International Journal of Molecular and Theoretical Physics

Crystal structures of {[Cd(μ-ox) (H ade) (H₂O)]. H₂O}n, {[Cu(μ-ox) (3Meade) (H₂O)].H₂O}n and {[Cu(ox) (H₂O)₂(9Megua)].2.5H₂O}n complexes are linked by bidentate oxalato ligands. Density functional theory calculation has been performed on the above complexes to investigate their electronic structures and to explore the stability of the monomer and complexes. The geometrical parameters calculated by DFT method are found to have reasonably good agreement with the x-ray crystallographic data. The investigation includes a variety of theoretical analyses such as interaction energy, electrostatic potential map, topological, NBO, and NMR analyses. The present calculations provide an important physicochemical insight into the structure and properties of metal oxalato ligands, 3 methyl adenine and 9-methyl guanine. The results help to understand the active role of coordinated water molecules in modulating the binding of the oxalato ligands through hydrogen bonds.

Keywords: Bidentate oxalato ligands; Density functional theory; Interaction energy; Electrostatic potential map; Topological analysis;

For the past few decades many research efforts have been examined to understand the binding properties of nucleic acids and their constituents with metal ions, which aid to develop the new biologically active metallo drug. The interaction of DNA/ RNA constituents and their derivatives with both organic and inorganic molecules help to design the biomimetic systems [1- 4] and the development of artificial nucleobase receptors used as specific nucleotide sensors [5]. Plenty of structural studies concerning metal complexes with purine-like ligands are focused on mixed-ligand metal complexes, where the metal binding pattern is deliberated for the configuration of a M-N (purine) bond, in some cases it is reinforced by a suitable intra-molecular interligand hydrogen bonding interaction [6-12]. Owing to the increasing interest in the non-bonding interactions (hydrogen bonds [13], π,π-stacking [14, 15] and C–H/π interactions [16,17]), our attention determined to examine their behaviour in the metal-ligand interaction, intramolecular and inter molecular ligand interactions. These are the cases of a variety of ternary metal complexes involving Nucleobases [9-11] and the metal ion binding pattern is targeted as the main goal.

Galindo, et al. [2] have reported a model for metal ion- DNA interactions and molecular architecture of metal complexes capable of forming base-pair hydrogen bonding. Garcia-Teran, et al. [18] have characterized three M(II) oxalato complexes containing the adenanium nucleobase. Dance, et al. [19] have demonstrated the importance of extended structures with metal building blocks based on the use of intermolecular forces such as hydrogen bond and /or π-π interactions. Sonia Perez-Yanez, et al. [20] have studied the metal oxalato and malanato systems, which act as receptors of adenine and cytosine by means of the covalent anchoring of nucleobases to the metal centers [18, 21-23]. They have synthesized and reported the supramolecular structure of compounds {[Cd(μ-ox) (H ade) (H₂O)]. H₂O}n, {[Cu(μ-ox) (3Meade) (H₂O)].H₂O}n and {[Cu(ox)(H₂O)₂(9Megua)].2.5H₂O}n n, containing the non-modified adenine nucleobase (H ade), the 3 methyl adenine (3 me ade) and the model 9-methyl guanine (9 me gua ) which act as monodentate ligands. The 3 methyl adenine is highly cytotoxic and mutageni, since it can able to arrest the replication of DNA, where the methyl group N3 project into the minor groove of DNA double helix and thereby prevent the replication [24]. Hence, the design and structural analyses of coordination compounds containing the methylated adenine can able to predict useful information, which assist to understand the conformational damages induced through the nucleobase alkylation in biological systems and the molecular identification procedure to restore them.

In the present study an attempt has been made to recognize the structural behavior and characteristic properties of crystal compounds {[Cd(μ-ox) (H ade) (H₂O)]. H₂O} n, {[Cu(μ-ox) (3Meade) (H₂O)].H₂O}n and {[Cu(ox) (H₂O)₂(9Megua)].2.5H₂O}n, with CCDC numbers: 779251, 779252 and 779253 by using density functional theory by employing LANL2DZ basis set. We are interested to examine the binding strength formed through hydrogen bonds in through mixed-metal ligand and hence the crystal compounds have been investigated through two ways i). Hydrogen bonding arrangement and ii). Stacking arrangement. In extension to our previous work on the interaction of biomolecules with water [25], drugs [26-29] and metal ions [30-32], this work is concerned with the investigation of available X-ray crystallographic data [20] with the results of the theoretical methods. In order to know the potency of mixed-metal-ligand binding and the influence of water molecules on their binding affinity the interaction energy calculations have been examined for the hydrogen bonding and stacking arrangement. The active sites of heavy atoms responsible for the binding strength in hydrogen bonding and π-π stacking of supramolecular architecture for all the complexes were analyzed using electrostatic potential map. The role of individual hydrogen bonds and their contribution for the stable nature was analyzed through AIM and NBO analyses. The nature of hydrogen atoms was examined through NMR chemical shift.

The crystal compounds of all the complexes used in this work were extracted from the Cambridge Crystal Structure Database (CCSD) and the molecular geometries of {[Cd(μ- ox) (H ade) (H₂O)]. H₂O}n, {[Cu(μ-ox) (3Meade) (H₂O)].H₂O}n and {[Cu(ox)(H₂O)₂(9Megua)].2.5H₂O}n, monomers and their complexes were fully optimized using the Density functional theory at B3LYP and M05 [33] levels of theory with LANL2DZ basis set. The choice of the LANL2DZ basis set for metal complexes is based on the accurate results obtained for metal– ligand interactions [34, 35]. The vibrational frequency analysis computed for all the optimized structures reveal the structures are observed with real local minima and no structures are found with imaginary frequencies. The interaction (binding) energies of all the hydrogen bonding and stacking arrangement of the complexes are corrected using a Counterpoise correction [36] to a basis set superposition error. The interaction energies were performed for these complexes by using the formula: $${\Delta }^{2}E(AB)=E_{AB}-[E_{(A)}+E_{(B)}]\text{ (1)}$$ where E(AB) is the total energy of two monomers and EA, EB, are the total energy of individual monomer. Note that while calculating interaction energies the BSSE was corrected.

In turn to accomplish an extra precise energy evaluation between the metal-ligand complexes considered, single point interaction energy calculation at MP2/LANL2DZ level of theory was performed for the optimized geometries at M05/LANL2DZ level of theory. To confirm the presence of hydrogen bonding a topological analysis has been carried out to calculate the charge density ρ(r) and its second derivative Laplacian of charge density ^2ρ(r) for bonds using Baders Atoms in molecules (AIM) theory [37-41]. The NBO analysis has also been carried out for all the molecules using the same level of theory employing the NBO 3.1 Program [42]. Electrostatic potential maps have been produced for the monomer and complexes. NMR calculations have been carried out for all the complexes based on the Cheeseman coworkers [43] method at M05/LANL2DZ level of theory, where isotropic H values are taken into account. All the calculations have been performed using Gaussian 09 W package [44].

The experimental crystalline atomic coordinates of {[Cd(μ-ox) (H ade) (H₂O)]. H₂O}n, {[Cu(μ-ox) (3Meade) (H₂O)]. H₂O}n and {[Cu(ox)(H₂O)₂(9Megua)].2.5H₂O}n,,complexes were used as the starting point for geometry optimization, and protonation has been included at the end of oxalato group for ideal geometries. All the complexes were optimized at B3LYP/ LANL2DZ and M05/LANL2DZ levels of theory and are given in Figures. 1-3.

The Table 1 and 2 compares the results of geometrical parameters and hydrogen bond lengths calculated by theoretical and experimental methods for all the three complexes. In the present study, in order to occur more structural details the complexes were divided into two categories based on hydrogen bonding and stacking arrangement. {[Cd(μ-ox) (H ade) (H₂O)]. H₂O}n, {[Cu(μ-ox) (3Meade) (H₂O)].H₂O}n and {[Cu(ox) (H₂O)₂(9Megua)].2.5H₂O}n, were named as complex 1, complex 2 and complex 3 respectively.

i) {[Cd(μ-ox) (H ade) (H2O)]. H2O}n: As seen from, it is renowned that the metal atoms display an unclear octahedral arrangement produced by four oxygen atoms as of two connecting oxalato ligands, a single water molecule and a nitrogen atom having endocylic property of the adenine ring. This complex proliferates to form the 1D zig-zag chain, where the nucleobase is coordinated perpendicular to the propagating direction [20]. In case of monomer the M-O (M=Cd) bond distance originates from 2.29 to 2.34 Å and 2.20 to 2.47 Å, where the adenine nucleobase bonded through N11 atom has the M-N11 bond distance of 2.29 Å and 2.28 Å at B3LYP and M05 levels of theory respectively. This agrees well with the experimental crystal data and the previously reported values of crystal compound [20, 45, 46]. The dihedral angle between two consecutive oxalato bridging ligands (O₃-Cd₁- O₄-C₂) are 82.27° and 81.16° at above levels of theory respectively which were underestimated by 7° compared to those observed in X-ray crystallography. The dihedral angle between the adenine moiety and the oxalato ligands O₆-Cd₁-N₁₁-C₉ is 103.29° and 102.91° at the above levels of theory respectively, which are in agreement with the experimental value of 103.76°.

While considering the {[Cd(μ-ox) (H ade) (H2O)]. H2O} n complex, it is renowned that inter and intramolecular hydrogen bonds were created in hydrogen bonding arrangement. From the Table 2 it is observed that from the metal oxalato complex containing adenine nucleobase the intra molecular hydrogen bond length (Ade O22-H24….. N21 (W)) is 1.66 Å and 1.53 Å at the above levels of theory respectively which is underestimated by crystallography data of 0.3 Å. The intermolecular hydrogen bond length plays a significant contribution in the configuration of polymeric chain compound [20]. The nucleobase of the two polymeric chains be interlinked by hydrogen bonding interaction between two Watson-crick faces of two nucleobases and is shown in Figure. 1b.

In the complex, the adenine ligands are oriented in such a way to form an intramolecular hydrogen bond involving the coordinated water molecule (donor) and the N46 atom (acceptor), which strengthen the observed metal-binding pattern of the nucleobase [20]. Furthermore, the proton transfer from N₄₆ to N₄₂ atom favors the formation of a hydrogen bond between the Hoogsteen face [N₃₉, N₄₂] of the nucleobase as donor and a crystallization water molecule as acceptor with asymmetric N…O distances of 3.12 Å and 2.77 Å at the above levels of theory. These values agree with the experimental values. The π-π stacking between adenine base of the {[Cd(μ-ox) (H ade) (H₂O)]. H₂O}n complex is so long to form face to face or edge to face interaction between the π system, but the coordinated nucleobases establishes π-π stacking of the above complex and is shown in Figure. 1c. The distance between two adjacent stacked nucleobase is 3.52 Å and 3.64 Å at B3LYP and MO5 levels of theory, which is comparable with the experimental value of 3.6 Å. Moreover the interaction energy observed for hydrogen bonding and stacking arrangement is -71.58, -77.63, -77.53 and -60.23, -59.98, -65.48 kcal/mol at B3LYP, MO5 and MP2 levels of theory indicating the stability and strength of the interaction.

ii). {[Cu(μ-ox) (3Meade) (H2O)].H2O}n: As seen from the Figure. 2a, in case of monomer, the fragments are joined by bisbidentate oxalato ligands. The metal centre exhibits a tetragonally elongated CuNO₃₀O₂₆w chromophore wherein three oxygen atoms of two oxalato ligands is in the equatorial plane and the imidazole N₂₂ atom of the 3-methyl adenine20. The apical positions of the octahedral coordination are filled by the remaining O₇ oxygen atom of the oxalato bridging ligand and the O₂₆w coordinated water molecule with calculated metal-ligand bond distances are 2.16 Å and 2.17 Å at B3LYP and M05 levels of theory respectively. The perpendicular position of 3-methyl adenine with metal oxalato arrangement permits the establishment of face-toface π-π interactions between adjacent pyrimidinic rings. For monomer, the bond length of Cu1-O₂₆(w) is 2.16 Å and 2.17 Å, and for metal coordinated oxygen atom, it is 1.94 to 2.48 Å and 1.94 to 2.42 Å at above levels of theory respectively, which agree well with the x-ray crystallographic data. The adenine base coordinated to the metal atom by N₂₂ and the bond distance of Cu1-N₂₂ is 2.05 Å (B3LYP), 2.021 Å (MO5) and the experimental value is 1.98 Å. The layers of polymeric chains are held together by an intricate network of hydrogen bonding interactions and are given in Figure. 2b. The Watson-Crick face of the nucleobases form a layer by hydrogen bond to the adjacent ones by means of a N₂₆–H₆₈…O20 (1.986, 2.159Å) and N₂₆–H₅₅…O₃₈ (1.914, 2.323Å) interaction between the exocyclic amino group and the oxalato ligand, and by a weak C5–H65…N28 (2.013, 2.299Å) base-base association.

The N₃₅ nitrogen atom of the imidazole ring acts as acceptor of a hydrogen bonding interaction with the coordinated water molecule of a neighbouring chain (Figure. 2b). The stacking arrangement of the above complex is shown in Figure. 2c and their stacking distance is 4.37 Å and 4.13Å at the above levels of theory respectively. Finally the interaction energy for hydrogen bonding and stacking arrangement is -54.35, -56.34, -55.82 and -45.31, -47.35, 48.58 kcal/mol at B3LYP, M05 and MP2 levels of theory, which influences the stability of the structure.

is 4.37 Å and 4.13Å at the above levels of theory respectively. Finally the interact

iii).{[Cu(ox)(H₂O)₂(9Megua)].2.5H₂O}n: The supramolecular structure of {[Cu(ox)(H₂O)₂(9Megua)].2.5H₂O}n complex is quite different from the above complexes and the optimized structures are shown in Figure. 3.

The metal core assume a indistinct square pyramidal nature coordination, wherein the basal plane is engaged by two oxygen atoms from a bidentate oxalato ligand, one water molecule , and the nucleobase having N₁₉ site is the most common coordination metal binding model intended for the 9-methylguanine ligand [20]. In case of monomer the apical positions occupied by water molecules with Cu-O₂₈w distance is 2.15 Å and 2.18 Å at B3LYP and MO5 levels of theory respectively. As observed from Figure. 3b the Watson-Crick face of the nucleobase establishes a triple hydrogen bonding interaction with three oxygen atoms, one from the coordinated water molecule and the other ones from a carboxylate group of the oxalato ligand. The metal to oxygen Cu- O₂₈w bond length is 2.10 Å and 2.12 Å at B3LYP and M05 levels of theory respectively, which underestimates the experimental value around 0.2 Å. The guanine base is coordinated by Cu- N₁₉ bond and the bond length is 2.03 Å and 2.10 Å at the above levels of theory respectively which overestimates by 0.1 Å. The keto group of the guanine ligand establishes an intramolecular hydrogen bond with the coordinated water molecule, where the N8H9 and N₁₁H₁₃ sites are connected to the non-coordinated oxygen atoms from an adjacent unit to form hydrogen bonded motif. In this complex O₂₇-H₂₉…..O₅₀ interaction is 1.90 Å, 2.21 Å at above levels of theory respectively, which is overestimated by 2-4 Å. The interaction energy of the complex is -13.17, -8.13 and -18.23 kcal/mol at B3LYP, M05 and MP2 levels of theory indicating the strength of the interaction.

The electrostatic potentials (ESPs) disclose the significant contribution on the structural behaviour and properties of the considered metal-ligand complexes. In general Electrostatic property of nucleotides rule the directional behaviour of stacking interactions and this is vital for the dependability of DNA polymerase. Chin, et al. [47] proposed that the electrostatic potential will give a reliable contribution in understanding the nature of each individual atoms in nucleic acid identification and stabilization. The position of abnormal electrostatic features reveals the importance of functional regions, for instance, the binding spot intended for the metal ions are characterized by a typically negative electrostatic potential. The electrostatic potential maps was drawn for the monomers and complexes and are shown in Figures 4 and 5, where the red regions stand for the most electron rich regions and blue region correspond to the most electron poor region of the monomers. The projection of the electrostatic potential on the 0.0004 a.u electron density surface clearly shows noteworthy concentration of the negative charge around metal oxalato atoms. The overlapping of the charges between electronegative atoms and metal atoms in the complexes decreases from Cu to Cd complexes.

To gain further insight into the nature of hydrogen bond in the metal complexes, we have performed the electron density based topological analysis within the framework of

Bader’s Atoms in Molecule theory [28-32]. The interactions were studied by considering the values of the electron density (ρ)its Laplacian (∇^2ρ ) and bond ellipticity (ε ) at the bond critical points (BCP) of the O-H...O, O–H…N, N-H...N and N-H...O bonds in the metal complexes at M05/LANL2DZ level of theory, and these results are summarized in Table 3. The strong hydrogen bonds are to be linked with large electron density values at the bond critical points (BCPs), leading to high structural stability, and this is observed for all the complexes. In addition, small ellipticity values (e) at the BCPs for all the metal complexes indicate a strong interaction between the atoms. As can be seen from Table 3,

the values of (ρ) and (∇^2ρ )for all the metal complexes vary from 0.013-0.079 a.u. and 0.043-0.141 a.u, which proves that the complexes are having strong hydrogen bonds. Also as the ionic radius of the metal cation increases, (ρ) and (∇^2ρ) values of the metal to water oxygen distances are found to decrease from Cu to Cd complexes. In general E(2), the stabilization energy is related to the individual hydrogen bond strength that corresponds to the amount of charge transfer energy at M05/LANL2DZ level of theory and is given in Table 2. It is worthwhile to note that there is a correlation between bond length and stabilization energy E(2), i.e., smaller bond lengths (strong hydrogen bonds) have larger stabilization energy as seen in Table 2.

The calculation of NMR chemical shielding is an important tool to determine the structures of biomolecules. The relation between the shielding and chemical shift δ is given by,

δ= [(Shielding of carbon/hydrogen in TMS) – (Shielding value of carbon/hydrogen)] (1)

The calculated shielding value for hydrogen atoms in tetramethylsilane (TMS) at MO5/LANL2DZ is 28.49 ppm. By using these values, the δ values corresponding to the respective hydrogen atoms in hydrogen bond interactions have been calculated for all the complexes and are presented in Table 3. It is interesting to note that there is a correlation between bond length and chemical shift, i.e., smaller bond lengths (strong hydrogen bonds) have larger chemical shift (Figure. 6). During hydrogen bond formation the hydrogen atom loses electrons and gains positive charge, which results in large downfield chemical shift.

The present study gives better understanding to the metal oxalato complexes by comparing the theoretical and experimental data. The metal complexes of {[Cd(μ-ox) (H ade) (H₂O)]. H₂O}n,{[Cu(μ-ox)(3Meade)(H₂O)].H₂O}n and{[Cu(ox) (H₂O)₂(9Megua)].2.5H₂O}n were optimized at B3LYP/LANL2DZ and M05/LANL2DZ levels of theory and to get reliable comparison single point calculations has been carried out at MP2/LANL2DZ level of theory. The calculated geometrical parameters proved that all interatomic bond distances, bond angles and hydrogen bond lengths calculated at the above levels of theory agree well with the X-ray crystallographic data. The presence of hydrogen bond has been identified and studied through the interaction energy. Among the stacking and hydrogen bond arrangement, the interaction energy for the hydrogen bond arrangement is found to be more stable than stacking arrangement indicating the stability of the structure. The electrostatic potential map for hydrogen bonding and stacking arrangement reveals the concentration of the negative charge around the metal oxalato complexes. The results of the topological parameters and stabilization energy give a proper explanation for the stability of the individual hydrogen bonds. The harmonic vibrational analysis clearly indicates very good agreement of O-H, C-H and N-H stretching frequency with the X-ray crystal data. This work can give useful information to understand the conformational damages provoked by the nucleobase N alkylation occurring in biological systems.

This work was part of the Research Project (File Number: YSS/2015/000275) and Palanisamy Deepa, is thankful to Science and Engineering Research Board (SERB), Government of India, New Delhi for the award of the Project. Also authors express her sincere thanks to Prof. P. Kolandaivel, Department of Physics, Bharathiar University, and Coimbatore for the computational facility

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