Formation of atomic hydrogen in an amine—nitrobenzene donor—acceptor pair

We have studied by EPR the oxidation—reduction processes in an amine—nitrobenzene donor— acceptor pair which, when the material is exposed to UV radiation, lead to formation of atomic hydrogen in the system. __________ Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 42, No. 1, pp. 61–63, January–February, 2006.     

Simultaneous binding of minor groove binder and intercalator to dodecamer DNA: importance of relative orientation of donor and acceptor in FRET

In the present study, steady-state, picosecond time-resolved fluorescence and polarization gated anisotropy have been used to establish simultaneous binding of an intercalator (ethidium bromide, EtBr) and a minor groove binder (Hoeschst 33258, H258) to a dodecamer DNA of specific sequence. The F?rster resonance energy transfer (FRET) studies between the dyes H258 (donor) and EtBr (acceptor) in the dodecamer, where the ligands have a particular relative orientation of the transition dipoles, in contrast to the cases in sodium dodecyl sulfate (SDS) micelles and larger genomic DNA, where the orientations are random, reveal the effect of the binding geometry of the ligands in the constrained environment. Our study establishes that reconsideration of the value of the orientation factor (kappa2) is crucial for correct estimation of the donor-acceptor distance when the ligands are simultaneously bound to a specific region of biological macromolecules.     

Rational engineering of a DNA glycosylase specific for an unnatural cytosine:pyrene base pair

A novel site-specific cytosine DNA glycosylase has been rationally engineered from the active site scaffold of the DNA repair enzyme uracil DNA glycosylase (UDG). UDG, which operates by a nucleotide flipping mechanism, was first converted into a sequence nonspecific cytosine DNA glycosylase (CDG) by altering the base-specific hydrogen bond donor-acceptor groups in the active site. A second mutation that renders UDG defective in nucleotide flipping was then introduced, and the double mutant was rescued using a substrate with a "preflipped" cytosine base. Substrate-assisted flipping was engineered by incorporation of an unnatural pyrene nucleotide wedge (Y) into the DNA strand opposite to the target cytosine. This new enzyme, CYDG, can be used to target cleavage of specific cytosine residues in the context of a C/Y base pair in any DNA fragment.     

Photoinduced electron transfer between a donor and an acceptor separated by a capsular wall

The efficient photoinduced electron transfer from a stilbene derivative incarcerated within a negatively charged organic nanocapsule to positively charged acceptors (methyl viologen and a pyridinium salt) adsorbed outside and the back electron transfer were controlled by supramolecular effects.     

Manipulating active layer morphology of molecular donor/polymer acceptor based organic solar cells through ternary blends

The development of molecular donor/polymer acceptor blend(MD/PA)-type organic solar cells(OSCs) lags far behind other type OSCs. It is due to the large-size phase separation morphology of MD/PAblend, which results from the high crystallinity of molecular donors. In this article, to suppress the crystallinity of molecular donors, we use ternary blends to develop OSCs based on one polymer acceptor(P-BNBP-f BT) and two molecular donors(DR3 TBDTT and BTR) with similar chemical structures.The ternary OSC exhibits a power conversion efficiency(PCE) of 4.85%, which is higher than those of the binary OSCs(PCE=3.60% or 3.86%). To our best knowledge, it is the first report of ternary MD/PA-type OSCs and this PCE is among the highest for MD/PA-type OSCs reported so far. Compared with the binary blends, the ternary blend exhibits decreased crystalline size and improved face-on orientation of the donors. As a result, the ternary blend exhibits improved and balanced charge mobilities, suppressed charge recombination and increased donor/acceptor interfacial areas, which leads to the higher shortcircuit current density. These results suggest that using ternary blend is an effective strategy to manipulate active layer morphology and enhance photovoltaic performance of MD/PA-type OSCs.     

Effects of donor/acceptor strengths on the multiphoton absorption: an EOM-CCSD correction vector study

We have developed a correction method (CV) to calculate the single- and multiphoton absorption (MPA) spectra of organic pi-conjugated systems within the equation of motion coupled-cluster method with single and double excitations (EOM-CCSD). The effects of donor/acceptor strengths on the multiphoton absorption in a series of symmetrically substituted stilbene derivatives have been reinvestigated at both the ab initio and the semiempirical intermediate neglect of differential overlap (INDO) Hamiltonian levels. Both ab initio and INDO calculations show that the electron-donating or electron-withdrawing substituents lead to enhancements of two- and three-photon absorption cross sections, more pronounced for two-photon absorption than for three-photon absorption. The ab initio calculations usually produce larger excitation energies than the semiempirical, which lead to lower MPA cross sections.     

The photoluminescent graphene oxide serves as an acceptor rather than a donor in the fluorescence resonance energy transfer pair of Cy3.5-graphene oxide

We have systematically studied the fluorescence resonance energy transfer (FRET) efficiency between the photoluminescent graphene oxide (GO) and Cy3.5 dye by controlling the donor-acceptor distance with a double stranded DNA and demonstrated that the GO serves as an acceptor rather than a donor in this FRET system.     

Conformational conversion of DNA G-quadruplex induced by a cationic porphyrin

The interactions between cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the G-quadruplex (G4) of human telomeric single-strand oligonucleotide d(TTAGGG)₂ (S12) have been investigated by means of circular dichroism (CD), UV–visible absorption and fluorescence spectroscopies. It is found that TMPyP4 can preferentially induce the conformational conversion of the G4 structure from the parallel type to the parallel/antiparallel mixture in the presence of K⁺, and that it can directly induce the formation of antiparallel G4 structure from the single-strand oligonucleotide S12 in the absence of K⁺. Furthermore, the comparable experiments of TMPyP4 with two single-strand oligonucleotides S6 d(TTAGGG) and S24 d(TAGGG(TTAGGG)₃T) in the absence of K⁺ show that TMPyP4 can also induce the formation of antiparallel G4 from S24 but not from S6, indicating that the end-loops of the G4 structure are the key factors for the formation of G4 induced by TMPyP4.     

Photophysical properties of oligophenylene ethynylenes modified by donor and/or acceptor groups

To create highly fluorescent organic compounds in longer wavelength regions, and to gain physical chemistry insight into the photophysical characteristics, we investigated photophysical properties (Phi(f), lambda(em), tau, lambda(abs), epsilon, k(r), and k(d)) and their controlling factor dependence of the following pi-conjugated molecular rods consisting of p-phenyleneethynylene units modified by donor (OMe) and/or acceptor (CN): (1) side-donor modification systems (SD systems), (2) side-acceptor modification systems (SA systems), and (3) systems consisting of donor block and acceptor block (BL systems). As a result, very high Phi(f) values (>0.95) were obtained for BL systems. Bathochromic shifts of lambd(em) in the same pi conjugation length were largest for BL systems. Thus we succeeded in the creation of highly efficient light emitters in the longer wavelength region by block modification (e.g., Phi(f) = 0.97, lambda(em) = 464 nm for BL-9), contrary to expectation from energy gap law. Considerably intense solid emission (Phi(f) approximately 0.5) in the longer wavelength region (500-560 nm) was also found for BL systems, presumably because of molecular orientation that hinders the self-quenching of fluorescence in solids. From (1) a Lippert-Mataga plot, (2) density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations, and (3) the positive linear relationship between the optical transition energy (nu(em)) and the difference between the highest occupied molecular orbital of the donor and the lowest unoccupied molecular orbital of the acceptor (HOMO(D)-LUMO(A) difference), it is elucidated that the excited singlet (S1) state of BL systems has a high charge transfer nature. The number (n) of energetically equivalent dipolar structure (EEDS) units in the oligoarylene ethynylenes is shown to be a measure of the effective pi conjugation length in the S1 state. The S1 state planarity increases with n values of EEDS units and by the introduction of donor and/or acceptor groups. It is worth noting that the Phi(f) values increase linearly with the n values of EEDS units.     

Synthesis of a new pair of fluorescence resonance energy transfer donor and acceptor dyes and its use in a protease assay

A new, efficient and very robust fluorescence resonance energy transfer (FRET) system, which can be measured in a normal as well as in a time-resolved mode, was developed and its feasibility demonstrated in a protease assay format.     

Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study

The suitability of the GMIPp energy functional as a fast, efficient method for estimating the hydrogen-bond donor and acceptor propensities of a wide variety of organic compounds is examined. Comparison of the GMIPp values is made with two experimental hydrogen-bond scales: i) the hydrogen-bond basicity scale for N-heteroaromatics in carbon tetrachloride, and ii) the hydrogen-bond acidities for NH/OH donors and hydrogen-bond basicities of N/O acceptors determined in 1,1,1-trichloroethane. Attention is paid to i) the reliability of semiempirical versus ab initio treatments of the quantum mechanical molecule, ii) the role of solvation, and iii) the effect of including the polarization energy component in the calculation of the GMIPp functional. The statistical analysis of the results reveals that the GMIP functional, which combines electrostatic and steric energy components, predicts with reasonable accuracy and computational efficiency the hydrogen-bond strength for a wide variety of compounds.     

Specificity of DNA triple helix formation analyzed by a FRET assay

Background  

A third DNA strand can bind into the major groove of a homopurine duplex DNA to form a DNA triple helix. Sequence specific triplex formation can be applied for gene targeting, gene silencing and mutagenesis.     

Detection of specific noncovalent interaction of peptide with DNA by MALDI-TOF

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to obtain spectra of peptide-DNA complexes formed by basic domain (BD15) of c-Fos protein and DNA AP-1 site (5'-TGAGTCA-3'). The noncovalent interaction between single stranded DNA and BD15 was observed and confirmed to be an ionic one between the negatively charged sugar-phosphate backbone of DNA and positively charged side chains of Arg- and lys-rich peptides as demonstrated by Vertes and coworkers and Woods and coworkers. But the specific noncovalent interaction between DNA AP-1 site and the dimer of BD15 was firstly detected in this paper. Various different sequence DNAs were studied and it was found that this interaction is a sequence-specific one, and AP-1 site was essential for this interaction. This specific interaction depends on the matrix. It was only observed in the ATT matrix and not in the other two matrixes (CHCA and DHBA).     

Synthesis of C-nucleosides designed to participate in triplex formation with native DNA: specific recognition of an A:T base pair in DNA

[structure: see text] We have previously described a system of 2-aminoquinoline- and 2-aminoquinazoline-based C-deoxynucleosides (TRIPsides) that are designed to be incorporated into oligomers that can specifically bind in the major groove via Hoogsteen base pairing to any sequence of native DNA. The four TRIPsides are termed antiGC, antiCG, antiTA, and antiAT with respect to the Watson-Crick base pair targets that they bind. The first three TRIPsides have been prepared, characterized, and shown to form stable and sequence-specific triplexes. In the present study, we describe the preparation of two molecules, 2-amino-4-(2'-deoxy-beta-D-ribofuranosyl)quinazoline (7) and 2-amino-6-fluoro-4-(2'-deoxy-beta-D-ribofuranosyl)quinoline (14), that can serve as the remaining antiAT TRIPside. The phosphoramidites of 7 and 14 were prepared, but only the latter was successfully incorporated into DNA oligomers. It is demonstrated using UV-visible melting experiments that 14 forms sequence-specific intramolecular triplets with A:T base pairs at physiological pH.     

Thermodynamic consideration of the charge transfer interaction of the donor: acceptor type between chloranilic acid and haloperidol

The thermodynamic parameters of the charge transfer complex between chloranilic acid and haloperidol were studied. Haloperidol in pure form and in dosage form was assayed in this study. The method was based on charge transfer complex formation between the drug, which acted as an n-donor, and chloranilic acid, which acted as a pi acceptor in a non aqueous solvent. The complex stoichiometry was found to be 1:2 (haloperidol: chloranilic acid) with the maximum absorption band at a wavelength of 576 nm. The complex obeyed Beer's law. The thermodynamic parameters investigated included stability constant, molar absorptivity, free energy change, enthalpy, and entropy. The method was successfully applied in the analysis of commercially available haloperidol tablets without interference from its excipients, with good precision and reproducibility, compared with the official assay method (non aqueous titration) described for haloperidol in the compendium.     

CH...pi interaction for rhenium-based rectangles: an interaction that is rarely designed into a host-guest pair

Alkoxy- and thiolato-bridged Re(I) molecular rectangles [{(CO)3Re(mu-ER)2Re(CO)3}2(mu-bpy)2] (ER = SC4H9, 1a; SC8H17, 1b; OC4H9, 2a; OC12H25, 2b; bpy = 4,4'-bipyridine) exhibit strong interactions with several planar aromatic molecules. The nature of their binding was studied by spectral techniques and verified by X-ray diffraction analysis. Standard absorption and fluorescence titrations showed that a relatively strong 1:1 interaction occurs between aromatic guests such as pyrene and these rectangles. The results of a single-crystal X-ray diffraction analysis show that the recognition of 1 with a pyrene molecule is mainly due to CH...pi interactions and the face of the guest pyrene is located over the edges of the bpy linkers of 1. This is a fairly novel example of an interaction that is rarely designed into a host-guest pair. Furthermore, the interaction of 1 with Ag+ results in the self-organization of supramolecular arrays, as revealed by solid-state data.     

Donor-pi-acceptor conjugated copolymers for photovoltaic applications: tuning the open-circuit voltage by adjusting the donor/acceptor ratio

A class of new conjugated copolymers containing a donor (thiophene)-acceptor (2-pyran-4-ylidene-malononitrile) was synthesized via Stille coupling polymerization. The resulting copolymers were characterized by 1H NMR, elemental analysis, GPC, TGA, and DSC. UV-vis spectra indicated that the increase in the content of the thiophene units increased the interaction between the polymer main chains to cause a red-shift in the optical absorbance. Cyclic voltammetry was used to estimate the energy levels of the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) and the band gap (Eg) of the copolymers. The basic electronic structures of the copolymers were also studied by DFT calculations with the GGA/B3LYP function. Both the experimental and the calculated results indicated an increase in the HOMO energy level with increasing the content of thiophene units, whereas the corresponding change in the LUMO energy level was much smaller. Polymer photovoltaic cells of a bulk heterojunction were fabricated with the structure of ITO/PEDOT/PSS (30 nm)/copolymer-PCBM blend (70 nm)/Ca (8 nm)/Al (140 nm). It was found that the open-circuit voltage (Voc) increased (up to 0.93 V) with a decrease in the content of thiophene units. Although the observed power convention efficiency is still relatively low (up to 0.9%), the corresponding low fill factor (0.29) indicates considerable room for further improvement in the device performance. These results provided a novel concept for developing high Voc photovoltaic cells based on donor-pi-acceptor conjugated copolymers by adjusting the donor/acceptor ratio.