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.

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.

scholarly journals The crystal structures of two novel polymorphs of bis(oxonium) ethane-1,2-disulfonate

2019 ◽  
Vol 75 (11) ◽  
pp. 1586-1589
Author(s):  
Jaroslaw Mazurek ◽  
Ana Fernandez-Casares
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Acta Cryst ◽  
Crystal Forms ◽  
Crystal Density ◽  
Hydrogen Bonding Network

Two novel crystal forms of bis(oxonium) ethane-1,2-disulfonate, 2H3O−·C2H4O6S2 2−, are reported. Polymorph II has monoclinic (P21/n) symmetry, while the symmetry of form III is triclinic (P\overline{1}). Both structures display extensive networks of O—H...O hydrogen bonds. While this network in Form II is similar to that observed for the previously reported Form I [Mootz & Wunderlich (1970). Acta Cryst. B26, 1820–1825; Sartori et al. (1994). Z. Naturforsch. 49, 1467–1472] and extends in all directions, in Form III it differs significantly, forming layers parallel to the ab plane. The sulfonate molecule in all three forms adopts a nearly identical geometry. The other observed differences between the forms, apart from the hydrogen-bonding network, are observed in the crystal density and packing index.

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

2017 ◽  
Vol 73 (3) ◽  
pp. 287-297 ◽  
Author(s):  
Farahnaz Hamzehee ◽  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Duane Choquesillo-Lazarte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Neutral Hydrogen ◽  
The Other ◽  
Phosphorus Compounds ◽  
Database Study ◽  
Extensive Analysis ◽  
Structural Database

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.

Heterocyclic tautomerism: reassignment of two crystal structures of 2-amino-1,3-thiazolidin-4-one derivatives

2014 ◽  
Vol 70 (8) ◽  
pp. 812-816 ◽  
Author(s):  
Andrzej K. Gzella ◽  
Marcin Kowiel ◽  
Aneta Suseł ◽  
Magdalena N. Wojtyra ◽  
Roman Lesyk
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Heterocyclic Ring ◽  
Secondary Amide ◽  
Acta Cryst ◽  
Imine Group ◽  
Structural Database ◽  
Main Factor

The structures of 5-(2-hydroxyethyl)-2-[(pyridin-2-yl)amino]-1,3-thiazolidin-4-one, C10H11N3O2S, (I), and ethyl 4-[(4-oxo-1,3-thiazolidin-2-yl)amino]benzoate, C12H12N2O3S, (II), which are identical to the entries with refcodes GACXOZ [Váňaet al.(2009).J. Heterocycl. Chem.46, 635–639] and HEGLUC [Behbehani & Ibrahim (2012).Molecules,17, 6362–6385], respectively, in the Cambridge Structural Database [Allen (2002).Acta Cryst.B58, 380–388], have been redetermined at 130 K. This structural study shows that both investigated compounds exist in their crystal structures as the tautomer with the carbonyl–imine group in the five-membered heterocyclic ring and an exocyclic amine N atom, rather than the previously reported tautomer with a secondary amide group and an exocyclic imine N atom. The physicochemical and spectroscopic data of the two investigated compounds are the same as those of GACXOZ and HEGLUC, respectively. In the thiazolidin-4-one system of (I), the S and chiral C atoms, along with the hydroxyethyl group, are disordered. The thiazolidin-4-one fragment takes up two alternative locations in the crystal structure, which allows the molecule to adoptRandSconfigurations. The occupancy factors of the disordered atoms are 0.883 (2) (for theRconfiguration) and 0.117 (2) (for theSconfiguration). In (I), the main factor that determines the crystal packing is a system of hydrogen bonds, involving both strong N—H...N and O—H...O and weak C—H...O hydrogen bonds, linking the molecules into a three-dimensional hydrogen-bond network. On the other hand, in (II), the molecules are linkedviaN—H...O hydrogen bonds into chains.

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.

scholarly journals Bis(μ2-4-nitrophenolato)bis(4-nitrophenolato)di-μ3-oxido-octaphenyltetratin chloroform sesquisolvate [+ solvate]: a tetranuclear stannoxane

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Complex Molecules ◽  
Three Dimensional Structure

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

2021 ◽  
Vol 77 (2) ◽  
pp. 211-218
Author(s):  
Ivica Cvrtila ◽  
Vladimir Stilinović
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Two Dimensional ◽  
Structural Motifs ◽  
Supramolecular Isomerism ◽  
Other Hand ◽  
Π Stacking ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

2015 ◽  
Vol 71 (10) ◽  
pp. 921-928 ◽  
Author(s):  
Kulsoom Kamal ◽  
Hardesh K. Maurya ◽  
Atul Gupta ◽  
Prema G. Vasudev
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Cambridge Structural Database ◽  
Database Analysis ◽  
Molecular Conformations ◽  
Keto Esters ◽  
Organic Molecular Crystals ◽  
Structural Database

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013).RSC Adv.3, 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014).Angew. Chem. Int. Ed.53, 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple-bond]C interaction (X = F, Cl, Br or I),viz.the N...Xdistance and the C—X...N and C—N...Xangles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

scholarly journals Crystal structures of 4-methyl-2-oxo-2H-chromene-7,8-diyl diacetate and 4-methyl-2-oxo-2H-chromene-7,8-diyl bis(pent-4-ynoate)

2016 ◽  
Vol 72 (5) ◽  
pp. 704-708
Author(s):  
Akintunde Akinyemi ◽  
Courtney Thomas ◽  
Willis Marsh ◽  
Ray J. Butcher ◽  
Jerry P. Jasinski ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Triple Bond ◽  
The Other ◽  
Coumarin Derivatives ◽  
Extended Conformation ◽  
Π Stacking ◽  
Planar Part ◽  
Centrosymmetric Dimers

In the structures of the two title coumarin derivatives, C14H12O6, (1), and C20H16O6, (2), one with acetate and the other with pent-4-ynoate substituents, both the coumarin rings are almost planar. In (1), both acetate substituents are significantly rotated out of the coumarin plane to minimize steric repulsions. One acetate substituent is disordered over two equivalent conformations, with occupancies of 0.755 (17) and 0.245 (17). In (2), there are two pent-4-ynoate substituents, the C[triple-bond]C group of one being disordered over two positions with occupancies of 0.55 (2) and 0.45 (2). One of the pent-4-ynoate substituents is in an extended conformation, while the other is in a bent conformation. In this derivative, the planar part of both pent-4-ynoate substituents deviate from the coumarin plane. The packing of (1) is dominated by π–π stacking involving the coumarin rings and weak C—H...O contacts link the parallel stacks in the [101] direction. In contrast, in (2) the packing is dominated byR22(24) hydrogen bonds, involving the acidicspH atom and the oxo O atom, which link the molecules into centrosymmetric dimers. The bent conformation of one of the pent-4-ynoate substituents prevents the coumarin rings from engaging in π–π stacking.

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