Nitrogen-Containing Molecules: Natural and Synthetic Products Including Coordination Compounds

A special issue of Molbank (ISSN 1422-8599).

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 45866

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1. Department of Biomedical Sciences, University of West Attica, Egaleo Park Campus, 12243 Athens, Greece
2. Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, 15310 Athens, Greece
Interests: heterocyclic and medicinal chemistry; organic synthesis; antimicrobial agents; structure–activity relationships of bioactive compounds; curcuminoids; tetramic acids; pyrazolines
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Guest Editor
Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, 15310 Athens, Greece
Interests: nano-sized systems; drug encapsulation and delivery; drug targeting; surface functionalization; material characterization; controlled release; natural products; metal complexes; radiopharmaceuticals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nitrogen constitutes one of the most crucial elements in synthetic compounds, both organic and coordination. After all, urea is considered to be the first synthetic organic compound (it was first prepared in 1828 by Friedrich Wöhler from a mixture of the inorganic compounds silver cyanate (AgOCN) and ammonium chloride (NH4Cl)).

From a medicinal chemistry viewpoint, nitrogen is a very common element in every major class of active pharmaceutical ingredients existing in heterocyclic and in acyclic molecules. Functional groups like amines, imines, nitriles, amides, and carbamates dominate the libraries of bioactive compounds, whereas the total number of unique drugs containing at least one nitrogen heterocycle among FDA-approved pharmaceuticals is 910 (84% among 1035 unique small-molecule drugs). The top-5 most frequent nitrogen heterocycles in this list are piperidine, pyridine, piperazine, β-lactam, and pyrrolidine.

Until today, the combined use of synthetic organic chemistry and coordination chemistry has generated a number of new and effective synthetic methods of high-rate product formation for important classes of coordination compounds of several nitrogen-containing ligands with numerous metal ions, giving rise to novel materials with exceptional physicochemical, biological, medicinal, catalytic, and optical properties.

For the Special Issue “Nitrogen-Containing Molecules: Natural and Synthetic Products Including Coordination Compounds”, we welcome the submission of research articles related to one or more of the following: design and synthesis; structural characterization by means of NMR; X-ray crystallography; or other preliminary but significant results including but not limited to biological evaluation, theoretical calculations/molecular mechanics/computational studies, material or physicochemical properties of nitrogen-containing molecules, and/or coordination compounds of nitrogen-containing molecules.

Dr. Dimitrios Matiadis
Dr. Eleftherios Halevas
Guest Editors

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Keywords

  • nitrogen heterocycles
  • coordination compounds
  • amines
  • pyridine
  • Schiff bases
  • metal complexes
  • metal–organic coordination chemistry
  • organic chemistry

Published Papers (17 papers)

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Editorial

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5 pages, 207 KiB  
Editorial
Nitrogen-Containing Molecules: Natural and Synthetic Products including Coordination Compounds
by Dimitris Matiadis and Eleftherios Halevas
Molbank 2021, 2021(4), M1282; https://doi.org/10.3390/M1282 - 27 Sep 2021
Cited by 4 | Viewed by 1893
Abstract
Nitrogen constitutes one of the most crucial elements in synthetic compounds, both in organic and in coordination chemistry [...] Full article

Research

Jump to: Editorial

4 pages, 349 KiB  
Communication
Synthesis of 4-[(1H-Benzimidazol-2-yl)sulfanyl]benzaldehyde and 2-({4-[(1H-Benzimidazol-2-yl)sulfanyl]phenyl}methylidene)hydrazine-1-carbothioamide
by Mustafa Turki Ubeid, Hamdy Khamees Thabet and Mohamed Yousef Abu Shuheil
Molbank 2021, 2021(3), M1273; https://doi.org/10.3390/M1273 - 26 Aug 2021
Cited by 4 | Viewed by 2931
Abstract
Here we describe the preparation of 2-(4-((1H-benzo[d]imidazol-2-yl)thio)-benzylidene)-hydrazine-1-carbothioamide in two steps. In the first step, 1,3-dihydro-2H-1,3-benzimidazole-2-thione was reacted with 4-fluorobenzaldehyde in DMSO to get 4-[(1H-benzimidazol-2-yl)sulfanyl]benzaldehyde in high yield. The reaction of the obtained aldehyde with thiosemicarbazide in ethanol at reflux [...] Read more.
Here we describe the preparation of 2-(4-((1H-benzo[d]imidazol-2-yl)thio)-benzylidene)-hydrazine-1-carbothioamide in two steps. In the first step, 1,3-dihydro-2H-1,3-benzimidazole-2-thione was reacted with 4-fluorobenzaldehyde in DMSO to get 4-[(1H-benzimidazol-2-yl)sulfanyl]benzaldehyde in high yield. The reaction of the obtained aldehyde with thiosemicarbazide in ethanol at reflux temperature yielded 2-({4-[(1H-benzimidazol-2-yl)sulfanyl]phenyl}methylidene)hydrazine-1-carbothioamide. The structure of the synthesized compounds was established by NMR spectroscopy (1H, 13C), mass spectrometry, and infrared spectroscopy. Full article
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Scheme 1

6 pages, 388 KiB  
Short Note
4-Amino-2-(p-tolyl)-7H-chromeno[5,6-d]oxazol-7-one
by Evangelia-Eirini N. Vlachou, Thomas D. Balalas, Dimitra J. Hadjipavlou-Litina and Konstantinos E. Litinas
Molbank 2021, 2021(2), M1237; https://doi.org/10.3390/M1237 - 15 Jun 2021
Cited by 2 | Viewed by 1883
Abstract
The new 4-amino-2-(p-tolyl)-7H-chromeno[5,6-d]oxazol-7-one was successfully prepared through the Au/TiO2-catalyzed NaBH4 activation and chemoselective reduction of the new 4-nitro-2-(p-tolyl)-7H-chromeno[5,6-d]oxazol-7-one. The latter was synthesized by the one-pot tandem reactions of [...] Read more.
The new 4-amino-2-(p-tolyl)-7H-chromeno[5,6-d]oxazol-7-one was successfully prepared through the Au/TiO2-catalyzed NaBH4 activation and chemoselective reduction of the new 4-nitro-2-(p-tolyl)-7H-chromeno[5,6-d]oxazol-7-one. The latter was synthesized by the one-pot tandem reactions of 6-hydroxy-5,7-dinitrocoumarin with p-tolylmethanol under Au/TiO2 catalysis. The dinitrocoumarin was obtained by the nitration of 6-hydroxycoumarin with cerium ammonium nitrate (CAN). The structure of the synthesized compounds was confirmed by FT-IR, HR-MS, 1H-NMR and 13C-NMR analysis. Preliminary biological tests show low anti-lipid peroxidation activity for the title compound. Full article
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Scheme 1

7 pages, 1904 KiB  
Short Note
1-Methyl-8-phenyl-1,3-diazaspiro[4.5]decane-2,4-dione
by Vasiliki Pardali, Sotirios Katsamakas, Erofili Giannakopoulou and Grigoris Zoidis
Molbank 2021, 2021(2), M1228; https://doi.org/10.3390/M1228 - 4 Jun 2021
Cited by 1 | Viewed by 2194
Abstract
A simple, fast and cost-effective three-step synthesis of 1-methyl-8-phenyl-1,3-diazaspiro[4.5]decane-2,4-dione has been developed. The reactions described herein proceed readily, with high yields and no further purification. Therefore, the proposed method, with an overall yield of 60%, offers a facile pathway to the synthesis of [...] Read more.
A simple, fast and cost-effective three-step synthesis of 1-methyl-8-phenyl-1,3-diazaspiro[4.5]decane-2,4-dione has been developed. The reactions described herein proceed readily, with high yields and no further purification. Therefore, the proposed method, with an overall yield of 60%, offers a facile pathway to the synthesis of N-1 monosubstituted spiro carbocyclic imidazolidine-2,4-diones (hydantoins), which constitute a privileged class of heterocyclic scaffolds with pharmacological interest. Full article
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4 pages, 693 KiB  
Short Note
(E)-3-((2-Fluorophenyl)(hydroxy)methylene)imidazo[1,2-a]pyridin-2(3H)-one
by Giammarco Tenti, Ángel Cores, María Teresa Ramos and J. Carlos Menéndez
Molbank 2021, 2021(2), M1212; https://doi.org/10.3390/M1212 - 14 May 2021
Cited by 1 | Viewed by 1880
Abstract
Treatment of a N-2-pyridyl-β-ketoamide precursor with bromine afforded the first example of the 3-aryl(α-hydroxy)methylenelimidazo[1,2-a]pyridin-2(3H)-one framework. This transformation proceeded through a domino process comprising an initial bromination, cyclization via an intramolecular SN reaction, and a final keto-enol tautomerism, and [...] Read more.
Treatment of a N-2-pyridyl-β-ketoamide precursor with bromine afforded the first example of the 3-aryl(α-hydroxy)methylenelimidazo[1,2-a]pyridin-2(3H)-one framework. This transformation proceeded through a domino process comprising an initial bromination, cyclization via an intramolecular SN reaction, and a final keto-enol tautomerism, and allows generation of the fused heterocyclic system and installation of the acyl substituent in a single operation. Full article
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6 pages, 769 KiB  
Communication
Synthesis of Polar Aromatic Substituted Terminal Alkynes from Propargyl Amine
by Surya R. Banks, Kyung Min Yoo and Mark E. Welker
Molbank 2021, 2021(2), M1206; https://doi.org/10.3390/M1206 - 25 Apr 2021
Cited by 1 | Viewed by 3071
Abstract
A series of small molecules containing polar aromatic substituents and alkynes have been synthesized. One–pot preparations of polar aromatic molecules containing an alkynyl imine and alkynyl amide are reported. A one-pot preparation of a catechol containing an alkynyl amine was also attempted but [...] Read more.
A series of small molecules containing polar aromatic substituents and alkynes have been synthesized. One–pot preparations of polar aromatic molecules containing an alkynyl imine and alkynyl amide are reported. A one-pot preparation of a catechol containing an alkynyl amine was also attempted but in our hands it proved much better to synthesize this target molecule via a three step synthesis which we also report here. Full article
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Scheme 1

5 pages, 1138 KiB  
Short Note
Homopiperazine (Hexahydro-1,4-diazepine)
by R. Alan Aitken, Dheirya K. Sonecha and Alexandra M. Z. Slawin
Molbank 2021, 2021(2), M1200; https://doi.org/10.3390/M1200 - 10 Apr 2021
Cited by 3 | Viewed by 2468
Abstract
The X-ray structure of the title compound has been determined for the first time. Data on its 1H–13C-NMR coupling constants and 15N-NMR spectrum are also given. Full article
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5 pages, 1172 KiB  
Short Note
(1R,4S,5S)-5-((3-Hydroxypropyl)amino)-4-((1-methyl-1H-tetrazol-5-yl)thio)cyclopent-2-en-1-ol
by Milene A. G. Fortunato, Filipa Siopa and Carlos A. M. Afonso
Molbank 2021, 2021(2), M1199; https://doi.org/10.3390/M1199 - 1 Apr 2021
Cited by 1 | Viewed by 2177
Abstract
Using environmentally friendly conditions, the nucleophilic ring-opening reaction of 6-azabicyclo[3.1.0]hex-3-en-2-ol with 1-methyl-1H-tetrazole-5-thiol provided a novel thiol-incorporated aminocyclopentitol, (1R,4S,5S)-5-((3-hydroxypropyl)amino)-4-((1-methyl-1H-tetrazol-5-yl)thio)cyclopent-2-en-1-ol, in excellent yield (95%). The newly synthesized compound was analyzed and characterized via 1H, 13C-NMR, HSQC, and mass spectral data. Full article
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5 pages, 940 KiB  
Short Note
4′-(5-N-Propylthiophen-2-yl)-2,2′:6′,2″-terpyridine
by Jérôme Husson and Laurent Guyard
Molbank 2021, 2021(1), M1183; https://doi.org/10.3390/M1183 - 21 Jan 2021
Cited by 1 | Viewed by 2187
Abstract
A new thiophene-substituted terpyridine derivative has been prepared through the reaction between 5-n-propylthiophene-2-carboxaldehyde and 2-acetylpyridine. This terpyridine derivative bears an alkyl chain linked via a thiophene heterocycle. Full article
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Graphical abstract

5 pages, 2187 KiB  
Short Note
Cis-Bis(2,2′-Azopyridinido)dicarbonylruthenium(II)
by Tsugiko Takase, Shuya Kainuma, Takatoshi Kanno and Dai Oyama
Molbank 2021, 2021(1), M1182; https://doi.org/10.3390/M1182 - 18 Jan 2021
Cited by 1 | Viewed by 2032
Abstract
An [Ru(apy)2Cl2] precursor (apy = 2,2′-azopyridine) in 2-methoxyethanol was heated under a pressurized CO atmosphere to afford a diradical complex, [Ru(apy·)2(CO)2], containing one-electron-reduced azo anion radical ligands. The electronic states of the complex [...] Read more.
An [Ru(apy)2Cl2] precursor (apy = 2,2′-azopyridine) in 2-methoxyethanol was heated under a pressurized CO atmosphere to afford a diradical complex, [Ru(apy·)2(CO)2], containing one-electron-reduced azo anion radical ligands. The electronic states of the complex were characterized by spectroscopic techniques and computational studies. Magnetic measurements revealed the existence of antiferromagnetic interactions in the diradical complex. Full article
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Figure 1

9 pages, 1966 KiB  
Communication
Synthesis and Structural Characterization of (E)-4-[(2-Hydroxy-3-methoxybenzylidene)amino]butanoic Acid and Its Novel Cu(II) Complex
by Eleftherios Halevas, Antonios Hatzidimitriou, Barbara Mavroidi, Marina Sagnou, Maria Pelecanou and Dimitris Matiadis
Molbank 2021, 2021(1), M1179; https://doi.org/10.3390/M1179 - 6 Jan 2021
Cited by 4 | Viewed by 3276
Abstract
A novel Cu(II) complex based on the Schiff base obtained by the condensation of ortho-vanillin with gamma-aminobutyric acid was synthesized. The compounds are physico-chemically characterized by elemental analysis, HR-ESI-MS, FT-IR, and UV-Vis. The complex and the Schiff base ligand are further [...] Read more.
A novel Cu(II) complex based on the Schiff base obtained by the condensation of ortho-vanillin with gamma-aminobutyric acid was synthesized. The compounds are physico-chemically characterized by elemental analysis, HR-ESI-MS, FT-IR, and UV-Vis. The complex and the Schiff base ligand are further structurally identified by single crystal X-ray diffraction and 1H and 13C-NMR, respectively. The results suggest that the Schiff base are synthesized in excellent yield under mild reaction conditions in the presence of glacial acetic acid and the crystal structure of its Cu(II) complex reflects an one-dimensional polymeric compound. The molecular structure of the complex consists of a Cu(II) ion bound to two singly deprotonated Schiff base bridging ligands that form a CuN2O4 chelation environment, and a coordination sphere with a disordered octahedral geometry. Full article
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7 pages, 1370 KiB  
Short Note
6-Bromo-N-(3-(difluoromethyl)phenyl)quinolin-4-amine
by Christopher R. M. Asquith and Graham J. Tizzard
Molbank 2020, 2020(4), M1161; https://doi.org/10.3390/M1161 - 20 Oct 2020
Cited by 1 | Viewed by 2997
Abstract
A routine synthesis was performed to furnish the title compound which incorporates a versatile difluoromethyl group on the aniline substitution of a 4-anilinoquinoline kinase inhibitor motif. In addition, the small molecule crystal structure (of the HCl salt) was solved, which uncovered that the [...] Read more.
A routine synthesis was performed to furnish the title compound which incorporates a versatile difluoromethyl group on the aniline substitution of a 4-anilinoquinoline kinase inhibitor motif. In addition, the small molecule crystal structure (of the HCl salt) was solved, which uncovered that the difluoromethyl group was disordered within the packing arrangement and also a 126.08(7)° out of plane character between the respective ring systems within the molecule. The compound was fully characterized with 1H/13C-NMR and high-resolution mass spectra (HRMS), with the procedures described. Full article
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Graphical abstract

5 pages, 1140 KiB  
Short Note
Ethyl 11a,12-Dihydrobenzo[b]benzo[5,6][1,4]oxazino[2,3-e][1,4]oxazine-5a(6H)-carboxylate
by Lidia S. Konstantinova, Mikhail A. Tolmachev, Vadim V. Popov and Oleg A. Rakitin
Molbank 2020, 2020(3), M1149; https://doi.org/10.3390/M1149 - 21 Jul 2020
Cited by 2 | Viewed by 2526
Abstract
The 11a,12-dihydrobenzo[b]benzo[5,6][1,4]oxazino[2,3-e][1,4]oxazine heterocyclic system has been used in the construction of heteropropellanes, which attracted much attention not only on the possible modification of drugs, but also for novel materials with unusual and important physical properties. In this communication, the [...] Read more.
The 11a,12-dihydrobenzo[b]benzo[5,6][1,4]oxazino[2,3-e][1,4]oxazine heterocyclic system has been used in the construction of heteropropellanes, which attracted much attention not only on the possible modification of drugs, but also for novel materials with unusual and important physical properties. In this communication, the reaction of ethyl 2-(hydroxyimino)propanoate 1 with disulfur dichloride and o-aminophenol, which gave ethyl 11a,12-dihydrobenzo[b]benzo[5,6][1,4]oxazino[2,3-e][1,4]oxazine-5a(6H)-carboxylate in moderate yield, was described. The structure of the newly synthesized compound was established by means of elemental analysis, high resolution mass-spectrometry, 1H, 13C NMR and IR spectroscopy, mass-spectrometry and X-ray analysis. Full article
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Graphical abstract

10 pages, 499 KiB  
Communication
(E)-(1-(4-Ethoxycarbonylphenyl)-5-(3,4-dimethoxyphenyl)-3-(3,4-dimethoxystyryl)-2-pyrazoline: Synthesis, Characterization, DNA-Interaction, and Evaluation of Activity Against Drug-Resistant Cell Lines
by Dimitris Matiadis, Barbara Mavroidi, Angeliki Panagiotopoulou, Constantinos Methenitis, Maria Pelecanou and Marina Sagnou
Molbank 2020, 2020(1), M1114; https://doi.org/10.3390/M1114 - 30 Jan 2020
Cited by 12 | Viewed by 2885
Abstract
(E)-1-(4-Ethoxycarbonylphenyl)-5-(3,4-dimethoxyphenyl)-3-(3,4-dimethoxystyryl)-2-pyrazoline was synthesized via the cyclization reaction between the monocarbonyl curcuminoid (2E,6E)-2,6-bis(3,4-dimethoxybenzylidene)acetone and ethyl hydrazinobenzoate in high yield and purity (>95% by High-performance liquid chromatography (HPLC)). The compound has been fully characterized by 1H, 13C [...] Read more.
(E)-1-(4-Ethoxycarbonylphenyl)-5-(3,4-dimethoxyphenyl)-3-(3,4-dimethoxystyryl)-2-pyrazoline was synthesized via the cyclization reaction between the monocarbonyl curcuminoid (2E,6E)-2,6-bis(3,4-dimethoxybenzylidene)acetone and ethyl hydrazinobenzoate in high yield and purity (>95% by High-performance liquid chromatography (HPLC)). The compound has been fully characterized by 1H, 13C NMR, FTIR, UV-Vis and HRMS and its activity was evaluated in terms of its potential interaction with DNA as well as its cytotoxicity against resistant and non-resistant tumor cells. Both DNA thermal denaturation and DNA viscosity measurements revealed that a significant intercalation binding takes place upon treatment of the DNA with the synthesized pyrazoline, causing an increase in melting temperature by 3.53 ± 0.11 °C and considerable DNA lengthening and viscosity increase. However, neither re-sensitisation of Doxorubicin (DO X)-resistant breast cancer and multidrug resistance (MDR) reversal nor synergistic activity with DOX by potentially increasing the DOX cell killing ability was observed. Full article
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7 pages, 1295 KiB  
Short Note
2,2′-((1,4-Dimethoxy-1,4-dioxobutane-2,3-diylidene)bis(azanylylidene))bis(quinoline-3-carboxylic acid)
by Joanna Fedorowicz, Karol Gzella, Paulina Wiśniewska and Jarosław Sączewski
Molbank 2019, 2019(4), M1093; https://doi.org/10.3390/M1093 - 21 Nov 2019
Cited by 1 | Viewed by 2429
Abstract
The title compound, 2,2′-((1,4-dimethoxy-1,4-dioxobutane-2,3-diylidene)bis(azanylylidene))bis(quinoline-3-carboxylic acid) was synthesized from isoxazolo[3,4-b]quinolin-3(1H)-one and dimethyl acetylenedicarboxylate (DMAD) via a double aza-Michael addition followed by [1,3]-H shifts. The product was characterized by infrared and nuclear magnetic resonance spectroscopy, as well as elemental analysis and [...] Read more.
The title compound, 2,2′-((1,4-dimethoxy-1,4-dioxobutane-2,3-diylidene)bis(azanylylidene))bis(quinoline-3-carboxylic acid) was synthesized from isoxazolo[3,4-b]quinolin-3(1H)-one and dimethyl acetylenedicarboxylate (DMAD) via a double aza-Michael addition followed by [1,3]-H shifts. The product was characterized by infrared and nuclear magnetic resonance spectroscopy, as well as elemental analysis and high-resolution mass spectrometry (HRMS). The proposed reaction mechanism was rationalized by density functional theory (DFT) calculations. Full article
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Graphical abstract

8 pages, 2832 KiB  
Communication
Synthesis of 2-Cyanopyrimidines
by Andreas S. Kalogirou and Panayiotis A. Koutentis
Molbank 2019, 2019(4), M1086; https://doi.org/10.3390/M1086 - 22 Oct 2019
Cited by 4 | Viewed by 3196
Abstract
4,6-Dichloro-2-(methylthio)pyrimidine (7) was converted to 4-chloro-6-methoxy-2-(methylthio)pyrimidine (15) and 4,6-dimethoxy-2-(methylthio)pyrimidine (14). Chlorination of the latter with N-chlorosuccinimide (NCS) affords 5-chloro-4,6-dimethoxy-2-(methylthio)pyrimidine (16) in 56% yield. Both methylthiopyrimidines 15 and 14 were converted in two steps to [...] Read more.
4,6-Dichloro-2-(methylthio)pyrimidine (7) was converted to 4-chloro-6-methoxy-2-(methylthio)pyrimidine (15) and 4,6-dimethoxy-2-(methylthio)pyrimidine (14). Chlorination of the latter with N-chlorosuccinimide (NCS) affords 5-chloro-4,6-dimethoxy-2-(methylthio)pyrimidine (16) in 56% yield. Both methylthiopyrimidines 15 and 14 were converted in two steps to 4-chloro-6-methoxypyrimidine-2-carbonitrile (13) and 4,6-dimethoxypyrimidine-2-carbonitrile (12), respectively, after oxidation to sulfones and displacement of the sulfinate group with KCN. 4,6-Dimethoxypyrimidine-2-carbonitrile (12) was chlorinated with NCS to give 5-chloro-4,6-dimethoxypyrimidine-2-carbonitrile (10) in 53% yield. All new compounds were fully characterized. Full article
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5 pages, 1843 KiB  
Communication
Reactions of Polychlorinated Pyrimidines with DABCO
by Andreas S. Kalogirou and Panayiotis A. Koutentis
Molbank 2019, 2019(4), M1084; https://doi.org/10.3390/M1084 - 14 Oct 2019
Cited by 3 | Viewed by 2792
Abstract
The reaction of 2,4,5,6-tetrachloropyrimidine (4) and 4,5,6-trichloropyrimidine-2-carbonitrile (1) with DABCO (1 equiv.), in MeCN, at ca. 20 °C gives 2,4,5-trichloro-6-[4-(2-chloroethyl)piperazin-1-yl]pyrimidine (5) and 4,5-dichloro-6-[4-(2-chloroethyl)piperazin-1-yl]pyrimidine-2-carbonitrile (6) in 42% and 52% yields, respectively. The new compounds were fully characterized. Full article
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