There have been attempts, both experimental and based on density-functional theory (DFT) modeling, at understanding the factors that govern the electronic conductance behavior of single-stacking junctions formed by pi-conjugated materials in nanogaps. Here, a reliable description of relevant stacked configurations of some thiophene-cored systems is provided by means of high-level quantum chemical approaches. The minimal structures of these configurations, which are found using the dispersion-corrected DFT approach, are employed in calculations that apply the coupled cluster method with singles, doubles and perturbative triples [CCSD(T)] and extrapolations to the complete basis set (CBS) limit in order to reliably quantify the strength of intermolecular binding, while their physical origin is investigated using the DFT-based symmetry-adapted perturbation theory (SAPT) of intermolecular interactions. In particular, for symmetrized S-Tn dimers (where "S" and "T" denote a thiomethyl-containing anchor group and a thiophene segment comprising "n" units, respectively), the CCSD(T)/CBS interaction energies are found to increase linearly with n ≤ 6, and significant conformational differences between the flanking 2-thiophene group in S-T1 and S-T2 are described by the CCSD(T)/CBS and SAPT/CBS computations. These results are put into the context of previous work on charge transport properties of S-Tn and other types of supramolecular junctions.

Institute of Macromolecular Chemistry Czech Academy of Sciences Heyrovsky Square 2 16200 Prague Czech Republic

Zobrazit více v PubMed

Li T., Bandari V.K., Schmid O.G. Molecular Electronics: Creating and Bridging Molecular Junctions and Promoting Its Commercialization. Adv. Mater. 2023;35:2209088. doi: 10.1002/adma.202209088. PubMed DOI

Li X., Ge W., Guo S., Bai J., Hong W. Characterization and Application of Supramolecular Junctions. Angew. Chem. 2023;62:202216819. doi: 10.1002/anie.202216819. PubMed DOI

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. doi: 10.1039/D3QM00210A. DOI

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. doi: 10.1021/jacs.2c09656. PubMed DOI

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. doi: 10.1021/jacs.3c02050. PubMed DOI PMC

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. doi: 10.1002/anie.202200191. PubMed DOI

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. doi: 10.1021/nl080580e. PubMed DOI

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. doi: 10.1002/anie.201913344. PubMed DOI

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. doi: 10.1021/jacs.5b11605. PubMed DOI

Chen H., Stoddart J.F. From molecular to supramolecular electronics. Nat. Rev. Mater. 2021;6:804–828. doi: 10.1038/s41578-021-00302-2. DOI

Patkowski K. Recent developments in symmetry-adapted perturbation theory. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2020;10:e1452. doi: 10.1002/wcms.1452. DOI

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. doi: 10.1021/acsnano.1c11433. PubMed DOI

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. doi: 10.1021/jacs.0c07348. PubMed DOI

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. doi: 10.1021/jacs.9b00936. PubMed DOI

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. doi: 10.3390/ijms232415773. PubMed DOI PMC

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. doi: 10.1021/ct400036b. PubMed DOI PMC

Czernek J., Brus J., Czerneková V., Kobera L. Quantifying the Intrinsic Strength of C–H⋯O Intermolecular Interactions. Molecules. 2023;28:4478. doi: 10.3390/molecules28114478. PubMed DOI PMC

Řezáč J., Hobza P. Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications. Chem. Rev. 2016;116:5038–5071. doi: 10.1021/acs.chemrev.5b00526. PubMed DOI

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. doi: 10.1021/ct2002946. PubMed DOI PMC

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. doi: 10.1021/acs.jpcc.0c08428. DOI

Mejía L., Kleinekathöfer U., Franco I. Coherent and incoherent contributions to molecular electron transport. J. Chem. Phys. 2022;156:094302. doi: 10.1063/5.0079708. PubMed DOI

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. doi: 10.1063/1.3432765. PubMed DOI

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. doi: 10.1038/s41467-021-24119-3. PubMed DOI PMC

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. doi: 10.1021/acs.jpclett.7b03323. PubMed DOI

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. doi: 10.1021/acs.nanolett.0c02815. PubMed DOI PMC

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. doi: 10.1002/anie.202302693. PubMed DOI

Magyarkuti A., Adak O., Halbritter A., Venkataraman L. Electronic and mechanical characteristics of stacked dimer molecular junctions. Nanoscale. 2018;10:3562–3568. doi: 10.1039/C7NR08354H. PubMed DOI

Irikura K.K., National Institute of Standards and Technology Using the Output File from a Gaussian Frequency Calculation to Compute Ideal-Gas Thermodynamic Functions. [(accessed on 12 August 2023)]; Available online: https://www.nist.gov/mml/csd/chemical-informatics-research-group/products-and-services/program-computing-ideal-gas/

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. Gaussian, Inc.; Wallingford, CT, USA: 2019. Revision C.01.

Becke A. Density-Functional Thermochemistry. V. Systematic Optimization of Exchange-Correlation Functionals. J. Chem. Phys. 1997;107:8554–8560. doi: 10.1063/1.475007. DOI

Grimme S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 2006;27:1787–1799. doi: 10.1002/jcc.20495. PubMed DOI

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. doi: 10.1039/b508541a. PubMed DOI

Grimme S. Semiempirical hybrid density functional with perturbative second-order correlation. J. Chem. Phys. 2006;124:034108. doi: 10.1063/1.2148954. PubMed DOI

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. doi: 10.1039/C7CP04913G. PubMed DOI

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. doi: 10.1063/1.3382344. PubMed DOI

Rappoport D., Furche F. Property-optimized Gaussian basis sets for molecular response calculations. J. Chem. Phys. 2010;133:134105. doi: 10.1063/1.3484283. PubMed DOI

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. doi: 10.1021/acs.jctc.5b01144. PubMed DOI

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. doi: 10.1063/1.456153. DOI

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. doi: 10.1063/1.462569. DOI

Weigend F., Häser M. RI-MP2: First derivatives and global consistency. Theor. Chem. Acc. 1997;97:331–340. doi: 10.1007/s002140050269. DOI

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. doi: 10.1016/S0009-2614(98)00862-8. DOI

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. doi: 10.1063/5.0004635. PubMed DOI PMC

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. doi: 10.1063/5.0005081. PubMed DOI

Czernek J., Brus J., Czerneková V. A computational inspection of the dissociation energy of mid-sized organic dimers. J. Chem. Phys. 2022;156:204303. doi: 10.1063/5.0093557. PubMed DOI

Heßelmann A., Jansen G. First-order intermolecular interaction energies from Kohn—Sham orbitals. Chem. Phys. Lett. 2002;357:464–470. doi: 10.1016/S0009-2614(02)00538-9. DOI

Heßelmann A., Jansen G. Intermolecular dispersion energies from time-dependent density functional theory. Chem. Phys. Lett. 2003;367:778–784. doi: 10.1016/S0009-2614(02)01796-7. DOI

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. doi: 10.1016/S0009-2614(02)01097-7. DOI

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. doi: 10.1080/00268979650026262. DOI

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. doi: 10.1016/S0009-2614(98)00111-0. DOI

Riplinger C., Neese F. An efficient and near linear scaling pair natural orbital based local coupled cluster method. J. Chem. Phys. 2013;138:034106. doi: 10.1063/1.4773581. PubMed DOI

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. doi: 10.1063/1.4821834. PubMed DOI

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. doi: 10.1063/1.4939030. PubMed DOI

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. doi: 10.1063/1.4926879. PubMed DOI

Neese F. Software update: The ORCA program system—Version 5.0. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2022;12:e1606. doi: 10.1002/wcms.1606. DOI

Revisiting the Most Stable Structures of the Benzene Dimer

Reliable Dimerization Energies for Modeling of Supramolecular Junctions