Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products

Daniel E. Vicentes; Ricaurte Rodríguez; Justo Cobo; Christopher Glidewell

doi:10.1107/s2053229623003728

Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products

Daniel E. Vicentes, Ricaurte Rodríguez, Justo Cobo, Christopher Glidewell^*

^*Corresponding author for this work

School of Chemistry

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Abstract

A concise and versatile synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidines has been developed, starting from 4-(1H-benzo[d]imidazol-1-yl)pyrimidines, and we report here the synthesis and spectroscopic and structural characterization of three such products, along with those of two intermediates in the reaction pathway. The intermediates 4-[2-(4-chlorophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (II), and 4-[2-(4-bromophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (III), crystallize as the isostructural monohydrates C₁₈H₁₅ClN₅O·H₂O and C₁₈H₁₅BrN₅O·H₂O, respectively, in which the components are linked into complex sheets by O—H...N and N—H...O hydrogen bonds. In the product (E)-4-methoxy-5-[(4-nitrobenzylidene)amino]-6-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, which crystallizes as a 1:1 solvate with dimethyl sulfoxide, C₂₅H₁₈N₈O₅·C₂H₆OS, (IV), inversion-related pairs of the pyrimidine component are linked by N—H...N hydrogen bonds to form cyclic centrosymmetric R²₂(8) dimers to which pairs of solvent molecules are linked by N—H...O hydrogen bonds. (E)-4-Methoxy-5-[(4-methylbenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C₂₇H₂₄N₆O, (V), crystallizes with Z′ = 2 and the molecules are linked into a three-dimensional framework structure by a combination of N—H...N, C—H...N and C—H...π(arene) hydrogen bonds. The analogous product (E)-4-methoxy-5-[(4-chlorobenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C₂₆H₂₁ClN₆O, (VI), crystallizes from dimethyl sulfoxide in two forms: one, denoted (VIa), is isostructural with (V), and the other, denoted (VIb), crystallizes with Z′ = 1, but as an unknown solvate in which the pyrimidine molecules are linked by N—H...N hydrogen bonds to form a ribbon containing two types of centrosymmetric ring.

Original language	English
Article number	dv3022
Pages (from-to)	227-236
Number of pages	10
Journal	Acta Crystallographica Section C Structural Chemistry
Volume	79
Issue number	6
Early online date	4 May 2023
DOIs	https://doi.org/10.1107/s2053229623003728
Publication status	Published - 1 Jun 2023

Keywords

Synthesis
Pyrimidine
Heterocyclic hybrid
NMR spectroscopy
Crystal structure
Molecular structure
Molecular conformation
Hydrogen bonding
Supramolecular assembly

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Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products (dataset)
Glidewell, C. (Creator), Cambridge Crystallographic Data Centre, 2023
https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:2258807 and 5 more links, https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:2258808, https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:2258809, https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:2258810, https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:2258811, https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:2258812 (show fewer)
Dataset

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Vicentes, D. E., Rodríguez, R., Cobo, J., & Glidewell, C. (2023). Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products. Acta Crystallographica Section C Structural Chemistry, 79(6), 227-236. Article dv3022. https://doi.org/10.1107/s2053229623003728

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title = "Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products",

abstract = "A concise and versatile synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidines has been developed, starting from 4-(1H-benzo[d]imidazol-1-yl)pyrimidines, and we report here the synthesis and spectroscopic and structural characterization of three such products, along with those of two intermediates in the reaction pathway. The intermediates 4-[2-(4-chlorophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (II), and 4-[2-(4-bromophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (III), crystallize as the isostructural monohydrates C18H15ClN5O·H2O and C18H15BrN5O·H2O, respectively, in which the components are linked into complex sheets by O—H...N and N—H...O hydrogen bonds. In the product (E)-4-methoxy-5-[(4-nitrobenzylidene)amino]-6-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, which crystallizes as a 1:1 solvate with dimethyl sulfoxide, C25H18N8O5·C2H6OS, (IV), inversion-related pairs of the pyrimidine component are linked by N—H...N hydrogen bonds to form cyclic centrosymmetric R22(8) dimers to which pairs of solvent molecules are linked by N—H...O hydrogen bonds. (E)-4-Methoxy-5-[(4-methylbenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C27H24N6O, (V), crystallizes with Z′ = 2 and the molecules are linked into a three-dimensional framework structure by a combination of N—H...N, C—H...N and C—H...π(arene) hydrogen bonds. The analogous product (E)-4-methoxy-5-[(4-chlorobenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C26H21ClN6O, (VI), crystallizes from dimethyl sulfoxide in two forms: one, denoted (VIa), is isostructural with (V), and the other, denoted (VIb), crystallizes with Z′ = 1, but as an unknown solvate in which the pyrimidine molecules are linked by N—H...N hydrogen bonds to form a ribbon containing two types of centrosymmetric ring.",

keywords = "Synthesis, Pyrimidine, Heterocyclic hybrid, NMR spectroscopy, Crystal structure, Molecular structure, Molecular conformation, Hydrogen bonding, Supramolecular assembly",

author = "Vicentes, {Daniel E.} and Ricaurte Rodr{\'i}guez and Justo Cobo and Christopher Glidewell",

note = "Funding: Funding for this research was provided by: Spanish Ministerio de Ciencia, Innovac{\'i}on, y Universidades (R&D project No. RTI2018-098560-B-C22), co-financed by the FEDER funds of the European Union.",

year = "2023",

month = jun,

day = "1",

doi = "10.1107/s2053229623003728",

language = "English",

volume = "79",

pages = "227--236",

journal = "Acta Crystallographica Section C Structural Chemistry",

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publisher = "International Union of Crystallography",

number = "6",

}

Vicentes, DE, Rodríguez, R, Cobo, J & Glidewell, C 2023, 'Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products', Acta Crystallographica Section C Structural Chemistry, vol. 79, no. 6, dv3022, pp. 227-236. https://doi.org/10.1107/s2053229623003728

Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products. / Vicentes, Daniel E.; Rodríguez, Ricaurte; Cobo, Justo et al.
In: Acta Crystallographica Section C Structural Chemistry, Vol. 79, No. 6, dv3022, 01.06.2023, p. 227-236.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids

T2 - synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products

AU - Vicentes, Daniel E.

AU - Rodríguez, Ricaurte

AU - Cobo, Justo

AU - Glidewell, Christopher

N1 - Funding: Funding for this research was provided by: Spanish Ministerio de Ciencia, Innovacíon, y Universidades (R&D project No. RTI2018-098560-B-C22), co-financed by the FEDER funds of the European Union.

PY - 2023/6/1

Y1 - 2023/6/1

N2 - A concise and versatile synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidines has been developed, starting from 4-(1H-benzo[d]imidazol-1-yl)pyrimidines, and we report here the synthesis and spectroscopic and structural characterization of three such products, along with those of two intermediates in the reaction pathway. The intermediates 4-[2-(4-chlorophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (II), and 4-[2-(4-bromophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (III), crystallize as the isostructural monohydrates C18H15ClN5O·H2O and C18H15BrN5O·H2O, respectively, in which the components are linked into complex sheets by O—H...N and N—H...O hydrogen bonds. In the product (E)-4-methoxy-5-[(4-nitrobenzylidene)amino]-6-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, which crystallizes as a 1:1 solvate with dimethyl sulfoxide, C25H18N8O5·C2H6OS, (IV), inversion-related pairs of the pyrimidine component are linked by N—H...N hydrogen bonds to form cyclic centrosymmetric R22(8) dimers to which pairs of solvent molecules are linked by N—H...O hydrogen bonds. (E)-4-Methoxy-5-[(4-methylbenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C27H24N6O, (V), crystallizes with Z′ = 2 and the molecules are linked into a three-dimensional framework structure by a combination of N—H...N, C—H...N and C—H...π(arene) hydrogen bonds. The analogous product (E)-4-methoxy-5-[(4-chlorobenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C26H21ClN6O, (VI), crystallizes from dimethyl sulfoxide in two forms: one, denoted (VIa), is isostructural with (V), and the other, denoted (VIb), crystallizes with Z′ = 1, but as an unknown solvate in which the pyrimidine molecules are linked by N—H...N hydrogen bonds to form a ribbon containing two types of centrosymmetric ring.

AB - A concise and versatile synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidines has been developed, starting from 4-(1H-benzo[d]imidazol-1-yl)pyrimidines, and we report here the synthesis and spectroscopic and structural characterization of three such products, along with those of two intermediates in the reaction pathway. The intermediates 4-[2-(4-chlorophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (II), and 4-[2-(4-bromophenyl)-1H-benzo[d]imidazol-1-yl]-6-methoxypyrimidine-2,5-diamine, (III), crystallize as the isostructural monohydrates C18H15ClN5O·H2O and C18H15BrN5O·H2O, respectively, in which the components are linked into complex sheets by O—H...N and N—H...O hydrogen bonds. In the product (E)-4-methoxy-5-[(4-nitrobenzylidene)amino]-6-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, which crystallizes as a 1:1 solvate with dimethyl sulfoxide, C25H18N8O5·C2H6OS, (IV), inversion-related pairs of the pyrimidine component are linked by N—H...N hydrogen bonds to form cyclic centrosymmetric R22(8) dimers to which pairs of solvent molecules are linked by N—H...O hydrogen bonds. (E)-4-Methoxy-5-[(4-methylbenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C27H24N6O, (V), crystallizes with Z′ = 2 and the molecules are linked into a three-dimensional framework structure by a combination of N—H...N, C—H...N and C—H...π(arene) hydrogen bonds. The analogous product (E)-4-methoxy-5-[(4-chlorobenzylidene)amino]-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-amine, C26H21ClN6O, (VI), crystallizes from dimethyl sulfoxide in two forms: one, denoted (VIa), is isostructural with (V), and the other, denoted (VIb), crystallizes with Z′ = 1, but as an unknown solvate in which the pyrimidine molecules are linked by N—H...N hydrogen bonds to form a ribbon containing two types of centrosymmetric ring.

KW - Synthesis

KW - Pyrimidine

KW - Heterocyclic hybrid

KW - NMR spectroscopy

KW - Crystal structure

KW - Molecular structure

KW - Molecular conformation

KW - Hydrogen bonding

KW - Supramolecular assembly

U2 - 10.1107/s2053229623003728

DO - 10.1107/s2053229623003728

M3 - Article

SN - 2053-2296

VL - 79

SP - 227

EP - 236

JO - Acta Crystallographica Section C Structural Chemistry

JF - Acta Crystallographica Section C Structural Chemistry

IS - 6

M1 - dv3022

ER -

Vicentes DE, Rodríguez R, Cobo J, Glidewell C. Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products. Acta Crystallographica Section C Structural Chemistry. 2023 Jun 1;79(6):227-236. dv3022. Epub 2023 May 4. doi: 10.1107/s2053229623003728

Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products

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Synthesis of 5-(arylmethylideneamino)-4-(1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of two intermediates and three final products (dataset)

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