1
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Bowles J, Jähnigen S, Agostini F, Vuilleumier R, Zehnacker A, Calvo F, Clavaguéra C. Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases. Chemphyschem 2024; 25:e202300982. [PMID: 38318765 DOI: 10.1002/cphc.202300982] [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: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/07/2024]
Abstract
Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of the IR and VCD spectra is examined and found to be more demanding in the latter case. Comparisons with experimental frequencies are also provided for the condensed phases.
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Affiliation(s)
- Jessica Bowles
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Sascha Jähnigen
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Anne Zehnacker
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay UMR8214, 91405, Orsay, France
| | - Florent Calvo
- Université Grenoble Alpes, CNRS, LIPhy, 38000, Grenoble, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405, Orsay, France
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2
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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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3
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Bravin C, Mazzeo G, Abbate S, Licini G, Longhi G, Zonta C. Helicity control of a perfluorinated carbon chain within a chiral supramolecular cage monitored by VCD. Chem Commun (Camb) 2022; 58:2152-2155. [PMID: 35059695 DOI: 10.1039/d1cc06861j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Confinement within supramolecular systems is the leading technology to finely tune guest functional properties. In this communication we report the synthesis of a chiral supramolecular cage able to bias the helicity of a perfluorinated carbon chain hosted within the cage. We monitor the phenomenon of chiral induction by Vibrational Circular Dichroism (VCD) experiments complemented by DFT calculations over the possible conformers.
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Affiliation(s)
- Carlo Bravin
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova, PD, Italy.
| | - Giuseppe Mazzeo
- Department of Molecular and Translational Medicine, Università di Brescia, Viale Europa 11, 25123 Brescia, BS, Italy.
| | - Sergio Abbate
- Department of Molecular and Translational Medicine, Università di Brescia, Viale Europa 11, 25123 Brescia, BS, Italy.
| | - Giulia Licini
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova, PD, Italy.
| | - Giovanna Longhi
- Department of Molecular and Translational Medicine, Università di Brescia, Viale Europa 11, 25123 Brescia, BS, Italy.
| | - Cristiano Zonta
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova, PD, Italy.
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4
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An intensive and glow-type chemiluminescence of luminol-embedded, guanosine-derived hydrogel. Talanta 2021; 230:122351. [PMID: 33934799 DOI: 10.1016/j.talanta.2021.122351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 11/24/2022]
Abstract
In this paper, an intensive and glow-type chemiluminescence (CL) hydrogel was prepared by simultaneous incorporation of chemiluminescence reagent (luminol) and catalytic cofactor (hemin) into the scaffold of guanosine-derived hydrogel. The self-assembled hydrogel consisted of K+ stabilized hemin/G-quartet structures, showing significant enzyme-like activity to H2O2-mediated oxidation of luminol. After adding H2O2 into the hydrogel, blue light visible to naked eyes would come into being and last for over 8 h. The lasting-time CL emission of hydrogel was achieved due to a mechanism of slow-diffusion-controlled heterogeneous catalysis. Moreover, this self-assembled hydrogel performed a good response to H2O2 and the CL emission images could be recorded by smartphone. The hydrogel could remain excellent lifetime stability for months and the stable, enhanced and glow-type CL emission could improve the reliability and precision of CL detection, which has a promising application in cold light source and H2O2 detection of real biological samples.
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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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Boback K, Bacchi K, O’Neill S, Brown S, Dorsainvil J, Smith-Carpenter JE. Impact of C-Terminal Chemistry on Self-Assembled Morphology of Guanosine Containing Nucleopeptides. Molecules 2020; 25:E5493. [PMID: 33255230 PMCID: PMC7727710 DOI: 10.3390/molecules25235493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/16/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
Herein, we report the design and characterization of guanosine-containing self-assembling nucleopeptides that form nanosheets and nanofibers. Through spectroscopy and microscopy analysis, we propose that the peptide component of the nucleopeptide drives the assembly into β-sheet structures with hydrogen-bonded guanosine forming additional secondary structures cooperatively within the peptide framework. Interestingly, the distinct supramolecular morphologies are driven not by metal cation responsiveness common to guanine-based materials, but by the C-terminal peptide chemistry. This work highlights the structural diversity of self-assembling nucleopeptides and will help advance the development of applications for these supramolecular guanosine-containing nucleopeptides.
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Affiliation(s)
| | | | | | | | | | - Jillian E. Smith-Carpenter
- Department of Chemistry and Biochemistry, Fairfield University, 1073 N. Benson Rd, Fairfield, CT 06824, USA; (K.B.); (K.B.); (S.O.); (S.B.); (J.D.)
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7
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Xiao S, Paukstelis PJ, Ash RD, Zavalij PY, Davis JT. Drawing with Iron on a Gel Containing a Supramolecular Siderophore. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Songjun Xiao
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
| | - Paul J. Paukstelis
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
| | - Richard D. Ash
- Department of Geology University of Maryland College Park MD 20742 USA
| | - Peter Y. Zavalij
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
| | - Jeffery T. Davis
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
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8
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Xiao S, Paukstelis PJ, Ash RD, Zavalij PY, Davis JT. Drawing with Iron on a Gel Containing a Supramolecular Siderophore. Angew Chem Int Ed Engl 2019; 58:18434-18437. [DOI: 10.1002/anie.201910872] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Songjun Xiao
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
| | - Paul J. Paukstelis
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
| | - Richard D. Ash
- Department of Geology University of Maryland College Park MD 20742 USA
| | - Peter Y. Zavalij
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
| | - Jeffery T. Davis
- Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA
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9
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Thakur N, Sharma B, Bishnoi S, Jain S, Nayak D, Sarma TK. Biocompatible Fe3+ and Ca2+ Dual Cross-Linked G-Quadruplex Hydrogels as Effective Drug Delivery System for pH-Responsive Sustained Zero-Order Release of Doxorubicin. ACS APPLIED BIO MATERIALS 2019; 2:3300-3311. [DOI: 10.1021/acsabm.9b00334] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Neha Thakur
- Discipline of Chemistry, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Bhagwati Sharma
- Materials Research Centre, Malaviya National Institute of Technology Jaipur, Jaipur 302017, India
| | - Suman Bishnoi
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Siddarth Jain
- Discipline of Chemistry, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Debasis Nayak
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Tridib K. Sarma
- Discipline of Chemistry, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
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10
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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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11
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Chen CT, Liao YY, Salunke SB, Lin YH, Kuo TS. Directed Self-Assembly of C 4-Symmetric, Oxidovanadate-Centered, Vanadyl(V) Quadruplexes for Ba 2+- and Hg 2+-Specific Recognition, Transport, and Recovery. Inorg Chem 2018; 57:11511-11523. [PMID: 30183263 DOI: 10.1021/acs.inorgchem.8b01454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed assembly of loosely, Na+-bound, oxidovanadate-centered quartets of C4-symmetry from tailor-made chiral N-salicylidene-vanadyl(V) complexes, for the first time, allows for highly efficient Ba2+- or Hg2+-specific detection (by 51V NMR and VCD), transport (forming a unique helical capsule or a capped square planar complex, respectively), and green recovery from an aqueous phase containing 4 different alkaline earth ions or from at least 10 different metal ions of similar size and charge capacity into the CHCl3 layer without interference from oxa- or oxophilic ions like Mg2+, Ca2+, Cu2+, Cd2+, and Pb2+.
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Affiliation(s)
- Chien-Tien Chen
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan
| | - Yi-Ya Liao
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan
| | | | - Ya-Hui Lin
- National Taiwan Normal University , Taipei , Taiwan
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12
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Taniguchi T, Nakano K, Monde K. Stereochemistry (and Conformation) of Nucleosides and Their Synthetic Precursors by Vibrational Circular Dichroism. ACTA ACUST UNITED AC 2018; 72:7.29.1-7.29.9. [PMID: 29927125 DOI: 10.1002/cpnc.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The chemistry of artificial nucleosides is associated with the difficulties in the characterization of the stereochemistry and conformation of their furanose ring moiety. This unit describes how to use vibrational circular dichroism (VCD) spectroscopy to identify the three-dimensional structure of nucleosides. The experimental part of this protocol is dedicated to obtain a VCD spectrum of a sample with high S/N ratio. The computational part generally starts with a conformational search using molecular mechanics and the following structural optimization by density functional theory calculation. Then, theoretical VCD spectra of stable conformers are calculated and averaged on the basis of their Boltzmann population. Finally, the obtained experimental and theoretical VCD spectra are compared qualitatively or quantitatively. The agreement between these spectra leads to determination of the stereochemistry of the studied molecule. This protocol may also be useful for analyzing the conformation of nucleosides. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kie Nakano
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
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13
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Katoono R, Obara Y, Fujiwara K, Suzuki T. Enhanced circular dichroism at elevated temperatures through complexation-induced transformation of a three-layer cyclophane with dualistic dynamic helicity. Chem Sci 2018; 9:2222-2229. [PMID: 29719695 PMCID: PMC5897879 DOI: 10.1039/c7sc05242a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
When two planes stacked one above the other are twisted, they provide a dynamic pair of helical conformations with (M)- or (P)-helicity. We designed a three-layer cyclophane that consists of two such dynamic pairs: the top and middle planes, and the middle and bottom planes. Hence, several global conformations could be created for the overall molecule, e.g., double-helical forms with a pair with the same helicity [(M,M) or (P,P)], and a meso-like form with a pair with a different helicity (M,P). These conformations dynamically interconvert to each other in solution. Chiroptical properties were given by the helical-sense preference of the double-helical forms, which was brought about through complexation with a chiral hydrogen-bonding guest. In terms of the conformational energy in a complexed state, when a desirable relationship between double-helical and meso-like forms was attained, complexation-induced circular dichroism was enhanced at elevated temperatures and decreased at lowered temperatures.
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Affiliation(s)
- Ryo Katoono
- Department of Chemistry , Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan . ; ; Tel: +81 11 706 3396
| | - Yudai Obara
- Department of Chemistry , Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan . ; ; Tel: +81 11 706 3396
| | - Kenshu Fujiwara
- Department of Chemistry , Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan . ; ; Tel: +81 11 706 3396
| | - Takanori Suzuki
- Department of Chemistry , Faculty of Science , Hokkaido University , Sapporo 060-0810 , Japan . ; ; Tel: +81 11 706 3396
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Xiao S, Davis JT. G 4-quartet hydrogels from 5'-hydrazino-guanosine for the non-covalent and covalent remediation of contaminants from water. Faraday Discuss 2018; 209:97-112. [PMID: 29971308 DOI: 10.1039/c8fd00038g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The creation of supramolecular hydrogels from relatively simple building blocks demonstrates the power of molecular self-assembly to make functional materials. G4-quartet hydrogels are appealing for a number of applications, including the environmental remediation of pollutants in water. We find that the guanosine analog, 5'-deoxy-5'-hydrazinoguanosine (HG 2) self-assembles into a self-standing hydrogel in the presence of stoichiometric amounts (0.25 equiv.) of KCl. The higher water solubility of HG 2 (14.5 mM), compared to that of the parent compound G 1 (2.1 mM), likely contributes to its enhanced gelation. The structural basis for this HG 2·KCl hydrogel, confirmed by PXRD, IR and CD, is the G4·K+ quartet, which forms extended 1D ion-channel assemblies that entangle to give a stable and long-lived hydrogel. We also find that adding KCl to a saturated solution of HG 2 triggers the generation of colloidal G4·K+ assemblies in situ that selectively and efficiently binds the anionic dye naphthol blue black (NBB) over a cationic dye. In addition to this non-covalent electrostatic binding of anions, the nucleophilic 5'-hydrazino group in the HG 2·KCl hydrogel HG 2 enables the efficient absorption of propionaldehyde from both the gas phase and from water solution via the formation of covalent hydrazone linkages with the gel matrix.
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Affiliation(s)
- Songjun Xiao
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA.
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15
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Fagan P, Kocourková L, Tatarkovič M, Králík F, Kuchař M, Setnička V, Bouř P. Cocaine Hydrochloride Structure in Solution Revealed by Three Chiroptical Methods. Chemphyschem 2017; 18:2258-2265. [DOI: 10.1002/cphc.201700452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/31/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Patrik Fagan
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Lucie Kocourková
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Michal Tatarkovič
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - František Králík
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Martin Kuchař
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Vladimír Setnička
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Flemingovo náměstí 2 16610 Prague Czech Republic
- Departments of Analytical Chemistry and Chemistry of Natural Compounds and Forensic Laboratory of Biologically Active Substances; University of Chemistry and Technology; Technická 5 16628 Prague Czech Republic
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16
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Taniguchi T, Nakano K, Baba R, Monde K. Analysis of Configuration and Conformation of Furanose Ring in Carbohydrate and Nucleoside by Vibrational Circular Dichroism. Org Lett 2017; 19:404-407. [PMID: 28045273 DOI: 10.1021/acs.orglett.6b03626] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A reliable and convenient method for determining the configuration and conformation of the furanose ring in carbohydrates and nucleosides by vibrational circular dichroism (VCD) spectroscopy is described. Diastereomeric pairs of several furanose monosaccharides and nucleosides were prepared, and their VCD spectra were analyzed. The results revealed that VCD spectroscopy elucidates the equibrated state of the furanose ring puckers, which is often difficult to study by other techniques.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Kie Nakano
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Ryosuke Baba
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, and ‡Graduate School of Life Science, Hokkaido University , Kita 21 Nishi 11, Sapporo 001-0021, Japan
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17
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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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18
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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: 1266] [Impact Index Per Article: 140.7] [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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19
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Katoono R, Tanaka Y, Kusaka K, Fujiwara K, Suzuki T. Dynamic Figure Eight Chirality: Multifarious Inversions of a Helical Preference Induced by Complexation. J Org Chem 2015; 80:7613-25. [DOI: 10.1021/acs.joc.5b01206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryo Katoono
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Tanaka
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiichi Kusaka
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenshu Fujiwara
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takanori Suzuki
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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20
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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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21
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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: 277] [Impact Index Per Article: 27.7] [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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22
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Katoono R, Tanaka Y, Fujiwara K, Suzuki T. A Foldable Cyclic Oligomer: Chiroptical Modulation through Molecular Folding upon Complexation and a Change in Temperature. J Org Chem 2014; 79:10218-25. [PMID: 25265438 DOI: 10.1021/jo501883m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Ryo Katoono
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Tanaka
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenshu Fujiwara
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takanori Suzuki
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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23
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Katoono R, Kusaka K, Fujiwara K, Suzuki T. Controlled Dynamic Helicity of a Folded Macrocycle Based on a Bisterephthalamide with a Twofold Z-Shaped Structure. Chem Asian J 2014; 9:3182-7. [PMID: 25145967 DOI: 10.1002/asia.201402658] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Ryo Katoono
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo (Japan).
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24
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Wang Y, Lin HX, Chen L, Ding SY, Lei ZC, Liu DY, Cao XY, Liang HJ, Jiang YB, Tian ZQ. What molecular assembly can learn from catalytic chemistry. Chem Soc Rev 2014; 43:399-411. [DOI: 10.1039/c3cs60212e] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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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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26
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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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27
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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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28
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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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29
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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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30
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Kuang Y, Gao Y, Shi J, Lin HC, Xu B. Supramolecular hydrogels based on the epitope of potassium ion channels. Chem Commun (Camb) 2011; 47:8772-4. [PMID: 21701756 PMCID: PMC3526070 DOI: 10.1039/c1cc13115j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imparting aromatic-aromatic interactions to the potassium binding epitope affords a supramolecular hydrogelator that responds to the K(+) concentration by self-assembly into nanofibers of different widths and crosslinking patterns, which illustrates a simple approach to generate biomimic materials based on tunable, hierarchical self-assembly of small molecules.
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Affiliation(s)
| | | | | | | | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA. Fax: 781-736-2516; Tel: 781-736-5201
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31
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Andrushchenko V, Bouř P. Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides. Chirality 2011; 22 Suppl 1:E96-E114. [PMID: 21038400 DOI: 10.1002/chir.20872] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
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32
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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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33
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Barboiu M. Multistate and Phase Change Selection in Constitutional Multivalent Systems. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:33-53. [DOI: 10.1007/128_2011_196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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34
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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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35
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Bouchet A, Brotin T, Cavagnat D, Buffeteau T. Induced Chiroptical Changes of a Water-Soluble Cryptophane by Encapsulation of Guest Molecules and Counterion Effects. Chemistry 2010; 16:4507-18. [PMID: 20235244 DOI: 10.1002/chem.200902740] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Indexed: 11/07/2022]
Affiliation(s)
- Aude Bouchet
- Institut des Sciences Moléculaires (CNRS - UMR5255), Université Bordeaux 1, 351, Cours de la Libération, 33405 Talence (France), Fax: (+33) 540008402
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36
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Mihai S, Le Duc Y, Cot D, Barboiu M. Sol–gel selection of hybrid G-quadruplex architectures from dynamic supramolecular guanosine libraries. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/c0jm01248c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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37
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Barboiu M. Dynamic interactive systems: dynamic selection in hybrid organic–inorganic constitutional networks. Chem Commun (Camb) 2010; 46:7466-76. [DOI: 10.1039/c0cc00341g] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Li Y, Dong M, Otzen DE, Yao Y, Liu B, Besenbacher F, Mamdouh W. Influence of tunable external stimuli on the self-assembly of guanosine supramolecular nanostructures studied by atomic force microscope. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:13432-13437. [PMID: 19499943 DOI: 10.1021/la900640f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The self-assembly of guanosine (G) molecules on solid surfaces is investigated by tapping-mode atomic force microscopy (AFM) upon controlling and introducing external factors (stimuli) to the G stock solution such as incubation time, presence/absence of metal cations, and mechanical shaking. Surprisingly, at different stages of incubation time at room temperature and in the absence of any metal cations in the G stock solution, which are known to be one of the governing factors in forming G-nanostructures, two assembly pathways resulting into two distinct supramolecular nanostructures were revealed. Astonishingly, by introducing a mechanical shaking of the tube containing the G stock solution, one-dimensional (1D) wires of G molecules are observed by AFM, and very interestingly, novel "branched" supramolecular nanostructures are formed. We have also observed that the later branched G nanostructures can grow further into a two-dimensional (2D) thin film by increasing the incubation time of the G stock solution at room temperature after it is exposed to the external mechanical stimuli. The self-assembled nanostructures of G molecules are changed significantly by tuning the assembly conditions, which show that it is indeed possible to grow complex 2D nanostructures from simple nucleoside molecules.
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Affiliation(s)
- Yinli Li
- Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
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39
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Lena S, Masiero S, Pieraccini S, Spada GP. Guanosine hydrogen-bonded scaffolds: a new way to control the bottom-up realisation of well-defined nanoarchitectures. Chemistry 2009; 15:7792-7806. [PMID: 19421976 DOI: 10.1002/chem.200802506] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Over the last two decades, guanosine-related molecules have been of interest in different areas, ranging from structural biology to medicinal chemistry, supramolecular chemistry and nanotechnology. The guanine base is a multiple hydrogen-bonding unit, capable also of binding to cations, and fits very well with contemporary studies in supramolecular chemistry, self-assembly and non-covalent synthesis. This Concepts article, after reviewing on the diversification of self-organised assemblies from guanosine-based low-molecular-weight molecules, will mainly focus on the use of guanine moiety as a potential scaffold for designing functional materials of tailored physical properties.
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Affiliation(s)
- Stefano Lena
- Dipartimento di Chimica Organica A. Mangini, Alma Mater Studiorum-Università di Bologna, Via San Giacomo 11, 40126 Bologna, Italy
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40
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Aimé C, Tamoto R, Satoh T, Grelard A, Dufourc EJ, Buffeteau T, Ihara H, Oda R. Nucleotide-promoted morphogenesis in amphiphile assemblies: kinetic control of micrometric helix formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:8489-8496. [PMID: 19379002 DOI: 10.1021/la8043297] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Anionic nucleotides adenosine monophosphate or guanosine monophosphate interact with cationic vesicles, exchange with the counteranions of the amphiphiles in situ, and organize themselves at the membrane surfaces. Such organized nucleotides reciprocally transfer their chirality to membranes of nonchiral amphiphiles to induce the formation of right-handed micrometric helices on the time scale of hours. The kinetics of the nucleotide molecular organization and the formation of supramolecular helices was followed. We have shown that helix formation is a kinetic-dependent process that does not primarily result from ion exchange but from conformational reorganization and formation of weak interactions between confined nucleotides.
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Affiliation(s)
- Carole Aimé
- Institut Européen de Chimie et Biologie, UMR 5248 CBMN, CNRS-Université de Bordeaux - ENITAB, 2 rue Robert Escarpit, F-33607 Pessac, France
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41
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Mihai S, Cazacu A, Arnal-Herault C, Nasr G, Meffre A, van der Lee A, Barboiu M. Supramolecular self-organization in constitutional hybrid materials. NEW J CHEM 2009. [DOI: 10.1039/b908641m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Brizard A, Berthier D, Aimé C, Buffeteau T, Cavagnat D, Ducasse L, Huc I, Oda R. Molecular and supramolecular chirality in gemini-tartrate amphiphiles studied by electronic and vibrational circular dichroisms. Chirality 2009; 21 Suppl 1:E153-62. [DOI: 10.1002/chir.20790] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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C3-symmetrical self-assembled structures investigated by vibrational circular dichroism. Chirality 2008; 20:1016-22. [DOI: 10.1002/chir.20568] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Brotin T, Cavagnat D, Buffeteau T. Conformational changes in cryptophane having C1-symmetry studied by vibrational circular dichroism. J Phys Chem A 2008; 112:8464-70. [PMID: 18710194 DOI: 10.1021/jp804450w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Vibrational circular dichroism (VCD) measurements and density functional theory (DFT) calculations were used to obtain the absolute configuration of a cryptophane molecule having C1-symmetry (labeled cryptophane-H). This molecule exhibits chiroptical properties different from those published for cryptophane-A having D3-symmetry [Brotin et al. J. Am. Chem. Soc. 2006, 128, 5533-5540]. In particular, we have shown that the conformation of the aliphatic linkers is very dependent on the solvent used and its ability to enter (CDCl3 solution) or not (C2D2Cl4 solution) in the cryptophane cavity. Calculations performed at the DFT (B3PW91/6-31G*) level establish, besides the absolute configuration, the preferential anti and gauche conformations of the aliphatic linkers of the chloroform@cryptophane-H complex and the empty cryptophane-H molecule, respectively. Polarimetric measurements performed in several solvents reflect also the change of conformation of the bridges upon guest encapsulation.
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Affiliation(s)
- Thierry Brotin
- Laboratoire de Chimie de l'ENS-LYON (UMR 5182-CNRS), Ecole Normale Supérieure de Lyon, 69364 Lyon 07, France
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45
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Setnicka V, Nový J, Böhm S, Sreenivasachary N, Urbanová M, Volka K. Molecular structure of guanine-quartet supramolecular assemblies in a gel-state based on a DFT calculation of infrared and vibrational circular dichroism spectra. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:7520-7527. [PMID: 18553994 DOI: 10.1021/la800611h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The infrared (IR) and vibrational circular dichroism (VCD) spectra of guanosine-5'-hydrazide ( G-1), a powerful hydrogelator, have been measured and analyzed on the basis of ab initio modeling. B3LYP/6-31G** DFT calculations predict that G-1, forming a clear solution in deuterated DMSO, is present in monomeric form in this solvent, whereas strong gelation in a phosphate buffer is due to the formation of a guanine-quartet structure, ( G-1)4, in which the four G-1 are linked by hydrogen-bonded guanine moieties and stabilized by an alkali metal cation. The B3LYP/6-31G** IR and VCD spectra of the nearly planar G-quartet, whose structure is slightly distorted from the C4h symmetry, in which the G-bases interact via four Hoogsteen-type hydrogen bonds and a sodium cation is positioned in the middle of the G-quartet, are in very good agreement with the experimental spectra, indicating that this structure is the predominant structure in the gel state. The geometric parameters are discussed. This study is the first to use IR and VCD spectroscopies coupled with DFT calculations to elucidate the structure of a supramolecular species in a gel state and shows the VCD spectroscopy as a powerful method for investigating the structure of complex supramolecular self-assemblies where the use of other structural methods is limited.
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Affiliation(s)
- Vladimír Setnicka
- Institute of Chemical Technology, Technická 5, 166 28 Prague 6, Czech Republic
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46
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Graziano C, Masiero S, Pieraccini S, Lucarini M, Spada GP. A Cation-Directed Switch of Intermolecular Spin−Spin Interaction of Guanosine Derivatives Functionalized with Open-Shell Units. Org Lett 2008; 10:1739-42. [DOI: 10.1021/ol8003832] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carla Graziano
- Alma Mater Studiorum - Università di Bologna, Dipartimento di Chimica Organica “A. Mangini”, Via San Giacomo 11, I-40126 Bologna, Italy
| | - Stefano Masiero
- Alma Mater Studiorum - Università di Bologna, Dipartimento di Chimica Organica “A. Mangini”, Via San Giacomo 11, I-40126 Bologna, Italy
| | - Silvia Pieraccini
- Alma Mater Studiorum - Università di Bologna, Dipartimento di Chimica Organica “A. Mangini”, Via San Giacomo 11, I-40126 Bologna, Italy
| | - Marco Lucarini
- Alma Mater Studiorum - Università di Bologna, Dipartimento di Chimica Organica “A. Mangini”, Via San Giacomo 11, I-40126 Bologna, Italy
| | - Gian Piero Spada
- Alma Mater Studiorum - Università di Bologna, Dipartimento di Chimica Organica “A. Mangini”, Via San Giacomo 11, I-40126 Bologna, Italy
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47
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Nový J, Böhm S, Králová J, Král V, Urbanová M. Formation and temperature stability of G-quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations. Biopolymers 2008; 89:144-52. [PMID: 17960602 DOI: 10.1002/bip.20875] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Variations in the structure of d(GGGA)(5) oligonucleotide in the presence of Li(+), Na(+), and K(+) ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3-Lee-Yang-Parr functional at the 6-31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)(5) in the presence of Li(+) forms a nonplanar single tetramer, with angles of 102 degrees and 171 degrees between neighboring guanine bases. This tetramer changes its geometry at temperatures >50 degrees C, but does not form a quadruplex structure. In the presence of Na(+), the d(GGGA)(5) structure was optimized to almost planar tetramers with an angle of 177 degrees between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60 degrees C. The Hartree-Fock energies imply that d(GGGA)(5) prefers to form complexes with Na(+) rather than Li(+). The d(GGGA)(5) structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li(+) < Na(+) < K(+).
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Affiliation(s)
- Jakub Nový
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague, Czech Republic
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48
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Arnal-Hérault C, Pasc A, Michau M, Cot D, Petit E, Barboiu M. Functional G-quartet macroscopic membrane films. Angew Chem Int Ed Engl 2008; 46:8409-13. [PMID: 17912736 DOI: 10.1002/anie.200702605] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Carole Arnal-Hérault
- Adaptative Supramolecular Nanosystems, Institut Européen des Membranes, ENSCM/UM2/CNRS 5635, IEM/UM2, Place Eugène Bataillon, CC 047, 34095 Montpellier, France
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49
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Gottarelli G, Lena S, Masiero S, Pieraccini S, Spada GP. The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: An overview. Chirality 2008; 20:471-85. [DOI: 10.1002/chir.20459] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Arnal-Hérault C, Pasc A, Michau M, Cot D, Petit E, Barboiu M. Functional G-Quartet Macroscopic Membrane Films. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702605] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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