Experimental and Theoretical Charge Density Studies of Chalcogen

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Experimental and theoretical charge density studies of chalcogen bonding and other intermolecular contacts in 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline Mikolaj Pyziak, Jadwiga Pyziak, Marcin Hoffmann, and Maciej Kubicki Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.5b00676 • Publication Date (Web): 07 Oct 2015 Downloaded from http://pubs.acs.org on October 11, 2015

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Crystal Growth & Design

Experimental and theoretical charge density studies of chalcogen bonding and other intermolecular contacts in 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline Mikołaj Pyziak, Jadwiga Pyziak, Marcin Hoffmann, Maciej Kubicki* Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland High-resolution diffraction data have been used for modelling electron density distribution in the crystal structure of 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline. The results confirm the presence of intermolecular, electron pairs - σ-holes S···S bonding. The calculated minimum energy distance has value of 3.33 - 3.34 Å and agrees very well with the separation of 3.3300(11) Å, observed in the crystal structure. A large spectrum of weak interactions, including C-H···O, CH···S, π···π has been analysed by means of the electron density distribution details and Atoms-InMolecules approach. There is apparently a good agreement between the results obtained with the multipolar Hansen-Coppens model and a generic theoretical study. A comparison with the results of the best Independent Atom Model has revealed its deficiencies.

*

Prof. Maciej Kubicki, Faculty of Chemistry Adam Mickiewicz University Umultowska 89b 61-614 Poznań, Poland tel +48618291557 fax +48618291555 e-mail:[email protected]

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Experimental and theoretical charge density studies of chalcogen bonding and other intermolecular contacts in 4-[[4-(methoxy)-3-quinolinyl]thio]-3thiomethylquinoline Mikołaj Pyziak, Jadwiga Pyziak, Marcin Hoffmann, Maciej Kubicki* Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland e-mail: [email protected]

Abstract

High-resolution diffraction data have been used for modelling the electron density distribution in the crystal structure of 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline. The results confirm the presence of intermolecular, electron pairs - σ-holes S···S bonding. The calculated minimum energy distance is 3.33 - 3.34 Å and agrees very well with the separation of 3.3300(11) Å, observed in the crystal structure. A large spectrum of weak interactions, including C-H···O, CH···S, π···π has been analysed by means of electron density distribution details and Atoms-InMolecules approach. There is apparently a good agreement between the results obtained with the multipolar Hansen-Coppens model and theoretical study. At the same time, comparison with the results of the best Independent Atom Model has revealed its deficiencies.

Introduction ACS Paragon Plus Environment

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Intermolecular non-covalent interactions constitute one of the principal factors in the determination of architecture of a molecular crystal. Of course, the final structure is a consequence of fine interplay between a number of factors, including also space-group requirements, tendency towards close packing, etc. Therefore a prediction of the crystal structure of a given chemical compound is still a risky endeavour even though a significant progress has been achieved (one can compare the results of consecutive blind tests, organised by the IUCr commission1,2 in order to appreciate this progress). In any case, detailed knowledge of certain interactions is crucial for different scientific goals, including - besides crystal structure prediction - also construction of co-crystals, preparation of noncentrosymmetric crystals, in general for crystal engineering. In recent years a kind of ‘inflation’ of the specific (or the so-called specific) interactions has been observed. No wonder that a discussion has arisen if such a large inflation of the term was appropriate, and if we need to take a step back, to see the whole picture instead of a (growing) number of interactions. In a sense, the landmark paper by Dunitz and Gavezzotti3 set the stage for the discussion which is probably yet to come4-6. There are, in principle, two complementary ways of gathering information about a certain interaction (assuming that we have agreed on the need of such a procedure). One can rely on the enormous source of structural information which is provided by the Cambridge Crystallographic Data Center – the CDB7. Comparing thousands of structures may (and often does) lead to the identification, on the basis of statistics, of certain interactions and to the determination of their principal – although mainly geometrical - features. This approach has been widely used throughout the structural science community, and a number of reports describing such analyses is enormous (starting for instance from the landmark papers by Leiserowitz8-10). The weak point of this approach is a necessity of assuming the arbitrary criteria for classifying the contacts as interactions, and the potential non-representability of a sample under consideration. The second approach is connected with detailed analysis of electron density distribution in the crystals, finding the interaction paths and connecting them with the certain interactions by the topological, energetic and other


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quantitative characteristics (for instance, papers by Lecomte et al.11-13, Gatti et al.14, Wozniak et al.15,16, etc.). Here, the weaknesses are the high experimental demands, including very good quality of the crystals, and – recently stressed – insufficient flexibility of the models used17,18. Both experimental methods and theoretical investigation allowed, among others, the identification of quite interesting and not obvious interaction between chalcogen atoms, by analogy with the earlier identified hydrogen and halogen bonding called the chalcogen bonding19. In particular, the non-covalent interactions of divalent sulfur (bound to two atoms, neither of which is hydrogen) were postulated and their geometrical features characterized by Parthasarathy et al. in late 1970’s and early 1980’s20-22. The S···S interactions were regarded as mainly due to incipient formation of an attractive electrophile – nucleophile pairing, which was supported by the analysis of the angular dependence between S···S contact and the angles of approach of the two engaged atoms. Recently, two groups have reported the results of charge density analyses of such interactions. Espinosa et al.23 have investigated the experimental electron density distribution for selenophthalic anhydride, C8H4O2Se, and characterized directionality and strength of Se··Se and Se···O chalcogen bonding and additionally those for Se···H hydrogen bonding interactions. They have found out that, similarly to halogen bonding, anisotropic distribution of the electron density around chalcogen atom (the σ-hole concept) is likely to be the origin of the chalcogen bonding (this idea was earlier put by Politzer et al.24). Interestingly, the reasonable bond paths and critical points were found for contacts with distances comparable with sums of van der Waals radii (Se···O 3.355Å, Se···Se 3.822Å). Ramamurthy, Guru Row et al.25 have determined the crystal structure of the donor-acceptor-donor structured organic conductor, 7,9-di(thiophen-2-yl)-8H-cyclopenta[a]acenaphtylen-8-one, and further performed with the single point periodic quantum mechanical calculations in order to obtain the details of the electron density distribution. They have also found the critical points related to S···S interactions (3.791Å and 3.578Å). Very recently, Guru Row et al.26 have reported the details of the charge density distribution in an intramolecular S···O chalcogen bonding in sulfomethizole


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sulfate salt. Similar conclusions (regarding the presence of such interactions) can be drawn from other studies of chalcogen-chalcogen bonding27-33. It is worth noting that tendencies towards participation in chalcogen bonding are more pronounced as the element’s atomic number increases.

H3C O S N N

S CH3

Scheme 1. Structure of 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline

Some time ago we have published34 the standard resolution structure of the title compound, 4-[[4(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline (Scheme 1, 1), in which a short intermolecular S···S contact, of ca. 3.35Å (much shorter than those described above) is observed, together with the S···O and S···S intramolecular contacts. As we finally succeeded in obtaining the high quality single crystals, which could be used for experimental determination of the charge density distribution in these crystals, we decided to attempt at characterization of these weak interactions.

Experimental section A colorless crystal with dimensions 0.4 x 0.4 x 0.1 mm was used for data collection at 110 K on an Oxford Diffraction XCalibur EOS four-circle κ-cradle diffractometer, equipped with the Sapphire CCD detector and the graphite-monochromated MoKα radiation (λ=0.71073Å). Temperature was controlled using an Oxford Instruments Cryosystem cooling device. Images were collected in 31 runs, with the exposition times depending on the theta angle. More details on data quality can be


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found in Table 1. Integration of the reflection intensities and data reduction were carried out with CrysAlisRed. Data sorting and merging was performed with WinGX suite35 (v. 1.80.05) sortmerge tool. Hirshfeld surface analysis was performed with Crystal Explorer36.

Figure 1. Anisotropic ellipsoid representation of the molecule with labelling scheme. Ellipsoids are drawn at 50% probability level, with hydrogens represented by spheres of arbitrary radii. Crystal data: C20H16N2OS2, Mr=364.47, triclinic P-1, a=9.2605(8)Å, b=10.5797(12)Å, c=10.7704(15)Å,

α=60.921(10)°,

β=85.569(12)°,

γ=65.892(9)°,

V=831.98(18)Å3,

Z=2,

F(000)=380, dx=1.46g·cm-3, µ(MoKα)=0.33mm-1. 82911 reflections collected up to 2Θ=135° (sinΘ/λ=1.31Å-1), of which 28749 symmetry-independent (Rint=2.30%), 18907 with I>2σ(I). Overall completeness 93.8%, mean redundancy 2.9.

Table 1. Details of data reduction characterization resolution (Å)

No. No. mean completeness theory unique redundancy

mean (F2/σ(F2))

Rint

inf-0.84

2880

2874

99.8

4.2

97.60

0.012

0.84-0.67

2884

2874

99.7

4.3

38.75

0.022


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0.67-0.59

2904

2874

99.0

3.1

19.17

0.034

0.59-0.53

2957

2874

97.2

2.6

11.82

0.053

0.53-0.49

2954

2874

97.3

3.6

9.04

0.099

0.49-0.46

2975

2874

96.6

3.4

6.37

0.141

0.46-0.44

3074

2874

93.5

2.1

4.30

0.149

0.44-0.42

3124

2874

92.0

2.0

3.27

0.193

0.42-0.40

3155

2874

91.1

1.9

2.55

0.244

0.40-0.38

3727

2883

77.4

1.7

2.06

0.273

Density Functional Theory (DFT) calculations were carried out using several functionals: two common functionals, pure Becke-Perdew 86 (BP86), the Becke three-parameter hybrid exchange functional combined with the Lee, Young and Parr (LYP) functional denoted as B3LYP37-39 used in connection with 6-31G and SDD basis40,41. They were also augmented with the original Grimme’s B97-D hybrid functional and empirical Grimme corrections (denoted as BP86+D and B3LYP+D). All computations were carried out with Gaussian0942. The S1···S1 bond interaction energy graph was calculated on the basis of a series of two symmetry-dependant molecules, with S1···S1 distance varying from 2.6 to 12.0 Å. To ensure that changes in free lone pairs overlapping would not distort the calculated bonding values, the molecules were shifted along the C18···C18 direction.

Refinement

The crystal structure was solved using SHELXS43 and standard Independent Atom Model (IAM) refinement was performed using SHELXL43. Non-H atoms were refined anisotropically; H atoms positions were found in the difference Fourier maps and isotropically refined. Atom positions are in satisfying agreement with previously reported34. Perspective view of the molecule with a labelling scheme is depicted in Figure 1. Final residuals for IAM: for all reflections R=7.05%, wR2=12.93%, for I>2σ(I) R=4.04%, wR2=11.05%, S=1.02. Max/min ∆ρ values in the final ∆F map 0.66/0.53e·Å-3, located on the covalent bonds.


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The electron density was subsequently refined against the structure-factor amplitudes with the MoPro software44,45 using the multipole Hansen–Coppens model46,47 for pseudoatom electron density:

ρ atom (r ) = ρ core (r ) + Pval κ 3 ρ val (κr ) + ∑ l κ '3 Rl (κ ' r )∑ m Plm ±Ylm± (θ , φ ) where the first two terms are the spherically averaged core and valence electron densities of the atom, and the last term corresponds to the non-spherical valence density which is described in terms of real spherical harmonic functions Ylm±. Pval is the valence population, Plm±’s are the multipole populations, and κ' and κ” are the contraction/expansion parameters for valence and multipolar

ξ ln + 3 l

population, respectively. Rl are radial Slater-type functions: R l ( r ) =

( n l + 2)!

r nl e −ξ l r , n l ≥ 1 . Before

introducing the multipolar model, hydrogen atoms were moved to the positions determined by neutron diffraction, and a few cycles of high-order refinement (sinΘ/λ>0.7 Å-1) were performed in order to achieve better deconvolution between the thermal motion and deformation effects48. The atomic displacement parameters of H atoms were constrained to the values obtained from the SHADE server49. Heteroatoms were refined up to hexadecapolar (l=4) level, carbon atoms up to octupolar (l=3) and hydrogen atoms up to dipolar (l=1) level. The positional and displacement parameters of hydrogen atoms were restrained until the end of refinement, their κ and κ' parameters were also restrained at the values of 1.16(1) and 1.18(1), respectively. Anharmonic refinement brought no apparent improvement in residual noise levels, but the values of some Gram-Charlier parameters were non-negligible (above 3σ level) and were thus incorporated into the model. More details on the refinement procedure can be found in Supplementary material. All charge density parameters are included in CIF file attached as supplementary material. For the sake of comparison of the models, as well as for the estimation of significance of charge density studies , the final model was used as a basis of the IAM-type model. Coordinates and thermal motion parameters of the final model were retained, but valence populations, multipoles, κ and κ' parameters were reset to the


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initial state. Differences in residual density maps between two IAM models and the multipolar model are depicted in Figure 2.

Figure 2. Comparison of residual electron density maps, left: the final model, middle: the final

model converted to IAM model, right: the initial IAM model obtained with SHELX. Cut-off I/σ(I) > 3, contours 0.05 eÅ-3, blue: negative and red: positive; s < 0.9 Å-1. Final

residuals

after

multipolar

refinement:

R(I)=2.33%,

wR2(I)=2.47%,

R(F)=3.25%,

wR(F)=1.29%, S=1.62, max/min ∆ρ values in the final ∆F map 0.36/-0.23e·Å-3, residual density randomly distributed throughout the cell.

Hirshfeld surface analysis

The analysis of normalised contact distances mapped on the Hirshfeld surface50-52 (Figure 3) brings attention to the S1 sulphur atom area, where there is a minimum of -0.15. In the same time, relatively short OCH3···N contacts breach van der Waals radii, giving normalised contact distances of -0.10 and -0.09. It is worth noting that, despite its steric hindrance, O1 atom stays in close contact with its symmetry generated counterpart, but not with the contacting hydrogen atoms. Fingerprint plots53 of the molecule’s Hirshfeld surface can be found in supporting information.


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Figure 3. Normalised contact distance mapped on the Hirshfeld surface. Most close contacts

mentioned in text are labelled. Intermolecular interactions

Numerous weak intermolecular bonds and contacts have been identified and investigated. The molecules have a total of 15 symmetry mates in their immediate vicinity, 4 of which participate in the particularly interesting interactions. They are depicted in Figure 4 and described in detail later on.

Figure 4. Selected symmetry mates and critical points of most relevant intermolecular interactions

(symmetry codes as given in text). The central molecule is drawn together with thermal ellipsoids,


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critical point depicted as lavender spheres. Atom colour codes: gold for carbon, white for hydrogen, green for sulphur, blue for nitrogen. Homoatomic interactions

There are four homoatomic binding intermolecular contacts, two of which deserve special attention: S1···S1i (i denotes symmetry operation 1-x,1-y,1-z) and O1···O1ii (ii 1-x,2-y,1-z). For both contacts, (3,-1) the critical points between the atoms, along with the appropriate interaction paths, have been found, which indicates the presence of intermolecular bonding. In previous studies of this system34, it has been signalled that S1···S1i distance is significantly smaller than the sum of van der Waals radii. Static total electron density at this location has value of 0.081 eÅ-3 – which is the highest of all intermolecular (3,-1) critical points within this lattice. Laplacian (0.75 eÅ-5) and λ1 (1.01 eÅ-5) values are smaller only than the corresponding values for the C-H···N bond. Detailed analysis based on both crystallographic data and DFT calculations shows the bonding mediated via sulphur free electron pairs and σ-holes54-58. The C4-S1···S1i angle of 158.7° lies within the typical range for chalcogen bonds reported earlier20-22,59,60. Bond strength has been calculated in the range 3.0 to -12.3 kcal/mol, depending on the functional and calculations base applied.

Figure 5. Experimental based sulphur electron pairs - σ-holes bonding depiction. Electrostatic

potential mapped over the electron density isosurface of 0.1 eÅ-3. Values scaled in eÅ-1.


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The S1···S1i distance of 3.3300(11) Å – as measured in the crystal - is, according to our in silico studies, optimal. The calculated minimum energy distance is 3.33 - 3.34 Å depending on the functional base applied. Figure shows the energy change with intermolecular distance, calculated for different functional bases. Minimum energy values are gathered in Table 2.

Figure 6. Energy changes upon variation of S1···S1i distance d between two units of the molecule. B3LYP 6-31G

B3LYP+D 6-31G

BP86 6-31G

BP86+D 6-31G

BP97D 6-31G

B3LYP SDD

BP86 SDD

BP97 SDD

B3LYP 6-31G(d,p)

B3LYP SDD(d,p)

-5.88

-14.16

-4.90

-13.32

-12.91

-5.52*

-4.12*

-11.16*

-5.90

-5.51*

Table 2. Energy values at minima for various functional bases. Values are marked with an asterisk identified as minimum at 3.34 Å. Full distance – bond energy table available in supporting information. The strength and privileged location of the S1···S1i interaction clearly indicates that it can play an important role in the crystal structure architecture determination and solid state stability. It is, to the best of our knowledge, the first report of symmetry-generated reciprocal σ-bonds between two sulphur atoms. The O1···O1ii interactions are relatively weak, with the static electron density of 0.028 e·Å-3 at the (3, -1) saddle point, but its relatively high second derivative parameters (−∇2ρ(r)=0.49 and λ1=0.57) suggest that this is a genuine interaction and not a modelling artefact. This critical point is ACS Paragon Plus Environment

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also, similarly to sulphur···sulphur (3,-1) critical point, placed at the inversion centre at ½ 0 ½ (S···Si at ½ ½ ½). However, it is a peculiar contact, and its share of only 0.1% of Hirshfeld surface strengthens the first impression of an accidental van der Waals radii sum breach, however, the deformation map (Figure ) confirms the possibility of the neighbouring, related by the centre of inversion, molecules attracting (or at least interacting with) each other. Shared lowest unoccupied orbital (LUMO) also indicates that these two oxygen atoms develop a weak bonding interaction.

Figure 7. Static deformation map of the O1···O1 contact area. Isovalues every 0.01 eÅ-3, blue -

negative, red – positive, yellow – neutral. There are two other homoatomic intermolecular interactions (or – strictly speaking – the contacts for which (3,-1) critical points and bonding paths could be found), namely H17···H17iii (iii: -x,3y,1-z) and H6···H16ii, both positioned at the different inversion centres. While the latter is characterised with parameters rather typical of H···H interactions61-63, the H17···H17iii bond critical point is connected with the electron density value of 0.044 eA-3 and λ1 value of 0.86. They , together with other numerical descriptors, are very similar to the C16-H16···O1ii contact (hydrogen bond) usually regarded as much stronger. Moreover, the H17···H17iii and H6···H16ii distances are nearly identical (2.20 and 2.21 Å, respectively), but the latter has – in contrast - one of the most electron-scarce (3, -1) saddle points of all contacts formed by the molecule while the H17···H17iii (3,-1) critical point is connected with the highest electron density of all hydrogen···hydrogen interactions found. This might be used as an argument for the necessity of a deeper analysis of interactions, not based solely on their geometrical features.


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Other intermolecular contacts

As the molecule studied lacks strong hydrogen bond donors, only the C-H···X weak hydrogen bonds can be formed. Each of sulphur, oxygen and nitrogen atoms accepts at least one such bond, with the nitrogen atoms being undoubtedly dominant. The N1 and N11 atoms interact with both methoxy and thiomethyl hydrogen atoms, forming relatively strong intermolecular bonds with total electron density at the saddle (3,-1) critical points ranging from 0.052 to 0.062 e·Å-3. Laplacian values place themselves amongst highest in this system, and - as one might expect - critical points are determined with a relatively high positional certainty. The contribution of the oxygen atom is small, as it is involved only in the C-H···O intermolecular bonds with electron density around 0.035 e·Å-3. We think that main reason for such a weak bonding can be related to the position of the oxygen atom in the lattice: its neighbours sterically hinder (Figure ) the access of for hydrogen atoms, necessary to form a stronger bond.

Figure 8. The oxygen O1 atom with its nearest neighbours. Long range interactions marked by grey

lines, with red crosses at the positions of critical points. The S2 sulphur atom takes part in C-H···S bonding with methoxy moiety, with saddle point parameters between those of C-H···N and C-H···O interactions. Electron density at the critical point, of 0.30 e·Å-3, is slightly higher than the value 0.25 e·Å-3 calculated for the O1···H22Bii


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contact. However, both the S2···H22Ai and O1-H22Bii distances are by about 0.2 Å longer than the sums of appropriate van der Waals radii (however one should bear in mind the fuzziness of the very concept of van der Waals radius…). Other C-H···S contacts are disputable, since the C-H bond is oriented perpendicular to the S···H line, and the bond path trajectory tends to fall in between carbon and hydrogen atoms (Figure ). Nevertheless, these contacts are treated here as C-H···S or σ C-H···S bonds, as the sulphur atom has little access to the carbon scaffold.

Figure 9. Static total electron density and trajectory plots for (top) S2···H17 contacts, (bottom)

S1···H18 contact. Saddle points are marked with the red asterisks, black contours mark electron density isovalues, plotted every 0.025 e·Å-3. Trajectory plots in grey. The area between the N1 and C7iv (iv 1-x,2-y,-z) atoms is characterised with relatively low electron density (approx. 0.3 eÅ-3), which is consistent with the values found for stacking interactions within the lattice. In general, the interactions of this type are characterised as weak, with total static electron density at 0.025 - 0.035 e·Å-3 level, and low Laplacian values at critical points. Even though it seems weaker than the other groups of intermolecular contacts, π-π stacking is not ACS Paragon Plus Environment

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localised in a small area. Thus, low electron density spread over relatively large space conceals the contribution of stacking in intermolecular interactions when the analysis is based solely on the values at the saddle points (cf. discussion in Dunitz, Gavezzotti3 and additional explanation in Supplementary material).

Figure 10. Total static electron density combined with trajectories plots. Black isovalues lines are

drawn at 0.025 eÅ-3 interval. Bond critical point is marked with a thin red cross. C-H···H-C interactions are numerous and, similarly to surprisingly scarce C-H···π ones,

fairly weak, having electron density at saddle point ranging between 0.030 and 0.045 eÅ-3. Laplacian values vary from 0.25 eÅ-5 up to 0.65 eÅ-5. Even though the crucial numerical values describing saddle point properties are similar to those of π-π stacking, their positional uncertainty is only a fraction of that of the latter. This is intuitively understandable, if only one takes into account the shape differences between π orbital and H atom.


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Figure 11. Static total electron density and trajectory plots for (left) H16···H7, H7···H22C,

H22C···H2 hydrogen contacts, (right) H16···π C5-C6 bond. Saddle points are marked with red crosses, black contours mark electron density isovalues at 0.025 eÅ-3 each.

Topological analysis of covalent bonds

The average measured length of three sulphur – sp2 carbon atom bonds is 1.77(1) A, with bond saddle points placed halfway for S1 and at off-centre positions for S2 sulphur atom. Bond critical points for S2 atom are shifted, in the case of S2-C3 bond - closer to the sulphur atom and in the case of S2-C21 - closer to the methyl carbon atom. These four bonds have the lowest total electron density at the saddle point from all covalent bonds within the molecule, with the densities averaging at 1.26(1) e·Å-3 (S2-C3 differs from the other bonds with its electron density of 1.30 eÅ-3). The oxygen atom O1 displays similar properties and topology with the total electron density at the saddle point O1-C22 still relatively low: 1.59 e·Å-3. However, its link to the sp2 C14 carbon is about as populous as the average of C-C phenyl bond within the molecule. Both nitrogen atoms show interesting and nearly identical topological features. The total electron densities at the (3, -1) saddle points of N1-C2 and N11-C12 bonds take the highest values from among all covalent bonds, with the mean value of 2.52(1) eÅ-3. This is by about 0.3 eÅ-3 higher than the values found for N1-C10 and N11-C20 bonds, yet all four bonds differ in length by not more than 0.05 Å. The critical points are positioned unsymmetrically, shifted towards the nitrogen near the sulphur atoms and towards the carbon near the phenyl ring. Basic characteristics of the covalent bond critical points are gathered in Table . In general, the carbon-carbon bonds within the quinoline system retain the expected bond lengths of 1.42 and 1.38 Å. Shorter bonds are positioned between the external α and β positions. All (3,-1) bond critical points are positioned halfway between the atoms concerned and lie directly on the bond axes. The average static electron density at the critical points takes the values of 2.05(2) eÅ-3


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and 2.20(2) for longer and shorter bonds, respectively. The bond between C6 and C7 displays unusual positioning of the critical point which is placed unsymmetrically: 0.78 Å from C6 and 0.60 Å from C7. Detailed analysis revealed an unexpected electron density peak near C7 (Figure ), which however disappeared after using s 4.0 cutoff. Therefore, the peak was interpreted as an effect of random noise mistakenly taken into account by the program and not spotted until topological analysis. However, different noise cutoff levels did not change the deformation density map and the shifts of the critical point position were less than 0.02 Å. This permitted us to claim that such an unexpected deviation of electron density results from the stacking interactions with nearby N1 nitrogen atom. The chemically identical C16 - C17 bond, which lacks neighbours with strong electronegativity, has its (3,-1) critical point positioned symmetrically. This speaks in favour of weak intermolecular interactions being responsible for the saddle point positional shift.

Table 3. Basic covalent bond critical points characterisation. Saddle point position coefficient is

calculated as (dA1-CP/dA1-A2)/(vdWrA1/( vdWrA1+ vdWrA2)). Quinoline C-C α-β include C16-C17, C8-C9 and C18-C19 bonds. Quinoline C-C and C-H include the corresponding bonds unmentioned elsewhere. Atom 1 Atom 2 S1 C4 S1 C13 S2 C3 S2 C21 O1 C22 O1 C14 N1. N11 C10. C20 N1. N11 C2. C12 C2. C12 C3. C13 C3 C4 C13 C14 Quinoline C-C Quinoline C-C α-β C6 C7 C2 H2

ρ (eÅ-3) 1.28 1.27 1.30 1.26 1.59 2.13 2.16 2.52 1.98 2.12 2.17 2.03 2.20 2.23 1.87

∇² (eÅ-5) -6.86 -7.02 -8.65 -6.31 -10.66 -17.27 -20.43 -27.60 -17.34 -19.27 -21.26 -18.38 -22.01 -23.93 -18.18

pos. coeff. 0.959 0.976 0.897 0.996 1.310 1.211 1.225 1.186 1.074 0.967 0.959 0.978 0.975 1.102 1.111


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C12 H12 C16 H16 C17 H17 C19 H19 Quinoline C-H Methyl C-H

1.82 1.75 1.81 1.70 1.77 1.77

-18.48 -15.63 -18.30 -16.00 -16.97 -14.55

1.086 1.107 1.078 1.105 1.093 1.040

Figure 12. (top) Laplacian map (logarithmic) with cp6 shifted towards C7 atom; (middle)

deformation map of the area, isovalues every 0.1 eÅ-3; (bottom) 1.25 Fo – 1.00 Fc map, no cutoff applied. Comparison of IAM and multipolar models ACS Paragon Plus Environment

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In comparison to standard IAM methods, multipolar refinement is demanding in terms of time consumption. High quality, high resolution and redundant data required for a reliable multipolar model analysis usually take several days to collect. The molecule studied, after refinement against basic 9 parameters per atom, has yet to be refined against additional 4 to 25 also repeating refinement of the first 9 parameters in the process. Noting differences between approaches and marking the line where extra work becomes sustainable is therefore important. Independent Atom Model gives, by definition, no information on atomic charges and valence electrons variations but can be reliably used as a template for DFT calculations. In contrast the multipolar model takes valence shells population and shapes into account, but its usefulness as a template remains unchanged. However, incorporating detailed information obtained by charge density studies gives a new insight into valence-dependent quantities such as local electron densities, potentials or intermolecular bond trajectories. Comparison of the atomic charges (Figure 5) shows that MM stays closer to DFT results than IAM does. It is worth noting that the hydrogen atoms taking part in intermolecular interactions with heteroatoms possess slight negative charges or stay approximately neutral in atomic basins integration approaches, but stay positive in DFT studies where modelling of the molecule together with all neighbours yields a system too big to be effectively modelled using a classical approach.


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Figure 5. Calculated atomic charges comparison. DFT charges calculated using Mulliken approach,

IAM and MM model based calculations rely on atomic basins integration. MM Pval depicts difference between nucleus charge and electron population. Critical points analysis reveals crucial differences between the IAM and MM approaches. As a natural consequence of the use of the independent atoms model, all covalent bond critical points are positioned at covalent radii. On the contrary, the multipolar model allows taking into account differences in atomic charge and additional charge distribution parameters. Thus, heteroatom binding carbon atoms usually have their bond critical points shifted from covalent radii contact point towards the carbon atom. Moreover, the C6-C7 bond saddle point in the system studied is positioned at the bond centre in IAM model, concealing the influence of a strong neighbouring nitrogen atom. Intermolecular bonding description also differs significantly: While the multipolar model yields 144 intermolecular saddle points, the same analysis in the independent atoms model yields only 130 points. What is important, differences occur at the crucial positions: the O1···O1 interaction described above is virtually non-existent in the IAM approach. A weak bond obtained in the MM approach is replaced by an even weaker, less localised (3,-1) intermolecular bond saddle point at the very edge (λ2=-0.002) of converting to the (3,+1) ring centre point. Close hydrogenhydrogen contacts, specifically H17···H17 and H6···H16 differ significantly between the models as shown in Table 1 and depicted in Figure . These differences reveal the inaccuracy of the standard model, rendering it less trustworthy for the detailed system analyses.

Table 1. A comparison of CP characteristics for selected H···H interactions. model

interaction ρ (eÅ-3) ∇2ρ (eÅ-5)

λ1

λ2

λ3

MM

H17···H17 0.0447

0.59

0.86

-0.13

-0.15

IAM

H17···H17 0.0787

0.63

1.09

-0.22

-0.24

MM

H6···H16

0.0305

0.55

0.73

-0.08

-0.09

IAM

H6···H16

0.0805

0.66

1.08

-0.18

-0.24


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Figure 14. C17···C17 and H6···H16 contact areas. Electron density isovalues every 0.01 e·Å-3 for MM (top) and IAM (middle), 0.001 e·ao-3 (ca. 0.00675 e·Å-3) for DFT (bottom) approach. Another difference between the models compared concerns the electrostatic potentials: in general, volume enclosed by isosurfaces compared rises when using the multipolar model approach. It is especially noticeable near intermolecular contacts, which again rises the issue of IAM being less appropriate for the detailed interactions studies. Figure

illustrates the effect on contacts

interpretation. It is not surprising, as without incorporating the charge density distribution variations, electrostatic potential values depend solely on the element type.


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Figure 15. A comparison of same electrostatic potential isosurfaces in the S1···S1 region. Inner surface for IAM, outer (semi-transparent) for MM.

The variations in IAM can be introduced using DFT calculations, giving an electrostatic potential map in satisfactory agreement with that obtained from the MM (Figure ). The most important features, σ-holes and lone electron pairs, as well as nitrogen atoms and other features, stay in good agreement. The main differences, such as phenyl ring hydrogen atoms charge, most probably stem from the theoretical studies conducted for a free molecule.


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Figure 16. Electrostatic potential mapped over same electron density isosurface: DFT - above, MM - below. Isosurface drawn for 0.5 e/Å-3, red colour for 0.1 e/Å, blue colour for 1.3 e/Å Theoretical and experimental models seem to be in very good agreement. Slight differences are present, but their distribution can be assigned to orbital functional characteristics: Slater-type and Gaussian-type functions produce different distribution far from the nucleus centre. Since our analysis focuses on intermolecular contacts, the calculated electron density is prone to stress out approach differences. The use of various basis sets for DFT approach yields changes in the contact electron density comparable in value to the DFT – MM differences or bigger.

Table 5. A comparison of electron density (in eÅ-3) in several chosen saddle points obtained using various methods Experimental

DFT


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S1···S1 O1···O1 O1···H22B H17···H17 H6···H16

IAM 0.084 0.035 0.040 0.079 0.081

MM 0.081 0.029 0.035 0.045 0.030

6-31G 0.057 0.021 0.034 0.304 0.026

LANL2DZ 0.061 0.033 0.024 0.028 0.022

STO-3G 0.044 0.011 0.018 0.036 0.039

Summary

Various intermolecular contacts were analysed and described, most notably a unique reciprocal chalcogen bond between two S1 atoms. In given conditions of not strong hydrogen bond donors, this chalcogen homoatomic bond proves to be the strongest within the system studied. Several different approaches were used and the results compared. The use of MM allows obtaining a model with lower discrepancy index than that of IAM, but – what is most important – a model giving reliable information about intermolecular contacts. The results are comparable to those obtained via in silico studies. Some differences, e.g. in molecule’s atomic charges and electrostatic potential map, are most probably a result of not considering symmetry mates during the process. While it might be perceived as a method defect, a typical in silico study does not apply any surrounding molecule if not necessary. Thus, our study compares and finds good agreement between the multipolar model and the generic theoretical study. Meanwhile, even the best obtainable IAM model occurs to be unreliable until applying further, more advanced approximations.

Supporting information is available for this manuscript: crystallographic details in the CIF-format, multipolar refinement procedure details, Hirshfeld surface fingerprint plots, DFT calculated S1-S1 bond strength - detailed data, intermolecular parameters details for IAM and MM, a justification of the scarcity of observed π-π stacking crital points.


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For Table of Contents Use Only.

Experimental and theoretical charge density studies of chalcogen bonding and other intermolecular contacts in 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline Mikołaj Pyziak, Jadwiga Pyziak, Marcin Hoffmann, Maciej Kubicki*

High-resolution diffraction data confirm the presence of intermolecular, electron pairs - σ-holes S···S bonding. The calculated minimum energy distance has value of 3.33 - 3.34 Å and agrees very well with the separation of 3.3300(11) Å, observed in the crystal structure.


31

Experimental and Theoretical Charge Density Studies of Chalcogen

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