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.
Your institute does not have access to this article
Subscribe to Nature+
Get immediate online access to the entire Nature family of 50+ journals
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Ziegler, T. & Möglich, A. Photoreceptor engineering. Front. Mol. Biosci. 2, 30 (2015).
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).
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).
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).
Beljonne, D. & Cornil, J. Multiscale Modelling of Organic and Hybrid Photovoltaics Vol. 352 (Springer, 2014).
Kilina, S., Kilin, D. & Tretiak, S. Light-driven and phonon-assisted dynamics in organic and semiconductor nanostructures. Chem. Rev. 115, 5929–5978 (2015).
Alberi, K. et al. The 2019 materials by design roadmap. J. Phys. D Appl. Phys. 52, 013001–013049 (2019).
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).
Rivail, J. L. & Rinaldi, D. A quantum chemical approach to dielectric solvent effects in molecular liquids. Chem. Phys. 18, 233–242 (1976).
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).
Gao, J. Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29, 298–305 (1996).
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).
Senn, H. M. & Thiel, W. QM/MM methods for biomolecular systems. Angew. Chem. Int. Ed. Engl. 48, 1198–1229 (2009).
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).
Morzan, U. N. et al. Spectroscopy in complex environments from QM–MM simulations. Chem. Rev. 118, 4071–4113 (2018).
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).
Cramer, C. J. & Truhlar, D. G. Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem. Rev. 99, 2161–2200 (1999).
Tomasi, J., Mennucci, B. & Cammi, R. Quantum mechanical continuum solvation models. Chem. Rev. 105, 2999–3094 (2005).
Mennucci, B. Continuum solvation models: what else can we learn from them? J. Phys. Chem. Lett. 1, 1666–1674 (2010).
Klamt, A. The COSMO and COSMO-RS solvation models. Wiley Interdiscip. Rev. Comput. Mol. Sci. 1, 699–709 (2011).
Mennucci, B. Polarizable continuum model. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 386–404 (2012).
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).
Aroca, R. F. Plasmon enhanced spectroscopy. Phys. Chem. Chem. Phys. 15, 5355–5319 (2013).
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).
Zrimsek, A. B. et al. Single-molecule chemistry with surface- and tip-enhanced raman spectroscopy. Chem. Rev. 117, 7583–7613 (2017).
Schlücker, S. Surface-enhanced raman spectroscopy: concepts and chemical applications. Angew. Chem. Int. Ed. 53, 4756–4795 (2014).
Zhang, R. et al. Chemical mapping of a single molecule by plasmon-enhanced Raman scattering. Nature 498, 82–86 (2013).
Arroyo, J. O. & Kukura, P. Non-fluorescent schemes for single-molecule detection, imaging and spectroscopy. Nat. Photon. 10, 11–17 (2016).
Lakowicz, J. R. et al. Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy. Analyst 133, 1308–1339 (2008).
Dong, J., Zhang, Z., Zheng, H. & Sun, M. Recent progress on plasmon-enhanced fluorescence. Nanophotonics 4, 1–19 (2015).
Mayer, K. M. & Hafner, J. H. Localized surface plasmon resonance sensors. Chem. Rev. 111, 3828–3857 (2011).
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).
Linic, S., Aslam, U., Boerigter, C. & Morabito, M. Photochemical transformations on plasmonic metal nanoparticles. Nat. Mater. 14, 567–576 (2015).
Zhang, Y. et al. Surface-plasmon-driven hot electron photochemistry. Chem. Rev. 118, 2927–2954 (2018).
Zhan, C. et al. From plasmon-enhanced molecular spectroscopy to plasmon-mediated chemical reactions. Nat. Rev. Chem. 2, 216–230 (2018).
Chikkaraddy, R. et al. Single-molecule strong coupling at room temperature in plasmonic nanocavities. Nature 535, 127–130 (2016).
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).
Sukharev, M. & Nitzan, A. Optics of exciton-plasmon nanomaterials. J. Phys. Condens. Matter 29, 443003 (2018).
Morton, S. M., Silverstein, D. W. & Jensen, L. Theoretical studies of plasmonics using electronic structure methods. Chem. Rev. 111, 3962–3994 (2011).
Corni, S. & Tomasi, J. Enhanced response properties of a chromophore physisorbed on a metal particle. J. Chem. Phys. 114, 3739–3713 (2001).
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).
Hohenester, U. & Trügler, A. MNPBEM – a Matlab toolbox for the simulation of plasmonic nanoparticles. Computer Phys. Commun. 183, 370–381 (2012).
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).
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).
Trautmann, S. et al. A classical description of subnanometer resolution by atomic features in metallic structures. Nanoscale 9, 391–401 (2017).
Piatkowski, L., Accanto, N. & van Hulst, N. F. Ultrafast meets ultrasmall: controlling nanoantennas and molecules. ACS Photon. 3, 1401–1414 (2016).
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).
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).
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).
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).
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).
Sakko, A., Rossi, T. P., Enkovaara, J. & Nieminen, R. M. Atomistic approach for simulating plasmons in nanostructures. Appl. Phys. A 115, 427–431 (2013).
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).
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).
Luque, F. J., Dehez, F., Chipot, C. & Orozco, M. Polarization effects in molecular interactions. Wiley Interdiscip. Rev. Comput. Mol. Sci. 1, 844–854 (2011).
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).
Hillier, I. H. Chemical reactivity studied by hybrid QM/MM methods. J. Mol. Struct. 463, 45–52 (1999).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Olsen, J. M. H. & Kongsted, J. in Advances in Quantum Chemistry Vol. 61 107–143 (Elsevier, 2011).
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).
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).
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).
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).
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).
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).
Cacelli, I. & Prampolini, G. Parametrization and validation of intramolecular force fields derived from DFT calculations. J. Chem. Theory Comput. 3, 1803–1817 (2007).
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).
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).
Gao, J. et al. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Acc. Chem. Res. 47, 2837–2845 (2014).
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).
Shen, L. & Yang, W. Molecular dynamics simulations with quantum mechanics/molecular mechanics and adaptive neural networks. J. Chem. Theory Comput. 14, 1442–1455 (2018).
Loco, D. et al. Hybrid QM/MM molecular dynamics with AMOEBA polarizable embedding. J. Chem. Theory Comput. 13, 4025–4033 (2017).
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).
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).
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).
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).
Curutchet, C. & Mennucci, B. Quantum chemical studies of light harvesting. Chem. Rev. 117, 294–343 (2017).
Mennucci, B. Modeling absorption and fluorescence solvatochromism with QM/Classical approaches. Int. J. Quantum Chem. 115, 1202–1208 (2015).
Olsen, J. M. H. Excited states in large molecular systems through polarizable embedding. Phys. Chem. Chem. Phys. 18, 20234–20250 (2016).
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).
Pelton, M. Modified spontaneous emission in nanophotonic structures. Nat. Photon. 9, 427–435 (2015).
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).
Liu, P., Chulhai, D. V. & Jensen, L. Single-molecule imaging using atomistic near-field tip-enhanced raman spectroscopy. ACS Nano 11, 5094–5102 (2017).
Kowalik, L. & Chen, J. K. Illuminating developmental biology through photochemistry. Nat. Chem. Biol. 13, 587–598 (2017).
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).
Mirkovic, T. et al. Light absorption and energy transfer in the antenna complexes of photosynthetic organisms. Chem. Rev. 117, 249–293 (2017).
Saikin, S. K., Eisfeld, A., Valleau, S. & Aspuru-Guzik, A. Photonics meets excitonics: natural and artificial molecular aggregates. Nanophotonics 2, 21–38 (2013).
Jang, S. J. & Mennucci, B. Delocalized excitons in natural light-harvesting complexes. Rev. Mod. Phys. 90, 035003 (2018).
Collini, E. Spectroscopic signatures of quantum-coherent energy transfer. Chem. Soc. Rev. 42, 4932–4916 (2013).
Chenu, A. & Scholes, G. D. Coherence in energy transfer and photosynthesis. Annu. Rev. Phys. Chem. 66, 69–96 (2015).
Scholes, G. D. et al. Using coherence to enhance function in chemical and biophysical systems. Nature 543, 647–656 (2017).
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).
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).
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).
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).
Law, C. J. et al. The structure and function of bacterial light-harvesting complexes (review). Mol. Membr. Biol. 21, 183–191 (2009).
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).
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).
Ferretti, M. et al. Dark states in the light-harvesting complex 2 revealed by two-dimensional electronic spectroscopy. Sci. Rep. 6, 20834 (2016).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Mackowski, S. et al. Metal-enhanced fluorescence of chlorophylls in single light-harvesting complexes. Nano Lett. 8, 558–564 (2008).
Caprasecca, S., Corni, S. & Mennucci, B. Shaping excitons in light-harvesting proteins through nanoplasmonics. Chem. Sci. 9, 6219–6227 (2018).
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).
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).
Warshel, A. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 53, 10020–10031 (2014).
Dans, P. D., Walther, J., Gómez, H. & Orozco, M. Multiscale simulation of DNA. Curr. Opin. Struct. Biol. 37, 29–45 (2016).
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).
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).
Curchod, B. F. E. & Martínez, T. J. Ab initio nonadiabatic quantum molecular dynamics. Chem. Rev. 118, 3305–3336 (2018).
Tully, J. C. Perspective: nonadiabatic dynamics theory. J. Chem. Phys. 137, 22A301 (2012).
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).
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).
Cole, D. J. & Hine, N. D. M. Applications of large-scale density functional theory in biology. J. Phys. Condens. Matter 28, 393001 (2016).
Giese, T. J. & York, D. M. Quantum mechanical force fields for condensed phase molecular simulations. J. Phys. Condens. Matter 29, 383002 (2017).
Thiel, W. Semiempirical quantum-chemical methods. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 145–157 (2013).
Elstner, M. & Seifert, G. Density functional tight binding. Philos. Trans. A Math. Phys. Eng. Sci. 372, 20120483 (2014).
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).
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).
Marrink, S. J. & Tieleman, D. P. Perspective on the Martini model. Chem. Soc. Rev. 42, 6801–6822 (2013).
Kmiecik, S. et al. Coarse-grained protein models and their applications. Chem. Rev. 116, 7898–7936 (2016).
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).
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).
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).
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).
Fofang, N. T. et al. Plexcitonic nanoparticles: plasmon−exciton coupling in nanoshell−J-aggregate complexes. Nano Lett. 8, 3481–3487 (2008).
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).
Jacob, Z. & Shalaev, V. M. Plasmonics goes quantum. Science 334, 463–464 (2011).
Tame, M. S. et al. Quantum plasmonics. Nat. Phys. 9, 329–340 (2013).
Libisch, F., Huang, C. & Carter, E. A. Embedded correlated wavefunction schemes: theory and applications. Acc. Chem. Res. 47, 2768–2775 (2014).
Wesolowski, T. A., Shedge, S. & Zhou, X. Frozen-density embedding strategy for multilevel simulations of electronic structure. Chem. Rev. 115, 5891–5928 (2015).
Sun, Q. & Chan, G. K.-L. Quantum embedding theories. Acc. Chem. Res. 49, 2705–2712 (2016).
Jacob, C. R. & Neugebauer, J. Subsystem density-functional theory. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 325–362 (2014).
König, C. & Neugebauer, J. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. ChemPhysChem 13, 386–425 (2011).
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).
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).
Rodríguez-Fernández, J., Pastoriza-Santos, I. & Funston, A. M. Modelling the optical response of gold nanoparticles. Chem. Soc. Rev. 37, 1792–1805 (2008).
Van Duijnen, P. T. & Swart, M. Molecular and atomic polarizabilities: Thole’s model revisited. J. Phys. Chem. A 102, 2399–2407 (1998).
Thole, B. T. Molecular polarizabilities calculated with a modified dipole interaction. Chem. Phys. 59, 341–350 (1981).
Yu, R., Liz-Marzán, L. M. & Garcia de Abajo, F. J. Universal analytical modeling of plasmonic nanoparticles. Chem. Soc. Rev. 46, 6710–6724 (2017).
Kreibig, U. & von Fragstein, C. The limitation of electron mean free path in small silver particles. Z. Physik. 224, 307–323 (1969).
Ciracì, C. et al. Probing the ultimate limits of plasmonic enhancement. Science 337, 1072–1074 (2012).
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).
Ciracì, C. & Della Sala, F. Quantum hydrodynamic theory for plasmonics: impact of the electron density tail. Phys. Rev. B 93, 205405 (2016).
Jensen, L. L. & Jensen, L. Atomistic electrodynamics model for optical properties of silver nanoclusters. J. Phys. Chem. C 113, 15182–15190 (2009).
Dexter, D. L. A theory of sensitized luminescence in solids. J. Chem. Phys. 21, 836 (1953).
Förster, T. 10th Spiers Memorial Lecture. Transfer mechanisms of electronic excitation. Discuss. Faraday Soc. 27, 7–17 (1959).
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).
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).
Difley, S. & Van Voorhis, T. Exciton/charge-transfer electronic couplings in organic semiconductors. J. Chem. Theory Comput. 7, 594–601 (2011).
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)
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.
The authors declare no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
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
Nature Machine Intelligence (2021)
Archives of Computational Methods in Engineering (2021)