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Singh H, Khatoon N, Bhardwaj SK, Kampani P, Nayak TK, Haridas V. Bispidine as a Versatile Scaffold: From Topological Hosts to Transmembrane Transporters. Chembiochem 2023; 24:e202300502. [PMID: 37708237 DOI: 10.1002/cbic.202300502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
The development of designer topological structures is a synthetically challenging endeavor. We present herein bispidine as a platform for the design of molecules with various topologies and functions. The bispidine-based acyclic molecule, which shows intriguing S-shape topology, is discussed. Single-crystal X-ray diffraction studies revealed that this molecule exists in the solid state as two conformational enantiomers. In addition, bispidine-based designer macrocycles were synthesized and investigated for ionophoric properties. Patch clamp experiments revealed that these macrocycles transport both anions and cations non-specifically with at least tenfold higher chloride conductance over the cations under the given experimental conditions. Ultramicroscopy and single-crystal X-ray crystallographic studies indicated that the self-assembling macrocycle forms a tubular assembly. Our design highlights the use of unconventional dihydrogen interactions in nanotube fabrication.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Nadira Khatoon
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Surya Kant Bhardwaj
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Pradeepti Kampani
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tapan K Nayak
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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Mocilac P, Pohl F, Gallagher JF. The unusual ( syn-/ anti-) 2 conformation of a di-meth-oxy-pyrimidyl-based tennimide. Acta Crystallogr E Crystallogr Commun 2023; 79:837-841. [PMID: 37693664 PMCID: PMC10483549 DOI: 10.1107/s2056989023006837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023]
Abstract
The tennimide macrocycle, (I) (C52H40N16O16.0.167H2O), was synthesized from 2-amino-4,6-di-meth-oxy-pyrimidine and pyridine-2,6-dicarbonyl dichloride. Compound (I) represents the first tennimide incorporating pyridine rings in the macrocycle scaffold. In the macrocycle ring, the carbonyl groups at each successive dicarbon-yl(pyridine) moiety adopt the (syn/anti)2 conformation. This contrasts with all previously reported tetra-imide macrocycles, which exhibit the (syn)4 conformation. The effect is to close any potential cavity or niche by having two of the central pyridine C5N rings aligned close to each other [with closest pyridine Cg⋯Cg ring centroid separations of 3.5775 (19) Å; closest C⋯C = 3.467 (5) Å]. A partial occupancy water mol-ecule (with s.o.f. = 0.167), resides with its oxygen atom on a twofold axis at hydrogen-bonding distances to the carbonyl O atom, in a mol-ecular niche between two pyridine rings. Macrocyles of (I) have all six C=O groups and all eight meth-oxy O atoms present on the macrocycle surface. However, all twelve N atoms are effectively shielded on steric grounds from any potential inter-molecular inter-actions. The remaining two C=O O atoms inter-act with the partial occupancy water mol-ecule via two O-H⋯O=C hydrogen bonds. Macrocycles of (I) stack as one-dimensional chains along the b-axis direction with primary inter-molecular inter-actions involving weak C-H⋯O=C/OCH3/H2O contacts. Chains inter-lock weakly via meth-oxy-meth-oxy C-H⋯O inter-actions into two-dimensional sheets.
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Affiliation(s)
- Pavle Mocilac
- School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
| | - Fabian Pohl
- School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
- Fakultät für Chemie und Mineralogie, Universität Leipzig, Johannisallee 29, 04103 Leipzig, Sachsen, Germany
| | - John F. Gallagher
- School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
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Dhawan S, Singh H, Dutta S, Haridas V. Designer peptides as versatile building blocks for functional materials. Bioorg Med Chem Lett 2022; 68:128733. [PMID: 35421579 DOI: 10.1016/j.bmcl.2022.128733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
Peptides and pseudopeptides show distinct self-assembled nanostructures such as fibers, nanotubes, vesicles, micelles, toroids, helices and rods. The formation of such molecular communities through the collective behavior of molecules is not fully understood at a molecular level. All these self-assembled nanostructured materials have a wide range of applications such as drug delivery, gene delivery, biosensing, bioimaging, catalysis, tissue engineering, nano-electronics and sensing. Self-assembly is one of the most efficient and a simple strategy to generate complex functional materials. Owing to its significance, the last few decades witnessed a remarkable advancement in the field of self-assembling peptides with a plethora of new designer synthetic systems being discovered. These systems range from amphiphilic, cyclic, linear and polymeric peptides. This article presents only selected examples of such self-assembling peptides and pseudopeptides.
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Affiliation(s)
- Sameer Dhawan
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Souvik Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India.
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Krut’ko DP, Medved’ko AV, Lyssenko KA, Churakov AV, Dalinger AI, Kalinin MA, Gudovannyy AO, Ponomarev KY, Suslov EV, Vatsadze SZ. Bispidine Platform as a Tool for Studying Amide Configuration Stability. Molecules 2022; 27:430. [PMID: 35056748 PMCID: PMC8779339 DOI: 10.3390/molecules27020430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this work, the solution conformations of seventeen 3,7-diacyl bispidines were studied by means of NMR spectroscopy including VT NMR experiments. The acyl groups included alkyl, alkenyl, aryl, hetaryl, and ferrocene moieties. The presence of syn/anti-isomers and their ratios were estimated, and some reasons explaining experimental facts were formulated. In particular, all aliphatic and heterocyclic units in the acylic R(CO) fragments led to an increased content of the syn-form in DMSO-d6 solutions. In contrast, only the anti-form was detected in DMSO-d6 and CDCl3 in the case when R = Ph, ferrocenyl, (R)-myrtenyl. In the case of a chiral compound derived from the natural terpene myrtene, a new dynamic process was found in addition to the expected inversion around the amide N-C(O) bond. Here, rotation around the CO-C=C bond in the acylic R fragment was detected, and its energy was estimated. For this compound, ΔG for amide N-C(O) inversion was found to be equal to 15.0 ± 0.2 kcal/mol, and for the rotation around the N(CO)-C2' bond, it was equal to 15.6 ± 0.3 kcal/mol. NMR analysis of the chiral bispidine-based bis-amide was conducted for the first time. Two X-ray structures are reported. For the first time, the unique syn-form was found in the crystal of an acyclic bispidine-based bis-amide. Quantum chemical calculations revealed the unexpected mechanism for amide bond inversion. It was found that the reaction does not proceed as direct N-C(O) bond inversion in the double-chair (CC) conformation but rather requires the conformational transformation into the chair-boat (CB) form first. The amide bond inversion in the latter requires less energy than in the CC form.
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Affiliation(s)
- Dmitry P. Krut’ko
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | | | - Konstantin A. Lyssenko
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry, 119991 Moscow, Russia;
| | - Alexander I. Dalinger
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | - Mikhail A. Kalinin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia;
| | - Alexey O. Gudovannyy
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
- High Chemical College, Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
| | - Konstantin Y. Ponomarev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 630090 Novosibirsk, Russia; (K.Y.P.); (E.V.S.)
| | - Eugeny V. Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 630090 Novosibirsk, Russia; (K.Y.P.); (E.V.S.)
| | - Sergey Z. Vatsadze
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
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Gallagher JF, Mocilac P. Pockets and channels in tennimide solvate structures: Influence of solvent on crystal packing behaviour. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mocilac P, Farrell M, Lough AJ, Jelsch C, Gallagher JF. Aggregation in isomeric imides: analysis of the weak interactions in six N-(benzoyl)-N-(2-pyridyl)benzamides. Struct Chem 2018. [DOI: 10.1007/s11224-018-1101-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lu X, Lee S, Hong Y, Phan H, Gopalakrishna TY, Herng TS, Tanaka T, Sandoval-Salinas ME, Zeng W, Ding J, Casanova D, Osuka A, Kim D, Wu J. Fluorenyl Based Macrocyclic Polyradicaloids. J Am Chem Soc 2017; 139:13173-13183. [DOI: 10.1021/jacs.7b07335] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuefeng Lu
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Sangsu Lee
- Spectroscopy
Laboratory for Functional π-Electronic Systems and Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Yongseok Hong
- Spectroscopy
Laboratory for Functional π-Electronic Systems and Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hoa Phan
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | | | - Tun Seng Herng
- Department of Materials Science & Engineering, National University of Singapore, 119260 Singapore
| | - Takayuki Tanaka
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - María Eugenia Sandoval-Salinas
- Departament
de Ciència de Materials i Química Física, Institut
de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea & Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, 20018 Donostia-San Sebastián, Euskadi, Spain
| | - Wangdong Zeng
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Jun Ding
- Department of Materials Science & Engineering, National University of Singapore, 119260 Singapore
| | - David Casanova
- Kimika Fakultatea, Euskal Herriko Unibertsitatea & Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, 20018 Donostia-San Sebastián, Euskadi, Spain
- IKERBASQUE - Basque Foundation for Science, Bilbao 48013, Euskadi, Spain
| | - Atsuhiro Osuka
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Dongho Kim
- Spectroscopy
Laboratory for Functional π-Electronic Systems and Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Jishan Wu
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
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