TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C60

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A TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C Complexes Sherif Abdulkader Tawfik, Xiang Y. Cui, Simon P. Ringer, and Catherine Stampfl J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.7b07442 • Publication Date (Web): 07 Nov 2017 Downloaded from http://pubs.acs.org on November 15, 2017

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The Journal of Physical Chemistry

A TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C60 Complexes Sherif Abdulkader Tawfik,∗,† X. Y. Cui,‡ S. P. Ringer,¶ and C. Stampfl† †School of Physics, The University of Sydney, New South Wales, 2006, Australia ‡Australian Centre for Microscopy and Microanalysis, and School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, New South Wales, 2006, Australia ¶Australian Institute for Nanoscale Science and Technology, and School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, New South Wales, 2006, Australia E-mail: [email protected]

Abstract

applying fullerenes as optical characterization agents for individual nucleic acid bases (NABs) is a desirable feature for DNA analysis, as an alternative to organic reagents. 3–5 In the field of DNA photocleavage, in which light triggers nuclease activity (the nuclease being an enzyme that cleaves phosphodiester bonds between nucleotides), 6,7 the application of C60 as photocleavage agents has attracted significant attention. This is because C60 , acting as an electronpoor photosensitizer, mediates the photocleavage reaction. 8–11 Another application of C60 DNA conjugation is cancer radiation therapy, where C60 has been proposed to serve as a future anti-radiation agent: it was reported that C60 -DNA conjugation protects against the side effects of cancer radiation therapy by quenching oxidative damage that occurs when DNA is exposed to radiation. 12 The optical response of C60 /DNA conjugates has, therefore, attracted a lot of attention. Several groups have reported experimental optical responses of C60 /DNA conjugates. The ultraviolet (UV)-visible optical characterization of C60 derivatives (functionalized by oxygen and hydroxyl groups) integrated into double-strand and single-strand DNA molecules was reported in Ref. 5, where the authors detected features in the visible absorption spectrum. The infrared (IR) characteristics of DNA/C60 in DNA hydro-

The potential of C60 as a nucleic acid base (NAB) optical sensor is theoretically explored. We investigate the adsorption of four NABs, namely adenine, cytosine, guanine and thymine on C60 in the gas phase. For the optimal NAB@C60 adsorption configurations, obtained using a dispersion-corrected density functional, we calculate the vis-near ultraviolet optical response using time-dependent density functional theory. While the isolated C60 and NAB molecules do not exhibit visible optical excitation, we find that C60 /NAB conjugation gives rise to distinct spectral features in the visible range. These results suggest that C60 conjugation can be applied for photodetection of individual NABs.

Introduction Fullerene-biomolecule conjugates have become an important area of biomedical research during the past two decades. 1,2 Such conjugation gives rise to many interesting biological and chemical phenomena owing to the unique optical, electrochemical and other physical properties of fullerenes. Consequently, fullerenes, in particular C60 , are promising for a wide range of biomedical applications. The possibility of

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(PBE), 19 and the local-density approximation (LDA). 20 To accurately account for the weak interaction between C60 and the NABs, we consider the VV 21 and the DRSLL 22 van der Waals self-consistent dispersion corrections. In addition, we perform PBE-GD2 Grimme dispersion potential calculations using GAUSSIAN09 23 for comparison. SIESTA uses basis sets comprised of numerical atomic orbitals, and approximates the atomic potential in terms of Troullier-Martins 24 norm-conserving pseudopotentials. The auxiliary basis uses a real–space mesh with a kinetic energy cutoff of 500 Ry, and the basis functions are radially confined using an energy shift of 0.005 Ry (see Ref. 18 for details). We allow full atomic relaxation until the forces on the atoms are less than 0.01 eV/˚ A. For the GAUSSIAN09 calculation, we apply the basis set 6311++G(d,p). The optical absorption spectra of the NABs and C60 /NABs are computed within a realspace real-time version of TDDFT, as implemented in the OCTOPUS code, version 4.1.2, 25 where we adopt the LDA 20 for the exchangecorrelation potential. The choice of the LDA in our TDDFT simulation is because it has been established as being the most numerically stable functional. 15 TDDFT is an efficient approach to calculate electronic excitations in finite systems, due to its simplicity and moderate computational cost, 15 and has provided good results for the optical response of a large set of molecular systems, including some biomolecules. 26–29 TDDFT does not rely on perturbation theory and is competitive with implementations in the frequency domain, 30,31 and in its linear-response form, is already a widely used approach for calculating optical spectra of small atom clusters and molecules. The optical response is computed in two steps. First, calculation of the ground state electronic structure is performed using the structures relaxed in SIESTA. Then, the ground state is perturbed with a small electric field (a delta kick) of magnitude k0 along the three principal Cartesian directions by applying the external potential V (x, t) = k0 xi δ(t), xi = x, y, z which shifts the wavefunctions by

gel were addressed in Ref. 13. The presence of C60 and C70 in an aqueous dispersion was found to induce effective visible-light DNA cleavage. 14 This growing potential of fullerenes in DNA research necessitates a critical investigation of the interaction between DNA bases, whether isolated or in solution, with pristine and functionalized fullerenes in order to assess the applicability of fullerenes as optical sensors (which would distinguish between different NABs via colors) as well as visible-light cleavage photosensitizers. In this respect, first-principles theoretical investigations can yield much insight, which is the subject of the present work. Optical absorption spectra are widely used to experimentally characterize the structural and dynamical properties of biomolecular systems, 15 including DNA and DNA-based compounds. 16 Therefore, the full characterization of the optical properties of DNA molecules and DNA-based complexes is of great interest. For the isolated DNA bases, there are numerous experimental and theoretical results concerning their optical response. 15,17 However, to the best of our knowledge, the investigation of the optical properties of DNA-fullerene conjugates has not been tackled theoretically. In the present paper, we perform densityfunctional theory (DFT) investigations of the adsorption of the four NABs, namely, adenine, cytosine, guanine and thymine on C60 , followed by calculation of the optical spectra of the energetically favorable NAB@C60 structures using time-dependent density functional theory (TDDFT). Our results reveal that unlike the C60 and individual NABs, NAB@C60 exhibit distinct spectral features in the visible range. This suggests that C60 can be used for optical probing of individual NABs.

Computational details To obtain the atomic and electronic structure of the NAB@C60 complexes, we perform spinunrestricted DFT calculations with the SIESTA code, 18 using the generalized gradient approximation for the exchange-correlation functional as developed by Perdew, Burke and Ernzerhof


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a small phase ψi −→ eik0 xi ψi . Next, the timedependent Kohn-Sham (KS) orbitals are propagated for a finite time, and the dynamical polarizability is obtained as Z 1 αi (ω) = − d3 xi δn(r, ω), (1) k0

Ead = E(NAB@C60 ) − E(NAB) − E(C60 ), (3) where E(NAB@C60 ) represents the total energy of the NAB@C60 complex, E(NAB) the total energy of the individual free NAB molecule and E(C60 ) the total energy of the C60 molecule. To identify the most favorable adsorption site of each NAB on C60 , we have compared the adsorption energies using GGA, LDA, DRSLL, VV and PBE-GD2 of four initial configurations (displayed in the Supplementary Material). Table 1 displays the adsorption energies for the most favorable structures using the five functionals mentioned above. Our calculations show that, in agreement with the results reported in Ref. 34 (where, in that reference, the authors compared the adsorption energies of six initial configurations and used a range of meta-GGA and a dispersion-corrected density functional), for thymine (T), guanine (G), and cytosine (C), adsorption on the bridge site is the most stable (the bridge site between two hexagons), while for adenine (A), the most stable site is the top site (cf. Fig. 2(b)). All the considered exchange-correlation functionals predict that G has the largest adsorption energy while A is the second largest. The inclusion of dispersion forces results in a notable increase in the calculated Ead relative to the values obtained using the GGA functional, making them closer to the values obtained using the LDA functional. The Ead computed with the DRSLL self-consistent dispersion potential, and those calculated within the PBE-GD2 dispersion correction, are consistently closer to each other for each of the four complexes, than to the Ead obtained with the LDA and VV. Owing to the different nature of the corrections, PBE-GD2 yields a lower (more favorable) adsorption energy of cytocine than thyamine, which is opposite to the results obtained with VV and DRSLL. It should be noted that the adsorption energies of T and C on C60 obtained using PBE-GD2 are very close (differ by only ∼ 0.007 eV, cf. Tab. 1) and would be sensitive to small variations in the atomic structure. Generally, the adsorp-

where δn(r, ω) is the Fourier transform of the relative density n(r, t) − nGS (r), and nGS (r) is the ground state density. The photoabsorption cross-section, the quantity usually measured in experiments, is proportional to the imaginary part of the polarizability, σ (ω), averaged over the three space directions 32 σ (ω) =

4πω 1 X Im αγ (ω) , c 3 γ

(2)

where c is the speed of light and the summation is over the three axial coordinates. The numerical parameters in the OCTOPUS calculations are the following: time step of 0.002 eV/¯h, total propagation steps of 10,000, spacing of realspace mesh points of 0.2 ˚ A and radius of wave function domain around each nucleus of 6 ˚ A.

Results and discussion The atomic structure of the four considered NAB molecules are shown in Fig. 2(a) along with that of C60 structures obtained using SIESTA. Within the GGA (LDA) functional, the calculated C−C bond lengths in C60 for the hexagon-hexagon (hh) and hexagon-heptagon (hp) bridges are 1.412 (1.400) ˚ A (hh) and 1.462 ˚ (1.448) A (hp), which compare very closely to those of 1.418 (1.406) ˚ A (hh) and 1.468 (1.453) ˚ A (hp) reported in Ref. 33. Using the VV(DRSLL) dispersion functionals, the calculated C−C bond lengths are 1.401 (1.399) ˚ A A (hp). The HOMO(hh) and 1.451 (1.449) ˚ LUMO gap of C60 obtained using the GGA and LDA functionals is 1.61 eV for both cases, as calculated by the SIESTA code, and is 1.55 eV as calculated with the OCTOPUS code, in agreement with the theoretical value quoted in Ref. 33. The adsorption energy, Ead , for the complexes NAB@C60 is defined as


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Table 1: The adsorption energies Ead of the NAB@C60 conjugates obtained using the LDA, GGA, DRSLL, VV and PBE-D2 exchange-correlation functionals, in units of eV. A@C60 C@C60 G@C60 T@C60

LDA −0.535 −0.491 −0.634 −0.498

GGA −0.185 −0.174 −0.217 −0.157

DRSLL −0.545 −0.473 −0.593 −0.496

VV −0.629 −0.552 −0.702 −0.563

PBE-GD2 −0.466 −0.428 −0.542 −0.421

Table 2: The adsorption distances, defined as the shortest separation between the atoms of the NAB and C60 , in units of ˚ A. A@C60 C@C60 G@C60 T@C60

LDA 2.784 2.807 2.773 2.713

GGA 3.180 3.441 3.184 3.217

DRSLL 3.104 3.301 3.085 3.076

VV 2.928 3.005 2.917 2.892

PBE-GD2 2.943 3.051 2.941 2.879

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tion energies of C@C60 and T@C60 are consistently very close for all functionals (differing in magnitude by less than 0.023 eV), in agreement with the behavior reported for calculations using dispersion-corrected and metaGGA functionals in Ref. 34. An important observation from Tab. 1 is the order of the binding strengths. In particular, spectroscopic measurements determined the binding order to be G > A > T > C, 35 as predicted by our DRSLL and VV calculations. Table 2 displays the adsorption distances, defined as the shortest separation between the atoms of the NAB and C60 . An interesting observation is that the values of the adsorption distances obtained using VV and PBE-GD2 are very close. The GGA values are larger than the LDA values, as would be expected, and the bond distance of the C@C60 is the largest in all of the functionals, most notably for GGA and DRSLL (larger than the other NAB by 0.2−0.3 ˚ A). The order of the distances in VV, DRSLL and PBE-GD2 is C > A > G > T. To understand the interactions between the NABs and C60 , we have calculated the total atoms projected density of states (pDOS) as shown in Fig. ??, using the PBE functional in SIESTA. The large C-related peaks are from C60 and the smaller peaks are NAB-related. For A@C60 and G@C60 , a peak of NAB molecular origin can be seen near the valence band max-

pDOS (arb. units)

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Figure 1: (Color online) The partial density of states for (a) A@C60 , (b) G@C60 , (c) C@C60 and (d) T@C60 , resolved by the atoms. The Fermi level is the zero enegy point. imum. For T@C60 , the highest occupied state is, however, C60 -related. The lowest unoccopied states are of C60 nature for all systems. The optical absorption spectra of the isolated C60 and NAB molecules in the gas phase is shown in Fig. 3. The spectrum of C60 (cf. Fig. 3(a)) is composed of a wide empty region up to about 2.5 eV, very small peaks between 2.5 eV to 3.0 eV, a series of clear peaks of increasing intensity at 3.38 eV, 4.32 eV, 5.32 eV, 5.92 eV, and some broader peaks at higher energy. These features are in good agreement with results reported in Ref. 33 which also uses the


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of NABs is that they have high UV absorption spectra, hence NABs are known as the primary chromophores of UV radiation. 39 (a) 14.00

DRSLL VV

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1.50 1.00 0.50 0.00 0.0

Figure 2: (Color online) (a) Relaxed atomic structures of the isolated C60 and the four NABs considered: adenine (A), cytosine (C), guanine (G), and thymine (T). (b) Relaxed atomic structures of the NAB@C60 systems, obtained using the GGA. Cyan spheres represent C, white spheres H, purple spheres N and red spheres O.

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Figure 3: (Color online) Optical spectra of (a) the C60 molecule calculated using the VV and DRSLL corrections, and (b) the four NAB molecules in the gas phase calculated using the VV correction. The curves have been vertically displaced from each other for better visibility. Interestingly, the NAB/C60 complexes gives rise to excitation spectra in the visible region (1.6 − 3.3 eV, 390 − 700 nm) as can be seen in Fig. 4, which displays the vertical excitation spectra from 0 to 4 eV. These same excitation energies are not present in either the individual NAB or C60 molecules. A clear C60 -related feature, however, common in all systems in the range 2.3-3.0 eV can be seen. This range of excitation energies is presented in Tab. 4. According to Tab. 4, there are characteristic yellow (590 nm, 2.10 eV) and blue (449 nm, 2.76 eV) absorption peaks in C@C60 , blue (451 nm, 2.75 eV) in A@C60 , green (512 nm, 2.42 eV) in G@C60 and red (725 nm, 1.71 eV) and blue (443 nm, 2.80 eV) in T@C60 . The green color in the spectrum of G@C60 , the yellow color in the visible spectrum of C@C60 and the red color in the visible spectrum of T@C60 indicate the potential of using the C60 to detect different NABs

same theoretical method to calculate optical excitation spectra. NABs (cf. Fig. 3(b)) have strong π −→ π ∗ transitions, which are responsible for the bands seen in their UV absorption spectra, 16 and lone electron pairs of the O and N are responsible for additional n −→ π ∗ excitations. The vertical excitation energies for the NAB molecules are listed in Tab. 3. It can be seen that the first excitation (π −→ π ∗ 15 ) is at 4.14 eV for C, 4.32 eV for T, at 4.43 eV for G and at 4.46 eV for A in fair agreement with calculations reported in Ref. 15 and experimental measurements. 36–38 The highest excitation peak in our calculations for both A and T occurs in the energy region around 6.72 eV, while the highest excitation energy for the other two NABs occur at lower energies (6.15 eV in C and 6.24 in G). A common feature in the excitation spectra


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Table 3: Calculated (TDDFT) and experimental (exp) vertical excitations energies for the four NABs: A, G, C and T, in units of eV. Experimental values are obtained from Ref. 15. A exp TDDFT 4.59 4.46 4.8-4.9 4.87 5.7-6.1 5.60 6.26 6.13 6.81 6.72 7.06 7.73 7.42

exp 4.5-4.7 5.0-5.1 5.8-6.0 6.3-6.6 7.00

T TDDFT 4.32 5.06 5.59 6.17 6.70 7.04 7.37

exp 4.60 5.0-5.3 5.4-5.8 6.1-6.3 6.7-7.1

C TDDFT 4.14 4.83 5.35 5.77 6.15 6.50 6.88 7.14 7.59

exp 4.4-4.5 4.9-5.0 5.7-5.8 6.1-6.3 6.6-6.7

G TDDFT 4.43 4.70 5.09 5.61 6.24 6.70 7.23

ergy peaks occur primarily in trasition between HOMO, HOMO-1 and LUMO, LUMO+1 except for T@C60 , where the lowest energy peak involves the LUMO+3 orbital. The calculations of the optical spectra in the present study are performed in the gas phase. It is important here to point out that the spectral results obtained in the gas phase might be slightly higher in energy (∼ 0.2 eV) than the situation in solution. 28,40 Such spectra would be rigidly shifted by that quantity, and therefore would slightly affect the specific color of some of the low energy peaks, but will not impact onset of new optical excitation in the conjugation systems. It should also be noted that the calculations performed in the present work might underestimate the optical excitations due to LDA functional, as shown in Table III, for the four NABs, most of the calculated vertical excitation energies are slightly underestimated compared with the experimental values. Nevertheless, there have been several reports on using rangeseparated-based approaches that have shown excellent agreement with experiment. 41,42

with distinctive visible optical features for the NABs, and that C60 could be used as an optical characterization agent for NABs.

Figure 4: (Color online) Optical spectra of the isolated, free NABs and C60 , and NAB@C60 complexes in the gas phase from 0.0 eV up to 4.0 eV. The curves have been vertically displaced from each other for better visibility. The colored circles inicate the absorption peak color. We have analyzed the spectral peaks of the NAB@C60 complexes in Fig. 4 in light of the energies of the frontier orbitals. Table 4 displays the assignment of orbital transitions for the visible spectral peaks. The band gaps of the molecules, given by, ELU M O−HOM O (HOMO is the highest occupied molecular orbital, LUMO is the lowest unoccupied molecular orbital) are 1.39 eV for A@C60 , 0.80 eV for C@C60 , 1.39 eV for G@C60 and 1.54 eV for T@C60 . The low en-

Conclusion In conclusion, we have explored the potential of C60 as a DNA optical sensor. We calculated the atomic structure of the C60 /NAB configurations using the GGA, LDA, as well as van der Waals corrections including the two


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Table 4: Vertical excitation energies and the corresponding vertical electron transitions for the four NAB@C60 conjugates: A, G, C and T, within the range 0 to 4 eV, in units of eV. A@C60 1.59 2.75

HOMO→LUMO+1 HOMO-1→LUMO+1

C@C60 0.80 2.1 2.76

HOMO→LUMO HOMO-3→LUMO HOMO-3→LUMO+2

self-consistent methods VV and DRSLL, and the Grimme-based DFT-D2 method. For the structures obtained using dispersion-corrected density-functionals, we calculate the vis-near UV optical response using TDDFT. We find that C60 /NAB conjugation gives rise to spectral features in the visible region for each of the NABs. These results suggest the potential of C60 /DNA conjugation in DNA optical characterization.

G@C60 1.39 2.42

HOMO→LUMO HOMO-3→LUMO

T@C60 1.71 2.80

HOMO→LUMO+3 HOMO-3→LUMO+3

(5) Kysil, O.; Sporysh, I.; Buzaneva, E.; Erb, T.; Gobsch, G.; Ritter, U. ; Scharff, P. The C60 Fullerene Molecules Integration by ds-, ss-DNA Molecules in Fluids: Optical Spectroscopy Characterization of the Biointerface Organization. Mat. Sci. Eng. B, 2010, 169, 85. (6) Joyce, L.E.; Aguirre, J. Dafhne; Angeles-Boza, Alfredo M.; Chouai, Abdellatif; Fu, Patty K.-L.; Dunbar Kim R.; Turro, Claudia. Photophysical Properties, DNA Photocleavage, and Photocytotoxicity of a Series of dppn Dirhodium (II, II) Complexes. Inorg. Chem., 2010, 49, 5371. (7) Ros, T. Da; Prato, M. Medicinal Chemistry with Fullerenes and Fullerene Derivatives. Chem. Comm., 1999, 663.

Acknowledgments This research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI), which is supported by the Australian Government.

(8) Bernstein, R.; Prat, F.; Foote, C. S. On the Mechanism of DNA Cleavage by Fullerenes Investigated in Model Systems: Electron Transfer from Guanosine and 8-oxo-guanosine Derivatives to C60 . J. Amer. Chem. Soc., 1998, 121, 464.

Supplementary Materials

(9) Boutorine, A. S.; Takasugi, M.; Helene, C.; Tokuyama, H.; Isobe, H.; Nakamura, E. FullereneOligonucleotide Conjugates: Photoinduced SequenceSpecific DNA Cleavage. Angew. Chemie Int. Ed. Eng., 1995, 33, 2462.

The atomic structure of the four conjugated structures NAB@C60 .

(10) Bosi, S.; Tatiana, D.; Spalluto, G.; Prato, M. Fullerene Derivatives: an Attractive tool for Biological Applications. Europ. J. Med. Chem., 2003, 38, 913.

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Cytosine

Adenine

Guanine

Thymine

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TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C60

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