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

2013 ◽  
Vol 69 (2) ◽  
pp. 184-194 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Maryam Toghraee ◽  
Vladimir Divjakovic ◽  
Arie van der Lee ◽  
Teresa Mancilla Percino ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structure Analysis ◽  
Cambridge Structural Database ◽  
Tetrahedral Environment ◽  
Phosphoric Triamide ◽  
Structural Database ◽  
C And N ◽  
New Compounds ◽  
Phosphoric Triamides ◽  
C Nmr

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.

Three new phosphoric triamides with a [C(O)NH]P(O)[N(C)(C)]2skeleton: a database analysis of C—N—C and P—N—C bond angles

2014 ◽  
Vol 70 (10) ◽  
pp. 998-1002 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arnold L. Rheingold ◽  
James A. Golen
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Database Analysis ◽  
Acta Cryst ◽  
Bond Angles ◽  
Cyclic Amide ◽  
Phosphoric Triamide ◽  
Structural Database ◽  
Phosphoric Triamides

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.

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

2013 ◽  
Vol 69 (2) ◽  
pp. 184-194
Author(s):  
Mehrdad Pourayoubi ◽  
Maryam Toghraee ◽  
Vladimir Divjakovic ◽  
Arie van der Lee ◽  
Teresa Mancilla Percino ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Structural Database ◽  
Phosphoric Triamides

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

Understanding distortions of inorganic substructures in chloridobismuthates(III)

2021 ◽  
Vol 77 (5) ◽  
Author(s):  
Maciej Bujak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Inorganic Anions ◽  
Cambridge Structural Database ◽  
Molar Ratio ◽  
Organic Cations ◽  
Hybrid Crystals ◽  
Structural Database ◽  
Distortion Parameters

The molar ratio variations of organic and inorganic reactants of chloridobismuthates(III) with N,N-dimethylethane-1,2-diammonium, [(CH3)2NH(CH2)2NH3]2+, and N,N,N′,N′-tetramethylguanidinium, [NH2C{N(CH3)2}2]+, cations lead to the formation of four different products, namely, tris(N,N-dimethylethane-1,2-diammonium) bis[hexachloridobismuthate(III)], [(CH3)2NH(CH2)2NH3]3[BiCl6]2 (1), catena-poly[N,N-dimethylethane-1,2-diammonium [[tetrachloridobismuthate(III)]-μ-chlorido]], {[(CH3)2NH(CH2)2NH3][BiCl5]} n (2), tris(N,N,N′,N′-tetramethylguanidinium) tri-μ-chlorido-bis[trichloridobismuthate(III)], [NH2C{N(CH3)2}2]3[Bi2Cl9] (3), and catena-poly[N,N,N′,N′-tetramethylguanidinium [[dichloridobismuthate(III)]-di-μ-chlorido]], {[NH2C{N(CH3)2}2][BiCl4]} n (4). The hybrid crystals 1–4, containing relatively large but different organic cations, are composed of four distinct anionic substructures. They are built up from isolated [BiCl6]3− octahedra in 1, from face-sharing bioctahedral [Bi2Cl9]3− units in 3, from polymeric corner-sharing {[BiCl5]2−} n chains in 2 and from edge-sharing {[BiCl4]−} n chains in 4. The distortions shown by the single [BiCl6]3− polyhedra in 1–4 are associated with intrinsic interactions within the anionic substructures and the organic...inorganic substructures interactions, namely, N/C—H...Cl hydrogen bonds. The first factor is the stronger, which is evident in comparison of the experimentally determined geometrical and calculated distortion parameters for the isolated octahedron in 1 to the more complex inorganic substructures in 2–4. The formation of N—H...Cl hydrogen bonds, in terms of their number and strength, is favoured for 1 and 3 containing relatively easily accessed hydrogen-bond acceptors of isolated [BiCl6]3− and [Bi2Cl9]3− units. The studies of the deviations from regularity of the [BiCl6]3− octahedra within inorganic substructures were supported by a survey of the Cambridge Structural Database, which confirmed the role played by different factors in the variations in geometry of the inorganic anions.

scholarly journals N,N′-Bis(4-bromophenyl)-N,N′-dimethylurea

IUCrData ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Alexandre Pocinho ◽  
Sonia Mallet-Ladeira ◽  
Christelle Hureau ◽  
Emmanuel Gras
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Cambridge Structural Database ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Compound C ◽  
Structural Database

The structure of the title compound, C15H14Br2N2O, at 180 K has monoclinic (P21/n) symmetry. It was obtained unexpectedly from the decomposition of the parent 4-bromo-N-tert-butoxycarbonyl-N-methyl-aniline. It exhibits an `endo' conformation with angles between the two aromatic rings slightly lower than the average values found for similar compounds on the Cambridge Structural Database. In the crystal, C—H...O hydrogen bonds and short Br...Br halogen bonds [3.444 (1) Å] are observed.

Zur Reaktion von 2,4-Dioxo-4-ferrocenyl-butansäureethylester mit primären aromatischen Aminen / On the Reaction of Ethyl 2,4-Dioxo-4-ferrocenyl-butanoate with Primary Aromatic Amines

1999 ◽  
Vol 54 (7) ◽  
pp. 849-857 ◽  
Author(s):  
Petra Prokop ◽  
Rainer Richter ◽  
Lothar Beyer
Keyword(s):  
Ethyl Ester ◽  
Carbonic Acid ◽  
Acid Ethyl Ester ◽  
Crystal Structure Analysis ◽  
Molecular Structures ◽  
Ferrocene Derivatives ◽  
Primary Aromatic Amines ◽  
New Compounds ◽  
C Nmr ◽  
Phenylene Diamine

Starting from ethyl 2,4-dioxo-4-ferrocenyl-butanoate (1) a series of new ferrocene derivatives has been prepared. While the reaction with o-phenylene diamine leads to two ferrocene-containing heterocyclic compounds, 4-ferrocenyl-3H-1,5-benzodiazepine-2-carbonic acid ethyl ester (3) and 3-(2-ferrocenyl-2-oxo-ethylidene)-3,4-dihydro-1H-quinoxalin-2-one · H20 (4), reactions with m- and p-phenylene diamine give both the mono- and disubstituted products 5 - 8, respectively. The conversion of 4 by Lawesson’s reagent results in 2-ferrocenvl-thieno[2,3- b]quinoxaline (9). The new compounds have been characterized by their 1H, 13C NMR, and mass spectra. The molecular structures of 4-ferrocenyl-4-oxo-2-phenylamino-but-2-enoic acid ethyl ester 2, and of 4 and 9 have been determined by X-ray crystal structure analysis.

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 ◽  
...  
Keyword(s):  
Lone Electron Pair ◽  
Electron Pair ◽  
Bond Angle ◽  
Carbonyl Groups ◽  
Database Analysis ◽  
Acta Cryst ◽  
Phosphoric Triamide ◽  
Minimal Deviation ◽  
Structural Database ◽  
Phosphoric Triamides

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.

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

2012 ◽  
Vol 68 (4) ◽  
pp. o164-o169 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Fatemeh Karimi Ahmadabad ◽  
Karla Fejfarová ◽  
Arie van der Lee ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Asymmetric Unit ◽  
Structural Database ◽  
Independent Molecules ◽  
Hydrogen Bond Patterns

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.

Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones

2016 ◽  
Vol 72 (3) ◽  
pp. 317-325 ◽  
Author(s):  
Dikima Bibelayi ◽  
Albert S. Lundemba ◽  
Frank H. Allen ◽  
Peter T. A. Galek ◽  
Juliette Pradon ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Crystal Engineering ◽  
Cambridge Structural Database ◽  
Bond Lengths ◽  
Partial Charges ◽  
Structural Database

In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database andab initiocalculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries andab initiopartial charges show that this bonding stems from resonance-induced Cδ+=Seδ−dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering.

scholarly journals Synthesis of N-substituted 3-(2-aryl-2-oxoethyl)-3-hydroxyindolin-2-ones and their conversion to N-substituted (E)-3-(2-aryl-2-oxoethylidene)indolin-2-ones: synthetic sequence, spectroscopic characterization and structures of four 3-hydroxy compounds and five oxoethylidene products

2020 ◽  
Vol 76 (5) ◽  
pp. 433-445
Author(s):  
Diana Becerra ◽  
Juan Castillo ◽  
Braulio Insuasty ◽  
Justo Cobo ◽  
Christopher Glidewell
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Spectroscopic Characterization ◽  
Crystal Structure Analysis ◽  
Dimensional Structure ◽  
Acidic Conditions ◽  
Synthetic Sequence ◽  
Hydroxy Compounds ◽  
Aryl Methyl ◽  
C Nmr

An operationally simple and time-efficient approach has been developed for the synthesis of racemic N-substituted 3-(2-aryl-2-oxoethyl)-3-hydroxyindolin-2-ones by a piperidine-catalysed aldol reaction between aryl methyl ketones and N-alkylisatins. These aldol products were used successfully as strategic intermediates for the preparation of N-substituted (E)-3-(2-hetaryl-2-oxoethylidene)indolin-2-ones by a stereoselective dehydration reaction under acidic conditions. The products have all been fully characterized by 1H and 13C NMR spectroscopy, by mass spectrometry and, for a representative selection, by crystal structure analysis. In each of (RS)-1-benzyl-3-hydroxy-3-[2-(4-methoxyphenyl)-2-oxoethyl]indolin-2-one, C24H21NO4, (Ic), and (RS)-1-benzyl-3-{2-[4-(dimethylamino)phenyl]-2-oxoethyl}-3-hydroxyindolin-2-one, C25H24N2O3, (Id), inversion-related pairs of molecules are linked by O—H...O hydrogen bonds to form R 2 2(10) rings, which are further linked into chains of rings by a combination of C—H...O and C—H...π(arene) hydrogen bonds in (Ic) and by C—H...π(arene) hydrogen bonds in (Id). The molecules of (RS)-1-benzyl-3-hydroxy-3-[2-oxo-2-(pyridin-4-yl)ethyl]indolin-2-one, C22H18N2O3, (Ie), are linked into a three-dimensional framework structure by a combination of O—H...N, C—H...O and C—H...π(arene) hydrogen bonds. (RS)-3-[2-(Benzo[d][1,3]dioxol-5-yl)-2-oxoethyl]-1-benzyl-3-hydroxyindolin-2-one, C24H19NO5, (If), crystallizes with Z′ = 2 in the space group P\overline{1} and the molecules are linked into complex sheets by a combination of O—H...O, C—H...O and C—H...π(arene) hydrogen bonds. In each of (E)-1-benzyl-3-[2-(4-fluorophenyl)-2-oxoethylidene]indolin-2-one, C23H16FNO2, (IIa), and (E)-1-benzyl-3-[2-oxo-2-(thiophen-2-yl)ethylidene]indolin-2-one, C21H15NO2S, (IIg), the molecules are linked into simple chains by a single C—H...O hydrogen bond, while those of (E)-1-benzyl-3-[2-oxo-2-(pyridin-4-yl)ethylidene]indolin-2-one, C22H16N2O2, (IIe), are linked by three C—H...O hydrogen bonds to form sheets which are further linked into a three-dimensional structure by C—H...π(arene) hydrogen bonds. There are no hydrogen bonds in the structures of either (E)-1-benzyl-3-[2-(4-methoxyphenyl)-2-oxoethylidene]indolin-2-one, C24H19NO3, (IIc), or (E)-1-benzyl-5-chloro-3-[2-(4-chlorophenyl)-2-oxoethylidene]indolin-2-one, C23H15Cl2NO2, (IIh), but the molecules of (IIh) are linked into chains of π-stacked dimers by a combination of C—Cl...π(arene) and aromatic π–π stacking interactions.

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