bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibitory effects of Korean plants on HIV‐1 activities
Authors: Min Byung Sun , Kim Young Ho , Tomiyama Miyuki , Nakamura Norio , Miyashiro Hirotsugu , Otake Toru , Hattori Masao
Published: August 2002

In the search for novel anti‐human immunodeficiency virus type 1 (anti‐HIV‐1) agents from natural sources, 49 MeOH extracts of Korean plants were screened for their inhibitory effects against RNA‐dependent DNA polymerase (RT) and ribonuclease H (RNase H) activities of HIV‐1 reverse transcriptase and HIV‐1 protease, and anti‐HIV‐1 activity. Regarding the HIV‐1 reverse transcriptase, Agrimonia ­pilosa (whole plant), Cornus kousa (stem and leaf), Limonium tetragonum (root) and Mallotus japonicus (stem) showed significant inhibitory activity on RT activity with 50% inhibitory activity (IC50) of 8.9, 6.3, 7.5 and 11.9 µg/mL, respectively, whereas Agrimonia pilosa was also active against RNase H activity (IC50 = 98.4 µg/mL). Four plants, namely Agrimonia pilosa (whole plant), Atractylodes japonica (root), Clematis heracleifolia (whole plant) and Syneilesis palmata (whole plant), were appreciably active (<35%) against recombinant HIV‐1 protease at a concentration of 100 µg/mL. Crinum asiaticum var. japonicum (root) showed significant anti‐HIV‐1 activity (ED50 = 12.5 µg/mL) with a favourable SI value of 16. Copyright © 2001 John Wiley & Sons, Ltd.
In vitro studies on antilithiatic activity of seeds of Dolichos biflorus Linn. and rhizomes of Bergenia ligulata Wall.
Authors: Garimella T. S. , Jolly C. I. , Narayanan S.
Published: August 2002

Soxhlet extracts of seeds of Dolichos biflorus and rhizomes of Bergenia ligulata were tested for their in vitro antilithiatic/anticalcification activity by the homogenous precipitation method. The extracts were compared with an aqueous extract of cystone (a marketed preparation) for their activities. Also a combination of the extracts of the two plants was tested. Extracts of Dolichus biflorus showed activity almost equivalent to cystone while Bergenia ligulata showed less activity and the combination was not as active as the individual extracts. Copyright © 2001 John Wiley & Sons, Ltd.
Implementing a quality management system in a global pharmacovigilance processing centre
Authors: Sayers Jacqueline
Published: August 2002

Quality Management (QM) initiatives are common within the pharmaceutical industry today, although such projects do not always result in the anticipated benefits. The Roche Pharmacovigilance Global Processing Centre (PC) has successfully introduced a QM system that allows it to demonstrate to its customers the accuracy and consistency of its end product—the coded adverse event (AE) case. Factors such as senior management support, the designation of a specific manager with responsibility for QM, and communication with all staff about the concept of quality, have all contributed to the success of the project. The importance placed on the QM system by senior management means that the resolution of those issues that remain outstanding is given an appropriately high priority. Copyright © 2001 John Wiley & Sons, Ltd.
Targeting R&D quality and compliance training for technology transfer into the GMP environment of production
Authors: Varma Shobha
Published: August 2002

For a long time, veterinary biological vaccine‐producing companies in the United States have been ruled by the quality and compliance requirements imposed by the United States Department of Agriculture (USDA). However, with the globalization of markets, companies now need to comply with quality and compliance guidelines of key foreign markets such as the European Union (EU), Japan and Canada. Since the quality of the final product is built in from inception, i.e. through all development phases, it is imperative that all research and development (R&D) personnel understand the basic global requirements for quality and compliance. This paper presents an innovative approach for designing a training program for R&D personnel in the basic quality and compliance requirements for global product development and technology transfer into production operating under strict good manufacturing practices (GMP) requirements. The training program integrated basic GMP requirements such as sourcing of raw materials, components, qualification of vendors, developing GMP compliant documentation for pilot batch production, setting specifications based on target countries and the proper use of change control. In addition the basics of good laboratory practice (GLP) requirements were incorporated into the training by including a section on the importance of the use of calibrated instrumentation/measuring devices and proper documented approved procedures. Copyright © 2001 John Wiley & Sons, Ltd.
VICH good clinical practice: preparing for study conduct change in the United States
Authors: Rogers Steve
Published: August 2002

The International Cooperation on Harmonization of Technical Requirements for Registration of Veterinary Medicinal Products (VICH) good clinical practice (GCP) guideline is scheduled to take effect by July 2001. The guideline will replace existing US guidance by the Food and Drug Administration's Center for Veterinary Medicine entitled ‘Good Target Animal Study Practices’. To abide by these new rules, researchers and clinical research facilities in the US must prepare themselves now for this impending change. Several key components of clinical trials, including the use of quality assurance practices, will need to be reviewed and changed as necessary. Copyright © 2001 John Wiley & Sons, Ltd.
What's new?
Authors: Bohaychuk Wendy
Published: August 2002

The What's New? section in the Quality Assurance Journal aims to draw your attention to items of importance to QA professionals. Each item will be linked to the relevant internet address which you might add to your ‘favorites’ folders and check regularly yourselves. If there is any other new information which should be brought to the attention of readers, please let us know by e‐mailing: gcrpc@compuserve.com Copyright © 2001 John Wiley & Sons, Ltd.
Contracts for clinical trial – related duties and functions: general points to consider
Authors: Nickols Pamela Charnley
Published: August 2002

During good clinical practice (GCP) audits and regulatory inspections of clinical research, a number of issues surrounding the use of contracts commonly arise:

No contract is in place.

Work begins before a contract is in place.

The contract is imprecise in terms of scope of work.

The contract is incorrectly authorised.

The contract omits essential considerations.

This article seeks to provide guidance on some of the important elements to be considered when drafting and implementing contracts. Copyright © 2001 John Wiley & Sons, Ltd.
Quality in the outsourcing process: part I. The quality outsourcer
Authors: Russell Yvonne
Published: August 2002

In clinical research, the definition of quality and overall responsibility for ensuring that performance parameters are adequately tracked and the necessary corrective action taken, lies firmly in the hands of the outsourcing project director/manager (outsourcer or sponsor). Meticulous planning of requirements prior to project start and strong ‘general management’ throughout the life of the outsourced project play a critical role in influencing both the outcome of the study and also in determining the quality of the research data. For ‘quality in the outsourcing process’, read ‘quality outsourcing’. The implementation of a carefully formulated project‐specific outsourcing strategy means that macromanagement (general management), not micromanagement (defined here as a form of ‘intensive therapy for the ailing project’ management), will be the primary task of the sponsor. A research team that is well‐defined, with all members (sponsor and vendor alike) mindful of their individual responsibilities, in addition to being well‐directed, will achieve consensus of opinion faster and deliver a quality product. An outsourcing strategy for the full clinical development program, clearly defined outsourcing standard operating procedures (SOPs) and a strategy tailored to each individually outsourced project form an integral part of the recipe to outsourcing success. Individual components of an outsourcing strategy and how one can safeguard that an outsourced project is brought to completion successfully, and to the prescribed quality standards, are addressed in detail in this article. Part two of this article, entitled ‘Quality in the Outsourcing Process: II. The Vendor Selection Process and The Quality Vendor’, will provide the quality outsourcer with tips and tools on how to make a quality decision in the vendor selection process and addresses further issues that are fundamental to the maintenance of quality in the outsourcing process. Copyright © 2001 John Wiley & Sons, Ltd.
An investigation on the reaction mechanism of the F2+Cl2→2ClF using the B3LYP method
Authors: Wang Zun Yao , Gong Xue Dong , Li Jin Shan , Xiao He Ming
Published: August 2002

The reaction mechanism of F2+Cl2→2ClF has been investigated with the density functional theory at the B3LYP/6‐311G* level. Six transition states have been found for the three possible reaction paths and verified by the normal mode vibrational and IRC analyses. Ab initio MP2/6‐311G* geometry optimizations and CCSD(T)/6‐311G(2df)//MP2/6‐311G* single‐point energy calculations have been performed for comparison. It is found that when the F2 (or Cl2) molecule decomposes into atoms first and then the F (or Cl) atom reacts with the molecule Cl2 (or F2) nearly along the molecular axis, the energy barrier is very low. The calculated energy barrier of F attacking Cl2 is zero and that of Cl attacking F2 is only 15.57 kJ⋅mol−1 at the B3LYP level. However, the calculated dissociation energies of F2 and Cl2 are as high as 145.40 and 192.48 kJ⋅mol−1, respectively. When the reaction proceeds through a bimolecular reaction mechanism, two four‐center transition states are obtained and the lower energy barrier is 218.69 kJ⋅mol−1. Therefore, the title reaction F2+Cl2→2ClF is most probably initiated from the atomization of the F2 molecule and terminated by the reaction of F attacking Cl2 nearly along the ClCl bond. MP2 calculations lead to the same conclusion, but the geometry of TS and the energy barrier are somewhat different. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Polarizability and chemical hardness—A combined study of wave function and density functional theory approach
Authors: Kolandaivel P. , Mahalingam T. , Sugandhi K.
Published: August 2002

A flexible model for generating the molecular wave function and electron density for diatomic molecules is developed employing the quadratic anharmonic oscillator and Morse potential. The chemical hardness, Fukui function, and polarizability were calculated using the electron density of the molecules, and the values are found to be reasonably good. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Statistical mechanics of energy transfer in gas–surface scattering: A dynamical Lie algebraic approach
Authors: Guan Daren , Yi Xizhang , Meng Qingtian , Zheng Yujun , Wu Jianzhong , Sun Jiazhong
Published: August 2002

The dynamical Lie algebraic (DLA) method is used to describe statistical mechanics of energy transfer in rotationally inelastic molecule–surface scattering. Statistical average values of an observable for the scattering system are calculated in terms of density operator formalism in statistical mechanics. Employing a cubic expansion procedure of molecule–surface interaction potential leads to generation of a dynamical Lie algebra. Thus these statistical average values as a function of the group parameters can be obtained analytically in this formulation. The group parameters can be found from solving a set of coupled nonlinear differential equations. The DLA method, which has no need for determination of transition probabilities in advance as made routinely in the calculation, offers an efficient alternative to the method for computing the statistical average values. This method is much less computationally intensive because most of calculations can be analytically carried out. The average final rotational energies and their dependence on the main dynamic variables and the average interaction potential are presented for the rotationally inelastic scattering of NO molecules from a flat, static Ag(111) surface. Direct comparison is made between the predictions of this model calculation and experiment. The model reproduces well the degree of rotational excitation and correlation between the average final translational and the average rotational energies. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Energy profiles for the rate‐limiting stage of the serine protease prototype reaction
Authors: Nemukhin Alexander V. , Topol Igor A. , Burt Stanley K.
Published: August 2002

The energy profiles of reaction, modeling the rate‐limiting stage of serine protease catalyzed transformations, have been computed by quantum chemistry methods. The model includes fragments of the residues of the catalytic triad (serine, histidine, and aspartic acid), two water molecules as an oxyanion hole, represented by effective fragment potentials, and a formamide molecule as a substrate. Geometry optimizations have been performed along the reaction coordinate, chosen as the distance between oxygen of serine and carbon of substrate, by using the Hartree–Fock method. The density functional theory B3LYP/6‐31+G(d,p) calculations have been employed to recalculate energies along the reaction path in the gas phase and in the dielectric environment. The computed barrier heights are fairly consistent with the data cited in the literature. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 34–40, 2002
Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models?*
Authors: Czaplewski Cezary , Ripoll Daniel R. , Liwo Adam , Rodziewicz‐Motowidło Sylwia , Wawak Ryszard J. , Scheraga Harold A.
Published: August 2002

The potential of mean force (PMF) of the hydrophobic association of pairs and triplets of nonpolar solute molecules with various sizes and strengths of van der Waals interactions has been studied by means of umbrella‐sampling molecular‐dynamic simulations combined with the weighted‐histogram analysis method. The TIP3P water model was used in these computations. It was found that the distance dependence of the PMF, including the three‐body (cooperative) contribution, is described qualitatively correctly by the variation of either the molecular surface area or the excluded solvation‐shell molecular volume with the distance between the solute molecules, while the solvent‐accessible surface and the hydration‐shell models, which are commonly used in mean‐field solvation approaches, give an incorrect distance dependence and the wrong sign of the cooperative contribution. The cooperative contribution to the PMF increases the strength of hydrophobic interactions and increases with the size of the solute. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 41–55, 2002
A protoporphyrin IX‐based model for cytochrome P‐450 iron‐binding inhibitors: SAM1 calculations of structure and complexation enthalpy*
Authors: Pudzianowski Andrew T.
Published: August 2002

A methyl diester protoporphyrin IX complex with ferric ion in a low‐spin doublet state and with ethyl sulfide as a constant axial ligand, is proposed as a model system for examining cytochrome P‐450 Fe‐binding inhibitors, e.g., imidazoles and pyridines, which can coordinate as a second axial ligand. The SAM1 semiempirical method was used to calculate optimized structures and complexation enthalpies for a variety of organic ligands, as well as for the resting state aquo complex, under the assumption that such inhibitors are stronger Fe ligands than a water molecule in the enzyme's resting state and thereby block the P‐450 catalytic cycle. The SAM1 structures agree qualitatively with X‐ray structures of P‐450cam with bound ligands, and are in reasonable agreement regarding details such as Fe‐ligand bond lengths. The enthalpy results and structures provide insights into how the inhibitory potency of imidazoles is decreased by substituents around the divalent nitrogen. In particular, a substituted imidazole may still intrinsically be able to bind to the resting state iron but with a lowered binding energy, so that it is thermodynamically unable to displace the bound water molecule. Qualitative predictions based on SAM1 binding enthalpies are in accord with experimental structural and inhibitory data. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 147–153, 2002
Effect of the orbitals of the bridging group on magnetic coupling
Authors: Hu Haiquan , Chen Zhida
Published: August 2002

With an AXB centrosymmetrical model system, the qualitative relationship was demonstrated among the coupling constant and the fourth power of S13, which is the overlap integral between the orbitals of the bridging group and the symmetrical combination of the singly occupied orbitals of magnetic centers in the local ligand field. By using density functional theory and the broken symmetry approach HHeH, [HFH]− and OTi2Cl4 systems were calculated to inspect the above conclusion. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 275–279, 2002
Improved generator coordinate Hartree–Fock method applied to generate Gaussian basis sets for the isoelectronic series of the atoms He to Ne
Authors: Canal Neto A. , Jorge F. E. , De Castro M.
Published: August 2002

We have generated Gaussian basis sets (GBSs) for the neutral and the first 20 cations members of the isoelectronic series of each ground state atom from He to Ne with the improved generator coordinate Hartree–Fock (IGCHF) method. For all atomic species studied here, our total energy errors are smaller than those calculated by the original GCHF method using GBSs of the same sizes. The largest difference between our total energy results and those computed with a numerical Hartree–Fock approach is equal to 215 μhartree for Co17+. We also compare the ionization potentials obtained with the IGCHF with the corresponding experimental values. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 252–262, 2002
Time‐dependent Fourier grid Hamiltonian method for studying the curve crossing dynamics: Dynamics of predissociation of NaI
Authors: Kumar Modal Chandan , Bhattacharyya S. P.
Published: August 2002

A time‐dependent Fourier route is proposed to study quantum dynamics in the presence of curve crossing. The method is tested on a model problem and is then used to study the predissociation dynamics of NaI by a femtosecond laser pulse. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Effect of trimethylsilyl substitution on the structure and properties of phthalocyanine: A density functional theory study
Authors: Dong Gong Xue , Ming Xiao He , Gao Pin , Tian He
Published: August 2002

The geometries of four isomers of the trimethylsilyl substituted phthalocyanine (Pc)—I, II, III, and IV—have been optimized at the B3LYP/3‐21G level of density functional theory. Normal‐mode vibrational analyses have been performed and their standard thermodynamic functions, molar fractions, and electronic absorption spectra calculated. Single‐point energies have been calculated at the B3LYP/6‐311G* level for all isomers to evaluate the heats of formation from an isodesmic reaction. It is found that substitution has little influence on the geometry and electronic structures of the Pc framework. The corresponding geometric parameters in various isomers are close. According to the B3LYP/6‐311G*//B3LYP/3‐21G results, substitution at the peripheral position of the isoindole with an inner hydrogen is most favorable. The energies increase in the order of IV < II < III < I, and the energy difference between IV and I is 5.75 kJ/mol. The molar fractions of IV, II, III, and I are 0.80, 0.17, 0.02, and 0.02 and the heats of formation are 2009.96, 2010.10, 2015.85, and 2016.52 kJ/mol, respectively. This indicates that nonperipheral substituted Pcs have higher energy and little production because they are not stable under the considered conditions. The electronic spectra of the substituted Pcs calculated using the ZINDO method have two strong Q absorption bands around 700 nm and one B band around 300 nm that are slightly shifted compared with those in Pc. The ratios of the oscillator strength of the B band to the Q bands are much lowered by trimethylsilyl substitution. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Gyroscopic tensor ab initio calculation of the molecular crystals: (Mo6X14)2−Y−(TTF+)3 (X=Br, Cl and Y=Br, Cl, I)
Authors: Dhouib A. , Essalah K. , Tangour B. , Abderraba M.
Published: August 2002

The aim of this study is the determination of the g tensor of the tetrathiafulvalene (TTF) molecule involved in chlorine and bromine radical–ion salts. This work is based on ab initio calculations using several basis sets which enabled us to compare theoretical and experimental measurement data. The results show clearly the impact of the structural distortions on the g gyroscopic matrix elements and proves the important fact that even a small variation of the crystallographic parameters has major consequences on the physical–chemical properties. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Solution of the Kronig–Penney model using variational Monte Carlo
Authors: Alexander S. A. , Coldwell R. L.
Published: August 2002

Variance minimization and Monte Carlo integration are used to evaluate the energy bands of an electron in the presence of a periodic array of one‐dimensional square wells separated by finite‐width barriers. Our results for the ground state, as well as the first and second excited states, are in excellent agreement with the exact analytic results for this model system. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
New time‐independent perturbation theory for the multireference problem
Authors: Chen Feiwu , Davidson E. R. , Iwata Suehiro
Published: August 2002

A new time‐independent perturbation theory is developed for the multireference problem. In the derivation, neither perturbed wave function nor intermediate normalization condition is required. In the single‐reference case, the present approach gives the same perturbation expressions as Rayleigh–Schrödinger perturbation theory. In the multireference case, the perturbation expressions are derived with two kinds of partitions and can be applied to those cases with or without the definition of the zeroth Hamiltonian \documentclass{article}\pagestyle{empty}\begin{document}$\hat{H}_{0}$\end{document}. As the size of the reference space is decreased to 1, one multireference expansion returns to the single‐reference one with Epstein–Nesbet partition, while another is reduced to a new expansion. These two multireference perturbation expansions are further expressed with the eigenvectors of the Hamiltonian within the reference space for an efficient implementation. The correspondences between the single‐reference and multireference perturbation expansion are discussed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Adsorption of water in mordenite—An ab initio study
Authors: Demuth Th. , Benco L. , Hafner J. , Toulhoat H.
Published: August 2002

The adsorption of water in mordenite has been investigated using density functional theory using gradient corrections to the exchange–correlation functional. In the neutral complex water is strongly physisorbed through two different hydrogen bonds, the stronger between the acid site and the water oxygen atom, the weaker between a hydrogen atom of the adsorbed molecule and a framework oxygen atom. Strong polarizations and structural distortions of both the acid site and the molecule have been observed. To elucidate the question if a chemisorbed complex (creation of a hydroxonium ion) is possible, ab initio molecular dynamics have been performed, indicating that a protonation of water occurs even for the low coverage of one water molecule per unit cell. However, this ionic configuration cannot be stabilized by the electrostatic field of the zeolite framework and is therefore not a minimum of the potential energy surface. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 110–116, 2001
Explicitly correlated SCF study of small hydrides
Authors: Shillady Donald D. , Craig John , Rutan Sarah
Published: August 2002

The “soft Coulomb hole” method of Chakravorty and Clementi has been implemented in a Gaussian lobe‐orbital (GLO) program to include explicit electron–electron correlation in molecules according to a modified form of Coulomb's law in a program for workstations and personal computers (PCLOBE):
f(R12)=(1−exp (−w(R12)2))/R12,  w=scaling parameter.
Twice as many two‐electron integrals must be calculated compared to the usual Hartree–Fock–Roothaan algorithm, but this “correlated self‐consistent field (SCF)” method may be embedded within well‐known SCF computer codes and yields more than 90% of the correlation energy in run times less than twice that of the restricted Hartree–Fock (RHF) method. A two‐parameter model of correlation is calibrated on HF and LiH using the 6‐311G** basis as Gaussian lobe orbitals. The quantum Monte Carlo energies of LiH and HF were fitted to within 150 cal/mol, but the scaling model for first‐row atoms is less good for H2. This work shows promise as a fast way to modify the Hartree–Fock–Roothaan method for accuracy approaching quantum Monte Carlo methods. This proof‐of‐concept work offers extension to modeling solvation properties of water solutions in high‐pressure liquid chromatography (HPLC). © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Accuracy and precision of flowing afterglow mass spectrometry for the determination of the deuterium abundance in the headspace of aqueous liquids and exhaled breath water
Authors: Španel Patrik , Smith David
Published: August 2002

We have assessed the accuracy and precision of our flowing afterglow mass spectrometric method (FA‐MS) for absolute measurements of deuterium abundance in water using standardised tap water/D2O mixtures within the D/H range from 155 ppm (local tap water) to 1104 ppm, prepared by the gravimetric method. The results of this study show that a precision and accuracy of 1% can be achieved for the deuterium abundance in water samples. This is quite adequate for the main application, which is the rapid, non‐invasive measurement of total body water by deuterium analysis of breath water vapour using the D2O dilution method. Copyright © 2001 John Wiley & Sons, Ltd.
Comparison of electron capture dissociation and collisionally activated dissociation of polycations of peptide nucleic acids
Authors: Olsen Jesper V. , Haselmann Kim F. , Nielsen Michael L. , Budnik Bogdan A. , Nielsen Peter E. , Zubarev Roman A.
Published: August 2002

Electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry coupled with electrospray ionization enhances the sequence elucidation of peptide nucleic acids compared with conventional low‐energy collisionally activated dissociation (CAD). Examples are shown where ECD produced complete or extensive sequence coverage in PNAs six to ten nucleobases long. However, facile base losses from the reduced species and low abundances of backbone ECD fragments presented a significant problem. This was rationalized through the lower degree of charge solvation on the backbone compared to polypeptides. Combination of both CAD and ECD data is advantageous, as these techniques produce cleavages at different sites. Copyright© 2001 John Wiley & Sons, Ltd.
Aldehyde analysis by high performance liquid chromatography/tandem mass spectrometry
Authors: O'Brien‐Coker Ivan C. , Perkins George , Mallet Anthony I.
Published: August 2002

This paper describes the development of a high performance liquid chromatography/tandem mass spectrometric (MS/MS) procedure for the specific qualitative and quantitative analysis of lipid aldehydes in biological matrices. A derivatisation method, which results in molecules that exhibit a common product ion on MS/MS, permits informative precursor ion scans, at high sensitivity. This has been applied to the examination of plasma in order to examine the production of aldehydes consequent on in vitro lipid oxidation. Quantitative analysis of target molecules using multiple reaction monitoring has been developed to permit quantitation in the same matrices. Copyright© 2001 John Wiley & Sons, Ltd.
Electrospray ionisation tandem mass spectrometry in the characterisation of isomeric benzofurocoumarins
Authors: Begala M. , Delogu G. , Maccioni E. , Podda G. , Tocco G. , Quezada E. , Uriarte E. , Fedrigo M. A. , Favretto D. , Traldi P.
Published: August 2002

A set of aminoalkoxy‐substituted, differently annullated furocoumarins, differing in the position of the aminoalkoxy chain and in the unsaturation level of the fused ring, has been subjected to electron impact and electrospray ionisation (ESI) experiments. In order to achieve a distinct characterisation of isomeric compounds, which partially failed under electron impact conditions, collision‐induced dissociation experiments were performed on protonated molecules. The breakdown curves obtained by varying the tickle voltage on an ion trap ESI instrument led to the desired characterisation. Copyright © 2001 John Wiley & Sons, Ltd.
Development of a high‐pressure gradient pumping system for parallel liquid chromatography/mass spectrometry for the analysis of combinatorial libraries
Authors: Tolson David , Organ Andrew , Shah Ajit
Published: August 2002

Parallel liquid chromatography/mass spectrometer (LC/MS) systems such as the Micromass MUX™ have been commercially available for several years. Until recently, the LC pumping systems available have been a serious limitation to the more widespread adoption of such systems, particularly in good laboratory practice (GLP) environments. In this work, we compare the performance of the Jasco PAR‐1500 pumping system, which delivers an equal gradient flow to eight individual flow channels, to that of a conventional system, where the flow is split post pump. Both systems were coupled to a Micromass LCT™ liquid chromatography/electrospray ionisation time‐of‐flight (LC/ESI‐TOF) mass spectrometer equipped with a parallel MUX™ inlet system, used for the analysis of combinatorial libraries. In addition to flow stability, the Jasco system has resulted in a dramatic improvement in chromatographic performance. Copyright © 2001 John Wiley & Sons, Ltd.
Dynamically assisted gated trapping for Fourier transform ion cyclotron mass spectrometry
Authors: Gorshkov Michael V. , Masselon Christophe D. , Anderson Gordon A. , Udseth Harold R. , Smith Richard D.
Published: August 2002

An efficient approach for trapping ions and enhancing signal based on ‘adiabatic amplitude reduction’ for Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is described and evaluated. This method is a modification to the widely used gated trapping technique in which the trapping potential is raised adiabatically rather than instantaneously (non‐adiabatically). Compared with non‐adiabatic gated trapping, the final amplitudes of ion axial oscillations and energies are lower in the proposed method. All performance aspects of the FTICR spectrum (e.g., peak intensities, mass resolution, and mass accuracy) improve significantly compared to the conventional gated trapping technique. Copyright © 2001 John Wiley & Sons, Ltd.
Characterization of phosphopeptides from protein digests using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and nanoelectrospray quadrupole time‐of‐flight mass spectrometry
Authors: Ma Yuliang , Lu Yun , Zeng Huiqing , Ron David , Mo Wenjun , Neubert Thomas A.
Published: August 2002

A two‐step mass spectrometric method for characterization of phosphopeptides from peptide mixtures is presented. In the first step, phosphopeptide candidates were identified by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) based on their higher relative intensities in negative ion MALDI spectra than in positive ion MALDI spectra. The detection limit for this step was found to be 18 femtomoles or lower in the case of unfractionated in‐solution digests of a model phosphoprotein, β‐casein. In the second step, nanoelectrospray tandem mass (nES‐MS/MS) spectra of doubly or triply charged precursor ions of these candidate phosphopeptides were obtained using a quadrupole time‐of‐flight (Q‐TOF) mass spectrometer. This step provided information about the phosphorylated residues, and ruled out nonphosphorylated candidates, for these peptides. After [32P] labeling and reverse‐phase high‐performance liquid chromatography (RP‐HPLC) to simplify the mixtures and to monitor the efficiency of phosphopeptide identification, we used this method to identify multiple autophosphorylation sites on the PKR‐like endoplasmic reticulum kinase (PERK), a recently discovered mammalian stress‐response protein. Copyright © 2001 John Wiley & Sons, Ltd.
Electrospray ionization with ambient pressure ion mobility separation and mass analysis by orthogonal time‐of‐flight mass spectrometry
Authors: Steiner Wes E. , Clowers Brian H. , Fuhrer Katrin , Gonin Marc , Matz Laura M. , Siems William F. , Schultz Albert J. , Hill Herbert H.
Published: August 2002

Rapid screening and identification of drug and other mixtures are possible using a novel ambient pressure high‐resolution ion mobility (APIMS) orthogonal reflector time‐of‐flight mass spectrometer (TOFMS). Departing ions from the APIMS drift tube traversed a pressure interface between the APIMS and TOFMS where they were subjected to numerous gas collisions that could produce selective fragmentation. By increasing the accelerating field in the pressure interface region, the ions generated using water‐cooled electrospray ionization (ESI) underwent collision‐induced dissociation (CID). Mixtures of ESI ions were separated by APIMS based on their respective size‐to‐charge (s/z) ratios while CID and analysis of mass‐to‐charge (m/z) ratios occurred in the pressure interface and TOFMS. Product ions that were formed in this pressure interface region could be readily assigned to precursor ions by matching the mobility drift times. This process was demonstrated by the examination of a mixture of amphetamines and the resulting fragmentation patterns of the mobility‐separated precursor ion species [M + H]+. Copyright © 2001 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric observation of a peptide triplet induced by thermal cleavage of cystine
Authors: Kim Jong‐Seo , Kim Hie‐Joon
Published: August 2002

Heat‐induced (90 °C, 30 min) β‐elimination of a cystine residue leads to cleavage of a disulfide bond and produces a set of three peptides with a cysteine residue, a thiocysteine residue (+32Da), and a dehydroalanine residue (−34Da). This characteristic feature was observed from somatostatin and insulin by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Mass spectrometric observation of this triplet is useful in identifying the presence of a cystine residue in a peptide, and could assist mass spectrometric identification of the peptide from a database. Copyright © 2001 John Wiley & Sons, Ltd.
Gas‐phase ion chemistry of Glu/Met systems
Authors: Wincel H. , Fokkens R. H.
Published: August 2002

A combined chemical ionisation and tandem mass spectrometry (MS/MS) approach has been used for investigation of the gas‐phase ion chemistry of systems containing the amino acids Glu and Met, and the dipeptides γ‐Glu‐Met and Met‐Glu. The metastable fragmentation of the protonated dimer, (Glu)2H+, reveals an intracluster reaction leading to the elimination of the Glu residue. The main features of the ion‐molecule reactions observed in the systems containing Glu and Glu + Met can be described in terms of sequential adduct formation. The results obtained for the thermal dehydration of Glu were used to rationalise the formation of the proton‐bound structures (Glu − H2O)···H+··· (Glu − H2O) and (Glu − H2O)3·H+. The adduct ions, [(Glu − H2O) + H + Glu]+ and [(Glu − H2O) + H + Met]+, and further association products were also observed. The results lead to a reconsideration of the structural aspects proposed earlier for these species in the sense that they suggest that the systems correspond to a mixture of isomeric covalent and proton‐bound structures.

The thermal effects on the decomposition of the neutral (γ‐Glu‐Met) and its protonated form, (γ‐Glu‐Met)H+, at m/z 279 were investigated, and dramatic changes in the MI spectra of the m/z 279 ion with temperature were found. A mechanistic explanation for the observed evolution of higher mass ion peaks in the mass spectra is developed. Copyright © 2001 John Wiley & Sons, Ltd.
Silver stain removal using H2O2 for enhanced peptide mass mapping by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Sumner Lloyd W. , Wolf‐Sumner Barbara , White Steven P. , Asirvatham Victor S.
Published: August 2002

Hydrogen peroxide solutions are reported for the removal of silver stain from proteins isolated in polyacrylamide gels. Removal of silver stain prior to in‐gel digestion is shown to enhance sensitivity and sequence coverage of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) peptide mass maps. The rate of silver removal using H2O2 is influenced by H2O2 concentration and increases with increasing pH. The presence of complexation reagents such as ammonia from mass spectrometry compatible ammonium bicarbonate solutions enhances the efficiency and speed of H2O2‐mediated silver removal. H2O2‐mediated silver removal using the described procedure does not appear to have any detrimental effects on proteins but is observed to produce a slightly elevated level of methionine oxidization over that usually observed in in‐gel tryptic digestion. Copyright © 2001 John Wiley & Sons, Ltd.
Microwave‐assisted protein staining: mass spectrometry compatible methods for rapid protein visualisation
Authors: Nesatyy Victor J. , Dacanay Andrew , Kelly John F. , Ross Neil W.
Published: August 2002

The effects of microwave irradiation on the staining of electrophoresed and electroblotted proteins have been assessed using currently available detection methods. Although the absorption of microwave radiation was found to be uneven, band intensity following microwave‐assisted protein staining (MAPS) was comparable and in some cases exceeded the intensity of the bands visualised by the original staining methods. It was found that microwave treatment drastically reduced the duration of the staining protocols for visualisation of the proteins separated by both one‐ and two‐dimensional electrophoresis. Application of MAPS methods did not affect peptide mass fingerprinting analysis by mass spectrometry and subsequent identification of the protein by database searching. The peptide mass maps corresponding to the proteins visualised using both the conventional and MAPS methods did not show significant difference in signal/noise ratio. Moreover, it appeared that microwave treatment of the gels resulted in the increased recovery of the peptides following in‐gel trypsin digestion. Briefly, microwave‐assisted protein staining methods were rapid, compatible with mass spectrometry and were equally effective on thin (0.75 mm) and thick (1.5 mm) gels (such as those used in 2D electrophoresis). Copyright © 2002 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.
Derivatization of small oligosaccharides prior to analysis by matrix‐assisted laser desorption/ionization using glycidyltrimethylammonium chloride and Girard's reagent T
Authors: Gouw Joost W. , Burgers Peter C. , Trikoupis Moschoula A. , Terlouw Johan K.
Published: August 2002

In matrix‐assisted laser desorption/ionization (MALDI) analyses of small oligosaccharides a very large increase in sensitivity (by a factor of 1000) may be obtained by introducing a quaternary ammonium center (‘quaternization’). Such a quaternary ammonium center may be introduced into the saccharide by reaction with commercially available glycidyltrimethylammonium chloride (GTMA), or by using Girard's reagent T (Naven and Harvey, Rapid Commun. Mass Spectrom. 1996; 10: 829). GTMA reacts with alcohol functionalities, whereas Girard's reagent T is specific for aldehyde and keto groups. Thus reducing saccharides can be derivatized by both GTMA and Girard's reagent T. For example, glucose or cellobiose having a stock concentration of 3 × 10−5 M (5 µg/mL) produces no sugar‐derived signals in conventional MALDI, but their quaternized derivatives, also at 3 × 10−5 M, yield intense signals, with the matrix‐derived signals only being weak. Similar results were obtained for glucosamine. Non‐reducing saccharides as well as sugar alcohols can be derivatized using GTMA; thus, although sucrose, raffinose and sorbitol do not react with Girard's reagent T, they all produce intense signals after derivatization with GTMA. An example of the application of these derivatization reactions is provided by the analysis of oligosaccharides in beer. Copyright © 2002 John Wiley & Sons, Ltd.
Analysis of protein ions in the range 3000–12000 Th under partial (no discharge) atmospheric pressure chemical ionization conditions using ion trap mass spectrometry
Authors: Cristoni Simone , Bernardi Luigi Rossi , Biunno Ida , Guidugli Federico
Published: August 2002

A new approach, based on the use of atmospheric pressure chemical ionization ion trap mass spectrometry (APCI‐ITMS), but without a corona discharge, was investigated for application to creating and monitoring protein ions. It must be emphasized that APCI is not usually used in protein analysis. In order to verify the applicability of the proposed method to the analysis of proteins, two standard proteins (horse cytochrome c and horse myoglobin) were analyzed. A mixture of the two proteins was also analyzed showing that this novel approach, based on the use of APCI, can be used in the analysis of protein mixtures. Copyright © 2002 John Wiley & Sons, Ltd.
Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis
Authors: Sørensen Helle Aagaard , Sperotto Maria Maddalena , Petersen Marianne , Keşmir Can , Radzikowski Louise , Jacobsen Susanne , Søndergaard Ib
Published: August 2002

The performance of matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry with neural networks in wheat variety classification is further evaluated.1 Two principal issues were studied: (a) the number of varieties that could be classified correctly; and (b) various means of pre‐processing mass spectrometric data. The number of wheat varieties tested was increased from 10 to 30. The main pre‐processing method investigated was based on Gaussian smoothing of the spectra, but other methods based on normalisation procedures and multiplicative scatter correction of data were also used. With the final method, it was possible to classify 30 wheat varieties with 87% correctly classified mass spectra and a correlation coefficient of 0.90. Copyright © 2002 John Wiley & Sons, Ltd.
Centrifugal Bioreactors and Their Application in Remediation
Authors: Herman Heath H. , Lin Weimin , Petrecca Peter J. , Herman Tod M. , Bates Christopher , Simmons Robert , Houghton John
Published: August 2002

A new approach to the maintenance of large microbial populations for bioremediation purposes has been
developed in which a centrifugal bioreactor is used to immobilize microbial populations at extremely high
density. The cells are ordered into a three‐dimensional array through which wastewater or groundwater
volumes may be flowed, unimpeded by frits or screens. The process methodology is independent of the type, shape,
or viability of the individual cells immobilized and, thus, may be adapted to many different bioremediation
needs. The utilization of this new process has been explored for three different types of remediation: the
removal of heavy metals from wastewater, the aerobic degradation of
methyl‐tert‐butyl ether (MTBE), and the anaerobic reduction of nitrate
to nitrogen gas. This article discusses the use of centrifugal bioreactors and their application in remediation.
© 2001 John Wiley & Sons, Inc.
Field Trial of Biosparging with Oxygen for Bioremediation of Volatile Organic Compounds
Authors: Sperry Kenneth L. , Stanley Christian , Kay James
Published: August 2002

Xpert Design & Diagnostics, LLC (XDD), & Conestoga‐Rovers and Associates
(CRA) conducted a biosparging field trial at a Superfund site in New Jersey. The biosparging field
trial proved that biosparging with oxygen was very effective in promoting the biological destruction of benzene.
The approximately 265‐day period of oxygen injection successfully reduced benzene concentrations by
several orders of magnitude, or even to non‐detect values, at least 40 feet from the point of injection.
Through co‐precipitation of arsenic with oxidized iron, biosparging also effectively reduced total
concentrations of arsenic and iron in groundwater. Based on the results of the biosparging field trial, the
final remedy for the site has been amended to include the use of biosparging technology as an alternative to
groundwater pumping and aboveground treatment in select locations. © 2001 John Wiley & Sons,Inc.
Full‐scale in‐situ biobarrier demonstration for containment and treatment of MTBE
Authors: Miller Karen D. , Johnson Paul C. , Bruce Cristin L.
Published: August 2002

The Naval Facilities Engineering Service Center (NFESC), Arizona State University, and Equilon
Enterprises LLC are partners in an innovative Environmental Security Technology Certification Program cleanup
technology demonstration designed to contain dissolved MTBE groundwater plumes. This full‐scale
demonstration is being performed to test the use of an oxygenated biobarrier at Naval Base Ventura County, in Port
Hueneme, California. Surprisingly, few cost‐effective in‐situ remedies are known for the cleanup of
MTBE‐impacted aquifers, and remediation by engineered in‐situ biodegradation was thought to be an
unlikely candidate just a few years ago. This project demonstrates that MTBE‐impacted groundwater can be
remediated in‐situ through engineered aerobic biodegradation under natural‐flow conditions. With
respect to economics, the installation and operation costs associated with this innovative biobarrier system are
at least 50 percent lower than those of a conventional pump and treat system. Furthermore, although it has been
suggested that aerobic MTBE biodegradation will not occur in mixed MTBE‐BTEX dissolved plumes, this project
demonstrates otherwise. The biobarrier system discussed in this article is the largest of its kind ever
implemented, spanning a dissolved MTBE plume that is over 500 feet wide. This biobarrier system has achieved an
in‐situ treatment efficiency of greater than 99.9 percent for dissolved MTBE and BTEX concentrations.
Perhaps of greater importance is the fact that extensive performance data has been collected, which is being used
to generate best‐practice design and cost information for this biobarrier technology. © 2001 John
Wiley & Sons, Inc.