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Synthesis, crystal structure, and in silico mol­ecular docking studies of 4-hy­droxy-3,5-di­meth­oxy­benzaldehyde (6-chloro­pyridazin-3-yl)hydrazone monohydrate
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S205698902500252X
Muhammed Rafi Ummer , M. NizamMohideen , Mohammed Nazrudeen Noorulla , Abubacker Sidhik Moolan Khaja
The synthesis, mol­ecular X-ray structure and in silico EGFR and HER2 mol­ecular docking studies are reported for 4-hy­droxy-3,5-di­meth­oxy­benzaldehyde (6-chloro­pyridazin-3-yl)hydrazone hydrate, which constitutes a new pyridazine-based compound incorporating a syringaldehyde moiety by condensation of the hydrazine linker with the aldehyde function.
In the title compound, C13H13ClN4O3·H2O, the organic mol­ecule has an E configuration with regard to the C=N bond of the hydrazone bridge. The phenyl and pyridazine rings subtend a dihedral angle of 2.1 (1)° between their mean planes, while the hydrazone moiety makes dihedral angles of 1.6 (2) and 3.0 (2)°, respectively, with these aromatic rings. This renders the entire mol­ecule comparably flat. A C—H⋯N hydrogen bond generates an inversion dimer with a large R22(14) ring motif. Within this ring, a further C—H⋯N hydrogen bond establishes a smaller R22(8) ring. The mol­ecules of a dimer are thereby firmly linked by four hydrogen bonds. A bifurcated O—H⋯(O,O) hydrogen bond is formed between a water hydrogen atom and the hydroxyl and meth­oxy oxygen atoms of an adjacent mol­ecule, leading to the formation of an R21(5) membered ring. C—H⋯π and face-to-face π–π stacking inter­actions are also present in the two-dimensional framework, which may be of relevance for the packing. In a complementary analysis, the compound was docked in silico to EGFR and HER2 receptors and the results imply that the compound targets EGFR preferentially over HER2.
{"title":"Synthesis, crystal structure, and in silico mol­ecular docking studies of 4-hy­droxy-3,5-di­meth­oxy­benzaldehyde (6-chloro­pyridazin-3-yl)hydrazone monohydrate","authors":"Muhammed Rafi Ummer ,&nbsp;M. NizamMohideen ,&nbsp;Mohammed Nazrudeen Noorulla ,&nbsp;Abubacker Sidhik Moolan Khaja","doi":"10.1107/S205698902500252X","DOIUrl":"10.1107/S205698902500252X","url":null,"abstract":"<div><div>The synthesis, mol­ecular X-ray structure and <em>in silico</em> EGFR and HER2 mol­ecular docking studies are reported for 4-hy­droxy-3,5-di­meth­oxy­benzaldehyde (6-chloro­pyridazin-3-yl)hydrazone hydrate, which constitutes a new pyridazine-based compound incorporating a syringaldehyde moiety by condensation of the hydrazine linker with the aldehyde function.</div></div><div><div>In the title compound, C<sub>13</sub>H<sub>13</sub>ClN<sub>4</sub>O<sub>3</sub>·H<sub>2</sub>O, the organic mol­ecule has an <em>E</em> configuration with regard to the C=N bond of the hydrazone bridge. The phenyl and pyridazine rings subtend a dihedral angle of 2.1 (1)° between their mean planes, while the hydrazone moiety makes dihedral angles of 1.6 (2) and 3.0 (2)°, respectively, with these aromatic rings. This renders the entire mol­ecule comparably flat. A C—H⋯N hydrogen bond generates an inversion dimer with a large <em>R</em><sub>2</sub><sup>2</sup>(14) ring motif. Within this ring, a further C—H⋯N hydrogen bond establishes a smaller <em>R</em><sub>2</sub><sup>2</sup>(8) ring. The mol­ecules of a dimer are thereby firmly linked by four hydrogen bonds. A bifurcated O—H⋯(O,O) hydrogen bond is formed between a water hydrogen atom and the hydroxyl and meth­oxy oxygen atoms of an adjacent mol­ecule, leading to the formation of an <em>R</em><sub>2</sub><sup>1</sup>(5) membered ring. C—H⋯π and face-to-face π–π stacking inter­actions are also present in the two-dimensional framework, which may be of relevance for the packing. In a complementary analysis, the compound was docked <em>in silico</em> to EGFR and HER2 receptors and the results imply that the compound targets EGFR preferentially over HER2.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 336-340"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crystal structure and Hirshfeld surface analysis of aqua­(1H-imidazole-κN3)[N-(2-oxido­benzyl­idene)threonato-κ3O,N,O′]zinc(II)
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025002385
Fumishi Yoshizawa , Anna Okui , Daisuke Nakane , Takashiro Akitsu
The crystal structure of the amino acid Schiff base zinc(II) complex synthesized from salicyl­aldehyde, l-threonine and zinc(II) acetate is reported.
The title complex, [Zn(C11H11NO4)(C3H4N2)(H2O)], which includes a tridentate ligand, was synthesized from l-threonine and salicyl­aldehyde. One water mol­ecule and one imidazole mol­ecule additionally coordinate the zinc(II) center in a distorted trigonal–bipyramidal geometry. The crystal structure features N—H⋯O and O—H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H/H⋯H (50.7%) and O⋯H/H⋯O (25.0%) contacts.
{"title":"Crystal structure and Hirshfeld surface analysis of aqua­(1H-imidazole-κN3)[N-(2-oxido­benzyl­idene)threonato-κ3O,N,O′]zinc(II)","authors":"Fumishi Yoshizawa ,&nbsp;Anna Okui ,&nbsp;Daisuke Nakane ,&nbsp;Takashiro Akitsu","doi":"10.1107/S2056989025002385","DOIUrl":"10.1107/S2056989025002385","url":null,"abstract":"<div><div>The crystal structure of the amino acid Schiff base zinc(II) complex synthesized from salicyl­aldehyde, <span>l</span>-threonine and zinc(II) acetate is reported.</div></div><div><div>The title complex, [Zn(C<sub>11</sub>H<sub>11</sub>NO<sub>4</sub>)(C<sub>3</sub>H<sub>4</sub>N<sub>2</sub>)(H<sub>2</sub>O)], which includes a tridentate ligand, was synthesized from <span>l</span>-threonine and salicyl­aldehyde. One water mol­ecule and one imidazole mol­ecule additionally coordinate the zinc(II) center in a distorted trigonal–bipyramidal geometry. The crystal structure features N—H⋯O and O—H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H/H⋯H (50.7%) and O⋯H/H⋯O (25.0%) contacts.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 332-335"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
(5,6-Dimethyl-1,10-phenanthroline)(2-{[2-(di­phenyl­phosphan­yl)benzyl­idene]amino}­ethan-1-amine)­platinum(II) dinitrate methanol disolvate
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025001847
Ashley Jurisinec , Yingjie Zhang , Janice R. Aldrich-Wright
The title platinum(II) complex exhibits a distorted square-planar geometry. Intra- and inter­molecular π-stacking inter­actions are observed between the phenanthroline and phosphine rings while hydrogen bonding is observed between the complex ion, nitrate counter-ions and solvent mol­ecules.
The title compound, [Pt(C14H12N2)(C21H21N2P)](NO3)2·2CH3OH, is a platinum(II) complex, which crystallizes in a monoclinic (P21/c) space group. The complex exhibits a distorted square-planar geometry, which includes a monodentate 5,6-dimethyl-1,10-phenanthroline ligand and a tridentate 2-{[2-(di­phenyl­phosphan­yl)benzyl­idene]amino}­ethan-1-amine ligand. The structure reveals both intra- and inter­molecular π-stacking inter­actions between the phenanthroline and phosphine rings. Hydrogen bonding is observed between the complex ion, nitrate counter-ions and solvent mol­ecules.
{"title":"(5,6-Dimethyl-1,10-phenanthroline)(2-{[2-(di­phenyl­phosphan­yl)benzyl­idene]amino}­ethan-1-amine)­platinum(II) dinitrate methanol disolvate","authors":"Ashley Jurisinec ,&nbsp;Yingjie Zhang ,&nbsp;Janice R. Aldrich-Wright","doi":"10.1107/S2056989025001847","DOIUrl":"10.1107/S2056989025001847","url":null,"abstract":"<div><div>The title platinum(II) complex exhibits a distorted square-planar geometry. Intra- and inter­molecular π-stacking inter­actions are observed between the phenanthroline and phosphine rings while hydrogen bonding is observed between the complex ion, nitrate counter-ions and solvent mol­ecules.</div></div><div><div>The title compound, [Pt(C<sub>14</sub>H<sub>12</sub>N<sub>2</sub>)(C<sub>21</sub>H<sub>21</sub>N<sub>2</sub>P)](NO<sub>3</sub>)<sub>2</sub>·2CH<sub>3</sub>OH, is a platinum(II) complex, which crystallizes in a monoclinic (<em>P</em>2<sub>1</sub>/<em>c</em>) space group. The complex exhibits a distorted square-planar geometry, which includes a monodentate 5,6-dimethyl-1,10-phenanthroline ligand and a tridentate 2-{[2-(di­phenyl­phosphan­yl)benzyl­idene]amino}­ethan-1-amine ligand. The structure reveals both intra- and inter­molecular π-stacking inter­actions between the phenanthroline and phosphine rings. Hydrogen bonding is observed between the complex ion, nitrate counter-ions and solvent mol­ecules.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 275-278"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis and crystal structure of 5-{(E)-[(1H-indol-3-ylformamido)­imino]­meth­yl}-2-meth­oxy­phenyl propane-1-sulfonate
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025002087
Reham A. Mohamed-Ezzat , Benson M. Kariuki , Aisha A. K. Al-Ashmawy , Aladdin M. Srour
The crystal structure is characterized by a three-dimensional hydrogen-bonding network. Chains formed through N—H⋯O contacts are linked by additional inter­molecular bonds to complete the structure.
In the title mol­ecule, C20H21N3O5S, the methyl­ideneformohydrazide and meth­oxy­benzene groups are almost coplanar, with the indolyl group being rotated farther from the plane. The mol­ecules in the crystal structure form chains parallel to the a-axis direction through N—H⋯O hydrogen-bonding inter­actions. Neighbouring chains are linked by N—H⋯O contacts to form a three-dimensional network.
{"title":"Synthesis and crystal structure of 5-{(E)-[(1H-indol-3-ylformamido)­imino]­meth­yl}-2-meth­oxy­phenyl propane-1-sulfonate","authors":"Reham A. Mohamed-Ezzat ,&nbsp;Benson M. Kariuki ,&nbsp;Aisha A. K. Al-Ashmawy ,&nbsp;Aladdin M. Srour","doi":"10.1107/S2056989025002087","DOIUrl":"10.1107/S2056989025002087","url":null,"abstract":"<div><div>The crystal structure is characterized by a three-dimensional hydrogen-bonding network. Chains formed through N—H⋯O contacts are linked by additional inter­molecular bonds to complete the structure.</div></div><div><div>In the title mol­ecule, C<sub>20</sub>H<sub>21</sub>N<sub>3</sub>O<sub>5</sub>S, the methyl­ideneformohydrazide and meth­oxy­benzene groups are almost coplanar, with the indolyl group being rotated farther from the plane. The mol­ecules in the crystal structure form chains parallel to the <em>a-</em>axis direction through N—H⋯O hydrogen-bonding inter­actions. Neighbouring chains are linked by N—H⋯O contacts to form a three-dimensional network.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 310-313"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crystal structures and Hirshfeld surface analyses of methyl (2Z)-(4-bromo­phen­yl)[2-(4-methyl­phen­yl)hydrazinyl­idene]acetate, methyl (2Z)-(4-bromophen­yl)[2-(3,5-di­methyl­phen­yl)hydrazinyl­idene]acetate, methyl (2Z)-[2-(4-meth­oxy­phen­yl)hydrazinyl­idene](3-nitro­phen­yl)acetate, methyl (2E)-(4-chlorophen­yl)(2-phenyl­hydrazinyl­idene)acetate and methyl (2Z)-[2-(4-bromo­phen­yl)hydrazinylidene](4-chloro­phen­yl)acetate
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025002051
Namiq Q. Shikhaliyev , Aliyar A. Babazade , Gulnar T. Atakishiyeva , Irada M. Shikhaliyeva , Abel M. Maharramov , Victor N. Khrustalev , Zeliha Atioğlu , Mehmet Akkurt , Ajaya Bhattarai
Mol­ecules (1), (2), (3) and (5) adopt a Z configuration with respect to the central C=N bond, while (4) adopts an E configuration.
Mol­ecules of the title compounds, methyl (Z)-2-(4-bromo­phen­yl)-2-[2-(4-methyl­phen­yl)hydrazin-1-yl­idene]acetate, C16H15BrN2O2, (1), methyl (Z)-2-(4-bromo­phen­yl)-2-[2-(3,5-di­methyl­phen­yl)hydrazin-1-yl­idene]acetate, C17H17BrN2O2, (2), methyl (Z)-2-[2-(4-meth­oxy­phen­yl)hydrazin-1-yl­idene]-2-(3-nitro­phen­yl)acetate, C16H15N3O5, (3), and methyl (Z)-2-[2-(4-bromo­phen­yl)hydrazin-1-yl­idene]-2-(4-chloro­phen­yl)acetate, C15H12BrClN2O2, (5), adopt a Z configuration with respect to the central C=N bond, while methyl (E)-2-(4-chloro­phen­yl)-2-(2-phenyl­hydrazin-1-yl­idene)acetate, C15H13ClN2O2, (4), adopts an E configuration. The atoms of the phenyl ring of the bromo­phenyl group of (1) are disordered over two sets of sites with equal occupancies. In the crystal structure of (1), mol­ecules connected by C—H⋯N hydrogen bonds are further linked by C—H⋯π inter­actions, forming ribbons parallel to [010]. In (2), pairs of mol­ecules are linked by C—H⋯π inter­actions parallel to [100]. In (3), C—H⋯O hydrogen bonds form ribbons parallel to [010], while in (4), the mol­ecules are bonded together by C—H⋯N, C—H⋯Cl, C—H⋯O and C—H⋯π inter­actions parallel to [010]. In (5), C—H⋯Br, C—H⋯O and C—H⋯Cl inter­actions lead to the formation of layers parallel to (002). C—H⋯π inter­actions also occur between these planes. Hirshfeld surface analyses were performed to investigate and qu­antify the inter­molecular inter­actions between the mol­ecules of all compounds.
{"title":"Crystal structures and Hirshfeld surface analyses of methyl (2Z)-(4-bromo­phen­yl)[2-(4-methyl­phen­yl)hydrazinyl­idene]acetate, methyl (2Z)-(4-bromophen­yl)[2-(3,5-di­methyl­phen­yl)hydrazinyl­idene]acetate, methyl (2Z)-[2-(4-meth­oxy­phen­yl)hydrazinyl­idene](3-nitro­phen­yl)acetate, methyl (2E)-(4-chlorophen­yl)(2-phenyl­hydrazinyl­idene)acetate and methyl (2Z)-[2-(4-bromo­phen­yl)hydrazinylidene](4-chloro­phen­yl)acetate","authors":"Namiq Q. Shikhaliyev ,&nbsp;Aliyar A. Babazade ,&nbsp;Gulnar T. Atakishiyeva ,&nbsp;Irada M. Shikhaliyeva ,&nbsp;Abel M. Maharramov ,&nbsp;Victor N. Khrustalev ,&nbsp;Zeliha Atioğlu ,&nbsp;Mehmet Akkurt ,&nbsp;Ajaya Bhattarai","doi":"10.1107/S2056989025002051","DOIUrl":"10.1107/S2056989025002051","url":null,"abstract":"<div><div>Mol­ecules (<strong>1</strong>), (<strong>2</strong>), (<strong>3</strong>) and (<strong>5</strong>) adopt a <em>Z</em> configuration with respect to the central C=N bond, while (<strong>4</strong>) adopts an <em>E</em> configuration.</div></div><div><div>Mol­ecules of the title compounds, methyl (<em>Z</em>)-2-(4-bromo­phen­yl)-2-[2-(4-methyl­phen­yl)hydrazin-1-yl­idene]acetate, C<sub>16</sub>H<sub>15</sub>BrN<sub>2</sub>O<sub><em>2</em></sub>, (<strong>1</strong>), methyl (<em>Z</em>)-2-(4-bromo­phen­yl)-2-[2-(3,5-di­methyl­phen­yl)hydrazin-1-yl­idene]acetate, C<sub>17</sub>H<sub>17</sub>BrN<sub>2</sub>O<sub>2</sub>, (<strong>2</strong>), methyl (<em>Z</em>)-2-[2-(4-meth­oxy­phen­yl)hydrazin-1-yl­idene]-2-(3-nitro­phen­yl)acetate, C<sub>16</sub>H<sub>15</sub>N<sub>3</sub>O<sub>5</sub>, (<strong>3</strong>), and methyl (<em>Z</em>)-2-[2-(4-bromo­phen­yl)hydrazin-1-yl­idene]-2-(4-chloro­phen­yl)acetate, C<sub>15</sub>H<sub>12</sub>BrClN<sub>2</sub>O<sub>2</sub>, (<strong>5</strong>), adopt a <em>Z</em> configuration with respect to the central C=N bond, while methyl (<em>E</em>)-2-(4-chloro­phen­yl)-2-(2-phenyl­hydrazin-1-yl­idene)acetate, C<sub>15</sub>H<sub>13</sub>ClN<sub>2</sub>O<sub>2</sub>, (<strong>4</strong>), adopts an <em>E</em> configuration. The atoms of the phenyl ring of the bromo­phenyl group of (<strong>1</strong>) are disordered over two sets of sites with equal occupancies. In the crystal structure of (<strong>1</strong>), mol­ecules connected by C—H⋯N hydrogen bonds are further linked by C—H⋯π inter­actions, forming ribbons parallel to [010]. In (<strong>2</strong>), pairs of mol­ecules are linked by C—H⋯π inter­actions parallel to [100]. In (<strong>3</strong>), C—H⋯O hydrogen bonds form ribbons parallel to [010], while in (<strong>4</strong>), the mol­ecules are bonded together by C—H⋯N, C—H⋯Cl, C—H⋯O and C—H⋯π inter­actions parallel to [010]. In (<strong>5</strong>), C—H⋯Br, C—H⋯O and C—H⋯Cl inter­actions lead to the formation of layers parallel to (002). C—H⋯π inter­actions also occur between these planes. Hirshfeld surface analyses were performed to investigate and qu­antify the inter­molecular inter­actions between the mol­ecules of all compounds.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 314-323"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(2,4-di­methyl­benz­yl)sulfan­yl]pyrimidine-4,6-di­amine
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025002440
Gulrukh Salieva , Tursunali Kholikov , Rasul Ya Okmanov , Alimjon Matchanov , Khamid U Khodjaniyazov , Shakhnoza Kadirova , Batirbay Torambetov
The mol­ecular and crystal structures of 2-[(2,4-di­methyl­benz­yl)thio]­pyrimidine-4,6-di­amine were studied and Hirshfeld surfaces and fingerprint plots were generated to investigate the various inter­molecular inter­actions.
The title compound, C13H16N4S (DAMP-DMB), was synthesized through the reaction of 2,4-di­methyl­benzyl chloride with di­amino­pyrimidine-thiol. Single-crystal X-ray diffraction analysis confirmed that the compound crystallizes in the monoclinic crystal system, space group P21/c. The asymmetric unit contains a single mol­ecular entity. Structural examination revealed the presence of a dimeric arrangement consolidated by N—H⋯N hydrogen-bonding inter­actions. Additionally, Hirshfeld surface analysis indicated that H⋯H, N⋯H, C⋯H, and S⋯H contacts account for 98.9% of the total inter­molecular inter­actions to the Hirshfeld surface.
{"title":"Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(2,4-di­methyl­benz­yl)sulfan­yl]pyrimidine-4,6-di­amine","authors":"Gulrukh Salieva ,&nbsp;Tursunali Kholikov ,&nbsp;Rasul Ya Okmanov ,&nbsp;Alimjon Matchanov ,&nbsp;Khamid U Khodjaniyazov ,&nbsp;Shakhnoza Kadirova ,&nbsp;Batirbay Torambetov","doi":"10.1107/S2056989025002440","DOIUrl":"10.1107/S2056989025002440","url":null,"abstract":"<div><div>The mol­ecular and crystal structures of 2-[(2,4-di­methyl­benz­yl)thio]­pyrimidine-4,6-di­amine were studied and Hirshfeld surfaces and fingerprint plots were generated to investigate the various inter­molecular inter­actions.</div></div><div><div>The title compound, C<sub>13</sub>H<sub>16</sub>N<sub>4</sub>S (DAMP-DMB), was synthesized through the reaction of 2,4-di­methyl­benzyl chloride with di­amino­pyrimidine-thiol. Single-crystal X-ray diffraction analysis confirmed that the compound crystallizes in the monoclinic crystal system, space group <em>P</em>2<sub>1</sub>/<em>c</em>. The asymmetric unit contains a single mol­ecular entity. Structural examination revealed the presence of a dimeric arrangement consolidated by N—H⋯N hydrogen-bonding inter­actions. Additionally, Hirshfeld surface analysis indicated that H⋯H, N⋯H, C⋯H, and S⋯H contacts account for 98.9% of the total inter­molecular inter­actions to the Hirshfeld surface.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 328-331"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fluorine–hydrogen inter­actions observed in a helix structure having an orn-free gramicidin S sequence incorporating 4-trans-fluoro­proline
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025002592
Asano Akiko , Mizuki Sakata , Kato Takuma , Mitsunobu Doi
Decapeptide having a gramicidin S sequence forms a helix structure supported by a fluorine–H inter­action.
The deca­peptide Boc-(d-Phe-tFPro-Val-Leu-Leu)2—OMe (1) (Boc is tert-but­oxy­carbonyl, tFPro is 4-trans-fluoro-l-proline d-Phe is d-phenyl­alanine, Val is valine and Leu is leucine) crystallized in a methanol-solvated form (C68H104F2N10O13·CH4O). Peptide 1 has a sequence similar to gramicidin S (GS) incorporating tFPro. GS is a cyclic peptide, with the d-Phe-Pro unit known as a strong β-turn inducer in previous studies. Thus, it was initially assumed that 1 would bend at the d-Phe6-tFPro7 position, potentially forming a sheet-like structure. However, the structure of 1 was a helix, a surprising finding in GS-related structural studies. A factor enabling this helical formation could be the fluorine–H inter­actions between tFPro and the aromatic rings of d-Phe residues.
{"title":"Fluorine–hydrogen inter­actions observed in a helix structure having an orn-free gramicidin S sequence incorporating 4-trans-fluoro­proline","authors":"Asano Akiko ,&nbsp;Mizuki Sakata ,&nbsp;Kato Takuma ,&nbsp;Mitsunobu Doi","doi":"10.1107/S2056989025002592","DOIUrl":"10.1107/S2056989025002592","url":null,"abstract":"<div><div>Decapeptide having a gramicidin S sequence forms a helix structure supported by a fluorine–H inter­action.</div></div><div><div>The deca­peptide Boc-(<span>d</span>-Phe-tFPro-Val-Leu-Leu)<sub>2</sub>—OMe (<strong>1</strong>) (Boc is <em>tert</em>-but­oxy­carbonyl, tFPro is 4-<em>trans</em>-fluoro-<span>l</span>-proline <span>d</span>-Phe is <span>d</span>-phenyl­alanine, Val is valine and Leu is leucine) crystallized in a methanol-solvated form (C<sub>68</sub>H<sub>104</sub>F<sub>2</sub>N<sub>10</sub>O<sub>13</sub>·CH<sub>4</sub>O). Peptide <strong>1</strong> has a sequence similar to gramicidin S (GS) incorporating tFPro. GS is a cyclic peptide, with the <span>d</span>-Phe-Pro unit known as a strong β-turn inducer in previous studies. Thus, it was initially assumed that <strong>1</strong> would bend at the <span>d</span>-Phe6-tFPro7 position, potentially forming a sheet-like structure. However, the structure of <strong>1</strong> was a helix, a surprising finding in GS-related structural studies. A factor enabling this helical formation could be the fluorine–H inter­actions between tFPro and the aromatic rings of <span>d</span>-Phe residues.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 345-349"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis and structure of tris­(2-methyl-1H-imidazol-3-ium) 5-carb­oxy­benzene-1,3-di­carboxyl­ate 3,5-di­carb­oxy­benzoate
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025002063
Lina Maria Asprilla-Herrera , Simone Techert , Jose de Jesus Velazquez-Garcia
The structure of a tris­(2-methyl-1H-imidazol-3-ium) di­hydrogenetrimesate mono­hydrogentrimesate2− compound was determined by single-crystal X-ray diffraction. The compound is mixture of protonated and deprotonated mol­ecules.
The structure of the title salt, 3C4H7N2+·C9H5O6·C9H4O62−, 1, consists of three 2-methyl-imidazolium cations and both a single and a doubly deprotonated form of trimesic acid as anions. A detailed analysis of the bond lengths and angles reveals both differences and similarities between compound 1 and the previously reported 2-methyl-1H-imidazol-3-ium 3,5-di­carb­oxy­benzoate structure [Baletska et al. (2023). Acta Cryst. E79, 1088–109], as well as the neutral counterpart of the ions. Examination of the crystal packing shows the formation of infinite chains by the anions, which, along with the cations, form zigzag planes parallel to the ab plane. The packing inter­actions are primarily driven by π–π inter­actions and hydrogen bonding between anions.
{"title":"Synthesis and structure of tris­(2-methyl-1H-imidazol-3-ium) 5-carb­oxy­benzene-1,3-di­carboxyl­ate 3,5-di­carb­oxy­benzoate","authors":"Lina Maria Asprilla-Herrera ,&nbsp;Simone Techert ,&nbsp;Jose de Jesus Velazquez-Garcia","doi":"10.1107/S2056989025002063","DOIUrl":"10.1107/S2056989025002063","url":null,"abstract":"<div><div>The structure of a tris­(2-methyl-1<em>H</em>-imidazol-3-ium) di­hydrogenetrimesate<sup>−</sup> mono­hydrogentrimesate<sup>2−</sup> compound was determined by single-crystal X-ray diffraction. The compound is mixture of protonated and deprotonated mol­ecules.</div></div><div><div>The structure of the title salt, 3C<sub>4</sub>H<sub>7</sub>N<sub>2</sub><sup>+</sup>·C<sub>9</sub>H<sub>5</sub>O<sub>6</sub><sup>−</sup>·C<sub>9</sub>H<sub>4</sub>O<sub>6</sub><sup>2−</sup>, <strong>1</strong>, consists of three 2-methyl-imidazolium cations and both a single and a doubly deprotonated form of trimesic acid as anions. A detailed analysis of the bond lengths and angles reveals both differences and similarities between compound <strong>1</strong> and the previously reported 2-methyl-1<em>H</em>-imidazol-3-ium 3,5-di­carb­oxy­benzoate structure [Baletska <em>et a</em>l. (2023). <em>Acta Cryst.</em> E<strong>79</strong>, 1088–109], as well as the neutral counterpart of the ions. Examination of the crystal packing shows the formation of infinite chains by the anions, which, along with the cations, form zigzag planes parallel to the <em>ab</em> plane. The packing inter­actions are primarily driven by π–π inter­actions and hydrogen bonding between anions.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 303-309"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Polymorphism and Hirshfeld surface analysis of tetra­oxa[2]perfluoro­arene[2]triazine
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S205698902500194X
Tadashi Kawasaki , Akiko Hori
Tetra­oxa[2]perfluoro­arene[2]triazine (C20H6F8N6O6), composed of two tetra­fluoro­phenyl­ene and two triazine moieties connected by four oxygen atoms, was crystallized via slow evaporation of a di­chloro­methane solution, yielding two polymorphs with block- and plate-shaped crystals.
The title compound, tetra­oxa[2]perfluoro­arene[2]triazine (C20H6F8N6O6), composed of two tetra­fluoro­phenyl­ene and two triazine moieties connected by four oxygen atoms, was crystallized via slow evaporation of a di­chloro­methane solution, yielding two polymorphs: block- (I) and plate-shaped (II) crystals. Polymorph I (triclinic, P1, V = 516 Å3 at 173 K) was previously reported by Yang et al. [(2015. Org. Lett.15, 4414–4417] whereas the newly identified polymorph II (triclinic, P1, V = 1085 Å3 at 100 K) shares the same space group but has a unit-cell volume twice as large, accommodating two symmetrically distinct mol­ecules, Mol­ecule-1 and Mol­ecule-2, with a different mol­ecular arrangement. Since these crystals are expected to exhibit the characteristics of non-porous adaptive crystals, detailed analyses of inter­molecular inter­actions were conducted, revealing that C—F⋯π-hole inter­actions are more pronounced in II than in I. Hirshfeld surface analysis at 100 K revealed that the primary contributions to the crystal packing in polymorph I were F⋯F (17.1%), F⋯H/H⋯F (21.5%), C⋯H/H⋯C (6.3%), C⋯F/F⋯C (4.5%) and C⋯O/O⋯C (9.2%) inter­actions, whereas in polymorph II, these inter­actions were F⋯F (9.9% and 10.0%), F⋯H/H⋯F (20.9% and 26.5%), C⋯H/H⋯C (6.3% and 2.9%), C⋯F/F⋯C (8.5% and 10.0%) and C⋯O/O⋯C (4.9% and 4.6%) for Mol­ecule-1 and Mol­ecule-2, respectively. Powder X-ray diffraction analysis indicates that polymorph I is the more stable crystalline form, predominantly obtained through rapid precipitation or by grinding the crystals.
{"title":"Polymorphism and Hirshfeld surface analysis of tetra­oxa[2]perfluoro­arene[2]triazine","authors":"Tadashi Kawasaki ,&nbsp;Akiko Hori","doi":"10.1107/S205698902500194X","DOIUrl":"10.1107/S205698902500194X","url":null,"abstract":"<div><div>Tetra­oxa[2]perfluoro­arene[2]triazine (C<sub>20</sub>H<sub>6</sub>F<sub>8</sub>N<sub>6</sub>O<sub>6</sub>), composed of two tetra­fluoro­phenyl­ene and two triazine moieties connected by four oxygen atoms, was crystallized <em>via</em> slow evaporation of a di­chloro­methane solution, yielding two polymorphs with block- and plate-shaped crystals.</div></div><div><div>The title compound, tetra­oxa[2]perfluoro­arene[2]triazine (C<sub>20</sub>H<sub>6</sub>F<sub>8</sub>N<sub>6</sub>O<sub>6</sub>), composed of two tetra­fluoro­phenyl­ene and two triazine moieties connected by four oxygen atoms, was crystallized <em>via</em> slow evaporation of a di­chloro­methane solution, yielding two polymorphs: block- (<strong>I</strong>) and plate-shaped (<strong>II</strong>) crystals. Polymorph <strong>I</strong> (triclinic, <em>P</em>1, <em>V</em> = 516 Å<sup>3</sup> at 173 K) was previously reported by Yang <em>et al.</em> [(2015. <em>Org. Lett.</em><strong>15</strong>, 4414–4417] whereas the newly identified polymorph <strong>II</strong> (triclinic, <em>P</em>1, <em>V</em> = 1085 Å<sup>3</sup> at 100 K) shares the same space group but has a unit-cell volume twice as large, accommodating two symmetrically distinct mol­ecules, <em>Mol­ecule-1</em> and <em>Mol­ecule-2</em>, with a different mol­ecular arrangement. Since these crystals are expected to exhibit the characteristics of non-porous adaptive crystals, detailed analyses of inter­molecular inter­actions were conducted, revealing that C—F⋯π-hole inter­actions are more pronounced in <strong>II</strong> than in <strong>I</strong>. Hirshfeld surface analysis at 100 K revealed that the primary contributions to the crystal packing in polymorph <strong>I</strong> were F⋯F (17.1%), F⋯H/H⋯F (21.5%), C⋯H/H⋯C (6.3%), C⋯F/F⋯C (4.5%) and C⋯O/O⋯C (9.2%) inter­actions, whereas in polymorph <strong>II</strong>, these inter­actions were F⋯F (9.9% and 10.0%), F⋯H/H⋯F (20.9% and 26.5%), C⋯H/H⋯C (6.3% and 2.9%), C⋯F/F⋯C (8.5% and 10.0%) and C⋯O/O⋯C (4.9% and 4.6%) for <em>Mol­ecule-1</em> and <em>Mol­ecule-2</em>, respectively. Powder X-ray diffraction analysis indicates that polymorph <strong>I</strong> is the more stable crystalline form, predominantly obtained through rapid precipitation or by grinding the crystals.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 289-295"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crystal structure and Hirshfeld surface analysis of 6-[4-(1-cyclo­hexyl-1H-tetra­zol-5-yl)but­oxy]-8-nitro-3,4-di­hydro­quinolin-2(1H)-one
IF 0.5 Q4 CRYSTALLOGRAPHY Pub Date : 2025-04-01 DOI: 10.1107/S2056989025001793
Arnab Dutta , Yogesh Dhasmana , T. P. Mohan , B. Selvakumar , Deepak Chopra
The composition of the nitro-substituted compound 6-[4-(1-cyclo­hexyl-1H-tetra­zol-5-yl)but­oxy]-8-nitro-3,4-di­hydro­quinolin-2(1H)-one has been unequivocally established from single-crystal X-ray diffraction. The mol­ecular conformation and the role of the different inter­molecular inter­actions in the crystal packing has also been explored.
The crystal structure of 6-[4-(1-cyclo­hexyl-1H-tetra­zol-5-yl)but­oxy]-8-nitro-3,4-di­hydro­quinolin-2(1H)-one, C20H26N6O4 (I), was characterized by single-crystal X-ray diffraction. The primary focus was to establish the position of the nitro group, the mol­ecular conformation, and the role of inter­molecular inter­actions towards the crystal packing of I. The crystalline structure is mainly consolidated by π–π, C—H⋯O, C—H⋯N, N⋯C(π) and O⋯C(π) inter­actions. The contributions of different inter­actions towards the crystal packing were further analyzed using Hirshfeld surface and fingerprint plots.
{"title":"Crystal structure and Hirshfeld surface analysis of 6-[4-(1-cyclo­hexyl-1H-tetra­zol-5-yl)but­oxy]-8-nitro-3,4-di­hydro­quinolin-2(1H)-one","authors":"Arnab Dutta ,&nbsp;Yogesh Dhasmana ,&nbsp;T. P. Mohan ,&nbsp;B. Selvakumar ,&nbsp;Deepak Chopra","doi":"10.1107/S2056989025001793","DOIUrl":"10.1107/S2056989025001793","url":null,"abstract":"<div><div>The composition of the nitro-substituted compound 6-[4-(1-cyclo­hexyl-1<em>H</em>-tetra­zol-5-yl)but­oxy]-8-nitro-3,4-di­hydro­quinolin-2(1<em>H</em>)-one has been unequivocally established from single-crystal X-ray diffraction. The mol­ecular conformation and the role of the different inter­molecular inter­actions in the crystal packing has also been explored.</div></div><div><div>The crystal structure of 6-[4-(1-cyclo­hexyl-1<em>H</em>-tetra­zol-5-yl)but­oxy]-8-nitro-3,4-di­hydro­quinolin-2(1<em>H</em>)-one, C<sub>20</sub>H<sub>26</sub>N<sub>6</sub>O<sub>4</sub> (<strong>I</strong>), was characterized by single-crystal X-ray diffraction. The primary focus was to establish the position of the nitro group, the mol­ecular conformation, and the role of inter­molecular inter­actions towards the crystal packing of <strong>I</strong>. The crystalline structure is mainly consolidated by π–π, C—H⋯O, C—H⋯N, N⋯C(π) and O⋯C(π) inter­actions. The contributions of different inter­actions towards the crystal packing were further analyzed using Hirshfeld surface and fingerprint plots.</div></div>","PeriodicalId":7367,"journal":{"name":"Acta Crystallographica Section E: Crystallographic Communications","volume":"81 4","pages":"Pages 284-288"},"PeriodicalIF":0.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143768149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Acta Crystallographica Section E: Crystallographic Communications
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