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Welcome to OPEN - the Repository of Open Scientific Publications, run by the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, previously operating as the CeON Repository. The Repository enables Polish researchers from all fields to openly share their articles, books, conference materials, reports, doctoral theses, and other scientific texts.

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22936 archived items

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Carboxylated Pillar[6]arene Emulates Pillar[5]arene in the Host–Guest Crystal Complexes and Shows Conformational Flexibility in the Solution/Gas Phase

(American Chemical Society, 2023) Butkiewicz, Helena; Kosiorek, Sandra; Sashuk, Volodymyr; Zimnicka, Magdalena M.; Danylyuk, Oksana; Institute of Physical Chemistry, Polish Academy of Sciences; Institute of Organic Chemistry, Polish Academy of Sciences

Despite the thriving interest in the aqueous complexation properties of carboxylated pillar[6]arene, its solid state supramolecular chemistry has remained a mystery. Here, overcoming challenging crystallogenesis, we report the first crystallographic authentication of carboxylated pillar[6]arene in the form of two host–guest inclusion complexes with methyl viologen and pentamidine. The key to the successful crystallization of carboxylated pillar[6]arene is the mixed ionization state of its 12 carboxylic substituents. The deprotonation of several but not all substituents enables intermolecular hydrogen bonding and, as a result, “gluing” and crystallization of pillar[6]arene complexes with the aid of carboxylic-carboxylate, carboxylic-carboxylic, and amidinium-carboxylate supramolecular synthons. Single crystal X-ray diffraction analysis revealed that upon guest inclusion pillar[6]arene adopts a quasi-pentagonal shape rather than the expected hexagonal shape. The squeezed quasi-pentagonal conformation of the six-membered macrocycle is stabilized by two intramolecular hydrogen bonds between pillar[6]arene substituents. Moreover, the distinctive deviation of the macrocycle from hexagonal shape stays operative in the solution/gas phase as concluded from ion mobility mass spectrometry (IM-MS) studies and theoretical calculations. These results provide the first insight into how to gain control over the conformation of flexible pillar[6]arene with a view of solid state design of more advanced supramolecular host–guest structures.

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Carboxylated Pillar[5]arene Meets Medicinal Biguanides: Host–Guest Complexes with Alexidine and Phenformin in the Crystal and Solution/Gas Phase

Here, we discuss crystal and solution/gas-phase complexes of carboxylated pillar[5]arene with two cationic guests, alexidine and phenformin, revealing host–guest and assembly curiosities, the role of hydrogen bonding, and cavity inclusion versus exo-mode binding. We show that the combination of carboxylated pillar[5]arene with bis(biguanidinium) guest alexidine results in the crystallization of open-type supramolecular architecture. This is also the first crystal structure of alexidine ever reported. The crystallization of pillar[5]arene with biguanidinium drug phenformin affects a rare solid-state complex comprising two cavity inclusion modes within the same crystal lattice. The winner in the competition between ethanol molecules and an organic cation (phenformin) for access to the cavity of pillar[5]arene is undecided, visualized as a “snapshot” of these two inclusion possibilities in one crystal structure. Our results demonstrate that carboxylated pillar[n]arenes can be a useful addition to the macrocyclic toolkit for the facilitation of the crystallization of bio(macro)molecules. Moreover, the IM-MS analysis of the precrystallization solutions of pillar[5]arene host and biguanide guests has shown the presence of structures and conformations closely related to those observed in the crystal forms. The most intriguing results obtained for a pillar[5]arene–alexidine complex imply a conformational evolution of the complex over 24 h. The IM-MS analysis complemented by theoretical calculations may be applied to predict and examine the crystallization process of host–guest systems, complementing crystallographic studies.

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Carboxylated Pillar[5]arene Meets Medicinal Biguanides: Host−Guest Complexes with Alexidine and Phenformin in the Crystal and Solution/Gas Phase

(American Chemical Society, 2023-10-12) Butkiewicz, Helena; Kosiorek, Sandra; Sashuk, Volodymyr; Zimnicka, Magdalena; Danylyuk, Oksana; Institute of Physical Chemistry Polish Academy of Sciences; Institute of Organic Chemistry Polish Academy of Sciences

Here we discuss crystal and solution/gas phase complexes of carboxylated pillar[5]arene with two cationic guests, alexi-dine and phenformin, revealing host-guest and assembly curiosities, the role of hydrogen bonding and cavity inclusion versus exo-mode binding. We show that the combination of carboxylated pillar[5]arene with bis(biguanidinium) guest alexidine results in the crystallization of open-type supramolecular architecture. This is also the first crystal structure of alexidine ever reported. The crystallization of pillar[5]arene with biguanidinium drug phenformin effects a rare solid state complex comprising two cavity inclusion modes within the same crystal lattice. The winner in the competition between ethanol molecules and organic cation (phenformin) for the access to the cavity of pillar[5]arene is undecided, visualized as ‘snapshot’ of these two inclusion possibilities in one crystal structure. Our results demonstrate that carbox-ylated pillar[n]arenes can be useful addition to the macrocyclic toolkit for the facilitation of the crystallization of bio(macro)molecules. Moreover, the IM-MS analysis of the pre-crystallization solutions of pillar[5]arene host and bigua-nide guests have shown the presence of structures and conformations closely related to those observed in the crystal forms. The most intriguing results obtained for pillar[5]arene-alexidine complex imply a conformational evolution of the complex over 24 h. The IM-MS analysis complemented by theoretical calculations may be applied to predict and examine the crystallization process of host-guest systems, complementing crystallographic studies

Item

Carboxylated Pillar[6]arene Emulates Pillar[5]arene in the Host–Guest Crystal Complexes and Shows Conformational Flexibility in the Solution/Gas Phase

(American Chemical Society, 2022-12-08) Butkiewicz, Helena; Kosiorek, Sandra; Sashuk, Volodymyr; Zimnicka, Magdalena; Danylyuk, Oksana; Instytut Chemii Fizycznej Polskiej Akademii Nauk; Instytut Chemii Organicznej Polskiej Akademii Nauk

Despite the thriving interest in the aqueous complexation properties of carboxylated pillar[6]arene, its solid state supramolecular chemistry has remained a mystery. Here, overcoming challenging crystallogenesis, we report the first crystallographic authentication of carboxylated pillar[6]arene in the form of two host−guest inclusion complexes with methyl viologen and pentamidine. The key to the successful crystallization of carboxylated pillar[6]arene is the mixed ionization state of its 12 carboxylic substituents. The deprotonation of several but not all substituents enables intermolecular hydrogen bonding and, as a result, “gluing” and crystallization of pillar[6]arene complexes with the aid of carboxylic-carboxylate, carboxylic-carboxylic, and amidinium-carboxylate supramolecular synthons. Single crystal X-ray diffraction analysis revealed that upon guest inclusion pillar[6]arene adopts a quasi-pentagonal shape rather than the expected hexagonal shape. The squeezed quasi-pentagonal conformation of the six-membered macrocycle is stabilized by two intramolecular hydrogen bonds between pillar[6]arene substituents. Moreover, the distinctive deviation of the macrocycle from hexagonal shape stays operative in the solution/gas phase as concluded from ion mobility mass spectrometry (IM-MS) studies and theoretical calculations. These results provide the first insight into how to gain control over the conformation of flexible pillar[6]arene with a view of solid state design of more advanced supramolecular host−guest structures.

Item

NHC–BIAN–Cu(I)-Catalyzed Friedländer-Type Annulation of 2-Amino-3-(per)fluoroacetylpyridines with Alkynes on Water

(American Chemical Society, 2022) Dolna, Magdalena; Nowacki, Michał; Danylyuk, Oksana; Brotons-Rufes, Artur; Poater, Albert; Michalak, Michał; Institute of Organic Chemistry, Polish Academy of Sciences; Institute of Physical Chemistry, Polish Academy of Sciences; Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Spain

The direct catalytic alkynylation/dehydrative cyclization of 2-amino-3-trifluoroacetyl-pyridines on water was developed for the efficient synthesis of a broad range of fluorinated 1,8-naphthyridines from terminal alkynes. A novel N-heterocyclic carbene (NHC) ligand system that combines a π-extended acenaphthylene backbone with sterically bulky pentiptycene pendant groups was successfully utilized in a copper- or silver-mediated cyclization. Computational analysis of the reaction pathway supports our explanation of the different experimental conversions and yields for the set of copper and silver catalysts. The impact of steric hindrance at the metal center and the flexibility of substituents on the imidazole ring of the NHC on catalytic performance are also discussed.

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