Hexahydropyrimidine Ring Research Articles

Synthesis, crystal structure, Hirshfeld surface, DFT calculations, Z-scan and nonlinear optical studies of novel flourinated hexahydropyrimidine

A new fluorinated hexahydropyrimidine was synthesized and its crystal structure was elucidated using single crystal X-ray diffraction technique. This compound, C15H17F3N2O6 crystallizes in monoclinic space group P21/c with cell parameters a = 10.6345(3) Å, b = 14.7074(4) Å, c = 10.6677(4) Å, β= 101.453(2)° and V= 1635.27 (9) Å3. In this compound the hexahydropyrimidine ring (C7/C8/C12/N1/C14/N2) adopts sofa conformation. The puckering parameters are Q = 0.5117Å, Ɵ = 129.59° and φ =304.0802°. The analysis of Hirshfeld surface indicates the presence of hydrogen bonds C‒H•••F, C‒H•••O, O‒H•••O, N‒H•••O and π•••π stacking stabilizes the system. The energy optimized structure was calculated using Density Functional Theory (DFT) and were employed by hybrid functional theory (B3LYP) at 6-311++G(d,p) basis set in the Gaussian09_revision C0.1 program package. The natural bond orbital analysis results state that the highest energy transfer of 604.21 kJ/mol occur between the donor σ(O4‒H43) to acceptor σ*(C34‒H36) through carboxylate chain. Moreover, the vibrational assignments, global reactivity descriptors, energy gap and molecular electrostatic potential (MEP) also gives clear insight about chemical and biological activity of the molecule. The first hyperpolarizability value 7.2987 × 10−30 esu of the synthesized compound is twenty times greater than that of urea (0.3728 × 10−30 esu). The one electron excitation of the synthesized crystal calculated by the time dependent-density functional theory (TD-DFT) calculation and comparatively studied using recorded UV spectrum. The single beam Z-scan unit equipped with 532 nm continuous Nd:YAG wave laser with 5ns pulse width was used to measure third order nonlinear optical property reveal that the investigated molecule possess effective two photon absorption with higher effective absorption coefficient. The imaginary and real parts of the third-order susceptibility values determined as Im χ3 = 2.31 × 10−6 cm W−1 and Re χ3 = 8.74 × 10−8 cm2 W−1 respectively.

A concise route to 4-aminomethylpyrazoles and 4-aminomethylisoxazoles from acetylacetone-derived hexahydropyrimidines under mild conditions

AbstractAcetylacetone was successfully used as a precursor of 4-aminomethylpyrazoles and 4-aminomethylisoxazoles in a two step process at ambient temperature. In the first step, acetylacetone was transformed to the corresponding hexahydropyrimidines (1,3-diazinanes) via two consecutive one-pot Mannich aminomethylations. Hexahydropyrimidines were then treated with hydrazine, phenylhydrazine, and hydroxylamine, respectively, to obtain the corresponding 4-aminomethylpyrazoles and 4-aminomethylisoxazoles in good yields. The hexahydropyrimidine ring decomposed providing the title compounds and a reasonable mechanism has been proposed.

Crystal structure of (E)-2-(4-meth-oxy-styr-yl)-2,3-di-hydro-1H-perimidine aceto-nitrile monosolvate.

The title compound, C20H18N2O·CH3CN, a perimidine deriv­ative, crystallized as an aceto­nitrile monosolvate. The planes of the naphthalene ring system and the meth­oxy­phenyl ring are oriented almost perpendicular to one another, with a dihedral angle of 87.61 (6)°. The conformation about the C=C bond is E. The hexa­hydro­pyrimidine ring has an envelope conformation, with the methine C atom as the flap. In the crystal, the mol­ecules are linked by N—H⋯N hydrogen bonds involving the aceto­nitrile solvent mol­ecule as acceptor, forming zigzag chains propagating along [100].

PJS, a novel isocoumarin with hexahydropyrimidine ring from Bacillus subtilis PJS

PJS, a novel isocoumarin with hexahydropyrimidine ring from Bacillus subtilis PJS

Stereoselective synthesis and structural analysis of polycyclic lactams derived from tetrahydroisoquinoline 1,2- and 1,3-diamines

By means of the domino ring-closure reactions of (1S*,1′S*)-1-(1′-aminoethyl)-, (1R*,1′R*)-1(2′-amino-1′-methylethyl)and 1-(2-aminophenyl)-6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline with acyclic and aromatic γor δ-oxo acids, angularly-condensed tetra-, pentaand hexacyclic lactam derivatives were formed with practically full diastereoselectivities (de ~100%), containing the substituents at the annelations of the saturated heterocyclic rings in cis position. The structure and relative stereochemistry of the products were determined with H and C NMR spectroscopy. Further, the tetrahydropyridine ring (ring B) was observed to prefer cis fusion with the condensed imidazolidine or hexahydropyrimidine ring (ring C), with one exception preferring trans fusion (namely, the tetracyclic imidazolidine derivative bearing a methyl substituent at the C/D ring annelation, cmpd. 11). These two conformations can interconvert via simultaneous nitrogen inversion at the B/C annelation and ring inversion of the ring B, and their populations could be roughly estimated from the J-coupling constant data for each lactam derivative. The compounds gave fragment ions that were typical for the structures of the compounds.

Eudistomidins H–K, new β-carboline alkaloids from the Okinawan marine tunicate Eudistoma glaucus

Four new β-carboline alkaloids, eudistomidins H-K (1-4), were isolated from an Okinawan marine tunicate Eudistoma glaucus and the structures of 1-4 were elucidated on the basis of spectroscopic data. Eudistomidins H (1) and I (2) were new β-carboline alkaloids possessing a unique fused-tetracyclic ring system consisting of a tetrahydro β-carboline ring and a hexahydropyrimidine ring. Eudistomidin J (3) showed relatively potent cytotoxicity against murine leukemia cells P388 and L1210, and human epidermoid carcinoma cells KB in vitro.

2-Phenyl-2-(pyridin-2-yl)hexahydropyrimidine

The title compound, C15H17N3, was prepared by reaction of benzoyl­pyridine and hexahydropyrimidine. The 1,3-diazinane ring adopts a chair conformation with one N—H group axial and the other equatorial. The axial N—H group participates in very weak hydrogen bonding to the lone pair of electrons of the N atom with the equatorial H atom producing a very weakly hydrogen-bonded dimer. The pyridine N atom accepts an inter­nal hydrogen bond from the equatorial H atom. The phenyl ring adopts an equatorial position while the pyridine ring is axial. The phenyl ring exhibits a slight twist (ca 25°) relative to the hexahydropyrimidine ring. The pyridine ring stacks with symmetry-related pyridine rings.

Complexation to FeII, NiII, and ZnII of Multidentate Ligands Resulting from Condensation of 2-Pyridinecarboxaldehyde with α,ω-Triamines: Selective Imidazolidine/Hexahydropyrimidine Ring Opening Revisited

The condensation reaction between 2-pyridinecarboxaldehyde and diethylenetriamine, 3-[(2-aminoethyl)amino]propylamine, and 3,3'-iminobis(propylamine) in a 2:1 molar ratio yields ligands that may be isolated exclusively in the dissymmetric (cyclic) isomeric forms L(A), L(B)/L(B*), and L(C). The template effect of a metal center (Fe(II), Ni(II), and Zn(II)) results in the ring opening of L(C) including one hexahydropyrimidine ring and one (long) propylene bridge. The resulting symmetric bis-Schiff base isomeric form L(C') is stabilized through pentacoordination, yielding [Fe(II)L(C')(NCS)](NCS) (3), [Ni(II)L(C')(NCS)](NCS) (6), and [Zn(II)L(C')(NCS)](NCS) (9). The same metal centers are too bulky to exert a template effect on L(A) including one imidazolidine ring and one (short) ethylene bridge. L(A) acts as a tetradentate ligand yielding [Fe(II)L(A)(NCS)2] (1), [Ni(II)L(A)(NCS)2] (4), and [Zn(II)L(A)(NCS)2] (7). The template effect of the metal center is selective toward the ligand L(B)/L(B*) including a hexahydropyrimidine (imidazolidine) ring and the shorter ethylene (longer propylene) bridge. The Fe(II) cation is small enough to exert a template effect, resulting in the ring opening of L(B)/L(B*). The resulting bis-Schiff base L(B') is stabilized through pentacoordination, yielding [Fe(II)L(B')(NCS)](NCS) (2). Ni(II) is too bulky to promote the ring opening of L(B)/L(B*): L(B) acts as a tetradentate ligand, yielding [Ni(II)L(B)(NCS)2] (5) (the L(B*) isomer is totally converted to L(B)). The coordinative requirements and stereochemical preference of the bulkier Zn(II) cation allow neither the ring opening of L(B)/L(B*) nor the tetracoordination of L(B) or L(B*) but stabilize the novel tetradentate dissymmetric form L(B degrees) in [Zn(II)L(B degrees)(NCS)2].H2O (8) (L(B degrees) results from MeOH addition across the imine bond of L(B)). Density functional theory calculations performed for Ni(II) and Zn(II) complexes of the L(B)/L(B*)/L(B degrees) set of ligands allowed one to compare the relative stabilities of all possible isomers, showing that the most stable ones correspond to those experimentally obtained: isomerization, or methanol addition across the imine bond, of the tetradentate ligand depends on the relative stabilities of all possible isomeric complexes.

Triazene derivatives of (1,x)-diazacycloalkanes. Part V.1 Synthesis and characterization of 4-ethyl-3-({6-ethyl-3-[2-aryl-1-diazenyl]hexahydro-1-pyrimidinyl}methyl)-1-[2-aryl-1-diazenyl)hexa- hydropyrimidines from the reaction of diazonium salts with mixtures of formaldehyde and 1,3-diaminopentane

A new series of bistriazenes has been synthesized from a general reaction of diazonium salts with a mixture of 1,3-diaminopentane (DYTEK® EP diamine) and formaldehyde, which affords the 4-ethyl-3-({6-ethyl-3-[2-aryl-1-diazenyl]hexahydro-1-pyrimidinyl}methyl)-1-[2-aryl-1-diazenyl]hexahydropyrimidines (1). Each of the molecules of type 1 is built up of two equivalent 3-(aryldiazenyl)-6-ethylhexahydro-1-pyrimidinyl groups attached to a central methylene group. The importance of this study is in part due to the fact that the formaldehyde–1,3-diaminopentane system has not previously been investigated. All new compounds have been characterized by IR and NMR spectroscopy, with elemental analysis for selected compounds; one example from the series has been unequivocally characterized by X-ray crystallography. Although analysis of the NMR spectra is made somewhat difficult because of broadness and coalescence of signals due to the rotational dynamics of the N—N single bonds, it is possible to fully assign the proton spectra of all compounds and to detect 94% of all carbon signals. The fine structure within the proton spectra illustrate the diastereotopic nature of the methylene group protons because of the presence of a stereocenter in each hexahydropyrimidine ring. The general conclusion of this study is that alkanediamines with three carbon atoms in the spacer link between the nitrogen atoms give rise to the linear bicyclic molecules of type 1, 2, and 3, in contrast to the case of ethylenediamine (spacer link has two carbon atoms), which affords molecules of type 7 that exemplify the bridged bicyclic bistriazene structure. The new compounds of series 1 represent an extension of a broad ranging study of the synthesis of new bistriazene derivatives of (1,x)-diazacycloalkanes.Key words: triazene, diazonium coupling, hexahydropyrimidine, diaminopentane, diazacycloalkanes, stereocenter, diastereotopic protons.

Mirror symmetry in 7,9-dibenzyl-1-tert-butoxycarbonyl-1,7,9-triazaspiro[4.5]dec-3-en-2-one

The crystal structure of tert-butyl 7,9-dibenzyl-2-oxo-1,7,9-triazaspiro[4.5]dec-3-ene-1-carboxylate, C 26 H 31 N 3 O 3 , is reported. The molecule has imposed mirror symmetry and the hexahydropyrimidine ring adopts a chair conformation with two benzyl substituents bonded equatorially to the ring N atoms. The 3-pyrrolin-2-one is attached as a spiro-skeleton to the hexahydropyrimidine ring by one axial C-C and one equatorial C-N bond.

Deprotonation-Induced Enantioselective Aggregation and Deprotonation-Induced Ligand Rearrangement of Copper(II) Complexes Yield 1D Homochiral and Heterochiral Chains and a Cyclic Tetramer, Respectively.

The copper(II) complexes of protonated pentadentate Schiff-base ligands with [Cu(H(2)L(n))](ClO(4))(2) formula (n = 3-6, 3-6) have been synthesized and characterized (H(2)L(3) = N-((2-methylimidazol-4-yl)methylene)-3-aminpropyl-N'-((2-methylimidazol-4-yl)methylene)-4'-aminobutylamine, H(2)L(4) = N-((2-phenylimidazol-4-yl)methylene)-3-aminpropyl-N'-((2-phenyl-imidazol-4-yl)methylene)-4'-aminobutylamine, H(2)L(5) = N,N'-bis((2-phenylimidazol-4-yl)methylene)-3,3'-diaminodipropylmethylamine, H(2)L(6) = N-((2-methylimidazol-4-yl)methylene)-2-aminoethyl-N'-((2-methylimidazol-4-yl)methylene)-3'-aminopropylamine. The mono-deprotonated complexes 3', 4', and 5' contain one imidazole and one imidazolate groups per unit and are Delta (clockwise) or Lambda (anticlockwise) enantiomorphs due to the spiral arrangement of the ligand around copper(II) ion. They function as chiral building components for a self-assembly process resulting from the formation of hydrogen bonds between the imidazole and imidazolate groups of adjacent units to yield 1D zigzag-chain structures. The distance between hydrogen-bonded nitrogen atoms is 2.81(2), 2.832(9), and 2.875(9) Å for 3', 4', and 5', respectively. The crystal lattice of 3' yielded either.DeltaDeltaDelta. or.LambdaLambdaLambda. isotactic 1D zigzag-chains, while the crystal lattices of 4' and 5' yielded.DeltaLambdaDeltaLambda. syndiotactic 1D zigzag-chains. In 3', two adjacent methyl groups at the 2-position connected by hydrogen bond array in the same direction, thus allowing homochiral aggregation of the complex molecules in a 1D chain. On the other hand, in 4' and 5', two adjacent bulky phenyl groups require opposite orientations, thus allowing heterochiral aggregation. Enantioselective aggregation with homochirality or heterochirality can thus be controlled with suitable substituents. While its mononuclear precursor 6 is pentacoordinated with the N(5) donor set of the pentadentate ligand H(2)L(6), the deprotonated complex 6' has an imidazolate-bridged tetranuclear cyclic structure with a Cu-Cu distance of 6.086(2) Å. The ligand in 6' is tetradentate and includes an hexahydropyrimidine ring resulting from a deprotonation induced rearrangement reaction.

ChemInform Abstract: Synthesis and Transformation of Polyhedral Compounds. Part 14. Opening of the Hexahydropyrimidine Ring of 2‐Substituted 1,3‐Diazaadamantanes by Electrophilic Reagents.

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Synthesis and transformations of polyhedral compounds. 14. Opening of hexahydropyrimidine ring of 2-substituted 1,3-diazaadamantanes by electrophilic reagents

It was found that a cleavage of the N-C bonds of C-mono- and C,C-disubstituted methylenediammo groups of 1,3-diazaadamantanes takes place by the action of electrophilic reagents.

ChemInform Abstract: Synthesis of Imidazo[1,2‐a]pyridine and Pyrido[1,2‐a]pyrimidine Derivatives by the Addition and Cyclocondensation Reactions of Ketenaminals Containing Imidazolidine or Hexahydropyrimidine Ring with Esters of α,β‐Unsaturated Acids.

AbstractDurch Addition der Alkin‐ (II) bzw. Alkencarbonsäureester (V) an die Ketenaminale (I) und nachfolgende Cyclisierung der Addukte wie (III) werden die heterocyclischen Systeme (IV) bzw. (VI) aufgebaut.

Synthesis of Imidazo[1,2-a]pyridine and Pyrido[1,2-a]pyrimidine Derivatives by the Addition and Cyclocondensation Reactions of Ketenaminals Containing Imidazolidine or Hexahydropyrimidine Ring with Esters of a,b-Unsaturated Acids

Synthesis of Imidazo[1,2-a]pyridine and Pyrido[1,2-a]pyrimidine Derivatives by the Addition and Cyclocondensation Reactions of Ketenaminals Containing Imidazolidine or Hexahydropyrimidine Ring with Esters of a,b-Unsaturated Acids

Hydropyrimidines. V. Hexahydropyrimidines. The reaction of aldehydes and ketones with 1,3-diaminopropanes

Hexahydropyrimidine and some N-alkylated derivatives have been obtained from the reaction of the corresponding trimethylenediamine or its monoprotonated salt with formaldehyde. A variety of spectroscopic evidence supports a cyclic structure for these compounds in preference to a tautomeric open-chain form. The chemical behaviour of hexahydropyrimidine is explicable in terms of a cyclic di-secondary amine structure. The cyclic structure is destabilized with respect to the open- chain form if the hydrogen atoms attached to C2 of the hexahydropyrimidine ring are replaced by alkyl groups and cannot be detected when, in addition, one of the hydrogen atoms attached to nitrogen is replaced by the bulkier t-butyl group. Hexahydro-2-methylpyrimidine is dehydrogenated to 1,4,5,6- tetrahydro-2-methylpyrimidine on shaking with Adams catalyst and hydrogen under laboratory conditions. Hexahydropyrimidines which are tautomeric mixtures are reduced to the corresponding N-alkyl-1,3- diaminopropanes, while those possessing cyclic structures are inert.