Using SPARK as a Solver for Modelica (open access)

Using SPARK as a Solver for Modelica

Modelica is an object-oriented acausal modeling language that is well positioned to become a de-facto standard for expressing models of complex physical systems. To simulate a model expressed in Modelica, it needs to be translated into executable code. For generating run-time efficient code, such a translation needs to employ algebraic formula manipulations. As the SPARK solver has been shown to be competitive for generating such code but currently cannot be used with the Modelica language, we report in this paper how SPARK's symbolic and numerical algorithms can be implemented in OpenModelica, an open-source implementation of a Modelica modeling and simulation environment. We also report benchmark results that show that for our air flow network simulation benchmark, the SPARK solver is competitive with Dymola, which is believed to provide the best solver for Modelica.
Date: June 30, 2008
Creator: Wetter, Michael; Wetter, Michael; Haves, Philip; Moshier, Michael A. & Sowell, Edward F.
Object Type: Article
System: The UNT Digital Library
An Aerial Radiological Survey of Selected Areas of the City of North Las Vegas (open access)

An Aerial Radiological Survey of Selected Areas of the City of North Las Vegas

As part of the proficiency training for the Radiological Mapping mission of the Aerial Measuring System (AMS), a survey team from the Remote Sensing Laboratory-Nellis (RSL-Nellis) conducted an aerial radiological survey of selected areas of the city of North Las Vegas for the purpose of mapping natural radiation background and locating any man-made radioactive sources. Survey areas were selected in collaboration with the City Manager's office and included four separate areas: (1) Las Vegas Motor Speedway (10.6 square miles); (2) North Las Vegas Downtown Area (9.2 square miles); (3) I-15 Industrial Corridor (7.4 square miles); and (4) Future site of University of Nevada Las Vegas campus (17.4 square miles). The survey was conducted in three phases: Phase 1 on December 11-12, 2007 (Areas 1 and 2), Phase 2 on February 28, 2008 (Area 3), and Phase 3 on March 19, 2008 (Area 4). The total completed survey covered a total of 44.6 square miles. The flight lines (without the turns) over the surveyed areas are presented in Figures 1, 2, 3, and 4. A total of eight 2.5-hour-long flights were performed at an altitude of 150 ft above ground level (AGL) with 300 feet of flight-line spacing. Water line and …
Date: June 1, 2008
Creator: Wasiolek, Piotr
Object Type: Report
System: The UNT Digital Library
Measurement of Fast Voltage Transients in High-Performance Nb3Sn Magnets (open access)

Measurement of Fast Voltage Transients in High-Performance Nb3Sn Magnets

The Superconducting Magnet group at Lawrence Berkeley National Laboratory has been developing Nb{sub 3}Sn high-field accelerator magnet technology for the last fifteen years. In order to support the magnet R&D effort, we are developing a diagnostic system that can help identify the causes of performance limiting quenches by recording small flux-changes within the magnet prior to quench-onset. These analysis techniques were applied to the test results from recent Nb{sub 3}Sn magnets. This paper will examine various types of events and their distinguishing characteristics. The present measurement techniques are discussed along with the design of a new data acquisition system that will substantially improve the quality of the recorded signals.
Date: June 1, 2008
Creator: Lietzke, A. F.; Sabbi, G. L.; Ferracin, P.; Caspi, S.; Zimmerman, S.; Joseph, J. et al.
Object Type: Article
System: The UNT Digital Library
Initial Operation of the High Temperature Electrolysis Integrated Laboratory Scale Experiment at INL (open access)

Initial Operation of the High Temperature Electrolysis Integrated Laboratory Scale Experiment at INL

An integrated laboratory scale, 15 kW high-temperature electrolysis facility has been developed at the Idaho National Laboratory under the U.S. Department of Energy Nuclear Hydrogen Initiative. Initial operation of this facility resulted in over 400 hours of operation with an average hydrogen production rate of approximately 0.9 Nm3/hr. The integrated laboratory scale facility is designed to address larger-scale issues such as thermal management (feed-stock heating, high-temperature gas handling), multiple-stack hot-zone design, multiple-stack electrical configurations, and other “integral” issues. This paper documents the initial operation of the ILS, with experimental details about heat-up, initial stack performance, as well as long-term operation and stack degradation.
Date: June 1, 2008
Creator: Stoots, C. M.; O'Brien, J. E.; Condie, K. G.; Herring, J. S. & Hartvigsen, J. J.
Object Type: Article
System: The UNT Digital Library
Computational Science Research in Support of Petascale Electromagnetic Modeling (open access)

Computational Science Research in Support of Petascale Electromagnetic Modeling

Computational science research components were vital parts of the SciDAC-1 accelerator project and are continuing to play a critical role in newly-funded SciDAC-2 accelerator project, the Community Petascale Project for Accelerator Science and Simulation (ComPASS). Recent advances and achievements in the area of computational science research in support of petascale electromagnetic modeling for accelerator design analysis are presented, which include shape determination of superconducting RF cavities, mesh-based multilevel preconditioner in solving highly-indefinite linear systems, moving window using h- or p- refinement for time-domain short-range wakefield calculations, and improved scalable application I/O.
Date: June 20, 2008
Creator: Lee, L.; Akcelik, V.; Ge, L.; Chen, S.; Schussman, G.; Candel, A. et al.
Object Type: Article
System: The UNT Digital Library
Modeling Approach/Strategy for Corrective Action Unit 99: Rainier Mesa and Shoshone Mountain, Nevada Test Site, Nye County, Nevada, Revision 1, with ROTC-1 (open access)

Modeling Approach/Strategy for Corrective Action Unit 99: Rainier Mesa and Shoshone Mountain, Nevada Test Site, Nye County, Nevada, Revision 1, with ROTC-1

This document describes an approach for preliminary (Phase I) flow and transport modeling for the Rainier Mesa/Shoshone Mountain (RMSM) Corrective Action Unit (CAU). This modeling will take place before the planned Phase II round of data collection to better identify the remaining data gaps before the fieldwork begins. Because of the geologic complexity, limited number of borings, and large vertical gradients, there is considerable uncertainty in the conceptual model for flow; thus different conceptual models will be evaluated, in addition to different framework and recharge models. The transport simulations will not be used to formally calculate the Contaminant Boundary at this time. The modeling (Phase II) will occur only after the available data are considered sufficient in scope and quality.
Date: June 1, 2008
Creator: Ruskauff, Greg
Object Type: Report
System: The UNT Digital Library
Atmospheric Properties from the 2006 Niamey Deployment and Climate Simulation with a Geodesic Grid Coupled Climate Model Third Quarter 2008 (open access)

Atmospheric Properties from the 2006 Niamey Deployment and Climate Simulation with a Geodesic Grid Coupled Climate Model Third Quarter 2008

In 2008, the Atmospheric Radiation Measurement (ARM) Program and the Climate Change Prediction Program (CCPP) have been asked to produce joint science metrics. For CCPP, the metrics will deal with a decade-long control simulation using geodesic grid-coupled climate model. For ARM, the metrics will deal with observations associated with the 2006 deployment of the ARM Mobile Facility (AMF) to Niamey, Niger. Specifically, ARM has been asked to deliver data products for Niamey that describe cloud, aerosol, and dust properties. This report describes the aerosol optical depth (AOD) product.
Date: June 30, 2008
Creator: Mather, JH; Randall, DA & Flynn, CJ
Object Type: Report
System: The UNT Digital Library
Sigma: Web Retrieval Interface for Nuclear Reaction Data (open access)

Sigma: Web Retrieval Interface for Nuclear Reaction Data

The authors present Sigma, a Web-rich application which provides user-friendly access in processing and plotting of the evaluated and experimental nuclear reaction data stored in the ENDF-6 and EXFOR formats. The main interface includes browsing using a periodic table and a directory tree, basic and advanced search capabilities, interactive plots of cross sections, angular distributions and spectra, comparisons between evaluated and experimental data, computations between different cross section sets. Interactive energy-angle, neutron cross section uncertainties plots and visualization of covariance matrices are under development. Sigma is publicly available at the National Nuclear Data Center website at www.nndc.bnl.gov/sigma.
Date: June 24, 2008
Creator: Pritychenko,B. & Sonzogni, A.A.
Object Type: Article
System: The UNT Digital Library
Investigation of possible csr induced energy spread effects with the A0 photoinjector bunch compressor (open access)

Investigation of possible csr induced energy spread effects with the A0 photoinjector bunch compressor

The bunch compressor of the A0 Photoinjector at Fermilab was removed this past spring to install a transverse to longitudinal emittance exchange experiment. Prior to its removal questions arose about the possibility of observing the effects of Coherent Synchrotron Radiation on the compressed beam. The energy spread of the beam with and without compression was measured to observe any changes. Various beam charges were used to look for square law effects associated with CSR. No direct observation of CSR in the compressor was attempted because the design of the vacuum chamber did not allow it. In this paper we report the results of these experiments and comparison with simulations using ASTRA and CSRTrack. The results are also compared with analytical approximations.
Date: June 1, 2008
Creator: Edwards, H.; Kazakevich, G.; Thurman-Keup, R. M. & Ruan, J.
Object Type: Article
System: The UNT Digital Library
Survey of Dynamic Simulation Programs for Nuclear Fuel Reprocessing (open access)

Survey of Dynamic Simulation Programs for Nuclear Fuel Reprocessing

The absence of any industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other industries. Modeling programs to simulate the dynamic behavior of nuclear fuel separations and processing were originally developed to support the US government’s mission of weapons production and defense fuel recovery. Consequently there has been little effort is the US devoted towards improving this specific process simulation capability during the last two or three decades. More recent work has been focused on elucidating chemical thermodynamics and developing better models of predicting equilibrium in actinide solvent extraction systems. These equilibrium models have been used to augment flowsheet development and testing primarily at laboratory scales. The development of more robust and complete process models has not kept pace with the vast improvements in computational power and user interface and is significantly behind simulation capability in other chemical processing and separation fields.
Date: June 1, 2008
Creator: Tranter, Troy J. & Haefner, Daryl R.
Object Type: Report
System: The UNT Digital Library
Supersymmetry Searches at the Tevatron (open access)

Supersymmetry Searches at the Tevatron

None
Date: June 1, 2008
Creator: Strologas, John
Object Type: Article
System: The UNT Digital Library
Shot-Noise Seeded Microbunching Instability: Second-Order Correction to the Gain Function (open access)

Shot-Noise Seeded Microbunching Instability: Second-Order Correction to the Gain Function

We determine the second-order correction to the gain function of the microbunching instability in single-pass systems of interest for the next generation of light sources. The calculation applies to the case where the instability is seeded by shot noise. We examine an analytically treatable model of beam dynamics where collective forces are active only in non-dispersive sections of the linac. We find that the second order term can augment the linear gain significantly while affecting the spectrum of the overall gain only marginally. The weight of the second-order correction relative to the linear gain is found to scale quadratically with respect to R56. The qualitative behavior predicted by the model is consistent with exact numerical solutions of the Vlasov equations for realistic lattices.
Date: June 30, 2008
Creator: Venturini, Marco
Object Type: Article
System: The UNT Digital Library
TESTING OF A ROTARY MICROFILTER TO SUPPORT HANFORD APPLICATIONS (open access)

TESTING OF A ROTARY MICROFILTER TO SUPPORT HANFORD APPLICATIONS

Savannah River National Laboratory (SRNL) researchers are investigating and developing a rotary microfilter for solid-liquid separation applications at the Savannah River Site (SRS). Because of the success of that work, the Hanford Site is evaluating the use of the rotary microfilter for its Supplemental Pretreatment process. The authors performed rotary filter testing with a full-scale, 25-disk unit with 0.5 {micro} filter media manufactured by Pall Corporation using a Hanford AN-105 simulant at solids loadings of 0.06, 0.29, and 1.29 wt%. The conclusions from this testing are: (1) The filter flux at 0.06 wt% solids reached a near constant value at an average of 0.26 gpm/ft{sup 2} (6.25 gpm total). (2) The filter flux at 0.29 wt% solids reached a near constant value at an average of 0.17 gpm/ft{sup 2} (4 gpm total). (3) The filter flux at 1.29 wt% solids reached a near constant value at an average of 0.10 gpm/ft{sup 2} (2.4 gpm total). (4) Because of differences in solids loadings, a direct comparison between crossflow filter flux and rotary filter flux is not possible. The data show the rotary filter produces a higher flux than the crossflow filter, but the improvement is not as large as seen in …
Date: June 26, 2008
Creator: Poirier, M; David Herman, D; David Stefanko, D & Samuel Fink, S
Object Type: Report
System: The UNT Digital Library
New Results on Leptonic B Meson Decays at BaBar (open access)

New Results on Leptonic B Meson Decays at BaBar

The authors present selected new results on leptonic B meson decays from the BABAR experiment: searches for the decays B{sup 0} {yields} {ell}{sup +}{ell}{sup -}, B{sup +} {yields} {ell}{sup +}{nu} and B{sup 0} {yields} {ell}{sup +}{tau}{sup -}, and B {yields} K{nu}{bar {nu}}, where {ell} = e or {mu}. They observe no evidence for these decays and set upper limits on their branching fractions.
Date: June 9, 2008
Creator: Kim, Hojeong
Object Type: Article
System: The UNT Digital Library
A Virtual Engineering Framework for Simulating Advanced Power System (open access)

A Virtual Engineering Framework for Simulating Advanced Power System

In this report is described the work effort performed to provide NETL with VE-Suite based Virtual Engineering software and enhanced equipment models to support NETL's Advanced Process Engineering Co-simulation (APECS) framework for advanced power generation systems. Enhancements to the software framework facilitated an important link between APECS and the virtual engineering capabilities provided by VE-Suite (e.g., equipment and process visualization, information assimilation). Model enhancements focused on improving predictions for the performance of entrained flow coal gasifiers and important auxiliary equipment (e.g., Air Separation Units) used in coal gasification systems. In addition, a Reduced Order Model generation tool and software to provide a coupling between APECS/AspenPlus and the GE GateCycle simulation system were developed. CAPE-Open model interfaces were employed where needed. The improved simulation capability is demonstrated on selected test problems. As part of the project an Advisory Panel was formed to provide guidance on the issues on which to focus the work effort. The Advisory Panel included experts from industry and academics in gasification, CO2 capture issues, process simulation and representatives from technology developers and the electric utility industry. To optimize the benefit to NETL, REI coordinated its efforts with NETL and NETL funded projects at Iowa State University, Carnegie …
Date: June 18, 2008
Creator: Bockelie, Mike; Swensen, Dave; Denison, Martin & Borodai, Stanislav
Object Type: Report
System: The UNT Digital Library
High Resolution Upgrade of the ATF Damping ring BPM System (open access)

High Resolution Upgrade of the ATF Damping ring BPM System

None
Date: June 5, 2008
Creator: Terunuma, N.; Urakawa, J.; Frisch, J.; May, J.; McCormick, D.; Nelson, J. et al.
Object Type: Article
System: The UNT Digital Library
Microwave Transmission Measurements of the Electron Cloud density In the Positron Ring of PEP-II (open access)

Microwave Transmission Measurements of the Electron Cloud density In the Positron Ring of PEP-II

Clouds of electrons in the vacuum chambers of accelerators of positively charged particle beams present a serious limitation for operation of these machines at high currents. Because of the size of these accelerators, it is difficult to probe the low energy electrons clouds over substantial lengths of the beam pipe. We applied a novel technique to directly measure the electron cloud density via the phase shift induced in a TE wave which is independently excited and transmitted over a straight section of the accelerator. The modulation in the wave transmission which appears to increase in depth when the clearing solenoids are switched off, seem to be directly correlated to the electron cloud density in the section. Furthermore, we expect a larger phase shift of a wave transmitted through magnetic dipole field regionsif the transmitted wave couples with the gyration motion of the electrons. We have used this technique to measure the average electron cloud density (ECD) specifically for the first time in magnetic field regions of a new 4-dipole chicane in the positron ring of the PEP-II collider at SLAC. In this paper we present and discuss the measurements taken in the Low Energy Ring (LER) between 2006 and 2008.
Date: June 18, 2008
Creator: Pivi, Mauro T.F.; Krasnykh, Anatoly K.; Byrd, John; De Santis, Stefano; Sonnaad, Kiran G.; Caspers, Fritz et al.
Object Type: Article
System: The UNT Digital Library
Decays of B_s Mesons and b Baryons: A Review of Recent First Observations and Branching Fractions (open access)

Decays of B_s Mesons and b Baryons: A Review of Recent First Observations and Branching Fractions

Recent rate measurements of B{sub s}{sup 0} mesons and {Lambda}{sub b}{sup 0} baryons produced in {radical}s = 1.96 TeV proton-antiproton and {Upsilon}(5S) electron-positron collisions are reviewed, including the first observations of six new decay modes: B{sub s}{sup 0} {yields} D{sub s}{sup +} K{sup -} (CDF), B{sub s}{sup 0} {yields} D{sub s}{sup -} D{sub s}{sup +} (CDF), B{sub s}{sup 0} {yields} D{sub s1}{sup -}(2536){mu}{sup +} {nu}{sub {mu}} X (DZero), B{sub s}{sup 0} {yields} {phi}{gamma} (Belle)< {Lambda}{sub b}{sup 0} {yields} p{pi}{sup -} (CDF), and {Lambda}{sub b}{sup 0} {yields} pK{sup -} (CDF). Also examined are branching-fraction measurements or limits for the B{sub s}{sup 0} {yields} D{sub s}{sup (*)} D{sub s}{sup (*)} modes (Belle, CDF, and DZero), the B{sub s}{sup 0} {yields} {gamma}{gamma} radiative penguin decay (Belle), and three two-body charmless B{sub s}{sup 0} meson decay channels (CDF). Implications for the phenomenology of electroweak and QCD physics, as well as searches for physics beyond the Standard Model, are identified where applicable.
Date: June 1, 2008
Creator: Warburton, Andreas
Object Type: Article
System: The UNT Digital Library
GIS Method for Developing Wind Supply Curves (open access)

GIS Method for Developing Wind Supply Curves

This report describes work conducted by the National Renewable Energy Laboratory (NREL) as part of the Wind Technology Partnership (WTP) sponsored by the U.S. Environmental Protection Agency (EPA). This project has developed methods that the National Development and Reform Commission (NDRC) intends to use in the planning and development of China's 30 GW of planned capacity. Because of China's influence within the community of developing countries, the methods and the approaches here may help foster wind development in other countries.
Date: June 1, 2008
Creator: Kline, D.; Heimiller, D. & Cowlin, S.
Object Type: Report
System: The UNT Digital Library
Early Brain Response to Low-Dose Radiation Exposure Involves Molecular Networks and Pathways Associated with Cognitive Functions, Advanced Aging and Alzheimer's Disease (open access)

Early Brain Response to Low-Dose Radiation Exposure Involves Molecular Networks and Pathways Associated with Cognitive Functions, Advanced Aging and Alzheimer's Disease

Understanding the cognitive and behavioral consequences of brain exposures to low-dose ionizing radiation has broad relevance for health risks from medical radiation diagnostic procedures, radiotherapy, environmental nuclear contamination, as well as earth orbit and space missions. Analyses of transcriptome profiles of murine brain tissue after whole-body radiation showed that low-dose exposures (10 cGy) induced genes not affected by high dose (2 Gy), and low-dose genes were associated with unique pathways and functions. The low-dose response had two major components: pathways that are consistently seen across tissues, and pathways that were brain tissue specific. Low-dose genes clustered into a saturated network (p < 10{sup -53}) containing mostly down-regulated genes involving ion channels, long-term potentiation and depression, vascular damage, etc. We identified 9 neural signaling pathways that showed a high degree of concordance in their transcriptional response in mouse brain tissue after low-dose radiation, in the aging human brain (unirradiated), and in brain tissue from patients with Alzheimer's disease. Mice exposed to high-dose radiation did not show these effects and associations. Our findings indicate that the molecular response of the mouse brain within a few hours after low-dose irradiation involves the down-regulation of neural pathways associated with cognitive dysfunctions that are also …
Date: June 6, 2008
Creator: Lowe, Xiu R; Bhattacharya, Sanchita; Marchetti, Francesco & Wyrobek, Andrew J.
Object Type: Article
System: The UNT Digital Library
Transatlantic transport of Fermilab 3.9 GHz cryomodule for TTF/FLASH to DESY (open access)

Transatlantic transport of Fermilab 3.9 GHz cryomodule for TTF/FLASH to DESY

In an exchange of technology agreement, Fermilab built and will deliver a 3.9 GHz (3rd harmonic) cryomodule to DESY to be installed in the TTF/FLASH beamline. This cryomodule delivery will involve a combination of flatbed air ride truck and commercial aircraft transport to Hamburg Germany. A description of the isolation and damping systems that maintain alignment during transport and protect fragile components is provided. Initially, transport and corresponding alignment stability studies were performed in order to assess the risk associated with transatlantic travel of a fully assembled cryomodule. Shock loads were applied to the cryomodule by using a coldmass mockup to prevent subjecting actual critical components (such as the cavities and input couplers) to excessive forces. Accumulative and peak shock loads were applied through over-the-road testing and using a pendulum hammer apparatus, respectively. Finite Element Analysis (FEA) studies were implemented to define location of instrumentation for transport studies and provide modal frequencies and shapes. Shock and vibration measurement results of transport studies and stabilization techniques are discussed.
Date: June 1, 2008
Creator: McGee, M. W.; Vocean, V.; Grimm, C. & Schappert, W.
Object Type: Article
System: The UNT Digital Library
Thermal-fluid and electrochemical modeling and performance study of a planar solid oxide electrolysis cell : analysis on SOEC resistances, size, and inlet flow conditions. (open access)

Thermal-fluid and electrochemical modeling and performance study of a planar solid oxide electrolysis cell : analysis on SOEC resistances, size, and inlet flow conditions.

Argonne National Laboratory and Idaho National Laboratory researchers are analyzing the electrochemical and thermal-fluid behavior of solid oxide electrolysis cells (SOECs) for high temperature steam electrolysis using computational fluid dynamics (CFD) techniques. The major challenges facing commercialization of steam electrolysis technology are related to efficiency, cost, and durability of the SOECs. The goal of this effort is to guide the design and optimization of performance for high temperature electrolysis (HTE) systems. An SOEC module developed by FLUENT Inc. as part of their general CFD code was used for the SOEC analysis by INL. ANL has developed an independent SOEC model that combines the governing electrochemical mechanisms based on first principals to the heat transfer and fluid dynamics in the operation of SOECs. The ANL model was embedded into the commercial STAR-CD CFD software, and is being used for the analysis of SOECs by ANL. The FY06 analysis performed by ANL and reported here covered the influence of electrochemical properties, SOEC component resistances and their contributing factors, SOEC size and inlet flow conditions, and SOEC flow configurations on the efficiency and expected durability of these systems. Some of the important findings from the ANL analysis are: (1) Increasing the inlet mass …
Date: June 25, 2008
Creator: Yildiz, B.; Smith, J. & Sofu, T.
Object Type: Report
System: The UNT Digital Library
Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein (open access)

Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

{sup 13}C-based metabolic flux analysis provides valuable information about bacterial physiology. Though many biological processes rely on the synergistic functions of microbial communities, study of individual organisms in a mixed culture using existing flux analysis methods is difficult. Isotopomer-based flux analysis typically relies on hydrolyzed amino acids from a homogeneous biomass. Thus metabolic flux analysis of a given organism in a mixed culture requires its separation from the mixed culture. Swift and efficient cell separation is difficult and a major hurdle for isotopomer-based flux analysis of mixed cultures. Here we demonstrate the use of a single highly-expressed protein to analyze the isotopomer distribution of amino acids from one organism. Using the model organism E. coli expressing a plasmid-borne, his-tagged Green Fluorescent Protein (GFP), we show that induction of GFP does not affect E. coli growth kinetics or the isotopomer distribution in nine key metabolites. Further, the isotopomer labeling patterns of amino acids derived from purified GFP and total cell protein are indistinguishable, indicating that amino acids from a purified protein can be used to infer metabolic fluxes of targeted organisms in a mixed culture. This study provides the foundation to extend isotopomer-based flux analysis to study metabolism of individual strains …
Date: June 27, 2008
Creator: Shaikh, Afshan; Shaikh, Afshan S.; Tang, Yinjie; Mukhopadhyay, Aindrila & Keasling, Jay D.
Object Type: Article
System: The UNT Digital Library
SYNTHESIS OF THE FULLY PROTECTED PHOSPHORAMIDITE OF THE BENZENE-DNA ADDUCT, N2- (4-HYDROXYPHENYL)-2'-DEOXYGUANOSINE AND INCORPORATION OF THE LATER INTO DNA OLIGOMERS (open access)

SYNTHESIS OF THE FULLY PROTECTED PHOSPHORAMIDITE OF THE BENZENE-DNA ADDUCT, N2- (4-HYDROXYPHENYL)-2'-DEOXYGUANOSINE AND INCORPORATION OF THE LATER INTO DNA OLIGOMERS

N2-(4-Hydroxyphenyl)-2'-deoxyguanosine-5'-O-DMT-3'-phosphoramidite has been synthesized and used to incorporate the N2-(4-hydroxyphenyl)-2'-dG (N2-4-HOPh-dG) into DNA, using solid-state synthesis technology. The key step to obtaining the xenonucleoside is a palladium (Xantphos-chelated) catalyzed N2-arylation (Buchwald-Hartwig reaction) of a fully protected 2'-deoxyguanosine derivative by 4-isobutyryloxybromobenzene. The reaction proceeded in good yield and the adduct was converted to the required 5'-O-DMT-3'-O-phosphoramidite by standard methods. The latter was used to synthesize oligodeoxynucleotides in which the N2-4-HOPh-dG adduct was incorporated site-specifically. The oligomers were purified by reverse-phase HPLC. Enzymatic hydrolysis and HPLC analysis confirmed the presence of this adduct in the oligomers.
Date: June 9, 2008
Creator: Chenna, Ahmed; Gupta, Ramesh C.; Bonala, Radha R.; Johnson, Francis & Huang, Bo
Object Type: Article
System: The UNT Digital Library