Combination of X-ray crystallography and theoretical study to evaluate the effect of NH⋯OP versus NH⋯OC hydrogen bonds on the NH stretching frequencies

Pourayoubi, Mehrdad; Izadyar, Mohammad; Elahi, Behrouz; Parvez, Masood

doi:10.1016/j.molstruc.2012.10.055

Cited by 16 publications

(12 citation statements)

References 20 publications

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“…In 5 In the IR spectra the absorption bands in the range 3024-3075 cm À1 in (1)-(5) and the bands at 3344, 3347 and 3362 cm À1 for (1), (2) and (3) are assigned to the corresponding N CP -H and N-H stretching modes, respectively. The lower N CP -H stretching frequencies with respect to the N-H stretching frequencies are attributed to the strengths of N CP -HÁ Á ÁO P relative to N-HÁ Á ÁO C hydrogen bonds, which was discussed in a recently published paper (Pourayoubi et al, 2013) by considering the experimental and theoretical evidence.…”

Section: Nmr and Ir Studiesmentioning

confidence: 94%

Analysis of N—H...O hydrogen bonds in new C(O)—NH—P(O)-based phosphoric triamides and analogous structures deposited in the Cambridge Structural Database

Pourayoubi

Toghraee

Divjaković

et al. 2013

Acta Crystallogr B Struct Sci Cryst Eng Mater

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Five new compounds belonging to the phosphoric triamide family have been synthesized: two of them with the formula XC(O)NHP(O)Y [X = CF3 (1) and CClF2 (2), Y = NHCH2C(CH3)2CH2NH] involving a 1,3-diazaphosphorinane ring part, and three 2,6-Cl2C6H3C(O)NHP(O)Z2 phosphoric triamides [Z = NHC(CH3)3 (3), N(CH3)(C6H11) (4) and N(CH3)(CH2C6H5) (5)]. The characterization was performed by (31)P{(1)H}, (1)H, (13)C NMR, IR spectroscopy besides (19)F NMR for fluorine containing compounds (1) and (2), and X-ray single-crystal structure analysis for (1), (3), (4) and (5). In each molecule the P atom has a distorted tetrahedral environment. The N atoms bonded to P atom have mainly sp(2) character with a very slight tendency to a pyramidal coordination for some amido groups. Different types of N-H···O hydrogen bonds have been analyzed for (1), (3), (4) and (5) and 118 other structures (including 194 hydrogen bonds) deposited in the Cambridge Structural Database, containing either C(O)-NH-P(O)[N(C)(C)]2 or C(O)-NH-P(O)[NH(C)]2. The participation of N(CP)-H···O=P [N(CP) = the nitrogen atom of the C(O)-NH-P(O) fragment], N-H···O=P, N-H···O=C and N(CP)-H···O=C hydrogen bonds in different hydrogen-bonded motifs are discussed. Moreover, the involvement of the O atoms of C=O or P=O in the [N(CP)-H][N-H]···O=P, [N-H]2···O=P, [N-H]2···O=C and [N-H]3···O=C groups are considered. A histogram of N···O distances, the distribution of N-H···O angles and the scatterplot of N-H···O angles versus N···O distances are studied.

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Section: Nmr and Ir Studiesmentioning

confidence: 94%

Analysis of N—H...O hydrogen bonds in new C(O)—NH—P(O)-based phosphoric triamides and analogous structures deposited in the Cambridge Structural Database

Pourayoubi

Toghraee

Divjaković

et al. 2013

Acta Crystallogr B Struct Sci Cryst Eng Mater

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“…The difference between the envelope and half-chair conformations is mostly related to the 4 parameter which is 0 or 180 for the envelope conformation, and 90 or 270 for the half-chair conformation. An example of a typical "C2N2P" structure is that with refcode DIGHEI 44 (Q ¼ 0.209 (2) and 4 ¼ 112.5 (5) ). A set of 18 structures with a "C6" (6 structures) or "C5N" (12 structures) group was investigated and all of them show a near chair conformation, with a slight deviation from the ideal chair of cyclohexane caused by the bulk phosphorus-containing group in the equatorial position of the ring.…”

Section: Puckering Behavior Of C(o)nhp(o)-based Phosphoric Triamides mentioning

confidence: 99%

“…44 The stretching frequency assigned to the N CP eH vibration shows a blue shift in 2 with respect to that of 1, due to the weaker intermolecular N CP eH/O]C hydrogen bond in 2 compared to the N CP eH/O]P hydrogen bond in 1. This band includes a shoulder in the higher frequency attributed to the N P eH units.…”

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confidence: 94%

Puckering behavior in six new phosphoric triamides containing aliphatic six- and seven-membered ring groups and a database survey of analogous ring-containing structures

et al. 2018

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The influence of a N heteroatom on the ring conformations of six-and seven-membered aliphatic rings in six new C(O)NHP(O)-based phosphoric triamide structures (analysed by X-ray crystallography) is investigated. Additionally the influence of steric and crystal packing effects is also studied by the analysis of Hirshfeld surfaces. The results are compared to analogous structures with three-to seven-aliphatic membered rings deposited in the Cambridge Structural Database. In the newly determined structures, the six-membered rings only show the near-chair conformation with a maximum deviation of the q puckering parameter of 4.4 from the ideal chair value of 0 /180 , while the seven-membered rings are found in different conformations such as near-chair, twist chair and twist sofa.

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“…In both compounds, the lower stretching frequencies are related to N CP -H, engaged in hydrogen bonding interactions with the P=O group (with greater hydrogen bond strengths with respect to the N P -H···O=C hydrogen bond), as demonstrated by a comparison of IR spectra in various compounds and supported by quantum chemical calculations (Pourayoubi et al 2013). The reason for the higher N P -H stretching frequency of 1 with respect to that of 2 is related to the involvement of N P -H units in weaker hydrogen bonds as will be discussed in the X-ray crystallography section.…”

Section: Ir and Nmr Studymentioning

confidence: 68%

Different molecular assemblies in two new phosphoric triamides with the same C(O)NHP(O)(NH)2 skeleton: crystallographic study and Hirshfeld surface analysis

et al. 2017

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Different molecular assemblies were compared in two new structures [4-CH 3 -C 6 H 4 C(O)NH]P(O) [NH] 2 (-CH 2 ) 3 , 1, and [4-CH 3 -C 6 H 4 C(O)NH]P(O) [NHC 6 H 3 (3, ) 2 ] 2 , 2, belonging to the families of "cyclic phosphoric triamide" and "phosphoric triamide", respectively. The differences in the hydrogen bond motifs were discussed (by single crystal X-ray diffraction) as a result of three factors: (1) action of two N atoms with a non-planar environment in 1 as an H-bond acceptor, (2) different orientations of three N-H bond vectors in two molecules and (3) different conformations of C=O and P=O groups. These differences lead to more complicated hydrogen bond pattern of 1, with respect to that of 2, as structure 1 may be considered as a model of four-acceptor-three-donor versus a two-acceptorthree-donor system in 2. The main discrepancies of 1 and 2, monitored by the Hirshfeld surface analysis, are related to the contribution portions of O···H/H···O contacts, in which compound 1 not only involves the greater existence of classical hydrogen bonds but also contains the further C-H···O weak interactions in its crystal packing with respect to compound 2. Instead, in 2, the shortage of O···H/H···O contacts has been partially compensated by the C···H/H···C interactions, due to the presence of more unsaturated carbon acceptors. The differences in assemblies are also reflected in the solid-state IR spectra, especially for the N-H vibration frequencies. The new compounds were further studied by 1D NMR experiments ( 1 H, 13 C, 31 P), 2D NMR techniques [HMQC and HMBC (H-C correlation), HSQC (N-H correlation)], high-resolution ESI-MS, EI-MS spectrometry and IR spectroscopy.

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Combination of X-ray crystallography and theoretical study to evaluate the effect of NH⋯OP versus NH⋯OC hydrogen bonds on the NH stretching frequencies

Cited by 16 publications

References 20 publications

Analysis of N—H...O hydrogen bonds in new C(O)—NH—P(O)-based phosphoric triamides and analogous structures deposited in the Cambridge Structural Database

Analysis of N—H...O hydrogen bonds in new C(O)—NH—P(O)-based phosphoric triamides and analogous structures deposited in the Cambridge Structural Database

Puckering behavior in six new phosphoric triamides containing aliphatic six- and seven-membered ring groups and a database survey of analogous ring-containing structures

Different molecular assemblies in two new phosphoric triamides with the same C(O)NHP(O)(NH)2 skeleton: crystallographic study and Hirshfeld surface analysis

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