Analysis of P–O–C, P–S–C and P–O–P angles: a database survey completed with four new X-ray crystal structures

Sabbaghi, Fahimeh; Pourayoubi, Mehrdad; Dušek, Michal; Eigner, Václav; Bayat, Sahar; Damodaran, Krishnan; Nečas, Marek

doi:10.1007/s11224-016-0809-7

Cited by 10 publications

(16 citation statements)

References 41 publications

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“…The C-O-P angles are 119.6 (2) (C12-O11-P1) and 122.8 (2) (C10-O12-P1) for molecule 1 and 119.9 (2) (C23-O22-P2) and 122.4 (2) (C25-O21-P2) for molecule 2. These values are similar to those reported in analogous structures with a similar P (Sabbaghi et al, 2016). Fig.…”

Section: Figuresupporting

confidence: 91%

“…The P atom is bonded in a distorted tetrahedral P[S][O] 2 [N] environment, with the surrounding bond angles at the P atom ranging from 99.04 (13) (O11-P1-O12) to 117.29 (10) (O11-P1-S1) for molecule 1 and from 99.10 (12) (O22-P2-O21) to 116.85 (10) (O22-P2-S2) for molecule 2. The maximum and minimum bond angles at the P atom are similar to those reported for an analogous structure with a similar (Sabbaghi et al, 2016). The N atoms adopt a practically planar environment (sp 2 hybridization state), which is reflected in the bond-angle sums at the N atoms (P-N-C + C-N-H + H-N-P ' 360 ).…”

Section: Figuresupporting

confidence: 79%

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Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

et al. 2018

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In the crystal structure of O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate, CHNOPS, two symmetrically independent thiophosphoramide molecules are linked through N-H...S and N-H...π hydrogen bonds to form a noncentrosymmetric dimer, with Z' = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06-2X level within the 6-311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N-H...S hydrogen bond is slightly stronger than the N-H...π hydrogen bond. This is reflected in differences between the calculated N-H stretching frequencies of the isolated molecules and the frequencies of the same N-H units involved in the different hydrogen bonds of the hydrogen-bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.

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Section: Figuresupporting

confidence: 91%

Section: Figuresupporting

confidence: 79%

Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

et al. 2018

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“…The P O, P-O and P-N bond lengths are within the ranges observed in analogous structures (Hamzehee et al, 2016). The P-N-C and P-O-C angles show a little more 's' character with respect to sp 2 hybridization, as has been reported previously by a Cambridge Structural Database (CSD) analysis and by quantum chemical calculations for analogous structures (Sabbaghi et al, 2016;Vahdani Alviri et al, 2018). At the P atom, the narrowest and widest bond angles correspond to O2-P1-O3 and O1-P1-O3, with the values in the structure (I) being typical at 93.09 7 Computer programs: CrystalClear-SM Expert (Rigaku, 2014), CrysAlis PRO (Rigaku OD, 2015), SHELXT2014 (Sheldrick, 2015a), SHELXL2018 (Sheldrick, 2015b), Mercury (Macrae et al, 2008) and enCIFer (Allen et al, 2004).…”

Section: Description Of the Crystal Structuressupporting

confidence: 85%

Two single-enantiomer amidophosphoesters: a database study on the chirality of (O)₂P(O)(N)-based structures

et al. 2019

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The crystal structures of two single-enantiomer amidophosphoesters with an (O) 2 P(O)(N) skeleton, i.e. diphenyl [(R)-(+)--methylbenzylamido]phosphate, (I), and diphenyl [(S)-(À)--methylbenzylamido]phosphate, (II), both C 20 H 20 -NO 3 P, are reported. In both structures, chiral one-dimensional hydrogenbonded architectures, along [010], are mediated by N-HÁ Á ÁOP interactions. The statistically identical assemblies include the noncentrosymmetric graph-set motif C(4) and the compounds crystallize in the chiral space group P2 1 . As a result of synergistic co-operation from C-HÁ Á ÁO interactions, a two-dimensional superstructure is built including a noncentrosymmetric R 4 4 (22) hydrogenbonded motif. A Cambridge Structural Database survey was performed on (O) 2 P(O)(N)-based structures in order to review the frequency of space groups observed in this family of compounds; the hydrogen-bond motifs in structures with chiral space groups and the types of groups inducing chirality are discussed. The 2,3 J X-P (X = H or C) coupling constants from the NMR spectra of (I) and (II) have been studied. In each compound, the two diastereotopic C 6 H 5 O groups are different, which is reflected in the different chemical shifts and some coupling constants.

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“…In the hydrogen bonds formed, the P O group has a better acceptor capability than the other acceptor groups that usually exist in the structures, typically C O (Vahdani Alviri et al, 2018), S O (Pourayoubi et al, 2011) and N O/N-O (Gholivand et al, 2009), and a much better capability than ISSN 2053ISSN -2296 # 2018 International Union of Crystallography acceptors such as P S (Cupertino et al, 1998), C S (Omrani et al, 2015) and OAr (Ar = aryl) (Sabbaghi et al, 2016) groups. Thus, the P O group usually dictates the hydrogen-bond pattern as the best hydrogen-bond acceptor in the molecule.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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Analysis of P–O–C, P–S–C and P–O–P angles: a database survey completed with four new X-ray crystal structures

Cited by 10 publications

References 41 publications

Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

Two single-enantiomer amidophosphoesters: a database study on the chirality of (O)₂P(O)(N)-based structures

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

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Analysis of P–O–C, P–S–C and P–O–P angles: a database survey completed with four new X-ray crystal structures

Cited by 10 publications

References 41 publications

Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

Two single-enantiomer amidophosphoesters: a database study on the chirality of (O)2P(O)(N)-based structures

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

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Product

Resources

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Two single-enantiomer amidophosphoesters: a database study on the chirality of (O)₂P(O)(N)-based structures

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