Three new [XC(O)NH]P(O)[N(CH2C6H5)2]2phosphoric triamides (X= CClF2, 3-F-C6H4and 3,5-F2-C6H3): a database analysis of tertiary N-atom geometry in compounds with a C(O)NHP(O)[N]2core

2012 ◽  
Vol 68 (10) ◽  
pp. o399-o404 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Jerry P. Jasinski ◽  
Samad Shoghpour Bayraq ◽  
Hossein Eshghi ◽  
Amanda C. Keeley ◽  
...  

In the phosphoric triamidesN,N,N′,N′-tetrabenzyl-N′′-(2-chloro-2,2-difluoroacetyl)phosphoric triamide, C30H29ClF2N3O2P, (I),N,N,N′,N′-tetrabenzyl-N′′-(3-fluorobenzoyl)phosphoric triamide, C35H33FN3O2P, (II), andN,N,N′,N′-tetrabenzyl-N′′-(3,5-difluorobenzoyl)phosphoric triamide, C35H32F2N3O2P, (III), the tertiary N atoms of the dibenzylamido groups havesp2character with minimal deviation from planarity. The sums of the three bond angles about the N atoms in (I)–(III) deviate by less than 8° from the planar value of 360°. The geometries of the tertiary N atoms in all phosphoric triamides with C(O)NHP(O)[N]2skeletons deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388] have been examined and the bond-angle sums at the two tertiary N atoms (SUM1 and SUM2) and the parameter ΔSUM (= SUM1 − SUM2) considered. It was found that in compounds with a considerable ΔSUM value, the more pyramidal N atoms are usually oriented so that the corresponding lone electron pair isantiwith respect to the P=O group. In (I), (II) and (III), the phosphoryl and carbonyl groups, separated by an N atom, areantiwith respect to each other. In the C(O)NHP(O) fragment of (I)–(III), the P—N bond is longer and the O—P—N angle is contracted compared with the other two P—N bonds and the O—P—N angles in the molecules. These effects are also seen in analogous compounds deposited in the CSD. Compounds with [C(O)NH]P(O)[N]X(X≠ N), such as compounds with a [C(O)NH]P(O)[N][O] skeleton, have not been considered here. Also, compounds with a [C(O)NH]2P(O)[N] fragment have not been reported to date. In the crystal structures of all three title compounds, adjacent molecules are linkedviapairs of P=O...H—N hydrogen bonds, forming dimers withCisymmetry.

2014 ◽  
Vol 70 (10) ◽  
pp. 998-1002 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arnold L. Rheingold ◽  
James A. Golen

InN,N,N′,N′-tetraethyl-N′′-(4-fluorobenzoyl)phosphoric triamide, C15H25FN3O2P, (I), andN-(2,6-difluorobenzoyl)-N′,N′′-bis(4-methylpiperidin-1-yl)phosphoric triamide, C19H28F2N3O2P, (II), the C—N—C angle at each tertiary N atom is significantly smaller than the two P—N—C angles. For the other new structure,N,N′-dicyclohexyl-N′′-(2-fluorobenzoyl)-N,N′-dimethylphosphoric triamide, C21H33FN3O2P, (III), one C—N—C angle [117.08 (12)°] has a greater value than the related P—N—C angle [115.59 (9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]2skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with theN-methylcyclohexylamide substituent, similar to (III), one structure with the seven-membered cyclic amide azepan-1-yl substituent and one structure with anN-methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linkedviapairs of N—H...O=P hydrogen bonds to form dimers.


2014 ◽  
Vol 70 (12) ◽  
pp. 1147-1152 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Mozhgan Abrishami ◽  
Václav Eigner ◽  
Marek Nečas ◽  
Michal Dušek ◽  
...  

The compoundN,N′,N′′-tricyclohexylphosphorothioic triamide, C18H36N3PS or P(S)[NHC6H11]3, (I), crystallizes in the space groupPnmawith 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 anantiorientation 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]3skeleton; 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. InO,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]3skeleton. 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]3and P(S)[O]2[N] segments were studied through a CSD analysis.


2009 ◽  
Vol 65 (3) ◽  
pp. 401-402 ◽  
Author(s):  
Vasyl Sidey

Systematic variations of the bond-valence sums calculated from the poorly determined bond-valence parameters [Sidey (2008), Acta Cryst. B64, 515–518] have been illustrated using a simple graphical scheme.


2008 ◽  
Vol 64 (3) ◽  
pp. 393-396 ◽  
Author(s):  
Peter A. Wood ◽  
Simon J. Borwick ◽  
David J. Watkin ◽  
W. D. Samuel Motherwell ◽  
Frank H. Allen

The Cambridge Structural Database (CSD) has been used to study nonbonded interactions between dipolar cyano groups. The analysis shows that C[triple-bond]N...C[triple-bond]N interactions form in an analogous manner to those involving carbonyl groups, and with the same interaction motifs: a dominant antiparallel dimer (57.5%) together with smaller populations of perpendicular (19.4%) and sheared parallel (23.0%) motifs. Ab initio calculations using intermolecular perturbation theory (IMPT) show an attractive C[triple-bond]N...C[triple-bond]N interaction in the dominant antiparallel dimer, with E t = −20.0 kJ mol−1 at d(C...N) = 3.30 Å and with the motif having a shear angle close to 102°. The antiparallel C[triple-bond]N...C[triple-bond]N interaction is therefore slightly weaker than the analogous C=O...C=O dimer (−23.5 kJ mol−1), but both interactions have attractive energies similar to that of a medium-strength hydrogen bond and, where sterically favoured, they are important in the stabilization of extended crystal structures.


Author(s):  
Mehrdad Pourayoubi ◽  
Maryam Toghraee ◽  
Vladimir Divjakovic ◽  
Arie van der Lee ◽  
Teresa Mancilla Percino ◽  
...  

Five new compounds belonging to the phosphoric triamide family have been synthesized: two of them with the formulaXC(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)Z2phosphoric triamides [Z= NHC(CH3)3(3), N(CH3)(C6H11) (4) and N(CH3)(CH2C6H5) (5)]. The characterization was performed by31P{1H},1H,13C NMR, IR spectroscopy besides19F 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 mainlysp2character 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)]2or C(O)—NH—P(O)[NH(C)]2. The participation of NCP—H...O=P [NCP= the nitrogen atom of the C(O)—NH—P(O) fragment], N—H...O=P, N—H...O=C and NCP—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 [NCP—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 anglesversusN...O distances are studied.


2008 ◽  
Vol 64 (4) ◽  
pp. 515-518 ◽  
Author(s):  
Vasyl Sidey

Applicability of the Wang–Liebau polyhedron eccentricity parameter in the bond-valence model [Wang & Liebau (2007). Acta Cryst. B63, 216–228] has been found to be doubtful: the correlations between the values of the polyhedron eccentricity parameters and the bond-valence sums calculated for the cations with one lone electron pair are probably an artifact of the poorly determined bond-valence parameters.


2021 ◽  
Vol 25 ◽  
Author(s):  
Evgenia S. Veligina ◽  
Nataliya V. Obernikhina ◽  
Stepan G. Pilyo ◽  
Oleksiy D. Kachkovsky ◽  
Volodymyr S. Brovarets

: Background: Synthesis of a series of 2-(dichloromethyl)pyrazolo[1,5- a][1,3,5]triazines was carried out and evaluated in vitro for their anticancer activity against a panel of 60 cell lines derived from nine cancer types. The joint quantum-chemical and experimental study of the influence of the extended πconjugated phenyl substituents on the electron structure of the pyrazolo[1,5-a][1,3,5]triazines as Pharmacophores were performed. It is shown that the decrease in the barriers to the rotation of phenyl substituents in compounds 1-7 possibly leads to an increase in the anti-cancer activity, which is in agreement with the change in the parameter biological affinity ϕ0. Analysis of the S0 → S1 electronic transitions (π→π*) of the pyrazolo[1,5-a][1,3,5]triazines shows that an increase in their intensity correlates with anti-cancer activity. Thus, the introduction of phenyl substituents increases the likelihood of investigated pyrazolo[1,5-a][1,3,5]triazines interacting with protein molecules (Biomolecule) by the π stacking mechanism. In both methyl and phenyl derivatives of pyrazolo[1,5-a][1,3,5]triazines, the second electronic transition includes the n-MO (the level of the lone electron pair in two-coordinated nitrogen atoms). The highest intensity of the η→π* electronic transition is observed in pyrazolo[1,5-a][1,3,5]triazine with pyridine residue, which does not exhibit anti-cancer activity, but exhibits antiviral activity [13]. It can be assumed that the possibility of the formation of [Pharmacophore-Biomolecule] complex by hydrogen bonding ([H-B]) mechanism with protein molecules increases.


2017 ◽  
Vol 73 (10) ◽  
pp. 1409-1413 ◽  
Author(s):  
Robert Rosin ◽  
Wilhelm Seichter ◽  
Monika Mazik

The syntheses and crystal structures ofN-(7-bromomethyl-1,8-naphthyridin-2-yl)acetamide dioxane hemisolvate, C11H10BrN3O·0.5C4H8O2, (I), and bis[N-(7-dibromomethyl-1,8-naphthyridin-2-yl)acetamide] dioxane hemisolvate, 2C11H9Br2N3O·0.5C4H8O2, (II), are described. The molecules adopt a conformation with the N—H hydrogen pointing towards the lone electron pair of the adjacent naphthyridine N atom. The crystals of (I) are stabilized by a three-dimensional supramolecular network comprising N—H...N, C—H...N and C—H...O hydrogen bonds, as well as C—Br...π halogen bonds. The crystals of compound (II) are stabilized by a three-dimensional supramolecular network comprising N—H...N, C—H...N and C—H...O hydrogen bonds, as well as C—H...π contacts and C—Br...π halogen bonds. The structure of the substituent attached in the 7-position of the naphthyridine skeleton has a fundamental influence on the pattern of intermolecular noncovalent bonding. While the Br atom of (I) participates in weak C—Br...Oguestand C—Br...π contacts, the Br atoms of compound (II) are involved in host–host interactionsviaC—Br...O=C, C—Br...N and C—Br...π bonding.


Author(s):  
Miroslaw Gilski ◽  
Jianbo Zhao ◽  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Douglas H. Turner ◽  
...  

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.


2012 ◽  
Vol 8 (2) ◽  
pp. 1566-1580 ◽  
Author(s):  
Hiba Khili ◽  
Najla Chaari ◽  
Mohamed Fliyou ◽  
Slaheddine Chaabouni

The [C8H12N]2 BiCl5 compound crystallised in the triclinic system with space group  P-1  with a = 9,833(4),                     b = 10,044(7), c = 12,225(7) Å, a= 78.82(4), β = 75,42(4), g= 76.89°(5)  and Z = 2. The average density value, ρx = 1.518 g.cm-3  is in agreement with the calculated one, ρx = 1.494 g.cm-3. The atomic arrangement can be described as an alternation of organic and inorganic layers. The anionic layer is built up of octahedral [Bi2Cl10]-4. The organic layers are arranged in sandwich between the anionic ones. The crystal packing is governed by means of the ionic N–H---Cl hydrogen bonds, forming a three dimensional network. The nature of the distortion of the inorganic polyhedra has been studied and can be attributed to the stereo activity of the Bi(III) lone electron pair. The infrared and Raman spectra was recorded in the 4000–400 cm-1 frequency region.


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