181
Session Assigned: W&Th P
Title: DSPNet - A Distributed, Networked NMR Acquisition System with Digital Signal Processing

Institute: University of Florida, Gainesville, Florida, USA
Keywords:
Abstract:
In our laboratory, we have been using a Web-operated NMR spectrometer (1)for both interdisciplinary research and teaching. To improve the performance of the instrument, especially for high-volume undergraduate education, we have designed and implemented a distributed, network-based data acquisition system, additionally equipped with a digital signal processing (DSP) front end.

The DSPNet data acquisition system comprises a PC computer populated with a DSP board and connected, via the 100 MBit/s Ethernet network, with a high-performance UNIX system. The UNIX system, a Sun Ultra 2, equipped with two 300 MHz UltraSPARC microprocessors, runs a Web server for providing a browser-based user interface to the system. The PC, executing the single task of reading data off the DSP board and sending them to the UNIX system, operates under Microsoft DOS operating system, upgraded to provide the TCP/IP connectivity. The DSP board operating under a real-time kernel performs the actual NMR data collection; the presence of a dedicated DSP processor allows for on-the-fly data processing, including oversampling and filtering.

Distribution of the independent tasks of data collecting and user interaction among different computers brings a considerable improvement in overall performance, compared to the original, single-computer Web interface. In addition, since the ubiquitous Ethernet protocol can be implemented on nearly any computing platform, individual components of the networked system can run different operating systems, and can be optimized for high performance or selected for availability of tools or price range.

1. M.L. Buszko and D.C. Wang: A World-Wide Web Interface to an NMR Spectrometer, Appl. Magn. Reson. 12, 95-101 (1997)

182
Session Assigned: W&Th P
Title: Java Software and Programmable Logic for a Versatile Pulse Programmer

Institute: University of Florida, Gainesville, Florida.
Keywords: programmable logic; VHDL; Java; pulse programmer
Abstract:
New hardware and software solutions for a versatile pulse programmer have been developed. The core hardware design of the pulse programmer uses only two complex programmable integrated circuits and features a 12.5 ns timing resolution. Developed using a hardware description language (HDL) and the state-machine paradigm, the hardware design can be modified to accommodate a wide range of design specifications. The software is a Java-based client-server package that allows for intuitive controlling and programming of the pulse programmer via a Web browser.

The pulse programmer is programmed and controlled using a printer (parallel) port, and it can be attached to either a PC or a UNIX workstation. The software package consists of two parts - the server and the client. The server is a Java application running on the computer that the pulse programmer is attached to. Its task is to communicate with both the client software and the pulse programmer; the server also performs all the necessary processing of the data. The client is a Java applet that the user interacts with on her local computer. The main task of the applet is to provide the end user with an interface for efficient utilization of the pulse programmer.

Writing the software in Java has several advantages for both the designer and the end user. Since Java is platform independent, the server part can be easily ported to other platforms. Having the client as a Java applet means that anyone with a Java-capable browser and a network connection can use the pulse programmer. The small size of the applet makes the loading and initialization fast, even over slow communication lines. The pulse programmer can be used in high-performance stationary systems as well as in small desktops or even portable spectrometers of magnetic resonance.

Institute: "Jozef Stefan" Institute, University of Ljubljana
Keywords:
Abstract:
Several carboxylic acids form dimers in the solid state. The two molecules of a dimer are bound by two O-H...O hydrogen bonds.In some carboxylic acid dimers the two hydrogen bonds are observed to be significantly disordered.Various models are proposed describing the origin of the proton disorder. ¹⁷O nuclear quadrupole resonance (NQR) seeems to be a suitable technique to investigate proton disorder in the O-H...O hydrogen bonds. We therefore performed a ¹⁷O NQR studie of benzoic acid, 4-hydroxybenzoic acid, 4-nitrobenzoic acid, and 2-nitrobenzoic acid by a field-cycling double resonance technique. The experimental results support the model of a concerted two-proton jump. The O-H...O hydrogen bonds are observed to be slightly asymmetric. The energy difference of the two proton configurations is of the order of 1kJ/mole. It is temperature independent in 4-nitrobenzoic acid and in 2-nitrobenzoic acid whereas it decreases with increasing temperature in benzoic acid and in 4-hydroxybenzoic acid. A model for the temperature variation of the energy difference is proposed.

184
Session Assigned: W&Th P
Title: New Insights in the Structure of Ribonucleic Acids Using Carbon Chemical Shifts - an Experimental and Theoretical Study.

Institute: University of Nebraska at Lincoln
Keywords:
Abstract:
The conformation of RNA nucleotides and nucleosides can be described with a fair degree of accuracy by three structural variables - the sugar pucker, the exocyclic angle between C4– and C5–, and the glycosidic angle between base and sugar. The three torsional minima of the glycosidic angle (gg, gt and tg), the two major families of sugar pucker (N and S), and the two principal base orientations (anti and syn) could in principle combine to give a total of twelve possible major conformations. Of these twelve, only four are found in crystalline nucleotides and nucleosides. CP-MAS measurements of these four conformations allows us to parameterize their chemical shifts, and we can determine at least two of the three structural variables from these chemical shifts alone.

However, other conformations, for which no corresponding crystalline structures have been identified, are found to fit NOE constraints from liquid state NMR data sets. To characterize the chemical shifts of these less accessible conformations, ab initio calculations must be carried out. We set out to calculate these carbon chemical shifts by density functional theory (DFT). Chemical shifts were determined using the 6-311+G(2d,p) and B3LYP correlation functionals following a minimization with a lower 6-31G(d) basis set. Remarkably, the calculated chemical shifts of the four major solid state conformations coincide essentially perfectly with experimental values for crystalline nucleotides and nucleosides, and therefore we can calculate experimentally less accessible structures with a high degree of confidence.

Presently, we are calculating the chemical shifts of the remaining structures and exploring in more detail the relationships between structure and chemical shift in RNA. Up to date advances will be presented at the meeting.

185
Session Assigned: W&Th P
Title: NMR solution structure of a complementary undecanucleotide duplex, containing a 10S benzo[a]pyrene adduct

Institute: National Institutes of Health
Keywords: carcinogenesis PAH
Abstract:
Benzo[a]pyrene (BaP) diol epoxides are carcinogenic metabolites of hydrocarbon pollutants that chemically modify DNA. Structural features of DNA adducts are important to out understanding of the mechanisms underlying the formation of tumor cells. We present here the results on the NMR solution structure of an undecanucleotide duplex, d(CGGTC[BaP]ACGAGG d(CCTCGTGACCG), in which (+)-(7S,8R,9S,10R)- 7, 8 dihydroxy 9,10 epoxy 7,8,9,10 tetrahydro benzo[a] pyrene is covalently bonded to the exocyclic N6 amino group of deoxyadenosine, dA6, through trans addition at C10 of the epoxide (to give a 10S adduct). The undecanucleotide duplex under study, is the first example of a BaP-dA adduct with matched complementary dT opposite dA and with a 10S absolute configuration at C10 of the epoxide. NMR assignments for both exchangeable and nonexchangeable protons of the DNA-BaP duplex was accomplished from TOCSY (in D20) and NOESY spectra (in H20 and D20). Sequential NOEs expected for a B-type DNA conformation with typical Watson-Crick base pairing are observed along the duplex, except at the lesion site. In particular, a strong intraresidue NOE cross peak between H1 and H8 of the modified dA6 is noticed. Also, the dA6 H8 chemical shift appears at a higher field than that of H2. The NOE and chemical shift values of the dA6 are indicative of a syn glycosidic bond at the modified base. The solution conformation of the DNA-BaP adduct was characterized by molecular mechanics and molecular dynamics computations. Results from the molecular dynamics calculations will be presented.

186
Session Assigned: W&Th P
Title: Structure and Dynamics of DNA Three-Way Junctions; Hybrid-Hybrid Relaxation Matrix Analysis

Institute: University of Texas Medical Branch at Galveston
Keywords:
Abstract:
As the simplest DNA junctions, three way junctions (3WJ) can provide information about the principles underlying the folding and stabilization of branched DNA structures. The solution structure of a DNA 3WJ has been probed using a hybrid-hybrid complete relaxation matrix refinement method using 3D NOESY-NOESY data. The results indicate that the DNA 3WJ exists in a folded conformation with two of the helical stems stacked upon each other. The third stem extends away from the junction exposing the unpaired bases to the solvent. The helical stems making the 3WJ show mobility indicating dynamic processes around the junction region. To study the dynamics, we performed molecular dynamics simulations with complete particle mesh Ewald treatment. Changes in the inter-helical angles were monitored over time during the long MD trajectory. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. Our results also indicate that the 3D hybrid-hybrid MORASS refinement of the 3D NOESY-NOESY data gives higher quality structures compared to the 2D complete relaxation matrix refinement of 2D NOESY data alone.

187
Session Assigned: W&Th P
Title: Structure of Peroxide-Cobalt(III)Bleomycin Bound to GC-Containing DNA Oligomers and Properties of the Peroxide Binding Site in Related Structures

Institute: University of Wisconsin-Milwaukee
Keywords:
Abstract:
Bleomycin (Blm) is a complex glycopeptide antibiotic used in the treatment of human cancer. HO₂^-Fe(III)Blm induces single and double strand DNA damage at guanine-pyrimidine sites. Using HO₂^-Co(III)Blm as a model, the structures of 3 HO₂^-Co(III)Blm-DNA oligomer adducts were determined by 2-dimensional NMR spectroscopy. The oligomers were d(GGAAGCTTCC)₂, d(GAGCTC)₂, and d(AGCT)₂. Structures were calculated using X-Plor (Axel T. Brunger, Version 3.1). As in a previous work (Wu et al, JACS (1996) 118, 1281), the structures show that there are two hydrogen bonds between the pyrimidinyl ligand of cobalt in the drug and the guanine base of the GC binding site. Specific binding is lost on the NMR time scale when inosine is substituted for guanine, indicating the importance of at least one of these hydrogen bonds for site specific binding. In addition, another hydrogen bond connection was located between the sulfonium tail amide proton of Blm and N7 of guanine base paired to C at the binding site. Substitution of 7-deazaguanine for this guanine base did not alter the slow exchange rate of the drug. Binding HO₂^-CoBlm to the 10- and 6-mers caused substantial bending of the DNA structure away from the minor groove binding site of the drug. The 4-mer is single stranded in the absence of drug and becomes double stranded as it binds to HO₂^-CoBlm, showing that the drug stabilizes the oligomer even as it distorts it. Similar structures result from modelling in which the fifth axial position of cobalt is occupied by the primary amine or the mannose-carbamoyl nitrogen atom, leaving some ambiguity as to the coordination structure of the metal center.

The drug-DNA adduct contains a sterically restricted pocket in which the peroxide ligand is located and projects toward its reaction target on DNA. The orientations of the principal plane of the cobalt coordination site and of peroxide are very similar to those of the coordination plane and bound external ligand in NO-Fe(II)Blm-DNA and O₂-Co(II)Blm-DNA adducts. Nevertheless, the size of this pocket is such that larger ligands or ligands without the correct binding geometry can not be fit into this space. Thus, whereas Fe(III)Blm binds to the 10-mer in slow exchange like HO₂^-CoBlm, HPO₄^-Fe(III)Blm and CN^-Fe(III)Blm bind in fast exchange because, presumably, they can not make the same pyrimidinyl-guanine hydrogen bonds that exist in HO₂^-CoBlm-DNA. Depending on the concentration of phosphate or cyanide, these ligands dissociate from the adducts to produce Fe(III)Blm-DNA, which forms the slow exchange adduct because the pyrimidinyl-guanine hydrogen bonds are sterically free to form.

Supported by NIH grant CA-22184 to DHP.

188
Session Assigned: W&Th P
Title: Binding of Lexitropsins to Okazaki Fragments Studied by VAST and PFG-NMR.

Institute: University of Nebraska Medical Center, Omaha, NE
Keywords:
Abstract:
Okazaki fragments occur as intermediates during lagging strand DNA replication. Alterations in Okazaki fragment structure may contribute to the anticancer activities of nucleoside analogs such as cytarabine, a potent anti-leukemic agent that inhibits lagging strand replication. We recently reported the NMR solution structures for two model Okazaki fragments, [OKA] and [ARAC] (Gmeiner et al., (1999) Biochemistry, In Press). These sequences are derived from a frequent initiation site for primase during replication of the SV-40 viral genome. The sequence of [ARAC] differs from [OKA] only by substitution of cytarabine for one deoxycytidine. The structure of each model Okazaki fragment was elucidated using NMR spectroscopy and restrained molecular dynamics simulations. The solution structures of [OKA] and [ARAC] each consist of two distinct domains: a DNA duplex region (DDR) and an RNA:DNA hybrid duplex region (HDR). The DDR of [OKA] adopts geometry similar to B-form except for variations in helical parameters, especially twist and roll, which occur in the purine-tract increasing base overlap among the five consecutive purines. The helical axes for the DDR and HDR of [OKA] are bent 22^o relative to one another. We recently have applied a variety of solution NMR techniques including VAST and PFG-NMR to analyze the binding of a variety of lexitropsins to [OKA]. Lexitropsins are oligopeptidic molecules designed to bind in the minor groove of duplex DNA. The variability in minor groove width between the DDR and HDR, and the bending of the helical axis, makes the identification of structural motifs that bind these unusual structures a challenging NMR structural problem.

189
Session Assigned: W&Th P
Title: Quantum Chemical Predictions of Spectroscopic Properties of Amino Acids: Chemical Shielding, Charge Density Topology, and Electrostatics

Institute:
Keywords:
Abstract:
In our continued effort to express the structure dependence of ¹³C chemical shifts in proteins, we present our latest calculated Ramachandran .sigma_iso and .DELTA.sigma shielding surfaces. At little additional cost, a quantum chemical electron density (ED) is available from the same calculations used to produce the shieldings. We compare the topology of such a ED in L-asparagine to that obtained by high-angle x-ray diffraction, and compare calculated and experimental molecular electrostatic potentials. Using an icosahedral representation, we show that quantum chemical calculations accurately predict the orientation of electric field gradient tensors in amino acids. This validation of quantum chemical methodology, using diverse electronic properties, lends support to the idea that such methods will be of use not only in structure determination, but in probing more fundamental properties, such as the detailed structure of hydrogen bonds, and enzyme mechanisms in proteins.

190
Session Assigned: W&Th P
Title:Crystal Structure and Solid State NMR (⁹³Nb MAS, ¹⁹F MAS, ⁹³Nb Frequency Swept) of [NH₄]₅[NbF₄O][NbF₇]₂

Institute: Louisiana State University, Baton Rouge, LA
Keywords:
Abstract:
[NH₄]₅[NbF₄O][NbF₇]₂ has six- and seven-coordinate niobium sites which are observed crystallographically and by two variable-temperature solid-state ⁹³Nb NMR techniques: a spin-echo pulse sequence with frequency stepping and very short pulse static NMR. These NMR techniques are used to cover large spectral widths, and thus observe the quadrupolar powder patterns from which quadrupolar information may be extracted. The crystal structure determined at 333 K shows a six-coordinate site which forms linear chains composed of square pyramidal NbF₄O^- units bridged by oxygen. Also present is a discrete mirror-symmetric NbF₇^-2 unit which shows evidence of motion for a fluoride site. At 100 K, this fluoride site exhibits an ambiguous resolved disorder across the mirror, with half-populated sites. Thus at low temperatures the symmetry of the NbF₇^-2 unit is reduced from mirror to asymmetric. The ⁹³Nb sites are assigned based on a) temperature dependence, b) asymmetry parameters, c) integrated intensity, and d) J-coupling to ¹⁹F. At 333 K the NbF₇^-2 site acts like a [NbF₆^-]F^- complex with six equivalent ¹⁹F sites bound to ⁹³Nb and one ¹⁹F with a spin-spin coupling constant near zero. The commercially available product "ammonium hexafluoroniobate(V)" was the source of the sample.

191
Session Assigned: W&Th P
Title: Isotope Effects in NMR Spectra as Indication of Conformational Change upon Protonation of Imino and Azo Group in Model Compounds

Institute: Rugjer Boskovic Institute, Zagreb, Croatia
Keywords: protonation, conformation, imines, azo compounds, deuterium isotope effects
Abstract:
The protonation of both imino and azo group plays a very important role in many chemical and biochemical processes and transformations. In this work trans-N-benzylideneaniline, trans-N-salicylideneaniline and trans-azobenzene were chosen as model molecules for aromatic compounds containing imino and azo group, respectively.

In order to study deuterium isotope effects in ¹³C NMR spectra a number of deuterium labeled isotopomers were synthesized. The protonation of studied compounds was performed using trifluoroacetic acid (CF₃COOH), where no decomposition of samples due to hydrolysis was observed. The deuterated species were also prepared using CF₃COOD.

There is an indication that the long range deuterium isotope effect over six bonds (⁶.DELTA) in para deuterium labeled isotopomers can be well correlated with the N-Ph torsional angle in the molecules studied. On the other hand, the range of effects could be used as an indication of conformational change upon protonation (deuteration). The general idea is that longer range of effects indicates a better overlapping of .pi orbitals, which is more effective at smaller torsional angle. Taking this into account, one can predict trends of conformational changes upon protonation in binuclear aromatic compounds containing imino or azo group.

192
Session Assigned: W&Th P
Title: Structure and Dynamics of Deuterated Polyamidoamine Dendrimers

Institute: College of W&M, Williamsburg, VA, U.S.A.
Keywords: distribution of voids, arm localization, two-frame motion simulation
Abstract:
Quadruple echo spectra of high generation chlorinated polyamidoamine salts (G=5,7, 9) will be presented and compared with previous results for lower generations¹. For all generations the spectra consist of three broadened overlapping powder patterns. The widest powder pattern is assigned to secondary amides (-ND...O=C-) and provides information on the distribution of hydrogen bond lengths throughout the dendrimer. The next widest powder pattern complements this information with the distribution of hydrogen bond lengths between partially deuterated interior tertiary amines (>N⁺D-) and the chloride counterion, Cl^-. For generation 2 the spectra obtained upon substitution of Cl^- by Br^- demonstrate that both types of hydrogen bonding, which are responsible for stabilizing the dendrimer structure, are counterion dependent. The narrowest powder pattern is characteristic of mobile surface ammonium groups (-N⁺D₃). For generations G=2, 3 and 9, in the temperature range from -30^oC to +60^oC, the spectra are indicative of a broad melting transition. For N⁺D₃ groups of G=2, 3 and 9 dendrimers the temperature dependent anisotropy of the Zeeman relaxation time, T_1Z, will be presented and discussed. For all generations the recovery is biexponential, with a nearly isotropic fast component and anisotropic slow component. The anisotropy of the slow T_1Z cannot be modeled by simple three-site N⁺D₃ rotation. The data for low and high dendrimer generations can only be interpreted using complex models which include libration, large amplitude jumps and unequal site populations.⁽¹⁾D.I.Malyarenko, R.L.Vold, and G.L.Hoatson, Poster presented at 39th ENC, Asilomar, CA (1998).

Institute: Rutgers University
Keywords:
Abstract:
AutoAssign is a constraint-based expert system for automating the analysis of resonance assignments using NMR spectra of small proteins. We originally developed AutoAssign in the Lisp programming language to automate backbone resonance assignments [1]. We now have a new AutoAssign reimplemented in C++ on an SGI computer system (platform) together with a graphical user interface (GUI) implemented in Java for multiplatform use. This new version of AutoAssign is more portable, more efficient, and expandably designed to handle future enhancements. The C++ AutoAssign server is written to be easily portable to other Unix platforms. The Java GUI already supports multiple platforms including SGI, Solaris, Linux, and others.

The new C++/Java AutoAssign currently automates the assignments of HN, NH, CO, C-alpha, C-beta, and H-alpha resonances. The AutoAssign GUI also provides a set of validation tools and graphical displays of the resonances and assignments. There is also a full web-based help and tutorial. We illustrate AutoAssign^,s performance on several independently-collected triple-resonance NMR data sets of proteins ranging in size from ~6 to ~18 kD. AutoAssign obtains nearly complete resonance assignments (~98%) with virtually no errors (<0.5%). The constraint-based algorithm limits assignments to only those with significant evidence. AutoAssign performs the automated analysis of assignments in only seconds on current RISC and Pentium-based platforms.

Future enhancements of AutoAssign are forthcoming. They will include: (i) complete and automatic assignment of sidechain resonances, (ii) expanding AutoAssign^,s spectral repertoir, (iii) homology-based automatic assignment, (iv) improving the Java-based GUI, (v) strip plot representations of frequency-domain spectral data, and (iv) a macro language for easy user specialization and expansion.

[1] Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tahiro, M., Shimotakahara, S., Chien, C., Powers, R., Montelione, G.T., J.Mol.Biol. 269, 592-610 (1997).

194
Session Assigned: W&Th P
Title: High Resolution in the Indirectly Detected Dimension Exploiting the Processing of Folded Spectra

Institute: University of Geneva
Keywords: HSQC, folding, aliasing, computer processing
Abstract:
HSQC spectra are very often used in combination with one-dimensional proton spectra to assign carbon resonances. Whereas the resolution of the directly detected dimension can attain the high resolution of proton spectra, the resolution in the indirectly detected dimension is low and limits the unambiguous assignment to carbon atoms differing by several ppm in chemical shift. The principle exploited here consists in taking advantage of the fact the spectral resolution increases when the spectral width of the indirectly detected dimension is reduced. The price to pay for the enhancement is that folded signals show up in the smaller window. Removing these ambiguities requires comparison with a reference spectrum. The computer program presented here performs this task and thereby permits the attainment of the same high resolution as normally available only in one-dimensional spectra. The efficiency is demonstrated for a steroid.

195
Session Assigned: W&Th P
Title: Application of Deconvolution to Crosspeaks of DQF-COSY Spectra for the Determination of Spin Networks

Institute: University of Geneva
Keywords: COSY, coupling network, deconvolution, steroid
Abstract:
Scalar coupling constants can be extracted from the crosspeaks of correlation spectra by applying deconvolution to the frequency domain. This requires a high resolution in the directly detected dimension. A three step automated procedure is presented as a free package running in combination with a major commercial processing software. The initial step allows one to measure coupling constants in an interactive manner in high-resolution cross-peak multiplets of weakly coupled spin systems. The user can follow the recursive analysis to assess the reliability of the results. If needed, he can change the course of the automatic procedure. A second module compiles the data of the cross-peak analysis and assembles the proton spin network. The algorithm assigns data to a given nucleus if it encounters full consistency of both chemical shifts and coupling constants in all relevant crosspeaks. The pairing of signals symmetric with respect to the diagonal defines the connectivity of the spin network. The last module displays the coupling network in a pleasing presentation. Application to androst-4-ene-3,17-dione is presented. This example shows that assignment of the coupling network to the molecular structure becomes straightforward.

196
Session Assigned: W&Th P
Title: A Customization of VNMR which Facilitates the Structure Elucidation of Organic Compounds

Institute: University of Florida
Keywords:
Abstract:
We introduce a program which facilitates the structure elucidation of organic compounds, where several 1D and 2D spectra are used. The program does what a spectroscopist would do with a pencil and a ruler on top of the spectra, but nicer and faster.

First, the chemical shifts and the splitting patterns are marked by clicking on the spectrum and in the menus. For 2D spectra, chemical shifts in both f1 and f2 can be marked in this way. The data can then be saved, displayed/plotted with the spectrum, or written in an ascii file which can be imported in any text editor.

All the operations are menu-driven. Although the usage is self-explanatory, help files are provided. The program is implemented as an optional customization of vnmr, by providing alternate paths to maclib, menulib and help.

197
Session Assigned: W&Th P
Title: Automated Platform for Spectral Analysis of H NMR Spectra via Prediction based on the 3D-Molecular Structure

Institute: Dept. of Chemistry, Univ. of Kuopio, Finland
Keywords: software, spectral analysis, H NMR prediction, structure elucidation
Abstract:
The recent progress in automation of the NMR spectrometer instrumentation results in an increasing output of data, raising the need for more automation of the structure elucidation and verification of the spectral data. This is often done either by matching database entries with the experimental data or by predicting the spectral data from a possible structure and comparing the predicted spectrum with the experimental one.

While these approaches work quite well for ¹³C NMR, H NMR spectra depend much more on the solvent, temperature and last not least on the 3D-structure of the molecule, making the prediction of H NMR spectra much more difficult and a simple database/match approach impracticable.

We now present a method using a prediction algorithm based on the 3D-structure obtained via MM- and randomized by MD-calculations in combination with an automatic assignment based on an iterative verification algorithm using integral transforms. The present model provides a shift prediction with a standard deviation of 0.15 ppm for non-aromatic protons and 0.1 ppm for aromatic protons. The assignment is based on a modified integral transform algorithm (1) which is now able to automatically correct wrong order in the shift prediction and evaluate the possibility of the spectrum/structure match in a much more competent way than a simple pattern recognition.

The complete procedure from the processing of the spectral data over the structure editor, MM/MD-calculations and spectral parameter prediction to the automated assignment and verification is now available in the software package

PERCH (2).

1. R. Laatikainen, M. Niemitz, U. Weber, J. Sundelin, T. Hassinen and J. Vepsalainen, J.Magn.Reson., A120, 1-10, 1996
2. R. Laatikainen, M. Niemitz, J. Sundelin and T. Hassinen, PERCH Software, PERCH Project, University of Kuopio, Kuopio, Finland, 1996

198
Session Assigned: W&Th P
Title: SESAME - an experiment management system for NMR spectrometers

Institute: NMRFAM, Department of Biochemistry, UW - Madison,
Keywords:
Abstract:
SESAME - an experiment management system for NMR spectrometers Peter T. Lee, William M. Westler, Michael R. Chapman, John L. Markley and Zsolt Zolnai NMRFAM, Department of Biochemistry, UW - Madison, 433 Babcock Drive, Madison, WI 53706, USA

An experiment management system (SESAME) has been created as an elegant solution to various problems associated with a multi-user NMR resource, including storing, recovering, and disseminating parameters associated with NMR data collection and processing and with reservation requests for data collection time. SESAME has been implemented as a 3-tier Java/Corba client/server application. The user interface allows simple access to the centralized database that stores all information needed to run a particular experiment (pulse program, gradient files, etc.). The database content can be queried and downloaded. This makes it possible to rerun any experiment in the database or to use one as the starting point for developing a new experiment. In the case of time requests, the system stores project numbers, abstracts, scheduling preferences, etc. These data are used in scheduling and in preparing reports on spectrometer activity. For security, access to stored data is controlled by privileges. In addition to the public and private categories, virtual groups can be formed by users of the system to allow easy sharing of information among collaborators.

199
Session Assigned: W&Th P
Title: GWEnter: An Alternative Interface for Varian Automation

Institute: Glaxo Wellcome, Inc. RTP, NC USA
Keywords:
Abstract:
Since Varian adopted Tcl/Tk as the user interface programming language for automation with VNMR 5.3, this has given the user added flexibility for customization. At Glaxo Wellcome, we have designed an alternative interface to meet our needs for multi-user, high-throughput, rapid NMR automation. The program, GWEnter, can be used with both traditional SMS automation, or the new tubeless VAST system. Through active monitoring of the Varian sample queues, the program provides the chemist with readily interpretable information about the status of samples  submitted, running, and finished. Through the interface, the administrator can easily configure available experiments, solvents, and many other multiuser features including e-mail notification when samples are complete. The program has proven itself very successful as our user base has grown to over 150 chemists and four automated NMR instruments.

Institute: National High Magnetic Field Laboratory
Keywords:
Abstract:
NMR data acquired using the YBCO- based High Temperature Superconducting (HTS) probe operating at 400 MHz are presented. The HTS probe, also known as super proton probe, is on loan from Varian. Measurements showed an impressive S/N that is nearly 4 times higher than that for a conventional probe at this frequency. However, the high Q (quality factor) of the probe renders substantial non-linearity in its performance and mandates careful calibrations in routine use. Experiments that highlight strengths and strangeness of this probe are presented.

201
Session Assigned: W&Th P
Title: A User-Friendly System for the Routine Application of Cryogenic NMR Probes: Technology and Results

Institute: Bruker AG, Faellanden, Switzerland
Keywords:
Abstract:
Due to steady improvements and refinements in both the probe and cooling technology, cryogenic high-resolution NMR probes developed in the past few years are becoming routine analytical tools.

Cooling of the probes is achieved by a sophisticated closed-cycle cooling system, which requires no liquid cryogens. The system is self-contained and capable of completely unattended operation. Owing to its fully automated push-button operation, it is transparent to the user who can concentrate on the experiment being performed without having to divert his or her attention to the technical details of the cooling.

The entire cryogenic platform has been extensively tested and has proven to be very stable and reliable. We have achieved months of routine operation while performing highly demanding experiments.

We present data from inverse probes with carbon or nitrogen decoupling channels, as well as from carbon-observe probes with proton decoupling. In addition to the probes for standard 5-mm sample tubes, microprobes for 2.5-mm samples have been produced. All of these probes achieve very high S/N (3 to 5 times that of conventional probes) and are equipped with a sensitive lock channel and a z-gradient. The probes have found a wealth of useful applications in biological NMR, investigations of natural products, and even in fullerene chemistry. The experiments performed range from very insensitive experiments such as INADEQUATE to highly demanding inverse experiments using 13C spinlock. Measurements will be presented which demonstrate the high performance and stability of the complete system.

202
Session Assigned: W&Th P
Title: Application of a 2.5-mm CryoProbe to Metabolite Studies

Institute: Roche Bioscience, Palo Alto, CA USA
Keywords: cryogenic
Abstract:
We will present data obtained from metabolite samples in a 2.5-mm, 500-MHz CryoProbe (Bruker Instruments, Fremont, CA USA).

The carbon-inverse microprobe, equipped with a pulsed Z gradient, has a proton sensitivity of >1200 (0.1% ethylbenzene) and an ASTM carbon sensitivity of >150. The proton 90^o pulse length is <10 &micro;s and the carbon 90^o pulse length is <20 &micro;s. The RF homogeneity is characterized by 810^o/90^o ratios of over 70% for both proton and carbon.

Starting with a few micrograms of a low-molecular-weight metabolite in about 75 microliters of solvent, we collected HMQC data. The sample was then diluted and new HMQC data collected until a reasonable detection limit was established. COSY and HMBC data will also be presented, as will spectra obtained from peptide and protein samples.

203
Session Assigned: W&Th P
Title: Superconducting RF Coils

Institute: DuPont Superconductivity, Wilmington, Delaware
Keywords: Cryogenic
Abstract:
DuPont Superconductivity has developed superconducting RF coils for various magnetic resonance applications. We fabricate imaging coils from yttrium barium copper oxide and thallium barium calcium copper oxide thin films grown epitaxially on sapphire and lanthanum aluminate substrates. We realize signal-to-noise improvement approaching an order of magnitude when these superconducting RF coils replace conventional nonsuperconducting RF coils in magnetic resonance imaging experiments. We will summarize data collected using DuPont materials. We will also compare and contrast the performance of different superconducting material and substrate combinations. We believe that this technology is advantageous for many magnetic resonance applications.

204
Session Assigned: W&Th P
Title: Thin-Film HTS Probe Coils for NQR Detection Systems

Institute: Penn State University, University Park, PA USA
Keywords: NQR, thin-film HTS coils
Abstract:
Nuclear quadrupole resonance (NQR) provides a noninvasive method for detecting explosives and narcotics by revealing the presence of ¹⁴N. Although ¹⁴N is essentially 100% abundant, the small zero-field NQR splitting results in a low signal to noise ratio (SNR) that places a lower bound on the minimal detectable quantity. Under the right conditions, the SNR of an NQR measurement is proportional to the square root of the Quality factor (Q) of the tuned probe coil. As a result, it may be possible to significantly improve the sensitivity of the NQR detection system by increasing the Q of the tuned detection circuit. In the low-MHz frequency range of interest for narcotics and explosives, resonators fabricated from thin films of the high-temperature superconductor (HTS) material Y₁Ba₂Cu₃O_7-d can achieve Q factors that are much higher than conventional copper resonators. In fact, the resonator bandwidth can be narrower than the NQR line-width in the so-called super-Q regime. Even in this limit, the SNR has been predicted to improve by further increasing resonator Q (Suits et. al. 1998)..

We are developing an NQR spectrometer that operates in the super-Q limit and which demonstrates the potential SNR gain that has been predicted. The system is based on a YBCO resonator that has an unmatched Q of about 500,000 at a frequency of 3.6 MHz. The resonator bandwidth is about hundred times narrower than the NQR line-width..

There are two engineering issues that must be addressed. First, the high resonator Q results in a ringdown time that is much longer than T₂^*. We present and evaluate an approach to reducing the ringdown time of the resonator to a useful value. Second, the frequency of the NQR response of a material is temperature dependent. This causes the resonant frequency of the material to vary in a range of about 60 kHz for normal environmental temperatures. Although the HTS resonant frequency is fixed by its physical parameters, it must somehow be tuned to the desired NQR resonance. We evaluate a technique to introduce a small external reactance as a means of changing the frequency of the HTS resonator..

205
Session Assigned: W&Th P
Title: RF Measurements of High-Temperature-Superconducting NMR Probe Coils in a 25-T Resistive Magnet

Institute: Conductus, Inc., Sunnyvale, CA
Keywords:
Abstract:
The National High Magnetic Field Laboratory (NHMFL) is developing for high-resolution NMR a 21.1-T magnet, equivalent to a 900-MHz proton resonance. In addition to the wide spectral dispersion and the possibility of exploiting dipolar ordering in liquids, the 21.1-T magnet will yield a sensitivity that has been exceeded only by 500 and 600 MHz spectrometers using superconductive probes. To take full advantage of the potential sensitivity of the instrument will require a superconductive RF probe. While high-sensitivity NMR probes based on the high-temperature superconductive (HTS) material Y₁Ba₂Cu₃O_7-.delta. (YBCO) have been demonstrated at proton frequencies up to 600 MHz, it was not clear that the material would have favorable RF properties at higher fields. To answer this question, we have recently performed RF tests of YBCO in a resistive magnet at the NHMFL at up to 25 T (corresponding to a proton frequency of 1.065 GHz) to determine if this material will be appropriate to use in superconductive RF probes for the next generation of high-field NMR magnets.

To prepare for the test, thin films of the HTS material YBCO were deposited on dielectric substrates using the co-evaporation technique, and were patterned into RF coils using designs developed for NMR at Conductus and Bruker. Two coils, one at 900 MHz and the other at 650 MHz, were then tested at the NHMFL. Tests were made both at zero field and in a resistive magnet. Coil temperature was maintained at 4.2 K during all tests. The 900-MHz coil had a matched quality factor (Q) of 25,800 at zero field, which dropped to 22,900 at 21.1 T (900-MHz proton frequency) and 19,900 at 25 T. The 650-MHz coil yielded a Q of 23,900 at fields up to 25 T. The 900-MHz coil carried over 12 amperes of RF current at 21.1 T (sufficient for 90-degree pulses shorter than 10 microseconds), while the 650-MHz coil carried more than 15 amperes at 25 T.

Based on these tests, we conclude that HTS materials are suitable for use in ultra-high-sensitivity NMR probes at fields beyond 1 GHz.

This work sponsored by the National Science Foundation, Grant No. DMI-9761221. The National High Magnetic Field Laboratory is supported by NSF Cooperative Agreement No. DMR-9527035 and by the State of Florida.

206
Session Assigned: W&Th P
Title: Low-field NMR and MRI of room temperature samples detected with a high T_c SQUID

Institute: UC Berkeley and LBNL, Berkeley, CA, USA
Keywords:
Abstract:
We have constructed a high-T_c SQUID spectrometer to detect NMR signals from samples at room temperature in magnetic fields up to 3 mT. The multiloop SQUID magnetometer is operated in vacuum at 77 K, and is separated from the sample, which is less than 1.5 mm away, by a sapphire window. We present NMR spectra of protons, fluorine, and hyperpolarized, isotopically-enriched ¹²⁹Xe. In a magnetic field comparable to the field of the earth, we can resolve the proton spin echo produced by 1 ml of mineral oil at 2.5 kHz after 2000 averages. When the field is increased to 2 mT we can detect the proton spin echo at 86 kHz in a single shot. We were also able to detect protons in human tissue in vivo. In addition to the spectroscopic data we present images obtained from proton signals in filled phantoms. With the thermal polarization of 0.6 ml mineral oil in a field  of 2 mT we are able to obtain two-dimensional images with a spatial resolution of about 0.6 mm x 0.6 mm. Supported by the U.S. Department of Energy under Grant No. OE-AC03-76SF00098, the Deutsche Forschungsgemeinschaft, and the Brazilian Agency for Research CNPq

207
Session Assigned: W&Th P
Title: NMR Applications at Very High Fields

Institute: NHMFL, Tallahassee, Florida, USA
Keywords:
Abstract:
As an important step in high field NMR development, high field magnets with reasonable field homogeneity for NMR applications are becoming available at the National High Magnetic Field Laboratory (NHMFL). Fields ranging from a high resolution 89 mm 600 MHz system to a resistive magnet with a H-1 frequency of 1066 MHz are available. Unique hardware for RF consoles and NMR probes associated with sophisticated NMR systems are also becoming available. An effort to develop a braod range of NMR applications at these high fields is underway. In this presentation, we will demonstrate our recent experimental results and simulations based on these high fields, showing the challenges and potential of high fields.

208
Session Assigned: W&Th P
Title: Development of Resistive Magnets for NMR Applications

Institute: Natl High Magnetic Field Lab, Tallahassee, FL, USA
Keywords:
Abstract:
The realization of field strengths beyond the realm of current superconducting technology can only be achieved either in a purely resistive magnet or in a hybrid (resistive and superconducting) magnet. To that aim, the characterization and improvement of the temporal stability and spatial homogeneity of high field (20 to 33 Tesla) resistive magnets is crucial.

The factors that influence the temporal characteristics of resistive magnets are the power supply ripple (short term) and the temperature of the inlet magnet cooling water (long term). Initially, the peak to peak variation of the power supply ripple, monitored by NMR, was 20 ppm. In order to improve the short term temporal stability, modifications to the power supplies were made that resulted in a factor of 4 reduction. Flux stabilization was then introduced which resulted in a 2 ppm peak to peak variation over short periods of time. For the long term variation that arises from fluctuations in the temperature of the cooling water, current density redistribution, etc, we have used a field frequency lock unit to obtain one order of magnitude reduction on the temporal variation. We extrapolate that given a starting point of 2 ppm, we will achieve less than 0.5 ppm temporal stability at 25 T for several hours.

Based on our preliminary results on a 24 T, 32 mm bore resistive magnet, the Keck Foundation supported the construction of a 25 T, 52 mm magnet. It is in this magnet that we plan to demonstrate a fraction of a ppm temporal stability and 1 ppm spatial homogeneity over 10 mm DSV after the introduction of a combination of passive and active shims in collaboration with Resonance Research. The knowledge acquired, coupled with our working solutions will be applied to the realization of a stable, moderately homogeneous 1.5 GHz magnet for structural biology applications.

209
Session Assigned: W&Th P
Title: Development of a Small Permanent Magnet for Biomedical MRI

Institute: University of Illinois, Urbana, IL, USA
Keywords: imaging, homogeneity, MR
Abstract:
Recent interest in the use of MR microscopy to analyze changes of embryonic and adult genetic models opens a very large base of applications. Standard protocols require imaging of hundreds of specimen for valid results. Clearly, the number of standard MR microscopy systems would be overwhelmed with such demands. To this end, we are designing a series of small permanent magnet systems suitable for MRI.

The design and calculations are based on methods outlined by Abele (1). A cylinder of hard magnetic material is magnetized perpendicular to its axis. In the case of cylindrical magnet geometry high degree of field uniformity can be achieved by making the magnet long enough. However, in real life one has to account for magnet openings that severely cripple field homogeneity. Corrections to the field in central imaging region of the magnet are introduced by adding even number of symmetrical cuts in cylindrical bore. Calculations are performed that optimize their widths and positions in order to eliminate higher order field harmonics.

A fist-sized prototype magnet has been constructed of Nd-Fe-B material with remanent magnetization of 1.2T. The prototype is about 4 cm long and has 2 cm clearance. Its 20 ppm homogeneous imaging region is 1 x 1.5 x 2.2 mm, with a field strength similar to that of a remanence value. The design may be scaled to the application of interest. Recent results and data will be shown.

References:

1. M.G.Abele, "Structures of Permanent Magnets", John Willey & Sons, Inc., New York, 1993.

210
Session Assigned: W&Th P
Title: NMR and MRI Superconductive Magnets : an Analysis Method of Active Shielding Efficiency

Institute: UNIVERSITE CLAUDE BERNARD -LYON I, FRANCE
Keywords: magnets, active shielding, stray field
Abstract:
An actively shielded, superconducting magnet for NMR or MRI has an inner coil system and an outer coil system supplied with current of opposite polarities in order to achieve a very efficient stray field limitation. The magnet remains then compact and lightweight and a shielded room for containment of magnetic fringe fields is no more needed.

On the other hand, a conventional superconducting magnet used in persistent mode provides a good rejection of low frequency external magnetic fields, because of the conservation of the total magnetic flux. The shielding factor associated with this rejection of magnetic field fluctuation is then high.

The main drawback of short-circuited actively shielded magnets is the drastic reduction of this shielding factor and hence the poor compensation of externally generated field variations.

The method to compute these shielding factors will be described. We will present several applications using computer generated field maps in order to assess the stray field suppression. Self-inductance and flux computations will be presented as well as shielding factors derivations for different magnetic configurations in order to clearly illustrate and compare the different solutions.

211
Session Assigned: W&Th P
Title: How Stable under the (Active) Shield ?

Institute: Carnegie Mellon University, Pittsburgh, Pa, USA
Keywords:
Abstract:
The availability of a new generation of superconducting magnets with active shielding dramatically lessens the demands on NMR lab siting. There is, though, a concern about their stability. Our recent experience with 600 MHz systems employing such actively shielded magnets is very encouraging. Spectra will be presented showing excellent field stability and homogeneity stability after an "aging" period.

212
Session Assigned: W&Th P
Title: Stand-alone Point-to-Point Mapping and Shimming System with Ultrasonic Motors

Institute: JEOL Ltd. Akishima, Tokyo, Japan
Keywords: shim mapping shimming
Abstract:
A stand-alone magnetic field mapping and shimming system has been developed to set 44 shim values by moving two micro samples from point to point. The spectral frequency of Fourier transformed ¹H signal is related to the magnetic field at the sample position.

The samples are moved by two computer-controlled, nonmagnetic ultrasonic motors. This makes the mechanical driving unit simple and decreases the risk of failure from repeated operations. A commercial spectrometer was adapted for the NMR signal measurement.

A large number of measurement positions is needed to represent the many terms in the field analysis and precise mapping over wide distance is needed for high order term analysis (n = 5,6,... or m = 3,4,...). The high order terms become large and change rapidly at positions far from the origin. One sample is moved along the center axis of RT shim coil for axial mapping and the other sample is moved on the cylindrical plane of the center axis (radius 7.5 mm) for radial mapping. The shimming system has following features.

The range of axial direction is 0-100 mm and the range of radial direction is 0-360 deg. The position accuracy of each direction is 0.1 mm and 0.2 deg . A typical mapping speed is 2 s/point. The mapping sample is doped water (half width 10 Hz). The field range is 270-800 MHz.

Optimized values of shims are determined from the analysis of mapping result by a least squares method. In practice, moving 40 mm in axial direction and 900 points in 30 min is sufficient for precise analysis and shimming for 44 field terms.

213
Session Assigned: W&Th P
Title: Gradient Amplifier Design using Power Operational Amplifiers

Institute: Penn State University, University Park, PA USA
Keywords: Gradient amplifier, power operational amplifier, defined rise-time
Abstract:
The development of small MRI systems for research laboratories presents the need for low-cost gradient amplifiers. We developed an inexpensive gradient system that uses a single power operational amplifier per channel. Using an external +/-50 V power supply, the amplifier can achieve a 20 &micro;s rise-time for a gradient coil of 0.5 Ohms and 150 &micro;H. This rise-time is thirty times smaller than that obtained by applying a step change in voltage across the gradient coil. The reduction in rise-time is achieved by incorporating the gradient coil in a feedback loop that shapes the current response by controlling the voltage applied across the gradient coil. The theory and equations that describe the operation of the amplifier are presented along with experimentally measured electrical characteristics of the system.

214
Session Assigned: W&Th P
Title: An Inquiry into the Thermal Nature of NMR

Institute: The Ohio State University
Keywords:
Abstract:
Recently, it was reported that the amount of RF power required for a 90 degree spin excitation in the human head on a whole body 8 Tesla system is much less than predicted by NMR theory (NMR Biomed. 11, 263-265, 1998). In order to evaluate the consistency of this finding with our current understanding of magnetic resonance, we have decided to measure the power density spectrum of liquids using a high resolution spectrometer and a homemade saddle coil. In part, we have undertaken this task since this early report claimed that these findings could be explained based on the thermal nature of NMR, Planck blackbody radiation and thermodynamics principles. We observed that the power density spectrum measured from 40-400 MHz through the ramping of a high resolution magnet, did indeed demonstrate a maximum in RF power near 200 MHz. RF power was substantially reduced at 400 MHz. Most importantly, we report the following noteworthy findings at 200 MHz. First, that the use of a radiation shield surrounding the RF coil has the effect of making the 180 degree pulse independent on sample volume. Consequently, whether the sample holder is filled with about 10 cc of water, or containing only a few microliters of water (in a capillary), the 180 degree pulse length did not change and remained constant at 38 usec. Even if the glass sample holder was removed and only the capillary remained, the 180 degree pulse length was 38 usec. When the radiation shield was removed, the 180 degree pulse length did not change when examining only the capillary and the sample holder. However, the 180 degree pulse length increased to 70 usec when the sample holder was filled with water. Most importantly, when the temperature of water was increased from room temperature (as above) to near boiling, the 180 degree pulse length decreased from 70 usec to less than 50 usec. None of the aforementioned results could be explained by changes in the q value of the coil. This appears to be firm confirmation that a thermal process is involved.