bluuebunny/crossref_metadata_2025 huggingface dataset:
An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems
Authors: Shi Shenghua , Yan Lisa , Yang Yang , Fisher‐Shaulsky Jodi , Thacher Tom
Published: May 2003

ESFF is a rule‐based force field designed for modeling organic, inorganic, and organometallic systems. To cover this broad range of molecular systems, ESFF was developed in an extensible and systematic manner. Several unique features were introduced including pseudoangle and a dot product function representing torsion energy terms. The partial atomic charges that are topology‐dependent are determined fromab initio(DFT) calculated electronegativity and hardness for valence orbitals. The van der Waals parameters are charge‐dependent, and correlated with the ionization potential for atoms in various valence states. To obtain a set of well‐defined and physically meaningful parameters, ESFF employs semiempirical rules to translate atomic‐based parameters to parameters typically associated with a covalent valence force field. The atomic parameters depend not only on atom type, but also on internal type, thus resulting in a more accurate force field. This article presents the theory and the method used to develop the force field. The force field has been applied to molecular simulations of a wide variety of systems including nucleic acids, peptides, hydrocarbons, porphyrins, transition metal complexes, zeolites, and organometallic compounds. Agreement with the experimental results indicates that ESFF is a valuable tool in molecular simulations for understanding and predicting both crystal and gas phase molecular structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1059–1076, 2003
A density functional study of the hydrogen‐bond network within the HIV‐1 protease catalytic site cleft
Authors: Sirois S. , Proynov E. I. , Truchon J.‐F. , Tsoukas C. M. , Salahub D. R.
Published: May 2003

The relative energy between two different protonation sites of the Asp25′ catalytic site residue is computed and analyzed for various HIV‐1 Protease/inhibitor complexes and compared to the wild‐type structure. By comparing calculations of negatively charged fragments of gradually increasing size up to 105 atoms we show that correct modeling of the HIV‐1 Protease active site requires much larger models than the commonly used acetic acid/acetate moieties. The energy difference between the two proposed protonation sites decreases as the size of the system increases and tends to converge only when the entire catalytic triad of both monomers is taken into account. The importance of the Gly27 backbone amine groups in the stabilization of the negative charge within the catalytic site cleft is revealed. Comparison of the wild‐type structure with the structures from various Pr/drug complexes indicates that the HIV‐1 protease has a particular catalytic site flexibility. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1110–1119, 2003
Localized basis orbitals: Minimization of 2‐electron integrals array and orthonormality of basis set
Authors: Anikin N. A. , Bugaenko V. L. , Frash M. V. , Gorb L. , Leszczynski J.
Published: May 2003

A new scheme for deriving localized basis orbitals (LBOs) and for obtaining integral transformations from the basis orbitals (BOs) to the LBOs has been introduced. The scheme was tested at the ab initio Hartree‐Fock level using the STO‐3G basis set. It has been revealed that it provides results that are close to the conventional ab initio approximations for various physical‐chemical properties. At the same time, both the number of differential overlaps and the number of electron repulsion integrals (ERIs) grow with the system size notably slower than those calculated for the usual BOs. The power exponent for ERI/LBO is typically smaller by 0.3–0.6 than that for ERI/BO. The exponent reaches the value of 1.69 even for triglycine (24 atoms only), which represents a relatively small molecular model. Thus, the localization of the BOs (using LBOs) may result in additional improvements in efficiency even for electronically delocalized systems. It was shown that ERI/LBO is particularly efficient for systems with complex spatial structures (including conjugated species). The obtained results indicate that the proposed scheme could be included in computational methods targeted at calculating large molecular systems (which achieve linear scaling for more distant interactions). Neglecting ERI/LBO does not depend on the delocalization of the localized MO using ERI/LBO. The orthogonality and locality of the LBOs should make them useful in methods based on dividing the system into orthogonal subsystems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1132–1141, 2003
A novel approach for designing simple point charge models for liquid water with three interaction sites
Authors: Glättli Alice , Daura Xavier , Van Gunsteren Wilfred F.
Published: May 2003

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard–Jones and Coulomb interaction functions and without including a self‐energy correction in the effective pair‐potential as is done in the SPC/E model. Here, a different approach to circumvent this problem is presented. A short‐range interaction term, which corrects the oxygen–oxygen energy at small distances by small amounts of energy, was introduced in the nonbonded interaction function. This additional force‐field term allows to derive new parameter sets for SPC‐like water models that yield better agreement with experimental data on liquid water. Based on previous investigations of the force‐field parameter dependence of the water properties of SPC‐like models, the necessary parameter changes to obtain a lower diffusion coefficient and a larger dielectric permittivity were specified and accordingly six new models were developed. They all represent an improvement over SPC in terms of structural and diffusional properties, four of them show better dielectric properties also. One model, SPC/S, has been characterized in more detail, and represents most properties of liquid water better than SPC while avoiding the larger discrepancies with experimental values regarding density, thermal compressibility, energy, and free energy of the SPC/E model. We conclude that the use of a simple, short‐ranged additional oxygen–oxygen interaction term makes a simultaneous improvement of the diffusion coefficient and the dielectric properties of water feasible. © 2003 Wiley Periodicals, Inc. J Comput Chem 9: 1087–1096, 2003
Development of new pseudopotential methods: Improved model core potentials for the first‐row transition metals
Authors: Lovallo Christopher C. , Klobukowski Mariusz
Published: May 2003

We have recently developed new nonrelativistic and scalar‐relativistic pseudopotentials for the first‐row transition metal and several main‐group elements. These improved Model Core Potentials were tested on a variety of transition metal complexes to determine their accuracy in reproducing electronic structures, bond lengths, and harmonic vibrational frequencies with respect to both all‐electron reference data as well as experimental data. The new potentials are also compared with the previous model core potentials available for the first‐row transition metals. The new potentials do a superior job at reproducing atomic data, reproduce molecular data as well as the previous version, and in conjunction with new main‐group pseudopotentials that have L‐shell structure of the valence basis set, they are slightly faster. © 2003 Wiley Periodicals, Inc. J Comput Chem 9: 1009–1015, 2003
A local interpolation scheme using no derivatives in potential sampling: Application to O(1D) + H2 system
Authors: Ishida Toshimasa , Schatz George C.
Published: May 2003

We recently proposed a local interpolation scheme, in which interpolant moving least squares (IMLS) and Shepard interpolation are employed to describe potential energy surfaces. This IMLS/Shepard scheme is used to interpolate quantum chemical potential energy surfaces for which analytical derivatives are not available. In this study, we apply the scheme to the highly exothermic O(1D) + H2 → H + OH reaction and compare it with results based on Shepard interpolation using second‐order Taylor expansions. An analytical surface is used to define the potential function so that errors in the interpolation function may accurately be determined. We find that the present scheme reproduces the correct reactive cross‐sections more accurately than the Shepard scheme, and with rms errors for energy and gradients that are significantly smaller than those from Shepard interpolation. This occurs even though the present scheme does not utilize derivative and Hessian information, whereas the Shepard interpolation does. The Bayesian approach proposed by Bettens and Collins does not improve the IMLS/Shepard results significantly, although it does the Shepard‐only approach. The accuracy of the IMLS/Shepard scheme is surprising, but can be explained by the more global nature of the interpolation. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1077–1086, 2003
Powder pattern indexing using the weighted crosscorrelation and genetic algorithms
Authors: Hageman J. A. , Wehrens R. , De Gelder R. , Buydens L. M. C.
Published: May 2003

X‐ray diffraction is a powerful technique for investigating the structure of crystals and crystalline powders. Unfortunately, for powders, the first step in the structure elucidation process, retrieving the unit cell parameters (indexing), is still very critical. In the present article, an improved approach to powder pattern indexing is presented. The proposed method matches peak positions from experimental X‐ray powder patterns with peak positions from trial cells using a recently published method for pattern comparison (weighted crosscorrelation). Trial cells are optimized with Genetic Algorithms. Patterns are not pretreated to remove any existing zero point shift, as this is determined during optimization. Another improvement is the peak assignment procedure. This assignment is needed for determining the similarity between lines from trial cells and experiment. It no longer allows calculated peaks to be assigned twice to different experimental peaks, which is beneficial for the indexing process. The procedure proves to be robust with respect to false peaks and accidental or systematic absensences of reflections, and is successfully applied to powder patterns originating from orthorhombic, monoclinic, and triclinic compounds measured with synchrotron as well as with conventional laboratory X‐ray diffractometers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1043–1051, 2003
Optimized Slater‐type basis sets for the elements 1–118
Authors: Van Lenthe E. , Baerends E. J.
Published: May 2003

Seven different types of Slater type basis sets for the elements H (Z = 1) up to E118 (Z = 118), ranging from a double zeta valence quality up to a quadruple zeta valence quality, are tested in their performance in neutral atomic and diatomic oxide calculations. The exponents of the Slater type functions are optimized for the use in (scalar relativistic) zeroth‐order regular approximated (ZORA) equations. Atomic tests reveal that, on average, the absolute basis set error of 0.03 kcal/mol in the density functional calculation of the valence spinor energies of the neutral atoms with the largest all electron basis set of quadruple zeta quality is lower than the average absolute difference of 0.16 kcal/mol in these valence spinor energies if one compares the results of ZORA equation with those of the fully relativistic Dirac equation. This average absolute basis set error increases to about 1 kcal/mol for the all electron basis sets of triple zeta valence quality, and to approximately 4 kcal/mol for the all electron basis sets of double zeta quality. The molecular tests reveal that, on average, the calculated atomization energies of 118 neutral diatomic oxides MO, where the nuclear charge Z of M ranges from Z = 1–118, with the all electron basis sets of triple zeta quality with two polarization functions added are within 1–2 kcal/mol of the benchmark results with the much larger all electron basis sets, which are of quadruple zeta valence quality with four polarization functions added. The accuracy is reduced to about 4–5 kcal/mol if only one polarization function is used in the triple zeta basis sets, and further reduced to approximately 20 kcal/mol if the all electron basis sets of double zeta quality are used. The inclusion of g‐type STOs to the large benchmark basis sets had an effect of less than 1 kcal/mol in the calculation of the atomization energies of the group 2 and group 14 diatomic oxides. The basis sets that are optimized for calculations using the frozen core approximation (frozen core basis sets) have a restricted basis set in the core region compared to the all electron basis sets. On average, the use of these frozen core basis sets give atomic basis set errors that are approximately twice as large as the corresponding all electron basis set errors and molecular atomization energies that are close to the corresponding all electron results. Only if spin‐orbit coupling is included in the frozen core calculations larger errors are found, especially for the heavier elements, due to the additional approximation that is made that the basis functions are orthogonalized on scalar relativistic core orbitals. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1142–1156, 2003
Hydrogen bonding in diols and binary diol–water systems investigated using DFT methods. II. Calculated infrared OH‐stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding
Authors: Klein Roger A.
Published: May 2003

Although the two hydroxyl groups in 1,2‐diols interact as evidenced by NMR and IR spectroscopic shifts, electron density topological analysis has shown a bond critical point (BCP) and atomic bond path to be absent (Klein, R. A.; J Comp Chem 2002, 23, 585–599; J Am Chem Soc 2002, 124, 13931–13937), indicating that no intramolecular hydrogen bond is formed. Here, we demonstrate that small NMR or IR shifts are neither necessarily diagnostic nor sufficient as indicators of hydrogen bond formation; moreover, modified van der Waals atomic radii are needed for estimating maximum nuclear interaction distances and nuclear interpenetration. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1120–1131, 2003
Development of polyphosphate parameters for use with the AMBER force field
Authors: Meagher Kristin L. , Redman Luke T. , Carlson Heather A.
Published: May 2003

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed‐phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6‐31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas‐phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1016–1025, 2003
Methyl dynamics in crystalline amino acids: MD and NMR
Authors: Chatfield David C. , Augsten Alberto , D'Cunha Cassian , Wong Sergio E.
Published: May 2003

Correlation times for rotation of deuterated methyls in crystalline leucine, valine, and cyclo‐L‐alanyl‐L‐alanine are calculated with molecular dynamics and compared with NMR data. The simulations distinguish between methyls having different steric environments in the crystal, yielding correlation times differing by a factor of up to 30 for methyls within a given crystal. MD and NMR correlation times agree to within a factor of 2. However, averaging over nonequivalent methyls can yield correlation functions that, although actually multiexponential, are well fit by single exponentials. This may have significance for interpreting NMR data; previous NMR data did not distinguish between the methyls in these crystals. Adiabatic rotational barriers calculated with the X‐ray structure differ from effective barriers during simulation by up to ±1 kcal/mol; the difference indicates that dynamical effects have a significant role in determining rotational correlation times. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1052–1058, 2003
Peptide models. XXXIII. Extrapolation of low‐level Hartree–Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory
Authors: Perczel András , Farkas Ödön , Jákli Imre , Topol Igor A. , Csizmadia Imre G.
Published: May 2003

At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X‐ray‐based 3D‐stucture determinations in silico methods are now widely accepted. Homology‐based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low‐ and medium‐level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3‐21G, 6‐31+G(d) and 6‐311++G(d,p)] serves as a suitable test. Minima, first‐order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6‐311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3‐21G) to more complex results [CCSD(T)/6‐311+G(d,p)//B3LYP/6‐311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1026–1042, 2003
Complete graph conjecture for inner‐core electrons: Homogeneous index case
Authors: Pogliani Lionello
Published: May 2003

The complete graph conjecture that encodes the inner‐core electrons of atoms with principal quantum number n ≥ 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen‐suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher‐order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner‐core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two “quantum” algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED50 of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model. © 2003 Wiley Periodicals, Inc. J Comput Chem 9: 1097–1109, 2003
Self‐efficacy changes in groups: effects of diversity, leadership, and group climate
Authors: Choi Jin Nam , Price Richard H. , Vinokur Amiram D.
Published: May 2003

Self‐efficacy belief is a significant predictor of behavioral choices in terms of goal setting, the amount of effort devoted to a particular task, and actual performance. This study conceives of formation and change of self‐efficacy as a social and context‐dependent process. We hypothesized that different group factors (discretionary and ambient group stimuli) influence changes in members' self‐efficacy through differing routes (individual‐level and cross‐level processes). We tested our hypotheses using data from individuals in 169 training groups who attended a 5‐day workshop designed to increase participants' job‐search skills and efficacy. Specifically, we examined the degree of change in participants' job‐search efficacy before and after the workshop. The results showed that (a) membership diversity in education was positively related to increases in job‐search efficacy, (b) supportive leadership contributed to job‐search efficacy at the individual level of analysis with no cross‐level effects, and (c) open group climate contributed to job‐search efficacy through both individual‐level and cross‐level processes. Limitations and directions for future research are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Becoming an undercover police officer: a note on fairness perceptions, behavior, and attitudes
Authors: Farmer Suzanne J. , Beehr Terry A. , Love Kevin G.
Published: May 2003

Reactions to an undercover police officer selection system were analyzed for 271 officers. Officers given undercover assignments had higher procedural justice perceptions and outcome satisfaction than others awaiting assignment in a qualified applicant pool. Procedural and distributive justice perceptions were subsequently related to the undercover officer's job performance, job satisfaction, and organizational commitment. Copyright © 2003 John Wiley & Sons, Ltd.
Relationships between psychological climate perceptions and work outcomes: a meta‐analytic review
Authors: Parker Christopher P. , Baltes Boris B. , Young Scott A. , Huff Joseph W. , Altmann Robert A. , LaCost Heather A. , Roberts Joanne E.
Published: May 2003

In this study, meta‐analytic procedures were used to examine the relationships between individual‐level (psychological) climate perceptions and work outcomes such as employee attitudes, psychological well‐being, motivation, and performance. Our review of the literature generated 121 independent samples in which climate perceptions were measured and analyzed at the individual level. These studies document considerable confusion regarding the constructs of psychological climate, organizational climate, and organizational culture and reveal a need for researchers to use terminology that is consistent with their level of measurement, theory, and analysis. Our meta‐analytic findings indicate that psychological climate, operationalized as individuals' perceptions of their work environment, does have significant relationships with individuals' work attitudes, motivation, and performance. Structural equation modeling analyses of the meta‐analytic correlation matrix indicated that the relationships of psychological climate with employee motivation and performance are fully mediated by employees' work attitudes. We also found that the James and James (1989) PCg model could be extended to predict the impact of work environment perceptions on employee attitudes, motivation, and performance. Despite the number of published individual‐level climate studies that we found, there is a need for more research using standardized measures so as to enable analyses of the organizational and contextual factors that might moderate the effects of psychological climate perceptions. Finally, we argue for a molar theory of psychological climate that is rooted in the psychological processes by which individuals make meaning or their work experiences. Copyright © 2003 John Wiley & Sons, Ltd.
Reducing subjectivity in the assessment of the job environment: development of the Factual Autonomy Scale (FAS)
Authors: Spector Paul E. , Fox Suzy
Published: May 2003

Self‐report measures of job stressors have been criticized for being too subjective, rendering relations with other variables inconclusive. The Factual Autonomy Scale (FAS) was developed to reduce subjectivity by careful choice of fact‐based items. Results of two studies showed that when compared to the Job Diagnostic Survey autonomy scale, the FAS demonstrated superior convergent validity with alternate sources (supervisors in Study 1 and coworkers in Study 2), and discriminant validity when correlated with the remaining JDS core characteristics subscales. In addition, the FAS was correlated to a lesser extent than the JDS autonomy scale with job satisfaction. Incumbent FAS scores and not JDS scores correlated significantly with job performance as assessed by supervisors. It is suggested that it is feasible to develop fact‐based items for scales of the work environment that reduce the degree of subjectivity of responses. Copyright © 2003 John Wiley & Sons, Ltd.
Microflora involved in textile dye waste removal
Authors: Abd El–Rahim Wafaa M. , Moawad Hassan , Khalafallah M.
Published: May 2003

Textile dyes are heavily used in factories for coloring different cloth materials. This work was designed to identify microorganisms capable of removing textile dyes, either by biodegradation or by biosorption.

We expected to isolate microorganisms adapted to high dye concentrations from sites near textile industry complex. An experiment was conducted to study the efficiency of the isolates in removing textile dyes. The tested dyes were used as carbon and nitrogen sources for isolation of soil and/or water microorganisms capable of removing textile dyes wastes from factories effluent. The results indicated the low efficiency of both bacteria and actinomycetes in clean‐up the effluent from the waste dyes in 10–21 days. On the other hand six fungal isolates were obtained by plating factory effluent on Martin's medium and media containing dyes as the sole source of carbon and nitrogen for growth. These isolates fell in two genera, Aspergillus and Trichoderma. Results of these studies revealed the potential capacity of these fungi to decolorize the tested dyes in comparatively short time (2–24 hours) indicating strong efficiency of dye bioremediation by the fungal isolates. Since the process involved is mostly fast interaction between the fungal mycelium and the dye in the media, the possible mechanism could be based on a biosorption of such chemicals on the intact fungal biomass, rather than direct biodegradation of the compounds.
Distribution of zoosporic fungi in the mud of major Egyptian lakes
Authors: Ali Esam H. , Abdel–Raheem Ahmed
Published: May 2003

Twenty‐six identified and three unidentified species belonging to eight genera of zoosporic fungi were recovered from seventy‐six mud samples of Egyptian lakes using sesame seeds as baits. Nineteen samples were collected along the borders of four major lakes. Pythium, Phytophthora and Allomyces, yielded the highest spectra of zoosporic species, while Aqualinderella, Blastocladia and Dictyuchus, had one species. Pythium, Aphanomyces, Allomyces, Aqualinderella, Phytophthora and Saprolegnia were the dominant zoosporic genera while Blastocladia and Dictyuchus were rare. The most prevalent species of zoosporic fungi were Aqualinderella fermentans, Aphanomyces laevis and unidentified Pythium species while the other isolated species in this study were rare. Menzalah was the richest lake with zoosporic species followed by Borolous and Karoon. Some zoosporic fungal genera were recovered from the mud of the four tested lakes (participator genera) and others from three lakes or from only two lakes. Physicochemical characteristics of the mud samples (pH, total soluble salts and organic matter) revealed no correlation with the fungal occurrence and distribution in these lakes.
Occurrence of yeasts in municipal wastes and their behaviour in presence of cadmium, copper and zinc
Authors: Balsalobre Luz , De Silóniz María‐Isabel , Valderrama María‐José , Benito Teresa , Larrea María‐Teresa , Peinado José‐Martínez
Published: May 2003

Seven yeasts strains have been isolated from sewage sludge. Also six samples of compost with different sieving, composting times and origins, have been analysed. Apparently, composting processes negatively affect the viability of yeasts, as none could be isolated from the compost samples. The margins of tolerance of the yeasts to Cd, Cu and Zn have been determined. The physiological response to metals was similar in all the species studied, and in general, kinetic parameters (μ and lag) were affected. Metal uptake ability was also studied and inter‐ and intra‐specific heterogeneity was detected, thus indicating that both the tolerance to metals and the capacity of the uptake were dependent on ionic metal and yeast species. The effect of the presence of multi‐metal ions on the uptake capacity of each individual metal was assayed for two selected yeasts, Pichia guilliermondii and Torulaspora delbrueckii. The uptake of each individual metal varied with the combination assayed, and when both strains were compared different results were also found.
Evaluation of SDS‐polyacrylamide gel systems for the study of outer membrane protein profiles of clinical strains of Acinetobacter baumannii
Authors: Cuenca Felipe Fernández , Pascual Alvaro , Martínez Luis Martínez , Conejo Ma Carmen , Perea Evelio J.
Published: May 2003

The outer membrane protein (OMP) profiles of 23 blood isolates of Acinetobacter baumannii representing all the different antimicrobial susceptibility patterns observed during a 3‐year period in a Spanish hospital were studied. OMPs extracted from envelopes of sonicated cells after solubilisation with 2% of N‐lauryl‐sarcosinate were analysed by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE) using the Laemmli's buffers. Eight running gel systems differing in the concentration of polyacrylamide (8%, 10% and 12%) and in the absence or presence of urea (4 M and 6 M) were used in a preliminary study analysing the OMP profiles of four clonally unrelated strains of A. baumannii. When this study was completed, the OMPs of the 23 A. baumannii were analysed in 10% SDS‐polyacrylamide gels with 6 M urea and in 12% SDS‐polyacrylamide gels. Ten OMP profiles were observed in 10% SDS‐polyacrylamide gels with 6 M urea, whereas only 5 OMP profiles were visualised using 12% SDS‐polyacrylamide gels. The OMP profiles obtained in 10% SDS‐polyacrylamide gels with 6 M urea only partially correlated with those observed in 12% SDS‐polyacrylamide gels. In conclusion, the use of 10% SDS‐polyacrylamide gels with 6 M urea is recommended for the study of OMP profiles of A. baumannii.
Molecular diversity of mesophilic and thermophilic bacteria in a membrane bioreactor determined by fluorescent in situ hybridization with mxaF‐ and rRNA‐targeted probes
Authors: Dias João Carlos T. , Silva Cláudio M. , Mounteer Ann H. , Passos Flavia M. L. , Linardi Valter R.
Published: May 2003

An evaluation of the efficiency of treatment of kraft mill foul condensates in a membrane bioreactor was carried out in the laboratory. Efficiency and rate of methanol removal were quantified at operating temperatures of 35, 45 and 55 °C. The structure of the bacterial community present in the reactor biomass at the different operating temperatures was evaluated by in situ hybridization of the biomass samples with fluorescently‐labelled probes (FISH) targeting the Eubacteria, the alpha, beta and gamma subclasses of the Proteobacteria, the low G + C content Gram‐positive bacteria (Bacillus spp.), while community function was evaluated by in situ hybridization with a methanol dehydrogenase gene (mxaF) probe. Methanol removal efficiency decreased from 99.4 to 92%, and removal rate from 2.69 mg MeOH/l × min to 2.49 mg MeOH/l × min when the operating temperature was increased from 35 to 55 °C. This decrease in methanol removal was accompanied by a decrease (from 58% to 42%) in the relative proportion of cells that hybridized with the mxaF probe. The relative proportion of Bacillus spp. increased from 5 to 20% while the proportion of members of the alpha subclass of Proteobacteria decreased from 16% to 6% when the bioreactor operating temperature was raised from 35 to 55 °C. The relative proportions of bacteria belonging to the beta (22–25%) and gamma (18–20%) subclasses of the Proteobacteria remained relatively constant regardless of operating temperature. Proteobacteria (alpha, beta and gamma subclasses) and Bacillus spp. represented 61, 67 and 71% of the Eubacteria in the biomass sampled at 35, 45 and 55 °C, respectively. The FISH technique was shown to be an efficient method for detection of both structural and functional changes in the bacterial communities that could be related to efficiency of methanol removal in a membrane bioreactor operating at different temperatures.
Effect of carbon source on alkaline phosphatase production and excretion in Aspergillus caespitosus
Authors: Guimarães Luis Henrique Souza , Jorge João Atilio , Terenzi Héctor Francisco , Jamur Maria Célia , Oliver Constance , De Lourdes Teixeira De Moraes Polizeli Maria
Published: May 2003

The effect of several carbon sources on the production of alkaline phosphatase by the thermotolerant Aspergillus caespitosus was analysed. The fungus released high levels of alkaline phosphatases into the medium after being cultured for long periods with xylan or industrial residues such as wheat raw and sugar cane bagasse in the culture media. In contrast, the alkaline phosphatase activities were found only intracellulary when the fungus was cultured in glucose‐supplemented media. The pH of the medium likely affects the process of enzyme secretion according to the carbon source used. Addition of xylan or industrial residues in the culture medium stimulated the secretion of phosphatases. In contrast, media supplemented with glucose or disaccharides promoted retention of these enzymes into the cells. The subcellular location activities of alkaline phosphatases were studied using histochemical and immunochemical methods and showed that alkaline phosphatases were present in the mycelial walls and septa.
Evaluation of biotoxicity of textile dyes using two bioassays
Authors: Moawad Hassan , El–Rahim Wafaa M. Abd , Khalafallah M.
Published: May 2003

The toxicity of eight textile dyes was evaluated using two bioassays namely: Ames test and seed germination test. The Ames test is widely used for the evaluation of hazardous mutagenic effect of different chemicals, as a short‐term screening test for environmental impact assessment. The eight‐textile dyes and Eithidium bromide dye (as positive control) were tested with five “his” Salmonella typhimurium strains: TA 100; TA 98; TA 1535; TA 1537; TA 1538. Using six concentrations of each dye (2.5 μg/ml, 4.5 μg/ml, 9 μg/ml, 13.5 μg/ml, 18 μg/ml, and 22.5 μg/ml) revealed that, most of the dyes were mutagenic for the test strains used in this study. The high concentrations of dye eliminated microbial colonies due to the high frequency of mutation causing lethal effect on the cells.

In this work the phytotoxicity of different soluble textile dyes was estimated by measuring the relative changes in seed germination of four plants: clover, wheat, tomato and lettuce. The changes in shooting percentages and root length as affected by dye were also measured. Seed germination percent and shoot growth as well as root length were recorded after 6 days of exposure to different concentrations of textile dyes in irrigation water. The results show that high concentrations of dyes were more toxic to seed germination as compared with the lower concentrations. However, the low concentrations of the tested dyes adversely affected the shooting percent significantly.
Biomass and exopolysaccharide production in submerged cultures of Pleurotus ostreatoroseusSing. and Pleurotus ostreatus “florida” (Jack.: Fr.) Kummer
Authors: Rosado Fábio Rogério , Germano Sandro , Carbonero Elaine R. , da Costa Sandra Maria Gomes , Iacomini Marcello , Kemmelmeier Carlos
Published: May 2003

The species of the genus Pleurotus produce large amounts of biomass and exopolysaccharide (EPS) in submerged cultures, which may be used for biotechnological purposes. In the present work two Brazilian autochthonous strains of edible Pleurotus (P. ostratoroseus Sing. and P. ostreatus “florida”) were used. The fungi grown in liquid Potato Dextrose medium (PD) were used as inocula to cultivate those microorganisms in the POL culture medium. After a 9‐day incubation, the optimal growth time for biomass production, P. ostreatus “florida” presented higher biomass production (22.8 g d.w./l) than P. ostreatoroseus (16.8 g d.w./l). After a 7‐day incubation, the optimal growth time for EPS production, P. ostreatoroseus produced higher amounts of crude EPS (5.8 g d.w./l) than P. ostreatus “florida” (1.4 g d.w./l). Relative carbohydrate composition for P. ostreatoroseus and P. ostreatus “florida” EPS were: glucose (95.5–87.7), galactose (traces – 4.9), mannose (traces – 3.1), xylose (1.3–2.5), and arabinose (3.2–1.8). Lower ammonium sulfate concentration in the POL culture medium increased the exopolysaccharides production by P. ostreatoroseus.
Phenol degradation by a Graphium sp. FIB4 isolated from industrial effluents
Authors: Santos Vera L. , Heilbuth Nádia M. , Braga Danúbia T. , Monteiro Andrea S. , Linardi Valter R.
Published: May 2003

In this work, we show that the fungal strain Graphium sp. FIB4 was able to use phenol as the sole carbon source. Higher degradation of phenol was accomplished by alginate‐immobilized mycelial mass than by mycelial suspensions of Graphium sp. FIB4. Free mycelium exhibited higher degradation rates when compared with the alginate‐immobilized mycelium in the presence of 14 mM of phenol or less. Above this concentration, degradation rates by free mycelium decreased and the immobilized mycelium showed higher values. The maximum degradation rate for 8 mM phenol was found to be 20.13 mg/l × h by free mycelia and 16.24 mg/l × h by immobilized mycelial mass in the presence of 18 mM phenol. When the fungus was grown on medium without phenol, catechol 1,2‐dioxygenase activity was not detected. This enzyme activity was induced at phenol concentrations as low as 0.05 mM and up to 6 mM at 24 h incubation at 30 °C, suggesting that catechol was oxidized by the ortho type of ring fission. Addition of glucose reduced phenol consumption rate, and both substrates were used simultaneously. Glucose concentrations higher than 0.075% repressed the induction of phenol oxidation by Graphium sp. FIB4 grown on glucose. But glucose did not fully repress utilization of phenol by phenol‐pre‐induced cells. Immobilization and addition of calcium and barium ions were detrimental to the stability of catechol 1,2‐dioxygenase activity and phenol degradation by Graphium sp. FIB4.
Nucleotide sequence of MPB63 gene in Mycobacterium bovis BCG Tokyo
Authors: Kobayashi Kohmei , Kamiie Katsuyoshi , Kobayashi Akihiro , Matsuda Satoru
Published: May 2003

Mycobacterium bovis BCG has been used for the prevention of tuberculosis and as therapy for bladder tumor. MPB63 in M. bovis BCG is one of the immunogenic proteins and is secreted in large quantities. Therefore, it is of interest that the MPB63 gene be examined for the determination of its nucleotide sequence. A fragment of 820 base pairs (bp) including the MPB63 gene was prepared by amplification using polymerase chain reaction (PCR) employing M. bovis BCG Tokyo chromosomal DNA as a template and its nucleotide sequence was determined. The nucleotide sequence of mpb63 in M. bovis BCG was then compared with that of mpt63 in M. tuberculosis. The result indicated that the nucleotide sequences between two protein genes were quite agreeable in the genes' structural and upstream regions, except that one base change from C in mpt63 to G in mpb63 was detected in the downstream trailer sequence. This suggests that the genetic information of M. bovis BCG is not entirely identical to that of M. tuberculosis, although the characteristics of both microorganism are very similar to each other.
Chemical Modification of Chitosan, 17
Authors: Sashiwa Hitoshi , Yamamori Naoki , Ichinose Yoshifumi , Sunamoto Junzo , Aiba Sei‐ichi
Published: May 2003

The Michael reaction of chitosan with acrylic acid was carried out successfully, even in water alone as the reaction medium. As a consequence of its good solubility in water, the reaction product, N‐carboxyethylchitosan, showed excellent biodegradable properties with standard activated sludge.

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Laccase‐Catalyzed Oxidative Polymerization of Phenols
Authors: Mita Naruyoshi , Tawaki Shin‐ichiro , Uyama Hiroshi , Kobayashi Shiro
Published: May 2003

Laccase‐catalyzed oxidative polymerization of phenol and its derivatives has been performed in aqueous organic solvents at room temperature in air. Laccase derived from Pycnoporus coccineus efficiently induced the polymerization to produce polyphenols consisting of a mixture of phenylene and oxyphenylene units. The unit ratio of the polymer could be precisely controlled by selection of the solvent and the monomer substituent.

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Synthesis of Graft Bacterial Polyesters for Nanoparticles Preparation
Authors: Renard Estelle , Ternat Céline , Langlois Valérie , Guerin Philippe
Published: May 2003

Graft copolymers of bacterial polyesters were prepared by direct condensation of poly(3‐hydroxyoctanoate‐co‐9‐carboxy‐3‐hydroxydecanoate) (PHOD) and poly(ethylene glycol) (PEG) or poly(lactic acid) (PLA). Nanoparticles from PHO, PHOD, PHOD‐g‐PEG, and PHOD‐g‐PLA were obtained by solvent displacement without stabilizer, and their stability in different aqueous media with different salt concentrations were studied. The results showed that the presence of hydrophilic PEG on the particle surface prevents the aggregation promotion by salts in aqueous solution. PHOD‐g‐PEG appears to be a promising candidate for site‐specific drug delivery systems.

1H NMR spectrum of PHOD‐g‐PLA in CDCl3.

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1H NMR spectrum of PHOD‐g‐PLA in CDCl3.
Effect of Light Exposure on UV‐Vis Spectrum of [(nBuCp)2ZrCl2] Based Catalyst
Authors: Mäkelä‐Vaarne Nora I. , Kallio Kalle , Reichert Karl‐Heinz , Leskelä Markku A.
Published: May 2003

UV‐vis spectroscopic study revealed that vinylcyclohexane interaction with zirconocene catalyst is enhanced on light exposure. If oxygen is present it interacts with the catalyst, hindering vinylcyclohexane interaction and consequently lowering the catalyst activity. The catalyst activity can be recovered with light exposure if low O2 concentrations are used since in light the zirconocene‐vinylcyclohexane interaction is favoured over the zirconocene‐O2 interaction. Moreover, 1H NMR studies of the reaction products showed that the structures of the vinylcyclohexane‐based species produced with light irradiation were identical to the species produced in dark. This indicates that light exposure of the catalytic system does not change the reaction mechanism.

Absorption spectrum of [(nBuCp)2ZrCl2]/MAO/VCH. (a) reaction in dark, (b) reaction with irradiation, (c) reaction with O2 treatment in dark and (d) reaction with O2 treatment with irradiation.

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Absorption spectrum of [(nBuCp)2ZrCl2]/MAO/VCH. (a) reaction in dark, (b) reaction with irradiation, (c) reaction with O2 treatment in dark and (d) reaction with O2 treatment with irradiation.
Water‐Soluble Building Blocks for Terpyridine‐Containing Supramolecular Polymers: Synthesis, Complexation, and pH Stability Studies of Poly(ethylene oxide) Moieties
Authors: Lohmeijer Bas G. G. , Schubert Ulrich S.
Published: May 2003

Poly(ethylene oxide) of various molecular weights (Mn = 3 000, 5 200, 10 000, 16 500 g · mol−1) has been modified with terpyridine end groups as building blocks for water‐soluble metallo‐supramolecular polymers. Metallo‐supramolecular A–A homopolymers have been prepared and characterized by complexing the terpyridine units of one selected poly(ethylene oxide) (Mn = 3 000 g · mol−1) with the following transition metal ions in their 2+ oxidation state: Fe, Ru, Co, Ni, Cu, Zn, and Cd. In addition, the stability of the supramolecular connection with respect to pH variations has been investigated.

Schematic representation of the product of poly(ethylene oxide) modification with terpyridine end groups and the metal complexation.

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Schematic representation of the product of poly(ethylene oxide) modification with terpyridine end groups and the metal complexation.
1H and 13C NMR Study of the Intermediates Formed by (Cp‐R)2ZrCl2 Activation with MAO and AlMe3/[CPh3][B(C6F5)4]. Correlation of Spectroscopic and Ethene Polymerization Data
Authors: Bryliakov Konstantin P. , Semikolenova Nina V. , Yudaev Dmitrii V. , Ystenes Martin , Rytter Erling , Zakharov Vladimir A. , Talsi Evgenii P.
Published: May 2003

Using 1H and 13C NMR spectroscopy, cationic intermediates formed by activation of (Cp‐R)2ZrCl2 (R = nBu, tBu and 1,2,3‐Me3) with MAO in toluene were monitored at Al/Zr ratios from 50 to 1 000. The catalysts (Cp‐R)2ZrCl2/AlMe3/CPh3+B(C6F5)4− (nBu, tBu and 1,2,3‐Me3) were also studied for comparison of spectroscopic and polymerization data with MAO based systems. Complexes of type (Cp‐R)2ZrMe+ ← Me−‐AlMAO (IV) with different Me‐MAO− counter anions have been identified in the (Cp‐R)2ZrCl2/MAO systems at low Al/Zr ratios. At Al/Zr ratios of 200–1 000, the complex [(Cp‐R)2Zr(μ‐Me)2AlMe2]+ Me‐MAO− (III) dominates in all MAO‐based reaction systems. Ethene polymerization activity strongly depends on the Al/Zr ratio (Al/Zr = 200–1 000) for the systems (Cp‐nBu)2ZrCl2/MAO and (Cp‐tBu)2ZrCl2/MAO, while it is virtually constant in the same range of Al/Zr ratios for the catalytic system (Cp‐1,2,3‐Me3)2ZrCl2/MAO. The data obtained are interpreted on the assumption that complex III is the actual precursor of active centers of polymerization in MAO based systems.

Formation of cationic intermediates by activation with MAO.

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Formation of cationic intermediates by activation with MAO.