2‐Amino‐4‐chloro‐6‐[N‐methyl‐N‐(4‐methylphenyl)amino]pyrimidine: formation versus fragmentation of hydrogen‐bonded chains of edge‐fused R22(8) rings in 4,6‐disubstituted 2‐aminopyrimidines

Molecules of the title compound, C₁₂H₁₃ClN₄, are linked by two independent N—H...N hydrogen bonds into a chain of edge‐fused R₂²(8) rings. The significance of this study lies in its attempt to rationalize the patterns of supramolecular aggregation in the title compound and in a range of analogous 4,6‐disubstituted 2‐aminopyrimidines.     

2‐Amino‐3‐methyl‐6‐[methyl(phenyl)amino]‐5‐nitropyrimidin‐4(3H)‐one: polarized molecules within hydrogen‐bonded sheets

The pyrimidinone ring in the title compound, C₁₂H₁₃N₅O₃, is effectively planar, despite the presence of five substituents. The bond distances provide evidence for significant polarization of the electronic structure, with charge separation, and the molecules are linked into sheets by a combination of N—H...O and N—H...π(arene) hydrogen bonds. Comparisons are made with the molecular and supramolecular structures of the precursor compound 2‐amino‐6‐[methyl(phenyl)amino]‐5‐nitropyrimidin‐4(3H)‐one.     

The diastereoisomers 2‐[(S/R)‐2‐chloro‐3‐quinolyl]‐2‐[(R)‐1‐(4‐methoxyphenyl)ethylamino]acetonitrile at 100 K

In the structures of the two enantiopure diastereoisomers of the title compound, C₂₀H₁₈ClN₃O, which crystallize in different space groups, the molecules are very similar as far as bond distances and angles are concerned, but more substantial differences are observed in some torsion angles. The crystal structures of both molecules can be described as zigzag layers along the c axis. The packing is stabilized by hydrogen‐bond interactions of N—H...O, C—H...Cl and C—H...π types for 2‐[(R)‐2‐chloro‐3‐quinolyl]‐2‐[(R)‐1‐(4‐methoxyphenyl)ethylamino]acetonitrile, and of N—H...N, C—H...O and C—H...π types for 2‐[(S)‐2‐chloro‐3‐quinolyl]‐2‐[(R)‐1‐(4‐methoxyphenyl)ethylamino]acetonitrile, resulting in the formation of two‐ and three‐dimensional networks.     

(E)‐3‐{2‐Amino‐4‐ethoxy‐6‐[N‐(4‐methoxyphenyl)‐N‐methylamino]pyrimidin‐5‐yl}‐1‐phenylprop‐2‐en‐1‐one: a boat‐shaped pyrimidine ring and a chain of hydrogen‐bonded R42(8) and R22(20) rings

In the title compound, C₂₃H₂₄N₄O₃, the pyrimidine ring adopts an almost perfect boat conformation, and the bond distances provide evidence for some polarization of the molecular–electronic structure. Two independent N—H...O hydrogen bonds link the molecules into chains of edge‐fused R²₄(8) and R²₂(20) rings.     

2‐Amino‐5‐nitro­thia­zole monoethanol solvate: triply‐interwoven hydrogen‐bonded sheets containing centrosymmetric R(8) and R(38) rings

2‐Amino‐5‐nitro­thia­zole crystallizes from solution in ethanol as a monosolvate, C₃H₃N₃O₂S·C₂H₆O, in which the thia­zole component has a strongly polarized molecular–electronic structure. The thia­zole mol­ecules are linked into centrosymmetric dimers by paired N—H⋯N hydrogen bonds [H⋯N = 2.09 Å, N⋯N = 2.960 (6) Å and N—H⋯N = 169°], and these dimers are linked by the ethanol mol­ecules, via a two‐centred N—H⋯O hydrogen bond [H⋯O = 1.98 Å, N⋯O = 2.838 (5) Å and N—H⋯O = 164°] and a planar asymmetric three‐centred O—H⋯(O)₂ hydrogen bond [H⋯O = 2.07 and 2.53 Å, O⋯O = 2.900 (5) and 3.188 (5) Å, O—H⋯O = 169 and 136°, and O⋯H⋯O = 55°], into sheets built from alternating (8) and (38) rings. These sheets are triply interwoven.     

Hydrogen bonding in nitroaniline analogues: hydrogen‐bonded sheets in 2‐amino‐4,6‐dimethoxy‐5‐nitropyrimidine and π‐stacked hydrogen‐bonded sheets in 4‐amino‐2,6‐dimethoxy‐5‐nitropyrimidine

In 2‐amino‐4,6‐di­methoxy‐5‐nitro­pyrimidine, C₆H₈N₄O₄, the mol­ecules are linked by one N—H⋯N and one N—H⋯O hydrogen bond to form sheets built from alternating R(8) and R(32) rings. In isomeric 4‐amino‐2,6‐di­methoxy‐5‐nitro­pyrimidine, C₆H₈N₄O₄, which crystallizes with Z′ = 2 in P, the two independent mol­ecules are linked into a dimer by two independent N—H⋯N hydrogen bonds. These dimers are linked into sheets by a combination of two‐centre C—H⋯O and three‐centre C—H⋯(O)₂ hydrogen bonds, and the sheets are further linked by two independent aromatic π–π‐stacking interactions to form a three‐dimensional structure.     

Anomeric effect and hydrogen‐bonded supramolecular motif in 5‐(3‐fluoro‐4‐methoxyphenyl)‐1‐[(3‐fluoro‐4‐methoxyphenyl)aminomethyl]‐1,3,5‐triazinane‐2‐thione

In the title compound, C₁₈H₂₀F₂N₄O₂S, the triazinane‐2‐thione ring adopts an envelope conformation, the ring substituents lie on the same side of the mean plane of the heterocyclic ring and the exo lp—N—C—N_triaz unit (lp is a lone pair and triaz is the triazinane ring) exhibits an antiperiplanar orientation, which is shown to be governed by strong anomeric effects. Molecules are linked into a complex three‐dimensional framework by a combination of two N—H...S hydrogen bonds, three C—H...F hydrogen bonds and a π–π stacking interaction.     

2‐Amino‐6‐chloro‐4‐(1‐phenyl­ethyl­amino)­pyrimidine

The structure of the title compound, C₁₂H₁₃ClN₄, (I), comprises a racemic mixture of chiral mol­ecules associated by N—H?N hydrogen‐bonding interactions. The dihedral angle between the two rings is 77.90 (6)°.     

Synthesis and Herbicidal Activity of 2‐Alkyl(aryl)‐4‐amino‐3‐[alkyl(alkoxy)carbonyl]‐5‐cyano‐6‐[(3‐trifluoromethyl)phenoxy]‐pyridines

To find novel bleaching herbicide lead compounds, a series of novel 2‐alkyl(aryl)‐4‐amino‐3‐[alkyl(alkoxy)carbonyl]‐5‐cyano‐6‐[(3‐trifluoromethyl)phenoxy]‐pyridines was designed and synthesized by the multistep reactions. N,S‐acetal 1 reacted with 2 to obtain multisubstituted pyridines 3 in the presence of zinc nitrate as the catalyst. The target compounds 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j , 5k , 5l were formed by the oxidation of 3 , followed by the substitution with 3‐(trifluoromethyl)phenol in the presence of potassium carbonate. Their structures were confirmed by IR, ¹H NMR, EI‐MS, and elemental analyses. The preliminary bioassays indicated that some of them displayed moderate herbicidal activity against dicotyledonous weed Brassica campestris L at the concentration of 100 mg/L.     

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.     

5‐Amino‐3‐tert‐butyl‐1‐(4‐nitro­phen­yl)‐1H‐pyrazole forms hydrogen‐bonded sheets of alternating R(20) and R(32) rings

Molecules of the title compound, C₁₃H₁₆N₄O₂, are linked by one N—H⋯O hydrogen bond [H⋯O = 2.47 Å, N⋯O = 3.326 (2) Å and N—H⋯O = 166°] and one N—H⋯N hydrogen bond [H⋯N = 2.19 Å, N⋯N = 3.063 (2) Å and N—H⋯N = 173°] into sheets containing alternating (20) and (32) rings, both types of which are centrosymmetric.     

Two polymorphs,with Z′ = 1 and 2, of 2‐amino‐4‐chloro‐6‐morpholino­pyrimidine in P21/c,and 2‐amino‐4‐chloro‐6‐piperidino­pyrimidine,which is isomorphous and almost isostructural with the Z′ = 2 polymorph

Crystallization of 2‐amino‐4‐chloro‐6‐morpholino­pyrimidine, C₈H₁₁ClN₄O, (I), yields two polymorphs, both with space group P2₁/c, having Z′ = 1 (from diethyl ether solution) and Z′ = 2 (from di­chloro­methane solution), denoted (Ia) and (Ib), respectively. In polymorph (Ia), the mol­ecules are linked by an N—H⋯O and an N—H⋯N hydrogen bond into sheets built from alternating R(8) and R(40) rings. In polymorph (Ib), one mol­ecule acts as a triple acceptor of hydrogen bonds and the other acts as a single acceptor; one N—H⋯O and three N—H⋯N hydrogen bonds link the mol­ecules in a complex chain containing two types of R(8) and one type of R(18) ring. 2‐Amino‐4‐chloro‐6‐piperidino­pyrimidine, C₉H₁₃ClN₄, (II), which is isomorphous with polymorph (Ib), also has Z′ = 2 in P2₁/c, and the mol­ecules are linked by three N—­H⋯N hydrogen bonds into a centrosymmetric four‐mol­ecule aggregate containing three R(8) rings.     

4‐Amino‐2,6‐di­methoxy­pyrimidine: hydrogen‐bonded sheets of R22(8) and R66(28) rings,reinforced by an aromatic π–π‐stacking interaction

Molecules of the title compound, C₆H₉N₃O₂, are linked by an N—H⃛O hydrogen bond [H⃛O = 2.29 Å, N⃛O = 3.169 (2) Å and N—H⃛O = 173°] and an N—H⃛N hydrogen bond [H⃛N = 2.12 Å, N⃛N = 2.999 (2) Å and N—H⃛N = 175°] into sheets containing centrosymmetric R(8) and R(28) rings; the sheets are reinforced by a single aromatic π–π‐stacking interaction.     

Supramolecular hydrogen‐bonding patterns in the organic–inorganic hybrid compound bis(4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium) tetrathiocyanatozinc(II)–4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–water (1/2/2)

Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one‐, two‐ and three‐dimensional polymeric metal–thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate–aminopyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium cation, a 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine molecule and a water molecule. The Zn^II atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water molecules and the metal‐coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base‐pair‐like structures with an R₂²(8) ring motif via N—H…N hydrogen bonds. The crystal structure is further stabilized by intermolecular N—H…O, O—H…S, N—H…S and O—H…N hydrogen bonds, by intramolecular N—H…Cl and C—H…Cl hydrogen bonds, and also by π–π stacking interactions.     

A three‐dimensional hydrogen‐bonded framework in 2‐amino‐6‐(N‐methylanilino)pyrimidin‐4(3H)‐one and a ribbon of fused hydrogen‐bonded rings in 2‐amino‐6‐(N‐methylanilino)‐5‐nitropyrimidin‐4(3H)‐one

The molecular dimensions of both 2‐amino‐6‐(N‐methylanilino)pyrimidin‐4(3H)‐one, C₁₁H₁₂N₄O, (I), and 2‐amino‐6‐(N‐methylanilino)‐5‐nitropyrimidin‐4(3H)‐one, C₁₁H₁₁N₅O₃, (II), are consistent with considerable polarization of the molecular–electronic structures. The molecules of (I) are linked into a three‐dimensional framework by a combination of one N—H...N hydrogen bond, two independent N—H...O hydrogen bonds and one C—H...π(arene) hydrogen bond. The molecules of (II) are linked into ribbons containing three types of edge‐fused ring by the combination of two independent three‐centre N—H...(O)₂ hydrogen bonds.     

2‐Amino‐5‐nitro‐4,6‐dipiperidinopyrimidinium hydrogen­sulfate monohydrate: hydrogen‐bonded sheets containing highly distorted cations

In the title compound, C₁₄H₂₃N₆O₂⁺·HSO₄⁻·H₂O, the pyrimidinium ring of the cation adopts a twist‐boat conformation, induced by steric clashes between adjacent ring substituents; the anions and the water mol­ecules are linked by three O—H⃛O hydrogen bonds [H⃛O = 1.70–1.78 Å, O⃛O = 2.548 (2)–2.761 (2) Å and O—H⃛O = 161–168°] into chains of edge‐fused R(12) rings, which are linked into sheets by the cations, via three N—H⃛O hydrogen bonds [H⃛O = 1.96–2.17 Å, N⃛O = 2.820 (2)–2.935 (2) Å and N—H⃛O = 145–173°].     

Redetermination of 6‐amino‐5‐formyl‐1,3‐dimethyluracil monohydrate at 120 K: a polarized molecular structure and two interwoven hydrogen‐bonded frameworks

The title compound [systematic name: 6‐amino‐5‐formyl‐1,3‐dimethylpyrimidine‐2,4(1H,3H)‐dione monohydrate], C₇H₉N₃O₃·H₂O, has been reexamined at 120 K. The improved precision of the intramolecular dimensions provides evidence for a polarized molecular–electronic structure, and the molecular components are linked by one N—H...O and two O—H...O hydrogen bonds into two interwoven three‐dimensional frameworks, which are weakly linked by the longer component of a three‐centre N—H...(O)₂ hydrogen bond.     

5‐Methyl‐N‐[2‐nitro‐4‐(trifluoromethyl)phenyl]‐1H‐pyrazole‐3‐amine: a chain of hydrogen‐bonded R22(6) and R22(16) rings

The molecular skeleton of the title compound, C₁₁H₉F₃N₄O₂, is almost planar and exhibits a polarized (charge‐separated) electronic structure in the nitroaniline portion. Molecules are linked by N—H...N and C—H...O hydrogen bonds to form a chain in which centrosymmetric R₂²(6) and R₂²(16) rings alternate.     

Hydrogen‐bonded ribbons in ethyl (E)‐3‐[2‐amino‐4,6‐bis(dimethylamino)pyrimidin‐5‐yl]‐2‐cyanoacrylate and 2‐[(2‐amino‐4,6‐di‐1‐piperidylpyrimidin‐5‐yl)methylene]malononitrile

The pyrimidine rings in ethyl (E)‐3‐[2‐amino‐4,6‐bis(dimethylamino)pyrimidin‐5‐yl]‐2‐cyanoacrylate, C₁₄H₂₀N₆O₂, (I), and 2‐[(2‐amino‐4,6‐di‐1‐piperidylpyrimidin‐5‐yl)methylene]malononitrile, C₁₈H₂₃N₇, (II), which crystallizes with Z′ = 2 in the space group, are both nonplanar with boat conformations. The molecules of (I) are linked by a combination of N—H...N and N—H...O hydrogen bonds into chains of edge‐fused R₂²(8) and R₄⁴(20) rings, while the two independent molecules in (II) are linked by four N—H...N hydrogen bonds into chains of edge‐fused R₂²(8) and R₂²(20) rings. This study illustrates both the readiness with which highly‐substituted pyrimidine rings can be distorted from planarity and the significant differences between the supramolecular aggregation in two rather similar compounds.     

A hydrogen‐bonded chain of rings in 5‐amino‐1‐(4‐methoxybenzoyl)‐3‐methylpyrazole and a three‐dimensional hydrogen‐bonded framework in 5‐amino‐3‐methyl‐1‐(2‐nitrobenzoyl)pyrazole

The molecules of 5‐amino‐1‐(4‐methoxybenzoyl)‐3‐methylpyrazole, C₁₂H₁₃N₃O₂, (I), and 5‐amino‐3‐methyl‐1‐(2‐nitrobenzoyl)pyrazole, C₁₁H₁₀N₄O₃, (II), both contain intramolecular N—H...O hydrogen bonds. The molecules of (I) are linked into a chain of rings by a combination of N—H...N and N—H...π(arene) hydrogen bonds, while those of (II) are linked into a three‐dimensional framework structure by N—H...N and C—H...O hydrogen bonds.