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Article

Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te)

by
Fengying Lei
1,
Qingyu Liu
1,
Yeshuang Zhong
1,
Xinai Cui
1,
Jie Yu
1,
Zuquan Hu
1,
Gang Feng
2,
Zhu Zeng
1,* and
Tao Lu
1,*
1
School of Basic Medical Sciences/School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China
2
School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2023, 24(22), 16193; https://doi.org/10.3390/ijms242216193
Submission received: 16 October 2023 / Revised: 3 November 2023 / Accepted: 9 November 2023 / Published: 10 November 2023
(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)
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Abstract

:
In recent years, the non-covalent interactions between chalcogen centers have aroused substantial research interest because of their potential applications in organocatalysis, materials science, drug design, biological systems, crystal engineering, and molecular recognition. However, studies on π-hole-type chalcogen∙∙∙chalcogen interactions are scarcely reported in the literature. Herein, the π-hole-type intermolecular chalcogen∙∙∙chalcogen interactions in the model complexes formed between XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) were systematically studied by using quantum chemical computations. The model complexes are stabilized via one primary X∙∙∙Y chalcogen bond (ChB) and the secondary C−H∙∙∙O hydrogen bonds. The binding energies of the studied complexes are in the range of −21.6~−60.4 kJ/mol. The X∙∙∙Y distances are significantly smaller than the sum of the van der Waals radii of the corresponding two atoms. The X∙∙∙Y ChBs in all the studied complexes except for the SO2∙∙∙CH3OCH3 complex are strong in strength and display a partial covalent character revealed by conducting the quantum theory of atoms in molecules (QTAIM), a non-covalent interaction plot (NCIplot), and natural bond orbital (NBO) analyses. The symmetry-adapted perturbation theory (SAPT) analysis discloses that the X∙∙∙Y ChBs are primarily dominated by the electrostatic component.

Graphical Abstract

1. Introduction

A chalcogen bond (ChB) [1,2,3,4] is an attractive non-covalent interaction (NCI) between an electron-deficient region related to a chalcogen atom (mainly S, Se, and Te) as Lewis acids and any electron-rich region (lone pairs, π-electrons, anions) as Lewis bases. These electron-deficient regions corresponding to the positive electrostatic potentials can be divided into two categories: σ-holes and π-holes [5,6,7,8,9]. The former is generally located along the extension of the covalent σ-bond involving a chalcogen atom, while the latter is generally located perpendicular to the σ-framework of the molecular entity. Both σ-holes and π-holes are capable of interacting attractively with Lewis bases, and the formed NCIs are called the σ-hole interactions and π-hole interactions [6,7,10,11,12,13], respectively. Previous studies disclose that the attractive nature of such interactions is mainly composed of electrostatic, dispersion, and charge transfer interactions [1,14]. In analogy to the halogen bonds (HaBs) [15,16] which involve group VII element atoms (mainly Cl, Br, and I) as Lewis acid sites, the ChBs exhibit a strong directional nature as a result of the existence of the σ-hole. In addition, the ChBs also exhibit comparable strength to that of the HaBs or hydrogen bonds (HBs) [17] and in some cases even exceed that of the HBs [18,19]. Additionally, it should be noted that the chalcogen atoms can serve not only as the ChB donors owing to the existence of an σ-hole [20,21,22,23] or π-hole [24,25,26] on the chalcogen atoms, but also as the ChB acceptors thanks to the presence of lone pairs of electrons on the chalcogen atoms as in chalcoethers [20,26].
Among the various ChBs, the non-covalent chalcogen∙∙∙chalcogen interactions have received substantial research interest in recent years because of their potential applications in organocatalysis [27,28,29,30], materials science [31], drug design [32], biological systems [33,34,35,36], crystal engineering [37,38,39], and molecular recognition [40,41]. Experimental and theoretical studies concerning such interactions have suggested that both the chalcogen atom size and the substituents covalently attached to the chalcogen atom can affect the strength of the ChBs [37,42,43]. Specifically, the ChB becomes stronger in strength as the ChB donor atom increases in size and progressively becomes weaker in strength as the ChB acceptor atom increases in size. Moreover, the strength of the ChB becomes greater as the electron-withdrawing capacity of the substituent covalently linked to the ChB donor atom and the electron-donating capacity of the substituent adjoined with the ChB acceptor atom increase. Gleiter and colleagues [42,43] theoretically studied the binary complexes of CH3YCH3 and CH3YZ (Y = S, Se, Te; Z = CH3, CN), and symmetry-adapted perturbation theory (SAPT) analysis demonstrated that dispersion and induction forces are responsible for the formation of chalcogen∙∙∙chalcogen interactions. Additionally, statistical analyses of crystal structure surveys have also shown that there is a great number of chalcogen∙∙∙chalcogen interactions in small molecules, nucleic acids, proteins, and protein–ligand complexes [33,35,36,44,45,46,47], further suggesting the importance of such chalcogen∙∙∙chalcogen interactions.
Currently, the vast majority of investigations concerning ChBs focus on the divalent chalcogen atoms as the ChB donors [18,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50]. However, the chalcogen atoms can also frequently participate in hypervalent bonding such as tetravalent bonding [21,51,52,53]. Taking the S atom as an example, it behaves as a tetravalent bond in both SF4 and SO2. The former acts as a ChB donor to form the σ-hole interactions with Lewis bases [19,54], while the latter acts as a ChB donor to form the π-hole interactions with Lewis bases [24,26,55,56]. Scheiner and coworkers theoretically studied the heterodimers of SF4 and nitrogen-containing Lewis bases and revealed that the S∙∙∙N ChB are stronger in strength than that of a classical hydrogen bond [19]. The same group also computationally studied the S∙∙∙O ChBs between SO2 and a series of carbonyl-containing molecules, and the results show that the most stable isomer of each complex is mainly stabilized by one S∙∙∙O ChB as the primary interaction, supplemented by weak C−H∙∙∙O HBs [55]. Recently, Feng and coworkers applied microwave spectroscopy and theoretical calculations to investigate the gas-phase binary complex of SO2 with cyclohexanol and found that the two moieties within the four detected isomers are connected together via one dominant S∙∙∙O ChB and secondary weak C/O−H∙∙∙O=S HBs [56]. Microwave spectroscopic investigation on the SO2∙∙∙CH3SCH3 complex demonstrated that the S∙∙∙S ChB is the primary interaction with the determined distance of 2.947(3) Å [26]. The SAPT analysis results indicate that the electrostatic interactions mainly dominate the attractive nature of both S∙∙∙O and S∙∙∙S ChBs in the two above-mentioned complexes [26,56].
To sum up, the investigations on chalcogen∙∙∙chalcogen interactions so far mainly correspond to σ-hole interactions. However, reports on π-hole-type chalcogen∙∙∙chalcogen interactions are still very scarce [25,26,55,56]. In addition, as far as we know, no studies have been reported on such interactions containing the heavy chalcogen atom Te as a ChB donor or ChB acceptor. Herein, we used quantum chemical calculations to systematically investigate the strength and nature of the π-hole-type intermolecular chalcogen∙∙∙chalcogen interactions in the model complexes between XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te), which was frequently used as a nucleophile to engage in various NCIs like hydrogen bonds [57,58], chalcogen bonds [20,26], and pnictogen bonds [59]. Additionally, the molecular electrostatic surface potential (MESP) [60], quantum theory of atoms in molecules (QTAIM) [61], non-covalent interaction plot (NCIplot) [62], natural bond orbital (NBO) [63], and symmetry-adapted perturbation theory (SAPT) [64] analyses were also conducted to gain a deeper understanding of the π-hole-type chalcogen∙∙∙chalcogen interactions. Simultaneously, we have also compared the strength and nature of such interactions with those of the σ-hole-type chalcogen∙∙∙chalcogen interactions within the CH3YCH3∙∙∙CH3YZ (Y = S, Se, Te; Z = CH3, CN) complexes [42,43].

2. Results and Discussion

2.1. Molecular Electrostatic Surface Potential (MESP)

For the sake of identifying the potential interaction sites in each monomer, the MESPs of the XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) monomers were computed at the MP2/aug-cc-pVTZ(PP) level of theory. The MESP maps of these monomers are shown in Figure 1. For all the monomers, the positive potential corresponds to the red-colored region and the negative potential corresponds to the blue-colored region. For the XO2 (X = S, Se, Te) monomers, the positive potential regions (π-holes) are located above the chalcogen atoms on both sides of the monomeric plane, exhibiting a perpendicular orientation to the molecular plane. The negative potential regions are located at the surfaces of two O atoms. The most positive electrostatic potential values (VS,max) are 183.0, 217.8, and 257.7 kJ/mol for the SO2, SeO2, and TeO2 molecules, respectively. The VS,max values related to the chalcogen atom become more positive as the chalcogen atom increases in size. This can be primarily attributed to the fact that the polarizability of the X atom becomes larger, and its electronegativity becomes smaller as the size of the chalcogen atom increases. Conversely, the negative potential regions are distributed around the chalcogen atoms for the CH3YCH3 (Y = O, S, Se, Te) monomers, and the positive potential regions are located on the H atoms of each CH3 group. The absolute value of the VS,min associated with the chalcogen atom decreases as the chalcogen atomic radius increases. The most negative potential values (VS,min) are −143.9, −103.6, −99.2, and −91.4 kJ/mol for the CH3OCH3, CH3SCH3, CH3SeCH3, and CH3TeCH3 molecules, respectively. Accordingly, we can predict that the intermolecular π-hole-type chalcogen∙∙∙chalcogen interactions between the X atom of XO2 and the Y atom of CH3YCH3 and the C−H∙∙∙O interactions between the O atoms of XO2 and the H atoms of CH3YCH3 can be formed.

2.2. Geometrical Structures and Binding Energies of the Studied Complexes

Based on the interaction sites identified by the MESP analysis, the initial structures of the studied 12 complexes were obtained by changing the relative positions between XO2 and CH3YCH3 monomers. Figure 2 shows the geometrically optimized structures of these 12 complexes, and the corresponding Cartesian coordinates for each complex are provided in Tables S1–S3 in the Supplementary Materials. The binding energies (EB) and the key geometrical parameters associated with the ChBs within these complexes are summarized in Table 1. One can clearly find that the complexes of CH3OCH3 with XO2 (X = S, Se, Te) possess C1 symmetry and the remaining complexes have Cs symmetry. Interestingly, it should be pointed out that the structures possessing Cs symmetry for the XO2∙∙∙CH3OCH3 (X = S, Se, Te) complexes are unstable, with imaginary frequencies. The distances (RChB) between two interacting chalcogen atoms in all these complexes vary from 2.603 Å to 3.210 Å (Table 1), which are obviously smaller than the sum (Rsum,1) of van der Waals radii of the corresponding two atoms by 18.6% to 29.4% [65], thus suggesting the formation of a strong π-hole-type chalcogen∙∙∙chalcogen interaction. However, it should be also noted that these distances are bigger than the sum (Rsum,2) of covalent radii of the two interacting chalcogen atoms by 18.0% to 56.8% [66]. The π-hole-type X∙∙∙Y distances in this work are all significantly shorter than the σ-hole-type X∙∙∙Y distances in CH3XCN∙∙∙CH3YCH3 (X = S, Se, Te; Y = O, S, Se, Te) complexes [42,43], suggesting that the π-hole-type X∙∙∙Y ChBs are stronger in strength than those of the σ-hole-type X∙∙∙Y ChBs. In addition, Obenchain and collaborators investigated the π-hole chalcogen-bonded complex formed between SO2 and CH3SCH3 using high-resolution microwave spectroscopy in the gas phase and experimentally determined the intermolecular S∙∙∙S distance of 2.947(3) Å [26]. This is in good accordance with the computed theoretical value of 2.920 Å, demonstrating the reliability of the theoretical method utilized in this paper. We also calculated the ratio (λ) between RChB and Rsum,1 to qualitatively evaluate the strength of the π-hole-type chalcogen∙∙∙chalcogen interactions. The calculated λ values range from 0.71 to 0.81 for all the studied complexes, further indicating that the relatively strong π-hole-type chalcogen∙∙∙chalcogen interactions are formed in the studied complexes. The O∙∙∙H distances between one of the O atoms of XO2 and one of the H atoms of CH3YCH3 are determined to be in the range of 2.021–2.704 Å (see Table S4). These O∙∙∙H distances in all the studied complexes except for the SO2∙∙∙CH3OCH3 complex are significantly lower than the sum (2.62 Å) of van der Waals radii of the corresponding two atoms. The ∠C−H∙∙∙O angle has been determined to be in the range of 102.4–151.8° (see Table S4). It is important to point out that the O∙∙∙H distance gradually decreases and the ∠C−H∙∙∙O angle becomes bigger as the Y atomic radius increases for a given XO2 (X = S, Se, or Te) subunit. This suggests that the strength of the C−H∙∙∙O HB becomes progressively stronger as the size of the Y atom increases.
One can see from Table 1 that the EB values of the studied complexes vary from −21.6 kJ/mol for the SO2∙∙∙CH3OCH3 complex to −60.4 kJ/mol for the TeO2∙∙∙CH3TeCH3 complex. For a given ChB acceptor, the EB in absolute value gradually increases with increases in the X atom size, which is very consistent with the above-mentioned MESP analysis results. For the same ChB donor, the EB value becomes more negative as the Y atomic radius increases. It is worth noting that there is a good linear correlation between the EB and the VS,max values (Figure S1) of XO2 as well as the VS,min values (Figure S2) of CH3YCH3. In addition, a linear correlation is also found between the EB and the X∙∙∙Y distance (Figure S3).
It should be also noted that although there exist other isomers involving only hydrogen bonds for the studied model complexes on the potential energy surface, all these hydrogen-bonded isomers are not true minima due to the existence of an imaginary vibrational frequency. This suggests that the π-hole-type chalcogen bonds play a crucial role in stabilizing the studied model complexes. Furthermore, this work mainly focuses on the π-hole-type chalcogen···chalcogen interactions; thus, the discussion on these hydrogen-bonded isomers has been omitted for simplicity.

2.3. Quantum Theory of Atoms in Molecules (QTAIM) Analysis

For the purpose of estimating the strength and nature of the π-hole-type chalcogen∙∙∙chalcogen interactions present in the studied complexes, we performed the QTAIM analysis on the basis of the optimized structures at the MP2/aug-cc-pVTZ(PP) level. One bond critical point (BCP) and bond path (BP) between the two interacting chalcogen atoms in each complex was identified (see Figure 3), demonstrating the formation of the π-hole-type chalcogen∙∙∙chalcogen interaction. Interestingly, no BCPs and BPs associated with the C−H∙∙∙O HBs were found in the SO2∙∙∙CH3OCH3 complex, and there only exists one BCP and BP associated with one C−H∙∙∙O HB in the SeO2∙∙∙CH3OCH3 complex. However, for all the other complexes, two BCPs and BPs related to two C−H∙∙∙O HBs between each O atom of XO2 and one H atom of each CH3 group of CH3YCH3 were identified. Table 2 lists the calculated topological parameters at the BCPs including the electron density (ρ(r)), Laplacian of electron density (∇2ρ(r)), and total energy density (H(r)). The absolute ratio between local kinetic energy density (G(r)) and local potential energy density (V(r)) was also computed and is given in Table 2. One can see that the ρ(r) value varies from 0.0290 a.u for the SO2∙∙∙CH3OCH3 complex to 0.0438 a.u for the TeO2∙∙∙CH3OCH3 complex, and the corresponding ∇2ρ(r) value varies between 0.0184 and 0.0911 a.u, suggesting the formation of a relatively strong interaction between two chalcogen atoms. In addition, the ρ(r) value gradually decreases in the order of Y = O > S > Se > Te for the same Lewis acids (XO2). Similarly, for the same Lewis bases (CH3YCH3), the ρ(r) value gradually becomes larger as the X atom increases in size. This is in good accordance with the above-mentioned MESP analysis results. The QTAIM analysis results reveal that the π-hole-type chalcogen∙∙∙chalcogen interactions in all the studied complexes are moderate strong closed-shell interactions owing to the positive ∇2ρ(r) values. Apart from the SO2∙∙∙CH3OCH3 complex, the H(r) values are all negative and the |G(r)/V(r)| values are less than 1, demonstrating that the natures of these chalcogen∙∙∙chalcogen interactions have partial covalent characters.

2.4. Non-Covalent Interaction Plot (NCIplot) Analysis

The intermolecular interactions between XO2 and CH3YCH3 were also characterized and visualized by performing the NCIplot analysis, which is based on the electron density and its derivatives. The NCIplot analysis results are graphically displayed in Figure 4, where the weak and strong attractive interactions are represented in green-colored and blue-colored regions, respectively, and the repulsive interactions correspond to the red-colored regions. One can see that one dark blue isofurface between the X atom and Y atom in each studied complex was found, indicating the existence of a strong attractive chalcogen∙∙∙chalcogen interaction. Additionally, two green(-blush) isosurfaces between the O and H atoms were also found in all the studied complexes, suggesting the presence of two weak attractive C−H∙∙∙O HBs. It should be noted that the attractive HBs in the XO2∙∙∙CH3OCH3 (X = S, Se, Te) complexes are the weakest among these HBs. Figure 4 also displays the scatter plots of the electronic reduced density gradient (RDG) vs. the sign(λ2)ρ for the twelve studied complexes. It is seen that the sign(λ2)ρ values associated with the X∙∙∙Y ChBs and the C−H∙∙∙O HBs are all negative, further confirming the presence of intermolecular attractive interactions. However, the sign(λ2)ρ values for the X∙∙∙Y ChBs are significantly more negative than those for the C−H∙∙∙O HBs, indicating the strengths of the X∙∙∙Y ChBs are obviously stronger than those of the C−H∙∙∙O HBs in all the studied complexes. Furthermore, it is worth mentioning that for the given ChB acceptor, the sign(λ2)ρ value becomes more negative upon going from the S to Te, demonstrating that the X∙∙∙Y ChBs are stronger in strength in the order of X = S < Se < Te. This matches very well with the MESP and QTAIM analysis results.

2.5. Natural Bond Orbital (NBO) Analysis

To further understand the nature of the X∙∙∙Y ChBs in terms of orbital interactions and the corresponding second-order perturbation energy (E(2)), which can qualitatively represent the strength of the X∙∙∙Y ChBs, NBO analysis has been implemented for the studied complexes. Table 3 summarizes the obtained E(2) values for orbital interactions associated with the X∙∙∙Y ChBs. The results disclose that the interactions between the lone pair (LP) of the Y atoms of CH3YCH3 and π*(O=X, X = S, Se, Te) antibonding orbital of XO2 are the largest contribution to the stabilization of these twelve complexes. One can note that the E(2) values for all the LP(Y)→π*(O=X) orbital interactions except for the LP(O)→π*(O=S) orbital interaction in the SO2∙∙∙CH3OCH3 complex are relatively large. Indeed, the X∙∙∙Y ChB is so strong that the NBO judges it to be a covalent bond in the SeO2∙∙∙CH3TeCH3, TeO2∙∙∙CH3SeCH3, and TeO2∙∙∙CH3TeCH3 complexes. In other words, the NBO considers these three complexes as one single molecular entity. For the same ChB donor, e.g., SO2, the E(2) value becomes larger as the Y atom becomes bigger in size. Similarly, for the same ChB acceptor, e.g., CH3OCH3, the E(2) value increases upon going from the S atom to the Te atom. The changing trend of the E(2) values is in qualitative accordance with that of the EB values and the NCIplot findings described above. In addition, Figure 5 also graphically displays the NBO analysis results for the three selected representative complexes. One can clearly see that there exists a large overlap between the LP orbital of the S atom of CH3SCH3 and the π*(O=X) antibonding orbital of XO2 (X = S, Se, Te), suggesting the existence of strong X∙∙∙S ChBs.

2.6. Symmetry-Adapted Perturbation Theory (SAPT) Analysis

We also carried out the SAPT analysis to gain an in-depth understanding of the intrinsic nature of the studied intermolecular interactions. This method can decompose the total interaction energies (Etotal) of the studied complexes into the three attractive components including electrostatics (Eelec), induction (Eind), and dispersion (Edisp) interactions and one repulsive component of exchange–repulsion (Eex-re) interaction. Table 4 collects the resulting energetical values for each component. It is evident that the electrostatic component is the largest contributor for the attraction of these interactions, which stabilize the studied complexes. The contribution of this component to the total attractive interaction energy varies between 41% and 51%. The dispersion component is dominant over the induction component in the SO2∙∙∙CH3OCH3 complex, whilst the induction component is superior to the dispersion component for all the remaining complexes. It is estimated that these two components account for about 49–59% of the total attractive interaction energies. Conversely, the σ-hole-type chalcogen∙∙∙chalcogen interactions are mainly dominated by induction and dispersion components in the CH3XCN∙∙∙CH3YCH3 (X = S, Se, Te; Y = O, S, Se, Te) complexes [42,43]. The results of the SPAT analysis also indicate that the total interaction energies range from −31.3 kJ/mol for the SO2∙∙∙CH3OCH3 complex to −129.8 kJ/mol for the TeO2∙∙∙CH3TeCH3 complex. For the same Lewis acid, the Etotal value becomes more negative with increasing Y atom size. For the same Lewis base, the Etotal value also becomes more negative upon moving from X = S to Te atom. In addition, the changing trend of the total interaction energies obtained from the SAPT analysis has a linear correlation with that of the binding energies in Table 1 (Figure S4).

3. Computational Methods

Full geometry optimizations of both monomers and complexes have been carried out via the MP2 method [67] in combination with the aug-cc-pVTZ basis set [68]. The MP2/aug-cc-pVTZ level of theory has been frequently employed to investigate various chalcogen-bonded complexes owing to its accuracy and reliability, which have been demonstrated in the past [24,25,48,49,54]. The pseudopotential aug-cc-pVTZ-PP basis set [69] obtained from the EMSL new Basis Set Exchange (BSE) library [70] was employed for the Te atom to consider the relativistic effects. The same level was also utilized for conducting harmonic vibrational frequency calculations to verify that all the optimized geometrical structures are real minima with no imaginary frequencies. The binding energies (EB) of the complexes were computed by applying the following equation:
EB = EAB − EA − EB + BSSE
where EAB denotes the energy of the complex, and EA and EB represent the energy of the isolated optimized monomers. The counterpoise method [71] was utilized to correct the binding energies by removing the basis set superposition error (BSSE). The Gaussian 16 program [72] was used to execute all the computations described above.
The Multiwfn program [73] was employed to compute the molecular electrostatic surface potentials (MESPs) of the monomers on the electron/Bohr3 isosurface and the resulting MESP isosurfaces were visualized utilizing the VMD software (version 1.9.3) [74]. The Bader’s QTAIM analysis was performed at the MP2/aug-cc-pVTZ(PP) level of theory via the Multiwfn program to identity bond paths (BPs) and obtain their topological properties including the electron density (ρ(r)), Laplacian of electron density (∇2ρ(r)), local kinetic energy density (G(r)), local potential energy density (V(r)), and total energy density (H(r)) at the bond critical points (BCPs). The Johnson’s NCIplot approach was applied for characterizing the intermolecular interactions occurring in the studied complexes using the Multiwfn program, and the NCIplot analysis results were also visualized with the VMD program. The information on the charge transfer, orbital interactions, and second-order perturbation energy (E(2)) in the studied complexes was obtained by performing the NBO analysis using the NBO 3.1 module embedded into Gaussian16 program at the B3LYP-D3(BJ)/def2-TZVP level. The SAPT2+3/aug-cc-pVTZ(PP) level [64] was chosen to perform the SAPT analysis in the PSI4 software (version 1.3.2) [75] for quantitatively understanding the nature of the studied intermolecular interactions.

4. Conclusions

In summary, we systematically studied the π-hole-type chalcogen∙∙∙chalcogen interactions in a series of model complexes of XO2 (X = S, Se, Te) with CH3YCH3 (Y = O, S, Se, Te) using ab initio calculations in conjunction with QTAIM, NCIplot, NBO, and SAPT methodologies in this work. The binding energies range from −21.55 kJ/mol for the SO2∙∙∙CH3OCH3 complex to −61.38 kJ/mol for the TeO2∙∙∙CH3TeCH3 complex. The X∙∙∙Y distance varies between 2.526 Å and 3.210 Å, which is obviously less than the sum of the van der Waals radii of the corresponding two chalcogen atoms. The QTAIM analysis results suggest that all the X∙∙∙Y ChBs are closed-shell interactions, and simultaneously, the X∙∙∙Y ChBs possess some degree of covalent character in all the studied complexes, except for the SO2∙∙∙CH3OCH3 complex. The strengths of the X∙∙∙Y ChBs are clearly stronger than those of the C−H∙∙∙O HBs, revealed by performing the NCIplot and NBO analyses. In addition, the π-hole-type X∙∙∙Y ChBs are stronger in strength than those of the σ-hole-type X∙∙∙Y ChBs in the CH3XCN∙∙∙CH3YCH3 (X = S, Se, Te; Y = O, S, Se, Te) complexes [42,43]. The findings of the SAPT analysis indicate that electrostatic interactions are the largest contributor to the stabilization of the studied complexes, but the induction and dispersion interactions also play a key role in stabilizing the studied complexes. Hopefully, the findings obtained from this work will prove valuable to the scientific community engaged in crystal engineering, materials science, drug design, organocatalysis, molecular recognition, and biological systems.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms242216193/s1.

Author Contributions

Conceptualization, T.L.; methodology, F.L., Q.L. and Y.Z.; software, G.F. and T.L.; validation, F.L., Q.L., Y.Z., X.C. and T.L.; formal analysis, F.L., Q.L. and Y.Z.; investigation, F.L., Q.L., Y.Z., X.C., J.Y. and T.L.; resources, T.L.; data curation, F.L., Q.L., Y.Z., J.Y. and T.L.; writing—original draft preparation, F.L., Q.L. and Y.Z.; writing—review and editing, Z.H., G.F., Z.Z. and T.L.; visualization, F.L., Q.L., Y.Z. and J.Y.; supervision, Z.Z. and T.L.; project administration, T.L.; funding acquisition, T.L. All authors have read and agreed to the published version of the manuscript.

Funding

This word was supported by the National Natural Science Foundation of China (Grant No. 22263003), the Natural Science Foundation of Guizhou Province (ZK2022-369, ZK2022-406), the Youth Science and Technology Talents Growth Project of Guizhou Ordinary Colleges and Universities (2022-188, 2022-222), the Science and Technology Fund Project of Guizhou Provincial Health Commission (gzwkj2022-513), and the High-Level Talent Initiation Project of Guizhou Medical University (J[2021]039, J[2022]060, J[2023]007).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data that support the findings of this study are available within the article and its Supplementary Materials.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Pascoe, D.J.; Ling, K.B.; Cockroft, S.L. The Origin of Chalcogen-Bonding Interactions. J. Am. Chem. Soc. 2017, 139, 15160–15167. [Google Scholar] [CrossRef]
  2. Aakeroy, C.B.; Bryce, D.I.; Desiraju, G.R.; Frontera, A.; Legon, A.C.; Nicotra, F.; Rissanen, K.K.; Scheiner, S.; Terraneo, G.; Metrangolo, P.; et al. Definition of the chalcogen bond (IUPAC Recommendations 2019). Pure Appl. Chem. 2019, 91, 1889–1892. [Google Scholar] [CrossRef]
  3. Vogel, L.; Wonner, P.; Huber, S.M. Chalcogen Bonding: An Overview. Angew. Chem. Int. Ed. 2018, 58, 1880–1891. [Google Scholar] [CrossRef]
  4. Scilabra, P.; Terraneo, G.; Resnati, G. The Chalcogen Bond in Crystalline Solids: A World Parallel to Halogen Bond. Acc. Chem. Res. 2019, 52, 1313–1324. [Google Scholar] [CrossRef]
  5. Murray, J.S.; Lane, P.; Clark, T.; Riley, K.E.; Politzer, P. σ-Holes, π-holes and electrostatically-driven interactions. J. Mol. Model. 2012, 18, 541–548. [Google Scholar] [CrossRef] [PubMed]
  6. Bauzá, A.; Mooibroek, T.J.; Frontera, A. The bright future of unconventional σ/π-hole interactions. ChemPhysChem 2015, 16, 2496–2517. [Google Scholar] [CrossRef]
  7. Wang, H.; Wang, W.; Jin, W.J. σ-Hole bond vs π-hole bond: A comparison based on halogen bond. Chem. Rev. 2016, 116, 5072–5104. [Google Scholar] [CrossRef]
  8. Politzer, P.; Murray, J.S.; Clark, T.; Resnati, G. The σ-hole revisited. Phys. Chem. Chem. Phys. 2017, 19, 32166–32178. [Google Scholar] [CrossRef]
  9. Politzer, P.; Murray, J.S. An Overview of Strengths and Directionalities of Noncovalent Interactions: σ-Holes and π-Holes. Crystals 2019, 9, 165. [Google Scholar] [CrossRef]
  10. Politzer, P.; Murray, J.S.; Clark, T. Halogen bonding and other σ-hole interactions: A perspective. Phys. Chem. Chem. Phys. 2013, 15, 11178–11189. [Google Scholar] [CrossRef]
  11. Politzer, P.; Murray, J.S. σ-Hole Interactions: Perspectives and Misconceptions. Crystals 2017, 7, 212. [Google Scholar] [CrossRef]
  12. Frontera, A. σ- and π-Hole Interactions. Crystals 2020, 10, 721. [Google Scholar] [CrossRef]
  13. Scheiner, S. Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage. J. Phys. Chem. A 2021, 125, 6514–6528. [Google Scholar] [CrossRef]
  14. Tsuzuki, S.; Sato, N. Origin of attraction in chalcogen–nitrogen interaction of 1,2,5-chalcogenadiazole dimers. J. Phys. Chem. B 2013, 117, 6849–6855. [Google Scholar] [CrossRef]
  15. Desiraju, G.R.; Ho, P.S.; Kloo, L.; Legon, A.C.; Marquardt, R.; Metrangolo, P.; Politzer, P.; Resnati, G.; Rissanen, K. Definition of the halogen bond (IUPAC Recommendations 2013). Pure Appl. Chem. 2013, 85, 1711–1713. [Google Scholar] [CrossRef]
  16. Cavallo, G.; Metrangolo, P.; Milani, R.; Pilati, T.; Priimagi, A.; Resnati, G.; Terraneo, G. The halogen bond. Chem. Rev. 2016, 116, 2478–2601. [Google Scholar] [CrossRef] [PubMed]
  17. Gilli, G.; Gilli, P. The Nature of the Hydrogen Bond; Oxford University Press: Oxford, UK, 2009. [Google Scholar]
  18. Adhikari, U.; Scheiner, S. Effects of charge and substituent on the S···N chalcogen bond. J. Phys. Chem. A 2014, 118, 3183–3192. [Google Scholar] [CrossRef] [PubMed]
  19. Nziko, V.d.P.N.; Scheiner, S. Chalcogen Bonding between Tetravalent SF4 and Amines. J. Phys. Chem. A 2014, 118, 10849–10856. [Google Scholar] [CrossRef]
  20. Geboes, Y.; De Vleeschouwer, F.; De Proft, F.; Herrebout, W.A. Exploiting the σ-hole concept: An Infrared and Raman-based characterization of the S···O chalcogen bond between 2,2,4,4-tetrafluoro-1,3-dithiethane and dimethyl ether. Chem. Eur. J. 2017, 23, 17384–17392. [Google Scholar] [CrossRef]
  21. Zierkiewicz, W.; Wysokiński, R.; Michalczyk, M.; Scheiner, S. Chalcogen bonding of two ligands to hypervalent YF4 (Y = S, Se, Te, Po). Phys. Chem. Chem. Phys. 2019, 21, 20829–20839. [Google Scholar] [CrossRef] [PubMed]
  22. Lu, T.; Zheng, Y.; Gou, Q.; Hou, G.-L.; Feng, G. Rotational characterization of S···F chalcogen bonds in the complex of 2,2,4,4-tetrafluoro-1,3-dithietane and difluoromethane. Phys. Chem. Chem. Phys. 2019, 21, 24659–24665. [Google Scholar] [CrossRef]
  23. Santos, L.d.A.; Ramalho, T.C.; Hamlin, T.A.; Bickelhaupt, F.M. Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study. J. Comput. Chem. 2021, 42, 688–698. [Google Scholar] [CrossRef] [PubMed]
  24. Esrafili, M.D.; Vakili, M.; Solimannejad, M. Cooperative interaction between π-hole and single-electron σ-hole interactions in O2S···NCX···CH3 and O2Se···NCX···CH3 complexes (X = F, Cl, Br and I). Mol. Phys. 2014, 112, 2078–2084. [Google Scholar] [CrossRef]
  25. Esrafili, M.D.; Mohammadian-Sabet, F. Homonuclear chalcogen–chalcogen bond interactions in complexes pairing YO3 and YHX molecules (Y = S, Se; X = H, Cl, Br, CCH, NC, OH, OCH3): Influence of substitution and cooperativity. Int. J. Quantum Chem. 2016, 116, 529–536. [Google Scholar] [CrossRef]
  26. Obenchain, D.A.; Spada, L.; Alessandrini, S.; Rampino, S.; Herbers, S.; Tasinato, N.; Mendolicchio, M.; Kraus, P.; Gauss, J.; Puzzarini, C.; et al. Unveiling the Sulfur–Sulfur Bridge: Accurate Structural and Energetic Characterization of a Homochalcogen Intermolecular Bond. Angew. Chem. Int. Ed. 2018, 57, 15822–15826. [Google Scholar] [CrossRef]
  27. Wang, W.; Zhu, H.; Liu, S.; Zhao, Z.; Zhang, L.; Hao, J.; Wang, Y. Chalcogen–Chalcogen Bonding Catalysis Enables Assembly of Discrete Molecules. J. Am. Chem. Soc. 2019, 141, 9175–9179. [Google Scholar] [CrossRef]
  28. Wang, W.; Zhu, H.; Feng, L.; Yu, Q.; Hao, J.; Zhu, R.; Wang, Y. Dual chalcogen–chalcogen bonding catalysis. J. Am. Chem. Soc. 2020, 142, 3117–3124. [Google Scholar] [CrossRef] [PubMed]
  29. Pale, P.; Mamane, V. Chalcogen Bonding Catalysis: Tellurium, the Last Frontier? Chem. Eur. J. 2023, 29, e202302755. [Google Scholar] [CrossRef]
  30. Zhao, Z.; Pang, Y.; Zhao, Z.; Zhou, P.-P.; Wang, Y. Supramolecular catalysis with ethers enabled by dual chalcogen bonding activation. Nat. Commun. 2023, 14, 6347. [Google Scholar] [CrossRef]
  31. Ho, P.C.; Wang, J.Z.; Meloni, F.; Vargas-Baca, I. Chalcogen bonding in materials chemistry. Coordin. Chem. Rev. 2020, 422, 213464. [Google Scholar] [CrossRef]
  32. Beno, B.R.; Yeung, K.-S.; Bartberger, M.D.; Pennington, L.D.; Meanwell, N.A. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J. Med. Chem. 2015, 58, 4383–4438. [Google Scholar] [CrossRef]
  33. Carugo, O.; Resnati, G.; Metrangolo, P. Chalcogen Bonds Involving Selenium in Protein Structures. ACS Chem. Biol. 2021, 16, 1622–1627. [Google Scholar] [CrossRef]
  34. Piña, M.d.L.N.; Frontera, A.; Bauza, A. Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study. ACS Chem. Biol. 2021, 16, 1701–1708. [Google Scholar] [CrossRef] [PubMed]
  35. Riveras, J.A.F.; Frontera, A.; Bauzá, A. Selenium chalcogen bonds are involved in protein–carbohydrate recognition: A combined PDB and theoretical study. Phys. Chem. Chem. Phys. 2021, 23, 17656–17662. [Google Scholar] [CrossRef]
  36. Biswal, H.S.; Sahu, A.K.; Galmés, B.; Frontera, A.; Chopra, D. Se···O/S and S···O chalcogen bonds in small molecules and proteins: A combined CSD and PDB study. ChemBioChem 2022, 23, e202100498. [Google Scholar] [CrossRef] [PubMed]
  37. Gleiter, R.; Haberhauer, G.; Werz, D.B.; Rominger, F.; Bleiholder, C. From Noncovalent Chalcogen–Chalcogen Interactions to Supramolecular Aggregates: Experiments and Calculations. Chem. Rev. 2018, 118, 2010–2041. [Google Scholar] [CrossRef]
  38. Fourmigué, M.; Dhaka, A. Chalcogen bonding in crystalline diselenides and selenocyanates: From molecules of pharmaceutical interest to conducting materials. Coordin. Chem. Rev. 2020, 403, 213084. [Google Scholar] [CrossRef]
  39. Mahmudov, K.T.; Gurbanov, A.V.; Aliyeva, V.A.; da Silva, M.F.C.G.; Resnati, G.; Pombeiro, A.J. Chalcogen bonding in coordination chemistry. Coordin. Chem. Rev. 2022, 464, 214556. [Google Scholar] [CrossRef]
  40. Lim, J.Y.; Beer, P.D. Sigma-Hole Interactions in Anion Recognition. Chem 2018, 4, 731–783. [Google Scholar] [CrossRef]
  41. Biot, N.; Bonifazi, D. Chalcogen-bond driven molecular recognition at work. Coordin. Chem. Rev. 2020, 413, 213243. [Google Scholar] [CrossRef]
  42. Bleiholder, C.; Werz, D.B.; Köppel, H.; Gleiter, R. Theoretical Investigations on Chalcogen−Chalcogen Interactions: What Makes These Nonbonded Interactions Bonding? J. Am. Chem. Soc. 2006, 128, 2666–2674. [Google Scholar] [CrossRef] [PubMed]
  43. Bleiholder, C.; Gleiter, R.; Werz, D.B.; Köppel, H. Theoretical Investigations on Heteronuclear Chalcogen—Chalcogen Interactions: On the Nature of Weak Bonds between Chalcogen Centers. Inorg. Chem. 2007, 46, 2249–2260. [Google Scholar] [CrossRef] [PubMed]
  44. Kříž, K.; Fanfrlík, J.; Lepšík, M. Chalcogen Bonding in Protein−Ligand Complexes: PDB Survey and Quantum Mechanical Calculations. Chemphyschem 2018, 19, 2540–2548. [Google Scholar] [CrossRef] [PubMed]
  45. Lundemba, A.S.; Bibelayi, D.D.; Tsalu, P.V.; Wood, P.A.; Cole, J.; Kayembe, J.S.; Yav, Z.G. Chalcogen Bonds in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD). Cryst. Struct. Theory Appl. 2021, 10, 57–69. [Google Scholar] [CrossRef]
  46. Carugo, O.I. Chalcogen bonds formed by protein sulfur atoms in proteins. A survey of high-resolution structures deposited in the protein data bank. J. Biomol. Struct. Dyn. 2022, 91, 1–7. [Google Scholar] [CrossRef]
  47. Piña, M.d.L.N.; Bauzá, A. On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective. Int. J. Mol. Sci. 2023, 24, 13035. [Google Scholar] [CrossRef]
  48. Esrafili, M.D.; Saeidi, N.; Baneshi, M.M. Chalcogen–chalcogen interactions in furan-YHX and thiophene-YHX complexes (X = F, Cl, Br; Y = S, Se): An ab initio study. Bull. Chem. Soc. Jpn. 2015, 88, 1683–1692. [Google Scholar] [CrossRef]
  49. Yan, N.; Huo, S.; Li, X.; Zeng, Y.; Meng, L. The chalcogen bond in F2P(S)N···SX2, F2PNS···SX2, F2PSN···SX2 (X = F, Cl, Br, OH, CH3, NH2) complexes. J. Mol. Model. 2019, 25, 19. [Google Scholar]
  50. Weiss, R.; Aubert, E.; Groslambert, L.; Pale, P.; Mamane, V. Evidence for and evaluation of fluorine–tellurium chalcogen bonding. Chem. Sci. 2023, 14, 7221–7229. [Google Scholar] [CrossRef]
  51. Matsumoto, K.; Gerken, M. Recent advances in sulfur tetrafluoride chemistry: Syntheses, structures, and applications. Dalton Trans. 2021, 50, 12791–12799. [Google Scholar] [CrossRef]
  52. Liang, J.; Shi, Y.; Lu, Y.; Xu, Z.; Liu, H. Square tetravalent chalcogen bonds in dimeric aggregates: A joint crystallographic survey and theoretical study. CrystEngComm 2022, 24, 975–986. [Google Scholar] [CrossRef]
  53. Franconetti, A.; Quiñonero, D.; Frontera, A.; Resnati, G. Unexpected chalcogen bonds in tetravalent sulfur compounds. Phys. Chem. Chem. Phys. 2019, 21, 11313–11319. [Google Scholar] [CrossRef] [PubMed]
  54. Ibrahim, M.A.A.; Saeed, R.R.A.; Shehata, M.N.I.; Moussa, N.A.M.; Tawfeek, A.M.; Ahmed, M.N.; El-Rahman, M.K.A.; Shoeib, T. Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases. ACS Omega 2023, 8, 32828–32837. [Google Scholar] [CrossRef] [PubMed]
  55. Azofra, L.M.; Scheiner, S. Substituent effects in the noncovalent bonding of SO2 to molecules containing a carbonyl group. The dominating role of the chalcogen bond. J. Phys. Chem. A 2014, 118, 3835–3845. [Google Scholar] [CrossRef]
  56. Jin, Y.; Saragi, R.T.; Juanes, M.; Feng, G.; Lesarri, A. Interaction topologies of the S···O chalcogen bond: The conformational equilibrium of the cyclohexanol···SO2 cluster. Phys. Chem. Chem. Phys. 2021, 23, 10799–10806. [Google Scholar] [CrossRef]
  57. Tulsiyan, K.D.; Jena, S.; Dutta, J.; Biswal, H.S. Hydrogen bonding with polonium. Phys. Chem. Chem. Phys. 2022, 24, 17185–17194. [Google Scholar] [CrossRef] [PubMed]
  58. Pal, D.; Charaya, H.; Chakraborty, S. An experimental exploration of C−H···X hydrogen bond in [CHCl3−X(CH3)2] complexes (X= O, S, and Se). ChemPhysChem 2023, 24, e202300124. [Google Scholar] [CrossRef]
  59. Beckmann, J.L.; Krieft, J.; Vishnevskiy, Y.V.; Neumann, B.; Stammler, H.-G.; Mitzel, N.W. A bidentate antimony pnictogen bonding host-system. Angew. Chem. Int. Ed. 2023, 62, e202310439. [Google Scholar] [CrossRef]
  60. Politzer, P.; Murray, J.S.; Concha, M.C. σ-hole bonding between like atoms; a fallacy of atomic charges. J. Mol. Model. 2008, 14, 659–665. [Google Scholar] [CrossRef]
  61. Bader, R.F.W. A quantum theory of molecular structure and its applications. Chem. Rev. 1991, 91, 893–928. [Google Scholar] [CrossRef]
  62. Johnson, E.R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A.J.; Yang, W. Revealing Noncovalent Interactions. J. Am. Chem. Soc. 2010, 132, 6498–6506. [Google Scholar] [CrossRef] [PubMed]
  63. Glendening, E.D.; Landis, C.R.; Weinhold, F. Natural bond orbital methods. WIREs Comput. Mol. Sci. 2011, 2, 1–42. [Google Scholar] [CrossRef]
  64. Parker, T.M.; Burns, L.A.; Parrish, R.M.; Ryno, A.G.; Sherrill, C.D. Levels of symmetry adapted perturbation theory (SAPT). I. Efficiency and performance for interaction energies. J. Chem. Phys. 2014, 140, 094106. [Google Scholar] [CrossRef] [PubMed]
  65. Mantina, M.; Chamberlin, A.C.; Valero, R.; Cramer, C.J.; Truhlar, D.G. Consistent van der Waals Radii for the Whole Main Group. J. Phys. Chem. A 2009, 113, 5806–5812. [Google Scholar] [CrossRef]
  66. Cordero, B.; Gómez, V.; Platero-Prats, A.E.; Revés, M.; Echeverría, J.; Cremades, E.; Barragán, F.; Alvarez, S. Covalent radii revisited. Dalton Trans. 2008, 21, 2832–2838. [Google Scholar] [CrossRef]
  67. Møller, C.; Plesset, M.S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. B 1934, 46, 618–622. [Google Scholar] [CrossRef]
  68. Woon, D.E.; Dunning, T.H., Jr. Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. J. Chem. Phys. 1993, 98, 1358–1371. [Google Scholar] [CrossRef]
  69. Peterson, K.A.; Figgen, D.; Goll, E.; Stoll, H.; Dolg, M. Systematically convergent basis sets with relativistic pseudopotentials. II. Small-core pseudopotentials and correlation consistent basis sets for the post-d group 16–18 elements. J. Chem. Phys. 2003, 119, 11113–11123. [Google Scholar] [CrossRef]
  70. Pritchard, B.P.; Altarawy, D.; Didier, B.T.; Gibson, T.D.; Windus, T.L. New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community. J. Chem. Inf. Model. 2019, 59, 4814–4820. [Google Scholar] [CrossRef] [PubMed]
  71. Boys, S.F.; Bernardi, F.D. The Calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 1970, 19, 553–566. [Google Scholar] [CrossRef]
  72. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Petersson, G.A.; Nakatsuji, H.; et al. Gaussian 16, Revision A.03; Gaussian, Inc.: Wallingford, CT, USA, 2016. [Google Scholar]
  73. Lu, T.; Chen, F. Multiwfn: A multifunctional wavefunction analyzer. J. Comput. Chem. 2012, 33, 580–592. [Google Scholar] [CrossRef] [PubMed]
  74. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph. 1996, 14, 33–38. [Google Scholar] [CrossRef] [PubMed]
  75. Parrish, R.M.; Burns, L.A.; Smith, D.G.A.; Simmonett, A.C.; DePrince, A.E., III; Hohenstein, E.G.; Bozkaya, U.; Sokolov, A.Y.; Di Remigio, R.; Richard, R.M.; et al. Psi4 1.1: An open-source electronic structure program emphasizing automation, advanced libraries, and interoperability. J. Chem. Theory Comput. 2017, 13, 3185–3197. [Google Scholar] [CrossRef] [PubMed]
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Figure 1. The MESP maps of the XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) monomers. The red-colored region indicates the positive potential and the blue-colored region indicates the negative potential. The VS,max and VS,min values (in kJ/mol) denote the most positive potential and the most negative potential, respectively.
Figure 1. The MESP maps of the XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) monomers. The red-colored region indicates the positive potential and the blue-colored region indicates the negative potential. The VS,max and VS,min values (in kJ/mol) denote the most positive potential and the most negative potential, respectively.
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Figure 2. The optimized geometrical structures of the studied complexes. The chalcogen∙∙∙chalcogen distances are given in Å. The binding energies in kJ/mol are displayed using blue numbers.
Figure 2. The optimized geometrical structures of the studied complexes. The chalcogen∙∙∙chalcogen distances are given in Å. The binding energies in kJ/mol are displayed using blue numbers.
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Figure 3. The diagrams of the QTAIM analysis for the studied complexes. The orange and yellow dots represent the bond critical points (BCPs) and ring critical points (RCPs), respectively. The brown lines denote the bond paths.
Figure 3. The diagrams of the QTAIM analysis for the studied complexes. The orange and yellow dots represent the bond critical points (BCPs) and ring critical points (RCPs), respectively. The brown lines denote the bond paths.
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Figure 4. The NCI isosurfaces (S = 0.55) and scatter plots of the RDG vs. sign(λ2)ρ of the twelve studied complexes.
Figure 4. The NCI isosurfaces (S = 0.55) and scatter plots of the RDG vs. sign(λ2)ρ of the twelve studied complexes.
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Figure 5. The NBO plots of the donor–acceptor interaction for the three selected representative complexes.
Figure 5. The NBO plots of the donor–acceptor interaction for the three selected representative complexes.
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Table 1. The binding energies (EB, kJ/mol) and geometrical parameters associated with the ChBs for the studied complexes.
Table 1. The binding energies (EB, kJ/mol) and geometrical parameters associated with the ChBs for the studied complexes.
ComplexesEBChBsRChB (Å)Rsum,1 a (Å)λ bRsum,2 c (Å)
SO2∙∙∙CH3OCH3−21.6S∙∙∙O2.6033.32 (21.6%) d0.781.66 [56.8%] e
SO2∙∙∙CH3SCH3−27.3S∙∙∙S2.9203.60 (18.9%)0.812.06 [41.7%]
SO2∙∙∙CH3SeCH3−27.8S∙∙∙Se2.9823.70 (19.4%)0.812.19 [36.2%]
SO2∙∙∙CH3TeCH3−28.3S∙∙∙Te3.1433.86 (18.6%)0.812.39 [31.5%]
SeO2∙∙∙CH3OCH3−28.2Se∙∙∙O2.5353.42 (25.9%)0.741.79 [41.6%]
SeO2∙∙∙CH3SCH3−40.3Se∙∙∙S2.8853.70 (22.0%)0.782.19 [31.7%]
SeO2∙∙∙CH3SeCH3−42.4Se∙∙∙Se2.9563.80 (22.2%)0.782.32 [27.4%]
SeO2∙∙∙CH3TeCH3−45.5Se∙∙∙Te3.1213.96 (21.2%)0.792.52 [23.8%]
TeO2∙∙∙CH3OCH3−37.4Te∙∙∙O2.5263.58 (29.4%)0.711.99 [26.9%]
TeO2∙∙∙CH3SCH3−52.8Te∙∙∙S2.9543.86 (23.5%)0.772.39 [23.6%]
TeO2∙∙∙CH3SeCH3−56.0Te∙∙∙Se3.0373.96 (23.3%)0.772.52 [20.5%]
TeO2∙∙∙CH3TeCH3−60.4Te∙∙∙Te3.2104.12 (22.1%)0.782.72 [18.0%]
a Rsum,1 denotes the sum of the van der Waals radii of the corresponding two chalcogen atoms, and the van der Waals radii of the O, S, Se, and Te atoms are 1.52, 1.80, 1.90, and 2.06 Å, respectively [65]. b λ denotes the ratio of RChB and Rsum,1. c Rsum,2 denotes the sum of the covalent radii of the corresponding two chalcogen atoms, and the covalent radii of the O, S, Se, and Te atoms are 0.63, 1.03, 1.16, and 1.36 Å, respectively [66]. d The values in parentheses are the percentage differences between |RChB − Rsum,1| and Rsum,1. e The values in square brackets are the percentage differences between |RChB − Rsum,2| and Rsum,2.
Table 2. Topological properties of the BCPs related to the chalcogen∙∙∙chalcogen interactions in all twelve complexes. All the values are reported in a.u.
Table 2. Topological properties of the BCPs related to the chalcogen∙∙∙chalcogen interactions in all twelve complexes. All the values are reported in a.u.
ComplexesBCPρ(r)∇2ρ(r)H(r)|G(r)/V(r)|
SO2∙∙∙CH3OCH3S∙∙∙O0.0290 0.0831 0.0002 1.0087
SO2∙∙∙CH3SCH3S∙∙∙S0.0307 0.0463 −0.00310.8266
SO2∙∙∙CH3SeCH3S∙∙∙Se0.0315 0.0395 −0.00370.7864
SO2∙∙∙CH3TeCH3S∙∙∙Te0.0292 0.0303 −0.00340.7654
SeO2∙∙∙CH3OCH3Se∙∙∙O0.0377 0.0911 −0.00230.9172
SeO2∙∙∙CH3SCH3Se∙∙∙S0.0370 0.0420 −0.00530.7479
SeO2∙∙∙CH3SeCH3Se∙∙∙Se0.0371 0.0345 −0.00570.7153
SeO2∙∙∙CH3TeCH3Se∙∙∙Te0.0340 0.0254 −0.00510.6923
TeO2∙∙∙CH3OCH3Te∙∙∙O0.0438 0.0893 −0.00630.8202
TeO2∙∙∙CH3SCH3Te∙∙∙S0.0383 0.0328 −0.00690.6871
TeO2∙∙∙CH3SeCH3Te∙∙∙Se0.0378 0.0255 −0.00690.6576
TeO2∙∙∙CH3TeCH3Te∙∙∙Te0.0346 0.0184 −0.00580.6419
Table 3. The donor–acceptor orbital interactions and the corresponding E(2) value (kJ/mol) related to the X∙∙∙Y ChBs in all the studied complexes a.
Table 3. The donor–acceptor orbital interactions and the corresponding E(2) value (kJ/mol) related to the X∙∙∙Y ChBs in all the studied complexes a.
ComplexesDonorAcceptor E(2)
SO2∙∙∙CH3OCH3LP(O)BD*(O=S)7.7
SO2∙∙∙CH3SCH3LP(S)BD*(O=S)55.3
SO2∙∙∙CH3SeCH3LP(Se)BD*(O=S)66.2
SO2∙∙∙CH3TeCH3LP(Te)BD*(O=S)70.1
SeO2∙∙∙CH3OCH3LP(O)BD*(O=Se)44.0
SeO2∙∙∙CH3SCH3LP(S)BD*(O=Se)109.3
SeO2∙∙∙CH3SeCH3LP(Se)BD*(O=Se)131.5
SeO2∙∙∙CH3TeCH3LP(Te)BD*(O=Se)NA b
TeO2∙∙∙CH3OCH3LP(O)BD*(O=Te)74.1
TeO2∙∙∙CH3SCH3LP(S)BD*(O=Te)137.3
TeO2∙∙∙CH3SeCH3LP(Se)BD*(O=Te)NA b
TeO2∙∙∙CH3TeCH3LP(Te)BD*(O=Te)NA b
a LP represents lone pair, and BD* represents antibonding orbital. b The corresponding ChB is so strong that the NBO judges it to be a covalent bond.
Table 4. The energetical values of the attractive and repulsion components as well as total interaction energies for the studied complexes obtained by using the SAPT approach at the SAPT2+3/aug-cc-pVTZ(PP) level of calculation a.
Table 4. The energetical values of the attractive and repulsion components as well as total interaction energies for the studied complexes obtained by using the SAPT approach at the SAPT2+3/aug-cc-pVTZ(PP) level of calculation a.
ComplexesEelecEindEdispEex-reEtotal
SO2∙∙∙CH3OCH3−58.9(49%) b−27.5(22%)−35.0(29%)90.1−31.3
SO2∙∙∙CH3SCH3−79.2(43%)−55.3(30%)−48.2(27%)139.6−43.2
SO2∙∙∙CH3SeCH3−88.6(43%)−65.4(32%)−52.8(25%)160.3−46.4
SO2∙∙∙CH3TeCH3−87.6(42%)−65.5(31%)−55.2(27%)160.3−48.0
SeO2∙∙∙CH3OCH3−95.2(49%)−53.4(27%)−47.5(24%)147.2−48.9
SeO2∙∙∙CH3SCH3−120.3(43%)−95.8(34%)−65.5(23%)206.6−75.0
SeO2∙∙∙CH3SeCH3−134.4(43%)−108.5(34%)−71.0(23%)230.9−83.0
SeO2∙∙∙CH3TeCH3−129.8(41%)−114.4(36%)−74.4(23%)228.7−89.9
TeO2∙∙∙CH3OCH3−145.7(51%)−80.3(28%)−59.3(21%)204.6−80.7
TeO2∙∙∙CH3SCH3−154.9(46%)−104.4(31%)−77.9(23%)228.7−108.5
TeO2∙∙∙CH3SeCH3−166.1(45%)−117.4(32%)−83.6(23%)248.2−119.0
TeO2∙∙∙CH3TeCH3−161.8(44%)−119.5(32%)−87.8(24%)239.2−129.8
a All the energetical values are given in kJ/mol. b The parenthesized values indicate the proportion of each attractive component contributing to the total attractive interactions.
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Lei, F.; Liu, Q.; Zhong, Y.; Cui, X.; Yu, J.; Hu, Z.; Feng, G.; Zeng, Z.; Lu, T. Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te). Int. J. Mol. Sci. 2023, 24, 16193. https://doi.org/10.3390/ijms242216193

AMA Style

Lei F, Liu Q, Zhong Y, Cui X, Yu J, Hu Z, Feng G, Zeng Z, Lu T. Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te). International Journal of Molecular Sciences. 2023; 24(22):16193. https://doi.org/10.3390/ijms242216193

Chicago/Turabian Style

Lei, Fengying, Qingyu Liu, Yeshuang Zhong, Xinai Cui, Jie Yu, Zuquan Hu, Gang Feng, Zhu Zeng, and Tao Lu. 2023. "Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te)" International Journal of Molecular Sciences 24, no. 22: 16193. https://doi.org/10.3390/ijms242216193

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