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Site Model (site + model)
Selected AbstractsStereoselective Hydrolysis of Quaternary Quinuclidinium Benzoates Catalyzed by ButyrylcholinesteraseEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 2 2003Ines Primoz Abstract Four chiral, quaternary, N -methyl and N -benzyl derivatives of (R)- and (S)-quinuclidin-3-yl benzoates were synthesized and studied as substrates of horse serum butyrylcholinesterase (BChE). The kcat for the substrates decreased in the order (R)- N -methyl > (R)- N -benzyl (2.3-fold slower) >> (S)- N -methyl (70.5-fold slower reaction), while for the (S)- N -benzyl ester inhibition of the enzyme was observed. The kinetics of inhibition (Ka = 3.3 ,M) indicated that binding to the catalytic site of BChE occurred. From the ratio of the kcat/KM values of both enantiomers an enantiomeric excess of 95% was calculated for N -methyl derivatives. Thus, BChE is suitable as a biocatalyst for the resolution of racemic quaternary quinuclidinium esters. In order to explain the experimental data, combined quantum chemical (HF/3,21G*) and semiempirical (PM3) calculations within the ONIOM scheme of the stable species in the acylation step were performed. Geometry optimizations were carried out for all benzoate esters for an assumed active site model of BChE. It was confirmed that hydrolysis is affected to an appreciable extent by a proper geometrical orientation of substrates at the choline subsite. The energies of the optimized systems were in good agreement with the experimental data. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Assessing and managing contaminated sediments: Part I, developing an effective investigation and risk evaluation strategyINTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT, Issue 1 2005Sabine E. Apitz Abstract This is the first of a two-part review of the current state-of-the-science pertaining to the assessment and management of contaminated sediments. The goal of this review is to introduce some of the major technical and policy issues stemming from the assessment and management of contaminated sediments, highlight a number of aspects of contaminated sediment assessment and management found to be successful, and, when appropriate, address the barriers that still exist for improving contaminated sediment management. In this paper, Part I, the many key elements of an effective investigation and risk evaluation strategy are reviewed, beginning with the development of a conceptual site model (CSM) and including a discussion of some of the key factors influencing the design of sediment investigations and ecological risk assessment of sediment-bound chemicals on aquatic biota. In Part II of this paper (Apitz et al. 2005), various approaches are reviewed for evaluating sediment risk and monitoring sediment remedy effectiveness. While many of the technical and policy issues described in this review are relevant to dredged material management, the focus of this paper is on sediment assessment for environmental management. [source] Comparative study of electrostatic solvent response by RISM and PCM methods,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2007S. Chiodo Abstract The solvent response on the solute is calculated by the reference interaction site model (RISM) and by the polarizable continuum model (PCM) methods. The linearized RISM technique is developed to treat free energies of atomic and polyatomic ions in water. An empirical repulsive bridge is used for the RISM calculations. The solvent electrostatic potential is approximated by a linear dependence on the solute atomic charges. For a series of monovalent polyatomic cations and anions, the method provides free energies deviating by few percent from the experimental data. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] PM3-compatible zinc parameters optimized for metalloenzyme active sitesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2004Edward N. Brothers Abstract Recent studies have shown that semiempirical methods (e.g., PM3 and AM1) for zinc-containing compounds are unreliable for modeling structures containing zinc ions with ligand environments similar to those observed in zinc metalloenzymes. To correct these deficiencies a reparameterization of zinc at the PM3 level was undertaken. In this effort we included frequency corrected B3LYP/6-311G* zinc metalloenzyme ligand environments along with previously utilized experimental data. Average errors for the heats of formation have been reduced from 46.9 kcal/mol (PM3) to 14.2 kcal/mol for this new parameter set, termed ZnB for "Zinc, Biological." In addition, the new parameter sets predict geometries for the Bacillus fragilis active site model and other zinc metalloenzyme mimics that are qualitatively in agreement with high-level ab initio results, something existing parameter sets failed to do. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1677,1692, 2004 [source] Evaluation of the silanol-suppressing potency of ionic liquidsJOURNAL OF SEPARATION SCIENCE, JSS, Issue 8 2006Micha, Piotr Marsza Abstract Recently, increasing attention has been paid to the use of ionic liquids for high-performance liquid chromatography (HPLC) and capillary electrophoresis. In the present study, the silanol-suppressing potency of ionic liquids was evaluated by HPLC using the two-retention site model proposed previously by Nahum and Horváth (J. Chromatogr. 1981, 203, 53,63). The binding constant, KA, in that approach has been demonstrated to reliably reflect the ability of the ionic liquids to block the silanols of the silica support material of the stationary phase. The determinations were carried out for ionic liquids of the 1-alkyl-3-methylimidazolium group with the use of a series of basic drugs as the test analytes. Comparison of ionic liquids with standard mobile phase additives such as triethylamine showed the former to possess advantages as silanol suppressors in HPLC. The main advantage of the method is that it provides a simple and fast determination of the silanol complex stability, which allowed comparison of the suppressing efficiency of several ionic liquids. [source] Linear lower bounds for ,c(p) for a class of 2D self-destructive percolation modelsRANDOM STRUCTURES AND ALGORITHMS, Issue 4 2009J. van den Berg Abstract The self-destructive percolation model is defined as follows: Consider percolation with parameter p > pc. Remove the infinite occupied cluster. Finally, give each vertex (or, for bond percolation, each edge) that at this stage is vacant, an extra chance , to become occupied. Let ,c(p) be the minimal value of ,, needed to obtain an infinite occupied cluster in the final configuration. This model was introduced by van den Berg and Brouwer. They showed, for the site model on the square lattice (and a few other 2D lattices satisfying a special technical condition) that ,c(p) , . In particular, ,c(p) is at least linear in p , pc. Although the arguments used by van den Berg and Brouwer look very lattice-specific, we show that they can be suitably modified to obtain similar linear lower bounds for ,c(p) (with p near pc) for a much larger class of 2D lattices, including bond percolation on the square and triangular lattices, and site percolation on the star lattice (or matching lattice) of the square lattice. © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2009 [source] Continuous water-level monitoring in the assessment of groundwater remediation and refinement of a conceptual site modelREMEDIATION, Issue 4 2005John J. Quinn An Erratum has been published for this article in Remediation 16(1) 2005, 155,157. Water-level data collection is a fundamental component of groundwater investigations and remediation. While the locations and depths of monitored wells are important, the frequency of data collection may have a large impact on conclusions made about site hydrogeology. Data-logging water-level probes may be programmed to record water levels at frequent intervals, providing site decision makers with abundant, detailed information on the response of an aquifer to both anticipated and unforeseen stresses. In this study, a network of movable probes has provided several years of hourly water- level data. The understanding of the site's phytoremediation system has been enhanced by the continuous data, but subsequent insights into an unexpected situation regarding the site's infrastructure have been the most valuable result of the monitoring program. © 2005 Wiley Periodicals, Inc. [source] Systematic planning for Triad projectsREMEDIATION, Issue 1 2004Robert Howe This article examines specific systematic planning steps that can be used for designing and controlling Triad projects. Triad work strategies act to limit decision uncertainty, expedite schedules to meet project milestones, and reduce costs associated with cleanup activities. As a result, the Triad approach is rapidly increasing in popularity. Good project planning has always been seen as the cornerstone of successful Triad projects. However, the specific steps in the systematic planning process have not been extensively published. Demands of Triad projects, which attempt to make maximum use of innovative technologies and sequencing of activities in a learn- as-you-go framework, put new demands on regulators and project managers alike. Specific activities and relationships are identified to assist project managers with dynamic work strategies and real-time measurements to support improved decision making. These include: assembly of stakeholders, a core technical team, and key decisions; development and refinement of a site model; use of demonstrations of methods applicability; development of dynamic work strategies and project sequencing; real-time data management assessment and presentation; and unitized procurement of technologies and services. © 2004 Wiley Periodicals, Inc. [source] Triad case study: Marine Corps Base Camp PendletonREMEDIATION, Issue 1 2004Adrianne V. Saboya The U.S. Navy Public Works Center (PWC) Environmental Department, San Diego, California, is home to the Navy West Coast Site Characterization and Analysis Penetrometer System (SCAPS). SCAPS has been extensively used at several Navy sites since 1995 to provide real-time, high-density data sets. The U.S. Environmental Protection Agency's Triad approach provided an ideal framework for optimizing the use of the Navy SCAPS during a volatile organic compound (VOC) source investigation at Installation Restoration Site 1114 at Marine Corps Base Camp Pendleton. All three elements of Triad,systematic planning, dynamic work strategy, and use of real-time measurement tools,were implemented to manage decision uncertainty and expedite the site management process. The investigation was conducted using the Navy SCAPS, outfitted with a cone penetrometer, membrane interface probe, and a direct sampling ion trap mass spectrometry detector, which allowed for real- time collection of over 690 feet of continuous lithologic information and VOC concentration data. These data were used collaboratively with 24-hour turnaround US EPA 8260B VOC groundwater results from temporary direct- push wells to support the conclusion of a limited source area. Implementation of the Triad approach for this investigation provided an expedited high-density data set and a refined conceptual site model (CSM) in real time that resulted in cost savings estimated at $2.5M and reduction of the site characterization and cleanup schedule by approximately three years. This project demonstrates how the US EPA's Triad approach can be applied to streamline the site characterization and cleanup process while appropriately managing decision uncertainty in support of defensible site decisions. © 2004 Wiley Periodicals, Inc. [source] Quantifying the condition of Hawaiian coral reefsAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 1 2010Ku'ulei S. Rodgers Abstract (1)This investigation developed and tested descriptive models designed to evaluate coral reef ecological condition based on data developed using the basic techniques most often used in coral reef surveys. (2)Forty-three variables at 184 stations were analysed in order to identify specific factors that are useful metrics for describing reef condition. (3)The common practice of using ,reference sites' for paired site comparisons was evaluated by developing a reference site model (RSM). This use of reference sites proved to be subjective and unreliable, especially when multiple factors and multiple sites are involved. However, in some cases the RSM is appropriate in demonstrating severe degradation based on factors such as sediment, coral cover and fish abundance. (4)An objective ecological gradient model (EGM) was developed based on a wide range of metrics at numerous sites. A computer program was developed that allows a quantitative ranking of reef condition along a continuum and can be used to compare reefs across a wide range of conditions. Further, this approach permits the operator to alter and define criteria appropriate to a specific question. (5)Results of this investigation provide ecological insights into the importance of natural and anthropogenic ecological factors in determining coral reef condition. Copyright © 2009 John Wiley & Sons, Ltd. [source] | ||||||||||