The double H-atom acceptability of the P=O group in new XP(O)(NHCH2C6H4-2-Cl)2 phosphoramidates [X = C6H5O- and CF3C(O)NH-]: a database analysis of compounds having a P(O)(NHR) group

Structural and Molecular Packing study of Three New Amidophosphoric Acid Esters and Assessment of Their Inhibiting Activity Against SARS-CoV-2 by Molecular Docking

Three new compounds of amidophosphoric acid esters with a [OCH2C(CH3)2CH2O]P(O)[X] segment (where X=cyclopentylamido (1), 2-aminopyridinyl (2) and pyrrolidinyl (3)) were synthesized and studied using FT-IR and 31P/13C/1H NMR spectroscopies and single-crystal X-ray diffraction analysis. The compounds crystallize in the triclinic space groups P 1 ‾ for 1 and 3 and in the orthorhombic space group Pca21 for 2, where the asymmetric unit consists of three symmetrically-independent molecules for 1 and one molecule for 2 and 3. The intermolecular interactions and supramolecular assemblies are assessed by Hirshfeld surface analysis and enrichment ratios. The results reveal that the substituent effect plays an important role in directing the supramolecular structures. The presence of the aromatic substituent aminopyridine in 2 providing the C-H…π interactions leads to a larger variety in interactions including H…H, H…O/O…H, H…C/C…H and H…N/N…H contacts, whereas the packings of the compounds 1 and 3 bearing aliphatic substituents only include H…H and H…O/O…H contacts. The enrichment ratios affirm the importance of O…H/H…O contacts reflecting the hydrogen bond N-H…O interactions to be the enriched contacts. Compounds 1-3 were also investigated along with five similar reported structures with a [OCH2C(CH3)2CH2O]P(O) segment for their inhibitory behavior against SARS-CoV-2. The molecular docking results illustrate that the presence of the aromatic amido substituent versus the aliphatic type provides a more favorable condition for their biological activities.

Three new amidophosphoric acid esters with a P(O)[OCH2C(CH3)2CH2O] segment: X-ray diffraction, DFT, AIM and Hirshfeld surface investigations of bi- and tri-furcated (three and four-center) hydrogen bond interactions

Structural and packing features of three new amidophosphoric acid esters having a common part XP(O)[OCH2C(CH3)2CH2O], with X = [(CH3)3CNH] (1), [(CH3)2HCNH] (2) and [C6H11(CH3)N] (3), are investigated by single crystal X-ray diffraction. The results illustrate that the compounds 1 and 3 crystallize with one independent molecule in the asymmetric unit; whereas, for 2, the compound crystallizes with three independent molecules in the asymmetric unit. The crystal structures are mostly stabilized via tri-furcated hydrogen bond interactions (C–H · · ·)2(N–H · · ·)O=P in 1 and (C–H · · ·)3O=P in 3, while the stability is given by bi-furcated hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P in 2. For a better understanding of the nature, strength and energetics associated with the formation of the quoted multi-center hydrogen bond interactions, the Natural Bond Order (NBO) method from Density Functional Theory (DFT) and a topological analysis by means of Atoms In Molecules (AIM) and Hirshfeld surface procedures were performed. These studies reveal that the studied multi-center hydrogen bond interactions of the type O · · · H are favoured in the crystal packing displaying enrichment ratios larger than unity. The detailed nature of the different interactions in these multi-center interactions is studied for the first time in such compounds. It is shown that the N–H · · · O interaction is rather non-covalent closed-shell whereas the C–H · · · O interaction is more van der Waals closed-shell. Stronger hydrogen bond interactions are observed for a lower multiple H-atom acceptor oxygen in three-center hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P of 2 than for four-center interactions in 1 [i.e. (C–H · · ·)2(N–H · · ·)O=P] and 3 [i.e. (C–H · · ·)3O=P]. The better H-atom acceptability of the O atom of P=O compared with the esteric O atom is explained by the richer s-character of the hybrid orbital of the O atom acceptor of P=O coupled with enhance of the polarization and charge. The obtained results are also confirmed by Molecular Electrostatic Potential (MEP).

A combined X-ray crystallography and theoretical study of N-H...OX (X is =P and -C) hydrogen bonds in two new structures with a (C-O)2(N)P(=Y) (Y is O and S) skeleton

The crystal structures of N,N'-(cyclohexane-1,4-diyl)bis(O,O'-diphenylphosphoramide), C₃₀H₃₂N₂O₆P₂ or (C₆H₅O)₂P(O)(1-NH)(C₆H₁₀)(4-NH)P(O)(OC₆H₅)₂, (I), and N,N'-(1,4-phenylene)bis(O,O'-dimethylthiophosphoramide), C₁₀H₁₈N₂O₄P₂S₂ or (CH₃O)₂P(S)(1-NH)(C₆H₄)(4-NH)P(S)(OCH₃)₂, (II), have been investigated. In the structure of (I), with an (O)₂(N)P(O) skeleton, two symmetry-independent phosphoramide molecules are linked through N-H...O=P hydrogen bonds. In the structure of (II), with an (O)₂(N)P(S) skeleton, the ester O atoms take part in N-H...O-C hydrogen bonds as acceptors; the P=S groups do not participate in hydrogen-bonding interactions. The strengths of these hydrogen bonds were evaluated, using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6-311G(d,p) level of theory. For this, LP(O) to σ*(NH) charge transfers were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology, for a three-component cluster of hydrogen-bonded molecules for both structures, including all of the independent N-H...O hydrogen bonds observed in the crystal packing. The details of the intermolecular interactions were studied by Hirshfeld surface maps and two-dimensional fingerprint plots.

Chiral one-dimensional hydrogen-bonded architectures constructed from single-enantiomer phosphoric triamides

The two single-enantiomer phosphoric triamides N-(2,6-difluorobenzoyl)-N',N''-bis[(S)-(-)-α-methylbenzyl]phosphoric triamide, [2,6-F₂-C₆H₃C(O)NH][(S)-(-)-(C₆H₅)CH(CH₃)NH]₂P(O), denoted L-1, and N-(2,6-difluorobenzoyl)-N',N''-bis[(R)-(+)-α-methylbenzyl]phosphoric triamide, [2,6-F₂-C₆H₃C(O)NH][(R)-(+)-(C₆H₅)CH(CH₃)NH]₂P(O), denoted D-1, both C₂₃H₂₄F₂N₃O₂P, have been investigated. In their structures, chiral one-dimensional hydrogen-bonded architectures are formed along [100], mediated by relatively strong N-H...O(P) and N-H...O(C) hydrogen bonds. Both assemblies include the noncentrosymmetric graph-set motifs R₂²(10), R₂¹(6) and C₂²(8), and the compounds crystallize in the chiral space group P1. Due to the data collection of L-1 at 120 K and of D-1 at 95 K, the unit-cell dimensions and volume show a slight difference; the contraction in the volume of D-1 with respect to that in L-1 is about 0.3%. The asymmetric units of both structures consist of two independent phosphoric triamide molecules, with the main difference being seen in one of the torsion angles in the OPNHCH(CH₃)(C₆H₅) part. The Hirshfeld surface maps of these levo and dextro isomers are very similar; however, they are near mirror images of each other. For both structures, the full fingerprint plot of each symmetry-independent molecule shows an almost asymmetric shape as a result of its different environment in the crystal packing. It is notable that NMR spectroscopy could distinguish between compounds L-1 and D-1 that have different relative stereocentres; however, the differences in chemical shifts between them were found to be about 0.02 to 0.001 ppm under calibrated temperature conditions. In each molecule, the two chiral parts are also different in NMR media, in which chemical shifts and P-H and P-C couplings have been studied.

A novel tubular hydrogen-bond pattern in a new diazaphosphole oxide: a combination of X-ray crystallography and theoretical study of hydrogen bonds

In the structure of 2-(4-chloroanilino)-1,3,2λ⁴-diazaphosphol-2-one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N-H)₂...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R³₃(12) and R₄³(14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N-H groups of the diazaphosphole ring, not co-operating in classical hydrogen bonding, takes part in an N-H...π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen-bond pattern. The energies of the N-H...O and N-H...π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen-bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen-bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J_H-P coupling constant.

A new Z′=(2+0.5+0.5) amidophosphoester structure: Hirshfeld surface analysis of symmetry-independent molecules

Tetraethyl 1,3-phenylenebis(phosphoramidate) was synthesized and characterized by 1H, 13C, 31P NMR, IR and mass spectroscopies. The asymmetric unit is composed of two half-molecules, each residing on a two-fold axis, and two complete molecules, thus leading to a Z′=(2+0.5+0.5)=3 structure. The most plausible explanation for the occurrence of multiple independent molecules is a frustration between relatively strong hydrogen bond interactions and weaker CH···π interactions. In each of the molecules, the P atoms are in a similar distorted tetrahedral environment. The N atoms bonded to P atoms have mainly sp2 character tending towards a planar environment. In the crystal structure, the phosphoryl O atoms are involved in classical N–H···O=P and weaker C–H···O=P hydrogen bonds as (N–H)(C–H) ···O=P, acting as a double hydrogen-bond acceptor. These hydrogen bonds along with other C–H···O hydrogen bonds and C–H···π interactions create a 3D crystalline network. Hirshfeld surfaces and two-dimensional (2D) fingerprint plots are calculated for analyzing intermolecular interactions in each of the independent molecules of the title compound. For all four independent molecules, the contribution of H···H contacts to the total interactions is decisive, being larger than 60% for each molecule. The O···H/H···O contacts are the characteristic intermolecular contacts in the corresponding molecules. Furthermore, the C···H/H···C, including the C–H···π interactions, and N···H/H···N contacts cover other intermolecular contacts in the crystal lattice.

Extensive analysis of N-H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study

The N-H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N'-(p-tolyl)phosphonic diamide, C₂₀H₂₁N₂OP or (C₆H₅)P(O)(NHCH₂C₆H₅)(NHC₆H₄-p-CH₃), (I), diphenylphosphinic 1-methylpropylamide, C₁₆H₂₀NOP or (C₆H₅)₂P(O)[NHCH(CH₃)(C₂H₅)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C₈H₁₂N⁺·C₁₄H₁₅NO₂P^- or [S-(C₆H₅)CH(CH₃)NH₃][(C₆H₅)P(O){S-NHCH(CH₃)(C₆H₅)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C₈H₁₂N⁺·C₁₂H₁₀O₂P^- or [4-CH₃-C₆H₄CH₂NH₃][(C₆H₅)₂P(O)(O)], (IV). This article focuses on the N-H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)₂, 102 (C)₂P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)₂P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)₂ segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)₂P(O)(O) structures were particularly noticeable for a high number of cation-anion compounds. The overall tendencies of N...O distances in neutral and cation-anion compounds were compared. The N-H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

Two new thiophosphoramide structures: N,N',N''-tricyclohexylphosphorothioic triamide and O,O'-diethyl (2-phenylhydrazin-1-yl)thiophosphonate

The compound N,N',N''-tricyclohexylphosphorothioic triamide, C18H36N3PS or P(S)[NHC6H11]3, (I), crystallizes in the space group Pnma with the molecule lying across a mirror plane; one N atom lies on the mirror plane, whereas the bond-angle sum at the other N atom has a deviation of some 8° from the ideal value of 360° for a planar configuration. The orientation of the atoms attached to this nonplanar N atom corresponds to an anti orientation of the corresponding lone electron pair (LEP) with respect to the P=S group. The P=S bond length of 1.9785 (6) Å is within the expected range for compounds with a P(S)[N]3 skeleton; however, it is in the region of the longest bond lengths found for analogous structures. This may be due to the involvement of the P=S group in N-H···S=P hydrogen bonds. In O,O'-diethyl (2-phenylhydrazin-1-yl)thiophosphonate, C10H17N2O2PS or P(S)[OC2H5]2[NHNHC6H5], (II), the bond-angle sum at the N atom attached to the phenyl ring is 345.1°, whereas, for the N atom bonded to the P atom, a practically planar environment is observed, with a bond-angle sum of 359.1°. A Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B58, 380-388] analysis shows a shift of the maximum population of P=S bond lengths in compounds with a P(S)[O]2[N] skeleton to the shorter bond lengths relative to compounds with a P(S)[N]3 skeleton. The influence of this difference on the collective tendencies of N···S distances in N-H···S hydrogen bonds for structures with P(S)[N]3 and P(S)[O]2[N] segments were studied through a CSD analysis.

Newrac-XP(O)(OC6H5)(NHC6H4-p-CH3) [X= N(CH3)(cyclo-C6H11) and NH(C3H5)] andrac-(C6H5CH2NH)P(O)(OC6H5)(NH-cyclo-C6H11) mixed-amide phosphinates

The mixed-amide phosphinates,rac-phenyl (N-methylcyclohexylamido)(p-tolylamido)phosphinate, C20H27N2O2P, (I), andrac-phenyl (allylamido)(p-tolylamido)phosphinate, C16H19N2O2P, (II), were synthesized from the racemic phosphorus–chlorine compound (R,S)-(Cl)P(O)(OC6H5)(NHC6H4-p-CH3). Furthermore, the phosphorus–chlorine compound ClP(O)(OC6H5)(NH-cyclo-C6H11) was synthesized for the first time and used for the synthesis ofrac-phenyl (benzylamido)(cyclohexylamido)phosphinate, C19H25N2O2P, (III). The strategies for the synthesis of racemic mixed-amide phosphinates are discussed. The P atom in each compound is in a distorted tetrahedral (N1)P(=O)(O)(N2) environment. In (I) and (II), thep-tolylamido substituent makes a longer P—N bond than those involving theN-methylcyclohexylamido and allylamido substituents. In (III), the differences between the P—N bond lengths involving the cyclohexylamido and benzylamido substituents are not significant. In all three structures, the phosphoryl O atom takes part with the N—H unit in hydrogen-bonding interactions,viz.an N—H...O=P hydrogen bond for (I) and (N—H)(N—H)...O=P hydrogen bonds for (II) and (III), building linear arrangements along [001] for (I) and along [010] for (III), and a ladder arrangement along [100] for (II).

Hirshfeld surface analysis of new phosphoramidates

Hirshfeld surfaces and two-dimensional fingerprint plots are used to visualize and analyze intermolecular interactions in six new phosphoramidate structures, [2,6-F2-C6H3C(O)NH]P(O)[X]2 {X = N(C2H5)2 (1), [X]2 = NHCH2C(CH3)2CH2NH and with one CH3OH solvated molecule (2)}, [C6H5O]2P(O)Y [Y = NC4H8O (3), NHC6H4(3-Br) (4)] and [Z]2P(O)OP(O)[Z]2 [Z = N(CH3)(CH2C6H5) (5), NHC6H4(4-CH3) (6)]. Study of the short intermolecular contacts in structures (1)-(6) by Hirshfeld surfaces demonstrate that the O atom of P=O is a better H-atom acceptor than the O atom of C=O for (1) and (2), and also relative to the O atom of the C6H5O group for (3) and (4), and relative to the bridge O atom of the P(O)OP(O) segment for (5) and (6). The results confirm that the crystal packing is related to the kind of substituent linked to the P atom. Compounds (1), (2), (4) and (6), with characteristic N-H···O hydrogen bonds, show a pair of intense spikes (including the intermolecular H···O contacts) in the fingerprint plots, summarizing the major features of each structure in the related two-dimensional plot. For (3) and (5), without any N-H unit, the two short spikes are observed for (3) but are absent for (5). The upper d(e) and d(i) values (distances to the Hirshfeld surfaces for the nearest atoms outside and inside) in the fingerprint plots are more compact in (3) than in (4), and in (5) than in (6), reflecting the more efficient packing in (3) and (5). The tertiary N atoms of (3) and (5) do not take part in any intermolecular contacts involving H atoms. Moreover, structures (3)-(6) show greater contribution from C···H contacts relative to O···H contacts. Finally, Hirshfeld surfaces and fingerprint plots are employed for a comparison of the two independent molecules in the asymmetric unit of (1) and also, for a comparison of (6), in the orthorhombic crystal system, with the previously reported monoclinic polymorph (Pourayoubi, Fadaei et al., 2012).

Diphenyl (methylamido)phosphate

The N—H bond in the title compound, C₁₃H₁₄NO₃P, is syn-oriented relative to the P=O bond. The N atom deviates somewhat from planarity, the sum of the bond angles being 353.3°. The P atom has a distorted tetra­hedral coordination; its bond angles are in the range 93.96 (5)–116.83 (6)°. In the crystal, mol­ecules form centrosymmetric dimers through P=O⋯H—N hydrogen bonds.

N,N'-Dibenzyl-N''-(2-chloro-2,2-difluoro-acet-yl)phospho-ric triamide

In the title mol-ecule, C(16)H(17)ClF(2)N(3)O(2)P, the N-H unit of the C(=O)NHP(=O) fragment adopts a syn orientation with respect to the P=O group. The two F atoms and the Cl atom of the ClF(2)C group are disordered over two sets of sites with refined occupancies of 0.605 (6) and 0.395 (6). In the crystal, mol-ecules are linked via N-H⋯O=C hydrogen bonds the and the (N-H⋯)(N-H⋯)O=P group into chains along [010].

N,N-Dimethyl-N',N''-bis-(2-methyl-phenyl)phospho-ric triamide mono-hydrate

In the title compound, C₁₆H₂₂N₃OP·H₂O, the P atom adopts a distorted tetra­hedral environment with the bond angles around the P atom in the range 99.98 (7)–116.20 (7)°. The P—N bond length in the [(CH₃)₂N]P(O) fragment [1.6392 (14) Å] is slightly shorter than two other P—N bonds [1.6439 (15) and 1.6530 (14) Å]. In the (CH₃)₂NP(O) fragment, one of the methyl groups is syn to the P=O bond, whereas the other one is anti to the P=O bond [C—N—P=O torsion angles = 4.80 (17) and −174.57 (15)°]. In the crystal, the water mol­ecules form hydrogen bonds to the O atoms of the P=O bond of two different mol­ecules and act as acceptors for the two amino H atoms of the same mol­ecule. As a result, chains parallel to [010] are formed.

A second monoclinic polymorph of N-[bis-(morpholin-4-yl)phosphino-yl]-4-fluoro-benzamide with the P2(1)/n space group

A second monoclinic polymorph of the title mol­ecule, C₁₅H₂₁FN₃O₄P, is reported in the space group P2₁/n and compared to the previously reported C2/c space group [Gholivand et al. (2006 ▶). Polyhedron, 25, 711–721]. The asymmetric unit of the title compound consists of two independent mol­ecules. The P atoms adopt a distorted tetra­hedral environment. In the C(O)NHP(O) fragment, the P=O and the N—H groups are in a syn conformation with respect to each other and in the crystal, inter­molecular N—H⋯O=P hydrogen bonds form dimeric aggregates.

Cyclo-hexyl-ammonium acetate-N,N',N''-tricyclo-hexyl-phospho-ric triamide (1/1)

In the phospho­ric triamide mol­ecule of the title compound, C₆H₁₄N⁺·C₂H₃O₂⁻·C₁₈H₃₆N₃OP, the P atom displays a distorted tetra­hedral geometry and the cyclo­hexyl rings adopt chair conformations with the NH groups in equatorial positions. In the crystal, the cations, anions and phosphoric triamide mol­ecules are linked via N—H⋯O hydrogen bonds into a two-dimensional array parallel to the bc plane. The O atom of the P(O) group acts as a double-hydrogen-bond acceptor.

N,N'-Bis(4-methyl-phen-yl)-N''-(2,2,2-trichloro-acet-yl)phospho-ric triamide

The P atom in the title compound, C(16)H(17)Cl(3)N(3)O(2)P, is bonded in a distorted tetra-hedral geometry with the phosphoryl and carbonyl groups anti with respect to one another. In the crystal, mol-ecules are linked through (N-H)(2)⋯O(=P) and N-H⋯O(=C) hydrogen bonds into chains along [001]. The phosphoryl O atom acts as a double hydrogen-bond acceptor.

Two newXP(O)[NHC(CH3)3]2phosphoramidates, withX= (CH3)2N and [(CH3)3CNH]2P(O)(O)

InN,N′-di-tert-butyl-N′′,N′′-dimethylphosphoric triamide, C10H26N3OP, (I), andN,N′,N′′,N′′′-tetra-tert-butoxybis(phosphonic diamide), C16H40N4O3P2, (II), the extended structures are mediated by P(O)...(H—N)2interactions. The asymmetric unit of (I) consists of six independent molecules which aggregate through P(O)...(H—N)2hydrogen bonds, givingR21(6) loops and forming two independent chains parallel to theaaxis. Of the 12 independenttert-butyl groups, five are disordered over two different positions with occupancies ranging from 1 \over 6 to 5 \over 6. In the structure of (II), the asymmetric unit contains one molecule. P(O)...(H—N)2hydrogen bonds giveS(6) andR22(8) rings, and the molecules form extended chains parallel to thecaxis. The structures of (I) and (II), along with similar structures having (N)P(O)(NH)2and (NH)2P(O)(O)P(O)(NH)2skeletons extracted from the Cambridge Structural Database, are used to compare hydrogen-bond patterns in these families of phosphoramidates. The strengths of P(O)[...H—N]x(x= 1, 2 or 3) hydrogen bonds are also analysed, using these compounds and previously reported structures with (N)2P(O)(NH) and P(O)(NH)3fragments.