Tokita, Y., Shimura, J., Nakajima, H., Goto, Y. & Watanabe, Y. Mechanism of intramolecular electron transfer in the photoexcited Zn-substituted cytochrome c: theoretical and experimental perspective. J. Am. Chem. Soc. 130, 5302–5310 (2008).
Google Scholar
Sariciftci, N. S., Smilowitz, L., Heeger, A. J. & Wudl, F. Photoinduced electron transfer from a conducting polymer to buckminsterfullerene. Science 258, 1474–1476 (1992).
Google Scholar
Murphy, C. J. et al. Long-range photoinduced electron transfer through a DNA helix. Science 262, 1025–1029 (1993).
Google Scholar
Lindstrom, C. D. & Zhu, X.-Y. Photoinduced electron transfer at molecule–metal interfaces. Chem. Rev. 106, 4281–4300 (2006).
Google Scholar
Ma, W., Ma, H., Peng, Y. Y., Tian, H. & Long, Y. T. An ultrasensitive photoelectrochemical platform for quantifying photoinduced electron-transfer properties of a single entity. Nat. Protoc. 14, 2672–2690 (2019).
Google Scholar
Jones, A. L., Jiang, J. & Schanze, K. S. Excitation-wavelength-dependent photoinduced electron transfer in a π-conjugated diblock oligomer. J. Am. Chem. Soc. 142, 12658–12668 (2020).
Google Scholar
O’Dea, J. R., Brown, L. M., Hoepker, N., Marohn, J. A. & Sadewasser, S. Scanning probe microscopy of solar cells: from inorganic thin films to organic photovoltaics. MRS Bull. 37, 642–650 (2012).
Giridharagopal, R., Cox, P. A. & Ginger, D. S. Functional scanning probe imaging of nanostructured solar energy materials. Acc. Chem. Res. 49, 1769–1776 (2016).
Google Scholar
Gerster, D. et al. Photocurrent of a single photosynthetic protein. Nat. Nanotechnol. 7, 673–676 (2012).
Google Scholar
Takeuchi, O. et al. Microscopic description of the current–voltage characteristics of a bulk-heterojunction organic solar cell under illumination. Appl. Phys. Express 7, 021602 (2014).
Google Scholar
Coffey, D. C., Reid, O. G., Rodovsky, D. B., Bartholomew, G. P. & Ginger, D. S. Mapping local photocurrents in polymer/fullerene solar cells with photoconductive atomic force microscopy. Nano Lett. 7, 738–744 (2007).
Google Scholar
Imada, H. et al. Single-molecule laser nanospectroscopy with micro-electron volt energy resolution. Science 373, 95–98 (2021).
Google Scholar
Jaculbia, R. B. et al. Single-molecule resonance Raman effect in a plasmonic nanocavity. Nat. Nanotechnol. 15, 105–110 (2020).
Google Scholar
Wu, S. W., Ogawa, N. & Ho, W. Atomic-scale coupling of photons to single-molecule junctions. Science 312, 1362–1365 (2006).
Google Scholar
Zhu, S.-E. et al. Self-decoupled porphyrin with a tripodal anchor for molecular-scale electroluminescence. J. Am. Chem. Soc. 135, 15794–15800 (2013).
Google Scholar
Cocker, T. L., Peller, D., Yu, P., Repp, J. & Huber, R. Tracking the ultrafast motion of a single molecule by femtosecond orbital imaging. Nature 539, 263–267 (2016).
Google Scholar
Yoshioka, K. et al. Real-space coherent manipulation of electrons in a single tunnel junction by single-cycle terahertz electric fields. Nat. Photonics 10, 762–765 (2016).
Google Scholar
Garg, M. & Kern, K. Attosecond coherent manipulation of electrons in tunneling microscopy. Science 367, 411–415 (2020).
Google Scholar
Zhang, R. et al. Chemical mapping of a single molecule by plasmon-enhanced Raman scattering. Nature 498, 82–86 (2013).
Google Scholar
Zhang, Y. et al. Visualizing coherent intermolecular dipole–dipole coupling in real space. Nature 531, 623–627 (2016).
Google Scholar
Imada, H. et al. Real-space investigation of energy transfer in heterogeneous molecular dimers. Nature 538, 364–367 (2016).
Google Scholar
Doppagne, B. et al. Vibronic spectroscopy with submolecular resolution from STM-induced electroluminescence. Phys. Rev. Lett. 118, 127401 (2017).
Google Scholar
Kimura, K. et al. Selective triplet exciton formation in a single molecule. Nature 570, 210–213 (2019).
Google Scholar
Imada, H. et al. Single-molecule investigation of energy dynamics in a coupled plasmon–exciton system. Phys. Rev. Lett. 119, 013901 (2017).
Google Scholar
Murray, C. et al. Infrared and Raman spectroscopy of free-base and zinc phthalocyanines isolated in matrices. Phys. Chem. Chem. Phys. 12, 10406–10422 (2010).
Google Scholar
Murray, C. et al. Visible luminescence spectroscopy of free-base and zinc phthalocyanines isolated in cryogenic matrices. Phys. Chem. Chem. Phys. 13, 17543–17554 (2011).
Google Scholar
Imai-Imada, M. et al. Energy-level alignment of a single molecule on ultrathin insulating film. Phys. Rev. B 98, 201403 (2018).
Google Scholar
Doppagne, B. et al. Electrofluorochromism at the single-molecule level. Science 361, 251–255 (2018).
Google Scholar
Repp, J., Meyer, G., Stojković, S. M., Gourdon, A. & Joachim, C. Molecules on insulating films: scanning-tunneling microscopy imaging of individual molecular orbitals. Phys. Rev. Lett. 94, 026803 (2005).
Google Scholar
Ikeda, T., Iino, R. & Noji, H. Real-time fluorescence visualization of slow tautomerization of single free-base phthalocyanines under ambient conditions. Chem. Commun. 50, 9443–9446 (2014).
Google Scholar
Liljeroth, P., Repp, J. & Meyer, G. Current-induced hydrogen tautomerization and conductance switching of naphthalocyanine molecules. Science 317, 1203–1206 (2007).
Google Scholar
Doppagne, B. et al. Single-molecule tautomerization tracking through space- and time-resolved fluorescence spectroscopy. Nat. Nanotechnol. 15, 207–211 (2020).
Google Scholar
Böckmann, H. et al. Direct observation of photoinduced tautomerization in single molecules at a metal surface. Nano Lett. 16, 1034–1041 (2016).
Google Scholar
Miwa, K., Najarian, A. M., Mccreery, R. L. & Galperin, M. Hubbard nonequilibrium Green’s function analysis of photocurrent in nitroazobenzene molecular junction. J. Phys. Chem. Lett. 10, 1550–1557 (2019).
Google Scholar
Miwa, K. et al. Many-body state description of single-molecule electroluminescence driven by a scanning tunneling microscope. Nano Lett. 19, 2803–2811 (2019).
Google Scholar
Yang, B. et al. Sub-nanometre resolution in single-molecule photoluminescence imaging. Nat. Photonics 14, 693–699 (2020).
Google Scholar
Qiu, X. H., Nazin, G. V. & Ho, W. Vibrationally resolved fluorescence excited with submolecular precision. Science 299, 542–546 (2003).
Google Scholar
Kuhnke, K., Große, C., Merino, P. & Kern, K. Atomic-scale imaging and spectroscopy of electroluminescence at molecular interfaces. Chem. Rev. 117, 5174–5222 (2017).
Google Scholar
Yang, B., Kazuma, E., Yokota, Y. & Kim, Y. Fabrication of sharp gold tips by three-electrode electrochemical etching with high controllability and reproducibility. J. Phys. Chem. C 122, 16950–16955 (2018).
Google Scholar
Miwa, K., Imada, H., Kawahara, S. & Kim, Y. Effects of molecule–insulator interaction on geometric property of a single phthalocyanine molecule adsorbed on an ultrathin NaCl film. Phys. Rev. B 93, 165419 (2016).
Google Scholar
Neuman, T., Esteban, R., Casanova, D., García-Vidal, F. J. & Aizpurua, J. Coupling of molecular emitters and plasmonic cavities beyond the point-dipole approximation. Nano Lett. 18, 2358–2364 (2018).
Google Scholar
Frisch, M. J. et al. Gaussian 16, revision C.01 (Gaussian, Inc., 2016); https://gaussian.com.
Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007–1023 (1989).
Google Scholar
Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648–5652 (1993).
Google Scholar
Henderson, T. M., Izmaylov, A. F., Scalmani, G. & Scuseria, G. E. Can short-range hybrids describe long-range-dependent properties? J. Chem. Phys. 131, 044108 (2009).
Google Scholar
Baer, R., Livshits, E. & Salzner, U. Tuned range-separated hybrids in density functional theory. Annu. Rev. Phys. Chem. 61, 85–109 (2010).
Google Scholar
Runge, E. & Gross, E. K. U. Density-functional theory for time-dependent systems. Phys. Rev. Lett. 52, 997–1000 (1984).
Google Scholar
Casida, M. E. Time-dependent density functional response theory for molecules. In Recent Advances in Density Functional Methods: Part I (ed. Chong, D. P.) 155–192 (World Scientific, 1995).
Hirata, S. & Head-Gordon, M. Time-dependent density functional theory within the Tamm–Dancoff approximation. Chem. Phys. Lett. 314, 291–299 (1999).
Google Scholar
Santoro, F., Improta, R., Lami, A., Bloino, J. & Barone, V. Effective method to compute Franck–Condon integrals for optical spectra of large molecules in solution. J. Chem. Phys. 126, 084509 (2007).
Google Scholar
Santoro, F., Lami, A., Improta, R. & Barone, V. Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution. J. Chem. Phys. 126, 184102 (2007).
Google Scholar
Santoro, F., Lami, A., Improta, R., Bloino, J. & Barone, V. Effective method for the computation of optical spectra of large molecules at finite temperature including the Duschinsky and Herzberg–Teller effect: the Qx band of porphyrin as a case study. J. Chem. Phys. 128, 224311 (2008).
Google Scholar
Barone, V., Bloino, J., Biczysko, M. & Santoro, F. Fully integrated approach to compute vibrationally resolved optical spectra: from small molecules to macrosystems. J. Chem. Theory Comput. 5, 540–554 (2009).
Google Scholar
Scivetti, I. & Persson, M. Frontier molecular orbitals of a single molecule adsorbed on thin insulating films supported by a metal substrate: electron and hole attachment energies. J. Phys. Condens. Matter 29, 355002 (2017).
Galperin, M. Photonics and spectroscopy in nanojunctions: a theoretical insight. Chem. Soc. Rev. 46, 4000–4019 (2017).
Google Scholar
Miwa, K., Chen, F. & Galperin, M. Towards noise simulation in interacting nonequilibrium systems strongly coupled to baths. Sci. Rep. 7, 9735 (2017).
Google Scholar
Chen, F., Ochoa, M. A. & Galperin, M. Nonequilibrium diagrammatic technique for Hubbard Green functions. J. Chem. Phys. 146, 92301 (2017).
Cohen, G. & Galperin, M. Green’s function methods for single molecule junctions. J. Chem. Phys. 152, 090901 (2020).
Google Scholar
White, A. J., Ochoa, M. A. & Galperin, M. Nonequilibrium atomic limit for transport and optical response of molecular junctions. J. Phys. Chem. C 118, 11159–11173 (2014).
Google Scholar
Schulz, F. et al. Many-body transitions in a single molecule visualized by scanning tunnelling microscopy. Nat. Phys. 11, 229–234 (2015).
Google Scholar
Ervasti, M. M., Schulz, F., Liljeroth, P. & Harju, A. Single- and many-particle description of scanning tunneling spectroscopy. J. Electron Spectros. Relat. Phenom. 219, 63–71 (2017).
Google Scholar
Seldenthuis, J. S., van der Zant, H. S. J., Ratner, M. A. & Thijssen, J. M. Electroluminescence spectra in weakly coupled single-molecule junctions. Phys. Rev. B 81, 205430 (2010).
Google Scholar
Fatayer, S. et al. Reorganization energy upon charging a single molecule on an insulator measured by atomic force microscopy. Nat. Nanotechnol. 13, 376–380 (2018).
Google Scholar
Yu, P., Kocić, N., Repp, J., Siegert, B. & Donarini, A. Apparent reversal of molecular orbitals reveals entanglement. Phys. Rev. Lett. 119, 56801 (2017).
Google Scholar
Wu, S. W., Nazin, G. V., Chen, X., Qiu, X. H. & Ho, W. Control of relative tunneling rates in single molecule bipolar electron transport. Phys. Rev. Lett. 93, 236802 (2004).
Google Scholar
Novotny, L. A. & Hecht, B. Principles of Nano-Optics (Cambridge Univ. Press, 2012).