Nucleobase Stacking at Clay Edges, a Favorable Interaction for RNA

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Nucleobase Stacking at Clay Edges, a Favorable Interaction for RNA/DNA Oligomerization Pierre Mignon, Javier Navarro-Ruiz, Albert Rimola, and Mariona Sodupe ACS Earth Space Chem., Just Accepted Manuscript • DOI: 10.1021/ acsearthspacechem.9b00021 • Publication Date (Web): 11 Apr 2019 Downloaded from http://pubs.acs.org on April 18, 2019

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ACS Earth and Space Chemistry

Nucleobase Stacking at Clay Edges, a Favorable Interaction for RNA/DNA Oligomerization

Pierre Mignon†*, Javier Navarro-Ruiz‡§, Albert Rimola‡, Mariona Sodupe‡*

†

Institut Lumière Matière, UMR 5306, Université Claude Bernard Lyon 1, CNRS, Université de Lyon, 69622 Villeurbanne cedex, France ‡ Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain § Institute of Chemical Research of Catalonia, ICIQ, and The Barcelona Institute of Science and Technology, BIST, Av. Països Catalans 16, 43007 Tarragona, Spain

Corresponding Authors: *[email protected] ; [email protected]

Keywords: Nucleobase, nucleotide, adsorption, clay, edge, hydrogen bond, DFT

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Abstract Periodic DFT calculations have been performed to model the adsorption of nucleobases at clay edges as potential adsorption sites for DNA/RNA oligomerization. According to the accessibility and availability of hydroxyl groups and water molecules at clay edges numerous adsorption conformations via H-bonding, in a similar way to the Watson-Crick base pairing in DNA strands, have been considered. It is found that guanine and cytosine are mainly adsorbed through three H-bonds with edge’s hydroxyls and water molecules, while adenine and thymine do generally engage two H-bonds. As a result, largest adsorption energies were found for guanine and cytosine (-32 to -35 kcal mol-1) in comparison to most adsorbed modes with adenine and thymine (-22 to -24 kcal mol-1). For thymine, a three H-bond tilted adsorption mode has also been observed with an exceptionally large adsorption energy of -35 kcal mol-1. Significant stabilizing dispersive forces with the surface are present in all the explored adducts, around 30 % of the total adsorption energy (-6 to -10 kcal mol-1). The stacking of an additional nucleobase and its adsorption via H-bonding on the edge surface has also been studied. The large stabilizing interactions of the complexes, arising from both H-bonding and stacking interactions, range between -44 and -66 kcal mol-1, the dispersion component accounting for around -20 kcal mol-1, while no cooperative effects are observed. A significant number of strong H-bonds (

adenosine. The IR spectra highlighted that adenine interacts through the NH2 group irrespective of the salt concentration. X-ray diffraction patterns indicated that the interlayer distance is not affected by the nucleotide, which thus do not enter interlayers. Overall, experimental studies suggest that nucleotides’ binding on phyllosilicates occurs through H-bonding with hydroxyl groups at the edges or through metal cations bridging present at the negatively charged basal surface sites, depending on experimental conditions. The important contribution of theoretical works investigating the interaction and reactivity of prebiotic molecules with mineral surfaces has been shown in a wide number of studies 28,29. In particular, nucleobases adsorption on a dry Na+-montmorillonite basal surface has been first modelled by using DFT methods.30 It was shown that nucleobases can adopt either an orthogonal conformation through cation bridging or a parallel adsorption configuration, allowing for both cation coordination and dispersion interactions with the surface. Such configurations were also identified on hydrated Na+montmorillonite interlayer with cytosine, by means of ab-initio molecular dynamics simulations, although the interaction with the surface in the orthogonal configuration was not mediated by the metal cation.31 On the other hand, nucleobases adsorption on kaolinite tetrahedral and octahedral surfaces was found to occur via cation bridges and/or H-bonding interactions with hydroxyl groups32 whereas on the acidic external surfaces of H+-montmorillonite a spontaneous proton transfer to the nucleobase was observed during the adsorption.33 Finally, from approximated models using parameterized force fields, it was possible to simulate interactions between hydrated

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Ca2+ cation and nucleotides via phosphate coordination in the montmorillonite interlayer.34 To the best of our knowledge all studies concerning molecular adsorption on phyllosilicates only considered the basal surface and not clay edges. Montmorillonite, one of the most studied clays, is part of the 2:1 phyllosilicates’ family with two tetrahedral sheets sandwiching an octahedral one.35 Isomorphic substitutions leads to negatively charged layers, which are compensated by interlayer cations. Montmorillonite is a swelling clay; i.e., initially stacked layers of montmorillonite open in the presence of water leading to interlayer cations hydration and allowing for cation exchange. On the contrary, pyrophyllite is a 2:1 phyllosilicate non-swelling clay since it neither contains exchangeable cations nor isomorphous substitution. Nucleotide adsorption on swelling and non-swelling clays showed similar adsorption properties at pH > 4 on broken edges.24 Thus, pyrophyllite constitutes a good prototype to model phyllosilicate edges. In the present theoretical work, we propose a model in which the nucleotide adsorption occurs via nucleobase H-bonding, instead of interaction via the phosphate group. The adsorption of four nucleobases (i.e., guanine, cytosine, adenine and thymine, see Figure 1) at phyllosilicate edges is addressed by studying the nucleobase-surface H-bond interactions. The interaction with the edge surface has been clearly shown experimentally,23 however there is no clear data evidencing the phosphate ligand exchange mechanism. Furthermore, as observed via IR spectroscopy for adsorbedbased adenine nucleotides on montmorillonite, the interaction of the nucleobase occurs through H-bonding via the NH2 group.27 Nucleobases are indeed species that can be engaged in rather strong H-bonds as in double stranded DNA-RNA within Watson-Crick base pairing: Adenine and Thymine are involved in two H-bonds while Cytosine and Guanine in three. These H-bonds interactions can reach 24 kcal mol-1 and are responsible for the secondary structure of double stranded DNA-RNA.36,37 In addition, with the aim of inducing RNA polymerization, the phosphate group needs to be freely available. Most importantly, as identified in the catalytic mechanism of phosphodiester bond formation of RNA polymerase, the reaction is likely if nucleobases are engaged in stacking and H-bonding interaction between each other.38–40 In this work, we show that

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hydroxyl groups and water molecules of the clay edges can provide suitable nucleobases anchoring points (via H-bonding), which in turn can allow for RNA/DNA elongation.

Methods Montmorillonite model The pyrophyllite unit cell [Al4(OH)4(Si4O10)2] has been taken from X-Ray refinement of pyrophyllite-1Tc from Lee and Guggenheim (cell parameters: a=5.160Å, b=8.966Å, c=9.347Å, =90.587, !=100.46, "=89.64).41 Bulk cell parameters variations are rather minor after optimization (less than 1.5% as compared to the Lee and Guggenheim structure). However, these variations reach 3.3% after optimization of the edge model due to important hydrogen bonding between clay platelets edges (Figure 2). Cell parameters are kept fixed to these values in all calculations. The edge model surface was generated by doubling the cell in the a direction and cleave along the [110] direction. The edge (110) faces were chosen because DFT calculations showed that pyrophyllite crystals are predicted to have a prismatic habit dominated by the (110) edge facets, although the surface energy of the (010) edges was observed to be slightly lower in energy.42 An integer number of water molecules were added to both edges of the model, through molecular coordination to Al atoms or through water splitting (OH + H), to saturate silanol or hydroxyl dangling bonds (see Figure 2), according to a high water coverage, as described in previous calculations.42–44 Cell dimension in the b direction is increased to 25 Å, so that there is a 14 Å vacuum space between edge slabs. One can notice that the orientation of the conventional cell, as found in the CIF file, and the one used in the calculations differs somehow from the cell that is used to define Miller indices and cleavage planes (Fig. 2 Left); i.e., the (110) plane of the conventional cell corresponds to the (010) plane of the cell used in this work. For calculations with stacked bases the cell has been doubled along the a and c parameters. Calculations with isolated nucleobases have been performed in a cubic cell with side length of 20 Å. Computational Details The settings applied in the present work are similar to those applied in previous studies 30,31,33.

Periodic DFT calculations were performed with the VASP Package,45,46 by using 6


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the projector augmented wave (PAW) method to describe ionic cores and valence electrons through a plane wave basis.47,48 The Perdew-Burke-Ernzerhof (PBE) form of the generalized gradient approximation (GGA) was used for the exchange and correlation functional.49 This functional has been shown to provide accurate results for silica-based materials.50,51 The Brillouin zone sampling was restricted to the Y=,

and

the cut-off energy was fixed to 400 eV.30,31,33 No dipolar corrections were not applied and smearing parameters used correspond to Gaussian smearing for insulators. Dispersion forces were accounted for by applying the D3 Grimme’s scheme.52 Ionic relaxation was performed at the DFT+D3 level until a 0.01 eV/Å threshold is reached. Adsorption energies ( Eads) correspond to the difference between the energy of the complex and the energy of the isolated species optimized separately. Interaction energies ( Eint*) are obtained considering isolated species at the same geometry as that found in the complex. The deformation energy ( Edef) corresponds to the difference between the energy of the isolated species at the geometry optimized in the complex and that of the isolated optimized species. The deformation energy allows to gauge the energy change induced by molecular interactions in the complex. The cooperative energy for the stacked nucleobases complex ( Ecoop) is computed as the difference between the energy of the complex and the energies of each species and interactions between pairs, as found in the complex. See the supporting information (SI) for a more detailed explanation.

Results and Discussion Adsorption of single nucleobases on pyrophyllite edges As can be seen in Figure 2, pyrophyllite edges are composed by Si-OH silanol groups, Albound hydroxyl groups and Al-coordinated water molecules. A total of 48 adsorption configurations via H-bonding have been found for the four nucleobases. All of them were initially positioned to allow H-bonds in a similar way as those found in the WatsonCrick base pairing in DNA. In such orientations, a nucleotide would exhibit a free phosphate group allowing for the phosphodiester bond formation. As in the WatsonCrick base pairing, adenine and thymine can be engaged in two H-bonds, each giving and 7



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receiving one H-bond, and cytosine and guanine can be engaged in three H-bonds, guanine giving two and receiving one H-bond and vice-versa for cytosine. (see Figure 1 for nucleobases atoms’ numbering). Among all computed configurations the most stable ones are presented in Figures 3 and 4. Energies and optimized geometries of all computed structures are given in Tables S1-S2 and Figures S1- S4 of SI. For adenine (Table 1 and Figure 3), total adsorption energies ( Eads(DFT+D3)), comprising DFT ( Eads(DFT)) and dispersion ( Eads(D3)) contributions, of the five most stable configurations range from -17.7 to -23.8 kcal mol-1. Analysis of DFT and dispersion (D3) contributions shows that differences mainly arise from DFT values, as the dispersion contribution varies by 2 kcal mol-1 at the most. In all cases, adenine exhibits a strong Hbond through N1 with either Al-OH2 (A1, A2 and A5) or SiOH (A3 and A4), with H-bond distances ranging from 1.52 to 1.61 Å. Moreover, in all cases except for A5, the amine group establishes rather strong H-bonds with an Al-OH group, H-bond distances being around 1.77 and 1.89 Å. Several factors determine the relative stability of these configurations, such as the availability of H-bond donors. At the edge, Al-bound water molecules show naturally available H atoms as compared to silanols, which are involved in intramolecular H-bonds (see Figure 2). Thus H-bonding to a silanol, as donor, requires a disruption of the H-bond network at the pyrophyllite edge and thus a lower adsorption energy may be obtained in comparison with H-bonding with Al-OH2. On the other hand, this may be balanced by the fact that the silanol groups are more acidic than AlOH2 (1 pKa unit larger) and AlOH (4 pKa units larger) as computed from ab-initio simulations.53 For the A5 configuration, although having a strong Al-OH2··N1 H-bond, shows a smaller interaction energy, in which adenine gives and accepts a H-bond from a unique Al bound water molecule, playing both the role of donor and acceptor. As a result, the hydrogen bond of the adenine amino group is significantly longer than in A1-A4. Most of thymine adsorbed complexes show two hydrogen bonds, one through O4 as proton acceptor and another one via N3-H as proton donor (Fig. 3). Adsorption energies for the five located most stable structures range from -14.3 to -34.7 kcal mol-1. For the T1 configuration H-bond distances (1.64 Å for O4··AlOH2 and 1.44 Å for N3H··AlOH) are indicative of strong interactions. Furthermore, thymine is also involved in a third H-bond (1.78 Å) via O2 with a silanol group (not shown in Figure 3), and is not fully orthogonal 8


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to the surface, which enhances dispersive interactions. Overall, this leads to a DFT adsorption energy of -22.4 kcal mol-1 significantly larger than that obtained for adenine and the other thymine configurations. The non-orthogonal orientation of T1 leads to the largest dispersive contribution (-12.2 kcal mol-1, Table 1). As a result, thymine is the nucleobase with the largest adsorption energy. In the remaining thymine configurations, O4 and N3 are involved in H-bonding with either Al bound water molecules or silanols with H-bond distances in the range of ~1.6-1.9 Å. As found for A5, the T4 configuration exhibits a small interaction energy despite the rather strong O4···AlOH2 hydrogen bond (1.70 Å) due to the fact that O4 and N3H are both bound to a single water molecule. With the exception of T1 with three H-bonds, DFT adsorption energies for adenine and thymine are comparable with an interaction energy of the adenine thymine WatsonCrick H-bonded base pair at -13.9 kcal/mol at the PBE level, BSSE corrected with triple zeta basis. 54 In the case of cytosine (Table 1 and Figure 4), Eads(DFT+D3) values range between -28.6 and -35.4 kcal mol-1. The adsorption takes place through three H-bonds: two in which cytosine acts as proton acceptor through O2 and N3 and one in which it acts as proton donor through the N4 amino group. Numerous configurations have been found with all three H-bonds formed with the edge hydroxyls or water molecules. The strongest adsorption, found for C1, involves H-bonds with two different Al-bound water molecules (with O2 and N3) with rather small H-bond distances (1.67 and 1.77 Å, respectively). Hbonds with O2, N3 and NH2 are in the range of 1.69-2.01Å, 1.68-1.98Å and 1.56-1.79Å, respectively. As found for previous nucleobases, the amino group preferentially establishes a H-bond with an Al-OH hydroxyl group because it is the most accessible and flexible. For guanine, all three H-bonds are formed by N1-H and N2-H amino group, as proton donor, and by O6 as proton acceptor. The five reported configurations show Eads(DFT+D3) values lying between -30.0 and -32.2 kcal mol-1. The most important interaction at pure DFT level amounts to almost -24 kcal mol-1 with a rather short H-bond (1.49 Å) between O6 and Al-OH2 (G2 configuration in Figure 4). In G1-G4 configurations, O6 is also strongly H-bonded to Al-OH2 with bond distances in the 1.51-1.56 Å range and only in G5, O6 is H-bonded to Si-OH (1.55 Å). The adsorption energy is somewhat smaller (-21.3 kcal mol9



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1) since the O6···HO-Si H-bond formation implies the disruption of surface edge H-bonds.

Similarly, the N2 amino group of guanine establishes H-bonds with Al-OH2 in G1-G4 and with Si-OH in G5. The guanine-cytosine interaction energy as computed in a H-bonded Watson-Crick base pair in gas phase are -26.9 kcal mol-1.54 These values, corresponding to a strong H-bonding between guanine and cytosine are somehow larger but still comparable with those found here ( Eads(DFT) = -21.0 to -24.0 kcal mol-1), indicating rather strong nucleobase-edges’ H-bond interactions. These interactions are further enhanced by the stabilizing dispersive forces between the nucleobase and the surface, which account for an additional 8-9 kcal mol-1. For all configurations, the dispersion interaction is around 6-12 kcal mol-1 which is nearly one third of the total adsorption energy. However, dispersion contributions are independent of the chemical groups’ orientation, and computed values may be overestimated because no solvent or water molecules are present at the surface and around nucleobases which would counterbalance the interaction with the surface. On the other hand, the rather important DFT adsorption energy shows that the availability of hydroxyl groups and water molecules at pyrophyllite edges can lead to adsorption modes that can maximize H-bond interactions similarly to those observed in a WatsonCrick H-bonded pairs. Furthermore, present calculations show that Al bound water molecules are the main H-bond donor at edges’ surface while Al-OH groups are the principal H-bonds acceptors. The shortest H-bonds are observed with Si-OH and Al-OH2 acting as donors, with mean distances of 1.59 and 1.62 Å, respectively. This shows that the adsorption of nucleotides at edges through nucleobases is clearly possible and comparable (or even larger) to the cation bridging adsorption that may occur at phyllosilicate basal surfaces. Indeed, these last adsorption modes have been evaluated at the same computational level at about -20 kcal mol-1 for adenine and thymine, and 27 kcal mol-1 for cytosine and guanine.30 Adsorption of stacked nucleobases on pyrophyllite edges The RNA oligomerization at pyrophyllite edges would only be possible if a second nucleobase gets involved in a stacking interaction with the first one, while both are Hbonded with the surface, leaving the phosphate group available for the phosphodiester bond formation. In addition, solution cations may play the role of reaction catalysts as 10


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observed in the mechanism of the RNA polymerase enzyme.38–40 In this context, we modelled the adsorption of a second nucleobase aside the first one to investigate if this is energetically feasible in terms of stacking interaction between nucleobases and if the availability of surface water molecule and hydroxyls allows for the correct H-bonding with the surface. Starting from the adsorbed complexes with a single nucleobase, a second one aside and parallel to the first one at about 3.5 Å was added and pointing toward the edge surface to allow H-bonding with the same atoms as those involved in H-bonded Watson-Crick base pair. The starting single nucleobase configurations have been chosen to represent various types of orientation on the edge surface and various kinds of H-bond patterns (with hydroxyls bound to Si or Al atoms or water molecules). Although they do not necessarily correspond to the lowest energy configurations for single nucleobase complexes (shown Table 1), it allows to explore multiple stacking conformations and may lead to new minimum energy complexes. The chosen configurations are A1, A4, C2, C5, G2, G3, T2 and T3 as named in Table 1 and Figures 3 and 4. These configurations have been used to construct the ten possible stacking complexes between two bases as shown in Figure 5 and Table 2. Ade/Ade complex has been formed from A1; Ade/Gua from A4; Ade/Cyt, Cyt/Cyt and Cyt/Thy from C2; Ade/Thy from T2; Cyt/Gua from C5; Gua/Gua from G3; Gua/Thy from G2 and Thy/Thy from T3. For each initial guess structure, the second nucleobase was added on both sides of the first one. For the sake of clarity, only the most stable structures are presented here (all energetics can be found in the SI Table S3). For these calculations, the cell has been doubled along a and c parameters to avoid interactions between nucleobases of adjacent cells (a=20.640 Å, c=18.694 Å), and accordingly, two pyrophyllite layers are included in the model. Energetics of the two stacked nucleobases adsorbed on the montmorillonite edges (calculated according to the definitions in the Methods section and the equations of SI) are given in Table 2, while structures and parameters are shown in Figure 5. The total adsorption energy corresponds to the energy required to bring the nucleobases and montmorillonite together as found in the complex, from fully relaxed isolated species. Various interaction energies components are given, corresponding to the difference in energy between species as found in the complex. The montmorillonite deformation

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energies correspond to the change in energy from the isolated geometry of montmorillonite to the one found in the optimized complexes. All various components can be found in Table S4 of the SI. Stabilization of the adsorbed molecules, i.e. the adsorption energy ( Eads), depends on various factors, among which the most important ones are the number and strength of H-Bonds between the nucleobases and the surface, the interaction between stacked nucleobases and deformation energy of montmorillonite. The dispersion component of the adsorption energy is almost constant for all adsorbed/stacked complexes, in the range -19.3 to -22.7 kcal mol-1. In the five adsorbed pairs with lowest Eads(DFT+D3); i.e., Cyt/Gua (-66.4 kcal mol-1), Gua/Thy (-60.2 kcal mol-1), Ade/Gua (-60.3 kcal mol-1), Gua/Gua (-57.3 kcal mol-1) and Cyt/Cyt (-56.3 kcal mol-1), guanine and/or cytosine is present and involved in 3 H-bonds < 1.6 Å for the two formers and 2 H-bonds < 1.6 Å for the three later complexes. The Cyt/Gua is the most stable complex with a relatively small deformation energy and the largest interaction between stacked nucleobases ( Eint*(Cyt/Gua) = -13.2 kcal mol-1, see Table 2). The four other complexes show a large montmorillonite deformation energy which can be related to the strong H-bonds formed with the surface. Calculated

Eads(DFT+D3) values for Cyt/Cyt and Gua/Gua

complexes are somehow lower because of the negligible interaction between the stacked nucleobases ( Eint*(Gua/Gua) = -0.6 kcal mol-1 and Eint*(Cyt/Cyt) = +1.5 kcal mol-1). In these cases both nucleobases show the same orientation which maximize the electrostatic repulsion, as shown in previous theoretical study of stacked nucleobases.55 In the Cyt/Cyt complex, one can see the largest distance (d=3.96 Å) and the less coplanar orientation between stacked nucleobases F]V$#^G6 In contrast, in Cyt/Gua, the most stable complex, nucleobases are 3.53 Å distant in an almost coplanar orientation, maximizing the DFT and dispersion components of the stabilizing contributions to the energy. The dispersion component of the interaction between stacked nucleobases ( ED3 component in the Eint*(B1/B2) terms) is around -6 kcal mol-1 for all systems. This value is somehow smaller but still comparable to that calculated at the MP2 level for stacked bases in a DNA strand F_ 5.1-11.9 kcal mol-1).55 Distances between stacked nucleobases (around 3.4-4.4 Å) are also comparable to those found in RNA/DNA strands. This shows that the stacking interaction participates in a non-negligible way to the 12


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stabilization of adsorbed nucleobase pairs, as they could be found in RNA/DNA strands. It is still important to note that the adsorption of stacked bases is energetically favored in all cases. Indeed, H-bonds with edge hydroxyls or water molecules are still rather strong in Ade/Ade and Thy/Thy complexes with one H-bond < 1.6 Å. According to previous studies showing that the stacking interaction between two nucleobases may be favored over the H-bonded complexes in condensed phase 56–58, one thus may predict that the present studied stacked complexes as clearly probable adsorption structures. The adsorption of the second nucleobase may modify the interaction of the first one with the surface. Indeed, the adsorption energy of the first one, as observed for Ade/Gua, Cyt/Cyt, Cyt/Gua, Gua/Thy and Thy/Thy, is significantly lowered by around 8 to 18 kcal mol-1 compared with the adsorption energy of a single nucleobase, respectively. For comparison, adsorption energies values of single and stacked nucleobases complexes can be found in Table S4 of the SI; the change in H-bonding of the first nucleobase from the single to stacked complexes can be found in Table 3. There are different cases, for example, in Ade/Gua, Cyt/Cyt and Thy/Thy complexes, the change in adsorption energies (8.2, 8.7 and 7.5 kcal.mol-1, respectively) is mainly due to the montmorillonite deformation energy to form H-bonds with the second nucleobase. There are weak changes in the H-bonds with the first nucleobase (Table 3). For the Cyt/Gua and Gua/Thy complexes however, changes in adsorption energies are larger (13.0 and 18.3 kcal.mol-1, respectively) and the H-bonding interactions of the first nucleobases are much more modified. For example, cytosine in the Cyt/Gua complex, initially involved in three H-bonds in the C5 adsorption mode (O2-[AlOH2], N3-[AlOH], N4-[SiOH], see Figure 4 and Table 3), is only involved in two H-bonds in the stacked complex. In these last two cases, upon adsorption of the second nucleobase, the rearrangement of the first one disfavors its interaction with the surface, and at the same time, stacking interactions are established between the two nucleobases. This rearrangement is visible from the relatively high MNT deformation energy values because of the reorganization of H-bonds network at the edges surface. However, this energetic balance results in no significant cooperative effects in the adsorption of two nucleobases, as indicated the estimated Ecoop values of Table 2; calculated values are

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positive or negative but, in all cases, very small (between -1.3 and 2.7 kcal mol-1) compared with the total adsorption energies. Adsorption of TpT on pyrophyllite edges A final calculation with a thymine dinucleotide unit (TpT) was performed to gauge the ability of previous model calculations to represent nucleobases orientation as found in polynucleotides. The dinucleotide geometry was taken from a DFT benchmark study on RNA backbone conformation of UpU dinucleotides,59 where restrained backbone dihedral angles relaxations were performed and compared with experimental data.60 A methyl group was added to model thymine and the TpT dinucleotide was optimized in gas phase at the TPSS-D3/Def2TZV level of theory with the Gaussian package,61 keeping fixed the backbone dihedral angles similarly to the theoretical benchmark study.59 The dinucleotide was superimposed on the Thy/Thy adsorbed complex described above by matching nucleobase atoms involved in the strongest H-bonds. The obtained geometry was relaxed via DFT periodic calculations, as described in the computational details section, and the obtained geometry is shown in Figure 6. In this case only the interaction energy was computed since the geometry of the isolated dinucleotide was constrained. The interaction energy amounts to -68.2 kcal mol-1 which is rather close to what was found for the interaction energy of the Thy/Thy complex (-65.0 kcal mol-1, see Table 2). DFT and D3 contributions are also quite similar in TpT (-50.0 and -18.2 kcal mol-1) to Thy/Thy complex (-45.0 and -20.0 kcal mol-1). The first thymine reinforces its strong Hbond via N3 (from 1.52 Å in Thy/Thy to 1.37 Å in TpT complex), while O4 is involved in H-bonds with two water molecules among which one is involved in H-bonding with the second thymine. The second thymine is involved in only one H-bond (1.62 Å) in TpT complex as compared with the Thy/Thy complex. This is due to the twist angle between stacked bases imposed by the backbone torsion. Nucleobase have flipped a little to maximize H-bonds with the edge, the nucleobase distance being: 3.87 Å and the angle between nucleobase planes: 23°. The DFT and D3 interaction energies between the bases, computed after removing the sugar-phosphate moieties and adding and optimizing the position of a H at N1, are Eint(DFT)=7.3 and aXint(D3)= -5.2 kcal mol-1. As already found in DNA,55 the electrostatic interaction between the stacked bases is repulsive. The stacking interaction is thus maintained by a non-negligible dispersion 14


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contribution and by H-bonding interaction with the edge hydroxyl groups and water molecules. This final calculation shows that the adsorption of nucleotides through nucleobase H-bonding is energetically favorable and that the stacking interaction between nucleobases is possible and participates to the overall complex stabilization.

Conclusions The adsorption of nucleobases at the pyrophyllite edge through H-bonding has been addressed by means of plane wave periodic DFT calculations. Nucleobase interactions with the clay edge surfaces follow the same H-bond patterns as those observed in the Watson-Crick base pairing in DNA strands, that is, guanine and cytosine are mainly involved in three H-bonds with edge’s hydroxyl groups and water molecules, while adenine and thymine do engage two H-bonds. Accordingly, DFT adsorption energies for guanine and cytosine (-23.9 and -25.5 kcal mol-1) and for adenine and thymine (-15.5 and -14.4 kcal mol-1) are similar to those computed for guanine-cytosine and adeninethymine Watson-Crick base pairs computed in gas phase (-25.2 and -12.3 kcal mol-1, respectively). For thymine, the most stable structure exhibits a third H-bond between O2 and a surface silanol, which leads to a DFT interaction energy rather similar (-22.4 kcal mol-1) to those computed for guanine and cytosine with three hydrogen bonds. Dispersion interactions with the surface are significant and amount to 6 - 12 kcal mol-1, leading to total DFT+D3 adsorption energies of -23.8 kcal mol-1 for adenine, -34.7 kcal mol-1 for thymine, -35.4 kcal mol-1 for cytosine and -32.2 kcal mol-1 for guanine. At the edge montmorillonite surface, Al bound water molecules and hydroxyl groups are observed to be the main H-bond donors and acceptors, respectively. The adsorption of two stacked nucleobases, in which both nucleobases are involved in H-bonding with the edge surface, shows a total adsorption energy that ranges between -44 and -66 kcal mol-1, the dispersion component (both between bases and between each nucleobase and the surface) accounting for -20 kcal mol-1. This clearly shows that the availability of hydroxyl groups and water molecules at clay edges allows for a sideby-side nucleobase adsorption. Such adsorption requires H-bond restructuration at the surface to maximize the H-bonding interaction with nucleobases, which is possible due 15



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to the distribution of OH groups (mainly H-bonds acceptors) and water molecules (mainly H-bond donors). Moreover, a rather important number of strong H-bonds (

Nucleobase Stacking at Clay Edges, a Favorable Interaction for RNA

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