bluuebunny/crossref_metadata_2025 huggingface dataset:
Purification and characterization of cytochrome c′ from Neisseria meningitidis
Authors: Huston W.M. , Lowe E.C. , Butler C.S. , Moir J.W.B.
Published: February 2005

Cytochrome c′, a c-type cytochrome with unique spectroscopic and magnetic properties, has been characterized in a variety of denitrifying and photosynthetic bacteria. Cytochrome c′ has a role in defence and/or removal of NO but the mechanism of action is not clear. To examine the function of cytochrome c′ from Neisseria meningitidis, the protein was purified after heterologous overexpression in Escherichia coli. The electronic spectra of the oxidized c′ demonstrated a pH-dependent transition (over the pH range of 6–10) typical of known c′-type cytochromes. Interestingly, the form in which NO is supplied determines the redox state of the resultant haem-nitrosyl complex. Fe(III)–NO complexes were formed when Fe(II) or Fe(III) cytochrome c′ was sparged with NO gas, whereas an Fe(II)–NO complex was generated when NO was supplied using DEA NONOate (diazeniumdiolate).
Electron transport through nitrate and nitrite reductases in Campylobacter jejuni
Authors: Pittman M.S. , Kelly D.J.
Published: February 2005

Campylobacter jejuni is a small genome pathogen that is incapable of growing strictly anaerobically due to its dependence on an oxygen-requiring ribonucleotide reductase for DNA synthesis. Nevertheless, it has a complex branched respiratory chain, which allows the use of several alternative electron acceptors for growth under oxygen-limited conditions. C. jejuni is equipped with both nitrate reductase (Nap) and nitrite reductase (Nrf) located in the periplasm, each predicted to receive electrons from menaquinol through distinct redox proteins. The pathways of electron transport to nitrate and nitrite are reviewed in this paper. Nitrate is considered as a potential in vivo electron acceptor and a role for nitrite reductase in NO detoxification is suggested.
Transcriptional regulation of nitric oxide reduction in Ralstonia eutropha H16
Authors: Büsch A. , Strube K. , Friedrich B. , Cramm R.
Published: February 2005

Nitric oxide reduction in Ralstonia eutropha H16 is catalysed by the quinol-dependent NO reductase NorB. norB and the adjacent norA form an operon that is controlled by the σ54-dependent transcriptional activator NorR in response to NO. A NorR derivative containing MalE in place of the N-terminal domain binds to a 73 bp region upstream of norA that includes three copies of the putative upstream activator sequence GGT-(N7)-ACC. Mutations altering individual bases of this sequence resulted in an 80–90% decrease in transcriptional activation by wild-type NorR. Similar motifs are present in several proteobacteria upstream of genes encoding proteins of NO metabolism. The N-terminal domain of NorR contains a GAF module and is hypothesized to interact with a signal molecule. A NorR derivative lacking this domain activates the norAB promoter constitutively. Amino acid exchanges within the GAF module identified a cysteine residue that is essential for promoter activation by NorR. Signal sensing by NorR is negatively modulated by the iron-containing protein NorA.
Transcriptional regulation of a hybrid cluster (prismane) protein
Authors: Filenko N.A. , Browning D.F. , Cole J.A.
Published: February 2005

HCP (hybrid-cluster protein) contains two Fe/S clusters, one of which is a hybrid [4Fe-2S-2O] cluster. Despite intensive study, its physiological function has not been reported. The Escherichia coli hcp gene is located in a two-gene operon with hcr, which encodes an NADH-dependent HCP reductase. E. coli HCP is detected after anaerobic growth with nitrate or nitrite: possible roles for it in hydroxylamine or nitric oxide reduction have been proposed. To study the regulation and role of HCP, an hcp::lacZ fusion was constructed and transformed into fnr, arcA and norR mutant strains of E. coli. Transcription from the hcp promoter was induced during anaerobic growth. Only the fnr mutant was defective in hcp expression. Nitrate- and nitrite-induced transcription from the hcp promoter was activated by the response regulator proteins NarL and NarP. Gel retardation assays were used to show that FNR (fumarate-nitrate regulation) and NarL form a complex with the hcp promoter. Transcription of the hcp-hcr operon initiates at a thymine nucleotide located 31 bp upstream of the translation-initiation codon. HCP has been overexpressed from a recombinant plasmid for physiological studies.
Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria
Authors: Van de Pas-Schoonen K.T. , Schalk-Otte S. , Haaijer S. , Schmid M. , Op den Camp H. , Strous M. , Gijs Kuenen J. , Jetten M.S.M.
Published: February 2005

In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.
Evolution of the bacterial phosphotransferase system: from carriers and enzymes to group translocators
Authors: Saier M.H. , Hvorup R.N. , Barabote R.D.
Published: February 2005

The bacterial phosphotransferase system (PTS) is a structurally and functionally complex system with a surprising evolutionary history. The substrate-recognizing protein constituents of the PTS (Enzymes II) derive from at least four independent sources. Some of the non-PTS precursor constituents have been identified, and evolutionary pathways taken have been proposed. Our analyses suggest that two of these independently evolving systems are still in transition, not yet having acquired the full-fledged characteristics of PTS Enzyme II complexes. The work described provides detailed insight into the process of catalytic protein evolution.
Thyroid hormone transporters
Authors: Friesema E.C.H. , Jansen J. , Visser T.J
Published: February 2005

Thyroid hormone is important for development of various tissues, in particular brain, and for regulation of metabolic processes throughout life. The follicular cells of the thyroid gland produce predominantly T4 (thyroxine), but the biological activity of thyroid hormone is largely exerted by T3 (3,3′,5-tri-iodothyronine). The deiodinases involved in T4-to-T3 conversion or T4 and T3 degradation, as well as the T3 receptors, are located intracellularly. Therefore the action and metabolism of thyroid hormone require transport of iodothyronines across the cell membrane via specific transporters. Recently, a number of transporters capable of cellular uptake of iodothyronines have been identified. The most specific transporters identified so far are OATP1C1 and MCT8, which appear to be involved in T4 transport across the blood–brain barrier, and in T3 transport into brain neurons, respectively. The MCT8 gene is located on human chromosome Xq13, and mutations in MCT8 are associated with X-linked severe psychomotor retardation and elevated serum T3 levels.
Neutral amino acid transport in epithelial cells and its malfunction in Hartnup disorder
Authors: Bröer S. , Cavanaugh J.A. , Rasko J.E.J.
Published: February 2005

Hartnup disorder is an autosomal recessive abnormality of renal and gastrointestinal neutral amino acid transport. A corresponding transport activity has been characterized in kidney and intestinal cells and named system B0. The failure to resorb amino acids in this disorder is thought to be compensated by a protein-rich diet. However, in combination with a poor diet and other factors, more severe symptoms can develop in Hartnup patients, including a photosensitive pellagra-like skin rash, cerebellar ataxia and other neurological symptoms. Homozygosity mapping in a Japanese family and linkage analysis on six Australian pedigrees placed the Hartnup disorder gene at a locus on chromosome 5p15. This fine mapping facilitated a candidate gene approach within the interval, which resulted in the cloning and characterization of a novel member of the sodium-dependent neurotransmitter transporter family (B0AT1, SLC6A19) from mouse and human kidney, which shows all properties of system B0. Flux experiments and electrophysiological recording showed that the transporter is Na+ dependent and Cl− independent, electrogenic and actively transports most neutral amino acids. In situ hybridization showed strong expression in intestinal villi and in the proximal tubule of the kidney. Expression of B0AT1 was restricted to kidney, intestine and skin. A total of ten mutations have been identified in SLC6A19 that co-segregate with disease in the predicted recessive manner, with the majority of affected individuals being compound heterozygotes. These mutations lead to altered neutral amino acid transport function compared to the wild-type allele in vitro. One of the mutations occurs in members of the original Hartnup family described in 1956, thereby defining SLC6A19 as the ‘Hartnup’-gene.
Biological functions of SLC5A8, a candidate tumour suppressor
Authors: Ganapathy V. , Gopal E. , Miyauchi S. , Prasad P.D.
Published: February 2005

SLC5A8 is a candidate tumour suppressor gene that is silenced in colon cancer, gastric cancer and possibly other cancers in humans. This gene codes for a transporter belonging to the Na+/glucose co-transporter gene family (SLC5). The cancer-associated silencing of the gene involves hypermethylation of CpG islands present in exon 1 of the gene. SLC5A8 is expressed in colon, ileum, kidney and thyroid gland. The protein coded by the gene mediates the Na+-coupled and electrogenic transport of a variety of monocarboxylates, including short-chain fatty acids, lactate and nicotinate. It may also transport iodide. The normal physiological function of this transporter in the intestinal tract and kidney is likely to facilitate the active absorption of short-chain fatty acids, lactate and nicotinate. One of the short-chain fatty acids that serves as a substrate for SLC5A8 is butyrate. This fatty acid is an inhibitor of histone deacetylases and is known to induce apoptosis in a variety of tumours including colonic tumour. Since butyrate is produced in the colonic lumen at high concentrations by bacterial fermentation of dietary fibre, we speculate that the ability of SLC5A8 to mediate the entry of this short-chain fatty acid into colonic epithelial cells underlies the potential tumour suppressor function of this transporter.
ABC transporters in the balance: is there a role in multidrug resistance?
Authors: Polgar O. , Bates S.E.
Published: February 2005

Drug resistance can occur at several levels and is the major cause of treatment failure in oncology. The ABC (ATP-binding cassette) transporters, beginning with the discovery of P-gylcoprotein (Pgp) almost 30 years ago, have been intensively studied as potential mediators of drug resistance. Although we understand that drug resistance is almost certainly multifactorial, investigators have attempted to link anticancer drug resistance to overexpression of ABC transporters and the consequent reduction in drug accumulation. A body of evidence implicated Pgp as being important in clinical outcome; however, critical studies aimed at proving the hypothesis using Pgp inhibitors in clinical trials have to date failed. Identification of the MRP (multidrug resistance protein)/ABCC subfamily expanded the possible mechanisms of reduced drug accumulation, and the discovery of ABCG2 added a new chapter in these investigations. Correlative studies examining ABCG2 and the ABCC subfamily members in clinical drug resistance have been less avidly pursued, while basic molecular studies of structure and function have proceeded briskly. Recently, studies have focused on how single nucleotide polymorphism in multidrug transporters might affect the pharmacokinetics and pharmacodynamics of anticancer agents. These studies suggest an important role for ABC transporters in pharmacology, independent of the ultimate determination of their role in multidrug resistance.
Nutrient sensing systems for rapid activation of the protein kinase A pathway in yeast
Authors: Thevelein J.M. , Geladé R. , Holsbeeks I. , Lagatie O. , Popova Y. , Rolland F. , Stolz F. , Van de Velde S. , Van Dijck P. , Vandormael P. , Van Nuland A. , Van Roey K. , Van Zeebroeck G. , Yan B.
Published: February 2005

The cAMP-protein kinase A (PKA) pathway in the yeast Saccharomyces cerevisiae controls a variety of properties that depend on the nutrient composition of the medium. High activity of the pathway occurs in the presence of rapidly fermented sugars like glucose or sucrose, but only as long as growth is maintained. Growth arrest of fermenting cells or growth on a respirative carbon source, like glycerol or ethanol, is associated with low activity of the PKA pathway. We have studied how different nutrients trigger rapid activation of the pathway. Glucose and sucrose activate cAMP synthesis through a G-protein-coupled receptor system, consisting of the GPCR Gpr1, the Gα protein Gpa2 and its RGS protein Rgs2. Glucose is also sensed intracellularly through its phosphorylation. Specific mutations in Gpr1 abolish glucose but not sucrose signalling. Activation of the PKA pathway by addition of a nitrogen source or phosphate to nitrogen- or phosphate-starved cells, respectively, is not mediated by an increase in cAMP. Activation by amino acids is triggered by the general amino acid permease Gap1, which functions as a transporter/receptor. Short truncation of the C-terminus results in constitutively activating alleles. Activation by ammonium uses the ammonium permeases Mep1 and Mep2 as receptor. Specific point mutations in Mep2 uncouple signalling from transport. Activation by phosphate is triggered a.o. by the Pho84 phosphate permease. Several mutations in Pho84 separating transport and signalling or triggering constitutive activation have been obtained.
Amino acid sensing by Ssy1
Authors: Poulsen P. , Wu B. , Gaber R.F. , Ottow Kim , Andersen H.A. , Kielland-Brandt M.C.
Published: February 2005

Saccharomyces cerevisiae senses extracellular amino acids using two members of the family of amino acid transporters, Gap1 or Ssy1; aspects of the latter are reviewed here. Despite resemblance with bona fide transporters, Ssy1 appears unable to facilitate transport. Exposure of yeast to amino acids results in Ssy1-dependent transcriptional induction of several genes, in particular some encoding amino acid transporters. Amino acids differ strongly in their potency, leucine being the most potent one known. Using a selection system in which potassium uptake was made dependent on amino acid signalling, our laboratory has obtained and described gain-of-function mutations in SSY1. Some alleles conferred inducer-independent signalling; others increased apparent affinity for inducers. These results revealed that amino acid transport is not required for signalling and support the notion that sensing by Ssy1 occurs via its direct interaction with extracellular amino acids. Current work includes development of quantitative assays of sensing. We use the finding by Per Ljungdahl's laboratory that the signal transduction from Ssy1 involves proteolytic removal of an inhibitory part of the transcriptional activator Stp1. Protein-A Z-domain fused to the C-terminus of Stp1 and Western analysis using antibody against horseradish peroxidase allow quantification of sensing.
Sugar sensing and signalling networks in plants
Authors: Rolland F. , Sheen J.
Published: February 2005

Plant sugar signalling operates in a complex network with plant-specific hormone signalling pathways. Hexokinase was identified as an evolutionarily conserved glucose sensor that integrates light, hormone and nutrient signalling to control plant growth and development.
Nitrate and glutamate sensing by plant roots
Authors: Filleur S. , Walch-Liu P. , Gan Y. , Forde B.G.
Published: February 2005

The architecture of a root system plays a major role in determining how efficiently a plant can capture water and nutrients from the soil. Growth occurs at the root tips and the process of exploring the soil volume depends on the behaviour of large numbers of individual root tips at different orders of branching. Each root tip is equipped with a battery of sensory mechanisms that enable it to respond to a range of environmental signals, including nutrients, water potential, light, gravity and touch. We have previously identified a MADS (MCM1, agamous, deficiens and SRF) box gene (ANR1) in Arabidopsis thaliana that is involved in modulating the rate of lateral root growth in response to changes in the external NO3− supply. Transgenic plants have been generated in which a constitutively expressed ANR1 protein can be post-translationally activated by treatment with dexamethasone (DEX). When roots of these lines are treated with DEX, lateral root growth is markedly stimulated but there is no effect on primary root growth, suggesting that one or more components of the regulatory pathway that operate in conjunction with ANR1 in lateral roots may be absent in the primary root tip. We have recently observed some very specific effects of low concentrations of glutamate on root growth, resulting in significant changes in root architecture. Experimental evidence suggests that this response involves the sensing of extracellular glutamate by root tip cells. We are currently investigating the possible role of plant ionotropic glutamate receptors in this sensory mechanism.
Carbon source induced yeast-to-hypha transition in Candida albicans is dependent on the presence of amino acids and on the G-protein-coupled receptor Gpr1
Authors: Maidan M.M. , Thevelein J.M. , Van Dijck P.
Published: February 2005

Yeast-to-hypha transition in Candida albicans can be induced by a wide variety of factors, including specific nutrients. We have started to investigate the mechanism by which some of these nutrients may be sensed. The G-protein-coupled receptor Gpr1 is required for yeast-to-hypha transition on various solid hypha-inducing media. Recently we have shown induction of Gpr1 internalization by specific amino acids, e.g. methionine. This suggests a possible role for methionine as a ligand of CaGpr1. Here we show that there is a big variation in methionine-induced hypha formation depending on the type of carbon source present in the medium. In addition high glucose concentrations repress hypha formation whereas a concentration of 0.1%, which mimics the glucose concentration present in the bloodstream, results in maximal hypha formation. Hence, it remains unclear whether Gpr1 senses sugars, as in Saccharomyces cerevisiae, or specific amino acids like methionine.
Nutrient sensing in pancreatic β cells suppresses mitochondrial superoxide generation and its contribution to apoptosis
Authors: Martens G. , Cai Y. , Hinke S. , Stangé G. , Van De Casteele M. , Pipeleers D.
Published: February 2005

Excessively high glucose concentrations have been shown to damage tissues through stimulation of mitochondrial superoxide generation. This effect has therefore been considered as a potential cause for dysfunction and death of pancreatic β cells in diabetes. We have examined whether the rate of glucose metabolism in isolated rat β cells is correlated with their formation of oxygen radicals. It was found that high rates of glucose metabolism did not stimulate the formation of superoxide and H2O2 but suppressed it. The higher rates of superoxide production in β cells with lower mitochondrial metabolic activity contributed to the susceptibility of these cells to apoptosis.
Expression of sweet taste receptors of the T1R family in the intestinal tract and enteroendocrine cells
Authors: Dyer J. , Salmon K.S.H. , Zibrik L. , Shirazi-Beechey S.P.
Published: February 2005

The composition of the intestinal luminal content varies considerably with diet. It is important therefore that the intestinal epithelium senses and responds to these significant changes and regulates its functions accordingly. Although it is becoming evident that the gut epithelium senses and responds to luminal nutrients, little is known about the nature of the nutrient sensing molecule and the downstream cellular events. A prototype example is the modulation in the capacity of the gut to absorb monosaccharides via the intestinal luminal membrane Na+/glucose cotransporter, SGLT1. The experimental evidence suggests that luminal sugar is sensed by a glucose sensor residing on the luminal membrane of the gut epithelium and linked to a G-protein-coupled receptor, cAMP/PKA (protein kinase A) pathway, resulting ultimately in modulation of intestinal monosaccharide absorption. Here we report the expression, at mRNA and protein levels, of members of the T1R sweet taste receptors, and the α-subunit of the G-protein gustducin, in the small intestine and the enteroendocrine cell line, STC-1. In the small intestine, there is a highly coordinated expression of sweet taste receptors and gustducin, a G-protein implicated in intracellular taste signal transduction, throughout the gut. The potential involvement of these receptors in sugar sensing in the intestine will facilitate our understanding of intestinal nutrient sensing, with implications for better nutrition and health maintenance.
Impact of flowering on bird community dynamics in some central Victorian eucalypt forests
Authors: MCGOLDRICK J. M. , MACNALLY R.
Published: February 2005

Many species of Eucalyptus in Australia provide copious amounts of nectar during their reproductive seasons. The nectar is used by many animal species but especially by birds, insects and some bats, which act as pollinators. One of the major features of eucalypt flowering in southern Australia is the patchy, asynchronous flowering of different species, which appears to drive mass nomadism of nectarivorous birds among regions and among habitats. Here we explore whether flowering asynchrony or climate is primarily responsible for the influxes and effluxes of vast numbers of nectarivorous birds in central Victoria, Australia. By using a structured sampling program, we show that winter flowering by red ironbark Eucalyptus tricarpa is the most likely agent controlling avian‐nectarivore dynamics rather than climatic differences among regions. Densities and species richness of nectarivores, and numbers of nectarivory events, are all closely related to measures of flowering intensity. However, non‐ nectarivores, such as insectivores and granivores, show no relationships with either habitat or region. We discuss how dependence on a patchily distributed but highly rewarding resource such as nectar influences population densities and community structure in birds.
Improvement of efficiency and stability of polymer light-emitting devices by modifying indium tin oxide anode surface with ultrathin tetrahedral amorphous carbon film
Authors: Chen B. J. , Sun X. W. , Tay B. K. , Ke L. , Chua S. J.
Published: February 2005

Poly(p-phenylene vinylene)-based polymer light-emitting devices using different thicknesses of tetrahedral amorphous carbon ultrathin films between indium tin oxide and polyethylenedioxythiophene hole transporting layer have been fabricated. The device with a 0.5nm tetrahedral amorphous carbon (ta-C) layer has the highest luminance and current efficiency compared to that of other devices. The current efficiency of a standard device without a ta-C layer is 1.1cd∕A at 5V, however, the current efficiency of a device with a ta-C layer thickness of 0.5nm is 2.7cd∕A; the current efficiency is improved about 2.5 times compared to the standard device. The improvement of the efficiency is due to blocking the hole injection from anode and balancing the hole and electron current. The lifetime of a device with a ta-C layer is significantly much longer than the standard device, and the device with a 0.5nm ta-C layer has the longest lifetime.
Experimental study of the K2392Πg3 state by perturbation facilitated infrared-infrared double resonance and two-photon excitation spectroscopy
Authors: Chu Yizhuo , Xie Feng , Li Dan , Li Li , Sovkov V. B. , Ivanov V. S. , Lyyra A. M.
Published: February 2005

The K2392Πg3 state has been observed by perturbation facilitated infrared-infrared double resonance and two-photon excitations. The vibrational numbering of the 2Πg3 levels was determined by resolved fluorescence into the bound levels as well as to the continuum of the aΣu+3 state. The rotational assignment of the 2Πg3 levels excited by two-photon transitions was determined from excitation frequencies and resolved fluorescence into the bound levels of the aΣu+3 and bΠu3 states. Molecular constants obtained from these observed levels agree with theoretical constants.
Connection between the regular approximation and the normalized elimination of the small component in relativistic quantum theory
Authors: Filatov Michael , Cremer Dieter
Published: February 2005

The regular approximation to the normalized elimination of the small component (NESC) in the modified Dirac equation has been developed and presented in matrix form. The matrix form of the infinite-order regular approximation (IORA) expressions, obtained in [Filatov and Cremer, J. Chem. Phys. 118, 6741 (2003)] using the resolution of the identity, is the exact matrix representation and corresponds to the zeroth-order regular approximation to NESC (NESC-ZORA). Because IORA (=NESC-ZORA) is a variationally stable method, it was used as a suitable starting point for the development of the second-order regular approximation to NESC (NESC-SORA). As shown for hydrogenlike ions, NESC-SORA energies are closer to the exact Dirac energies than the energies from the fifth-order Douglas–Kroll approximation, which is much more computationally demanding than NESC-SORA. For the application of IORA (=NESC-ZORA) and NESC-SORA to many-electron systems, the number of the two-electron integrals that need to be evaluated (identical to the number of the two-electron integrals of a full Dirac–Hartree–Fock calculation) was drastically reduced by using the resolution of the identity technique. An approximation was derived, which requires only the two-electron integrals of a nonrelativistic calculation. The accuracy of this approach was demonstrated for heliumlike ions. The total energy based on the approximate integrals deviates from the energy calculated with the exact integrals by less than 5×10−9hartree units. NESC-ZORA and NESC-SORA can easily be implemented in any nonrelativistic quantum chemical program. Their application is comparable in cost with that of nonrelativistic methods. The methods can be run with density functional theory and any wave function method. NESC-SORA has the advantage that it does not imply a picture change.
Tetra-t-butyl magnesium phthalocyanine on gold: Electronic structure and molecular orientation
Authors: Biswas I. , Peisert H. , Schwieger T. , Dini D. , Hanack M. , Knupfer M. , Schmidt T. , Chassé T.
Published: February 2005

In this work we have investigated the electronic structure and the molecular orientation of (t-Bu)4PcMg (tetra-t-butyl magnesium phthalocyanine) on polycrystalline and single crystalline gold substrates using photoemission spectroscopy and x-ray absorption spectroscopy, and we compare the results to the unsubstituted PcCu (copper phthalocyanine). The C 1s photoemission spectrum is described similar to unsubstituted relatives with an additional component for the aliphatic substituents. The variation of the excitation energy causes distinct differences in the shape of the C 1s spectrum, which is very useful for the analysis of the molecular orientation in the uppermost layer. It is shown that despite of the sterically demanding substituents, ordered sublimed films of (t-Bu)4PcMg are accessible, the orientation of the molecules, however, is different from the orientation of the unsubstituted relatives.
Finite length nanotubes: Ground state degeneracy and single-electron spectrum
Authors: Mestechkin M. M.
Published: February 2005

By means of the Rutherford method it is found that in zigzag carbon nanotubes with an even number n=2j of hexagons in a tube ring the gap between occupied and empty single-electron levels disappears. The frontier level is shown to be at least doubly degenerate. The reason for the loss of the zero level (for n=2j) upon reaching the infinite length limit is discussed. The existence of a lot of states, specific for finite nanotubes, with the energy very close to the Fermi level is shown, and the number of these states is estimated. The existence of a narrow (of order 10−4eV) conduction band, formed by edge states, is demonstrated in tight binding approximation. If the Coulomb interaction is taken into account, the half-filled degenerate π-electronic level continues to exist. The open shell Hartree–Fock theory demonstrates the degenerate configuration splitting onto three equidistant terms: two singlets with the seniority numbers 0 and 1, and the lowest triplet in accordance with the Hund rule. The behavior of the single-electron gap is alike for all three terms: the gap is of the order 0.2–0.01 eV. The Rutherford method gives analytical results for armchair nanotubes as well, which explains the gap oscillations as a function of the tube length with a period of three rings. Application of the degenerate open shell Hartree–Fock theory supports this explanation.
The energetics and structural properties of diazomethyl (HCNN) and cyanomidyl (HNCN) radicals and their related cations and anions from ab initio calculations
Authors: Puzzarini Cristina , Gambi Alberto
Published: February 2005

The molecular structures and energetics of diazomethyl (HCNN) and cyanomidyl (HNCN) radicals and their related cations (HCNN+,HNCN+) and anions (HCNN−,HNCN−) are reported at a high level of accuracy. The singles and doubles coupled-cluster method including a perturbational correction for connected triple excitations with systematic sequences of correlation consistent basis sets have been employed. Extrapolation to the complete basis set limit has been used with accurate treatments of core-valence correlation effects in order to accurately predict molecular properties, ionization potentials, electron affinities as well as C–H and N–H bond dissociation energies. For all the species studied, harmonic vibrational frequencies have also been evaluated in order to obtain zero-point corrections to ionization potentials, electron affinities, and dissociation energies.
Configurational temperatures and interactions in charge-stabilized colloid
Authors: Han Yilong , Grier David G.
Published: February 2005

A system’s temperature can be expressed in terms of its constituents’ instantaneous positions rather than their momenta. Such configurational temperature definitions offer substantial benefits for experimental studies of soft condensed matter systems, most notably their applicability to overdamped systems whose instantaneous momenta may not be accessible. We demonstrate that the configurational temperature formalism can be derived from the classical hypervirial theorem, and introduce a hierarchy of hyperconfigurational temperature definitions, which are particularly well suited for experimental studies. We then use these analytical tools to probe the electrostatic interactions in monolayers of charge-stabilized colloidal spheres confined by parallel glass surfaces. The configurational and hyperconfigurational temperatures, together with a thermodynamic sum rule, provide previously lacking self-consistency tests for interaction measurements based on digital video microscopy, and thereby cast light on controversial reports of confinement-induced like-charge attractions. We further introduce a method to determine unknown parameters in a model potential by using consistency of the configurational and hyperconfigurational temperatures as a set of constraints. This approach, in principle, also should provide the basis for a model-free estimation of the pair potential.
Superexchange and electron correlations in alkali fullerides AC60, A=K, Rb, Cs
Authors: Nikolaev A. V. , Michel K. H.
Published: February 2005

Superexchange interactions in alkali fullerides AC60 are derived for C60 molecular ions separated by interstitial alkali-metal ions. We use a multiconfiguration approach which comprises the lowest molecular orbital states of the C60 molecule and the excited s and d states of the alkali-metal atom A. Interactions are described by the valence bond (Heitler–London) method for a complex (C60–A–C60)– with two valence electrons. The electronic charge transfer between the alkali-metal atom and a neighboring C60 molecule is not complete. The occupation probability of excited d and s states of the alkali atom is not negligible. In correspondence with the relative positions of the C60 molecules and A atoms in the polymer crystal, we consider 180° and 90° (angle) superexchange pathways. For the former case the ground state is found to be a spin singlet separated from a triplet at ∼20K. For T<20K there appear strong spin correlations for the 180° superexchange pathway. The results are related to spin lattice relaxation experiments on CsC60 in the polymerized and in the quenched cubic phase.
Real-space post-Hartree–Fock correlation models
Authors: Becke Axel D.
Published: February 2005

Real-space models of nondynamical correlation between electrons of opposite spin and of parallel spin in multicenter (molecular) systems are discussed. These models are designed to be partnered with Hartree–Fock or exact Kohn–Sham exchange. Thus the numerous and well-known problems of local density-functional exchange-correlation approximations, especially in stretched odd-electron systems, are circumvented.
Correlation effects due to an axial propagation of projectiles in a dusty plasma
Authors: Ali S. , Nasim M. H. , Murtaza G.
Published: February 2005

Generalized expressions for the Debye potential and the wake field potential are derived due to an axial propagation of dust grain projectiles. The dust grain projectiles are assumed to lie on sets of concentric circles propagating through the dusty plasma with a constant velocity along the z axis. Each circle carries N number of dust grain projectiles having radius rl and angular position (2πm)∕N. A couple of specific cases of electrostatic potential due to four and eight projectiles are studied in some detail both analytically and numerically.
Aging and free surface flow of a thixotropic fluid
Authors: Huynh H. T. , Roussel N. , Coussot P.
Published: February 2005

Free surface flows of thixotropic fluids such as paints, self-compacting concrete, or natural mudflows are of noticeable practical interest. Here we study the basic characteristics of the uniform flow of a layer of thixotropic fluid under gravity. A theoretical approach relying on a simple thixotropy constitutive equation shows that after some time at rest over a small slope angle the fluid layer should start to flow rather abruptly beyond a new, larger, critical slope angle. The theory also predicts that the critical time at which the layer velocity should significantly increase is proportional to the duration of the preliminary rest and tends to infinity when the new slope approaches the critical slope. Experiments carried out with different suspensions show that the qualitative trends of the flows are in very good agreement with the theoretical predictions, except that the critical time for flow start appears to be proportional to a power 0.6 of the time of rest whereas the theory predicts a linear dependence. We show that this indicates a restructuration process at rest differing from the restructuration process under flow.
Relativistic corrections to the diamagnetic term of the nuclear magnetic shielding: Analysis of contributions from localized orbitals
Authors: Gómez Sergio S. , Melo Juan I. , Romero Rodolfo H. , Aucar Gustavo A. , de Azúa Martín Ruiz
Published: February 2005

We have calculated the relativistic corrections to the diamagnetic term of the nuclear magnetic shielding constants for a series of molecules containing heavy atoms. An analysis of the contributions from localized orbitals is performed. We establish quantitatively the relative importance of inner core and valence shell molecular orbitals in each correcting term. Contributions from the latter are much less important than those from the former. The calculated values of the correction σL-PSO, first derived within the linear response elimination of small component formalism, show a power-law dependence on the nuclear charge ∼Z3.5, in contrast with the ∼Z3.1 behavior of the mass-velocity external-field correction to the paramagnetic term previously reported.
Evaluating changes of writhe in computer simulations of supercoiled DNA
Authors: de Vries Renko
Published: February 2005

We compute changes in the writhe of a polygonal space curve when one of the vertices is displaced. The resulting expressions can be used in simulations of supercoiled DNA. For Brownian dynamics simulations, the expressions can be used to eliminate the explicit twisting degree of freedom. For Monte Carlo simulations, they can be used in fast local moves. Preliminary Monte Carlo simulations using only such fast local moves show that these can be used to efficiently simulate small DNA supercoils.
Stability limits in binary fluids mixtures
Authors: Imre Attila R. , Kraska Thomas
Published: February 2005

The stability limits in binary fluid mixtures are investigated on the basis of the global phase diagram approach employing a model for the attracting hard-sphere fluid. In addition to the diffusion spinodals the mechanical spinodals are included. As a result one finds topologically different types of the diffusion spinodals while only one shape exists for the mechanical spinodals which are present in the region of liquid-vapor equilibria only. The diffusion spinodals represent the underlying properties of the phase behavior. The types of stable phase behavior therefore resemble that of the spinodal behavior. The different shapes of the spinodals can be important for nonequilibrium processes in nature and technology.
Neutron scattering study of the H-bond network in amorphous N-methylformamide
Authors: Hammami Férid , Nasr Salah , Bellissent-Funel Marie-Claire
Published: February 2005

Original investigations of structural properties in noncrystalline solid N-methylformamide (HCONHCH3) are presented in this paper. After description of the sample preparation, the elastic neutron scattering formalism is applied to deduce the coherent scattering cross section for amorphous N-methylformamide. The contribution of each possible monomer (cis or trans) is computed and the corresponding distinct structure factor is deduced. Our measurements clearly show that the hydrogen-bond network occurs in amorphous N-methylformamide between CO and N–H groups. The experimental spectra are consistent with an open-chain structure similar to the one existing in the crystalline form. The more probable clusters that have been identified in the liquid are also examined.
Matching-pursuit/split-operator-Fourier-transform computations of thermal correlation functions
Authors: Chen Xin , Wu Yinghua , Batista Victor S.
Published: February 2005

A rigorous and practical methodology for evaluating thermal-equilibrium density matrices, finite-temperature time-dependent expectation values, and time-correlation functions is described. The method involves an extension of the matching-pursuit∕split-operator-Fourier-transform method to the solution of the Bloch equation via imaginary-time propagation of the density matrix and the evaluation of Heisenberg time-evolution operators through real-time propagation in dynamically adaptive coherent-state representations.
Lattice vibrations in cubic, tetragonal, and monoclinic phases of ZrO2
Authors: Sternik M. , Parlinski K.
Published: February 2005

First principles calculations of the phonon dispersion relations and the phonon density of states for three zero-pressure zirconia phases are presented. The phonon dispersion relations of the tetragonal and monoclinic phases do not exhibit the imaginary frequencies, contrary to the cubic phase for which the imaginary soft mode is seen. For tetragonal and monoclinic phases the free energies versus temperature are calculated in harmonic approximation. They cross at 1560K indicating the phase transition.
Optical transverse excitation in quaterthiophene crystals by ultraviolet-visible internal and attenuated total reflection
Authors: Raimondo L. , Laicini M. , Tavazzi S. , Borghesi A. , Spearman P.
Published: February 2005

We report internal and attenuated total reflection of light at the interface between glass and a quaterthiophene crystal in the spectral region of the electronic transitions. The bands corresponding to the absorption of the au and bu Frenkel exciton states are detected for different polarization of the incident light. In particular, the wave-normal vector being almost perpendicular to the bu transition dipole moment allows its transverse component to be accessed, whose excitation in conventional external reflection or transmission spectroscopies is forbidden.
Virtual state scattering with cold electrons: para-xylene and para-difluorobenzene
Authors: Jones N. C. , Field D. , Ziesel J.-P. , Field T. A.
Published: February 2005

The scattering of electrons with kinetic energies down to a few meV by para-xylene and para-difluorobenzene has been observed experimentally with an electron beam energy resolution of 0.95to1.5meV (full width half maximum). At low electron energies the collisions can be considered as cold scattering events because the de Broglie wavelength of the electron is considerably larger than the target dimensions. The scattering cross sections measured rise rapidly at low energy due to virtual state scattering. The nature of this scattering process is discussed using s- and p-wave phase shifts derived from the experimental data. Scattering lengths are derived of, respectively, −9.5±0.5 and −8.0±0.5a.u. for para-xylene and para-difluorobenzene. The virtual state effect is interpreted in terms of nuclear diabatic and partially adiabatic models, involving the electronic and vibronic symmetries of the unoccupied orbitals in the target species. The concept of direct and indirect virtual state scattering is introduced, through which the present species, in common with carbon dioxide and benzene, scatter through an indirect virtual state process, whereas other species, such as perfluorobenzene, scatter through a direct process.
Inelastic collisions in para-H2: Translation-rotation state-to-state rate coefficients and cross sections at low temperature and energy
Authors: Maté B. , Thibault F. , Tejeda G. , Fernández J. M. , Montero S.
Published: February 2005

We report an experimental determination of the k00→02 rate coefficient for inelastic H2:H2 collisions in the temperature range from 2to110K based on Raman spectroscopy data in supersonic expansions of para-H2. For this purpose a more accurate method for inverting the master equation of rotational populations is presented. The procedure permits us to reduce the measured k00→02 rate coefficient to the corresponding σ00→02 cross section in the range of precollisional energy from 360to600cm−1. Numerical calculations of σ00→02 carried out in the frame of the coupled channel method are also reported for different intermolecular potentials of H2. A good agreement is found between the experimental cross section and the numerical one derived from Diep and Johnson’s potential [J. Chem. Phys. 112, 4465 (2000)].
Dynamical and statistical effects of the intrinsic curvature of internal space of molecules
Authors: Teramoto Hiroshi , Takatsuka Kazuo
Published: February 2005

The Hamilton dynamics of a molecule in a translationally and/or rotationally symmetric field is kept rigorously constrained in its phase space. The relevant dynamical laws should therefore be extracted from these constrained motions. An internal space that is induced by a projection of such a limited phase space onto configuration space is an intrinsically curved space even for a system of zero total angular momentum. In this paper we discuss the general effects of this curvedness on dynamics and structures of molecules in such a manner that is invariant with respect to the selection of coordinates. It is shown that the regular coordinate originally defined by Riemann is particularly useful to expose the curvature correction to the dynamics and statisitcal properties of molecules. These effects are significant both qualitatively and quantitatively and are studied in two aspects. One is the direct effect on dynamics: A trajectory receives a Lorentz-like force from the curved space as though it was placed in a magnetic field. The well-known problem of the trapping phenomenon at the transition state is analyzed from this point of view. By showing that the trapping force is explicitly described in terms of the curvature of the internal space, we clarify that the physical origin of the trapped motion is indeed originated from the curvature of the internal space and hence is not dependent of the selection of coordinate system. The other aspect is the effect of phase space volume arising from the curvedness: We formulate a general expression of the curvature correction of the classical density of states and extract its physical significance in the molecular geometry along with reaction rate in terms of the scalar curvature and volume loss (gain) due to the curvature. The transition state theory is reformulated from this point of view and it is applied to the structural transition of linear chain molecules in the so-called dihedral angle model. It is shown that the curvature effect becomes large roughly linearly with the size of molecule.
Calculating energy levels of isomerizing tetra-atomic molecules. II. The vibrational states of acetylene and vinylidene
Authors: Kozin Igor N. , Law Mark M. , Tennyson Jonathan , Hutson Jeremy M.
Published: February 2005

A general, full-dimensional computational method for the accurate calculation of rotationally and vibrationally excited states of tetra-atomic molecules is further developed. The resulting computer program may be run in serial and parallel modes and is particularly appropriate for molecules executing wide-amplitude motions and isomerizations. An application to the isomerizing acetylene∕vinylidene system is presented. Large-scale calculations using a coordinate system based on orthogonal satellite vectors have been performed in six dimensions and vibrational term values and wave functions for acetylene and vinylidene states up to ≈23000cm−1 above the potential minimum have been determined. This has permitted the characterization of acetylene and vinylidene states at and above the isomerization barrier. These calculations employ more extensive vibrational basis sets and hence consider a much higher density of states than in any variational calculations reported hitherto for this system. Comparison of the calculated density of states with that determined empirically suggests that our calculations are the most realistic achieved for this system to date. Indeed more states have been converged than in any previous study of this system. Calculations on lower lying excited states of acetylene based on HC–CH diatom-diatom coordinates give nearly identical results to those based on orthogonal satellite vectors. Comparisons are also made with calculations based on HH–CC diatom-diatom coordinates.