Phys. 1996, 88, 741–758. [Google Scholar] [CrossRef]
- Halkier, A.; Helgaker, T.; Jørgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A.K. Basis-set convergence in correlated calculations on Ne, N2, and H2O. Chem. Phys. Lett. 1998, 286, 243–252. [Google Scholar] [CrossRef]
- Riplinger, C.; Neese, F. An efficient and near linear scaling pair natural orbital based local coupled cluster method. J. Chem. Phys. 2013, 138, 034106. [Google Scholar] [CrossRef]
- Riplinger, C.; Sandhoefer, B.; Hansen, A.; Neese, F. Natural triple excitations in local coupled cluster calculations with pair natural orbitals. J. Chem. Phys. 2013, 139, 134101. [Google Scholar] [CrossRef]
- Riplinger, C.; Pinski, P.; Becker, U.; Valeev, E.F.; Neese, F. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory. J. Chem. Phys. 2016, 144, 024109. [Google Scholar] [CrossRef]
- Pinski, P.; Riplinger, C.; Valeev, E.F.; Neese, F. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals. J. Chem. Phys. 2015, 143, 034108. [Google Scholar] [CrossRef] [PubMed]
- Neese, F. Software update: The ORCA program system—Version 5.0. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2022, 12, e1606. [Google Scholar] [CrossRef]
Configuration | Supermolecular | SAPT-DFT/CBS | |||||||
---|---|---|---|---|---|---|---|---|---|
unsymmetric | 29.7 (25.5) | −105.2 (−99.4) | 25.1 (23.6) | −50.5 (−50.4) | −38.9 (−33.0) | 87.1 (74.7) | −10.9 (−9.5) | −87.5 (−82.5) | −50.1 (−50.2) |
symmetric | 35.3 (33.5) | −107.5 (−105.9) | 27.2 (26.7) | −45.0 (−45.7) | −32.1 (−31.2) | 80.6 (77.6) | −9.7 (−9.0) | −84.8 (−83.8) | −46.0 (−46.3) |
Configuration | Supramolecular | SAPT-DFT/CBS | |||||||
---|---|---|---|---|---|---|---|---|---|
unsymmetric | 51.6 | −160.7 | 41.9 | −67.2 | −41.9 | 113.6 | −12.7 | −124.9 | −65.9 |
symmetric | 52.3 | −159.7 | 42.7 | −64.6 | −38.8 | 106.9 | −10.5 | −121.8 | −64.2 |
Configuration | ||||
---|---|---|---|---|
unsymmetric | 71.1 (74.8) | −224.8 (−259.6) | 61.0 (68.5) | −92.8 (−116.3) |
symmetric | 68.3 (81.3) | −215.0 (−261.6) | 59.2 (74.6) | −87.6 (−105.8) |
System | (cc) | (SS) |
---|---|---|
S-T1 | 395 (399) | 1025 (834) |
S-T2 | 380 (359) | 1396 (1225) |
S-T3 | 391 (297) | 1784 (1538) |
S-T4 | 400 (241) | 2189 (1724) |
S-T5 | 402 | 2260 |
S-T6 | 445 | 2585 |
System (in Ci Symmetry) | (CC) | |||
---|---|---|---|---|
S-T5 | 101.2 | −314.1 | 89.0 | −123.9 |
S-T6 | 108.1 | −329.3 | 94.4 | −126.7 |
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Czernek, J.; Brus, J. On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions. Int. J. Mol. Sci. 2023, 24, 13349. https://doi.org/10.3390/ijms241713349
Czernek J, Brus J. On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions. International Journal of Molecular Sciences. 2023; 24(17):13349. https://doi.org/10.3390/ijms241713349
Chicago/Turabian StyleCzernek, Jiří, and Jiří Brus. 2023. "On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions" International Journal of Molecular Sciences 24, no. 17: 13349. https://doi.org/10.3390/ijms241713349