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At least 415 records · Page 23Linked to original sources
PubMed2004

Importance of intermolecular interactions in assessing hopping mobilities in organic field effect transistors: pentacene versus dithiophene-tetrathiafulvalene.

We report on a computational study to understand the high mobility found in dithiophene-tetrathiafulvalene (DT-TTF) transistors, with respect to that known for pentacene, using an extended measure of the reorganization energy (lambdareorg). We demonstrate the high importance of considering intermolecular interactions to assess hole-hopping mobilities. We find that due to the steric, polarizable environment and the structural changes induced by local intermolecular charge delocalization, the calculated lambdareorg for DT-TTF decreases from 0.574 eV in the isolated molecule to 0.042 eV in the crystal embedded molecule, which is of the same order of the previously reported value found for the isolated pentacene molecule, 0.098 eV.

Journal Article↗
PubMed2005

Conformationally gated switching between superexchange and hopping within oligo-p-phenylene-based molecular wires.

We observe well-defined regions of superexchange and thermally activated hopping in the temperature dependence of charge recombination (CR) in a series of donor-bridge-acceptor (D-B-A) systems, where D = phenothiazine (PTZ), B = p-phenylene (Ph(n)), n = 1-4, and A = perylene-3,4:9,10-bis(dicarboximide) (PDI). A fit to the thermally activated CR rates of the n = 3 and n = 4 compounds yields activation barriers of 1290 and 2030 cm(-1), respectively, which match closely with theoretically predicted and experimentally observed barriers for the planarization of terphenyl and quaterphenyl. Negative activation of CR in the temperature regions dominated by superexchange charge transport is the result of a fast conformational equilibrium that increasingly depopulates the reactive state for CR as temperature is increased. The temperature dependence of the effective donor-acceptor superexchange coupling, V(DA), measured using magnetic field effects on the efficiency of the charge recombination process, shows that CR occurs out of the conformation with lower V(DA) via the energetically favored triplet pathway.

Crystallography, X-Ray↗
PubMed2006

Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates.

The mechanism and dynamics of photoinduced charge separation and charge recombination have been investigated in synthetic DNA hairpins possessing donor and acceptor stilbenes separated by one to seven A:T base pairs. The application of femtosecond broadband pump-probe spectroscopy, nanosecond transient absorption spectroscopy, and picosecond fluorescence decay measurements permits detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge-separated intermediates. When the donor and acceptor are separated by a single A:T base pair, charge separation occurs via a single-step superexchange mechanism. However, when the donor and acceptor are separated by two or more A:T base pairs, charge separation occurs via a multistep process consisting of hole injection, hole transport, and hole trapping. In such cases, hole arrival at the electron donor is slower than hole injection into the bridging A-tract. Rate constants for charge separation (hole arrival) and charge recombination are dependent upon the donor-acceptor distance; however, the rate constant for hole injection is independent of the donor-acceptor distance. The observation of crossover from a superexchange to a hopping mechanism provides a "missing link" in the analysis of DNA electron transfer and requires reevaluation of the existing literature for photoinduced electron transfer in DNA.

Adenine↗
PubMed2006

Electron hopping in pi-stacked covalent and self-assembled perylene diimides observed by ENDOR spectroscopy.

We have carried out room-temperature, solution-phase electron paramagnetic resonance and electron-nuclear double resonance studies on a series of radical anions based upon perylene-3,4:9,10-bis(dicarboximide) (PDI). The following systems were studied: two PDI monomers, a covalent, cofacial dimer, and two covalent trefoil-PDI3 molecules, one of which self-assembles into pi-stacked dimers. Full sharing of the unpaired electron in the covalent and self-assembled dimers is revealed by a halving of the hyperfine coupling constants in these species, relative to those of the monomers. These results and the electronic absorption spectra show that electron hopping on a >107 Hz time scale occurs between a reduced and neutral chromophoric pair.

Journal Article↗
PubMed2006

Electron hopping dynamics in Au38 nanoparticle langmuir monolayers at the air/water interface.

The electron-transfer dynamics between nanoparticles has been studied as a function of interparticle distance by in situ voltammetry of well-defined monolayers of a metal quantum dot nanoparticle Au38(hexanethiolate)24. The interparticle distance is precisely controlled by the Langmuir technique and addition of various lengths of dithiol linkers (HS(CH2)nSH; n = 5, 6, 8, and 9). Voltammograms of Au38 monolayers display a well-defined single-electron charging peak that increases remarkably with decreasing the interparticle distance. The diffusion coefficient and rate constant calculated from the peak current for core-core electron hopping reaction both exponentially increase respectively, from 3.3 x 10-10 to 5.2 x 10-9 cm2/s and 2.2 x 104 to 5.0 x 105 s-1 as the distance decreases from 13.3 to 9.5 A and then levels off at 8.0 A. These rate constants are in good agreement with the literature values, demonstrating that the present experimental approach provides a powerful way to investigate the correlation between the electron-transfer dynamics and nanoparticle assembly structure.

Journal Article↗
PubMed2003

Hop (Humulus lupulus L.) proanthocyanidins characterized by mass spectrometry, acid catalysis, and gel permeation chromatography.

Proanthocyanidins extracted from hops (Humulus lupulus L. cv. Willamette) were subjected to Sephadex LH-20 column chromatography using a step gradient of methanol, water, and acetone. The resulting fractions were analyzed by acid catalysis, electrospray ionization and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and gel permeation chromatography (GPC). The proanthocyanidins contained catechin and epicatechin as monomers and as terminal and extension units. Epigallocatechin was found as extension units. The mean degree of polymerization (mDP) of the crude proanthocyanidins was 7.8, but heptamers were the largest oligomers visible in mass spectra of the whole. In the last-eluted fraction (mDP = 22.2), polymers as large as 20-mers were detected by MALDI-TOF-MS, demonstrating the effectiveness of prior separation in improving MS detection. GPC data correlated well with acid catalysis results, confirming the presence of large polymers that were not detected by MS.

Anthocyanins↗
PubMed2005

Activation of proestrogens from hops (Humulus lupulus L.) by intestinal microbiota; conversion of isoxanthohumol into 8-prenylnaringenin.

Hop, an essential ingredient in most beers, contains a number of prenylflavonoids, among which 8-prenylnaringenin (8-PN) would be the most potent phytoestrogen currently known. Although a number of health effects are attributed to these compounds, only a few reports are available about the bioavailability of prenylflavonoids and the transformation potency of the intestinal microbial community. To test these transformations, four fecal samples were incubated with xanthohumol, isoxanthohumol (IX), and 8-PN. Upon incubation with IX, present in strong ales up to 4 mg/L, 36% was converted into 8-PN in one fecal sample and the estrogenic properties of the sample drastically increased. In an experiment with 12 fecal cultures, this conversion was observed in one-third of the samples, indicating the importance of interindividual variability in the intestinal microbial community. Eubacterium limosum was identified to be capable of this conversion (O-demethylation) of IX into 8-PN, and after strain selection, a conversion efficiency of 90% was achieved. Finally, strain supplementation to a nonconverting fecal sample led to rapid and high 8-PN production at only 1% (v/v) addition. Up to now, the concentration of 8-PN in beer was considered too low to affect human health. However, these results show that the activity of the intestinal microbial community could more than 10-fold increase the exposure concentration. Because prenylflavonoids are present in many beers with IX being the major constituent, the results raise the question whether moderate beer consumption might contribute to increased in vivo levels of 8-PN and even influence human health.

Adult↗
PubMed2006

Effects of beer and hop on ionotropic gamma-aminobutyric acid receptors.

Beer induced the response of the ionotropic gamma-aminobutyric acid receptors (GABA(A) receptors) expressed in Xenopus oocytes, indicating the presence of gamma-aminobutyric acid (GABA)-like activity. Furthermore, the pentane extract of the beer, hop (Humulus lupulus L.) oil, and myrcenol potentiated the GABA(A) receptor response elicited by GABA. The GABA(A) receptor responses were also potentiated by the addition of aliphatic esters, most of which are reported to be present in beer flavor. Aliphatic esters showed the tendency to decrease in the potentiation of the GABA(A) receptor response with an increase in their carbon chain length. When myrcenol was injected to mice prior to intraperitoneal administration of pentobarbital, the pentobarbital-induced sleeping time of mice increased additionally. Therefore, the beer contained not only GABA-like activity but also the modulator(s) of the GABA(A) receptor response.

Acyclic Monoterpenes↗
PubMed2004

Scaffold hopping in de novo design. Ligand generation in the absence of receptor information.

We report here the de novo generation of chemotypes and scaffolds for the estrogen receptor, without use of the receptor structure in the assembly phase. Through use of ligand superpositions or a single bound conformation of a known active, a pseudoreceptor can be generated as a design envelope, within which novel structures are readily assembled. Many of these structures have high similarity to known chemotypes. Scaffold hopping is readily achieved within this pseudoreceptor, indicating the advantages of such an approach in discovery research.

Benzene Derivatives↗
PubMed2005

A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction.

In this paper, we describe the first prospective application of the shape-comparison program ROCS (Rapid Overlay of Chemical Structures) to find new scaffolds for small molecule inhibitors of the ZipA-FtsZ protein-protein interaction, a proposed antibacterial target. The shape comparisons are made relative to the crystallographically determined, bioactive conformation of a high-throughput screening (HTS) hit. The use of ROCS led to the identification of a set of novel, weakly binding inhibitors with scaffolds presenting synthetic opportunities to further optimize biological affinity and lacking development issues associated with the HTS lead. These ROCS-identified scaffolds would have been missed using other structural similarity approaches such as ISIS 2D fingerprints. X-ray crystallographic analysis of one of the new inhibitors bound to ZipA reveals that the shape comparison approach very accurately predicted the binding mode. These experimental results validate this use of ROCS for chemotype switching or "lead hopping" and suggest that it is of general interest for lead identification in drug discovery endeavors.

Algorithms↗
PubMed2005

Scaffold hopping with molecular field points: identification of a cholecystokinin-2 (CCK2) receptor pharmacophore and its use in the design of a prototypical series of pyrrole- and imidazole-based CCK2 antagonists.

A new molecular modeling approach has been used to derive a pharmacophore of the potent and selective cholecystokinin-2 (CCK(2)) receptor antagonist 5 (JB93182), based on features shared with two related series. The technique uses "field points" as simple and effective descriptions of the electrostatic and van der Waals maxima and minima surrounding a molecule equipped with XED (extended electron distribution) charges. Problems associated with the high levels of biliary elimination of 5 in vivo required us to design a compound with significantly lower molecular weight without sacrificing its nanomolar levels of in vitro activity. Two new series of compounds were designed to mimic the arrangement of field points present in the pharmacophore rather than its structural elements. In a formal sense, two of the three amides in 5 were replaced with either a simple pyrrole or imidazole, while some features thought to be essential for the high levels of in vitro activity of the parent compounds were retained and others deleted. These compounds maintained activity and selectivity for this receptor over CCK(1). In addition, the reduction in molecular weight coupled with lower polarities greatly reduced levels of biliary elimination associated with 5. This makes them good lead compounds for development of drug candidates whose structures are not obviously related to those of the parents and represents the first example of scaffold hopping using molecular field points.

Animals↗
PubMed2006

Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring.

The ability to find novel bioactive scaffolds in compound similarity-based virtual screening experiments has been studied comparing Tanimoto-based, ranking-based, voting, and consensus scoring protocols. Ligand sets for seven well-known drug targets (CDK2, COX2, estrogen receptor, neuraminidase, HIV-1 protease, p38 MAP kinase, thrombin) have been assembled such that each ligand represents its own unique chemotype, thus ensuring that each similarity recognition event between ligands constitutes a scaffold hopping event. In a series of virtual screening studies involving 9969 MDDR compounds as negative controls it has been found that atom pair descriptors and 3D pharmacophore fingerprints combined with ranking, voting, and consensus scoring strategies perform well in finding novel bioactive scaffolds. In addition, often superior performance has been observed for similarity-based virtual screening compared to structure-based methods. This finding suggests that information about a target obtained from known bioactive ligands is as valuable as knowledge of the target structures for identifying novel bioactive scaffolds through virtual screening.

Cyclin-Dependent Kinase 2↗
PubMed2006

Discovery of nonpeptidic small-molecule AP-1 inhibitors: lead hopping based on a three-dimensional pharmacophore model.

We designed and synthesized small-molecule activator protein-1 (AP-1) inhibitors based on a three-dimensional (3D) pharmacophore model that we had previously derived from a cyclic decapeptide exhibiting AP-1 inhibitory activity. New AP-1 inhibitors with a 1-thia-4-azaspiro[4.5]decane or a benzophenone scaffold, which inhibit the DNA-binding and transactivation activities of AP-1, were discovered using a "lead hopping" procedure. An additional investigation of the benzophenone analogues confirmed the reliability of the pharmacophore model, its utility to discover AP-1 inhibitors, and the potency of the benzophenone derivatives as a lead series.

Animals↗
PubMed2006

Subtle side-chain modifications of the hop phytoestrogen 8-prenylnaringenin result in distinct agonist/antagonist activity profiles for estrogen receptors alpha and beta.

In search of therapeutic agents for estrogen-related pathologies, phytoestrogens are being extensively explored. In contrast to naringenin, 8-prenylnaringenin is a potent hop-derived estrogenic compound, highlighting the importance of the prenyl group for hormonal activity. We investigated the effects of substituting the prenyl group at C(8) with alkyl chains of varying lengths and branching patterns on estrogen receptor (ER) subtype ERalpha- and ERbeta-binding affinities and transcriptional activities. In addition, features of the ligand-induced receptor conformations were explored using a set of specific ER-binding peptides. The new 8-alkylnaringenins were found to span an activity spectrum ranging from full agonism to partial agonism to antagonism. Most strikingly, 8-(2,2-dimethylpropyl)naringenin exhibited full agonist character on ERalpha, but pronounced antagonist character on ERbeta. Knowledge on how ER-subtype-selective activities can be designed provides valuable information for future drug or tool compound discovery.

Binding, Competitive↗
PubMed2005

Theoretical rate constants of super-exchange hole transfer and thermally induced hopping in DNA.

Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].

DNA↗
PubMed2005

Toward an accurate and efficient semiclassical surface hopping procedure for nonadiabatic problems.

The derivation of a semiclassical surface hopping procedure from a formally exact solution of the Schrodinger equation is discussed. The fact that the derivation proceeds from an exact solution guarantees that all phase terms are completely and accurately included. Numerical evidence shows the method to be highly accurate. A Monte Carlo implementation of this method is considered, and recent work to significantly improve the statistical accuracy of the Monte Carlo approach is discussed.

Journal Article↗
PubMed2006

Charge hopping in organic semiconductors: influence of molecular parameters on macroscopic mobilities in model one-dimensional stacks.

We present a Monte Carlo approach to estimate how molecular parameters impact hopping rates and charge mobilities in organic pi-conjugated materials. Our goal is to help in establishing structure-properties relationships. As a first step, our approach is illustrated by considering a model system made of a one-dimensional array of pentacene molecules; we describe the variations of the electron-transfer rates and of the resulting charge mobilities as a function of electric field and of the presence of molecular disorder and traps. The results highlight that there is no direct relationship between the degree of spatial overlap among adjacent molecules and charge mobility.

Journal Article↗
PubMed2006

Toroidal hopping of a single hole through the circularly-arrayed naphthyl groups in hexanaphthylbenzene cation radical.

Synthesis of a dendritic (soluble) hexanaphthylbenzene derivative is described in which the six naphthyl groups are connected to the central benzene ring in a propeller-shaped arrangement. Observation of multiple oxidation waves in its cyclic voltammogram as well as an intense charge-resonance transition (extending beyond 1600 nm) in its cation radical, generated by laser-flash photolysis using photoexcited chloranil as an oxidant, suggests that a single hole is mobilized via electron transfer (or hopping) over six identical (circularly arrayed) redox centers.

Journal Article↗