bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antarctic genomics
Authors: Clark Melody S. , Clarke Andrew , Cockell Charles S. , Convey Peter , Detrich H. William , Fraser Keiron P. P. , Johnston Ian A. , Methe Barbara A. , Murray Alison E. , Peck Lloyd S. , Römisch Karin , Rogers Alex D. 
Published: April 2004

AbstractWith the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. Copyright © 2004 John Wiley & Sons, Ltd.
Functional genomics in chickens: development of integrated‐systems microarrays for transcriptional profiling and discovery of regulatory pathways
Authors: Cogburn L. A. , Wang X. , Carre W. , Rejto L. , Aggrey S. E. , Duclos M. J. , Simon J. , Porter T. E. 
Published: April 2004

AbstractThe genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver‐specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri‐hatch transition and during a strong metabolic perturbation — fasting and re‐feeding — in divergently selected broiler chickens (fast vs. slow‐growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken. Copyright © 2004 John Wiley & Sons, Ltd.
Residual Topological Isomerism of Intertwined Molecules
Authors: Lukin Oleg , Godt Adelheid , Vögtle Fritz 
Published: April 2004

AbstractThe growing number of molecular assemblies with unusual geometry and topology requires from time to time a revision of certain aspects of stereochemistry. The present paper analyzes several representatives of intertwined molecules that have bridges connecting their loops. In spite of the experimentally proven chirality, these species lack elements of both classical and topological chirality. Due to the relationship of these types of molecules to the well‐recognized topologically nontrivial compounds, such as catenanes and knots, we propose the term “residual topology” illustrated by a simple scheme of excessive or missing bridges that could be excluded or included, respectively, in molecular graphs of these species to render them topologically nontrivial. This concept paper represents, therefore, an update on the currently applied nomenclature.
Mechanism of Homogeneously and Heterogeneously Catalysed Meerwein–Ponndorf–Verley–Oppenauer Reactions for the Racemisation of Secondary Alcohols
Authors: Klomp Dirk , Maschmeyer Thomas , Hanefeld Ulf , Peters Joop A. 
Published: April 2004

AbstractThe mechanism of hydrogen transfer from alcohols to ketones, catalysed by lanthanide(III) isopropoxides or zeolite Beta has been studied. For the lanthanide catalysed reactions, (S)‐1‐phenyl‐(1‐2H1)ethanol and acetophenone were used as case studies to determine the reaction pathway for the hydrogen transfer. Upon complete racemisation all deuterium was present at the 1‐position, indicating that the reaction exclusively takes place via a carbon‐to‐carbon hydrogen transfer. Zeolite Beta with different Si/Al ratios was applied in the racemisation of (S)‐1‐phenylethanol. In this case the racemisation does not proceed via an oxidation/reduction pathway but via elimination of the hydroxy group and its re‐addition. This mechanism, however, is not characteristic for all racemisation reactions with zeolite Beta. When 4‐tert‐butyl cyclohexanone is reduced with this catalyst, a classical MPV reaction takes place exclusively. This demonstrates that zeolite Beta has a substrate dependent reaction pathway.
Multiple Recognition of Barbiturate Guests by “Hamilton‐Receptor”‐Functionalized Dendrimers
Authors: Dirksen Anouk , Hahn Uwe , Schwanke Frank , Nieger Martin , Reek Joost N. H. , Vögtle Fritz , De Cola Luisa 
Published: April 2004

AbstractThe well‐known unsubstituted “Hamilton receptor” was monofunctionalized with an amino group and attached at the periphery of poly(propyleneamine) dendrimers through the use of an activated ester. Four generations of Hamilton‐receptor‐functionalized dendrimers (HR‐dendrimers) were synthesized and characterized by 1H and 13C NMR spectroscopy and MALDI‐TOF mass spectrometry. The photophysical properties of the HR‐dendrimers were investigated by UV/Vis as well as with steady‐state and time‐resolved fluorescence spectroscopy. The dendrimers were used as multivalent hosts for the barbiturate guests Barbital (7) and [Re(Br)(CO)3(barbi‐bpy)] (8; barbi‐bpy=5‐[4‐(4′‐methyl)‐2,2′‐bipyridyl]methyl‐2,4,6‐(1 H,3 H,5 H)‐pyrimidinetrione). The stable adducts formed between the dendritic architectures (the hosts) and the barbiturate guests 7 and 8 were investigated by 1H NMR spectroscopy and photophysical methods. The binding constants of the barbiturate guests for binding to reference compound 2 (with a single receptor unit) in chloroform were found to be 1.4×103 M−1 and 1.5×105 M−1 for 7 and 8, respectively. Binding of 7 to the dendrimers enhances the weak emission of the Hamilton receptor. This increase in emission is also generation dependent; it was found to be most pronounced in the case of 2 and the least in the case of the fourth‐generation dendrimer 6. The unexpected increase in the quantum yield of emission from the HR‐dendrimers with increasing generation could be caused by the rather rigid conformation of the Hamilton receptors in later‐generation compounds, which is a result of intramolecular aggregation and steric hindrance at the periphery of the dendrimer. The photoinduced energy transfer from the excited state of the HR‐dendrimers to the lower‐lying excited state of the guest 8 was used to probe the formation of host–guest complexes. The rate of energy transfer was calculated to be 3.6×1010 s−1. Energy transfer in 2⊂8 only occurred in the presence of a strong base, which shows that the basic amine core in the HR‐dendrimers is crucial for this photoinduced process. The binding of 8 to the dendrimers is completely reversible: 8 can be exchanged with a competitive guest such as 7 and the emission of the HR‐dendrimer is restored.
Electrochemically Induced Sol–Gel Deposition of Zirconia Thin Films
Authors: Shacham Ronen , Mandler Daniel , Avnir David 
Published: April 2004

AbstractA novel electrochemical method for deposition of ZrO2 thin films is described. The films, 50–600 nm thick, were obtained by applying moderate positive or negative potentials (+2.5 V to −1.5 V versus SHE) on conducting surfaces immersed in a 2‐propanol solution of zirconium tetra‐n‐propoxide [Zr(OPr)4] in the presence of minute quantities of water (water/monomer molar ratios in the range of 10−5 to 10−1), which was the limiting reagent. Oxidative electrochemical formation of solvated H+ and reductive formation of OH− catalyze the hydrolysis and condensation of the metal alkoxide precursor. The magnitude of the applied potential and its duration provide a convenient way of controlling the film thickness. The films consist of an amorphous phase, as revealed by XRD measurements. The effects of different parameters, such as the applied potential and its duration, the amount of added water and the current–time characteristics, were studied. A mechanism for the electrodeposition of the zirconia films which is in accordance with our findings is proposed.
Structure‐Switching Signaling Aptamers: Transducing Molecular Recognition into Fluorescence Signaling
Authors: Nutiu Razvan , Li Yingfu 
Published: April 2004

AbstractThe development of aptamer technology considerably broadens the utility of nucleic acids as molecular recognition elements, because it allows the creation of DNA or RNA molecules for binding a wide variety of analytes (targets) with high affinity and specificity. Several recent studies have focused on developing rational design strategies for transducing aptamer–target recognition events into easily detectable signals, so that aptamers can be widely exploited for detection directed applications. We have devised a generalizable strategy for designing nonfluorescent aptamers that can be turned into fluorescence‐signaling reporters. The resultant signaling probes are denoted “structure‐switching signaling aptamers” as they report target binding by switching structures from DNA/DNA duplex to DNA/target complex. The duplex is formed between a fluorophore‐labeled DNA aptamer and an antisense DNA oligonucleotide modified with a quencher (denoted QDNA). In the absence of the target, the aptamer hybridizes with QDNA, bringing the fluorophore into close proximity of the quencher for efficient fluorescence quenching. When this system is exposed to the target, the aptamer switches its binding partner from QDNA to the target. This structure‐switching event is coupled to the generation of a fluorescent signal through the departure of QDNA, permitting the real‐time monitoring of the aptamer–target recognition. In this article, we discuss the conceptual framework of the structure‐switching approach, the essential features of structure‐switching signaling aptamers as well as remaining challenges and possible solutions associated with this new methodology.
Synthesis, Structure, and Characterisation of a New Phenolato‐Bridged Manganese Complex [Mn2(mL)2]2+: Chemical and Electrochemical Access to a New Mono‐μ‐Oxo Dimanganese Core Unit
Authors: Hureau Christelle , Sabater Laurent , Anxolabéhère‐Mallart Elodie , Nierlich Martine , Charlot Marie‐France , Gonnet Florence , Rivière Eric , Blondin Geneviève 
Published: April 2004

AbstractThe dinuclear phenolato‐bridged complex [(mL)MnIIMnII(mL)](ClO4)2 (1(ClO4)2) has been obtained with the new [N4O] pentadentate ligand mL− (mLH=N,N′‐bis‐(2‐pyridylmethyl)‐N‐(2‐hydroxybenzyl)‐N′‐methyl‐ethane‐1,2‐diamine) and has been characterised by X‐ray crystallography. X‐ and Q‐band EPR spectra were recorded and their variation with temperature was examined. All spectra exhibit features extending over 0–800 mT at the X band and over 100–1450 mT at the Q band, features that are usually observed for dinuclear MnII complexes. Cyclic voltammetry of 1 exhibits two irreversible oxidation waves at E${{{\rm p}\hfill \atop 1\hfill}}$=0.89 V and E${{{\rm p}\hfill \atop 2\hfill}}$=1.02 V, accompanied on the reverse scan by an ill‐defined cathodic wave at E${{{\rm p}\hfill \atop 1^{\prime}\hfill}}$=0.56 V (all measured versus the saturated calomel electrode (SCE)). Upon chemical oxidation with tBuOOH (10 equiv) at 20 °C, 1 is transformed into the mono‐μ‐oxo species [(mL)MnIII‐(μ‐O)‐MnIII(mL)]2+ (2), which eventually partially evolves into the di‐μ‐oxo species [(mL)MnIII‐(μ‐O)2‐MnIV(mL)]n+ (3) in which one of the aromatic rings of the ligand is decoordinated. The UV/Vis spectrum of 2 displays a large absorption band at 507 nm, which is attributed to a phenolate→MnIII charge‐transfer transition. The cyclovoltammogram of 2 exhibits two reversible oxidation waves, at 0.65 and 1.16 V versus the SCE, corresponding to the MnIIIMnIII/MnIIIMnIV and MnIIIMnIV/MnIVMnIV oxidation processes, respectively. The one‐electron electrochemical oxidation of 2 leads to the mono‐μ‐oxo mixed‐valent species [(mL)MnIII‐(μ‐O)‐MnIV(mL)]3+ (2 ox). The UV/Vis spectrum of 2 ox exhibits one large band at 643 nm, which is attributed to the phenolate→MnIV charge‐transfer transition. 2 ox can also be obtained by the direct electrochemical oxidation of 1 in the presence of an external base. The 2 ox and 3 species exhibit a 16‐line EPR signal with first peak to last trough widths of 125 and 111 mT, respectively. Both spectra have been simulated by using colinear rhombic Mn‐hyperfine tensors. Mechanisms for the chemical formation of 2 and the electrochemical oxidation of 1 into 2 ox are proposed.
Competition between π and Non‐π Cation‐Binding Sites in Aromatic Amino Acids: A Theoretical Study of Alkali Metal Cation (Li+, Na+, K+)–Phenylalanine Complexes
Authors: Siu Fung Ming , Ma Ngai Ling , Tsang Chun Wai 
Published: April 2004

AbstractTo understand the cation–π interaction in aromatic amino acids and peptides, the binding of M+ (where M+ = Li+, Na+, and K+) to phenylalanine (Phe) is studied at the best level of density functional theory reported so far. The different modes of M+ binding show the same order of binding affinity (Li+>Na+>K+), in the approximate ratio of 2.2:1.5:1.0. The most stable binding mode is one in which the M+ is stabilized by a tridentate interaction between the cation and the carbonyl oxygen (OC), amino nitrogen (NH2), and aromatic π ring; the absolute Li+, Na+, and K+ affinities are estimated theoretically to be 275, 201, and 141 kJ mol−1, respectively. Factors affecting the relative stabilities of various M+–Phe binding modes and conformers have been identified, with ion–dipole interaction playing an important role. We found that the trend of π and non‐π cation bonding distances (Na+–π>Na+–N>Na+–O and K+–π>K+–N>K+–O) in our theoretical Na+/K+–Phe structures are in agreement with the reported X‐ray crystal structures of model synthetic receptors (sodium and potassium bound lariat ether complexes), even though the average alkali metal cation–π distance found in the crystal structures is longer. This difference between the solid and the gas‐phase structures can be reconciled by taking the higher coordination number of the cations in the lariat ether complexes into account.
Highly Conjugated p‐Quinonoid π‐Extended Tetrathiafulvalene Derivatives: A Class of Highly Distorted Electron Donors
Authors: Díaz Marta C. , Illescas Beatriz M. , Martín Nazario , Viruela Rafael , Viruela Pedro M. , Ortí Enrique , Brede Ortwin , Zilbermann Israel , Guldi Dirk M. 
Published: April 2004

AbstractA new class of π‐extended TTF‐type electron donors (11 a–c) has been synthesized by Wittig–Horner olefination of bianthrone (9) with 1,3‐dithiole phosphonate esters (10 a–c). In cyclic voltammetry experiments, donors 11 a–c reveal a single, electrochemically irreversible oxidation—yielding the corresponding dicationic products—at relatively low oxidation potentials (∼0.7–0.8 V). Theoretical calculations, performed at the DFT level (B3 P86/6‐31 G*), predict a highly‐folded C2h structure for 11 a. In the ground state, the molecule adopts a double saddle‐like conformation to compensate the steric hindrance. The calculations suggest that the intramolecular charge transfer associated with the HOMO→LUMO transition is responsible for an absorption band observed above 400 nm. While the radical cation 11 a.+ retains the folded C2h structure predicted for the neutral molecule as the most stable conformation, the dication 11 a2+ has a fully aromatic D2 structure, formed by an orthogonal 9,9′‐bianthryl central unit to which two singly‐charged dithiole rings are attached. The drastic conformational changes that compounds 11 undergo upon oxidation account for their electrochemical properties. By means of pulse radiolysis measurements, radical‐induced one‐electron oxidation of 11 a–c was shown to lead to the radical cation species (11 a–c.+), which were found to disproportionate with generation of the respective dication species (11 a–c2+) and the neutral molecules (11 a–c).
Effects of Chain Length and Au Spin‐Orbit Coupling on 3(ππ*) Emission from Bridging Cn2− Units: Theoretical Characterization of Spin‐Forbidden Radiative Transitions in Metal‐Capped One‐Dimensional Carbon Chains [H3PAu(CC)nAuPH3]
Authors: Cao Zexing , Zhang Qianer 
Published: April 2004

AbstractDensity functional theory and CASSCF calculations have been used to optimize the geometries of binuclear gold(I) complexes [H3PAu(CC)nAuPH3] (n=1–6) in their ground states and selected lowest energy 3(ππ*) excited states. Vertical excitation energies obtained by time‐dependent density functional calculations for the spin‐forbidden singlet–triplet transitions have exponential‐decay size dependence. The predicted singlet–triplet splitting limit of [H3PAu(CC)∝AuPH3] is about 8317 cm−1. Calculated singlet–triplet transition energies are in reasonable agreement with available experimental observations. The effect of the heavy atom Au spin‐orbit coupling on the 3(ππ*) emission of these metal‐capped one‐dimensional carbon allotropes has been investigated by MRCI calculations. The contribution of the spin‐ and dipole‐allowed singlet excited state to the spin‐orbit‐coupling wave function of the 3(ππ*) excited state makes the low‐lying acetylenic triplet excited states become sufficiently allowed so as to appear in both electronic absorption and emission.
Photochemical and Electronic Properties of Conjugated Bis(azo) Compounds: An Experimental and Computational Study
Authors: Cisnetti Federico , Ballardini Roberto , Credi Alberto , Gandolfi Maria Teresa , Masiero Stefano , Negri Fabrizia , Pieraccini Silvia , Spada Gian Piero 
Published: April 2004

AbstractWe have investigated the photophysical, photochemical and electrochemical properties of two bis(azo) derivatives, (E,E)‐m‐1 and (E,E)‐p‐1. The two compounds, which can be viewed as being composed of a pair of azobenzene units sharing one of their phenyl rings, differ only for the relative position of the two azo groups on the central phenyl ring—meta and para for m‐1 and p‐1, respectively. The UV‐visible absorption spectra and photoisomerisation properties are noticeably different for the two structural isomers; (E,E)‐m‐1 behaves similarly to (E)‐azobenzene, while (E,E)‐p‐1 exhibits a substantial red shift in the absorption bands and a decreased photoreactivity. The three geometric isomers of m‐1, namely the E,E, E,Z and Z,Z isomers, cannot be resolved in a mixture by absorption spectroscopy, while the presence of three distinct species can be revealed by analysis of the absorption changes observed upon photoisomerisation of (E,E)‐p‐1. Quantum chemical ZINDO/1 calculations of vertical excitation energies nicely reproduce the observed absorption changes and support the idea that, while the absorption spectra of the geometrical isomers of m‐1 are approximately given by the sum of the spectra of the constituting azobenzene units in their relevant isomeric form, this is not the case for p‐1. From a detailed study on the E→Z photoisomerisation reaction it was observed that the photoreactivity of an azo unit in m‐1 is influenced by the isomeric state of the other one. Such observations indicate a different degree of electronic coupling and communication between the two azo units in m‐1 and p‐1, as confirmed by electrochemical experiments and quantum chemical calculations. The decreased photoisomerisation efficiency of (E,E)‐p‐1 compared to (E,E)‐m‐1 is rationalised by modelling the geometry relaxation of the lowest π–π* state. These results are expected to be important for the design of novel oligomers and polymers, based on the azobenzene unit, with predetermined photoreactivity.
Supramolecular Recognition: Protonmotive‐Driven Switches or Motors?
Authors: Crowley James D. , Goshe Andrew J. , Steele Ian M. , Bosnich Brice 
Published: April 2004

AbstractA dicationic molecular receptor bearing two cofacially disposed terpyridyl‐Pd‐Cl units forms stable 1:1 host–guest complexes with planar, neutral platinum(II) complexes. When the guest is modified to incorporate a pyridine group, the now basic guest is protonated by trifluoroacetic acid in acetonitrile solutions. The basic yellow guest forms a stable, deep red 1:1 host–guest complex with the yellow palladium receptor. Addition of trifluoroacetic acid to this host–guest complex leads to the displacement of the guest from the receptor. It is proposed that the dissociation of the guest is caused by electrostatic repulsion between the dicationic receptor and the positively charged protonated guest. Addition of base restores the host–guest complex. This protonmotive translocation of the guest from the host to the solution is discussed in terms of the mechanisms that drive molecular motors, the power stroke and the Brownian ratchet. It is concluded that the system is best described as a molecular switch that operates by the same mechanism as one stroke of a molecular motor
Ferrocene‐Modified Purines as Potential Electrochemical Markers: Synthesis, Crystal Structures, Electrochemistry and Cytostatic Activity of (Ferrocenylethynyl)‐ and (Ferrocenylethyl)purines
Authors: Hocek Michal , Štěpnička Petr , Ludvík Jiří , Císařová Ivana , Votruba Ivan , Řeha David , Hobza Pavel 
Published: April 2004

AbstractPalladium‐catalyzed Sonogashira cross‐coupling reactions of halopurines 9‐benzyl‐6‐chloropurine (2 a), 9‐benzyl‐8‐bromoadenine (2 b), and 9‐benzyl‐2‐chloroadenine (2 c) with ethynylferrocene (1) gave the corresponding (ferrocenylethynyl)purines 3 a–c in moderate to good yields. Catalytic hydrogenation of these alkynes over Pd/C afforded the respective saturated [2‐(ferrocenyl)ethyl]purines 4 a–c. The crystal structures 3 a, 3 b, 4 a and 4 b as determined by X‐ray diffraction show interesting solid‐state interactions, markedly different for purines 3 a and 4 a on one hand and adenines 3 b and 4 b that possess a free amino group on the other. Electrochemistry of electrochemically labelled purines 3 and 4 has been studied by voltammetry and cyclic voltammetry on platinum disc electrode and the experimental oxidation potentials were confirmed and explained by ionization potentials from theoretical DFT calculations. Several compounds of this series exhibited a considerable cytostatic effect.