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Dobšíková K, Taušová T, Fagan P, Paškanová N, Kuchař M, Čejka J, Setnička V. Solid-state vibrational circular dichroism: Methodology and application for amphetamine derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123486. [PMID: 37820493 DOI: 10.1016/j.saa.2023.123486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/22/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023]
Abstract
Amphetamine derivatives are considered most seized substances worldwide. In this study, solid-state vibrational circular dichroism (VCD) measurements of enantiomerically pure substances were performed for spectroscopic discrimination between (S)- and (R)-enantiomers. First, we have developed a universal experimental approach to obtain reliable and reproducible solid-state VCD spectra. First, the samples were prepared as pellets composed of mixtures of camphor as a model compound and a crystalline matrix powder. In order to obtain the best results without artifacts and with a maximum signal-to-noise ratio, the following experimental conditions were optimized: pellet thickness and diameter and sample rotation speed. The optimized parameters were then used for the analysis of amphetamine and its derivatives (methamphetamine and 3,4-methylendioxymethamphetamine). Our high-quality spectra and results suggest that solid-state VCD spectroscopy represents a cost-effective and easy-to-use method for the analysis of conformation changes and molecular packing in solid-state with potential applications in pharmaceutical and forensic practice.
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Affiliation(s)
- K Dobšíková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - T Taušová
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - P Fagan
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - N Paškanová
- Forensic Laboratory of Biologically Active Substances, Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - M Kuchař
- Forensic Laboratory of Biologically Active Substances, Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic; Psychedelic Research Centre, National Institute of Mental Health, Topolová 748, Klecany 250 67, Czech Republic
| | - J Čejka
- Department of Solid State Chemistry, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic
| | - V Setnička
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6 166 28, Czech Republic.
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2
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Van Lommel R, De Borggraeve WM, De Proft F, Alonso M. Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels. Gels 2021; 7:87. [PMID: 34287290 PMCID: PMC8293097 DOI: 10.3390/gels7030087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
Supramolecular gels form a class of soft materials that has been heavily explored by the chemical community in the past 20 years. While a multitude of experimental techniques has demonstrated its usefulness when characterizing these materials, the potential value of computational techniques has received much less attention. This review aims to provide a complete overview of studies that employ computational tools to obtain a better fundamental understanding of the self-assembly behavior of supramolecular gels or to accelerate their development by means of prediction. As such, we hope to stimulate researchers to consider using computational tools when investigating these intriguing materials. In the concluding remarks, we address future challenges faced by the field and formulate our vision on how computational methods could help overcoming them.
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Affiliation(s)
- Ruben Van Lommel
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F Leuven Chem & Tech, P.O. Box 2404, 3001 Leuven, Belgium;
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium;
| | - Wim M. De Borggraeve
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F Leuven Chem & Tech, P.O. Box 2404, 3001 Leuven, Belgium;
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium;
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium;
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3
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Mal M, Mandal D. Molecular Rotors as Guest Fluorophores Probing the Local Environment inside Host G4 Supramolecular Hydrogels. J Phys Chem B 2021; 125:219-230. [PMID: 33370116 DOI: 10.1021/acs.jpcb.0c07954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fluorescent molecular rotors with a high binding affinity toward the guanosine quartet (G4) were incorporated as guest fluorophores into host supramolecular hydrogels based on the self-assembly of G4 units, to probe the local environment. Torsional dynamics of the rotors were severely inhibited inside the hydrogels in comparison with aqueous solutions, although the hydrogels were composed of >95% water. Moreover, even though all the gels were rigid bodies with no spontaneous deformation or flow property at room temperature, torsional dynamics in G4 borate gels was found to be consistently several orders of magnitude slower than those in the other G4 gels, irrespective of the identity of the molecular rotor probe. This clear difference in the molecular mobilities of the guest fluorophore could be attributed to systematic differences in the internal structure between the two categories of host G4 hydrogels. In specific terms, the borate groups in G4 borate hydrogels serve as bridging units between separate G4 quadruplex strands, generating additional cross-links that reinforce the network structure of the gel. The results demonstrate that molecular rotors act as efficient fluorescent probes for the quantitative assessment of the molecular-level environment and dynamics inside the hydrogels, an aspect that is missed out by most other analytical methods that are routinely employed for studying them.
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Affiliation(s)
- Madhushree Mal
- Department of Chemistry, University of Calcutta, 92, APC Road, Kolkata 700009, India
| | - Debabrata Mandal
- Department of Chemistry, University of Calcutta, 92, APC Road, Kolkata 700009, India
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4
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Interaction of (G4)2 and (X4)2 DNA quadruplexes with Cu+, Ag+ and Au+ metal cations: a quantum chemical calculation on structural, energetic and electronic properties. Struct Chem 2019. [DOI: 10.1007/s11224-019-01421-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Chen M, Lin W, Hong L, Ji N, Zhao H. The Development and Lifetime Stability Improvement of Guanosine-Based Supramolecular Hydrogels through Optimized Structure. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6258248. [PMID: 31312660 PMCID: PMC6595390 DOI: 10.1155/2019/6258248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/12/2019] [Accepted: 04/24/2019] [Indexed: 02/05/2023]
Abstract
Guanosine is an important building block for supramolecular gels owing to the unique self-assembly property that results from the unique hydrogen bond acceptors and donor groups. Guanosine-derived supramolecular hydrogels have promise in the fields of drug delivery, targeted release, tissue engineering applications, etc. However, the property of poor longevity and the need for excess cations hinder the widespread applications of guanosine hydrogels. Although guanosine-derived supramolecular hydrogels have been reviewed previously by Dash et al., the structural framework of this review is different, as the modification of guanosine is described at the molecular level. In this review, we summarize the development and lifetime stability improvement of guanosine-based supramolecular hydrogels through optimized structure and elaborate on three aspects: sugar modification, base modification, and binary gels. Additionally, we introduce the concept and recent research progress of self-healing gels, providing inspiration for the development of guanosine-derived supramolecular hydrogels with longer lifespans, unique physicochemical properties, and biological activities.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Le Hong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ning Ji
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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6
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Villani G. Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere. ACS OMEGA 2018; 3:9934-9944. [PMID: 31459122 PMCID: PMC6644616 DOI: 10.1021/acsomega.8b01678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/09/2018] [Indexed: 05/17/2023]
Abstract
The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na+ and K+ ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM—CNR
(UOS Pisa), Area della Ricerca di Pisa, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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7
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Sato H, Yajima T, Yamagishi A. Stereochemical effects on dynamics in two-component systems of gelators with perfluoroalkyl and alkyl chains as revealed by vibrational circular dichroism. Phys Chem Chem Phys 2018; 20:3210-3215. [DOI: 10.1039/c7cp06264h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The VCD method was applied to the gelation processes of chiral two-component gel systems.
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Affiliation(s)
- Hisako Sato
- Graduated School of Science and Engineering
- Ehime University
- Matsuyama
- Japan
| | - Tomoko Yajima
- Faculty of Science
- Department of Chemistry
- Ochanomizu University
- Tokyo 112-8610
- Japan
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8
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Hashemnejad S, Huda MM, Rai N, Kundu S. Molecular Insights into Gelation of Di-Fmoc-l-Lysine in Organic Solvent-Water Mixtures. ACS OMEGA 2017; 2:1864-1874. [PMID: 31457548 PMCID: PMC6640949 DOI: 10.1021/acsomega.7b00108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/25/2017] [Indexed: 05/21/2023]
Abstract
Despite significant interest in molecular gels due to their intriguing structure formation through self-assembly and their stimuli-responsive behavior, our understanding of the gel formation mechanism of a low-molecular-weight gelator (LMWG) is incomplete. Here, we report a combined experimental and computational study on a LMWG, di-Fmoc-l-lysine, that has two aromatic moieties and multiple hydrogen bond donors and acceptors. Gelation in various organic solvent-water mixtures was obtained through the solvent-triggered technique. We show that an approach based on approximate cohesive energy density derived from density functional theory (DFT) calculations can capture the experimental solubility trend of LMWGs in different organic solvents. Furthermore, DFT calculations indicate parallel and helical structures to be the preferred structural motifs for gelator dimers. We believe that these motifs can potentially lead to fiber formation as observed with microscopy. Our work provides a relatively simple yet effective approach to quantify interactions between solvents and complex gelators that can help rationalize solubility and gelation behavior.
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Affiliation(s)
- Seyed
Meysam Hashemnejad
- Dave
C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Md Masrul Huda
- Dave
C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Neeraj Rai
- Dave
C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Santanu Kundu
- Dave
C. Swalm School of Chemical Engineering and Center for Advanced Vehicular Systems, Mississippi State University, Mississippi State, Mississippi 39762, United States
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9
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Abstract
Minima of the electric field and positions of K+ and Na+ (zero of the x-coordinate is the center of the cavity).
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici
- ICCOM – UOS Pisa
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
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10
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Vibrational and electronic circular dichroism as powerful tools for the conformational analysis of cationic antimicrobial peptides. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1807-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Corradini MG, Rogers MA. Molecular gels: improving selection and design through computational methods. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Peters GM, Davis JT. Supramolecular gels made from nucleobase, nucleoside and nucleotide analogs. Chem Soc Rev 2016; 45:3188-206. [PMID: 27146863 DOI: 10.1039/c6cs00183a] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supramolecular or molecular gels are attractive for various applications, including diagnostics, tissue scaffolding and targeted drug release. Gelators derived from natural products are of particular interest for biomedical purposes, as they are generally biocompatible and stimuli-responsive. The building blocks of nucleic acids (i.e. nucleobases, nucleosides, and nucleotides) are desirable candidates for supramolecular gelation as they readily engage in reversible, noncovalent interactions. In this review, we describe a number of organo- and hydrogels formed through the assembly of nucleosides, nucleotides, and their derivatives. While natural nucleosides and nucleotides generally require derivatization to induce gelation, guanosine and its corresponding nucleotides are well known gelators. This unique gelating ability is due to propensity of the guanine nucleobase to self-associate into stable higher-order assemblies, such as G-ribbons, G4-quartets, and G-quadruplexes.
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Affiliation(s)
- Gretchen Marie Peters
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, Stop A5300, Austin, Texas 78712-1224, USA.
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13
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Du X, Zhou J, Shi J, Xu B. Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials. Chem Rev 2015; 115:13165-307. [PMID: 26646318 PMCID: PMC4936198 DOI: 10.1021/acs.chemrev.5b00299] [Citation(s) in RCA: 1292] [Impact Index Per Article: 143.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Indexed: 12/19/2022]
Abstract
In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping address fundamental questions about the mechanisms or the consequences of the self-assembly of molecules, including low molecular weight ones. Finally, we provide a perspective on supramolecular hydrogelators. We hope that this review will serve as an updated introduction and reference for researchers who are interested in exploring supramolecular hydrogelators as molecular biomaterials for addressing the societal needs at various frontiers.
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Affiliation(s)
- Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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14
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Sato H, Yajima T, Yamagishi A. Chiroptical Studies on Supramolecular Chirality of Molecular Aggregates. Chirality 2015; 27:659-66. [DOI: 10.1002/chir.22482] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Hisako Sato
- Graduated of Science and Engineering; Ehime University; Matsuyama Japan
| | - Tomoko Yajima
- Department of Chemistry; Ochanomizu University; Tokyo Japan
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15
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Yajima T, Tabuchi E, Nogami E, Yamagishi A, Sato H. Perfluorinated gelators for solidifying fluorous solvents: effects of chain length and molecular chirality. RSC Adv 2015. [DOI: 10.1039/c5ra12656h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
With a purpose of solidifying fluorous solvents, a novel series of perfluorinated gelators based on 1,2-diaminocyclohexane (denoted as CFn: n = the number of carbon chain in perfluoroalkanoyl moiety) were developed.
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Affiliation(s)
- Tomoko Yajima
- Department of Chemistry
- Ochanomizu University
- Tokyo
- Japan
| | - Erika Tabuchi
- Department of Chemistry
- Ochanomizu University
- Tokyo
- Japan
| | - Emiko Nogami
- Department of Chemistry
- Ochanomizu University
- Tokyo
- Japan
| | | | - Hisako Sato
- Graduated School of Science and Engineering
- Ehime University
- Matsuyama
- Japan
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16
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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17
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Sato H, Yajima T, Yamagishi A. An intermediate state in gelation as revealed by vibrational circular dichroism spectroscopy. RSC Adv 2014. [DOI: 10.1039/c4ra02526a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Sato H, Nogami E, Yajima T, Yamagishi A. Terminal effects on gelation by low molecular weight chiral gelators. RSC Adv 2014. [DOI: 10.1039/c3ra44070b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Afrasiabi R, Kraatz HB. Small-Peptide-Based Organogel Kit: Towards the Development of Multicomponent Self-Sorting Organogels. Chemistry 2013; 19:15862-71. [DOI: 10.1002/chem.201303116] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Indexed: 11/06/2022]
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20
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Castaings A, Marchon JC, Cavagnat D, Buffeteau T. Conformational Equilibria of Bridled Chiroporphyrins in Solution Investigated by Vibrational Circular Dichroism. Chirality 2013; 25:480-6. [DOI: 10.1002/chir.22196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/10/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Castaings
- Laboratoire de Chimie Inorganique et Biologique (UMR E3 CEA-UJF); Institut Nanosciences et Cryogénie, CEA Grenoble; Grenoble France
| | - Jean-Claude Marchon
- Laboratoire de Chimie Inorganique et Biologique (UMR E3 CEA-UJF); Institut Nanosciences et Cryogénie, CEA Grenoble; Grenoble France
| | - Dominique Cavagnat
- Institut des Sciences Moléculaires; Université de Bordeaux 1 (CNRS UMR5255); Talence France
| | - Thierry Buffeteau
- Institut des Sciences Moléculaires; Université de Bordeaux 1 (CNRS UMR5255); Talence France
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21
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Goncharova I, Novotná J, Urbanová M. Stacked and continuous helical self-assemblies of guanosine monophosphates detected by vibrational circular dichroism. Anal Bioanal Chem 2012; 403:2635-44. [PMID: 22573058 DOI: 10.1007/s00216-012-6014-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/02/2012] [Accepted: 04/02/2012] [Indexed: 11/25/2022]
Abstract
The aim of this study was to characterize self-assembled structures of guanosine derivatives in aqueous solutions by vibrational circular dichroism (VCD) and electronic circular dichroism (ECD). Three guanosine derivatives were studied [5'-guanosine monophosphate (GMP), diphosphate (GDP), and triphosphate (GTP)] using a broad range of concentrations and various metal/guanosine ratios. VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. It can also help to determine the impact that the cations have, when added to the solution, on the versatile structures of guanine derivatives in terms of their association and disassociation. Based on the markedly different intensities and signs of the VCD signals observed for different concentrations of guanosine derivatives, we propose various structures based on guanine quartets for high guanosine concentrations and high K(+)/guanosine ratios (i.e., columnar helical organization of the quartets, which are rearranged into a continuous helix). We performed a degenerate coupled oscillator (DCO) calculation to interpret the VCD spectra obtained and how they vary during the assembly of guanosine derivatives. The calculations correctly predicted the VCD spectra and enabled us to identify the structures of the metal cation/guanosine monophosphate aggregates. ECD in the ultraviolet region was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the guanine derivative assemblies and the molecular systems studied here. These studies revealed that the VCD technique is a powerful new method for determining the structures of optically active guanosine motifs.
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Affiliation(s)
- Iryna Goncharova
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Czech Republic
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22
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Novotná J, Goncharova I, Urbanová M. Supramolecular arrangement of guanosine/5-guanosine monophosphate binary mixtures studied by methods of circular dichroism. Chirality 2012; 24:432-8. [PMID: 22517502 DOI: 10.1002/chir.22045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/23/2012] [Accepted: 02/28/2012] [Indexed: 11/10/2022]
Abstract
Self-assembly of molecules is one of the fundamental processes in biology and in supramolecular chemistry. Guanosine (Guo) and its derivatives are among the widely studied molecules because of self-assembly abilities. Their tetrameric associates are the nature of telomeric DNA, and furthermore they are fundamental building blocks of supramolecular reversible gels, which may arise in certain physical and chemical conditions. Although poorly soluble in water, Guo forms interesting structures with guanosine 5'-monophosphate salt (GMP) in the TRIS buffer. We used electronic circular dichroism and vibrational circular dichroism to describe the thermal response of gels formed by the Guo/GMP binary mixture. Using these complementary techniques suitable to study conformational changes of chiral compounds, we obtained information about the involvement of functional groups and weak interactions in the guanosine quartet (G(4)) and stacked G(4) structures.
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Affiliation(s)
- Jana Novotná
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
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Kohno K, Morimoto K, Manabe N, Yajima T, Yamagishi A, Sato H. Promotion effects of optical antipodes on the formation of helical fibrils: chiral perfluorinated gelators. Chem Commun (Camb) 2012; 48:3860-2. [PMID: 22398874 DOI: 10.1039/c2cc18164a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chiral gelator, RR- or SS-N,N'-diperfluorooctanoyl-1,2-diaminocyclohexane, gelated racemic 2-butanol. The gel was most stable at the racemic mixture, its stability lowered with the increase in the optical purity of the gelator. Notably, characteristic helically coiled fibrils were formed in the narrow region of enantiomer excess (ee = 0.2-0.4). Promotion effects of the antipodal enantiomers are proposed.
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Affiliation(s)
- Kazuhiro Kohno
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
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24
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Wu J, Fu Y, He Z, Han Y, Zheng L, Zhang J, Li W. Growth mechanisms of fluorescent silver clusters regulated by polymorphic DNA templates: a DFT study. J Phys Chem B 2012; 116:1655-65. [PMID: 22242908 DOI: 10.1021/jp206251v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The aggregation behaviors of silver atoms modulated by polymorphic DNA templates involving i-motif, G-quadruplex, and the Watson-Crick duplex, were investigated by using the density functional theory (DFT) calculations, combining with the experimental characterizations of CD, UV, fluorescence measurements and TEM, in order to understand the reason in the molecular level that polymorphic DNA templates affect the fluorescence emitting species of Ag nanomaterials. First, the affinity sites of silver ions on different DNA templates were analyzed by using DFT calculations, and the conformational variations of DNA templates caused by silver ions and atoms were disclosed. Second, the aggregation behaviors of silver atoms constrained by the polymorphic DNA templates were studied by DFT modeling, and distinct fluorescence property of nanosilvers templated by polymorphic DNA were evaluated using the time-dependent DFT calculations. It is illustrated that with the DNA template adopting i-motif or the duplex the silver atoms tend to aggregate inside the encapsulated spaces of nucleobases, and the formed silver nanoclusters are positively charged with high fluorescent spectral features; whereas with the template of the G-quadruplex the silver atoms are preferential to aggregate outside of the G-tetrad, which results in the formation of larger silver crystals without fluorescence property. The results obtained here are useful to explore the nucleation and growth mechanism of silver nanomaterials regulated by the structure-specific DNA templates, which is important to rational design of desirable fluorescent emitters for sensing in the field from biology to nanoscience.
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Affiliation(s)
- Jiangjiexing Wu
- Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
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25
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Setnička V, Hlaváček J, Urbanová M. Oligopeptide-porphyrin interactions studied by circular dichroism spectroscopy: the effect of metalloporphyrin axial ligands on peptide matrix conformation. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424608000650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Vibrational (VCD) and electronic circular dichroism (ECD) spectroscopies were used to investigate non-covalent interactions between the cationic tripeptide L-lysyl-L-alanyl-L-alanine (KAA) and the anionic porphyrin meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) in aqueous solution. Also studied were the interactions between KAA and the three metal derivatives of TPPS (copper(II), iron(III), and manganese(III)), each of which has a different number of axial ligands. VCD spectra in the amide I' ( C = O stretching vibration) region are extremely sensitive to peptide conformation, and, consequently, provide direct information about the conformational changes of host oligopeptide matrices caused by electrostatic interaction with guest porphyrin molecules. We found that pure KAA adopts a left-handed polyproline II (PPII) helical conformation when dissolved in aqueous solution at near-neutral pH values. When mixed with metal-free TPPS under the same conditions, VCD intensities were markedly reduced in the amide I' region and a new negative band was observed at 1634 cm−1; both findings indicating the transition of the PPII conformation into a less compact structure having similarities to β-sheet, herein termed a β-sheet-like conformation. In the case of the metal derivatives of TPPS studied, only variations in the VCD intensities in the amide I' region were observed. Compared to the results for pure KAA, the binding of Cu (II) TPPS , which has no axial ligand, resulted in the greatest decrease in amide I' VCD intensity. Nevertheless, the shape of a VCD spectrum characteristic for a PPII conformation was maintained, thereby indicating the presence of an “extended” PPII conformation in the Cu (II) TPPS -KAA complex. Conversely, Mn (III) TPPS , which has two axial ligands, did not significantly affect the PPII conformation of KAA in the Mn (III) TPPS -KAA complex. The effects of the metalation and axial ligation of TPPS on the conformation of KAA in peptide-porphyrin complexes are discussed, together with the results of our ECD study.
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Affiliation(s)
- Vladimír Setnička
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, Prague 6, 166 28, Czech Republic
| | - Jan Hlaváček
- Department of Natural Products, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, Prague 6, 166 10, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Technická 5, Prague 6, 166 28, Czech Republic
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26
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Sato H, Nakae T, Morimoto K, Tamura K. Critical effects of alkyl chain length on fibril structures in benzene-trans(RR)- or (SS)-N,N′-alkanoyl-1,2-diaminocyclohexane gels. Org Biomol Chem 2012; 10:1581-6. [DOI: 10.1039/c1ob06460f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Sato H, Sakurai T, Yamagishi A. Comparison of Vibrational Circular Dichroism between the Langmuir–Blodgett Films and Gels of 12-Hydroxyoctadecanoic Acid. CHEM LETT 2011. [DOI: 10.1246/cl.2011.25] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Buchs (née Levrand) B, Fieber W, Vigouroux-Elie F, Sreenivasachary N, Lehn JM, Herrmann A. Release of bioactive volatiles from supramolecular hydrogels: influence of reversible acylhydrazone formation on gel stability and volatile compound evaporation. Org Biomol Chem 2011; 9:2906-19. [DOI: 10.1039/c0ob01139h] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Taylor A, Taylor J, Watson GW, Boyd RJ. Electronic Energy Changes Associated with Guanine Quadruplex Formation: An Investigation at the Atomic Level. J Phys Chem B 2010; 114:9833-9. [DOI: 10.1021/jp912013k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexis Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Justine Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Graeme W. Watson
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
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30
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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31
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Kudo M, Hanashima T, Muranaka A, Sato H, Uchiyama M, Azumaya I, Hirano T, Kagechika H, Tanatani A. Identification of Absolute Helical Structures of Aromatic Multilayered Oligo(m-phenylurea)s in Solution. J Org Chem 2009; 74:8154-63. [DOI: 10.1021/jo901934r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mayumi Kudo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Takayuki Hanashima
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Atsuya Muranaka
- Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisako Sato
- Faculty of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency (JST), Japan
| | - Masanobu Uchiyama
- Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomoya Hirano
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroyuki Kagechika
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- PRESTO, Japan Science and Technology Agency (JST), Japan
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32
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Lopes LMF, Garcia AR, Fidalgo A, Ilharco LM. Encapsulation of ruthenium nitrosylnitrate and DNA purines in nanostructured sol-gel silica matrices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:10243-10250. [PMID: 19499946 DOI: 10.1021/la901046f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The interactions between DNA purines (guanine and adenine) and the ruthenium complex Ru(NO)(NO(3))(3) were studied within nanostructured silica matrices prepared by a two-step sol-gel process. By infrared analysis in diffuse reflectance mode, it was proved that encapsulation induces a profound modification on the complex, whereas guanine and adenine preserve their structural integrity. The complex undergoes nitrate ligand exchange and co-condenses with the silica oligomers, but the nitrosyl groups remain stable, which is an unusual behavior in Ru nitrosyl complexes. In turn, the doping molecules affect the sol-gel reactions and eventually the silica structure as it forms: the complex yields a microporous structure, and the purine bases are responsible for the creation of macropores due to hydrogen bonding with the silanol groups of the matrix. In a confined environment, the interactions are much stronger for the coencapsulated pair guanine complex. While adenine only establishes hydrogen bonds or van der Waals interactions with the complex, guanine bonds covalently to Ru by one N atom of the imidazole ring, which becomes strongly perturbed, resulting in a deformation of the complex geometry.
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Affiliation(s)
- Luís M F Lopes
- Centro de Quimica-Fisica Molecular (CQFM) and Institute of Nanoscience and Nanotechnology (IN), Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal
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33
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Buerkle LE, Li Z, Jamieson AM, Rowan SJ. Tailoring the properties of guanosine-based supramolecular hydrogels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:8833-8840. [PMID: 19371040 DOI: 10.1021/la900746w] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We demonstrate that very stable hydrogels can be formed in aqueous potassium chloride solution by mixing a well-known gelator (guanosine, G) with a nongelator of similar structure (2',3',5'-tri-O-acetylguanosine, TAcG), and through a variety of characterization methods including rheology, small-angle neutron scattering, differential scanning calorimetry, and atomic force microscopy, we report substantial progress toward elucidating the factors that control the structure and stability of this fibrous gel system. The results suggest that the tailorability, long lifetime stability, and thermomechanical behavior of these gels derives from a reduction in the driving force toward crystallization with increased hydrophobic (TAcG) content, accompanied by a simultaneous decrease in fiber length and an increase in fiber width.
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Affiliation(s)
- Lauren E Buerkle
- Department of Macromolecular Science and Engineering, Case Western Reserve University, 2100 Adelbert Road, Cleveland, Ohio 44106-7202, USA
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