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Uji H, Ogawa J, Itabashi K, Imai T, Kimura S. Compartmentalized host spaces accommodating guest aromatic molecules in a chiral way in a helix-peptide-aromatic framework. Chem Commun (Camb) 2018; 54:12483-12486. [PMID: 30338328 DOI: 10.1039/c8cc07380e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A novel host molecular assembly of a free-standing flat nanosheet with compartmentalized spaces was prepared using a bolaamphiphilic peptide composed of two amphiphilic helical peptides and an oligo(naphthaleneethynylene) (ONE) unit at the center of the molecule. The nanosheet possesses void host spaces that can accommodate two mol-equivalent ONE groups to form columns of ONE groups in a right-handed helical way and ONE channels over a long distance. The present molecular system therefore can provide a chiral pore channel for relatively large molecules.
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Affiliation(s)
- Hirotaka Uji
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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2
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Dutta S, Gellman AJ. Enantiomer surface chemistry: conglomerate versus racemate formation on surfaces. Chem Soc Rev 2018; 46:7787-7839. [PMID: 29165467 DOI: 10.1039/c7cs00555e] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Research on surface chirality is motivated by the need to develop functional chiral surfaces for enantiospecific applications. While molecular chirality in 3D has been the subject of study for almost two centuries, many aspects of 2D chiral surface chemistry have yet to be addressed. In 3D, racemic mixtures of chiral molecules tend to aggregate into racemate (molecularly heterochiral) crystals much more frequently than conglomerate (molecularly homochiral) crystals. Whether chiral adsorbates on surfaces preferentially aggregate into heterochiral rather than homochiral domains (2D crystals or clusters) is not known. In this review, we have made the first attempt to answer the following question based on available data: in 2D racemic mixtures adsorbed on surfaces, is there a clear preference for homochiral or heterochiral aggregation? The current hypothesis is that homochiral packing is preferred on surfaces; in contrast to 3D where heterochiral packing is more common. In this review, we present a simple hierarchical scheme to categorize the chirality of adsorbate-surface systems. We then review the body of work using scanning tunneling microscopy predominantly to study aggregation of racemic adsorbates. Our analysis of the existing literature suggests that there is no clear evidence of any preference for either homochiral or heterochiral aggregation at the molecular level by chiral and prochiral adsorbates on surfaces.
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Affiliation(s)
- Soham Dutta
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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3
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Nuermaimaiti A, Ning Y, Cramer JL, Svane KL, Hammer B, Gothelf KV, Linderoth TR. Influence of CH···N Interaction in the Self-Assembly of an Oligo(isoquinolyne-ethynylyne) Molecule with Distinct Conformational States. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10782-10791. [PMID: 28968110 DOI: 10.1021/acs.langmuir.7b02207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular conformational flexibility can play an important role in supramolecular self-assembly on surfaces, affecting not least chiral molecular assemblies. To explicitly and systematically investigate the role of molecular conformational flexibility in surface self-assembly, we synthesized a three-bit conformational switch where each of three switching units on the molecules can assume one of two distinct binary positions on the surface. The molecules are designed to promote C-H···N type hydrogen bonds between the switching units. While supramolecular self-assembly based on strong hydrogen-bonding interactions has been widely explored, less is known about the role of such weaker directional interactions for surface self-assembly. The synthesized molecules consist of three nitrogen-containing isoquinoline (IQ) bits connected by ethynylene spokes and terminated by tert-butyl (tBu) groups. Using high-resolution scanning tunnelling microscopy, we investigate the self-assembly of the IQ-tBu molecules on a Au(111) surface under ultrahigh-vacuum conditions. The molecules form extended domains of brick-wall structure where the molecular backbones are packed regularly but without selection of specific molecular conformations. However, statistical analysis of the extended network demonstrates alignment/correlation for the orientations of the switching units indicating specific interactions. The primary interaction motifs in the structure are quantified from DFT calculations, showing that the brick-wall structure is indeed stabilized by two types of weak C-H···N bonds, involving either aromatic hydrogens on the IQ groups or nonaromatic hydrogens on the tBu groups. Analysis of the C-H···N interactions in the brick-wall structure explains the observed distribution and alignment of molecular conformations as well as the overall organization of the molecular surface structures.
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Affiliation(s)
- Ajiguli Nuermaimaiti
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
| | - Yanxiao Ning
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
| | - Jacob L Cramer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
- Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
| | - Katrine L Svane
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
- Department of Physics and Astronomy, Aarhus University , 8000 Aarhus C, Denmark
| | - Bjørk Hammer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
- Department of Physics and Astronomy, Aarhus University , 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
- Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
| | - Trolle R Linderoth
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
- Department of Physics and Astronomy, Aarhus University , 8000 Aarhus C, Denmark
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Husch T, Seebach D, Beck AK, Reiher M. Rigorous Conformational Analysis of Pyrrolidine Enamines with Relevance to Organocatalysis. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700182] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tamara Husch
- Laboratorium für Physikalische Chemie ETH Zürich Vladimir‐Prelog‐Weg 3 8093 Zürich Switzerland
| | - Dieter Seebach
- Laboratorium für Organische Chemie ETH Zürich Vladimir‐Prelog‐Weg 2 8093 Zürich Switzerland
| | - Albert K. Beck
- Laboratorium für Organische Chemie ETH Zürich Vladimir‐Prelog‐Weg 2 8093 Zürich Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Vladimir‐Prelog‐Weg 3 8093 Zürich Switzerland
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5
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Yang X. Conformational dynamics play important roles upon the function of N-acetylglutamate kinase. Appl Microbiol Biotechnol 2017; 101:3485-3492. [PMID: 28341883 DOI: 10.1007/s00253-017-8237-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/04/2017] [Accepted: 03/09/2017] [Indexed: 12/14/2022]
Abstract
N-acetylglutamate kinase (NAGK) catalyzes the phosphorylation of N-acetylglutamate. In many bacteria, NAGK catalysis is the rate controlling step in the L-arginine biosynthesis pathway from glutamate to L-arginine and is allosterically inhibited by L-arginine. Many data show that conformational dynamics of NAGKs are essential for their function. The demonstration of the conformational mechanism provides a potential way to improve the yield of arginine. Due to the lack of NAGK catalysis step in arginine synthesis route of mammals, the elucidation of the dynamic mechanism can also provide a way to design a new antivirus drug. This paper reviews how the dynamics affect the activity of NAGKs and are controlled by the effectors. X-ray crystallography and modeling data have shown that in NAGKs, the structural elements required for inhibitor and substrate binding, catalysis and product release, are highly mobile. It is possible to eliminate the inhibition of the arginine and/or block the synthesis of arginine by disturbing the flexibility of the NAGKs. Amino acid kinase family is thought to share some common dynamic features; the flexible structural elements of NAGKs have been identified, but the details of the dynamics and the signal transfer pathways are yet to be elucidated.
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Affiliation(s)
- Xiaorong Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Key Laboratory of Renewable Energy, Chinese Academy of Sciences, Guangzhou, 510640, People's Republic of China.
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Li N, Gu G, Zhang X, Song D, Zhang Y, Teo BK, Peng LM, Hou S, Wang Y. Packing fractal Sierpiński triangles into one-dimensional crystals via a templating method. Chem Commun (Camb) 2017; 53:3469-3472. [DOI: 10.1039/c7cc00566k] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystalline structures with Sierpiński triangles as building blocks were constructedviaa templating method in ultra-high vacuum and studied by low-temperature scanning tunneling microscopy.
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Affiliation(s)
- Na Li
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Gaochen Gu
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Xue Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Daoliang Song
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Yajie Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Boon K. Teo
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Lian-mao Peng
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Shimin Hou
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
| | - Yongfeng Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices
- Department of Electronics
- Peking University
- Beijing 100871
- China
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