Comment pubs.acs.org/JPCC
Comment on “Breakdown of Exciton Splitting through Electron Donor−Acceptor Interaction: A Caveat for the Application of Exciton Chirality Method in Macromolecules” Gennaro Pescitelli* and Lorenzo Di Bari* Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 3, I-56124 Pisa, Italy
J. Phys. Chem. C 2013, 117 (35), 17927−17939. DOI: 10.1021/jp403431w
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n a paper recently published by this Journal, Joy et al. reported the spectroscopic characterization of a number of oligonucleotides capped at the 5′-end with a bichromophoric naphthalenimide−perylenimide dyad (NP, Scheme 1).1 The Scheme 1. Structure of the NP Dyad Appended to Oligonucleotide (ODN) Considered by Joy et al.a
a
The double arrows represent the transition dipoles considered in the NDEC. Figure 1. Idealized consequences of the exciton coupling between two different chromophores (NDEC) in absorption and CD spectra. It is assumed that the isolated (uncoupled) chromophores are associated with negligible CD spectra.
authors claimed to observe a “breakdown of the exciton coupling between the naphthalenimide and the perylenimide transition dipoles upon the formation of the charge transfer state between one of the participating dipoles (naphthalenimide) and the adjacent GC base pair”. Their conclusion is however plagued by (1) a severe misunderstanding of the principles of the exciton coupling (EC) mechanism; (2) an erroneous application of the EC method and EC equations to the specific case; and (3) an uncritical analysis of their calculation results. We will discuss these three problems in sequence. (1) Appearance of the ECD spectrum for nondegenerate exciton coupling − The so-called nondegenerate exciton coupling (NDEC) mechanism occurs between two distinct transitions localized on separate chromophores and consists of a throughspace interaction between the excited states of the two chromophores.2−4 As a result of this interaction, the two absorption bands are (slightly) shifted in energy toward opposite sides and altered in intensity. More importantly, each transition acquires a rotational strength which is opposite in sign and, in the ideal case, similar in magnitude for the two transitions. As a result, a CD band is generated in correspondence of each transition or, in other words, a single CD couplet with the two opposite components well separated in energy.2,4 An idealized picture of the situation described above, for two generic transitions differing by 150 nm, is represented in Figure 1. The authors of the commented paper incorrectly identify the two bisignate features in the naphthalenimide and perylenimide absorption regions (around 400 and 550 nm, respectively)1 as the signature of NDEC. Two (apparent) © XXXX American Chemical Society
couplets means at least four dif ferent transitions and four distinct excited states. (2) Exciton coupling of transitions whose electric dipoles are parallel − The fundamental equation relating the intensity and sign of the two CD bands associated with NDEC and the system geometry is2a,3b (corresponding to eq 2 in the paper)1 R1,2 = ±
2πν1̃ ν2̃ ν2̃ 2 − ν1̃ 2
V12 R12·μ1 × μ2
(1)
where μ1 and μ2 are the electric transition dipoles (vectors) giving rise to the exciton coupling, R12 the reciprocal distance vector, V12 the coupling potential, and ν̃1,2 the transition wavenumbers. The transitions discussed by the authors are “the S0−S3 transition of the naphthalenimide (...) oriented parallel to the short axis of naphthalenimide, and the S0−S1 transition of the perylenimide (...), oriented parallel to the long axis of perylenimide”. A simple inspection of the molecular structure of the NP dyad (Scheme 1) reveals that these two transition dipoles lie parallel regardless of the dihedral angle assumed by the dyad. In this case, the vector product μ1 × μ2 in eq 1 is vanishing. Some deviation from perfect parallelism between the two vectors is conceivable because of structural distortions and/ or substituent effects, but it is likely to be minor. Therefore, the Received: June 9, 2014 Revised: August 18, 2014
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dx.doi.org/10.1021/jp505703k | J. Phys. Chem. C XXXX, XXX, XXX−XXX
The Journal of Physical Chemistry C
Comment
2093−2096. (e) Di Bari, L.; Pescitelli, G.; Reginato, G.; Salvadori, P. Chirality 2001, 13, 548−555. (f) Fishkin, N.; Pescitelli, G.; Sparrow, J. R.; Nakanishi, K.; Berova, N. Chirality 2004, 16, 637−641. (g) Tanaka, K.; Pescitelli, G.; Di Bari, L.; Xiao, T. L.; Nakanishi, K.; Armstrong, D. W.; Berova, N. Org. Biomol. Chem. 2004, 2, 48−58. (5) Goerigk, L.; Grimme, S. J. Chem. Phys. 2010, 132, 184103. (6) Magyar, R. J.; Tretiak, S. J. Chem. Theory Comput. 2007, 3, 976− 987. (7) Pescitelli, G.; Di Bari, L.; Berova, N. Chem. Soc. Rev. 2011, 40, 4603−4625.
two transitions discussed by the authors give rise to no or only very small NDEC. As a consequence, the calculated and experimental CD spectra for the dyad and nucleotides (Figures 2 and 5 in the paper,1 respectively) must be attributed to different mechanisms of optical activity rather than to degenerate or nondegenerate exciton coupling occurring within a single NP dyad. (3) TDDFT calculations: choice of the f unctional and analysis of results − The authors calculated the CD spectra of the NP dyad at various dihedral angles using time-dependent density functional theory (TDDFT) with the B3LYP functional and an extended basis set. However, B3LYP has well-known deficiencies in treating these kinds of systems,5 which are expected to introduce spurious transitions (especially of the charge-transfer type, CT)6 in the investigated region. It is likely that a more critical examination of the calculation results, also in terms of transition and population analysis, would have helped the authors to better understand the origin of the CD spectra. In particular, the presence of several distinct transitions localized on the two chromophores, including CT ones, must be sought as the reason for the emergence of multiple CD bands in the 320−450 nm and 500−600 nm regions, which appear for some dihedral angles as couplet-like features.1 (Notice that we are referring to CT transitions occurring within the dyad, e.g., between perylenimide and naphthalenimide.) In summary, the assumed NDEC mechanism is negligible for the dyad, and it cannot significantly account for the observed spectra. Consequently, the present case does not constitute any breakdown of the EC method, very simply because the CD spectrum does not originate from intramolecular exciton coupling. The use of the “exciton chirality method in predicting the structure of complex macromolecules and the nature of binding between small molecules and macromolecular structures like DNA and proteins” does not need any special caution, apart from those always necessary in any application,7 that is, the consideration of a reliable geometry and the accurate knowledge of the involved transition dipoles.
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AUTHOR INFORMATION
Corresponding Authors
*E-mail:
[email protected]. *E-mail:
[email protected]. Notes
The authors declare no competing financial interest.
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REFERENCES
(1) Joy, J.; Cheriya, R. T.; Nagarajan, K.; Shaji, A.; Hariharan, M. J. Phys. Chem. C 2013, 117, 17927−17939. (2) (a) Harada, N.; Nakanishi, K. Circular Dichroic Spectroscopy Exciton Coupling in Organic Stereochemistry; University Science Books: Mill Valley, CA, 1983. (b) Harada, N.; Nakanishi, K.; Berova, N. Electronic CD Exciton Chirality Method: Principles and Applications. In Comprehensive Chiroptical Spectroscopy; Berova, N., Polavarapu, P. L., Nakanishi, K., Woody, R. W., Eds.; John Wiley & Sons, Inc.: Hoboken (NJ), 2012; pp 115−166. (3) (a) For general discussion on NDEC, see ref 2a, §3.1D, pp 85− 87, and ref 2b, §§4.8.3−4.8.4, pp 143−146. (b) For NDEC theory, see ref 2a, §10.9, pp 353−361. (4) For examples of NDEC see: (a) Harada, N.; Iwabuchi, J.; Yokota, Y.; Uda, H.; Nakanishi, K. J. Am. Chem. Soc. 1981, 103, 5590−5591. (b) Wiesler, W. T.; Nakanishi, K. J. Am. Chem. Soc. 1990, 112, 5574− 5583. (c) Gawronski, J.; Kazmierczak, F.; Gawronska, K.; Rychlewska, U.; Nordén, B.; Holmén, A. J. Am. Chem. Soc. 1998, 120, 12083− 12091. (d) Superchi, S.; Donnoli, M. I.; Rosini, C. Org. Lett. 1999, 1, B
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