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582 KiB

Open AccessArticle

Lessons from Chlorophylls: Modifications of Porphyrinoids Towards Optimized Solar Energy Conversion

by Dariusz Karcz, Bożena Boroń, Arkadiusz Matwijczuk, Justyna Furso, Jakub Staroń, Alicja Ratuszna and Leszek Fiedor

Molecules 2014, 19(10), 15938-15954; https://doi.org/10.3390/molecules191015938 - 3 Oct 2014

Cited by 43 | Viewed by 12481

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 S₁state 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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1628 KiB

Open AccessArticle

On Tuning the Fluorescence Emission of Porphyrin Free Bases Bonded to the Pore Walls of Organo-Modified Silica

by Rosa I. Y. Quiroz-Segoviano, Iris N. Serratos, Fernando Rojas-González, Salvador R. Tello-Solís, Rebeca Sosa-Fonseca, Obdulia Medina-Juárez, Carmina Menchaca-Campos and Miguel A. García-Sánchez

Molecules 2014, 19(2), 2261-2285; https://doi.org/10.3390/molecules19022261 - 21 Feb 2014

Cited by 31 | Viewed by 10044

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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765 KiB

Open AccessArticle

[15]aneN₄S: Synthesis, Thermodynamic Studies and Potential Applications in Chelation Therapy

by Nuno Torres, Sandrina Gonçalves, Ana S. Fernandes, J. Franco Machado, Maria J. Villa De Brito, Nuno G. Oliveira, Matilde Castro, Judite Costa and Maria F. Cabral

Molecules 2014, 19(1), 550-567; https://doi.org/10.3390/molecules19010550 - 3 Jan 2014

Cited by 2 | Viewed by 7994

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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2164 KiB

Open AccessArticle

Orbital Interaction and Electron Density Transfer in Pd^II([9]aneB₂A)L₂ Complexes: Theoretical Approaches

by Ock Keum Kwak, Mahreen Arooj, Yong-Jin Yoon, Euh Duck Jeong and Jong Keun Park

Molecules 2013, 18(10), 12687-12706; https://doi.org/10.3390/molecules181012687 - 14 Oct 2013

Cited by 1 | Viewed by 7850

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 a_1g(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 a_1g(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)

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991 KiB

Open AccessArticle

A Macrocyclic Peptide that Serves as a Cocrystallization Ligand and Inhibits the Function of a MATE Family Transporter

by Christopher J. Hipolito, Yoshiki Tanaka, Takayuki Katoh, Osamu Nureki and Hiroaki Suga

Molecules 2013, 18(9), 10514-10530; https://doi.org/10.3390/molecules180910514 - 30 Aug 2013

Cited by 43 | Viewed by 8866

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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1705 KiB

Open AccessArticle

A Lead (II) 3D Coordination Polymer Based on a Marine Cyclic Peptide Motif

by Subrata Chakraborty, Pooja Tyagi, Dar-Fu Tai, Gene-Hsiang Lee and Shie-Ming Peng

Molecules 2013, 18(5), 4972-4985; https://doi.org/10.3390/molecules18054972 - 26 Apr 2013

Cited by 10 | Viewed by 6525

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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504 KiB

Open AccessArticle

Evaluation of the Interaction between Long Telomeric DNA and Macrocyclic Hexaoxazole (6OTD) Dimer of a G-quadruplex Ligand

by Keisuke Iida, Satoki Majima, Takahiro Nakamura, Hiroyuki Seimiya and Kazuo Nagasawa

Molecules 2013, 18(4), 4328-4341; https://doi.org/10.3390/molecules18044328 - 12 Apr 2013

Cited by 32 | Viewed by 7298

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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1200 KiB

Open AccessReview

Macrocyclic Drugs and Synthetic Methodologies toward Macrocycles

by Xufen Yu and Dianqing Sun

Molecules 2013, 18(6), 6230-6268; https://doi.org/10.3390/molecules18066230 - 24 May 2013

Cited by 188 | Viewed by 16439

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)

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364 KiB

Open AccessReview

Dynamic Motion and Rearranged Molecular Shape of Heme in Myoglobin: Structural and Functional Consequences

by Saburo Neya

Molecules 2013, 18(3), 3168-3182; https://doi.org/10.3390/molecules18033168 - 11 Mar 2013

Cited by 8 | Viewed by 7734

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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