bluuebunny/crossref_metadata_2025 huggingface dataset:
The Kinetics of Detonation of Nitroguanidine
Authors: Leiper G. A. , Cooper J.
Published: May 2005

A slightly divergent flow detonation model has been used to model previously published charge diameter data for nitroguanidine. The kinetic form at low density is shown to be of the hot spot/grain burning type. At higher densities the kinetics become progressively thermal explosion in form. The kinetics are discussed in terms of the pressure dependent rate law used in the model and models of hot spot formation in powder explosives. The particular crystal size and form of nitroguanidine used shows characteristics which suggest it to be of the type described by Price as Group 2 at low density but to show a change to Group 1 type behaviour at higher density. The analysis suggests reasons for this and for the observation that an alternative crystal size and form appears to show only Group 1 characteristics.
Theoretical Study on Pyrolysis and Sensitivity of Energetic Compounds. Part I: Simple model molecules containing NO2 Group
Authors: Heming Xiao , Jianfen Fan , Xuedong Gong
Published: May 2005

UHF (Unrestricted Hartree‐Fock) Molecular Orbital calculations have been first performed for studying the pyrolysis mechanism of five compounds (nitromethane, methyl nitrate, nitroamine, methyl nitroamine and dimethyl nitroamine) containing NO2 group as the simple models of organic explosives by using PM3 and AM1 methods. The potential energy curves and activation energies of the five pyrolysis reactions (into radicals) have been obtained. The activation energies are consistent with the experimental impact sensitivity of these three kinds of explosives: C‐nitro < N‐nitro < O‐nitro compounds. It is found that there is a parallel linear relationship between the bond orders of NNO2 bond in the molecules of three nitroamine compounds and the activation energies of their initiation reactions breaking NNO2 bond. The obtained correlation coefficients between bond orders and activation energies from PM3 and AM1 calculations are 0.9962 and 0.9999, respectively.
Two trifluoperazine‐binding sites on calmodulin predicted from comparative molecular modeling with troponin‐C
Authors: Strynadka Natalie C. J. , James Michael N. G.
Published: May 2005

Among the known regulatory proteins that are conformationally sensitive to the binding of calcium ions, calmodulin and troponin‐C have the greatest primary sequence homology. This observation has led to the conclusion that the most accurate predicted molecular model of calmodulin would be based on the X‐ray crystallographic coordinates of the highly refined structure of turkey skeletal troponin‐C. This paper describes the structure of calmodulin built from such a premise. The resulting molecular model was subjected to conjugate gradient energy minimization to remove unacceptable intramolecular non‐bonded contacts. In the analysis of the resulting structure, many features of calmodulin, including the detailed conformation of the Ca2+‐binding loops, the amino‐ and carboxy‐terminal hydrophobic patches of the Ca2+‐bound form, and the several clusters of acidic residues can be reconciled with much of the previously published solution data. Calmodulin in missing the N‐terminal helix characteristic of troponin‐C. The deletion of three residues from the central helical linker (denoted D/E in troponin‐D) shortens the molecule and changes the orientation of the two domains of calmodulin by 60° relative to those in troponin‐C. The molecular model has been used to derive two possible binding sites for the antipsychotic drug trifluoperazine, a potent competitive inhibitor of calmodulin activity.
Hydrophobicity of amino acid subgroups in proteins
Authors: Lesser Glenn J. , Rose George D.
Published: May 2005

Protein folding studies often utilize areas and volumes to assess the hydrophobic contribution to conformational free energy (Richards, F. M. Annu. Rev. Biophys. Bioeng. 6:151–176, 1977). We have calculated the mean area buried upon folding for every chemical group in each residue within a set of X‐ray elucidated proteins. These measurements, together with a standard state cavity size for each group, are documented in a table. It is observed that, on average, each type of group buries a constant fraction of its standard state area. The mean area buried by most, though not all, groups can be closely approximated by summing contributions from three characteristic parameters corresponding to three atom types: (1) carbon or sulfur, which turn out to be 86% buried, on average; (2) neutral oxygen or nitrogen, which are 40% buried, on average; and (3) charged oxygen or nitrogen, which are 32% buried, on average.
Comparison of the structures of globins and phycocyanins: Evidence for evolutionary relationship
Authors: Pastore Annalisa , Lesk Arthur M.
Published: May 2005

Globins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3–10 C helix and the unusual “crossed‐ridge” packing pattern at the B/E helix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phycocyanins.
Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins
Authors: Nakashima Hiroshi , Nishikawa Ken , Ooi Tatsuo
Published: May 2005

A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt‐proteins) were examined in the 20‐dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt‐proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G‐C‐rich base composition.
Stereochemical quality of protein structure coordinates
Authors: Morris Anne Louise , MacArthur Malcolm W. , Hutchinson E. Gail , Thornton Janet M.
Published: May 2005

Methods have been developed to assess the stereochemical quality of any protein structure both globally and locally using various criteria. Several parameters can be derived from the coordinates of a given structure. Global parameters include the distribution of ϕ,ψ and χ1 torsion angles, and hydrogen bond energies. There are clear correlations between these parameters and resolution; as the resolution improves, the distribution of the parameters becomes more clustered. These features show a broad distribution about ideal values derived from high‐resolution structures. Some structures have tightly clustered distributions even at relatively low resolutions, while others show abnormal scatter though the data go to high resolution. Additional indicators of local irregularity include proline ϕ angles, peptide bond planarities, disulfide bond lengths, and their χ3 torsion angles. These stereochemical parameters have been used to generate measures of stereochemical quality which provide a simple guide as to the reliability of a structure, in addition to the most important measures, resolution and R‐factor. The parameters used in this evaluation are not novel, and are easily calculated from structure coordinates. A program suite is currently being developed which will quickly check a given structure, highlighting unusual stereochemistry and possible errors.
The molecular structure of UDP‐galactose 4‐epimerase from Escherichia coli determined at 2.5 Å resolution
Authors: Bauer Alan J. , Rayment Ivan , Frey Perry A. , Holden Hazel M.
Published: May 2005

UDP‐galactose 4‐epimerase catalyzes the conversion of UDP‐galactose to UDP‐glucose during normal galactose metabolism. The molecular structure of UDP‐galactose 4‐epimerase from Escherichia coli has now been solved to a nominal resolution of 2.5 Å. As isolated from E. coli, the molecule is a dimer of chemically identical subunits with a total molecular weight of 79,000. Crystals of the enzyme used for this investigation were grown as a complex with the substrate analogue, UDP‐benzene, and belonged to the space group P212121 with unit cell dimensions of a = 76.3 Å, b = 83.1 Å, c = 132.1 Å, and one dimer per asymmetric unit. An interpretable electron density map calculated to 2.5 Å resolution was obtained by a combination of multiple isomorphous replacement with six heavy atom derivatives, molecular averaging, and solvent flattening.

Each subunit of epimerase is divided into two domains. The larger N‐terminal domain, composed of amino acid residues 1–180, shows a classic NAD+ binding motif with seven strands of parallel β‐pleated sheet flanked on either side of α‐helices. The seventh strand of the β‐pleated sheet is contributed by amino acid residues from the smaller domain. In addition, this smaller C‐terminal domain, consisting of amino acid residues 181–338, contains three strands of β‐pleated sheet, two major α‐helices and one helical turn. The substrate analogue, UDP‐benzene, binds in the cleft located between the two domains with its phenyl ring in close proximity to the nicotinamide ring of NAD+. Contrary to the extensive biochemical literature suggesting that epimerase binds only one NAD+ per functional dimer, the map clearly shows electron density for two nicotinamide cofactors binding in symmetry‐related positions in the dimer. Likewise, each subunit in the dimer also binds one substrate analogue.
Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation
Authors: Ikura Teikichi , Gō Nobuhiro , Kohda Daisuke , Inagaki Fuyuhiko , Yanagawa Hiroshi , Kawabata Masuyo , Kawabata Shun‐ichiro , Iwanaga Sadaaki , Noguti Tosiyuki , Gō Mitiko
Published: May 2005

Proteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24–52) and M3 (52–73) by 2D NMR studies. Some local secondary structures, α‐helix, and β‐turns in M2 and β‐turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase. © 1993 Wiley‐Liss, Inc.
Molecular dynamics study of structure and stability of a model coiled coil
Authors: Zhang Li , Hermans Jan
Published: May 2005

This paper employs methods used earlier to study helix propensity in a model α‐helix. The methods are extended to simulations of a motif structure of the α‐helical coiled coil, i.e., a structure with a simple amino acid sequence, containing only alanine, leucine, and valine, with leucine and valine forming hydrophobic contacts in the helix interface (positions “d” and “a”). Dynamic simulations of the model coiled‐coil structure reproduce characteristic features of the coiled‐coil motif seen in experimental studies. Free energy simulations were used to assess the change in stability of the model when a leucine pair or a valine pair in the helix interface was replaced with an alanine pair. A leucine pair at position d was found to contribute 3.4 kcal/mol to the stability of the coiled coil relative to an alanine pair, and a valine pair at postion a was found to contribute 0.8 kcal/mol relative to an alanine pair. The value for the leucine pair agrees with reports in two experimental studies with molecules having different amino sequence. The value for the valine pair is reasonable given the smaller size of the valine side chain and the intrinsic low helix propensity of valine. No experimental value was available for comparison. © 1993 Wiley‐Liss, Inc.
A hypothetical complex between crystalline flavocytochrome b2 and Cytochrome c
Authors: Tegoni Mariella , White Scott A. , Roussel Alain , Mathews F. Scott , Cambillau Christian
Published: May 2005

Flavocytochrome b2 and cytochrome c are physiological electron transfer partners in yeast mitochondria. The formation of a stable complex between them has been demonstrated both in solution and in the crystalline state. On the basis of the three‐dimensional structures, using molecular modeling and energy minimization, we have generated a hypothetical model for the interaction of these redox partners in the crystal lattice. General criteria such as good charge and surface complementarity, plausible orientation, and separation distance of the prosthetic groups, as well as more specific criteria such as the stoichiometry determined in the crystal, and the involvement of both domains and of more than one subunit of flavocytochrome b2 led us to discriminate between several possible interaction sites. In the hypothetical model we present, four cytochrome c molecules interact with a tetramer of flavocytochrome b2. The b2 and c hemes are coplanar, with an edge‐to‐edge distance of 14 Å. the contact surface area is ca. 800 Å2. Several electrostatic interactions involving the flavin and the heme domains of flavocytochrome b2 stabilize the binding of cytochrome c. © 1993 Wiley‐Liss, Inc.
Normal mode analysis of mouse epidermal growth factor: Characterization of the harmonic motion
Authors: Ikura Teikichi , Gō Nobuhiro
Published: May 2005

Normal mode analysis of mouse epidermal growth factor (mEGF) has been carried out at room temperature. The value of the lowest frequency is 4.1 cm−1. This mode corresponds to hinge‐bending motion between the N‐terminal and C‐terminal domains of mEGF. This hinge‐bending motion corresponds to the “mitten mode.” In this motion, the N‐terminal domain is almost rigid. However, the C‐terminal domain is found to consist of three rigid segments. Two segments, C33‐D46 and G51‐R53, are observed moving in the same direction, but L47‐W50 moves in the opposite direction. For this mode, the effective Young's modulus turned out to be 1.1 × 109 dyn·−2. This value is a little larger than that of the mode with the lowest frequency 4.4 cm−1 of BPTI. The difference may be related to the fraction of residues involved in β‐sheets in the molecule. Similar analyses are carried out for other low frequency modes.
A monoclonal antibody fab fragment crystallized with and without a peptide epitope from HIV
Authors: Pfeffer‐Hennig Sabine , Wessner Helga , Hennig Michael , Dauter Zbigniew , Hausdorf Gert , Höhne Wolfgang E.
Published: May 2005

The Fab fragment of CB 4‐1, a monoclonal murine antibody against HIV protein p24, has been produced. It forms a complex with a synthetic antigen, an epitope of p24 made up of 11 amino acids, with the binding constant kd = 3.6 × 10−9 M. Crystals of hexagonal and orthorhombic space group has been obtained by cocrystallization of the Fab with the epitope and crystallization without the epitope, respectively. In either case, the crystals are suitable for X‐ray structural analysis. Crystals of the Fab fragment cocrystallized with the peptide have the space group P 6322 with cell dimensions of a = b = 105 Å, c = 297 Å. Fab crystals without the epitope are in space group C 222 with cell dimensions a = 110.1 Å, b = 110.2 c Å = 150.1 Å. © 1993 Wiley‐Liss, Inc.
Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways
Authors: Camacho Carlos J. , Thirumalai D.
Published: May 2005

The role of disulfide bonds in directing protein folding is studied using lattice models. We find that the stability and the specificity of the disulfide bond interactions play quite different roles in the folding process: Under some conditions, the stability decreases the overall rate of folding; the specificity, however, by yielding a simpler connectivity of intermediates, always increases the rate of folding. This conclusion is intimately related to the selection mechanism entailed by entropic driving forces, such as the loop formation probability, and entropic barriers separating the native and the many native‐like metastable states. The folding time is found to be a minimum for a certain range of the effective disulfide bond interaction. Examination of a model, which allows for the formation of disulfide bonded intermediates, suggests that folding proceeds via a threestage multiple pathways kinetics. We show that there are pathways to the native state involving only native‐like intermediates, as well as those that are mediated by nonnative intermediates. These findings are interpreted in terms of the appropriate energy landscape describing the barriers connecting low energy conformations. The consistency of our conclusions with several experimental studies is also discussed. © 1995 Wiley‐Liss, Inc.
The essential dynamics of thermolysin: Confirmation of the hinge‐bending motion and comparison of simulations in vacuum and water
Authors: van Aalten D. M. F. , Amadei A. , Linssen A. B. M. , Eijsink V. G. H. , Vriend G. , Berendsen H. J. C.
Published: May 2005

Comparisons of the crystal structures of thermolysin and the thermolysin‐like protease produced by B. cereus have recently led to the hypothesis that neutral proteases undergo a hinge‐bending motion. We have investigated this hypothesis by analyzing molecular dynamics simulations of thermolysin in vacuum and water, using the essential dynamics method. This method is able to extract large concerted atomic motions of biological importance from a molecular dynamics trajectory. The analysis of the thermolysin trajectories indeed revealed a large rigid body hinge‐bending motion of the Nterminal and C‐terminal domains, similar to the motion hypothesized from the crystal structure comparisons. In addition, it appeared that the essential dynamics properties derived from the vacuum simulation were similar to those derived from the solvent simulation. © 1995 Wiley‐Liss, Inc.
Laser microprobe fourier transform mass spectrometry. Preliminary results for feasibility and evaluation
Authors: Pelletier M. , Kreier G. , Muller J. F. , Weil D. , Johnston M. , MarshalI A. G.
Published: May 2005

The feasibility is reported of coupling a laser microprobe sampling system with a Fourier transform mass spectrometer (FTMS) for surface characterization. Analysis of an integrated circuit chip demonstrates capabilities for focusing the laser on a selected spot on a sample surface. Analysis of a model glass sample for which high resolution is required to separate metal ions from metal oxide ions emphasizes the advantages of coupling such a sampling system to an FTMS instrument.
Differentiation of type 1 and type 2 chain linkages of native glycosphingolipids by positive‐ion fast‐atom bombardment mass spectrometry with collision‐induced dissociation and linked scanning
Authors: Salyan Mary Ellen K. , Stroud Mark R. , Baillie T. A. , Levery Steven B.
Published: May 2005

Two underivatized glycosphingolipids, Leb and Ley, isomeric in carbohydrate structure (Fucα1 → 2Galβ1 → 3[Fucα1 → 4]GlcNAcβ1 → 3Glcβ1 → 4Glcβ1 → 1Cer and Fucα1 → 2Galβ1 → 4[Fucα1 → 3]GlcNAcβ1 → 3Galβ1 → 4Glcβ1 → 1Cer, respectively), were analyzed by positive‐ion fast‐atom bombardment (FAB) mass spectrometry with high energy collision‐induced dissociation (CID) and linked scanning. The two isomers were distinguishable by the abundance of product ions derived from the non‐reducing terminal tetrasaccharide fragment via sequential β‐eliminations of vivinaliy linked saccharide residues. Following earlier studies from other laboratories, which have dealt primarily with positive‐ion FAB‐CID mass spectrometry of simple model oligosaccharides, these results exemplify the practical application of two‐sector methodology to underivatized complex glycoconjugates commonly encountered in the biomedical field.
Analysis of peptides and proteins by capillary electrophoresis/mass spectrometry using acidic buffers and coated capillaries
Authors: Thibault P. , Paris C. , Pleasance S. , Caprioli R. M.
Published: May 2005

The direct coupling of capillary electrophoresis (CE) and mass spectrometry, combined with ionspray ionization using a coaxial capillary arrangement, is described. The CE/mass spectrometer interface is shown to be effective for the analysis of native and tryptic peptides and of proteins of high molecular weight such as bovine serum apotransferrin ( ≈78kDa). Adsorption of cationic analytes under acidic buffer conditions is minimized through the use of a non‐covalent coated capillary possessing an overall positive charge. Since the direction of the electroosmotic flow is thus reversed, compared to that in conventional CE separation on uncoated capillaries, migration of cations is achieved by applying a negative voltage (typically − 30kV) at the injector end of the capillary. In addition to the inherent advantage of providing pre‐formed cationic species for mass spectral detection, this arrangement permits analysis of proteins of high isoelectric points even at low pH. The ability to conduct electrophoesis of globular proteins under acidic conditions also provides a means of monitoring their conformational changes, as reflected both by the variation of migration times and by concurrent changes in the multiply charged ion envelopes.
Positive‐ion fast‐atom bombardment mass spectrometry of nitrogen macrocycles
Authors: Aubagnac J.‐L. , Marzin C. , Tarrago G.
Published: May 2005

Fast‐atom bombardment (FAB) mass Spectra of nitrogen macrocycles studied in this work show fragmentations which occur by loss of neutral molecules from the protonated molelcule to give even‐electron ions. Furthermore, both the neutral molecules and the even‐electron ions characterize substructures of each compound studied. Thus, it is easy to identify an unknown nitrogen macrocycle from its FAB mass Spectrum.
The electron affinity of UO3
Authors: Rudnyi E. B. , Kaibicheva E. A. , Sidorov L. N.
Published: May 2005

The ion/molecule equilibria method was applied to study negative ions while U3O8 was being vaporized. No UO opms were found. This has led to the conclusion that the electron affinity (EA) of UO3 is less than 205kJ mol−1, in complete contradiction to Gurvich's prediction that EA(UO3)=500±50kJ mol−1.
Analysis by a combination of gas chromatography and tandem mass spectrometry: Development of quantitative tandem‐in‐time ion trap mass spectrometry: Isotope dilution quantification of 11‐nor‐delta‐9‐tetrahydrocannabinol‐9‐carboxylic acid
Authors: Phinney Curtis S. , Welch Michael J.
Published: May 2005

Collision‐induced dissociation (CID) was performed in an ion‐trap mass spectrometer to investigate quantification by isotope dilution and gas Chromatography coupled with tandem mass spectrometry (GC/MS/MS). The operating system software was modified to allow simutaneous CID of two ions differing only slightly in mass/ charge ratios. Simultaneous excitation of the base peaks of the parent compound and its deuterated analog in a co‐eluting GC peak leads to quantitative and reproducible formation of daughter ions. Changing conditions in the mass analyzer as the GC peak elutes required broadening of the CID excitation frequency pattern. This had to be done so that relatively uniform dissociation energy would be imparted to both parent ions during the concentration changes associated with the elution of a GC peak. A commonly measured human metabolite of marijuana, 11‐nor‐delta‐9‐tetrahydrocannabinol‐9‐carboxylic acid, was analyzed in freeze‐dried urine. The mean value, 14.0±0.61 (1 standard deviation) ng/mL, agrees very well with the GC/MS mean measured value of 14.1±0.45 ng/mL. The overall coefficient of variation for the individual ion‐trap MS/MS sample measurements is 4.3%.
Quantitative attenuated total reflection (ATR) spectroscopy of films with an absorption gradient
Authors: Stuchebryukov S. D. , Vavkushevsky A. A. , Rudoy V. M.
Published: May 2005

A method for quantitatively studying the absorption gradients in films of a thickness of an incident radiation wavelength, by means of attenuated total reflection (ATR) spectroscopy is proposed. The possibilities and limitations of the method are discussed.
A practical method for determining backscattering factors and matrix correction in quantitative aes analysis of binary alloys
Authors: Streubel Peter , Berndt Helga
Published: May 2005

The composition‐dependent backscattering factor in quantitative AES analysis is investigated by comparing experimental results from different approaches with several theoretical methods. Backscattering factor ratios are presented as a function of the composition of homogeneous CuPd alloys cleaned in situ by scribing. The values were calculated in a simple way by the proposed approximation method which takes into account the importance of the primary electron incident angle. This approach can be recommended for practical use in determining matrix correction. Application of the approximation method for matrix correction to different binary alloy systems gives a better agreement with the experimental matrix correction factor than Reuter's backscattering factor equation. Matrix correction factors for binary alloys were evaluated by a simple equation considering the weak linear composition dependence which was found experimentally. With matrix correction the accuracy of quantitative AES analysis can be improved by 5% or more as was shown for the CuPd alloys.
XPS: Energy calibration of electron spectrometers. 2—Results of an interlaboratory comparison
Authors: Anthony M. T. , Seah M. P.
Published: May 2005

An interlaboratory test of the NPL calibration values and methodology for the energy scale of XPS instruments, given in Part 1, has been completed. The NPL calibration values are given for the Cu 3p, Au 4f7/2, Ag 3d5/2, Cu LMM, Cu 2p3/2, and Ag MNN peaks for A1 and Mg Kα radiations to an accuracy of 20 me V. Thirteen participants reported with their values for these peaks from seven instrument models representative of four manufacturers. These results are analysed in terms of random errors, voltage scaling errors and zero offset errors. The random errors are the smallest of these errors and amount to 30 me V, showing that instrument users can assign peak positions with very high precision. However, the voltage scaling and zero errors range up to 700 ppm and 1363 me V respectively showing that the weakest link in the commercial measurement chains is in the electronics. It is not clear if this is mainly due to drift in the electronics after the manufacturer's installation or inadequte calibration at that time. A detailed analysis of the measurements confirms the linearity of each of the instrument energy scales to within the accuracy of their random errors.
Spatially multidimensional SIMS analysis
Authors: Rüdenauer F. G.
Published: May 2005

A review of the instrumental development of spatially multidimensional elemental SIMS analysis is given. This new method makes use of fast image digitization, digital image storage and digital image processing techniques and is applicable to both scanning ion microprobes and ion microscopes. A variety of physical processes may produce image artifacts which distort image signal modulation, prevent correct spatial registration and relocate sample atoms in the interior of the sample from their original positions. Attempts at correction of these artifacts are described.
Quantitative XPS analysis considering elastic scattering
Authors: Ebel H. , Ebel M. F. , Wernisch J. , Jablonski A.
Published: May 2005

Up to now the equations for both quantitative XPS analysis and those for the determination of reduced thicknesses of thin overlayers have been derived according to the assumption of a well‐defined photoelectron escape length. Escape length distributions are caused by a variety of influences. The consequences of this are demonstrated by the example of thin overlayers. Additionally, an approximation is developed which accounts for elastic electron scattering. The ratio Λ/λel of mean free path is the characteristic quantity of this approximation, which is quantified by comparison of Monte Carlo calculations and thin film experiments. This approximation allows us to conclude that elastic electron scattering does not influence quantitative XPS analysis, so long as it is performed without any kind of references.
Observation of CuNi alloy surfaces by low wattage glow discharge emission spectrometry
Authors: Wagatsuma Kazuaki , Hirokawa Kichinosuke
Published: May 2005

Glow discharge sputtering on CuNi alloy surfaces is studied by optical emission spectroscopy and Auger electron spectroscopy. The relative intensity of Cu emission lines against Ni lines increases with a decrease in supplied power in very low wattage regions. These changes of the relative intensities principally depend on the sputtering parameters of constituent elements in CuNi alloy; that is, the preferential sputtering of copper. Surface analysis by Auger electron spectroscopy shows that when samples are sputtered by glow discharges in very low power operations, the deformation layer which has a nickel‐enriched composition exists on alloy surfaces. We discuss the effect of glow discharge sputterings on surface compositions using the two analytical methods described above.
Analytical application of XPS for surface characterization of coal fly ash and coal
Authors: Hirokawa K. , Danzaki Y.
Published: May 2005

Surface observation of coal and coal ashes was performed by XPS. S, P and N in coal and coal fly ashes were especially noticed as environmental contaminating elements, S in SO type and P in PO type in fly ash, and S in thiophene type and oxide type, N in pyrrole and pyridine type in coal were found, respectively. The some S compounds in coal and fly ash, and N compounds in coal were dissolved in water by leaching, but P in fly ash remained in the residue as PO type.
Depth profiling on a sputtered bevel of sub‐degree slope angle
Authors: Gries W. H.
Published: May 2005

A new method is described whereby a surface can be bevel‐sectioned by means of sputtering at a slope angle of any desired sharpness. In contrast with other proposals of sputter‐bevelling this method produces an elevated bevel section. Measurements on a shallow diffusion profile of boron in a silicon wafer using this method show the profile reproduction to be very satisfactory. Distorting effects on the projection of the depth profile on the sputtered bevel are discussed. Scanning Auger and ion microprobes are compared for their suitability for reproducing a depth profile from its projection on a sputtered bevel.
Scanning ion imaging as a diagnostic tool for an ion microscope
Authors: Brown J. D. , Vandervorst W.
Published: May 2005

A scanning system has been installed on a Cameca IMS 3f ion microscope. The system has been invaluable for alignment of secondary ion extraction to the centre of the crater during depth profiling, detection of inclusions and lateral inhomogeneities during depth profiling and compensation of charging of insulators using an electron flood gun. Limitations of the standard gun have become apparent.
Stabilization of charge on electrically insulating surfaces during SIMS experiments—experimental and theoretical studies of the specimen isolation method
Authors: Lau W. M. , McIntyre N. S. , Metson J. B. , Cochrane D. , Brown J. D.
Published: May 2005

Recent experiments have shown that secondary ion mass spectrometric (SIMS) measurements of insulator surfaces can be greatly facilitated by the use of a charged aperture located immediately above the analysis area (the ‘specimen isolation technique’). This allows the surface potential within the aperture area to be stabilized. Charging is stabilized when the potential difference between the surface and the aperture becomes large enough that excessive charge, in the form of secondary electrons, is drained away from the surface to the aperture. The potential difference generated on such insulating surfaces can be measured experimentally by varying the voltages applied to the electrostatic analyzer to measure the secondary ion intensity as a function of kinetic energy. Such measurements have been carried out on a Cameca IMS‐3F instrument for a range of aperture dimensions and for different primary and secondary ions. The surface potential can be stabilized at a potential readily measurable by the electrostatic analyzer for both O− and Cs+ ion beams. The mechanism for this stabilization has been analyzed through calculations of two dimensional contours for the region around the specimen holder. For surfaces with a very high charging potential (>600 V), potential wells which can trap ions of low kinetic energy develop near the surface. Element and oxide secondary ion kinetic energy distribution curves, taken under specimen isolation conditions, which differ from those obtained under normal non‐charging SIMS conditions, are evidence for such ion trapping.
Quantitative analysis of complex Auger spectra by least‐squares fitting with prefiltering of spectra
Authors: Sekine T. , Mogami A.
Published: May 2005

The ‘filter‐fit’ method, which was originally developed for the analysis of energy dispersive x‐ray data, has been applied to the quantitative analysis of Auger spectra for the first time. It is a digital peak deconvolution technique in the presence of the continuum background using least‐squares fitting calculations, including the prefiltering of spectra. To evaluate this method, composite‐known spectra digitally composed of Cr, O and Ni standard spectra were prepared. For the deconvolution of Cr and O peaks under the influence of the Ni peak tail, the present method showed remarkable advantage over the conventional least‐squares fitting without prefiltering. As a digital filter for prefiltering, derivative filters of different orders and ‘top‐hat’ filter were examined. In derivative filters, it was found that there is an optimum order in the balance of advantage of suppressing the background and disadvantage of losing peak intensity. The ‘top‐hat’ filter is a very practical filter in both background suppression and noise attenuation.
Quantitative AES depth profiling of very thin overlayers
Authors: Sanz J. M. , Hofmann S.
Published: May 2005

A model calculation is proposed which quantitatively evaluates measured AES sputtering profiles of very thin overlayers in terms of the original elemental depth distribution. The model is based on the sequential layer sputtering model, including the escape depth of the Auger electrons. A proposal for the incorporation of a site dependent sputtering yield and of preferential sputtering effects is presented and the limitations and capabilities are discussed. Applications to experimental data are shown for oxide films on tantalum, for an oxidefilm on a NiCr20 alloy and for a passive film on FeCr18Ni9.
Spatial chemical analysis of polymer laminates and conducting organic films using SIMS
Authors: deVries J. E. , Holubka J. W. , Prater T. J. , Kaberline S. L. , Schuetzle D. , McIntyre N. S. , Chauvin W.
Published: May 2005

Secondary ion mass spectrometry (SIMS) has been used to generate images of polymeric materials including a polymer laminate and metal‐chelated organic materials cured on Teflon substrates. Metal‐chelation facilitated the imaging of organic materials by monitoring of the metallic tag. Incorporation of the metal into the organic complex made the sample conductive therefore circumventing charging difficulties normally associated with SIMS analysis of organics. Each layer of the polymer laminate could be easily identified by monitoring molecular fragment ions that were distinctive for each polymer type. Images were acquired at a resolution of approximately 5–10 μm.
Quantitative non‐destructive in‐depth composition information from XPS
Authors: Tougaard S.
Published: May 2005

The XPS peak shape from inhomogeneous transition metals is studied theoretically under variation of the path length R travelled by the photoelectron in the solid, the XPS peak energy Ep, and the particular metal M. The variation in peak shape is characterized by a single parameter D = Ap/B which is the ratio of the peak area to the increase in background signal 30 eV below the peak energy. It is found that D is a strong function of R, a moderate function of Ep and to first order independent of M. This gives theoretical support to the idea suggested previously of using D for fast non‐destructive extraction of in‐depth composition information. To a good approximation we have D(R,Ep) = (425+Ep) × R, with Ep in eV, R in Å and D(R,Ep) in eV. The practical use of this function in the analysis of experimental data is discussed.
Auger electron spectroscopy depth profiling during sample rotation
Authors: Zalar A.
Published: May 2005

There are many factors that affect depth resolution of AES compositional depth profiles; quite often, it is degraded mostly by the sample surface roughness. We differentiate between the initial roughness of the sample surface and the roughness induced by ion sputtering during depth profiling. The influence of the ion beam incidence angle and of the ion energy on the depth resolution of multilayer Cr/Ni thin film structures was initially investigated on the samples that were stationary during AES depth profiling. The sputtering induced surface topography was investigated by transmission electron microscopy. In order to diminish topographical effects, we applied sample rotation during AES depth profiling. The sample holder of a commercial AES instrument was equipped with a mechanism that enabled sample rotation (1 rpm) during the simultaneous ion sputtering and AES analysis. The influence of sample rotation on depth resolution was studied on multilayer Cr/Ni thin film structures deposited on smooth substrate and on SiO2/Si samples. In all the cases studied, sample rotation during depth profiling improved depth resolution. This improvement was in some cases surprisingly large, whereas in other cases it was less substantial, depending on the type of sample and its original surface topography, on the ion beam incidence angle, on the ion beam energy, and on the sputer depth. The main reasons for improved depth resolution resulting from sample rotation during depth profiling are the decrease of the angular dependence of the sputtering yield for variously oriented microplanes with respect to the ion beam direction, and the decrease of the roughness induced during ion sputtering.
Wetting and spreading of liquid metals: the rôle of surface composition
Authors: Smith Graham C. , Lea Colin
Published: May 2005

Quantitative measurements of the surface compositional changes which occur during the wetting of copper substrates in vacuum by liquid SnPb solder alloys have been made in situ, by Auger electron spectroscopy. Five different spatial regions associated with the wetting front have been identified. Away from the spreading front, the liquid solder shows a surface enhancement of lead. Approaching the front, adjacent bands of Cu3Sn intermetallic compound, and tin‐depleted liquid occur, both of width ∼ 20 μm. The lead‐enriched surface of the solder extends over these two regions, and out over the copper to form approximately 50% monolayer ‘halo’ of ∼ 80 μm width. Beyond the halo, in the fifth region, very small amounts of tin and lead were detected. The lead halo forms rapidly by surface diffusion, and precedes wetting. In the absence of other limitations, it is the reduction of the copper substrate surface energy by the lead halo that restricts the spread of the molten alloy. Intermetallic compound formation is relatively slow and only takes place once spreading has ceased and a quasiequilibrium reached.
Depth profiling of carbonaceous films, produced in situ in the Tokamak TEXTOR
Authors: Tschersich K. G. , Littmark U. , Fleischhauer H. P.
Published: May 2005

Samples of Si, Ni and Cr exposed to an in situ ‘carbonization’ in the Tokamak TEXTOR have been investigated. Depth profiles have been measured by argon ion sputter etching and AES. From the AES energy spectra (direct counting), the relative AES signals (peak to background ratios) have been derived by properly fitting the background and the peaks. The depth profiles are discussed in light of a ballistic‐mixing model for sputter etching and a standard exponential Auger escape probability.
SIMS analysis of AlxGa1–xas/gaas layered structures grown by metal‐organic vapour phase Epitaxy
Authors: Boudewijn P. R. , Leys M. R. , Roozeboom F.
Published: May 2005

For AlxGa1‐xAs/GaAs layered structures, grown by MOVPE, abrupt interfaces in the order of one atomic distance were observed. These structures are well suited to serve as test samples for studying the influence of bombardment conditions on the quality of SIMS depth profiles. The results of such a study are presented and it is shown that depth profiles can be obtained with a depth resolution of about 25 Å. It was found that beyond the interface secondary ion signals decrease exponentially; from the variation of the slope of this exponential decay as a function of primary ion energy it can be concluded that depth resolution is determined by a purely collisional mixing process. From this type of data we can derive a minimal layer thickness in AlxGa1‐xAs/GaAs quantum well structures for which quantitative SIMS analysis of the Al content is possible.
The application of secondary Ion mass spectrometry to surface analysis of semiconductor substrates and devices
Authors: Brown A. , van den Berg J. A. , Vickerman J. C.
Published: May 2005

The application of static, dynamic and imaging SIMS to semiconductor starting materials and devices is discussed. Static SIMS is used to examine the effect of various chemical preparation methods on the surface of the III‐V compounds InAs, InP and GaAs prior to epitaxial growth of device structures. Dynamic SIMS profiles from a superlattice structure involving alternative GaAlAs ‐ GaAs layers are presented along with an examination of the factors affecting depth resolution for low‐dimensional devices. Finally the importance of imaging or scanning SIMS for chemical mapping and microanalysis of final device structures is discussed.
Application of GDOS (glow discharge optical spectroscopy) and SIMS to the analysis of surface corrosion products on stainless steel after exposure to liquid alkali metals
Authors: Barker Marten G. , Schreinlechner Inge E.
Published: May 2005

Corrosion of steels by liquid alkali metals involves the transfer of non metals, such as C, N or O, from solution in the alkali metal to the surface of the steel. Surface corrosion products may then be formed. With oxygen in sodium these products may be ternary oxides, with nitrogen in lithium the ternary nitride Li9CrN5 is formed and with carbon binary carbides are formed in both alkalies. Along with the surface corrosion products, element depletions and carbon or nitrogen diffusion profiles are created. The analyses of thin corrosion product layers and the determination of the concentration profiles of carbon and nitrogen are important requirements for the understanding of the corrosion process. Lithium penetration into steel is also a major problem in lithium corrosion. Lithium is extremely difficult to determine by conventional analytical methods, due to its low atomic number. In this paper the use of glow discharge optical spectroscopy (GDOS) and SIMS for the study of surface corrosion products, is described, together with a quantitative determination of the carbon‐depth profile in type 316 steel exposed to liquid sodium.
ESCA study of the oxidation of a nickel–molybdenum alloy
Authors: Marcus P. , Olefjord I.
Published: May 2005

The surface composition of Ni–6at% Mo (110) alloy was analysed by ESCA after surface preparation treatments and after oxidation at 25°C and 500°C (p = 10−4 Torr). Ion etching causes a marked enrichment of molybdenum on the surface. After annealing at 500°, the concentration of segregated molybdenum is ˜25%. At 800°C there is no segregation of the metal elements, but sulphur segregates to the surface. Oxidation at 25°C gives a thin oxide layer (5–6 Å) with a composition which reflects the composition of the initial surface, so that the oxidation of a surface enriched with molybdenum gives a molybdenum‐rich oxide. Oxidation at 500°C gives a molybdenum‐enriched oxide. The Mo concentration of the oxide is 12%, i.e. twice that in the bulk. The lateral growth of oxide islands seems to be already complete after a very short oxidation time (2 min) and then a parabolic growth of the oxide layer is observed. The chemical shifts of Ni2+ (2p3/2) and Mo6+ (3d5/2) in the oxide formed on the alloy are respectively 2.1 eV and 4.2 eV, while they are 1.6 eV for NiO and 4.8 eV for MoO3. Adsorbed sulphur has a marked influence on the oxidation. The oxide growth (also parabolic) is faster in the presence of sulphur at 500°C. The oxide film grows on top of the sulphur layer.
A high‐performance low‐cost computer interface for AES/XPS
Authors: Tomich D. H. , Grazulis L. , Grant J. T.
Published: May 2005

An Auger/XPS system has been automated using a mircocomputer. Some considerations in the design of the interface which could be used for a variety of spectroscopies will be presented and should be of general interest. The spectrometer used in this work was a Perkin–Elmer Physical Electronics Model 550 SAM/XPS. The computer used was a Zenith Z‐100 but the interface was designed for use with any microcomputer having two parallel I/O ports. Hardware details will be discussed with emphasis on the versatility, efficiency, and cost. The sweep control for the electron energy analyzer utilizes two 12 bit DAC's, one for the starting energy and another for the energy sweep range, thereby allowing 12 bits of resolution in both the sweep and offset. The software has been written in Microsoft FORTRAN, a subset of FORTRAN 77. The versatility of this system is illustrated with XPS data from Ag and a high kinetic energy backscattered primary.