1
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Singh H, Chenna A, Gangwar U, Dutta S, Kurur ND, Goel G, Haridas V. Bispidine as a promising scaffold for designing molecular machines. Org Biomol Chem 2023; 21:9054-9060. [PMID: 37937510 DOI: 10.1039/d3ob01406a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The development of artificial molecular machines is a challenging endeavor. Herein, we have synthesized a series of bispidine diamides D1-D6 that exhibit rotation reminiscent of a motor motion. Dynamic NMR, X-ray diffraction, quantum mechanical calculations, and molecular dynamics simulations provided insights into their rotational dynamics. All the diamides D1-D6 exhibited mutually independent rotation around the two bispidine arms. However, the rate of rotation and the presence or absence of directionality in amide bond rotation were found to depend on the solvent, temperature, and nature of substitution on the amide carbonyl. These engineered systems may aid in the development of biologically relevant synthetic molecular motors. Studies on homochiral and heterochiral bispidine-peptides revealed that the direction of rotation can be controlled by chirality and the nature of the amino acid.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India
| | - Upanshu Gangwar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Souvik Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Narayanan D Kurur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Gaurav Goel
- Department of Chemical Engineering, 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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2
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Ramos-Enríquez MA, Vazquez-Chavez J, Campos-Xolalpa N, Pérez-Gutiérrez S, Iglesias-Arteaga MA. Synthesis, NMR characterization and cytotoxic activity of hybrid spirostanic sapogenins-estradiol dimers. Steroids 2023; 199:109286. [PMID: 37517593 DOI: 10.1016/j.steroids.2023.109286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Four hybrid steroid dimers were obtained by BF3·Et2O-catalyzed aldol condensation of acetylated steroid sapogenins with 2-formyl-estradiol diacetate. The structures of the obtained dimers were unambiguously established by NMR. The hybrid dimers 9a (IC50 18.37 μM) and 9c (IC50 9.4 μM) with the 5α configuration at the A/B rings junction showed the higher cytotoxicity against HeLa, with selectivity index of 4.36 and 11.8 respectively. The presence of a carbonyl function at position C-12 produced the highest cytotoxic effect, which is in line with our previous reports.
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Affiliation(s)
- Manuel A Ramos-Enríquez
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Josué Vazquez-Chavez
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Nimsi Campos-Xolalpa
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Coyoacán, 04960 Ciudad de México, Mexico
| | - Salud Pérez-Gutiérrez
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Coyoacán, 04960 Ciudad de México, Mexico
| | - Martín A Iglesias-Arteaga
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico.
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3
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Xiao Y, Woods RJ. Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation. J Chem Theory Comput 2023; 19:5503-5515. [PMID: 37493980 PMCID: PMC10448718 DOI: 10.1021/acs.jctc.3c00300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 07/27/2023]
Abstract
Here, we develop an empirical energy function based on quantum mechanical data for the interaction between methane and benzene that captures the contribution from CH-π interactions. Such interactions are frequently observed in protein-ligand crystal structures, particularly for carbohydrate ligands, but have been hard to quantify due to the absence of a model for CH-π interactions in typical molecular mechanical force fields or docking scoring functions. The CH-π term was added to the AutoDock Vina (AD VINA) scoring function enabling its performance to be evaluated against a cohort of more than 1600 occurrences in 496 experimental structures of protein-ligand complexes. By employing a conformational grid search algorithm, inclusion of the CH-π term was shown to improve the prediction of the preferred orientation of flexible ligands in protein-binding sites and to enhance the detection of carbohydrate-binding sites that display CH-π interactions. Last but not least, this term was also shown to improve docking performance for the CASF-2016 benchmark set and a carbohydrate set.
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Affiliation(s)
- Yao Xiao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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4
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Gallarati S, Fabregat R, Juraskova V, Inizan TJ, Corminboeuf C. How Robust Is the Reversible Steric Shielding Strategy for Photoswitchable Organocatalysts? J Org Chem 2022; 87:8849-8857. [PMID: 35762705 PMCID: PMC9295146 DOI: 10.1021/acs.joc.1c02991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A highly appealing strategy to modulate a catalyst's activity and/or selectivity in a dynamic and noninvasive way is to incorporate a photoresponsive unit into a catalytically competent molecule. However, the description of the photoinduced conformational or structural changes that alter the catalyst's intrinsic reactivity is often reduced to a handful of intuitive static representations, which can struggle to capture the complexity of flexible organocatalysts. Here, we show how a comprehensive exploration of the free energy landscape of N-alkylated azobenzene-tethered piperidine catalysts is essential to unravel the conformational characteristics of each configurational state and explain the experimentally observed reactivity trends. Mapping the catalysts' conformational space highlights the existence of false ON or OFF states that lower their switching ability. Our findings expose the challenges associated with the realization of a reversible steric shielding for the photocontrol of Brønsted basicity of piperidine photoswitchable organocatalysts.
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Affiliation(s)
- Simone Gallarati
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Raimon Fabregat
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Veronika Juraskova
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Theo Jaffrelot Inizan
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.,National Center for Competence in Research─Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.,National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
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5
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Labra-Vázquez P, Ochoa ME, Alfonso-Herrera LA, Vera MA, Farfán N, Santillan R. A Steroidal Molecular Rotor with Fast Solid‐State Dynamics Obtained by Crystal Engineering: Role of the Polarity of the Stator. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Pablo Labra-Vázquez
- UNAM Facultad de Quimica: Universidad Nacional Autonoma de Mexico Facultad de Quimica Química orgánica 04510 Ciudad de México, México MEXICO
| | - María E. Ochoa
- Centro de Investigacion y de Estudios Avanzados Unidad Zacatenco: Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional Química Apdo. Postal 14-740, 07000, Ciudad de México, México MEXICO
| | - Luis A. Alfonso-Herrera
- Universidad Autónoma de Nuevo León: Universidad Autonoma de Nuevo Leon Departamento de Ecomateriales y Energía Av. Universidad S/N Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, MEXICO
| | - Marco A. Vera
- Universidad Autonoma Metropolitana Iztapalapa Lab. de RMN MEXICO
| | - Norberto Farfán
- UNAM Facultad de Quimica: Universidad Nacional Autonoma de Mexico Facultad de Quimica Química orgánica 04510 Ciudad de México, México MEXICO
| | - Rosa Santillan
- Centro de Investigacion y de Estudios Avanzados Unidad Zacatenco: Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional Química Apdo. Postal 14-740, 07000, Ciudad de México, México 07000 Ciudad de México MEXICO
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6
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Joshi H, Meena N, Kumar S, Shinde VN, Reddy SR, Bhuvanesh N, Kumar A. Bulky selenium ligand stabilized trans-palladium dichloride complexes as catalyst for silver-free decarboxylative coupling of coumarin-3-carboxylic acids. Chem Asian J 2021; 17:e202101199. [PMID: 34919329 DOI: 10.1002/asia.202101199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/14/2021] [Indexed: 11/06/2022]
Abstract
This report describes synthesis of three new trans -palladium dichloride complexes of bulky selenium ligands. These complexes possess a Cl-Pd-Cl rotor spoke attached to a Se-Pd-Se axle. The new ligands and palladium complexes ( C1 - C3 ) were characterized with the help of NMR, HRMS, UV-Vis., IR, and elemental analysis. The single crystal structure of metal complex C2 confirmed a square planer geometry of complex with trans -orientation. The X-ray structure revealed intramolecular secondary interactions (SeCH---Cl) between chlorine of PdCl 2 and CH 2 proton of selenium ligand. Variable temperature NMR data shows coalescence of diastereotopic protons, which indicates pyramidal inversion of selenium atom at elevated temperature. The relaxed potential energy scan of C2 suggests a rotational barrier of ~12.5 kcal/mol for rotation of chlorine atom through Cl-Pd-Cl rotor. The complex C3 possess dual intramolecular secondary interactions (OCH 2 ---Cl and SeCH 2 ---Cl) with stator ligand. Molecular rotor C2 was found to be most efficient catalyst for the decarboxylative Heck-coupling under mild reaction conditions. The protocol is applicable to a broad range of substrates with large functional group tolerance and low catalyst loading (2.5 mol %). The mechanism of decarboxylative Heck-coupling reaction was investigated through experimental and computational studies. Importantly the reaction works under silver-free conditions which reduces the cost of overall protocol. Further, the catalyst also worked for decarboxylative arylation and decarboxylative Suzuki-Miyaura coupling reactions with good yields of the coupled products.
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Affiliation(s)
- Hemant Joshi
- Central University of Rajasthan, Ajmer, Chemistry, Department of Chemistry, Central University of Rajasthan, 305817, Bandarsindri, Ajmer, INDIA
| | - Neha Meena
- BITS Pilani: Birla Institute of Technology and Science, Chemistry, INDIA
| | - Sunil Kumar
- Central University of Rajasthan, Chemistry, INDIA
| | - Vikki N Shinde
- BITS: Birla Institute of Technology and Science Pilani, Chemistry, INDIA
| | | | - Nattamai Bhuvanesh
- Texas A&M University College Station: Texas A&M University, Chemistry, UNITED STATES
| | - Anil Kumar
- BITS: Birla Institute of Technology and Science Pilani, Chemistry, INDIA
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7
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Sohrabi H, Javanbakht S, Oroojalian F, Rouhani F, Shaabani A, Majidi MR, Hashemzaei M, Hanifehpour Y, Mokhtarzadeh A, Morsali A. Nanoscale Metal-Organic Frameworks: Recent developments in synthesis, modifications and bioimaging applications. CHEMOSPHERE 2021; 281:130717. [PMID: 34020194 DOI: 10.1016/j.chemosphere.2021.130717] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Porous Metal-Organic Frameworks (MOFs) have emerged as eye-catching materials in recent years. They are widely used in numerous fields of chemistry thanks to their desirable properties. MOFs have a key role in the development of bioimaging platforms that are hopefully expected to effectually pave the way for accurate and selective detection and diagnosis of abnormalities. Recently, many types of MOFs have been employed for detection of RNA, DNA, enzyme activity and small-biomolecules, as well as for magnetic resonance imaging (MRI) and computed tomography (CT), which are valuable methods for clinical analysis. The optimal performance of the MOF in the bio-imaging field depends on the core structure, synthesis method and modifications processes. In this review, we have attempted to present crucial parameters for designing and achieving an efficient MOF as bioimaging platforms, and provide a roadmap for researchers in this field. Moreover, the influence of modifications/fractionalizations on MOFs performance has been thoroughly discussed and challenging problems have been extensively addressed. Consideration is mainly focused on the principal concepts and applications that have been achieved to modify and synthesize advanced MOFs for future applications.
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Affiliation(s)
- Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Siamak Javanbakht
- Faculty of Chemistry, Shahid Beheshti University, G.C., P.O. Box 19396-4716, Tehran, Iran
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Farzaneh Rouhani
- Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Ahmad Shaabani
- Faculty of Chemistry, Shahid Beheshti University, G.C., P.O. Box 19396-4716, Tehran, Iran
| | - Mir Reza Majidi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Mahmoud Hashemzaei
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Zabol University of Medical Sciences, Zabol. Iran
| | - Younes Hanifehpour
- Department of Chemistry, Sayyed Jamaleddin Asadabadi University, Asadabad, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Ali Morsali
- Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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8
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Zhai L, Nara M, Otani Y, Ohwada T. Unexpectedly rigid short peptide foldamers in which NH-π and CH-π interactions are preserved in solution. Chem Commun (Camb) 2021; 57:8344-8347. [PMID: 34328149 DOI: 10.1039/d1cc02998c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NH-π and CH-π interactions, due to their weak character, are not easily identified in solution. We report a group of isolable short peptides with stable folds, in which NH-π and CH-π main chain-side chain interactions can be detected in solution by means of NMR and ATR-IR spectroscopy.
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Affiliation(s)
- Luhan Zhai
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ko, Tokyo, 113-0033, Japan.
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9
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Ehnbom A, Gladysz JA. Gyroscopes and the Chemical Literature, 2002–2020: Approaches to a Nascent Family of Molecular Devices. Chem Rev 2021; 121:3701-3750. [DOI: 10.1021/acs.chemrev.0c01001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Andreas Ehnbom
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842-3012, United States
| | - John A. Gladysz
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842-3012, United States
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10
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Liepuoniute I, Jellen MJ, Garcia-Garibay MA. Correlated motion and mechanical gearing in amphidynamic crystalline molecular machines. Chem Sci 2020; 11:12994-13007. [PMID: 34094484 PMCID: PMC8163207 DOI: 10.1039/d0sc04495d] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
In this review we highlight the recent efforts towards the development of molecular gears with an emphasis on building molecular gears in the solid state and the role that molecular gearing and correlated motions may play in the function of crystalline molecular machines. We discuss current molecular and crystal engineering strategies, challenges associated with engineering correlated motion in crystals, and outline experimental and theoretical tools to explore gearing dynamics while highlighting key advances made to date.
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Affiliation(s)
- Ieva Liepuoniute
- Department of Chemistry and Biochemistry, University of California Los Angeles CA 90095-1569 USA
| | - Marcus J Jellen
- Department of Chemistry and Biochemistry, University of California Los Angeles CA 90095-1569 USA
| | - Miguel A Garcia-Garibay
- Department of Chemistry and Biochemistry, University of California Los Angeles CA 90095-1569 USA
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11
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Vargas-Romero K, Martínez-Torres FC, Aguilar-Granda A, Pérez-Estrada S, Flores-Alamo M, Rodríguez-Molina B, Iglesias-Arteaga MA. Synthesis and Solid-State Dynamics of a Crystalline Steroid Molecular Rotor without the Alkyne Axle: Steroid Dimers Based on a 1,4-Di(1,3-dioxan-2-yl)benzene Moiety. J Org Chem 2020; 85:8501-8509. [PMID: 32475112 DOI: 10.1021/acs.joc.0c00867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two diastereomeric crystalline steroid dimers were obtained by acid-catalyzed double acetalization of (20S)-5α-pregnan-3β,16β,20-triol 3-monoacetate with terephtalaldehyde. These compounds were characterized by NMR in solution, MS, single-crystal X-ray diffraction, and variable-temperature solid-state NMR by 13C cross-polarization magic angle spinning (CPMAS). While the phenylene rotator in the SR diastereomer remains static even at 373 K, the RR isomer shows a slow rotational process of the phenylene ring at temperatures above room temperature and thus may be considered the first crystalline steroid molecular rotor without the alkyne axle.
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Affiliation(s)
- Katherine Vargas-Romero
- Facultad de Quı́mica, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Fátima C Martínez-Torres
- Facultad de Quı́mica, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Andrés Aguilar-Granda
- Instituto de Quı́mica, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior, 04510 Ciudad de México, México
| | - Salvador Pérez-Estrada
- Área Académica de Quı́mica, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km 4.5, Mineral de la Reforma, Hidalgo CP 42076, Mexico
| | - Marcos Flores-Alamo
- Facultad de Quı́mica, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Braulio Rodríguez-Molina
- Instituto de Quı́mica, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior, 04510 Ciudad de México, México
| | - Martín A Iglesias-Arteaga
- Facultad de Quı́mica, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
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12
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Aguilar-Valdez N, Esturau-Escofet N, González-Antonio O, Romero-Ávila M, Flores-Pérez B, Leyva MA, Díaz D, Santillan R, Farfán N. Synthesis, complete NMR assignment and structural study of a steroidal dimer of 17α-ethynyl-5α,10α-estran-17β-ol with diethynylbenzene spacer. Steroids 2020; 157:108606. [PMID: 32084503 DOI: 10.1016/j.steroids.2020.108606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/04/2020] [Accepted: 02/14/2020] [Indexed: 11/16/2022]
Abstract
A phenylene-bridged steroidal dimer derived from 17α-ethynyl-5α,10α-estran-17β-ol with molecular rotor-like architecture was synthesized to investigate the supramolecular interactions directing the crystallization of these systems. Structures with varying importance in complementarity between H-bonding and hydrophobic interactions can be observed directing the packing of the obtained crystals, depending on the synthetic stage, though conserving the same space group for both systems. Such behavior clearly shows the versatility achievable using steroids as crystal packing directors. Alongside this structural study, the complete NMR assignment is presented for the dimer, and precursors, in which the steroids present an unconventional and noteworthy A-B ring fusion.
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Affiliation(s)
- Nancy Aguilar-Valdez
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Nuria Esturau-Escofet
- Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Oscar González-Antonio
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Margarita Romero-Ávila
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Blas Flores-Pérez
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Marco A Leyva
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Apdo. Postal 14-740, 07000, Mexico
| | - David Díaz
- Facultad de Química, Departamento de Química Inorgánica y Nuclear, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Rosa Santillan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Apdo. Postal 14-740, 07000, Mexico
| | - Norberto Farfán
- Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
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13
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Zhang H, Du L, Wang L, Liu J, Wan Q, Kwok RTK, Lam JWY, Phillips DL, Tang BZ. Visualization and Manipulation of Molecular Motion in the Solid State through Photoinduced Clusteroluminescence. J Phys Chem Lett 2019; 10:7077-7085. [PMID: 31663748 DOI: 10.1021/acs.jpclett.9b02752] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The development of molecular machines has long been a dream of scientists and is expected to revolutionize many aspects of technology and medicine. As the prerequisite of a practicable molecular machine, studies on the solid-state molecular motion (SSMM) are not only of scientific importance but also practically useful. Herein, two nonconjugated molecules, 1,2-diphenylethane (s-DPE) and 1,2-bis(2,4,5-trimethylphenyl)ethane (s-DPE-TM), are synthesized, and their SSMM is investigated. Experimental and calculation results reveal that s-DPE and s-DPE-TM are capable of performing light-driven SSMM to form excited-state through-space complexes (ESTSC). The radiative decay of ESTSC generates an unexpected visible emission termed clusteroluminescence, which serves as a tool to visualize the process of SSMM. Meanwhile, the original packing structure can be recovered from ESTSC after the removal of light irradiation. This work provides a new strategy to manipulate and "see" the SSMM and gains new insights into clusteroluminescence.
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Affiliation(s)
- Haoke Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong SAR, China
- HKUST-Shenzhen Research Institute , No. 9 Yuexing First Road , South Area, Hi-tech Park, Nanshan, Shenzhen 518057 , China
| | - Lili Du
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Pok Fu Lam , Hong Kong SAR, China
- Institute of Life Sciences , Jiangsu University , Zhenjiang 212013 , China
| | - Lin Wang
- School of Biomedical Sciences, Faculty of Medicine , The Chinese University of Hong Kong , Shatin , NT, Hong Kong SAR, China
| | - Junkai Liu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong SAR, China
- HKUST-Shenzhen Research Institute , No. 9 Yuexing First Road , South Area, Hi-tech Park, Nanshan, Shenzhen 518057 , China
| | - Qing Wan
- Center for Aggregation-Induced Emission, State Key Laboratory of Luminescent Materials and Devices, SCUT-HKUST Joint Research Institute , South China University of Technology , Tianhe Qu, Guangzhou 510640 , China
| | - Ryan T K Kwok
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong SAR, China
- HKUST-Shenzhen Research Institute , No. 9 Yuexing First Road , South Area, Hi-tech Park, Nanshan, Shenzhen 518057 , China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong SAR, China
- HKUST-Shenzhen Research Institute , No. 9 Yuexing First Road , South Area, Hi-tech Park, Nanshan, Shenzhen 518057 , China
| | - David Lee Phillips
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Pok Fu Lam , Hong Kong SAR, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction and Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong SAR, China
- HKUST-Shenzhen Research Institute , No. 9 Yuexing First Road , South Area, Hi-tech Park, Nanshan, Shenzhen 518057 , China
- Center for Aggregation-Induced Emission, State Key Laboratory of Luminescent Materials and Devices, SCUT-HKUST Joint Research Institute , South China University of Technology , Tianhe Qu, Guangzhou 510640 , China
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14
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Banerjee A, Dey A, Chandrakumar N. Motional Dynamics of Halogen-Bonded Complexes Probed by Low-Field NMR Relaxometry and Overhauser Dynamic Nuclear Polarization. Chem Asian J 2019; 14:2785-2789. [PMID: 31210020 DOI: 10.1002/asia.201900754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/14/2019] [Indexed: 11/07/2022]
Abstract
Halogen bonding is a subject of considerable interest owing to wide-ranging chemical, materials and biological applications. The motional dynamics of halogen-bonded complexes play a pivotal role in comprehending the nature of the halogen-bonding interaction. However, not many attempts appear to have been made to shed light on the dynamical characteristics of halogen-bonded species. For the first time, we demonstrate here that the combination of low-field NMR relaxometry and Overhauser dynamic nuclear polarization (ODNP) makes it possible to obtain a cogent picture of the motional dynamics of halogen-bonded species. We discuss here the advantages of this combined approach. Low-field relaxometry allows us to infer the hydrodynamic radius and rotational correlation time, whereas ODNP probes the molecular translational correlation times (involving the substrate as well as the organic radical) with high sensitivity at low field.
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Affiliation(s)
- Abhishek Banerjee
- MRI-MRS Centre and Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India
| | - Arnab Dey
- MRI-MRS Centre and Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India
| | - N Chandrakumar
- MRI-MRS Centre and Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India
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15
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Valdez-García RM, Alarcón-Manjarrez C, Galano A, Rodríguez-Molina B, Flores-Álamo M, Iglesias-Arteaga MA. Synthesis of Dimeric Steroid Trioxabispiroacetals Scaffolds by Gold(I)-Catalyzed Hydroalkoxylation-Hydration of Diynediols. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ricardo M. Valdez-García
- Facultad de Química; Universidad Nacional Autónoma de México, Ciudad Universitaria; 04510 Ciudad de México México
| | - Carlos Alarcón-Manjarrez
- Facultad de Química; Universidad Nacional Autónoma de México, Ciudad Universitaria; 04510 Ciudad de México México
| | - Annia Galano
- Departamento de Química; División de Ciencias Básicas e Ingeniería; Universidad Autónoma Metropolitana-Iztapalapa; Av. San Rafael Atlixco No.186, C.P. 09340, Ciudad de México México
| | - Braulio Rodríguez-Molina
- Instituto de Química; División de Ciencias Básicas e Ingeniería; Universidad Nacional Autónoma de México; 04510 Ciudad de México México
| | - Marcos Flores-Álamo
- Facultad de Química; Universidad Nacional Autónoma de México, Ciudad Universitaria; 04510 Ciudad de México México
| | - Martín A. Iglesias-Arteaga
- Facultad de Química; Universidad Nacional Autónoma de México, Ciudad Universitaria; 04510 Ciudad de México México
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16
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Hamer S, Röhricht F, Jakoby M, Howard IA, Zhang X, Näther C, Herges R. Synthesis of dipolar molecular rotors as linkers for metal-organic frameworks. Beilstein J Org Chem 2019; 15:1331-1338. [PMID: 31293682 PMCID: PMC6604738 DOI: 10.3762/bjoc.15.132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/31/2019] [Indexed: 12/02/2022] Open
Abstract
We report the synthesis of five dicarboxylic acid-substituted dipolar molecular rotors for the use as linker molecules in metal-organic frameworks (MOFs). The rotor molecules exhibit very low rotational barriers and decent to very high permanent, charge free dipole moments, as shown by density functional theory calculations on the isolated molecules. Four rotors are fluorescent in the visible region. The linker designs are based on push-pull-substituted phenylene cores with ethynyl spacers as rotational axes, functionalized with carboxylic acid groups for implementation in MOFs. The substituents at the phenylene core are chosen to be small to leave rotational freedom in solids with confined free volumes. The dipole moments are generated by electron-donating substituents (benzo-1,3-dioxole, benzo-1,4-dioxane, or benzo-2,1,3-thiadiazole annelation) and withdrawing substituents (difluoro, or dicyano substitution) at the opposite positions of the central phenylene core. A combination of 1,4-dioxane annelation and dicyano substitution generates a theoretically predicted, very high dipole moment of 10.1 Debye. Moreover, the molecules are sufficiently small to fit into cavities of 10 Å3. Hence, the dipolar rotors should be ideally suited as linkers in MOFs with potential applications as ferroelectric materials and for optical signal processing.
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Affiliation(s)
- Sebastian Hamer
- Otto-Diels-Institut für Organische Chemie, Kiel University, Otto-Hahn-Platz 4, D-24118 Kiel, Germany
| | - Fynn Röhricht
- Otto-Diels-Institut für Organische Chemie, Kiel University, Otto-Hahn-Platz 4, D-24118 Kiel, Germany
| | - Marius Jakoby
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ian A Howard
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Xianghui Zhang
- Fakultät für Physik, Universität Bielefeld,Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Christian Näther
- Institut für Anorganische Chemie, Kiel University, Max-Eyth-Str. 2, D-24118 Kiel, Germany
| | - Rainer Herges
- Otto-Diels-Institut für Organische Chemie, Kiel University, Otto-Hahn-Platz 4, D-24118 Kiel, Germany
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17
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Yu B, Liu D, Zhang J, Li Z, Zhang YM, Li M, Zhang SXA. Emissions and the application of a series of twisted fluorophores with intramolecular weak hydrogen bonds. RSC Adv 2019; 9:13214-13219. [PMID: 35520777 PMCID: PMC9063768 DOI: 10.1039/c9ra01244c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/15/2019] [Indexed: 01/30/2023] Open
Abstract
A series of twisted fluorophores of CEOCH (((2,5-dimethoxy-1,4-phenylene)bis(ethene-2,1,1-triyl))-tetra-benzene) derivatives with intramolecular weak hydrogen bonds (IMWHBs) were synthesized to investigate how different substituents on outer benzenes influence their emissive properties. Because of the twisted structure and weak intermolecular interactions, the emissions of the CEOCH derivatives were intense in the aggregated state but as the flexibility and electronic effect of the substituents changed, their quantum yields (QYs) changed from over 40% to 1% in solution. Based on the adjustable QYs of CEOCHs with different substituents in solutions, a fluorescent sensor for hydrazine with an extremely strong light and dark contrast was obtained via the conversion of dicyanovinyl groups to hydrazone groups.
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Affiliation(s)
- Binhong Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun 130012 PR China .,College of Chemistry, Jilin University Changchun 130012 PR China
| | - Danyang Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun 130012 PR China .,College of Chemistry, Jilin University Changchun 130012 PR China
| | - Jinyan Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun 130012 PR China .,College of Chemistry, Jilin University Changchun 130012 PR China
| | - Zhize Li
- College of Chemistry, Jilin University Changchun 130012 PR China
| | - Yu-Mo Zhang
- College of Chemistry, Jilin University Changchun 130012 PR China
| | - Minjie Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun 130012 PR China .,College of Chemistry, Jilin University Changchun 130012 PR China
| | - Sean Xiao-An Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun 130012 PR China .,College of Chemistry, Jilin University Changchun 130012 PR China
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18
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Ousaka N, Yamamoto S, Iida H, Iwata T, Ito S, Hijikata Y, Irle S, Yashima E. Water-mediated deracemization of a bisporphyrin helicate assisted by diastereoselective encapsulation of chiral guests. Nat Commun 2019; 10:1457. [PMID: 30926811 PMCID: PMC6441078 DOI: 10.1038/s41467-019-09443-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/06/2019] [Indexed: 11/19/2022] Open
Abstract
Deracemization is a powerful method by which a racemic mixture can be transformed into an excess of one enantiomer with the aid of chiral auxiliaries, but has been applied only to small chiral molecular systems. Here we report a deracemization of a racemic double-stranded spiroborate helicate containing a bisporphyrin unit upon encapsulation of chiral aromatic guests between the bisporphyrin. The chiral guest-included helicate is kinetically stable, existing as a mixture of right- and left-handed double helices, which eventually undergo an inversion of the helicity triggered by water resulting from the water-mediated reversible diastereoselective B-O bond cleavage/reformation of the spiroborate groups, thus producing an optically-active helicate with a high enantioselectivity. Quantum chemical calculations suggest that the stereospecific CH-π interactions between the porphyrin hydrogen atoms of the helicate and an aromatic pendant group of the chiral guest play a key role in the enhancement of the helical handedness of the helicate.
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Affiliation(s)
- Naoki Ousaka
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Shinya Yamamoto
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Hiroki Iida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
- Department of Chemistry, Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue, 690-8504, Japan
| | - Takuya Iwata
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Shingo Ito
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yuh Hijikata
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Stephan Irle
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
- Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, 37831-6493, TN, USA
| | - Eiji Yashima
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
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19
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Nikitin K, O'Gara R. Mechanisms and Beyond: Elucidation of Fluxional Dynamics by Exchange NMR Spectroscopy. Chemistry 2019; 25:4551-4589. [PMID: 30421834 DOI: 10.1002/chem.201804123] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 12/31/2022]
Abstract
Detailed mechanistic information is crucial to our understanding of reaction pathways and selectivity. Dynamic exchange NMR techniques, in particular 2D exchange spectroscopy (EXSY) and its modifications, provide indispensable intricate information on the mechanisms of organic and inorganic reactions and other phenomena, for example, the dynamics of interfacial processes. In this Review, key results from exchange NMR studies of small molecules over the last few decades are systemised and discussed. After a brief introduction to the theory, the key types of dynamic processes are identified and fundamental examples given of intra- and intermolecular reactions, which, in turn, could involve, or not, bond-making and bond-breaking events. Following that logic, internal molecular rotation, intramolecular stereomutation and molecular recognition will first be considered because they do not typically involve bond breaking. Then, rearrangements, substitution-type reactions, cyclisations, additions and other processes affecting chemical bonds will be discussed. Finally, interfacial molecular dynamics and unexpected combinations of different types of fluxional processes will also be highlighted. How exchange NMR spectroscopy helps to identify conformational changes, coordination and molecular recognition processes as well as quantify reaction energy barriers and extract detailed mechanistic information by using reaction rate theory in conjunction with computational techniques will be shown.
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Affiliation(s)
- Kirill Nikitin
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Ryan O'Gara
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
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20
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Yu B, Liu D, Wang Y, Zhang T, Zhang YM, Li M, Zhang SXA. Strong and insusceptible photo-emissions from an intramolecular weak hydrogen bond strengthened twisted fluorophore. Phys Chem Chem Phys 2018; 20:23851-23855. [PMID: 30211408 DOI: 10.1039/c8cp04242j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Intramolecular weak hydrogen bonds of CHO and CH/Pi were introduced into a twisted fluorophore backbone of 1,4-bis(2,2-diphenylvinyl)benzene, which enables the fluorophore to emit violently and stably in both solubilized and aggregated states, and be inert to solvent environments and preserve over 10% quantum yield at temperature as high as 90 °C in solution.
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Affiliation(s)
- Binhong Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry Jilin University, Changchun 130012, P. R. China.
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21
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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22
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Hossain A, Dey A, Seth SK, Ray PP, Ballester P, Pritchard RG, Ortega-Castro J, Frontera A, Mukhopadhyay S. Enhanced Photosensitive Schottky Diode Behavior of Pyrazine over 2-Aminopyrimidine Ligand in Copper(II)-Phthalate MOFs: Experimental and Theoretical Rationalization. ACS OMEGA 2018; 3:9160-9171. [PMID: 31459050 PMCID: PMC6644610 DOI: 10.1021/acsomega.8b01111] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/31/2018] [Indexed: 05/26/2023]
Abstract
Two novel Cu(II)-based metal-organic frameworks [C40H34Cu2N6O18 (1) and C20H18CuN2O10 (2)] have been synthesized using 2-aminopyrimidine or pyrazine ligands and phthalate ion and characterized spectroscopically and by X-ray single-crystal diffraction. Both 1 and 2 show electrical conductivity and photosensitivity, evidencing their potentiality in optoelectronic device applications. Experimental and theoretical investigations revealed that the electrical conductivity under irradiation of visible light increases compared to that under dark condition (photosensitive Schottky barrier diode behavior), especially in complex 2. Both 1 and 2 have been successfully applied in technologically challenging thin-film active devices.
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Affiliation(s)
- Anowar Hossain
- Department
of Chemistry and Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Arka Dey
- Department
of Chemistry and Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Saikat Kumar Seth
- Department
of Chemistry and Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Partha Pratim Ray
- Department
of Chemistry and Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Pablo Ballester
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, Tarragona 43007, Spain
- Catalan
Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys, 23, Barcelona 08010, Spain
| | - Robin G. Pritchard
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PI, United
Kingdom
| | - Joaquín Ortega-Castro
- Departament
de Química, Universitat de les Illes
Balears, Crta. de Valldemossa
km 7.5, Palma Baleares 07122, Spain
| | - Antonio Frontera
- Departament
de Química, Universitat de les Illes
Balears, Crta. de Valldemossa
km 7.5, Palma Baleares 07122, Spain
| | - Subrata Mukhopadhyay
- Department
of Chemistry and Department of Physics, Jadavpur University, Kolkata 700032, India
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23
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Kharel S, Joshi H, Bhuvanesh N, Gladysz JA. Syntheses, Structures, and Thermal Properties of Gyroscope-like Complexes Consisting of PtCl2 Rotators Encased in Macrocyclic Dibridgehead Diphosphines P((CH2)n)3P with Extended Methylene Chains (n = 20/22/30) and Isomers Thereof. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00345] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sugam Kharel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - Hemant Joshi
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - Nattamai Bhuvanesh
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - John A. Gladysz
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
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24
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Abstract
Despite having significant applications in building nanomachines, molecular rotors with the rotational speed modulations to multiple stages in a wide range of frequency have not yet been well established. Here, we report the discovery of a stimuli-responsive molecular rotor, the rotational speed of which in the slow-to-fast range could be modulated to at least four stages triggered by acid/base and metal cations. The rotor itself rotates rapidly at ambient or elevated temperature but displays a restricted rotation after deprotonation due to the produced intramolecular electrostatic repulsion. Subsequent addition of Li+ or Na+ cations introduces an electrostatic bridge to stabilize the transition state of the deprotonated rotor, thus giving a cation-radius-dependent acceleration of the rotation to render the rotor running at a mid-speed. All the stimuli are highly reversible. Our studies provide a conceptual approach for constructing multistage rotational-speed-changing molecular rotors, and further, the practical nanomachines. Molecular rotors with rotational speed modulation have not yet been well established. Here, the authors report a pH and metal cation triggered molecular rotor, which allows for a four stage speed modulation in the slow-to-fast frequency range.
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25
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Vannay L, Meyer B, Petraglia R, Sforazzini G, Ceriotti M, Corminboeuf C. Analyzing Fluxional Molecules Using DORI. J Chem Theory Comput 2018; 14:2370-2379. [PMID: 29570294 DOI: 10.1021/acs.jctc.7b01176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Density Overlap Region Indicator (DORI) is a density-based scalar field that reveals covalent bonding patterns and noncovalent interactions in the same value range. This work goes beyond the traditional static quantum chemistry use of scalar fields and illustrates the suitability of DORI for analyzing geometrical and electronic signatures in highly fluxional molecular systems. Examples include a dithiocyclophane, which possesses multiple local minima with differing extents of π-stacking interactions and a temperature dependent rotation of a molecular rotor, where the descriptor is employed to capture fingerprints of CH-π and π-π interactions. Finally, DORI serves to examine the fluctuating π-conjugation pathway of a photochromic torsional switch (PTS). Attention is also placed on postprocessing the large amount of generated data and juxtaposing DORI with a data-driven low-dimensional representation of the structural landscape.
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26
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Mayorquín-Torres MC, Colin-Molina A, Pérez-Estrada S, Galano A, Rodríguez-Molina B, Iglesias-Arteaga MA. Synthesis, Characterization, and Solid State Dynamic Studies of a Hydrogen Bond-Hindered Steroidal Molecular Rotor with a Flexible Axis. J Org Chem 2018; 83:3768-3779. [PMID: 29504766 DOI: 10.1021/acs.joc.8b00134] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel steroid molecular rotor was obtained in four steps from the naturally occurring spirostane sapogenin diosgenin. The structural and dynamic characterization was carried out by solution NMR, VT X-ray diffraction, solid state 13C CPMAS, and solid state 2H NMR experiments. They allowed the identification of a fast dynamic process with a frequency of 14 MHz at room temperature, featuring a barrier to rotation Ea = 7.87 kcal mol-1. The gathered experimental evidence indicated the presence of a hydrogen bond that becomes stronger as the temperature lowers. This interaction was characterized using theoretical calculations, based on topological analyses of the electronic density and energies. In addition, combining theoretical calculations with experimental measurements, it was possible to propose a partition to Ea (∼8 kcal/mol) into three contributions, that are the cost of the intrinsic rotation (∼2 kcal/mol), the hydrogen bond interaction (∼2 kcal/mol), and the packing effects (∼2-3 kcal/mol). The findings from the present work highlight the relevance of the individual components in the function of molecular machines in the solid state.
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Affiliation(s)
- Martha C Mayorquín-Torres
- Facultad de Química , Universidad Nacional Autónoma de México , Ciudad Universitaria , 04510 Ciudad de México , México
| | - Abraham Colin-Molina
- Instituto de Química , Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria , 04510 Ciudad de México , México
| | - Salvador Pérez-Estrada
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Annia Galano
- Departamento de Química, División de Ciencias Básicas e Ingeniería , Universidad Autónoma Metropolitana-Iztapalapa , Av. San Rafael Atlixco No.186 , C.P.09340 Ciudad de México , México
| | - Braulio Rodríguez-Molina
- Instituto de Química , Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria , 04510 Ciudad de México , México
| | - Martín A Iglesias-Arteaga
- Facultad de Química , Universidad Nacional Autónoma de México , Ciudad Universitaria , 04510 Ciudad de México , México
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27
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Abstract
Rotational motion within molecular crystals is a prototypical concept to build future functional materials and solid-state molecular machines.
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Affiliation(s)
- Luca Catalano
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - Panče Naumov
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
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28
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Dong Z, Sun Y, Chu J, Zhang X, Deng H. Multivariate Metal-Organic Frameworks for Dialing-in the Binding and Programming the Release of Drug Molecules. J Am Chem Soc 2017; 139:14209-14216. [PMID: 28898070 DOI: 10.1021/jacs.7b07392] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report the control of guest release profiles by dialing-in desirable interactions between guest molecules and pores in metal-organic frameworks (MOFs). The interactions can be derived by the rate constants that were quantitatively correlated with the type of functional group and its proportion in the porous structure; thus the release of guest molecules can be predicted and programmed. Specifically, three probe molecules (ibuprofen, rhodamine B, and doxorubicin) were studied in a series of robust and mesoporous MOFs with multiple functional groups [MIL-101(Fe)-(NH2)x, MIL-101(Fe)-(C4H4)x, and MIL-101(Fe)-(C4H4)x(NH2)1-x]. The release rate can be adjusted by 32-fold [rhodamine from MIL-101(Fe)-(NH2)x], and the time of release peak can be shifted by up to 12 days over a 40-day release period [doxorubicin from MIL-101(Fe)-(C4H4)x(NH2)1-x], which was not obtained in the physical mixture of the single component MOF counterparts nor in other porous materials. The corelease of two pro-drug molecules (ibuprofen and doxorubicin) was also achieved.
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Affiliation(s)
- Zhiyue Dong
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, and ‡UC Berkeley-Wuhan University Joint Innovative Center, The Institute of Advanced Studies, Wuhan University , Luojiashan, Wuhan 430072, China
| | - Yangzesheng Sun
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, and ‡UC Berkeley-Wuhan University Joint Innovative Center, The Institute of Advanced Studies, Wuhan University , Luojiashan, Wuhan 430072, China
| | - Jun Chu
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, and ‡UC Berkeley-Wuhan University Joint Innovative Center, The Institute of Advanced Studies, Wuhan University , Luojiashan, Wuhan 430072, China
| | - Xianzheng Zhang
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, and ‡UC Berkeley-Wuhan University Joint Innovative Center, The Institute of Advanced Studies, Wuhan University , Luojiashan, Wuhan 430072, China
| | - Hexiang Deng
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, and ‡UC Berkeley-Wuhan University Joint Innovative Center, The Institute of Advanced Studies, Wuhan University , Luojiashan, Wuhan 430072, China
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29
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Synthesis, structural characterization and photoluminescent properties of 2D multilayer Cu + coordination polymers via C H⋯π and π⋯π interactions. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.04.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Hess GD, Fiedler T, Hampel F, Gladysz JA. Octahedral Gyroscope-like Molecules Consisting of Rhenium Rotators within Cage-like Dibridgehead Diphosphine Stators: Syntheses, Substitution Reactions, Structures, and Dynamic Properties. Inorg Chem 2017; 56:7454-7469. [DOI: 10.1021/acs.inorgchem.7b00909] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gisela D. Hess
- Institut
für Organische Chemie and Interdisciplinary Center for Molecular
Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Tobias Fiedler
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842-3012, United States
| | - Frank Hampel
- Institut
für Organische Chemie and Interdisciplinary Center for Molecular
Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - John A. Gladysz
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842-3012, United States
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31
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Kumar R, Gaurav A, Pal S, Kumar KR, Sridhar B, Tewari AK. Reverse Intramolecular Stacking in o-Xylene Bridge Symmetrical Dimers of 2-Thiopyridine Derivative: Assessment of the Conformational Stability. ChemistrySelect 2017. [DOI: 10.1002/slct.201700269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ranjeet Kumar
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Archana Gaurav
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Shiv Pal
- Indian Institute of Science Education and Research, Pune; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Krishnan R. Kumar
- Laboratory of X-ray Crystallography; Indian Institute of Chemical Technology; Hyderabad 500 607 India
| | - Balasubramanian Sridhar
- Laboratory of X-ray Crystallography; Indian Institute of Chemical Technology; Hyderabad 500 607 India
| | - Ashish K. Tewari
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
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32
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Kumar R, Gaurav A, Pal S, Tewari AK. A Case of Folding Pattern in Flexible Tripodal of N-Substituted Bisethylenamine Bridged Pyridazinone Dimers. ChemistrySelect 2017. [DOI: 10.1002/slct.201601897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ranjeet Kumar
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Archana Gaurav
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Shiv Pal
- Indian Institute of Science Education and Research, Pune; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Ashish Kumar Tewari
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
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33
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Fujiwara A, Inagaki Y, Momma H, Kwon E, Yamaguchi K, Kanno M, Kono H, Setaka W. A crystalline molecular gyrotop with a biphenylene dirotor and its temperature-dependent birefringence. CrystEngComm 2017. [DOI: 10.1039/c7ce01081h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A crystalline molecular gyrotop with a biphenylene dirotor showed a reduction in the birefringence with increasing temperature.
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Affiliation(s)
- Atsushi Fujiwara
- Division of Applied Chemistry
- Faculty of Urban Environmental Sciences
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Yusuke Inagaki
- Division of Applied Chemistry
- Faculty of Urban Environmental Sciences
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Hiroyuki Momma
- Research and Analytical Center for Giant Molecules
- Graduate School of Science
- Tohoku University
- Sendai
- Japan
| | - Eunsang Kwon
- Research and Analytical Center for Giant Molecules
- Graduate School of Science
- Tohoku University
- Sendai
- Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus
- Tokushima Bunri University
- Sanuki
- Japan
| | - Manabu Kanno
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai
- Japan
| | - Hirohiko Kono
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai
- Japan
| | - Wataru Setaka
- Division of Applied Chemistry
- Faculty of Urban Environmental Sciences
- Tokyo Metropolitan University
- Hachioji
- Japan
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34
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Lang GM, Bhuvanesh N, Reibenspies JH, Gladysz JA. Syntheses, Reactivity, Structures, and Dynamic Properties of Gyroscope-like Iron Carbonyl Complexes Based on Dibridgehead Diarsine Cages. Organometallics 2016. [DOI: 10.1021/acs.organomet.6b00447] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgette M. Lang
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
| | - Nattamai Bhuvanesh
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
| | - Joseph H. Reibenspies
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
| | - John A. Gladysz
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
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35
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Lang GM, Shima T, Wang L, Cluff KJ, Skopek K, Hampel F, Blümel J, Gladysz JA. Gyroscope-Like Complexes Based on Dibridgehead Diphosphine Cages That Are Accessed by Three-Fold Intramolecular Ring Closing Metatheses and Encase Fe(CO)3, Fe(CO)2(NO)+, and Fe(CO)3(H)+Rotators. J Am Chem Soc 2016; 138:7649-63. [DOI: 10.1021/jacs.6b03178] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Georgette M. Lang
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
| | - Takanori Shima
- Institut für Organische Chemie and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Leyong Wang
- Institut für Organische Chemie and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Kyle J. Cluff
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
| | - Katrin Skopek
- Institut für Organische Chemie and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Frank Hampel
- Institut für Organische Chemie and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Janet Blümel
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
| | - John A. Gladysz
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77843-3012, United States
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36
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Jiang X, O’Brien ZJ, Yang S, Lai LH, Buenaflor J, Tan C, Khan S, Houk KN, Garcia-Garibay MA. Crystal Fluidity Reflected by Fast Rotational Motion at the Core, Branches, and Peripheral Aromatic Groups of a Dendrimeric Molecular Rotor. J Am Chem Soc 2016; 138:4650-6. [PMID: 26973017 PMCID: PMC5155508 DOI: 10.1021/jacs.6b01398] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Low packing densities are key structural features of amphidynamic crystals built with static and mobile components. Here we report a loosely packed crystal of dendrimeric rotor 2 and the fast dynamics of all its aromatic groups, both resulting from the hyperbranched structure of the molecule. Compound 2 was synthesized with a convergent strategy to construct a central phenylene core with stators consisting of two layers of triarylmethyl groups. Single crystal X-ray diffraction analysis confirmed a low-density packing structure consisting of one molecule of 2 and approximately eight solvent molecules per unit cell. Three isotopologues of 2 were synthesized to study the motion of each segment of the molecule in the solid state using variable temperature quadrupolar echo (2)H NMR spectroscopy. Line shape analysis of the spectra reveals that the central phenylene, the six branch phenylenes, and the 18 periphery phenyls all display megahertz rotational dynamics in the crystals at ambient temperature. Arrhenius analysis of the data gives similar activation energies and pre-exponential factors for different parts of the structure. The observed pre-exponential factors are 4-6 orders of magnitude greater than those of elementary site-exchange processes, indicating that the dynamics are not dictated by static energetic potentials. Instead, the activation energies for rotations in the crystals of 2 are controlled by temperature dependent local structural fluctuations and crystal fluidity.
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Affiliation(s)
- Xing Jiang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Zachary J. O’Brien
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Lan Huong Lai
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Jeffrey Buenaflor
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Colleen Tan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Saeed Khan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Miguel A. Garcia-Garibay
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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37
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38
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Petraglia R, Nicolaï A, Wodrich MD, Ceriotti M, Corminboeuf C. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry. J Comput Chem 2016; 37:83-92. [PMID: 26228927 PMCID: PMC5324590 DOI: 10.1002/jcc.24025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/09/2023]
Abstract
Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.
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Affiliation(s)
- Riccardo Petraglia
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Adrien Nicolaï
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modelling, Institut des Materiaux, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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39
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Xu Y, Southern SA, Szell PMJ, Bryce DL. The role of solid-state nuclear magnetic resonance in crystal engineering. CrystEngComm 2016. [DOI: 10.1039/c6ce01206j] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This Highlight article discusses the role of solid-state NMR spectroscopy in crystal engineering with the aid of several examples from the literature.
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Affiliation(s)
- Yijue Xu
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa, Ontario K1N6N5 Canada
| | - Scott A. Southern
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa, Ontario K1N6N5 Canada
| | - Patrick M. J. Szell
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa, Ontario K1N6N5 Canada
| | - David L. Bryce
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa, Ontario K1N6N5 Canada
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40
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Sk B, Patra A. C–C coupling over Schiff base condensation: a rational design strategy for a strongly fluorescent molecular material. CrystEngComm 2016. [DOI: 10.1039/c5ce02489g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Lang GM, Skaper D, Hampel F, Gladysz JA. Synthesis, reactivity, structures, and dynamic properties of gyroscope like iron complexes with dibridgehead diphosphine cages: pre- vs. post-metathesis substitutions as routes to adducts with neutral dipolar Fe(CO)(NO)(X) rotors. Dalton Trans 2016; 45:16190-16204. [DOI: 10.1039/c6dt03258c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Substitution reactions of 4c+ BF4− afford the title complexes 9c-X, the Fe(CO)(NO)(X) moieties of which rapidly rotate within the diphosphine cage. Trends are interpreted in terms of horizontal/vertical van der Waals clearance.
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Affiliation(s)
| | - Dirk Skaper
- Institut für Organische Chemie and Interdisciplinary Center for Molecular Materials
- Friedrich-Alexander-Universität Erlangen-Nürnberg
- 91054 Erlangen
- Germany
| | - Frank Hampel
- Institut für Organische Chemie and Interdisciplinary Center for Molecular Materials
- Friedrich-Alexander-Universität Erlangen-Nürnberg
- 91054 Erlangen
- Germany
| | - John A. Gladysz
- Department of Chemistry
- Texas A&M University
- Texas 77842-3012
- USA
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42
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Kaleta J, Kaletová E, Císařová I, Teat SJ, Michl J. Synthesis of Triptycene-Based Molecular Rotors for Langmuir–Blodgett Monolayers. J Org Chem 2015; 80:10134-50. [DOI: 10.1021/acs.joc.5b01753] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Kaleta
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Eva Kaletová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Ivana Císařová
- Department
of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 12840 Prague 2, Czech Republic
| | - Simon J. Teat
- Advanced
Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Josef Michl
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
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