A quantum assessment of the interaction between Glycine amino acid with pristine and B&amp;N doped silicon carbide nanocage (Si 12 C 12 )

doi:10.21203/rs.3.rs-2478331/v1

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A quantum assessment of the interaction between Glycine amino acid with pristine and B&N doped silicon carbide nanocage (Si 12 C 12 )

https://doi.org/10.21203/rs.3.rs-2478331/v1

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Density functional theory is utilized for scrutinizing the interaction of Glycine amino acid (Gly) with the Si₁₂C₁₂, BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ nanocages. The adsorption and deformation energy, solvent effect, topological parameters of atom in the molecule (AIM), time-dependent (TD-DFT), reduced density gradient (RDG), natural bonding (NBO), and quantum descriptors for all considered complexes of Gly&SiC nanocages are computed. The adsorption and enthalpy energy of formation all considered Gly&SiC nanocage complexes are exothermic, and interaction of Gly from oxygen site (C = O) with NSi₁₁C₁₂ and BSi₁₂C₁₁ nanocage is more favorable than other complexes. In the presence of water solvent, the formation of Gly&SiC nanocage complexes is non-spontaneous. The NBO charge and electrostatic potential (ESP) results display that the Gly molecule has a donor electron effect on the SiC nanocage surface. The gap energy and hardness property of Gly&SiC nanocage complexes depict that the conductivity and reactivity complex increases. The AIM and RDG parameters confirm that the bonding between Gly and SiC nanocage is partially covalent or electrostatic type. The electrical and optical properties of Gly with BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ nanocages change more than Si₁₂C₁₂ nanocages, and these nanocages can be applied as a selective sensor and absorber for Gly.

SiC nanocage

B and N doped

Glycine amino acid

DFT

AIM

One of the important and most abundant proteins in the body of humans and animals is the Glycine amino acid (Gly). It is used as a precursor of various important low molecular weights, such as glutathione, glyphosine, porphyrins, imiprothrin, eglinazine, heme, purines, and creatine [1]. Gly has immunomodulatory, cytoprotective, anti-inflammatory, and anti-oxidant roles in both the central nervous system and peripheral tissues. It is used as an intermediate compound to produce medicines and thiamphenicol [2–4]. After the discovery of carbon nanoparticles, great attention focused on other nanoparticles such as silicon carbide due to thermal stability, high conductivity, high hardness, gas sensing, hydrogen storage, electronic devices, and other adsorption properties [5–8]. Sun and coworkers [9] synthesized the SiC nanotubes successfully via a reaction of Si oxide with carbon nanotubes with the ratio of 1:1 Si to C atom. The theoretical study indicated that the aromaticity and stability of SiC nanotubes are lower than carbon nanotubes, and the electrical properties of SiC nanotubes are independent of their chirality, lengths, and tubular diameter [10–11]. Reports of various research on the pristine and doped silicon carbide nanotube with various elements and compounds (such as Fe, Ga, O₂, Fe, Co, Ni, and dichlorocarbon) demonstrated that SiC nanoparticles have valuable potential for special applications in the manufacture of electronic devices as a sensor and absorber of various compounds[12–18]. The interaction of SiC nanotube with NH₃BH₃ [19] CO [20–21], HCN [22], H₂ [23–25], O₂ [26], CO₂ [27], formic acid [28], NH₃ [29], CH₄ [30], formamide [31], phenol [32] are scrutinized by density functional theory. The results demonstrate that the electrical properties of SiC nanotube change significantly with different compounds, and this nanotube is a favorable candidate for preparing adsorbent, catalyst, and sensitive sensor. Another structure of silicon carbide is the Si₁₂C₁₂ nanocage, which has recently attracted a lot of research and its electronic structure has been studied in the interaction of different compounds. Zhao et al. [33] and Duan et al. [34] reported the structural, electrical, stabilities, and optical properties of Si₁₂C₁₂ nanocage, their results show that Si₁₂C₁₂ nanocage is more stable and reactive. Solimannejad et al. [35–36] by using the DFT methods investigated the nonlinear optical (NLO) response of Si₁₂C₁₂ nanocage decorated with alkali metals (M = Li, Na, and K), and sensing performance of Cu-decorated Si₁₂C₁₂ nanocage towards toxic cyanogen gas. They found that nonlinear optical properties of SiC nanocage increase with decorating with alkali metals and Cu atoms. In the other work, Solimannejad et al [37] studied the hydrazine trapping ability of Si₁₂C₁₂ nanocage, the calculated results confirmed that the adsorption of a monomer of hydrazine on the Si₁₂C₁₂ nanocage was more appropriate than the corresponding dimers, and this nanocage was a good candidate for removal of hydrazine molecule from environmental systems. Jouypazadeh et al. [38–39] studied the interaction of Tabun and sulfur mustard chemical warfare agent with various nanocages such as C₂₄, Si₁₂C₁₂, Al₁₂N₁₂, Al₁₂P₁₂, Be₁₂O₁₂, B₁₂N_12, and Mg₁₂O₁₂. The results revealed that the C₂₄, Be₁₂O₁₂, Al₁₂P₁₂, and B₁₂N₁₂ nanocages have a good potential for adsorbing Tabun and sulfur mustard. Following our previous study on the interaction of ammonia molecule, nitrate ion, Cd ion, and H₂S gas with boron nitride and HCN molecule with beryllium oxide nanotube BeONTs [40–44], in this work, the interaction of Glycine amino acid with the Si₁₂C₁₂, BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ nanocages are investigated at cam-B3LYP/6-31G (p, d) level of density functional theory. The results of this study determine the capability of pristine and doped SiC nanocages for adsorbing and detecting Gly in chemical and biological systems.

In this study, the geometrical structures of the Si₁₂C₁₂, BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ nanocages and complexes of Glycine amino acid (Gly) from O = C site (a label), O‒C site (b label) and N‒C site (c label) with above nanocages are selected and are optimized at the cam-B3LYP/6-31G (p, d) level of theory (see Fig. 1) by Gaussian 09 software [45]. The Maximum force and displacement in this study are 0.00042 Ha, 0.00015 Ha/Bohr. The stable complexes without imaginary frequency are selected and other calculations are done (see Fig. 2). The A, B, C, D, E, and F labels are denoted for adsorption Gly to Si₁₂C₁₂ (from Si and C site), BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ respectively. The adsorption energy, thermodynamic parameters (ΔH and ΔG), deformation energy of nanocage (E_{def-SiC nanocage}), Gly (E_def-Gly), and interaction energy (E_int) are calculated for all studied complexes by Eqs. 1‒4.

\(\begin{gathered} {E_{ads}}={E_{Gly\& SiC\,nanocage}} - {E_{SiC\,nanocage}} - {E_{Gly}}+BSSE\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(1) \hfill \\ {E_{def\,A}}\,=\,{E_A}\, - \,{E_{A\,in\,\,complex}}\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,A:\,SiC\,nanocage,\,\,Gly\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(2) \hfill \\ {E_{\operatorname{int} }}={E_{Gly\& SiC\,nanocage}}\, - {E_{SiC\,nanocage\,in\,complex}} - {E_{Gly\,incomplex}}\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(3) \hfill \\ \Delta Q={Q_{Gly\& SiC\,nanocage\,}}\, - {Q_{SiC\,nanocage\,}} - {Q_{Gly\,}}\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,Q:\,H,G\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(4) \hfill \\ \end{gathered}\)

The adsorption energy of all studied complexes is corrected with basis set superposition error (BSSE) of theoretical level. The electrical properties of all Gly&SiC nanocages complexes are examined by using results of the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energies, quantum descriptive such as gap energy (E_g), hardness of complex (η), electrochemical potential (µ) and maximum charge transfer (ΔN) [41–44], and calculated results are tabulated in Table 2.

\(\begin{gathered} {E_{gap}}=\,{E_{LUMO}} - {E_{HOMO}}\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(5) \hfill \\ \mu \,=({E_{HOMO}}+{E_{LUMO}})/2\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(6) \hfill \\ \eta =({E_{LUMO}} - {E_{LUMO}})/2\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(7) \hfill \\ \Delta N= - \frac{\mu }{\eta }\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(8) \hfill \\ \end{gathered}\)

To investigate the type of bonding between Gly…SiC nanocage, the atom in molecule (AIM) topological parameters, reduced density gradient (RDG) plots, electron localization function (ELF), localized orbital locator (LOL) and natural bond orbital (NBO) [46–47] for all Gly&SiC nanocages complex have been calculated using Multiwfn. 3.4 [48]. For computing, the solvent (water) effect, the PCM (polarizable continuum) method is applied for all studied complexes [49].

3.1 Geometrical and structural properties

The optimized structures of A-a to F-c complexes are shown in Fig. 2. Based on the optimized structures at all complexes except D-c, E-c, and F-c models the Gly is strongly adsorbed on the surface of the nanocage. In the D-c, E-c, and F-c due to the repulsion effect, the Gly molecule localizes far from the nanocage. The Si-C bond length and Si-C-Si bond angle of Si₁₂C₁₂ nanocage and distance between Gly… SiC nanocages are calculated and results are presented in Figs. S1 and S2. Inspection of results indicates that the bond length Si-C in the pristine models is 1.83 Å and is in agreement with other reports [10–15] and with doping B and N despite on the Si and C sites nanocage the Si-B, C-B, Si-N and C-N bond lengths around adsorption sites are 1.94, 1.61, 1.83, and 1.48 Å respectively. The bond distance between Gly….Si nanocage in the A-a to F-c complexes (except D-c, E-c, and F-c models) is in the range of 1.56 to 1.99 Å. In the D-c, E-c, and F-c models due to repulsion interaction, the bond distance between nanocage and Gly increased significantly from 1.83 Å to 3.37, 4.79, and 3.87 Å respectively. The bond distance between Gly….SiC nanocage in the D-b, E-b, and F-a models is 1.56 Å and is lower than other models, so the adsorption of Gly on the surface of nanocage in these states is stronger than in other models. The NBO charge density (∆ρ_(NBO))around the Gly molecule is positive, and it indicates that the Gly has a donor electron effect, and electron charge transfer has taken place from the Gly molecule toward the nanocage. The calculated electrostatic potential (ESP) plots for all studied complexes are displayed in Fig. S3. In the ESP plots, the red and blue colors represent the negative and positive regions around the adsorption site. The ESP results show that the positive charge density is concentrated on the Gly molecule while the negative charge density is concentrated around the nanocage, which indicates that the charge transfer has occurred from the Gly surface toward the nanocage surface, and this result is in a good agreement with the NBO, HOMO and LUMO results. The E_ads, E_def, and E_int of all studied complexes are calculated (by Eqs. 1‒3) and the results are listed in Table 1. According to the results of Table 1, it can be seen that the amount of adsorption energy for all studied complexes is negative and the adsorption process is exothermic and thermodynamically favorable. The highest and lowest absolute values of E_ads are related to D-a (‒34.45 Kcal/mol) and E-c (‒1.39 Kcal/mol) complexes, respectively. Whereas the E_ads values in the D-c, E-c, and F-c models are 1.55, 1.39, and 1.76 Kcal/mol, respectively, and the adsorption process is endothermic and thermodynamically unfavorable due to the repulsion effect between nanocage and Gly. In the a direction of the drug, the E_ads of the A-a, B-a, C-a, D-a, E-a and F-a complexes decrease in order: D-a (‒34.45 Kcal/mol) > A-a(‒29.46 Kcal/mol) > B-a(‒26.85 Kcal/mol) > F-a(‒19.71 Kcal/mol) > E-a(‒17.09 Kcal/mol) > C-a(‒34.45 Kcal/mol). These results indicate that with doping N atom despite Si atom of nanocage (NSi₁₁C₁₂) the interaction and adsorption of Gly from carbonyl (C = O) site on the surface of nanocage is stronger than other complexes. While with doping boron atom despite Si atom of nanocage (BSi₁₁C₁₂) the interaction and adsorption of Gly is weaker than other complexes. The E_def is the amount of energy exchanged in the deformation of the structure of the material in the Free State to a combined state. If the amount of deformation energy of the substance is large, it shows that the structure of the substance changes more due to combining with another substance. The results of Table 1 indicate that the E_def of nanocage and Gly is negative in all complexes and the deformation process is spontaneous. The highest E_def for SiC nanocage structure has occurred in C-a (‒14.53 Kcal/mol) and F-a (‒13.48 Kcal/mol) complex, while the lowest E_def has appeared in the F-c (‒0.03 Kcal/mol) model. These results confirm that Si₁₂C₁₂ nanocages in the C-a and F-a models are more affected by the interaction of Gly and its structure changes. The E_def absolute value of Gly&SiC nanocage complex changes in order C-a (‒14.53 Kcal/mol) > F-a (‒13.48 Kcal/mol) > D-a (‒10.08 Kcal/mol) > E-a(‒10.03 Kcal/mol) > A-a = B-a (‒4.03 Kcal/mol). The lowest change in the structure of the nanocage takes place in pristine Si₁₂C₁₂ nanocage, whereas the highest deformation of nanocage is observed in the C-a (B doped despite the Si atom of nanocage). The E_def absolute values of Gly in the B-c (‒12.50 Kcal/mol) and C-c (‒11.93 Kcal/mol) models are more than other complexes. In the B-c and C-c models, the structure of Gly is deformed significantly from its original values due to interaction with the nanocage effect. The interaction energy (E_int) values for all studied complexes except the E-c and F-c models are negative, so the interaction of Gly with Si₁₂C₁₂ nanocage is thermodynamically favorable. Most of the interaction energy is observed in D-a (‒34.45 kcal/mol) and B-c (‒49.88 kcal/mol) models, and in these models, most of the interaction between nanocage and Gly has occurred. The E_int of Gly&Si₁₂C₁₂ nanocage complexes change decrease for a site of Gly: D-a (‒38.95 Kcal/mol) > F-a (‒34.09 Kcal/mol) > A-a (‒33.66 Kcal/mol) > B-a (‒33.26 Kcal/mol) > C-a (‒25.04 Kcal/mol) > E-a (‒15.44 Kcal/mol). A comparison of results confirms that the NSi₁₁C₁₂ nanocage (D-a model) is suitable for Gly interaction in the biological system. According to the ∆H, and ∆G results of Table 1, it can be seen that the ∆H and ∆G values of all studied complexes except the D-c, E-c, and F-c models are negative and the adsorption processes are exothermic, spontaneous, and favorable. Therefore the interaction of Gly from the NH₂ site with NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ nanocage is unspontaneous and unfavorable. For understanding the solvent (water) effects on the interaction of Gly with nanocage the ΔΔG _(w) (ΔΔG_(w) = ΔG _{(Gly@nanocage)} ‒ ΔG _(Gly) ‒ΔG_(nanocage)) values of A-a, B-a, C-a, D-a, E-a, and F-a studied complexes by using PCM model [49] are computed and the result is tabulated in Table S1. The ΔG _{(w)(Gly@nanocage)} values of A-a, B-a, C-a, D-a, E-a, and F-a studied complexes are negative and solvent coating of the compound is spontaneous. While the ΔΔG _(w) values of formation Gly@nanocage complex from SiC nanocage and Gly are positive and this process is thermodynamically unspontaneous.

Table 1

Adsorption energy (E_ads), deformation energy of Gly (E_{def (GLY)}), nanocage (E_{def (nano)}), interaction energy E_int (Kcal/mol), thermodynamic parameters (ΔH and ΔG (Kcal/mol) Gly@Si₁₂C₁₂ complex for A-a to F-c models.
	E_def.Nano	E_{def. Gly}	E_int	E_ads	∆H	∆G	∆ρ_(NBO)
A-a	‒4.03	‒2.77	‒33.66	‒29.46	‒28.57	‒54.03	0.23
A-b	‒7.47	‒3.84	‒23.60	‒17.04	‒16.34	‒43.75	0.18
A-c	‒2.72	‒7.70	‒32.39	‒22.27	‒20.18	‒47.81	0.21
B-a	‒4.03	‒2.77	‒33.26	‒26.85	‒25.43	‒51.92	0.22
B-b	‒2.51	‒3.66	‒23.15	‒16.66	‒16.01	‒43.92	0.18
B-c	‒3.74	‒12.50	‒49.88	‒33.64	‒32.17	‒57.67	0.17
C-a	‒14.53	‒2.91	‒25.04	‒7.59	‒5.95	‒6.48	0.31
C-b	‒3.64	‒4.40	‒40.25	‒32.19	‒30.16	‒17.53	0.21
C-c	‒15.49	‒11.93	‒46.40	‒18.97	‒17.08	3.61	0.24
D-a	‒10.08	‒2.71	‒38.95	‒34.45	‒35.58	‒22.93	0.21
D-b	‒3.76	‒3.98	‒28.50	‒8.57	‒53.65	‒38.84	0.18
D-c	‒10.95	‒11.05	19.24	1.55	2.29	6.83	0.20
E-a	‒10.03	‒10.01	‒15.44	‒17.09	‒35.58	‒22.93	0.22
E-b	‒10.49	‒3.21	‒30.80	‒5.98	‒53.65	‒38.84	0.50
E-c	‒8.91	‒4.87	19.77	1.39	2.29	6.83	0.05
F-a	‒13.48	‒2.88	‒34.09	‒19.71	‒15.99	‒4.36	0.31
F-b	‒3.49	‒5.16	‒29.16	‒20.5	‒5.74	‒5.14	0.31
F-c	‒0.03	‒0.09	1.88	1.76	0.28	5.72	0.07

3.2 QTAIM and RDG

QTAIM (quantum theory of atoms in molecules) is an important method for explaining the molecular structure and type of bonding between two compounds by electron density [46]. By applying the QTAIM method, the total electron density (ρ), electron density Laplacian (∇²ρ), electronic energy (H_r), and ellipticity (ε) factor for A-a to F-a stable complexes are computed and results are listed in Table 2. Based on the calculated results of QTAIM (Table 2) the sign ∇²ρ and H_r for A-a to F-a complexes in the bond critical point are positive and negative respectively, so the type of bonding between Gly and nanocage is a partially covalent or van der Walls. The absolute value of ρ for the D-a complex is more than other complexes and so the interaction of Gly with NSi₁₁C₁₂ nanocage (D-a model) is strong, this result is in agreement with E_ads and ∆H. The ε values of A-a to F-a are < 0.1, so the bonding Gly and nanocage is σ. The localized orbital locator (LOL) plots for A-a, B-a, C-a, D-a, E-a, and F-a complexes are displayed in Fig. 3.

In the LOL topological plots, the red, yellow, and blue colors illustrate the highest, low, and lowest density electron localized, respectively. A close inspection of LOL plots shows that the localized electron density between the Gly and SiC nanocage is low, which confirms that the interaction between the two above compounds is non-covalent or electrostatic type. To examine the nature of the non-covalent bond, the RDG (reduced density gradient) scatter is calculated according to Eq. 9 [43, 50], and the scatter plots for A-a to F-a complexes are shown in Fig. 4.

\(RDG(r)=\frac{1}{{2{{(3{\pi ^2})}^{1/3}}}}\,\frac{{\left| {\nabla \rho (r)} \right|}}{{\rho {{(r)}^{4/3}}}}\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(9)\)

In the RDG scatter plots, the sign(λ₂)ρ(r) < 0, sign(λ₂)ρ(r) > 0, and sign(λ₂)ρ(r) = 0 indicate that the interaction between two compounds is electrostatic or hydrogen bond, repulsion, and van der Waals type. A close inspection of RDG results confirms that the more RDG density localizes in the sign (λ₂) ρ(r) < 0, and sign (λ₂) ρ(r) = 0 regions. These results prove that the nature of the bond between Gly and SiC nanocage is electrostatic and van der Waals type.

3.3 UV-visible spectrum

Using the time-dependent density function method, it is possible to determine the states of electron transfer at the excited states and to extract the ultraviolet or visible spectrum of a compound. These spectra can also be used to identify compounds and trace them in biological systems [51–53]. The excited states and UV-visible spectra for studied complexes at 30 states are computed by cam-B3LYP/6-31G (d, p) level of DFT theory, and results are tabulated in Table 3 and are shown in Fig. 5. Based on the results, it can be seen that the λ_max of all studied complexes are in the range of 400 to 1162 nm. This wavelength locates in the visible region of spectroscopy. It is interested that with doping B and N atoms instead of carbon and silicon atoms of nanocage as well as Gly adsorption, the λ_max increases significantly from original values, which can be used to track Gly associated with nanocage. Inspection of λ_max results indicates that the most λ_max (1162.19 nm) is observed for the E-a complex, which is related to the excited state S0→S1 with (0.96(H→L) + 0.04(H‒1→L)) with oscillator strength 0.017. The λ_max of studied complexes decrease in order: E-a > C-a > D-a > F-a > B-a > A-a. This result confirms that doping of the B atom despite Si and C atoms of nanocage increase the λ_max from 525.32 to 1162.19 nm (BSi₁₂C₁₁) and from 443.07 to 960.76 nm (BSi₁₁C₁₂). For detecting the interaction of Gly with SiC nanocages the BSi₁₂C₁₁ and BSi₁₁C₁₂ nanocages should be used.

3.4 HOMO and LUMO

In this section, to further investigate the electronic structure of the interaction of Gly with Si₁₂C₁₂ nanocage, HOMO and LUMO orbitals of all studied complexes are computed and the results are shown in Figs. 6, and S3. A close inspection of the HOMO and LUMO orbitals structures of Fig. 6 displays that the density of HOMO orbitals is localized on the SiC nanocage surface, so this surface is favorable for interaction with the electrophilic compound. While the density of LUMO orbitals is localized on the Gly molecule, so this surface is suitable for interaction with nucleophilic compounds. It is noteworthy that with the replacement of carbon and silicon atoms of nanocage with boron and nitrogen atoms the electron spin of orbitals is divided into two alpha and beta. In these models, it is observed that the most density of HOMO and LUMO orbitals is localized around the adsorption sites. The most density of LUMO orbital in the B-a, E-a_(α), and F-a_(β) is localized on the Gly surface and this region is suitable for interacting with nucleophile compounds. By using the energy of HOMO and LUMO, the E_gap, η, µ, and ∆N for studied complexes are computed by Eqs. 5–8 and the results are listed in Tables 4 and S2. From Table 4 it is seen that the amount of E_gap and η are in the range of 1.16 to 3.16 eV and 0.58 to 2.45 eV respectively. With doping of B and N atoms and adsorbing of Gly the E_gap and η values of Si₁₂C₁₂ nanocage are significantly reduced from pristine Si₁₂C₁₂ nanocage, as a result the conductivity Gly&SiC nanocage according to \(\sigma \propto {e^{ - Eg/2KT}}\)equation [54] increases, which indicates that the B and N doped Si₁₂C₁₂ nanocage are more reactive and conductive than pristine model and it can be a suitable sensor for the detection of glycine in the chemical and biochemical system. The negative values of chemical potential indicate that the formation of the Gly&SiC nanocage complex is stable. The maximum charge transfer (∆N) values of Gly&SiC nanocage complexes are positive and in the range of 2.38 to 7.41, as a result, the charge transfer from Gly toward SiC nanocage, so the surface of the nanocage has a negative charge and may be interaction with electrophile compound. Using GaussSum software, the density of state (DOS) diagrams for studied complexes are determined and the results are displayed in Figs. 7 and S5. Inspection of DOS diagrams (see Fig. 7) with doping of B and N atoms the HOMO and LUMO electron spin is separated into α and β, so the number of DOS states increases. The number of electron transitions between the levels increases, and as a result the optical behavior of the material increases. In these cases, with the appearance of a few small peaks in the gap region, the E_gap decreases significantly from the pristine state, which increases the conductivity of the nanocage.

3.5 NBO analysis

To understand the electrical and donor and acceptor properties of Gly and Si₁₂C₁₂, BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ nanocage the natural bonding orbital (NBO) parameters are computed. The stabilization energy E⁽²⁾ [55–56] of the bonding and antibonding orbitals are computed by Eq. 10.

\({E^{(2)}}={q_i}\,\frac{{F_{{ij}}^{2}}}{{{\varepsilon _j} - {\varepsilon _i}}}\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(10)\)

The F_ij, q_i, and ԑ_j-ԑ_i are the off-diagonal, orbital occupancy, and difference orbital energies, respectively. The computation results are tabulated in Table S3 and S4. From Table S3, it is observed that with doping B and N atoms despite Si and C atoms of Si₁₂C₁₂ nanocage the electrons density between Si-C bonding of nanocage decrease from a pure state, so the polarizability and stability of SiC nanocage decrease significantly from pristine models. On the other hand, maximum values of E⁽²⁾ between donor and acceptor orbital in the A-a model σSi₅–C₁₀ → σ*Si₁–C₁₃ (9.98 kcal/mol), B-a model σSi₁–C₁₈ → σ*Si₁–C₁₃ (10.11 kcal/mol), C-a model σC₁₇– B₃₄ → σ*Si₁₁– C₁₂ (2.89 kcal/mol), D-a model πC₁₅–N₃₄→σ*Si₃–C₁₃(6.55 kcal/mol), E-a model σSi₅–B₃₄→σ*Si₁–C₁₃ (3.97 kcal/mol), and F-a model σSi₈–N₃₄→n*Si₃₃ (3.28 kcal/mol). The ∆ρ_NBO values demonstrate the charge value of the Gly surface is positive and the SiC nanocage surface is negative, this result confirms the quantum parameters.

In this work, the interaction of Glycine amino acid with Si₁₂C₁₂, BSi₁₁C₁₂, NSi₁₁C₁₂, BSi₁₂C₁₁, and NSi₁₂C₁₁ is investigated at the density functional theory. The geometrical results demonstrate that the bond length between Gly….SiC nanocage in the D-b, E-b, and F-a complexes is 1.56 Å and is lower than other complexes, so the interaction of Gly with SiC nanocage in these complexes is stronger than in other complexes. The negative values of E_ads, ∆H, and ∆G for all complexes reveal that the formation of the Gly&SiC nanocage complex is exothermic and spontaneous. The absolute values E_ads of studied complexes in the a site increase in order: D-a (‒34.45 kcal/mol) > A-a(‒29.46 kcal/mol) > B-a(‒26.85 kcal/mol) > F-a(‒19.71 kcal/mol) > E-a(‒17.09 kcal/mol) > C-a(‒34.45 kcal/mol). The ∆∆G_(w) of the formation of Gly&SiC nanocage complexes in the water media are positive and unspontaneous in the thermodynamic approach. The AIM, LOL, and RDG results demonstrate that bonding between Gly and SiC nanocage is partially covalent or van der Waals type. The E_gap and η values of Si₁₂C₁₂ nanocage with adsorbing of Gly and doping of B and N atoms reduce significantly from the pristine state, therefore the conductivity and reactivity of the complex are more than pure state. The results of this study demonstrate that the NSi₁₁C₁₂ nanocage is a good candidates for adsorbing and detecting Gly in chemical and biochemical systems.

Supplementary data

Figs. S1- S6 and Tables S1- S5 are given in supplementary data.

Ethics approval: All authors state that the manuscript is not be submitted simultaneously to another journal. The submitted work is original and has not been published elsewhere in any form or language.

Consent to participate: Not applicable.

Consent for publication: All authors agreed with the content and that all gave explicit consent to submit and we obtained consent from the responsible authorities at the organization where the work has been carried out.

Availability of data and materials: The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Competing interests: The authors have no relevant financial or non-financial interests to disclose.

Funding: The authors declare that no funds, grants or other support were received during the preparation of this manuscript.

Authors' contributions: Allauthors contributed to the study conception and design. Data collection and analysis were performed by M. Rezaei-Sameti and M. Barandisheh Naghibi. The first draft of the manuscript was written by M. Rezaei-Sameti. All authors read and approved the final manuscript.

Acknowledgment

The author thanks the Computational information center of Malayer University for providing the necessary facilities to carry out the research.

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Supplementary Figs. S1- S6 and Tables S1- S5 are not available with this version.

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A quantum assessment of the interaction between Glycine amino acid with pristine and B&N doped silicon carbide nanocage (Si 12 C 12 )

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Abstract

Figures

1. Introduction

2. Details Of The Computational Method

3. Results And Discussion

3.1 Geometrical and structural properties

3.2 QTAIM and RDG

3.3 UV-visible spectrum

3.4 HOMO and LUMO

3.5 NBO analysis

4. Conclusions

Declarations

References

Supplementary data

Additional Declarations

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