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Special Issue "Macrocyclic Chemistry"

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A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (30 November 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Jurriaan Huskens

Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, University of Twente, TNW/MNF, PO Box 217, 7500AE Enschede, The Netherlands
Website | E-Mail
Fax: +31 53 4894645
Interests: host-guest chemistry; cyclodextrins; multivalency; supramolecular surface chemistry; supramolecular materials; nanolithography; soft lithography

Special Issue Information

Dear Colleagues,

Macrocycles constitute the archetypical components of supramolecular chemistry. Many fundamental aspects of molecular recognition and supramolecular science have been and are being reveiled using macrocycles. From the start, both naturally occurring (e.g. cyclodextrins, porphyrins) as well as synthetic macrocycles (such as crown ethers, calixarenes, phthalocyanines) have been employed. Thermodynamic phenomena such as the chelate effect, multivalency and cooperativity, have been and still are topics of thorough investigation. Synthetic procedures have been developed in order to create macrocycles, such as high-dilution synthesis and template-directed synthesis, and to functionalize them in order to introduce functional groups at one or more positions selectively and/or to control the conformation of the macrocycle. Macrocycles are applied in ion and molecular sensing, metal ion protection in biomedical imaging, treatment of heavy metal waste streams, drug delivery and increase of drug efficacy, and many, many others. Modern topics of investigation encompass dynamic covalent chemistry with macrocycles to provide evolutionary amplification of optimal receptors, the design of vehicles for drug and gene delivery, and receptor-functionalized platforms as models for cell membrane interactions. These examples show that macrocylic chemistry is still and will remain a vibrant area of chemistry for the foreseeable future!

This special issue of Molecules welcomes previously unpublished manuscripts covering all aspects of natural and synthetic macrocycles including their design, synthesis, functionalization, molecular recognition, and applications.

Prof. Dr. Jurriaan Huskens
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs).

Keywords

  • macrocycles
  • macrocyclization
  • template synthesis
  • host-guest recognition
  • cation and anion recognition
  • neutral molecule recognition

Published Papers (9 papers)

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Research

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Open AccessArticle Lessons from Chlorophylls: Modifications of Porphyrinoids Towards Optimized Solar Energy Conversion
Molecules 2014, 19(10), 15938-15954; doi:10.3390/molecules191015938
Received: 21 April 2014 / Revised: 20 August 2014 / Accepted: 5 September 2014 / Published: 3 October 2014
Cited by 5 | PDF Full-text (582 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Practical applications of photosynthesis-inspired processes depend on a thorough understanding of the structures and physiochemical features of pigment molecules such as chlorophylls and bacteriochlorophylls. Consequently, the major structural features of these pigments have been systematically examined as to how they influence the S
[...] Read more.
Practical applications of photosynthesis-inspired processes depend on a thorough understanding of the structures and physiochemical features of pigment molecules such as chlorophylls and bacteriochlorophylls. Consequently, the major structural features of these pigments have been systematically examined as to how they influence the S1 state energy, lifetimes, quantum yields, and pigment photostability. In particular, the effects of the macrocyclic π-electron system, central metal ion (CMI), peripheral substituents, and pigment aggregation, on these critical parameters are discussed. The results obtained confirm that the π-electron system of the chromophore has the greatest influence on the light energy conversion capacity of porphyrinoids. Its modifications lead to changes in molecular symmetry, which determine the energy levels of frontier orbitals and hence affect the S1 state properties. In the case of bacteriochlorophylls aggregation can also strongly decrease the S1 energy. The CMI may be considered as another influential structural feature which only moderately influences the ground-state properties of bacteriochlorophylls but strongly affects the singlet excited-state. An introduction of CMIs heavier than Mg2+ significantly improves pigments' photostabilities, however, at the expense of S1 state lifetime. Modifications of the peripheral substituents may also influence the S1 energy, and pigments’ redox potentials, which in turn influence their photostability. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
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Open AccessArticle On Tuning the Fluorescence Emission of Porphyrin Free Bases Bonded to the Pore Walls of Organo-Modified Silica
Molecules 2014, 19(2), 2261-2285; doi:10.3390/molecules19022261
Received: 24 December 2013 / Revised: 29 January 2014 / Accepted: 7 February 2014 / Published: 21 February 2014
Cited by 6 | PDF Full-text (1628 KB) | HTML Full-text | XML Full-text
Abstract
A sol-gel methodology has been duly developed in order to perform a controlled covalent coupling of tetrapyrrole macrocycles (e.g., porphyrins, phthalocyanines, naphthalocyanines, chlorophyll, etc.) to the pores of metal oxide networks. The resulting absorption and emission spectra intensities in the UV-VIS-NIR range
[...] Read more.
A sol-gel methodology has been duly developed in order to perform a controlled covalent coupling of tetrapyrrole macrocycles (e.g., porphyrins, phthalocyanines, naphthalocyanines, chlorophyll, etc.) to the pores of metal oxide networks. The resulting absorption and emission spectra intensities in the UV-VIS-NIR range have been found to depend on the polarity existing inside the pores of the network; in turn, this polarization can be tuned through the attachment of organic substituents to the tetrapyrrrole macrocycles before bonding them to the pore network. The paper shows clear evidence of the real possibility of maximizing fluorescence emissions from metal-free bases of substituted tetraphenylporphyrins, especially when these molecules are bonded to the walls of functionalized silica surfaces via the attachment of alkyl or aryl groups arising from the addition of organo-modified alkoxides. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
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Open AccessArticle [15]aneN4S: Synthesis, Thermodynamic Studies and Potential Applications in Chelation Therapy
Molecules 2014, 19(1), 550-567; doi:10.3390/molecules19010550
Received: 2 December 2013 / Revised: 23 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014
PDF Full-text (765 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The purpose of this work was to synthesize and characterize the thiatetraaza macrocycle 1-thia-4,7,10,13-tetraazacyclopentadecane ([15]aneN4S). Its acid-base behaviour was studied by potentiometry at 25 °C and ionic strength 0.10 M in KNO3. The protonation sequence of this ligand was
[...] Read more.
The purpose of this work was to synthesize and characterize the thiatetraaza macrocycle 1-thia-4,7,10,13-tetraazacyclopentadecane ([15]aneN4S). Its acid-base behaviour was studied by potentiometry at 25 °C and ionic strength 0.10 M in KNO3. The protonation sequence of this ligand was investigated by 1H-NMR titration that also allowed the determination of protonation constants in D2O. Binding studies of [15]aneN4S with Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+ and Pb2+ metal ions were further performed under the same experimental conditions. The results demonstrated that this compound has a higher selectivity and thermodynamic stability for Hg2+ and Cu2+, followed by Ni2+. The UV-visible-near IR spectroscopies and magnetic moment data for the Co(II) and Ni(II) complexes indicated a tetragonal distorted coordination geometry for both metal centres. The value of magnetic moment and the X-band EPR spectra of the Cu(II) complex are consistent with a distorted square pyramidal geometry. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
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Open AccessArticle Orbital Interaction and Electron Density Transfer in PdII([9]aneB2A)L2 Complexes: Theoretical Approaches
Molecules 2013, 18(10), 12687-12706; doi:10.3390/molecules181012687
Received: 29 July 2013 / Revised: 13 September 2013 / Accepted: 29 September 2013 / Published: 14 October 2013
PDF Full-text (2164 KB) | HTML Full-text | XML Full-text
Abstract
The geometric structures of Pd-complexes {Pd([9]aneB2A)L2 and Pd([9]aneBAB)L2 where A = P, S; B = N; L = PH3, P(CH3)3, Cl}, their selective orbital interaction
[...] Read more.
The geometric structures of Pd-complexes {Pd([9]aneB2A)L2 and Pd([9]aneBAB)L2 where A = P, S; B = N; L = PH3, P(CH3)3, Cl}, their selective orbital interaction towards equatorial or axial (soft A…Pd) coordination of macrocyclic [9]aneB2A tridentate to PdL2, and electron density transfer from the electron-rich trans L-ligand to the low-lying unfilled a1g(5s)-orbital of PdL2 were investigated using B3P86/lanl2DZ for Pd and 6-311+G** for other atoms. The pentacoordinate endo-[Pd([9]aneB2A)(L-donor)2]2+ complex with an axial (soft A--Pd) quasi-bond was optimized for stability. The fifth (soft A--Pd) quasi-bond between the σ-donor of soft A and the partially unfilled a1g(5s)-orbital of PdL2 was formed. The pentacoordinate endo-Pd([9]aneB2A)(L-donor)2]2+ complex has been found to be more stable than the corresponding tetracoordinate endo-Pd complexes. Except for the endo-Pd pentacoordinates, the tetracoordinate Pd([9]aneBAB)L2 complex with one equatorial (soft A-Pd) bond is found to be more stable than the Pd([9]aneB2A)L2 isomer without the equatorial (A-Pd) bond. In particular, the geometric configuration of endo-[Pd([9]anePNP)(L-donor)2]2+ could not be optimized. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
Open AccessArticle A Macrocyclic Peptide that Serves as a Cocrystallization Ligand and Inhibits the Function of a MATE Family Transporter
Molecules 2013, 18(9), 10514-10530; doi:10.3390/molecules180910514
Received: 18 June 2013 / Revised: 24 August 2013 / Accepted: 27 August 2013 / Published: 30 August 2013
Cited by 17 | PDF Full-text (991 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The random non-standard peptide integrated discovery (RaPID) system has proven to be a powerful approach to discover de novo natural product-like macrocyclic peptides that inhibit protein functions. We have recently reported three macrocyclic peptides that bind to Pyrococcus furiosus multidrug and toxic compound
[...] Read more.
The random non-standard peptide integrated discovery (RaPID) system has proven to be a powerful approach to discover de novo natural product-like macrocyclic peptides that inhibit protein functions. We have recently reported three macrocyclic peptides that bind to Pyrococcus furiosus multidrug and toxic compound extrusion (PfMATE) transporter and inhibit the transport function. Moreover, these macrocyclic peptides were successfully employed as cocrystallization ligands of selenomethionine-labeled PfMATE. In this report, we disclose the details of the RaPID selection strategy that led to the identification of these three macrocyclic peptides as well as a fourth macrocyclic peptide, MaD8, which is exclusively discussed in this article. MaD8 was found to bind within the cleft of PfMATE’s extracellular side and blocked the path of organic small molecules being extruded. The results of an ethidium bromide efflux assay confirmed the efflux inhibitory activity of MaD8, whose behavior was similar to that of previously reported MaD5. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
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Open AccessArticle A Lead (II) 3D Coordination Polymer Based on a Marine Cyclic Peptide Motif
Molecules 2013, 18(5), 4972-4985; doi:10.3390/molecules18054972
Received: 26 March 2013 / Revised: 16 April 2013 / Accepted: 24 April 2013 / Published: 26 April 2013
Cited by 4 | PDF Full-text (1705 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-L-Ser-L-Pro-L-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network
[...] Read more.
The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-L-Ser-L-Pro-L-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network in the crystalline state. The polymerization of a heavy metal ion with a rigid asymmetric cyclic tetrapeptide represents the first example of a new class of macrocyclic complexes. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
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Open AccessArticle Evaluation of the Interaction between Long Telomeric DNA and Macrocyclic Hexaoxazole (6OTD) Dimer of a G-quadruplex Ligand
Molecules 2013, 18(4), 4328-4341; doi:10.3390/molecules18044328
Received: 12 March 2013 / Revised: 2 April 2013 / Accepted: 9 April 2013 / Published: 12 April 2013
Cited by 11 | PDF Full-text (504 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Macrocyclic hexaoxazole dimer of L2H2-6OTD-dimer (3) was newly synthesized as a telomeric G-quadruplex (G4) ligand, and interaction with long telomeric DNAs telo48, 72, and 96 was evaluated by means of electrophoresis mobility shift assay, CD spectra analysis, and CD melting experiments.
[...] Read more.
Macrocyclic hexaoxazole dimer of L2H2-6OTD-dimer (3) was newly synthesized as a telomeric G-quadruplex (G4) ligand, and interaction with long telomeric DNAs telo48, 72, and 96 was evaluated by means of electrophoresis mobility shift assay, CD spectra analysis, and CD melting experiments. The L2H2-6OTD-dimer (3) interacted with the long telomeric DNAs by inducing anti-parallel type G4 structure of each unit of 24 bases, i.e., (TTAGGG)4 sequences. Dimer 3 stabilizes long telomeric DNAs more efficiently than the corresponding monomer of L2H2-6OTD (2). It showed potent inhibitory activity against telomerase, with an IC50 value of 7.5 nm. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
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Review

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Open AccessReview Macrocyclic Drugs and Synthetic Methodologies toward Macrocycles
Molecules 2013, 18(6), 6230-6268; doi:10.3390/molecules18066230
Received: 3 April 2013 / Revised: 15 May 2013 / Accepted: 20 May 2013 / Published: 24 May 2013
Cited by 44 | PDF Full-text (1200 KB) | HTML Full-text | XML Full-text
Abstract
Macrocyclic scaffolds are commonly found in bioactive natural products and pharmaceutical molecules. So far, a large number of macrocyclic natural products have been isolated and synthesized. The construction of macrocycles is generally considered as a crucial and challenging step in the synthesis of
[...] Read more.
Macrocyclic scaffolds are commonly found in bioactive natural products and pharmaceutical molecules. So far, a large number of macrocyclic natural products have been isolated and synthesized. The construction of macrocycles is generally considered as a crucial and challenging step in the synthesis of macrocyclic natural products. Over the last several decades, numerous efforts have been undertaken toward the synthesis of complex naturally occurring macrocycles and great progresses have been made to advance the field of total synthesis. The commonly used synthetic methodologies toward macrocyclization include macrolactonization, macrolactamization, transition metal-catalyzed cross coupling, ring-closing metathesis, and click reaction, among others. Selected recent examples of macrocyclic synthesis of natural products and druglike macrocycles with significant biological relevance are highlighted in each class. The primary goal of this review is to summarize currently used macrocyclic drugs, highlight the therapeutic potential of this underexplored drug class and outline the general synthetic methodologies for the synthesis of macrocycles. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)
Open AccessReview Dynamic Motion and Rearranged Molecular Shape of Heme in Myoglobin: Structural and Functional Consequences
Molecules 2013, 18(3), 3168-3182; doi:10.3390/molecules18033168
Received: 18 February 2013 / Revised: 7 March 2013 / Accepted: 7 March 2013 / Published: 11 March 2013
Cited by 3 | PDF Full-text (364 KB) | HTML Full-text | XML Full-text
Abstract
Myoglobin, a simple oxygen binding protein, was reconstituted with various types of synthetic hemes to manipulate the heme-globin interactions. From the paramagnetic NMR analysis, small heme was found to rotate rapidly about the iron-histidine bond upon. This is a novel and typical example
[...] Read more.
Myoglobin, a simple oxygen binding protein, was reconstituted with various types of synthetic hemes to manipulate the heme-globin interactions. From the paramagnetic NMR analysis, small heme was found to rotate rapidly about the iron-histidine bond upon. This is a novel and typical example for the fluctuation of protein. The dynamic NMR analysis indicated that the 360° rotational rate of a small heme was 1,400 s−1 at room temperature. The X-ray analyses revealed that the tertiary structure of globin containing the smallest heme was closely similar to that of native protein despite extensive destruction of the specific heme-globin interactions. The functional analyses of O2 binding showed that the loose heme-globin contacts do not significantly affect the oxygen binding. On the other hand, the rearrangement of tetrapyrrole array and the non-planar deformation in porphyrin ring significantly affect the functional properties of myoglobin. These results, taken together, indicate that the essential factors to regulate the myoglobin function are hidden under the molecular shape of prosthetic group rather than in the nonbonded heme-globin contacts. Full article
(This article belongs to the Special Issue Macrocyclic Chemistry)

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