Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Multiscale modelling of photoinduced processes in composite systems

Nature Reviews Chemistry volume 3, pages 315–330 (2019)Cite this article

Subjects

Abstract

In the past few decades, quantum mechanical (QM) modelling has moved from isolated molecules made of few atoms to large supramolecular aggregates embedded in complex environments. The integration of QM methods within classical descriptions in multiscale models made such advances possible. One of the first examples of this integration is represented by continuum solvation models that have been largely and successfully applied to predict properties and processes of solvated molecules since the 1980s. Almost in the same years, an alternative classical description based on molecular mechanics (MM) was coupled to QM methods in hybrid QM/MM approaches. Since their first formulations, these QM/classical models have seen great development in terms of accuracy, robustness and generalizability. This progress has enabled their application to systems of increasing complexity and processes never studied before within a QM framework, such as photoinduced processes in biomolecules, nanomaterials and, more generally, composite systems. These systems bring together components of different sizes — molecular, nano and mesoscopic — and multiscale approaches enable their simultaneous investigation. In this Review, we highlight potentials and limitations of multiscale approaches for the modelling of photoinduced processes in composite systems. We discuss the developments that are still needed to elevate the QM-based multiscale strategy to a gold standard for the prediction of light-activated events in composite systems and the analysis of the outputs of novel advanced spectroscopies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: QM/classical strategy.
Fig. 2: Multiscale modelling of surface-enhanced spectroscopy.
Fig. 3: Multiscale modelling of the LH2 complex.
Fig. 4: Plasmonic effects on excitons of the LH2 complex.

Similar content being viewed by others

References

  1. Ziegler, T. & Möglich, A. Photoreceptor engineering. Front. Mol. Biosci. 2, 30 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Xu, L., Mou, F., Gong, H., Luo, M. & Guan, J. Light-driven micro/nanomotors: from fundamentals to applications. Chem. Soc. Rev. 46, 6905–6926 (2017).

    Article  CAS  PubMed  Google Scholar 

  3. van Leeuwen, T., Lubbe, A. S., Štacko, P., Wezenberg, S. J. & Feringa, B. L. Dynamic control of function by light-driven molecular motors. Nat. Rev. Chem. 1, 0096 (2017).

    Article  CAS  Google Scholar 

  4. Wang, J., Xiong, Z., Zheng, J., Zhan, X. & Tang, J. Light-driven micro/nanomotor for promising biomedical tools: principle, challenge, and prospect. Acc. Chem. Res. 51, 1957–1965 (2018).

    Article  CAS  PubMed  Google Scholar 

  5. Beljonne, D. & Cornil, J. Multiscale Modelling of Organic and Hybrid Photovoltaics Vol. 352 (Springer, 2014).

  6. Kilina, S., Kilin, D. & Tretiak, S. Light-driven and phonon-assisted dynamics in organic and semiconductor nanostructures. Chem. Rev. 115, 5929–5978 (2015).

    Article  CAS  PubMed  Google Scholar 

  7. Alberi, K. et al. The 2019 materials by design roadmap. J. Phys. D Appl. Phys. 52, 013001–013049 (2019).

    Article  CAS  Google Scholar 

  8. Warshel, A. & Levitt, M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103, 227–249 (1976).

    Article  CAS  PubMed  Google Scholar 

  9. Rivail, J. L. & Rinaldi, D. A quantum chemical approach to dielectric solvent effects in molecular liquids. Chem. Phys. 18, 233–242 (1976).

    Article  CAS  Google Scholar 

  10. Miertuš, S., Scrocco, E. & Tomasi, J. Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem. Phys. 55, 117–129 (1981).

    Article  Google Scholar 

  11. Gao, J. Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29, 298–305 (1996).

    Article  CAS  Google Scholar 

  12. Lin, H. & Truhlar, D. G. QM/MM: what have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 117, 185–199 (2006).

    Article  CAS  Google Scholar 

  13. Senn, H. M. & Thiel, W. QM/MM methods for biomolecular systems. Angew. Chem. Int. Ed. Engl. 48, 1198–1229 (2009).

    Article  CAS  PubMed  Google Scholar 

  14. Brunk, E. & Rothlisberger, U. Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states. Chem. Rev. 115, 6217–6263 (2015).

    Article  CAS  PubMed  Google Scholar 

  15. Morzan, U. N. et al. Spectroscopy in complex environments from QM–MM simulations. Chem. Rev. 118, 4071–4113 (2018).

    Article  CAS  PubMed  Google Scholar 

  16. Tomasi, J. & Persico, M. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem. Rev. 94, 2027–2094 (1994).

    Article  CAS  Google Scholar 

  17. Cramer, C. J. & Truhlar, D. G. Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem. Rev. 99, 2161–2200 (1999).

    Article  CAS  PubMed  Google Scholar 

  18. Tomasi, J., Mennucci, B. & Cammi, R. Quantum mechanical continuum solvation models. Chem. Rev. 105, 2999–3094 (2005).

    Article  CAS  PubMed  Google Scholar 

  19. Mennucci, B. Continuum solvation models: what else can we learn from them? J. Phys. Chem. Lett. 1, 1666–1674 (2010).

    Article  CAS  Google Scholar 

  20. Klamt, A. The COSMO and COSMO-RS solvation models. Wiley Interdiscip. Rev. Comput. Mol. Sci. 1, 699–709 (2011).

    Article  CAS  Google Scholar 

  21. Mennucci, B. Polarizable continuum model. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 386–404 (2012).

    Article  CAS  Google Scholar 

  22. Cammi, R., Mennucci, B. & Tomasi, J. On the calculation of local field factors for microscopic static hyperpolarizabilities of molecules in solution with the aid of quantum-mechanical methods. J. Phys. Chem. A 102, 870–875 (1998).

    Article  CAS  Google Scholar 

  23. Aroca, R. F. Plasmon enhanced spectroscopy. Phys. Chem. Chem. Phys. 15, 5355–5319 (2013).

    Article  CAS  PubMed  Google Scholar 

  24. Klingsporn, J. M., Sonntag, M. D., Seideman, T. & Van Duyne, R. P. Tip-enhanced raman spectroscopy with picosecond pulses. J. Phys. Chem. Lett. 5, 106–110 (2014).

    Article  CAS  PubMed  Google Scholar 

  25. Zrimsek, A. B. et al. Single-molecule chemistry with surface- and tip-enhanced raman spectroscopy. Chem. Rev. 117, 7583–7613 (2017).

    Article  CAS  PubMed  Google Scholar 

  26. Schlücker, S. Surface-enhanced raman spectroscopy: concepts and chemical applications. Angew. Chem. Int. Ed. 53, 4756–4795 (2014).

    Article  CAS  Google Scholar 

  27. Zhang, R. et al. Chemical mapping of a single molecule by plasmon-enhanced Raman scattering. Nature 498, 82–86 (2013).

    Article  CAS  PubMed  Google Scholar 

  28. Arroyo, J. O. & Kukura, P. Non-fluorescent schemes for single-molecule detection, imaging and spectroscopy. Nat. Photon. 10, 11–17 (2016).

    Article  CAS  Google Scholar 

  29. Lakowicz, J. R. et al. Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy. Analyst 133, 1308–1339 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Dong, J., Zhang, Z., Zheng, H. & Sun, M. Recent progress on plasmon-enhanced fluorescence. Nanophotonics 4, 1–19 (2015).

    Article  CAS  Google Scholar 

  31. Mayer, K. M. & Hafner, J. H. Localized surface plasmon resonance sensors. Chem. Rev. 111, 3828–3857 (2011).

    Article  CAS  PubMed  Google Scholar 

  32. Saha, K., Agasti, S. S., Kim, C., Li, X. & Rotello, V. M. Gold nanoparticles in chemical and biological sensing. Chem. Rev. 112, 2739–2779 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Linic, S., Aslam, U., Boerigter, C. & Morabito, M. Photochemical transformations on plasmonic metal nanoparticles. Nat. Mater. 14, 567–576 (2015).

    Article  CAS  PubMed  Google Scholar 

  34. Zhang, Y. et al. Surface-plasmon-driven hot electron photochemistry. Chem. Rev. 118, 2927–2954 (2018).

    Article  CAS  PubMed  Google Scholar 

  35. Zhan, C. et al. From plasmon-enhanced molecular spectroscopy to plasmon-mediated chemical reactions. Nat. Rev. Chem. 2, 216–230 (2018).

    Article  Google Scholar 

  36. Chikkaraddy, R. et al. Single-molecule strong coupling at room temperature in plasmonic nanocavities. Nature 535, 127–130 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Ruggenthaler, M., Tancogne-Dejean, N., Flick, J., Appel, H. & Rubio, A. From a quantum-electrodynamical light–matter description to novel spectroscopies. Nat. Rev. Chem. 2, 0118 (2018).

    Article  CAS  Google Scholar 

  38. Sukharev, M. & Nitzan, A. Optics of exciton-plasmon nanomaterials. J. Phys. Condens. Matter 29, 443003 (2018).

    Article  Google Scholar 

  39. Morton, S. M., Silverstein, D. W. & Jensen, L. Theoretical studies of plasmonics using electronic structure methods. Chem. Rev. 111, 3962–3994 (2011).

    Article  CAS  PubMed  Google Scholar 

  40. Corni, S. & Tomasi, J. Enhanced response properties of a chromophore physisorbed on a metal particle. J. Chem. Phys. 114, 3739–3713 (2001).

    Article  CAS  Google Scholar 

  41. Garcia de Abajo, F. J. & Howie, A. Retarded field calculation of electron energy loss in inhomogeneous dielectrics. Phys. Rev. B Condens. Matter 65, 4156–4117 (2002).

    Article  CAS  Google Scholar 

  42. Hohenester, U. & Trügler, A. MNPBEM – a Matlab toolbox for the simulation of plasmonic nanoparticles. Computer Phys. Commun. 183, 370–381 (2012).

    Article  CAS  Google Scholar 

  43. Delgado, A., Corni, S. & Goldoni, G. Modeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticle. J. Chem. Phys. 139, 024105–024112 (2013).

    Article  PubMed  CAS  Google Scholar 

  44. Neaton, J. B., Hybertsen, M. S. & Louie, S. G. Renormalization of molecular electronic levels at metal-molecule interfaces. Phys. Rev. Lett. 97, 98–94 (2006).

    Article  CAS  Google Scholar 

  45. Trautmann, S. et al. A classical description of subnanometer resolution by atomic features in metallic structures. Nanoscale 9, 391–401 (2017).

    Article  CAS  PubMed  Google Scholar 

  46. Piatkowski, L., Accanto, N. & van Hulst, N. F. Ultrafast meets ultrasmall: controlling nanoantennas and molecules. ACS Photon. 3, 1401–1414 (2016).

    Article  CAS  Google Scholar 

  47. Andrade, X. et al. Time-dependent density-functional theory in massively parallel computer architectures: the octopus project. J. Phys. Condens. Matter 24, 233202–233212 (2012).

    Article  PubMed  CAS  Google Scholar 

  48. Goings, J. J., Lestrange, P. J. & Li, X. Real-time time-dependent electronic structure theory. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1341–1319 (2017).

    Article  CAS  Google Scholar 

  49. Coccia, E., Troiani, F. & Corni, S. Probing quantum coherence in ultrafast molecular processes: an ab initioapproach to open quantum systems. J. Chem. Phys. 148, 204112 (2018).

    Article  PubMed  CAS  Google Scholar 

  50. Chen, H., McMahon, J. M., Ratner, M. A. & Schatz, G. C. Classical electrodynamics coupled to quantum mechanics for calculation of molecular optical properties: a RT-TDDFT/FDTD approach. J. Phys. Chem. C 114, 14384–14392 (2010).

    Article  CAS  Google Scholar 

  51. Gao, Y. & Neuhauser, D. Communication: dynamical embedding: correct quantum response from coupling TDDFT for a small cluster with classical near-field electrodynamics for an extended region. J. Chem. Phys. 138, 181105 (2013).

    Article  PubMed  CAS  Google Scholar 

  52. Sakko, A., Rossi, T. P., Enkovaara, J. & Nieminen, R. M. Atomistic approach for simulating plasmons in nanostructures. Appl. Phys. A 115, 427–431 (2013).

    Article  CAS  Google Scholar 

  53. Smith, H. T., Karam, T. E., Haber, L. H. & Lopata, K. Capturing plasmon–molecule dynamics in dye monolayers on metal nanoparticles using classical electrodynamics with quantum embedding. J. Phys. Chem. C 121, 16932–16942 (2017).

    Article  CAS  Google Scholar 

  54. Corni, S., Pipolo, S. & Cammi, R. Equation of motion for the solvent polarization apparent charges in the polarizable continuum model: application to real-time TDDFT. J. Phys. Chem. A 119, 5405–5416 (2015).

    Article  CAS  Google Scholar 

  55. Luque, F. J., Dehez, F., Chipot, C. & Orozco, M. Polarization effects in molecular interactions. Wiley Interdiscip. Rev. Comput. Mol. Sci. 1, 844–854 (2011).

    Article  CAS  Google Scholar 

  56. Rick, S. W., Stuart, S. J. & Berne, B. J. Dynamical fluctuating charge force fields: application to liquid water. J. Chem. Phys. 101, 6141–6156 (1994).

    Article  CAS  Google Scholar 

  57. Hillier, I. H. Chemical reactivity studied by hybrid QM/MM methods. J. Mol. Struct. 463, 45–52 (1999).

    Article  CAS  Google Scholar 

  58. Patel, S. & Brooks, C. L. III Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems. Mol. Simulat. 32, 231–249 (2006).

    Article  CAS  Google Scholar 

  59. Lipparini, F. & Barone, V. Polarizable force fields and polarizable continuum model: a fluctuating charges/PCM approach. 1. Theory and implementation. J. Chem. Theory Comput. 7, 3711–3724 (2011).

    Article  CAS  PubMed  Google Scholar 

  60. Lipparini, F., Cappelli, C. & Barone, V. Linear response theory and electronic transition energies for a fully polarizable QM/classical Hamiltonian. J. Chem. Theory Comput. 8, 4153–4165 (2012).

    Article  CAS  PubMed  Google Scholar 

  61. Lamoureux, G., MacKerell, A. D. & Roux, B. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 119, 5185–5113 (2003).

    Article  CAS  Google Scholar 

  62. Boulanger, E. & Thiel, W. Solvent boundary potentials for hybrid QM/MM computations using classical drude oscillators: a fully polarizable model. J. Chem. Theory Comput. 8, 4527–4538 (2012).

    Article  CAS  PubMed  Google Scholar 

  63. Lemkul, J. A., Huang, J., Roux, B. & MacKerell, A. D. Jr. An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications. Chem. Rev. 116, 4983–5013 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Thompson, M. A. & Schenter, G. K. Excited states of the bacteriochlorophyll b dimer of rhodopseudomonas viridis: a QM/MM study of the photosynthetic reaction center that includes MM polarization. J. Phys. Chem. 99, 6374–6386 (1995).

    Article  CAS  Google Scholar 

  65. van Duijnen, P. T. & de Vries, A. H. Direct reaction field force field: a consistent way to connect and combine quantum-chemical and classical descriptions of molecules. Int. J. Quantum Chem. 60, 1111–1132 (1996).

    Article  Google Scholar 

  66. Illingworth, C. J. R., Parkes, K. E. B., Snell, C. R., Ferenczy, G. G. & Reynolds, C. A. Toward a consistent treatment of polarization in model QM/MM calculations. J. Phys. Chem. A 112, 12151–12156 (2008).

    Article  CAS  PubMed  Google Scholar 

  67. Curutchet, C. et al. Electronic energy transfer in condensed phase studied by a polarizable QM/MM model. J. Chem. Theory Comput. 5, 1838–1848 (2009).

    Article  CAS  PubMed  Google Scholar 

  68. Olsen, J. M. H. & Kongsted, J. in Advances in Quantum Chemistry Vol. 61 107–143 (Elsevier, 2011).

  69. Jensen, L., van Duijnen, P. T. & Snijders, J. G. A discrete solvent reaction field model for calculating molecular linear response properties in solution. J. Chem. Phys. 119, 3800–3811 (2003).

    Article  CAS  Google Scholar 

  70. Loco, D. et al. A QM/MM approach using the AMOEBA polarizable embedding: from ground state energies to electronic excitations. J. Chem. Theory Comput. 12, 3654–3661 (2016).

    Article  CAS  PubMed  Google Scholar 

  71. van Duijnen, P. T., de Vries, A. H., Swart, M. & Grozema, F. Polarizabilities in the condensed phase and the local fields problem: a direct reaction field formulation. J. Chem. Phys. 117, 8442–8453 (2002).

    Article  CAS  Google Scholar 

  72. List, N. H., Jensen, H. J. X. R. A. & Kongsted, J. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding. Phys. Chem. Chem. Phys. 18, 10070–10080 (2016).

    Article  CAS  PubMed  Google Scholar 

  73. Chandrasekaran, S., Aghtar, M., Valleau, S., Aspuru-Guzik, A. & Kleinekathöfer, U. Influence of force fields and quantum chemistry approach on spectral densities of BChl ain solution and in FMO proteins. J. Phys. Chem. B 119, 9995–10004 (2015).

    Article  CAS  PubMed  Google Scholar 

  74. Andreussi, O., Prandi, I. G., Campetella, M., Prampolini, G. & Mennucci, B. Classical force fields tailored for QM applications: is it really a feasible strategy? J. Chem. Theory Comput. 13, 4636–4648 (2017).

    Article  CAS  PubMed  Google Scholar 

  75. Cacelli, I. & Prampolini, G. Parametrization and validation of intramolecular force fields derived from DFT calculations. J. Chem. Theory Comput. 3, 1803–1817 (2007).

    Article  CAS  PubMed  Google Scholar 

  76. Xu, P., Guidez, E. B., Bertoni, C. & Gordon, M. S. Perspective: Ab initio force field methods derived from quantum mechanics. J. Chem. Phys. 148, 090901 (2018).

    Article  CAS  Google Scholar 

  77. Gordon, M. S., Fedorov, D. G., Pruitt, S. R. & Slipchenko, L. V. Fragmentation methods: a route to accurate calculations on large systems. Chem. Rev. 112, 632–672 (2012).

    Article  CAS  PubMed  Google Scholar 

  78. Gao, J. et al. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Acc. Chem. Res. 47, 2837–2845 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Maurer, P., Laio, A., Hugosson, H. W., Colombo, M. C. & Rothlisberger, U. Automated parametrization of biomolecular force fields from quantum mechanics/molecular mechanics (QM/MM) simulations through force matching. J. Chem. Theory Comput. 3, 628–639 (2007).

    Article  CAS  PubMed  Google Scholar 

  80. Shen, L. & Yang, W. Molecular dynamics simulations with quantum mechanics/molecular mechanics and adaptive neural networks. J. Chem. Theory Comput. 14, 1442–1455 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Loco, D. et al. Hybrid QM/MM molecular dynamics with AMOEBA polarizable embedding. J. Chem. Theory Comput. 13, 4025–4033 (2017).

    Article  CAS  PubMed  Google Scholar 

  82. Morton, S. M. & Jensen, L. A discrete interaction model/quantum mechanical method to describe the interaction of metal nanoparticles and molecular absorption. J. Chem. Phys. 135, 134103–134112 (2011).

    Article  PubMed  CAS  Google Scholar 

  83. Chen, X., Moore, J. E., Zekarias, M. & Jensen, L. Atomistic electrodynamics simulations of bare and ligand-coated nanoparticles in the quantum size regime. Nat. Commun. 6, 8921 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Li, X. et al. Optical properties of gold nanoclusters functionalized with a small organic compound: modeling by an integrated quantum-classical approach. J. Chem. Theory Comput. 12, 3325–3339 (2016).

    Article  CAS  PubMed  Google Scholar 

  85. Walsh, T. R. & Knecht, M. R. Biointerface structural effects on the properties and applications of bioinspired peptide-based nanomaterials. Chem. Rev. 117, 12641–12704 (2017).

    Article  CAS  PubMed  Google Scholar 

  86. Curutchet, C. & Mennucci, B. Quantum chemical studies of light harvesting. Chem. Rev. 117, 294–343 (2017).

    Article  CAS  PubMed  Google Scholar 

  87. Mennucci, B. Modeling absorption and fluorescence solvatochromism with QM/Classical approaches. Int. J. Quantum Chem. 115, 1202–1208 (2015).

    Article  CAS  Google Scholar 

  88. Olsen, J. M. H. Excited states in large molecular systems through polarizable embedding. Phys. Chem. Chem. Phys. 18, 20234–20250 (2016).

    Article  PubMed  CAS  Google Scholar 

  89. Darby, B. L., Auguié, B., Meyer, M., Pantoja, A. E. & Le Ru, E. C. Modified optical absorption of molecules on metallic nanoparticles at sub-monolayer coverage. Nat. Photon. 10, 40–45 (2015).

    Article  CAS  Google Scholar 

  90. Pelton, M. Modified spontaneous emission in nanophotonic structures. Nat. Photon. 9, 427–435 (2015).

    Article  CAS  Google Scholar 

  91. Vukovic, S., Corni, S. & Mennucci, B. Fluorescence enhancement of chromophores close to metal nanoparticles. Optimal setup revealed by the polarizable continuum model. J. Phys. Chem. C 113, 121–133 (2009).

    Article  CAS  Google Scholar 

  92. Liu, P., Chulhai, D. V. & Jensen, L. Single-molecule imaging using atomistic near-field tip-enhanced raman spectroscopy. ACS Nano 11, 5094–5102 (2017).

    Article  CAS  PubMed  Google Scholar 

  93. Kowalik, L. & Chen, J. K. Illuminating developmental biology through photochemistry. Nat. Chem. Biol. 13, 587–598 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Kottke, T., Xie, A., Larsen, D. S. & Hoff, W. D. Photoreceptors take charge: emerging principles for light sensing. Annu. Rev. Biophys. 47, 291–313 (2018).

    Article  CAS  PubMed  Google Scholar 

  95. Mirkovic, T. et al. Light absorption and energy transfer in the antenna complexes of photosynthetic organisms. Chem. Rev. 117, 249–293 (2017).

    Article  CAS  PubMed  Google Scholar 

  96. Saikin, S. K., Eisfeld, A., Valleau, S. & Aspuru-Guzik, A. Photonics meets excitonics: natural and artificial molecular aggregates. Nanophotonics 2, 21–38 (2013).

    Article  CAS  Google Scholar 

  97. Jang, S. J. & Mennucci, B. Delocalized excitons in natural light-harvesting complexes. Rev. Mod. Phys. 90, 035003 (2018).

    Article  CAS  Google Scholar 

  98. Collini, E. Spectroscopic signatures of quantum-coherent energy transfer. Chem. Soc. Rev. 42, 4932–4916 (2013).

    Article  CAS  PubMed  Google Scholar 

  99. Chenu, A. & Scholes, G. D. Coherence in energy transfer and photosynthesis. Annu. Rev. Phys. Chem. 66, 69–96 (2015).

    Article  CAS  PubMed  Google Scholar 

  100. Scholes, G. D. et al. Using coherence to enhance function in chemical and biophysical systems. Nature 543, 647–656 (2017).

    Article  CAS  PubMed  Google Scholar 

  101. Jumper, C. C., Rafiq, S., Wang, S. & Scholes, G. D. From coherent to vibronic light harvesting in photosynthesis. Curr. Opin. Chem. Biol. 47, 39–46 (2018).

    Article  CAS  PubMed  Google Scholar 

  102. Li, X., Parrish, R. M., Liu, F., Kokkila Schumacher, S. I. L. & Martínez, T. J. An Ab initio exciton model including charge-transfer excited states. J. Chem. Theory Comput. 13, 3493–3504 (2017).

    Article  CAS  PubMed  Google Scholar 

  103. Nottoli, M. et al. The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria. Photosynth. Res. 15, 209–212 (2018).

    Google Scholar 

  104. Cupellini, L. et al. Coupling to charge transfer states is the key to modulate the optical bands for efficient light harvesting in purple bacteria. J. Phys. Chem. Lett. 9, 6892–6899 (2018).

    Article  CAS  PubMed  Google Scholar 

  105. Law, C. J. et al. The structure and function of bacterial light-harvesting complexes (review). Mol. Membr. Biol. 21, 183–191 (2009).

    Article  CAS  Google Scholar 

  106. Cleary, L., Chen, H., Chuang, C., Silbey, R. J. & Cao, J. Optimal fold symmetry of LH2 rings on a photosynthetic membrane. Proc. Natl Acad. Sci. USA 110, 8537–8542 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Kunz, R. et al. Exciton self trapping in photosynthetic pigment–protein complexes studied by single-molecule spectroscopy. J. Phys. Chem. B 116, 11017–11023 (2012).

    Article  CAS  PubMed  Google Scholar 

  108. Ferretti, M. et al. Dark states in the light-harvesting complex 2 revealed by two-dimensional electronic spectroscopy. Sci. Rep. 6, 20834 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Herek, J. L. et al. B800→B850 energy transfer mechanism in bacterial LH2 complexes investigated by B800 pigment exchange. Biophys. J. 78, 2590–2596 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Abramavicius, D., Valkunas, L. & van Grondelle, R. Exciton dynamics in ring-like photosynthetic light-harvesting complexes: a hopping model. Phys. Chem. Chem. Phys. 6, 3097–3099 (2004).

    Article  CAS  Google Scholar 

  111. Novoderezhkin, V. I., Rutkauskas, D. & van Grondelle, R. Dynamics of the emission spectrum of a single LH2 complex: interplay of slow and fast nuclear motions. Biophys. J. 90, 2890–2902 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Harel, E. & Engel, G. S. Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2). Proc. Natl Acad. Sci. USA 109, 706–711 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Smyth, C., Oblinsky, D. G. & Scholes, G. D. B800-B850 coherence correlates with energy transfer rates in the LH2 complex of photosynthetic purple bacteria. Phys. Chem. Chem. Phys. 17, 30805–30816 (2015).

    Article  CAS  PubMed  Google Scholar 

  114. van der Vegte, C. P., Prajapati, J. D., Kleinekathöfer, U., Knoester, J. & Jansen, T. L. C. Atomistic modeling of two-dimensional electronic spectra and excited-state dynamics for a light harvesting 2 complex. J. Phys. Chem. B 119, 1302–1313 (2015).

    Article  PubMed  CAS  Google Scholar 

  115. Cupellini, L. et al. An ab initio description of the excitonic properties of LH2 and their temperature dependence. J. Phys. Chem. B 120, 11348–11359 (2016).

    Article  CAS  PubMed  Google Scholar 

  116. Segatta, F. et al. A quantum chemical interpretation of two-dimensional electronic spectroscopy of light-harvesting complexes. J. Am. Chem. Soc. 139, 7558–7567 (2017).

    Article  CAS  PubMed  Google Scholar 

  117. Ma, Y.-Z., Cogdell, R. J. & Gillbro, T. Energy transfer and exciton annihilation in the B800−850 antenna complex of the photosynthetic purple bacterium Rhodopseudomonas acidophila (Strain 10050). A femtosecond transient absorption study. J. Phys. Chem. B 101, 1087–1095 (1997).

    Article  CAS  Google Scholar 

  118. Andreussi, O., Biancardi, A., Corni, S. & Mennucci, B. Plasmon-controlled light-harvesting: design rules for biohybrid devices via multiscale modeling. Nano Lett. 13, 4475–4484 (2013).

    Article  CAS  PubMed  Google Scholar 

  119. Caprasecca, S., Guido, C. A. & Mennucci, B. Control of coherences and optical responses of pigment-protein complexes by plasmonic nanoantennae. J. Phys. Chem. Lett. 7, 2189–2196 (2016).

    Article  CAS  PubMed  Google Scholar 

  120. Mackowski, S. et al. Metal-enhanced fluorescence of chlorophylls in single light-harvesting complexes. Nano Lett. 8, 558–564 (2008).

    Article  CAS  PubMed  Google Scholar 

  121. Caprasecca, S., Corni, S. & Mennucci, B. Shaping excitons in light-harvesting proteins through nanoplasmonics. Chem. Sci. 9, 6219–6227 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Wientjes, E., Renger, J., Curto, A. G., Cogdell, R. & van Hulst, N. F. Strong antenna-enhanced fluorescence of a single light-harvesting complex shows photon antibunching. Nat. Commun. 5, 4236 (2014).

    Article  CAS  PubMed  Google Scholar 

  123. Wientjes, E., Renger, J., Curto, A. G., Cogdell, R. & van Hulst, N. F. Nanoantenna enhanced emission of light-harvesting complex 2: the role of resonance, polarization, and radiative and non-radiative rates. Phys. Chem. Chem. Phys. 16, 24739–24746 (2014).

    Article  CAS  PubMed  Google Scholar 

  124. Warshel, A. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 53, 10020–10031 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Dans, P. D., Walther, J., Gómez, H. & Orozco, M. Multiscale simulation of DNA. Curr. Opin. Struct. Biol. 37, 29–45 (2016).

    Article  CAS  PubMed  Google Scholar 

  126. Chiricotto, M., Sterpone, F., Derreumaux, P. & Melchionna, S. Multiscale simulation of molecular processes in cellular environments. Philos. Trans. A Math. Phys. Eng. Sci. 374, 20160225 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  127. Amaro, R. E. & Mulholland, A. J. Multiscale methods in drug design bridge chemical and biological complexity in the search for cures. Nat. Rev. Chem. 2, 0148 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Curchod, B. F. E. & Martínez, T. J. Ab initio nonadiabatic quantum molecular dynamics. Chem. Rev. 118, 3305–3336 (2018).

    Article  CAS  PubMed  Google Scholar 

  129. Tully, J. C. Perspective: nonadiabatic dynamics theory. J. Chem. Phys. 137, 22A301 (2012).

    Article  CAS  PubMed  Google Scholar 

  130. Wu, X., Clavaguéra, C., Lagardère, L., Piquemal, J.-P. & de la Lande, A. AMOEBA polarizable force field parameters of the heme cofactor in its ferrous and ferric forms. J. Chem. Theory Comput. 14, 2705–2720 (2018).

    Article  CAS  PubMed  Google Scholar 

  131. Akimov, A. V. & Prezhdo, O. V. Large-scale computations in chemistry: a bird’s eye view of a vibrant field. Chem. Rev. 115, 5797–5890 (2015).

    Article  CAS  PubMed  Google Scholar 

  132. Cole, D. J. & Hine, N. D. M. Applications of large-scale density functional theory in biology. J. Phys. Condens. Matter 28, 393001 (2016).

    Article  PubMed  CAS  Google Scholar 

  133. Giese, T. J. & York, D. M. Quantum mechanical force fields for condensed phase molecular simulations. J. Phys. Condens. Matter 29, 383002 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  134. Thiel, W. Semiempirical quantum-chemical methods. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 145–157 (2013).

    Article  CAS  Google Scholar 

  135. Elstner, M. & Seifert, G. Density functional tight binding. Philos. Trans. A Math. Phys. Eng. Sci. 372, 20120483 (2014).

    Article  PubMed  CAS  Google Scholar 

  136. Lipparini, F. et al. Quantum calculations in solution for large to very large molecules: a new linear scaling QM/continuum approach. J. Phys. Chem. Lett. 5, 953–958 (2014).

    Article  CAS  PubMed  Google Scholar 

  137. Lagardère, L. et al. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem. Sci. 9, 956–972 (2018).

    Article  PubMed  Google Scholar 

  138. Marrink, S. J. & Tieleman, D. P. Perspective on the Martini model. Chem. Soc. Rev. 42, 6801–6822 (2013).

    Article  CAS  PubMed  Google Scholar 

  139. Kmiecik, S. et al. Coarse-grained protein models and their applications. Chem. Rev. 116, 7898–7936 (2016).

    Article  CAS  PubMed  Google Scholar 

  140. Sokkar, P., Boulanger, E., Thiel, W. & Sanchez-Garcia, E. Hybrid quantum mechanics/molecular mechanics/coarse grained modeling: a triple-resolution approach for biomolecular systems. J. Chem. Theory Comput. 11, 1809–1818 (2015).

    Article  CAS  PubMed  Google Scholar 

  141. Ricci, C. G., Li, B., Cheng, L.-T., Dzubiella, J. & McCammon, J. A. ‘Martinizing’ the variational implicit solvent method (VISM): solvation free energy for coarse-grained proteins. J. Phys. Chem. B 121, 6538–6548 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Duster, A. W., Wang, C.-H., Garza, C. M., Miller, D. E. & Lin, H. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? Wiley Interdiscip. Rev. Comput. Mol. Sci. 103, e1310–e1321 (2017).

    Article  CAS  Google Scholar 

  143. Sugawara, Y., Kelf, T. A., Baumberg, J. J., Abdelsalam, M. E. & Bartlett, P. N. Strong coupling between localized plasmons and organic excitons in metal nanovoids. Phys. Rev. Lett. 97, 266808 (2006).

    Article  CAS  PubMed  Google Scholar 

  144. Fofang, N. T. et al. Plexcitonic nanoparticles: plasmon−exciton coupling in nanoshell−J-aggregate complexes. Nano Lett. 8, 3481–3487 (2008).

    Article  CAS  PubMed  Google Scholar 

  145. Beane, G., Brown, B. S., Johns, P., Devkota, T. & Hartland, G. V. Strong exciton–plasmon coupling in silver nanowire nanocavities. J. Phys. Chem. Lett. 9, 1676–1681 (2018).

    Article  CAS  PubMed  Google Scholar 

  146. Jacob, Z. & Shalaev, V. M. Plasmonics goes quantum. Science 334, 463–464 (2011).

    Article  CAS  PubMed  Google Scholar 

  147. Tame, M. S. et al. Quantum plasmonics. Nat. Phys. 9, 329–340 (2013).

    Article  CAS  Google Scholar 

  148. Libisch, F., Huang, C. & Carter, E. A. Embedded correlated wavefunction schemes: theory and applications. Acc. Chem. Res. 47, 2768–2775 (2014).

    Article  CAS  PubMed  Google Scholar 

  149. Wesolowski, T. A., Shedge, S. & Zhou, X. Frozen-density embedding strategy for multilevel simulations of electronic structure. Chem. Rev. 115, 5891–5928 (2015).

    Article  CAS  PubMed  Google Scholar 

  150. Sun, Q. & Chan, G. K.-L. Quantum embedding theories. Acc. Chem. Res. 49, 2705–2712 (2016).

    Article  CAS  PubMed  Google Scholar 

  151. Jacob, C. R. & Neugebauer, J. Subsystem density-functional theory. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 325–362 (2014).

    Article  CAS  Google Scholar 

  152. König, C. & Neugebauer, J. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. ChemPhysChem 13, 386–425 (2011).

    Article  PubMed  CAS  Google Scholar 

  153. Spata, V. A. & Carter, E. A. Mechanistic insights into photocatalyzed hydrogen desorption from palladium surfaces assisted by localized surface plasmon resonances. ACS Nano 12, 3512–3522 (2018).

    Article  CAS  PubMed  Google Scholar 

  154. Andreussi, O., Corni, S., Mennucci, B. & Tomasi, J. Radiative and nonradiative decay rates of a molecule close to a metal particle of complex shape. J. Chem. Phys. 121, 10190–10113 (2004).

    Article  CAS  PubMed  Google Scholar 

  155. Rodríguez-Fernández, J., Pastoriza-Santos, I. & Funston, A. M. Modelling the optical response of gold nanoparticles. Chem. Soc. Rev. 37, 1792–1805 (2008).

    Article  PubMed  CAS  Google Scholar 

  156. Van Duijnen, P. T. & Swart, M. Molecular and atomic polarizabilities: Thole’s model revisited. J. Phys. Chem. A 102, 2399–2407 (1998).

    Article  Google Scholar 

  157. Thole, B. T. Molecular polarizabilities calculated with a modified dipole interaction. Chem. Phys. 59, 341–350 (1981).

    Article  CAS  Google Scholar 

  158. Yu, R., Liz-Marzán, L. M. & Garcia de Abajo, F. J. Universal analytical modeling of plasmonic nanoparticles. Chem. Soc. Rev. 46, 6710–6724 (2017).

    Article  CAS  PubMed  Google Scholar 

  159. Kreibig, U. & von Fragstein, C. The limitation of electron mean free path in small silver particles. Z. Physik. 224, 307–323 (1969).

    Article  CAS  Google Scholar 

  160. Ciracì, C. et al. Probing the ultimate limits of plasmonic enhancement. Science 337, 1072–1074 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  161. Raza, S., Wubs, M., Søndergaard, T., Bozhevolnyi, S. I. & Mortensen, N. A. A generalized non-local optical response theory for plasmonic nanostructures. Nat. Commun. 5, 3809 (2014).

    Article  PubMed  CAS  Google Scholar 

  162. Ciracì, C. & Della Sala, F. Quantum hydrodynamic theory for plasmonics: impact of the electron density tail. Phys. Rev. B 93, 205405 (2016).

    Article  CAS  Google Scholar 

  163. Jensen, L. L. & Jensen, L. Atomistic electrodynamics model for optical properties of silver nanoclusters. J. Phys. Chem. C 113, 15182–15190 (2009).

    Article  CAS  Google Scholar 

  164. Dexter, D. L. A theory of sensitized luminescence in solids. J. Chem. Phys. 21, 836 (1953).

    Article  CAS  Google Scholar 

  165. Förster, T. 10th Spiers Memorial Lecture. Transfer mechanisms of electronic excitation. Discuss. Faraday Soc. 27, 7–17 (1959).

    Article  Google Scholar 

  166. Iozzi, M. F., Mennucci, B., Tomasi, J. & Cammi, R. Excitation energy transfer (EET) between molecules in condensed matter: a novel application of the polarizable continuum model (PCM). J. Chem. Phys. 120, 7029–7040 (2004).

    Article  CAS  PubMed  Google Scholar 

  167. Hsu, C. P., You, Z. Q. & Chen, H. C. Characterization of the short-range couplings in excitation energy transfer. J. Phys. Chem. C 112, 1204–1212 (2008).

    Article  CAS  Google Scholar 

  168. Difley, S. & Van Voorhis, T. Exciton/charge-transfer electronic couplings in organic semiconductors. J. Chem. Theory Comput. 7, 594–601 (2011).

    Article  CAS  PubMed  Google Scholar 

  169. Giovannini, T., Rosa, M., Corni, S. & Cappelli, C. A classical picture of subnanometer junctions: an atomistic Drude approach to nanoplasmonics. Nanoscale 11, 6004-6015 (2019)

Download references

Acknowledgements

B.M. acknowledges funding from the European Research Council under the grant ERC-AdG-786714 (LIFETimeS). S.C. acknowledges funding from the European Research Council under the grant ERC-CoG-681285 (TAME-Plasmons). The authors thank S. Caprasecca for the sketch in Fig. 4a and L. Cupellini for the sketch of LH2 in the graphical abstract.

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Pisa, Pisa, Italy

    Benedetta Mennucci

  2. Department of Chemical Sciences, University of Padova, Padova, Italy

    Stefano Corni

  3. CNR Institute of Nanoscience, Modena, Italy

    Stefano Corni

Authors
  1. Benedetta Mennucci
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stefano Corni
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed equally to the preparation of this manuscript.

Corresponding authors

Correspondence to Benedetta Mennucci or Stefano Corni.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mennucci, B., Corni, S. Multiscale modelling of photoinduced processes in composite systems. Nat Rev Chem 3, 315–330 (2019). https://doi.org/10.1038/s41570-019-0092-4

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41570-019-0092-4

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing