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Wang Y, Li C, Zheng X. Markov State Models Reveal How Folding Kinetics Influence Absorption Spectra of Foldamers. J Chem Theory Comput 2024; 20:5396-5407. [PMID: 38900275 DOI: 10.1021/acs.jctc.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Self-assembly of platinum(II) complex foldamers is an essential approach to fabricate advanced luminescent materials. However, a comprehensive understanding of folding kinetics and their absorption spectra remains elusive. By constructing Markov state models (MSMs) from large-scale molecular dynamics simulations, we reveal that two largely similar dinuclear alknylplatinum(II) terpyridine foldamers, Pt-PEG and Pt-PE with slightly different bridges, exhibit distinctive folding kinetics. Particularly, Pt-PEG bears bridge-dominant, plane-dominant, and cooperative pathways, while Pt-PE only prefers the plane-dominant pathway. Such preference originates from their difference in intrabridge electrostatic interactions, leading to contrastive distributions of metastable states. We also found that the bridge-dominant pathway for Pt-PEG becomes more favorable when lowering the temperature. Interestingly, based on the comprehensive conformation ensembles from our MSMs, we reveal the conformation-dependent absorption spectra of Pt-PEG and Pt-PE. Our theoretical spectra not only align with experimental results but also reveal the contributions of diverse conformations to the overall absorption bands explicitly, facilitating the rational design of stimuli-responsive smart luminescent molecules.
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Affiliation(s)
- Yijia Wang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chu Li
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoyan Zheng
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering of Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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2
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Koehler V, Bruschera G, Merlet E, Mandal PK, Morvan E, Rosu F, Douat C, Fischer L, Huc I, Ferrand Y. High-Affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water. Angew Chem Int Ed Engl 2023; 62:e202311639. [PMID: 37804233 DOI: 10.1002/anie.202311639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
We prepared a series of water-soluble aromatic oligoamide sequences all composed of a segment prone to form a single helix and a segment prone to dimerize into a double helix. These sequences exclusively assemble as antiparallel duplexes. The modification of the duplex inner rim by varying the nature of the substituents borne by the aromatic monomers allowed us to identify sequences that can hybridize by combining two chemically different strands, with high affinity and complete selectivity in water. X-ray crystallography confirmed the expected antiparallel configuration of the duplexes whereas NMR spectroscopy and mass spectrometry allowed us to assess precisely the extent of the hybridization. The hybridization kinetics of the aromatic strands was shown to depend on both the nature of the substituents responsible for strand complementarity and the length of the aromatic strand. These results highlight the great potential of aromatic hetero-duplex as a tool to construct non-symmetrical dynamic supramolecular assemblies.
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Affiliation(s)
- Victor Koehler
- CBMN (UMR 5248) Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, 2 rue Escarpit, 33600, Pessac, France
| | - Gabrielle Bruschera
- CBMN (UMR 5248) Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, 2 rue Escarpit, 33600, Pessac, France
| | - Eric Merlet
- CBMN (UMR 5248) Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, 2 rue Escarpit, 33600, Pessac, France
| | - Pradeep K Mandal
- Department Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Estelle Morvan
- IECB, UAR3033 Univ. ćBordeaux, CNRS, INSERM, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Frédéric Rosu
- IECB, UAR3033 Univ. ćBordeaux, CNRS, INSERM, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Céline Douat
- Department Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Lucile Fischer
- CBMN (UMR 5248) Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, 2 rue Escarpit, 33600, Pessac, France
| | - Ivan Huc
- Department Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Yann Ferrand
- CBMN (UMR 5248) Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, 2 rue Escarpit, 33600, Pessac, France
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3
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Park J, Lee HS, Kim H, Choi JM. Conformational landscapes of artificial peptides predicted by various force fields: are we ready to simulate β-amino acids? Phys Chem Chem Phys 2023; 25:7466-7476. [PMID: 36848062 DOI: 10.1039/d2cp05998c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
With the introduction of artificial peptides as antimicrobial agents and organic catalysts, numerous efforts have been made to design foldamers with desirable structures and functions. Computational tools are a helpful proxy for revealing the dynamic structures at atomic resolution and understanding foldamer's complex structure-function relationships. However, the performance of conventional force fields in predicting the structures of artificial peptides has not been systematically evaluated. In this study, we critically assessed three popular force fields, AMBER ff14SB, CHARMM36m, and OPLS-AA/L, in predicting conformational propensities of a β-peptide foldamer at monomer and hexamer levels. Simulation results were compared to those obtained from quantum chemistry calculations and experimental data. We also utilised replica exchange molecular dynamics simulations to investigate the energy landscape of each force field and assess the similarities and differences between force fields. We compared different solvent systems in the AMBER ff14SB and CHARMM36m frameworks and confirmed the unanimous role of hydrogen bonds in shaping energy landscapes. We anticipate that our data will pave the way for further improvements to force fields and for understanding the role of solvents in peptide folding, crystallisation, and engineering.
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Affiliation(s)
- Jihye Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hee-Seung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea. .,Center for Multiscale Chiral Architectures, KAIST, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea.
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4
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Sawato T, Yamaguchi M. Synthetic Chemical Systems Involving Self‐Catalytic Reactions of Helicene Oligomer Foldamers. Chempluschem 2020; 85:2017-2038. [DOI: 10.1002/cplu.202000489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/18/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Tsukasa Sawato
- Department of Organic Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Aoba Sendai 980-8578 Japan
| | - Masahiko Yamaguchi
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Department of Organic Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Aoba Sendai 980-8578 Japan
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5
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Orłowski R, Cichowicz G, Staszewska-Krajewska O, Schilf W, Cyrański MK, Gryko DT. Covalently Linked Bis(Amido-Corroles): Inter- and Intramolecular Hydrogen-Bond-Driven Supramolecular Assembly. Chemistry 2019; 25:9658-9664. [PMID: 30990230 DOI: 10.1002/chem.201901254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Indexed: 11/08/2022]
Abstract
Four bis-corroles linked by diamide bridges were synthesized through peptide-type coupling of a trans-A2 B-corrole acid with aliphatic and aromatic diamines. In the solid state, the hydrogen-bond pattern in these bis-corroles is strongly affected by the type of solvent used in the crystallization process. Although intramolecular hydrogen bonds play a decisive role, they are supported by intermolecular hydrogen bonds and weak N-H⋅⋅⋅π interactions between molecules of toluene and the corrole cores. In an analogy to mono(amido-corroles), both in crystalline state and in solutions, the aliphatic or aromatic bridge is located directly above the corrole ring. When either ethylenediamine or 2,3-diaminonaphthalene are used as linkers, incorporation of polar solvents into the crystalline lattice causes a roughly parallel orientation of the corrole rings. At the same time, both NHCO⋅⋅⋅NH corrole hydrogen bonds are intramolecular. In contrast, solvation in toluene causes a distortion with one of the hydrogen bonds being intermolecular. Interestingly, intramolecular hydrogen bonds are always formed between the -NHCO- functionality located further from the benzene ring present at the position 10-meso. In solution, the hydrogen-bonds pattern of the bis(amido-corroles) is strongly affected by the type of the solvent. Compared with toluene (strongly high-field shifted signals), DMSO and pyridine disrupt self-assembly, whereas hexafluoroisopropanol strengthens intramolecular hydrogen bonds.
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Affiliation(s)
- Rafał Orłowski
- Institute of Organic Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka str., 01224, Warsaw, Poland
| | - Grzegorz Cichowicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093, Warsaw, Poland
| | - Olga Staszewska-Krajewska
- Institute of Organic Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka str., 01224, Warsaw, Poland
| | - Wojciech Schilf
- Institute of Organic Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka str., 01224, Warsaw, Poland
| | - Michał K Cyrański
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093, Warsaw, Poland
| | - Daniel T Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka str., 01224, Warsaw, Poland
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Kielesiński Ł, Morawski OW, Sobolewski AL, Gryko DT. The synthesis and photophysical properties of tris-coumarins. Phys Chem Chem Phys 2019; 21:8314-8325. [PMID: 30951072 DOI: 10.1039/c9cp00978g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A structurally unique cyclic tris-coumarin possessing three identical coumarin units bridged by amide linkers as well as two linear analogs has been synthesized. There is a remarkable agreement between crystallographic data, 1H NMR and results of calculations for the cyclic tris-coumarin, showing in all cases a non-symmetric arrangement of identical coumarin moieties. Weak polarization of the coumarin subunits, resulting from the presence of only CONH- groups as electron-donors, results in a hypsochromic shift of both absorption and emission in this dye. We have proven that in non-cyclic, head-to-tail linked tris-coumarins, the photophysics is controlled not only by the substituents but also by the conformation of the molecule, which in turn depends on the nature of the linker's interactions. These can be controlled by the presence/absence of an amide-type hydrogen atom responsible for the formation of intramolecular hydrogen bonds. The presence of a hydrogen bond favors a stretched trans conformation of the dye, while in its absence, folding of the molecule occurs leading to a more compact conformation. Although, the increased number of covalently linked coumarin units does not drastically change the preferred conformation, the fluorescence quantum yields of tris-coumarins are significantly lower than for analogous bis-coumarins composed of the same units.
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Affiliation(s)
- Łukasz Kielesiński
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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7
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Double helical conformation and extreme rigidity in a rodlike polyelectrolyte. Nat Commun 2019; 10:801. [PMID: 30778067 PMCID: PMC6379425 DOI: 10.1038/s41467-019-08756-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 01/25/2019] [Indexed: 11/13/2022] Open
Abstract
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures appear widely in nature, only rarely are these found in synthetic non-chiral macromolecules. Here we report a double helical conformation in the densely charged aromatic polyamide poly(2,2′-disulfonyl-4,4′-benzidine terephthalamide) or PBDT. This double helix macromolecule represents one of the most rigid simple molecular structures known, exhibiting an extremely high axial persistence length (~1 micrometer). We present X-ray diffraction, NMR spectroscopy, and molecular dynamics (MD) simulations that reveal and confirm the double helical conformation. The discovery of this extreme rigidity in combination with high charge density gives insight into the self-assembly of molecular ionic composites with high mechanical modulus (~ 1 GPa) yet with liquid-like ion motions inside, and provides fodder for formation of other 1D-reinforced composites. Double helix structures appear widely in nature, but only rarely in synthetic non-chiral macromolecules. Here the authors describe a double helix in a densely charged aromatic polyamide, which exhibits an axial rigidity persistence length of ~ 1 μm, much higher than that of DNA (~ 50 nm).
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Debnath S, Sengupta A, Jose KVJ, Raghavachari K. Fragment-Based Approaches for Supramolecular Interaction Energies: Applications to Foldamers and Their Complexes with Anions. J Chem Theory Comput 2018; 14:6226-6239. [DOI: 10.1021/acs.jctc.8b00525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sibali Debnath
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arkajyoti Sengupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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9
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Kielesiński Ł, Gryko DT, Sobolewski AL, Morawski OW. Effect of conformational flexibility on photophysics of bis-coumarins. Phys Chem Chem Phys 2018; 20:14491-14503. [DOI: 10.1039/c8cp01084f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The fluorescence of bis-coumarins linked via CONH and COO functionalities is strongly dependant on solvent polarity.
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Affiliation(s)
- Łukasz Kielesiński
- Institute of Organic Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
- Institute of Physics
| | - Daniel T. Gryko
- Institute of Organic Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | | | - Olaf W. Morawski
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
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