A novel amido–pyrophosphate MnII chelate complex with the synthetic ligand O{P(O)[NHC(CH3)3]2}2 (L): [Mn(L)2{OC(H)N(CH3)2}2]Cl2·2H2O

The title complex, trans‐bis(dimethylformamide‐κO)bis{N,N′‐N′′,N′′′‐tetra‐tert‐butyl[oxybis(phosphonic diamide‐κO)]}manganese(II) dichloride dihydrate, [Mn(C₁₆H₄₀N₄O₃P₂)₂(C₃H₇NO)₂]Cl₂·2H₂O, is the first example of a bis‐chelate amido–pyrophosphate (pyrophosphoramide) complex containing an O[P(O)(NH)₂]₂ fragment. Its asymmetric unit contains half of the complex dication, one chloride anion and one water molecule. The Mn^II atom, located on an inversion centre, is octahedrally coordinated, with a slight elongation towards the monodentate dimethylformamide ligand. Structural features of the title complex, such as the P=O bond lengths and the planarity of the chelate ring, are compared with those of previously reported complexes with six‐membered chelates involving the fragments C(O)NHP(O), (X)NP(O) [X = C(O), C(S), S(O)₂ and P(O)] and O[P(O)(N)₂]₂. This analysis shows that the six‐membered chelate rings are less puckered in pyrophosphoramide complexes containing a P(O)OP(O) skeleton, such as the title compound. The extended structure of the title complex involves a linear aggregate mediated by N—H...O and N—H...Cl hydrogen bonds, in which the chloride anion is an acceptor in two additional O—H...Cl hydrogen bonds.     

The double H‐atom acceptability of the P=O group in new XP(O)(NHCH2C6H4‐2‐Cl)2 phosphoramidates [X = C6H5O– and CF3C(O)NH–]: a database analysis of compounds having a P(O)(NHR) group

In the hydrogen‐bond patterns of phenyl bis(2‐chlorobenzylamido)phosphinate, C₂₀H₁₉Cl₂N₂O₂P, (I), and N,N′‐bis(2‐chlorobenzyl)‐N′′‐(2,2,2‐trifluoroacetyl)phosphoric triamide, C₁₆H₁₅Cl₂F₃N₃O₂P, (II), the O atoms of the related phosphoryl groups act as double H‐atom acceptors, so that the P=O...(H—N)₂ hydrogen bond in (I) and the P=O...(H—N_amide)₂ and C=O...H—N_C(O)NHP(O) hydrogen bonds in (II) are responsible for the aggregation of the molecules in the crystal packing. The presence of a double H‐atom acceptor centre is a result of the involvement of a greater number of H‐atom donor sites with a smaller number of H‐atom acceptor sites in the hydrogen‐bonding interactions. This article also reviews structures having a P(O)NH group, with the aim of finding similar three‐centre hydrogen bonds in the packing of phosphoramidate compounds. This analysis shows that the factors affecting the preference of the above‐mentioned O atom to act as a double H‐atom acceptor are: (i) a higher number of H‐atom donor sites relative to H‐atom acceptor centres in molecules with P(=O)(NH)₃, (N)P(=O)(NH)₂, C(=O)NHP(=O)(NH)₂ and (NH)₂P(=O)OP(=O)(NH)₂ groups, and (ii) the remarkable H‐atom acceptability of this atom relative to the other acceptor centre(s) in molecules containing an OP(=O)(NH)₂ group, with the explanation that the N atom bound to the P atom in almost all of the structures found does not take part in hydrogen bonding as an acceptor. Moreover, the differences in the H‐atom acceptability of the phosphoryl O atom relative to the O atom of the alkoxy or phenoxy groups in amidophosphoric acid esters may be illustrated by considering the molecular packing of compounds having (O)₂P(=O)(NH) and (O)P(=O)(NH)(N)groups, in which the unique N—H unit in the above‐mentioned molecules almost always selects the phosphoryl O atom as a partner in forming hydrogen‐bond interactions. The P atoms in (I) and (II) are in tetrahedral coordination environments, and the phosphoryl and carbonyl groups in (II) are anti with respect to each other (the P and C groups are separated by one N atom). In the crystal structures of (I) and (II), adjacent molecules are linked via the above‐mentioned hydrogen bonds into a linear arrangement parallel to [100] in both cases, in (I) by forming R₂²(8) rings and in (II) through a combination of R₂²(10) and R₂¹(6) rings.     

New rac‐XP(O)(OC6H5)(NHC6H4‐p‐CH3) [X = N(CH3)(cyclo‐C6H11) and NH(C3H5)] and rac‐(C6H5CH2NH)P(O)(OC6H5)(NH‐cyclo‐C6H11) mixed‐amide phosphinates

The mixed‐amide phosphinates, rac‐phenyl (N‐methylcyclohexylamido)(p‐tolylamido)phosphinate, C₂₀H₂₇N₂O₂P, (I), and rac‐phenyl (allylamido)(p‐tolylamido)phosphinate, C₁₆H₁₉N₂O₂P, (II), were synthesized from the racemic phosphorus–chlorine compound (R,S)‐(Cl)P(O)(OC₆H₅)(NHC₆H₄‐p‐CH₃). Furthermore, the phosphorus–chlorine compound ClP(O)(OC₆H₅)(NH‐cyclo‐C₆H₁₁) was synthesized for the first time and used for the synthesis of rac‐phenyl (benzylamido)(cyclohexylamido)phosphinate, C₁₉H₂₅N₂O₂P, (III). The strategies for the synthesis of racemic mixed‐amide phosphinates are discussed. The P atom in each compound is in a distorted tetrahedral (N¹)P(=O)(O)(N²) environment. In (I) and (II), the p‐tolylamido substituent makes a longer P—N bond than those involving the N‐methylcyclohexylamido and allylamido substituents. In (III), the differences between the P—N bond lengths involving the cyclohexylamido and benzylamido substituents are not significant. In all three structures, the phosphoryl O atom takes part with the N—H unit in hydrogen‐bonding interactions, viz. an N—H...O=P hydrogen bond for (I) and (N—H)(N—H)...O=P hydrogen bonds for (II) and (III), building linear arrangements along [001] for (I) and along [010] for (III), and a ladder arrangement along [100] for (II).     

Different cyclic motifs in phosphoric triamides containing a C(O)NHP(O)(NH)2 skeleton and an R22(10) graph set in three new compounds: a database analysis of hydrogen‐bond strengths based on motifs

In the crystal networks of N,N′‐bis(2‐chlorobenzyl)‐N′′‐(2,6‐difluorobenzoyl)phosphoric triamide, C₂₁H₁₈Cl₂F₂N₃O₂P, (I), N‐(2,6‐difluorobenzoyl)‐N′,N′′‐bis(4‐methoxybenzyl)phosphoric triamide, C₂₃H₂₄F₂N₃O₄P, (II), and N‐(2‐chloro‐2,2‐difluoroacetyl)‐N′,N′′‐bis(4‐methylphenyl)phosphoric triamide, C₁₆H₁₇ClF₂N₃O₂P, (III), C=O...H—N_C(O)NHP(O) and P=O...H—N_amide hydrogen bonds are responsible for the aggregation of the molecules. This is the opposite result from that commonly observed for carbacylamidophosphates, which show a tendency for the phosphoryl group, rather than the carbonyl counterpart, to form hydrogen bonds with the NH group of the C(O)NHP(O) skeleton. This hydrogen‐bond pattern leads to cyclic R₂²(10) motifs in (I)–(III), different from those found for all previously reported compounds of the general formula RC(O)NHP(O)[NR¹R²]₂ with the syn orientation of P=O versus NH [R₂²(8)], and also from those commonly observed for RC(O)NHP(O)[NHR¹]₂ [a sequence of alternate R₂²(8) and R₂²(12) motifs]. In these cases, the R₂²(8) and R₂²(12) graph sets are formed through similar kinds of hydrogen bond, i.e. a pair of P=O...H—N_C(O)NHP(O) hydrogen bonds for the former and two C=O...H—N_amide hydrogen bonds for the latter. This article also reviews 102 similar structures deposited in the Cambridge Structural Database and with the International Union of Crystallography, with the aim of comparing hydrogen‐bond strengths in the above‐mentioned cyclic motifs. This analysis shows that the strongest N—H...O hydrogen bonds exist in the R₂²(8) rings of some molecules. The phosphoryl and carbonyl groups in each of compounds (I)–(III) are anti with respect to each other and the P atoms are in a tetrahedral coordination environment. In the crystal structures, adjacent molecules are linked via the above‐mentioned hydrogen bonds in a linear arrangement, parallel to [010] for (I) and (III) and parallel to [100] for (II). Formation of the N_C(O)NHP(O)—H...O=C instead of the N_C(O)NHP(O)—H...O=P hydrogen bond is reflected in the higher N_C(O)NHP(O)—H vibrational frequencies for these molecules compared with previously reported analogous compounds.     

The synergistic co‐operation of N—H…O=P hydrogen bonds and C—H…OX weak intermolecular interactions (X is =P or —C) in the (CH3O)2P(O)(NH–NHC6F5) amidophosphoester: a combined X‐ray crystallographic and theoretical study

The asymmetric unit of O,O′‐dimethyl [(2,3,4,5,6‐pentafluorophenyl)hydrazinyl]phosphonate, C₈H₈F₅N₂O₃P, is composed of two symmetry‐independent molecules with significant differences in the orientations of the C₆F₅ and OMe groups. In the crystal structure, a one‐dimensional assembly is mediated from classical N—H…O hydrogen bonds, which includes R₂²(8), D(2) and some higher‐order graph‐set motifs. By also considering weak C—H…O=P and C—H…O—C intermolecular interactions, a two‐dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6‐311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge‐transfer interactions were examined according to second‐order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen‐bonded clusters of molecules, including N—H…O and C—H…O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N—H…O [R₂²(8)] > N—H…O [D(2)] > C—H…O. The decomposed fingerprint plots show that the contribution portions of the F…H/H…F contacts in both molecules are the largest.     

Three new [XC(O)NH]P(O)[N(CH2C6H5)2]2 phosphoric triamides (X = CClF2, 3‐F‐C6H4 and 3,5‐F2‐C6H3): a database analysis of tertiary N‐atom geometry in compounds with a C(O)NHP(O)[N]2 core

In the phosphoric triamides N,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), and N,N,N′,N′‐tetrabenzyl‐N′′‐(3,5‐difluorobenzoyl)phosphoric triamide, C₃₅H₃₂F₂N₃O₂P, (III), the tertiary N atoms of the dibenzylamido groups have sp² character 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]₂ skeletons deposited in the Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B 58 , 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 is anti with respect to the P=O group. In (I), (II) and (III), the phosphoryl and carbonyl groups, separated by an N atom, are anti with 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 linked via pairs of P=O...H—N hydrogen bonds, forming dimers with C_i symmetry.     

trans‐Diaquabis(nicotinamide‐κN)bis(salicylato‐κO)cobalt(II)

The title compound, [Co(C₇H₅O₃)₂(C₆H₆N₂O)₂(H₂O)₂], forms a three‐dimensional hydrogen‐bonded supramolecular structure. The Co^II ion is in an octahedral coordination environment comprising two pyridyl N atoms, two carboxylate O atoms and two O atoms from water molecules. Intermolecular N—H...O and O—H...O hydrogen bonds produce R₂²(8), R₂²(12) and R₂²(14) rings, which lead to two‐dimensional chains. An extensive three‐dimensional supramolecular network of C—H...O, N—H...O and O—H...O hydrogen bonds and C—H...π interactions is responsible for crystal structure stabilization. This study is an example of the construction of a supramolecular assembly based on hydrogen bonds in mixed‐ligand metal complexes.     

Two Fe3(μ3‐S)2(CO)8 clusters with terminal N‐heterocyclic carbenes

The title compounds with terminal N‐heterocyclic carbenes, namely octacarbonyl(imidazolidinylidene‐κC²)di‐μ₃‐sulfido‐triiron(II)(2 Fe—Fe), [Fe₃(C₃H₆N₂)(μ₃‐S)₂(CO)₈], (I), and octacarbonyl(1‐methylimidazo[1,5‐a]pyridin‐3‐ylidene‐κC³)di‐μ₃‐sulfido‐triiron(II)(2 Fe—Fe), [Fe₃(C₈H₈N₂)(μ₃‐S)₂(CO)₈], (II), have been synthesized. Each compound contains two Fe—Fe bonds and two S atoms above and below a triiron triangle. One of the eight carbonyl ligands deviates significantly from linearity. In (I), dimers generated by an N—H...S hydrogen bond are linked into [001] double chains by a second N—H...S hydrogen bond. These chains are packed by a C—H...O hydrogen bond to yield [101] sheets. In (II), dimers generated by an N—H...S hydrogen bond are linked by C—H...O hydrogen bonds to form [111] double chains.     

Two isomorphous ZnII/CoII complexes with tri‐tert‐butoxysilanethiol and histamine,and (4‐hydroxymethyl‐1H‐imidazole‐κN)bis(tri‐tert‐butoxysilanethiolato‐κ2O,S)zinc(II)

The complexes [2‐(1H‐imidazol‐4‐yl‐κN³)ethylamine‐κN]bis(tri‐tert‐butoxysilanethiolato‐κS)cobalt(II), [Co(C₁₂H₂₇O₃SSi)₂(C₅H₉N₃)], and [2‐(1H‐imidazol‐4‐yl‐κN³)ethylamine‐κN]bis(tri‐tert‐butoxysilanethiolato‐κS)zinc(II), [Zn(C₁₂H₂₇O₃SSi)₂(C₅H₉N₃)], are isomorphous. The central Zn^II/Co^II ions are surrounded by two S atoms from the tri‐tert‐butoxysilanethiolate ligand and by two N atoms from the chelating histamine ligand in a distorted tetrahedral geometry, with two intramolecular N—H...O hydrogen‐bonding interactions between the histamine NH₂ groups and tert‐butoxy O atoms. Molecules of the complexes are joined into dimers via two intermolecular bifurcated N—H...(S,O) hydrogen bonds. The Zn^II atom in [(1H‐imidazol‐4‐yl‐κN³)methanol]bis(tri‐tert‐butoxysilanethiolato‐κ²O,S)zinc(II), [Zn(C₁₂H₂₇O₃SSi)₂(C₄H₆N₂O)], is five‐coordinated by two O and two S atoms from the O,S‐chelating silanethiolate ligand and by one N atom from (1H‐imidazol‐4‐yl)methanol; the hydroxy group forms an intramolecular hydrogen bond with sulfur. Molecules of this complex pack as zigzag chains linked by N—H...O hydrogen bonds. These structures provide reference details for cysteine‐ and histidine‐ligated metal centers in proteins.     

trans‐Diaquabis(3‐hydroxybenzoato‐κO1)bis(nicotinamide‐κN1)copper(II)

The title compound, [Cu(C₇H₅O₃)₂(C₆H₆N₂O)₂(H₂O)₂], is a two‐dimensional hydrogen‐bonded supramolecular complex. The Cu^II ion resides on a centre of symmetry and is in an octahedral coordination environment comprising two pyridine N atoms, two carboxylate O atoms and two O atoms from water molecules. Intermolecular N—H...O and O—H...O hydrogen bonds produce R₂²(4), R₂²(8) and R₂²(15) rings which lead to one‐dimensional polymeric chains. An extensive two‐dimensional network of N—H...O and O—H...O hydrogen bonds and C—H...π interactions are responsible for crystal stabilization.     

Diaquabis(4‐fluorobenzoato‐κO)bis(nicotinamide‐κN)cobalt(II)

The title compound, [Co(C₇H₄FO₂)₂(C₆H₆N₂O)₂(H₂O)₂], is a three‐dimensional hydrogen‐bonded supramolecular complex. The Co^II ion resides on a centre of symmetry and is in an octahedral coordination environment comprising two pyridyl N atoms, two carboxylate O atoms and two O atoms from water molecules. Intermolecular N—H...O and O—H...O hydrogen bonds produce R₃²(6), R₂²(12) and R₂²(16) rings, which lead to two‐dimensional chains. An extensive three‐dimensional network of C—H...F, N—H...O and O—H...O hydrogen bonds and π–π interactions are responsible for crystal stabilization.     

Two scandium–biuret complexes: [Sc(C2H5N3O2)(H2O)5]Cl3·H2O and [Sc(C2H5N3O2)4](NO3)3

The scandium(III) cations in the structures of pentaaqua(biuret‐κ²O,O′)scandium(III) trichloride monohydrate, [Sc(C₂H₅N₃O₂)(H₂O)₅]Cl₃·H₂O, (I), and tetrakis(biuret‐κ²O,O′)scandium(III) trinitrate, [Sc(C₂H₅N₃O₂)₄](NO₃)₃, (II), are found to adopt very different coordinations with the same biuret ligand. The roles of hydrogen bonding and the counter‐ion in the establishment of the structures are described. In (I), the Sc³⁺ cation adopts a fairly regular pentagonal bipyramidal coordination geometry arising from one O,O′‐bidentate biuret molecule and five water molecules. A dense network of N—H...Cl, O—H...O and O—H...Cl hydrogen bonds help to establish the packing, resulting in dimeric associations of two cations and two water molecules. In (II), the Sc³⁺ cation (site symmetry 2) adopts a slightly squashed square‐antiprismatic geometry arising from four O,O′‐bidentate biuret molecules. A network of N—H...O hydrogen bonds help to establish the packing, which features [010] chains of cations. One of the nitrate ions is disordered about an inversion centre. Both structures form three‐dimensional hydrogen‐bond networks.     

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate, 2C₂H₇N₄O⁺·FO₃P²⁻·2H₂O, are presented. Polymorph (I), crystallizing in the space group Pnma, is slightly less densely packed than polymorph (II), which crystallizes in Pbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen‐bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation of R⁴₄(10) graph‐set motifs. These motifs extend along the a axis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three‐dimensional hydrogen‐bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen‐bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen‐bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).     

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

In N,N,N′,N′‐tetraethyl‐N′′‐(4‐fluorobenzoyl)phosphoric triamide, C₁₅H₂₅FN₃O₂P, (I), and N‐(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)]₂ skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B 58 , 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with the N‐methylcyclohexylamide substituent, similar to (III), one structure with the seven‐membered cyclic amide azepan‐1‐yl substituent and one structure with an N‐methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linked via pairs of N—H...O=P hydrogen bonds to form dimers.     

2‐Ethyl‐1‐[5‐(4‐methylphenyl)pyrazol‐3‐yl]‐3‐(thiophene‐2‐carbonyl)isothiourea: molecular ribbons containing three types of hydrogen‐bonded ring

The title compound, C₁₈H₁₈N₄OS₂, was prepared by reaction of S,S‐diethyl 2‐thenoylimidodithiocarbonate with 5‐amino‐3‐(4‐methylphenyl)‐1H‐pyrazole using microwave irradiation under solvent‐free conditions. In the molecule, the thiophene unit is disordered over two sets of atomic sites, with occupancies of 0.814 (4) and 0.186 (4), and the bonded distances provide evidence for polarization in the acylthiourea fragment and for aromatic type delocalization in the pyrazole ring. An intramolecular N—H...O hydrogen bond is present, forming an S(6) motif, and molecules are linked by N—H...O and N—H...N hydrogen bonds to form a ribbon in which centrosymmetric R₂²(4) rings, built from N—H...O hydrogen bonds and flanked by inversion‐related pairs of S(6) rings, alternate with centrosymmetric R₂²(6) rings built from N—H...N hydrogen bonds.     

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5‐fluorocytosine

Three new metal(II)–cytosine (Cy)/5‐fluorocytosine (5FC) complexes, namely bis(4‐amino‐1,2‐dihydropyrimidin‐2‐one‐κN³)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI₂(C₄H₅N₃O)₂], ( I ), bis(4‐amino‐1,2‐dihydropyrimidin‐2‐one‐κN³)bis(nitrato‐κ²O,O′)cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO₃)₂(C₄H₅N₃O)₂], ( II ), and (6‐amino‐5‐fluoro‐1,2‐dihydropyrimidin‐2‐one‐κN³)aquadibromidozinc(II)–6‐amino‐5‐fluoro‐1,2‐dihydropyrimidin‐2‐one (1/1) or (6‐amino‐5‐fluorocytosine)aquadibromidozinc(II)–4‐amino‐5‐fluorocytosine (1/1), [ZnBr₂(C₄H₅FN₃O)(H₂O)]·C₄H₅FN₃O, ( III ), have been synthesized and characterized by single‐crystal X‐ray diffraction. In complex ( I ), the Cd^II ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr₂(C₄H₅N₃O)₂] [Muthiah et al. (2001). Acta Cryst. E 57 , m558–m560]. In compound ( II ), each of the two cytosine molecules coordinates to the Cd^II ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N—H…O hydrogen bond involving two cytosine molecules is also present. In compound ( III ), one zinc‐coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The Zn^II atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)—H tautomer of 5FC mimics N(3)‐protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R₂²(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a‐axis direction, forming the rungs of a ladder motif, whereas Zn—Br bonds and N—H…Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O—H…O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound ( III ), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N—H…O, N—H…N, O—H…O, N—H…I and N—H…Br hydrogen bonds, and stacking interactions.     

Methanol[1‐(methoxymethanimidoyl)‐2‐(pyridin‐2‐ylmethyl)guanidine]bis(perchlorato)copper(II)

The title complex, [Cu(ClO₄)₂(C₉H₁₃N₅O)(CH₃OH)], was synthesized from a methanolysis reaction of N‐(methylpyridin‐2‐yl)cyanoguanidine (L³) and copper(II) perchlorate hexahydrate in a 1:1 molar ratio. The Cu^II ion is six‐coordinated by an N₃O₃ donor set which confers a highly distorted and asymmetric octahedral geometry. Three N‐donor atoms from the chelating 1‐(methoxymethanimidoyl)‐2‐(pyridin‐2‐ylmethyl)guanidine (L^3m) ligand and one O atom from the methanol molecule define the equatorial plane, with two perchlorate O atoms in the apical sites, one of which has a long Cu—O bond of 2.9074 (19) Å. The dihedral angle between the five‐ and six‐membered chelate rings is 8.21 (8)°. Two molecules are associated into a dimeric unit by intermolecular N—H...O(perchlorate) hydrogen bonds. Additionally, the weakly coordinated perchlorate anions also link adjacent [Cu(ClO₄)₂(L^3m)(CH₃OH)] dimers by hydrogen‐bonding interactions, resulting in a two‐dimensional layer in the (100) plane. Further C—H...O hydrogen bonds link the two‐dimensional layers along [100] to generate a three‐dimensional network.     

Syntheses and Spectroscopic Study of Some New N‐4‐Fluorobenzoyl Phosphoric Triamides; Crystal Structures of 4‐F‐C6H4C(O)N(H)P(O)R2, R = NH‐C(CH3)3, NH‐CH2C6H5, N(CH3)(CH2C6H5)

Some new N‐4‐Fluorobenzoyl phosphoric triamides with formula 4‐F‐C₆H₄C(O)N(H)P(O)X₂, X = NH‐C(CH₃)₃ ( 1 ), NH‐CH₂‐CH=CH₂ ( 2 ), NH‐CH₂C₆H₅ ( 3 ), N(CH₃)(C₆H₅) ( 4 ), NH‐CH(CH₃)(C₆H₅) ( 5 ) were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR and Mass spectroscopy and elemental analysis. The structures of compounds 1 , 3 and 4 were investigated by X‐ray crystallography. The P=O and C=O bonds in these compounds are anti. Compounds 1 and 3 form one dimensional polymeric chain produced by intra‐ and intermolecular ‐P=O···H‐N‐ hydrogen bonds. Compound 4 forms only a centrosymmetric dimer in the crystalline lattice via two equal ‐P=O···H‐N‐ hydrogen bonds. ¹H and ¹³C NMR spectra show two series of signals for the two amine groups in compound 1 . This is also observed for the two α‐methylbenzylamine groups in 5 due to the presence of chiral carbon atom in molecule. ¹³C NMR spectrum of compound 4 shows that ²J(P,C_aliphatic) coupling constant for CH₂ group is greater than for CH₃ in agreement with our previous study. Mass spectra of compounds 1 ‐ 3 (containing 4‐F‐C₆H₄C(O)N(H)P(O) moiety) indicate the fragments of amidophosphoric acid and 4‐F‐C₆H₄CN⁺ that formed in a pseudo McLafferty rearrangement pathway. Also, the fragments of aliphatic amines have high intensity in mass spectra.     

{μ‐N,N′‐Bis[3‐(dimethyl­amino)prop­yl]­oxamidato(2–)‐κ6N,N′,O′:N′′,N′′′,O}­bis­[(1H‐imidazole‐κN3)(methanol‐κO)copper(II)] bis­(perchlorate)

The structure of the title compound, [Cu₂(C₁₂H₂₄N₄O₂)(C₃H₄N₂)₂(CH₄O)₂](ClO₄)₂ or [Cu₂(dmoxpn)(HIm)₂(CH₃OH)₂](ClO₄)₂, where dmoxpn is the dianion of N,N′‐bis­[3‐(dimethyl­amino)prop­yl]oxamide and HIm is imidazole, consists of a centrosymmetric trans‐oxamidate‐bridged copper(II) binuclear cation, having an inversion centre at the mid‐point of the central C—C bond, and two perchlorate anions. The Cu^II atom has square‐pyramidal coordination geometry involving two N atoms and an O atom from the dmoxpn ligand, an N atom from an imidazole ring, and an O atom from a methanol mol­ecule. The crystal structure is stabilized by O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds and imidazole π–π stacking inter­actions to form a three‐dimensional supra­molecular array.     

(6‐Oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylato‐κ2O5,O6)bis[2‐(2‐pyridyl)‐1H‐benzimidazole‐κ2N2,N3]manganese(II) monohydrate

In the title compound, [Mn(C₅H₂N₂O₄)(C₁₂H₉N₃)₂]·H₂O, the Mn^II centre is surrounded by three bidentate chelating ligands, namely, one 6‐oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylate (or uracil‐5‐carboxylate, Huca²⁻) ligand [Mn—O = 2.136 (2) and 2.156 (3) Å] and two 2‐(2‐pyridyl)‐1H‐benzimidazole (Hpybim) ligands [Mn—N = 2.213 (3)–2.331 (3) Å], and it displays a severely distorted octahedral geometry, with cis angles ranging from 73.05 (10) to 105.77 (10)°. Intermolecular N—H...O hydrogen bonds both between the Hpybim and the Huca²⁻ ligands and between the Huca²⁻ ligands link the molecules into infinite chains. The lattice water molecule acts as a hydrogen‐bond donor to form double O...H—O—H...O hydrogen bonds with the Huca²⁻ O atoms, crosslinking the chains to afford an infinite two‐dimensional sheet; a third hydrogen bond (N—H...O) formed by the water molecule as a hydrogen‐bond acceptor and a Hpybim N atom further links these sheets to yield a three‐dimensional supramolecular framework. Possible partial π–π stacking interactions involving the Hpybim rings are also observed in the crystal structure.