Understanding the Interaction of Nucleobases with Chiral

Article pubs.acs.org/JPCC

Understanding the Interaction of Nucleobases with Chiral Semiconducting Single-Walled Carbon Nanotubes: An Alternative Theoretical Approach Based on Density Functional Reactivity Theory Amrit Sarmah and Ram Kinkar Roy* Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani 333031, Rajasthan, India S Supporting Information *

ABSTRACT: The present study describes an alternative and computationally cost-effective theoretical approach to explore the interaction of nucleobases with different semiconducting chiral single-walled carbon nanotubes (SWCNTs). Implementing density functional reactivity theory (DFRT) based CDASE (comprehensive decomposition analysis of stabilization energy, Bagaria et al. Phys. Chem. Chem. Phys. 2009, 11, 8306), scheme kinetic and thermodynamic aspects of the interaction between different DNA bases as well as Watson−Crick base pairs (AT and GC) with SWCNTs are investigated and that is also without performing computationally intensive transition state optimization or thermochemistry calculation. The trend of interaction generated by reactivity parameters (based on the CDASE scheme) follows the experimentally as well as theoretically verified order, G⟩A⟩T⟩C⟩U, observed earlier. Conventional binding energy calculations on some of the chosen systems using the ONIOM QM:MM approach generate a reasonably satisfactory trend of interaction. Reported theoretical findings can be exploited as an alternative (albeit qualitative but rapid) technique to understand the functionalization of CNTs with DNA bases.

1. INTRODUCTION One of the most exciting allotropes of carbon discovered recently is the carbon nanotube (CNT).1,2 This cylindrical tube-shaped material consists of a long series of sp2-hybridized carbon atoms3 and typically has a diameter ranging from less than 1 to 50 nm.4 Conceptually, CNTs are considered as hollow graphene sheets designed in a rolled-up fashion. When only one layer of graphene sheet is present, it is called a singlewalled carbon nanotube (SWCNT), and multilayer structures are known as multiwalled carbon nanotubes (MWCNTs).1 Extraordinary mechanical, optoelectronic, and thermal properties of CNTs uncorked its application in biosensors,5,6 biocompatible agents,7 DNA and protein transporters,8 and many more. However, the chemical inertness of a SWCNT constricts its application to a major extent. Thus, to enhance the chemical reactivity of CNTs some chemical modifications need to be done on the surface of the SWCNT, and this whole procedure is termed “functionalization of SWCNTs”.9−13 One of the most promising techniques to carry out the SWCNT functionalization is to exploit the noncovalent interaction of SWCNTs with DNA or protein.10 Recently, studies on the DNA/CNT combination have become an emerging area in the field of nanotechnology as it finds some potential applications in the electrochemical detection of DNA,14 DNA sensors,15 DNA encapsulation,16 transformations of DNA conformation,17 etc. The DNA/CNT complexes showed promising activity in the antitumor drug delivery system and enzyme immobilization.18 © XXXX American Chemical Society

To offer a detailed insight into the interaction of semiconducting SWCNTs with DNA, a considerable increase in the experimental as well as the theoretical studies has been observed in the past few years. The isolation of SWCNTs from synthetic aggregates is a major technical concern. Zheng et al. reported the formation of a stable DNA/CNT complex, which can efficiently disperse CNTs in the aqueous solution.19,20 A thorough study on the adsorption of nucleobases adenine and thymine and their radicals on the SWCNT surface has been performed by Shtogun et al.21 The interaction between the π-orbitals of nucleobases and SWCNTs plays a crucial role during the physisorption process of nucleobases on SWCNTs. Wang has reported22 that the cross-stacking gas-phase binding energy of nucleobases with both (10,0) and (5,5) SWCNTs follows the order G⟩A⟩T⟩C. However, in the aqueous phase the order of binding energies changes to A⟩G⟩T⟩C for the isomer (10,0).22 In a combined theoretical and experimental study Das et al.23 have observed that the binding energy variation in the gas phase for four nucleobases A, T, G, and C with the isomer (5,5) follows the order G⟩A⟩T⟩C⟩U. In an experimental study, Sowerby et al.24 reported the adsorption isotherm for purine and pyrimidine bases in a solid−liquid interface. The observed trend in the Received: June 14, 2013 Revised: September 16, 2013

A

dx.doi.org/10.1021/jp4058803 | J. Phys. Chem. C XXXX, XXX, XXX−XXX

The Journal of Physical Chemistry C

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2. THEORETICAL DEVELOPMENT The formalism of energy lowering (i.e., stabilization energy (SE)) for an adduct formation process between the electron acceptor A and the electron donor B, considering a small amount of electron transfer (ΔN), was developed by Parr and Pearson25 as 1 EA + E B = EAo + E Bo + (μAo − μBo )ΔN + (ηA + ηB) 2 2 (ΔN ) + ... (1)

variation of adsorption behavior of nucleobases on a crystalline graphite surface followed the order G⟩A⟩hypoxanthine⟩T⟩C⟩U. In the last three decades a substantial growth of computational chemistry has been observed with the development of various local and global reactivity descriptors25−40 in the context of density functional reactivity theory (DFRT).41−47 In recent years, newly proposed reactivity descriptors are widely used to explain the mechanisms of different types of chemical reactions.48−60 Local reactivity indices include Fukui function [f(r)],26,31 local softness (S+k , S−k , and S0k ),30 local hardness [η(r)],32,38−40 relative electrophilicity (S+k /S−k ) and relative nucleophilicity (Sk−/Sk+),33,34 local electrophilicity,58−60 etc. Global reactivity descriptors such as chemical potential61 (i.e., the negative of electronegativity62), chemical hardness25(η), global electrophilicity index,63,64 nucleophilicity,65−67 electrofugality and nucleofugality,68,69 etc., are mainly used for intermolecular reactivity study. Recently, Roy and collaborators proposed a new energy decomposition scheme,70 termed CDASE (comprehensive decomposition analysis of stabilization energy). This scheme has been effectively used to explore different types of chemically as well as biologically important reactive interactions.70−73 They have also argued that the global electrophilicity descriptor (w),64 proposed by Parr et al., can be conceptually correlated to the expression of stabilization energy25 when the donor is a perfect one. Considering certain approximations (i.e., the chemical potential and the chemical hardness of the prefect donor to be zero), Roy and collaborators proposed a new reactivity descriptor, “internal assistance”,70 as it depends solely on the structural and electronic properties of the two isolated chemical species. More appropriately it can be called the “kinetic assistance” as it can play a key role in determining the rate of a chemical reaction. The study as described in the present article will be centered on the theoretical investigation of the kinetic and thermodynamic factors associated with the interaction between the nucleobases and the semiconducting SWCNTs. The strategy as described here can be considered as an alternative methodology to perform comprehensive investigations on relatively large systems without explicitly going through computationally intensive transition state or thermochemistry calculations. Still it is possible to obtain relevant kinetic and thermodynamic information in the process of complex formation between the two interacting systems. Traditional binding energy calculations on some selected systems are also carried out (using the ONIOM QM:MM approach) to justify the qualitative trend obtained from the five CDASE scheme based parameters. The article is organized in the following way: A brief discussion on the theoretical background of the proposed CDASE scheme is presented in Section 2. Adopted computational methodology is described in Section 3. Section 4(a) deals with the values of different kinetic and thermodynamic reactivity parameters generated from the CDASE scheme. These values are analyzed in a systematic way, critically acclaiming their roles in explaining the interaction of nucleobases with semiconducting chiral SWCNTs. The calculation of binding energy for four different SWCNTs with five nucleobases using the ONIOM QM:MM approach is discussed in Section 4(b). Finally, in Section 5 we have summarized our entire study on the interaction of nucleobases with SWCNTs.

where ΔN = NA − N0A = N0B − NB (which indicates that B is an electron donor and A is an electron acceptor). The terms E0A and E0B denote the energies of systems, A and B, respectively, before the electron transfer. Similarly, EA and EB denote the corresponding quantities after the electron transfer. The reactivity descriptors μ and η are known as chemical potential61 and chemical hardness,25 respectively, of the two interacting species. The state of maximal flow of electrons can be achieved by applying the chemical potential equalization principle (i.e., μA = μB or χA = χB; here χ denotes the electronegativity values).61,62 When

ΔE/ΔΝ = 0

(2)

the stabilization energy (ΔESE) can be written as ΔESE = −

(μBo − μAo )2 2(ηA + ηB)

(3)

and the corresponding electron transfer (ΔN) as ΔN =

μBo − μAo (ηA + ηB)

(4)

In another paper, Parr et al. considered “an electrophilic ligand immersed in an idealized zero-temperature free electron sea of zero chemical potential”, and in such a situation it was shown that 64

ΔE = −

μ2 2η

(5)

and

ΔNmax = −

μ η

(6)

In this case μ and η refer to the chemical potential and chemical hardness, respectively, of the electrophilic ligand only. Parr et al. proposed a new reactivity descriptor, global electrophilicity (w),64 which is negative of ΔE for an energetically favorable charge transfer process (i.e., η > 0, ΔE > 0) as

w = −ΔE =

μ2 2η

(7)

Taking the analogy from the global reactivity descriptor, w, some other reactivity descriptors such as nucleophilicity,65−67 electrofugality, and nucleofugality68,69 are also proposed subsequently. Chattaraj et al.29 explore various kinetic and thermodynamic aspects of w to establish a good correlation with the relative experimental trends in different types of reactive interactions. The works of Perez et al.58 show that the empirical measure of B



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Figure 1. Optimized structures [at the B3LYP/6-31G(d) level of theory] of Me-capped nucleobases and base pairs.

The negative of this stabilization energy (i.e., (μoA)2/2ηA) is the “global electrophilicity” of the acceptor A (i.e., wA) as defined before.64 Thus, global electrophilicity (w), which emerges out to be a fundamental descriptor of a chemical species, originates from the expression of stabilization energy25 when the donor is a perfect one. Roy and collaborators70 proposed modified expression of stabilization energy (SE) as well as its different components when interaction takes place between donors and acceptors of comparable size. For such a system, the mutual effect of interacting species on each other cannot be neglected. Then, the expression for the overall stabilization energy can be denoted more appropriately as

electrophilicity (based on experimental kinetic data) correlates well with the theoretical global as well as local electrophilicity. Domingo et al.60 used the global electrophilicity index (w) to test the intrinsic electronic contributions to the Hammett substituent constant. The substituent effect on the fragments and intermediates (in the process of indigo dye formation) has been evaluated by Lamsabhi et al. using global and local electrophilicity descriptors.59 However, Roy and collaborators70 argued that conceptually the global electrophilicity descriptor (w) as proposed by Parr et al.64 can be derived from the overall stabilization energy expression (i.e., eq 3) after taking into consideration the fact that the chemical potential (μ) as well as chemical hardness (η) of the perfect donor were assumed to be zero. That is ΔESE = −

ΔESE(AB) = ΔEA(B) + ΔEB(A) = −

(μAo )2 2ηA

(μBo − μAo )2 2(ηA + ηB)

(9)

The corresponding electron transfer (ΔN) can be expressed as usual by eq 4. The expressions for the change of individual energy components (i.e., ΔEB and ΔEA) can be denoted as

(8) C



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Table I. Values of the Global Electrophilicity Difference (Δw) (in kcal mol−1) for a Different Combination of Chosen SWCNTs (Considered As Acceptor, A) and Nucleobases (Considered As Donor, B)a DNA bases

a

SWCNT

guanine

adenine

thymine

cytosine

uracil

A−T

G−C

m:n m:n m:n m:n m:n m:n m:n m:n

114.58 134.13 142.03 158.30 165.65 174.91 217.66 231.87

111.82 131.36 141.75 155.55 162.88 172.16 214.89 229.10

108.85 128.39 141.45 151.16 159.92 167.77 211.92 226.13

104.46 124.00 141.01 148.20 155.52 164.80 207.53 221.74

101.71 121.26 140.74 145.43 152.78 162.03 204.78 218.99

106.06 125.61 141.17 151.14 157.13 167.75 209.12 223.35

108.87 128.42 141.45 153.95 159.94 170.55 211.94 226.15

6, 5 9, 7 9, 5 9, 2 7, 6 8, 3 10, 2 7, 5

The values are generated at the B3LYP/6-31G(d) level of theory.

ΔE B(A) =

⎛ μ o − μ o ⎞⎤ μBo − μAo ⎡ o A ⎥ ⎢ −μ + 1 η ⎜⎜ B ⎟⎟ ηA + ηB ⎢⎣ B 2 B⎝ ηA + ηB ⎠⎥⎦

(10)

⎛ μ o − μ o ⎞⎤ μBo − μAo ⎡ o A ⎥ ⎢μ + 1 η ⎜⎜ B ⎟⎟ ηA + ηB ⎢⎣ A 2 A ⎝ ηA + ηB ⎠⎥⎦

(11)

structures of different SWCNTs are shown in the Supporting Information. The numerical values are generated by using the hybrid B3LYP functional (Becke 3-Parameter exchange functional79−82 along with correlation functional as proposed by Lee, Yang, and Parr83) as implemented in the Gaussian 09, Revision C.01 software package.84 As mentioned in Section 2, the kinetic aspects are studied using the difference of global electrophilicity descriptor between the acceptor and the donor (i.e., Δw = wA − wB) and the energy raising component, ΔEB(A)(eq 10). The thermodynamic aspects are investigated using ΔEA(B) (eq 11) and ΔESE(AB) (eq 9). The charge transfer values ΔN (eq 4) can be used to study both kinetic and thermodynamic aspects because it is formally linked to ΔEB(A) (eq 10), ΔEA(B) (eq 11), and ΔESE(AB) (eq 9). That is, ΔN can be considered as both a kinetic and thermodynamic descriptor of reactivity. The geometries of eight SWCNTs, nucleobases, as well as base pairs have been optimized (without imposing any constraint) at the B3LYP/6-31g(d)85−88 level of theory. Subsequent single-point calculations are carried out at the same level of theory. Vertical ionization potential (IP) and electron affinity (EA) values are considered in the present study (i.e., calculations of cationic and anionic systems are performed using the geometries of the neutral systems only). While the restricted level of theory (RB3LYP/6-31G(d)) is used for the neutral systems, the unrestricted level of the same theory (UB3LYP/6-31G(d)) is chosen for calculations of the corresponding ionic systems. The details of binding energy calculations on some of the chosen SWCNTs with DNA bases using the ONIOM QM:MM approach are given in Section 4(b).

and ΔEA(B) =

Argued further, it was also shown how ΔEB(A) can be used to study the kinetics, whereas ΔEA(B) is for thermodynamics of chemical reactions.70 In the present study kinetic aspects of the interaction between the SWCNTs (i.e., the acceptors, A) and the DNA bases (i.e., the donors, B) are investigated by using Δw (i.e., the difference of global electrophilicity values between the acceptors and the donors) and ΔEB(A), whereas ΔEA(B) and ΔESE(AB) are exploited to understand the thermodynamic stability of the resultant adducts. The electron transfer values (i.e., ΔN) are used to explain both the rate of interaction as well as stability of the adducts as it is formally linked to all the kinetic and thermodynamic descriptors as shown by eqs 9−11. To compare the trend of stabilities of the resultant complexes, as generated by ΔEA(B) and ΔESE(AB) values, conventional binding energy (BE) calculations are also performed on some of the chosen systems. The equation used here is ΔE = Enucleobase+SWCNT − (Enucleobase + ESWCNT)

(12)

3. ADOPTED MODELS AND COMPUTATIONAL METHODOLOGY To carry out the investigation, eight different types of semiconducting chiral SWCNTs are chosen as prototype electron acceptors, whereas five nucleobases, A, T, G, C, and U along with two Watson−Crick (W−C) base pairs, A−T and G−C, are chosen as electron donors. Selected SWCNTs, consisting of lattice vectors (10,2), (8,3), (9,2), (6,5), (9,5), (7,6), (7,5), and (9,7), belong to the chiral SWCNT conformation. For convenience, nucleobases are modeled after capping N1 (pyrimidines) and N9 (purines) nitrogen atoms with a methyl group. Although the absence of phosphate and sugar moieties, which connect the nucleobases, changes the environment of the systems significantly, it is a well-accepted modeling technique74−78 and provides valuable information for qualitative understanding of interactions related to DNA. The methyl-capped DNA bases and base pairs are shown in Figure 1. The vertical, horizontal, and inside views of the optimized

4. RESULTS AND DISCUSSION Normally, genetic DNA consists of four bases, adenine (A), guanine (G), cytosine (C), and thymine (T). However, another component uracil (U), which is a constituent of RNA, is also considered as a mutagenic base in DNA sequence. Both A and G are purine bases, containing one six-membered pyrimidine ring fused with a five-membered imidazole ring. Adenine has the functional group −NH2, and guanine contains both −NH2 and −CO as functional groups. On the other hand, T and C are known as pyrimidine bases consisting of a single sixmembered pyrimidine ring. These four bases are arranged in stable complementary base pair sequence as A−T and G−C by strong H-bonding interaction between them in double-helical DNA structure. In a number of reported literatures74−78 DNA bases are taken as the prototype of DNA sequence to D



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Table II. Values of Positive Energy Component, ΔEB(A) (Equation 10) (in kcal mol−1), for Different Combinations of Chosen SWCNTs (Considered As Acceptor, A) and Nucleobases (Considered As Donor, B)a DNA bases SWCNT m:n m:n m:n m:n m:n m:n m:n m:n a

9, 7 6, 5 7, 6 7, 5 10, 2 9, 5 9, 2 8, 3

guanine

adenine

thymine

cytosine

uracil

A−T

G−C

10.42 10.89 13.94 14.91 15.41 18.00 27.15 29.67

7.94 8.51 11.42 12.24 12.78 14.88 21.70 24.32

5.13 5.79 8.55 9.20 9.77 11.36 15.84 18.53

1.54 2.34 4.50 5.44 6.06 7.10 9.16 12.00

−1.61 −0.73 1.72 2.04 2.69 3.23 3.32 6.14

7.187 7.85 11.08 11.98 12.58 14.93 23.19 26.37

11.40 11.92 15.54 16.78 17.35 20.83 35.61 38.71


species, it assists to overcome the activation barrier (hence it is called the “internal assistance” or more appropriately called the “kinetic assistance”). So, the higher the positive value of ΔEB(A) the higher will be the rate of interaction between a particular pair of interacting SWCNT and nucleobase. Table II contains the ΔEB(A) values calculated on the basis of the CDASE scheme for various combinations of SWCNTs and nucleobases. The generated ΔEB(A) values clearly show that the fastest interaction is between DNA bases with chiral SWCNTs (8,3). The rate of interaction of nucleobases with semiconducting SWCNTs, as per data in Table II, follows the sequence, G⟩A⟩T⟩C⟩U. It is encouraging to note that the above trend closely resembles those reported recently by some experimental as well as theoretical studies.21−24 For example, Shtogun et al.21 reported a DFT-based study on the adsorption behavior of purine and pyrimidine bases (considering adenine and thymine as the model systems) along with their radicals on the surface of SWCNTs. Observations in that study exhibit the higher value of adsorption energy for the purine/SWCNT combination (i.e., adenine/SWCNT) compared to that between pyrimidine and SWCNTs (i.e., thymine/SWCNT). They also concluded that the DNA−CNT interaction is mainly controlled by the nucleobases, and the rest of the composite DNA system plays a secondary role.21 It is gratifying to note that the results generated from CDASE scheme based calculations also provide a similar variation in the rate of interaction, showing a higher value of ΔEB(A) for the purine/SWCNT combination and a lower value for that between pyrimidine and SWCNT. Some interesting observations are made on the rate of interaction of mutagenic base uracil with SWCNTs. In the case of interaction of SWCNTs (6,5) and (9,7) with uracil the ΔEB(A) values are found to be negative. The physical interpretation of these observations is that the interaction between uracil and these two SWCNTs might not be kinetically feasible or probably occurs due to the reversal of charge transfer that was initially assumed to be, i.e., from uracil to SWCNTs. However, positive Δw values for the interaction of uracil with these two SWCNTs (Table I) strengthen the argument that the direction of charge transfer is from uracil to SWCNTs only, and negative values of ΔEB(A) might have been generated due to some theoretical artifact. This last argument seems to be more justified as these two values becomes positive (hence as expected) when a higher level of basis sets [6-31G (d,p)] is used. For SWCNT (9,7) the value of ΔEB(A) is 0.42 kcal/mol, whereas for the one having lattice vector (6,5) the value is 0.44 kcal/mol. (iii). Understanding the Interaction Between SWCNTs and Nucleobases on the Basis of the Charge Transfer Value (i.e.,

understand the interaction of DNA with different surfaces (semiconducting or metallic). Semiconducting SWCNTs are constituted as networks formed by a series of sp2-hybridized carbon atoms. The delocalized π-orbitals of this network structure of carbon atoms are perpendicular to the plane of carbon atoms. At this insistence, the paradigm of interaction between SWCNTs and nucleobases can be considered as the interplay between the carbon π systems of SWCNTs and nitrogenous π systems of DNA bases. (a). Critical Evaluation of the Five CDASE Scheme Based Parameters in Explaining Interaction between Nucleobases and SWCNTs. The said interaction can be investigated under two aspects. The first one is the kinetic aspect, i.e., comparison of the rate of interaction between different pairs of SWCNTs and DNA bases. The second one is the thermodynamic aspect, i.e., comparison of the stability of the complexes formed due to this interaction. In the next few subsections the generated values of different kinetic and thermodynamic parameters will be analyzed to have a general idea of the trend of interaction between different pairs of SWCNTs and DNA bases (as well as base pairs). (i). Understanding the Rate of Interaction between SWCNTs and Nucleobases on the Basis of Difference in Their Global Electrophilicity Values (i.e., Δw). The values of Δw, calculated for different combinations of SWCNTs (i.e., the acceptors, A) and nucleobases (i.e., the donors, B), are reported in Table I. A positive value of Δw indicates that the choice of the donor and the acceptor is justified. Also, the higher the value of Δw, the kinetically more favorable the interaction is. It is obvious from Table I that the choice of donors and acceptors is physically justified (functionalized SWCNT usually behaves as an electron acceptor, and this fact is widely exploited in the photoinduced electron transfer systems in combination with a nitrogen donor such as phthalocyanines)89 and that the interactions of purine bases (guanine and adenine) with semiconducting SWCNTs are kinetically more favorable than the pyrimidine bases cytosine and thymine. Also, another earlier study claims relatively higher immobilization of purine bases, rather than pyrimidine ones, on the surface of the SWCNT.21 Moreover, according to Δw values the interaction between the G−C base pair and SWCNTs is faster when compared to that between the A−T base pair and SWCNTs. (ii). Understanding the Rate of Interaction between SWCNTs and Nucleobases on the Basis of the Positive Energy Component (i.e., ΔEB(A)). As ΔEB(A) is an energy raising term (i.e., positive quantity) and generated from the electronic parameters (e.g., IP and EA, indirectly) of the interacting E



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Table III. CDASE Scheme Based on Charge Transfer (ΔN, Equation 4) Values for Different Combinations of Chosen SWCNTs (Considered As Acceptor, A) and Nucleobases (Considered As Donor, B)a DNA bases SWCNT m:n m:n m:n m:n m:n m:n m:n m:n a

9, 7 6, 5 7, 6 7, 5 10, 2 9, 5 9, 2 8, 3

guanine

adenine

thymine

cytosine

uracil

A−T

G−C

0.140 0.146 0.182 0.193 0.199 0.228 0.323 0.348

0.103 0.110 0.144 0.153 0.159 0.183 0.254 0.281

0.064 0.072 0.104 0.111 0.118 0.135 0.183 0.210

0.018 0.028 0.058 0.063 0.070 0.081 0.104 0.133

−0.019 −0.008 0.019 0.023 0.030 0.036 0.037 0.067

0.091 0.099 0.137 0.147 0.154 0.180 0.267 0.298

0.152 0.159 0.202 0.216 0.223 0.262 0.413 0.442


Table IV. Values of the Negative Energy Component (ΔEA(B), Equation 11) (in kcal mol−1) for Different Combinations of Chosen SWCNTs (Considered As Acceptor, A) And Nucleobases (Considered As Donor, B)a DNA bases

a

SWCNT

guanine

adenine

thymine

cytosine

uracil

A−T

G−C

m:n m:n m:n m:n m:n m:n m:n m:n

−11.70 −12.32 −16.07 −17.21 −17.87 −20.86 −30.99 −34.25

−8.63 −9.33 −12.77 −13.70 −14.37 −16.74 −24.13 −27.35

−5.39 −6.14 −9.26 −9.99 −10.66 −12.40 −17.12 −20.28

−1.56 −2.39 −5.18 −5.69 −6.37 −7.47 −9.58 −12.70

1.59 0.72 −1.74 −2.08 −2.75 −3.31 −3.37 −6.32

−7.67 −8.45 −12.17 −13.17 −13.91 −16.50 −25.361 −29.17

−12.69 −13.36 −17.77 −19.20 −19.95 −23.92 −40.23 −44.24

9, 7 6, 5 7, 6 7, 5 10, 2 9, 5 9, 2 8, 3


Table V. Values of Overall Stabilization Energy (ΔESA(AB), Equation 9) (in kcal mol−1) for a Different Combination of Chosen SWCNTs (Considered As Acceptor, A) And Nucleobases (Considered As Donor, B)a DNA bases SWCNT m:n m:n m:n m:n m:n m:n m:n m:n a

9, 7 6, 5 7, 6 7, 5 10, 2 9, 5 9, 2 8, 3

guanine

adenine

thymine

cytosine

uracil

A−T

G−C

−1.28 −1.43 −2.13 −2.30 −2.46 −2.85 −3.84 −4.58

−0.67 −0.82 −1.35 −1.46 −1.60 −1.85 −2.42 −3.03

−0.27 −0.36 −0.71 −0.78 −0.88 −1.03 −1.28 −1.75

−0.02 −0.05 −0.22 −0.25 −0.31 −0.37 −0.41 −0.70

−0.02 −0.01 −0.03 −0.03 −0.06 −0.08 −0.06 −0.19

−0.49 −0.60 −1.09 −1.20 −1.33 −1.57 −2.17 −2.81

−1.28 −1.45 −2.22 −2.42 −2.60 −3.10 −4.62 −5.52


ΔN). According to eq 4, for a favorable interaction process (both kinetically and thermodynamically, see Sections 2 and 3), ΔN value should be positive, and this is possible when μ0B > μ0A or (χ0A > χ0B). Thus, it can be argued that a higher value of ΔN for a particular pair of SWCNT and nucleobase implies a greater extent of interaction between the pair. The charge transfer (ΔN) values for different combinations of SWCNTs and nucleobases, calculated on the basis of CDASE scheme, are presented in Table III. The generated ΔN values clearly show that the nucleobase guanine exhibits significantly higher value of charge transfer against all SWCNTs chosen in the present study. This important observation justifies that among the nucleobases guanine interacts fastest with SWCNTs as well as forms the most stable complex followed by adenine, thymine, cytosine, and uracil, respectively (i.e., G > A > T > C > U). Also, SWCNT (8,3) exhibits the highest ΔN values against all the

nucleobases. Hence, it can be argued that SWCNT (8,3) interacts fastest as well as forms the most stable complex with all the nucleobases compared to other chiral SWCNTs chosen here. Another important observation from the generated ΔN values is that the base pair G−C forms more stable complexes with all SWCNTs than the A−T pair. It is worth mentioning here that similar trends of interaction were also observed by Xiao et al.90 Unexpected negative values of ΔN for SWCNT (9,7) and SWCNT (6,5) with uracil are corrected by performing the calculations at higher-order basis sets (i.e., 631 G(d,p) level), and the corresponding values are 0.0048 and 0.0050, respectively. (iv). Stabilities of the Complexes Formed between SWCNTs and Nucleobases on the Basis of the Negative Energy Component (ΔEA(B)). As per eq 11, ΔEA(B) is an energy lowering term; i.e., the values are negative. This is because ΔEB(A) is a positive quantity, whereas, the overall process of F



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Figure 2. Selected higher and lower level region for the implementation of QM/MM ONIOM model calculation in the four SWCNTs.

generated using eq 9 and demonstrated in Table V. For a favorable interaction (i.e., a spontaneous charge transfer process) ΔESE(AB) will be a negative quantity, and in this way a stable complex will be formed. If the ΔESE(AB) value is high (i.e., more negative) for a particular interacting pair (of SWCNT and nucleobase) the stability of the corresponding complex formed will be more. From the observation of ΔESE(AB) values in Table V it is obvious that the order of stabilities of the corresponding complexes follows the trend as G > A > T > C > U; i.e., the most and the least stable adducts are formed with nucleobases guanine and uracil, respectively. Very recently, Das et al.23 performed an extensive theoretical and experimental investigation on the binding interaction of nucleobases with SWCNT (5,5). They have observed that the variation in binding energy in the gas phase for the four nucleobases with the SWCNT follows the order G > A > T > C.23 The values of the stabilization energy for the interaction between nucleobases and semiconducting chiral SWCNTs calculated using the CDASE scheme (Table V) also generate the same trend as observed by Das et al. and Sowerby et al.24 (see Section 4(iv)). It is also observed that the SWCNT (8,3) produces the highest values of ΔESE(AB) for all the nucleobases as well as for A−T and G−C base pairs. This indicates SWCNT (8,3) is capable of forming thermodynamically more stable complexes with nucleobases compared to other SWCNTs chosen in the present study. Similar is the observation with ΔN and ΔEA(B) values also, and as far as the rate of interaction is concerned the ΔEB(A) values also predict the same trend.

interaction should be an energy lowering one (i.e., the net energy change, ΔESE(AB), should be a negative quantity). A large negative value of ΔEA(B) indicates higher thermodynamic stability of the resultant complex. The calculated ΔEA(B) values for different combinations of SWCNTs and nucleobases are reported in Table IV. As per the data in Table IV, the complexes formed by the G−C base pair with SWCNTs are more stable than those formed between the A−T base pair and SWCNTs. Also, the stabilities of the complexes formed by the individual DNA bases with SWCNTs follow the order, G > A > T > C > U. It is worth mentioning here that Sowerby et al.24 had a similar observation in one of their experimental studies. On the basis of the adsorption of nucleobases on the crystalline graphite−water interface they observed the highest surface adsorption for nucleobase guanine, followed by adenine, thymine, cytosine, and the mutagenic base uracil showing the lowest one. Phenomenologically, a particular adsorption on the solid−liquid interface can be viewed as a thermodynamically controlled one. Thus, it can be argued that the CDASE scheme based energy component ΔE A(B) can be used as a thermodynamic parameter to predict the stability of complexes formed during chemical interaction. The unexpected positive ΔEA(B) values generated by the interaction of SWCNTs (9,7) and (6,5) with the mutagenic base uracil come out to be negative when calculations are performed at the 6-31G (d,p) level of basis sets, and the values are −0.4241 and −0.442 kcal/ mol, respectively. (v). Stabilities of the Complexes Formed between SWCNTs and Nucleobases on the Basis of Stabilization Energy [i.e., ΔESE(AB)]. The stabilization energy values (i.e., ΔESE(AB)) are G



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(b). Brief Discussion on the ONIOM (QM:MM) Calculation for the Interaction between SWCNT and Nucleobases. It is evident from the earlier studies that ONIOM QM:MM91,92 type of calculation is the best possible approach to explore the noncovalent interaction in large systems like nucleobases and SWCNTs.93−95 We have performed ONIOM QM:MM model calculation (implemented in Gaussian09)84 on the interaction between four different types of SWCNTs with five nucleobases. To account for the order of preferential binding interaction of the five nucleobases with SWCNTs, we have chosen SWCNT (7,5), SWCNT (7,6), SWCNT (8,3), and SWCNT (9,2) as our model systems. In a conventional ONIOM model calculation it is possible to implement two or three different levels of theory in two or three different regions of the particular system for the calculation. The flexibility of assembling a high-level ab initio calculation for a particular domain (area of highest importance) of the system with a relatively lower level of computation to the rest provides more emancipation to perform a theoretical study on large systems with greater efficiency at a lower computational cost. In the present calculation we have defined two ONIOM regions for the combined SWCNT−nucleobases system. The high and low layers of the SWCNTs, according to the standard practice of ONIOM model computation, are represented in Figure 2. The high level zone of the calculation includes the nucleobase and extends up to four hexagonal rings of SWCNT, whereas the rest of the SWCNT is considered as the low level zone. The density functional theory based B3LYP method is being used with the 6-31G(d) basis set for the highlevel zone along with universal force-field (UFF) molecular mechanics which has been adopted for the low-level zone of the system. It is worth mentioning here that an earlier study suggests an improvement of the result obtained from the ONIOM B3LYP:UFF method in comparison to that of the ONIOM B3LYP:AM1 alternative.94 The optimized structures of the SWCNTs with different nucleobases represent a parallel orientation of the nucleobase over the SWCNT surface in a slight wrap-around fashion (Figure 2 in the Supporting Information). Table VI represents

interaction strength of the two nucleobases cytosine and thymine with SWCNT (7,0) is also evident from another comprehensive study by Shukla et al.97 The binding energy data computed for both SWCNT (7,5) and SWCNT (7,6) with five different nucleobases produce a good agreement with the trend obtained from CDASE scheme based calculations. In these two types of SWCNTs, we have got the highest negative value of binding energy for the interaction with nucleobase guanine succeeded by adenine, thymine, cytosine, and uracil (i.e., G > A > T > C > U). However, the trend of interaction obtained for SWCNT (8,3) with five nucleobases is marginally away from the anticipation. Here, we have found that nucleobase adenine has the highest affinity for SWCNT (8,3) and followed by thymine, cytosine, guanine, and uracil. A more extensive study may resolve the anomaly in the generated binding energy values of SWCNT (8,3) with nucleobases and that can be exploited to understand the exceptional behavior of the other armchair SWCNTs in this category. Perhaps, the interaction of SWCNT (8,3) with different nucleobases could be inexplicitly justified from the reported study of Varghese et al.98 Thus, excluding guanine, computed data for adenine, thymine, and cytosine in our present ONIOM QM:MM calculation reproduce similar trends as obtained by Varghese et al.96 in the case of carbon nanosystems. It is worth mentioning here that the trend of interaction of SWCNT (9,2) and SWCNT (8,3) with nucleobases, when evaluated by the CDASE scheme, reproduces the experimental trends correctly. Possibly higher level of theory along with intelligent layer selection in the ONIOM QM:MM approach will reproduce the experimental trends.

5. CONCLUSIONS The results obtained from the CDASE scheme based calculations provide some useful insights to understand the binding interaction of nucleobases with semiconducting chiral SWCNTs. The interaction is explained on the basis of five reactivity descriptors (i.e., Δw, ΔN, ΔEB(A), ΔEA(B), and ΔESE(AB)) derived from the CDASE scheme. It is worth mentioning here that the data generated from both the kinetic (i.e., Δw and ΔEB(A)) and thermodynamic (i.e., ΔEA(B) and ΔESE(AB)) descriptors as well as charge transfer values (i.e., ΔN, which plays the role of both kinetic and thermodynamic descriptor) produce a similar trend of the rate of interaction and complex stability when nucleobases interact with chiral SWCNTs. As far as nucleobases are concerned the trend is as, G > A > T > C > U, which is observed experimentally. However, the rate of complex formation of different SWCNTs with a particular nucleobase differs when different kinetic parameters (i.e., Δw and ΔEB(A)) are used. As observed from the generated data in Table I (i.e., Δw values) the rate of adduct formation of SWCNTs with a particular nucleobase varies as, (7,5) > (10,2) > (8,3) > (7,6) > (9,2) > (9,5) > (9,7) > (6,5). However, the trend changes to (8,3) > (9,2) > (9,5) > (10,2) > (7,5) > (7,6) > (6,5) > (9,7) when the corresponding ΔEB(A) values are compared. In the absence of any earlier reported results (either experimental or theoretical) it is difficult to conclude which one is the more appropriate trend. The functionalization of carbon nanotube (CNT) with active biomolecules is an emerging area of research from both experimental and theoretical points of view. A theoretical study on large systems like carbon nanotubes is a challenging task. Minimization of computational cost without compromising the reliability of the obtained results is a highly demanding aspect

Table VI. Binding Energies (kcal/mol) of SWCNT− Nucleobase Complexes at the ONIOM (B3LYP/631G(d):UFF) Level of Theorya guanine SWCNT SWCNT SWCNT SWCNT a

(9,2), (7,5), (7,6), (8,3),

−553.61 −300.80 −182.89 −17.38

adenine

thymine

cytosine

uracil

−268.34 −289.54 −175.18 −78.55

−318.75 −288.82 −121.86 −76.20

−301.47 −262.97 −121.85 −24.52

−235.18 −262.84 −121.41 −9.16

Binding energy, ΔE = ENucleobase+SWCNT − (ESWCNT + ENucleobase).

the binding energy (ΔE) values calculated for the interaction between nucleobases with four SWCNTs. The graphical representation of the variation in binding energy between the four SWCNTs with nucleobase is also included in Figure 3. The observed variation of binding energy of the five nucleobases with SWCNT (9,2) follows the trend G > T > C > A > U. This order of binding energy variation is reasonably close to that of the earlier reported theoretical observations of Stepanian et al.96 and Shukla et al.97 except that of adenine. According to the study of Stepanian et al. the relative interaction of nucleobase cytosine and thymine with SWCNT (10,0) appeared to be almost equal.96 The equivalent H



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Figure 3. Graphical representation of the variation in binding energy values for nucleobase−SWCNT complexes computed at the ONIOM (B3LYP/ 6-31G(d):UFF) level.

cytosine, thymine) of DNA. The mutagenic base uracil shows the least interaction. (2) Interaction of SWCNTs with Watson−Crick complementary base pair G−C is both kinetically and thermodynamically more favorable than that with the A−T pair. (3) Some unusual interaction behavior is exhibited by the mutagenic base uracil with few of the semiconducting SWCNTs [e.g., (6,5) and (9,7)]. The generated values of the descriptors (ΔEB(A), ΔN, and ΔEA(B)) claim that during interaction with these two SWCNTs uracil behaves as an electron acceptor and the two SWCNTs as electron donors. However, with the Δw values this unusual trend is not observed, and an unusual observation by CDASE scheme based parameters is attributed to the theoretical artifact incurred during generation of these values. This argument seems to be justified because use of a higher level of basis set [i.e., 6-31G (d,p)] corrects the trend. (4) The calculated values of all five parameters justify the experimentally verified trend of interaction of nucleobases with semiconducting SWCNTs (i.e., G > A > T > C > U).

of theoretical research in recent times. In the present study we have focused on the effective application of the CDASE scheme as a computationally cost-effective (as it avoids computationally intensive transition state optimizations or thermochemistry calculations), simple, and alternative approach to study the interaction between nucleobases and chiral SWCNTs. The worthiness of the study is evident from the fact that the observed trend of interaction, both kinetic and thermodynamic (obtained from the systematic analysis of the CDASE scheme based reactivity parameters), between the chosen semiconducting chiral SWCNTs and nucleobases matches satisfactorily with earlier reported experimental as well as related theoretical results.99 The study also highlights the fact that the CDASE scheme based charge transfer value is an essential parameter to judge the direction of spontaneous electron flow. This is because for a particular interaction the numerical value of ΔN helps to determine the donor and the acceptor systems involved in the process of interaction. The binding energy values (calculated by the ONIOM QM:MM approach) for four SWCNTs with five nucleobases generate reasonably satisfactory trends as observed earlier as well as by the CDASE scheme. We have found that for SWCNT (7,5) and SWCNT (7,6) the trends are similar to those observed experimentally as well as by the CDASE scheme. However, the trends of interaction for SWCNT (9,2) and SWCNT (8,3) with five nucleobases generated on the basis of the ONIOM QM:MM approach differ in one or two cases from the experimental observations. However, these minor deviations are expected to be resolved by considering either higher level of theories or redefining the different layers in the ONIOM model. Also, in such a situation the most reliable benchmark should be the experimental trends. Finally, the overall theoretical findings from the present study can be summarized by the following points: (1) The calculated values of reactivity parameters establish the fact that SWCNTs interact more effectively with purine bases (i.e., guanine and adenine) than with pyrimidines (i.e.,

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ASSOCIATED CONTENT

S Supporting Information *

The geometries of eight SWCNTs in three different orientations optimized at the B3LYP/6-31G (d) level and the geometry of combined structures for four different SWCNTs with five nucleobases optimized at the ONIOM (B3LYP/631G(d):UFF) level of theory. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: rkroy2@rediffmail.com; [email protected]. Notes

The authors declare no competing financial interest. I



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ACKNOWLEDGMENTS The authors would like to thank the Reviewer for his valuable suggestions which have improved the standard of the manuscript significantly. A.S. is grateful to the DST and UGC-BSR, Government of India, for granting him research fellowships. R.K.R. acknowledges financial support of this research from DST (Project ref. No. SR/S1/PC-41/2008) and Departmental Research Support under University Grants Commission (UGC) Special Assistance Program (SAP) [Project ref. No. F. 540/14/DRS/2007 (SAP-I)], Government of India, New Delhi. Computational facilities extended by the Department of Chemistry, BITS-PILANI, Pilani, are also gratefully acknowledged.

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