bluuebunny/crossref_metadata_2025 huggingface dataset:
Clustering of null mutations in the EcoRI endonuclease
Authors: Yanofsky Stephen D. , Love Robert , McClarin Judith A. , Rosenberg John M. , Boyer Herbert W. , Greene Patricia J.
Published: May 2005

EcoRI endonuclease mutants were isolated in a methylase‐deficient background following in vitro hydroxylamine mutagenesis of plasmid pKG2 (Kuhn et al.: Gene 44:253–263, 1986). Mutants which survived high‐level endonuclease expression (IPTG induction) were termed null mutants. Sixtytwo of 121 null mutants tested by Western blot contained normal levels of endonuclease cross‐reacting protein. The complete endonuclease gene was scquenced for 27 null mutants. This group was found to consist of 20 signle base‐change missense mutations, 6 double mutations, and 1 triple mutation. Ten of the 20 signle mutations were clustered between residues 139 and 144. When examined with respect to the structure of the EcoRI‐DNA complex (McClarin et al.: Science 234:1526–1541, 1986), these alterations werre found to fall predominantly into two classes: substitutions at the protein‐DNA interface or substitutions at the protein‐protein (dimer) interface. Protein from several of the mutants was purified and sized by using HPLC. Wild‐type EcoRI endonuclease and protein from three of the DNA interface mutations (A1a139→Thr, Gly140→Ser, Arg203→Gln) appeared to be dimeric, while protein from subunit interface mutations (Glu144→Lys, Glu152→Lys, Gly210→Arg) migrated as monomers.
Stability of wild‐type and mutant RTEM‐1 β‐lactamases: Effect of the disulfide bond
Authors: Schultz Steve C. , Dalbadie‐McFarland Gloria , Neitzel James J. , Richards John H.
Published: May 2005

Uniquely among class A β‐lactamases, the RTEM‐1 and RTEM‐2 enzymes contain a single disulfide bond between Cys 77 and Cys 123. To study the possible role of this naturally occurring disulfide in stabilizing RTEM‐1 β‐lactamase and its mutants at residue 71, this bond was removed by introducing a Cys 77 → Ser mutation. Both the wild‐type enzyme and the single mutant Cys 77 → Ser confer the same high levels of resistance to ampicillin in vivo to Echerichia coli; at 30°C the specific activity of purified Cys 77 → Ser mutant is also the same as that of the wild‐type enzyme. Also, neither wild‐type enzyme nor the Cys 77 → Ser mutant is inactivated by brief exposure to p‐hydroxymercuri‐benzoate. However, above 40°C the mutant enzyme is less stable than wild‐type enzyme. After introduction of the Cys 77 → Ser mutation, none of the double mutants (containing the second mutations at residue 71) confer resistance to ampicillin in vivo at 37°C; proteins with Ala, Val, Leu, Ile, Met, Pro, His, Cys, and Ser at residue 71 confer low levels of resistance to ampicillin in vivo at 30°C. The use of electrophoretic blots stained with antibodies against β‐lactamase to analyze the relative quantities of mutant proteins in whole‐cell extracts of E. coli suggests that all 19 of the doubly mutant enzymes are proteolyzed much more readily than their singly mutant analogues (at Thr 71) that contain a disulfide bond. Thus, the disulfide bond of the RTEM‐1 β‐lactamase seems able to reduce the destabilizing effect of mutations at Thr 71. These results also emphasize the unique and essential role that Thr 71 performs in the stable folding of RTEM‐1 β‐lactamase and presumably the other class A β‐lactamases.
Functionally acceptable substitutions in two α‐helical regions of λ repressor
Authors: Reidharr‐Olson John F. , Sauer Robert T.
Published: May 2005

A method of targeted random mutagenesis has been used in investigate the informational content of 25 residue positions in two α‐helical regions of the N‐terminal domain of λ repressor. Examination of the functionally allowed sequences indicates that there is a wide range in tolerance to amino acid substitution at these position. At position that are buried in the structure, there are severe limitations on the number and type of residues allowed. At most surface positions, many different residues and residue types are tolerated. However, at several surface positions there is a string preference for hydrophilic amino acids, and at one surface position proline is absolutely conserved. The results reveal the high level of degeneracy in the information that specifies a particular protein fold.
Crystal structure of myoglobin form a synthetic gene
Authors: Phillips George N. , Arduini Robert M. , Springer Barry A. , Sligar Stephen G.
Published: May 2005

Crystal have been grown of myoglobin produced in Escherichia coli from a synthetic gene, and the structure has been solved to 1.9 Å resolution. The space group of the crystals is P6, which is different from previously solved myoglobin crystal forms. The synthetic myoglobin is essentially identical to myoglobin isolated from sperm whale tissue, except for the retention of the initiator methionine at the N‐terminus and the substitution of asparagine for aspartic acid at position 122. Superposition of the coordinates of native and synthetic sperm whale myoglobins reveals only minor changes in the positions of main chain atoms and roeientation of some surface side chains. Crystals of variant of the “synthetic” myoglobin have also been grown for structural analysis of the role of key amino acid residues in ligand and specificity.
Solvent structure in crystals of trypsin determined by X‐ray and neutron diffraction
Authors: Finer‐Moore Janet S. , Kossiakoff Anthony A. , Hurley James H. , Earnest Thomas , Stroud Robert M.
Published: May 2005

The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X‐ray diffraction to 1.35 Å resolution and by neutron diffraction to 2.1 Å resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X‐ray diffraction, which were verified by comparison to D2OH2O difference neutron scattering density. Six of 184 water molecules in the X‐ray structure, all with B‐factors greater than 50 Å2, were found to be spurious after comparison with neutron results. Roughly two‐thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one‐half of the water of hydration was located by X‐ray diffraction. Polar regions of the protein are well hydrated, and significant D2OH2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures.

Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X‐ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two β‐strands, which may resemble an intermediate in the formation of β sheets during the folding of a protein.
β‐Sheet coil transitions in a simple polypeptide model
Authors: Yapa Kanthi , Weaver David L. , Karplus Martin
Published: May 2005

A simplified model of a polypeptide chain is used to study the dynamics of the β‐sheet–coil transition. Each amino acid residue is treated as a single quasiparticle in an effective potential that approximates the potential of mean force in solution. The model is used to study the equilibrium and dynamic aspects of the sheet–coil transition. Systems studied include ones with both strands free to move (two‐strand sheet), and ones with either strand fixed in position (multistrand sheet). The equilibrium properties examined include sheet–coil equilibrium constants and their dependence on chain position. Dynamic properties are investigated by a stochastic simulation of the Brownian motion of the chain in its solvent surroundings. Time histories of the dihedral angles and residue–residue cross‐strand distances are used to study the behavior of the sheet structure. Auto‐and cross‐correlation functions are calculated from the time histories with relaxation times of tens to hundreds of picoseconds. Sheet–coil rate constants of tens of ns−1 were found for the fixed strand cases.
A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding
Authors: Bass Michael B. , Hopkins Derek F. , Jaquysh W. Andrew N. , Ornstein Rick L.
Published: May 2005

An automated method for the optimal placement of polar hydrogens in a protein structure is described. This method treats the polar, side chain hydrogens of lysine, serine, threonine, and tyrosine and the amino terminus of a protein. The program, called NETWORK, divides the potential hydrogen‐bonding pairs of a protein into groups of interacting donors and acceptors. A search is conducted on each of the local groups to find an arrangement which forms the most hydrogen bonds. If two or more arrangements have the same number of hydrogen bonds, the arrangement with the shortest set of hydrogen bonds is selected. The polar hydrogens of the histidyl side chain are specifically treated, and the ionization state of this residue is allowed to change, if this change results in additional hydrogen bonds for the local group. The program will accept Protein Data Bank as well as Biosym‐format coordinate files. Input and output routines can be easily modified to accept other coordinate file formats. The predictions from this method are compared to known hydrogen positions for bovine pancreatic trypsin inhibitor, insulin, RNase‐A, and trypsin for which the neutron diffraction structures have been determined. The usefulness of this program is further demonstrated by a comparison of molecular dynamics simulations for the enzyme cytochrome P‐450cam with and without using NETWORK.
Comparison of the hemocyanin β‐barrel with other greek key β‐barrels: Possible importance of the “β‐zipper” in protein structure and folding
Authors: Hazes Bart , Hol Wim G. J.
Published: May 2005

The Greek key β‐barrel topology is a folding motif observed in many proteins of widespread evolutionary origin. The arthropodan hemocyanins also have such a Greek key β‐barrel, which forms the core of the third domain of this protein. The hemocyanin β‐barrel was found to be structurally very similar to the β‐barrels of the immunoglobulin domains, Cu,Zn‐superoxide dismutase and the chromophore carrying antitumor proteins. The structural similarity within this group of protein families is not accompanied by an evolutionary or functional relationship. It is therefore possible to study structure–sequence relations without bias from nonstructural constraints. The present study reports a conserved pattern of features in these Greek key β‐barrels that is strongly suggestive of a folding nucleation site. This proposed nucleation site, which we call a “β‐zipper,” shows a pattern of well‐conserved, large hydrophobic residues on two sequential β‐strands joined by a short loop. Each β‐zipper strand is near the center of one of the β‐sheets, so that the two strands face each other from opposite sides of the barrel and interact through their hydrophobic side chains, rather than forming a hydrogen‐bonded β‐hairpin. Other protein families with Greek key β‐barrels that do not as strongly resemble the immunoglobulin fold—such as the azurins, plastocyanins, crystallins, and prealbumins—also contain the β‐zipper pattern, which might therefore be a universal feature of Greek key β‐barrel proteins.
Long timestep dynamics of peptides by the dynamics driver approach
Authors: Derreumaux Philippe , Schlick Tamar
Published: May 2005

Previous experience with the Langevin/implicit‐Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high‐frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13‐residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small‐time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time‐dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all‐atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full αR‐helix starting structure, and a high‐temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA‐generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two‐state model for helix–coil transition. The good, near‐Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley‐Liss, Inc.
A lipoamide dehydrogenase from Neisseria meningitidis has a lipoyl domain
Authors: Bringas Ricardo , Fernandez Julio
Published: May 2005

A protein of molecular weight of 64 kDa (p64k) found in the outer membrane of Neisseria meningitidis shows a high degree of homology with both the lipoyl domain of the acetyltransferase and the entire sequence of the lipoamide dehydrogenase, the E2 and E3 components of the dehydrogenase multienzyme complexes, respectively. The alignment of the p64k with lipoyl domains and lipoamide dehydrogenases from different species is presented. The possible implications of this protein in binding protein‐dependent transport are discussed. This is the first lipoamide dehydrogenase reported to have a lipoyl domain. © 1995 Wiley‐Liss, Inc.
Effect of chlorimuron‐ethyl on Bradyrhizobium japonicum and its symbiosis with soybean
Authors: Zawoznik Myriam S , Tomaro María L
Published: May 2005

Possible side‐effects of the acetolactate synthase (ALS)‐inhibiting herbicide chlorimuron‐ethyl on Bradyrhizobium japonicum (Kirchner & Jordan) in pure culture and on inoculated soybean plants growing under controlled conditions were investigated. Growth of B japonicum strain E109 was not affected by this herbicide even when exposed to concentrations 150 times higher than recommended field doses. However, nodulation of soybean plants treated 5 days after emergence with chlorimuron‐ethyl at standard application rates was impaired: a 38% decrease in the number of nodules per plant was observed four weeks after treatment. Despite nodule number decrease, no changes in shoot nitrogen content could be detected. Total fresh biomass was diminished by 25% in herbicide‐treated plants. Leghemoglobin content in nodules did not vary; nevertheless total nodule protein was diminished by 40% in the herbicide‐treated group. ALS activity in different soybean tissues and their relative sensitivity to chlorimuron‐ethyl were also investigated. Roots and bacteroids had the greatest specific ALS activities. On a fresh weight basis, the bacteroid fraction displayed the highest ALS activity and was also the most tolerant to in vitro chlorimuron addition: 72% of its activity was retained after including 10 µM chlorimuron‐ethyl in the reaction mixture. These results indicate that standard application rates of chlorimuron‐ethyl will have limited incidence on B japonicum survival, and effects on nodulation may have little long‐term consequences on soybean nitrogen fixation potential. The differences found among soybean tissues not only in intrinsic ALS activity but also in their relative sensitivity to this herbicide suggests that, in leguminous plants living in symbiosis with rhizobia, nodules may contribute to an enhanced tolerance to ALS inhibitors. Copyright © 2005 Society of Chemical Industry
Kinetics of matrix/sample interactions in fast‐atom bombardment
Authors: Vékey Kàroly , Colombo Luigi , Zerilli Luigi F. , Székely Györgyi
Published: May 2005

Addition of a hydroxy‐containing matrix to an aldehyde was observed in fast‐atom bombardment (FAB). This FAB‐induced interference reaction, observed in the case of a microbial alkaline protease inhibitor, shows a characteristic time behaviour. This can be explained by a first‐order reaction kinetics scheme which leads to quilibrium, for which rate and equilibrium constants were also determined. These data suggest that in situ reaction kinetics can be studied by FAB mass spectrometry.
The ion‐trap mass spectrometer in ion structure studies. The case of [MH]+ ions from chalcone
Authors: Ardanaz C. E. , Traldi P. , Vettori U. , Kavka J. , Guidugli F.
Published: May 2005

Ion‐structure investigation of the [MH]+ ions from chalcone has been carried out by collision experiments performed with an ion‐trap mass spectrometer (ITMS), operating with the application of a supplementary RF voltage. The data so obtained, together with those achieved by comparison with labelled model compounds, have led to a clear identification of the [MH]+ ion structure, proving the high potentialities of the ITMS in such a field.
The methane dication revisited
Authors: Nagesha K. , Marathe V. R. , Mathur D.
Published: May 2005

All‐electron, ab initio molecular orbital calculations have been performed on electronic states of CH using perturbative configuration interaction procedures and large sets of Gaussian basis functions with a view to attempting reconciliation between contemporary quantum‐chemical information and different sets of experimen‐tal data from charge‐stripping, threshold photoionization, and double‐charge‐transfer mass spectrometry. Metastable electronic states of CH are predicted for D4h and D2d symmetries, with charge‐stripping experiments likely to populate spin singles of the former symmetry. Investigation of the dissociation of CH (D4h) to CH (D3h)+ H+ along the C2v symmetry pathway indicates that theoretical and experimental data on metastable states of this dication are in accord only if non‐Frank‐Condon transitions are postulated.
Analysis of a mass‐analysed ion kinetic energy peak profile for a metastable ion decomposition occurring in a collision cell floated at high voltage
Authors: Kim Young Hwan , Kim Myung Soo
Published: May 2005

A numerical method has been developed to obtain the kinetic energy release distribution from a mass‐analysed ion kinetic energy peak profile for a metastable ion decomposition occurring in a collision cell floated at high voltage. The method has been applied to the unimolecular dissociation of the tert‐butylbenzene molecular ion. The kinetic energy release distribution thus obtained was nearly invariant to the applied voltage. Peak tailing due to dissociation in the field region could be reproduced adequately The method may be useful for the investigation of unimolecular ion decomposition in narrow time‐ and energy‐windows.
A new matrix for fast‐atom bombardment analysis of corrins
Authors: Staempfli A. A. , Schlunegger U. P.
Published: May 2005

2,3‐dihydroxypropyl benzyl ether, a glycerol derivative, is a suitable matrix for fast‐atom bombardment analysis. It has been shown to be superior to glycerol and thioglycerol for the detection of molecular ions of cobyrates.
Comparison between a quadrupole and an emission spectrometer in the determination of low level 15N abundance
Authors: Cervelli S. , DiGiovanni F. , Ferrari S.
Published: May 2005

The use of stable isotopes in ecosystem studies is increasing, due to the possibility of obtaining information on source/sink balances in the environment. Carbon, nitrogen oxygen and sulphur all have more than one stable isotope, and their isotopic concentration can be measured with precision by mass spectrometry. The use of this technique in environmental studies is not yet extensive, due both to the lack of a chemical and geochemical background of many ecologists, and the high cost of mass spectrometers. In this paper we report some experiments on the determination of 15N abundance in low ‐enriched nitrogenous materials (0.366–0.998% abundance) by two comparable low‐cost instruments: an emission spectrometer (Jasco NIA I) and a quadrupole mass spectrometer (Rial QM 130‐CS).
Distinguishing N‐ and C‐terminus ions for mass spectrometry sequencing of proteins without prior degradation
Authors: Aaserud David J. , Little Daniel P. , O'Connor Peter B. , McLafferty Fred W.
Published: May 2005

Identifying complementary pairs of fragment ions, b‐type vs y‐type, is a key step in mass spectral sequencing of proteins without degradation prior to ionization. Observations that b‐type ions tend to be less stable than y‐type have been extended to carbonic anhydrase (29kDa) as a model protein. Infrared multiphoton dissociation (IRMPD) of 24+, 27+, 30+ molecular ions shows y‐type ions from complementary pairs require, on average, 27% longer irradiation times for onset of abundance decrease, while in nozzle/skimmer dissociation of all charge states, y‐type ions require a 20% higher potential difference. In some cases, b‐ion dissociation appears to accompany its formation, as its rate of increase with increasing energy deposition is far less than that of its y‐complement.
Identification of organogermanium compounds as matrix complexes in fast‐atom bombardment mass spectrometry
Authors: Akiba Mitsuo , Sasaki Yoshinori , Kakimoto Norihiro , Ohnishi‐Kameyama Mayumi , Nagata Tadahiro
Published: May 2005

The application of aqueous matrices to fast‐atom bombardment mass spectrometry enables the detection of several organogermanium compounds as specific complexes with matrices. In the positive‐ion mode, the organogermanium compounds showed a dominant ion [M+matrix‐3 · H2O+H]+ whose dehydration involved atoms attached to the germanium atom. On the other hand, two types of fragmentation were observed in the negative‐ion mode The first was a group of compounds, with a carboxy group, that formed a lactone ring and showed a dominant ion at [M+matrix ‐3 · H2O‐H]−. The other group, without carboxy, attached another matrix molecule and showed a dominant fragment ion at [M+2 · matrix‐3 · H2O‐H]−. The investigation of these complex structures was performed using various matrices and D2O treatment.
Sequencing of oligonucleotides using high performance liquid chromatography and electrospray mass spectrometry
Authors: Glover Robert P. , Roberts Gordon C. K. , Sweetman Gavain M. A. , Farmer Peter B.
Published: May 2005

We report the sequence analysis of an oligodeoxyribonucleotide by electrospray mass spectrometry (ES‐MS). For full sequence analysis of the oligomer, d(CGTAGCTACG), an enzyme digestion step followed by off‐line high performance liquid chromatography was used. For ES‐MS analysis, introducing the sample in an imidazole buffer with 70% acetonitrile increased the electrospray ion currents and helped reduce sodium‐adduct ion peaks.
Visualization of craters in a Langmuir–Blodgett film from the impact of 23 MeV C ions
Authors: Tomaschko Ch. , Schurr M. , Berger R. , Saemann‐Ischenko G. , Voit H. , Brunelle A. , Della‐Negra S. , Lebeyec Y.
Published: May 2005

Atomic force microscopy (AFM) images taken from an Fe‐arachidate Langmuir‐Blodgett film irradiated with 23 MeV fullerene ions gives clear evidence that craters are formed as a result of the cluster‐ion impact. The crater diameter fits into a systematic formula already found for atomic ions. The AFM images indicate that even the largest molecular ions desorbed stem from the crater volume.
Endgroup analysis of polyethylene glycol polymers by matrix‐assisted laser desorption/ionization Fourier‐transform ion cyclotron resonance mass spectrometry
Authors: de Koster Chris G. , Duursma Marc C. , van Rooij Gerard J. , Heeren Ron M. A. , Boon Jaap J.
Published: May 2005

Fourier‐transform ion cyclotron resonance mass spectrometry (FTICR‐MS) by external injection of matrix‐assisted laser desorbed and ionized (MALDI) polymers offers good possibilities for characterization of low molecular weight homopolymers (MW range up to 10 kDa). The molecular masses of the molecular weight distribution (MWD) components of underivatized and derivatized (dimethyl, dipropyl, dibutyl and diacetyl) polyethylene giycol (PEG) 1000 and 4000 were measured by MALDI‐FTICR‐MS. These measurements have been performed using a commercial FTICR spectrometer with a home‐built external ion source. MALDI of the samples with a 2,5‐dihydroxybenzoic acid matrix in a 1000: 1 matrix‐to‐analyte molar ratio produces sodiated molecules in a sufficient yield to trap the ions in the ICR cell. The masses of the molecular weight distribution of PEG components were measured in broad‐band mode with a mass accuracy of < 5 ppm in the mass range around 1000 u and within 40 ppm accuracy around 4000 u. From these measurements, the endgroup mass of the polymer was determined by correlation of the measured component mass with the degree of polymerization. The masses of the PEG endgroups have been determined within a deviation of 3–10 millimass units for the PEG1000 derivatives and 10–100 millimass units for the PEG4000 derivatives, thus confirming the identity of the distal parts of the model compounds.
Mass spectrometric methodologies in plant analysis: The case of flavonols in Sedum telephium L. Juice
Authors: Mulinacci N. , Vincieri F. F. , Baldi A. , Romani A. , Favretto D. , Traldi P.
Published: May 2005

Negative‐ion fast‐atom bombardment mass spectrometry together with precursor and product‐ion spectroscopies has been validly employed in the identification of six flavonol glycosides present in the juice of Sedum telephium leaves. The proposed technique proved to be a valuable alternative to the combination of high performance liquid chromatography and mass spectrometry in the analysis of the complex polyphenol mixtures present in some medicinal plants.
Surface studies of conversion coated steel after corrosion induced paint deadhesion
Authors: deVries J. E. , Riley T. L. , Holubka J. W. , Dickie R. A.
Published: May 2005

Secondary ion mass spectorscopy (SIMS) and scanning electron microscopy (SEM) have been used to characterize the surface composition and morphology of zinc‐phosphated steel before application of organic coatings and after corrosion‐induced delamination of these coatings. Imaging SIMS and SEM results confirm the presence of a cystalline zinc‐iron‐phosphate layer on the phosphated steel before coating application. During the corrosion process, dissolution of the crystal structure occurs between the initial corrosion site and the progressing edge of corrosion induced delamination. Beyond this edge the crystal structure remains intact.
Surface chemistry of a microcoated energetic material, pentaerythritoltetranitrate (PETN)
Authors: Worley C. M. , Vannet M. D. , Ball G. L. , Moddeman W. E.
Published: May 2005

A microcoating technique was used to apply a polymer to an energetic explosive material. The explosive was pentaerythritoltetranitrate (PETN), and the coating was a copolymer consisting of vinylchloride/trifluorochloroethylene in a 1.5/1.0 molecular ratio. X‐ray photoelectron spectroscopy (XPS) and ion scattering spectroscopy (ISS) were used to study the surface and interfacial chemistry of PETN powders and pellets made from compressed powders having either 0.5 or 20 wt% coating. Two simple models were used to discuss the nature of the copolymer film on the PETN. Model I shows the copolymer completely coating PETN; Model II depicts the copolymer as only partially covering PETN. Model II was applicable in explaining the 0.5 and 20 wt% microcoating of powders, as well as the 0.5 wt% coated pellets. However, the pellets with 20 wt% coating showed the copolymer to completely coat PETN (Model I), suggesting copolymer redistribution during pelletization. XPS and ISS results showed the copolymer film to be thin. An XPS expression modified to accommodate ISS data was developed for the calculation of the average copolymer thickness of PETN. The thicknesses were determined to be 10 Å and 6 Å for 0.5 wt% coated PETN powders and pellets, respectively. Bonding between the copolymer and PETN was concluded to be mechanical.
On the N KLL spectra of some nitrides
Authors: Berghe R. Vanden , Vlaeminck R.
Published: May 2005

The N KLL peak in the electron‐stimulated Auger spectrum of some (transition metal) nitrides is shown. A tentative explanation for the observations is presented, referring to literature data.
Applications of in situ SIMS during processing of electronic materials
Authors: Webb A. P. , Smith J. A.
Published: May 2005

An in situ SIMS system is described that is capable of providing accurate and reliable control in determining the termination of processes whilst etching through multi‐layer structures. The instrumentation is described and how progressive alterations have been implemented to improve the sensitivity. Various applications are described which show the wide range of material systems that have already been addressed.
SiO2 in 6:3 (stishovite) and 4:2 Co‐ordination—Characterization by core level spectroscopy (XPS/XAES)
Authors: Finster J.
Published: May 2005

A comprehensive XPS/XAES investigation of the dense 6:3 co‐ordinated SiO2 polymorph stishovite in comparison with different SiO4/2 samples and Si was carried out for the first time. By evaluation of initial state and final state shift contributions, effective charges and extra‐atomic relaxation energies were determined and discussed in the context of the electronic structure for different co‐ordination numbers. The reduced binding energies of Si and O lines for stishovite are due to the higher extra‐atomic relaxation energy in comparison to SiO4/2, which correlates with the higher dielectric constant and the lower gap energy in SiO6/3. The effective charges are only slightly higher in stishovite than e.g. in quartz.
Calculations of electorn inelastic mean free paths. II. Data for 27 elements over the 50–2000 eV range
Authors: Tanuma S. , Powell C. J. , Penn D. R.
Published: May 2005

We report calculations of electron inelastic mean free paths (IMFPs) for 50–2000 eV electrons in a group of 27 elements (C, Mg, Al, Si, Ti, V, Cr, Fe, Ni, Cu, Y, Zr, Nb, Mo, Ru, Rh, Pd, Ag, Ta, W, Re, Os, Ir, Pt, Au and Bi). This work extends our previous calculations (Surf. Interface Anal. 11, 57 (1988)) for the 200–2000 eV range. Substantial variations were found in the shapes of the IMFP versus energy curves from element to element over the 50–2000 eV range and we attribute these variations to the different inelastic scattering properties of each material. Our calculated IMFPs wee fitted to a modified form of the Bethe equation for inelastic electron scattering in matter; this equation has four parameters. These four parameters could be empirically related to several material parameters for our group of elements (atomic weight, bulk density and number of valence electron per atom). IMFPs and those initially calculated was 13%. The modified Bethe equation and our expressions for the four parameters can therefore be used to estimate IMFPs in other materials. The uncertainties in the algorithm used for our IMFP calculation are difficult to estimate but are believed to be largely systematic. Since the same algorithm has been used for calculating IMFPs, our predictive IMFP formula is considered to be particularly useful for predicting the IMFP dependence on energy in the 50–2000 eV range and the material dependence for a given energy.
Laser Raman and XPS analyses of molybdenum–rare earth oxide catalysts
Authors: Nieto J. M. López , Corberán V. Cortés , Fierro J. L. G.
Published: May 2005

Laser Raman spectroscopy (LRS) and x‐ray photoelectron spectroscopy (XPS), combined with x‐ray diffraction (XRD), have been used to characterize the phases in Mo–RE–O (RE = Sm, Tb, Yb) systems. Two clearly differentiated composition regions were observed, namely the RE‐rich region (x < 0.5–0.6, where x represents the Mo/(Mo + RE) atomic ratio), in which the RE oxide was always present as a separate phase, and the Mo‐rich region (x > 0.6) in which MoO3 appeared as a separate phase. The broadening of the Raman bands in the RE‐rich region is indicative of the presence of ill‐defined structures. However, as the RE oxide content increased, crystalline molybdates with decreasing Mo/RE ratios were found in each system. XPS surface composition was roughly similar to that of the bulk for the Mo–Sm–O and Mo–Yb–O series, while relevance of MoO3 and molybdate phases in the Mo‐rich composition regions is discussed in the context of allylic oxidation of light olefins.
Partial intensity analysis (PIA) for quantitative electron spectroscopy
Authors: Werner Wolfgang S. M.
Published: May 2005

An approach is developed to separate the spectral contributions of electrons that have experienced a certain number of inelastic collisions and together constitute the observable lineshape in AES/XPS. The only assumption concerning the emission process that is made in this general approach is that energy losses and deflections occur separately. This means that the method can account for elastic scattering with arbitrary sophistication, while it can also be applied to spectra from samples exhibiting surface roughness or specimens with an arbitrary depth profile and even single crystals where diffraction effects dominate the peak intensities. If the details of the emission process are properly understood, such a so‐called partial intensity analysis may serve to assess the structural characteristics of an unknown specimen. Conversely, if the sample structure is known, it can be employed to assess experimentally the details of the emission process (elastic scattering, roughness, diffraction). At any rate, a partial intensity analysis allows proper background correction of the spectral lineshape to be performed if this is the ultimate aim of analysis. This again holds true without regard to the emission process and is possible without any kind of fitting or ad hoc assumptions. On a very similar basis, a method is derived to gain accurate information about the inelastic transport characteristics from reflection experiments in the case when the other quantities governing the particle transfer are known. The results are general in that the starting point of the method, i.e. the yield equation, in principle also describes the fundamentals of other techniques employing particle–solid interaction.
Advances in the use of molybdenum compounds as smoke suppressants for PVC
Authors: Moore Fred W. , Weber Thomas R. , Tsigdinos George A.
Published: May 2005

Molybdenum‐based compounds are effective smoke suppressants for rigid and flexible polyvinyl chloride formulations, both unfilled and filled with calcium carbonate and alumina trihydrate. These compounds, two of which are new compounds based on zinc molybdate with or without a phosphite synergist, are useful as is or extended onto core materials such as clay or talc. The addition of molybdenum‐containing additives to flexible PVCs containing antimony trioxide usually raises the oxygen index and thus improves flame retardancy. Tests indicate that molybdenum acts as a flame and smoke suppressant in the solid phase.
Antimony‐based flame retardant systems in plasticized polyvinyl chloride compounds
Authors: Furnivall James C. , Kupfer Alan D. , Irvine John L.
Published: May 2005

A method of choosing the most effective way to meet specific flame retardant requirements in polyvinyl chloride compounds, which uses flammability tests based on oxygen indexes, shows that antimony‐based and non‐antimony retardants perform as well as commonly used antimony oxide retardants, and at a reduced cost.
Marketplace synergies for PVC additives—how the supplier alliance is working in PVC markets
Authors: Goodman Donald
Published: May 2005

PVC is the only major plastic that needs additives to enhance its properties. Without additives, PVC would not enjoy its robust business and wide range of applications. This paper considers how additive suppliers have been able to bring out the best in PVC in an alliance that has been mutually beneficial. The alliance also comes with challenges to meet new and expanded regulations, as well as opportunities to develop tomorrow's materials. Some emerging concepts of “Responsible Care” are presented, which concern how resin and additive suppliers will have to provide product stewardship of compounds and products throughout their useful application lifetimes and provide options for proper disposal.
An evaluation of the suitability of X‐ray fluorescence spectroscopy in the analysis of complex alloy systems
Authors: Bäckerud L.
Published: May 2005

An attempt has been made to evaluate on the basis of simple physical theories the principal possibilities and limitations of the X‐ray fluorescence method in determining both principal components and other alloying elements as well as impurities in relatively complex alloy systems. The text refers specifically to the analysis of copper‐based alloys, but the principles are general ones and the arguments can easily be applied to other systems.
Notes and comments: The training of X‐ray spectroscopists
Authors: Chessin H.
Published: May 2005

One of the current problems in the application of the X‐ray spectrometer is the training of operators in the use of instrumentation and techniques. One of the usual consequences of rapid expansion in the use of any instrumental procedure is the lack of general experience and expertise, and in this X‐ray spectrometry is no exception. As a technique it has only recently been introduced into the syllabus of the appropriate university course of study and, at the present time, this only at a very few universities. Training in X‐ray spectrometry has therefore become very much an extra‐mural course of study and among the more successful groups to offer courses in the U.S.A. has been the State University of New York at Albany. The following short report by Professor Chessin gives an informal description of the background of his ‘Clinics’ and describes some of his experiences.
The loss of br from thin‐film samples during X‐ray fluorescence analysis
Authors: O'Connor B. H. , Kerrigan G. C. , Hinchliffe P.
Published: May 2005

The loss of Br during X‐ray fluorescence analysis presents problems in thin‐film determinations such as those employed in this laboratory for environmental particulate samples and in machine calibration with spotted filter standards. The occurrence of Br losses is easily overlooked unless appropriate measures are taken during calibration and analysis. Losses may be reduced to c. 2% by sealing the samples with adhesive tape, and by limiting the duration of the analysis to several minutes.
Identification of unconverted oxide phases in a synthetic clay mineral by scanning electron microscopy and the x‐ray microprobe
Authors: Patel Mahendra
Published: May 2005

The difficulty of identifying unconverted oxide phases, present in synthetic clay minerals, by classical techniques is discussed. It is shown that scanning electron microscopy, combined with the x‐ray microprobe, is very effective in such a study. Some representative micrographs of oxide phases in a synthetic vermiculite are presented.
Quantitative electron probe microanalysis in the system Fe–Sn–C using the Claisse–Quintin relation
Authors: Fredriksz W. , Koster H. , Kolster B. H.
Published: May 2005

Quantitative interpretation of EPMA measurements was required for the construction of the Fe–Sn–C phase diagram. This involved the conversion of measured x‐ray intensities into concentrations, which is difficult for a light element (such as C) being present among heavier elements (Fe and Sn). To meet this problem, firstly the various intensity–concentration conversion methods from the literature have been studied and are briefly surveyed. The Claisse–Quintin relation with constant influence coefficients was selected as the algorithm for multiple regression purposes, which was applied to reference standard data. Calibration functions are obtained for Sn and C, which are used in a simple iteration procedure. This procedure has been used for the conversion of Sn and C x‐ray intensities into concentrations. The method shows a relative accuracy of about 5%.
Spectral distribution of backseattered electrons: Application to electron probe microanalysis
Authors: Del Giorgio M. , Trincavelli J. , Riveros J. A.
Published: May 2005

The parameters ϕ0 and γ0 of the Gaussian model for the depth distribution of characteristic x‐ray production ϕ(ρz) were evaluated using an analytical expression for the energy distribution of backscatrered electrons. The expressions obtained were compared with those which do not take into account this distribution. A test of the usefulness of both models was performed for microanalysis corrections.
Determination of potassium and calcium in milk powder by energy‐dispersive x‐ray fluorescence spectrometry
Authors: Alvarez M. , Mazo‐Gray V.
Published: May 2005

A rapid method for the simultaneous determination of potassium and calcium in milk powder by energy‐dispersive x‐ray fluorescence (EDXRF) spectrometry was developed. The measurement system consists of a Si(Li) detector, an x‐ray tube coupled with titanium as a secondary target, a DEC‐350 computer and a nonlinear fitting least‐squares program. The methods of calibration and standard preparation are discussed. Milk powder was analysed as pressed pellets using counting times of 100 s. Concentrations were determined by a standard calibration graph method using synthetic standards. The minimum detection limits are 0.011% and 0.007% for potassium and calcium, respectively. The accuracy was ascertained by analysing standard reference materials from the International Atomic Energy Agency. Good agreement was found between the certified and measured values. Potential applications of this method are indicated.
Monte Carlo simulation of the grain size and edge effects in x‐ray fluorescence microanalysis of geological samples
Authors: Lankosz Marek
Published: May 2005

A Monte Carlo model was developed for simulation of x‐ray fluorescence from cylindrical mineral grains in geological samples including primary and secondary fluorescence events. The inter‐element and geometrical effects in XRF microanalysis of mineral grains were studied. Calculations were performed for grains of ZnS located in a CaCO3 matrix. The results of calculation indicated that the intensities of excited characteristic x‐rays depend strongly on the diameter and thickness of the irradiated grains.
Validation of sulphide‐bearing certified reference samples by primary calibration as applied to x‐ray fluorescence
Authors: Staats Gotthard , Strieder Stefan
Published: May 2005

Sulphide‐bearing certified reference samples were validated by multi‐element wavelength‐dispersive XRF based on the SI units kilogram and mole. An oxidizing borate fusion ensured complete oxidation of the test samples and provided for identical physical and chemical conditions for reference and test samples. Matrix effects were successfully overcome by computer‐aided generation and production of perfectly adapted multi‐element calibration samples. The trueness of the validated results was achieved by the application of pure elements or their compounds having quality assured assays. Detailed and accurate analytical information on certified reference samples CCu‐19 and CZN‐1 (CANMET, Canada) and BCR 26, 27, 28 (Community Bureau of Reference, Belgium) are reported.
A comparative radiorespirometric study of glucose metabolism in yeasts
Authors: Bruinenberg Peter M. , Waslander Gerrit W. , Van Dijken Johannes P. , Scheffers W. Alexander
Published: May 2005

A comparative radiorespirometric study of glucos emetabolism in glucose‐limited chemostat cultures of Saccharomyces cerevisiae, Candida utilis and Rhodosporidium toruloides was performed in an attempt to estimate the contribution of the hexose monophosphate (HMP) pathway to glucose metabolism. Radioactively labelled glucose was administered directly to the cultures in a constant substrate feed, without disturbance of the steady state. The 14CO2 yields from [1‐14C]‐ and [6‐14C]‐glucose demonstrated that the HMP pathway activities for the three yeasts were very similar. Furthermore, a quantitative analysis of results indicated that the HMP pathway activities were close to the theoretical minimum needed to cover the NADPH requirement for biomass formation.
Reduced efficiency in the glycosylation of the first sequon of Saccharomyces cerevisiae exoglucanase leads to the synthesis and secretion of a new glycoform of the molecule
Authors: Basco Ricardo D. , Muñoz M. Dolores , Hernández Luis M. , De Aldana Carlos Vazquez , Larriba Germán
Published: May 2005

In addition to exoglucanases (EXGs) I and II, old cultures of Saccharomyces cerevisiae secreted into the culture medium a new immunologically‐related material that exhibited exoglucanase activity. The new exoglucanase (EXGII1/2) was purified from stationary‐phase cultures. It turned out to be a glycoprotein whose protein portion was identical to that of the other two isoenzymes in terms of ionic properties, size, amino acid composition and NH2‐terminal sequence (25 residues). Disruption of the structural gene encoding EXGs I and II resulted in a strain unable to secrete all three isoenzymes. EXGII1/2 was indistinguishable in terms of molecular weight from the single intermediate detected during the deglycosylation (mediated by endo H) of EXGII by sodium dodecyl sulphate–polyacrylamide gel electrophoresis. Thus, the new isoenzyme contains only one of the two slightly elongated mannan inner cores present in enzyme II. Two intermediates were, however, detected when the deglycosylation of EXGII was monitored by ion‐exchange chromatography (high‐pressure liquid chromatography). Site‐directed mutagenesis indicated that the major intermediate, which eluted at about the same position as enzyme II1/2, corresponded to protein molecules carrying the oligosaccharide attached to the Asn of the second sequon, whereas the minor one carried the oligosaccharide in the first potential glycosylation site. Several lines of evidence indicate that EXGII1/2 is a biosynthetic product resulting from an imbalance between the rate of protein synthesis and the glycosylation capabilities of the glycosylation machinery.