Introduction

Nanoparticles (NPs) are “fickle” and have diverse biological effects depending on their size, chemical composition, shape, surface charge density, hydrophobicity, and aggregation. These complex effects make it extremely difficult to understand nanoparticles’ toxicities in different situations. As a result, nanotoxicity remains poorly understood, and a systematic approach to assessing the potential toxicology of nanomaterials is still non-existent [1, 2].

Experimentalists have made great progress (for very recent reviews, see [3–13]), especially in evaluating the toxicity of basic nanomaterials in vitro [14]. In stark contrast, computational studies aimed at understanding the toxicity of NPs are scarce [15–25], but are giving us rather instructive information. For example, by molecular dynamics (MD) simulations, Zhao et al. [16] suggested that C60 can bind tightly to single-strand (ssDNA) or double-strand DNA (dsDNA) in aqueous solution and significantly affect the nucleotides. Zhao further found that three typical water-soluble C60 derivatives can associate strongly with ssDNA segments and that they exhibit different binding features depending on their different functional groups [17].

Given the rapid growth of nanotechnologies and the massive production of NPs in the near future, it is impossible to test the biological effects of all the nanoscale products in vivo. Thus, fundamental theoretical research on nanotoxicity prediction is urgently required. Probing interactions between NPs and biological systems is the first critical step in understanding and ultimately predicting nanotoxicity.

Aluminum, a widely used metal, caught our great attention. People are exposed to aluminum in daily life through food and water consumption as well as through the use of many commercial products, such as antacids and antiperspirants. High aluminum concentrations in the human body can lead to anemia, bone disease, and dementia [26–28]. Besides, aluminum may be associated with neurological disorders such as dialysis encephalopathy, Parkinson’s dementia, and, especially, Alzheimer’s disease [29, 30]. Very recent in vitro experimental studies show that Al NPs impair the cell’s natural ability to respond to a respiratory pathogen regardless of NP composition (Al or Al2O3) [31].

Not surprisingly, theoretical and experimental studies have been performed to address the interactions between aluminum and nucleobases/base pairs or nucleotides. For example, using photoionization efficiency spectra, Pedersen et al. [32] found that Al atoms can stabilize an unusual tautomer of guanine that is incompatible with the formation of Watson-Crick base pairs (BPs). The theoretical studies of Mazzuca et al. [22] indicate that aluminum ions and nucleobases, as well as the corresponding nucleotides, can form stable complexes with large binding energies. Single aluminum atoms and trications were found to have high affinity to nucleic acid bases and monophosphate nucleotides [22, 33, 34]. However, all these studies considered only Al atoms and trications—no study involving Al NPs has been reported to the best of our knowledge.

Upon entering cells, Al NPs may coordinate with DNA and RNA nucleobases and disrupt their formation, replication and cleavage, and consequently, cause adverse effects to human health. To understand the possible toxicity of aluminum-based NPs in the human body, a detailed study on the interactions between Al NPs and DNA nucleobases as well as the corresponding BPs is urgently needed.

Choosing an appropriate NP model is crucial to the investigation of the bonding mechanism between Al NPs and DNA. Bare Al13 is a well-known magic cluster that has gained much attention for many years. Its neutral form is one electron deficient compared to the closed 40-electron shell given by the jellium model [35]. The icosahedral configuration is generally considered the most energetically favorable structure of neutral Al13. Substituting the inner aluminum atom of Al13 (I h ) with a tetravalent atom such as C (or Si) leads to a closed shell configuration, just as in a noble gas superatom [36–39]. On the other hand, doping with an atom with five valence electrons such as P (or N) results in a super alkali-metal atom with one extra electron [39, 40]. Having similar sizes and shapes but diverse redox properties, these doped Al12X clusters (X = Al, C, N and P) are ideal models of Al-based NPs. A comparison of these four NPs will also provide information on how the properties of NP binding to biosystems may change with different electronic configurations.

Thus, in this work, we used neutral bare Al12X clusters as simple NP models to investigate theoretically their interactions with adenine (A), thymine (T), guanine (G) and cytosine (C) as well as AT and GC pairs. The goal was to shed light on the possible biotoxicity caused by different NP configurations. Issues such as the geometries, electronic properties and binding Gibbs free energies of the complexes of bases/BPs with Al12X clusters are addressed. The mechanisms of Al NP binding as well as potential adverse effects on human biosystems are also suggested.

Computational methods

First, full geometry optimizations without symmetry constraints were carried out using the M05-2X functional [41] with the standard 6-31G* basis set. The M05-2X functional has exhibited outstanding performance in evaluating the geometries and energies of systems involving DNA bases [41, 42], and the optimized geometries of Al12X clusters at this level also agree well with earlier studies [43]. Several possible binding sites on nucleobases and BPs (Fig. 1, individual bases have the same numbering schemes) were considered to interact with Al12X (I h ) clusters, although in practice some sites may be blocked by sugar residues (ssDNA) or by intermolecular hydrogen bonds (dsDNA). All isomers were characterized as local minima by harmonic vibrational frequency analysis at the same theoretical level after the optimization. Then, the lowest-energy structures were reoptimized with the larger 6-311+G* basis set using polarizable continuum model (PCM) [44] to take the effect of solvent (water) into account. Charge distributions were studied with the aid of the natural bond order (NBO) analysis of Weinhold et al. [45].

Fig. 1
figure 1

Geometries and numbering schemes for the Watson-Crick base pairs AT [adenine (A)–thymine (T)] and GC [guanine (G)–cytosine (C)]

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To evaluate the binding strength at room temperature, we computed the binding Gibbs free energy (ΔG b, 298.15 K and 1 atm ) at the M05-2X/6-311+G* level of theory. ΔG b is defined as the difference in Gibbs free energy between a base/BP-Al12X complex and the separate base/BP and Al cluster (i.e., ΔG b = G(base/BP-Al12X) − [G(base/BP) + G(Al12X)]). The computed ΔG b values were adjusted for basis set superposition error (BSSE) using the Boys-Bernardi counterpoise correction scheme [46]. The Gaussian 03 package was employed throughout our density functional theory (DFT) computations [47]. The molecular orbitals were plotted using the gOpenmol program [48, 49].

Results and discussion

Geometries and energetics of base-Al12X complexes

In DNA nucleobases, electron-rich N and O atoms are conventionally favored for metal binding, while the exocyclic amino groups in A, G and C can bind with metals only after deprotonation or in tautomer structures [50, 51]. Thus, we considered the initial isomers by binding Al12X to the principal sites (either endocyclic N atoms or exocyclic carbonyl O atoms) in bases, namely, N1, N3, N7 of adenine, O2, O4 of thymine, N3, N7, O6 of guanine, and O2, N3 of cytosine. The lowest-energy complexes screened from the M05-2X/6-31G* optimized geometries (Table S1 summarizes all isomers, see Supporting Information) were reoptimized at the M05-2X/6-311+G* level of theory using PCM, and are presented in Fig. 2.

Fig. 2
figure 2

Optimized geometries of the lowest-energy complexes of DNA base-Al12X and computed natural bond order (NBO) charges for selected atoms at the M05-2X/6-311+G* level of theory. Black C, red O, blue N, white H, pink Al, yellow P. The nearest base-Al12X distances (R b-Al, unit: Å) and charges are given in blue (in parentheses) and black, respectively

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Adenine has three endocyclic nitrogen atoms (namely N1, N3 and N7, Fig. 1), all of which are potential sites for metal binding. The complexes with Al12X bound to the N3 site of adenine are the most favorable energetically (Table S1). The nearest base-Al12X distances (R b−Al) have the order A-Al13 (1.96 Å) < A-Al12N (1.98 Å) < A-Al12C (2.00 Å) = A-Al12P (2.00 Å) (Fig. 2). The BSSE corrected ΔG b values at 298.15 K (Table 1, −16.0, −7.3, −16.9 and −14.5 kcal mol−1 for A-Al13, A-Al12C, A-Al12N and A-Al12P, respectively) also suggest substantial interactions between adenine and the Al12X. Clearly, A-Al12C has a relatively larger ΔG b due to the closed shell configuration of the metal cluster.

Table 1 Basis set superposition error (BSSE)-corrected binding Gibbs free energies ΔG b (kcal mol−1) of the base/BP-Al12X complexes computed at the M05-2X/6-311+G* level of theory
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For T-Al12X complexes, the isomers with the metal bound to the O2 atom of thymine have more favorable energies. In contrast, σ bonding to O4 was preferred in other reports involving single Al atoms in either neutral or ionic form [22, 52]. T-Al12X has the same ΔG b and similar R b−A1 orders as A-Al12X, i.e., for ΔG b, T-Al12N (−12.5 kcal mol−1) < T−Al13 (−10.9 kcal mol−1) < T-Al12P (−9.6 kcal mol−1) < T-Al12C (5.2 kcal mol−1), and for R b−A1, T-Al13 (1.84 Å) = T-Al12C (1.84 Å) < T-Al12N (1.86 Å) < T−Al12P (1.87 Å). However, the T-Al12X complexes have larger ΔG b values than A-Al12X.

The G-Al12X complexes binding guanine via O6 sites are all most favorable energetically. Basically, their ΔG b values are all slightly smaller than those of A-Al12X and T-Al12X. G-Al12P has the smallest ΔG b (−19.7 kcal mol−1), followed by G-Al12N (−17.3 kcal mol−1). Although relatively large, the ΔG b of G-Al12C is still considerable (−8.7 kcal mol−1). Like that of A-Al12X, the R b−Al obeys the order of G-Al13 (1.82 Å) < G-Al12N (1.84 Å) < G-Al12C (1.85 Å) = G-Al12P (1.85 Å). Earlier studies proposed that a single Al atom or ion can bridge the O6 and the N7 atoms to form a stable structure [22, 32, 53]. As in the case of the G-Al12X complexes studied here, the metal binding to the O6 site may distort GC pairing and lead to the formation of globular DNA [54–57].

Generally, neutral cytosine favors N3 or O2 sites for binding with metals, depending on the nature of the metal and steric factors. When an Al12X cluster attaches to cytosine, Al13, Al12C and Al12N prefer the O2 site, whereas Al12P forms a bicoordinated complex with the N3 and O2 sites, adopting a similar binding pattern to the complex between cytosine and a single Al atom (or its cation and anion) [22, 33].

Energetically, the most stable complex is C-Al12P (ΔG b −21.3 kcal mol−1), followed by C-Al12N (−18.3 kcal mol−1), C-Al13 (−16.9 kcal mol−1) and C-Al12C (−9.5 kcal mol−1). These complexes have the smallest ΔG b values among all the base-Al12X complexes studied here. A large binding energy of cytosine-Al (neutral atom) was observed experimentally and suggested theoretically [33, 34]. R b−Al has the order of C-Al13 (1.81 Å) < C-Al12N (1.82 Å) < C-Al12C (1.83 Å) < C-Al12P (1.89 Å, 1.98 Å). The high stability of C-Al12P may be due to the two-fold intracluster interactions (from both N–Al and O–Al bonds).

From the above, we can draw the following conclusions:

  1. (1)

    Al12X clusters prefer to bind to O atoms over N atoms in the bases. A similar behavior was also found when hard transition metals interact with DNA bases [58].

  2. (2)

    Based on ΔG b, the relative affinities of individual bases to the same Al12X cluster are ordered as T < A < G < C. In addition, ΔG b has the order Al12P < Al12N (or Al12N < Al12P) < Al13 < Al12C for the same bases. Thus, T-Al12C has the largest ΔG b (5.2 kcal mol−1) of all the base-Al12X complexes. The special case of C-Al12P features bicoordination and the smallest binding Gibbs free energy (−21.3 kcal mol–1).

  3. (3)

    Basically, R b−Al has the order Al13 < Al12N < Al12C < Al12P for a single base and the order C < G < T < A for a single Al12X. Thus, C-Al13 and A-Al12P have the shortest (1.81 Å) and the longest R b−Al values (2.00 Å), respectively, among all the base-Al12X complexes. The shortest R b−Al is attributed to the interaction between the lone pairs (from O or N atoms) on the bases and the electron-deficient outer orbitals of Al13.

Geometries and energetics of BP-Al12X complexes

Similar patterns are apparent in the interactions between DNA BPs and Al12X clusters. Figure 3 illustrates the optimized structures of the complexes at the M05-2X/6-311+G* level of theory, while Table 1 summarizes the corresponding binding Gibbs free energies, ΔG b. In the AT-Al12X complexes, Al13, Al12C or Al12N bound to the N3 site of the adenine moiety have the lowest energy, whereas Al12P prefers the O2 site of thymine (Table S2). In the case of GC-Al12X complexes, however, all four Al12X clusters prefer binding at the O6 and the N7 sites of the guanine moiety in a bridging fashion.

Fig. 3
figure 3

Optimized geometries of the lowest-energy isomers of base pair (BP)-Al12X complexes and computed NBO charges for selected atoms at the M05-2X/6-311+G* level of theory. Coloring and labeling scheme as in Fig. 2

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The BSSE-corrected ΔG b values (−14.5, −8.0, −22.3 and −11.0 kcal mol−1 for AT-Al13, AT-Al12C, AT-Al12N and AT-Al12P, respectively) suggest that the interaction between AT and Al12N is the strongest, while that between AT and Al12C is the weakest. The R BP-Al values of AT-Al13 and AT-Al12C are exactly the same as the R b-Al values of the corresponding A-Al12X complexes (1.96 and 2.00 Å, respectively), while the R BP-Al values of AT-Al12N (1.97 Å) and AT-Al12P (1.82 Å) decrease by 0.01 and 0.05 Å compared to the R b-Al values of A-Al12N (1.98 Å) and T-Al12P (1.87 Å), respectively. AT-Al12C has the longest R BP-Al and the largest ΔG b because of the high chemical stability of Al12C, while AT-Al12P and AT-Al12N have the shortest R BP-Al and the smallest binding Gibbs free energy, respectively.

With the Al12X clusters simultaneously bridging O6 and N7 of guanine, GC-Al13, GC-Al12C, GC-Al12N and GC-Al12P all have considerable ΔG b values (−10.2, −4.0, −17.9 and −16.2 kcal mol−1, respectively). The average bond lengths (to O6 and N7 sites) are 1.94, 1.97, 1.95 and 1.93 Å, respectively, for Al13, Al12C, Al12N and Al12P, leading to the order: GC-Al12P < GC-Al13 < GC-Al12N < GC-Al12C. Among these, GC-Al12N has the strongest binding strength and is energetically the most stable.

Intermolecular hydrogen bonds play an important role in the stabilities of BPs and their associated complexes. Thus, we computed the intermolecular hydrogen bond distances in the BP-Al12X complexes in comparison with pure BPs (Table 2). Our computed hydrogen-bond parameters in BPs are consistent with previous high-level computations [59, 60].

Table 2 Computed hydrogen bond lengths (Å) and BSSE corrected base–base interaction energies ΔE (kcal mol−1) in BP-Al12X complexes at the M05-2X/6-311+G* level of theorya. BP Base pair
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For AT-Al13, AT-Al12C and AT-Al12N, with respect to normal AT, the N6(A)···O4(T) hydrogen bond distances decrease slightly, by 1.3%, whereas the N1(A)···N3(T) distances increase by 2.4%. However, these two hydrogen bonds become shorter (by 3.7 and 3.5%, respectively) in the AT-Al12P complex. Interestingly, in binding with the Al12P, H3 (T) approaches the adenine moiety more closely [H3(T)–N1(A) and H3(T)–N3(T) are 1.05 and 1.74 Å, respectively, see Fig. 3]. In the GC-Al12X complexes, the hydrogen bond distances of O6(G)···N4(C) increase dramatically (by 8.5, 7.4, 8.8 and 4.9% for GC-Al13, GC-Al12C, GC-Al12N and GC-Al12P, respectively), whereas most of the N1(G)···N3(C) distances are enlarged slightly (except GC-Al12N). In contrast, the N2(G)···O2(C) bonds shorten considerably (by 5.1, 4.8, 3.7 and 4.1% for GC-Al13, GC-Al12C, GC-Al12N and GC-Al12P, respectively). Compared to free GC, in GC-Al12X complexes the O6(G)···N4(C) bond is weakened and N2(G)···O2(C) is reinforced, whereas N1(G)···N3(C) changes only slightly. Clearly, depending on the nature of the metal clusters, the intermolecular H bonds of BPs can be reinforced, weakened, or even altered remarkably. This conclusion is further confirmed by the computational comparisons between the base–base interaction energies for BP-Al12X complexes and those for the free BPs (Table 2).

Electronic properties

Charge distributions and redox properties

Detailed analyses of NBO charge distributions were performed (Table 3). Clearly, Al12X clusters have negative charges in all complexes except C-Al12P. Considerable charge transfers occur in all complexes, with the smallest amount of 0.16 e in T-Al12P. Surprisingly, the largest charge transfer occurs in the C-Al12P complex, in which the C moiety obtains a substantial amount of negative charge (−0.51 e) from the Al12P.

Table 3 Total NBO charges (e) in the base/BP-Al12X complexes computed at the M05-2X/6-311+G* level of theory
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We then computed the vertical and adiabatic ionization potentials (VIPs, AIPs) of the individual bases and BPs. The IP values (VIPs 8.58, 9.33, 8.30, and 9.06 eV for A, T, G and C, respectively; the corresponding AIP values are 8.32, 9.02, 7.87 and 8.92 eV) have the order G < A < C < T, which agrees very well with previous high accuracy computations [61]. Thus, in the case of AT-Al12X, the T moiety can gain an electron from A and become negatively charged. However, in the GC-Al12X complex, G loses an electron more easily than C, so G contributes most of the negative charge localized on the Al12X. GC has a VIP of 7.56 eV and AIP of 7.14 eV, smaller than those of AT (VIP 8.35 eV, AIP 8.00 eV). Thus, Al12X can obtain more electrons (ca. 0.1 e, Table 3) from GC than from AT.

In addition, we computed the vertical and adiabatic electron affinities (VEAs, AEAs) for the Al12X clusters. The EA values (VEAs 3.23, 1.43, 2.28 and 1.44 eV, respectively, for Al13, Al12C, Al12N and Al12P; the corresponding AEA values are 3.49, 1.44, 2.28 and 1.45 eV) have the order Al12C < Al12P < Al12N < Al13. Thus, we can expect that both T and AT have small affinities to bind Al12C, which is in line with the above discussions of ΔG b. Moreover, we can also anticipate that Al13 can gain some electrons from the BPs due to its large EA, which was confirmed by the computed NBO charge (Table 3), although all four Al12X clusters obtain electrons from the BPs, regardless of whether the Al12X cluster is electron deficient or abundant.

On the other hand, the Al atom(s) bound to the bases/BPs all exhibit positive charge (Figs. 2, 3). For example, the charges on the relevant Al atoms are 0.24, 0.14, 0.12 and 0.13 e in A-Al13, A-Al12C, A-Al12N and A-Al12P, respectively. Thus, although the whole NP can attract electrons from the base, locally the Al atom attached to the base is positively charged, due mainly to the connecting electronegative O or N atom.

For complexes with both bases and BPs, the charges on the inner X atoms change little for the same Al12X (Figs. 2, 3). These complexes manifest a large electronic shielding effect of the outer Al shells. From the geometrical parameters and the charge distributions of the studied complexes, we conclude that all Al12X NPs are coordinated to bases and BPs through both covalent bonds and electrostatic interactions.

Frontier molecular orbitals

To derive useful information about the reactivity of the complexes under study, we plotted their frontier molecular orbitals, especially the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). The HOMOs and LUMOs are localized around the Al12X NP in almost all of the base–Al12X complexes (Fig. 4) with the exception of C-Al12C, whose LUMO locates mainly on the cytosine moiety. Thus, oxidation as well as reduction reactions occur mostly on the metal clusters.

Fig. 4
figure 4

Plots of the frontier orbitals for the base–Al12X complexes and the corresponding HOMO−LUMO gap energies (eV, in parentheses) computed at the M05-2X/6-311+G* level of theory

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Similarly, most of the frontier orbitals of the BP-Al12X complexes locate on the Al clusters. The exceptions are the LUMOs in GC-Al12X (X = Al, C and P), which are localized mainly on the BPs (Fig. 5). Furthermore, all of the base/BP-Al12X complexes have sizable HOMO−LUMO gap energies (ranging from 2.58 to 4.21 eV and 2.38 to 4.16 eV for base–Al12X and BP-Al12X, respectively), suggesting high kinetic stabilities.

Fig. 5
figure 5

Plots of the frontier orbitals for the BP-Al12X complexes and the corresponding HOMO−LUMO gap energies (eV, in parentheses) computed at the M05-2X/6-311+G* level of theory

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Implications to the nanotoxicity of aluminum clusters

Our computations reveal that the Al12X clusters have very strong interactions with DNA bases and base pairs (To confirm this, ΔG b values at higher temperatures (298.15–318.15 K) and BSSE-corrected binding energies were also estimated (summarized in Fig. S1 and Table S3, respectively, see Supporting Information). Notably, the typically highly stable magic cluster Al12C is also very reactive and interacts strongly with DNA, and the redox properties of the Al12X clusters do not have significant effects. It is the rather robust interaction between the surface Al atoms and the elements with high electronegativity (N and O) that binds the Al12X cluster and DNA. Thus, it is expected that larger Al NPs also tightly attach to DNA. Such interactions will most likely cause structural damage and electronic property changes in the DNA, and consequently lead to adverse effects on DNA function.

Conclusions

In summary, we performed a detailed theoretical study of complexes composed of DNA bases/BPs and Al12X (X = Al, C, N and P) clusters by means of DFT computations. All of these Al12X clusters attach tightly to the bases/BPs with negative binding Gibbs free energies due to the strong interactions between the outer Al atoms and the related binding sites, but the different redox properties of Al12X NPs have an insignificant effect. All four NPs (one is closed shell, three are open shell) can attract electrons from the BPs. The intermolecular H bonds of the BPs can be reinforced, weakened, or altered markedly depending on the nature of the metal cluster. All these findings suggest that the bound Al12X clusters, as well as larger Al nanoparticles, can affect the structure and stability of DNA, and may cause negative effects on its function. We hope this study sheds light on nanotoxicology research and stimulates more theoretical studies on the toxicities of NPs.