[en] The chiroptical properties of multi-chromophoric systems are governed by the intermolecular arrangement of the monomeric units. We report on a computational and experimental study of the linear optical properties and supramolecular structure of a rhodamine heterodimer assembled on a DNA scaffold. The experimental absorption and circular dichroism (CD) profiles confirm the dimer formation. Computationally, starting from low-cost DFT/TDDFT simulations of the bare dimer we attribute the measured -/+ CD sign sequence of the S1/S2 bands to a specific chiral conformation of the heterodimer. In the monomers, as typical for rhodamine dyes, the electric transition dipole of the lowest π-π* transition is parallel to the long axis of the xanthene planes. We show that in the heterodimer the sign sequence of the two CD bands is related to the orientation of these long axes. To account explicitly for environment effects, we use molecular dynamics (MD) simulations for characterizing the supramolecular structure of the two optical isomers tethered on DNA. Average absorption and CD-profiles were modeled using ab initio TDDFT calculations at the geometries sampled along a few nanosecond MD run. The absorption profiles computed for both optical isomers are in good agreement with the experimental absorption spectrum and do not allow one to discriminate between them. The computed averaged CD profiles provide the orientation of monomers in the enantiomer that is dominant under the experimental conditions.
Disciplines :
Chemistry
Author, co-author :
Rukin, P. S.; Theoretical Physical Chemistry, University of Liege, Liege, B4000, Belgium
Komarova, K. G.; Theoretical Physical Chemistry, University of Liege, Liege, B4000, Belgium
Fresch, B.; Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
Collini, E.; Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
Remacle, Françoise ; Université de Liège - ULiège > Département de chimie (sciences) > Laboratoire de chimie physique théorique
Language :
English
Title :
Chirality of a rhodamine heterodimer linked to a DNA scaffold: an experimental and computational study
Publication date :
2020
Journal title :
Physical Chemistry Chemical Physics
ISSN :
1463-9076
eISSN :
1463-9084
Publisher :
NLM (Medline)
Volume :
22
Issue :
14
Pages :
7516-7523
Peer reviewed :
Peer reviewed
Tags :
CÉCI : Consortium des Équipements de Calcul Intensif
Funders :
DG RDT - European Commission. Directorate-General. Research and Innovation [BE] FNR - Fonds National de la Recherche [LU]
B. L. Cannon L. K. Patten D. L. Kellis P. H. Davis J. Lee E. Graugnard B. Yurke W. B. Knowlton J. Phys. Chem. A 2018 122 2086 2095
B. L. Cannon D. L. Kellis L. K. Patten P. H. Davis J. Lee E. Graugnard B. Yurke W. B. Knowlton J. Phys. Chem. A 2017 121 6905 6916
F. Nicoli M. K. Roos E. A. Hemmig M. Di Antonio R. de Vivie-Riedle T. Liedl J. Phys. Chem. A 2016 120 9941 9947
D. G. Singleton R. Hussain G. Siligardi P. Kumar P. J. Hrdlicka N. Berova E. Stulz Org. Biomol. Chem. 2016 14 149 157
G. Pescitelli L. Di Bari N. Berova Chem. Soc. Rev. 2014 43 5211 5233
N. Berova L. D. Bari G. Pescitelli Chem. Soc. Rev. 2007 36 914 931
M. Balaz B. C. Li J. D. Steinkruger G. A. Ellestad K. Nakanishi N. Berova Org. Biomol. Chem. 2006 4 1865 1867
F. Segatta L. Cupellini M. Garavelli B. Mennucci Chem. Rev. 2019 119 9361 9380
D. Padula S. Jurinovich L. Di Bari B. Mennucci Chem.-Eur. J. 2016 22 17011 17019
H. Gattuso A. Spinello A. Terenzi X. Assfeld G. Barone A. Monari J. Phys. Chem. B 2016 120 3113 3121
W. W. Parson, Modern Optical Spectroscopy, Springer, Heidelberg, 2007
J. A. Schellman Chem. Rev. 1975 75 323 331
F. C. Spano J. Am. Chem. Soc. 2009 131 4267 4278
T. Brixner R. Hildner J. Köhler C. Lambert F. Würthner Adv. Energy Mater. 2017 7 1700236
R. S. Stoll N. Severin J. P. Rabe S. Hecht Adv. Mater. 2006 18 1271 1275
L. I. Markova V. L. Malinovskii L. D. Patsenker R. Häner Chem. Commun. 2013 49 5298 5300
K. Watanabe Z. Sun K. Akagi Chem. Mater. 2015 27 2895 2902
M. Cipolloni B. Fresch I. Occhiuto P. Rukin K. G. Komarova A. Cecconello I. Willner R. D. Levine F. Remacle E. Collini Phys. Chem. Chem. Phys. 2017 19 23043 23051
R. Szabla H. Kruse P. Stadlbauer J. Sponer A. L. Sobolewski Chem. Sci. 2018 9 3131 3140
D. Fazzi M. Barbatti W. Thiel J. Phys. Chem. Lett. 2017 8 4727 4734
J. J. Nogueira F. Plasser L. Gonzalez Chem. Sci. 2017 8 5682 5691
V. A. Spata W. Lee S. Matsika J. Phys. Chem. Lett. 2016 7 976 984
W. Arbelo-Gonzalez R. Crespo-Otero M. Barbatti J. Chem. Theory Comput. 2016 12 5037 5049
V. A. Spata S. Matsika Phys. Chem. Chem. Phys. 2015 17 31073 31083
C. M. Isborn A. W. Götz M. A. Clark R. C. Walker T. J. Martínez J. Chem. Theory Comput. 2012 8 5092 5106
R. Crespo-Otero M. Barbatti Theor. Chem. Acc. 2012 131 1237
V. A. Spata S. Matsika J. Phys. Chem. A 2014 118 12021 12030
M. Barbatti K. Sen Int. J. Quantum Chem. 2016 116 762 771
N. De Mitri S. Monti G. Prampolini V. Barone J. Chem. Theory Comput. 2013 9 4507 4516
P. V. Komarov V. G. Plotnikov Int. J. Quantum Chem. 2012 112 3039 3045
K. G. Komarova S. N. Sakipov V. G. Plotnikov M. V. Alfimov J. Lumin. 2015 164 57 63
A. V. Marenich C. J. Cramer D. G. Truhlar J. Phys. Chem. B 2015 119 958 967
J. Tomasi B. Mennucci R. Cammi Chem. Rev. 2005 105 2999 3094
M. Kasha H. R. Rawls M. Ashraf El-Bayoumi Pure Appl. Chem. 1965 11 371 392
N. J. Hestand F. C. Spano Chem. Rev. 2018 118 7069 7163
T. Yanai D. P. Tew N. C. Handy Chem. Phys. Lett. 2004 393 51 57
G. Stefan E. Stephan G. Lars J. Comput. Chem. 2011 32 1456 1465
R. Krishnan J. S. Binkley R. Seeger J. A. Pople J. Chem. Phys. 1980 72 650 654
M. M. Francl W. J. Pietro W. J. Hehre J. S. Binkley M. S. Gordon D. J. DeFrees J. A. Pople J. Chem. Phys. 1982 77 3654 3665
D. Feller J. Comput. Chem. 1996 17 1571 1586
K. L. Schuchardt B. T. Didier T. Elsethagen L. Sun V. Gurumoorthi J. Chase J. Li T. L. Windus J. Chem. Inf. Model. 2007 47 1045 1052
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, 2009
A. Pérez I. Marchán D. Svozil J. Sponer T. E. Cheatham C. A. Laughton M. Orozco Biophys. J. 2007 92 3817 3829
W. L. Jorgensen J. Chandrasekhar J. D. Madura R. W. Impey M. L. Klein J. Chem. Phys. 1983 79 926 935
J. Wang R. M. Wolf J. W. Caldwell P. A. Kollman D. A. Case J. Comput. Chem. 2004 25 1157 1174
T. J. Macke and D. A. Case, Molecular Modeling of Nucleic Acids, American Chemical Society, 1997, ch. 24, vol. 682, pp. 379-393
T. Darden D. York L. Pedersen J. Chem. Phys. 1993 98 10089 10092
S. Miyamoto P. A. Kollman J. Comput. Chem. 1992 13 952 962
D. A. Case, T. A. Darden, T. E. Cheatham, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Gotz, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko and P. A. Kollman, AMBER 12, 2012
R. L. Martin J. Chem. Phys. 2003 118 4775 4777
M. J. G. Peach P. Benfield T. Helgaker D. J. Tozer J. Chem. Phys. 2008 128 044118
B. Fresch F. Remacle Phys. Chem. Chem. Phys. 2014 16 14070 14082
A. Pohorille C. Jarzynski C. Chipot J. Phys. Chem. B 2010 114 10235 10253
