tools for teaching crystallography\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 79| Part 4| April 2023| Pages 246-253
https://doi.org/10.1107/S2056989023002700

A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model

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Sean Parkin,a* Jeremy Cunningham,b Brian Rawls,b John E. Bender,b Richard J. Staplesc and Shannon M. Birosb*

aDepartment of Chemistry, University of Kentucky, Lexington, KY, 40506, USA, bDepartment of Chemistry, Grand Valley State University, Allendale, MI 49401, USA, and cCenter for Crystallographic Research, Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
*Correspondence e-mail: s.parkin@uky.edu, biross@gvsu.edu

Edited by G. Diaz de Delgado, Universidad de Los Andes Mérida, Venezuela (Received 27 February 2023; accepted 22 March 2023; online 28 March 2023)

This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis­(di­phenyl­phosphan­yl)ethyl­ene, namely, 1,2-(ethene-1,2-di­yl)bis­(di­phenyl­phoshpine sulfide/selenide), C26H22P2S1.13Se0.87. A sequence of processes are presented to ascertain the composition of the crystal, along with strategies for which aspects of the model to inspect to ensure a chemically and crystallographically realistic structure. Criteria include mis-matches between Fobs2 and Fcalc2, plots of |Fobs| vs |Fcalc|, residual electron density, checkCIF alerts, pitfalls of the OMIT command used to suppress ill-fitting data, comparative size of displacement ellipsoids, and critical inspection of inter­atomic distances. Since the structure is quite small, solves easily, and presents a number of readily expressible refinement concepts, we feel that it would make a straightforward and concise instructional piece for students learning how to determine if their model provides the best fit for the data and show students how to critically assess their structures.

CCDC reference: 2231833

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1. Chemical context

Our research group has synthesized a number of phosphine chalogenide derivatives and explored their chemistry in regard to their coordination with both d-block and f-block metals (Luster et al., 2022[Luster, T., Van de Roovaart, H. J., Korman, K. J., Sands, G. G., Dunn, K. M., Spyker, A., Staples, R. J., Biros, S. M. & Bender, J. E. (2022). Dalton Trans. 51, 9103-9115.]; Mugemana et al., 2018[Mugemana, J., Bender, J., Staples, R. J. & Biros, S. M. (2018). Acta Cryst. E74, 998-1001.]; Morse et al., 2016[Morse, P. T., Staples, R. J. & Biros, S. M. (2016). Polyhedron, 114, 2-12.]; Neils et al., 2022[Neils, T., LaDuca, A., Bender, J. E., Staples, R. J. & Biros, S. M. (2022). Acta Cryst. E78, 1044-1047.]). A few years ago, we worked with the rigid diphosphine cis-1,2-bis­(di­phenyl­phosphine)ethyl­ene 1 (cis-dppe), and developed conditions for the synthesis of the di-sulfide 2 (Rawls et al., 2023[Rawls, B., Cunningham, J., Bender, J. E., Staples, R. J. & Biros, S. M. (2023). Acta Cryst. E79, 28-32.]) and the di-selenide 3 (Jones et al., 2015[Jones, P. G., Hrib, C. & du Mont, W.-W. (2015). Private Communication (refcode YOWTIP) CCDC, Cambridge, England.]) (Fig. 1[link]). We obtained X-ray diffraction data for both 2 and 3, and the structures were isomorphic, having the symmetry of the ortho­rhom­bic space group P212121. Our synthetic efforts then turned to preparation of mono-selenide 4 as a way to gain access to the mixed sulfide-selenide system, 5.

[Scheme 1]
[Figure 1]
Figure 1
A generalized reaction scheme to prepare the compounds studied in this work.

2. Structure solution and model building trials

We obtained diffraction data for crystals grown directly from the reaction mixture. The structure solved easily in P212121 using SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]) with included scattering factors for C, H, P, Se and a unit cell that was clearly related to those of compounds 2 and 3. In the initial solution, however, SHELXT had assigned scattering factors for phospho­rus to both chalcogen sites, a chemical impossibility. In terms of similarity of scattering factors, sulfur would be the obvious next choice for the chalcogen, but the pnictogen-to-chalcogen distances (vide infra) were much longer than in the di-sulfide structure 2 (Rawls et al., 2023[Rawls, B., Cunningham, J., Bender, J. E., Staples, R. J. & Biros, S. M. (2023). Acta Cryst. E79, 28-32.]). Given the available electron density at the chalcogen site, a disordered mono-selenide model seemed plausible. Of paramount importance here is that any trial model must be chemically plausible, thus knowledge of chemistry and information from other spectroscopic techniques (if available) should be used to rule out alternatives.

2.1. Trial 1: a mono-selenide model

Manual editing of the chalcogen sites to accommodate a single Se atom split over the two sites gave a model that refined smoothly using SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), giving a disordered Se occupancy ratio of 0.526 (2):0.474 (2) (Fig. 2[link]a). The P=Se distances were 2.063 (2) and 2.035 (2) Å, and the model converged to an R1 value of 0.0494.

[Figure 2]
Figure 2
(a) An ellipsoid (50% probability) plot for the major component of the mono-selenide model. (b) A plot of |Fobs| vs |Fcalc| values for the mono-selenide model. Note the extent of scatter in the plot. (c) A difference-electron density map reveals positive (green) electron density at the chalcogen site and negative (red) contours at the phospho­rus sites. Small peaks within the positive density are represented by coloured dots. The single Se atom in trial 1 is split with occupancies of 0.526 (2) and 0.474 (2) over the two chalcogen sites.

This model passed all the typical checkCIF tests, apart from returning a B-level alert indicating the presence of a few reflections with a poor fit between Fobs2 and Fcalc2. The SHELXL list of `most disagreeable reflections' (i.e, mis-matches between observed and calculated data) showed a striking difference for four reflections (Table 1[link], Fig. 2[link]b). At this point, it might be tempting to simply remove the top few poorly fitting reflections (i.e., those having error/s.u. > 10) using the OMIT command in SHELXL and be satisfied with the structure. However, all of the worst outliers (see Table 1[link]) have Fobs2 >> Fcalc2 and are at resolutions far removed from the beamstop shadow. Thus, the commonly blamed culprit of `obscured by the beamstop' would not provide any justification for omission. Unfortunately, uncritical omission of the worst-offending reflections in order to suppress unfavourable checkCIF alerts has become all too common. When Fobs2 >> Fcalc2, however, such ill-fitting intensities are precisely the datapoints that are most sensitive to any model deficiencies. Modern data-reduction software includes facilities to identify the particular frame for any such outliers for manual inspection. In the present case, the offending reflections appeared to have been measured properly; no justification for omission was apparent. A closer look at the model showed that the displacement ellipsoids for the Se atoms were a little on the small side relative to neighbouring atoms, and that the residual difference-Fourier map showed pronounced electron density with several small embedded difference-map peaks (each less than 0.9 e Å−3) clustered near the chalcogen sites (Fig. 2[link]c). These `features' suggest that this model did not fully account for all the electron density present in the data.

Table 1
List of the top four poorly fitting reflections for the model of the mono-selenide shown in Fig. 2[link]

h k l F2obs F2calc error/s.u. Fcalc/Fcalc(max) d–spacing (Å)
1 0 2 250.91 6.81 10.42 0.012 6.16
0 3 2 1787.72 504.88 10.20 0.101 3.74
2 0 3 335.44 41.35 9.52 0.029 3.76
1 4 0 671.93 175.18 8.75 0.060 3.18
All of the worst fitting reflections above have Fobs2 >> Fcalc2 and none would be obscured by a well-designed beamstop.

2.2. Trial 2: a di-selenide model

To better account for the residual electron density, we built a model that corresponded to the di-selenide 3, in which each Se atom had a fixed occupancy of 1.0 (Table 2[link] and Fig. 3[link]). The resulting P=Se distances were (unsurprisingly) similar to those for the previous model at 2.061 (2) and 2.030 (2) Å. However, the R1 value for this model jumped to 0.0632 and the mis-match between the values of the displacement parameter tensors for the Se atoms and those for the rest of the atoms in the structure became wholly unrealistic (Fig. 3[link]a). Moreover, the discrepancy between the top four `disagreeable' reflections became even larger, and the |Fobs| vs |Fcalc| plot was a little more scattered (Fig. 3[link]b). By any measure, the di-selenide model is demonstrably worse than the mono-selenide model. Comparison of these two models, however, suggests that the electron density for the chalcogen atom sites present in the crystal that produced the diffraction data was insufficient to support two fully occupied selenium atoms, but it was too much for a mono-selenide model.

Table 2
List of the top four poorly fitting reflections for the model of the di-selenide shown in Fig. 3[link]

h k l F2obs F2calc error/s.u. Fcalc/Fcalc(max) d–spacing (Å)
1 2 0 14663.16 2109.28 11.62 0.181 5.80
4 2 0 1787.72 13.29 10.10 0.014 2.78
0 4 3 335.44 114.61 10.00 0.042 2.71
0 2 0 671.93 1634.82 9.55 0.159 6.58
Three of the worst fitting reflections above have Fobs2 >> Fcalc2 and none would be obscured by a well-designed beamstop.
[Figure 3]
Figure 3
(a) An ellipsoid (50% probability) plot for the di-selenide model. Note the unrealistically large ellipsoids at the chalcogen sites and the small highly eccentric ellipsoids for the carbon atoms. (b) A plot of |Fobs| vs |Fcalc| values for the di-selenide model. Note the extent of scatter in the plot.

2.3. Trial 3: a mono-selenide/di-selenide solid-solution model

Since atomic scattering factors are (to a first approximation) proportional to atomic number, refinement of the occupancies at the chalcogen sites should give a good estimate of the amount of available density. Thus, to better fit the available electron density, the occupancies at each Se atom were refined freely, which gave occupancies of 0.712 (2) and 0.655 (2) for the two chalcogen sites (Fig. 4[link]a). The R1 value dropped quite precipitously to 0.0236 and the displacement ellipsoids for all atoms appeared to be acceptable. For this model, the checkCIF report revealed no B-level alerts, and the discrepancy between the top four observed vs calculated mis-matches was correspondingly much smaller than for any of the previous models (Table 3[link] and Fig. 4[link]b).

Table 3
List of the top four poorly fitting reflections for the model of the mixed mono/di-selenide shown in Fig. 4[link]

h k l F2obs F2calc error/s.u. Fcalc/Fcalc(max) d–spacing (Å)
6 3 0 275.52 151.58 7.71 0.053 1.86
1 0 2 344.63 207.43 7.69 0.062 6.16
0 0 2 118.70 64.07 5.83 0.034 7.12
0 2 1 20.03 3.69 5.55 0.008 5.98
There are no egregious Fobs2 >> Fcalc2 mis-matches for this model.
[Figure 4]
Figure 4
(a) An ellipsoid (50% probability) plot for the mixed mono-selenide/di-selenide model. Note that all ellipsoids appear quite normal. (b) A plot of |Fobs| vs |Fcalc| values for the mixed mono-selenide/di-selenide model. Note the much reduced scatter in the plot relative to Figs. 2[link] and 3[link].

2.4. Trial 4: a mixed selenide/sulfide solid-solution model

At this point, the statistics for the model were acceptable and checkCIF raised no red flags. Nonetheless, a critical comparison of the P=Se distances in the model shown in Fig. 4[link]a to values listed in Inter­national Tables for Crystallography vol. C (Table 9.5.1.1; Prince, 2006[Prince, E. (2006). International Tables for Crystallography, vol. C. Table 9.5.1.1. Chester: International Union of Crystallography.]) and updated information in the CSD (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) available via MOGUL (Bruno et al., 2004[Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E. & Orpen, A. G. (2004). J. Chem. Inf. Comput. Sci. 44, 2133-2144.]) revealed additional chemical evidence that the outwardly acceptable model was subtly flawed. The average length for P=Se bonds is listed in these resources as 2.093 Å, while that of P=S bonds is 1.954 Å. The lengths of the P=Se bonds in the model shown in Fig. 4[link]a are in between these two values at 2.060 (8) and 2.0328 (8) Å. This observation is reminiscent of work by Gerard Parkin and co-workers in de-bunking the bond-stretch isomerism theory (Parkin, 1992[Parkin, G. (1992). Acc. Chem. Res. 25, 455-460.]), in which improbable `bond lengths' were shown to result from undiagnosed chemical inhomogeneity rather than unrealistic bond-length differences.

In a similar vein, one logical explanation for the discrepancy in the present case was that the sample could have been contaminated with some di-sulfide 2. These compounds were all synthesized several years ago, and the mixed Se/S compound had been one of the synthetic goals (vide supra). Modification of the model to include selenium and sulfur at both sites, where the occupancies of these atoms were refined to sum to unity, resulted in the model shown in Fig. 5[link]a and 6. This model has an R1 value of 0.0209, notably lower than the previous selenide-only model, with the relative sulfur-to-selenium occupancies for each site being 0.513 (3):0.487 (3) and 0.614 (3):0.386 (3). The bond lengths for this final model are also in reasonable agreement with literature averages, the P=Se distances being 2.082 (8) and 2.088 (11) Å, while the P=S distances are 2.021 (19) and 1.953 (16) Å, directly from refinement, i.e., without distance restraints. Since the literature P=S distance is only ∼0.934 that of P=Se (i.e., 1.954/2.093 vide supra), had the relative sulfur occupancy been much lower, then a restraint to tie the P=Se/S distances via an FVAR parameter in SHELXL might have been necessary. A look at the list of `disagreeable' reflections also shows an improvement (Tables 1[link]–4[link][link][link]). Note in particular that none of the worst offenders in Table 1[link] or 2 show up in Table 4[link]. Based on these features and statistics, the structure for 5 shown in Fig. 6[link] is demonstrably the superior model for this crystal.

Table 4
List of the top four poorly fitting reflections for the model of the di-selenide shown in Fig. 5[link]

h k l F2obs F2calc error/s.u. Fcalc/Fcalc(max) d–spacing (Å)
6 3 0 270.87 165.41 7.11 0.055 1.86
0 8 0 301.14 215.46 5.07 0.063 1.65
0 6 2 784.43 965.40 4.86 0.133 2.10
2 5 1 57.90 29.40 4.80 0.023 2.39
There are no egregious Fobs2 >> Fcalc2 mis-matches for this model.
[Figure 5]
Figure 5
(a) An ellipsoid (50% probability) plot for the mixed selenide/sulfide model. Note that all ellipsoids appear quite normal. (b) A plot of |Fobs| vs |Fcalc| values for the mixed selenide/sulfide model. Note the much reduced scatter in the plot relative to Figs. 2[link] and 3[link].
[Figure 6]
Figure 6
An ellipsoid (50% probability) plot for the final mixed selenide/sulfide model showing the atom-numbering scheme.

3. Structural commentary

The structure of 5 (Fig. 6[link]) shares many similarities with the di-sulfide 2 (structure I in Rawls et al., 2023[Rawls, B., Cunningham, J., Bender, J. E., Staples, R. J. & Biros, S. M. (2023). Acta Cryst. E79, 28-32.]) and the di-selenide 3 (Jones et al., 2015[Jones, P. G., Hrib, C. & du Mont, W.-W. (2015). Private Communication (refcode YOWTIP) CCDC, Cambridge, England.]). As stated in section 2.4, in spite of the superpositional disorder of Se and S at both chalcogen sites, the unrestrained pnictogen-to-chalcogen bond distances [P1=Se1 = 2.0818 (8), P2=Se2 = 2.0879 (11), P1=S1 = 2.021 (19), P2=S2 = 1.953 (16) Å] are within or close to the normal ranges. All other bond distances and angles are also normal. There is a slight twist out of planarity at C1=C2, which gives a P1—C1—C2—P2 torsion angle of 9.0 (5)°. This, and torsion angles C9—P1—C1—C2 [−35.3 (3)°] and C1—C2—P2—C21 [−34. (3)°] effectively place phenyl rings C9–C14 and C12–C26 into an intra­molecular π–π-stacking arrangement. The dihedral angle between these overlapped phenyl rings is only 5.45 (3)° although the stacking is skewed, leading to a ring centroid–centroid distance of 3.737 (4) Å.

4. Supra­molecular features

The mol­ecular packing in 5 is similar to that in the di-sulfide 2 (Rawls et al., 2023[Rawls, B., Cunningham, J., Bender, J. E., Staples, R. J. & Biros, S. M. (2023). Acta Cryst. E79, 28-32.]) and the di-selenide 3 (Jones et al., 2015[Jones, P. G., Hrib, C. & du Mont, W.-W. (2015). Private Communication (refcode YOWTIP) CCDC, Cambridge, England.]). Since all hydrogen atoms are bound to carbon, there are no strong hydrogen bonds. There are also no inter­molecular π–π inter­actions, though there are numerous weak C—H⋯π contacts. A Hirshfeld-surface analysis mapped over dnorm (Fig. 7[link]) shows that inter­molecular contacts are dominated by hydrogen, either to other hydrogen atoms (55.0% of contacts), or to carbon (24.6%), or Se/S sites (16.4%). The remainder of the contacts (C⋯C at 3.3% and C⋯Se/S at 0.7%) are negligible. The strongest inter­actions, however, i.e. those in which distances are appreciably less than the sum of van der Waals radii (see intense red spots in Fig. 7[link]a) are from C—H⋯Se/S contacts (Table 5[link]).

Table 5
C—H⋯chalcogen close-contact geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C1—H1⋯Se2i 0.95 2.87 3.752 (13) 155.1
C1—H1⋯S2i 0.95 2.89 3.76 (2) 153.4
C8—H8⋯Se1 0.95 2.95 3.443 (8) 113.8
C8—H8⋯S1 0.95 2.82 3.325 (18) 114.5
C10—H10⋯Se1 0.95 2.92 3.459 (8) 117.4
C10—H10⋯S1 0.95 2.81 3.349 (19) 117.2
C20—H20⋯Se2 0.95 2.93 3.431 (13) 114.5
C20—H20⋯S2 0.95 2.92 3.40 (2) 112.6
C26—H26⋯Se2 0.95 3.00 3.524 (11) 116.6
C26—H26⋯S2 0.95 2.85 3.361 (17) 114.8
Symmetry code: (i) x + [{1\over 2}], −y + [{3\over 2}], −z.
[Figure 7]
Figure 7
(a) A Hirshfeld-surface plot mapped over dnorm for the final model. Red spots and dashed lines highlight close contacts between C—H groups and the Se/S sites (see also Table 5[link]). (b) Hirshfeld-surface fingerprint plot showing H⋯H contacts (55.0%). (c) Hirshfeld-surface fingerprint plot showing H⋯C contacts (24.6%). (d) Hirshfeld-surface fingerprint plot showing H⋯Se/S contacts (16.4%). (e) Hirshfeld-surface fingerprint plot showing C⋯C contacts (3.3%). (f) Hirshfeld-surface fingerprint plot showing C⋯Se/S contacts (0.7%).

5. Database survey

The Cambridge Structural Database (CSD, v5.43 with all updates through Nov. 2022; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) returns 5727 entries for a search fragment consisting of the dppe mol­ecule. Of these, 895 have `any atom' single bonded to the phospho­rus and 267 are double bonded. There are 35 entries with two P=S bonds and 17 with two P=Se bonds. There are also some mixed species; 33 entries have just one P=S and two entries have just one P=Se, though these mixed structures have little else in common with structure 5 discussed herein. The closest structures to 5 are the di-selenide structures YOWTIP (Jones et al., 2015[Jones, P. G., Hrib, C. & du Mont, W.-W. (2015). Private Communication (refcode YOWTIP) CCDC, Cambridge, England.]) and the di-sulfide CAMCUR01 (Rawls et al., 2023[Rawls, B., Cunningham, J., Bender, J. E., Staples, R. J. & Biros, S. M. (2023). Acta Cryst. E79, 28-32.]).

6. Refinement

A summary of data collection details and structure refinement statistics is given in Table 6[link]. Hydrogen atoms were found in difference-Fourier maps, but subsequently included in the refinement using riding models, with constrained distances set to 0.95 Å. Uiso(H) values were set to 1.2Ueq of the attached carbon atom. To ensure satisfactory refinement, constraints (SHELXL command EADP) were used to equalize displacement parameters of superimposed Se/S atoms.

Table 6
Experimental details

Crystal data
Chemical formula C26H22P2S1.13Se0.87
Mr 501.46
Crystal system, space group Orthorhombic, P212121
Temperature (K) 173
a, b, c (Å) 12.2833 (2), 13.1643 (2), 14.2478 (2)
V (Å3) 2303.88 (6)
Z 4
Radiation type Cu Kα
μ (mm−1) 4.32
Crystal size (mm) 0.49 × 0.45 × 0.34
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.587, 0.754
No. of measured, independent and observed [I > 2σ(I)] reflections 24246, 4187, 4155
Rint 0.026
(sin θ/λ)max (Å−1) 0.617
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.053, 1.10
No. of reflections 4187
No. of parameters 279
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.25, −0.23
Absolute structure Flack x determined using 1619 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.]).
Absolute structure parameter 0.018 (5)
Computer programs: APEX2 (Bruker, 2013[Bruker (2013). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2019/2 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]; Bourhis et al., 2015[Bourhis, L. J., Dolomanov, O. V., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2015). Acta Cryst. A71, 59-75.]), Mercury (Macrae et al., 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]), ShelXle (Hübschle et al., 2011[Hübschle, C. B., Sheldrick, G. M. & Dittrich, B. (2011). J. Appl. Cryst. 44, 1281-1284.]), CrystalExplorer (Spackman et al., 2021[Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006-1011.]), CrystalMaker (Palmer, 2007[Palmer, D. (2007). CrystalMaker. CrystalMaker Software Ltd, Yarnton, England.]), SHELX (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

7. Conclusions

This crystal structure can serve as a straightforward instructional tool to demonstrate the varied pieces of information used to determine the quality and ultimately the correctness of a model. Here we investigated residual electron density, size of displacement ellipsoids, Fobs2 and Fcalc2 mis-matches, plots of |Fobs| vs |Fcalc| and comparison of inter­atomic distances to literature averages. Of particular importance is that the analysis highlights the dangers of uncritical suppression of outliers by inappropriate use of the OMIT command in SHELXL. Since the path to determining the best model inevitably varies from one structure to the next, a few additional points to consider, along with some background and, where appropriate, strategies to deal with them are included in the supporting information.

8. Related literature

The supporting information includes a number of references that are not cited in the main paper. These sources are not exhaustive, but might serve as a useful starting point for further enquiry by an inter­ested student. They are grouped by their respective contexts and cited here:

General advice on structure and refinement strategy: Watkin, 1994[Watkin, D. (1994). Acta Cryst. A50, 411-437.]; Clegg, 2019[Clegg, W. (2019). Acta Cryst. E75, 1812-1819.]; Linden, 2020[Linden, A. (2020). Acta Cryst. E76, 765-775.]; Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.].

Twinning: Hahn & Klapper, 2006[Hahn, Th. & Klapper, H. (2006). International Tables for Crystallography, vol. D, pp. 393-448. Chester: International Union of Crystallography.]; Donnay & Donnay, 1959[Donnay, J. D. H. & Donnay, G. (1959). International Tables for X-ray Crystallography, vol. II, p104. Birmingham, Kynoch Press.]; Nespolo & Ferraris, 2003[Nespolo, M. & Ferraris, G. (2003). Z. Kristallogr. 218, 178-181.]; Nespolo, 2015[Nespolo, M. (2015). Cryst. Res. Technol. 50, 362-371.], 2019[Nespolo, M. (2019). Acta Cryst. A75, 551-573.]; Nespolo et al., 2020[Nespolo, M., Smaha, R. W. & Parkin, S. (2020). Acta Cryst. B76, 643-649.]; Herbst-Irmer & Sheldrick, 1998[Herbst-Irmer, R. & Sheldrick, G. M. (1998). Acta Cryst. B54, 443-449.], 2002[Herbst-Irmer, R. & Sheldrick, G. M. (2002). Acta Cryst. B58, 477-481.]; Parsons, 2003[Parsons, S. (2003). Acta Cryst. D59, 1995-2003.]; Parkin, 2021[Parkin, S. R. (2021). Acta Cryst. E77, 452-465.]; Spek, 2020[Spek, A. L. (2020). Acta Cryst. E76, 1-11.]; Cooper et al., 2002[Cooper, R. I., Gould, R. O., Parsons, S. & Watkin, D. J. (2002). J. Appl. Cryst. 35, 168-174.].

Mol­ecular geometry and crystal symmetry: Parkin, 1992[Parkin, G. (1992). Acc. Chem. Res. 25, 455-460.]; Allen et al., 1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-S19.]; Orpen et al., 1989[Orpen, A. G., Brammer, L., Allen, F. H., Kennard, O., Watson, D. G. & Taylor, R. (1989). J. Chem. Soc. Dalton Trans. pp. S1.]; Prince, 2006[Prince, E. (2006). International Tables for Crystallography, vol. C. Table 9.5.1.1. Chester: International Union of Crystallography.]; Baur & Kassner, 1992[Baur, W. H. & Kassner, D. (1992). Acta Cryst. B48, 356-369.]; Marsh, 1997[Marsh, R. E. (1997). Acta Cryst. B53, 317-322.]; Marsh & Spek, 2001[Marsh, R. E. & Spek, A. L. (2001). Acta Cryst. B57, 800-805.]; Le Page, 1987[Le Page, Y. (1987). J. Appl. Cryst. 20, 264-269.], 1988[Le Page, Y. (1988). J. Appl. Cryst. 21, 983-984.]; Mohamed et al. (2016[Mohamed, S. K., Younes, S. H. H., Abdel-Raheem, E. M. M., Horton, P. N., Akkurt, M. & Glidewell, C. (2016). Acta Cryst. C72, 57-62.]); Parkin et al., 2023[Parkin, S., Glidewell, C. & Horton, P. N. (2023). Acta Cryst. C79, 77-82.]; Vinaya et al. (2023[Vinaya, Basavaraju, Y. B., Srinivasa, G. R., Shreenivas, M. T., Yathirajan, H. S. & Parkin, S. (2023). Acta Cryst. E79, 54-59.]); Artioli et al. (1997[Artioli, G., Masciocchi, N. & Galli, E. (1997). Acta Cryst. B53, 498-503.]); Parkin & Hope (1998[Parkin, S. & Hope, H. (1998). Acta Cryst. B54, 339-344.]).

Rigid-body motion and TLS analysis: Schomaker & Trueblood, 1968[Schomaker, V. & Trueblood, K. N. (1968). Acta Cryst. B24, 63-76.]; Haestier et al., 2008[Haestier, J., Sadki, M., Thompson, A. L. & Watkin, D. (2008). J. Appl. Cryst. 41, 531-536.].

Absorption correction: de Meulenaer & Tompa, 1965[Meulenaer, J. de & Tompa, H. (1965). Acta Cryst. 19, 1014-1018.]; Blessing, 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.].

Extinction correction: Darwin, 1914a[Darwin, C. G. (1914a). London, Edinb. Dubl. Philos. Mag. J. Sci. 27, 315-333.],b[Darwin, C. G. (1914b). London, Edinb. Dubl. Philos. Mag. J. Sci. 27, 675-690.]; Becker & Coppens, 1974[Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147.]; Larson, 1967[Larson, A. C. (1967). Acta Cryst. 23, 664-665.].

SQUEEZE: van der Sluis & Spek, 1990[Sluis, P. van der & Spek, A. L. (1990). Acta Cryst. A46, 194-201.]; Spek, 2015[Spek, A. L. (2015). Acta Cryst. C71, 9-18.].

Spherical scattering factor approximation: Doyle & Turner, 1968[Doyle, P. A. & Turner, P. S. (1968). Acta Cryst. A24, 390-397.]; Dawson, 1964a[Dawson, B. (1964a). Acta Cryst. 17, 990-996.],b[Dawson, B. (1964b). Acta Cryst. 17, 997-1009.]; Coppens et al., 1969[Coppens, P., Sabine, T. M., Delaplane, G. & Ibers, J. A. (1969). Acta Cryst. B25, 2451-2458.].

Multiple diffraction: Renninger, 1937[Renninger, M. (1937). Z. Phys. 106, 141-176.].

λ/2 effects: Kirschbaum et al., 1997[Kirschbaum, K., Martin, A. & Pinkerton, A. A. (1997). J. Appl. Cryst. 30, 514-516.].

Radiation damage: Abrahams, 1973[Abrahams, S. C. (1973). Acta Cryst. A29, 111-116.]; Hope, 1975[Hope, H. (1975). In Anomalous Scattering edited by S. Ramaseshan & S. C. Abrahams, Copenhagen: IUCr, Munksgaard.]; Abrahams & Marsh, 1987[Abrahams, S. C. & Marsh, P. (1987). Acta Cryst. A43, 265-269.]; Moon et al., 2011[Moon, D. K., Tripathi, A., Sullivan, D., Siegler, M. A., Parkin, S. & Posner, G. H. (2011). Bioorg. Med. Chem. Lett. 21, 2773-2775.]; Christensen et al., 2019[Christensen, J., Horton, P. N., Bury, C. S., Dickerson, J. L., Taberman, H., Garman, E. F. & Coles, S. J. (2019). IUCrJ, 6, 703-713.].

Diffuse scatter and satellite reflections: Bürgi, 2022[Bürgi, H.-B. (2022). Acta Cryst. B78, 283-289.]; Stevens, 1974[Stevens, E. D. (1974). Acta Cryst. A30, 184-189.]; Dornberger-Schiff, 1956[Dornberger-Schiff, K. (1956). Acta Cryst. 9, 593-601.]; Zachariasen, 1967[Zachariasen, W. H. (1967). Acta Cryst. 23, 44-49.]; Wagner & Schönleber, 2009[Wagner, T. & Schönleber, A. (2009). Acta Cryst. B65, 249-268.]; Petříček et al., 2014[Petříček, V., Dušek, M. & Plášil, J. (2014). Z. Kristallogr. 229, 345-352.].

Supporting information

CCDC reference: 2231833

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989023002700/dj2064sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023002700/dj2064Isup2.hkl

Background, points to consider and strategies for determining the best model. DOI: https://doi.org/10.1107/S2056989023002700/dj2064sup3.pdf

the .res file for the mono-selenide model. DOI: https://doi.org/10.1107/S2056989023002700/dj2064sup4.txt

the .res file for the di-selenide model. DOI: https://doi.org/10.1107/S2056989023002700/dj2064sup5.txt

the .res file for the free occupancy selenide model. DOI: https://doi.org/10.1107/S2056989023002700/dj2064sup6.txt

the .res file for the mixed selenide/sulfide model. DOI: https://doi.org/10.1107/S2056989023002700/dj2064sup7.txt

checkCIF report


Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: APEX2 (Bruker, 2013); data reduction: APEX2 (Bruker, 2013); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2019/2 (Sheldrick, 2015b); molecular graphics: Olex2 (Dolomanov et al., 2009; Bourhis et al., 2015), Mercury (Macrae et al., 2020), ShelXle (Hübschle et al., 2011), CrystalExplorer (Spackman et al., 2021), CrystalMaker (Palmer, 2007); software used to prepare material for publication: SHELX (Sheldrick, 2008) and publCIF (Westrip, 2010).

1,2-(Ethene-1,2-diyl)bis(diphenylphoshpine sulfide/selenide) top
Crystal data top
C26H22P2S1.13Se0.87Dx = 1.446 Mg m−3
Mr = 501.46Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, P212121Cell parameters from 9858 reflections
a = 12.2833 (2) Åθ = 3.1–72.1°
b = 13.1643 (2) ŵ = 4.32 mm−1
c = 14.2478 (2) ÅT = 173 K
V = 2303.88 (6) Å3Block, yellow
Z = 40.49 × 0.45 × 0.34 mm
F(000) = 1023
Data collection top
Bruker APEXII CCD
diffractometer		4187 independent reflections
Radiation source: microsource4155 reflections with I > 2σ(I)
Detector resolution: 7.41 pixels mm-1Rint = 0.026
φ and ω scansθmax = 72.0°, θmin = 4.6°
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)		h = −13→14
Tmin = 0.587, Tmax = 0.754k = −15→16
24246 measured reflectionsl = −17→17
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.053 w = 1/[σ2(Fo2) + (0.0259P)2 + 0.6437P]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
4187 reflectionsΔρmax = 0.25 e Å−3
279 parametersΔρmin = −0.23 e Å−3
0 restraintsAbsolute structure: Flack x determined using 1619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.018 (5)
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement progress was checked using Platon (Spek, 2020) and by an R-tensor (Parkin, 2000). The final model was further checked with the IUCr utility checkCIF.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Se10.5609 (7)0.3728 (6)0.1269 (5)0.0324 (6)0.487 (3)
S10.5543 (16)0.3748 (14)0.1378 (11)0.0324 (6)0.513 (3)
Se20.3955 (11)0.8180 (7)−0.0416 (9)0.0290 (8)0.386 (3)
S20.3917 (16)0.8053 (11)−0.0401 (14)0.0290 (8)0.614 (3)
P10.53848 (5)0.52619 (4)0.15679 (4)0.02193 (15)
P20.44544 (5)0.67007 (4)−0.07209 (4)0.02106 (15)
C10.6036 (2)0.60331 (18)0.06839 (17)0.0247 (5)
H10.6781660.6152650.0820460.030*
C20.5726 (2)0.64761 (18)−0.01138 (17)0.0238 (5)
H20.6328730.674300−0.0450920.029*
C30.6118 (2)0.56693 (18)0.26141 (17)0.0236 (5)
C40.6416 (2)0.6674 (2)0.2747 (2)0.0348 (6)
H40.6224850.7170860.2292260.042*
C50.6993 (3)0.6958 (2)0.3544 (2)0.0400 (7)
H50.7194720.7648420.3631640.048*
C60.7273 (2)0.6241 (2)0.42085 (19)0.0340 (6)
H60.7674530.6433370.4750210.041*
C70.6967 (2)0.5248 (2)0.4079 (2)0.0368 (7)
H70.7153020.4755750.4538540.044*
C80.6394 (2)0.4953 (2)0.3293 (2)0.0317 (6)
H80.6187310.4263100.3215020.038*
C90.3993 (2)0.56668 (18)0.17259 (17)0.0218 (5)
C100.3177 (2)0.4942 (2)0.17614 (18)0.0283 (6)
H100.3352740.4241960.1700700.034*
C110.2103 (2)0.5237 (2)0.1886 (2)0.0351 (6)
H110.1542010.4740940.1900520.042*
C120.1851 (2)0.6251 (2)0.1987 (2)0.0352 (6)
H120.1114750.6451330.2071030.042*
C130.2660 (2)0.6977 (2)0.1968 (2)0.0328 (6)
H130.2481080.7673970.2048460.039*
C140.3735 (2)0.6691 (2)0.18307 (18)0.0284 (6)
H140.4292570.7190550.1808300.034*
C150.4883 (2)0.65684 (19)−0.19416 (17)0.0249 (5)
C160.5588 (2)0.5791 (2)−0.22096 (19)0.0330 (6)
H160.5875850.533907−0.1752760.040*
C170.5868 (2)0.5682 (3)−0.3148 (2)0.0455 (8)
H170.6355680.515905−0.3334090.055*
C180.5438 (3)0.6331 (3)−0.3812 (2)0.0478 (8)
H180.5618130.624394−0.4454940.057*
C190.4755 (3)0.7097 (3)−0.3548 (2)0.0427 (8)
H190.4471160.754619−0.4009290.051*
C200.4470 (2)0.7225 (2)−0.26115 (19)0.0322 (6)
H200.3993830.775975−0.2432100.039*
C210.3461 (2)0.56962 (18)−0.05739 (17)0.0241 (5)
C220.3769 (2)0.46794 (19)−0.06166 (18)0.0308 (6)
H220.4517770.450049−0.0641550.037*
C230.2976 (3)0.3930 (2)−0.0622 (2)0.0379 (7)
H230.3182270.323468−0.0647790.045*
C240.1892 (3)0.4188 (2)−0.0591 (2)0.0431 (8)
H240.1353320.367069−0.0605000.052*
C250.1579 (2)0.5197 (3)−0.0541 (2)0.0434 (7)
H250.0828740.536992−0.0515750.052*
C260.2364 (2)0.5956 (2)−0.05262 (19)0.0308 (6)
H260.2153890.664886−0.0483980.037*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Se10.0372 (10)0.0261 (4)0.0338 (16)0.0063 (5)0.0091 (10)−0.0022 (9)
S10.0372 (10)0.0261 (4)0.0338 (16)0.0063 (5)0.0091 (10)−0.0022 (9)
Se20.0335 (8)0.017 (2)0.0367 (4)0.0043 (14)−0.0011 (5)−0.0014 (14)
S20.0335 (8)0.017 (2)0.0367 (4)0.0043 (14)−0.0011 (5)−0.0014 (14)
P10.0201 (3)0.0209 (3)0.0248 (3)0.0025 (2)0.0022 (2)0.0025 (2)
P20.0204 (3)0.0208 (3)0.0220 (3)0.0002 (3)0.0002 (2)0.0000 (2)
C10.0179 (11)0.0297 (13)0.0266 (12)−0.0028 (10)0.0015 (10)0.0006 (10)
C20.0188 (12)0.0270 (12)0.0257 (12)−0.0018 (9)0.0015 (9)−0.0016 (9)
C30.0199 (12)0.0272 (12)0.0238 (12)0.0052 (10)0.002 (1)0.0034 (10)
C40.0413 (16)0.0288 (13)0.0342 (14)0.0031 (12)−0.0110 (12)0.0067 (11)
C50.0461 (17)0.0342 (15)0.0397 (16)0.0021 (13)−0.0112 (14)0.0000 (13)
C60.0269 (13)0.0500 (16)0.0253 (13)0.0059 (13)−0.0039 (11)0.0015 (12)
C70.0303 (14)0.0482 (17)0.0318 (14)0.0078 (13)−0.0021 (12)0.0178 (13)
C80.0287 (14)0.0316 (13)0.0350 (14)0.0038 (11)0.0024 (12)0.0119 (11)
C90.0195 (11)0.0240 (11)0.0219 (11)0.0003 (10)0.0022 (10)0.0004 (9)
C100.0276 (13)0.0263 (13)0.0312 (13)−0.0050 (11)0.0045 (11)−0.0004 (11)
C110.0237 (13)0.0425 (16)0.0393 (16)−0.0091 (12)0.0070 (12)−0.0019 (13)
C120.0206 (13)0.0506 (16)0.0345 (14)0.0065 (13)0.0053 (11)−0.0017 (13)
C130.0298 (15)0.0299 (14)0.0387 (15)0.0083 (12)0.0024 (12)−0.0046 (11)
C140.0256 (13)0.0267 (12)0.0329 (13)−0.0022 (11)0.0002 (11)−0.0014 (11)
C150.0196 (12)0.0323 (14)0.0227 (12)−0.0076 (10)−0.0006 (9)−0.0024 (10)
C160.0255 (13)0.0417 (14)0.0318 (13)−0.0013 (13)−0.0001 (12)−0.0085 (12)
C170.0290 (16)0.064 (2)0.0436 (18)−0.0032 (15)0.0073 (13)−0.0202 (15)
C180.0373 (17)0.080 (2)0.0257 (14)−0.0235 (18)0.0070 (13)−0.0069 (15)
C190.0452 (18)0.0580 (19)0.0250 (13)−0.0177 (15)−0.0022 (13)0.0084 (13)
C200.0331 (14)0.0324 (13)0.0310 (13)−0.0065 (12)−0.0036 (13)0.0025 (11)
C210.0245 (12)0.0256 (12)0.0223 (12)−0.0031 (10)0.0015 (10)−0.001 (1)
C220.0333 (15)0.0271 (13)0.0321 (14)0.0001 (11)0.0062 (12)−0.0013 (11)
C230.0496 (18)0.0292 (14)0.0348 (15)−0.0089 (13)0.0087 (13)−0.0036 (12)
C240.0457 (18)0.0461 (17)0.0375 (16)−0.0249 (15)0.0081 (14)−0.0064 (14)
C250.0254 (14)0.0600 (19)0.0448 (17)−0.0114 (14)0.0044 (13)−0.0066 (15)
C260.0255 (13)0.0344 (14)0.0327 (14)−0.0004 (11)0.0045 (11)−0.0032 (11)
Geometric parameters (Å, º) top
Se1—P12.082 (8)C11—H110.9500
S1—P12.021 (19)C12—C131.379 (4)
Se2—P22.088 (11)C12—H120.9500
S2—P21.953 (16)C13—C141.387 (4)
P1—C11.805 (2)C13—H130.9500
P1—C91.805 (2)C14—H140.9500
P1—C31.822 (3)C15—C201.384 (4)
P2—C21.810 (2)C15—C161.394 (4)
P2—C211.812 (2)C16—C171.388 (4)
P2—C151.826 (2)C16—H160.9500
C1—C21.333 (3)C17—C181.379 (5)
C1—H10.9500C17—H170.9500
C2—H20.9500C18—C191.364 (5)
C3—C41.386 (4)C18—H180.9500
C3—C81.392 (4)C19—C201.390 (4)
C4—C51.389 (4)C19—H190.9500
C4—H40.9500C20—H200.9500
C5—C61.381 (4)C21—C261.391 (4)
C5—H50.9500C21—C221.392 (4)
C6—C71.373 (4)C22—C231.387 (4)
C6—H60.9500C22—H220.9500
C7—C81.378 (4)C23—C241.375 (5)
C7—H70.9500C23—H230.9500
C8—H80.9500C24—C251.384 (5)
C9—C101.385 (4)C24—H240.9500
C9—C141.393 (3)C25—C261.389 (4)
C10—C111.386 (4)C25—H250.9500
C10—H100.9500C26—H260.9500
C11—C121.378 (4)
C1—P1—C9109.91 (11)C12—C11—C10119.9 (3)
C1—P1—C3100.74 (12)C12—C11—H11120.0
C9—P1—C3106.22 (11)C10—C11—H11120.0
C1—P1—S1114.8 (5)C11—C12—C13120.5 (3)
C9—P1—S1113.5 (6)C11—C12—H12119.7
C3—P1—S1110.6 (6)C13—C12—H12119.7
C1—P1—Se1110.1 (2)C12—C13—C14120.0 (3)
C9—P1—Se1115.9 (2)C12—C13—H13120.0
C3—P1—Se1112.8 (2)C14—C13—H13120.0
C2—P2—C21114.01 (12)C13—C14—C9119.7 (2)
C2—P2—C15100.99 (11)C13—C14—H14120.2
C21—P2—C15103.59 (11)C9—C14—H14120.2
C2—P2—S2109.2 (6)C20—C15—C16119.8 (2)
C21—P2—S2114.3 (6)C20—C15—P2119.4 (2)
C15—P2—S2114.0 (6)C16—C15—P2120.7 (2)
C2—P2—Se2107.8 (4)C17—C16—C15119.6 (3)
C21—P2—Se2117.3 (4)C17—C16—H16120.2
C15—P2—Se2111.9 (4)C15—C16—H16120.2
C2—C1—P1135.6 (2)C18—C17—C16120.1 (3)
C2—C1—H1112.2C18—C17—H17120.0
P1—C1—H1112.2C16—C17—H17120.0
C1—C2—P2136.5 (2)C19—C18—C17120.3 (3)
C1—C2—H2111.7C19—C18—H18119.8
P2—C2—H2111.7C17—C18—H18119.8
C4—C3—C8119.1 (2)C18—C19—C20120.6 (3)
C4—C3—P1121.56 (19)C18—C19—H19119.7
C8—C3—P1119.3 (2)C20—C19—H19119.7
C3—C4—C5120.2 (3)C15—C20—C19119.6 (3)
C3—C4—H4119.9C15—C20—H20120.2
C5—C4—H4119.9C19—C20—H20120.2
C6—C5—C4120.2 (3)C26—C21—C22120.1 (2)
C6—C5—H5119.9C26—C21—P2118.59 (19)
C4—C5—H5119.9C22—C21—P2120.9 (2)
C7—C6—C5119.3 (3)C23—C22—C21119.6 (3)
C7—C6—H6120.3C23—C22—H22120.2
C5—C6—H6120.3C21—C22—H22120.2
C6—C7—C8121.2 (3)C24—C23—C22120.2 (3)
C6—C7—H7119.4C24—C23—H23119.9
C8—C7—H7119.4C22—C23—H23119.9
C7—C8—C3119.8 (3)C23—C24—C25120.5 (3)
C7—C8—H8120.1C23—C24—H24119.7
C3—C8—H8120.1C25—C24—H24119.7
C10—C9—C14119.9 (2)C24—C25—C26119.9 (3)
C10—C9—P1119.12 (19)C24—C25—H25120.1
C14—C9—P1120.98 (19)C26—C25—H25120.1
C9—C10—C11120.0 (2)C25—C26—C21119.7 (3)
C9—C10—H10120.0C25—C26—H26120.2
C11—C10—H10120.0C21—C26—H26120.2
C9—P1—C1—C2−35.3 (3)C11—C12—C13—C141.0 (4)
C3—P1—C1—C2−147.1 (3)C12—C13—C14—C9−0.9 (4)
S1—P1—C1—C294.1 (7)C10—C9—C14—C13−0.2 (4)
Se1—P1—C1—C293.6 (4)P1—C9—C14—C13−178.8 (2)
P1—C1—C2—P29.0 (5)C2—P2—C15—C20−140.0 (2)
C21—P2—C2—C1−34.1 (3)C21—P2—C15—C20101.8 (2)
C15—P2—C2—C1−144.5 (3)S2—P2—C15—C20−23.0 (7)
S2—P2—C2—C195.1 (6)Se2—P2—C15—C20−25.5 (4)
Se2—P2—C2—C198.1 (5)C2—P2—C15—C1642.5 (2)
C1—P1—C3—C438.4 (3)C21—P2—C15—C16−75.8 (2)
C9—P1—C3—C4−76.2 (2)S2—P2—C15—C16159.5 (6)
S1—P1—C3—C4160.2 (6)Se2—P2—C15—C16156.9 (4)
Se1—P1—C3—C4155.8 (3)C20—C15—C16—C17−0.1 (4)
C1—P1—C3—C8−141.1 (2)P2—C15—C16—C17177.4 (2)
C9—P1—C3—C8104.3 (2)C15—C16—C17—C18−0.9 (4)
S1—P1—C3—C8−19.3 (6)C16—C17—C18—C191.4 (5)
Se1—P1—C3—C8−23.7 (3)C17—C18—C19—C20−0.9 (5)
C8—C3—C4—C50.7 (4)C16—C15—C20—C190.6 (4)
P1—C3—C4—C5−178.8 (2)P2—C15—C20—C19−177.0 (2)
C3—C4—C5—C60.0 (5)C18—C19—C20—C150.0 (4)
C4—C5—C6—C7−0.7 (5)C2—P2—C21—C26145.1 (2)
C5—C6—C7—C80.6 (4)C15—P2—C21—C26−106.1 (2)
C6—C7—C8—C30.1 (4)S2—P2—C21—C2618.5 (7)
C4—C3—C8—C7−0.8 (4)Se2—P2—C21—C2617.7 (5)
P1—C3—C8—C7178.8 (2)C2—P2—C21—C22−42.3 (2)
C1—P1—C9—C10133.8 (2)C15—P2—C21—C2266.5 (2)
C3—P1—C9—C10−118.1 (2)S2—P2—C21—C22−168.9 (7)
S1—P1—C9—C103.7 (6)Se2—P2—C21—C22−169.7 (4)
Se1—P1—C9—C108.1 (3)C26—C21—C22—C230.8 (4)
C1—P1—C9—C14−47.5 (2)P2—C21—C22—C23−171.8 (2)
C3—P1—C9—C1460.6 (2)C21—C22—C23—C240.4 (4)
S1—P1—C9—C14−177.6 (5)C22—C23—C24—C25−0.9 (5)
Se1—P1—C9—C14−173.2 (3)C23—C24—C25—C260.4 (5)
C14—C9—C10—C111.1 (4)C24—C25—C26—C210.7 (4)
P1—C9—C10—C11179.8 (2)C22—C21—C26—C25−1.3 (4)
C9—C10—C11—C12−0.9 (4)P2—C21—C26—C25171.4 (2)
C10—C11—C12—C13−0.1 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···Se2i0.952.873.752 (13)155
C1—H1···S2i0.952.893.76 (2)153
C8—H8···Se10.952.953.443 (8)114
C8—H8···S10.952.823.325 (18)115
C10—H10···Se10.952.923.459 (8)117
C10—H10···S10.952.813.349 (19)117
C20—H20···Se20.952.933.431 (13)115
C20—H20···S20.952.923.40 (2)113
C26—H26···Se20.953.003.524 (11)117
C26—H26···S20.952.853.361 (17)115
Symmetry code: (i) x+1/2, −y+3/2, −z.
List of the top four poorly fitting reflections for the model of the mono-selenide shown in Fig. 2 top
h k lFobs2Fcalc2error/s.u.Fcalc/Fcalc(max)d–spacing (Å)
1 0 2250.916.8110.420.0126.16
0 3 21787.72504.8810.200.1013.74
2 0 3335.4441.359.520.0293.76
1 4 0671.93175.188.750.0603.18
All of the worst fitting reflections above have Fobs2 >> Fcalc2 and none would be obscured by a well-designed beamstop.
List of the top four poorly fitting reflections for the model of the di-selenide shown in Fig. 3 top
h k lFobs2Fcalc2error/s.u.Fcalc/Fcalc(max)d–spacing (Å)
1 2 014663.162109.2811.620.1815.80
4 2 01787.7213.2910.100.0142.78
0 4 3335.44114.6110.000.0422.71
0 2 0671.931634.829.550.1596.58
Three of the worst fitting reflections above have Fobs2 >> Fcalc2 and none would be obscured by a well-designed beamstop.
List of the top four poorly fitting reflections for the model of the mixed mono/di-selenide shown in Fig. 4 top
h k lFobs2Fcalc2error/s.u.Fcalc/Fcalc(max)d–spacing (Å)
6 3 0275.52151.587.710.0531.86
1 0 2344.63207.437.690.0626.16
0 0 2118.7064.075.830.0347.12
0 2 120.033.695.550.0085.98
There are no egregious Fobs2 vs Fcalc2 mis-matches for this model.
List of the top four poorly fitting reflections for the model of the di-selenide shown in Fig. 5 top
h k lFobs2Fcalc2error/s.u.Fcalc/Fcalc(max)d–spacing (Å)
6 3 0270.87165.417.110.0551.86
0 8 0301.14215.465.070.0631.65
0 6 2784.43965.404.860.1332.10
2 5 157.9029.404.800.0232.39
There are no egregious Fobs2 vs Fcalc2 misfits for this model.
C—H···chalcogen close-contact geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C1—H1···Se2i0.952.873.752 (13)155.1
C1—H1···S2i0.952.893.76 (2)153.4
C8—H8···Se10.952.953.443 (8)113.8
C8—H8···S10.952.823.325 (18)114.5
C10—H10···Se10.952.923.459 (8)117.4
C10—H10···S10.952.813.349 (19)117.2
C20—H20···Se20.952.933.431 (13)114.5
C20—H20···S20.952.923.40 (2)112.6
C26—H26···Se20.953.003.524 (11)116.6
C26—H26···S20.952.853.361 (17)114.8
Symmetry code: (i) x + 1/2, -y + 3/2, -z.
 

Acknowledgements

We are grateful to the GVSU Chemistry Department Weldon Fund for support of this work. The CCD-based X-ray diffractometers at Michigan State University were upgraded and/or replaced using departmental funds.

Funding information

Funding for this research was provided by: NSF (RUI CHE-2102576) to SB at GVSU) and GVSU CSCE Research Grant-in-Aid to B. Rawls.

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Volume 79| Part 4| April 2023| Pages 246-253
https://doi.org/10.1107/S2056989023002700
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