Optical Response of Sila-Fulleranes in Interaction With Glycoproteins for Environmental Monitoring

In this paper, we introduce new features of silicon in fullerane structures. Silicon, when placed in a fullerane structure, increases its electron affinity and electrophilicity index, compared to placement in a diamondoids structure. These nanoparticles can be used to make optical sensors to detect viral environments. In this work, we theoretically examine the changes in the UV-Visible spectrum of sila-fulleranes by interacting with viral spikes. As a result, we find out how the color of silicon nanoparticles changes when they interact with viruses. We apply N- and O-Links for viral glycoprotein structures, and Si20H20 silicon dodecahedrane, respectively. Our computational method to obtain optimal structures and their energy in the ground and excited states, is density functional theory (DFT). Besides, to get the UV-Visible spectrum, time-dependent density functional theory (TD-DFT) approach has been used. Our results show that the color of sila-dodecahedrane is white, and turns green in the face of viral spikes. We can use the optical sensitivity of silicon nanoparticles, especially to identify environments infected with the novel coronavirus.


INTRODUCTION
If environmental health can reduce the role of viruses, the complex issue of treating viral patients will be removed from its critical state. But with the spread of human societies, can old methods clean the environment from microbial contamination? These methods are based on disinfecting suspicious, susceptible, and busy places. These are very costly due to the large statistical target population; as a result, it is sometimes impossible to do so [1]. Therefore, the need for substances that detect microbial contamination of the environment, whether viral or bacterial, etc., is felt more and more.
Nanoparticles can be sensitive to the viral environment. This sensitivity can appear as changes in color, light or even electrical properties. Metal nanoparticles have previously been studied to identify a variety of microbes. However, they usually have high chemical softness, which not only causes them to be unstable, but also causes unpredictable changes in biological systems [2,3]. From non-metallic nanoparticles, carbon can be affected by the environment, if it is located in a structure with sp 2 orbital hybridization, such as graphene, fullerenes, etc., due to the resonance of unlocated electrons, and so can be used as a sensor [4][5][6][7]. But graphene-based nanoparticles also always tend to oxidize [8].
Silicon, as the most popular metalloid, exhibits significant properties when placed in the form of nanoparticles. In 2013, Moore et al. showed that silicon nanoparticles can be used as optical sensors [9]. Biocompatibility and sensitivity to surface factors make silicon nanoparticles more attractive to therapeutic agents in biological systems [10][11][12]. In this study, we investigate the sensitivity of silicon nanoparticles to biological contamination, and introduce a type of nanoparticles as a virus-sensitive identifier [13][14][15][16]. We indicate that when silicon is placed in a fullerane structure, its electron sensitivity increases, so that we do our study on sila-fulleranes [17][18][19][20][21]. Since the electronic properties of sila-fulleranes with sizes between 1 and 2 nm, are very close to each other, we focus on our smallest samples to save on computational costs [22]. Also, to remove the edge factors, we have selected the most symmetric sila-fullerane for this purpose [23][24][25]. As a result, we select the sila-dodecahedrane with the chemical formula Si 20 H 20 , which has icosahedral (Ih) symmetry [26,27]. Finally, we generalize the results to a set of sila-fulleranes.

COMPUTATIONAL METHOD
Our calculations are based on density functional theory. We obtain the optimal and stable geometry of the structures and their energy in the ground and excited states, by B3LYP hybrid functional [28][29][30]. Using time-dependent density functional theory, we obtained the UV-visible spectrum for the studied structures [31,32]. We describe the orbitals of the atoms by basis set, which include the split valence, polarized and diffuse functions, that is 6-31 + G (d,p) basis set [33,34,35]. The calculations are performed by the Gaussian package [36,37]. We also used AIM2000 software to analyze the interaction between the structure of the sensor and the glycoproteins studied [38].

RESULTS
Virus spikes are usually made up of glycoproteins. Glycoprotein is a combination of protein and carbohydrate. There are different types of glycoproteins, however, the most common glycoproteins that make virus spikes, like the spike of the coronaviruses, are O-Link and N-Link types [39][40][41][42][43]. If the causative of carbohydrate-binding to protein is oxygen atoms, it is called O-Link, and if it is nitrogen atoms, it is called N-Link. The structure of these two types of glycoproteins is shown in Figure 1.
In this study, we propose that silicon nanoparticles have the ability to sense N-Link and O-Link glycoproteins. Because, in addition to biocompatibility, they are also electron sensitive. Although silicon is usually placed in the diamond structure, but when silicon placed in a fullerane structure, the rate of quantum confinement effect will be smaller. Unlike siladiamondoids, sila-fulleranes does not consist of pure sp 3 hybridization structure. Especially if fulleranes structures consist of a number of fused hexagon rings (NFHR), deviation from sp 3 hybridization occurs more frequently [22]. Finally, this deviation causes difference in the electronic properties of silafullerans and sila-diamondoids.
Using the following equations [44][45][46][47], we can obtain electronic information, such as the HOMO-LUMO gap, chemical potential, chemical hardness, and finally an estimate of electron affinity: (2) The new index, electrophilicity, can be obtained using chemical potential and chemical hardness through Eq. 6. Regarding electrophilicity, the difference between the type of structures is clearly visible [48,49].
We calculated the above electronic information for the six structures of sila-fulleranes. You can see the electronic information of them in Table 1.
Our previous researches on silicon nanoparticles shows that diagram of quantum confinement effect (QCE) for sila-fulleranes smoothly change than sila-diamondoids, especially in the range of 1-2 nm [22]. As a result, the HOMO-LUMO gap of fulleranes close to each other in this range, and because many properties such as chemical hardness, chemical potential and indexes such as electrophilicity are derived from this gap, so the properties of   In the following, the structures of the studied sila-fulleranes are shown in Figure 2.
According to the data in Table 1. It can be concluded that the high chemical hardness combined with significant electron affinity of the sila-fulleranes, make them a good candidate for chemical sensors due to increased electronic interaction with the environment. To determine the advantage of fullerane structures over diamond structures, Figure 3 shows the HOMO and LUMO orbitals in the smallest diamondoids, siladiamondoids, and sila-fulleranes. The localized orbitals of HOMO and LUMO in diamonds and their silicon analogues mean that the electrons in their structure have less impact on the environment.
As mentioned earlier, we used the most symmetrical structures, to remove the effect of the edges. The formulas for our structures are Si 20 H 20 and Si 60 H 60 , which have an icosahedral symmetry. The geometry of these two types of structures is shown in Figure 4. Now, according to the data given in Table 1, our selected sample to save time in calculations, is the sila-dodecahedrane with the chemical formula Si 20 H 20 . We investigate the ability of the Si 20 H 20 to see if it can sense the presence of the desired glycoproteins. We examine the reaction of Si 20 H 20 to the presence of the desired glycoproteins with the probable changes in the density of states (DOS) diagram. Figure 5 shows the changes in the diagram of the density of states of the Si 20 H 20 , due to the presence of N-and O-Link glycoproteins. The diagrams of this study are plotted with Gauss Sum software [50].
Silicon nanostructures have a very sensitive surface, so that in the face of high electronegative factors such as oxygen, its HOMO energy level increases, which is also confirmed by the density of states diagram, which it is confirmed by the density of states diagram. This is because the presence of oxygen increases the chemical potential of the structure and causes the electron to ionize or excite with less energy than before. So, changes in the DOS indicate differences in properties related to the electronic behaviors, such as optical properties. Now, we want to show how the color of the Si 20 H 20 changes due to the presence of N-and O-Link glycoproteins? Due to its large E Gap of about 4.5 eV, the color of our nanoparticle should be white. In other words, since the spectrum of visible light, about 1.6-3.2 eV, does not have enough energy to act on the electrons of the Si 20 H 20 , the total radiation returned to space at each wavelength, without any absorption.
The calculation of the optical gap also confirms our results. Optical gaps are usually smaller than HOMO-LUMO gaps. The optical absorption gap can be calculated by subtracting the total energy of the optimized-ground state from the total energy of the excited state in the same ground state geometry, as shown in Figure 6.
Because the number of electrons of the Si 20 H 20 is even, its spin state will be singlet, in the ground state. The lower-energy triplet excited-state is optically inactive, according to the ΔS 0 selection rule. Therefore, the lowest-energy allowed optical transition excites the system into the singlet excited state [51][52][53][54][55].
The energy of the singlet excited state is higher than the triplet state, due to larger repulsive Coulomb interactions between antiparallel spins. Therefore, the excited system may relax from the singlet state into the triplet one. Therefore, we calculate the emission bandgap from the relaxed excited triplet state to the ground state at the same energy, as shown in Figure 6.
In Table 2, we present the calculated absorption and emission gaps of the Si 20 H 20 . The difference between the absorption and emission gaps shows the Stokes shift.
The calculated absorption and emission gaps confirm our prediction, that the color of the Si 20 H 20 is white. Because the absorption gap is about 3.7 eV, and also, the emission gap is about 3.3 eV, none of them are in the range of the visible spectrum.
Our investigates show, the optimal distance between glycoprotein and sila-dodecahedrane depends on the condition and orientation of the glycoprotein relative to the sensor structure. But in general, it can be concluded that when the distance of hydrogens of both strucures have more than 2 A of together, the energy of the correlation between them is close to zero. Table 3 shows the electron properties of sila-dodecahedrane intracted to the studied glycoproteins.
Our calculations using AIM software analysis show that intermolecular interactions can take place between siladodecahedrane and glycoproteins in four zones (see Figure 7): Zone (a): Between the hydroxyl oxygen of carbohydrate part of glycoprotein and the hydrogen sila-dodecahedrane, the distance between which is about 7.8 A. At the critical point of this interaction, the electron density is about 0.0001 e.bohr −3 and the Laplacein density is about −0.0001 e.bohr −5 .
Zone (b): Between the carbonyl oxygen of carbohydrate part of glycoprotein and the hydrogen sila-dodecahedrane, the distance between which is about 2.2 A. At the critical point of this    The following Figure 8 shows the distance between atoms that interact with each other: Now, by obtaining the UV-Visible spectrum for the desired glycoproteins, we see that these structures also have no absorption in the visible spectrum [56]. The absorption range of N-Link and O-Link glycoproteins is in the ultraviolet part. But, interestingly, when van der Waals interaction between the Si 20 H 20 and the desired glycoproteins is established, the absorption of the new combined system enters the visible region, as shown in Figure 9.
The details of our final absorption spectra for the complex system of sila-dodecahedrane and O and N-Linke glycoproteins are given below in Table 4 using Gauss Sum software.
Since the absorption spectrum of the combined system of Si 20 H 20 and desired glycoproteins also includes violet light, we expect to see the composite system in yellowish-green, based on the complementary wavelength [57][58][59][60][61][62][63][64].   Our investigations show that what is effective in changing the spectrum of optical absorption is the distance of oxygen of the protein part or the carbohydrate part of the glycoprotein from the surface of silicon nanoparticles. Because the presence of oxygen changes the electron density around the silicon nanoparticles, and it increases the dipole moment of the system from 0.002 about to 10 debye.
Since the electronic properties of silicon nanoparticles can be easily engineered, significant changes and desired color can be achieved by functionalizing the Si-nanoparticle surface. It should be noted that in 2015, Wagner et al. synthesized silicon dodecahedrane as a sila-fullerane with an endohedral chlorideIon [65].

CONCLUSION
The present study includes two crucial applications. First, the diagnosis of viral diseases by using diagnostic kits based on silicon nanoparticles, which are biocompatible, in addition to high electrical and optical sensitivity. Second, for environmental hygiene in the facades of houses, schools, etc. or urban structures, or at least handles or gloves, the coating of silicon nanoparticles can be used to detect viral contamination. Coronavirus (COVID-19) is an example of a viral infection that becomes a global problem today.

DATA AVAILABILITY STATEMENT
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

AUTHOR CONTRIBUTIONS
All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.