Structural analysis of an iron-assisted carbon monolayer for delivery of 2-thiouracil

Abstract

An idea of employing an iron-assisted carbon (FeC) monolayer for delivery of 2-thiouracil (2TU) was examined in this work by analyzing structural features for singular and bimolecular models. Density functional theory (DFT) calculations were performed for optimizing the structures and evaluating molecular and atomic descriptors for analyzing the models systems. Two bimolecular models were obtained assigning by S-FeC and O-FeC models, in which each of S and O atom of 2TU was relaxed towards the Fe region of FeC surface in the mentioned models, respectively. The results indicated that both models were achievable with slightly more favorability for formation of S-FeC model. The obtained molecular orbital properties revealed the dominant role of FeC monolayer for managing future interactions of attached 2TU, which is indeed a major role for employing nanomaterials for targeted drug delivery purposes. In addition to energies and molecular orbital features, atomic quadrupole coupling constants indicated the benefit of employing FeC monolayer for drug delivery of 2TU.

Keywords

2-Thiouracil nanocarbon graphene drug delivery density functional theory

1 Introduction

After pioneering characterization of the nucleic acid structure by Watson and Crick, considerable efforts have been dedicated to innovate biological applications for relatives of nucleic acid building blocks [1 –3]. As known, purine nucleobases of adenine and guanine and pyrimidine nucleobases of cytosine, thymine and uracil, are those building blocks of nucleic acid structures for constructing each of DNA and RNA macromolecules [4 –8]. Synthetic derivatives of such nucleobases have been seen achievable for doing specific functions in living systems [9 –11]. Several structures of purine and pyrimidine nucleobases relatives have been proposed for the pharmaceutical purposes with suitable efficacy of medication in living systems [12 –14]. 2-thiouracil (2TU) is one of pharmaceutical derivatives of uracil nucleobase with function of medication for diseases such as thyroid misfunction [15 –17]. In this structure, one oxygen atom of uracil (number 2) was substituted by one sulfur atom to generate 2TU structure (Fig. 1). Earlier works indicated that 2TU should be still improved for showing better efficacy for medication of thyroid disease [18]. Therefore, examining structural features and combinations with possible drug carriers could be an advantage for providing insightful information about the investigated pharmaceutical compounds [19 –21]. To this aim, carbon layer structures have been already proposed for working as carriers in drug delivery process to increase efficiency of such pharmaceutical compounds [22 –24]. Indeed, innovation of carbon nanotubes (CNTs) have leaded to examining such idea of carrier function for carbon materials in drug delivery processes [25]. In this regard, several attempts have been dedicated to recognize features of CNTs for achieving the purpose in addition to performing further explorations to invent new carbon based nanomaterials [26 –28].

Fig. 1

The models representations with two side views, HOMO and LUMO distribution patterns, and ESP surfaces.

Graphene carbon monolayer was recognized as a remarkable innovation of new nanomaterials with characteristic features of electronic and structural aspects for applications in various fields of industries and living systems [29 –31]. In this case, the surface of such monolayer system has been seen useful for adsorption of other substances in atomic and molecular scales to show new function as carriers especially in drug delivery purposes [32 –34]. Both of experimental and computational works approved such idea of graphene applications for drug delivery purposes; however, such idea has been still under development to reach more insightful details about the investigated systems in very much important living systems [35 –37]. In this work, such idea was examined for 2TU focusing on application of a carbon monolayer for its drug delivery process. To this aim, a molecular scale representative of graphene, called coronene, was used to provide an interacting surface for 2TU substance (Fig. 1) [38]. As indicated by earlier works, metallic modifications of carbon nanomaterials could bear more useful features for the investigated system, in which metal nano particle (MNP) has been seen as proper materials especially for targeted drug delivery processes [39 –41]. Furthermore, atomic-doped models of nanomaterials have been seen more usable than those of pure nanomaterials for various applications especially for interacting environments for better adsorbing the external substances [42 –44]. One of the serious issues about applications of carbon-based nanostructures in biological systems is their toxicity arisen from insolubility in water, in which doped models have been seen more useful for such applications [45 –47]. Accordingly, the investigated coronene model of this work was modified by an iron dopant atom to construct FeC model for providing an interaction surface for 2TU substance. It is noted that iron-modification has been seen as an advantage of constructing MNPs with specified applications in drug delivery processes [48 –50]. To this point, capability of such FeC model was investigated here for drug delivery of 2TU. It is important to mention that both covalent and non-covalent loading of drugs on carriers could be expected; however, the specified purpose of reversible or irreversible drug delivery could define the type of drug loading [51 –53]. This work was done by benefit of performing high-level quantum chemical calculations to generate detailed information about materials systems especially for this of complicated nanomaterials in interacting environments [54 –56]. As a consequence, the required information to approach the purpose of structural analysis of FeC monolayer for drug delivery of 2TU were obtained through performing quantum chemical calculations, in which the obtained numeric results were summarized in Table 1 and those of visual representations were exhibited in Fig. 1 for enabling a careful discussion. The models were analyzed in singular and bimolecular modes to show the impacts of participating in such intermolecular interactions on the original features of each of 2TU and FeC models using the evaluated molecular and atomic descriptors.

Table 1

Optimized descriptors for the models^*

Descriptor	2TU	FeC	S-FeC	O-FeC
E _t	–20072.67	–58420.96	–78495.56	–78495.55
E _ads	–	–	–1.94	–1.92
E _BSSE	–	–	0.18	0.22
E _HOMO	–8.42	–6.74	–6.51	–6.49
E _LUMO	0.32	–0.71	–0.53	–0.67
E _g	8.74	6.03	5.98	5.82
η	4.37	3.02	2.99	2.91
σ	0.23	0.33	0.33	0.34
D _m	4.78	2.26	4.69	5.31
Q_cc (N1)	3.64	–	3.14	3.23
Q_cc (N2)	3.32	–	2.94	3.17
Q_cc (S)	37.09	–	31.61	33.73
Q_cc (O)	9.49	–	9.46	8.78
Q_cc (Fe)	–	51.58	24.61	32.71

^*The models were preseneted in Figure 1. Values of all E parameters and η are in eV, σ is in eV^-1, D_m is in Debye, and Q_cc is in MHz.

2 Materials and methods

The investigated materials of this work were 2TU and FeC models, in which both of them were stabilized by performing quantum chemical calculations, in which the models were exhibited in Fig. 1. Afterwards, the singular optimized models were used for constructing bimolecular models to make possible intermolecular interactions between 2TU and FeC. To reach stabilized bimolecular models, further optimizations calculations were performed to obtain the best relaxation mode of 2TU-FeC system in two orientations of sulfur atom localization towards the iron-doped region (S-FeC) or oxygen atom localization towards the iron-doped region (O-FeC). By doing such calculations, four stabilized models were obtained including 2TU, FeC, S-FeC, and O-FeC models as exhibited in Fig. 1. The employed method of calculations was the wb97xd/6-31g^* of density functional theory (DFT) as implemented in the Gaussian program [57]. In addition to obtaining values of total energy (E_t), other values such as adsorption energy (E_ads) and basis set superposition error correction to energy (E_BSSE) were obtained for the models. Molecular orbital based energy levels were obtained for the models including energies of the highest occupied and the lowest unoccupied molecular orbitals (E_HOMO and E_LUMO), energy gap (E_g) of these two HOMO and LUMO levels, chemical hardness (η) and chemical softness (σ). Distribution patterns of HOMO and LUMO and electrostatic potential (ESP) surfaces were also visualized for the models. Dipole moment (D_m) was also evaluated for showing the electric charge orientation variations. Values of atomic quadrupole coupling constant (Q_cc) were obtained for N, O, S, and Fe atoms of the optimized models to recognize the structural features at the atomic scales [58 –60]. As a result, all obtained values of optimized molecular and atomic descriptors were summarized in Table 1 in addition to visual representations of models in Fig. 1.

3 Results and discussion

Structural analysis of an iron-assisted carbon (FeC) monolayer for delivery of 2-thiouracil (2TU) was carried out in this work to provide insightful information at the molecular and atomic scales for the investigated systems employing quantum chemical calculations. To achieve this purpose, singular and bimolecular models were stabilized by performing optimization calculations yielding 2TU, FeC, S-FeC, and O-FeC models as exhibited in Fig. 1. The singular models were those of 2TU and FeC, in which both of them were first optimized to obtain the minimized energy structures. Two atomic regions of 2TU were suitable for participating in interactions with the FeC surface, in which two bimolecular models of were obtained calling S-FeC and O-FeC regarding the localization of each of S and O atoms towards the Fe region of surface. Here it could be asked how these sites of interactions were determined for bimolecular formation. This is indeed an important question making a challenge for reliability of the models. As shown at the bottom row panel of Fig. 1, ESP surfaces of singular and bimolecular models were exhibited, in which green color means almost neutral, yellow and red colors mean negative part and blue color means positive part. It was mentioned earlier that such doped nanomaterials could work better than the pure models, in which it could be clearly seen here with the ESP surfaces that the doped Fe atom made a positive part for the singular FeC surface possible for participating in interactions more than other green parts. Additionally, the ESP surface of singular 2TU showed somehow yellow and red colors for those regions of S and O atoms but blue color for the opposite side of molecule. As a consequence, possible interactions of 2TU with the FeC surface could be leaded through localization of each of S or O atoms towards the Fe religion of surface. In this regard, two bimolecular models were obtained for the interacting system including S-FeC and O-FeC models with nearest interacting distances of 2.30 and 1.96 Å, respectively, indicated by dashed lines of the first row panel of Fig. 1. Comparing values of total energy, assigned by E_t in Table 1, could show that the S-FeC model was slightly better than the O-FeC model in bimolecular formation strength, in which comparing values of adsorption energy, assigned by E_ads, confirmed this achievement. However, difference of values of E_t was not very much significant for the models revealing possibility of formation for both of S or O relaxations towards the Fe region of surface. Errors of such bimolecular energy calculations were almost negligible found by small vales of E_BSSE.

Molecular orbital features could reveal important information for the original reactivity characterization of molecules, in which they could be obtained by benefit of performing quantum chemical calculations. Each of energy values and visual representations for HOMO and LUMO levels could have its own meaning for characterization of the investigated molecular system. To this aim, values of E_HOMO, E_LUMO and E_g were evaluated for the models systems as listed in Table 1, in addition to HOMO and LUMO distribution patterns as exhibited in Fig. 1. The results indicated that each of singular and bimolecular models show different molecular orbital features regarding their existence in different molecular modes. HOMO is a level with electrons and LUMO is a level without electrons; therefore, energy of HOMO is important for contribution of a substance to ionization process for electron donating whereas that of LUMO implies for such contribution of a substance to electron affinity for electron accepting. As a consequence, such energy levels and their difference value (E_g) could be used for analyzing the reactivity favorability of a substance. For the models of this work, distribution patterns exhibited the HOMO and LUMO were distributed for whole structures of singular 2TU and FeC; however, the HOMO pattern of 2TU was almost moved to the FeC surface in both of S-FeC and O-FeC models. This achievement is very much important because of benefits of employing nanomaterials for conducting targeted drug delivery purposes reducing the side effects and increasing the efficacy. Movement of HOMO of 2TU to the surface could meant that the drug cannot interact with any target anymore, but it can interact with already known targets. For achieving such purpose, LUMO pattern of 2TU was still remained at this molecular substance for future recognition of the correct target for interactions. Comparing values of E_HOMO and E_LUMO could show favorability of 2TU to interact with FeC surface, in which such favorability was somehow reduced by bimolecular formations revealing the benefit of employing FeC surface for managing the interaction environment of 2TU. Further analyzing the structures by values of chemical hardness and softness, assigned by η and σ, could show that the difficulty of participating in reaction was reduced by bimolecular formation and the ease of such situation was increased in the same way. Therefore, bimolecular models of 2TU and FeC could work better for the purpose of reactions by the managing role of FeC for participation of attached 2TU to further interactions with other external substances. Values of D_m also showed different situations of electric charge orientations for the model systems, in which suitability of FeC model for involving in watery media was increased by such 2TU attachment.

Values of atomic quadrupole coupling constant, assigned by Q_cc in Table 1, of N, O, S, and Fe atoms were evaluated for the optimized models to make possible performing analyses of structures at regarding the features of atomic sites. The magnitude of Q_cc is proportional to electron density at the atomic site, in which any perturbations to the atomic sites could be very well recognized by variations of magnitudes of such Q_cc descriptors. For the interacting systems of this work, such descriptors could help in two steps. For the first step, the atomic features of singular models could be recognized. For the second step, impacts of interactions of bimolecular formations could be recognized by comparing the magnitudes of Q_cc in bimolecular and singular modes. To this point, the results indicated that the atoms of original 2TU detect different electronic environments in singular mode, in which such environments were changed in bimolecular mode. It is important to mention here that the variations of atomic Q_cc descriptors could also confirm formation of interacting systems, in which the magnitudes would be changed for the models before and after participating in interactions. Indeed, the electronic densities of atomic site would be deviated from a certain axis or shared between two atomic sites of interacting counterparts resulting the changes of magnitudes of Q_cc. For the FeC model, magnitudes of Q_cc for Fe atoms in singular and bimolecular models indicated participation of this atom in interaction with S or O atom of 2TU. As described about the magnitudes, Q_cc of Fe of bimolecular models were smaller than that of singular model confirming such interaction with the smallest magnitude for S-FeC model, which was already determined as the most favorable bimolecular formation regarding the energy values. Analyzing the results of 2TU could mean that each of N1 and N2 atoms detect indirect impacts of such interactions for bimolecular formations, in which the magnitudes of Q_cc were reduced for both of them in bimolecular models with the most significant variation for the atoms of S-FeC model. Analyzing the magnitudes of Q_cc for each of S and O atoms could show that the impacts of interactions were in the most significant mode for S in S-FeC model and for O in O-FeC model revealing the direct contribution of each atom to interaction participation with Fe atom. As a consequence, bimolecular formation was approved by changes of the magnitudes of Q_cc for atoms of 2TU and FeC before and after participating in interaction. Moreover, reduction of Q_cc magnitudes was in agreement with the achievement of HOMO distribution patterns, in which the HOMO distribution of 2TU was moved to the FeC surface as shown by lower magnitudes of Q_cc for N atoms of 2TU, which were not directly bonded to the surface.

4 Conclusion

This work was performed to analyze structural features of FeC monolayer for 2TU delivery by means of computed values of molecular and atomic descriptors for describing each of singular and bimolecular models. 2TU, FeC, S-FeC, and O-FeC were those investigated models, in which the values of various types of energies indicated stability for all the model systems. Additional energy values indicated that formation of S-FeC model was slightly more favorable than that of O-FeC model, in which atomic Q_cc descriptors confirmed better such achievement. HOMO and LUMO distribution patterns indicated that the HOMO pattern of 2TU was moved to the FeC surface in both of S-FeC and O-FeC models showing benefit of employing such FeC surface for managing interaction situations of 2TU regarding the side effects reductions and efficacy improvement. Moreover, variations of magnitudes Q_cc of non-interacting N atoms of 2TU indicated the important role of FeC surface for drug delivery of 2TU. As a final remark, structural analyses of the investigated models indicated that the idea of employing FeC monolayer for drug delivery of 2TU could be achievable regarding the obtained molecular and atomic descriptors with possibility of formations of S-FeC and O-FeC models with more favorability for S-FeC model.

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