Simple Functionalization of a Donor Monomer to Enhance Charge Transfer in Porous Polymer Networks for Photocatalytic Hydrogen Evolution

Porous polymer networks (PPNs) are promising candidates as photocatalysts for hydrogen production. Constructing a donor-acceptor structure is known to be an effective approach for improving photocatalytic activity. However, the process of how a functional group of a monomer can ensure photoexcited charges transfer and improve the hydrogen evolution rate (HER) has not yet been studied on the molecular level. Herein, we design and synthesize two kinds of triazatruxene (TAT)-based PPNs: TATR-PPN with a hexyl (R) group and TAT-PPN without the hexyl group, to understand the relationship between the presence of the functional group and charge transfer. The hexyl group on the TAT unit was found to ensure the transfer of photoexcited electrons from a donor unit to an acceptor unit and endowed the TATR-PPN with stable hydrogen production.

From truxenes to heterotruxenes: playing with heteroatoms and the symmetry of molecules

As a result of the modification of truxene, we can change the electronic structure or create multidimensional materials. Thus, the use of truxenes is very wide.

Functionalization at Nonperipheral Positions of Triazatruxene: Modular Construction of 1,6,11-Triarylated-Triazatruxenes for Potentially Organic Electronics and Optoelectronics

Functionalization from nonperipheral positions of triazatruxene is representing a challenge. Triarylation of the nonperipheral positions (1, 6, and 11) in triazatruxene scaffold has been achieved for the first time via two approaches. The transformations involve arylation/cyclotrimerization and cyclotrimerization/arylation sequences. POCl₃-mediated direct cyclotrimerization of oxindoles containing electron-deficient substituents on the aryl group at the C7-position resulted in the formation of 2-chloroindoles, whereas oxindoles containing electron-donating substituents gave the triazatruxenes. Furthermore, desired triazatruxenes were achieved through cyclotrimerization of 7-bromooxindole followed by coupling with arylboronic acids. NMR structural analysis exhibited that two of the suitably substituted oxindole and triazatuxene may have atropisomerism at room temperature. As a representative triazatruxene scaffold, the optoelectronic properties of 9a have also been studied via ultraviolet-visible (UV-vis) absorption spectra and fluorescence spectra of 9a thin films. Also, density functional theory calculation was realized to get knowledge about frontier molecular orbitals. In the light of the information obtained, an organic light-emitting diode (OLED) device utilizing 9a as an emissive layer was applied to obtain white emission. In brief, this study provides the first examples of the synthesis of triazatruxenes bearing aryl substituents at the nonperipheral positions as candidate compounds for organic electronics, optoelectronics, and material chemistry.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Learning to Model G-Quadruplexes: Current Methods and Perspectives

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.

DNA binding studies of novel diazatruxenones analogs as potential anticancer agents: Synthesis, antitumor investigation, DNA binding, SAR and molecular modeling calculation

A series of polycyclic skeleton of truxene and triazatruxene analogs has been synthesized and evaluated for antitumor and DNA binding activities. The synthesized structures were confirmed by different spectroscopic techniques such as IR, ¹HNMR, ¹³CNMR, and mass spectroscopy. The antitumor screening was performed adopting the NCI protocol against 60 different cell lines. Compounds 2 and 8 proved to be the most active ones among the other target compounds. In a trial to investigate the mechanism of action of the target compounds, DNA binding activity was also investigated. Compounds 3f, 4-8 exhibited good binding activity explaining their mechanism. In addition, molecular modeling studies were also performed for more clearance of the data obtained from the biological screening.

Toward Soluble 5,10-Diheterotruxenes: Synthesis and Reactivity of 5,10-Dioxatruxenes, 5,10-Dithiatruxenes, and 5,10-Diazatruxenes

The following work presents three general approaches allowing, for the first time, the synthesis of 5,10-diheterotruxene derivatives containing two identical heteroatoms, namely, oxygen OOC, nitrogen NNC, or sulfur SSC. Two of described pathways involve the photocyclization of the corresponding triene 2 as a key step leading to a heptacyclic aromatic system. The third approach is based on the acidic condensation between ninhydrin 14 and benzo[b]heteroole 15. Typical functionalizations of the 5,10-diheterotruxene core have also been presented. In addition, the article discusses the advantages and limitations of the three suggested paths for receiving specific 5,10-diheterotruxene derivatives because the universal method suitable for obtaining molecules with any type of heteroatoms is not known so far.

Triazatruxene-Rhodamine-Based Ratiometric Fluorescent Chemosensor for the Sensitive, Rapid Detection of Trivalent Metal Ions: Aluminium (III), Iron (III) and Chromium (III)

We investigated the ability of a novel triazatruxene-rhodamine-based (TAT-ROD) chemosensor to detect the trivalent metal ions aluminium (Al³⁺), iron (Fe³⁺) and chromium (Cr³⁺). Operating via the through-bond energy transfer (TBET) pathway, the chemosensor exhibited low detection limits of 23.0, 25.0 and 170.0 nM for Al³⁺, Fe³⁺ and Cr³⁺, respectively, along with high sensitivity and selectivity during a brief period (<15 s). The binding ratio of the chemosensor and trivalent metal ions achieved by Job's method was 3:1, and when we added ethylenediaminetetraacetic acid (EDTA), the sensing process reversed. Altogether, our TAT-ROD chemosensor marks the first triazatruxene-based colorimetric and fluorometric metal ion sensor reported in the literature.

Designing triazatruxene-based donor materials with promising photovoltaic parameters for organic solar cells

To address the increasing demand of efficient photovoltaic compounds for modern hi-tech applications, efforts have been made herein to design and explore triazatruxene-based novel donor materials with greater efficiencies. Five new molecules, namely M1-M5, were designed by structural modification of acceptor moiety (rhodanine-3-acetic acid) of well known experimentally synthesized JY05 dye (reference R), and their optoelectronic properties are evaluated to be used as donor molecules in organic solar cells. In these molecules M1-M5, triazatruxene acts as a donor unit and benzene spaced different end-capped moieties including 2-(4-(dicyanomethylene)-2-thioxothiazolidin-3-yl)acetic acid (A1), (E)-2-(4-(1-cyano-2-methoxy-2-oxoethylidene)-2-thioxothiazolidin-3-yl)acetic acid (A2), (Z)-2-(3'-ethyl-4'-oxo-2,2'-dithioxo-3',4'-dihydro-2'H,5H-[4,5'-bithiazolylidene]-3(2H)-yl)acetic acid (A3), (Z)-2-(4'-(dicyano-methylene)-3'-ethyl-2,2'-dithioxo-3',4'-dihydro-2'H,5H-[4,5'-bithiazol-ylidene]-3(2H)-yl)acetic acid (A4) and 2-((4Z,4'E)-4'-(1-cyano-2-methoxy-2-oxoethylidene)-3'-ethyl-2,2'-dithioxo-3',4'-dihydro-2'H,5H-[4,5'-bithiazolylidene]-3(2H)-yl)acetic acid (A5) respectively, as acceptor units. The electronic, photophysical and photovoltaic properties of the designed molecules M1-M5 have been compared with reference molecule R. All designed molecules exhibit reduced energy gap in the region of 1.464-2.008 eV as compared to reference molecule (2.509 eV). Frontier molecular orbital (FMO) surfaces confirm the transfer of charge from donor to acceptor units. All designed molecules M1-M5 exhibited an absorption spectrum in the visible region and they were broader as compared to that of reference R. Especially, M5 with highest λ max value 649.26 nm and lowest transition energy value 1.90 eV was accredited to the strong electron withdrawing end-capped acceptor moiety A5. The highest value of open circuit voltage (V oc) 1.02 eV with respect to HOMOdonor-LUMOBTP-4Cl was shown by M5 among all investigated molecules which was 0.15 V larger than reference molecule R. The designed molecule M5 is proven to be the best candidate for both electron and hole transport mobilities due to its smallest λ e (0.0212 eV) and λ h (0.0062 eV) values among all studied molecules.

An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex

Aberrant activation of RAS signalling pathways contributes to aggressive phenotypes of cancer cells. The RAS-targeted therapies for cancer, therefore, have been recognised to be effective; however, current developments on targeting RAS have not advanced due to structural features of the RAS protein. Here, we show that expression of NRAS, a major isoform of RAS, can be controlled by photo-irradiation with an anionic phthalocyanine, ZnAPC, targeting NRAS mRNA. In vitro experiments reveal that ZnAPC binds to a G-quadruplex-forming oligonucleotide derived from the 5'-untranslated region of NRAS mRNA even in the presence of excess double-stranded RNA, which is abundant in cells, resulting in selective cleavage of the target RNA's G-quadruplex upon photo-irradiation. In line with these results, upon photo-irradiation, ZnAPC decreases NRAS mRNA and NRAS expression and thus viability of cancer cells. These results indicate that ZnAPC may be a prominent photosensitiser for a molecularly targeted photodynamic therapy for cancer.

Efficient synthesis of 5-oxatruxene and the unusual influence of oxygen heteroatom on its physico-chemical properties

5-Oxatruxene presents new quality among the truxenes. It is a promising compound for the new class of optoelectronic materials.

Investigation of the interactions between methylene blue and intramolecular G-quadruplexes: an explicit distinction in electrochemical behavior

An explicit difference for binding affinity between MB and different intramolecular G-quadruplexes was quickly and easily obtained by an electrochemical method.

Triazatruxene radical cation: a trigonal class III mixed valence system

The highly symmetric and stable triazatruxene radical cation was generated chemically for the first time.

Efficiency enhancement of perovskite solar cells via incorporation of phenylethenyl side arms into indolocarbazole-based hole transporting materials

Small-molecule hole transporting materials based on an indolocarbazole core were synthesized and incorporated into perovskite solar cells, which displayed a power conversion efficiency up to 15.24%. The investigated hole transporting materials were synthesized in three steps from commercially available and relatively inexpensive starting materials without using expensive catalysts. Various electro-optical measurements (UV-vis, CV, hole mobility, DSC, TGA, ionization potential) have been carried out to characterize the new hole transporting materials.

Thermodynamics of binding of di- and tetrasubstituted naphthalene diimide ligands to DNA G-quadruplex

Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of G-quadruplex high order structures has become an important strategy to develop novel anticancer therapeutics. In this study four naphthalene diimide based ligands were analyzed in order to elucidate the principal factors determining contributions to G-quadruplex-ligand binding. Three possible modes of binding and their respective Gibbs free energies for two naphthalene diimide based di-N-alkylpyridinium substituted ligands have been determined using a molecular docking technique and compared to experimental results. The structures obtained from the molecular docking calculations, were analyzed using the ab initio based fragment molecular orbital (FMO) method in order to determine the major enthalpic contributions to the binding and types of interactions between the ligand and specific residues of the G-quadruplex. A computational methodology for the efficient and inexpensive ligand optimization as compared to fully ab initio methods based on the estimation of binding affinities of the naphthalene diimide derived ligands to G-quadruplex is proposed.

Xanthene and xanthone derivatives as G-quadruplex stabilizing ligands

Following previous studies on anthraquinone and acridine-based G-quadruplex ligands, here we present a study of similar aromatic cores, with the specific aim of increasing G-quadruplex binding and selectivity with respect to duplex DNA. Synthesized compounds include two and three-side chain xanthone and xanthene derivatives, as well as a dimeric “bridged” form. ESI and FRET measurements suggest that all the studied molecules are good G-quadruplex ligands, both at telomeres and on G-quadruplex forming sequences of oncogene promoters. The dimeric compound and the three-side chain xanthone derivative have been shown to represent the best compounds emerging from the different series of ligands presented here, having also high selectivity for G-quadruplex structures with respect to duplex DNA. Molecular modeling simulations are in broad agreement with the experimental data.

Design, synthesis, and anti-tumor activities of novel triphenylethylene-coumarin hybrids, and their interactions with Ct-DNA

Novel triphenylethylene-coumarin hybrid derivatives containing different amounts of amino side chains were designed and synthesized in good yields under microwave radiation. The derivatives 5b-d which possessed two amino side chains (except morpholinyl) showed a broad-spectrum and good anti-proliferative activity against five tumor cells and low cytotoxicity in osteoblast. UV-vis, fluorescence, and circular dichroism (CD) spectroscopies and thermal denaturation exhibited that compounds 10 c, 5c, and 13c bearing amino side chain (except morpholinyl) on 4-phenyl had significant interactions with Ct-DNA by the intercalative mode of binding. Structure-activity relationships (SARs) analysis suggested that the amino alkyl chain would play an important role both in the compounds against tumor cells proliferation and their interactions with DNA.

Light up G-quadruplex DNA with a [2.2.2]heptamethinecyanine dye

The interactions of a triangle-shaped [2.2.2]heptamethinecyanine dye 1, namely 1,5,7-tris-[3-methylbenzothiazol-2-yl]-[2.2.2]heptamethindiium, with quadruplex DNA were studied with photometric and fluorimetric titrations, thermal DNA denaturation, CD and (1)H-NMR spectroscopy. The ligand binds to the quadruplex DNA with moderate affinity (K = 8 × 10(5) M(-1)), mainly by terminal π stacking. Remarkably, the ligand 1 exhibits a selectivity for quadruplex DNA relative to duplex DNA. Whereas the cyanine dye is very weakly fluorescent in aqueous solution, the emission intensity increases by a factor of >100 upon association with quadruplex DNA. Thus, it is shown that trinuclear cyanine derivatives may be employed as selective probes for the fluorimetric detection of quadruplex DNA.

Energetics of ligand binding to G-quadruplexes

G-quadruplex ligands are potential anticancer agents as telomerase inhibitors and potential transcriptional regulators of oncogenes. The search for best-in-class drugs is addressed to identify small molecules able to promote and stabilize G-quadruplex structures. What features should the G-quadruplex ligands possess? They should have selective antiproliferative effects on cancer cells and induce telomerase inhibition or oncogene suppression. One of the main challenges in their design and synthesis is to make the ligands selective for G-quadruplex DNA. These features should be amplified by careful analyses of physico-chemical aspects of G-quadruplex-drug interactions. In particular, the study of the energetics of G-quadruplex-drug interactions can enhance drug design by providing thermodynamic parameters that give quantitative information on the biomolecular interactions important for binding. The main methodologies used to gain information on energetics of binding are based on spectroscopic or calorimetric principles. Spectroscopic techniques such as fluorescence and circular dichroism are rapid and cheap methods, but are not sufficient to characterize completely the thermodynamics of interaction. Calorimetric techniques such as isothermal titration calorimetry offer a direct measure of binding enthalpy, in addition to the stoichiometry and affinity constants. With the complete thermodynamic signature of drug-target interaction, dissecting the enthalpic and entropic components of binding is possible, which can be a useful aid to decision-making during drug optimization.

Mass spectrometry of G-quadruplex DNA: formation, recognition, property, conversion, and conformation

G-quadruplexes are special secondary structures formed from G-rich sequences of DNA, and have proven to play important roles in a number of biological systems, including the regulation of gene transcription and translation. The highly distinctive nature of G-quadruplex structures and their functions suggest that G-quadruplexes can act as novel targets for drug development. As a highly sensitive analytical tool, mass spectrometry has been widely used for the analysis of G-quadruplex structures. Electrospray-ionization mass spectrometry, in particular, has found captivating applications to probe interactions between small molecules and G-quadruplex DNA. In this review, we will discuss: (1) mass spectrometry probing of the formation, binding affinity, and stoichiometry between G-quadruplexes and small molecules; (2) stabilization and collision-dissociation behavior of G-quadruplex DNA; (3) the exploration of the equilibrium transfer between a G-quadruplex and duplex DNA; and (4) the ESI-MS analysis of the conversion of intramolecular and intermolecular G-quadruplexes. Finally, we will also introduce the application of new techniques in the analysis of G-quadruplex conformation, such as ion-mobility and infrared multiphoton-dissociation mass spectrometry. We believe that, with the new technical developments, mass spectrometry will play an unparalleled role in the analysis of the G-quadruplex structures.

Methods for investigating G-quadruplex DNA/ligand interactions

DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions.