Synthesis and Self-Assembly of Donor-Acceptor-Donor Based Oligothiophenes and Their Optoelectronic Properties

In this work, the synthesis of an oligothiophene having a donor acceptor donor (D-A-D) chromophore with hydrogen bonding groups is described. The D-A-D molecule was demonstrated to self-organize via intermolecular H-bonding between barbituric acid units. Interactions between the oligothiophene subunits were also found to be important, affording nanoribbons that could be observed by atomic force and transmission electron microscopy. The applicability of the oligothiophene for organic electronic applications was investigated by fabricating organic field-effect transistors (OFETs) and organic photovoltaic devices. The OFET measurements yielded p-type mobility of 7 x 10(-7) cm(2)/(Vs), and when blended with C(60)-PCBM, the photovoltaic efficiency was observed to be 0.18%.

Synthesis and DNA binding studies of Ni(II), Co(II), Cu(II) and Zn(II) metal complexes of N(1),N(5)-bis[pyridine-2-methylene]-thiocarbohydrazone Schiff-base ligand

The thiocarbohydrazone Schiff-base ligand with a nitrogen and sulphur donor was synthesized through condensation of pyridine-2-carbaldehyde and thiocarbohydrazide. Schiff-base ligands have the ability to conjugate with metal salts. A series of metal complexes with a general formula [MCl(2)(H(2)L)]center dot nH(2)O (M=Ni, Co, Cu and Zn) were synthesized by forming complexes of the N(1),N5-bis[pyridine-2-methylene]thiocarbohydrazone (H2L) Schiff-base ligand. These metal complexes and ligand were characterized by using ultraviolet-visible (UV-Vis), Fourier Transform Infrared (FT-IR), (1)H and (13)C NMR spectroscopy and mass spectroscopy, physicochemical characterization, CHNS and conductivity. The biological activity of the synthesized ligand was investigated by using Escherichia coli DNA as target. The DNA interaction of the synthesized ligand and complexes on E. coli plasmid DNA was investigated in the aqueous medium by UV-Vis spectroscopy and the binding constant (K(b)) was calculated. The DNA binding studies showed that the metal complexes had an improved interaction due to trans-geometrical isomers of the complexes than ligand isomers in cis-positions. (C) 2011 Elsevier B.V. All rights reserved.

Influence of the highest occupied molecular orbital energy level of the donor material on the effectiveness of the anode buffer layer in organic solar cells

Efficiency of organic photovoltaic cells based on organic electron donor/organic electron acceptor junctions can be strongly improved when the transparent conductive Anode is coated with a Buffer Layer (ABL). Here, the effects of a metal (gold) or oxide (molybdenum oxide) ABL are reported, as a function of the Highest Occupied Molecular Orbital (HOMO) of different electron donors. The results indicate that a good matching between the work function of the anode and the highest occupied molecular orbital of the donor material is the major factor limiting the hole transfer efficiency. Indeed, gold is efficient as ABL only when the HOMO of the organic donor is close to its work function Phi(Au). Therefore we show that the MoO(3) oxide has a wider field of application as ABL than gold. (C) 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Cu(II)-azide polymers with various molar equivalents of blocking diamine ligands: synthesis, structures, magnetic properties with DFT studies

Four new neutral copper-azido polymers [Cu(4)(N(3))(8)(Me-hmpz)(2)](n) (1), [Cu(4)(N(3))(8)(men)(2)](n) (2), [Cu(5)(N(3))(10)(N,N-dmen)(2)](n) (3) and [Cu(5)(N(3))(10)(N,N'-dmen)(5)](n) (4) [Me-hmpz = 1-methylhomopiperazine; men = N-methylethylenediamine; N, N-dmen = N, N-dimethylethylenediamine and N, N'-dmen = N, N'-dimethylethylenediamine] have been synthesized by using various molar equivalents of the chelating diamine ligands with Cu(NO(3))(2)center dot 3H(2)O and an excess of NaN(3). Single-crystal X-ray structures show that the basic asymmetric units of 1 and 2 are very similar, but the overall 1D structures were found to be quite different. Complex 3 with a different composition was found to be 2D in nature, while the 1D complex 4 with 1 : 1 metal to diamine ratio presented several new structural features. Cryomagnetic susceptibility measurements over a wide range of temperature were corroborated with density functional theory calculations (B3LYP functional) performed on the complexes 1-3 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands

The enzyme telomerase synthesizes the G-rich DNA strands of the telomere and its activity is often associated with cancer. The telomerase may be therefore responsible for the ability of a cancer cell-to escape apoptosis. The G-rich DNA sequences often adopt tetra-stranded structure, known as the G-quadruplex DNA (G4-DNA). The stabilization of the telomeric DNA into the G4-DNA structures by small molecules has been the focus of many researchers for the design and development of new anticancer agents. The compounds which stabilize the G-quadruplex in the telomere inhibit the telomerase activity. Besides telomeres, the G4-DNA forming sequences are present in the genomic regions of biological significance including the transcriptional regulatory and promoter regions of several oncogenes. Inducing a G-quadruplex structure within the G-rich promoter sequences is a potential way of achieving selective gene regulation. Several G-quadruplex stabilizing ligands are known. Minor groove binding ligands (MGBLs) interact with the double-helical DNA through the minor grooves sequence-specifically and interfere with several DNA associated processes. These MGBLs when suitably modified switch their preference sometimes from the duplex DNA to G4-DNA and stabilize the G4-DNA as well. Herein, we focus on the recent advances in understanding the G-quadruplex structures, particularly made by the human telomeric ends, and review the results of various investigations of the interaction of designed organic ligands with the G-quadruplex DNA while highlighting the importance of MGBL-G-quadruplex interactions.

Binding of BIS like and other ligands with the GSK-3 beta kinase: a combined docking and MM-PBSA study

Binding of several bisindolylmaleimide (BIS) like (BIS-3, BIS-8 and UCN1) and other ligands (H89, SB203580 and Y27632) with the glycogen synthase kinase-3 (GSK-3 beta) has been studied using combined docking, molecular dynamics and Poisson-Boltzmann surface area analysis approaches. The study generated novel binding modes of these ligands that can rationalize why some ligands inhibit GSK-3 beta while others do not. The relative binding free energies associated with these binding modes are in agreement with the corresponding measured specificities. This study further provides useful insight regarding possible existence of multiple conformations of some ligands like H89 and BIS-8. It is also found that binding modes of BIS-3, BIS-8 and UCN1 with GSK-3 beta and PDK1 kinases are similar. These new insights are expected to be useful for future rational design of novel, more potent GSK-3 beta-specific inhibitors as promising therapeutics.

First-Principles Study of the Effect of Organic Ligands on the Crystal Structure of CdS Nanoparticles

We show with the aid of first-principles electronic structure calculations that suitable choice of the capping ligands may be an important control parameter for crystal structure engineering of nanoparticles. Our calculations on CdS nanocrystals reveal that the binding energy of model trioctylphosphine molecules on the (001) facets of zincblende nanocrystals is larger compared to that on wurtzite facets. Similarly, the binding energy of model cis-oleic acid is found to be dominant for the (10 (1) over bar0) facets of wurtzite structure. As a consequence, trioctylphosphine as a capping agent stabilizes the zincblende structure while cis-oleic acid stabilizes the wurtzite phase by influencing the surface energy, which has a sizable contribution to the energetics of a nanocrystal. Our detailed analysis suggests that the binding of molecules on the nanocrystalline facets depends on the surface topology of the facets, the coordination of the surface atoms where the capping molecule is likely to attach, and the conformation of the capping molecule.

Coordination-Driven Self-Assembly of 2D-Metallamacrocycles Using a New Carbazole-Based Dipyridyl Donor: Synthesis, Characterization, and C-60 Binding Study

A new carbazole-based 90 degrees dipyridyl donor 3,6-di(4-pyridylethynyl)carbazole (L) containing carbazole-ethynyl functionality is synthesized in reasonable yield using the Sonagashira coupling reaction. Multinuclear NMR, electrospray ionization-mass spectrometry (ESI-MS), including single crystal X-ray diffraction analysis characterized this 90 degrees building unit. The stoichiometry combination of L with several Pd(II)/Pt(II)-based 90 degrees acceptors (1a-1d) yielded 2 + 2] self-assembled metallacycles (2a-2d) under mild conditions in quantitative yields 1a = cis-(dppf)Pd(OTf)(2); 1b = cis-(dppf)Pt(OTf)(2); 1c = cis-(tmen)Pd(NO3)(2); 1d = 3,6-bis{trans-Pt(C C) (PEt3)(2)(NO3))carbazole]. All these macrocycles were characterized by various spectroscopic techniques, and the molecular structure of 2a was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of ethynyl functionality to the carbazole backbone causes the resulted macrocycles (2a-2d) to be pi-electron rich and thereby exhibit strong emission characteristics. The macrocycle 2a has a large internal concave aromatic surface. The fluorescence quenching study suggests that 2a forms a similar to 1:1 complex with C-60 with a high association constant of K-sv = 1.0 X 10(5) M-1.

Molecular Docking Studies of Novel Palmitoyl-ligands for Cyclooxygenase-2

An in silico approach was adopted to identify potential cyclooxygenase-2 inhibitors through molecular docking studies. The in vivo studies indicated that synthetic palmitoyl derivatives of salicylic acid, para amino phenol, para amino benzoic acid, and anthranilic acid possessed significant pharmacological activities like anti-inflammatory, analgesic, and antipyretic activities. None of the tested substances produced any significant gastric lesions in experimental animals. In an attempt to understand the ligandprotein interactions in terms of the binding affinity, the above synthetic molecules were subjected to docking analysis using AutoDock. The palmitoyl derivatives palmitoyl anthranilic acid, palmitoyl para amino benzoic acid, palmitoyl para amino phenol, and palmitoyl salicylic acid showed better binding energy than the known inhibitor diclofenac bound to 1PXX. All the palmitoyl derivatives made similar interactions with the binding site residues of cyclooxygenase-2 as compared to that of the known inhibitor. Thus, structure-based drug discovery approach was successfully employed to identify some promising pro-drugs for the treatment of pain and inflammation.

Carrier concentration dependence of donor activation energy in n-type GaN epilayers grown on Si (111) by plasma-assisted MBE

The n-type GaN layers were grown by plasma-assisted MBE and either intentionally doped with Si or unintentionally doped. The optical characteristics of a donor level in Si-doped, GaN were studied in terms of photoluminescence (PL) spectroscopy as a function of electron concentration. Temperature dependent PL measurements allowed us to estimate the activation energy of a Si-related donor from temperature-induced decay of PL intensity. PL peak positions, full width at half maximum of PL and activation energies are found to be proportional to the cube root of carrier density. The involvement of donor levels is supported by the temperature-dependent electron concentration measurements. (C) 2012 Elsevier Ltd. All rights reserved.

Electrochemical, phosphate hydrolysis, DNA binding and DNA cleavage properties of new polyaza macrobicyclic dinickel(II) complexes

A new class of macrobicyclic dinickel(II) complexes Ni2L1,2 B](ClO4)(4) (1-6), where L-1,L-2 are polyaza macrobicyclic binucleating ligands, and B is a N,N-donor heterocyclic base (viz. 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)) are synthesized and characterized. The redox, catalytic, DNA binding and DNA cleavage properties were studied. They exhibit two irreversible waves in the cathodic region around E-pc = -0.95 V and E-pa = -0.85 V vs. Ag/Ag+ in CH3CN-0.1 M TBAP, respectively. The first order rate constants for the hydrolysis of 4-nitrophenylphosphate to 4-nitrophenolate by the dinickel(II) complexes 1-6 are in the range from 3.36 x 10(-5) to 10.83 x 10(-5) Ms-1. The complexes 3 and 6 show good binding propensity to calf thymus DNA giving binding constant values (K-b) in the range from 3.08 x 10(5) to 5.37 x 10(5) M-1. The binding site sizes and viscosity data suggest the DNA intercalative and/or groove binding nature of the complexes. The complexes display significant hydrolytic cleavage of supercoiled pBR322DNA at pH 7.2 and 37 degrees C. The hydrolytic cleavage of DNA by the complexes is supported by the evidence from free radical quenching and T4 ligase ligation. The pseudo Michaelis-Menten kinetic parameters k(cat) = 5.44 x 10(-2) h(-1) and K-M = 6.23 x 10(-3) M for complex 3 were obtained. Complex 3 also shows an enormous enhancement of the cleavage rate, of 1.5 x 10(6), in comparison to the uncatalysed hydrolysis rate (k = 3.6 x 10(-8) h(-1)) of ds-DNA.

Nanoindentation as a probe for mechanically-induced molecular migration in layered organic donor-acceptor complexes

Nanoindentation and scratch experiments on 1:1 donor-acceptor complexes, 1 and 2, of 1,2,4,5-tetracyanobenzene with pyrene and phenanthrene, respectively, reveal long-range molecular layer gliding and large interaction anisotropy. Due to the layered arrangements in these crystals, these experiments that apply stress in particular directions result in the breaking of interlayer interactions, thus allowing molecular sheets to glide over one another with ease. Complex 1 has a layered crystal packing wherein the layers are 68° skew under the (002) face and the interlayer space is stabilized by van der Waals interactions. Upon indenting this surface with a Berkovich tip, pile-up of material was observed on just one side of the indenter due to the close angular alignment of the layers with the half angle of the indenter tip (65.35°). The interfacial differences in the elastic modulus (21 ) and hardness (16 ) demonstrate the anisotropic nature of crystal packing. In 2, the molecular stacks are arranged in a staggered manner; there is no layer arrangement, and the interlayer stabilization involves C-H�N hydrogen bonds and ��� interactions. This results in a higher modulus (20 ) for (020) as compared to (001), although the anisotropy in hardness is minimal (4 ). The anisotropy within a face was analyzed using AFM image scans and the coefficient of friction of four orthogonal nanoscratches on the cleavage planes of 1 and 2. A higher friction coefficient was obtained for 2 as compared to 1 even in the cleavage direction due to the presence of hydrogen bonds in the interlayer region making the tip movement more hindered. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Raman study of the interaction of electron-donor and -acceptor molecules with chemically doped graphene

Effect of interaction of tetracyanoethylene (TCNE) and tetrathia fulvalene (TTF) with boron- and nitrogen-doped graphene has been investigated by Raman spectroscopy. The G- and 2D bands of boron- and nitrogen-doped graphenes in the Raman spectra show significantly different changes on interaction with electron-donor and -acceptor molecules. Thus, tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF) have different effects on the Raman spectra of boron- and nitrogen-doped graphenes. The changes in the Raman spectra brought about by electron-donor and -acceptor molecules can be understood in general terms on the basis of molecular charge transfer. (c) 2012 Elsevier B.V. All rights reserved.

Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites

Background: Transthyretin (TTR) is a homotetrameric serum and cerebrospinal fluid protein that transports thyroxine (T4) and retinol by binding to retinol binding protein. Rate-limiting tetramer dissociation and rapid monomer misfolding and disassembly of TTR lead to amyloid fibril formation in different tissues causing various amyloid diseases. Based on the current understanding of the pathogenesis of TTR amyloidosis, it is considered that the inhibition of amyloid fibril formation by stabilization of TTR in native tetrameric form is a viable approach for the treatment of TTR amyloidosis. Methodology and Principal Findings: We have examined interactions of the wtTTR with a series of compounds containing various substitutions at biphenyl ether skeleton and a novel compound, previously evaluated for binding and inhibiting tetramer dissociation, by x-ray crystallographic approach. High resolution crystal structures of five ligands in complex with wtTTR provided snapshots of negatively cooperative binding of ligands in two T4 binding sites besides characterizing their binding orientations, conformations, and interactions with binding site residues. In all complexes, the ligand has better fit and more potent interactions in first T4 site i.e. (AC site) than the second T4 site (BD site). Together, these results suggest that AC site is a preferred ligand binding site and retention of ordered water molecules between the dimer interfaces further stabilizes the tetramer by bridging a hydrogen bond interaction between Ser117 and its symmetric copy. Conclusion: Novel biphenyl ether based compounds exhibit negative-cooperativity while binding to two T4 sites which suggests that binding of only single ligand molecule is sufficient to inhibit the TTR tetramer dissociation.

DNA targeting polyaza macrobicyclic dizinc(II) complexes promoting high in vitro caspase dependent anti-proliferative activity against human carcinoma cancer cells

A series of macrobicyclic dizinc(II) complexes Zn2L1-2B](ClO4)(4) (1-6) have been synthesized and characterized (L1-2 are polyaza macrobicyclic binucleating ligands, and B is the N,N-donor heterocyclic base (viz. 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)). The DNA and protein binding, DNA hydrolysis and anticancer activity of these complexes were investigated. The interactions of complexes 1-6 with calf thymus DNA were studied by spectroscopic techniques, including absorption, fluorescence and CD spectroscopy. The DNA binding constant values of the complexes were found to range from 2.80 x 10(5) to 5.25 x 10(5) M-1, and the binding affinities are in the following order: 3 > 6 > 2 > 5 > 1 > 4. All the dizinc(II) complexes 1-6 are found to effectively promote the hydrolytic cleavage of plasmid pBR322 DNA under anaerobic and aerobic conditions. Kinetic data for DNA hydrolysis promoted by 3 and 6 under physiological conditions give observed rate constants (k(obs)) of 5.56 +/- 0.1 and 5.12 +/- 0.2 h(-1), respectively, showing a 10(7)-fold rate acceleration over the uncatalyzed reaction of dsDNA. Remarkably, the macrobicyclic dizinc(II) complexes 1-6 bind and cleave bovine serum albumin (BSA), and effectively promote the caspase-3 and caspase-9 dependent deaths of HeLa and BeWo cancer cells. The cytotoxicity of the complexes was further confirmed by lactate dehydrogenase enzyme levels in cancer cell lysate and content media.