1932

Abstract

Most processes triggered by ultraviolet (UV) or visible (vis) light in nature take place in complex biological environments. The first step in these photophysical events is the excitation of the absorbing system or chromophore to an electronically excited state. Such an excitation can be monitored by the UV-vis absorption spectrum. A precise calculation of the UV-vis spectrum of a chromophore embedded in an environment is a challenging task that requires the consideration of several ingredients, besides an accurate electronic-structure method for the excited states. Two of the most important are an appropriate description of the interactions between the chromophore and the environment and accounting for the vibrational motion of the whole system. In this contribution, we review the most common theoretical methodologies to describe the environment (including quantum mechanics/continuum and quantum mechanics/molecular mechanics models) and to account for vibrational sampling (including Wigner sampling and molecular dynamics). Further, we illustrate in a series of examples how the lack of these ingredients can lead to a wrong interpretation of the electronic features behind the UV-vis absorption spectrum.

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2018-04-20
2024-04-26
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Literature Cited

  1. Nelson N, Ben-Shem A. 1.  2004. The complex architecture of oxygenic photosynthesis. Nat. Rev. Mol. Cell Biol. 5:971–82 [Google Scholar]
  2. Palczewski K. 2.  2012. Chemistry and biology of vision. J. Biol. Chem. 287:1612–19 [Google Scholar]
  3. Bikle DD. 3.  2014. Vitamin D metabolism, mechanism of action, and clinical applications. Chem. Biol. 21:319–29 [Google Scholar]
  4. Legates TA, Fernandez DC, Hattar S. 4.  2014. Light as a central modulator of circadian rhythms, sleep and affect. Nat. Rev. Neurosci. 15:443–54 [Google Scholar]
  5. Holick MF. 5.  2016. Biological effects of sunlight, ultraviolet radiation, visible light, infrared radiation and vitamin D for health. Anticancer Res 36:1345–56 [Google Scholar]
  6. Besaratinia A, Synold TW, Chen HH, Chang C, Xi B. 6.  et al. 2005. DNA lesions induced by UV A1 and B radiation in human cells: comparative analyses in the overall genome and in the p53 tumor suppressor gene. PNAS 102:10058–63 [Google Scholar]
  7. Marquetand P, Nogueira JJ, Mai S, Plasser F, González L. 7.  2017. Challenges in simulating light-induced processes in DNA. Molecules 22:49 [Google Scholar]
  8. Curutchet C, Mennucci B. 8.  2017. Quantum chemical studies of light harvesting. Chem. Rev. 117:294–343 [Google Scholar]
  9. Schapiro I, Ruhman S. 9.  2014. Ultrafast photochemistry of Anabaena Sensory Rhodopsin: experiment and theory. Biochim. Biophys. Acta 1837:589–97 [Google Scholar]
  10. Zobel JP, Nogueira JJ, González L. 10.  2017. The IPEA dilemma in CASPT2. Chem. Sci. 8:1482–99 [Google Scholar]
  11. Laurent AD, Jacquemin D. 11.  2013. TD-DFT benchmarks: a review. Int. J. Quantum Chem. 113:2019–39 [Google Scholar]
  12. Wiebeler C, Borin V, Sanchez de Araújo AV, Schapiro I, Borin AC. 12.  2017. Excitation energies of canonical nucleobases computed by multiconfigurational perturbation theories. Photochem. Photobiol. 93:888–902 [Google Scholar]
  13. González L, Escudero D, Serrano-Andrés L. 13.  2012. Progress and challenges in the calculation of electronic excited states. ChemPhysChem 13:28–51 [Google Scholar]
  14. König C, Neugebauer J. 14.  2012. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. ChemPhysChem 13:386–425 [Google Scholar]
  15. Tomasi J, Mennucci B, Cammi R. 15.  2005. Quantum mechanical continuum solvation models. Chem. Rev. 105:2999–3093 [Google Scholar]
  16. Tomasi J, Persico M. 16.  1994. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem. Rev. 94:2027–94 [Google Scholar]
  17. Cramer CJ, Truhlar DG. 17.  1999. Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem. Rev. 99:2161–200 [Google Scholar]
  18. Orozco M, Luque FJ. 18.  2000. Theoretical methods for the description of the solvent effect in biomolecular systems. Chem. Rev. 100:4187–225 [Google Scholar]
  19. Mennucci B. 19.  2012. Polarizable continuum model. WIREs Comput. Mol. Sci. 2:386–404 [Google Scholar]
  20. Klamt A. 20.  2011. The COSMO and COSMO-RS solvation models. WIREs Comput. Mol. Sci. 1:699–709 [Google Scholar]
  21. Thompson JD, Cramer CJ, Truhlar DG. 21.  2004. New universal solvation model and comparison of the accuracy of the SM5.42R, SM5.43R, C-PCM, D-PCM, and IEF-PCM continuum solvation models for aqueous and organic solvation free energies and for vapor pressures. J. Phys. Chem. A 108:6532–42 [Google Scholar]
  22. Wong MW, Frisch MJ, Wiberg KB. 22.  1991. Solvent effects. 1. The mediation of electrostatic effects by solvents. J. Am. Chem. Soc. 113:4776–82 [Google Scholar]
  23. Wong MW, Wiberg KB, Frisch MJ. 23.  1992. Solvent effects. 2. Medium effect on the structure, energy, charge density, and vibrational frequencies of sulfamic acid. J. Am. Chem. Soc. 114:523–29 [Google Scholar]
  24. Senn HM, Thiel W. 24.  2009. QM/MM methods for biomolecular systems. Angew. Chem. Int. Ed. 48:1198–229 [Google Scholar]
  25. Brunk E, Rothlisberger U. 25.  2015. Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states. Chem. Rev. 115:6217–63 [Google Scholar]
  26. Friesner RA, Guallar V. 26.  2005. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annu. Rev. Phys. Chem. 56:389–427 [Google Scholar]
  27. Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. 27.  2012. Fragmentation methods: a route to accurate calculations on large systems. Chem. Rev. 112:632–72 [Google Scholar]
  28. Wesolowski TA, Shedge S, Zhou X. 28.  2015. Frozen-density embedding strategy for multilevel simulations of electronic structure. Chem. Rev. 115:5891–928 [Google Scholar]
  29. Barbatti M, Sen K. 29.  2016. Effects of different initial condition samplings on photodynamics and spectrum of pyrrole. Int. J. Quant. Chem. 116:762–71 [Google Scholar]
  30. Adcock SA, McCammon JA. 30.  2006. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106:1589–615 [Google Scholar]
  31. Wigner E. 31.  1932. On the quantum correction for thermodynamic equilibrium. Phys. Rev. 40:749–59 [Google Scholar]
  32. Ruckenbauer M, Barbatti M, Sellner B, Muller T, Lischka H. 32.  2010. Azomethane: nonadiabatic photodynamical simulations in solution. J. Phys. Chem. A 114:12585–90 [Google Scholar]
  33. Ruckenbauer M, Barbatti M, Müller T, Lischka H. 33.  2013. Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment. J. Phys. Chem. A 117:2790–99 [Google Scholar]
  34. Mennucci B. 34.  2013. Modeling environment effects on spectroscopies through QM/classical models. Phys. Chem. Chem. Phys. 15:6583–94 [Google Scholar]
  35. Curutchet C, Muñoz-Losa A, Monti S, Kongsted J, Scholes GD, Mennucci B. 35.  2009. Electronic energy transfer in condensed phase studied by a polarizable QM/MM model. J. Chem. Theory Comput. 5:1838–48 [Google Scholar]
  36. Improta R, Scalmani G, Frisch MJ, Barone V. 36.  2007. Toward effective and reliable fluorescence energies in solution by a new state specific polarizable continuum model time dependent density functional theory approach. J. Chem. Phys. 127:074504 [Google Scholar]
  37. Mewes J-M, Herbert JM, Dreuw A. 37.  2017. On the accuracy of the general, state-specific polarizable-continuum model for the description of correlated ground- and excited states in solution. Phys. Chem. Chem. Phys. 19:1644–54 [Google Scholar]
  38. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr.. 38.  et al. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179–97 [Google Scholar]
  39. MacKerell AD Jr., Bashford D, Bellott M, Dunbrack RL Jr., Evanseck JD. 39.  et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102:3586–616 [Google Scholar]
  40. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. 40.  2004. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25:1656–76 [Google Scholar]
  41. Jorgensen WL, Maxwell DS, Tirado-Rives J. 41.  1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225–36 [Google Scholar]
  42. Lopes PEM, Roux B, MacKerell AD Jr. 42.  2009. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications. Theor. Chem. Acc. 124:11–28 [Google Scholar]
  43. Vreven T, Byun KS, Komáromi I, Dapprich S, Montgomery JA. 43.  et al. 2006. Combining quantum mechanics methods with molecular mechanics methods in ONIOM. J. Chem. Theory Comput. 2:815–26 [Google Scholar]
  44. Hall KF, Vreven T, Frisch MJ, Bearpark MJ. 44.  2008. Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181. J. Mol. Biol. 383:106–21 [Google Scholar]
  45. Ponder JW, Wu C, Ren P, Pande VS, Chodera JD. 45.  et al. 2010. Current status of the AMOEBA polarizable force field. J. Phys. Chem. B 114:2549–64 [Google Scholar]
  46. Steindal AH, Ruud K, Frediani L, Aidas K, Kongsted J. 46.  2011. Excitation energies in solution: the fully polarizable QM/MM/PCM method. J. Phys. Chem. B 115:3027–37 [Google Scholar]
  47. Lipparini F, Barone V. 47.  2011. Polarizable force fields and polarizable continuum model: a fluctuating charges/PCM approach. 1. Theory and implementation. J. Chem. Theory Comput. 7:3711–24 [Google Scholar]
  48. Patel S, Brooks CL III. 48.  2004. CHARMM fluctuating charge force field for proteins: I Parameterization and application to bulk organic liquid simulations. J. Comput. Chem. 25:1–15 [Google Scholar]
  49. Patel S, Mackerell AD Jr., Brooks CL III. 49.  2004. CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comput. Chem. 25:1504–14 [Google Scholar]
  50. Boulanger E, Thiel W. 50.  2014. Toward QM/MM simulation of enzymatic reactions with the Drude oscillator polarizable force field. J. Chem. Theory Comput. 10:1795–809 [Google Scholar]
  51. Lamoureux G, MacKerell AD Jr., Roux B. 51.  2003. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 119:5185–97 [Google Scholar]
  52. Miertuš S, Scrocco E, Tomasi J. 52.  1981. Electrostatic interaction of a solute with a continuum. A direct utilization of AB initio molecular potentials for the prevision of solvent effects. Chem. Phys. 55:117–29 [Google Scholar]
  53. Barone V, Cossi M. 53.  1998. Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A 102:1995–2001 [Google Scholar]
  54. Cancès E, Mennucci B, Tomasi J. 54.  1997. A new integral equation formalism for the polarizable continuum model: theoretical background and applications to isotropic and anisotropic dielectrics. J. Chem. Phys. 107:3032–41 [Google Scholar]
  55. Klamt A. 55.  1995. Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J. Phys. Chem. 99:2224–35 [Google Scholar]
  56. Chipman DM. 56.  1999. Simulation of volume polarization in reaction field theory. J. Chem. Phys. 110:8012–18 [Google Scholar]
  57. Kuechler ER, Giese TJ, York DM. 57.  2015. Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations. J. Chem. Phys. 143:234111 [Google Scholar]
  58. Tomasi J, Cancès E, Pomelli CS, Caricato M, Scalmani G. 58.  et al. 2007. Modern theories of continuum models. Continuum Solvation Models in Chemical Physics: From Theory to Applications B Mennucci, R Cammi 1–123 Chichester, UK: Wiley [Google Scholar]
  59. Improta R, Barone V, Scalmani G, Frisch MJ. 59.  2006. A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution. J. Chem. Phys. 125:054103 [Google Scholar]
  60. Li Q, Mennucci B, Robb MA, Blancafort L, Curutchet C. 60.  2015. Polarizable QM/MM multiconfiguration self-consistent field approach with state-specific corrections: environment effects on cytosine absorption spectrum. J. Chem. Theory Comput. 11:1674–82 [Google Scholar]
  61. Olsen JM, Aidas K, Kongsted J. 61.  2010. Excited states in solution through polarizable embedding. J. Chem. Theory Comput. 6:3721–34 [Google Scholar]
  62. Loco D, Polack E, Caprasecca S, Lagardère L, Lipparini F. 62.  et al. 2016. A QM/MM approach using the AMOEBA polarizable embedding: from ground state energies to electronic excitations. J. Chem. Theory Comput. 12:3654–61 [Google Scholar]
  63. Caricato M. 63.  2013. A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method. J. Chem. Phys. 139:044116 [Google Scholar]
  64. Mewes JM, You ZQ, Wormit M, Kriesche T, Herbert JM, Dreuw A. 64.  2015. Experimental benchmark data and systematic evaluation of two a posteriori, polarizable-continuum corrections for vertical excitation energies in solution. J. Phys. Chem. A 119:5446–64 [Google Scholar]
  65. Cossi M. 65.  1999. A direct procedure for the evaluation of solvent effects in MC-SCF calculations. J. Chem. Phys. 111:5295–302 [Google Scholar]
  66. Roberto C, Benedetta M. 66.  1999. Linear response theory for the polarizable continuum model. J. Chem. Phys. 110:9877–86 [Google Scholar]
  67. Cossi M, Barone V. 67.  2001. Time-dependent density functional theory for molecules in liquid solutions. J. Chem. Phys. 115:4708–17 [Google Scholar]
  68. Caricato M, Mennucci B, Tomasi J, Ingrosso F, Cammi R. 68.  et al. 2006. Formation and relaxation of excited states in solution: a new time dependent polarizable continuum model based on time dependent density functional theory. J. Chem. Phys. 124:124520 [Google Scholar]
  69. Schinke R. 69.  1995. Photodissociation Dynamics: Spectroscopy and Fragmentation of Small Polyatomic Molecules Cambridge, UK: Cambridge Univ. Press
  70. Dahl JP, Springborg M. 70.  1988. The Morse oscillator in position space, momentum space, and phase space. J. Chem. Phys. 88:4535–47 [Google Scholar]
  71. Du L, Lan Z. 71.  2015. An on-the-fly surface-hopping program jade for nonadiabatic molecular dynamics of polyatomic systems: implementation and applications. J. Chem. Theory Comput. 11:1360–74 [Google Scholar]
  72. 72.  Deleted in proof
  73. Crespo-Otero R, Barbatti M. 73.  2012. Spectrum simulation and decomposition with nuclear ensemble: formal derivation and application to benzene, furan and 2-phenylfuran. Theor. Chem. Acc. 131:1237 [Google Scholar]
  74. Barbatti M, Aquino AJA, Lischka H. 74.  2010. The UV absorption of nucleobases: semi-classical ab initio spectra simulations. Phys. Chem. Chem. Phys. 12:4959–67 [Google Scholar]
  75. Mitlief R, Hartmann M, Stanca B, Bonacic-Koutecky V, Fantucci P. 75.  2001. Ab initio adiabatic dynamics combined with Wigner distribution approach to femtosecond pump-probe negative ion to neutral to positive ion (NeNePo) spectroscopy of Ag2Au, Ag4, and Au4 clusters. J. Phys. Chem. A 105:8892–905 [Google Scholar]
  76. Peccati F, Mai S, González L. 76.  2017. Insights into the deactivation of 5-bromouracil after ultraviolet excitation. Phil. Trans. R. Soc. A 375:20160202 [Google Scholar]
  77. Carlos Borin A, Mai S, Marquetand P, González L. 77.  2017. Ab initio molecular dynamics relaxation and intersystem crossing mechanisms of 5-azacytosine. Phys. Chem. Chem. Phys. 19:5888–94 [Google Scholar]
  78. Mai S, Pollum M, Martínez-Fernández L, Dunn N, Marquetand P. 78.  et al. 2016. The origin of efficient triplet state population in sulfur-substituted nucleobases. Nat. Commun. 7:13077 [Google Scholar]
  79. Mai S, Marquetand P, González L. 79.  2016. Intersystem crossing pathways in the noncanonical nucleobase 2-thiouracil: a time-dependent picture. J. Phys. Chem. Lett. 7:1978–83 [Google Scholar]
  80. Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S. 80.  et al. 2015. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J. Am. Chem. Soc. 137:4368–81 [Google Scholar]
  81. Cardozo TM, Aquino AJA, Barbatti M, Borges I, Lischka H. 81.  2015. Absorption and fluorescence spectra of poly(p-phenylenevinylene) (PPV) oligomers: an ab initio simulation. J. Phys. Chem. A 119:1787–95 [Google Scholar]
  82. Karsili TNV, Marchetti B, Ashfold MNR. 82.  2016. Mechanistic insights into excited state intramolecular proton transfer in isolated and metal chelated supramolecular chemosensors. Dalton Trans 45:18921–30 [Google Scholar]
  83. Wiebeler C, Plasser F, Hedley GJ, Ruseckas A, Samuel IDW, Schumacher S. 83.  2017. Ultrafast electronic energy transfer in an orthogonal molecular dyad. J. Phys. Chem. Lett. 8:1086–92 [Google Scholar]
  84. Fazzi D, Barbatti M, Thiel W. 84.  2016. Unveiling the role of hot charge-transfer states in molecular aggregates via nonadiabatic dynamics. J. Am. Chem. Soc. 138:4502–11 [Google Scholar]
  85. Barbatti M, Ruckenbauer M, Plasser F, Pittner J, Granucci G. 85.  et al. 2014. Newton-X: a surface-hopping program for nonadiabatic molecular dynamics. WIREs Comput. Mol. Sci. 4:26–33 [Google Scholar]
  86. Mai S, Marquetand P, González L. 86.  2015. A general method to describe intersystem crossing dynamics in trajectory surface hopping. Int. J. Quant. Chem. 115:1215–31 [Google Scholar]
  87. Richter M, Marquetand P, González-Vázquez J, Sola I, González L. 87.  2011. SHARC: ab initio molecular dynamics with surface hopping in the adiabatic representation including arbitrary couplings. J. Chem. Theory Comput. 7:1253–58 [Google Scholar]
  88. Tuckerman ME, Martyna GJ. 88.  2000. Understanding modern molecular dynamics: techniques and applications. J. Phys. Chem. B 104:159–78 [Google Scholar]
  89. Swope WC, Andersen HC, Berens PH, Wilson KR. 89.  1982. A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters. J. Chem. Phys. 76:637–49 [Google Scholar]
  90. Nogueira JJ, Corani A, El Nahhas A, Pezzella A, d'Ischia M. 90.  et al. 2017. Sequential proton-coupled electron transfer mediates excited-state deactivation of a eumelanin building block. J. Phys. Chem. Lett. 8:1004–8 [Google Scholar]
  91. Nogueira JJ, Meixner M, Bittermann M, González L. 91.  2017. Impact of lipid environment on photodamage activation of methylene blue. ChemPhotoChem 1:178–82 [Google Scholar]
  92. Nogueira JJ, Oppel M, González L. 92.  2015. Enhancing intersystem crossing in phenotiazinium dyes by intercalation into DNA. Angew. Chem. Int. Ed. 54:4375–78 [Google Scholar]
  93. Zobel JP, Nogueira JJ, González L. 93.  2015. Quenching of charge transfer in nitrobenzene induced by vibrational motion. J. Phys. Chem. Lett. 6:3006–11 [Google Scholar]
  94. Rauer C, Nogueira JJ, Marquetand P, González L. 94.  2016. Cyclobutane thymine photodimerization mechanism revealed by nonadiabatic molecular dynamics. J. Am. Chem. Soc. 138:15911–16 [Google Scholar]
  95. Nogueira JJ, Plasser F, González L. 95.  2017. Electronic delocalization, charge transfer and hypochromism in the UV absorption spectrum of polyadenine unravelled by multiscale computations and quantitative wavefunction analysis. Chem. Sci. 8:5682–91 [Google Scholar]
  96. Lan Z, Lu Y, Fabiano E, Thiel W. 96.  2011. QM/MM nonadiabatic decay dynamics of 9H-adenine in aqueous solution. ChemPhysChem 12:1989–98 [Google Scholar]
  97. Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. 97.  2012. Electronic absorption spectra from MM and ab initio QM/MM molecular dynamics: environmental effects on the absorption spectrum of photoactive yellow protein. J. Chem. Theory Comput. 8:5092–106 [Google Scholar]
  98. Grozema FC, Swart M, Zijlstra RWJ, Piet JJ, Siebbeles LDA, van Duijnen PT. 98.  2005. QM/MM study of the role of the solvent in the formation of the charge separated excited state in 9,9′-bianthryl. J. Am. Chem. Soc. 127:11019–28 [Google Scholar]
  99. Parac M, Doerr M, Marian CM, Thiel W. 99.  2010. QM/MM calculation of solvent effects on absorption spectra of guanine. J. Comput. Chem. 31:90–106 [Google Scholar]
  100. Etienne T, Very T, Perpète EA, Monari A, Assfeld X. 100.  2013. A QM/MM study of the absorption spectrum of harmane in water solution and interacting with DNA: the crucial role of dynamic effects. J. Phys. Chem. B 117:4973–80 [Google Scholar]
  101. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 101.  1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926–35 [Google Scholar]
  102. Finley J, Malmqvist PA, Roos BO, Serrano-Andrés L. 102.  1998. The multi-state CASPT2 method. Chem. Phys. Lett. 288:299–306 [Google Scholar]
  103. Becke AD. 103.  1993. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98:5648–52 [Google Scholar]
  104. Mellish KJ, Cox RD, Vernon DI, Griffiths J, Brown SB. 104.  2002. In vitro photodynamic activity of a series of methylene blue analogues. Photochem. Photobiol. 75:392–97 [Google Scholar]
  105. Nogueira JJ, González L. 105.  2014. Molecular dynamics simulations of binding modes between methylene blue and DNA with alternating GC and at sequences. Biochemistry 53:2391–412 [Google Scholar]
  106. Tuite E, Nordén B. 106.  1994. Sequence-specific interactions of methylene blue with polynucleotides and DNA: a spectroscopic study. J. Am. Chem. Soc. 116:7548–56 [Google Scholar]
  107. Bacellar IOL, Pavani C, Sales EM, Itri R, Wainwright M, Baptista MS. 107.  2014. Membrane damage efficiency of phenothiazinium photosensitizers. Photochem. Photobiol. 90:801–13 [Google Scholar]
  108. Lower SK, El-Sayed MA. 108.  1966. The triplet state and molecular electronic processes in organic molecules. Chem. Rev. 66:199–241 [Google Scholar]
  109. Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K. 109.  et al. 2014. Lipid14: the amber lipid force field. J. Chem. Theory Comput. 10:865–79 [Google Scholar]
  110. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. 110.  2004. Development and testing of a general amber force field. J. Comput. Chem. 25:1157–74 [Google Scholar]
  111. Hawkins GD, Cramer CJ, Truhlar DG. 111.  1995. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246:122–29 [Google Scholar]
  112. Roos BO, Taylor PR, Sigbahn PEM. 112.  1980. A complete active space SCF method (CASSCF) using a density matrix formulated super-CI approach. Chem. Phys. 48:157–73 [Google Scholar]
  113. Adamo C, Barone V. 113.  1999. Toward reliable density functional methods without adjustable parameters: the PBE0 model. J. Chem. Phys. 110:6158–70 [Google Scholar]
  114. Hariharan PC, Pople JA. 114.  1973. The influence of polarization functions on molecular orbital hydrogenation energies. Theoret. Chim. Acta 28:213–22 [Google Scholar]
  115. Krishnan R, Binkley JS, Seeger R, Pople JA. 115.  1980. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J. Chem. Phys. 72:650–54 [Google Scholar]
  116. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA. 116.  et al. 2013. Gaussian 09, Revision D.01 Wallingford, CT: Gaussian [Google Scholar]
  117. Case DA, Berryman JT, Betz RM, Cerutti DS, Cheatham TE III. 117.  et al. 2015. Amber 2015 Reference Manual Univ. Calif., San Francisco. http://ambermd.org/doc12/Amber15.pdf
  118. Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. 118.  2015. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11:3696–713 [Google Scholar]
  119. Yanai T, Tew DP, Handy NC. 119.  2004. A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem. Phys. Lett. 393:51–57 [Google Scholar]
  120. Buchvarov I, Wang Q, Raytchev M, Trifonov A, Fiebig T. 120.  2007. Electronic energy delocalization and dissipation in single- and double-stranded DNA. PNAS 104:4794–97 [Google Scholar]
  121. Markovitsi D, Onidas D, Gustavsson T, Talbot F, Lazzarotto E. 121.  2005. Collective behavior of Franck–Condon excited states and energy transfer in DNA double helices. J. Am. Chem. Soc. 127:17130–31 [Google Scholar]
  122. Kwok WM, Ma C, Phillips DL. 122.  2006. Femtosecond time- and wavelength-resolved fluorescence and absorption spectroscopic study of the excited states of adenosine and an adenine oligomer. J. Am. Chem. Soc. 128:11894–905 [Google Scholar]
  123. Tonzani S, Schatz GC. 123.  2008. Electronic excitations and spectra in single-stranded DNA. J. Am. Chem. Soc. 130:7607–12 [Google Scholar]
  124. Emanuele E, Markovitsi D, Millié P, Zakrzewska K. 124.  2005. UV spectra and excitation delocalization in DNA: influence of the spectral width. ChemPhysChem 6:1387–92 [Google Scholar]
  125. Santoro F, Barone V, Improta R. 125.  2007. Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations. PNAS 104:9931–36 [Google Scholar]
  126. Plasser F, Lischka H. 126.  2012. Analysis of excitonic and charge transfer interactions from quantum chemical calculations. J. Chem. Theory Comput. 8:2777–89 [Google Scholar]
  127. Bouvier B, Dognon JP, Lavery R, Markovitsi D, Millié P. 127.  et al. 2003. Influence of conformational dynamics on the exciton states of DNA oligomers. J. Phys. Chem. B 107:13512–22 [Google Scholar]
  128. Voityuk AA. 128.  2013. Effects of dynamic disorder on exciton delocalization and photoinduced charge separation in DNA. Photochem. Photobiol. Sci. 12:1303–9 [Google Scholar]
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