Nile blue and Nile red optical properties predicted by TD-DFT and CASPT2 methods: static and dynamic solvent effects

详细信息    查看全文

• 作者：Marco Marazzi ; Hugo Gattuso ; Antonio Monari
• 关键词：Excited states ; Solvent effects ; Absorption ; Emission ; TD ; DFT ; CASPT2 ; Fluorescent dyes
• 刊名：Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：135
• 期：3
• 全文大小：1,783 KB
• 参考文献：1.Yang W (2011) Surviving the sun: repair and bypass of DNA UV lesions. Protein Sci 20(11):1781–1789CrossRef
  2.Dumont E, Monari A (2015) Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 3:43CrossRef
  3.Clauson C, Schaerer OD, Niedernhofer L (2013) Advances in understanding the complex mechanisms of DNA interstrand cross-link repair. Cold Spring Harb Perspect Biol 5:a012732CrossRef
  4.Barbatti M, Aquino AJA, Szymczak JJ, Nachtigallová D, Hobza P, Lischka H (2010) Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases. Proc Natl Acad Sci USA 107(50):21453–21458CrossRef
  5.Sauri V, Gobbo JP, Serrano-Pérez JJ, Lundberg M, Coto PB, Serrano-Andrés L, Borin AC, Lindh R, Merchan M, Roca-Sanjuan D (2013) Proton/hydrogen transfer mechanisms in the guanine–cytosine base pair: photostability and tautomerism. J Chem Theory Comput 9:481–496CrossRef
  6.Kwok WM, Ma C, Phillips DL (2008) A doorway state leads to photostability or triplet photodamage in thymine DNA. J Am Chem Soc 130(15):5131–5139CrossRef
  7.Cuquerella MC, Lhiaubet-Vallet V, Cadet J, Miranda MA (2012) Benzophenone photosensitized DNA Damage. Acc Chem Res 45(9):1558–1570CrossRef
  8.Ravanat J, Douki T, Cadet J (2001) Direct and indirect effects of UV radiation on DNA and its components. J Photochem Photobiol B Biol 63:88–102CrossRef
  9.Epe B (2012) DNA damage spectra induced by photosensitization. Photochem Photobiol Sci 11(1):98–106CrossRef
  10.Mie Y, Kowata K, Kojima N, Komatsu Y (2012) Electrochemical properties of interstrand cross-linked DNA duplexes labeled with Nile blue. Langmuir 28:17211–17216CrossRef
  11.Mitra RK, Sinha SS, Maiti S, Pal SK (2009) Sequence dependent ultrafast electron transfer of Nile blue in oligonucleotides. J Fluoresc 19(2):353–361CrossRef
  12.Hirakawa K, Ota K, Hirayama J, Oikawa S, Kawanishi S (2014) Nile blue can photosensitize DNA damage through electron transfer. Chem Res Toxicol 27:649–655CrossRef
  13.Beyer C, Wagenknecht H-A (2010) In situ azide formation and ‘click’ reaction of Nile red with DNA as an alternative postsynthetic route. Chem Commun 46(13):2230–2231CrossRef
  14.Yotapan N, Charoenpakdee C, Wathanathavorn P, Ditmangklo B, Wagenknecht H-A, Vilaivan T (2014) Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label. Beilstein J Org Chem 10:2166–2174CrossRef
  15.Okamoto A, Tainaka K, Fujiwara Y (2006) Nile Red nucleoside: design of a solvatofluorochromic nucleoside as an indicator of micropolarity around DNA. J Org Chem 71(9):3592–3598CrossRef
  16.Prokhorenko IA, Dioubankova NN, Korshun VA (2004) Oligonucleotide conjugates of Nile red. Nucleosides Nucleotides Nucleic Acids 23(1–2):509–520CrossRef
  17.Greenspan P, Fowler SD (1985) Spectrofluorometric studies of the lipid probe, Nile red. J Lipid Res 26(7):781–789
  18.Ghoneim N (2000) Photophysics of Nile red in solution. Steady state spectroscopy. Spectrochim Acta A 56(5):1003–1010CrossRef
  19.Cser A, Nagy K, Biczok L (2002) Fluorescence lifetime of Nile Red as a probe for the hydrogen bonding strength with its microenvironment. Chem Phys Lett 360:473–478CrossRef
  20.Ghanadzadeh Gilani A, Hosseini SE, Moghadam M, Alizadeh E (2012) Excited state electric dipole moment of Nile blue and brilliant cresyl blue: a comparative study. Spectrochim Acta A Mol Biomol Spectrosc 89:231–237CrossRef
  21.Lachmann D, Berndl S, Wolfbeis OS, Wagenknecht H-A (2010) Synthetic incorporation of Nile blue into DNA using 2′-deoxyriboside substitutes: representative comparison of (R)-and (S)-aminopropanediol as an acyclic linker. Beilstein J Org Chem 6(13):1–7
  22.Rama Raju B, Naik S, Coutinho PJG, Gonçalves MST (2013) Novel Nile blue derivatives as fluorescent probes for DNA. Dye Pigment 99(1):220–227CrossRef
  23.Chen QY, Li DH, Zhao Y, Yang HH, Zhu QZ, Xu JG (1999) Interaction of a novel red-region fluorescent probe, Nile blue, with DNA and its application to nucleic acids assay. Analyst 124(6):901–906CrossRef
  24.Greenspan P, Mayer EP, Fowler SD (1985) Nile red: a selective fluorescent stain for intracellular lipid droplets. J Cell Biol 100(10):965–973CrossRef
  25.Mitra RK, Sinha SS, Pal SK (2008) Interactions of Nile blue with micelles, reverse micelles and a genomic DNA. J Fluoresc 18(2):423–432CrossRef
  26.Varghese R, Wagenknecht H-A (2010) Non-covalent versus covalent control of self-assembly and chirality of Nile red-modified nucleoside and DNA. Chem A Eur J 16(30):9040–9046CrossRef
  27.Hebda E, Jancia M, Kajzar F, Niziol J, Pielichowski J, Rau I, Tane A (2012) Optical properties of thin films of DNA-CTMA and DNA-CTMA doped with Nile blue. Mol Cryst Liq Cryst 556(1):309–316CrossRef
  28.Andersson K, Malmqvist PA, Roos BO, Sadlej AJ, Wolinski K (1990) Second-order perturbation theory with a CASSCF reference function. J Phys Chem 94(14):5483–5488CrossRef
  29.Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys Rev A 38:3098–3100CrossRef
  30.Perdew JP (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 33:8822–8824CrossRef
  31.Lee C, Yang W, Parr RG (1988) Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789CrossRef
  32.Lee TJ, Taylor PR (1989) A diagnostic for determining the quality of single-reference electron correlation methods. Int J Quantum Chem Quant Chem Symp S23:199–207
  33.Wilson PJ, Bradley TJ, Tozer DJ (2001) Hybrid exchange-correlation functional determined from thermochemical data and ab initio potentials. J Chem Phys 115:9233–9242CrossRef
  34.Izmaylov AF, Scuseria G, Frisch MJ (2006) Efficient evaluation of short-range Hartree–Fock exchange in large molecules and periodic systems. J Chem Phys 125:104103CrossRef
  35.Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other function. Theory Chem Acc 120:215–241CrossRef
  36.Perdew JP, Burke K, Ernzerhof M (1997) Errata: generalized gradient approximation made simple. Phys Rev Lett 78:1396CrossRef
  37.Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3093CrossRef
  38.Forsberg N, Malmqvist P-Å (1997) Multiconfiguration perturbation theory with imaginary level shift. Chem Phys Lett 274:196–204CrossRef
  39.Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935CrossRef
  40.Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9):1157–1174CrossRef
  41.Singh UC, Kollman PA (1984) An approach to computing electrostatic charges for molecules. J Comput Chem 5:129–145CrossRef
  42.Besler BH, Merz KM Jr, Kollman PA (1990) Atomic charges derived from semiempirical methods. J Comput Chem 11:431–439CrossRef
  43.Aquilante F, De Vico L, Ferré N, Ghigo G, Malmqvist P-A, Neogrady P, Pedersen TB, Pitonak M, Reiher M, Roos BO, Serrano-Andres L, Urban M, Veryazov V, Lindh R (2010) MOLCAS 7: The Next Generation. J Comput Chem 31(1):224–247CrossRef
  44.Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Al E (2009) Gaussian09 revision D.01. Gaussian Inc., Wallingford
  45.Ponder J, Richards FM (1987) An efficient Newton-like method for molecular mechanics energy minimization of large molecules. J Comput Chem 8:1016–1024CrossRef
  46.Monari A, Rivail J-L, Assfeld X (2013) Theoretical modelling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations. Acc Chem Res 46(2):596–603CrossRef
  47.Marazzi M, Sancho U, Castaño O, Domcke W, Frutos LM (2010) Photoinduced proton transfer as a possible mechanism for highly efficient excited-state deactivation in proteins. J Phys Chem Lett 1(1):425–428CrossRef
  48.Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M (2014) Learning from photobiology how to design molecular devices using a computer. Chem Soc Rev 43(12):4019–4036CrossRef
  49.Gozem S, Huntress M, Schapiro I, Lindh R, Granovsky A, Angeli C, Olivucci M (2012) Dynamic electron correlation effects on the ground state potential energy surface of a retinal chromophore model. J Chem Theory Comput 8(11):4069–4080CrossRef
  50.Valsson O, Campomanes P, Tavernelli I, Rothlisberger U, Filippi C (2013) Rhodopsin absorption from first principles: bypassing common pitfalls. J Chem Theory Comput 9(5):2441–2454CrossRef
  51.Valsson O, Angeli C, Filippi C (2012) Excitation energies of retinal chromophores: critical role of the structural model. Phys Chem Chem Phys 14:11015–11020CrossRef
  52.Valsson O, Filippi C (2010) Photoisomerization of model retinal chromophores: insight from quantum monte carlo and multiconfigurational perturbation theory. J Chem Theory Comput 6(4):1275–1292CrossRef
  53.Etienne T, Assfeld X, Monari A (2014) Toward a quantitative assessment of electronic transitions’ charge-transfer character. J Chem Theory Comput 10:3896–3905CrossRef
  54.Etienne T, Assfeld X, Monari A (2014) New insight into the topology of excited states through detachment/attachment density matrices-based centroids of charge. J Chem Theory Comput 10(9):3906–3914CrossRef
  55.Etienne T (2015) Probing the locality of excited states with linear algebra. J Chem Theory Comput 11(4):1692–1699CrossRef
  56.Etienne T, Very T, Perpète EA, Monari A, Assfeld X (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 117:4973–4980CrossRef
  57.Buytendyk AM, Wang Y, Graham JD, Kandalam AK, Kiran B, Bowen KH (2015) Photoelectron spectrum of a polycyclic aromatic nitrogen heterocyclic anion: quinoline. Mol Phys 113(15–16):2095–2098CrossRef
  58.Avila Ferrer FJ, Cerezo J, Soto J, Improta R, Santoro F (2014) First-principle computation of absorption and fluorescent spectra in solution accounting for vibronic structure, temperature effects and solvent inhomogeneous broadening. Comp Theory Chem 1040–1041:328–337CrossRef
  59.Santoro F, Lami A, Improta R, Bloino J, Barone V (2008) Effective method for the computation of optical spectra of large molecules at finite temperature including the Duschinsky and Herzberg–Teller effect: the Q[sub x] band of porphyrin as a case study. J Chem Phys 128(22):224311–224317CrossRef
  60.Tajalli H, Gilani AG, Zakerhamidi MS, Tajalli P (2008) The photophysical properties of Nile red and Nile blue in ordered anisotropic media. Dye Pigment 78(1):15–24CrossRef
  
• 作者单位：Marco Marazzi (1) (2)
  Hugo Gattuso (1) (2)
  Antonio Monari (1) (2)
  
  1. Théorie-Modélisation-Simulation, Université de Lorraine, SRSMC, Boulevard des Aiguillettes, 54506, Vandoeuvre-lès-Nancy, Nancy, France
  2. Théorie-Modélisation-Simulation, CNRS, SRSMC, Boulevard des Aiguillettes, 54506, Vandoeuvre-lès-Nancy, Nancy, France
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Theoretical and Computational Chemistry
  Inorganic Chemistry
  Organic Chemistry
  Physical Chemistry
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-2234

文摘

The absorption and emission spectra of the fluorescent dyes Nile blue (NB) and Nile red (NR), widely used in biology and histology, were simulated with different methods, considering the effect of water as solvent. The aforementioned dyes are extremely significant because they also act as DNA sensitizers and hence can be used in photodynamic therapy. Especially, time dependent-density functional theory (TD-DFT) including different functionals, and ab initio single-state- and multi-state-complete active space perturbation theory (SS- and MS-CASPT2) including the effect of the basis set, were considered. The solvent environment was taken into account statically and dynamically: static optical properties were calculated with the polarizable continuum model as vertical transitions from the ground state equilibrium geometry, while dynamic properties were obtained by performing ground state molecular dynamics of NB and NR in explicit water, followed by hybrid quantum mechanics/molecular mechanics calculations of a statistical number of geometries along the trajectory. The results show that a dynamic treatment is required in order to reproduce the experimental absorption spectra, since the static approach gives rise to a hypsochromic shift of ca. 0.3 eV for NB and 0.2 eV for NR, at the TD-DFT and CASPT2 level of theory. This can be explained in terms of out-of-plane vibrational normal modes, which are properly taken into account only in the dynamic approach. Moreover, an exhaustive description of the charge transfer character in the excited state is given, at both TD-DFT and CASPT2 levels of theory.