Hydrogen Bonds of C=S, C=Se and C=Te with C-H in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD)

Abstract

Considerable interest in hydrogen bonding involving chalcogen has been growing since the IUPAC committee has redefined hydrogen bonding. Not only the focus is on unconventional acceptors, but also on donors not discussed before. It has been mentioned in previous studies that the proton of the H-C group could be involved in hydrogen bonding, but with conventional acceptors. In this study, we explored the ability of hydrogen bond formation of Se, S and Te acceptors with the H-C donor using Cambridge Structural Database in conjunction with Ab Initio calculations. In the CSD, there are respectively 256, 6249 and 11 R1,R2,-C=Se, R1,R2,-C=S and R1,R2,-C=Te structures that form hydrogen bonds, in which the N,N groups are majority. Except for C=S acceptor which can form a hydrogen bond with its C, C group, both C=Se and C=Te acceptors could form a hydrogen bond only with N,C and N,N groups. CSD analysis shows very similar d (norm) around -0.04 Å, while DFT-calculated interaction for N,C and N,N groups are also similar. Both interaction distances derived from CSD analysis and DFT-calculated interaction energies demonstrate that the acceptors form stable complexes with H-CF3. Besides hydrogen bonds, dispersion interactions are forces stabilizing the complexes since their contribution can reach 50%. Analysis of intra-molecular geometries and Ab Initio partial charges show that this bonding stems from resonance induced Cδ+=Xδ- dipoles. In many respects, both C=Se, C=S and C=Te are similar to C=S, with similar d (norm) and calculated interaction strengths.

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Bibelayi, D. , Lundemba, A. , Tsalu, P. , Kilunga, P. , Tshishimbi, J. and Yav, Z. (2022) Hydrogen Bonds of C=S, C=Se and C=Te with C-H in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD). Crystal Structure Theory and Applications, 11, 1-22. doi: 10.4236/csta.2022.111001.

1. Introduction

Selenium, sulphur and tellurium, of respectively atomic numbers 34, 16 and 52 are chalcogens and share properties with oxygen and polonium, all of which have six valence electrons, although oxygen is sometimes excluded from the collective term “chalcogen”. The importance of chalcogen is known and has been demonstrated [1] - [8]. Significant interest in hydrogen bonding involving chalcogen has been growing since the IUPAC committee has redefined hydrogen bonding. Not only the focus is on unconventional acceptors, but also on donors not discussed before. It has been mentioned in previous studies [9] [10] that the proton of the H-C group could be involved in hydrogen bonding, but with conventional acceptors.

Hydrogen bonding of divalent chalcogens compounds has also been studied computationally [11] [12] [13].

Due to the importance of both inorganic and organic chalcogens, we are embarking on a series of studies of the structural chemistry of small-molecule Se, S and Te compounds, with an emphasis on their intermolecular interactions in crystal structures. In this paper, we report a general survey of both three chalcogens in small-molecule crystal structures, before examining the ability of them to accept H-C hydrogen bonds in [(NH2)2-C=X], [(NH2),C-C=X, and [(C)2-C=X] models. This work builds on earlier studies of the hydrogen-bonding ability of analogous C=Se and C=S acceptors with O-H and N-H donors [14]. Surveys and analyses of the Cambridge Structural Database [15] [16] have been used in conjunction with AbInitio and DFT calculations of model systems using Gaussian 09 [17] to probe hydrogen bonding in terms of structure, energetics and electrostatics.

2. Methodology

2.1 CSD Analysis

We performed the CSD analysis using an analogous approach to that outlined elsewhere [14] using CSD version 5.41 (November 2019) including the November data update, which has a total of 1,034,174 structural entries. Geometric parameters (d distance, rho, phi and theta angles) for intermolecular interactions between H-bond acceptors (C=Se/S/Te) and donors (QA) were performed according to Figure 1.

In addition, we calculated the van der Waals normalized hydrogen-bond distances d (norm) to explore the bond-strength bond-length relationship according to the Equation (1):

Figure 1. Schematic illustration of electron delocalisation in N,R-C=X (R = C or N; X=S, Se or Te) systems.

d ( norm ) = d vdW ( H ) vdW ( X ) (1)

where d is the hydrogen bond distance, H and X are respectively the hydrogen and acceptor atoms, vdW(H) and vdW(X) are the van der Waals radii of the H and acceptor atoms respectively.

2.2. Computational Studies

To complement the database results, a series of calculations were carried out with the density-functional theory (DFT) method using Gaussian 09 [17]. The B3LYP [18] [19] [20] three-parameter hybrid functional and the B3LYP augmented with the D3 dispersion correction [21] were used with the basis set of 6-311++G(3df,2p). Use of this large basis set should minimize the problem of correction for the basis set superposition error [22] [23] [24]. Both approaches were used to calculate atomic partial charges, molecular electrostatic potentials and energies of interaction, but also to perform NBO analysis.

The electrostatic potential V(r) in the space around a molecule, created by the electrons and nuclei at any point r, was calculated according to the Equation (2), written in atomic units, a.u.:

V ( r ) = A Z A | R A r | ρ ( r ) d r | r r | (2)

ZA and ρ(r) are, respectively, the charge on nucleus A located at distance R and the electronic density of the molecule. | R A r | and | r r | respectively represent the nucleus distance from r, the distance of each electronic charge increment ρ ( r ) d r from r.

Interaction energies were calculated for the interactions of trifluoro-methane molecules with the hydrogen bonding acceptors R1,R2-C=X, where R = CH3CH2 or NHCH3 according to equation (3), as difference between the energy of the complex (Ecomplex) and the sum of the energies of the isolated h-bond donor (Edonor) and acceptor (Eacceptor) using optimised geometries:

E int = E complex ( E donor + E acceptor ) (3)

Ecomplex, Edonor, and Eacceptor are the energy minima at 0 K.

Vibrational analysis was also performed calculated with all DFT levels of theory to determine true minima and saddle points of different orders.

3. Initial Survey of Se Compounds in the CSD

We start with a brief overview of compounds containing the three chalcogens X (X = Se/S/Te) of CSD. The complete CSD (all inputs, without secondary filters applied) contains 13,787/208,565/5221 compounds of Se/S/Te which, 5692 (41.29%)/ 94421 (45.27%)/2858 (54.74%) are organic and, 8095 (58.71%)/114,144 (54.73%)/ 2363 (45.26%) are metallo-organic complexes respectively. When the secondary search criteria of Section 2.1 are applied, the total falls to 8625/128,636/3397 structures containing Se/S/Te which 4248 (49.25%)/68,890 (53.55%)/2052 (60.41%) are organic and 4377 (50.75%)/59,746 (46.45%)/1345 (39.59%) are organometallic. Among the Se/S/Te compounds that are classified as organic, we find respectively 7352/121,426/2874 independent selenium, sulphur and tellurium atoms (some structures contain X atoms in an environment of more than one coordination): 957 (22.53%)/10,818 (15.68%)/71(3.46%) structures are mono-coordinates Se (Se1)/S (S1)/Te (Te1), 2840 (66.85%)/32,951 (47.83%)/582 (28.36%) Se2/S2/Te2, 422 (9.93%)/5089 (7.39%)/369 (17.98%) Se3/S3/Te3, 226 (5.32%)/25,393 (36.86%)/ 687 (33.48%) Se4/S4/Te4, 24 (0.56%)/19 (0.03%)/174 (8.48%), Se5/S5/Te5, 31 (0.73%)/ 134 (0.19%)/258 (12.57%), Se6/S6/Te6, 0 (0.0%)/0 (0.0%)/11 (0.54%) Se7/S7/Te7 and one (0.0%)/1 (0.02%)/8 (0.39%) are, Se8/S8/Te8. Both three chalcogens can exist in −2, +2, +4, and +6 oxidation states, and the highest coordination type is taken from the highest of these states.

There are 890/10,348/38 structures containing 1254/14,226/49 fragments of Z = Se/S/Te in the CSD, where Z = any atom attached to the acceptor, (67/470/33 others structures have negatively charged mono-coordinated Se, S and Te atoms of the Z-Se-/Z-S-/Z-Te-type). In the Z = X subset, 420 (33.49%)/11,298 (79.42%)/14 (28.57%) fragments are C=Se, C=S and C=Te respectively, 808 (64.43%)/2843 (19.98%)/23 (46.94%) are P=Se, P=S and P=Te respectively, and in the 26 (2.07%)/85 (0.60%)/12 (24.49%) remaining Se/S/Te fragments, Z = Si, S, As or Te.

In the present work, we are concerned with organo-selenium (ii) compounds and therefore, we concentrate on those compounds featuring mono-coordinate Se atoms in C=Se/S/Te bonds. Preliminary analysis using ConQuest showed that the Se acceptors in the C=Se/S/Te subsets routinely form hydrogen bonds with N-H, O-H and C-H donors.

4. Intramolecular Geometry of the Systems R1,R2-C=Se, R1,R2-C=S and R1,R2-C=Te

In CSD there are 15 different combinations ofR1 and R2 bonded to C=Se. There are 21 and 3 respectively for C=S and C=Te. For C=Se, 7 combinations have N substituents, we can count 9 and 3 for C=S and C=Te respectively. The vast majority of these combinations have three-coordinate nitrogen atoms (N3), however, only two combinations (N3 with N3 and N3 with C) are common to all three chalcogens. The average bond lengths for these subgroups are collected in Tables 1-3 together with the data for R1 = C, and R2 = C.

Tables 1-3 generally show that the average lengths of the C=X and C-N bonds vary with the R1 and R2 substituents, and also with the hybridization of the carbon atom. This tendency is also presented by C=O acceptors [25] [26]. The length of the C=X bond increases in the sequence C4,C4-C=X 3,C 4-C=X 3, C 3-C=X 3,N 3-C=X. The average C-N bond is longer for N,N-C=X than for

Table 1. Mean bond lengths d (in Å) for subgroups of R1,R2 in R1,R2-C=Se systems with standard deviations in parentheses. Nf is the number of fragments contributing to the average.

Table 2. Mean bond lengths d (in Å) for subgroups of R1,R2 in R1,R2-C=S systems with standard deviations in parentheses. Nf is the number of fragments contributing to the average.

Table 3. Mean bond lengths d (in Å) for subgroups of R1,R2 in R1,R2-C=Te systems with standard deviations in parentheses. Nf is the number of fragments contributing to the average.

N,C-C=X, consistent with the data for the C=O and C=S analogues [26] and as expected from the resonance model.

In relation with our earlier work [14] and the previous studies by Allen [25] and Blessing [27], we analyzed the variations in bond length within the N,N-C=X subset by plotting d(C-N) vs d(C=Se), d(C=S) and d(C=Te) in Figures 2-4 respectively. Negative correlations between the two variables are observed, but with lower correlation coefficients of −0.672; −0.704; and −0.593 respectively for selenium, sulphur and tellurium, compared to −0.752 and −0.771 reported by Allen [25] for ureas and thioureas respectively, but higher than the value of −0.645 [14] for selenoureas.

Figure 2. Plot of the average C–N bond length [AVE(C-N)] (Å) vs. the C=Se bond length (Å) in selenoureas in the CSD. The line indicates a linear fit showing a correlation coefficient of −0.672, indicating some approximate relationship between the two quantities.

Figure 3. Plot of the average C–N bond length [AVE(C-N)] (Å) vs. the C=S bond length (Å) in thioureas in the CSD. The line indicates a linear fit showing a correlation coefficient of −0.704, indicating some approximate relationship between the two quantities.

Figure 4. Plot of the average C–N bond length [AVE(C-N)] (Å) vs. the C=Te bond length (Å) in telluroureas in the CSD. The line indicates a linear fit showing a correlation coefficient of −0.593, indicating some approximate relationship between the two quantities.

5. CSD Analyses of Hydrogen Bonding in C=X Acceptors

5.1. Occurrence of Hydrogen Bonds Involving C=S, C=Se and C=Te

An initial survey in the CSD showed that there are 7146 compounds R1,R2-C=S, with R1 and R2 assigned as any type of atom (X), which formed hydrogen bonds with OH, NH or CH donors, and 6249 of these compounds formed hydrogen bonds with C-H. In all cases, one or both of R1, R2 are three-coordinate nitrogen atoms. The overall frequency of occurrence (FoO) of hydrogen bond formation by C=S in CSD is 89.3% since we found 8002 structures in which a hydrogen bond to S could have been formed. The separate probability values for the structures of thioureas and thioamides, in which a hydrogen bond to S could have been formed, are quite different at 92.9% and 85.3% respectively. Of the 856 sulphur structures, where a hydrogen bond C=S···H is not formed, the available H donors bind to stronger acceptors in some cases, such as carbonyl and hydroxyl oxygen, in some others sulphur is involved in other types of interactions.

Furthermore, the equivalent frequencies of occurrence of hydrogen bond formation of the C=O analogues (urea and amide) were determined using CSD version 5.41 with an R-factor limit of 0.05. This resulted in overall FoO values of 94.3% and 94.8% respectively for the urea and amide analogues of C=O. Although these values are almost the same as those obtained for the C=Se compounds and less than of C=Te compounds, they should not be taken as an indication of the relative strengths of hydrogen bonds.

The CSD survey also showed that 278 compounds R1,R2-C=Se, with R1 and R2 assigned as any type of atom (X), formed hydrogen bonds withO-H, N-H and C-H donors, while there are 256 which formed with C-H donors. In all cases, one or both of R1, R2 are three-coordinate nitrogen atoms. In a separate search, we found 300 crystal structures that also contained O-H, N-H or C-H donors, i.e., structures in which a hydrogen bond to Se could have been formed. Thus, the overall occurrence frequency (FoO) of hydrogen bond formation by C=Se in CSD is 92.6%. The separate probability values for the structures of selenoureas and selenoamides, in which a hydrogen bond to Se could have been formed, are quite similar at 92.0% and 90.8% respectively. These results confirm that C=Se is an efficient hydrogen bond acceptor when Se is activated by resonance effects. Of the 22 selenium structures where a hydrogen bond C=Se···H does not form, the majority of available H donors bind to stronger acceptors, such as carbonyl and hydroxyl oxygen, or selenium is involved in other types of interactions.

Interestingly, there are 11 compounds R1,R2-C=Te, with R1 and R2 assigned as any type of atom (X) in CSD that have formed hydrogen bonds with O-H, N-H or C-H donors. All 11 compounds formed hydrogen bonds with C-H. One or both of R1, R2 are three-coordinate nitrogen atoms. Crystal structures also containing OH, NH or CH donors in which a hydrogen bond to Te could have been formed are 11. Thus, the overall occurrence frequency (Fo) of hydrogen bond formation by C=Te in CSD is of 100%. The separate probability values for tellurourea and telluroamide structures, in which a hydrogen bond to Te could have been formed, are 100% and 100% respectively.

In the present work, we are concerned with hydrogen-bonding of C-H donors at the monovalent chalcogen atoms, since those bonds report marked values of FoO. A similar study of the hydrogen-bonding of O-H and N-H donors will be reported shortly.

5.2. Hydrogen Bond Geometry

Tables 4-6 give geometric data for intermolecular hydrogen bonds with the acceptors C=Se, C=S and C=Te for C-H donors on the basis of the parameters defined in Figure 1. For comparison, the tables also report data for O-H and N-H.

Table 4. Mean geometry for hydrogen bonds from C-H, N-H and O-H donors to S acceptors in R1,R2-C=S systems. Nf is the number hydrogen bonds, while the parameters and the parameters d, ρ, φ and θ are defined in Figure 3. All distances are in Å, while angles are in ˚. Mean values are presented with estimate standard deviations in parentheses.

Table 5. Mean geometry for hydrogen bonds from C-H, N-H and O-H donors to Se acceptors in R1,R2-C=Se systems. Nf is the number hydrogen bonds, while the parameters and the parameters d, ρ, φ and θ are defined in Figure 3. All distances are in Å, while angles are in ˚. Mean values are presented with estimate standard deviations in parentheses.

Table 6. Mean geometry for hydrogen bonds from C-H, N-H and O-H donors to Te acceptors in R1,R2-C=Te systems. Nf is the number hydrogen bonds, while the parameters and the parameters d, ρ, φ and θ are defined in Figure 3. All distances are in Å, while angles are in ˚. Mean values are presented with estimate standard deviations in parentheses.

The first three rows of Tables 4-6 show hydrogen bonds for all angles ρ, while the rest of the tables only consider those structures where ρ ≥ 120.0˚, which is the recommended limit given by Wood [28]. Since the vast majority of the structures shown in these tables are those with N3 (three-coordinate N) and bonded to C-H donors, where the hydrogen bond angle ρ ≥ 120.0˚, the following analysis and discussion are limited to those hydrogen bonds.

We can note that C=Se and C=S could form hydrogen bonds with O-H, N-H and C-H donors, but C=Te could form only with C-H donors. The average hydrogen bond distance (d) of C=Te acceptors in Table 6 is approximately 0.16 Å and 0.25 Å longer than that of C=Se and C=S acceptors in Table 4 and Table 5 respectively, which is consistent with the larger van der Waals (vdW) radii of Te (2.06 Å) with respect to S (1.80 Å) and Se (1.90 Å) [29]. There is no significant difference between the hydrogen bond distances (d) observed in subgroups (N3, N3), and the subgroups (N3, C) for all acceptors. However, there is some indication that the hydrogen bond distances for CH···X interactions are longer than their NH···X and OH···X counterparts up to 0.33 Å and 0.51 Å respectively for selenium, 0.38 Å and 0.49 Å for sulphur. This situation has also been observed in previous studies of the C=S acceptor [25] [26] and C=Se acceptor [14]. This is an indication that the differences between the interaction energies between N-H and C-H donors could be greater than those between O-H and N-H donors.

An earlier comparative analysis of C = O and C = S acceptors [26] used standard van der Waals hydrogen bond distances, i.e.

d ( norm ) = d ( Hbond ) vdW ( H ) vdW ( X ) , where X represents the acceptor atom (O or S) and vdW (X) is the vdW radius of this atom. The value of 1.10 Å determined by Rowland and Taylor [30] was used for vdW (H), while the values of 1.52 Å for vdW (O) and 1.80 Å for vdW (S) were taken from Bondi [29]. For hydrogen bonds from NH with oxygen O of ureido and sulphur S of thioureido, a large and homogeneous subgroup for both acceptors, d(norm) values were −0.692 Å and −0.449 Å for the acceptors C = O and C = S respectively, which clearly indicates that the hydrogen bonds formed with C = O are much stronger compared to those with C = S. Calculation of d(norm) using the d values of 2.95 Å for the Se···HC bonds of selenoureido, of 2.86 Å for the S···HC bonds of thioureido and of 3.12 Å for the Te···HC bonds of telluroureido from Tables 4-6, vdW (S) = 1.80 Å [29], vdW (Se) = 1.90 Å [29] and vdW (H) = 1.10 Å [30], d(norm) gives −0.05 Å, −0.04 Å and −0.04 Å respectively for Se···HC, S···HC and Te···HC which values are lower than the values of -0.44 Å and -0.45 Å respectively for Se···HO and S···HO [14] [26]. Thus, we can deduce that the stabilization energy of both three acceptors C=X···H bonds should be similar with the CH donor.

The angular directionality parameters (ρ, φ and θ, Figure 1) for the C=X acceptors show remarkably similar mean values to each other. Thus, the angle on the donor atom of H is completely linear (ρ tends towards 180˚).This is an expected behaviour for hydrogen bonds [28].

In addition, the tendency for the hydrogen bond donor vector (C-H) to approach X in the plane of the >C=X group is typical. The θ values in Tables 4-6 show mean deviations of coplanarity around 37 (23)˚, 37 (24)˚ and 32 (22)˚ respectively. The most interesting angle is φ, the angle at which the hydrogen atom approaches with respect to the C=X bond, for which the mean values of 116 (26)˚, 119 (27)˚ and 116 (25)˚ are obtained for Se, S and Te acceptors respectively. These values, for the N-H and O-H donors, are slightly upper than those 103 (13)˚ and 97 (8) for selenium and than 107 (12)˚ and 103 (13)˚ for sulphur in Table 4 and Table 5, and all of these values can be attributed to interactions between Hδ+ and the lone pairs on the atoms of Se, S and Te. The finding that hydrogen bonding at C=Te acceptors shows directional properties like hydrogen bonding at C=Se and C=S, should also make Te atoms versatile tools to directing and controlling the structure of molecular systems, with consequences for the use in crystal engineering [9] [31] [32] [33] and its integration in pharmaceutical agents [34] [35] [36].

Furthermore, we note that intramolecular hydrogen bonds of acceptors N-C=Se, N-C=S and N-C=Te are formed in 216, 4533 and 9 structures respectively, with very variable geometries. Structures forming 5 to 8 membered hydrogen bond rings are observed. For these structures, the distances Se···H, S···H and Te···H vary from from 2.32 to 3.10 Å, 1.85 to 3.00 Å and from 2.75 to 3.25 Å respectively, but the hydrogen bond angles are significantly distorted from the intermolecular normal values discussed above by the constraints of ring formation: ρ values are in the ranges 79˚ - 174˚, 76˚ - 178˚ and 86˚ - 156˚, φ in the ranges 54˚ - 116˚, 44˚ - 173˚ and 58˚ - 92˚ and θ in the ranges 0˚ - 30˚, 0˚ - 83˚ and 1˚ - 62˚ respectively for Se, S and Te.

5.3. Hydrogen Bond Coordination

In the earlier comparative study by Allen [25], it was found that C=S and C=O normally accept one or two hydrogen bonds, but on rare occasions C=S accepts up to six hydrogen bonds, then C=O accepts up to five. This analysis was performed on all of the hydrogen bonds formed by the C=S or C=O acceptors at that time, and included both intramolecular and intermolecular hydrogen bonds. We performed a similar hydrogen bond coordination analysis of C=Se acceptors [14] and we saw that the coordination values 1 (66.3%) and 2 (25.5%) were the norm, while the maximum hydrogen bond coordination observed for C=Se was 3. The hydrogen bond coordination analysis performed for Se and S acceptors with C-H, N-H and O-H donors shows that these chalcogens can form up to eight and nine bonds respectively for Se and S.

6. Computational Results

6.1. Atomic Point Charges and Molecular Electrostatic Potential of Systems R1,R2-C=X

Table 7 reports the Mulliken and NBO partial charges on the O atom in formaldehyde, formamide and urea and on the Se and S atoms in their Se and S analogues, calculated using a variety of different methods, as described in section 2.2. Table 8 gives the Mulliken and NBO partial charges of Te.

The data in Table 7 show the expected trends in the electronegativity induced by the resonance in O, Se and S. The negative partial charge of the O atom increases due to the resonance moving from formaldehyde to formamide, then to

Table 7. Mulliken and NBO atomic partial charges on O, S and Se in R1,R2-C=X (X=O, S or Se) calculated using various levels of theory.

Table 8. Mulliken and NBO atomic partial charges on Te in R1,R2-C=Te calculated using various levels of theory.

urea, with both four theoretical levels and methods of calculating the partial charges, giving comparable results and trends. For Se and S with R1 and R2 as H atoms, the partial charges of the two atoms are quite small, in agreement with the similar electronegativities of Se, S and C. When we move to thioformamide and selenoformamide, then to thiourea and to selenourea, both Se and S have significant negative partial charges. These results and values are comparable to those previously reported for O and S by Allen [25] and for urea, thiourea and selenourea by Moudgil [37].

As for Te, the data in Table 8 show the same expected trend of electronegativity induced by resonance on Te. Indeed, the partial charge of Te tends more and more towards the negative when R1 and R2 move from C and C to N and N via C and N.

As shown by the above results, the Mulliken partial charges have lower values than the general NBO loads in Table 7, while in Table 8, the NBO partial charges have lower values than the Mulliken partial charges. This behaviour reflects the different approaches to obtaining atomic charges in each method. Indeed, all the methods of calculating the atomic charge are necessarily arbitrary, since it is not a quantum mechanical observable. There is then no rigorous physical basis for assigning charges to atoms in molecules, because assigning a single positive or negative value to each atom implicitly assumes that the charge distributions are spherical symmetrical [24].

The electrostatic potential has then been suggested as a significant representation of the electrostatic effects of molecular charge distribution [13].

Figure 5 shows the molecular electrostatic potential (MEP) for acetone, acetamide, urea and their selenium, sulphur and tellurium analogues. All molecules containing O exhibit a significant region of negative electrostatic potential, where the O atom will accept hydrogen bonds. For the Se, S and Te analogues, this region becomes more evident when the C atom bonded to the chalcogen has an N atom as a substituent. As previously reported for C=S [26], a marked fall-off in the negative charge density around Se and Te is observed in (CH3,CH3)-C=Se and (CH3,CH3)-C=Te, and explains the lack of hydrogen bonds to C=Se and C=Te in crystal structures when carbon bound to chalcogen has C as substituents. MEPs for selenourea, thiourea and, more clearly, for tellurourea also show a zone of positive electrostatic potential associated with the Se, S and Te atoms, which is directed outward along the C=Se, C=S and C=Te bondssuggesting the ability of chalcogen atoms to form both hydrogen bonds and positive hole-based bonds similar to sigma-hole interactions [24] [38] [39]. It was also find in chalcogen bonding in divalent Se, S and Te compounds [40] [41] [42] [43].

Figure 5. Molecular electrostatic potential (MEP) for acetone, acetamide and urea and their sulphur, selenium and tellurium analogues calculated using HF/6-311++G(3df,2p) for O, S, Se and B3LYP/3-21G for Te. Isovalue 0.04 u.a. Positive regions are in yellow, while negative regions are in orange.

6.2. Interaction Energies of Hydrogen Bonds to C=X Acceptors

DFT calculations were performed to determine the geometry and energy of interaction with trifluoro-methane as donors according to the scheme shown in Figure 6. The number of vibration frequencies (Nv) shows that all the complexes were true minima (Nv = 0).

Figure 6. Model systems used for calculating hydrogen bond interaction energies of C=X acceptors with trifluoromethan.

Structural information from the CSD and electrostatic data from AbInitio calculations suggest that the N-substituted C=Se acceptors should have hydrogen bond interaction strengths comparable to the corresponding C=S acceptors. Table 9 and Table 10 report the geometries and interaction energies (as defined in Figure 1 and Figure 6) of the complexes (NHCH3,NHCH3,)-C=Se···H-CF3 (I1), (NHCH3,CH3CH2)-C=Se···H-CF3 (I2), (CH3CH2,CH3CH2)-C=Se···H-CF3 (I3), (NHCH3,NHCH3,)-C=S···H-CF3 (II1), (NHCH3,CH3CH2)-C=S···H-CF3 (II2) and (CH3CH2,CH3CH2)-C=S···H-CF3 (II3) calculated with both B3LYP (EintB3LYP) and B3LYP-3D (EintB3LYP-3D). We were unable to calculate the interaction energies of the acceptor Te due to the failure of calculations.

The methyl groups of the substituents were placed cis at the Y–H···X interaction to avoid an interaction between the N–H and the donor molecule, after which all three systems were able to relax completely.

The results of Table 9 and Table 10 show that the interaction strength C=Se

Table 9. Values of total interaction energy (Eint) and geometric parameters d,φ and ρ for C–H···Se=C hydrogen bonds in N,N-, N,C- and C,C-disubstituted systems, as calculated using B3LYP/6-311++G(3df,2p) and B3LYP-GD3/6-311++G(3df,2p).

Table 10. Values of total interaction energy (Eint) and geometric parameters d,φ and ρ for C–H···S=C hydrogen bonds in N,N-, N,C- and C,C-disubstituted systems, as calculated using B3LYP/6-311++G(3df,2p) and B3LYP-GD3/6-311++G(3df,2p).

is very similar to that C=S for systems (NHCH3NHCH3)-C=X···H-CF3 and (NHCH3,CH3CH2)-C=X···H-CF3; and clearly shows that C=Se and C=S can form stabilizing hydrogen bonds. Indeed, values of −14.30 kJ/mole (EintB3LYP) and −27.76 kJ/mole (EintB3LYP-3D) of C=Se for the NN groups are similar with values of −14.29 kJ/mole (EintB3LYP) and −27.04 kJ/mole (EintB3LYP-3D) of C=S respectively, and those of −12.16 kJ/mole (EintB3LYP) and −22.37 kJ/mole (EintB3LYP-3D) of C=Se for the NC groups are similar with values of −12.55 kJ/mole (EintB3LYP) and −22.32 kJ/mole (EintB3LYP-3D) of C=S respectively.

As for the systems (CH3CH2,CH3CH2)-C=X···H-CF3, we notice the difference in interaction strength for the two acceptors C=Se and C=S, values of −9.81 kJ/mole (EintB3LYP) and −20.45 kJ/mole (EintB3LYP-3D) of C=Se are different from −5.20 kJ/mole (EintB3LYP) and −16.71 kJ/mole (EintB3LYP −3D) of C=S respectively.

The geometries parameters (d, φ and ρ) obtained in the DFT calculations much well with the trends observed in CSD (Table 4 and Table 5), but we can note a difference by 30˚ - 40˚ on φ angle for N,N groups. For example, an φ angle of 117 (26)˚ was found while the corresponding in calculation gives 89˚ for selenium acceptor.

The results of these Table 9 and Table 10 also show that the calculated energies follow the expected trend of the hydrogen bond strength already established on the basis of the geometry analysis of the structures in the CSD and are consistent with the partial charges and MEP of the groups C=Se and C=S substituted. Indeed, the trend of the interaction energies agrees well with that of CSD d (norm). One can expect from analysis of d (norm) values of three chalcogens that C=Te should be of comparable strength than C=Se.

Furthermore, insights into the nature of interaction involved in the complex formation can be provided by NBO interaction analysis. Table 11 and Table 12 report NBO interactions with values of the associated second order perturbation energies E(2) for C=Se and C=S respectively.

It appears from those Tables that all hydrogen bonds consist of charge transfer (CT) from a selenium or sulphur lone pair (LP) acting as hydrogen bond acceptor to a H-C antibonding orbital (BD*) of the hydrogen bond donor.

Table 11. NBO perturbation energy E(2) for C=Se···H-CF3 complexes calculated with B3LYP/6-311++ G(3df,2p) and B3LYP-GD3/6-311++G(3df,2p).

Table 12. NBO perturbation energy E(2) for C=S···H-CF3(CH3CH2,CH3CH2)-C=X···H-CF3 calculated with B3LYP/6-311++G(3df,2p) and B3LYP-GD3/6-311++G(3df,2p).

For C=Se acceptor, E(2) values range from 4.10 to 16.19 kJ∙mol−1 for B3LYP and from 2.85 to 21.13 kJ∙mol−1 for B3LYP-D3 depending on the hydrogen-bond donor and substituents bonded to carbon in C=X acceptors. Those calculated for C=S acceptor with B3LYP and B3LYP-D3 respectively vary from 2.89 to 14.69 kJ∙mol−1, and from 2.05 to 19.20 kJ∙mol−1.

7. Conclusions

The present study investigated the ability of C=Se, C=S and C=Te acceptors to form hydrogen bonds with C-H hydrogen bond donors using CSD analysis in conjunction with computational methods. Following relevant conclusions can be drawn:

· There are respectively 256, 6249 and 11R1,R2,-C=Se, R1,R2,-C=S and R1,R2,-C=Te structures in CSD that form hydrogen bonds, in which the majority groups are N,N compounds. Except for the C=S acceptor which can form the hydrogen bond with its C,C group, both C=Se and C=Te could form a hydrogen bond only with N,C and N,N groups.

· C-H hydrogen-bond donors approach C=X acceptors at greater angles than their corresponding N-H and O-H donors, and the hydrogen bonding to C=X acceptors is highly directional, like to N-H and O-H donors.

· Partial charges and electrostatic potentials calculated for Te atoms in C=Te acceptors, as well as intramolecular geometries, suggest that the hydrogen bond stems from the substituent groups inducing Cδ+=Teδ dipole as occurs in hydrogen bonding C=Se and C=S acceptors.

· Molecular electrostatic potential surfaces calculated for C=Te acceptors show remarkably similar patterns to those for C=Se acceptors and C=S with a negative area and a positive hole suggesting the ability of chalcogen atoms to form both hydrogen bonds and positive hole-based bonds similar to sigma-hole.

· Both interaction distances derived from CSD analysis and DFT-calculated interaction energies demonstrate that the acceptors strongly interact with H-CF3. Besides hydrogen bonds, dispersion interactions are forces stabilizing the complexes since their contribution can reach 50%.

· NBO interaction analysis shows that C=Se···H-Cand C=S···H-C interactions are characterized by the transfer of charge from lone pair of the proton acceptor to the antibonding orbital of the C-H covalent bond.

Acknowledgements

Didi D. Bibelayi is grateful to the CCDC for material support, and to Gaussian Inc, Wallingford, CT for providing Gaussian 09 software package.

Conflicts of Interest

The authors declare no conflicts of interest regarding the publication of this paper.

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