research papers
Conformational flexibility in amidophosphoesters: a CSD analysis completed with two new crystal structures of (C6H5O)2P(O)X [X = NHC7H13 and N(CH2C6H5)2]
aDepartment of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran, bDepartment of Atomic and Molecular Physics, Centre for Applied Nanosciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104, India, cDepartment of Chemistry, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic, dInstitut Européen des Membranes, Université de Montpellier, 34095 Montpellier, France, and eDepartment of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
*Correspondence e-mail: pourayoubi@um.ac.ir, abdul.ajees@manipal.edu
The crystal structures of diphenyl (cycloheptylamido)phosphate, C19H24NO3P or (C6H5O)2P(O)(NHC7H13), (I), and diphenyl (dibenzylamido)phosphate, C26H24NO3P or (C6H5O)2P(O)[N(CH2C6H5)2], (II), are reported. The NHC7H13 group in (I) provides two significant hydrogen-donor sites in N—H⋯O and C—H⋯O hydrogen bonds, needed for a one-dimensional hydrogen-bond pattern along [100] in the crystal, while (II), with a (C6H5CH2)2N moiety, lacks these hydrogen bonds, but its three-dimensional supramolecular structure is mediated by C—H⋯π interactions. The conformational behaviour of the phenyl rings in (I), (II) and analogous structures from the Cambridge Structural Database (CSD) were studied in terms of flexibility, volume of the other group attached to phosphorus and packing forces. From this study, synclinal (±sc), anticlinal (±ac) and antiperiplanar (±ap) conformations were found to occur. In the structure of (II), there is an intramolecular Cortho—H⋯O interaction that imposes a +sc conformation for the phenyl ring involved. For the structures from the CSD, the +sc and ±ap conformations appear to be mainly imposed by similar Cortho—H⋯O intramolecular interactions. The large contribution of the C⋯H/H⋯C contacts (32.3%) in the two-dimensional fingerprint plots of (II) is a result of the C—H⋯π interactions. The (DSC) analyses exhibit peak temperatures (Tm) at 109 and 81 °C for (I) and (II), respectively, which agree with the strengths of the intermolecular contacts and the melting points.
1. Introduction
Conformational studies are of great interest not only due to their importance in biological systems and drug design but also for purely scientific considerations, such as the study of nonrigid segments in the solid state and in solution (Mattern et al., 2000; Hopfinger & Battershell, 1976; Fang et al., 2014; Gholivand & Pourayoubi, 2004). The relationship between conformational behaviour and molecular packing has been extensively studied, and there are many examples of conformations imposed by intra- and intermolecular interactions and conformational preferences, typically in organotin systems (Buntine et al., 1998), and acids (Dauber & Hagler, 1980) and polypeptide chains (Gregoret & Cohen, 1991). The effect of conformational flexibility on the existence of two (or more) symmetry-independent molecules in the crystal, disordered structures and the formation of polymorphs were also studied (Toghraee et al., 2011; Keikha et al., 2017; Vahdani Alviri et al., 2018; Bernstein & Hagler, 1978).
The Cambridge Structural Database (CSD; Version 5.40, updated to November 2018; Groom et al., 2016) provides the opportunity to study conformational behaviour in analogous structures; in some recently published articles, we investigated conformational changes, typically in P(O)NHC(O)-based structures (Toghraee et al., 2011; Vahdani Alviri et al., 2018) and phosphate salts (Moghaddam et al., 2019), where, for example, the orientation of P(O) versus C(O) groups, the ring conformations of four-, five-, six- and seven-membered aliphatic rings, and the conformational flexibility of aliphatic and aromatic rings with respect to the other segments in the molecule/salt were considered.
With this background in mind, we present here the synthesis, 6H5O)2P(O) fragment and different in the type of amine fragment attached to phosphorus, in order to study conformational changes driven by the substituent effect and packing forces made by classical and/or nonclassical hydrogen bonds. The compounds are (C6H5O)2P(O)(NHC7H13), (I), and (C6H5O)2P(O)[N(CH2C6H5)2], (II) (see Scheme). The conformational flexibilities of the rings in (I) and (II), and analogous structures deposited in the CSD were investigated. The Hirshfeld surfaces, electrostatic energy frameworks and DSC analyses also detailed in this article.
and spectroscopic characterization of two amidophosphoesters with the same (C2. Experimental
Previous articles have described the synthesis of compounds (I) and (II) from the reaction between diphenylphosphoryl chloride and cycloheptylamine in the presence of neutral alumina (Al2O3) for (I) and from the reaction of [DBNP(O)(OPh)2]PF6 (DBN = N-acyl-1,5-diazabicyclo[4.3.0]non-5-ene) and dibenzylamine in CH3CN medium for (II). Melting points, selected IR bands and mass peaks for both (I) and (II), and 31P and 1H NMR data for (I) in CDCl3, and 31P, 1H and 13C NMR data for (II) in acetone-d6 were reported (Gupta et al., 2005, 2007; Jones et al., 2016). Here we report the single-crystal X-ray and some complementary spectroscopic features for (I) and (II). The NMR experiments were studied again in a different solvent (i.e. DMSO-d6).
2.1. Synthesis
2.1.1. Synthesis of (C6H5O)2P(O)(NHC7H13), (I)
Compound (I) was prepared from the reaction of diphenylphosphoryl chloride and cycloheptylamine (1:2 molar ratio, reaction time 4 h, ice-bath temperature) in dry CHCl3. The solvent was removed in a vacuum and the solid which formed was washed with distilled water. Colourless single crystals suitable for X-ray analysis were obtained at room temperature from a mixture of CH3OH and CHCl3 (4:1 v/v).
Analytical data: colourless prism-shaped crystal; m.p. 109 °C. IR (KBr, cm−1): 3240, 3052, 2918, 2860, 1591, 1488, 1317, 1242, 1196, 1162, 1075, 1013, 929, 894, 826, 779, 744, 686, 651. 31P{1H} NMR (243 MHz, DMSO-d6): δ −0.41. 1H NMR (601 MHz, DMSO-d6): δ 1.25–1.33 (m, 2H), 1.35–1.45 (m, 4H), 1.45–1.56 (m, 4H), 1.67–1.75 (m, 2H), 3.19–3.29 (m, 1H), 5.80 (dd, J = 13.7, 9.7 Hz, 1H, NH), 7.19 (t, J = 7.4 Hz, 2H), 7.21–7.25 (m, 4H), 7.36–7.42 (m, 4H). 13C{1H} NMR (151 MHz, DMSO-d6): δ 23.20, 27.61, 36.71 (d, J = 5.3 Hz), 52.84, 120.12 (d, J = 4.9 Hz), 124.62, 129.71, 150.79 (d, J = 6.4 Hz). MS (70 eV, EI): m/z (%) = 345 (2) [M]+, 344 (18) [M − 1]+, 286 (100) [M − C4H10 − H]+, 248 (56) [M − C7H13]+.
2.1.2. Synthesis of (C6H5O)2P(O)[N(CH2C6H5)2], (II)
Compound (II) was prepared from the reaction of diphenylphosphoryl chloride and dibenzylamine (1:2 molar ratio, reaction time 4 h, ice-bath temperature) in dry CHCl3. The solvent was removed in a vacuum and the solid which formed was washed with distilled water. Colourless single crystals suitable for X-ray analysis were obtained at room temperature from a mixture of CHCl3 and CH3CN (4:1 v/v).
Analytical data: colourless block-shaped crystal; m.p. 81 °C. IR (KBr, cm−1): 3434, 2999, 2790, 2630, 2483, 1745, 1629, 1592, 1490, 1454, 1369, 1244, 1210, 1099, 1017, 915, 751, 692. 31P{1H} NMR (122 MHz, DMSO-d6): δ −11.63. 1H NMR (301 MHz, DMSO-d6): δ 4.10 (m, 4H, CH2), 6.98–7.03 (m, 2H), 7.15–7.18 (m, 4H), 7.22–7.29 (m, 4H), 7.39–7.40 (m, 2H), 7.40–7.43 (m, 4H), 7.50–7.54 (m, 4H). 13C{1H} NMR (76 MHz, DMSO-d6): δ 50.35, 120.38 (d, J = 5.3 Hz), 122.66, 129.07, 129.34, 129.43, 130.52, 132.36, 154.05 (d, J = 6.8 Hz). MS (70 eV, EI): m/z (%) = 430 (54) [M + 1]+, 429 (52) [M]+, 428 (23) [M − 1]+, 336 (100) [M − OPh]+, 243 (36) [M − 2 OPh]+, 91 (95) [C7H7]+.
2.2. Refinement
Crystal data, data collection, and structure . The ab initio iterative charge-flipping method was used to solve the of (I); the parameters are described elsewhere (van der Lee, 2013). For both (I) and (II), all carbon-bound H atoms were placed at calculated positions and refined as riding, with Uiso(H) values set at 1.2Ueq of the respective carrier atoms. However, the position of atom H171 was refined with a soft distance and two angle restraints with respect to the parent N17 atom. All soft restraints used in these refinements have been described by Waser (1963) and Rollet (1965). The (s.u.) used for the N—H distance restraint was 0.02 Å and for the two angle restraints was 2°. The structure of (I) was refined in the Pn21a as an the structure solution in the centrosymmetric Pnma was investigated but was found to be much more disordered with respect to the cycloheptane ring than the model in Pn21a. The latter model is, however, not completely free from disorder, as is shown in the displacement ellipsoid plot (Fig. 1). A model with the cycloheptane ring disordered over two distinct positions was not significantly better than the model shown in Fig. 1, so the undisordered model was preferred, using some soft distance restraints (with an s.u. of 0.01 Å), as well as restraints on the atomic displacement parameters for the atoms in the cycloheptane ring. The s.u. values for the vibration restraints were taken between 0.001 and 0.005 Å2, and for the thermal similarity restraints between 0.01 and 0.02 Å2. The Flack (1983) parameter refined to 0.6 (3) and an a posteriori Hooft analysis based on estimation and Bayesian statistics gave a probability of the chance of having a racemic twin of 99.86%, with a Hooft parameter of 0.6 (1) (Hooft et al., 2008).
details are summarized in Table 13. Results and discussion
3.1. Structural description
The asymmetric units of amidophosphoesters (C6H5O)2P(O)(NHC7H13), (I), and (C6H5O)2P(O)[N(CH2C6H5)2], (II), consist of one complete molecule (Figs. 1 and 2). Selected geometric parameters and hydrogen-bond geometries of (I) and (II) are presented in Tables 2–5. In both structures, the P atoms are within a distorted tetrahedral (O)2(N)P(O) environment, with the angles at the P atoms ranging from 93.42 (10) to 115.5 (3)° for (I) and from 97.78 (5) to 116.27 (5)° for (II). The extreme values correspond to the O2—P1—O10 and O9—P1—O10 angles for (I), and the O2—P1—O3 and O1—P1—O3 angles for (II). The sum of the surrounding angles at the N atom, i.e. C—N—P + P—N—H + H—N—C for (I), shows a difference of about 2.5° with respect to the bond-angle sum for ideal sp2 (360°), while the bond-angle sum of 2 × P—N—C + C—N—C for (II) shows a practically planar environment at the N atom.
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The P=O bond lengths [1.4645 (18) Å for (I) and 1.4578 (10) Å for (II)] are comparable to those in analogous compounds (Sabbaghi et al., 2019) and are slightly longer than the normal P=O double-bond length (1.45 Å; Corbridge, 1995). The P—N bond lengths [1.607 (2) Å for (I) and 1.6232 (11) Å for (II)] are standard for structures with an (O)2P(O)(N) skeleton (Sabbaghi et al., 2019) and are smaller than a typical P—N single-bond length (Corbridge, 1995).
The P—O—C bond angles are 120.7 (3) (P1—O2—C3) and 119.7 (3)° (P1—O10—C11) in (I), and 122.79 (8) (C1—O2—P1) and 119.73 (8)° (C7—O3—P1) in (II) indicate an sp2-hybridization state for the O atoms, similar to the P—O—C angles in analogous structures with similar P(Y)(O–C)2(N) (Y = O and S) skeletons (Sabbaghi et al., 2016).
The similar torsion angles describing the environment around the P—N unit are close to each other for the two compounds. Thus, the O9—P1—N17—C18 torsion angle [0.96 (7)°] in (I) is close to the O1—P1—N1—C13 torsion angle [−4.83 (12)°] in (II) and, similarly, O2—P1—N17—C18 [129.9 (5)°] and O10—P1—N17—C18 [−129.4 (5)°] of (I) are close to the O2—P1—N1—C13 [122.07 (10)°] and O3—P1—N1—C13 [−134.84 (10)°] torsion angles of (II), respectively. In addition to these, the O9—P1—N17—H171 (162.39°), O2—P1—N17—H171 (−68.65°) and O10—P1—N17—H171 (32.05°) torsion angles of (I) have values close to the O1—P1—N1—C20 [173.29 (10)°], O2—P1—N1—C20 [−59.82 (11)°] and O3—P1—N1—C20 [43.28 (11)°] torsion angles of (II), respectively. On the other hand, the C20 atom of (II) occupies the equivalent position to the H171 atom of (I).
In the next section, the conformations of the phenyl rings in (I) and (II) and the varieties of conformations observed in analogous structures available in the CSD are investigated in order to depict a comparative study and understand the effects of substitution and packing forces on the conformations of the phenyl rings.
3.2. CSD analysis
3.2.1. Comparative studies with analogous compounds available in the CSD
The bond lengths of the 162 molecules obtained from the CSD were extracted (see Table S1 in the supporting information) and the averages of the bond lengths were compared with similar bond lengths in title compounds (I) and (II) (Fig. 3a). The bond lengths of (I) and (II) match with each other, as well as with the calculated averages (Fig. 3a). Slight but not significant variations are observed for (I) with respect to the C3—C4, C3—C8, C11—C12 and C11—C16 bonds, and all other bond lengths match with the standard deviations of the average values. In terms of bond angles, six were measured at the P atom and the data are listed in Table S2 in the supporting information. The averages of the bond angles calculated from the CSD structures are highly correlated with the title compounds, except for O2—P1—O10 of (I), which is smaller than all the other bond angles (Fig. 3b), due to the effect of the neighbouring bulky cycloheptyl ring. A comparative analysis of torsion angles/conformations was also provided which will be discussed in the next section (Fig. 3c and Table S3 in the supporting information).
Compounds (I) and (II) were superimposed with eight atoms constituting the (CCO)(O)P(O)(NC) skeleton [i.e. O2, P1, O9, O10, N17, C11, C16, and C18 of (I), and O2, P1, O1, O3, N1, C7, C12 and C13 of (II)], with an r.m.s. deviation of 0.08 Å. Phenyl rings C11–C16 of (I) and C7–C12 of (II) adopt a similar antiperiplanar (ap) conformation with a slight difference in the orientation [−ap for (I) and +ap for (II)]. The conformation is considered based on the C—O—P—O torsion angle and the angles ranging from ±150 to 180° denote an ±ap conformation. The seven-membered ring (atoms C18–C24) of (I) is closely aligned with the C14–C19 phenyl ring of (II) (Fig. 4). From the viewpoint of conformational changes, the significant difference between the two compounds arises due to the bulky C21–C26 phenyl-ring substituent at the N atom in (II). To accommodate this phenyl ring, another phenyl ring (C1–C6) rotates away and adopts a synclinal position (+sc), compared with an −ap orientation for the corresponding phenyl ring in (I). The distances between the rings are gathered in Table S4 of the supporting information. In (I), the seven-membered ring is located between the phenyl rings at almost equal distances from both, viz. 5.94 Å from phenyl ring C3–C8 and 5.71 Å from phenyl ring C11–C16 (see Fig. 4 and Table S4 in the supporting information).
3.2.2. The phenyl-ring conformations
In the previous section, the −ap conformation for phenyl rings 1 (atoms C3–C8) and 2 (C11–C16) of (I), and the +sc and +ap conformations, respectively, for phenyl rings 1 (C1–C6) and 2 (C7–C12) of (II) were introduced. Based on the torsion angles, the 162 molecules extracted from the CSD are divided into 22 groups. The −ap and +ap conformations are consistent with a trans orientation, so they can be combined together for a comparative study (Fig. 3c). From Fig. 3(c) and Table S3 in the supporting information, it is evident that 32 structures adopt +sc and ±ap conformations, and 46 structures adopt ±ap and ±ap conformations. Fig. 5(a) shows the superposition of the CSD structures corresponding to (I) and (II) with the structures of the title structures.
In (I), the angle between the planes of the phenyl rings is 26.1 (3)° and the torsion angles of −178.2 (4)° for C3—O2—P1—O10 and −179.7 (4)° for C11—O10—P1—O2 define the −ap conformation for phenyl rings 1 and 2, as noted. The 14 molecules ZIFYIW-Mol1 (Aparna et al., 1995), LEQRIK01-Mol2 (Gholivand et al., 2013), YEVSAT (Herrmann et al., 1994), FIBROY-Mol1 (Gholivand et al., 2005), OFESEZ-Mol2 (Safin et al., 2013), BIFYUN (Das et al., 2018), BIFXIA-Mol1 (Das et al., 2018), BOGPOC (Drewelies & Pritzkow, 1982), UREDUR-Mol1 (Sabbaghi et al., 2011b), KAVVAE-Mol1 (Zák et al., 1989), SOYCUE-Mol1 (Richter et al., 1991), SOYCUE-Mol2 (Richter et al., 1991), OFESAV-Mol1 (Safin et al., 2013) and WIBKUN-Mol1 (Rebrova et al., 1993) adopt a similar conformation (−ap and −ap) and their phenyl rings are similar to those in (I) (Fig. 5b and Table S3 in the supporting information). There are slight variations in some structures due to torsion-angle variations and bulk substitution in the phenyl rings or at the N atom, which are common and have been observed in previously reported structures (Simon et al., 2017). For example, YEVSAT and FIBROY-Mol1 have methyl substitution at the 4-position in the phenyl rings. Due to this effect, the phenyl rings are slightly disoriented with respect to the other structures. Similarly, UREDUR-Mol1 and FIBROY-Mol1 have a bulky phenyl group attached at an N-atom position and, due to this substitution, the phenyl rings are slightly twisted in comparison with the other structures.
As was discussed earlier, the ±ap conformations adopt a similar trans orientation. For example, OFESAV-Mol1 adopts −ap and −ap conformations, and OFESAV-Mol2 adopts +ap and +ap conformations, and both molecules are perfectly aligned with each other, as well as with compound (I). Similarly, KAVVAE-Mol1 (−ap/−ap), KAVVAE-Mol2 (+ap/+ap), LEQRIK01-Mol1 (+ap/+ap), LEQRIK01-Mol2 (−ap/−ap), SOYCUE-Mol1 (−ap/−ap), SOYCUE-Mol2 (−ap/−ap), WIBKUN-Mol1 (−ap/−ap) and WIBKUN-Mol2 (+ap/+ap), which adopt ±ap conformations, also fit well with (I) (Fig. 5c).
In (II), the planes of the phenyl rings make a dihedral angle of 59.40 (5)°, which is ∼33° greater than the corresponding angle in (I). There are 11 molecules in the CSD with conformations like those observed in (II) (i.e. +sc and +ap). These are WEWVUP (Allcock et al., 1994), WIHPIM (Balakrishna et al., 1994), UCOHID (Necas et al., 2001), UCOFOH-Mol1 (Necas et al., 2001), NOKHOL (Endeshaw et al., 2008), XABSEZ (Rybarczyk-Pirek et al., 2002a), OVUXAF-Mol2 (Chandrasekaran et al., 2011), MOPMIN (Rybarczyk-Pirek et al., 2002b), UCOHAV-Mol3 (Necas et al., 2001), NACJOR (Cadierno et al., 2004a) and BACVEH-Mol1 (Du et al., 2001), and there is no remarkable difference between these 11 molecules and (II).
Due to the similar orientation of the ±ap conformation, the +sc and −ap conformations are also aligned well with compound (II). There are 21 structures which adopt +sc and −ap conformations (Table S3 in the supporting information). For example, AFASIK (Krishna et al., 2007), VIDYUC (Ammon et al., 1991) and KABZIW (Attanasi et al., 1988) can also be superimposed with compound (II), and all are perfectly aligned with (II) (Fig. 5d). From the CSD comparison results, a trans (±ap) conformation is one of the preferred conformations for the two phenyl rings in molecules with the P(O)(OPh)2N skeleton. Out of 162 molecules, 46 molecules adopt ±ap/±ap conformations, which are similar to compound (I) (Fig. 3c). Similarly, 32 molecules adopt sc and ±ap conformations, which are similar to compound (II). The next most frequent conformations (25 molecules) are ±ap and −sc, which are the preferred alternative conformations similar to compound (II). Thus, for 124 out of 162 molecules either both phenyl rings or one of the phenyl rings adopts a trans conformation (Fig. 3c and Table S3 in the supporting information).
3.2.3. Intra- and intermolecular interactions
In the crystal of (I), adjacent molecules are linked through moderate N—H⋯O and weak C—H⋯O intermolecular hydrogen bonds, forming a linear arrangement along the a axis (Fig. 6a). The NHC7H13 group provides the two donor sites needed for these two hydrogen bonds. Compound (II) lacks an N—H group and a seven-membered ring, which prevents the formation of similar hydrogen bonds, except for the C6—H6A⋯O1 intramolecular hydrogen bond with an angle of 125°. This structure possesses more phenyl rings than that of (I), and its three-dimensional (3D) supramolecular assembly is built from C—H⋯π interactions (Table 5). Fig. 6(b) shows a view of the crystal packing in the structure of (II).
It is quite interesting that the recently published structure of diphenylcyclohexyl aminophosphonate (CSD refcodes BIFXIA and BIFYUN) is the closest structure to (I). The reference structure (Das et al., 2018) has a six-membered ring attached to the N atom, while compound (I) has a seven-membered ring. Both structures can be superimposed well, and the H atom attached to the N atom is oriented on the same side (Fig. 6c). The N—H⋯O hydrogen-bond pattern and the molecular packing of BIFYUN resemble those in compound (I) (Fig. 6d).
Another feature of the intramolecular interactions is related to the phenyl-ring conformation (with the assistance of the bulk effect, which was discussed previously). In the structure of (II), the phenyl ring with the +sc conformation is the one involved in intramolecular C—H⋯O hydrogen bonding. A CSD survey reveals that it is quite common that the O atom of the P=O group is involved in intramolecular C—H⋯O interactions with one of the phenyl rings when it adopts an +sc or ±ap conformation. For example, the typical structures with the CSD refcodes XABSEZ, UCOHAV-Mol3, QABZIF (Warren et al., 2016), IYAMEA-Mol1 (Cadierno et al., 2004b) and EROJAX (Sabbaghi et al., 2011a) form intramolecular C—H⋯O=P hydrogen bonds with an angle of ∼125°.
The hydrogen-bond network of (I) includes R21(7) and C(4) graph-set motifs, as shown in Fig. 7 (for graph-set notation, see Bernstein et al., 1995).
3.3. Hirshfeld surface analysis
3.3.1. Hirshfeld surface maps and fingerprint plots
The intermolecular interactions of (I) and (II) were further studied by Hirshfeld surface (HS) analysis, including 3D HS maps, two-dimensional (2D) fingerprint (FP) plots and electrostatic energy frameworks. The HSs mapped with dnorm and the corresponding shape-index-associated 2D FP plots of (I) and (II) were generated using the CrystalExplorer software (Version 3.1; Wolff et al., 2013), and the corresponding CIFs were used as the input files (Figs. 8 and 9). In the HS of (I), the N—H⋯O=P and C—H⋯O=P hydrogen bonds appear as large (label 1) and small (label 2) red areas (Fig. 8a), and in the HS of (II), the small and pale-red areas are related to C—H⋯π interactions (Fig. 9a). It should be noted that in the HS maps, the contacts shown in red highlight intermolecular interactions with distances shorter than the sum of the van der Waals radii (McKinnon et al., 2007).
Figs. 8(b)–(i) and 9(b)–(i) illustrate the FPs for (I) and (II), respectively. For both structures, the H⋯H contacts represent the largest relative contribution [66.3% for (I) (Fig. 8f) and 58.4% for (II) (Fig. 9f)], with one sharp spike for structure (I) (the shortest de = di ≃ 1.1 Å). The other interactions are O⋯H/H⋯O, C⋯H/H⋯C and C⋯C for both structures, and O⋯C/C⋯O and N⋯H/H⋯N for (II), with the percentages of contributions as given in the figures. It should be noted that the relatively large contribution of the C⋯H/H⋯C contacts (32.3%) (Fig. 9g) in (II) is a result of the presence of C—H⋯π interactions.
3.3.2. Energy frameworks
In order to better understand the crystal packing and visualize the interaction topologies of (I) and (II), an energy framework analysis was carried out using CrystalExplorer software (Thomas et al., 2018). The electrostatic, polarization, dispersion and exchange–repulsion energies of the interactions between the molecules are calculated for (I) (Fig. 10 and Table S5 in the supporting information) and (II) (Fig. 11 and Table S6 in the supporting information) using B3LYP/6-31G(d,p) electron-density functions. The energies between molecular pairs are represented as cylinders (scale size of 150) by joining the centroids of pairs of molecules. The energy frameworks for Eele (Figs. 10d–f), Edisp (Figs. 10g–i) and Etot (Figs. 10j–l) are shown in red, green and blue, respectively, for (I). Similarly, the energy frameworks for Eele (Figs. 11d–f), Edisp (Figs. 11g–i) and Etot (Figs. 11j–l) are shown for (II). The largest pairwise energies calculated are −89.9 (Table S5 in the supporting information) and −47.3 kJ mol−1 (Table S6 in the supporting information) for (I) and (II), respectively. In both structures, the energy distribution patterns are different. The energy frameworks for (I) form zigzag molecular sheets and for (II) form parallel sheets. However, the dispersion energies outweigh the electrostatic energies in all cases. In general, (I) has higher electrostatic energies than (II), which is visually evident from Figs. 10 and 11, and the 3D network topologies confirmed the significant contribution of the N—H⋯O and C—H⋯O interactions in (I), and the C—H⋯π interactions in (II). It should be noted that the energies can be affected by conformational changes, similar to what was observed for the relationship of the C6H5O segments in (I) and (II), which show the absence of C—H⋯π interactions in (I) but their presence in (II).
3.4. CSD data set
176 structures containing the P(O)(OPh)2N skeleton were extracted from the CSD. Of these structures, 58 were rejected due to the non-availability of 3D coordinates, disordered phenyl rings or both phenyl rings being fused via a single bond or the P=O group fused to other moieties. In the remaining 118 structures, some contain more than one molecule in the In total, 162 molecules from the 118 CSD structures were used for a comparative study with the title compounds (I) and (II). The figures were rendered using PyMOL (Schrödinger, 2015).
3.5. DSC study
The thermal properties of the two title structures were studied by (a) and 12(b) are at 109 and 81 °C for (I) and (II), respectively, and correspond to the melting of the compounds. The higher melting point of (I) can be directly correlated to the greater strength of the intermolecular contacts with respect to (II), as was discussed in the X-ray crystallography (§3.1) and energy framework (§3.3.2) sections. Furthermore, the thermal nature of the crystal is expected to be related to the flexibility of the molecule. The Hirshfeld rigid-bond test was also conducted for (I) and (II) (Hirshfeld, 1976) in order to understand the flexible natures of the structures. According to the rigid-bond test, the mean-squared displacement amplitudes do not show any significant bond deviation within 5.0 σ for both structures, except for three bonds of (I), namely P1—O2 (5.2 σ), C3—C4 (5.2 σ) and C11—C16 (6.0 σ), which show slight differences. In fact, this result is consistent with the CSD data, and these bond lengths vary slightly from the average obtained from the CSD data and the structure of (II) (Fig. 3a and Section §3.2.1). In any case, it is likely that there is conformational flexibility for these two structures and this is consistent with the CSD, Hirshfeld rigid-bond and energy framework studies.
(DSC) analysis. The peaks in the DSC plots in Figs. 12Supporting information
https://doi.org/10.1107/S2053229619016619/yo3071sup1.cif
contains datablocks I, II, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2053229619016619/yo3071Isup2.hkl
Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2053229619016619/yo3071IIsup3.hkl
Details and results of the CSD search. DOI: https://doi.org/10.1107/S2053229619016619/yo3071sup4.pdf
Data collection: CrysAlis PRO (Rigaku OD, 2015) for (I); Rigaku CrystalClear-SM Expert (Rigaku, 2011) for (II). For both structures, cell
CrysAlis PRO (Rigaku OD, 2015); data reduction: CrysAlis PRO (Rigaku OD, 2015). Program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007) for (I); SHELXT2014 (Sheldrick, 2015a) for (II). Program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003) for (I); SHELXL2018 (Sheldrick, 2015b) for (II). For both structures, molecular graphics: CAMERON (Watkin et al., 1996) and pyMOL (Schrödinger, 2015). Software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003) for (I); SHELXL2018 (Sheldrick, 2015b) for (II).C19H24NO3P | F(000) = 736 |
Mr = 345.36 | Dx = 1.295 Mg m−3 |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 3874 reflections |
a = 9.3538 (2) Å | θ = 2.1–27.1° |
b = 9.7899 (3) Å | µ = 0.17 mm−1 |
c = 19.3432 (5) Å | T = 175 K |
V = 1771.31 (5) Å3 | Prism, colourless |
Z = 4 | 0.35 × 0.25 × 0.15 mm |
Rigaku Xcalibur Sapphire3 Gemini diffractometer | 3411 independent reflections |
Graphite monochromator | 2964 reflections with I > 2.0σ(I) |
Detector resolution: 16.0143 pixels mm-1 | Rint = 0.035 |
ω scans | θmax = 28.0°, θmin = 2.1° |
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2015) | h = −7→12 |
Tmin = 0.979, Tmax = 1.000 | k = −9→11 |
9026 measured reflections | l = −23→23 |
Refinement on F2 | Hydrogen site location: difference Fourier map |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.052 | Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)] where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 19.6 25.7 7.98 |
wR(F2) = 0.103 | (Δ/σ)max = 0.001 |
S = 0.95 | Δρmax = 0.32 e Å−3 |
3338 reflections | Δρmin = −0.54 e Å−3 |
221 parameters | Absolute structure: Flack (1983), 1505 Friedel-pairs |
79 restraints | Absolute structure parameter: 0.6 (3) |
Primary atom site location: iterative |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier & Glazer, 1986) with a nominal stability of 0.1K. Cosier, J. & Glazer, A.M., 1986. J. Appl. Cryst. 105-107. |
Refinement. Data collection and crystal screening for (I) was performed on a Rigaku Oxford-Diffraction Gemini-S diffractometer with sealed-tube Mo-Kα radiation using the CrysAlisPro program (Rigaku Oxford-Diffraction, 2012). This program was also used for the integration of the data using default parameters, for the empirical absorption correction using spherical harmonics employing symmetry-equivalent and redundant data, and the correction for Lorentz and polarization effects. The ab-initio iterative charge flipping method was used to solve the crystal structure of (I) with parameters described elsewhere (van der Lee, 2013) employing the Superflip program (Palatinus&Chapuis, 2007) and it was refined using full-matrix least-squares procedures on squared structure factor amplitudes F2 as implemented in CRYSTALS (Betteridge et al., 2003) using all independent reflections with I>0. |
x | y | z | Uiso*/Ueq | ||
P1 | 0.35676 (6) | 0.84662 (6) | 0.00163 (13) | 0.0183 | |
O2 | 0.4415 (4) | 0.9225 (3) | 0.06247 (18) | 0.0205 | |
C3 | 0.4113 (6) | 0.8932 (5) | 0.1321 (3) | 0.0257 | |
C4 | 0.4887 (6) | 0.7907 (5) | 0.1653 (2) | 0.0305 | |
C5 | 0.4633 (8) | 0.7722 (6) | 0.2345 (3) | 0.0433 | |
C6 | 0.3634 (7) | 0.8486 (7) | 0.2706 (3) | 0.0431 | |
C7 | 0.2905 (8) | 0.9495 (7) | 0.2365 (3) | 0.0406 | |
C8 | 0.3173 (7) | 0.9711 (6) | 0.1665 (3) | 0.0333 | |
H81 | 0.2689 | 1.0405 | 0.1435 | 0.0500* | |
H71 | 0.2237 | 1.0015 | 0.2605 | 0.0500* | |
H61 | 0.3472 | 0.8316 | 0.3172 | 0.0500* | |
H51 | 0.5151 | 0.7058 | 0.2580 | 0.0500* | |
H41 | 0.5550 | 0.7374 | 0.1417 | 0.0500* | |
O9 | 0.20228 (18) | 0.87095 (18) | 0.0010 (3) | 0.0275 | |
O10 | 0.4444 (4) | 0.9209 (4) | −0.0573 (2) | 0.0288 | |
C11 | 0.4140 (5) | 0.8929 (5) | −0.1266 (3) | 0.0223 | |
C12 | 0.3098 (6) | 0.9729 (6) | −0.1603 (3) | 0.0323 | |
C13 | 0.2900 (8) | 0.9499 (8) | −0.2298 (3) | 0.0459 | |
C14 | 0.3672 (7) | 0.8504 (7) | −0.2635 (4) | 0.0488 | |
C15 | 0.4657 (7) | 0.7703 (7) | −0.2302 (3) | 0.0420 | |
C16 | 0.4909 (7) | 0.7958 (6) | −0.1596 (2) | 0.0358 | |
H161 | 0.5592 | 0.7455 | −0.1357 | 0.0500* | |
H151 | 0.5141 | 0.7017 | −0.2538 | 0.0500* | |
H141 | 0.3519 | 0.8376 | −0.3106 | 0.0500* | |
H131 | 0.2239 | 1.0023 | −0.2540 | 0.0500* | |
N17 | 0.3982 (2) | 0.6874 (2) | 0.0026 (3) | 0.0213 | |
C18 | 0.2936 (3) | 0.5742 (2) | 0.0018 (3) | 0.0232 | |
C19 | 0.3086 (7) | 0.4933 (6) | 0.0682 (3) | 0.0425 | |
C20 | 0.4369 (7) | 0.3947 (6) | 0.0702 (3) | 0.0671 | |
C21 | 0.4344 (6) | 0.2720 (4) | 0.0185 (3) | 0.0809 | |
C22 | 0.4727 (8) | 0.2979 (6) | −0.0558 (3) | 0.0828 | |
C23 | 0.4388 (6) | 0.4358 (5) | −0.0842 (3) | 0.0460 | |
C24 | 0.2980 (6) | 0.4913 (5) | −0.0638 (3) | 0.0330 | |
H241 | 0.2705 | 0.5513 | −0.1015 | 0.0500* | |
H242 | 0.2268 | 0.4196 | −0.0609 | 0.0500* | |
H231 | 0.4456 | 0.4317 | −0.1342 | 0.0500* | |
H232 | 0.5135 | 0.4971 | −0.0684 | 0.0500* | |
H191 | 0.2225 | 0.4394 | 0.0742 | 0.0500* | |
H192 | 0.3146 | 0.5558 | 0.1070 | 0.0500* | |
H181 | 0.1988 | 0.6165 | 0.0040 | 0.0500* | |
H201 | 0.5191 | 0.4478 | 0.0598 | 0.0830* | |
H202 | 0.4452 | 0.3584 | 0.1155 | 0.0830* | |
H211 | 0.4991 | 0.2058 | 0.0360 | 0.1300* | |
H212 | 0.3399 | 0.2364 | 0.0198 | 0.1300* | |
H221 | 0.5721 | 0.2813 | −0.0614 | 0.1047* | |
H222 | 0.4199 | 0.2331 | −0.0820 | 0.1047* | |
H121 | 0.2592 | 1.0429 | −0.1367 | 0.0436* | |
H171 | 0.484 (2) | 0.6673 (19) | −0.009 (2) | 0.0300* |
U11 | U22 | U33 | U12 | U13 | U23 | |
P1 | 0.0138 (3) | 0.0183 (3) | 0.0227 (3) | −0.0001 (2) | 0.0006 (7) | −0.0007 (6) |
O2 | 0.0227 (17) | 0.0164 (13) | 0.0223 (15) | −0.0076 (15) | −0.0063 (14) | −0.0020 (13) |
C3 | 0.029 (3) | 0.028 (2) | 0.020 (2) | −0.011 (2) | 0.002 (2) | −0.007 (2) |
C4 | 0.029 (3) | 0.024 (2) | 0.039 (3) | 0.008 (2) | −0.011 (2) | −0.003 (2) |
C5 | 0.055 (5) | 0.042 (3) | 0.033 (3) | 0.005 (3) | −0.014 (3) | 0.002 (3) |
C6 | 0.058 (5) | 0.055 (4) | 0.016 (3) | −0.018 (3) | 0.004 (3) | 0.003 (2) |
C7 | 0.045 (4) | 0.044 (3) | 0.033 (3) | 0.005 (3) | 0.018 (3) | −0.015 (3) |
C8 | 0.037 (3) | 0.034 (3) | 0.029 (3) | 0.006 (2) | 0.010 (2) | −0.007 (2) |
O9 | 0.0155 (8) | 0.0237 (9) | 0.0434 (11) | 0.0019 (7) | −0.004 (2) | −0.006 (2) |
O10 | 0.027 (2) | 0.0371 (17) | 0.0223 (15) | −0.0064 (19) | −0.0090 (16) | 0.0040 (15) |
C11 | 0.016 (3) | 0.026 (2) | 0.025 (2) | −0.003 (2) | 0.002 (2) | 0.003 (2) |
C12 | 0.023 (3) | 0.034 (3) | 0.040 (3) | −0.003 (2) | 0.003 (2) | 0.005 (3) |
C13 | 0.038 (4) | 0.058 (4) | 0.042 (3) | −0.011 (4) | −0.011 (3) | 0.012 (3) |
C14 | 0.043 (5) | 0.069 (5) | 0.034 (4) | −0.011 (3) | −0.009 (3) | 0.015 (3) |
C15 | 0.039 (4) | 0.055 (4) | 0.032 (3) | −0.008 (3) | 0.005 (3) | −0.010 (3) |
C16 | 0.036 (3) | 0.052 (3) | 0.020 (3) | −0.004 (3) | −0.008 (2) | 0.004 (2) |
N17 | 0.0128 (9) | 0.0206 (10) | 0.0305 (12) | 0.0018 (8) | 0.003 (3) | −0.006 (2) |
C18 | 0.0189 (12) | 0.0192 (12) | 0.0316 (13) | −0.0034 (10) | 0.008 (2) | 0.001 (2) |
C19 | 0.057 (3) | 0.040 (2) | 0.030 (2) | −0.018 (2) | 0.011 (3) | 0.007 (2) |
C20 | 0.056 (3) | 0.071 (3) | 0.074 (3) | −0.007 (3) | −0.019 (3) | 0.047 (2) |
C21 | 0.058 (3) | 0.0235 (17) | 0.161 (4) | 0.0095 (18) | 0.021 (4) | 0.037 (2) |
C22 | 0.065 (4) | 0.052 (2) | 0.131 (4) | 0.018 (3) | 0.001 (3) | −0.013 (2) |
C23 | 0.039 (2) | 0.053 (2) | 0.046 (2) | 0.002 (2) | −0.002 (2) | −0.0226 (17) |
C24 | 0.029 (2) | 0.036 (2) | 0.034 (2) | −0.006 (2) | −0.001 (2) | −0.0073 (19) |
P1—O2 | 1.601 (3) | C15—C16 | 1.409 (6) |
P1—O9 | 1.4645 (18) | C15—H151 | 0.930 |
P1—O10 | 1.581 (4) | C16—H161 | 0.930 |
P1—N17 | 1.607 (2) | N17—C18 | 1.479 (3) |
O2—C3 | 1.405 (6) | N17—H171 | 0.860 (18) |
C3—C4 | 1.394 (6) | C18—C19 | 1.514 (6) |
C3—C8 | 1.341 (7) | C18—C24 | 1.507 (6) |
C4—C5 | 1.371 (6) | C18—H181 | 0.980 |
C4—H41 | 0.930 | C19—C20 | 1.540 (7) |
C5—C6 | 1.385 (7) | C19—H191 | 0.970 |
C5—H51 | 0.930 | C19—H192 | 0.970 |
C6—C7 | 1.369 (7) | C20—C21 | 1.563 (6) |
C6—H61 | 0.930 | C20—H201 | 0.950 |
C7—C8 | 1.394 (6) | C20—H202 | 0.950 |
C7—H71 | 0.930 | C21—C22 | 1.502 (7) |
C8—H81 | 0.930 | C21—H211 | 0.950 |
O10—C11 | 1.399 (6) | C21—H212 | 0.950 |
C11—C12 | 1.409 (6) | C22—C23 | 1.491 (6) |
C11—C16 | 1.351 (7) | C22—H221 | 0.950 |
C12—C13 | 1.377 (6) | C22—H222 | 0.950 |
C12—H121 | 0.950 | C23—C24 | 1.478 (6) |
C13—C14 | 1.377 (7) | C23—H231 | 0.970 |
C13—H131 | 0.930 | C23—H232 | 0.970 |
C14—C15 | 1.370 (7) | C24—H241 | 0.970 |
C14—H141 | 0.930 | C24—H242 | 0.970 |
O2—P1—O9 | 114.8 (3) | P1—N17—H171 | 116.4 (13) |
O2—P1—O10 | 93.42 (10) | C18—N17—H171 | 116.5 (13) |
O9—P1—O10 | 115.5 (3) | N17—C18—C19 | 108.8 (4) |
O2—P1—N17 | 108.8 (2) | N17—C18—C24 | 113.2 (4) |
O9—P1—N17 | 113.34 (11) | C19—C18—C24 | 115.5 (2) |
O10—P1—N17 | 109.2 (2) | N17—C18—H181 | 106.4 |
P1—O2—C3 | 120.7 (3) | C19—C18—H181 | 105.6 |
O2—C3—C4 | 118.9 (5) | C24—C18—H181 | 106.8 |
O2—C3—C8 | 119.4 (5) | C18—C19—C20 | 114.9 (5) |
C4—C3—C8 | 121.4 (5) | C18—C19—H191 | 108.0 |
C3—C4—C5 | 117.0 (5) | C20—C19—H191 | 107.6 |
C3—C4—H41 | 121.7 | C18—C19—H192 | 109.3 |
C5—C4—H41 | 121.3 | C20—C19—H192 | 109.3 |
C4—C5—C6 | 122.5 (6) | H191—C19—H192 | 107.4 |
C4—C5—H51 | 118.6 | C19—C20—C21 | 117.0 (5) |
C6—C5—H51 | 118.8 | C19—C20—H201 | 106.3 |
C5—C6—C7 | 118.9 (6) | C21—C20—H201 | 107.4 |
C5—C6—H61 | 120.2 | C19—C20—H202 | 108.8 |
C7—C6—H61 | 120.9 | C21—C20—H202 | 107.8 |
C6—C7—C8 | 119.2 (6) | H201—C20—H202 | 109.5 |
C6—C7—H71 | 119.4 | C20—C21—C22 | 118.6 (4) |
C8—C7—H71 | 121.4 | C20—C21—H211 | 106.6 |
C7—C8—C3 | 120.9 (6) | C22—C21—H211 | 107.8 |
C7—C8—H81 | 119.3 | C20—C21—H212 | 106.2 |
C3—C8—H81 | 119.8 | C22—C21—H212 | 108.0 |
P1—O10—C11 | 119.7 (3) | H211—C21—H212 | 109.5 |
O10—C11—C12 | 118.3 (5) | C21—C22—C23 | 117.0 (5) |
O10—C11—C16 | 118.8 (5) | C21—C22—H221 | 108.2 |
C12—C11—C16 | 122.8 (5) | C23—C22—H221 | 108.7 |
C11—C12—C13 | 116.9 (6) | C21—C22—H222 | 105.8 |
C11—C12—H121 | 121.6 | C23—C22—H222 | 107.4 |
C13—C12—H121 | 121.4 | H221—C22—H222 | 109.5 |
C12—C13—C14 | 120.5 (7) | C22—C23—C24 | 115.1 (5) |
C12—C13—H131 | 119.4 | C22—C23—H231 | 108.4 |
C14—C13—H131 | 120.1 | C24—C23—H231 | 109.8 |
C13—C14—C15 | 122.4 (7) | C22—C23—H232 | 106.9 |
C13—C14—H141 | 118.5 | C24—C23—H232 | 109.3 |
C15—C14—H141 | 119.1 | H231—C23—H232 | 107.1 |
C14—C15—C16 | 117.8 (6) | C18—C24—C23 | 116.5 (4) |
C14—C15—H151 | 120.6 | C18—C24—H241 | 107.4 |
C16—C15—H151 | 121.6 | C23—C24—H241 | 105.0 |
C15—C16—C11 | 119.6 (6) | C18—C24—H242 | 108.8 |
C15—C16—H161 | 120.2 | C23—C24—H242 | 111.2 |
C11—C16—H161 | 120.2 | H241—C24—H242 | 107.4 |
P1—N17—C18 | 124.57 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
C23—H232···O9i | 0.97 | 2.57 | 3.516 (8) | 166 (1) |
N17—H171···O9i | 0.86 | 2.08 | 2.901 (8) | 159 (4) |
Symmetry code: (i) x+1/2, −y+3/2, z. |
C26H24NO3P | Z = 2 |
Mr = 429.43 | F(000) = 452 |
Triclinic, P1 | Dx = 1.320 Mg m−3 |
a = 8.3404 (3) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 9.5349 (5) Å | Cell parameters from 7627 reflections |
c = 14.9677 (7) Å | θ = 3.7–29.8° |
α = 76.280 (4)° | µ = 0.16 mm−1 |
β = 75.778 (4)° | T = 120 K |
γ = 72.055 (4)° | Block, colourless |
V = 1080.73 (9) Å3 | 0.25 × 0.20 × 0.20 mm |
AFC11 (Right): Eulerian 3 circle CCD diffractometer | 3578 reflections with I > 2σ(I) |
Radiation source: Rotating Anode MicroMax-007HF DW 1.2 kW | Rint = 0.018 |
Profile data from ω–scans | θmax = 25.4°, θmin = 3.2° |
Absorption correction: multi-scan CrysAlis PRO (Rigaku OD, 2015) | h = −10→10 |
Tmin = 0.722, Tmax = 1.000 | k = −11→11 |
9523 measured reflections | l = −18→18 |
3901 independent reflections |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.033 | H-atom parameters constrained |
wR(F2) = 0.086 | w = 1/[σ2(Fo2) + (0.0421P)2 + 0.4112P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max = 0.021 |
3901 reflections | Δρmax = 0.27 e Å−3 |
280 parameters | Δρmin = −0.34 e Å−3 |
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. Data collection and crystal screening for (I) was performed on a Rigaku Oxford-Diffraction Gemini-S diffractometer with sealed-tube Mo-Kα radiation using the CrysAlisPro program (Rigaku Oxford-Diffraction, 2012). This program was also used for the integration of the data using default parameters, for the empirical absorption correction using spherical harmonics employing symmetry-equivalent and redundant data, and the correction for Lorentz and polarization effects. The ab-initio iterative charge flipping method was used to solve the crystal structure of (I) with parameters described elsewhere (van der Lee, 2013) employing the Superflip program (Palatinus&Chapuis, 2007) and it was refined using full-matrix least-squares procedures on squared structure factor amplitudes F2 as implemented in CRYSTALS (Betteridge et al., 2003) using all independent reflections with I>0. |
x | y | z | Uiso*/Ueq | ||
P1 | 0.28992 (4) | 0.22585 (4) | 0.24553 (2) | 0.02034 (11) | |
O1 | 0.19646 (12) | 0.25264 (11) | 0.16998 (7) | 0.0268 (2) | |
O2 | 0.18570 (12) | 0.30054 (10) | 0.33444 (6) | 0.0242 (2) | |
O3 | 0.44766 (12) | 0.29786 (10) | 0.22264 (6) | 0.0229 (2) | |
N1 | 0.35880 (14) | 0.04977 (12) | 0.28829 (7) | 0.0210 (2) | |
C1 | 0.11701 (16) | 0.45642 (14) | 0.32925 (9) | 0.0216 (3) | |
C2 | 0.13891 (17) | 0.51758 (16) | 0.39864 (9) | 0.0251 (3) | |
H2A | 0.204474 | 0.457320 | 0.444418 | 0.030* | |
C3 | 0.06359 (18) | 0.66858 (16) | 0.40047 (10) | 0.0283 (3) | |
H3A | 0.077787 | 0.712423 | 0.447789 | 0.034* | |
C4 | −0.03204 (17) | 0.75573 (15) | 0.33386 (10) | 0.0279 (3) | |
H4A | −0.083810 | 0.859051 | 0.335667 | 0.033* | |
C5 | −0.05239 (18) | 0.69265 (16) | 0.26462 (10) | 0.0287 (3) | |
H5A | −0.117877 | 0.752952 | 0.218813 | 0.034* | |
C6 | 0.02249 (17) | 0.54132 (15) | 0.26162 (10) | 0.0264 (3) | |
H6A | 0.008991 | 0.497327 | 0.214182 | 0.032* | |
C7 | 0.58266 (16) | 0.26177 (14) | 0.14702 (9) | 0.0212 (3) | |
C8 | 0.55543 (18) | 0.31321 (15) | 0.05655 (9) | 0.0244 (3) | |
H8A | 0.444962 | 0.369332 | 0.044181 | 0.029* | |
C9 | 0.69321 (19) | 0.28115 (17) | −0.01621 (10) | 0.0311 (3) | |
H9A | 0.677120 | 0.314654 | −0.079222 | 0.037* | |
C10 | 0.8537 (2) | 0.2007 (2) | 0.00263 (11) | 0.0385 (4) | |
H10A | 0.947575 | 0.179286 | −0.047458 | 0.046* | |
C11 | 0.8781 (2) | 0.1512 (2) | 0.09426 (11) | 0.0395 (4) | |
H11A | 0.988814 | 0.096637 | 0.106884 | 0.047* | |
C12 | 0.74155 (18) | 0.18102 (16) | 0.16751 (10) | 0.0287 (3) | |
H12A | 0.756938 | 0.146579 | 0.230603 | 0.034* | |
C13 | 0.31490 (17) | −0.06607 (15) | 0.25673 (9) | 0.0241 (3) | |
H13A | 0.224230 | −0.017085 | 0.218789 | 0.029* | |
H13B | 0.267326 | −0.131358 | 0.312238 | 0.029* | |
C14 | 0.46539 (17) | −0.16227 (15) | 0.19938 (9) | 0.0227 (3) | |
C15 | 0.55410 (18) | −0.09884 (15) | 0.11602 (10) | 0.0256 (3) | |
H15A | 0.524078 | 0.006721 | 0.096448 | 0.031* | |
C16 | 0.68566 (19) | −0.18823 (18) | 0.06139 (11) | 0.0334 (3) | |
H16A | 0.744928 | −0.144031 | 0.004279 | 0.040* | |
C17 | 0.7312 (2) | −0.34247 (19) | 0.08992 (12) | 0.0399 (4) | |
H17A | 0.821881 | −0.403902 | 0.052550 | 0.048* | |
C18 | 0.6445 (2) | −0.40617 (17) | 0.17262 (13) | 0.0389 (4) | |
H18A | 0.675686 | −0.511682 | 0.192324 | 0.047* | |
C19 | 0.5118 (2) | −0.31677 (15) | 0.22719 (11) | 0.0302 (3) | |
H19A | 0.452266 | −0.361485 | 0.284001 | 0.036* | |
C20 | 0.47160 (16) | −0.00427 (14) | 0.35785 (9) | 0.0215 (3) | |
H20A | 0.491704 | 0.082604 | 0.374481 | 0.026* | |
H20B | 0.583807 | −0.065766 | 0.329936 | 0.026* | |
C21 | 0.39591 (16) | −0.09676 (14) | 0.44588 (9) | 0.0209 (3) | |
C22 | 0.48106 (18) | −0.24494 (16) | 0.47433 (10) | 0.0274 (3) | |
H22A | 0.589320 | −0.288210 | 0.439166 | 0.033* | |
C23 | 0.4090 (2) | −0.33073 (16) | 0.55406 (11) | 0.0327 (3) | |
H23A | 0.468936 | −0.431673 | 0.573441 | 0.039* | |
C24 | 0.2508 (2) | −0.26933 (17) | 0.60496 (10) | 0.0303 (3) | |
H24A | 0.200719 | −0.328244 | 0.658723 | 0.036* | |
C25 | 0.16556 (18) | −0.12152 (17) | 0.57722 (10) | 0.0281 (3) | |
H25A | 0.056824 | −0.078855 | 0.612209 | 0.034* | |
C26 | 0.23788 (17) | −0.03546 (15) | 0.49876 (9) | 0.0242 (3) | |
H26A | 0.179122 | 0.066360 | 0.480840 | 0.029* |
U11 | U22 | U33 | U12 | U13 | U23 | |
P1 | 0.01953 (18) | 0.02070 (19) | 0.01905 (18) | −0.00377 (13) | −0.00332 (13) | −0.00256 (13) |
O1 | 0.0258 (5) | 0.0293 (5) | 0.0242 (5) | −0.0051 (4) | −0.0080 (4) | −0.0022 (4) |
O2 | 0.0241 (5) | 0.0209 (5) | 0.0218 (5) | −0.0006 (4) | −0.0015 (4) | −0.0026 (4) |
O3 | 0.0243 (5) | 0.0224 (5) | 0.0217 (5) | −0.0070 (4) | −0.0007 (4) | −0.0062 (4) |
N1 | 0.0220 (5) | 0.0211 (6) | 0.0214 (5) | −0.0054 (4) | −0.0068 (4) | −0.0039 (4) |
C1 | 0.0166 (6) | 0.0214 (6) | 0.0229 (6) | −0.0039 (5) | 0.0013 (5) | −0.0032 (5) |
C2 | 0.0198 (6) | 0.0310 (7) | 0.0223 (7) | −0.0059 (5) | −0.0021 (5) | −0.0035 (6) |
C3 | 0.0255 (7) | 0.0319 (7) | 0.0292 (7) | −0.0098 (6) | −0.0009 (6) | −0.0103 (6) |
C4 | 0.0235 (7) | 0.0232 (7) | 0.0357 (8) | −0.0059 (5) | −0.0017 (6) | −0.0072 (6) |
C5 | 0.0257 (7) | 0.0253 (7) | 0.0316 (8) | −0.0027 (6) | −0.0077 (6) | −0.0014 (6) |
C6 | 0.0260 (7) | 0.0261 (7) | 0.0265 (7) | −0.0038 (6) | −0.0065 (6) | −0.0059 (6) |
C7 | 0.0236 (7) | 0.0189 (6) | 0.0220 (6) | −0.0085 (5) | −0.0007 (5) | −0.0056 (5) |
C8 | 0.0256 (7) | 0.0230 (7) | 0.0251 (7) | −0.0087 (5) | −0.0058 (5) | −0.0012 (5) |
C9 | 0.0336 (8) | 0.0394 (8) | 0.0220 (7) | −0.0149 (6) | −0.0033 (6) | −0.0039 (6) |
C10 | 0.0283 (8) | 0.0575 (10) | 0.0280 (8) | −0.0113 (7) | 0.0033 (6) | −0.0130 (7) |
C11 | 0.0228 (7) | 0.0564 (10) | 0.0349 (8) | −0.0029 (7) | −0.0048 (6) | −0.0100 (7) |
C12 | 0.0274 (7) | 0.0349 (8) | 0.0237 (7) | −0.0071 (6) | −0.0068 (6) | −0.0045 (6) |
C13 | 0.0262 (7) | 0.0250 (7) | 0.0248 (7) | −0.0112 (5) | −0.0067 (5) | −0.0035 (5) |
C14 | 0.0272 (7) | 0.0221 (6) | 0.0236 (7) | −0.0088 (5) | −0.0105 (5) | −0.0043 (5) |
C15 | 0.0297 (7) | 0.0246 (7) | 0.0247 (7) | −0.0080 (6) | −0.0082 (6) | −0.0042 (5) |
C16 | 0.0297 (8) | 0.0454 (9) | 0.0289 (8) | −0.0093 (7) | −0.0061 (6) | −0.0139 (7) |
C17 | 0.0337 (8) | 0.0429 (9) | 0.0492 (10) | 0.0049 (7) | −0.0182 (7) | −0.0290 (8) |
C18 | 0.0472 (9) | 0.0217 (7) | 0.0557 (10) | −0.0003 (7) | −0.0299 (8) | −0.0121 (7) |
C19 | 0.0406 (8) | 0.0224 (7) | 0.0341 (8) | −0.0122 (6) | −0.0180 (7) | −0.0009 (6) |
C20 | 0.0202 (6) | 0.0219 (6) | 0.0225 (6) | −0.0043 (5) | −0.0064 (5) | −0.0034 (5) |
C21 | 0.0224 (6) | 0.0222 (6) | 0.0207 (6) | −0.0065 (5) | −0.0073 (5) | −0.0042 (5) |
C22 | 0.0256 (7) | 0.0264 (7) | 0.0276 (7) | −0.0031 (6) | −0.0061 (6) | −0.0036 (6) |
C23 | 0.0378 (8) | 0.0240 (7) | 0.0338 (8) | −0.0063 (6) | −0.0127 (7) | 0.0031 (6) |
C24 | 0.0366 (8) | 0.0352 (8) | 0.0230 (7) | −0.0183 (6) | −0.0067 (6) | 0.0003 (6) |
C25 | 0.0266 (7) | 0.0367 (8) | 0.0237 (7) | −0.0104 (6) | −0.0033 (6) | −0.0090 (6) |
C26 | 0.0252 (7) | 0.0236 (7) | 0.0242 (7) | −0.0047 (5) | −0.0063 (5) | −0.0054 (5) |
P1—O1 | 1.4578 (10) | C12—H12A | 0.9500 |
P1—O2 | 1.5916 (9) | C13—C14 | 1.5127 (18) |
P1—O3 | 1.5948 (10) | C13—H13A | 0.9900 |
P1—N1 | 1.6232 (11) | C13—H13B | 0.9900 |
O2—C1 | 1.4092 (15) | C14—C19 | 1.3893 (19) |
O3—C7 | 1.4096 (15) | C14—C15 | 1.3907 (19) |
N1—C13 | 1.4693 (17) | C15—C16 | 1.383 (2) |
N1—C20 | 1.4707 (17) | C15—H15A | 0.9500 |
C1—C2 | 1.378 (2) | C16—C17 | 1.388 (2) |
C1—C6 | 1.3826 (19) | C16—H16A | 0.9500 |
C2—C3 | 1.386 (2) | C17—C18 | 1.378 (3) |
C2—H2A | 0.9500 | C17—H17A | 0.9500 |
C3—C4 | 1.382 (2) | C18—C19 | 1.387 (2) |
C3—H3A | 0.9500 | C18—H18A | 0.9500 |
C4—C5 | 1.382 (2) | C19—H19A | 0.9500 |
C4—H4A | 0.9500 | C20—C21 | 1.5151 (18) |
C5—C6 | 1.3913 (19) | C20—H20A | 0.9900 |
C5—H5A | 0.9500 | C20—H20B | 0.9900 |
C6—H6A | 0.9500 | C21—C22 | 1.3881 (19) |
C7—C8 | 1.3760 (19) | C21—C26 | 1.3919 (18) |
C7—C12 | 1.3791 (19) | C22—C23 | 1.393 (2) |
C8—C9 | 1.3880 (19) | C22—H22A | 0.9500 |
C8—H8A | 0.9500 | C23—C24 | 1.381 (2) |
C9—C10 | 1.382 (2) | C23—H23A | 0.9500 |
C9—H9A | 0.9500 | C24—C25 | 1.384 (2) |
C10—C11 | 1.384 (2) | C24—H24A | 0.9500 |
C10—H10A | 0.9500 | C25—C26 | 1.384 (2) |
C11—C12 | 1.384 (2) | C25—H25A | 0.9500 |
C11—H11A | 0.9500 | C26—H26A | 0.9500 |
O1—P1—O2 | 115.77 (5) | N1—C13—H13A | 108.8 |
O1—P1—O3 | 116.27 (5) | C14—C13—H13A | 108.8 |
O2—P1—O3 | 97.78 (5) | N1—C13—H13B | 108.8 |
O1—P1—N1 | 113.54 (6) | C14—C13—H13B | 108.8 |
O2—P1—N1 | 104.31 (5) | H13A—C13—H13B | 107.7 |
O3—P1—N1 | 107.44 (5) | C19—C14—C15 | 118.94 (13) |
C1—O2—P1 | 122.79 (8) | C19—C14—C13 | 120.19 (12) |
C7—O3—P1 | 119.73 (8) | C15—C14—C13 | 120.80 (12) |
C13—N1—C20 | 115.99 (10) | C16—C15—C14 | 120.52 (13) |
C13—N1—P1 | 121.10 (9) | C16—C15—H15A | 119.7 |
C20—N1—P1 | 122.88 (9) | C14—C15—H15A | 119.7 |
C2—C1—C6 | 121.90 (12) | C15—C16—C17 | 120.07 (15) |
C2—C1—O2 | 116.55 (12) | C15—C16—H16A | 120.0 |
C6—C1—O2 | 121.40 (12) | C17—C16—H16A | 120.0 |
C1—C2—C3 | 118.83 (13) | C18—C17—C16 | 119.78 (14) |
C1—C2—H2A | 120.6 | C18—C17—H17A | 120.1 |
C3—C2—H2A | 120.6 | C16—C17—H17A | 120.1 |
C4—C3—C2 | 120.38 (14) | C17—C18—C19 | 120.22 (14) |
C4—C3—H3A | 119.8 | C17—C18—H18A | 119.9 |
C2—C3—H3A | 119.8 | C19—C18—H18A | 119.9 |
C5—C4—C3 | 120.03 (13) | C18—C19—C14 | 120.47 (14) |
C5—C4—H4A | 120.0 | C18—C19—H19A | 119.8 |
C3—C4—H4A | 120.0 | C14—C19—H19A | 119.8 |
C4—C5—C6 | 120.37 (13) | N1—C20—C21 | 112.18 (10) |
C4—C5—H5A | 119.8 | N1—C20—H20A | 109.2 |
C6—C5—H5A | 119.8 | C21—C20—H20A | 109.2 |
C1—C6—C5 | 118.49 (13) | N1—C20—H20B | 109.2 |
C1—C6—H6A | 120.8 | C21—C20—H20B | 109.2 |
C5—C6—H6A | 120.8 | H20A—C20—H20B | 107.9 |
C8—C7—C12 | 122.33 (12) | C22—C21—C26 | 118.74 (12) |
C8—C7—O3 | 120.00 (12) | C22—C21—C20 | 120.71 (12) |
C12—C7—O3 | 117.59 (12) | C26—C21—C20 | 120.54 (11) |
C7—C8—C9 | 118.41 (13) | C21—C22—C23 | 120.54 (13) |
C7—C8—H8A | 120.8 | C21—C22—H22A | 119.7 |
C9—C8—H8A | 120.8 | C23—C22—H22A | 119.7 |
C10—C9—C8 | 120.28 (14) | C24—C23—C22 | 120.13 (13) |
C10—C9—H9A | 119.9 | C24—C23—H23A | 119.9 |
C8—C9—H9A | 119.9 | C22—C23—H23A | 119.9 |
C9—C10—C11 | 120.20 (14) | C23—C24—C25 | 119.63 (13) |
C9—C10—H10A | 119.9 | C23—C24—H24A | 120.2 |
C11—C10—H10A | 119.9 | C25—C24—H24A | 120.2 |
C12—C11—C10 | 120.16 (14) | C24—C25—C26 | 120.35 (13) |
C12—C11—H11A | 119.9 | C24—C25—H25A | 119.8 |
C10—C11—H11A | 119.9 | C26—C25—H25A | 119.8 |
C7—C12—C11 | 118.61 (13) | C25—C26—C21 | 120.60 (13) |
C7—C12—H12A | 120.7 | C25—C26—H26A | 119.7 |
C11—C12—H12A | 120.7 | C21—C26—H26A | 119.7 |
N1—C13—C14 | 113.73 (11) |
Cg1, Cg2 and Cg1 are the centroids of the C1–C6, C14–C19 and C7–C12 rings, respectively. |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2A···CG1i | 0.95 | 3.50 | 3.9798 (13) | 114 |
C13—H13B···CG1ii | 0.99 | 3.49 | 4.2048 (13) | 131 |
C18—H18A···CG3ii | 0.95 | 3.22 | 3.8839 (15) | 128 |
C8—H8A···CG2iii | 0.95 | 3.41 | 3.7716 (14) | 106 |
C6—H6A···O1 | 0.95 | 2.51 | 3.1488 (17) | 125 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, y−1, z; (iii) −x+1, −y, −z. |
Acknowledgements
Support of this investigation by the Ferdowsi University of Mashhad is gratefully acknowledged. The authors appreciatively acknowledge the Cambridge Crystallographic Data Centre for access to the CSD Enterprise suite. A CIISB research infrastructure project funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF X-ray diffraction and Bio-SAXS. Abdul Ajees Abdul Salam acknowledges the research grant provided by the Manipal Academy of Higher Education (MAHE), Manipal, India, under intramural funding.
Funding information
Funding for this research was provided by: Ferdowsi University of Mashhad (project No. 39847/3); MEYS CR (project No. LM2015043); Manipal Academy of Higher Education (grant No. MAHE/DREG/PhD/IMF/2019).
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