1
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Liao F, Wang H, Zhao J, Zhang B, Zhong H. Effectiveness evaluation of autotransplanted teeth after performing extraoral endodontic surgery instead of conventional root canal therapy. BMC Oral Health 2023; 23:1005. [PMID: 38097962 PMCID: PMC10722803 DOI: 10.1186/s12903-023-03733-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023] Open
Abstract
PURPOSE The aim of this study was to examine the viability and efficacy of utilizing extraoral apicoectomy and retrograde filling in combination to seal the root canal system of mature molars without the need for root canal therapy (RCT) during the autotransplantation of teeth (ATT). MATERIALS AND METHODS This study screened 27 patients who received ATT at the Department of Oral Surgery in the Hospital of Stomatology from 2019 to 2021. Extraoral apicoectomy and retrograde filling were performed, while RCT was temporarily not performed. The study analysed the periodontal status and masticatory function of transplanted teeth one to three years postoperation and used cone-beam computed tomography (CBCT) and periapical radiograph (PA) to evaluate the integrity of the periodontal space and intra/periapical inflammation. The potential predictors of survival/success were analysed statistically. We also conducted questionnaires and chewing efficiency tests. RESULTS In this study, 27 TTs from 27 patients were found to be fully functional in terms of chewing ability. The overall survival rate was 100% (27/27), and the success rate was 70.4% (19/27). A total of 90.9% (20/22) of patients reported being satisfied or very satisfied with their TTs. Additionally, the chewing efficiency of the transplantation side was on average 82.0% of that of the healthy side, with a significant difference between the two sides (P < 0.05). None of the potential predictors were found to significantly affect the success or survival of the transplanted tooth (TT). CONCLUSION The combination of extraoral apicoectomy and retrograde filling in TT showed promising outcomes, but further clinical cases and longer follow-up times are still required to validate the treatment plan.
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Affiliation(s)
- Fenglin Liao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hui Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihong Zhao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Biao Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
- Department of Endodontics,School and Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Haoyan Zhong
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China.
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2
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Lee H, Lee D. Assembling Molecular Clips To Build π-Stacks. Chemistry 2023; 29:e202302523. [PMID: 37658276 DOI: 10.1002/chem.202302523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/03/2023]
Abstract
Nature utilizes an intimate stacking of aromatic motifs to construct functional structures, as demonstrated in protein folding and polynucleotide assembly. However, organized π-stacks of artificial molecules are difficult to build, primarily due to the weak, non-directional, and context-sensitive nature of van der Waals forces. To overcome these challenges, chemists have invented ingenious architectural designs to construct π-stacked supramolecular assemblies using clip-like molecules. This Concept article focuses on molecular clips that enable precise spatial control over assembly patterns, beyond the scope of simple host-guest chemistry. Different design strategies are analyzed and compared that leverage non-covalent interactions to create multi-layer π-stacks. Particular emphasis is placed on the choice of spine units as they play a crucial role in controlling the (i) spacing, (ii) orientation, and (iii) conformational pre-organization of linked aromatics to achieve long-range spatial ordering.
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Affiliation(s)
- Hyun Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Dongwhan Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
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3
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Arévalo-Fester J, Briceño A. Insights into Selective Removal by Dye Adsorption on Hydrophobic vs Multivalent Hydrophilic Functionalized MWCNTs. ACS OMEGA 2023; 8:11233-11250. [PMID: 37008137 PMCID: PMC10061520 DOI: 10.1021/acsomega.2c08203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Hydrophilic functionalized carbon nanotubes (MWCNT-COOH) were developed via hydrothermal glucose-coated carbonization, mixing MWCNTs with glucose in different weight ratios. Methyl violet (MV), methylene blue (MB), alizarin yellow (AY), and methyl orange (MO) were used as dye models for adsorption studies. Comparative dye adsorption capacity onto the pristine (MWCNT-raw) and functionalized (MWCNT-COOH-11) CNTs was evaluated in aqueous solution. These results revealed that MWCNT-raw is capable of adsorbing either anionic or cationic dyes. In contrast, an induced selective cation dye adsorption capacity is significantly enhanced on multivalent hydrophilic MWCNT-COOH, in comparison to a pristine surface. This ability can be tuned to the selective adsorption of cations over anionic dyes or between anionic mixtures from binary systems. An insight into adsorbate-adsorbent interactions shows that hierarchical supramolecular interactions dominate the adsorption processes, which is ascribed to the chemical modification by switching from a hydrophobic to a hydrophilic surface, dye charge, temperature, and potential matching multivalent acceptor/donor capacity between chemical groups in the adsorbent interface. The dye adsorption isotherm and thermodynamics on both surfaces were also studied. Changes in the Gibbs free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) were evaluated. Thermodynamic parameters were endothermic on MWCNT-raw, whereas the adsorption process on MWCNT-COOH-11 revealed that adsorption processes were spontaneous and exothermic, accompanied by a significant reduction of entropy values as a consequence of a multivalent effect. This approach provides an eco-friendly, low-cost alternative for the preparation of supramolecular nanoadsorbents with unprecedented properties to achieve remarkable selective adsorption independent of the presence of intrinsic porosity.
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Affiliation(s)
- José Arévalo-Fester
- Instituto
Zuliano de Investigaciones Tecnológicas (INZIT), Km 15, La Cañada de Urdaneta, Estado Zulia 4001, Venezuela
- Instituto
Venezolano de Investigaciones Científicas (IVIC), Centro de
Química, Laboratorio de Síntesis y Caracterización
de Nuevos Materiales. P.O. Box 21817, Caracas 1020-A, Venezuela
| | - Alexander Briceño
- Instituto
Venezolano de Investigaciones Científicas (IVIC), Centro de
Química, Laboratorio de Síntesis y Caracterización
de Nuevos Materiales. P.O. Box 21817, Caracas 1020-A, Venezuela
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4
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Synthesis of Glycoluril Dimers with the Ability to Form Polymeric Self-Associates in Water. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Supramolecular self-assembly in water resulting in polymeric structures is emerging because of its potential in the preparation of adaptive materials with applications in biology and medicine. Here, we report the first example of host molecules based on glycoluril dimers, which self-associate into linear oligomers in water. The degree of polymerization for the resulting supramolecular aggregates was calculated using the isodesmic model and the Carothers equation. The model compound was prepared to enable a deeper understanding of the forces responsible for the self-association of the glycoluril dimer-based monomers in water.
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5
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Deng CL, Cheng M, Zavalij PY, Isaacs L. Thermodynamics of Pillararene•Guest Complexation: Blinded Dataset for the SAMPL9 Challenge. NEW J CHEM 2022; 46:995-1002. [PMID: 35250257 PMCID: PMC8896905 DOI: 10.1039/d1nj05209h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report an investigation of the complexation between a water soluble pillararene host (WP6) and a panel of hydrophobic cationic guests (G1 - G20) by a combination of 1H NMR spectroscopy and isothermal titration calorimetry in phosphate buffered saline. We find that WP6 forms 1:1 complexes with Ka values in the 104 - 109 M-1 range driven by favorable enthalpic contributions. This thermodynamic dataset serves as blinded data for the SAMPL9 challenge.
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Affiliation(s)
- Chun-Lin Deng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Ming Cheng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Peter Y Zavalij
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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6
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Bhosale SV, Al Kobaisi M, Jadhav RW, Morajkar PP, Jones LA, George S. Naphthalene diimides: perspectives and promise. Chem Soc Rev 2021; 50:9845-9998. [PMID: 34308940 DOI: 10.1039/d0cs00239a] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this review, we describe the developments in the field of naphthalene diimides (NDIs) from 2016 to the presentday. NDIs are shown to be an increasingly interesting class of molecules due to their electronic properties, large electron deficient aromatic cores and tendency to self-assemble into functional structures. Almost all NDIs possess high electron affinity, good charge carrier mobility, and excellent thermal and oxidative stability, making them promising candidates for applications in organic electronics, photovoltaic devices, and flexible displays. NDIs have also been extensively studied due to their potential real-world uses across a wide variety of applications including supramolecular chemistry, sensing, host-guest complexes for molecular switching devices, such as catenanes and rotaxanes, ion-channels, catalysis, and medicine and as non-fullerene accepters in solar cells. In recent years, NDI research with respect to supramolecular assemblies and mechanoluminescent properties has also gained considerable traction. Thus, this review will assist a wide range of readers and researchers including chemists, physicists, biologists, medicinal chemists and materials scientists in understanding the scope for development and applicability of NDI dyes in their respective fields through a discussion of the main properties of NDI derivatives and of the status of emerging applications.
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Affiliation(s)
- Sheshanath V Bhosale
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa-403 206, India.
| | - Mohammad Al Kobaisi
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Ratan W Jadhav
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa-403 206, India.
| | - Pranay P Morajkar
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa-403 206, India.
| | - Lathe A Jones
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Subi George
- New Chemistry Unit (NCU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur PO, Bangalore-560064, India
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7
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Higginbotham HF, Maniam S, Hsia T, Isaacs L, Langford SJ, Bell TDM. Self-assembled, optically-active {naphthalene diimide}U{cucurbit[8]uril} ensembles in an aqueous environment. Phys Chem Chem Phys 2021; 23:13434-13439. [PMID: 34105550 DOI: 10.1039/d1cp00659b] [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
Naphthalene diimides (NDIs) are shown to arrange spontaneously co-facially with cucurbit[8]uril (CB[8]) in an aqueous environment through purely non-covalent interactions. The resultant 2 : 2 supramolecular complex of NDI and CB[8] is highly fluorescent (>30 times more than the constituent NDIs) due to the formation of NDI-NDI excimers within the supramolecular complex.
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Affiliation(s)
| | - Subashani Maniam
- Applied Chemistry and Environmental Science, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
| | - Tina Hsia
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia.
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Steven J Langford
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering & Technology, Swinburne University of Technology, Victoria 3122, Australia.
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia.
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8
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Binding Properties of a Dinuclear Zinc(II) Salen-Type Molecular Tweezer with a Flexible Spacer in the Formation of Lewis Acid-Base Adducts with Diamines. INORGANICS 2021. [DOI: 10.3390/inorganics9060049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this paper we report the binding properties, by combined 1H NMR, optical absorption, and fluorescence studies, of a molecular tweezer composed of two Zn(salen)-type Schiff-base units connected by a flexible spacer, towards a series of ditopic diamines having a strong Lewis basicity, with different chain length and rigidity. Except for the 1,2-diaminoethane, in all other cases the formation of stable 1:1 Lewis acid-base adducts with large binding constants is demonstrated. For α,ω-aliphatic diamines, binding constants progressively increase with the increasing length of the alkyl chain, thanks to the flexible nature of the spacer and the parallel decreased conformational strain upon binding. Stable adducts are also found even for short diamines with rigid molecular structures. Given their preorganized structure, these latter species are not subjected to loss of degrees of freedom. The binding characteristics of the tweezer have been exploited for the colorimetric and fluorometric selective and sensitive detection of piperazine.
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9
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Heilmann M, Knezevic M, Piccini G, Tiefenbacher K. Understanding the binding properties of phosphorylated glycoluril-derived molecular tweezers and selective nanomolar binding of natural polyamines in aqueous solution. Org Biomol Chem 2021; 19:3628-3633. [PMID: 33908553 DOI: 10.1039/d1ob00379h] [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
A modular synthetic platform for the construction of flexible glycoluril-derived molecular tweezers was developed. The binding properties of four exemplary supramolecular hosts obtained via this approach towards 16 organic amines were investigated by means of 1H NMR titration. In this work, we compare the Ka values obtained this way with those of three structurally related molecular tweezers and provide a computational approach towards an explanation of the observed behavior of those novel hosts. The results showcase that certain structural modifications lead to very potent and selective binders of natural polyamines, with observed binding of spermine below 10 nM.
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Affiliation(s)
- Michael Heilmann
- University of Basel, Department of Chemistry, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Melina Knezevic
- University of Basel, Department of Chemistry, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - GiovanniMaria Piccini
- ETH Zurich, Department of Chemistry and Applied Biosciences, c/o USI campus, Via Guiseppe Buffi 13, 6900 Lugano, Switzerland
| | - Konrad Tiefenbacher
- University of Basel, Department of Chemistry, Mattenstrasse 24a, 4058 Basel, Switzerland. and ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
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10
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Shi Y, Laury ML, Wang Z, Ponder JW. AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. J Comput Aided Mol Des 2021; 35:79-93. [PMID: 33140208 PMCID: PMC7867568 DOI: 10.1007/s10822-020-00358-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022]
Abstract
As part of the SAMPL7 host-guest binding challenge, the AMOEBA force field was applied to calculate the absolute binding free energy for 16 charged organic ammonium guests to the TrimerTrip host, a recently reported acyclic cucurbituril-derived clip host structure with triptycene moieties at its termini. Here we report binding free energy calculations for this system using the AMOEBA polarizable atomic multipole force field and double annihilation free energy methodology. Conformational analysis of the host suggests three families of conformations that do not interconvert in solution on a time scale available to nanosecond molecular dynamics (MD) simulations. Two of these host conformers, referred to as the "indent" and "overlap" structures, are capable of binding guest molecules. As a result, the free energies of all 16 guests binding to both conformations were computed separately, and combined to produce values for comparison with experiment. Initial ranked results submitted as part of the SAMPL7 exercise had a mean unsigned error (MUE) from experimental binding data of 2.14 kcal/mol. Subsequently, a rigorous umbrella sampling reference calculation was used to better determine the free energy difference between unligated "indent" and "overlap" host conformations. Revised binding values for the 16 guests pegged to this umbrella sampling reference reduced the MUE to 1.41 kcal/mol, with a correlation coefficient (Pearson R) between calculated and experimental binding values of 0.832 and a rank correlation (Kendall τ) of 0.65. Overall, the AMOEBA results demonstrate no significant systematic error, suggesting the force field provides an accurate energetic description of the TrimerTrip host, and an appropriate balance of solvation and desolvation effects associated with guest binding.
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Affiliation(s)
- Yuanjun Shi
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Marie L Laury
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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11
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Wang J, Yang S, Zou Q, Wang H, Li H. X-ray structure of an unusual glycoluril derivative conformation: Structural analysis and influencing factors. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519820961019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The synthesis and X-ray structure of a novel glycoluril derivative are described. The crystal of the glycoluril derivative is obtained by slow evaporation in a refrigerator at about 5 °C. X-ray crystallographic analysis revealed that the compound crystallized in an unusual as conformation instead of the usual clip-shaped aa conformation. Structural analysis shows that the solvation effect, hydrogen bonding, and space-occupying effect influenced the crystallization conformation of the derivative. The X-ray crystallographic analysis in this work provides additional crystallographic evidence of the as conformation of the 3U glycoluril derivative and shows the effect of solvent water on the conformational behavior.
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Affiliation(s)
- Jungang Wang
- School of Chemical Engineering, Guizhou Minzu University, Guiyang, P.R. China
| | - Shanghui Yang
- School of Chemical Engineering, Guizhou Minzu University, Guiyang, P.R. China
| | - Qiling Zou
- School of Chemical Engineering, Guizhou Minzu University, Guiyang, P.R. China
| | - Huanjiang Wang
- School of Chemical Engineering, Guizhou Minzu University, Guiyang, P.R. China
| | - Hongqing Li
- School of Chemical Engineering, Guizhou Minzu University, Guiyang, P.R. China
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12
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Panshina SY, Ponomarenko OV, Bakibaev AA, Malkov VS. ANALYSIS OF XRD STRUCTURAL PARAMETERS OF GLYCOLURIL AND ITS DERIVATIVES. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620090012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Eggers DK, Fu S, Ngo DV, Vuong EH, Brotin T. Thermodynamic Contribution of Water in Cryptophane Host-Guest Binding Reaction. J Phys Chem B 2020; 124:6585-6591. [PMID: 32614599 PMCID: PMC10479154 DOI: 10.1021/acs.jpcb.0c05354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A detailed examination of binding thermodynamics is undertaken for the interaction between rubidium ion and a water-soluble cryptophane molecule using isothermal titration calorimetry. The equilibrium-binding quotient for this host-guest pair decreases with increasing product formation. When analyzed with a thermodynamic framework that considers water explicitly in the governing equation, the shift in equilibrium is ascribed to an unfavorable change in the free energy of solvation upon formation of the inclusion complex. A van't Hoff analysis of the binding data, as well as an observation of aggregation between inclusion complexes, suggests that charge-charge interactions between rubidium ion and the phenolate groups of the cryptophane host provide the driving force for association in water that overcomes a large and unfavorable change in solvent enthalpy.
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Affiliation(s)
- Daryl K. Eggers
- Department of Chemistry, San José State University, San José, CA 95192-0101, USA
| | - Sherry Fu
- Department of Chemistry, San José State University, San José, CA 95192-0101, USA
| | - Dominic V. Ngo
- Department of Chemistry, San José State University, San José, CA 95192-0101, USA
| | - Elizabeth H. Vuong
- Department of Chemistry, San José State University, San José, CA 95192-0101, USA
| | - Thierry Brotin
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
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14
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Herrera-España AD, Höpfl H, Morales-Rojas H. Boron-Nitrogen Double Tweezers Comprising Arylboronic Esters and Diamines: Self-Assembly in Solution and Adaptability as Hosts for Aromatic Guests in the Solid State. Chempluschem 2020; 85:548-560. [PMID: 32202393 DOI: 10.1002/cplu.201900717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/11/2019] [Indexed: 01/07/2023]
Abstract
The thermodynamic stability of 1 : 1 and 2 : 1 boron-nitrogen (B←N) adducts formed between aromatic boronic esters with mono- and diamines was studied in solution by NMR and UV-vis spectroscopy with association energies (ΔG°) ranging from -11 to -28 kJ mol-1 . The effect of different substituents in the boronic ester, the nature of the diamine linker, and the effect of the solvent was explored. Stable 2 : 1 B←N adducts with diamines such as 1,3-diaminopropane were produced in solutions of hydrogen-bonding acceptor solvents (acetonitrile and ethyl acetate), which can be isolated in the solid state as crystalline solvates, whereas the use of noncoordinating solvents such as 1,2-dichloroethane afforded mainly 1 : 1 B←N adducts. In suitable combinations, aromatic bis-pyridyl diamines produced stable 2 : 1 B←N adducts that were isolated either as solvent-free solids, solvates, or cocrystals. In these crystalline forms, double-tweezer hosts were observed with an exceptional syn/anti conformational guest-adaptability driven by simultaneous donor-acceptor and C-H⋅⋅⋅π interactions in the tweezer cavities, resembling preorganized covalent tweezer hosts. Interestingly, cocrystals with electron-rich guests such as tetrathiafulvalene and pyrene showed non-centrosymmetric crystal lattices with infinite π-stacked donor-acceptor columns.
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Affiliation(s)
- Angel D Herrera-España
- Centro de Investigaciones Químicas Instituto de Investigación en Ciencias Básicas y Aplicadas (IICBA), Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
| | - Herbert Höpfl
- Centro de Investigaciones Químicas Instituto de Investigación en Ciencias Básicas y Aplicadas (IICBA), Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
| | - Hugo Morales-Rojas
- Centro de Investigaciones Químicas Instituto de Investigación en Ciencias Básicas y Aplicadas (IICBA), Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
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15
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Yan Q, Liu W, Wen H, Zhibin X, Meng Z. A New Fluorescent Sensor for Fe
3+
Based on Glycoluril Molecular Clip. ChemistrySelect 2020. [DOI: 10.1002/slct.201904902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qiaoli Yan
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Wenjin Liu
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Hongliang Wen
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Xu Zhibin
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Zihui Meng
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
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16
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Heilmann M, Tiefenbacher K. A Modular Phosphorylated Glycoluril-Derived Molecular Tweezer for Potent Binding of Aliphatic Diamines. Chemistry 2019; 25:12900-12904. [PMID: 31348566 DOI: 10.1002/chem.201902556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/15/2019] [Indexed: 12/16/2022]
Abstract
A molecular tweezer based on a glycoluril-derived framework bearing four phosphate groups was synthesized and shown to be capable of binding organic amines in aqueous solution. This work reports the Ka values for 30 complexes of this molecular tweezer and amine guests, determined by means of 1 H NMR titrations. Both the hydrophobic cavity and the phosphate groups contribute to the binding. Bulkier molecules and molecules bearing negatively charged groups like carboxylates in amino acids bind less tightly due to a steric clash and coulombic repulsion. The narrow cavity and the strong ionic interactions of the phosphate groups with ammonium guests favor binding of aliphatic diamines. These binding properties clearly distinguish this system from structurally related molecular clips and tweezers.
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Affiliation(s)
- Michael Heilmann
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058, Basel, Switzerland
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
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17
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Trujillo P, González T, Brito JL, Briceño A. Surface Recognition Directed Selective Removal of Dyes from Aqueous Solution on Hydrophilic Functionalized Petroleum Coke Sorbents. A Supramolecular Perspective. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b02020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Pablo Trujillo
- Centro de Química, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21817, Caracas 1020-A, Venezuela
| | - Teresa González
- Centro de Química, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21817, Caracas 1020-A, Venezuela
| | - Joaquín L. Brito
- Centro de Química, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21817, Caracas 1020-A, Venezuela
- School of Chemical Sciences and Engineering, Yachay Tech University, Urcuqui 100119, Ecuador
| | - Alexander Briceño
- Centro de Química, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21817, Caracas 1020-A, Venezuela
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18
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Liu W, Lu X, Meng Z, Isaacs L. A glycoluril dimer-triptycene hybrid receptor: synthesis and molecular recognition properties. Org Biomol Chem 2019; 16:6499-6506. [PMID: 30155536 DOI: 10.1039/c8ob01575a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The strategic combination of the methylene bridged glycoluril dimer and triptycene skeletons delivers acyclic water soluble hybrid receptor 1 which is analogous to cucurbit[6]uril. The molecular recognition properties of host 1 toward hydrophobic cationic guests are investigated in detail by a combination of 1H NMR spectroscopy and isothermal titration calorimetry (ITC) studies. The fluorescence emission of 1 can be selectively and efficiently quenched upon the formation of 1·26 and 1·28 complexes.
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Affiliation(s)
- Wenjin Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, P. R. China
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19
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Bauer D, Andrae B, Gaß P, Trenz D, Becker S, Kubik S. Functionalisable acyclic cucurbiturils. Org Chem Front 2019. [DOI: 10.1039/c9qo00156e] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Functionalised acyclic cucurbiturils can be prepared in a straightforward fashion and provide access to a wide variety of substituted derivatives.
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Affiliation(s)
- Daniel Bauer
- Technische Universität Kaiserslautern
- Fachbereich Chemie - Organische Chemie
- 67663 Kaiserslautern
- Germany
| | - Beatrice Andrae
- Technische Universität Kaiserslautern
- Fachbereich Chemie - Organische Chemie
- 67663 Kaiserslautern
- Germany
| | - Patrick Gaß
- Technische Universität Kaiserslautern
- Fachbereich Chemie - Organische Chemie
- 67663 Kaiserslautern
- Germany
| | - Danjano Trenz
- Organic Chemistry II
- Saarland University
- 66123 Saarbrücken
- Germany
| | - Sabine Becker
- Technische Universität Kaiserslautern
- Fachbereich Chemie - Anorganische Chemie
- 67663 Kaiserslautern
- Germany
| | - Stefan Kubik
- Technische Universität Kaiserslautern
- Fachbereich Chemie - Organische Chemie
- 67663 Kaiserslautern
- Germany
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20
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Abstract
Two acyclic CB[n]-type hosts (1 and 2) which possess four 2° or 3° amide arms are reported; 1 and 2 are slightly soluble in water and do not self-associate. Host 2 has four 3° amide arms that exist as a mixture of E- and Z-isomers. 1H NMR was used to qualitatively investigate the binding properties of 1 and 2 which indicates they retain the essential binding features of macrocyclic CB[n] hosts (e.g. cavity binding of hydrophobic residues and portal binding of cationic groups). We measured the Ka values of 1 and 2 toward guests 6 - 12, methamphetamine, and fentanyl by ITC to evaluate their potential as in vivo sequestration agents. Neutral hosts 1 and 2 bind less tightly than tetraanionic hosts M1, ACB1, and ACB2. We attribute the lower Ka values to the absence of secondary ion-ion (ammonium•••sulfonate or ammonium•••carboxylate) electrostatic interactions for host•guest complexes of 1 and 2. The secondary amide functionality on 1 decreases affinity by formation of intramolecular NH•••O=C H-bonds. Tertiary amide host 2 binds even more weakly than 1 due to backfolding of the amide N-CH3-groups of 2 into its own cavity. The x-ray crystal structure of 2 supports this conclusion.
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Affiliation(s)
- Weijian Xue
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Peter Y Zavalij
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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21
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Ganapati S, Isaacs L. Acyclic cucurbit[n]urils capped with alkylene linkers: synthesis and molecular recognition properties. Supramol Chem 2018. [DOI: 10.1080/10610278.2018.1539228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shweta Ganapati
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, USA
| | - Lyle Isaacs
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, USA
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22
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Liu W, Lu X, Xue W, Samanta SK, Zavalij PY, Meng Z, Isaacs L. Hybrid Molecular Container Based on Glycoluril and Triptycene: Synthesis, Binding Properties, and Triggered Release. Chemistry 2018; 24:14101-14110. [PMID: 30044903 DOI: 10.1002/chem.201802981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/23/2018] [Indexed: 12/11/2022]
Abstract
We designed and synthesized a "hybrid" molecular container 1, which is structurally related to both cucurbit[n]uril (CB[n]) and pillar[n]arene type receptors. Receptor 1 was fully characterized by 1 H NMR, 13 C NMR, IR, MS and X-ray single crystal diffraction. The self-association behavior, host-guest recognition properties of 1, and the [salt] dependence of Ka were investigated in detail by 1 H NMR and isothermal titration calorimetry (ITC). Optical transmittance and TEM measurements provide strong evidence that receptor 1 undergoes co-assemble with amphiphilic guest C10 in water to form supramolecular bilayer vesicles (diameter 25.6±2.7 nm, wall thickness ≈3.5 nm) that can encapsulate the hydrophilic anticancer drug doxorubicin (DOX) and the hydrophobic dye Nile red (NR). The release of encapsulated DOX or NR from the vesicles can be triggered by hexamethonium (8 c) or spermine (10) which leads to the disruption of the supramolecular vesicles.
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Affiliation(s)
- Wenjin Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, P.R. China.,Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742, USA
| | - Xiaoyong Lu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742, USA
| | - Weijian Xue
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742, USA
| | - Soumen K Samanta
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742, USA
| | - Peter Y Zavalij
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742, USA
| | - Zihui Meng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, P.R. China
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742, USA
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23
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Ganapati S, Isaacs L. Acyclic Cucurbit[n]uril-type Receptors: Preparation, Molecular Recognition Properties and Biological Applications. Isr J Chem 2018; 58:250-263. [PMID: 29805180 PMCID: PMC5966040 DOI: 10.1002/ijch.201700098] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article traces the development of acyclic cucurbit[n]uril-type receptors with a focus on work from the Isaacs group. First, we describe the synthesis of methylene bridged glycoluril dimers capped with aromatic sidewalls which allowed us to probe the interconversion of the S- and C-shaped dimers which is a fundamental step in CB[n] formation. The C-shaped compounds were found to undergo discrete self-assembly (dimerization) in both water and organic solvents which lead us to investigate multicomponent self-sorting systems. We supressed the self-association of 8 by electrostatic repulsion in the putative dimer which allowed expression of its innate molecular recognition properties toward methylene blue and related planar cationic dyes. Longer glycoluril oligomers (trimer - hexamer, acyclic decamer) were prepared by starving the CB[n]-forming reaction of formaldehyde. The longer oligomers (e.g. 15 and 16) bind to alkylammonium ions in water ≈ 100-fold weaker than macrocyclic CB[n] highlighting the high preorganization of the acyclic but polycyclic framework. We prepared a wide variety of acyclic CB[n] compounds (wall variants, solubilizing group variants, linker variants) based on glycoluril trimer and tetramer. In particular, 26 and 27 have been shown to possess a wide variety of chemically and biologically interesting functions. For example, 26 was used to formulate the insoluble drug Albendazole and treat mice bearing SK-OV-3 xenograft tumors. Compound 27 binds tightly to the neuromuscular blocking agents rocuronium, vecuronium, and cisatracurium and acts as an in vivo reversal agent for these compounds in anesthetized rats. Container 27 was also found to modulate the hyperlocomotive effect of rats that had been treated with methamphetamine. Finally, 38 has been used as a cross reactive component of sensor arrays that are capable of classifying and quantifying cancer related nitroamines and a range of over the counter drugs. Overall, the work demonstrates that acyclic CB[n]-type compounds are nicely pre-organized and therefore retain the essential aspects of the recognition properties of macrocyclic CB[n] but allow for more straightforward tailoring of structure and solubility that enables a variety of chemically and biologically important applications.
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Affiliation(s)
- Shweta Ganapati
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA
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24
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Liu W, Johnson A, Smith BD. Guest Back-Folding: A Molecular Design Strategy That Produces a Deep-Red Fluorescent Host/Guest Pair with Picomolar Affinity in Water. J Am Chem Soc 2018; 140:3361-3370. [PMID: 29439578 DOI: 10.1021/jacs.7b12991] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
One of the major goals of modern supramolecular chemistry, with important practical relevance in many technical fields, is the development of synthetic host/guest partners with ultrahigh affinity and selectivity in water. Currently, most association pairs exhibit micromolar affinity or weaker, and there are very few host/guest systems with Ka > 109 M-1, apparently due to a barrier imposed by enthalpy/entropy compensation. This present study investigated the threading of a water-soluble tetralactam cyclophane by a deep-red fluorescent squaraine guest with flanking polyethylene glycol chains, an association process that is dominated by a highly favorable enthalpic driving force. A squaraine structure was rationally designed to permit guest back-folding as a strategy to greatly expand the hydrophobic surface area that could be buried upon complexation. Guided by computational modeling, an increasing number of N-benzyl groups were appended to the squaraine core, so that, after threading, the aromatic rings could fold back and stack against the cyclophane periphery. The final design iteration exhibited an impressive combination of fluorescence and supramolecular properties, including ratiometric change in deep-red emission, picomolar affinity ( Ka = 5.1 × 1010 M-1), and very rapid threading ( kon = 7.9 × 107 M-1 s-1) in water at 25 °C. Similar excellent behavior was observed in serum solution. A tangible outcome of this study is a new cyclophane/squaraine association pair that will be a versatile platform for many different types of fluorescence-based imaging and diagnostics applications. From a broader perspective, guest back-folding of aromatic groups is a promising new supramolecular stabilization strategy to overcome enthalpy/entropy compensation and produce ultrahigh affinity [2]pseudorotaxane complexes in water and biological media.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry , University of Notre Dame , 236 Nieuwland Science Hall , Notre Dame , Indiana 46556 , United States
| | - Andrew Johnson
- Division of Science , Lindsey Wilson College , 317 Fugitte Science Center , Columbia , Kentucky 42728 , United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry , University of Notre Dame , 236 Nieuwland Science Hall , Notre Dame , Indiana 46556 , United States
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25
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Jono K, Suzuki A, Akita M, Albrecht K, Yamamoto K, Yoshizawa M. A Polyaromatic Molecular Clip That Enables the Binding of Planar, Tubular, and Dendritic Compounds. Angew Chem Int Ed Engl 2017; 56:3570-3574. [PMID: 28225169 DOI: 10.1002/anie.201612489] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 12/27/2022]
Abstract
By the covalent linkage of two bent bisanthracene amphiphiles with a biphenyl spacer bearing hydrophilic pendants, we synthesized a new molecular clip with a C-shaped conformation. The molecular clip provides an acyclic, open cavity surrounded by four anthracene panels in water. In contrast to previous clip- and tweezers-like compounds as well as cage-shaped compounds, the C-shaped polyaromatic cavity displays unusual wide-ranging capturing abilities toward not only planar perylene-based pigments and cylindrical single-walled carbon nanotubes but also highly branched macromolecules (carbazole dendrimers).
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Affiliation(s)
- Keisuke Jono
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Akira Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Munetaka Akita
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Ken Albrecht
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Kimihisa Yamamoto
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
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26
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Jono K, Suzuki A, Akita M, Albrecht K, Yamamoto K, Yoshizawa M. A Polyaromatic Molecular Clip That Enables the Binding of Planar, Tubular, and Dendritic Compounds. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Keisuke Jono
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Akira Suzuki
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Munetaka Akita
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Ken Albrecht
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Kimihisa Yamamoto
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
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27
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Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des 2016; 31:1-19. [PMID: 27658802 DOI: 10.1007/s10822-016-9974-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/14/2016] [Indexed: 01/18/2023]
Abstract
The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein-ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods. Host-guest systems offer a valuable alternative class of test cases, as they exemplify noncovalent molecular recognition but are far smaller and simpler. As a consequence, host-guest systems have been part of the prior two rounds of SAMPL prediction exercises, and they also figure in the present SAMPL5 round. In addition to being blinded, and thus avoiding biases that may arise in retrospective studies, the SAMPL challenges have the merit of focusing multiple researchers on a common set of molecular systems, so that methods may be compared and ideas exchanged. The present paper provides an overview of the host-guest component of SAMPL5, which centers on three different hosts, two octa-acids and a glycoluril-based molecular clip, and two different sets of guest molecules, in aqueous solution. A range of methods were applied, including electronic structure calculations with implicit solvent models; methods that combine empirical force fields with implicit solvent models; and explicit solvent free energy simulations. The most reliable methods tend to fall in the latter class, consistent with results in prior SAMPL rounds, but the level of accuracy is still below that sought for reliable computer-aided drug design. Advances in force field accuracy, modeling of protonation equilibria, electronic structure methods, and solvent models, hold promise for future improvements.
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Affiliation(s)
- Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - David R Slochower
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Michael W Chiu
- Qualcomm Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David L Mobley
- Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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