Theoretical NMR correlations based Structure Discussion.

PubMed

Junker, Jochen

2011-07-28

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

An Accessible Two-Dimensional Solution Nuclear Magnetic Resonance Experiment on Human Ubiquitin

ERIC Educational Resources Information Center

Rovnyak, David; Thompson, Laura E.

2005-01-01

Solution-state nuclear magnetic resonance (NMR) is an invaluable tool in structural and molecular biology research, but may be underutilized in undergraduate laboratories because instrumentation for performing structural studies of macromolecules in aqueous solutions is not yet widely available for use in undergraduate laboratories. We have…

A closer look at the nitrogen next door: 1H-15N NMR methods for glycosaminoglycan structural characterization

NASA Astrophysics Data System (ADS)

Langeslay, Derek J.; Beni, Szabolcs; Larive, Cynthia K.

2012-03-01

Recently, experimental conditions were presented for the detection of the N-sulfoglucosamine (GlcNS) NHSO3- or sulfamate 1H and 15N NMR resonances of the pharmaceutically and biologically important glycosaminoglycan (GAG) heparin in aqueous solution. In the present work, we explore further the applicability of nitrogen-bound proton detection to provide structural information for GAGs. Compared to the detection of 15N chemical shifts of aminosugars through long-range couplings using the IMPACT-HNMBC pulse sequence, the more sensitive two-dimensional 1H-15N HSQC-TOCSY experiments provided additional structural data. The IMPACT-HNMBC experiment remains a powerful tool as demonstrated by the spectrum measured for the unsubstituted amine of 3-O-sulfoglucosamine (GlcN(3S)), which cannot be observed with the 1H-15N HSQC-TOCSY experiment due to the fast exchange of the amino group protons with solvent. The 1H-15N HSQC-TOCSY NMR spectrum reported for the mixture of model compounds GlcNS and N-acetylglucosamine (GlcNAc) demonstrate the broad utility of this approach. Measurements for the synthetic pentasaccharide drug Arixtra® (Fondaparinux sodium) in aqueous solution illustrate the power of this NMR pulse sequence for structural characterization of highly similar N-sulfoglucosamine residues in GAG-derived oligosaccharides.

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

PubMed Central

Huang, Rui; Ripstein, Zev A.; Augustyniak, Rafal; Lazniewski, Michal; Ginalski, Krzysztof; Kay, Lewis E.; Rubinstein, John L.

2016-01-01

The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded. PMID:27402735

Solution NMR Spectroscopy for the Study of Enzyme Allostery

PubMed Central

Lisi, George P.; Loria, J. Patrick

2016-01-01

Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery. PMID:26734986

Static and dynamic stereochemistry of the conformational atropisomers of tetra(o-tolyl)benzene.

PubMed

Lunazzi, Lodovico; Mazzanti, Andrea; Minzoni, Mirko

2005-11-25

[graph: see text] Whereas only one atropisomer of 1,2,4,5-tetra(o-tolyl)benzene was observed by X-ray diffraction in the solid, five conformational atropisomers were detected by low-temperature NMR in solution. Their structures were assigned by a combination of NOE experiments, solvent effect, and ab initio calculations. Variable temperature dynamic NMR and bidimensional EXSY experiments allowed the barrier for the interconversion of these atropisomers to be determined (deltaG(double dagger) = 15.3 kcal mol(-1)).

Magneto-optical contrast in liquid-state optically detected NMR spectroscopy

PubMed Central

Pagliero, Daniela; Meriles, Carlos A.

2011-01-01

We use optical Faraday rotation (OFR) to probe nuclear spins in real time at high-magnetic field in a range of diamagnetic sample fluids. Comparison of OFR-detected NMR spectra reveals a correlation between the relative signal amplitude and the fluid Verdet constant, which we interpret as a manifestation of the variable detuning between the probe beam and the sample optical transitions. The analysis of chemical-shift-resolved, optically detected spectra allows us to set constraints on the relative amplitudes of hyperfine coupling constants, both for protons at chemically distinct sites and other lower-gyromagnetic-ratio nuclei including carbon, fluorine, and phosphorous. By considering a model binary mixture we observe a complex dependence of the optical response on the relative concentration, suggesting that the present approach is sensitive to the solvent-solute dynamics in ways complementary to those known in inductive NMR. Extension of these experiments may find application in solvent suppression protocols, sensitivity-enhanced NMR of metalloproteins in solution, the investigation of solvent-solute interactions, or the characterization of molecular orbitals in diamagnetic systems. PMID:22100736

Parsimony and goodness-of-fit in multi-dimensional NMR inversion

NASA Astrophysics Data System (ADS)

Babak, Petro; Kryuchkov, Sergey; Kantzas, Apostolos

2017-01-01

Multi-dimensional nuclear magnetic resonance (NMR) experiments are often used for study of molecular structure and dynamics of matter in core analysis and reservoir evaluation. Industrial applications of multi-dimensional NMR involve a high-dimensional measurement dataset with complicated correlation structure and require rapid and stable inversion algorithms from the time domain to the relaxation rate and/or diffusion domains. In practice, applying existing inverse algorithms with a large number of parameter values leads to an infinite number of solutions with a reasonable fit to the NMR data. The interpretation of such variability of multiple solutions and selection of the most appropriate solution could be a very complex problem. In most cases the characteristics of materials have sparse signatures, and investigators would like to distinguish the most significant relaxation and diffusion values of the materials. To produce an easy to interpret and unique NMR distribution with the finite number of the principal parameter values, we introduce a new method for NMR inversion. The method is constructed based on the trade-off between the conventional goodness-of-fit approach to multivariate data and the principle of parsimony guaranteeing inversion with the least number of parameter values. We suggest performing the inversion of NMR data using the forward stepwise regression selection algorithm. To account for the trade-off between goodness-of-fit and parsimony, the objective function is selected based on Akaike Information Criterion (AIC). The performance of the developed multi-dimensional NMR inversion method and its comparison with conventional methods are illustrated using real data for samples with bitumen, water and clay.

Solution structure of an antifreeze protein CfAFP-501 from Choristoneura fumiferana.

PubMed

Li, Congmin; Guo, Xianrong; Jia, Zongchao; Xia, Bin; Jin, Changwen

2005-07-01

Antifreeze proteins (AFPs) are widely employed by various organisms as part of their overwintering survival strategy. AFPs have the unique ability to suppress the freezing point of aqueous solution and inhibit ice recrystallization through binding to the ice seed crystals and restricting their growth. The solution structure of CfAFP-501 from spruce budworm has been determined by NMR spectroscopy. Our result demonstrates that CfAFP-501 retains its rigid and highly regular structure in solution. Overall, the solution structure is similar to the crystal structure except the N- and C-terminal regions. NMR spin-relaxation experiments further indicate the overall rigidity of the protein and identify a collection of residues with greater flexibilities. Furthermore, Pro91 shows a cis conformation in solution instead of the trans conformation determined in the crystal structure.

Synthesis of Polystyrene and Molecular Weight Determination by [superscript 1]H NMR End-Group Analysis

ERIC Educational Resources Information Center

Wackerly, Jay Wm.; Dunne, James F.

2017-01-01

A procedure for the solution polymerization of styrene using di-"tert"-butyl peroxide (DTBP) as the initiator is described. The use of DTBP allows for end-group analysis by [superscript 1]H NMR spectroscopy and calculation of the number-average molecular weight of the polymer. This experiment was designed as a laboratory introduction to…

Improved Spin-Echo-Edited NMR Diffusion Measurements

NASA Astrophysics Data System (ADS)

Otto, William H.; Larive, Cynthia K.

2001-12-01

The need for simple and robust schemes for the analysis of ligand-protein binding has resulted in the development of diffusion-based NMR techniques that can be used to assay binding in protein solutions containing a mixture of several ligands. As a means of gaining spectral selectivity in NMR diffusion measurements, a simple experiment, the gradient modified spin-echo (GOSE), has been developed to reject the resonances of coupled spins and detect only the singlets in the 1H NMR spectrum. This is accomplished by first using a spin echo to null the resonances of the coupled spins. Following the spin echo, the singlet magnetization is flipped out of the transverse plane and a dephasing gradient is applied to reduce the spectral artifacts resulting from incomplete cancellation of the J-coupled resonances. The resulting modular sequence is combined here with the BPPSTE pulse sequence; however, it could be easily incorporated into any pulse sequence where additional spectral selectivity is desired. Results obtained with the GOSE-BPPSTE pulse sequence are compared with those obtained with the BPPSTE and CPMG-BPPSTE experiments for a mixture containing the ligands resorcinol and tryptophan in a solution of human serum albumin.

Using NMR to Determine the Boiling Point Diagram for a Non-Ideal Solution

ERIC Educational Resources Information Center

Allen, Fritz S.; And Others

1975-01-01

Describes an experiment that enables the student to concentrate on the fundamentals of the non-ideal liquid-vapor equilibrium. Presents typical student data and suggests features which might be added to the experiment. (GS)

Structural analysis of geochemical samples by solid-state nuclear magnetic resonance spectrometry. Role of paramagnetic material

USGS Publications Warehouse

Vassallo, A.M.; Wilson, M.A.; Collin, P.J.; Oades, J.M.; Waters, A.G.; Malcolm, R.L.

1987-01-01

An examination of coals, coal tars, a fulvic acid, and soil fractions by solid-state 13C NMR spectrometry has demonstrated widely differing behavior regarding quantitative representation in the spectrum. Spin counting experiments on coal tars and the fulvic acid show that almost all the sample carbon is observed in both solution and solid-state NMR spectra. Similar experiments on two coals (a lignite and a bituminous coal) show that most (70-97%) of the carbon is observed; however, when the lignite is ion exchanged with 3% (w/w) Fe3+, the fraction of carbon observed drops to below 10%. In additional experiments signal intensity from soil samples is enhanced by a simple dithionite treatment. This is illustrated by 13C, 27Al, and 29Si solid-state NMR experiments on soil fractions. ?? 1987 American Chemical Society.

Use of multi-coil parallel-gap resonators for co-registration EPR/NMR imaging

NASA Astrophysics Data System (ADS)

Kawada, Yuuki; Hirata, Hiroshi; Fujii, Hirodata

2007-01-01

This article reports experimental investigations on the use of RF resonators for continuous-wave electron paramagnetic resonance (cw-EPR) and proton nuclear magnetic resonance (NMR) imaging. We developed a composite resonator system with multi-coil parallel-gap resonators for co-registration EPR/NMR imaging. The resonance frequencies of each resonator were 21.8 MHz for NMR and 670 MHz for EPR. A smaller resonator (22 mm in diameter) for use in EPR was placed coaxially in a larger resonator (40 mm in diameter) for use in NMR. RF magnetic fields in the composite resonator system were visualized by measuring a homogeneous 4-hydroxy-2,2,6,6-tetramethyl-piperidinooxy (4-hydroxy-TEMPO) solution in a test tube. A phantom of five tubes containing distilled water and 4-hydroxy-TEMPO solution was also measured to demonstrate the potential usefulness of this composite resonator system in biomedical science. An image of unpaired electrons was obtained for 4-hydroxy-TEMPO in three tubes, and was successfully mapped on the proton image for five tubes. Technical problems in the implementation of a composite resonator system are discussed with regard to co-registration EPR/NMR imaging for animal experiments.

Transport Properties of Ibuprofen Encapsulated in Cyclodextrin Nanosponge Hydrogels: A Proton HR-MAS NMR Spectroscopy Study.

PubMed

Ferro, Monica; Castiglione, Franca; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco; Mele, Andrea

2016-08-15

The chemical cross-linking of β-cyclodextrin (β-CD) with ethylenediaminetetraacetic dianhydride (EDTA) led to branched polymers referred to as cyclodextrin nanosponges (CDNSEDTA). Two different preparations are described with 1:4 and 1:8 CD-EDTA molar ratios. The corresponding cross-linked polymers were contacted with 0.27 M aqueous solution of ibuprofen sodium salt (IP) leading to homogeneous, colorless, drug loaded hydrogels. The systems were characterized by high resolution magic angle spinning (HR-MAS) NMR spectroscopy. Pulsed field gradient spin echo (PGSE) NMR spectroscopy was used to determine the mean square displacement (MSD) of IP inside the polymeric gel at different observation times td. The data were further processed in order to study the time dependence of MSD: MSD = f(td). The proposed methodology is useful to characterize the different diffusion regimes that, in principle, the solute may experience inside the hydrogel, namely normal or anomalous diffusion. The full protocols including the polymer preparation and purification, the obtainment of drug-loaded hydrogels, the NMR sample preparation, the measurement of MSD by HR-MAS NMR spectroscopy and the final data processing to achieve the time dependence of MSD are here reported and discussed. The presented experiments represent a paradigmatic case and the data are discussed in terms of innovative approach to the characterization of the transport properties of an encapsulated guest within a polymeric host of potential application for drug delivery.

A general algorithm for peak-tracking in multi-dimensional NMR experiments.

PubMed

Ravel, P; Kister, G; Malliavin, T E; Delsuc, M A

2007-04-01

We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

PubMed Central

Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

2015-01-01

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC.

PubMed

Meier, Sebastian; Petersen, Bent O; Duus, Jens Ø; Sørensen, Ole W

2009-11-02

The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of (13)C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the (1)H spins, all in a single spectrum with good resolution and non-informative diagonal-type peaks suppressed. Clean HMBC is a remedy for the ubiquitous problem of strong coupling induced one-bond correlation artifacts in HMBC spectra of carbohydrates. Both experiments work well for one of the largest carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

Lee, Daniel; Chaudhari, Sachin R.; De Paëpe, Gaël

2017-05-01

Dynamic nuclear polarization (DNP) has become a powerful tool to substantially increase the sensitivity of high-field magic angle spinning (MAS) solid-state NMR experiments. The addition of dissolved hyperpolarizing agents usually results in the presence of solvent signals that can overlap and obscure those of interest from the analyte. Here, two methods are proposed to suppress DNP solvent signals: a Forced Echo Dephasing experiment (FEDex) and TRAnsfer of Populations in DOuble Resonance Echo Dephasing (TRAPDORED) NMR. These methods reintroduce a heteronuclear dipolar interaction that is specific to the solvent, thereby forcing a dephasing of recoupled solvent spins and leaving acquired NMR spectra free of associated resonance overlap with the analyte. The potency of these methods is demonstrated on sample types common to MAS-DNP experiments, namely a frozen solution (of L-proline) and a powdered solid (progesterone), both containing deuterated glycerol as a DNP solvent. The proposed methods are efficient, simple to implement, compatible with other NMR experiments, and extendable past spectral editing for just DNP solvents. The sensitivity gains from MAS-DNP in conjunction with FEDex or TRAPDORED then permits rapid and uninterrupted sample analysis.

Nuclear magnetic resonance studies of quadrupolar nuclei and dipolar field effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urban, Jeffry Todd

Experimental and theoretical research conducted in two areas in the field of nuclear magnetic resonance (NMR) spectroscopy is presented: (1) studies of the coherent quantum-mechanical control of the angular momentum dynamics of quadrupolar (spin I > 1/2) nuclei and its application to the determination of molecular structure; and (2) applications of the long-range nuclear dipolar field to novel NMR detection methodologies.The dissertation is organized into six chapters. The first two chapters and associated appendices are intended to be pedagogical and include an introduction to the quantum mechanical theory of pulsed NMR spectroscopy and the time dependent theory of quantum mechanics.more » The third chapter describes investigations of the solid-state multiple-quantum magic angle spinning (MQMAS) NMR experiment applied to I = 5/2 quadrupolar nuclei. This work reports the use of rotary resonance-matched radiofrequency irradiation for sensitivity enhancement of the I = 5/2 MQMAS experiment. These experiments exhibited certain selective line narrowing effects which were investigated theoretically.The fourth chapter extends the discussion of multiple quantum spectroscopy of quadrupolar nuclei to a mostly theoretical study of the feasibility of enhancing the resolution of nitrogen-14 NMR of large biomolecules in solution via double-quantum spectroscopy. The fifth chapter continues to extend the principles of multiple quantum NMR spectroscopy of quadrupolar nuclei to make analogies between experiments in NMR/nuclear quadrupolar resonance (NQR) and experiments in atomic/molecular optics (AMO). These analogies are made through the Hamiltonian and density operator formalism of angular momentum dynamics in the presence of electric and magnetic fields.The sixth chapter investigates the use of the macroscopic nuclear dipolar field to encode the NMR spectrum of an analyte nucleus indirectly in the magnetization of a sensor nucleus. This technique could potentially serve as an encoding module for the recently developed NMR remote detection experiment. The feasibility of using hyperpolarized xenon-129 gas as a sensor is discussed. This work also reports the use of an optical atomic magnetometer to detect the nuclear magnetization of Xe-129 gas, which has potential applicability as a detection module for NMR remote detection experiments.« less

A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

NASA Astrophysics Data System (ADS)

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff-based computation is employed in the scoring function to evaluate the probability of side-chain resonance assignments to generate the observed NMR spectra. The complexity of the assignment problem is first reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is used to find a set of optimal side-chain resonance assignments that best fit the NMR data. We have tested our algorithm on NMR data for five proteins, including the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), human ubiquitin, the ubiquitin-binding zinc finger domain of the human Y-family DNA polymerase Eta (pol η UBZ), and the human Set2-Rpb1 interacting domain (hSRI). Our algorithm assigns resonances for more than 90% of the protons in the proteins, and achieves about 80% correct side-chain resonance assignments. The final structures computed using distance restraints resulting from the set of assigned side-chain resonances have backbone RMSD 0.5 - 1.4 Å and all-heavy-atom RMSD 1.0 - 2.2 Å from the reference structures that were determined by X-ray crystallography or traditional NMR approaches. These results demonstrate that our algorithm can be successfully applied to automate side-chain resonance assignment and high-quality protein structure determination. Since our algorithm does not require any specific NMR experiments for measuring the through-bond interactions with side-chain protons, it can save a significant amount of both experimental cost and spectrometer time, and hence accelerate the NMR structure determination process.

NMR solution structure of the N-terminal domain of hERG and its interaction with the S4-S5 linker

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Qingxin; Gayen, Shovanlal; Chen, Angela Shuyi

Research highlights: {yields} The N-terminal domain (NTD, eag domain) containing 135 residues of hERG was expressed and purified from E. coli cells. {yields} Solution structure of NTD was determined with NMR spectroscopy. {yields} The alpha-helical region (residues 13-23) was demonstrated to possess the characteristics of an amphipathic helix. {yields} NMR titration confirmed the interaction between NTD and the peptide from the S4-S5 linker. -- Abstract: The human Ether-a-go-go Related Gene (hERG) potassium channel mediates the rapid delayed rectifier current (IKr) in the cardiac action potential. Mutations in the 135 amino acid residue N-terminal domain (NTD) cause channel dysfunction or mis-translocation.more » To study the structure of NTD, it was overexpressed and purified from Escherichia coli cells using affinity purification and gel filtration chromatography. The purified protein behaved as a monomer under purification conditions. Far- and near-UV, circular dichroism (CD) and solution nuclear magnetic resonance (NMR) studies showed that the purified protein was well-folded. The solution structure of NTD was obtained and the N-terminal residues 13-23 forming an amphipathic helix which may be important for the protein-protein or protein-membrane interactions. NMR titration experiment also demonstrated that residues from 88 to 94 in NTD are important for the molecular interaction with the peptide derived from the S4-S5 linker.« less

Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy

PubMed Central

Ramalhete, Susana M.; Nartowski, Karol P.; Sarathchandra, Nichola; Foster, Jamie S.; Round, Andrew N.; Angulo, Jesús

2017-01-01

Abstract Supramolecular hydrogels are composed of self‐assembled solid networks that restrict the flow of water. l‐Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi‐component hydrogels of l‐phenylalanine are used herein as model materials to develop an NMR‐based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid‐state NMR experiments and microscopic techniques. Solution‐state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high‐resolution magic angle spinning (HR‐MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties. PMID:28401991

Biomolecular solid state NMR with magic-angle spinning at 25K.

PubMed

Thurber, Kent R; Tycko, Robert

2008-12-01

A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution.

PubMed Central

Feigon, J; Wang, A H; van der Marel, G A; Van Boom, J H; Rich, A

1984-01-01

The deoxyribose hexanucleoside pentaphosphate (m5dC-dG)3 has been studied by 500 MHz 1H NMR in D2O (0.1 M NaCl) and in D2O/deuterated methanol mixtures. Two conformations, in slow equilibrium on the NMR time scale, were detected in methanolic solution. Two-dimensional nuclear Overhauser effect (NOE) experiments were used to assign the base and many of the sugar resonances as well as to determine structural features for both conformations. The results were consistent with the an equilibrium in solution between B-DNA and Z-DNA. The majority of the molecules have a B-DNA structure in low-salt D2O and a Z-DNA structure at high methanol concentrations. A cross-strand NOE between methyl groups on adjacent cytosines is observed for Z-DNA but not B-DNA. The B-DNA conformation predominates at low methanol concentrations and is stabilized by increasing temperature, while the Z-DNA conformation predominates at high methanol concentrations and low temperatures. 31P NMR spectra gave results consistent with those obtained by 1H NMR. Comparison of the 31P spectra with those obtained on poly(dG-m5dC) allow assignment of the lower field resonances to GpC in the Z conformation. PMID:6694910

Solid-state NMR spectroscopy of 18.5 kDa myelin basic protein reconstituted with lipid vesicles: spectroscopic characterisation and spectral assignments of solvent-exposed protein fragments.

PubMed

Zhong, Ligang; Bamm, Vladimir V; Ahmed, Mumdooh A M; Harauz, George; Ladizhansky, Vladimir

2007-12-01

Myelin basic protein (MBP, 18.5 kDa isoform) is a peripheral membrane protein that is essential for maintaining the structural integrity of the multilamellar myelin sheath of the central nervous system. Reconstitution of the most abundant 18.5 kDa MBP isoform with lipid vesicles yields an aggregated assembly mimicking the protein's natural environment, but which is not amenable to standard solution NMR spectroscopy. On the other hand, the mobility of MBP in such a system is variable, depends on the local strength of the protein-lipid interaction, and in general is of such a time scale that the dipolar interactions are averaged out. Here, we used a combination of solution and solid-state NMR (ssNMR) approaches: J-coupling-driven polarization transfers were combined with magic angle spinning and high-power decoupling to yield high-resolution spectra of the mobile fragments of 18.5 kDa murine MBP in membrane-associated form. To partially circumvent the problem of short transverse relaxation, we implemented three-dimensional constant-time correlation experiments (NCOCX, NCACX, CONCACX, and CAN(CO)CX) that were able to provide interresidue and intraresidue backbone correlations. These experiments resulted in partial spectral assignments for mobile fragments of the protein. Additional nuclear Overhauser effect spectroscopy (NOESY)-based experiments revealed that the mobile fragments were exposed to solvent and were likely located outside the lipid bilayer, or in its hydrophilic portion. Chemical shift index analysis showed that the fragments were largely disordered under these conditions. These combined approaches are applicable to ssNMR investigations of other peripheral membrane proteins reconstituted with lipids.

The NMR contribution to protein-protein networking in Fe-S protein maturation.

PubMed

Banci, Lucia; Camponeschi, Francesca; Ciofi-Baffoni, Simone; Piccioli, Mario

2018-03-22

Iron-sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe-S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe-2S], [3Fe-4S] and [4Fe-4S] clusters bound to proteins. After the first NMR structure of a paramagnetic protein was obtained for the reduced E. halophila HiPIP I, many NMR structures were determined for several Fe-S proteins in different oxidation states. It was found that differences in chemical shifts, in patterns of unobserved residues, in internal mobility and in thermodynamic stability are suitable data to map subtle changes between the two different oxidation states of the protein. Recently, the interaction networks responsible for maturing human mitochondrial and cytosolic Fe-S proteins have been largely characterized by combining solution NMR standard experiments with those tailored to paramagnetic systems. We show here the contribution of solution NMR in providing a detailed molecular view of "Fe-S interactomics". This contribution was particularly effective when protein-protein interactions are weak and transient, and thus difficult to be characterized at high resolution with other methodologies.

Development of a micro nuclear magnetic resonance system

NASA Astrophysics Data System (ADS)

Goloshevsky, Artem

Application of Nuclear Magnetic Resonance (NMR) to on-line/in-line control of industrial processes is currently limited by equipment costs and requirements for installation. A superconducting magnet generating strong fields is the most expensive part of a typical NMR instrument. In industrial environments, fringe magnetic fields make accommodation of NMR instruments difficult. However, a portable, low-cost and low-field magnetic resonance system can be used in virtually any environment. Development of a number of hardware components for a portable, low-cost NMR instrument is reported in this dissertation. Chapter one provides a discussion on a miniaturized Helmholtz spiral radio-frequency (RF) coil (average diameter equal to 3.5 mm) and an NMR probe built around a capillary (outer diameter = 1.59 mm and inner diameter = 1.02 mm) for flow imaging. Experiments of NMR spectroscopy, static and dynamic (flow) imaging, conducted with the use of the miniaturized coil, are described. Chapter two presents a microfabricated package of two biaxial gradient coils and a Helmholtz RF coil. Planar configuration of discrete wires was used to create magnetic field gradients. Performance of the microfabricated gradient coils while imaging water flow compared well with a commercial gradient set of much larger size. Chapter three reports on flow imaging experiments with power law fluids (aqueous solutions of sodium salt of carboxymethyl cellulose (CMC)) of different viscosities, carried out in the NMR probe with the miniaturized RF coil and capillary. Viscosities of the CMC solutions were determined based on the curve fits of the velocity profiles and simultaneous measurements of the flow rates. The curve fits were carried out according to the power law model equations. The NMR viscosity measurements compared well with measurements of the same CMC samples, performed on a conventional rotational rheometer. A portable, home-built transceiver, designed for NMR applications utilizing a miniaturized RF coil, is described in chapter four. The maximum RF power, occurring in the transceiver, was 21.5 dBm. Two transistor-transistor logic (TTL) switches functioned as an active duplexer. A quadrature detection scheme was used. The transceiver, combined with a filter/amplifier module, data acquisition (DAQ and RF generating PC boards, was successfully tested in NMR spectroscopy experiments at low magnetic field. It was demonstrated that, starting with the RF probe, a typical, large size NMR instrument can be miniaturized without impairment to the quality of the data. Such an instrument will be readily used in many industrial process control applications (e.g. for analysis of material properties and identification of chemicals).

NMR structure of biosynthetic engineered human insulin monomer B31(Lys)-B32(Arg) in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer.

PubMed

Bocian, Wojciech; Borowicz, Piotr; Mikołajczyk, Jerzy; Sitkowski, Jerzy; Tarnowska, Anna; Bednarek, Elzbieta; Głabski, Tadeusz; Tejchman-Małecka, Bozena; Bogiel, Monika; Kozerski, Lech

2008-10-01

A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, in H(2)O/CD(3)CN, 65/35 vol %, pH 3.6, is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55-64), that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. (c) 2008 Wiley Periodicals, Inc.

Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment.

PubMed

Ba, Yong; Mao, Yougang; Galdino, Luiz; Günsen, Zorigoo

2013-01-01

The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR microimaging experiment. The solutes studied include sodium chloride and glucose and the amino acids alanine, threonine, arginine, and aspartic acid. We found that the AFP is able to induce the bulk melting of the frozen AFP solutions at temperatures lower than 0 °C and can also keep the ice melted at higher temperatures in the AFP+solute solutions than those in the corresponding solute solutions. The latter shows that the ice phases were in super-heated states in the frozen AFP+solute solutions. We have tried to understand the first experimental phenomenon via the recent theoretical prediction that type I AFP can induce the local melting of ice upon adsorption to ice surfaces. The latter experimental phenomenon was explained with the hypothesis that the adsorption of AFP to ice surfaces introduces a less hydrophilic water-AFP-ice interfacial region, which repels the ionic/hydrophilic solutes. Thus, this interfacial region formed an intermediate chemical potential layer between the water phase and the ice phase, which prevented the transfer of water from the ice phase to the water phase. We have also attempted to understand the significance of the observed melting phenomena to the survival of organisms that express AFPs over cold winters.

Effects of CO2 injection and Kerogen Maturation on Low-Field Nuclear Magnetic Resonance Response

NASA Astrophysics Data System (ADS)

Prasad, M.; Livo, K.

2017-12-01

Low-field Nuclear Magnetic Resonance (NMR) is commonly used in petrophysical analysis of petroleum reservoir rocks. NMR experiments record the relaxation and polarization of in-situ hydrogen protons present in gaseous phases such as free-gas intervals and solution gas fluids, bulk fluid phases such as oil and aquifer intervals, and immovable fractions of kerogen and bitumen. Analysis of NMR relaxation spectra is performed to record how fluid composition, maturity, and viscosity change NMR experimental results. We present T1-T2 maps as thermal maturity of a water-saturated, sub-mature Woodford shale is increased at temperatures from 125 to 400 degrees Celsius. Experiments with applied fluid pressure in paraffinic mineral oil and DI water with varying fluid pH have been performed to mimic reservoir conditions in analysis of the relaxation of bulk fluid phases. We have recorded NMR spectra, T1-T2 maps, and fluid diffusion coefficients using a low-field (2 MHz) MagritekTM NMR. CO2 was injected at a pressure of 900 psi in an in house developed NMR pressure vessel made of torlon plastic. Observable 2D NMR shifts in immature kerogen formations as thermal maturity is increased show generation of lighter oils with increased maturity. CO2 injection leads to a decrease in bulk fluid relaxation time that is attributed to viscosity modification with gas presence. pH variation with increased CO2 presence were shown to not effect NMR spectra. From this, fluid properties have been shown to greatly affect NMR readings and must be taken into account for more accurate NMR reservoir characterization.

Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

PubMed

Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

2015-08-24

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective inclusion of PO4(3-) within persistent dimeric capsules of a tris(thiourea) receptor and evidence of cation/solvent sealed unimolecular capsules.

PubMed

Dey, Sandeep Kumar; Das, Gopal

2012-08-07

A tren-based tris(thiourea) receptor, L with electron-withdrawing p-nitrophenyl terminals has been established as a competent hydrogen-bonding scaffold that can selectively encapsulate PO(4)(3-) within persistent and rigid dimeric capsules, assembled by aromatic π-stacking interactions between the receptor side-arms. A quaternary ammonium salt of PO(4)(3-) capsules (complexes 1 and 1b, 2:1 host-guest) can reproducibly be obtained in quantitative yields by a solution-state deprotonation of [HL](+) moieties and a bound HPO(4)(2-) anion of complex 1a (HPO(4)(2-) complex of protonated L, 2:1 host-guest), induced by the presence of a large excess of anions such as HCO(3)(-), CH(3)CO(2)(-), and F(-). Qualitative as well as quantitative (1)H and (31)P NMR experiments (DMSO-d(6)) have been carried out in detail to demonstrate the selective and preferential inclusion of PO(4)(3-) by L in solution-states. Competitive crystallization experiments performed in the presence of an excess of anions such as HCO(3)(-), HSO(4)(-), CH(3)CO(2)(-), NO(3)(-) and halides (F(-) and Cl(-)) further establish the phenomenon of selective PO(4)(3-) encapsulation as confirmed by (1)H NMR, (31)P NMR, FT-IR and powder X-ray diffraction patterns of the isolated crystals. X-ray structural analyses and (31)P NMR studies of the isolated crystals of phosphate complexes (1, 1a and 1b) provide evidence of the binding discrepancy of inorganic phosphates with protonated and neutral form of L. Furthermore, extensive studies have been carried out with other anions of different sizes and dimensions in solid- and solution-states (complexes 2a, 3, 4 and 5). Crystal structure elucidation revealed the formation of a solvent (DMSO) sealed unimolecular capsule in the F(-) encapsulated complex, 2a (1:1 host-guest), a CO(3)(2-) encapsulated centrosymmetric molecular capsule in 3 (2:1 host-guest) and a cation (tetrabutylammonium) sealed SO(4)(2-) encapsulated unimolecular capsule in 4 (1:1 host-guest). 2D-NOESY NMR experiments carried out on these capsule complexes further confirm the relevant binding stoichiometry of complexes (2a-4) except for the PO(4)(3-)-encapsulated complex (1b) which showed a 1:1 host-guest stoichiometry in solution.

Organogold oligomers: Exploiting iClick and aurophilic cluster formation to prepare solution stable Au 4 repeating units

DOE PAGES

Yang, Xi; Wang, Shanshan; Ghiviriga, Ion; ...

2015-05-19

A novel synthetic method to create gold based metallo–oligomers/polymers via the combination of inorganic click (iClick) with intermolecular aurophilic interactions is demonstrated. Complexes [PEt 3Au] 4(μ-N 3C 2C 6H 5) (1) and [PPhMe 2Au] 43C 2C 6H 5) (2) and {[PEt 3Au] 4[(μ-N 3C 2) 2-9,9-dihexyl-9H-fluorene]} n (8) have been synthesized via iClick. The tetranuclear structures of 1 and 2, induced by aurophilic bonding, are confirmed in the solid state through single crystal X-ray diffraction experiments and in solution via variable temperature NMR spectroscopy. The extended 1D structure of 8 is constructed by aurophilic induced self-assembly. 1H DOSY NMR analysismore » reveals that the aurophilic bonds in 1, 2, and 8 are retained in the solution phase. The degree of polymerization within complex 8 is temperature and concentration dependent, as determined by 1H DOSY NMR. The complex 8 is a rare example of a solution stable higher ordered structure linked by aurophilic interactions.« less

A highly versatile automatized setup for quantitative measurements of PHIP enhancements

NASA Astrophysics Data System (ADS)

Kiryutin, Alexey S.; Sauer, Grit; Hadjiali, Sara; Yurkovskaya, Alexandra V.; Breitzke, Hergen; Buntkowsky, Gerd

2017-12-01

The design and application of a versatile and inexpensive experimental extension to NMR spectrometers is described that allows to carry out highly reproducible PHIP experiments directly in the NMR sample tube, i.e. under PASADENA condition, followed by the detection of the NMR spectra of hyperpolarized products with high spectral resolution. Employing this high resolution it is feasible to study kinetic processes in the solution with high accuracy. As a practical example the dissolution of hydrogen gas in the liquid and the PHIP kinetics during the hydrogenation reaction of Fmoc-O-propargyl-L-tyrosine in acetone-d6 are monitored. The timing of the setup is fully controlled by the pulse-programmer of the NMR spectrometer. By flushing with an inert gas it is possible to efficiently quench the hydrogenation reaction in a controlled fashion and to detect the relaxation of hyperpolarization without a background reaction. The proposed design makes it possible to carry out PHIP experiments in an automatic mode and reliably determine the enhancement of polarized signals.

Synthesis of Pyridine– and Pyrazine–BF 3 Complexes and Their Characterization in Solution and Solid State

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chénard, Etienne; Sutrisno, Andre; Zhu, Lingyang

2016-03-31

Following the discovery of the redox-active 1,4- bis-BF 3-quinoxaline complex, we undertook a structure- activity study with the objective to understand the active nature of the quinoxaline complex. Through systematic synthesis and characterization, we have compared complexes prepared from pyridine and pyrazine derivatives, as heterocyclic core analogues. This paper reports the structural requirements that give rise to the electrochemical features of the 1,4-bis-BF 3-quinoxaline adduct. Using solution and solidstate NMR spectroscopy, the role of aromatic ring fusion and nitrogen incorporation in bonding and electronics was elucidated. We establish the boron atom location and its interaction with its environment from 1Dmore » and 2D solution NMR, X-ray diffraction analysis, and 11B solid-state NMR experiments. Crystallographic analysis of single crystals helped to correlate the boron geometry with 11B quadrupolar coupling constant (CQ) and asymmetry parameter (ηQ), extracted from 11B solid-state NMR spectra. Additionally, computations based on density functional theory were performed to predict electrochemical behavior of the BF 3-heteroaromatic complexes. We then experimentally measured electrochemical potential using cyclic voltammetry and found that the redox potentials and CQ values are similarly affected by electronic changes in the complexes.« less

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide.

PubMed

Oktaviani, Nur Alia; Risør, Michael W; Lee, Young-Ho; Megens, Rik P; de Jong, Djurre H; Otten, Renee; Scheek, Ruud M; Enghild, Jan J; Nielsen, Niels Chr; Ikegami, Takahisa; Mulder, Frans A A

2015-06-01

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

MVAPACK: A Complete Data Handling Package for NMR Metabolomics

PubMed Central

2015-01-01

Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set. PMID:24576144

UV-vis, IR and 1H NMR spectroscopic studies and characterization of ionic-pair crystal violet-oxytetracycline

NASA Astrophysics Data System (ADS)

Orellana, Sandra; Soto, César; Toral, M. Inés

2010-01-01

The present study shows the formation and characterization of the ionic-pair between the antibiotic oxytetracycline and the dye crystal violet in ammonia solution pH 9.0 ± 0.2 extracted into chloroform. The characterization was demonstrated using UV-vis spectrophotometry, 1H NMR, measurement of relaxation times T1 and IR spectroscopy, using a comparison between the signals of individual pure compounds with the signals with the mixture CV-OTC in different alkaline media. The formation of ionic-pair was also corroborated by new signals and chemical shifts. (2D) NMR spectroscopy experiments show that the interaction is electrostatic.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xi; Wang, Shanshan; Ghiviriga, Ion

A novel synthetic method to create gold based metallo–oligomers/polymers via the combination of inorganic click (iClick) with intermolecular aurophilic interactions is demonstrated. Complexes [PEt 3Au] 4(μ-N 3C 2C 6H 5) (1) and [PPhMe 2Au] 43C 2C 6H 5) (2) and {[PEt 3Au] 4[(μ-N 3C 2) 2-9,9-dihexyl-9H-fluorene]} n (8) have been synthesized via iClick. The tetranuclear structures of 1 and 2, induced by aurophilic bonding, are confirmed in the solid state through single crystal X-ray diffraction experiments and in solution via variable temperature NMR spectroscopy. The extended 1D structure of 8 is constructed by aurophilic induced self-assembly. 1H DOSY NMR analysismore » reveals that the aurophilic bonds in 1, 2, and 8 are retained in the solution phase. The degree of polymerization within complex 8 is temperature and concentration dependent, as determined by 1H DOSY NMR. The complex 8 is a rare example of a solution stable higher ordered structure linked by aurophilic interactions.« less

Isotope Labeling for Solution and Solid-State NMR Spectroscopy of Membrane Proteins

PubMed Central

Verardi, Raffaello; Traaseth, Nathaniel J.; Masterson, Larry R.; Vostrikov, Vitaly V.; Veglia, Gianluigi

2013-01-01

In this chapter, we summarize the isotopic labeling strategies used to obtain high-quality solution and solid-state NMR spectra of biological samples, with emphasis on integral membrane proteins (IMPs). While solution NMR is used to study IMPs under fast tumbling conditions, such as in the presence of detergent micelles or isotropic bicelles, solid-state NMR is used to study the structure and orientation of IMPs in lipid vesicles and bilayers. In spite of the tremendous progress in biomolecular NMR spectroscopy, the homogeneity and overall quality of the sample is still a substantial obstacle to overcome. Isotopic labeling is a major avenue to simplify overlapped spectra by either diluting the NMR active nuclei or allowing the resonances to be separated in multiple dimensions. In the following we will discuss isotopic labeling approaches that have been successfully used in the study of IMPs by solution and solid-state NMR spectroscopy. PMID:23076578

Triple Resonance Solid State NMR Experiments with Reduced Dimensionality Evolution Periods

NASA Astrophysics Data System (ADS)

Astrof, Nathan S.; Lyon, Charles E.; Griffin, Robert G.

2001-10-01

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CON CA experiment establishes the correlation of 13Ci-1 to 13Cαi and 15Ni by simultaneously encoding the 13COi-1 and 15Ni chemical shifts. The CAN COCA experiment establishes the correlation 13Cai and 15COi to 13Cαi-1 and 15Ni-1 within a single experiment by simultaneous encoding of the 13Cαi and 15Ni chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.

Hydrogen bonds determine the signal arrangement in 13C NMR spectra of nicotinate

NASA Astrophysics Data System (ADS)

Gamov, G. A.; Kuranova, N. N.; Pogonin, A. E.; Aleksandriiskii, V. V.; Sharnin, V. A.

2018-02-01

Present work reports on studies of sodium nicotinate solutions in water and aqueous ethanol by means of 1H, 13C, 15N NMR spectroscopy. The H(2) nucleus was observed to be the least shielded among pyridine ring protons whilst C(6) signal placed in the lowest field in relation to the other pyridine carbons. The hydrogen bonds formation between nicotinate and water molecules was shown to be probable reason of signal arrangement in 13C NMR spectra of nicotinate. The heteronitrogen of nicotinate is less prone to the hydrogen bonding with water molecules than that of nicotinamide. The data on the change in the Gibbs energy of the nicotinate transfer and the results of the 13C NMR experiment are compared.

Nuclear magnetic resonance (NMR)-based metabolomics for cancer research.

PubMed

Ranjan, Renuka; Sinha, Neeraj

2018-05-07

Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research. Copyright © 2018 John Wiley & Sons, Ltd.

The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-binding Protein FepB*

PubMed Central

Chu, Byron C. H.; Otten, Renee; Krewulak, Karla D.; Mulder, Frans A. A.; Vogel, Hans J.

2014-01-01

The periplasmic binding protein (PBP) FepB plays a key role in transporting the catecholate siderophore ferric enterobactin from the outer to the inner membrane in Gram-negative bacteria. The solution structures of the 34-kDa apo- and holo-FepB from Escherichia coli, solved by NMR, represent the first solution structures determined for the type III class of PBPs. Unlike type I and II PBPs, which undergo large “Venus flytrap” conformational changes upon ligand binding, both forms of FepB maintain similar overall folds; however, binding of the ligand is accompanied by significant loop movements. Reverse methyl cross-saturation experiments corroborated chemical shift perturbation results and uniquely defined the binding pocket for gallium enterobactin (GaEnt). NMR relaxation experiments indicated that a flexible loop (residues 225–250) adopted a more rigid and extended conformation upon ligand binding, which positioned residues for optimal interactions with the ligand and the cytoplasmic membrane ABC transporter (FepCD), respectively. In conclusion, this work highlights the pivotal role that structural dynamics plays in ligand binding and transporter interactions in type III PBPs. PMID:25173704

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy

PubMed Central

Kheddo, Priscilla; Cliff, Matthew J.; Uddin, Shahid; van der Walle, Christopher F.; Golovanov, Alexander P.

2016-01-01

ABSTRACT Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins. PMID:27589351

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy.

PubMed

Kheddo, Priscilla; Cliff, Matthew J; Uddin, Shahid; van der Walle, Christopher F; Golovanov, Alexander P

2016-10-01

Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1 H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.

Studies of the Binding of Modest Modulators of the Human Enzyme, Sirtuin 6, by STD NMR.

PubMed

Bolívar, Beatriz E; Welch, John T

2017-05-18

Pyrazinamide (PZA), an essential constituent of short-course tuberculosis chemotherapy, binds weakly but selectively to Sirtuin 6 (SIRT6). Despite the structural similarities between nicotinamide (NAM), PZA, and pyrazinoic acid (POA), these inhibitors modulate SIRT6 by different mechanisms and through different binding sites, as suggested by saturation transfer difference (STD) NMR. Available experimental evidence, such as that derived from crystal structures and kinetic experiments, has been of only limited utility in elucidation of the mechanistic details of sirtuin inhibition by NAM or other inhibitors. For instance, crystallographic structural analysis of sirtuin binding sites does not help us understand important differences in binding affinities among sirtuins or capture details of such dynamic process. Hence, STD NMR was utilized throughout this study. Our results not only agreed with the binding kinetics experiments but also gave a qualitative insight into the binding process. The data presented herein suggested some details about the geometry of the binding epitopes of the ligands in solution with the apo- and holoenzyme. Recognition that SIRT6 is affected selectively by PZA, an established clinical agent, suggests that the rational development of more potent and selective NAM surrogates might be possible. These derivatives might be accessible by employing the malleability of this scaffold to assist in the identification by STD NMR of the motifs that interact with the apo- and holoenzymes in solution. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Egner, Timothy K.; Naik, Pranjali; Nelson, Nicholas C.

Engineering nanoparticle (NP) functions at the molecular level requires a detailed understanding of the dynamic processes occurring at the NP surface. Herein we show that a combination of dark-state exchange saturation transfer (DEST) and relaxation dispersion (RD) NMR experiments on gel-stabilized NP samples enables the accurate determination of the kinetics and thermodynamics of adsorption. We used the former approach to describe the interaction of cholic acid (CA) and phenol (PhOH) with ceria NPs with a diameter of approximately 200 nm. Whereas CA formed weak interactions with the NPs, PhOH was tightly bound to the NP surface. Interestingly, we found thatmore » the adsorption of PhOH proceeds via an intermediate, weakly bound state in which the small molecule has residual degrees of rotational diffusion. Here we believe the use of aqueous gels for stabilizing NP samples will increase the applicability of solution NMR methods to the characterization of nanomaterials.« less

Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel

DOE PAGES

Egner, Timothy K.; Naik, Pranjali; Nelson, Nicholas C.; ...

2017-06-22

Engineering nanoparticle (NP) functions at the molecular level requires a detailed understanding of the dynamic processes occurring at the NP surface. Herein we show that a combination of dark-state exchange saturation transfer (DEST) and relaxation dispersion (RD) NMR experiments on gel-stabilized NP samples enables the accurate determination of the kinetics and thermodynamics of adsorption. We used the former approach to describe the interaction of cholic acid (CA) and phenol (PhOH) with ceria NPs with a diameter of approximately 200 nm. Whereas CA formed weak interactions with the NPs, PhOH was tightly bound to the NP surface. Interestingly, we found thatmore » the adsorption of PhOH proceeds via an intermediate, weakly bound state in which the small molecule has residual degrees of rotational diffusion. Here we believe the use of aqueous gels for stabilizing NP samples will increase the applicability of solution NMR methods to the characterization of nanomaterials.« less

Using NMR Spectroscopy to Investigate the Solution Behavior of Nerve Agents and Their Binding to Acetylcholinesterase

DTIC Science & Technology

2016-01-01

USING NMR SPECTROSCOPY TO INVESTIGATE THE SOLUTION BEHAVIOR OF NERVE AGENTS AND THEIR BINDING TO...XX-01-2016 2. REPORT TYPE Final 3. DATES COVERED (From - To) Jan – Jun 2015 4. TITLE AND SUBTITLE Using NMR Spectroscopy to Investigate the...MOLECULAR MOTIONS AND NMR SPECTROSCOPY ...................................................................................................3 4. THE

Structure and Dynamics of Nonionic Surfactant Aggregates in Layered Materials.

PubMed

Guégan, Régis; Veron, Emmanuel; Le Forestier, Lydie; Ogawa, Makoto; Cadars, Sylvian

2017-09-26

The aggregation of surfactants on solid surfaces as they are adsorbed from solution is the basis of numerous technological applications such as colloidal stabilization, ore flotation, and floor cleaning. The understanding of both the structure and the dynamics of surfactant aggregates applies to the development of alternative ways of preparing hybrid layered materials. For this purpose, we study the adsorption of the triethylene glycol mono n-decyl ether (C 10 E 3 ) nonionic surfactant onto a synthetic montmorillonite (Mt), an aluminosilicate clay mineral for organoclay preparation with important applications in materials sciences, catalysis, wastewater treatment, or as drug delivery. The aggregation mechanisms follow those observed in an analogous natural Mt, with the condensation of C 10 E 3 in a bilayer arrangement once the surfactant self-assembles in a lamellar phase beyond the critical micelle concentration, underlining the importance of the surfactant state in solution. Solid-state 1 H nuclear magnetic resonance (NMR) at fast magic-angle spinning (MAS) and high magnetic field combined with 1 H- 13 C correlation experiments and different types of 13 C NMR experiments selectively probes mobile or rigid moieties of C 10 E 3 in three different aggregate organizations: (i) a lateral monolayer, (ii) a lateral bilayer, and (iii) a normal bilayer. High-resolution 1 H{ 27 Al} CP- 1 H- 1 H spin diffusion experiments shed light on the proximities and dynamics of the different fragments and fractions of the intercalated surfactant molecules with respect to the Mt surface. 23 Na and 1 H NMR measurements combined with complementary NMR data, at both molecular and nanometer scales, precisely pointed out the location of the C 10 E 3 ethylene oxide hydrophilic group in close contact with the Mt surface interacting through ion-dipole or van der Waals interactions.

High-field 95 Mo and 183 W static and MAS NMR study of polyoxometalates.

PubMed

Haouas, Mohamed; Trébosc, Julien; Roch-Marchal, Catherine; Cadot, Emmanuel; Taulelle, Francis; Martineau-Corcos, Charlotte

2017-10-01

The potential of high-field NMR to measure solid-state 95 Mo and 183 W NMR in polyoxometalates (POMs) is explored using some archetypical structures like Lindqvist, Keggin and Dawson as model compounds that are well characterized in solution. NMR spectra in static and under magic angle spinning (MAS) were obtained, and their analysis allowed extraction of the NMR parameters, including chemical shift anisotropy and quadrupolar coupling parameters. Despite the inherent difficulties of measurement in solid state of these low-gamma NMR nuclei, due mainly to the low spectral resolution and poor signal-to-noise ratio, the observed global trends compare well with the solution-state NMR data. This would open an avenue for application of solid-state NMR to POMs, especially when liquid-state NMR is not possible, e.g., for poorly soluble or unstable compounds in solution, and for giant molecules with slow tumbling motion. This is the case of Keplerate where we provide here the first NMR characterization of this class of POMs in the solid state. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Novel nuclear magnetic resonance techniques for studying biological molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laws, David Douglas

2000-06-01

Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. Inmore » this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13C a, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.« less

Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

PubMed

Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

2015-11-01

Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years. Copyright © 2015 John Wiley & Sons, Ltd.

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Li; Hanrahan, Michael P.; Chakravarty, Paroma

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is amore » powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.« less

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

DOE PAGES

Zhao, Li; Hanrahan, Michael P.; Chakravarty, Paroma; ...

2018-02-15

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is amore » powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.« less

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes

PubMed Central

Dias, David M.; Ciulli, Alessio

2014-01-01

Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets. PMID:25175337

Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

PubMed

Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

2010-12-08

Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

On the Analytical Superiority of 1D NMR for Fingerprinting the Higher Order Structure of Protein Therapeutics Compared to Multidimensional NMR Methods.

PubMed

Poppe, Leszek; Jordan, John B; Rogers, Gary; Schnier, Paul D

2015-06-02

An important aspect in the analytical characterization of protein therapeutics is the comprehensive characterization of higher order structure (HOS). Nuclear magnetic resonance (NMR) is arguably the most sensitive method for fingerprinting HOS of a protein in solution. Traditionally, (1)H-(15)N or (1)H-(13)C correlation spectra are used as a "structural fingerprint" of HOS. Here, we demonstrate that protein fingerprint by line shape enhancement (PROFILE), a 1D (1)H NMR spectroscopy fingerprinting approach, is superior to traditional two-dimensional methods using monoclonal antibody samples and a heavily glycosylated protein therapeutic (Epoetin Alfa). PROFILE generates a high resolution structural fingerprint of a therapeutic protein in a fraction of the time required for a 2D NMR experiment. The cross-correlation analysis of PROFILE spectra allows one to distinguish contributions from HOS vs protein heterogeneity, which is difficult to accomplish by 2D NMR. We demonstrate that the major analytical limitation of two-dimensional methods is poor selectivity, which renders these approaches problematic for the purpose of fingerprinting large biological macromolecules.

SIMPSON: A General Simulation Program for Solid-State NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Bak, Mads; Rasmussen, Jimmy T.; Nielsen, Niels Chr.

2000-12-01

A computer program for fast and accurate numerical simulation of solid-state NMR experiments is described. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, RF irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. These elements are implemented using the Tcl scripting language to ensure a minimum of programming overhead and direct interpretation without the need for compilation, while maintaining the flexibility of a full-featured programming language. Basicly, there are no intrinsic limitations to the number of spins, types of interactions, sample conditions (static or spinning, powders, uniaxially oriented molecules, single crystals, or solutions), and the complexity or number of spectral dimensions for the pulse sequence. The applicability ranges from simple 1D experiments to advanced multiple-pulse and multiple-dimensional experiments, series of simulations, parameter scans, complex data manipulation/visualization, and iterative fitting of simulated to experimental spectra. A major effort has been devoted to optimizing the computation speed using state-of-the-art algorithms for the time-consuming parts of the calculations implemented in the core of the program using the C programming language. Modification and maintenance of the program are facilitated by releasing the program as open source software (General Public License) currently at http://nmr.imsb.au.dk. The general features of the program are demonstrated by numerical simulations of various aspects for REDOR, rotational resonance, DRAMA, DRAWS, HORROR, C7, TEDOR, POST-C7, CW decoupling, TPPM, F-SLG, SLF, SEMA-CP, PISEMA, RFDR, QCPMG-MAS, and MQ-MAS experiments.

SIMPSON: A general simulation program for solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Bak, Mads; Rasmussen, Jimmy T.; Nielsen, Niels Chr.

2011-12-01

A computer program for fast and accurate numerical simulation of solid-state NMR experiments is described. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, RF irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. These elements are implemented using the Tel scripting language to ensure a minimum of programming overhead and direct interpretation without the need for compilation, while maintaining the flexibility of a full-featured programming language. Basicly, there are no intrinsic limitations to the number of spins, types of interactions, sample conditions (static or spinning, powders, uniaxially oriented molecules, single crystals, or solutions), and the complexity or number of spectral dimensions for the pulse sequence. The applicability ranges from simple ID experiments to advanced multiple-pulse and multiple-dimensional experiments, series of simulations, parameter scans, complex data manipulation/visualization, and iterative fitting of simulated to experimental spectra. A major effort has been devoted to optimizing the computation speed using state-of-the-art algorithms for the time-consuming parts of the calculations implemented in the core of the program using the C programming language. Modification and maintenance of the program are facilitated by releasing the program as open source software (General Public License) currently at http://nmr.imsb.au.dk. The general features of the program are demonstrated by numerical simulations of various aspects for REDOR, rotational resonance, DRAMA, DRAWS, HORROR, C7, TEDOR, POST-C7, CW decoupling, TPPM, F-SLG, SLF, SEMA-CP, PISEMA, RFDR, QCPMG-MAS, and MQ-MAS experiments.

Solution NMR Spectroscopy in Target-Based Drug Discovery.

PubMed

Li, Yan; Kang, Congbao

2017-08-23

Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

Gravity-driven pH adjustment for site-specific protein pKa measurement by solution-state NMR

NASA Astrophysics Data System (ADS)

Li, Wei

2017-12-01

To automate pH adjustment in site-specific protein pKa measurement by solution-state NMR, I present a funnel with two caps for the standard 5 mm NMR tube. The novelty of this simple-to-build and inexpensive apparatus is that it allows automatic gravity-driven pH adjustment within the magnet, and consequently results in a fully automated NMR-monitored pH titration without any hardware modification on the NMR spectrometer.

TDPAC and β-NMR applications in chemistry and biochemistry

NASA Astrophysics Data System (ADS)

Jancso, Attila; Correia, Joao G.; Gottberg, Alexander; Schell, Juliana; Stachura, Monika; Szunyogh, Dániel; Pallada, Stavroula; Lupascu, Doru C.; Kowalska, Magdalena; Hemmingsen, Lars

2017-06-01

Time differential perturbed angular correlation (TDPAC) of γ-rays spectroscopy has been applied in chemistry and biochemistry for decades. Herein we aim to present a comprehensive review of chemical and biochemical applications of TDPAC spectroscopy conducted at ISOLDE over the past 15 years, including elucidation of metal site structure and dynamics in proteins and model systems. β-NMR spectroscopy is well established in nuclear physics, solid state physics, and materials science, but only a limited number of applications in chemistry have appeared. Current endeavors at ISOLDE advancing applications of β-NMR towards chemistry and biochemistry are presented, including the first experiment on 31Mg2+ in an ionic liquid solution. Both techniques require the production of radioisotopes combined with advanced spectroscopic instrumentation present at ISOLDE.

Using solid 13C NMR coupled with solution 31P NMR spectroscopy to investigate molecular species and lability of organic carbon and phosphorus from aquatic plants in Tai Lake, China

USDA-ARS?s Scientific Manuscript database

Aquatic plants are involved in the storage and release capacity for organic matter and nutrients. In this study, solid 13C and solution 31P nuclear magnetic resonance (NMR) spectroscopy were used to characterize the biomass samples of six aquatic plants. Solid 13C NMR spectroscopy revealed the domin...

Analysis of the (Trimethylsilyl)propionic Acid-β(12-28) Peptide Binding Equilibrium with NMR Spectroscopy.

PubMed

Jayawickrama, D A; Larive, C K

1999-06-01

The binding of a small molecule, (trimethylsilyl)propionic acid (TSP), to a 17-residue peptide, β(12-28), is examined using (1)H NMR spectroscopy. β(12-28) (VHHQKLVFFAEDVGSNK) is a central fragment of the 40-42-residue Alzheimer's-associated Aβ peptide. This peptide has been previously shown to form soluble aggregates in low-pH aqueous solution. The TSP resonance is broadened appreciably in solutions containing relatively high concentrations (∼2 mM) of the peptide. The changes in TSP line width measured by titration of a peptide solution with TSP indicate a 1:1 binding stoichiometry. If the concentrations of both the peptide and TSP are reduced by 1 order of magnitude, the resonances of both species are sharp, suggesting that TSP binds predominately to the aggregated peptide. Nuclear Overhauser effect experiments indicate that the TSP interacts predominately with the side chains of the aliphatic peptide residues Leu(17) and Val(18). Pulsed-field gradient NMR measurements of TSP and peptide diffusion coefficients provide a more quantitative picture of the TSP-peptide binding equilibrium. The measured diffusion coefficients were used to calculate the fractions of the free and bound TSP. These results substantiate the conclusion that the stoichiometry of the TSP-peptide binding equilibrium is essentially 1:1 and further indicate anticooperative behavior in solutions containing an excess of TSP resulting in a dissociation of the peptide aggregates.

Evidence of formation of site-selective inclusion complexation between beta-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers.

PubMed

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M; Graham, Matthew J; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z D

2010-05-28

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with beta-cyclodextrin (beta-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state (13)C NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the beta-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in (13)C solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after beta-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of beta-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that beta-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using (1)H NMR, and a 3:1 (PO unit to beta-CD) was found for all inclusion complexes, which indicated that the number of threaded beta-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the beta-CD in the inclusion complex formed a channel-like structure that is different from the pure beta-CD crystal structure.

Evidence of formation of site-selective inclusion complexation between β-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers

NASA Astrophysics Data System (ADS)

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M.; Graham, Matthew J.; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z. D.

2010-05-01

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with β-cyclodextrin (β-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state C13 NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the β-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in C13 solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after β-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of β-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that β-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using H1 NMR, and a 3:1 (PO unit to β-CD) was found for all inclusion complexes, which indicated that the number of threaded β-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the β-CD in the inclusion complex formed a channel-like structure that is different from the pure β-CD crystal structure.

Human SLC26A4/Pendrin STAS domain is a nucleotide-binding protein: Refolding and characterization for structural studies.

PubMed

Sharma, Alok K; Krieger, Tobias; Rigby, Alan C; Zelikovic, Israel; Alper, Seth L

2016-12-01

Mutations in the human SLC26A4/Pendrin polypeptide (hPDS) cause Pendred Syndrome /DFNB4, syndromic deafness with enlargement of the vestibular aqueduct and low-penetrance goiter. Here we present data on cloning, protein overexpression and purification, refolding, and biophysical characterization of the recombinant hPDS STAS domain lacking its intrinsic variable sequence (STAS-ΔIVS). We report a reproducible protein refolding protocol enabling milligram scale expression and purification of uniformly 15 N- and 13 C /15 N-enriched hPDS STAS-ΔIVS domain suitable for structural characterization by solution NMR. Circular dichroism, one-dimensional 1 H, two-dimensional 1 H- 15 N HSQC, and 1 H- 13 C HSQC NMR spectra confirmed the well-folded state of purified hPDS STAS-ΔIVS in solution. Heteronuclear NMR chemical shift perturbation of select STAS-ΔIVS residues by GDP was observed at fast-to-intermediate NMR time scales. Intrinsic tryptophan fluorescence quench experiments demonstrated GDP binding to hPDS STAS-ΔIVS with K d of 178 μM. These results are useful for structure/function characterization of hPDS STAS, the cytoplasmic subdomain of the congenital deafness protein, pendrin, as well as for studies of other mammalian STAS domains.

[Ag115S34(SCH2C6H4 t Bu)47(dpph)6]: synthesis, crystal structure and NMR investigations of a soluble silver chalcogenide nanocluster.

PubMed

Bestgen, Sebastian; Fuhr, Olaf; Breitung, Ben; Kiran Chakravadhanula, Venkata Sei; Guthausen, Gisela; Hennrich, Frank; Yu, Wen; Kappes, Manfred M; Roesky, Peter W; Fenske, Dieter

2017-03-01

With the aim to synthesize soluble cluster molecules, the silver salt of (4-( tert -butyl)phenyl)methanethiol [AgSCH 2 C 6 H 4 t Bu] was applied as a suitable precursor for the formation of a nanoscale silver sulfide cluster. In the presence of 1,6-(diphenylphosphino)hexane (dpph), the 115 nuclear silver cluster [Ag 115 S 34 (SCH 2 C 6 H 4 t Bu) 47 (dpph) 6 ] was obtained. The molecular structure of this compound was elucidated by single crystal X-ray analysis and fully characterized by spectroscopic techniques. In contrast to most of the previously published cluster compounds with more than a hundred heavy atoms, this nanoscale inorganic molecule is soluble in organic solvents, which allowed a comprehensive investigation in solution by UV-Vis spectroscopy and one- and two-dimensional NMR spectroscopy including 31 P/ 109 Ag-HSQC and DOSY experiments. These are the first heteronuclear NMR investigations on coinage metal chalcogenides. They give some first insight into the behavior of nanoscale silver sulfide clusters in solution. Additionally, molecular weight determinations were performed by 2D analytical ultracentrifugation and HR-TEM investigations confirm the presence of size-homogeneous nanoparticles present in solution.

SIMPSON: a general simulation program for solid-state NMR spectroscopy.

PubMed

Bak, M; Rasmussen, J T; Nielsen, N C

2000-12-01

A computer program for fast and accurate numerical simulation of solid-state NMR experiments is described. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, RF irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. These elements are implemented using the Tcl scripting language to ensure a minimum of programming overhead and direct interpretation without the need for compilation, while maintaining the flexibility of a full-featured programming language. Basically, there are no intrinsic limitations to the number of spins, types of interactions, sample conditions (static or spinning, powders, uniaxially oriented molecules, single crystals, or solutions), and the complexity or number of spectral dimensions for the pulse sequence. The applicability ranges from simple 1D experiments to advanced multiple-pulse and multiple-dimensional experiments, series of simulations, parameter scans, complex data manipulation/visualization, and iterative fitting of simulated to experimental spectra. A major effort has been devoted to optimizing the computation speed using state-of-the-art algorithms for the time-consuming parts of the calculations implemented in the core of the program using the C programming language. Modification and maintenance of the program are facilitated by releasing the program as open source software (General Public License) currently at http://nmr.imsb.au.dk. The general features of the program are demonstrated by numerical simulations of various aspects for REDOR, rotational resonance, DRAMA, DRAWS, HORROR, C7, TEDOR, POST-C7, CW decoupling, TPPM, F-SLG, SLF, SEMA-CP, PISEMA, RFDR, QCPMG-MAS, and MQ-MAS experiments. Copyright 2000 Academic Press.

NMR 1D-imaging of water infiltration into mesoporous matrices.

PubMed

Le Feunteun, Steven; Diat, Olivier; Guillermo, Armel; Poulesquen, Arnaud; Podor, Renaud

2011-04-01

It is shown that coupling nuclear magnetic resonance (NMR) 1D-imaging with the measure of NMR relaxation times and self-diffusion coefficients can be a very powerful approach to investigate fluid infiltration into porous media. Such an experimental design was used to study the very slow seeping of pure water into hydrophobic materials. We consider here three model samples of nuclear waste conditioning matrices which consist in a dispersion of NaNO(3) (highly soluble) and/or BaSO(4) (poorly soluble) salt grains embedded in a bitumen matrix. Beyond studying the moisture progression according to the sample depth, we analyze the water NMR relaxation times and self-diffusion coefficients along its 1D-concentration profile to obtain spatially resolved information on the solution properties and on the porous structure at different scales. It is also shown that, when the relaxation or self-diffusion properties are multimodal, the 1D-profile of each water population is recovered. Three main levels of information were disclosed along the depth-profiles. They concern (i) the water uptake kinetics, (ii) the salinity and the molecular dynamics of the infiltrated solutions and (iii) the microstructure of the water-filled porosities: open networks coexisting with closed pores. All these findings were fully validated and enriched by NMR cryoporometry experiments and by performing environmental scanning electronic microscopy observations. Surprisingly, results clearly show that insoluble salts enhance the water progression and thereby increase the capability of the material to uptake water. Copyright © 2011 Elsevier Inc. All rights reserved.

Solution NMR views of dynamical ordering of biomacromolecules.

PubMed

Ikeya, Teppei; Ban, David; Lee, Donghan; Ito, Yutaka; Kato, Koichi; Griesinger, Christian

2018-02-01

To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Solution structures and backbone dynamics of Escherichia coli rhodanese PspE in its sulfur-free and persulfide-intermediate forms: implications for the catalytic mechanism of rhodanese.

PubMed

Li, Hongwei; Yang, Fan; Kang, Xue; Xia, Bin; Jin, Changwen

2008-04-15

Rhodanese catalyzes the sulfur-transfer reaction that transfers sulfur from thiosulfate to cyanide by a double-displacement mechanism, in which an active cysteine residue plays a central role. Previous studies indicated that the phage-shock protein E (PspE) from Escherichia coli is a rhodanese composed of a single active domain and is the only accessible rhodanese among the three single-domain rhodaneses in E. coli. To understand the catalytic mechanism of rhodanese at the molecular level, we determined the solution structures of the sulfur-free and persulfide-intermediate forms of PspE by nuclear magnetic resonance (NMR) spectroscopy and identified the active site by NMR titration experiments. To obtain further insights into the catalytic mechanism, we studied backbone dynamics by NMR relaxation experiments. Our results demonstrated that the overall structures in both sulfur-free and persulfide-intermediate forms are highly similar, suggesting that no significant conformational changes occurred during the catalytic reaction. However, the backbone dynamics revealed that the motional properties of PspE in its sulfur-free form are different from the persulfide-intermediate state. The conformational exchanges are largely enhanced in the persulfide-intermediate form of PspE, especially around the active site. The present structural and biochemical studies in combination with backbone dynamics provide further insights in understanding the catalytic mechanism of rhodanese.

High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pravdivtsev, Andrey N.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L., E-mail: ivanov@tomo.nsc.ru

2014-10-21

Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation timesmore » at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.« less

Determination of Unknown Concentrations of Sodium Acetate Using the Method of Standard Addition and Proton NMR: An Experiment for the Undergraduate Analytical Chemistry Laboratory

ERIC Educational Resources Information Center

Rajabzadeh, Massy

2012-01-01

In this experiment, students learn how to find the unknown concentration of sodium acetate using both the graphical treatment of standard addition and the standard addition equation. In the graphical treatment of standard addition, the peak area of the methyl peak in each of the sodium acetate standard solutions is found by integration using…

Characterization and elimination of undesirable protein residues in plant cell walls for enhancing lignin analysis by solution-state 2D gel-NMR methods

USDA-ARS?s Scientific Manuscript database

Proteins exist in every plant cell wall. Certain protein residues interfere with lignin characterization and quantification. The current solution-state 2D-NMR technique (gel-NMR) for whole plant cell wall structural profiling provides detailed information regarding cell walls and proteins. However, ...

NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes.

PubMed

Dias, David M; Ciulli, Alessio

2014-01-01

Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR.

PubMed

Sgourakis, Nikolaos G; May, Nathan A; Boyd, Lisa F; Ying, Jinfa; Bax, Ad; Margulies, David H

2015-11-27

As part of its strategy to evade detection by the host immune system, murine cytomegalovirus (MCMV) encodes three proteins that modulate cell surface expression of major histocompatibility complex class I (MHC-I) molecules: the MHC-I homolog m152/gp40 as well as the m02-m16 family members m04/gp34 and m06/gp48. Previous studies of the m04 protein revealed a divergent Ig-like fold that is unique to immunoevasins of the m02-m16 family. Here, we engineer and characterize recombinant m06 and investigate its interactions with full-length and truncated forms of the MHC-I molecule H2-L(d) by several techniques. Furthermore, we employ solution NMR to map the interaction footprint of the m06 protein on MHC-I, taking advantage of a truncated H2-L(d), "mini-H2-L(d)," consisting of only the α1α2 platform domain. Mini-H2-L(d) refolded in vitro with a high affinity peptide yields a molecule that shows outstanding NMR spectral features, permitting complete backbone assignments. These NMR-based studies reveal that m06 binds tightly to a discrete site located under the peptide-binding platform that partially overlaps with the β2-microglobulin interface on the MHC-I heavy chain, consistent with in vitro binding experiments showing significantly reduced complex formation between m06 and β2-microglobulin-associated MHC-I. Moreover, we carry out NMR relaxation experiments to characterize the picosecond-nanosecond dynamics of the free mini-H2-L(d) MHC-I molecule, revealing that the site of interaction is highly ordered. This study provides insight into the mechanism of the interaction of m06 with MHC-I, suggesting a structural manipulation of the target MHC-I molecule at an early stage of the peptide-loading pathway. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Citronellal assumes a folded conformation in solution due to dispersion interactions: A joint NMR-DFT analysis

NASA Astrophysics Data System (ADS)

Nardini, Viviani; Dias, Luis Gustavo; Palaretti, Vinicius; da Silva, Gil Valdo José

2018-04-01

Citronellal, an acyclic monoterpenoid, is a small molecule suitable for systematic scanning of its conformational geometric parameters in solution or in the gas phase. We have studied the conformational distribution of citronellal by correlating its structure and theoretical chemical shifts with nuclear magnetic resonance data. Interestingly, folded conformations were the most relevant, as confirmed by NOE experiments. We concluded that the conformational distribution is due to intramolecular dispersion interactions.

Identification of aquatically available carbon from algae through solution-state NMR of whole (13)C-labelled cells.

PubMed

Akhter, Mohammad; Dutta Majumdar, Rudraksha; Fortier-McGill, Blythe; Soong, Ronald; Liaghati-Mobarhan, Yalda; Simpson, Myrna; Arhonditsis, George; Schmidt, Sebastian; Heumann, Hermann; Simpson, André J

2016-06-01

Green algae and cyanobacteria are primary producers with profound impact on food web functioning. Both represent key carbon sources and sinks in the aquatic environment, helping modulate the dissolved organic matter balance and representing a potential biofuel source. Underlying the impact of algae and cyanobacteria on an ecosystem level is their molecular composition. Herein, intact (13)C-labelled whole cell suspensions of Chlamydomonas reinhardtii, Chlorella vulgaris and Synechocystis were studied using a variety of 1D and 2D (1)H/(13)C solution-state nuclear magnetic resonance (NMR) spectroscopic experiments. Solution-state NMR spectroscopy of whole cell suspensions is particularly relevant as it identifies species that are mobile (dissolved or dynamic gels), 'aquatically available' and directly contribute to the aquatic carbon pool upon lysis, death or become a readily available food source on consumption. In this study, a wide range of metabolites and structural components were identified within the whole cell suspensions. In addition, significant differences in the lipid/triacylglyceride (TAG) content of green algae and cyanobacteria were confirmed. Mobile species in algae are quite different from those in abundance in 'classic' dissolved organic matter (DOM) indicating that if algae are major contributors to DOM, considerable selective preservation of minor components (e.g. sterols) or biotransformation would have to occur. Identifying the metabolites and dissolved components within algal cells by NMR permits future studies of carbon transfer between species and through the food chain, whilst providing a foundation to better understand the role of algae in the formation of DOM and the sequestration/transformation of carbon in aquatic environments.

Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

R. James Kirkpatrick; Andrey G. Kalinichev

2008-11-25

Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches tomore » important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for significantly larger systems. These calculations have allowed us, for the first time, to study the effects of metal cations with different charges and charge density on the NOM aggregation in aqueous solutions. Other computational work has looked at the longer-time-scale dynamical behavior of aqueous species at mineral-water interfaces investigated simultaneously by NMR spectroscopy. Our experimental NMR studies have focused on understanding the structure and dynamics of water and dissolved species at mineral-water interfaces and in two-dimensional nano-confinement within clay interlayers. Combined NMR and MD study of H2O, Na+, and Cl- interactions with the surface of quartz has direct implications regarding interpretation of sum frequency vibrational spectroscopic experiments for this phase and will be an important reference for future studies. We also used NMR to examine the behavior of K+ and H2O in the interlayer and at the surfaces of the clay minerals hectorite and illite-rich illite-smectite. This the first time K+ dynamics has been characterized spectroscopically in geochemical systems. Preliminary experiments were also performed to evaluate the potential of 75As NMR as a probe of arsenic geochemical behavior. The 75As NMR study used advanced signal enhancement methods, introduced a new data acquisition approach to minimize the time investment in ultra-wide-line NMR experiments, and provides the first evidence of a strong relationship between the chemical shift and structural parameters for this experimentally challenging nucleus. We have also initiated a series of inelastic and quasi-elastic neutron scattering measurements of water dynamics in the interlayers of clays and layered double hydroxides. The objective of these experiments is to probe the correlations of water molecular motions in confined spaces over the scale of times and distances most directly comparable to our MD simulations and on a time scale different than that probed by NMR. This work is being done in collaboration with Drs. C.-K. Loong, N. de Souza, and A.I. Kolesnikov at the Intense Pulsed Neutron Source facility of the Argonne National Lab, and Dr. A. Faraone at the NIST Center for Neutron Research. A manuscript reporting the first results of these experiments, which are highly complimentary to our previous NMR, X-ray, and infra-red results for these phases, is currently in preparation. In total, in 2006-2007 our work has resulted in the publication of 14 peer-reviewed research papers. We also devoted considerable effort to making our work known to a wide range of researchers, as indicated by the 24 contributed abstracts and 14 invited presentations.« less

Flexible Stoichiometry and Asymmetry of the PIDDosome Core Complex by Heteronuclear NMR Spectroscopy and Mass Spectrometry

PubMed Central

Nematollahi, Lily A.; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V.; Driscoll, Paul C.

2015-01-01

Homotypic death domain (DD)–DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130–158 kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional 1H,15N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. 13C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640

The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments

PubMed Central

Chandak, Mahesh S; Nakamura, Takashi; Takenaka, Toshio; Chaudhuri, Tapan K; Yagi-Utsumi, Maho; Chen, Jin; Kato, Koichi; Kuwajima, Kunihiro

2013-01-01

Dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of proteins so far reported, lyophilization was used to remove D2O from the protein solution, and the lyophilized protein was dissolved in the DMSO solution to quench the H/D exchange reactions and to measure the amide proton signals by two-dimensional nuclear magnetic resonance (2D NMR) spectra. The denaturants or salts remaining after lyophilization thus prevent the measurement of good NMR spectra. In this article, we report that the use of spin desalting columns is a very effective alternative to lyophilization for the medium exchange from the D2O buffer to the DMSO solution. We show that the medium exchange by a spin desalting column takes only about 10 min in contrast to an overnight length of time required for lyophilization, and that the use of spin desalting columns has made it possible to monitor the H/D-exchange behavior of a fully unfolded protein in a concentrated denaturant. We report the results of unfolded ubiquitin in 6.0M guanidinium chloride. PMID:23339068

Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek

Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA,more » which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.« less

Solubilization of flurbiprofen within non-ionic Tween 20 surfactant micelles: a 19F and 1H NMR study.

PubMed

Saveyn, Pieter; Cocquyt, Ellen; Zhu, Wuxin; Sinnaeve, Davy; Haustraete, Katrien; Martins, José C; Van der Meeren, Paul

2009-07-14

The solubilization of the poorly water soluble anti-inflammatory drug flurbiprofen in non-ionic Tween 20 surfactant micellar solutions was studied by both (19)F and (1)H NMR spectroscopy in an acidic environment. These non-destructive techniques allowed us to investigate the effect of temperature cycling in situ. Using (19)F NMR, an increased solubilisation capacity was observed as the temperature increased. This effect became more pronounced above the cloud point, which was reduced by more than 30 degrees C in the presence of an excess of flurbiprofen. Upon clouding, peak splitting was observed in the (19)F spectrum, which indicates that two pools of solubilised flurbiprofen exist that are in slow exchange on the NMR frequency timescale. The clouding and solubilization processes were found to be reversible, albeit with slow kinetics. Based on chemical shift differences of both Tween 20 and flurbiprofen, as well as NOESY experiments, the flurbiprofen was found to be accumulated within the palisade layer of the Tween 20 micelles.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

High field hyperpolarization-EXSY experiment for fast determination of dissociation rates in SABRE complexes

NASA Astrophysics Data System (ADS)

Hermkens, Niels K. J.; Feiters, Martin C.; Rutjes, Floris P. J. T.; Wijmenga, Sybren S.; Tessari, Marco

2017-03-01

SABRE (Signal Amplification By Reversible Exchange) is a nuclear spin hyperpolarization technique based on the reversible concurrent binding of small molecules and para-hydrogen (p-H2) to an iridium metal complex in solution. At low magnetic field, spontaneous conversion of p-H2 spin order to enhanced longitudinal magnetization of the nuclear spins of the other ligands occurs. Subsequent complex dissociation results in hyperpolarized substrate molecules in solution. The lifetime of this complex plays a crucial role in attained SABRE NMR signal enhancements. Depending on the ligands, vastly different dissociation rates have been previously measured using EXSY or selective inversion experiments. However, both these approaches are generally time-consuming due to the long recycle delays (up to 2 min) necessary to reach thermal equilibrium for the nuclear spins of interest. In the cases of dilute solutions, signal averaging aggravates the problem, further extending the experimental time. Here, a new approach is proposed based on coherent hyperpolarization transfer to substrate protons in asymmetric complexes at high magnetic field. We have previously shown that such asymmetric complexes are important for application of SABRE to dilute substrates. Our results demonstrate that a series of high sensitivity EXSY spectra can be collected in a short experimental time thanks to the NMR signal enhancement and much shorter recycle delay.

Online structural elucidation of alkaloids and other constituents in crude extracts and cultured cells of Nandina domestica by combination of LC-MS/MS, LC-NMR, and LC-CD analyses.

PubMed

Iwasa, Kinuko; Takahashi, Teturo; Nishiyama, Yumi; Moriyasu, Masataka; Sugiura, Makiko; Takeuchi, Atsuko; Tode, Chisato; Tokuda, Harukuni; Takeda, Kazuyoshi

2008-08-01

The combination of NMR, MS, and CD data permitted the structural elucidation including the absolute configuration of the known alkaloids and unknown components in the extract matrix solution of Nandina domestica without isolation and sample purification prior to the coupling experiments. Unstable natural stereoisomers were identified by LC-NMR and LC-MS. Five known alkaloids, (S)-isoboldine, (S)-domesticine, (S)-nantenine, sinoacutine, and menispermine, were identified from N. domestica. O-Methylpallidine and (E, E)-, (E, Z)-, and (Z, Z)-terrestribisamide were also characterized for the first time from this plant. Known jatrorrhizine, palmatine, and berberine and unknown (R)-carnegine and (E, E)-, (E, Z)-, and (Z, Z)-terrestribisamide were identified in the callus of N. domestica.

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Characterization of nonderivatized plant cell walls using high-resolution solution-state NMR spectroscopy

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2008-01-01

A recently described plant cell wall dissolution system has been modified to use perdeuterated solvents to allow direct in-NMR-tube dissolution and high-resolution solution-state NMR of the whole cell wall without derivatization. Finely ground cell wall material dissolves in a solvent system containing dimethylsulfoxide-d6 and 1-methylimidazole-d6 in a ratio of 4:1 (v/...

Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 2, Non-catalyzed reactions with the wood cell wall

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2011-01-01

Solution-state NMR provides a powerful tool to observe the presence or absence of covalent bonds between wood and adhesives. Finely ground wood can be dissolved in an NMR compatible solvent system containing dimethylsulfoxide-d6 and N-methylimidazole-d6, in which the wood polymers remain largely intact. High-resolution...

A Routine Experimental Protocol for qHNMR Illustrated with Taxol⊥

PubMed Central

Pauli, Guido F.; Jaki, Birgit U.; Lankin, David C.

2012-01-01

Quantitative 1H NMR (qHNMR) provides a value-added dimension to the standard spectroscopic data set involved in structure analysis, especially when analyzing bioactive molecules and elucidating new natural products. The qHNMR method can be integrated into any routine qualitative workflow without much additional effort by simply establishing quantitative conditions for the standard solution 1H NMR experiments. Moreover, examination of different chemical lots of taxol and a Taxus brevifolia extract as working examples led to a blueprint for a generic approach to performing a routinely practiced 13C-decoupled qHNMR experiment, and for recognizing its potential and main limitations. The proposed protocol is based on a newly assembled 13C GARP broadband decoupled proton acquisition sequence that reduces spectroscopic complexity by removal of carbon satellites. The method is capable of providing qualitative and quantitative NMR data simultaneously and covers various analytes from pure compounds to complex mixtures such as metabolomes. Due to a routinely achievable dynamic range of 300:1 (0.3%) or better, qHNMR qualifies for applications ranging from reference standards to biologically active compounds to metabolome analysis. Providing a “cookbook” approach to qHNMR, acquisition conditions are described that can be adapted for contemporary NMR spectrometers of all major manufacturers. PMID:17298095

NMR-based conformational analysis of perezone and analogues.

PubMed

Zepeda, L Gerardo; Burgueño-Tapia, Eleuterio; Pérez-Hernández, Nury; Cuevas, Gabriel; Joseph-Nathan, Pedro

2013-04-01

Complete assignment of the (1)H NMR chemical shift and coupling constant values of perezone (1), O-methylperezone (2) and 6-hydroxyperezone (3) was carried out by total-line-shape-fitting calculations using the PERCH iterative spectra analysis software (PERCH Solutions Ltd., Kuopio, Finland). The resulting simulated spectra for the three compounds showed strong similarity to their corresponding experimental spectra. Particularly, all vicinal, allylic and homoallylic coupling constant values for the side chain of the three compounds were very similar, thus revealing that the conformation of these three molecules in solution is indeed almost identical. This fact is in agreement with extended side chain conformations over folded chain conformations because 1, 2 and 3 undergo completely different intramolecular cycloaddition reactions. In addition, results of double pulsed field gradient spin echo NOESY 1D experiments performed on perezone (1) were unable to provide evidence for folded conformers. Copyright © 2013 John Wiley & Sons, Ltd.

Combining Nuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations to Characterize Carvedilol Polymorphs.

PubMed

Rezende, Carlos A; San Gil, Rosane A S; Borré, Leandro B; Pires, José Ricardo; Vaiss, Viviane S; Resende, Jackson A L C; Leitão, Alexandre A; De Alencastro, Ricardo B; Leal, Katia Z

2016-09-01

The experiments of carvedilol form II, form III, and hydrate by (13)C and (15)N cross-polarization magic-angle spinning (CP MAS) are reported. The GIPAW (gauge-including projector-augmented wave) method from DFT (density functional theory) calculations was used to simulate (13)C and (15)N chemical shifts. A very good agreement was found for the comparison between the global results of experimental and calculated nuclear magnetic resonance (NMR) chemical shifts for carvedilol polymorphs. This work aims a comprehensive understanding of carvedilol crystalline forms employing solution and solid-state NMR as well as DFT calculations. Copyright © 2016. Published by Elsevier Inc.

Structural Changes Associated with Transthyretin Misfolding and Amyloid Formation Revealed by Solution and Solid-State NMR

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-03-21

Elucidation of structural changes involved in protein misfolding and amyloid formation is crucial for unraveling the molecular basis of amyloid formation. We report structural analyses of the amyloidogenic intermediate and amyloid aggregates of transthyretin using solution and solid-state nuclear magnetic resonance (NMR) spectroscopy. These NMR solution results show that one of the two main β-sheet structures (CBEF β-sheet) is maintained in the aggregation-competent intermediate, while the other DAGH β-sheet is more flexible on millisecond time scales. Magic-angle-spinning solid-state NMR revealed that AB loop regions interacting with strand A in the DAGH β-sheet undergo conformational changes, leading to the destabilized DAGHmore » β-sheet.« less

Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins.

PubMed

Jaremko, Matt J; Lee, D John; Patel, Ashay; Winslow, Victoria; Opella, Stanley J; McCammon, J Andrew; Burkart, Michael D

2017-10-10

In an effort to elucidate and engineer interactions in type II nonribosomal peptide synthetases, we analyzed biomolecular recognition between the essential peptidyl carrier proteins and adenylation domains using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics, and mutational studies. Three peptidyl carrier proteins, PigG, PltL, and RedO, in addition to their cognate adenylation domains, PigI, PltF, and RedM, were investigated for their cross-species activity. Of the three peptidyl carrier proteins, only PigG showed substantial cross-pathway activity. Characterization of the novel NMR solution structure of holo-PigG and molecular dynamics simulations of holo-PltL and holo-PigG revealed differences in structures and dynamics of these carrier proteins. NMR titration experiments revealed perturbations of the chemical shifts of the loop 1 residues of these peptidyl carrier proteins upon their interaction with the adenylation domain. These experiments revealed a key region for the protein-protein interaction. Mutational studies supported the role of loop 1 in molecular recognition, as mutations to this region of the peptidyl carrier proteins significantly modulated their activities.

Enantioselective complexation of chiral propylene oxide by an enantiopure water-soluble cryptophane.

PubMed

Bouchet, Aude; Brotin, Thierry; Linares, Mathieu; Ågren, Hans; Cavagnat, Dominique; Buffeteau, Thierry

2011-05-20

ECD and NMR experiments show that the complexation of propylene oxide (PrO) within the cavity of an enantiopure water-soluble cryptophane 1 in NaOH solution is enantioselective and that the (R)-PrO@PP-1 diastereomer is more stable than the (S)-PrO@PP-1 diastereomer with a free energy difference of 1.7 kJ/mol. This result has been confirmed by molecular dynamics (MD) and ab initio calculations. The enantioselectivity is preserved in LiOH and KOH solutions even though the binding constants decrease, whereas PrO is not complexed in CsOH solution.

Solid-state and solution /sup 13/C NMR in the conformational analysis of methadone-hydrochloride and related narcotic analgesics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sumner, S.C.J.

1986-01-01

Solid state and solution /sup 13/C NMR have been used to study the conformations of the racemic mixtures and single enantiomers of methadone hydrochloride, alpha and beta methadol hydrochloride, and alpha and beta acetylmethadol hydrochloride. The NMR spectra acquired for the compounds as solids, and in polar and nonpolar solvents are compared, in order to determine the conformation of the molecules in solution. To determine the reliability of assigning solution conformations by comparing solution and solid state chemical shift data, three bond coupling constants measured in solution are compared with those calculated from X-ray data. The conformations of the racemicmore » mixture and plus enantiomer of methadone hydrochloride have been shown to be very similar in the solid state, where minor differences in conformation can be seen by comparing NMR spectra obtained for the solids. Also shown is that the molecules of methadone hydrochloride have conformations in polar and in nonpolar solvents which are very similar to the conformation of the molecules in the solid state.« less

Utilizing a Water-Soluble Cryptophane with Fast Xenon Exchange Rates for Picomolar Sensitivity NMR Measurements

PubMed Central

Bai, Yubin; Hill, P. Aru; Dmochowski, Ivan J.

2012-01-01

Hyperpolarized 129Xe chemical exchange saturation transfer (129Xe Hyper-CEST) NMR is a powerful technique for the ultrasensitive, indirect detection of Xe host molecules (e.g., cryptophane-A). Irradiation at the appropriate Xe-cryptophane resonant radio frequency results in relaxation of the bound hyperpolarized 129Xe and rapid accumulation of depolarized 129Xe in bulk solution. The cryptophane effectively ‘catalyzes’ this process by providing a unique molecular environment for spin depolarization to occur, while allowing xenon exchange with the bulk solution during the hyperpolarized lifetime (T1 ≈ 1 min). Following this scheme, a triacetic acid cryptophane-A derivative (TAAC) was indirectly detected at 1.4 picomolar concentration at 320 K in aqueous solution, which is the record for a single-unit xenon host. To investigate this sensitivity enhancement, the xenon binding kinetics of TAAC in water was studied by NMR exchange lifetime measurement. At 297 K, kon ≈ 1.5 × 106 M−1s−1 and koff = 45 s−1, which represent the fastest Xe association and dissociation rates measured for a high-affinity, water-soluble xenon host molecule near rt. NMR linewidth measurements provided similar exchange rates at rt, which we assign to solvent-Xe exchange in TAAC. At 320 K, koff was estimated to be 1.1 × 103 s−1. In Hyper-CEST NMR experiments, the rate of 129Xe depolarization achieved by 14 pM TAAC in the presence of RF pulses was calculated to be 0.17 µM·s−1. On a per cryptophane basis, this equates to 1.2 × 104 129Xe atoms s−1 (or 4.6 × 104 Xe atoms s−1, all Xe isotopes), which is more than an order of magnitude faster than koff, the directly measurable Xe-TAAC exchange rate. This compels us to consider multiple Xe exchange processes for cryptophane-mediated bulk 129Xe depolarization, which provide at least 107-fold sensitivity enhancements over directly detected hyperpolarized 129Xe NMR signals. PMID:23106513

Flow-through lipid nanotube arrays for structure-function studies of membrane proteins by solid-state NMR spectroscopy.

PubMed

Chekmenev, Eduard Y; Gor'kov, Peter L; Cross, Timothy A; Alaouie, Ali M; Smirnov, Alex I

2006-10-15

A novel method for studying membrane proteins in a native lipid bilayer environment by solid-state NMR spectroscopy is described and tested. Anodic aluminum oxide (AAO) substrates with flow-through 175 nm wide and 60-mum-long nanopores were employed to form macroscopically aligned peptide-containing lipid bilayers that are fluid and highly hydrated. We demonstrate that the surfaces of both leaflets of such bilayers are fully accessible to aqueous solutes. Thus, high hydration levels as well as pH and desirable ion and/or drug concentrations could be easily maintained and modified as desired in a series of experiments with the same sample. The method allows for membrane protein NMR experiments in a broad pH range that could be extended to as low as 1 and as high as 12 units for a period of up to a few hours and temperatures as high as 70 degrees C without losing the lipid alignment or bilayers from the nanopores. We demonstrate the utility of this method by a solid-state 19.6 T (17)O NMR study of reversible binding effects of mono- and divalent ions on the chemical shift properties of the Leu(10) carbonyl oxygen of transmembrane pore-forming peptide gramicidin A (gA). We further compare the (17)O shifts induced by binding metal ions to the binding of protons in the pH range from 1 to 12 and find a significant difference. This unexpected result points to a difference in mechanisms for ion and proton conduction by the gA pore. We believe that a large number of solid-state NMR-based studies, including structure-function, drug screening, proton exchange, pH, and other titration experiments, will benefit significantly from the method described here.

Parameters and symbols for use in nuclear magnetic resonance (IUPAC recommendations 1997).

PubMed

Harris, R K; Kowalewski, J; Cabral de Menezes, S

1998-01-01

NMR is now frequently the technique of choice for the determination of chemical structure in solution. Its uses also span structure in solids and mobility at the molecular level in all phases. The research literature in the subject is vast and ever-increasing. Unfortunately, many articles do not contain sufficient information for experiments to be repeated elsewhere, and there are many variations in the usage of symbols for the same physical quantity. It is the aim of the present recommendations to provide simple check-lists that will enable such problems to be minimised in a way that is consistent with general IUPAC formulation. The area of medical NMR and imaging is not specifically addressed in these recommendations, which are principally aimed at the mainstream use of NMR by chemists (of all sub-disciplines) and by many physicists, biologists, materials scientists and geologists etc. working with NMR. The document presents recommended notation for use in journal publications involving a significant contribution of nuclear magnetic resonance (NMR) spectroscopy. The recommendations are in two parts: (1) Experimental parameters which should be listed so that the work in question can be repeated elsewhere. (2) A list of symbols (using Roman or Greek characters) to be used for quantities relevant to NMR.

NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vourtsis, Dionysios J.; Chasapis, Christos T.; Pairas, George

2014-07-18

Highlights: • A polypeptide, N-ALF{sub 233}, was overexpressed in E. coli and successfully isolated. • We produced {sup 2}H/{sup 15}N/{sup 13}C labeled protein samples. • Amino acid selective approaches were applied. • We acquired several heteronuclear NMR spectra, to complete the backbone assignment. • Prediction of the secondary structure was performed. - Abstract: NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successfulmore » overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.« less

Solution nuclear magnetic resonance spectroscopy on a nanostructured diamond chip.

PubMed

Kehayias, P; Jarmola, A; Mosavian, N; Fescenko, I; Benito, F M; Laraoui, A; Smits, J; Bougas, L; Budker, D; Neumann, A; Brueck, S R J; Acosta, V M

2017-08-04

Sensors using nitrogen-vacancy centers in diamond are a promising tool for small-volume nuclear magnetic resonance (NMR) spectroscopy, but the limited sensitivity remains a challenge. Here we show nearly two orders of magnitude improvement in concentration sensitivity over previous nitrogen-vacancy and picoliter NMR studies. We demonstrate NMR spectroscopy of picoliter-volume solutions using a nanostructured diamond chip with dense, high-aspect-ratio nanogratings, enhancing the surface area by 15 times. The nanograting sidewalls are doped with nitrogen-vacancies located a few nanometers from the diamond surface to detect the NMR spectrum of roughly 1 pl of fluid lying within adjacent nanograting grooves. We perform 1 H and 19 F nuclear magnetic resonance spectroscopy at room temperature in magnetic fields below 50 mT. Using a solution of CsF in glycerol, we determine that 4 ± 2 × 10 12 19 F spins in a 1 pl volume can be detected with a signal-to-noise ratio of 3 in 1 s of integration.Nitrogen vacancy (NV) centres in diamond can be used for NMR spectroscopy, but increased sensitivity is needed to avoid long measurement times. Kehayias et al. present a nanostructured diamond grating with a high density of NV centres, enabling NMR spectroscopy of picoliter-volume solutions.

Mechanisms of amyloid formation revealed by solution NMR

PubMed Central

Karamanos, Theodoros K.; Kalverda, Arnout P.; Thompson, Gary S.; Radford, Sheena E.

2015-01-01

Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein–protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology. PMID:26282197

Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Andrew Loyd

Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a βαβ-βαβ patternmore » of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition 15N T 1, T 2, and 15N/ 1H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone 1H, 13C, and 15N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and 15N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.« less

Multiphase flow experiments, mathematical modeling and numerical simulation of the water - gas - solute movement

NASA Astrophysics Data System (ADS)

Li, Y.; Ma, X.; Su, N.

2013-12-01

The movement of water and solute into and through the vadose zone is, in essence, an issue of immiscible displacement in pore-space network of a soil. Therefore, multiphase flow and transport in porous media, referring to three medium: air, water, and the solute, pose one of the largest unresolved challenges for porous medium fluid seepage. However, this phenomenon has always been largely neglected. It is expected that a reliable analysis model of the multi-phase flow in soil can truly reflect the process of natural movement about the infiltration, which is impossible to be observed directly. In such cases, geophysical applications of the nuclear magnetic resonance (NMR) provides the opportunity to measure the water movements into soils directly over a large scale from tiny pore to regional scale, accordingly enable it available both on the laboratory and on the field. In addition, the NMR provides useful information about the pore space properties. In this study, we proposed both laboratory and field experiments to measure the multi-phase flow parameters, together with optimize the model in computer programming based on the fractional partial differential equations (fPDE). In addition, we establish, for the first time, an infiltration model including solute flowing with water, which has huge influence on agriculture and soil environment pollution. Afterwards, with data collected from experiments, we simulate the model and analyze the spatial variability of parameters. Simulations are also conducted according to the model to evaluate the effects of airflow on water infiltration and other effects such as solute and absorption. It has significant meaning to oxygen irrigation aiming to higher crop yield, and shed more light into the dam slope stability. In summary, our framework is a first-time model added in solute to have a mathematic analysis with the fPDE and more instructive to agriculture activities.

How to tackle protein structural data from solution and solid state: An integrated approach.

PubMed

Carlon, Azzurra; Ravera, Enrico; Andrałojć, Witold; Parigi, Giacomo; Murshudov, Garib N; Luchinat, Claudio

2016-02-01

Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule. Copyright © 2016 Elsevier B.V. All rights reserved.

NMR investigation of the short-chain ionic surfactant-water systems.

PubMed

Popova, M V; Tchernyshev, Y S; Michel, D

2004-02-03

The structure and dynamics of surfactant molecules [CH3(CH2)7COOK] in heavy water solutions were investigated by 1H and 2H NMR. A double-exponential attenuation of the spin-echo amplitude in a Carr-Purcell-Meiboom-Gill experiment was found. We expect correspondence to both bounded and monomeric states. At high concentrations in the NMR self-diffusion measurements also a double-exponential decay of the spin-echo signal versus the square of the dc magnetic gradient was observed. The slow component of the diffusion process is caused by micellar aggregates, while the fast component is the result of the self-diffusion of the monomers through the micelles. The self-diffusion studies indicate that the form of micelles changes with increasing total surfactant concentration. The critical temperature range for self-association is reflected in the 1H transverse relaxation.

Characterization of Free Surface-Bound and Entrapped Water Environments in Poly(N-Isopropyl Acrylamide) Hydrogels via 1H HRMAS PFG NMR Spectroscopy

DOE PAGES

Alam, Todd Michael; Childress, Kimberly Kay; Pastoor, Kevin; ...

2014-09-19

We found that different water environments in poly(N-isopropyl acrylamide) (PNIPAAm) hydrogels are identified and characterized using 1H high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR). Local water environments corresponding to a “free” highly mobile species, along with waters showing restricted dynamics are resolved in these swollen hydro-gels. For photo-initiated polymerized PNIPAAm gels, an additional entrapped water species is observed. Spin–spin R 2 relaxation experiments support the argument of reduced mobility in the restricted and entrapped water species. Furthermore, by combining pulse field gradient techniques with HRMAS NMR it is possible to directly measure the self-diffusion rate for thesemore » different water environments. The behavior of the heterogeneous water environments through the lower critical solution temperature transition is described.« less

Collaborative development for setup, execution, sharing and analytics of complex NMR experiments.

PubMed

Irvine, Alistair G; Slynko, Vadim; Nikolaev, Yaroslav; Senthamarai, Russell R P; Pervushin, Konstantin

2014-02-01

Factory settings of NMR pulse sequences are rarely ideal for every scenario in which they are utilised. The optimisation of NMR experiments has for many years been performed locally, with implementations often specific to an individual spectrometer. Furthermore, these optimised experiments are normally retained solely for the use of an individual laboratory, spectrometer or even single user. Here we introduce a web-based service that provides a database for the deposition, annotation and optimisation of NMR experiments. The application uses a Wiki environment to enable the collaborative development of pulse sequences. It also provides a flexible mechanism to automatically generate NMR experiments from deposited sequences. Multidimensional NMR experiments of proteins and other macromolecules consume significant resources, in terms of both spectrometer time and effort required to analyse the results. Systematic analysis of simulated experiments can enable optimal allocation of NMR resources for structural analysis of proteins. Our web-based application (http://nmrplus.org) provides all the necessary information, includes the auxiliaries (waveforms, decoupling sequences etc.), for analysis of experiments by accurate numerical simulation of multidimensional NMR experiments. The online database of the NMR experiments, together with a systematic evaluation of their sensitivity, provides a framework for selection of the most efficient pulse sequences. The development of such a framework provides a basis for the collaborative optimisation of pulse sequences by the NMR community, with the benefits of this collective effort being available to the whole community. Copyright © 2013 Elsevier Inc. All rights reserved.

Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR) Methodology

PubMed Central

Wen, Jia-Long; Sun, Shao-Long; Xue, Bai-Liang; Sun, Run-Cang

2013-01-01

The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA), nitrobenzene oxidation (NBO), and derivatization followed by reductive cleavage (DFRC). Recent advances in nuclear magnetic resonance (NMR) technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ), as well as their applications are reviewed. PMID:28809313

High-resolution nuclear magnetic resonance measurements in inhomogeneous magnetic fields: A fast two-dimensional J-resolved experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yuqing; Cai, Shuhui; Yang, Yu

2016-03-14

High spectral resolution in nuclear magnetic resonance (NMR) is a prerequisite for achieving accurate information relevant to molecular structures and composition assignments. The continuous development of superconducting magnets guarantees strong and homogeneous static magnetic fields for satisfactory spectral resolution. However, there exist circumstances, such as measurements on biological tissues and heterogeneous chemical samples, where the field homogeneity is degraded and spectral line broadening seems inevitable. Here we propose an NMR method, named intermolecular zero-quantum coherence J-resolved spectroscopy (iZQC-JRES), to face the challenge of field inhomogeneity and obtain desired high-resolution two-dimensional J-resolved spectra with fast acquisition. Theoretical analyses for this methodmore » are given according to the intermolecular multiple-quantum coherence treatment. Experiments on (a) a simple chemical solution and (b) an aqueous solution of mixed metabolites under externally deshimmed fields, and on (c) a table grape sample with intrinsic field inhomogeneity from magnetic susceptibility variations demonstrate the feasibility and applicability of the iZQC-JRES method. The application of this method to inhomogeneous chemical and biological samples, maybe in vivo samples, appears promising.« less

Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2002-06-01

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.

Comparative NMR analysis of the decadeoxynucleotide d-(GCATTAATGC)2 and an analogue containing 2-aminoadenine.

PubMed Central

Chazin, W J; Rance, M; Chollet, A; Leupin, W

1991-01-01

The dodecadeoxynucleotide duplex d-(GCATTAATGC)2 has been prepared with all adenine bases replaced by 2-NH2-adenine. This modified duplex has been characterized by nuclear magnetic resonance (NMR) spectroscopy. Complete sequence-specific 1H resonance assignments have been obtained by using a variety of 2D NMR methods. Multiple quantum-filtered and multiple quantum experiments have been used to completely assign all sugar ring protons, including 5'H and 5'H resonances. The assignments form the basis for a detailed comparative analysis of the 1H NMR parameters of the modified and parent duplex. The structural features of both decamer duplexes in solution are characteristic of the B-DNA family. The spin-spin coupling constants in the sugar rings and the relative spatial proximities of protons in the bases and sugars (as determined from the comparison of corresponding nuclear Overhauser effects) are virtually identical in the parent and modified duplexes. Thus, substitution by this adenine analogue in oligonucleotides appears not to disturb the global or local conformation of the DNA duplex. PMID:1945828

The Use of Dodecylphosphocholine Micelles in Solution NMR

NASA Astrophysics Data System (ADS)

Kallick, D. A.; Tessmer, M. R.; Watts, C. R.; Li, C. Y.

Dodecylphosphocholine (DPC) micelles are useful as a model membrane system for solution NMR. Several new observations on dodecylphosphocholine micelles and their interactions with opioid peptides are described. The optimal lipid concentration has been investigated for small peptide NMR studies in DPC micelles for two opioid peptides, a 5-mer and a 17-mer. In contrast to reports in the literature, identical 2D spectra have been observed at low and high lipid concentrations. The chemical shift of resolved peptide proton resonances has been followed as a function of added lipid and indicates that there are changes in the chemical shifts above the critical micelle concentration and up to a ratio of 7:1 (lipid:peptide) for the 17-mer, and 9.6:1 for the 5-mer. These results suggest that conformational changes occur in the peptide significantly above the critical micelle concentration, up to a lipid:peptide ratio which is dependent upon the peptide, here ranging from 7:1 to 9.6:1. To address the stoichiometry more directly, the diffusion coefficients of the lipid alone and the lipid with peptide have been measured using pulsed-field gradient spin-echo NMR experiments. These data have been used to calculate the hydrodynamic radius and the aggregation number of the micelle with and without peptide and show that the aggregation number of the peptide-lipid complex increases at high lipid concentrations without a concomitant change in the peptide conformation. Last, several protonated impurities have been observed in the commercial preparation of DPC which resonate in the amide proton region of the NMR spectrum. These results are significant for researchers using DPC micelles and illustrate that both care in sample preparation and the stoichiometry are important issues with the use of DPC as a model membrane.

Proton NMR studies of functionalized nanoparticles in aqueous environments

NASA Astrophysics Data System (ADS)

Tataurova, Yulia Nikolaevna

Nanoscience is an emerging field that can provide potential routes towards addressing critical issues such as clean and sustainable energy, environmental remediation and human health. Specifically, porous nanomaterials, such as zeolites and mesoporous silica, are found in a wide range of applications including catalysis, drug delivery, imaging, environmental protection, and sensing. The characterization of the physical and chemical properties of nanocrystalline materials is essential to the realization of these innovative applications. The great advantage of porous nanocrystals is their increased external surface area that can control their biological, chemical and catalytic activities. Specific functional groups synthesized on the surface of nanoparticles are able to absorb heavy metals from the solution or target disease cells, such as cancer cells. In these studies, three main issues related to functionalized nanomaterials will be addressed through the application of nuclear magnetic resonance (NMR) techniques including: 1) surface composition and structure of functionalized nanocrystalline particles; 2) chemical properties of the guest molecules on the surface of nanomaterials, and 3) adsorption and reactivity of surface bound functional groups. Nuclear magnetic resonance (NMR) is one of the major spectroscopic techniques available for the characterization of molecular structure and conformational dynamics with atomic level detail. This thesis deals with the application of 1H solution state NMR to porous nanomaterial in an aqueous environment. Understanding the aqueous phase behavior of functionalized nanomaterials is a key factor in the design and development of safe nanomaterials because their interactions with living systems are always mediated through the aqueous phase. This is often due to a lack of fundamental knowledge in interfacial chemical and physical phenomena that occur on the surface of nanoparticles. The use of solution NMR spectroscopy results in high-resolution NMR spectra. This technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, 1H solution NMR spectroscopy was used to investigate the interface of the organic functional groups in D2O. The pKa for these functional groups covalently bound to the surface of nanoparticles was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The adsorption of toxic contaminants (chromate and arsenate anions) on the surface of functionalized silicalite-1 and mesoporous silica nanoparticles has been studied by 1H solution NMR spectroscopy. With this method, the surface bound contaminants are detected. The analysis of the intensity and position of these peaks allows quantitative assessment of the relative amounts of functional groups with adsorbed metal ions. These results demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups on porous nanomaterials.

High field hyperpolarization-EXSY experiment for fast determination of dissociation rates in SABRE complexes.

PubMed

Hermkens, Niels K J; Feiters, Martin C; Rutjes, Floris P J T; Wijmenga, Sybren S; Tessari, Marco

2017-03-01

SABRE (Signal Amplification By Reversible Exchange) is a nuclear spin hyperpolarization technique based on the reversible concurrent binding of small molecules and para-hydrogen (p-H 2 ) to an iridium metal complex in solution. At low magnetic field, spontaneous conversion of p-H 2 spin order to enhanced longitudinal magnetization of the nuclear spins of the other ligands occurs. Subsequent complex dissociation results in hyperpolarized substrate molecules in solution. The lifetime of this complex plays a crucial role in attained SABRE NMR signal enhancements. Depending on the ligands, vastly different dissociation rates have been previously measured using EXSY or selective inversion experiments. However, both these approaches are generally time-consuming due to the long recycle delays (up to 2min) necessary to reach thermal equilibrium for the nuclear spins of interest. In the cases of dilute solutions, signal averaging aggravates the problem, further extending the experimental time. Here, a new approach is proposed based on coherent hyperpolarization transfer to substrate protons in asymmetric complexes at high magnetic field. We have previously shown that such asymmetric complexes are important for application of SABRE to dilute substrates. Our results demonstrate that a series of high sensitivity EXSY spectra can be collected in a short experimental time thanks to the NMR signal enhancement and much shorter recycle delay. Copyright © 2017 Elsevier Inc. All rights reserved.

Dissolution of lignin in green urea aqueous solution

NASA Astrophysics Data System (ADS)

Wang, Jingyu; Li, Ying; Qiu, Xueqing; Liu, Di; Yang, Dongjie; Liu, Weifeng; Qian, Yong

2017-12-01

The dissolution problem is the main obstacle for the value-added modification and depolymerization of industrial lignin. Here, a green urea aqueous solution for complete dissolution of various lignin is presented and the dissolution mechanism is analyzed by AFM, DLS and NMR. The results show that the molecular interaction of lignin decreases from 32.3 mN/m in pure water to 11.3 mN/m in urea aqueous solution. The immobility of 1H NMR spectra and the shift of 17O NMR spectra of urea in different lignin/urea solutions indicate that the oxygen of carbonyl in urea and the hydrogen of hydroxyl in lignin form new hydrogen bonds and break the original hydrogen bonds among lignin molecules. The shift of 1H NMR spectra of lignin and the decrease of interactions in model compound polystyrene indicate that urea also breaks the π-π interactions between aromatic rings of lignin. Lignin dissolved in urea aqueous has good antioxidant activity and it can scavenge at least 63% free radicals in 16 min.

Conformational Aspects of the O-acetylation of C-tetra(phenyl)calixpyrogallol[4]arene.

PubMed

Casas-Hinestroza, José Luis; Maldonado, Mauricio

2018-05-20

Reaction between pyrogallol and benzaldehyde results in a conformational mixture of C- tetra(phenyl)pyrogallol[4]arene (crown and chair). The conformer mixture was separated using crystallization procedures and the structures were determined using FTIR, ¹H-NMR, and 13 C-NMR. O -acetylation of C- tetra(phenyl)pyrogallol[4]arene (chair) with acetic anhydride, in pyridine results in the formation of dodecaacetyl-tetra(phenyl)pyrogallol[4]arene. The structure was determined using ¹H-NMR and 13 C-NMR finding that the product maintains the conformation of the starting conformer. On the other hand, the O -acetylation reaction of C- tetra(phenyl)pirogallol[4]arene (crown) under same conditions proceeded efficiently, and its structure was determined using ¹H-NMR and 13 C-NMR. Dynamic ¹H-NMR of acetylated pyrogallolarene was studied by means of variable temperature in DMSO- d ₆ solution, and it revealed that two conformers are formed in the solution. Boat conformations for acetylated pyrogallolarene showed a slow interconversion at room temperature.

Synthesis, investigation of the new derivatives of dihydropyrimidines and determination of their biological activity

NASA Astrophysics Data System (ADS)

Maharramov, A. M.; Ramazanov, M. A.; Guliyeva, G. A.; Huseynzada, A. E.; Hasanova, U. A.; Shikhaliyev, N. G.; Eyvazova, G. M.; Hajiyeva, S. F.; Mamedov, I. G.; Aghayev, M. M.

2017-08-01

We reported of synthesis and investigation of the new biologically active derivatives of dihydropyrimidines 2 and 3. The investigation of structures of compounds by various experiments of NMR spectroscopy revealed the splitting of the signals to doublets and multiplets that confirms the presence of diastereomers in solution of compound 2 and the presence of diastereomers and tautomers in solution of compound 3. The individual diastereomer of compound 3 has been isolated. Biological activity of the synthesized compounds was studied on various species of genus Aspergillus fungi.

'Naked-eye' detection of biologically important anions in aqueous media by colorimetric receptor and its real life applications

NASA Astrophysics Data System (ADS)

Singh, Archana; Trivedi, Darshak R.

2017-05-01

A colorimetric receptor R 2-[(2-Hydroxy-naphthalen-1-ylmethylene)-hydrazonomethyl]-quinolin-8-ol has been designed and synthesized with good yield and characterized by the standard spectroscopic techniques such as FT-IR, UV-Visible, 1H NMR, 13C NMR and ESI-MS. The receptor R showed naked-eye detection and spectral change in the presence of F-, AcO- and H2PO4- over other anions. Interestingly, receptor R displaying high selective recognition towards F-, AcO- ion with a drastic color change from pale yellow to red in dry DMSO solvent and orange in mixed solvent DMSO/H2O (9:1, v/v). The behavior of receptor R towards F-, AcO- ion was investigated using UV-Vis and 1H NMR experiment. The detailed 1H NMR experiment result revealed that the receptor R is forming the hydrogen bonding between imine nitrogen and phenolic sbnd OH proton towards anions. The receptor R is able to detect sodium salts of flouride (NaF) and acetate (NaAcO) in aqueous medium and it exhibited dramatic color change from pale yellow to red. The receptor R demonstrated itself to be useful for real life application by detecting flouride and acetate ion in sea-water and commercially available product such as toothpaste, mouthwash and vinegar solution.

How well do force fields capture the strength of salt bridges in proteins?

PubMed Central

Ahmed, Mustapha Carab; Papaleo, Elena

2018-01-01

Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

On-line high-performance liquid chromatography-ultraviolet-nuclear magnetic resonance method of the markers of nerve agents for verification of the Chemical Weapons Convention.

PubMed

Mazumder, Avik; Gupta, Hemendra K; Garg, Prabhat; Jain, Rajeev; Dubey, Devendra K

2009-07-03

This paper details an on-flow liquid chromatography-ultraviolet-nuclear magnetic resonance (LC-UV-NMR) method for the retrospective detection and identification of alkyl alkylphosphonic acids (AAPAs) and alkylphosphonic acids (APAs), the markers of the toxic nerve agents for verification of the Chemical Weapons Convention (CWC). Initially, the LC-UV-NMR parameters were optimized for benzyl derivatives of the APAs and AAPAs. The optimized parameters include stationary phase C(18), mobile phase methanol:water 78:22 (v/v), UV detection at 268nm and (1)H NMR acquisition conditions. The protocol described herein allowed the detection of analytes through acquisition of high quality NMR spectra from the aqueous solution of the APAs and AAPAs with high concentrations of interfering background chemicals which have been removed by preceding sample preparation. The reported standard deviation for the quantification is related to the UV detector which showed relative standard deviations (RSDs) for quantification within +/-1.1%, while lower limit of detection upto 16mug (in mug absolute) for the NMR detector. Finally the developed LC-UV-NMR method was applied to identify the APAs and AAPAs in real water samples, consequent to solid phase extraction and derivatization. The method is fast (total experiment time approximately 2h), sensitive, rugged and efficient.

Probing the interaction of U (VI) with phosphonate-functionalized mesoporous silica using solid-state NMR spectroscopy

DOE PAGES

Uribe, Eva C.; Mason, Harris E.; Shusterman, Jennifer A.; ...

2016-05-30

The fundamental interaction of U (VI) with diethylphosphatoethyl triethoxysilane functionalized SBA-15 mesoporous silica is studied by macroscopic batch experiments and solid-state NMR spectroscopy. DPTS-functionalized silica has been shown to extract U (VI) from nitric acid solutions at or above pH 3. Extraction is dependent on pH and ionic strength. Single-pulse 31P NMR on U (VI) contacted samples revealed that U (VI)only interacts with a fraction of the ligands present on the surface. At pH 4 the U (VI) extraction capacity of the material is limited to 27–37% of the theoretical capacity, based on ligand loading. We combined single pulse 31Pmore » NMR on U (VI)-contacted samples with batch studies to measure a ligand-to-metal ratio of approximately 2 : 1 at pH 3 and 4. Batch studies and cross-polarization NMR measurements reveal that U (VI) binds to deprotonated phosphonate and/or silanol sites. We use 31P– 31P DQ-DRENAR NMR studies to compare the average dipolar coupling between phosphorus spins for both U (VI)-complexed and non-complexed ligand environments. Furthermore, these measurements reveal that U (VI) extraction is not limited by inadequate surface distribution of ligands, but rather by low stability of the surface phosphonate complex.« less

Effective rotational correlation times of proteins from NMR relaxation interference

NASA Astrophysics Data System (ADS)

Lee, Donghan; Hilty, Christian; Wider, Gerhard; Wüthrich, Kurt

2006-01-01

Knowledge of the effective rotational correlation times, τc, for the modulation of anisotropic spin-spin interactions in macromolecules subject to Brownian motion in solution is of key interest for the practice of NMR spectroscopy in structural biology. The value of τc enables an estimate of the NMR spin relaxation rates, and indicates possible aggregation of the macromolecular species. This paper reports a novel NMR pulse scheme, [ 15N, 1H]-TRACT, which is based on transverse relaxation-optimized spectroscopy and permits to determine τc for 15N- 1H bonds without interference from dipole-dipole coupling of the amide proton with remote protons. [ 15N, 1H]-TRACT is highly efficient since only a series of one-dimensional NMR spectra need to be recorded. Its use is suggested for a quick estimate of the rotational correlation time, to monitor sample quality and to determine optimal parameters for complex multidimensional NMR experiments. Practical applications are illustrated with the 110 kDa 7,8-dihydroneopterin aldolase from Staphylococcus aureus, the uniformly 15N-labeled Escherichia coli outer membrane protein X (OmpX) in 60 kDa mixed OmpX/DHPC micelles with approximately 90 molecules of unlabeled 1,2-dihexanoyl- sn-glycero-3-phosphocholine (DHPC), and the 16 kDa pheromone-binding protein from Bombyx mori, which cover a wide range of correlation times.

Probing the interaction of U (VI) with phosphonate-functionalized mesoporous silica using solid-state NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uribe, Eva C.; Mason, Harris E.; Shusterman, Jennifer A.

The fundamental interaction of U (VI) with diethylphosphatoethyl triethoxysilane functionalized SBA-15 mesoporous silica is studied by macroscopic batch experiments and solid-state NMR spectroscopy. DPTS-functionalized silica has been shown to extract U (VI) from nitric acid solutions at or above pH 3. Extraction is dependent on pH and ionic strength. Single-pulse 31P NMR on U (VI) contacted samples revealed that U (VI)only interacts with a fraction of the ligands present on the surface. At pH 4 the U (VI) extraction capacity of the material is limited to 27–37% of the theoretical capacity, based on ligand loading. We combined single pulse 31Pmore » NMR on U (VI)-contacted samples with batch studies to measure a ligand-to-metal ratio of approximately 2 : 1 at pH 3 and 4. Batch studies and cross-polarization NMR measurements reveal that U (VI) binds to deprotonated phosphonate and/or silanol sites. We use 31P– 31P DQ-DRENAR NMR studies to compare the average dipolar coupling between phosphorus spins for both U (VI)-complexed and non-complexed ligand environments. Furthermore, these measurements reveal that U (VI) extraction is not limited by inadequate surface distribution of ligands, but rather by low stability of the surface phosphonate complex.« less

High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids

PubMed Central

Nucci, Nathaniel V.; Valentine, Kathleen G.; Wand, A. Joshua

2014-01-01

High-resolution multi-dimensional solution NMR is unique as a biophysical and biochemical tool in its ability to examine both the structure and dynamics of macromolecules at atomic resolution. Conventional solution NMR approaches, however, are largely limited to examinations of relatively small (< 25 kDa) molecules, mostly due to the spectroscopic consequences of slow rotational diffusion. Encapsulation of macromolecules within the protective nanoscale aqueous interior of reverse micelles dissolved in low viscosity fluids has been developed as a means through which the ‘slow tumbling problem’ can be overcome. This approach has been successfully applied to diverse proteins and nucleic acids ranging up to 100 kDa, considerably widening the range of biological macromolecules to which conventional solution NMR methodologies may be applied. Recent advances in methodology have significantly broadened the utility of this approach in structural biology and molecular biophysics. PMID:24656086

Operando Solid-State NMR Observation of Solvent-Mediated Adsorption-Reaction of Carbohydrates in Zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Long; Alamillo, Ricardo; Elliott, William A.

Liquid-phase processing of molecules using heterogeneous catalysts – an important strategy for obtaining renewable chemicals sustainably from biomass – involves reactions that occur at solid-liquid interfaces. In glucose isomerization catalyzed by basic faujasite zeolites, the catalytic activity depends strongly on the solvent composition: initially, it declines precipitously when water is mixed with a small amount of the organic co-solvent γ-valerolactone (GVL), then recovers as the GVL content increases. Using solid-state 13C NMR spectroscopy, we observed glucose isomers located inside the zeolite pores directly, and followed their transformations into fructose and mannose in real time. At low GVL concentrations, glucose ismore » depleted in the zeolite pores relative to the liquid phase, while higher GVL concentrations in solution drive glucose inside the pores, resulting in up to a 32 enhancement in the local glucose concentration. Although their populations exchange rapidly, molecules present at the reactive interface experience a significantly different environment from the bulk solution.« less

Structure analysis and spectroscopic characterization of 2-Fluoro-3-Methylpyridine-5-Boronic Acid with experimental (FT-IR, Raman, NMR and XRD) techniques and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Alver, Özgür; Dikmen, Gökhan

2016-03-01

Possible stable conformers, geometrical molecular structures, vibrational properties as well as band assignments, nuclear magnetic shielding tensors of 2-Fluoro-3-Methylpyridine-5-Boronic Acid (2F3MP5BA) were studied experimentally and theoretically using FT-IR, Raman, (CP/MAS) NMR and XRD spectroscopic methods. FT-IR and Raman spectra were evaluated in the region of 3500-400 cm-1, and 3200-400 cm-1, respectively. The optimized geometric structures, vibrational wavenumbers and nuclear magnetic shielding tensors were examined using Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. 1H, 13C NMR chemical shifts were calculated using the gauge invariant atomic orbital (GIAO) method. 1H, 13C, APT and HETCOR NMR experiments of title molecule were carried out in DMSO solution. 13C CP/MAS NMR measurement was done with 4 mm zirconium rotor and glycine was used as an external standard. Single crystal of 2F3MP5BA was also prepared for XRD measurements. Assignments of vibrational wavenumbers were also strengthened by calculating the total energy distribution (TED) values using scaled quantum mechanical (SQM) method.

Partitioning of nitroxides in dispersed systems investigated by ultrafiltration, EPR and NMR spectroscopy.

PubMed

Krudopp, Heimke; Sönnichsen, Frank D; Steffen-Heins, Anja

2015-08-15

The partitioning behavior of paramagnetic nitroxides in dispersed systems can be determined by deconvolution of electron paramagnetic resonance (EPR) spectra giving equivalent results with the validated methods of ultrafiltration techniques (UF) and pulsed-field gradient nuclear magnetic resonance spectroscopy (PFG-NMR). The partitioning behavior of nitroxides with increasing lipophilicity was investigated in anionic, cationic and nonionic micellar systems and 10 wt% o/w emulsions. Apart from EPR spectra deconvolution, the PFG-NMR was used in micellar solutions as a non-destructive approach, while UF based on separation of very small volume of the aqueous phase. As a function of their substituent and lipophilicity, the proportions of nitroxides that were solubilized in the micellar or emulsion interface increased with increasing nitroxide lipophilicity for all emulsifier used. Comparing the different approaches, EPR deconvolution and UF revealed comparable nitroxide proportions that were solubilized in the interfaces. Those proportions were higher than found with PFG-NMR. For PFG-NMR self-diffusion experiments the reduced nitroxides were used revealing a high dynamic of hydroxylamines and emulsifiers. Deconvolution of EPR spectra turned out to be the preferred method for measuring the partitioning behavior of paramagnetic molecules as it enables distinguishing between several populations at their individual solubilization sites. Copyright © 2015 Elsevier Inc. All rights reserved.

Testing signal enhancement mechanisms in the dissolution NMR of acetone

NASA Astrophysics Data System (ADS)

Alonso-Valdesueiro, Javier; Elliott, Stuart J.; Bengs, Christian; Meier, Benno; Levitt, Malcolm H.

2018-01-01

In cryogenic dissolution NMR experiments, a substance of interest is allowed to rest in a strong magnetic field at cryogenic temperature, before dissolving the substance in a warm solvent, transferring it to a high-resolution NMR spectrometer, and observing the solution-state NMR spectrum. In some cases, negative enhancements of the 13C NMR signals are observed, which have been attributed to quantum-rotor-induced polarization. We show that in the case of acetone (propan-2-one) the negative signal enhancements of the methyl 13C sites may be understood by invoking conventional cross-relaxation within the methyl groups. The 1H nuclei acquire a relative large net polarization through thermal equilibration in a magnetic field at low temperature, facilitated by the methyl rotation which acts as a relaxation sink; after dissolution, the 1H magnetization slowly returns to thermal equilibrium at high temperature, in part by cross-relaxation processes, which induce a transient negative polarization of nearby 13C nuclei. We provide evidence for this mechanism experimentally and theoretically by saturating the 1H magnetization using a radiofrequency field pulse sequence before dissolution and comparing the 13 C magnetization evolution after dissolution with the results obtained from a conventional 1 H-13 C cross relaxation model of the CH3 moieties in acetone.

High-resolution solution-state NMR of unfractionated plant cell walls

Treesearch

John Ralph; Fachuang Lu; Hoon Kim; Dino Ress; Daniel J. Yelle; Kenneth E. Hammel; Sally A. Ralph; Bernadette Nanayakkara; Armin Wagner; Takuya Akiyama; Paul F. Schatz; Shawn D. Mansfield; Noritsugu Terashima; Wout Boerjan; Bjorn Sundberg; Mattias Hedenstrom

2009-01-01

Detailed structural studies on the plant cell wall have traditionally been difficult. NMR is one of the preeminent structural tools, but obtaining high-resolution solution-state spectra has typically required fractionation and isolation of components of interest. With recent methods for dissolution of, admittedly, finely divided plant cell wall material, the wall can...

Simple 1H NMR spectroscopic method for assay of salts of the contrast agent diatrizoate in commercial solutions.

PubMed

Hanna, G M; Lau-Cam, C A

1996-01-01

A simple, accurate, and specific 1H NMR spectroscopic method was developed for the assay of diatrizoate meglumine or the combination diatrizoate meglumine and diatrizoate sodium in commercial solutions for injection. A mixture of injectable solution and sodium acetate, the internal standard, was diluted with D2O and the 1H NMR spectrum of the solution was obtained. Two approaches were used to calculate the drug content, based on the integral values for the -N-CO-CH3 protons of diatrizoic acid at 2.23 ppm, and -N-CH3 protons of meglumine at 2.73 ppm, and the CH3-CO-protons of sodium acetate at 1.9 ppm. Recoveries (mean +/- standard deviation) of diatrizoic acid and meglumine from 10 synthetic mixtures of various amounts of these compounds with a fixed amount of internal standard were 100.3 +/- 0.55% and 100.1 +/- 0.98%, respectively. In addition to providing a direct means of simultaneously assaying diatrizoic acid and meglumine, the proposed NMR method can also be used to identify diatrizoate meglumine and each of its molecular components.

Fourier Analysis and Structure Determination. Part II: Pulse NMR and NMR Imaging.

ERIC Educational Resources Information Center

Chesick, John P.

1989-01-01

Uses simple pulse NMR experiments to discuss Fourier transforms. Studies the generation of spin echoes used in the imaging procedure. Shows that pulse NMR experiments give signals that are additions of sinusoids of differing amplitudes, frequencies, and phases. (MVL)

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

PubMed

Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

2008-02-01

We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

Experimental Aspects of Polarization Optimized Experiments (POE) for Magic Angle Spinning Solid-State NMR of Microcrystalline and Membrane-Bound Proteins.

PubMed

Gopinath, T; Veglia, Gianluigi

2018-01-01

Conventional NMR pulse sequences record one spectrum per experiment, while spending most of the time waiting for the spin system to return to the equilibrium. As a result, a full set of multidimensional NMR experiments for biological macromolecules may take up to several months to complete. Here, we present a practical guide for setting up a new class of MAS solid-state NMR experiments (POE or polarization optimized experiments) that enable the simultaneous acquisition of multiple spectra of proteins, accelerating data acquisition. POE exploit the long-lived 15 N polarization of isotopically labeled proteins and enable one to obtain up to eight spectra, by concatenating classical NMR pulse sequences. This new strategy propels data throughput of solid-state NMR spectroscopy of fibers, microcrystalline preparations, as well as membrane proteins.

Applications of ZVMo NMR spectroscopy. 17. ZVMo and UN relaxation time measurements confirming that (Mo(CN)8)U is dodecahedral in aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brownlee, R.T.; Shehan, B.P.; Wedd, A.G.

1987-07-01

Variable-temperature NMR line width measurements of ZVMo and UN in aqueous solutions of K4(Mo(CN)8) x 2H2O indicate that the stereochemistry of the (Mo(CN)8)U ion in solution is dodecahedral. A value for the ZVMo quadrupole coupling constant of 3.61 MHz is obtained. 27 references, 1 figure, 1 table.

In-depth investigation on quantitative characterization of pyrolysis oil by 31P NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben, Haoxi; Ferrell, III, Jack R.

The characterization of different heteroatom functional groups by employing 31P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigatedmore » by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.« less

In-depth investigation on quantitative characterization of pyrolysis oil by 31P NMR

DOE PAGES

Ben, Haoxi; Ferrell, III, Jack R.

2016-01-29

The characterization of different heteroatom functional groups by employing 31P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigatedmore » by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.« less

The structure investigations of dehydroacetic acid and 1,8-diaminonaphthalene condensation product by NMR, MS, and X-ray measurements

NASA Astrophysics Data System (ADS)

Kołodziej, B.; Morawiak, M.; Kamieński, B.; Schilf, W.

2016-05-01

A new unexpected product of condensation reaction of 1,8-diaminonaphthalene (DAN) and carbonyl compound (here: dehydroacetic acid (dha)) was synthesized. Discussion about the molecular structure of possible products of this reaction was done on the base of NMR studies. The structure of the titled product in both DMSO solution and in the solid state was resolved by analysis of its spectral data (X-ray structure analysis, multinuclear NMR in solution and solid state spectra) and MS measurements. The presented studies provided clear evidence that the titled product exists in diluted DMSO solution as the mixture of two kinetic free ionic species whereas in concentrated DMSO solution as well as in the solid state this system forms associated ionic pairs bonded together by hydrogen bonds.

Tunable Keplerate Type-Cluster "Mo132 " Cavity with Dicarboxylate Anions.

PubMed

Lai, Thanh-Loan; Awada, Mouhamad; Floquet, Sébastien; Roch-Marchal, Catherine; Watfa, Nancy; Marrot, Jérôme; Haouas, Mohamed; Taulelle, Francis; Cadot, Emmanuel

2015-09-14

The internal functionalization of the Keplerate-type capsule Mo132 has been carried out by ligand exchange leading to the formation of glutarate and succinate containing species isolated as ammonium or dimethylammonium salts. Solution NMR analysis is consistent with asymmetric inner dicarboxylate ions containing one carboxylato group grafted onto the inner side of the spheroidal inorganic shell while the second hangs toward the center of the cavity. Such a disposition has been confirmed by the single-crystal X-ray diffraction analysis of the glutarate containing {Mo132 } species. A detailed NMR solution study of the ligand-exchange process allowed determining the binding constant KL of acetate (AcO(-) ), succinate (HSucc(-) ) or glutarate (HGlu(-) ) ligands at the 30 inner coordinating sites, which vary such as K AcO -

Liquid and gas phase NMR spectra of 13CH313CHO acetaldehyde

NASA Astrophysics Data System (ADS)

Makulski, Włodzimierz; Wikieł, Agata J.

2018-01-01

The gas phase NMR experiments perform a vital role in establishing the magnetic shielding and spin-spin coupling constants which are free from intermolecular interactions, equivalent to the parameter of isolated molecules. This work is concerned with an acetaldehyde molecule. Small amounts of acetaldehyde 13CH313CHO in gaseous matrices of CO2 and Xe were studied using high-precision 1H and 13C NMR measurements. Results were extrapolated to the zero-density limit permitting the determinations of the 1H and 13C absolute nuclear magnetic shielding of an isolated acetaldehyde molecule. The difference between the experimental and recent theoretical DFT results is discussed. Several samples of 13CH313CHO dissolved in popular organic and inorganic solvents were also investigated. Gas-to-solution shifts show the influence of the association process when acetaldehyde is transferred from gas to liquid state. Several spin-spin coupling constants in the gas phase and in different solvents were precisely measured.

Partial homogeneity based high-resolution nuclear magnetic resonance spectra under inhomogeneous magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Zhiliang; Lin, Liangjie; Lin, Yanqin, E-mail: linyq@xmu.edu.cn, E-mail: chenz@xmu.edu.cn

2014-09-29

In nuclear magnetic resonance (NMR) technique, it is of great necessity and importance to obtain high-resolution spectra, especially under inhomogeneous magnetic fields. In this study, a method based on partial homogeneity is proposed for retrieving high-resolution one-dimensional NMR spectra under inhomogeneous fields. Signals from series of small voxels, which characterize high resolution due to small sizes, are recorded simultaneously. Then, an inhomogeneity correction algorithm is developed based on pattern recognition to correct the influence brought by field inhomogeneity automatically, thus yielding high-resolution information. Experiments on chemical solutions and fish spawn were carried out to demonstrate the performance of the proposedmore » method. The proposed method serves as a single radiofrequency pulse high-resolution NMR spectroscopy under inhomogeneous fields and may provide an alternative of obtaining high-resolution spectra of in vivo living systems or chemical-reaction systems, where performances of conventional techniques are usually degenerated by field inhomogeneity.« less

Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study

PubMed Central

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W.

2012-01-01

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 molal solution of α-D-glucopyranose, at a caffeine concentration of 0.083 molal; a single caffeine in a 3 molal solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 molal solution of sucrose (table sugar). Parallel Nuclear Magnetic Resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and that the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration, and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol. PMID:22897449

Caffeine and sugars interact in aqueous solutions: a simulation and NMR study.

PubMed

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W

2012-09-27

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 m solution of α-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 m solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

Didanosine polymorphism in a supercritical antisolvent process.

PubMed

Bettini, R; Menabeni, R; Tozzi, R; Pranzo, M B; Pasquali, I; Chierotti, M R; Gobetto, R; Pellegrino, L

2010-04-01

Solid-state properties of active ingredients are crucial in pharmaceutical development owing to their significant clinical and economical implications. In the present work we investigated the solid-state properties and the solubility in water of didanosine, DDI, re-crystallized from a dimethylsulfoxide solution using supercritical CO(2) as an antisolvent (SAS process) for comparison with the commercially available drug product. We also applied modern solid-state NMR (SS NMR) techniques, namely 2D (1)H DQ CRAMPS (Combined Rotation And Multiple Pulse Spectroscopy) and (1)H-(13)C on- and off-resonance CP (cross polarization) FSLG-HETCOR experiments, known for providing reliable information about (1)H-(1)H and (1)H-(13)C intra- and intermolecular proximities, in order to address polymorphism issues arising from the crystallization of a new form in the supercritical process. A new polymorph of didanosine was obtained from the supercritical antisolvent process and characterized by means of 1D and 2D multinuclear ((1)H, (13)C, (15)N) SS NMR. The particle size of the new crystal phase was reduced by varying the antisolvent density through a pressure increase. The structural differences between the commercial product and the SAS re-crystallized DDI are highlighted by X-ray diffractometry and well described by solid-state NMR. The carbon C6 (13)C chemical shift suggests that both commercial and re-crystallized didanosine samples are in the enol form. The analysis of homo- and heteronuclear proximities obtained by means of 2D NMR experiments shows that commercial and SAS re-crystallized DDI possess very similar molecular conformation and hydrogen bond network, but different packing. The new polymorph proved to be a metastable form at ambient conditions, showing higher solubility in water and lower stability to mechanical stress. 2009 Wiley-Liss, Inc. and the American Pharmacists Association

Detection of poly(ethylene glycol) residues from nonionic surfactants in surface water by1h and13c nuclear magnetic resonance spectrometry

USGS Publications Warehouse

Leenheer, J.A.; Wershaw, R. L.; Brown, P.A.; Noyes, T.I.

1991-01-01

??? Poly(ethylene glycol) (PEG) residues were detected in organic solute isolates from surface water by 1H nuclear magnetic resonance spectrometry (NMR), 13C NMR spectrometry, and colorimetric assay. PEG residues were separated from natural organic solutes in Clear Creek, CO, by a combination of methylation and chromatographic procedures. The isolated PEG residues, characterized by NMR spectrometry, were found to consist of neutral and acidic residues that also contained poly(propylene glycol) moieties. The 1H NMR and the colorimetric assays for poly(ethylene glycol) residues were done on samples collected in the lower Mississippi River and tributaries between St. Louis, MO, and New Orleans, LA, in July-August and November-December 1987. Aqueous concentrations for poly(ethylene glycol) residues based on colorimetric assay ranged from undetectable to ???28 ??g/L. Concentrations based on 1H NMR spectrometry ranged from undetectable to 145 ??g/L.

Forms and lability of phosphorus in algae and aquatic macrophytes characterized by solution 31P NMR coupled with enzymatic hydrolysis

USDA-ARS?s Scientific Manuscript database

Increased information on forms and lability of phosphorus (P) in aquatic macrophytes and algae is crucial for better understanding of P biogeochemical cycling in eutrophic lakes. In this work, solution 31P nuclear magnetic resonance (NMR) spectroscopy coupled with enzymatic hydrolysis (EH) was used ...

A solution-state NMR approach to elucidating pMDI-wood bonding mechanisms in loblolly pine

Treesearch

Daniel Joseph Yelle

2009-01-01

Solution-state NMR spectroscopy is a powerful tool for unambiguously determining the existence or absence of covalent chemical bonds between wood components and adhesives. Finely ground wood cell wall material dissolves in a solvent system containing DMSO-d6 and NMI-d6, keeping wood component polymers intact and in a near-...

NMR and rotational angles in solution conformation of polypeptides

NASA Astrophysics Data System (ADS)

Bystrov, V. F.

1985-01-01

Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin "bracelet", gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

A new titration system of a novel split-type superconducting magnet NMR spectrometer.

PubMed

Kitagawa, Isao; Tanaka, Hideki; Okada, Michiya; Kitaguchi, Hitoshi; Kohzuma, Takamitsu

2008-12-01

A new titration system for studying protein-ligand interactions has been developed. In this system, the sample solution is circulated in the route formed by an access path in a split superconducting magnet to maintain a constant protein concentration during the titration experiments. A concentration-control procedure for the ligand/protein ratio is devised, and the ligand/protein ratio is well controlled by this apparatus.

Accessible NMR Experiments Studying the Hydrodynamics of [subscript 15]N-Enriched Ubiquitin at Low Fields

ERIC Educational Resources Information Center

Thompson, Laura E.; Rovnyak, David

2007-01-01

We have recently developed and implemented two experiments in biomolecular NMR for an undergraduate-level biophysical chemistry laboratory with commercially available [subscript 15]N-enriched human ubiquitin. These experiments take advantage of [subscript 15]N direct detection of the NMR signal. The first experiment develops skills in acquiring…

Accessible NMR Experiments Studying the Hydrodynamics of [superscript 15]N-Enriched Ubiquitin at Low Fields

ERIC Educational Resources Information Center

Thompson, Laura E.; Rovnyak, David

2007-01-01

We have recently developed and implemented two experiments in biomolecular NMR for an undergraduate-level biophysical chemistry laboratory with commercially available [superscript 15]N-enriched human ubiquitin. These experiments take advantage of [superscript 15]N direct detection of the NMR signal. The first experiment develops skills in…

Application of geometric approximation to the CPMG experiment: Two- and three-site exchange.

PubMed

Chao, Fa-An; Byrd, R Andrew

2017-04-01

The Carr-Purcell-Meiboom-Gill (CPMG) experiment is one of the most classical and well-known relaxation dispersion experiments in NMR spectroscopy, and it has been successfully applied to characterize biologically relevant conformational dynamics in many cases. Although the data analysis of the CPMG experiment for the 2-site exchange model can be facilitated by analytical solutions, the data analysis in a more complex exchange model generally requires computationally-intensive numerical analysis. Recently, a powerful computational strategy, geometric approximation, has been proposed to provide approximate numerical solutions for the adiabatic relaxation dispersion experiments where analytical solutions are neither available nor feasible. Here, we demonstrate the general potential of geometric approximation by providing a data analysis solution of the CPMG experiment for both the traditional 2-site model and a linear 3-site exchange model. The approximate numerical solution deviates less than 0.5% from the numerical solution on average, and the new approach is computationally 60,000-fold more efficient than the numerical approach. Moreover, we find that accurate dynamic parameters can be determined in most cases, and, for a range of experimental conditions, the relaxation can be assumed to follow mono-exponential decay. The method is general and applicable to any CPMG RD experiment (e.g. N, C', C α , H α , etc.) The approach forms a foundation of building solution surfaces to analyze the CPMG experiment for different models of 3-site exchange. Thus, the geometric approximation is a general strategy to analyze relaxation dispersion data in any system (biological or chemical) if the appropriate library can be built in a physically meaningful domain. Published by Elsevier Inc.

Elucidation of solution state complexation in wet-granulated oven-dried ibuprofen and beta-cyclodextrin: FT-IR and 1H-NMR studies.

PubMed

Ghorab, M K; Adeyeye, M C

2001-08-01

The effect of oven-dried wet granulation on the complexation of beta-cyclodextrin with ibuprofen (IBU) in solution was investigated using Fourier transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance (1H NMR), and molecular modeling. Granulation was carried out using 5 mL of three different granulating solvents; water, ethanol (95% v/v), and isopropanol and the granules were oven-dried at 60 degrees C for 2 h. The granules were compared to oven-dried physical mixture and conventionally prepared complex. Phase solubility study was performed to investigate the stability of the granulation-formed complexes in solution. FT-IR was used to examine the complexation in the granules while 1H NMR, and molecular modeling studies were carried out to determine the mechanism of complexation in the water-prepared granules. The solubility studies suggested a 1:1 complex between IBU and betaCD. It also showed that the stability of the complex in solution was in the following order with respect to the granulating solvents: ethanol > water > isopropanol. The FT-IR study revealed a shift in the carboxylic acid stretching band and decrease in the intensities of the C-H bending bands of the isopropyl group and the out-of-plane aromatic ring, of IBU, in granules compared to the oven-dried physical mixture. This indicated that granules might have some extent of solid state complexation that could further enhance dissolution and the IBU-betaCD solution state complexation. 1H NMR showed that water prepared oven-dried granules had a different 1H NMR spectrum compared to similarly made oven-dried physical mixture, indicative of complexation in the former. The 1H NMR and the molecular modeling studies together revealed that solution state complexation from the granules occurred by inclusion of the isopropyl group together with part of the aromatic ring of IBU into the betaCD cavity probably through its wider side. These results indicate that granulation process induced faster complexation in solution which enhances the solubility and the dissolution rate of poorly soluble drugs. The extent of complexation in the granules was dependent on the type of solvent used.

Microwave temperature-jump nuclear magnetic resonance system for aqueous solutions

NASA Astrophysics Data System (ADS)

Kawakami, Masaru; Akasaka, Kazuyuki

1998-09-01

A microwave temperature-jump nuclear magnetic resonance (NMR) system suitable for aqueous solutions has been developed. A microwave pulse of a desired length is generated at a frequency of 2.46 GHz from a 1.3 kW magnetron, and is delivered through a waveguide and a coaxial cable to a coupling loop which works as an antenna to the dielectric resonator in the NMR probe. Inside the dielectric resonator, the microwave power is efficiently absorbed by the sample solution (about 100 μl) contained in a glass tube, causing a temperature jump by about 25 °C in less than 20 ms. The temperature after the jump can be maintained by applying intermittent microwave pulses of shorter length. A saddle-type radio-frequency coil is placed around the sample tube inside the hollow of the dielectric resonator to excite spins and detect NMR signals. Both the microwave pulses and the radio-frequency pulses are gated by a pulse programmer of the NMR spectrometer to form a desired temperature-jump pulse sequence. A mechanical mixing device is introduced, which significantly reduces the temperature gradient of the sample solution well within 100 ms after the jump. Application to an aqueous solution of ribonuclease A showed that the protein unfolds within 20 ms of microwave heating.

Two-dimensional NMR spectroscopy links structural moieties of soil organic matter to the temperature sensitivity of its decomposition

NASA Astrophysics Data System (ADS)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2015-04-01

Soil organic matter (SOM) represents a huge carbon pool, specifically in boreal ecosystems. Warming-induced release of large amounts of CO2 from the soil carbon pool might become a significant exacerbating feedback to global warming, if decomposition rates of boreal soils were more sensitive to increased temperatures. Despite a large number of studies dedicated to the topic, it has proven difficult to elucidate how the organo-chemical composition of SOM influences its decomposition, or its quality as a substrate for microbial metabolism. A great part of this challenge results from our inability to achieve a detailed characterization of the complex composition of SOM on the level of molecular structural moieties. 13C nuclear magnetic resonance (NMR) spectroscopy is a common tool to characterize SOM. However, SOM is a very complex mixture and the chemical shift regions distinguished in the 13C NMR spectra often represent many different molecular fragments. For example, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. We applied two-dimensional (2D) NMR to characterize SOM with highly increased resolution. We directly dissolved finely ground litters and forest floors'fibric and humic horizons'of both coniferous and deciduous boreal forests in dimethyl sulfoxide and analyzed the resulting solution with a 2D 1H-13C NMR experiment. In the 2D planes of these spectra, signals of CH groups can be resolved based on their 13C and 1H chemical shifts, hence the resolving power and information content of these NMR spectra is hugely increased. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra, so that hundreds of distinct CH groups could be observed and many molecular fragments could be identified. For instance, in the aromatics region, signals from individual lignin units could be recognized. It was hence possible to follow the fate of specific structural moieties in soils. We observed differences between litter and soil samples, and were able to relate them to the decomposition of identifiable moieties. Using multivariate data analysis, we aimed at linking the detailed chemical fingerprints of SOM to turnover rates in a soil incubation experiment. With the multivariate models, we were able to relate signal patterns in the 2D spectra and intensities of identifiable molecular moieties to variability in the temperature response of organic matter decomposition, as assessed by Q10. In conclusion, the characterization of SOM composition at the molecular level by solution-state 2D NMR spectroscopy is highly promising; it offers unprecedented possibilities to link SOM molecular composition to ecosystem processes, and their responses to environmental changes.

Improving the efficiency of branch-and-bound complete-search NMR assignment using the symmetry of molecules and spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernal, Andrés; Patiny, Luc; Castillo, Andrés M.

2015-02-21

Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed structure formula, wherein symmetric nuclei are grouped together; 2. partitioning of the solution space based on symmetry, that becomes the basis for an efficient branching procedure; and 3. a criterion of selection of input restrictions that leads to increased gaps between branches and thus faster pruningmore » of non-viable solutions. Although the examples chosen to illustrate this work focus on small-molecule NMR assignment, the results are generic and might help solving other combinatorial optimization problems.« less

NMR study on the network structure of a mixed gel of kappa and iota carrageenans.

PubMed

Hu, Bingjie; Du, Lei; Matsukawa, Shingo

2016-10-05

The temperature dependencies of the (1)H T2 and diffusion coefficient (D) of a mixed solution of kappa-carrageenan and iota-carrageenan were measured by NMR. Rheological and NMR measurements suggested an exponential formation of rigid aggregates of kappa-carrageenan and a gradual formation of fine aggregates of iota-carrageenan during two step increases of G'. The results also suggested that longer carrageenan chains are preferentially involved in aggregation, thus resulting in a decrease in the average Mw of solute carrageenans. The results of diffusion measurements for poly(ethylene oxide) (PEO) suggested that kappa-carrageenan formed thick aggregates that decreased hindrance to PEO diffusion by decreasing the solute kappa-carrageenan concentration in the voids of the aggregated chains, and that iota-carrageenan formed fine aggregates that decreased the solute iota-carrageenan concentration less. DPEO in a mixed solution of kappa-carrageenan and iota-carrageenan suggested two possibilities for the microscopic network structure: an interpenetrating network structure, or micro-phase separation. Copyright © 2016. Published by Elsevier Ltd.

Protein folding by NMR.

PubMed

Zhuravleva, Anastasia; Korzhnev, Dmitry M

2017-05-01

Protein folding is a highly complex process proceeding through a number of disordered and partially folded nonnative states with various degrees of structural organization. These transiently and sparsely populated species on the protein folding energy landscape play crucial roles in driving folding toward the native conformation, yet some of these nonnative states may also serve as precursors for protein misfolding and aggregation associated with a range of devastating diseases, including neuro-degeneration, diabetes and cancer. Therefore, in vivo protein folding is often reshaped co- and post-translationally through interactions with the ribosome, molecular chaperones and/or other cellular components. Owing to developments in instrumentation and methodology, solution NMR spectroscopy has emerged as the central experimental approach for the detailed characterization of the complex protein folding processes in vitro and in vivo. NMR relaxation dispersion and saturation transfer methods provide the means for a detailed characterization of protein folding kinetics and thermodynamics under native-like conditions, as well as modeling high-resolution structures of weakly populated short-lived conformational states on the protein folding energy landscape. Continuing development of isotope labeling strategies and NMR methods to probe high molecular weight protein assemblies, along with advances of in-cell NMR, have recently allowed protein folding to be studied in the context of ribosome-nascent chain complexes and molecular chaperones, and even inside living cells. Here we review solution NMR approaches to investigate the protein folding energy landscape, and discuss selected applications of NMR methodology to studying protein folding in vitro and in vivo. Together, these examples highlight a vast potential of solution NMR in providing atomistic insights into molecular mechanisms of protein folding and homeostasis in health and disease. Copyright © 2016 Elsevier B.V. All rights reserved.

Micromixer-based time-resolved NMR: applications to ubiquitin protein conformation.

PubMed

Kakuta, Masaya; Jayawickrama, Dimuthu A; Wolters, Andrew M; Manz, Andreas; Sweedler, Jonathan V

2003-02-15

Time-resolved NMR spectroscopy is used to studychanges in protein conformation based on the elapsed time after a change in the solvent composition of a protein solution. The use of a micromixer and a continuous-flow method is described where the contents of two capillary flows are mixed rapidly, and then the NMR spectra of the combined flow are recorded at precise time points. The distance after mixing the two fluids and flow rates define the solvent-protein interaction time; this method allows the measurement of NMR spectra at precise mixing time points independent of spectral acquisition time. Integration of a micromixer and a microcoil NMR probe enables low-microliter volumes to be used without losing significant sensitivity in the NMR measurement. Ubiquitin, the model compound, changes its conformation from native to A-state at low pH and in 40% or higher methanol/water solvents. Proton NMR resonances of the His-68 and the Tyr-59 of ubiquitin are used to probe the conformational changes. Mixing ubiquitin and methanol solutions under low pH at microliter per minute flow rates yields both native and A-states. As the flow rate decreases, yielding longer reaction times, the population of the A-state increases. The micromixer-NMR system can probe reaction kinetics on a time scale of seconds.

Determination of Structural Topology of a Membrane Protein in Lipid -Bilayers using Polarization Optimized Experiments (POE) for Static and MAS Solid State NMR Spectroscopy

PubMed Central

Mote, Kaustubh R.; Gopinath, T.; Veglia, Gianluigi

2013-01-01

The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments (POE), for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD ∼ 0.44 Å, a tilt angle of 24° ± 1°, and an azimuthal angle of 55° ± 6°. This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional O-ssNMR and MAS-ssNMR. PMID:23963722

Selective Injection of Magnetization by Slow Chemical Exchange in NMR

NASA Astrophysics Data System (ADS)

Boulat, Benoit; Epstein, David M.; Rance, Mark

1999-06-01

In a system in slow dynamic equilibrium two NMR methods are shown to be suitable for injecting magnetization from one resonance to another by means of slow chemical exchange. The combined outputs of the methods may be employed to measure the value of the off-rate constant κoff in the complex. The methods are implemented experimentally using the complex of molecules composed of the enzyme Esherichia coli dihydrofolate reductase (DHFR) and the ligand folate. In an equilibrium solution with DHFR, folate is known to undergo chemical exchange between a free state and a bound state. The modified synchronous nutation method is applied to a spin of the folate molecule in the free and bound states; magnetization transfer occurs between the two sites due to the underlying exchange process. As a preliminary step for the application of the synchronous nutation method, a new one-dimensional 1H NMR technique is proposed which facilitates the assignment of the resonance of a spin in the bound state, provided the resonance of its exchange partner in the free state is known. This experiment is also used to obtain quantitative estimates of the transverse relaxation rate constant of the bound resonance. The numerical procedure necessary to analyze the experimental results of the synchronous nutation experiment is presented.

Temperature invariance of NaCl solubility in water: inferences from salt-water cluster behavior of NaCl, KCl, and NH4Cl.

PubMed

Bharmoria, Pankaj; Gupta, Hariom; Mohandas, V P; Ghosh, Pushpito K; Kumar, Arvind

2012-09-27

The growth and stability of salt-water clusters have been experimentally studied in aqueous solutions of NaCl, KCl, and NH(4)Cl from dilute to near-saturation conditions employing dynamic light scattering and zeta potential measurements. In order to examine cluster stability, the changes in the cluster sizes were monitored as a function of temperature. Compared to the other cases, the average size of NaCl-water clusters remained almost constant over the studied temperature range of 20-70 °C. Information obtained from the temperature-dependent solution compressibility (determined from speed of sound and density measurements), multinuclear NMR ((1)H, (17)O, (35)Cl NMR), and FTIR were utilized to explain the cluster behavior. Comparison of NMR chemical shifts of saturated salt solutions with solid-state NMR data of pure salts, and evaluation of spectral modifications in the OH stretch region of saturated salt solutions as compared to that of pure water, provided important clues on ion pair-water interactions and water structure in the clusters. The high stability and temperature independence of the cluster sizes in aqueous NaCl shed light on the temperature invariance of its solubility.

Measuring molecular parity nonconservation using nuclear-magnetic-resonance spectroscopy

DOE PAGES

Eills, J.; Blanchard, J. W.; Bougas, L.; ...

2017-10-30

Here, the weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. We propose a nuclear-magnetic-resonance (NMR) experiment in which we titrate the chirality (enantiomeric excess) of a solvent and measure the diasteriomeric splitting in the spectra of a chiral solute in order to search for an anomalous offset due to parity nonconservation (PNC). We present a proof-of-principle experiment in which we search formore » PNC in the 13C resonances of small molecules, and use the 1H resonances, which are insensitive to PNC, as an internal reference. We set a constraint on molecular PNC in 13C chemical shifts at a level of 10 –5 ppm, and provide a discussion of important considerations in the search for molecular PNC using NMR spectroscopy.« less

Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR

PubMed Central

2015-01-01

We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as 1H–13C and 1H–15N HETCOR or 13C–13C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs. PMID:26393368

Measuring molecular parity nonconservation using nuclear-magnetic-resonance spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eills, J.; Blanchard, J. W.; Bougas, L.

Here, the weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. We propose a nuclear-magnetic-resonance (NMR) experiment in which we titrate the chirality (enantiomeric excess) of a solvent and measure the diasteriomeric splitting in the spectra of a chiral solute in order to search for an anomalous offset due to parity nonconservation (PNC). We present a proof-of-principle experiment in which we search formore » PNC in the 13C resonances of small molecules, and use the 1H resonances, which are insensitive to PNC, as an internal reference. We set a constraint on molecular PNC in 13C chemical shifts at a level of 10 –5 ppm, and provide a discussion of important considerations in the search for molecular PNC using NMR spectroscopy.« less

Characterization of D-glucaric acid using NMR, x-ray crystal structure, and MM3 molecular modeling analyses

USDA-ARS?s Scientific Manuscript database

D-glucaric acid was characterized in solution by comparing NMR spectra from the isotopically unlabeled molecule with those from D-glucaric acid labeled with deuterium or carbon-13 atoms. The NMR studies provided unequivocal assignments for all carbon atoms and non-hydroxyl protons of the molecule. ...

Intrinsic flexibility of West Nile virus protease in solution characterized using small-angle X-ray scattering.

PubMed

Garces, Andrea P; Watowich, Stanley J

2013-10-01

West Nile virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection can cause severe neurological disease and fatality in humans. Efforts are ongoing to develop antiviral drugs that inhibit the WNV protease, a viral enzyme required for polyprotein processing. Unfortunately, little is known about the solution structure of recombinant WNV protease (NS2B-NS3pro) used for antiviral drug discovery and development, although X-ray crystal structures and nuclear magnetic resonance (NMR) studies have provided valuable insights into the interactions between NS2B-NS3pro and peptide-based inhibitors. We completed small-angle X-ray scattering and Fourier transform infrared spectroscopy experiments to determine the solution structure and dynamics of WNV NS2B-NS3pro in the absence of a bound substrate or inhibitor. Importantly, these solution studies suggested that all or most of the NS2B cofactor was highly flexible and formed an ensemble of structures, in contrast to the NS2B tertiary structures observed in crystallographic and NMR studies. The secondary structure of NS2B-NS3pro in solution had high β-content, similar to the secondary structure observed in crystallographic studies. This work provided evidence of the intrinsic flexibility and conformational heterogeneity of the NS2B chain of the WNV protease in the absence of substratelike ligands, which should be considered during antiviral drug discovery and development efforts.

99 Tc NMR determination of the oxygen isotope content in 18 O-enriched water.

PubMed

Tarasov, Valerii P; Kirakosyan, Gayana А; German, Konstantin E

2018-03-01

99 Tc NMR has been suggested as an original method of evaluating the content of oxygen isotopes in oxygen-18-enriched water, a precursor for the production of radioisotope fluorine-18 used in positron emission tomography. To this end, solutions of NH 4 TcO 4 or NaTcO 4 (up to 0.28 mol/L) with natural abundance of oxygen isotopes in virgin or recycled 18 O-enriched water have been studied by 99 Tc NMR. The method is based on 16 O/ 17 O/ 18 O intrinsic isotope effects in the 99 Tc NMR chemical shifts, and the statistical distribution of oxygen isotopes in the coordination sphere of TcO 4 - and makes it possible to quantify the composition of enriched water by measuring the relative intensities of the 99 Tc NMR signals of the Tc 16 O 4-n 18 O n - isotopologues. Because the oxygen exchange between TcO 4 - and enriched water in neutral and alkaline solutions is characterized by slow kinetics, gaseous HCl was bubbled through a solution for a few seconds to achieve the equilibrium distribution of oxygen isotopes in the Tc coordination sphere without distortion of the oxygen composition of the water. Pertechnetate ion was selected as a probe due to its high stability in solutions and the significant 99 Tc NMR shift induced by a single 16 O→ 18 O substitution (-0.43 ± 0.01 ppm) in TcO 4 - and spin coupling constant 1 J( 99 Tc- 17 O) (131.46 Hz) favourable for the observation of individual signals of Tc 16 O 4-n 18 O n - isotopologues. Copyright © 2017 John Wiley & Sons, Ltd.

An Inversion Recovery NMR Kinetics Experiment

ERIC Educational Resources Information Center

Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

2011-01-01

A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

Solution structure of an artificial Fe8S8 ferredoxin: the D13C variant of Bacillus schlegelii Fe7S8 ferredoxin.

PubMed

Aono, S; Bentrop, D; Bertini, I; Cosenza, G; Luchinat, C

1998-12-01

The solution structure of the D13C variant of the thermostable Fe7S8 ferredoxin from Bacillus schlegelii has been determined by 1H-NMR spectroscopy in its oxidized form. In a variable-temperature NMR study the D13C variant was as thermostable (up to 90 degrees C) as the wild-type protein (WT). Seventy-five out of 77 amino acid residues and 81% of all theoretically expected proton resonances in the D13C Fe8S8 protein have been assigned. Its structure was determined through torsion angle dynamics calculations with the program DYANA, using 935 meaningful NOEs (from a total of 1251), hydrogen bond constraints, and NMR-derived dihedral angle constraints for the cluster-ligating cysteines. Afterwards, restrained energy minimization and restrained molecular dynamics were applied to each conformer of the family. The final family of 20 structures has RMSD values from the mean structure of 0.055 nm for the backbone atoms and of 0.099 nm for all heavy atoms. The overall folding of the WT is maintained in the mutant, except for the immediate vicinity of the new cysteine, which becomes much more similar to native Fe8S8 proteins. The two residues at positions 11 and 12, which constitute an insertion with respect to all known Fe8S8 proteins, assume a conformation that does not prevent the preceding and following residues from folding like in native Fe8S8 proteins. Clear evidence for the existence of two conformations involving almost half of the amino acid residues was found. The two conformations are structurally indistinguishable. Temperature-dependent NMR experiments show that one of them is thermodynamically more stable than the other.

Phase Composition and Disorder in La2(Sn,Ti)2O7 Ceramics: New Insights from NMR Crystallography.

PubMed

Fernandes, Arantxa; McKay, David; Sneddon, Scott; Dawson, Daniel M; Lawson, Sebastian; Veazey, Richard; Whittle, Karl R; Ashbrook, Sharon E

2016-09-15

An NMR crystallographic approach, involving the combination of 119 Sn NMR spectroscopy, XRD, and DFT calculations, is demonstrated for the characterization of La 2 Sn 2- x Ti x O 7 ceramics. A phase change from pyrochlore (La 2 Sn 2 O 7 ) to a layered perovskite phase (La 2 Ti 2 O 7 ) is predicted (by radius ratio rules) to occur when x ≈ 0.95. However, the sensitivity of NMR spectroscopy to the local environment is able to reveal a significant two-phase region is present, extending from x = 1.8 to ∼0.2, with limited solid solution at the two extremes, in broad agreement with powder XRD measurements. DFT calculations reveal that there is preferential site substitution of Sn in La 2 Ti 2 O 7 , with calculated shifts for Sn substitution onto Ti1 and Ti2 sites (in the "bulk" perovskite layers) in better agreement with experiment than those for Ti3 and Ti4 ("edge" sites). Substitution onto these two sites also produces structural models with lower relative enthalpy. As the Sn content decreases, there is a further preference for substitution onto Sn2. In contrast, the relative intensities of the spectral resonances suggest that Ti substitution into the pyrochlore phase is random, although only a limited solid solution is observed (up to ∼7% Ti). DFT calculations predict very similar 119 Sn shifts for Sn substitution into the two proposed models of La 2 Ti 2 O 7 (monoclinic ( P 2 1 ) and orthorhombic ( Pna 2 1 )), indicating it is not possible to distinguish between them. However, the relative energy of the Sn-substituted orthorhombic phase was higher than that of substituted monoclinic cells, suggesting that the latter is the more likely structure.

Comparison of phosphorus forms in three extracts of dairy feces by solution 31P NMR analysis

USDA-ARS?s Scientific Manuscript database

Using solution 31P NMR spectroscopy, we compared three extractants, deionized water, sodium acetate buffer (pH 5.0) with fresh sodium dithionite (NaAc-SD), and 0.25 M NaOH-0.05 M EDTA (NaOH-EDTA), for the profile of P compounds in two dairy fecal samples. Phosphorus extracted was 35% for water, and...

Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 1, Catalyzed reactions with wood models and wood polymers

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2011-01-01

To better understand adhesive interactions with wood, reactions between model compounds of wood and a model compound of polymeric methylene diphenyl diisocyanate (pMDI) were characterized by solution-state NMR spectroscopy. For comparison, finely ground loblolly pine sapwood, milled-wood lignin and holocellulose from the same wood were isolated and derivatized with...

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

PubMed

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A simple hand‐held magnet array for efficient and reproducible SABRE hyperpolarisation using manual sample shaking

PubMed Central

Richardson, Peter M.; Jackson, Scott; Parrott, Andrew J.; Nordon, Alison; Duckett, Simon B.

2018-01-01

Signal amplification by reversible exchange (SABRE) is a hyperpolarisation technique that catalytically transfers nuclear polarisation from parahydrogen, the singlet nuclear isomer of H2, to a substrate in solution. The SABRE exchange reaction is carried out in a polarisation transfer field (PTF) of tens of gauss before transfer to a stronger magnetic field for nuclear magnetic resonance (NMR) detection. In the simplest implementation, polarisation transfer is achieved by shaking the sample in the stray field of a superconducting NMR magnet. Although convenient, this method suffers from limited reproducibility and cannot be used with NMR spectrometers that do not have appreciable stray fields, such as benchtop instruments. Here, we use a simple hand‐held permanent magnet array to provide the necessary PTF during sample shaking. We find that the use of this array provides a 25% increase in SABRE enhancement over the stray field approach, while also providing improved reproducibility. Arrays with a range of PTFs were tested, and the PTF‐dependent SABRE enhancements were found to be in excellent agreement with comparable experiments carried out using an automated flow system where an electromagnet is used to generate the PTF. We anticipate that this approach will improve the efficiency and reproducibility of SABRE experiments carried out using manual shaking and will be particularly useful for benchtop NMR, where a suitable stray field is not readily accessible. The ability to construct arrays with a range of PTFs will also enable the rapid optimisation of SABRE enhancement as function of PTF for new substrate and catalyst systems. PMID:29193324

Apparatus for preparing a solution of a hyperpolarized noble gas for NMR and MRI analysis

DOEpatents

Pines, Alexander [Berkeley, CA; Budinger, Thomas [Berkeley, CA; Navon, Gil [Ramat Gan, IL; Song, Yi-Qiao [Berkeley, CA; Appelt, Stephan [Waiblingen, DE; Bifone, Angelo [Rome, IT; Taylor, Rebecca [Berkeley, CA; Goodson, Boyd [Berkeley, CA; Seydoux, Roberto [Berkeley, CA; Room, Toomas [Albany, CA; Pietrass, Tanja [Socorro, NM

2008-06-10

The present invention relates generally to nuclear magnetic resonance (NMR) techniques for both spectroscopy and imaging. More particularly, the present invention relates to methods in which hyperpolarized noble gases (e.g., Xe and He) are used to enhance and improve NMR and MRI. Additionally, the hyperpolarized gas solutions of the invention are useful both in vitro and in vivo to study the dynamics or structure of a system. When used with biological systems, either in vivo or in vitro, it is within the scope of the invention to target the hyperpolarized gas and deliver it to specific regions within the system.

Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.

PubMed

Takeda, Mitsuhiro; Chang, Chung-ke; Ikeya, Teppei; Güntert, Peter; Chang, Yuan-hsiang; Hsu, Yen-lan; Huang, Tai-huang; Kainosho, Masatsune

2008-07-18

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.

NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

PubMed

Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

2013-12-31

An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

Molecular simulations of multimodal ligand-protein binding: elucidation of binding sites and correlation with experiments.

PubMed

Freed, Alexander S; Garde, Shekhar; Cramer, Steven M

2011-11-17

Multimodal chromatography, which employs more than one mode of interaction between ligands and proteins, has been shown to have unique selectivity and high efficacy for protein purification. To test the ability of free solution molecular dynamics (MD) simulations in explicit water to identify binding regions on the protein surface and to shed light on the "pseudo affinity" nature of multimodal interactions, we performed MD simulations of a model protein ubiquitin in aqueous solution of free ligands. Comparisons of MD with NMR spectroscopy of ubiquitin mutants in solutions of free ligands show a good agreement between the two with regard to the preferred binding region on the surface of the protein and several binding sites. MD simulations also identify additional binding sites that were not observed in the NMR experiments. "Bound" ligands were found to be sufficiently flexible and to access a number of favorable conformations, suggesting only a moderate loss of ligand entropy in the "pseudo affinity" binding of these multimodal ligands. Analysis of locations of chemical subunits of the ligand on the protein surface indicated that electrostatic interaction units were located on the periphery of the preferred binding region on the protein. The analysis of the electrostatic potential, the hydrophobicity maps, and the binding of both acetate and benzene probes were used to further study the localization of individual ligand moieties. These results suggest that water-mediated electrostatic interactions help the localization and orientation of the MM ligand to the binding region with additional stability provided by nonspecific hydrophobic interactions.

Synthesis and Resolution of the Atropisomeric 1,1'-Bi-2-Naphthol: An Experiment in Organic Synthesis and 2-D NMR Spectroscopy

ERIC Educational Resources Information Center

Mak, Kendrew K. W.

2004-01-01

NMR spectroscopy is presented. It is seen that the experiment regarding the synthesis and resolution of 1,1'-Bi-2-naphtol presents a good experiment for teaching organic synthesis and NMR spectroscopy and provides a strategy for obtaining enantiopure compounds from achiral starting materials.

Using an NMR Spectrometer to Do Magnetic Resonance Imaging: An Undergraduate Physical Chemistry Laboratory Experiment

ERIC Educational Resources Information Center

Steinmetz, Wayne E.; Maher, M. Cyrus

2007-01-01

A conventional Fourier-transform NMR spectrometer with a triple-axis gradient probe can function as a MRI imager. In this experiment students gain hands-on experience with MRI while they learn about important principles underlying the practice of NMR, such as gradients, multi-dimensional spectroscopy, and relaxation. Students image a biological…

[Ag115S34(SCH2C6H4 tBu)47(dpph)6]: synthesis, crystal structure and NMR investigations of a soluble silver chalcogenide nanocluster† †Dedicated to Evamarie Hey-Hawkins on the occasion of her 60th birthday. ‡ ‡Electronic supplementary information (ESI) available: CCDC 1507868. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc04578b Click here for additional data file. Click here for additional data file.

PubMed Central

Fuhr, Olaf; Breitung, Ben; Kiran Chakravadhanula, Venkata Sei; Guthausen, Gisela; Hennrich, Frank; Yu, Wen; Kappes, Manfred M.; Roesky, Peter W.

2017-01-01

With the aim to synthesize soluble cluster molecules, the silver salt of (4-(tert-butyl)phenyl)methanethiol [AgSCH2C6H4 tBu] was applied as a suitable precursor for the formation of a nanoscale silver sulfide cluster. In the presence of 1,6-(diphenylphosphino)hexane (dpph), the 115 nuclear silver cluster [Ag115S34(SCH2C6H4 tBu)47(dpph)6] was obtained. The molecular structure of this compound was elucidated by single crystal X-ray analysis and fully characterized by spectroscopic techniques. In contrast to most of the previously published cluster compounds with more than a hundred heavy atoms, this nanoscale inorganic molecule is soluble in organic solvents, which allowed a comprehensive investigation in solution by UV-Vis spectroscopy and one- and two-dimensional NMR spectroscopy including 31P/109Ag-HSQC and DOSY experiments. These are the first heteronuclear NMR investigations on coinage metal chalcogenides. They give some first insight into the behavior of nanoscale silver sulfide clusters in solution. Additionally, molecular weight determinations were performed by 2D analytical ultracentrifugation and HR-TEM investigations confirm the presence of size-homogeneous nanoparticles present in solution. PMID:28507679

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

PubMed

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

PubMed

Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo; Murshudov, Garib N; Luchinat, Claudio

2014-04-01

The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

Characterization of the International Humic Substances Society standard and reference fulvic and humic acids by solution state carbon-13 (13C) and hydrogen-1 (1H) nuclear magnetic resonance spectrometry

USGS Publications Warehouse

Thorn, Kevin A.; Folan, Daniel W.; MacCarthy, Patrick

1989-01-01

Standard and reference samples of the International Humic Substances Society have been characterized by solution state carbon-13 and hydrogen-1 nuclear magnetic resonance (NMR) spectrometry. Samples included the Suwannee River, soil, and peat standard fulvic and humic acids, the Leonardite standard humic acid, the Nordic aquatic reference fulvic and humic acids, and the Summit Hill soil reference humic acid. Aqueous-solution carbon-13 NMR analyses included the measurement of spin-lattice relaxation times, measurement of nuclear Overhauser enhancement factors, measurement of quantitative carbon distributions, recording of attached proton test spectra, and recording of spectra under nonquantitative conditions. Distortionless enhancement by polarization transfer carbon-13 NMR spectra also were recorded on the Suwannee River fulvic acid in deuterated dimethyl sulfoxide. Hydrogen-1 NMR spectra were recorded on sodium salts of the samples in deuterium oxide. The carbon aromaticities of the samples ranged from 0.24 for the Suwannee River fulvic acid to 0.58 for the Leonardite humic acid.

Enhancing the resolution of 1H and 13C solid-state NMR spectra by reduction of anisotropic bulk magnetic susceptibility broadening.

PubMed

Hanrahan, Michael P; Venkatesh, Amrit; Carnahan, Scott L; Calahan, Julie L; Lubach, Joseph W; Munson, Eric J; Rossini, Aaron J

2017-10-25

We demonstrate that natural isotopic abundance 2D heteronuclear correlation (HETCOR) solid-state NMR spectra can be used to significantly reduce or eliminate the broadening of 1 H and 13 C solid-state NMR spectra of organic solids due to anisotropic bulk magnetic susceptibility (ABMS). ABMS often manifests in solids with aromatic groups, such as active pharmaceutical ingredients (APIs), and inhomogeneously broadens the NMR peaks of all nuclei in the sample. Inhomogeneous peaks with full widths at half maximum (FWHM) of ∼1 ppm typically result from ABMS broadening and the low spectral resolution impedes the analysis of solid-state NMR spectra. ABMS broadening of solid-state NMR spectra has previously been eliminated using 2D multiple-quantum correlation experiments, or by performing NMR experiments on diluted materials or single crystals. However, these experiments are often infeasible due to their poor sensitivity and/or provide limited gains in resolution. 2D 1 H- 13 C HETCOR experiments have previously been applied to reduce susceptibility broadening in paramagnetic solids and we show that this strategy can significantly reduce ABMS broadening in diamagnetic organic solids. Comparisons of 1D solid-state NMR spectra and 1 H and 13 C solid-state NMR spectra obtained from 2D 1 H- 13 C HETCOR NMR spectra show that the HETCOR spectrum directly increases resolution by a factor of 1.5 to 8. The direct gain in resolution is determined by the ratio of the inhomogeneous 13 C/ 1 H linewidth to the homogeneous 1 H linewidth, with the former depending on the magnitude of the ABMS broadening and the strength of the applied field and the latter on the efficiency of homonuclear decoupling. The direct gains in resolution obtained using the 2D HETCOR experiments are better than that obtained by dilution. For solids with long proton longitudinal relaxation times, dynamic nuclear polarization (DNP) was applied to enhance sensitivity and enable the acquisition of 2D 1 H- 13 C HETCOR NMR spectra. 2D 1 H- 13 C HETCOR experiments were applied to resolve and partially assign the NMR signals of the form I and form II polymorphs of aspirin in a sample containing both forms. These findings have important implications for ultra-high field NMR experiments, optimization of decoupling schemes and assessment of the fundamental limits on the resolution of solid-state NMR spectra.

Orientational ordering of a banana-shaped solute molecule in a nematic calamitic solvent by {sup 2}H-NMR spectroscopy: An indication of glasslike behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cinacchi, Giorgio; Domenici, Valentina

The Saupe ordering matrix of a banana-shaped mesogenic molecule as a solute in a common nematic calamitic solvent has been determined by {sup 2}H-NMR spectroscopy as a function of temperature. The temperature dependence of the Saupe ordering matrix element associated with the principal molecular axis is consistent with a glassy behavior in the reorientational motion of this particular solute molecule. The Haller expression, appropriately modified, provides a good fit to the experimental data.

Structural characterization of chemical warfare agent degradation products in decontamination solutions with proton band-selective (1)H-(31)P NMR spectroscopy.

PubMed

Koskela, Harri; Hakala, Ullastiina; Vanninen, Paula

2010-06-15

Decontamination solutions, which are usually composed of strong alkaline chemicals, are used for efficient detoxification of chemical warfare agents (CWAs). The analysis of CWA degradation products directly in decontamination solutions is challenging due to the nature of the matrix. Furthermore, occasionally an unforeseen degradation pathway can result in degradation products which could be eluded to in standard analyses. Here, we present the results of the application of proton band-selective (1)H-(31)P NMR spectroscopy, i.e., band-selective 1D (1)H-(31)P heteronuclear single quantum coherence (HSQC) and band-selective 2D (1)H-(31)P HSQC-total correlation spectroscopy (TOCSY), for ester side chain characterization of organophosphorus nerve agent degradation products in decontamination solutions. The viability of the approach is demonstrated with a test mixture of typical degradation products of nerve agents sarin, soman, and VX. The proton band-selective (1)H-(31)P NMR spectroscopy is also applied in characterization of unusual degradation products of VX in GDS 2000 solution.

Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves.

PubMed

Thurber, Kent R; Tycko, Robert

2014-05-14

We report solid state (13)C and (1)H nuclear magnetic resonance (NMR) experiments with magic-angle spinning (MAS) on frozen solutions containing nitroxide-based paramagnetic dopants that indicate significant perturbations of nuclear spin polarizations without microwave irradiation. At temperatures near 25 K, (1)H and cross-polarized (13)C NMR signals from (15)N,(13)C-labeled L-alanine in trinitroxide-doped glycerol/water are reduced by factors as large as six compared to signals from samples without nitroxide doping. Without MAS or at temperatures near 100 K, differences between signals with and without nitroxide doping are much smaller. We attribute most of the reduction of NMR signals under MAS near 25 K to nuclear spin depolarization through the cross-effect dynamic nuclear polarization mechanism, in which three-spin flips drive nuclear polarizations toward equilibrium with spin polarization differences between electron pairs. When T1e is sufficiently long relative to the MAS rotation period, the distribution of electron spin polarization across the nitroxide electron paramagnetic resonance lineshape can be very different from the corresponding distribution in a static sample at thermal equilibrium, leading to the observed effects. We describe three-spin and 3000-spin calculations that qualitatively reproduce the experimental observations.

Investigating the reactivity of pMDI with wood cell walls using high-resolution solution-state NMR spectroscopy

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2009-01-01

The objectives of this study are the following: (1) Use solution-state NMR to assign contours in HSQC spectra of the reaction products between pMDI model compounds and: (a) lignin model compounds, (b) milled-wood lignin, (c) ball-milled wood, (d) microtomed loblolly pine; (2) Determine where and to what degree urethane formation occurs with loblolly pine cell wall...

Preparation, spectroscopic and high field NMR relaxometry studies of gadolinium(III) complexes with the asymmetric tetraamine 1,4,7,11-tetraazaundecane

NASA Astrophysics Data System (ADS)

Hatzipanayioti, Despina; Veneris, Antonis

2009-10-01

The reaction of Gd(III) with asymmetric tetramine 1,4,7,11-tetraazaundecane (2,2,3-tet, L1) ligand has been studied via NMR spectroscopy. The ligand proton longitudinal relaxation rates ( R1) have been used to estimate the distances of these protons from the Gd(III) center, in Gd(III)- L1 reaction solutions, in H 2O/D 2O 5/1 mixtures. Two Gd(III) complexes [Gd(III)( L1)(NH 3)(H 2O) 4](CH 3COO) 3·2H 2O ( 1) and [Gd(III)( L1)(NH 3)(H 2O) 2]Cl 3·EtOH ( 2) have been isolated and characterized by elemental analyses, TGA, IR, NMR and relaxometry measurements. The NMR relaxation measurements of 2 in aqueous solutions have been performed, under various temperature or concentration conditions, and compared with those of the commercial contrast agents Gd(III)-DTPA and Gd(III)-DTPA-BMA. It has also been studied the influence of (i) the Gd(III) inner-sphere water molecule number ( q) alteration and (ii) the steric constraint enhancement on the metal site, over the relaxation rate values of the parent aqueous solution of Gd(III)-2,2,3-tet, and of the aqueous solutions of 2.

Enantioselective cyclization of racemic supramolecular polymers.

PubMed

ten Cate, A Tessa; Dankers, Patricia Y W; Kooijman, Huub; Spek, Anthony L; Sijbesma, Rint P; Meijer, E W

2003-06-11

Homochiral hydrogen-bonded cyclic assemblies are formed in dilute solutions of racemic supramolecular polymers based on the quadruple hydrogen bonding 2-ureido-4[1H]-pyrimidinone unit, as observed by 1H NMR and SEC experiments. Preorganization of the monomers and the combined binding strength of the eight hydrogen bonds result in a very high stability of the cyclic aggregates with pronounced selectivity between homochiral and heterochiral cyclic species, usually only observed in crystalline or liquid crystalline phases.

Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis

Treesearch

Daniel J. Yelle; Prasad Kaparaju; Christopher G. Hunt; Kolby Hirth; Hoon Kim; John Ralph; Claus Felby

2012-01-01

Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C-1H NMR correlation spectroscopy, via...

A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

ERIC Educational Resources Information Center

Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

2004-01-01

An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

Understanding Unimer Exchange Processes in Block Copolymer Micelles using NMR Diffusometry, Time-Resolved NMR, and SANS

NASA Astrophysics Data System (ADS)

Madsen, Louis; Kidd, Bryce; Li, Xiuli; Miller, Katherine; Cooksey, Tyler; Robertson, Megan

Our team seeks to understand dynamic behaviors of block copolymer micelles and their interplay with encapsulated cargo molecules. Quantifying unimer and cargo exchange rates micelles can provide critical information for determining mechanisms of unimer exchange as well as designing systems for specific cargo release dynamics. We are exploring the utility of NMR spectroscopy and diffusometry techniques as complements to existing SANS and fluorescence methods. One promising new method involves time-resolved NMR spin relaxation measurements, wherein mixing of fully protonated and 2H-labeled PEO-b-PCL micelles solutions shows an increase in spin-lattice relaxation time (T1) with time after mixing. This is due to a weakening in magnetic environment surrounding 1H spins as 2H-bearing unimers join fully protonated micelles. We are measuring time constants for unimer exchange of minutes to hours, and we expect to resolve times of <1 min. This method can work on any solution NMR spectrometer and with minimal perturbation to chemical structure (as in dye-labelled fluorescence methods). Multimodal NMR can complement existing characterization tools, expanding and accelerating dynamics measurements for polymer micelle, nanogel, and nanoparticle developers.

U.S. EPA High-Field NMR Facility with Remote Accessibility

EPA Science Inventory

EPA’s High-Field Nuclear Magnetic Resonance Research Facility housed in Athens, GA has two Varian 600 MHz NMR spectrometers used for conducting sophisticated experiments in environmental science. Off-site users can ship their samples and perform their NMR experiments remotely fr...

Investigations on the Crystal-Chemical Behavior of Transition-Metal-Bearing Aluminosilicate Garnet Solid Solutions Using 27Al and 29Si NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Palke, A. C.; Geiger, C. A.; Stebbins, J. F.

2015-12-01

The petrological importance of silicate garnet is derived from the presence of three distinct cation sites of varying size and coordination number. This allows for a wide range of trace, minor, and major element substitutions. However, a full and precise crystal-chemical understanding of the nature of transition metals in garnet is not at hand. Possible mechanisms of various charge-balanced substitutions (e.g. octahedral Ti4+ or tetrahedral Al3+) and the structural state of solid solutions (i.e. short- to long-range ordering) need study. We report on ongoing efforts in these directions using 27Al and 29Si Magic-Angle Spinning Nuclear Magnetic Resonance (MAS-NMR) spectroscopy. Early work on synthetic and natural Fe- and Mn-bearing pyrope- and grossular-rich garnets focused on the effect these paramagnetic transition metals have in measuring and interpreting NMR spectra. These results have been expanded with NMR measurements on synthetic pyrope-rich garnets containing other paramagnetic transition metals including Cr3+, V3+, Co2+, and Ni2+ as well as diamagnetic Ti4+. NMR peaks are severely broadened in the presence of even small concentrations of Cr3+, Mn2+, and Fe3+ leading to a loss of spectral resolution. On the other hand, the spectra of garnet containing V3+, Fe2+, Co2+, and Ni2+ have better resolution and show separate paramagnetically shifted NMR peaks. In some cases, crystal-chemical information can be obtained because of the large frequency separations between the NMR peaks that can be assigned to various local atomic configurations around Al and Si. Furthermore, the 27Al NMR spectrum of a synthetic pyrope garnet with about 2% diamagnetic Ti4+ on the octahedral site showed the absence of any tetrahedral Al3+, which rules out the substitution mechanism VITi + IVAl = VIAl + IVSi in the solid solution. Our NMR investigations on garnet are now being made at the exploratory level. We think that NMR spectra of diamagnetic garnet can provide information on a number of crystal-chemical properties. Spectra of garnet containing various paramagnetic transition elements can also, in some cases, give local structural information. With a better understanding of paramagnetic effects in NMR spectroscopy, this type of study can possibly be expanded to other geologically important paramagnetic minerals and phases.

Hydraulic characterisation of iron-oxide-coated sand and gravel based on nuclear magnetic resonance relaxation mode analyses

NASA Astrophysics Data System (ADS)

Costabel, Stephan; Weidner, Christoph; Müller-Petke, Mike; Houben, Georg

2018-03-01

The capability of nuclear magnetic resonance (NMR) relaxometry to characterise hydraulic properties of iron-oxide-coated sand and gravel was evaluated in a laboratory study. Past studies have shown that the presence of paramagnetic iron oxides and large pores in coarse sand and gravel disturbs the otherwise linear relationship between relaxation time and pore size. Consequently, the commonly applied empirical approaches fail when deriving hydraulic quantities from NMR parameters. Recent research demonstrates that higher relaxation modes must be taken into account to relate the size of a large pore to its NMR relaxation behaviour in the presence of significant paramagnetic impurities at its pore wall. We performed NMR relaxation experiments with water-saturated natural and reworked sands and gravels, coated with natural and synthetic ferric oxides (goethite, ferrihydrite), and show that the impact of the higher relaxation modes increases significantly with increasing iron content. Since the investigated materials exhibit narrow pore size distributions, and can thus be described by a virtual bundle of capillaries with identical apparent pore radius, recently presented inversion approaches allow for estimation of a unique solution yielding the apparent capillary radius from the NMR data. We found the NMR-based apparent radii to correspond well to the effective hydraulic radii estimated from the grain size distributions of the samples for the entire range of observed iron contents. Consequently, they can be used to estimate the hydraulic conductivity using the well-known Kozeny-Carman equation without any calibration that is otherwise necessary when predicting hydraulic conductivities from NMR data. Our future research will focus on the development of relaxation time models that consider pore size distributions. Furthermore, we plan to establish a measurement system based on borehole NMR for localising iron clogging and controlling its remediation in the gravel pack of groundwater wells.

On the influence of ion exchange on the local structure of the titanosilicate ETS-10.

PubMed

Pavel, Claudiu C; Zibrowius, Bodo; Löffler, Elke; Schmidt, Wolfgang

2007-07-14

The effect of ion exchange with different monovalent cations (NH(4)(+), K(+), Na(+) and Cs(+)) on the local structure of the titanosilicate ETS-10 has been studied by (29)Si MAS NMR and Raman spectroscopy. Although X-ray diffraction shows no significant influence of ion exchange on the long range order, ammonium exchange is found to result in substantial damage to the local structure. Ion exchange experiments with alkali cations under significantly more acidic conditions clearly show that the structural damage brought about by ammonium exchange is not caused by the low pH of the exchange solution. The exchange with potassium and caesium ions also leads to significant changes in the (29)Si NMR and Raman spectra. However, these changes can largely be reversed by sodium back-exchange.

Determining association constants from titration experiments in supramolecular chemistry.

PubMed

Thordarson, Pall

2011-03-01

The most common approach for quantifying interactions in supramolecular chemistry is a titration of the guest to solution of the host, noting the changes in some physical property through NMR, UV-Vis, fluorescence or other techniques. Despite the apparent simplicity of this approach, there are several issues that need to be carefully addressed to ensure that the final results are reliable. This includes the use of non-linear rather than linear regression methods, careful choice of stoichiometric binding model, the choice of method (e.g., NMR vs. UV-Vis) and concentration of host, the application of advanced data analysis methods such as global analysis and finally the estimation of uncertainties and confidence intervals for the results obtained. This tutorial review will give a systematic overview of all these issues-highlighting some of the key messages herein with simulated data analysis examples.

Ionic Liquid-Solute Interactions Studied by 2D NOE NMR Spectroscopy.

PubMed

Khatun, Sufia; Castner, Edward W

2015-07-23

Intermolecular interactions between a Ru(2+)(bpy)3 solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {(1)H-(19)F} HOESY and {(1)H-(1)H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru(2+)(bpy)3 solute is rather different from the bulk IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru(2+)(bpy)3 solute interacts with both the polar head and the nonpolar tail groups of the 1-butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.

Acid-base equilibrium in aqueous solutions of 1,3-dimethylbarbituric acid as studied by 13C NMR spectroscopy

NASA Astrophysics Data System (ADS)

Gryff-Keller, A.; Kraska-Dziadecka, A.

2011-12-01

13C NMR spectra of 1,3-dimethylbarbituric acid in aqueous solutions of various acidities and for various solute concentrations have been recorded and interpreted. The spectra recorded at pH = 2 and below contain the signals of the neutral solute molecule exclusively, while the ones recorded at pH = 7 and above only the signals of the appropriate anion, which has been confirmed by theoretical GIAO-DFT calculations. The signals in the spectra recorded for solutions of pH < 7 show dynamic broadenings. The lineshape analysis of these signals has provided information on the kinetics of the processes running in the dynamic acid-base equilibrium. The kinetic data determined this way have been used to clarify the mechanisms of these processes. The numerical analysis has shown that under the investigated conditions deprotonation of the neutral solute molecules undergoes not only via a simple transfer of the C-H proton to water molecules but also through a process with participation of the barbiturate anions. Moreover, the importance of tautomerism, or association, or both these phenomena for the kinetics of the acid-base transformations in the investigated system has been shown. Qualitatively similar changes of 13C NMR spectra with the solution pH variation have been observed for the parent barbituric acid.

Novel dimeric metabolites from Alternaria tagetica.

PubMed

Gamboa-Angulo, M M; Alejos-González, F; Escalante-Erosa, F; García-Sosa, K; Delgado-Lamas, G; Peña-Rodríguez, L M

2000-08-01

Two novel polyketides, bis-7-O-8' '.8-O-7' '- and bis-7-O-7' '. 8-O-8' '-zinniol (2 and 3, respectively) were isolated from the organic crude extract of culture filtrates from Alternaria tagetica. Both structures were determined on the basis of their spectroscopic data (IR, MS, (1)H NMR, (13)C NMR, and 2D NMR experiments) and confirmed by chemical synthesis. Zinniol (1) was isolated as a major component, and its (13)C NMR data was correctly assigned after careful analysis of data from its 2D NMR experiments (HMQC and HMBC).

Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies.

PubMed

Yang, Hongqin; Huang, Yanmei; He, Jiawei; Li, Shanshan; Tang, Bin; Li, Hui

2016-09-15

In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, (1)H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA. Copyright © 2016 Elsevier Inc. All rights reserved.

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Toward nanomolar detection by NMR through SABRE hyperpolarization.

PubMed

Eshuis, Nan; Hermkens, Niels; van Weerdenburg, Bram J A; Feiters, Martin C; Rutjes, Floris P J T; Wijmenga, Sybren S; Tessari, Marco

2014-02-19

SABRE is a nuclear spin hyperpolarization technique based on the reversible association of a substrate molecule and para-hydrogen (p-H2) to a metal complex. During the lifetime of such a complex, generally fractions of a second, the spin order of p-H2 is transferred to the nuclear spins of the substrate molecule via a transient scalar coupling network, resulting in strongly enhanced NMR signals. This technique is generally applied at relatively high concentrations (mM), in large excess of substrate with respect to metal complex. Dilution of substrate ligands below stoichiometry results in progressive decrease of signal enhancement, which precludes the direct application of SABRE to the NMR analysis of low concentration (μM) solutions. Here, we show that the efficiency of SABRE at low substrate concentrations can be restored by addition of a suitable coordinating ligand to the solution. The proposed method allowed NMR detection below 1 μM in a single scan.

Unprecedented Spectroscopic and Computational Evidence for Allenyl and Propargyl Titanocene(IV) Complexes: Electrophilic Quenching of Their Metallotropic Equilibrium.

PubMed

Ruiz-Muelle, Ana Belén; Oña-Burgos, Pascual; Ortuño, Manuel A; Oltra, J Enrique; Rodríguez-García, Ignacio; Fernández, Ignacio

2016-02-12

The synthesis and structural characterization of allenyl titanocene(IV) [TiClCp2 (CH=C=CH2 )] 3 and propargyl titanocene(IV) [TiClCp2 (CH2 -C≡C-(CH2 )4 CH3 )] 9 have been described for the first time. Advanced NMR methods including diffusion NMR methods (diffusion pulsed field gradient stimulated spin echo (PFG-STE) and DOSY) have been applied and established that these organometallics are monomers in THF solution with hydrodynamic radii (from the Stokes-Einstein equation) of 3.5 and 4.1 Å for 3 and 9, respectively. Full (1) H, (13) C, Δ(1) H, and Δ(13) C NMR data are given, and through the analysis of the Ramsey equation, the first electronic insights into these derivatives are provided. In solution, they are involved in their respective metallotropic allenyl-propargyl equilibria that, after quenching experiments with aromatic and aliphatic aldehydes, ketones, and protonating agents, always give the propargyl products P (when carbonyls are employed), or allenyl products A (when a proton source is added) as the major isomers. In all the cases assayed, the ratio of products suggests that the metallotropic equilibrium should be faster than the reactions of 3 and 9 with electrophiles. Indeed, DFT calculations predict lower Gibbs energy barriers for the metallotropic equilibrium, thus confirming dynamic kinetic resolution. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly sensitive and selective detection of Al(III) ions in aqueous buffered solution with fluorescent peptide-based sensor.

PubMed

In, Byunggyu; Hwang, Gi Won; Lee, Keun-Hyeung

2016-09-15

A fluorescent sensor based on a tripeptide (SerGluGlu) with a dansyl fluorophore detected selectively Al(III) among 16 metal ions in aqueous buffered solutions without any organic cosolvent. The peptide-based sensor showed a highly sensitive turn on response to aluminium ion with high binding affinity (1.84×10(4)M(-1)) in aqueous buffered solutions. The detection limit (230nM, 5.98ppb) of the peptide-based sensor was much lower than the maximum allowable level (7.41μM) of aluminium ions in drinking water demanded by EPA. The binding mode of the peptide sensor with aluminium ions was characterized using ESI mass spectrometry, NMR titration, and pH titration experiments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network.

PubMed

Xu, Xianzhong; Pulavarti, Surya V S R K; Eletsky, Alexander; Huang, Yuanpeng Janet; Acton, Thomas B; Xiao, Rong; Everett, John K; Montelione, Gaetano T; Szyperski, Thomas

2014-12-01

High-quality solution NMR structures of three homeodomains from human proteins ALX4, ZHX1 and CASP8AP2 were solved. These domains were chosen as targets of a biomedical theme project pursued by the Northeast Structural Genomics Consortium. This project focuses on increasing the structural coverage of human proteins associated with cancer.

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts III. 1H, 13C and 15N NMR studies at natural isotope abundance.

PubMed Central

Kozerski, L; Sierzputowska-Gracz, H; Krzyzosiak, W; Bratek-Wiewiórowska, M; Jaskólski, M; Wiewiórowski, M

1984-01-01

The 1H, 13C, 15N NMR spectra of cytidine /Cyd/, ethenocytidine /epsilon Cyd/ and their hydrochlorides /Cyd X HC1/ and /epsilon Cyd X HC1/ have been analysed to compare structural differences observed in solution with those existing in the crystalline state. The effects of ethenobridging and protonation of the hertero-aromatic base on the intramolecular stereochemistry, intermolecular interactions and electronic structure of the whole molecule are discussed on the basis of the NMR studies in DMSO solutions. Particular interest is devoted to the discussion of the conformation of the ribose ring, the presence of the intramolecular C-5'-0...H-6-C hydrogen bond, unambiguous assignment of the site of protonation, the mechanism of the 5C-H deuterium exchange in Cyd X HC1, and the intermolecular interactions in solution. PMID:6701098

A Novel Tri-Enzyme System in Combination with Laser-Driven NMR Enables Efficient Nuclear Polarization of Biomolecules in Solution

PubMed Central

Lee, Jung Ho; Cavagnero, Silvia

2013-01-01

NMR is an extremely powerful, yet insensitive technique. Many available nuclear polarization methods that address sensitivity are not directly applicable to low-concentration biomolecules in liquids and are often too invasive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is no exception. It needs high-power laser irradiation, which often leads to sample degradation, and photosensitizer reduction. Here, we introduce a novel tri-enzyme system that significantly overcomes the above challenges rendering photo-CIDNP a practically applicable technique for NMR sensitivity enhancement in solution. The specificity of the nitrate reductase (NR) enzyme is exploited to selectively in situ re-oxidize the reduced photo-CIDNP dye FMNH2. At the same time, the oxygen-scavenging ability of glucose oxidase (GO) and catalase (CAT) is synergistically employed to prevent sample photodegradation. The resulting tri-enzyme system (NR-GO-CAT) enables prolonged sensitivity-enhanced data collection in 1D and 2D heteronuclear NMR, leading to the highest photo-CIDNP sensitivity enhancement (48-fold relative to SE-HSQC) achieved to date for amino acids and polypeptides in solution. NR-GO-CAT extends the concentration limit of photo-CIDNP NMR down to the low micromolar range. In addition, sensitivity (relative to the reference SE-HSQC) is found to be inversely proportional to sample concentration, paving the way to the future analysis of even more diluted samples. PMID:23560683

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pecher, Oliver; Bayley, Paul M.; Liu, Hao

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insightmore » into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with “on-the-fly” re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na–Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.« less

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

NASA Astrophysics Data System (ADS)

Pecher, Oliver; Bayley, Paul M.; Liu, Hao; Liu, Zigeng; Trease, Nicole M.; Grey, Clare P.

2016-04-01

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insight into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with "on-the-fly" re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na-Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.

Boron environments in Pyrex® glass--a high resolution, Double-Rotation NMR and thermodynamic modelling study.

PubMed

Howes, A P; Vedishcheva, N M; Samoson, A; Hanna, J V; Smith, M E; Holland, D; Dupree, R

2011-07-07

It is shown, using the important technological glass Pyrex® as an example, that 1D and 2D (11)B Double-Rotation (DOR) NMR experiments, in combination with thermodynamic modelling, are able to provide unique structural information about complex glasses. (11)B DOR NMR has been applied to Pyrex® glass in order to remove both dipolar and quadrupolar broadening of the NMR lines, leading to high resolution spectra that allow unambiguous, accurate peak fitting to be carried out, of particular importance in the case of the 3-coordinated [BO(3)] (B3) trigonal planar environments. The data obtained are of sufficient quality that they can be used to test the distributions of borate and borosilicate superstructural units predicted by the thermodynamics-based Model of Associated Solutions. The model predicts the dominant boron-containing chemical groupings in Pyrex® glass to be those associated with B(2)O(3) and sodium tetraborate (with smaller amounts of sodium triborate, sodium diborate, sodium pentaborate, danburite and reedmergnerite). Excellent agreement is found between model and experiment provided the (11)B peaks with isotropic chemical shifts of -1.4 ppm and 0.5 ppm are assigned to B4 species from borosilicate units ([B(OSi)(4)] and [B(OSi)(3)(OB)]) and borate superstructural units (mainly triborate rings with some pentaborate and diborate) respectively. The peaks with isotropic shifts of 14 ppm and 18.1 ppm are then assigned to B3 in borate superstructural units (mainly triborate and pentaborate along with connecting B3) and boroxol rings respectively. The assignments of the DOR NMR peaks, are supported by the presence of cross-peaks in (11)B spin-diffusion DOR NMR spectra which can be used to develop a structural model in which B(2)O(3)-like regions are linked, via borate and borosilicate superstructural units, to the majority silica network. Pyrex® is thus shown to have a heterogeneous structure, with distinct molecular groupings that are far removed from a random distribution of network polyhedra with only short-range order. This journal is © the Owner Societies 2011

Using NMR to Determine Protein Structure in Solution

NASA Astrophysics Data System (ADS)

Cavagnero, Silvia

2003-02-01

Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

Surface characterization of hydrophobic core-shell QDs using NMR techniques

NASA Astrophysics Data System (ADS)

Zhang, Chengqi; Zeng, Birong; Palui, Goutam; Mattoussi, Hedi

2018-02-01

Using a few solution phase NMR spectroscopy techniques, including 1H NMR and 31P NMR, we have characterized the organic shell on CdSe-ZnS core-shell quantum dots and tracked changes in its composition when the QD dispersions are subjected to varying degrees of purification. Combining solution phase NMR with diffusion ordered spectroscopy (DOSY), we were able to distinguish between freely diffusing ligands in the sample from those bound on the surfaces. Additionally, matrix assisted laser desorption ionization (MALDI) and FTIR measurements were used to provide complementary and supporting information on the organic ligand coating for these nanocrystals. We found that the organic shell is dominated by monomeric or oligomeric n-hexylphosphonic acid (HPA), along with small portion of 1-hexadecyl amine (HDA). The presence of TOP/TOPO (tri-n-octylphosphine / tri-noctylphosphine oxide) molecules is much smaller, even though large excess of TOP/TOPO were used during the QD growth. These results indicate that HPA (alkyl phosphonate) exhibits the strongest coordination affinity to ZnS-rich QD surfaces grown using the high temperature injection route.

Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

PubMed Central

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

2011-01-01

One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

Analytical solution of the time-dependent Bloch NMR flow equations: a translational mechanical analysis

NASA Astrophysics Data System (ADS)

Awojoyogbe, O. B.

2004-08-01

Various biological and physiological properties of living tissue can be studied by means of nuclear magnetic resonance techniques. Unfortunately, the basic physics of extracting the relevant information from the solution of Bloch nuclear magnetic resource (NMR) equations to accurately monitor the clinical state of biological systems is still not yet fully understood. Presently, there are no simple closed solutions known to the Bloch equations for a general RF excitation. Therefore the translational mechanical analysis of the Bloch NMR equations presented in this study, which can be taken as definitions of new functions to be studied in detail may reveal very important information from which various NMR flow parameters can be derived. Fortunately, many of the most important but hidden applications of blood flow parameters can be revealed without too much difficulty if appropriate mathematical techniques are used to solve the equations. In this study we are concerned with a mathematical study of the laws of NMR physics from the point of view of translational mechanical theory. The important contribution of this study is that solutions to the Bloch NMR flow equations do always exist and can be found as accurately as desired. We shall restrict our attention to cases where the radio frequency field can be treated by simple analytical methods. First we shall derive a time dependant second-order non-homogeneous linear differential equation from the Bloch NMR equation in term of the equilibrium magnetization M0, RF B1( t) field, T1 and T2 relaxation times. Then, we would develop a general method of solving the differential equation for the cases when RF B1( t)=0, and when RF B1( t)≠0. This allows us to obtain the intrinsic or natural behavior of the NMR system as well as the response of the system under investigation to a specific influence of external force to the system. Specifically, we consider the case where the RF B1 varies harmonically with time. Here the complete motion of the system consists of two parts. The first part describes the motion of the transverse magnetization My in the absence of RF B( t) field. The second part of the motion described by the particular integral of the derived differential equation does not decay with time but continues its periodic behavior indefinitely. The complete motion of the NMR flow system is then quantitatively and qualitatively described.

Towards the elucidation of molecular determinants of cooperativity in the liver bile acid binding protein.

PubMed

Pedò, Massimo; D'Onofrio, Mariapina; Ferranti, Pasquale; Molinari, Henriette; Assfalg, Michael

2009-11-15

Bile acid binding proteins (BABPs) are cytosolic lipid chaperones contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Liver BABPs act in parallel with ileal transporters to ensure vectorial transport of bile salts in hepatocytes and enterocytes, respectively. We describe the investigation of ligand binding to liver BABP, an essential step in the understanding of intracellular bile salt transport. Binding site occupancies were monitored in NMR titration experiments using (15)N-labelled ligand, while the relative populations of differently bound BABP forms were assessed by mass spectrometry. This site-specific information allowed the determination of intrinsic thermodynamic parameters and the identification of an extremely high cooperativity between two binding sites. Protein-observed NMR experiments revealed a global structural rearrangement which suggests an allosteric mechanism at the basis of the observed cooperativity. The view of a molecular tool capable of buffering against significant concentrations of free bile salts in a large range of solution conditions emerges from the observed pH-dependence of binding. We set to determine the molecular determinants of cooperativity by analysing the binding properties of a protein containing a mutated internal histidine. Both mass spectrometry and NMR experiments are consistent with an overall decreased binding affinity of the mutant, while the measured diffusion coefficients of ligand species reveal that the affinity loss concerns essentially one of the two binding sites. We therefore identified a mutation able to disrupt energetic communication functional to efficient binding and conclude that the buried histidine establishes contacts that stabilize the ternary complex. 2009 Wiley-Liss, Inc.

Comprehensive multiphase NMR spectroscopy: Basic experimental approaches to differentiate phases in heterogeneous samples

NASA Astrophysics Data System (ADS)

Courtier-Murias, Denis; Farooq, Hashim; Masoom, Hussain; Botana, Adolfo; Soong, Ronald; Longstaffe, James G.; Simpson, Myrna J.; Maas, Werner E.; Fey, Michael; Andrew, Brian; Struppe, Jochem; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J.; Hume, Alan; Simpson, André J.

2012-04-01

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate 1H and 13C spectra for the different phases. In addition, 19F performance is also addressed. To illustrate the capability of 19F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state.

Comprehensive multiphase NMR spectroscopy: basic experimental approaches to differentiate phases in heterogeneous samples.

PubMed

Courtier-Murias, Denis; Farooq, Hashim; Masoom, Hussain; Botana, Adolfo; Soong, Ronald; Longstaffe, James G; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Andrew, Brian; Struppe, Jochem; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Hume, Alan; Simpson, André J

2012-04-01

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate (1)H and (13)C spectra for the different phases. In addition, (19)F performance is also addressed. To illustrate the capability of (19)F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state. Copyright © 2012 Elsevier Inc. All rights reserved.

A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra.

PubMed

Moseley, Hunter N B; Riaz, Nadeem; Aramini, James M; Szyperski, Thomas; Montelione, Gaetano T

2004-10-01

We present an algorithm and program called Pattern Picker that performs editing of raw peak lists derived from multidimensional NMR experiments with characteristic peak patterns. Pattern Picker detects groups of correlated peaks within peak lists from reduced dimensionality triple resonance (RD-TR) NMR spectra, with high fidelity and high yield. With typical quality RD-TR NMR data sets, Pattern Picker performs almost as well as human analysis, and is very robust in discriminating real peak sets from noise and other artifacts in unedited peak lists. The program uses a depth-first search algorithm with short-circuiting to efficiently explore a search tree representing every possible combination of peaks forming a group. The Pattern Picker program is particularly valuable for creating an automated peak picking/editing process. The Pattern Picker algorithm can be applied to a broad range of experiments with distinct peak patterns including RD, G-matrix Fourier transformation (GFT) NMR spectra, and experiments to measure scalar and residual dipolar coupling, thus promoting the use of experiments that are typically harder for a human to analyze. Since the complexity of peak patterns becomes a benefit rather than a drawback, Pattern Picker opens new opportunities in NMR experiment design.

Molecular interactions in ethyl acetate-chlorobenzene binary solution: Dielectric, spectroscopic studies and quantum chemical calculations.

PubMed

Karthick, N K; Kumbharkhane, A C; Joshi, Y S; Mahendraprabu, A; Shanmugam, R; Elangovan, A; Arivazhagan, G

2017-05-05

Dielectric studies using Time Domain Reflectometry method has been carried out on the binary solution of Ethyl acetate (EA) with Chlorobenzene (CBZ) over the entire composition range. Spectroscopic (FTIR and 13 C NMR) signatures of neat EA, CBZ and their equimolar binary solution have also been recorded. The results of the spectroscopic studies favour the presence of (CBZ) CH⋯OC (EA), (EA) methylene CH⋯π electrons (CBZ) and (EA) methyl CH⋯Cl (CBZ) contacts which have been validated using quantum chemical calculations. Dimerization of CBZ has been identified. Presence of β-clusters has been identified in all the solutions. Although EA and CBZ molecules have nearly equal molar volumes, CBZ molecules experience larger hindrance for the rotation than EA molecules. Very small excess dielectric constant (ε E ) values may be correlated with weak heteromolecular forces and/or closed heteromolecular association. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular interactions in ethyl acetate-chlorobenzene binary solution: Dielectric, spectroscopic studies and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Karthick, N. K.; Kumbharkhane, A. C.; Joshi, Y. S.; Mahendraprabu, A.; Shanmugam, R.; Elangovan, A.; Arivazhagan, G.

2017-05-01

Dielectric studies using Time Domain Reflectometry method has been carried out on the binary solution of Ethyl acetate (EA) with Chlorobenzene (CBZ) over the entire composition range. Spectroscopic (FTIR and 13C NMR) signatures of neat EA, CBZ and their equimolar binary solution have also been recorded. The results of the spectroscopic studies favour the presence of (CBZ) Csbnd H ⋯ Odbnd C (EA), (EA) methylene Csbnd H ⋯ π electrons (CBZ) and (EA) methyl Csbnd H ⋯ Cl (CBZ) contacts which have been validated using quantum chemical calculations. Dimerization of CBZ has been identified. Presence of β-clusters has been identified in all the solutions. Although EA and CBZ molecules have nearly equal molar volumes, CBZ molecules experience larger hindrance for the rotation than EA molecules. Very small excess dielectric constant (εE) values may be correlated with weak heteromolecular forces and/or closed heteromolecular association.

Influence of substituents on the solution conformation of the exopolysaccharide produced by Pseudomonas 'gingeri' strain Pf9.

PubMed

Gianni, R; Cescutti, P; Bosco, M; Fett, W F; Rizzo, R

1999-12-01

The influence of pyruvate ketals and acetyl groups on the conformational behaviour of the exopolysaccharide produced by Pseudomonas 'gingeri' strain Pf9 has been investigated experimentally through studies of intrinsic viscosity and circular dichroism experiments. A conformational variation was detected as a function of the ionic strength. Measurements carried out on the native polymer, as well as on both de-pyruvated and de-acetylated samples, suggested a critical role for the acetyl group on the solution conformation of the polysaccharide. Molecular mechanics calculations indicated the possibility of intramolecular hydrogen bonding between acetyl substituents on the mannose and the C(2)OH group of the preceding saccharidic unit. NMR linewidth measurements, carried out as a function of temperature, on the low molecular weight de-pyruvated sample indicated different polymeric backbone dynamics in aqueous solutions with respect to that observed in 0.3 M NaCl solutions.

Solution and solid-state effects on NMR chemical shifts in sesquiterpene lactones: NMR, X-ray, and theoretical methods.

PubMed

Dračínský, Martin; Buděšínský, Miloš; Warżajtis, Beata; Rychlewska, Urszula

2012-01-12

Selected guaianolide type sesquiterpene lactones were studied combining solution and solid-state NMR spectroscopy with theoretical calculations of the chemical shifts in both environments and with the X-ray data. The experimental (1)H and (13)C chemical shifts in solution were successfully reproduced by theoretical calculations (with the GIAO method and DFT B3LYP 6-31++G**) after geometry optimization (DFT B3LYP 6-31 G**) in vacuum. The GIPAW method was used for calculations of solid-state (13)C chemical shifts. The studied cases involved two polymorphs of helenalin, two pseudopolymorphs of 6α-hydroxydihydro-aromaticin and two cases of multiple asymmetric units in crystals: one in which the symmetry-independent molecules were connected by a series of hydrogen bonds (geigerinin) and the other in which the symmetry-independent molecules, deprived of any specific intermolecular interactions, differed in the conformation of the side chain (badkhysin). Geometrically different molecules present in the crystal lattices could be easily distinguished in the solid-state NMR spectra. Moreover, the experimental differences in the (13)C chemical shifts corresponding to nuclei in different polymorphs or in geometrically different molecules were nicely reproduced with the GIPAW calculations.

Two-dimensional NMR spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farrar, T.C.

1987-06-01

This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t/sub 0/; an evolution period, t/sub 1/; and a detection period, t/sub 2/.

A simple hand-held magnet array for efficient and reproducible SABRE hyperpolarisation using manual sample shaking.

PubMed

Richardson, Peter M; Jackson, Scott; Parrott, Andrew J; Nordon, Alison; Duckett, Simon B; Halse, Meghan E

2018-07-01

Signal amplification by reversible exchange (SABRE) is a hyperpolarisation technique that catalytically transfers nuclear polarisation from parahydrogen, the singlet nuclear isomer of H 2 , to a substrate in solution. The SABRE exchange reaction is carried out in a polarisation transfer field (PTF) of tens of gauss before transfer to a stronger magnetic field for nuclear magnetic resonance (NMR) detection. In the simplest implementation, polarisation transfer is achieved by shaking the sample in the stray field of a superconducting NMR magnet. Although convenient, this method suffers from limited reproducibility and cannot be used with NMR spectrometers that do not have appreciable stray fields, such as benchtop instruments. Here, we use a simple hand-held permanent magnet array to provide the necessary PTF during sample shaking. We find that the use of this array provides a 25% increase in SABRE enhancement over the stray field approach, while also providing improved reproducibility. Arrays with a range of PTFs were tested, and the PTF-dependent SABRE enhancements were found to be in excellent agreement with comparable experiments carried out using an automated flow system where an electromagnet is used to generate the PTF. We anticipate that this approach will improve the efficiency and reproducibility of SABRE experiments carried out using manual shaking and will be particularly useful for benchtop NMR, where a suitable stray field is not readily accessible. The ability to construct arrays with a range of PTFs will also enable the rapid optimisation of SABRE enhancement as function of PTF for new substrate and catalyst systems. © 2017 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Structural consequences of metallothionein dimerization: solution structure of the isolated Cd4-alpha-domain and comparison with the holoprotein dimer.

PubMed

Ejnik, John W; Muñoz, Amalia; DeRose, Eugene; Shaw, C Frank; Petering, David H

2003-07-22

The NMR determination of the structure of Cd(7)-metallothionein was done previously using a relatively large protein concentration that favors dimer formation. The reactivity of the protein is also affected under this condition. To examine the influence of protein concentration on metallothionein conformation, the isolated Cd(4)-alpha-domain was prepared from rabbit metallothionein-2 (MT 2), and its three-dimensional structure was determined by heteronuclear, (1)H-(111)Cd, and homonuclear, (1)H-(1)H NMR, correlation experiments. The three-dimensional structure was refined using distance and angle constraints derived from these two-dimensional NMR data sets and a distance geometry/simulated annealing protocol. The backbone superposition of the alpha-domain from rabbit holoprotein Cd(7)-MT 2 and the isolated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A. Nevertheless, the conformations of the two Cd-thiolate clusters were distinctly different at two of the cadmium centers. In addition, solvent access to the sulfhydryl ligands of the isolated Cd(4)-alpha cluster was 130% larger due to this small change in cluster geometry. To probe whether these differences were an artifact of the structure calculation, the Cd(4)-alpha-domain structure in rabbit Cd(7)-MT 2 was redetermined, using the previously defined set of NOEs and the present calculation protocol. All calculations employed the same ionic radius for Cd(2+) and same cadmium-thiolate bond distance. The newly calculated structure matched the original with an RMSD of 1.24 A. It is hypothesized that differences in the two alpha-domain structures result from a perturbation of the holoprotein structure because of head-to-tail dimerization under the conditions of the NMR experiments.

Water absorption of freeze-dried meat at different water activities: a multianalytical approach using sorption isotherm, differential scanning calorimetry, and nuclear magnetic resonance.

PubMed

Venturi, Luca; Rocculi, Pietro; Cavani, Claudio; Placucci, Giuseppe; Dalla Rosa, Marco; Cremonini, Mauro A

2007-12-26

Hydration of freeze-dried chicken breast meat was followed in the water activity range of aw=0.12-0.99 by a multianalytical approach comprising of sorption isotherm, differential scanning calorimetry (DSC), and nuclear magnetic resonance (NMR). The amount of frozen water and the shape of the T2-relaxogram were evaluated at each water content by DSC and NMR, respectively. Data revealed an agreement between sorption isotherm and DSC experiments about the onset of bulk water (aw=0.83-0.86), and NMR detected mobile water starting at aw=0.75. The origin of the short-transverse relaxation time part of the meat NMR signal was also reinvestigated through deuteration experiments and proposed to arise from protons belonging to plasticized matrix structures. It is proved both by D2O experiments and by gravimetry that the extra protons not contributing to the water content in the NMR experiments are about 6.4% of the total proton NMR CPMG signal of meat.

Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy

ERIC Educational Resources Information Center

Ruhayel, Rasha A.; Berners-Price, Susan J.

2010-01-01

2D [superscript 1]H NOESY NMR spectroscopy is routinely used to give information on the closeness of hydrogen atoms through space. This work is based on a 2D [superscript 1]H NOESY NMR spectrum of a 12 base-pair DNA duplex. This 6-h laboratory workshop aims to provide advanced-level chemistry students with a basic, yet solid, understanding of how…

NMR structure of navel orangeworm moth pheromone-binding protein (AtraPBP1): implications for pH-sensitive pheromone detection.

PubMed

Xu, Xianzhong; Xu, Wei; Rayo, Josep; Ishida, Yuko; Leal, Walter S; Ames, James B

2010-02-23

The navel orangeworm, Amyelois transitella (Walker), is an agricultural insect pest that can be controlled by disrupting male-female communication with sex pheromones, a technique known as mating disruption. Insect pheromone-binding proteins (PBPs) provide fast transport of hydrophobic pheromones through the aqueous sensillar lymph and promote sensitive delivery of pheromones to receptors. Here we present the three-dimensional structure of a PBP from A. transitella (AtraPBP1) in solution at pH 4.5 determined by nuclear magnetic resonance (NMR) spectroscopy. Pulsed-field gradient NMR diffusion experiments, multiangle light scattering, and (15)N NMR relaxation analysis indicate that AtraPBP1 forms a stable monomer in solution at pH 4.5 in contrast to forming mostly dimers at pH 7. The NMR structure of AtraPBP1 at pH 4.5 contains seven alpha-helices (alpha1, L8-L23; alpha2, D27-F36; alpha3, R46-V62; alpha4, A73-M78; alpha5, D84-S100; alpha6, R107-L125; alpha7, M131-E141) that adopt an overall main-chain fold similar to that of PBPs found in Antheraea polyphemus and Bombyx mori. The AtraPBP1 structure is stabilized by three disulfide bonds formed by C19/C54, C50/C108, and C97/C117 and salt bridges formed by H69/E60, H70/E57, H80/E132, H95/E141, and H123/D40. All five His residues are cationic at pH 4.5, whereas H80 and H95 become neutral at pH 7.0. The C-terminal helix (alpha7) contains hydrophobic residues (M131, V133, V134, V135, V138, L139, and A140) that contact conserved residues (W37, L59, A73, F76, A77, I94, V111, and V115) suggested to interact with bound pheromone. Our NMR studies reveal that acid-induced formation of the C-terminal helix at pH 4.5 is triggered by a histidine protonation switch that promotes rapid release of bound pheromone under acidic conditions.

PIC microcontroller based external fast analog to digital converter to acquire wide-lined solid NMR spectra by BRUKER DRX and Avance-I spectrometers.

PubMed

Koczor, Bálint; Rohonczy, János

2015-01-01

Concerning many former liquid or hybrid liquid/solid NMR consoles, the built in Analog-to-Digital Converters (ADCs) are incapable of digitizing the fids at sampling rates in the MHz range. Regarding both strong anisotropic interactions in the solid state and wide chemical shift dispersion nuclei in solution phase such as (195)Pt, (119)Sn, (207)Pb etc., the spectrum range of interest might be in the MHz range. As determining the informative tensor components of anisotropic NMR interactions requires nonlinear fitting over the whole spectrum including the asymptotic baseline, it is prohibited by low sampling rates of the ADCs. Wide spectrum width is also useful in solution NMR, since windowing of wide chemical shift ranges is avoidable. We built an external analog to digital converter with 10 MHz maximal sampling rate, which can work simultaneously with the built in ADC of the spectrometer. The ADC was tested on both Bruker DRX and Avance-I NMR consoles. In addition to the analog channels it only requires three external digital lines of the NMR console. The ADC sends data to PC via USB. The whole process is controlled by software written in JAVA which is implemented under TopSpin. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization of Non-Innocent Metal Complexes Using Solid-State NMR Spectroscopy: o-Dioxolene Vanadium Complexes

PubMed Central

Chatterjee, Pabitra B.; Goncharov-Zapata, Olga; Quinn, Laurence L.; Hou, Guangjin; Hamaed, Hiyam; Schurko, Robert W.; Polenova, Tatyana; Crans, Debbie C.

2012-01-01

51V solid-state NMR (SSNMR) studies of a series of non-innocent vanadium(V) catechol complexes have been conducted to evaluate the possibility that 51V NMR observables, quadrupolar and chemical shift anisotropies, and electronic structures of such compounds can be used to characterize these compounds. The vanadium(V) catechol complexes described in these studies have relatively small quadrupolar coupling constants, which cover a surprisingly small range from 3.4 to 4.2 MHz. On the other hand, isotropic 51V NMR chemical shifts cover a wide range from −200 ppm to 400 ppm in solution and from −219 to 530 ppm in the solid state. A linear correlation of 51V NMR isotropic solution and solid-state chemical shifts of complexes containing non-innocent ligands is observed. These experimental results provide the information needed for the application of 51V SSNMR spectroscopy in characterizing the electronic properties of a wide variety of vanadium-containing systems, and in particular those containing non-innocent ligands and that have chemical shifts outside the populated range of −300 ppm to −700 ppm. The studies presented in this report demonstrate that the small quadrupolar couplings covering a narrow range of values reflect the symmetric electronic charge distribution, which is also similar across these complexes. These quadrupolar interaction parameters alone are not sufficient to capture the rich electronic structure of these complexes. In contrast, the chemical shift anisotropy tensor elements accessible from 51V SSNMR experiments are a highly sensitive probe of subtle differences in electronic distribution and orbital occupancy in these compounds. Quantum chemical (DFT) calculations of NMR parameters for [VO(hshed)(Cat)] yield 51V CSA tensor in reasonable agreement with the experimental results, but surprisingly, the calculated quadrupolar coupling constant is significantly greater than the experimental value. The studies demonstrate that substitution of the catechol ligand with electron donating groups results in an increase in the HOMO-LUMO gap and can be directly followed by an upfield shift for the vanadium catechol complex. In contrast, substitution of the catechol ligand with electron withdrawing groups results in a decrease in the HOMO-LUMO gap and can directly be followed by a downfield shift for the complex. The vanadium catechol complexes were used in this work because the 51V is a half-integer quadrupolar nucleus whose NMR observables are highly sensitive to the local environment. However, the results are general and could be extended to other redox active complexes that exhibit similar coordination chemistry as the vanadium catechol complexes. PMID:21842875

Inclusion complex of benzocaine and β-cyclodextrin: 1H NMR and isothermal titration calorimetry studies

NASA Astrophysics Data System (ADS)

Mic, Mihaela; Pırnǎu, Adrian; Bogdan, Mircea; Turcu, Ioan

2013-11-01

The supramolecular structure of the inclusion complex of β-cyclodextrin with benzocaine in aqueous solution has been investigated by 1H NMR spectroscopy and isothermal titration nanocalorimetry (ITC). Analysis of 1H NMR data by continuous variation method indicates that the benzocaine: β-cyclodextrin inclusion complex occurs and has a 1:1 stoichiometry. Rotating frame NOE spectroscopy (ROESY) was used to ascertain the solution geometry of the host-guest complex which indicates that the benzocaine molecule was included with the aromatic ring into the cyclodextrin cavity. Although the affinity of benzocaine for cyclodextrin is relatively high, the association constant cannot be measured using ITC due to the low solubility of benzocaine in water.

Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy.

PubMed

Becker, Walter; Bhattiprolu, Krishna Chaitanya; Gubensäk, Nina; Zangger, Klaus

2018-04-17

Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Transformation of meta-stable calcium silicate hydrates to tobermorite: reaction kinetics and molecular structure from XRD and NMR spectroscopy

PubMed Central

2009-01-01

Understanding the integrity of well-bore systems that are lined with Portland-based cements is critical to the successful storage of sequestered CO2 in gas and oil reservoirs. As a first step, we investigate reaction rates and mechanistic pathways for cement mineral growth in the absence of CO2 by coupling water chemistry with XRD and NMR spectroscopic data. We find that semi-crystalline calcium (alumino-)silicate hydrate (Al-CSH) forms as a precursor solid to the cement mineral tobermorite. Rate constants for tobermorite growth were found to be k = 0.6 (± 0.1) × 10-5 s-1 for a solution:solid of 10:1 and 1.6 (± 0.8) × 10-4 s-1 for a solution:solid of 5:1 (batch mode; T = 150°C). This data indicates that reaction rates for tobermorite growth are faster when the solution volume is reduced by half, suggesting that rates are dependent on solution saturation and that the Gibbs free energy is the reaction driver. However, calculated solution saturation indexes for Al-CSH and tobermorite differ by less than one log unit, which is within the measured uncertainty. Based on this data, we consider both heterogeneous nucleation as the thermodynamic driver and internal restructuring as possible mechanistic pathways for growth. We also use NMR spectroscopy to characterize the site symmetry and bonding environment of Al and Si in a reacted tobermorite sample. We find two [4]Al coordination structures at δiso = 59.9 ppm and 66.3 ppm with quadrupolar product parameters (PQ) of 0.21 MHz and 0.10 MHz (± 0.08) from 27Al 3Q-MAS NMR and speculate on the Al occupancy of framework sites by probing the protonation environment of Al metal centers using 27Al{1H}CP-MAS NMR. PMID:19144195

Ionic Liquid–Solute Interactions Studied by 2D NOE NMR Spectroscopy

DOE PAGES

Khatun, Sufia; Castner, Edward W.

2014-11-26

Intermolecular interactions between a Ru²⁺(bpy)₃ solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {¹H-¹⁹F} HOESY and {¹H-¹H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru²⁺(bpy)₃ solute is rather different from the bulkmore » IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru²⁺(bpy)₃ solute interacts with both the polar head and the nonpolar tail groups of the 1- butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.« less

Beyond Fourier

NASA Astrophysics Data System (ADS)

Hoch, Jeffrey C.

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development.

Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand–protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency

PubMed Central

Delius, Judith; Frank, Oliver

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy is well-established in assessing the binding affinity between low molecular weight ligands and proteins. However, conventional NMR-based binding assays are often limited to small proteins of high purity and may require elaborate isotopic labeling of one of the potential binding partners. As protein–polyphenol complexation is assumed to be a key event in polyphenol-mediated oral astringency, here we introduce a label-free, ligand-focused 1H NMR titration assay to estimate binding affinities and characterize soluble complex formation between proteins and low molecular weight polyphenols. The method makes use of the effects of NMR line broadening due to protein–ligand interactions and quantitation of the non-bound ligand at varying protein concentrations by quantitative 1H NMR spectroscopy (qHNMR) using electronic reference to access in vivo concentration (ERETIC 2). This technique is applied to assess the interaction kinetics of selected astringent tasting polyphenols and purified mucin, a major lubricating glycoprotein of human saliva, as well as human whole saliva. The protein affinity values (BC50) obtained are subsequently correlated with the intrinsic mouth-puckering, astringent oral sensation imparted by these compounds. The quantitative NMR method is further exploited to study the effect of carboxymethyl cellulose, a candidate “anti-astringent” protein binding antagonist, on the polyphenol–protein interaction. Consequently, the NMR approach presented here proves to be a versatile tool to study the interactions between proteins and low-affinity ligands in solution and may find promising applications in the discovery of bioactives. PMID:28886151

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

NASA Technical Reports Server (NTRS)

Smith, G. K.; Jie, J.; Fox, G. E.; Gao, X.

1995-01-01

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

Interfacial Water at Protein Surfaces: Wide-Line NMR and DSC Characterization of Hydration in Ubiquitin Solutions

PubMed Central

Tompa, Kálmán; Bánki, Péter; Bokor, Mónika; Kamasa, Pawel; Lasanda, György; Tompa, Péter

2009-01-01

Wide-line 1H-NMR and differential scanning calorimetry measurements were done in aqueous solutions and on lyophilized samples of human ubiquitin between −70°C and +45°C. The measured properties (size, thermal evolution, and wide-line NMR spectra) of the protein-water interfacial region are substantially different in the double-distilled and buffered-water solutions of ubiquitin. The characteristic transition in water mobility is identified as the melting of the nonfreezing/hydrate water. The amount of water in the low-temperature mobile fraction is 0.4 g/g protein for the pure water solution. The amount of mobile water is higher and its temperature dependence more pronounced for the buffered solution. The specific heat of the nonfreezing/hydrate water was evaluated using combined differential scanning calorimetry and NMR data. Considering the interfacial region as an independent phase, the values obtained are 5.0–5.8 J·g−1·K−1, and the magnitudes are higher than that of pure/bulk water (4.2 J·g−1·K−1). This unexpected discrepancy can only be resolved in principle by assuming that hydrate water is in tight H-bond coupling with the protein matrix. The specific heat for the system composed of the protein molecule and its hydration water is 2.3 J·g−1·K−1. It could be concluded that the protein ubiquitin and its hydrate layer behave as a highly interconnected single phase in a thermodynamic sense. PMID:19348762

Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

ERIC Educational Resources Information Center

Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

2015-01-01

A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

Proton-Based Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy.

PubMed

Zhang, Rongchun; Mroue, Kamal H; Ramamoorthy, Ayyalusamy

2017-04-18

Protons are vastly abundant in a wide range of exciting macromolecules and thus can be a powerful probe to investigate the structure and dynamics at atomic resolution using solid-state NMR (ssNMR) spectroscopy. Unfortunately, the high signal sensitivity, afforded by the high natural-abundance and high gyromagnetic ratio of protons, is greatly compromised by severe line broadening due to the very strong 1 H- 1 H dipolar couplings. As a result, protons are rarely used, in spite of the desperate need for enhancing the sensitivity of ssNMR to study a variety of systems that are not amenable for high resolution investigation using other techniques including X-ray crystallography, cryo-electron microscopy, and solution NMR spectroscopy. Thanks to the remarkable improvement in proton spectral resolution afforded by the significant advances in magic-angle-spinning (MAS) probe technology, 1 H ssNMR spectroscopy has recently attracted considerable attention in the structural and dynamics studies of various molecular systems. However, it still remains a challenge to obtain narrow 1 H spectral lines, especially from proteins, without resorting to deuteration. In this Account, we review recent proton-based ssNMR strategies that have been developed in our laboratory to further improve proton spectral resolution without resorting to chemical deuteration for the purposes of gaining atomistic-level insights into molecular structures of various crystalline solid systems, using small molecules and peptides as illustrative examples. The proton spectral resolution enhancement afforded by the ultrafast MAS frequencies up to 120 kHz is initially discussed, followed by a description of an ensemble of multidimensional NMR pulse sequences, all based on proton detection, that have been developed to obtain in-depth information from dipolar couplings and chemical shift anisotropy (CSA). Simple single channel multidimensional proton NMR experiments could be performed to probe the proximity of protons for structure determination using 1 H- 1 H dipolar couplings and to evaluate the changes in chemical environments as well as the relative orientation to the external magnetic field using proton CSA. Due to the boost in signal sensitivity enabled by proton detection under ultrafast MAS, by virtue of high proton natural abundance and gyromagnetic ratio, proton-detected multidimensional experiments involving low-γ nuclei can now be accomplished within a reasonable time, while the higher dimension also offers additional resolution enhancement. In addition, the application of proton-based ssNMR spectroscopy under ultrafast MAS in various challenging and crystalline systems is also presented. Finally, we briefly discuss the limitations and challenges pertaining to proton-based ssNMR spectroscopy under ultrafast MAS conditions, such as the presence of high-order dipolar couplings, friction-induced sample heating, and limited sample volume. Although there are still a number of challenges that must be circumvented by further developments in radio frequency pulse sequences, MAS probe technology and approaches to prepare NMR-friendly samples, proton-based ssNMR has already gained much popularity in various research domains, especially in proteins where uniform or site-selective deuteration can be relatively easily achieved. In addition, implementation of the recently developed fast data acquisition approaches would also enable further developments in the design and applications of proton-based ultrafast MAS multidimensional ssNMR techniques.

Titration of Alanine Monitored by NMR Spectroscopy: A Biochemistry Laboratory Experiment

ERIC Educational Resources Information Center

Waller, Francis J.; And Others

1977-01-01

The experiment described here involves simultaneous monitoring of pH and NMR chemical shifts during an aqueous titration of alpha- and beta-alanine. This experiment is designed for use in an undergraduate biochemistry course. (MR)

Cryptophane Nanoscale Assemblies Expand 129Xe NMR Biosensing.

PubMed

Zemerov, Serge D; Roose, Benjamin W; Greenberg, Mara L; Wang, Yanfei; Dmochowski, Ivan J

2018-06-19

Cryptophane-based biosensors are promising agents for the ultrasensitive detection of biomedically relevant targets via 129 Xe NMR. Dynamic light scattering revealed that cryptophanes form water-soluble aggregates tens to hundreds of nanometers in size. Acridine orange fluorescence quenching assays allowed quantitation of the aggregation state, with critical concentrations ranging from 200 nM to 600 nM, depending on the cryptophane species in solution. The addition of excess carbonic anhydrase (CA) protein target to a benzenesulfonamide-functionalized cryptophane biosensor (C8B) led to C8B disaggregation and produced the expected 1:1 C8B-CA complex. C8B showed higher affinity at 298 K for the cytoplasmic isozyme CAII than the extracellular CAXII isozyme, which is a biomarker of cancer. Using hyper-CEST NMR, we explored the role of stoichiometry in detecting these two isozymes. Under CA-saturating conditions, we observed that isozyme CAII produces a larger 129 Xe NMR chemical shift change (δ = 5.9 ppm, relative to free biosensor) than CAXII (δ = 2.7 ppm), which indicates the strong potential for isozyme-specific detection. However, stoichiometry-dependent chemical shift data indicated that biosensor disaggregation contributes to the observed 129 Xe NMR chemical shift change that is normally assigned to biosensor-target binding. Finally, we determined that monomeric cryptophane solutions improve hyper-CEST saturation contrast, which enables ultrasensitive detection of biosensor-protein complexes. These insights into cryptophane-solution behavior support further development of xenon biosensors, but will require reinterpretation of the data previously obtained for many water-soluble cryptophanes.

Molecular structure in the solid state by X-ray crystallography and SSNMR and in solution by NMR of two 1,4-diazepines

NASA Astrophysics Data System (ADS)

Nieto, Carla I.; Sanz, Dionisia; Claramunt, Rosa M.; Torralba, M. Carmen; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

2018-03-01

The crystals of two 1,4-diazepines prepared from curcuminoid β-diketones and ethylenediamine were studied by X-ray crystallography and NMR. Their tautomerism, intramolecular hydrogen bonds and conformation were determined.

Mathematical Development and Computational Analysis of Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) Based on Bloch Nuclear Magnetic Resonance (NMR) Diffusion Model for Myocardial Motion.

PubMed

Dada, Michael O; Jayeoba, Babatunde; Awojoyogbe, Bamidele O; Uno, Uno E; Awe, Oluseyi E

2017-09-13

Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) is a tagged image analysis method that can measure myocardial motion and strain in near real-time and is considered a potential candidate to make magnetic resonance tagging clinically viable. However, analytical expressions of radially tagged transverse magnetization in polar coordinates (which is required to appropriately describe the shape of the heart) have not been explored because the physics required to directly connect myocardial deformation of tagged Nuclear Magnetic Resonance (NMR) transverse magnetization in polar geometry and the appropriate harmonic phase parameters are not yet available. The analytical solution of Bloch NMR diffusion equation in spherical geometry with appropriate spherical wave tagging function is important for proper analysis and monitoring of heart systolic and diastolic deformation with relevant boundary conditions. In this study, we applied Harmonic Phase MRI method to compute the difference between tagged and untagged NMR transverse magnetization based on the Bloch NMR diffusion equation and obtained radial wave tagging function for analysis of myocardial motion. The analytical solution of the Bloch NMR equations and the computational simulation of myocardial motion as developed in this study are intended to significantly improve healthcare for accurate diagnosis, prognosis and treatment of cardiovascular related deceases at the lowest cost because MRI scan is still one of the most expensive anywhere. The analysis is fundamental and significant because all Magnetic Resonance Imaging techniques are based on the Bloch NMR flow equations.

Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank

PubMed Central

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-01-01

Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution. PMID:21293729

Solution and Solid State Nuclear Magnetic Resonance Spectroscopic Characterization of Efavirenz.

PubMed

Sousa, Eduardo Gomes Rodrigues de; Carvalho, Erika Martins de; San Gil, Rosane Aguiar da Silva; Santos, Tereza Cristina Dos; Borré, Leandro Bandeira; Santos-Filho, Osvaldo Andrade; Ellena, Javier

2016-09-01

Samples of efavirenz (EFZ) were evaluated to investigate the influence of the micronization process on EFZ stability. A combination of X-ray diffraction, thermal analysis, FTIR, observations of isotropic chemical shifts of (1)H in distinct solvents, their temperature dependence and spin-lattice relaxation time constants (T1), solution (1D and 2D) (13)C nuclear magnetic resonance (NMR), and solid-state (13)C NMR (CPMAS NMR) provides valuable structural information and structural elucidation of micronized EFZ and heptane-recrystallized polymorphs (EFZ/HEPT). This study revealed that the micronization process did not affect the EFZ crystalline structure. It was observed that the structure of EFZ/HEPT is in the same form as that obtained from ethyl acetate/hexane, as shown in the literature. A comparison of the solid-state NMR spectra revealed discrepancies regarding the assignments of some carbons published in the literature that have been resolved. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Osmotic dehydration of organic kiwifruit pre-treated by pulsed electric fields and monitored by NMR.

PubMed

Traffano-Schiffo, Maria Victoria; Laghi, Luca; Castro-Giraldez, Marta; Tylewicz, Urszula; Rocculi, Pietro; Ragni, Luigi; Dalla Rosa, Marco; Fito, Pedro J

2017-12-01

Osmotic dehydration (OD) is a widely used preservation technique that consists in the reduction in food water activity by the immersion of the biological tissue in hypertonic solutions. The aim of this work was to analyze the effect of pulsed electric fields (PEF) in mass transfer as a pre-treatment of the OD using NMR. In this sense, PEF pre-treatments were done using three different voltages (100, 250 and 400V/cm) and 60 number of pulse. The OD of kiwifruit was carried out in 61.5% of sucrose solution at 25°C, for a contact period from 0 to 120min. The water distribution into the cellular tissue was studied by NMR relaxometry. In conclusion, NMR is an excellent technique for quantifying water molecules according to their interactions in the fruit tissue, obtaining the adsorbed water and opening the possibility to apply the BET model to fit the adsorbed isotherm over the whole range of water activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Correlations between the 1H NMR chemical shieldings and the pKa values of organic acids and amines.

PubMed

Lu, Juanfeng; Lu, Tingting; Zhao, Xinyun; Chen, Xi; Zhan, Chang-Guo

2018-06-01

The acid dissociation constants and 1 H NMR chemical shieldings of organic compounds are important properties that have attracted much research interest. However, few studies have explored the relationship between these two properties. In this work, we theoretically studied the NMR chemical shifts of a series of carboxylic acids and amines in the gas phase and in aqueous solution. It was found that the negative logarithms of the experimental acid dissociation constants (i.e., the pK a values) of the organic acids and amines in aqueous solution correlate almost linearly with the corresponding calculated NMR chemical shieldings. Key factors that affect the theoretically predicted pK a values are discussed in this paper. The present work provides a new way to predict the pK a values of organic/biochemical compounds. Graphical abstract The chemical shielding values of organic acids and amines correlate near linearly with their corresponding pK a values.

Rapid NMR method for the quantification of organic compounds in thin stillage.

PubMed

Ratanapariyanuch, Kornsulee; Shen, Jianheng; Jia, Yunhua; Tyler, Robert T; Shim, Youn Young; Reaney, Martin J T

2011-10-12

Thin stillage contains organic and inorganic compounds, some of which may be valuable fermentation coproducts. This study describes a thorough analysis of the major solutes present in thin stillage as revealed by NMR and HPLC. The concentration of charged and neutral organic compounds in thin stillage was determined by excitation sculpting NMR methods (double pulse field gradient spin echo). Compounds identified by NMR included isopropanol, ethanol, lactic acid, 1,3-propanediol, acetic acid, succinic acid, glycerophosphorylcholine, betaine, glycerol, and 2-phenylethanol. The concentrations of lactic and acetic acid determined with NMR were comparable to those determined using HPLC. HPLC and NMR were complementary, as more compounds were identified using both methods. NMR analysis revealed that stillage contained the nitrogenous organic compounds betaine and glycerophosphorylcholine, which contributed as much as 24% of the nitrogen present in the stillage. These compounds were not observed by HPLC analysis.

Anvil cell gasket design for high pressure nuclear magnetic resonance experiments beyond 30 GPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meier, Thomas; Haase, Jürgen

2015-12-15

Nuclear magnetic resonance (NMR) experiments are reported at up to 30.5 GPa of pressure using radiofrequency (RF) micro-coils with anvil cell designs. These are the highest pressures ever reported with NMR, and are made possible through an improved gasket design based on nano-crystalline powders embedded in epoxy resin. Cubic boron-nitride (c-BN), corundum (α-Al{sub 2}O{sub 3}), or diamond based composites have been tested, also in NMR experiments. These composite gaskets lose about 1/2 of their initial height up to 30.5 GPa, allowing for larger sample quantities and preventing damages to the RF micro-coils compared to precipitation hardened CuBe gaskets. It ismore » shown that NMR shift and resolution are less affected by the composite gaskets as compared to the more magnetic CuBe. The sensitivity can be as high as at normal pressure. The new, inexpensive, and simple to engineer gaskets are thus superior for NMR experiments at high pressures.« less

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

PubMed

Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

2018-01-02

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

Crankshaft motion in a highly congested bis(triarylmethyl)peroxide.

PubMed

Khuong, Tinh-Alfredo V; Zepeda, Gerardo; Sanrame, Carlos N; Dang, Hung; Bartberger, Michael D; Houk, K N; Garcia-Garibay, Miguel A

2004-11-17

Crankshaft motion has been proposed in the solid state for molecular fragments consisting of three or more rotors linked by single bonds, whereby the two terminal rotors are static and the internal rotors experience circular motion. Bis-[tri-(3,5-di-tert-butyl)phenylmethyl]-peroxide 2 was tested as a model in search of crankshaft motion at the molecular level. In the case of peroxide 2, the bulky trityl groups may be viewed as the external static rotors, while the two peroxide oxygens can undergo the sought after internal rotation. Evidence for this process in the case of peroxide 2 was obtained from conformational dynamics determined by variable-temperature (13)C and (1)H NMR between 190 and 375 K in toluene-d(8). Detailed spectral assignments for the interpretation of two coalescence processes were based on a correlation between NMR spectra obtained in solution at low temperature, in the solid state by (13)C CPMAS NMR, and by GIAO calculations based on a B3LYP/6-31G structure of 2 obtained from its X-ray coordinates as the input. Evidence supporting crankshaft rotation rather than slippage of the trityl groups was obtained from molecular mechanics calculations.

Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods

PubMed Central

Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

2013-01-01

Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L2-norm regularization. However, sparse representation methods via L1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72–88, 2013. PMID:23847452

Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods.

PubMed

Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

2013-05-01

Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L 2 -norm regularization. However, sparse representation methods via L 1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L 1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72-88, 2013.

CCR5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding.

PubMed

Chen, Bin; Longhini, Andrew P; Nußbaumer, Felix; Kreutz, Christoph; Dinman, Jonathan D; Dayie, T Kwaku

2018-04-11

Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13 C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced. This approach allowed the position-specific insertion of isotopic probes into a 96 nt CCR5 RNA fragment. Accurate measurements of functional dynamics using the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments enabled extraction of the exchange rates and populations of this RNA. NMR chemical shift perturbation analysis of the RNA/microRNA-1224 complex indicated that A90-C1' of the pseudoknot exhibits similar changes in chemical shift observed in the excited state. This work demonstrates the general applicability of a NMR-labeling strategy to probe functional RNA structural dynamics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE PAGES

Foston, Marcus B.; Samuel, Reichel; He, Jian; ...

2016-01-19

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foston, Marcus B.; Samuel, Reichel; He, Jian

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

Interaction Between Cyanine Dye IR-783 and Polystyrene Nanoparticles in Solution.

PubMed

Zhang, Yunzhi; Xu, Hui; Casabianca, Leah B

2018-05-17

The interactions between small molecule drugs or dyes and nanoparticles are important to the use of nanoparticles in medicine. Noncovalent adsorption of dyes on nanoparticle surfaces is also important to the development of nanoparticle dual-use imaging contrast agents. In the present work, solution-state NMR is used to examine the noncovalent interaction between a near-infrared cyanine dye and the surface of polystyrene nanoparticles in solution. Using 1D proton NMR, we can approximate the number of dye molecules that associate with each nanoparticle for different sized nanoparticles. Saturation-Transfer Difference (STD)-NMR was also used to show that protons near the positively-charged nitrogen in the dye are more strongly associated with the negatively-charged nanoparticle surface than protons near the negatively-charged sulfate groups of the dye. The methods described here can be used to study similar drug or dye molecules interacting with the surface of organic nanoparticles. This article is protected by copyright. All rights reserved.

Conformational distribution of baclofen analogues by 1H and 13C NMR analysis and ab initio HF MO STO-3G or STO-3G* calculations

NASA Astrophysics Data System (ADS)

Vaccher, Claude; Berthelot, Pascal; Debaert, Michel; Vermeersch, Gaston; Guyon, René; Pirard, Bernard; Vercauteren, Daniel P.; Dory, Magdalena; Evrard, Guy; Durant, François

1993-12-01

The conformations of 3-(substituted furan-2-yl) and 3-(substituted thien-2-yl)-γ-aminobutyric acid 1-9 in solution (D 2O) are estimated from high-resolution (300 MHz) 1H NMR coupling data. Conformations and populations of conformers are calculated by means of a modified Karplus-like relationship for the vicinal coupling constants. The results are compared with X-ray crystallographic investigations (torsion angles) and ab initio HF MO ST-3G or STO-3G* calculations. 1H NMR spectral analysis shows how 1-9 in solution retain the preferred g- conformation around the C3C4 bond, as found in the solid state, while a partial rotation is set up around the C2C3 bond: the conformations about C2C3 are all highly populated in solution. The 13C spin-lattice relaxation times are also discussed.

IR and NMR studies of hierarchical material obtained by the treatment of zeolite Y by ammonia solution

NASA Astrophysics Data System (ADS)

Gackowski, Mariusz; Kuterasiński, Łukasz; Podobiński, Jerzy; Sulikowski, Bogdan; Datka, Jerzy

2018-03-01

Ammonia treatment of ultrastable zeolite Y has a great impact on its features. XRD showed a partial loss of crystallinity coupled with a loss of long-distance zeolite ordering. However, a typical short-range zeolite ordering, in the light of 29Si NMR studies, was largely preserved. 27Al MAS NMR spectra evidenced that most of Al was located in zeolitic tetrahedral positions, but some of them adopted a distorted configuration. Evolution of zeolites acidity was followed quantitatively by using IR. In particular, such studies revealed the presence of strongly acidic Sisbnd OHsbnd Al groups. IR studies suggest also heterogeneity of these OH groups. The heterogeneity of Sisbnd OHsbnd Al groups was a consequence of the less ordered structure of zeolites treated with ammonia solutions. It was also found that the treatment with ammonia solutions yields hierarchical material. The samples revealed promising catalytic properties in the liquid phase isomerization of α-pinene. Zeolites desilicated with ammonia may constitute an inexpensive route yielding viable hierarchical catalysts.

Structural Evolution and Atom Clustering in β-SiAlON: β-Si 6–z Al z O z N 8–z

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cozzan, Clayton; Griffith, Kent J.; Laurita, Geneva

2017-02-06

SiAlON ceramics, solid solutions based on the Si 3N 4 structure, are important, lightweight structural materials with intrinsically high strength, high hardness, and high thermal and chemical stability. Described by the chemical formula β-Si 6–zAl zO zN 8–z, from a compositional viewpoint, these materials can be regarded as solid solutions between Si 3N 4 and Al 3O 3N. A key aspect of the structural evolution with increasing Al and O (z in the formula) is to understand how these elements are distributed on the β-Si 3N 4 framework. The average and local structural evolution of highly phase-pure samples of β-Simore » 6–zAl zO zN 8–z with z = 0.050, 0.075, and 0.125 are studied here, using a combination of X-ray diffraction, NMR studies, and density functional theory calculations. Synchrotron X-ray diffraction establishes sample purity and indicates subtle changes in the average structure with increasing Al content in these compounds. Solid-state magic-angle-spinning 27Al NMR experiments, coupled with detailed ab initio calculations of NMR spectra of Al in different AlO qN 4–q tetrahedra (0 ≤ q ≤ 4), reveal a tendency of Al and O to cluster in these materials. Independently, the calculations suggest an energetic preference for Al–O bond formation, instead of a random distribution, in the β-SiAlON system.« less

Hydrolysis Studies and Quantitative Determination of Aluminum Ions Using [superscript 27]Al NMR: An Undergraduate Analytical Chemistry Experiment

ERIC Educational Resources Information Center

Curtin, Maria A.; Ingalls, Laura R.; Campbell, Andrew; James-Pederson, Magdalena

2008-01-01

This article describes a novel experiment focused on metal ion hydrolysis and the equilibria related to metal ions in aqueous systems. Using [superscript 27]Al NMR, the students become familiar with NMR spectroscopy as a quantitative analytical tool for the determination of aluminum by preparing a standard calibration curve using standard aluminum…

Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r).

PubMed

Otten, Renee; Villali, Janice; Kern, Dorothee; Mulder, Frans A A

2010-12-01

To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ (1)H Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [(1)H, (13)C]-d-glucose in ∼100% D(2)O, which yields CHD(2) methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using (13)C TOCSY NMR spectroscopy, as was recently demonstrated (Otten, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure (1)H CPMG relaxation dispersion profiles for CHD(2) methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-δ1 and Thr-γ2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong (13)C scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone (15)N CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the (1)H line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 ± 0.5) × 10(3) per second (i.e., τ(ex) = 64.7 ± 1.9 μs). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by (1)H CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone (15)N relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins.

Complexation of rhodium(II) tetracarboxylates with aliphatic diamines in solution: 1H and 13C NMR and DFT investigations.

PubMed

Jaźwiński, Jarosław; Sadlej, Agnieszka

2013-10-01

The complexation of rhodium(II) tetraacetate, tetrakistrifluoroaceate and tetrakisoctanoate with a set of diamines (ethane-1,diamine, propane-1,3-diamine and nonane-1,9-diamine) and their N,N'-dimethyl and N,N,N',N'-tetramethyl derivatives in chloroform solution has been investigated by (1) H and (13) C NMR spectroscopy and density functional theory (DFT) modelling. A combination of two bifunctional reagents, diamines and rhodium(II) tetracarboxylates, yielded insoluble coordination polymers as main products of complexation and various adducts in the solution, being in equilibrium with insoluble material. All diamines initially formed the 2 : 1 (blue), (1 : 1)n oligomeric (red) and 1 : 2 (red) axial adducts in solution, depending on the reagents' molar ratio. Adducts of primary and secondary diamines decomposed in the presence of ligand excess, the former via unstable equatorial complexes. The complexation of secondary diamines slowed down the inversion at nitrogen atoms in NH(CH3 ) functional groups and resulted in the formation of nitrogenous stereogenic centres, detectable by NMR. Axial adducts of tertiary diamines appeared to be relatively stable. The presence of long aliphatic chains in molecules (adducts of nonane-1,9-diamines or rhodium(II) tetrakisoctanoate) increased adduct solubility. Hypothetical structures of the equatorial adduct of rhodium(II) tetraacetate with ethane-1,2-diamine and their NMR parameters were explored by means of DFT calculations. Copyright © 2013 John Wiley & Sons, Ltd.

Three-dimensional solution structure of lactoferricin B, an antimicrobial peptide derived from bovine lactoferrin.

PubMed

Hwang, P M; Zhou, N; Shan, X; Arrowsmith, C H; Vogel, H J

1998-03-24

The solution structure of bovine lactoferricin (LfcinB) has been determined using 2D 1H NMR spectroscopy. LfcinB is a 25-residue antimicrobial peptide released by pepsin cleavage of lactoferrin, an 80 kDa iron-binding glycoprotein with many immunologically important functions. The NMR structure of LfcinB reveals a somewhat distorted antiparallel beta-sheet. This contrasts with the X-ray structure of bovine lactoferrin, in which residues 1-13 (of LfcinB) form an alpha-helix. Hence, this region of lactoferricin B appears able to adopt a helical or sheetlike conformation, similar to what has been proposed for the amyloidogenic prion proteins and Alzheimer's beta-peptides. LfcinB has an extended hydrophobic surface comprised of residues Phe1, Cys3, Trp6, Trp8, Pro16, Ile18, and Cys20. The side chains of these residues are well-defined in the NMR structure. Many hydrophilic and positively charged residues surround the hydrophobic surface, giving LfcinB an amphipathic character. LfcinB bears numerous similarities to a vast number of cationic peptides which exert their antimicrobial activities through membrane disruption. The structures of many of these peptides have been well characterized, and models of their membrane-permeabilizing mechanisms have been proposed. The NMR solution structure of LfcinB may be more relevant to membrane interaction than that suggested by the X-ray structure of intact lactoferrin. Based on the solution structure, it is now possible to propose potential mechanisms for the antimicrobial action of LfcinB.

High Resolution NMR Studies of Encapsulated Proteins In Liquid Ethane

PubMed Central

Peterson, Ronald W.; Lefebvre, Brian G.; Wand, A. Joshua

2005-01-01

Many of the difficulties presented by large, aggregation-prone, and membrane proteins to modern solution NMR spectroscopy can be alleviated by actively seeking to increase the effective rate of molecular reorientation. An emerging approach involves encapsulating the protein of interest within the protective shell of a reverse micelle, and dissolving the resulting particle in a low viscosity fluid, such as the short chain alkanes. Here we present the encapsulation of proteins with high structural fidelity within reverse micelles dissolved in liquid ethane. The addition of appropriate co-surfactants can significantly reduce the pressure required for successful encapsulation. At these reduced pressures, the viscosity of the ethane solution is low enough to provide sufficiently rapid molecular reorientation to significantly lengthen the spin-spin NMR relaxation times of the encapsulated protein. PMID:16028922

Beyond Fourier.

PubMed

Hoch, Jeffrey C

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development. Copyright © 2017 Elsevier Inc. All rights reserved.

Magnetic resonance imaging (MRI) and relaxation spectrum analysis as methods to investigate swelling in whey protein gels.

PubMed

Oztop, Mecit H; Rosenberg, Moshe; Rosenberg, Yael; McCarthy, Kathryn L; McCarthy, Michael J

2010-10-01

Effective means for controlled delivery of nutrients and nutraceuticals are needed. Whey protein-based gels, as a model system and as a potential delivery system, exhibit pH-dependent swelling when placed in aqueous solutions. Understanding the physics that govern gel swelling is thus important when designing gel-based delivery platforms. The extent of swelling over time was monitored gravimetrically. In addition to gravimetric measurements, magnetic resonance imaging (MRI) a real-time noninvasive imaging technique that quantified changes in geometry and water content of these gels was utilized. Heat-set whey protein gels were prepared at pH 7 and swelling was monitored in aqueous solutions with pH values of 2.5, 7, and 10. Changes in dimension over time, as characterized by the number of voxels in an image, were correlated to gravimetric measurements. Excellent correlations between mass uptake and volume change (R(2)= 0.99) were obtained for the gels in aqueous solutions at pH 7 and 10, but not for gels in the aqueous solution at pH 2.5. To provide insight into the mechanisms for water uptake, nuclear magnetic resonance (NMR) relaxation times were measured in independent experiments. The relaxation spectrum for the spin-spin relaxation time (T(2)) showed the presence of 3 proton pools for pH 7 and 10 trials and 4 proton pools for pH 2.5 trials. Results demonstrate that MRI and NMR relaxation measurements provided information about swelling in whey protein gels that can constitute a new means for investigating and developing effective delivery systems for foods.

Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins.

PubMed

Sanders, C R; Oxenoid, K

2000-11-23

Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.

Light-induced yellowing of selectively 13C-enriched dehydrogenation polymers (DHPs). Part 2, NMR assignments and photoyellowing of aromatic ring 1-, 3-, 4-, and 5-13C DHPs

Treesearch

Jim Parkas; Magnus Paulsson; Terashima Noritsugu; Ulla Westermark; Sally Ralph

2004-01-01

Light-induced yellowing of lignocellulosicmaterials has been studied using 13C-enriched DHP (dehydrogenation polymer), selectively 13C-enriched at positions 1, 3, 4, and 5 in the aromatic ring, and quantitative solution state 13C NMR spectroscopy. The NMR study confirmed the results of previous studies using side-chain labeled DHP, mainly that coniferyl alcohol end...

Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: Application to microcrystalline and membrane protein preparations

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2015-04-01

Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes.

Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: application to microcrystalline and membrane protein preparations.

PubMed

Gopinath, T; Veglia, Gianluigi

2015-04-01

Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes. Copyright © 2015 Elsevier Inc. All rights reserved.

Multiple Acquisition of Magic Angle Spinning Solid-State NMR Experiments Using One Receiver: Application to Microcrystalline and Membrane Protein Preparations

PubMed Central

Gopinath, T.; Veglia, Gianluigi

2015-01-01

Solid-State NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POEs allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this Perspective, we describe the first generation of POEs, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic polarization, to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes. PMID:25797011

Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules

PubMed Central

Schanda, Paul; Ernst, Matthias

2016-01-01

Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution. PMID:27110043

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

Citrus Quality Control: An NMR/MRI Problem-Based Experiment

ERIC Educational Resources Information Center

Erhart, Sarah E.; McCarrick, Robert M.; Lorigan, Gary A.; Yezierski, Ellen J.

2016-01-01

An experiment seated in an industrial context can provide an engaging framework and unique learning opportunity for an upper-division physical chemistry laboratory. An experiment that teaches NMR/MRI through a problem-based quality control of citrus products was developed. In this experiment, using a problem-based learning (PBL) approach, students…

The U.S. Dairy Forage Research Center (USDFRC) condensed tannin NMR database

USDA-ARS?s Scientific Manuscript database

This perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, 1H and 13C chemical shifts of the condensed tan...

Organic solute changes with acidification in Lake Skjervatjern as shown by 1H-NMR spectroscopy

USGS Publications Warehouse

Malcolm, R.L.; Hayes, T.

1994-01-01

1H-NMR spectroscopy has been found to be a useful tool to establish possible real differences and trends between all natural organic solute fractions (fulvic acids, humic acids, and XAD-4 acids) after acid-rain additions to the Lake Skjervatjern watershed. The proton NMR technique used in this study determined the spectral distribution of nonexchangeable protons among four peaks (aliphatic protons; aliphatic protons on carbon ?? or attached to electronegative groups; protons on carbons attached to O or N heteroatoms; and aromatic protons). Differences of 10% or more in the respective peak areas were considered to represent a real difference. After one year of acidification, fulvic acids decreased 13% (relative) in Peak 3 protons on carbon attached to N and O heteratoms and exhibited a decrease in aromatic protons between 27% and 31%. Humic acids also exhibited an 11% relative decrease in aromatic protons as a result of acidification. After one year of acidification, real changes were shown in three of the four proton assignments in XAD-4 acids. Peak 1 aliphatic protons increased by 14% (relative), Peak 3 protons on carbons attached to O and N heteroatoms decreased by 13% (relative), and aromatic protons (Peak 4) decreased by 35% (relative). Upon acidification, there was a trend in all solutes for aromatic protons to decrease and aliphatic protons to increase. The natural variation in organic solutes as shown in the Control Side B of the lake from 1990 to 1991 is perhaps a small limitation to the same data interpretations of acid rain changes at the Lake Skjervatjern site, but the proton NMR technique shows great promise as an independent scientific tool to detect and support other chemical techniques in establishing organic solute changes with different treatments (i.e., additions of acid rain).

Conformational study on cyclic melanocortin ligands and new insight into their binding mode at the MC4 receptor.

PubMed

Grieco, Paolo; Brancaccio, Diego; Novellino, Ettore; Hruby, Victor J; Carotenuto, Alfonso

2011-09-01

The melanocortin receptors are involved in many physiological functions, including pigmentation, sexual function, feeding behavior, and energy homeostasis, making them potential targets to treat obesity, sexual dysfunction, etc. Understanding the basis of the ligand-receptor interactions is crucial for the design of potent and selective ligands for these receptors. The conformational preferences of the cyclic melanocortin ligands MTII (Ac-Nle(4)-c[Asp(5)-His(6)-DPhe(7)-Arg(8)-Trp(9)-Lys(10)]-NH(2)) and SHU9119 (Ac-Nle(4)-c[Asp(5)-His(6)-DNal(2')(7)-Arg(8)-Trp(9)-Lys(10)]-NH(2)), which show agonist and antagonist activity at the h-MC4R, respectively, were comprehensively investigated by solution NMR spectroscopy in different environments. In particular, water and water/DMSO (8:2) solutions were used as isotropic solutions and an aqueous solution of DPC (dodecylphosphocholine) micelles was used as a membrane mimetic environment. NMR-derived conformations of these two ligands were docked within h-MC4R models. NMR and docking studies revealed intriguing differences which can help explain the different activities of these two ligands. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Direct NMR Monitoring of Phase Separation Behavior of Highly Supersaturated Nifedipine Solution Stabilized with Hypromellose Derivatives.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Moribe, Kunikazu

2017-07-03

We investigated the phase separation behavior and maintenance mechanism of the supersaturated state of poorly water-soluble nifedipine (NIF) in hypromellose (HPMC) derivative solutions. Highly supersaturated NIF formed NIF-rich nanodroplets through phase separation from aqueous solution containing HPMC derivative. Dissolvable NIF concentration in the bulk water phase was limited by the phase separation of NIF from the aqueous solution. HPMC derivatives stabilized the NIF-rich nanodroplets and maintained the NIF supersaturation with phase-separated NIF for several hours. The size of the NIF-rich phase was different depending on the HPMC derivatives dissolved in aqueous solution, although the droplet size had no correlation with the time for which NIF supersaturation was maintained without NIF crystallization. HPMC acetate and HPMC acetate succinate (HPMC-AS) effectively maintained the NIF supersaturation containing phase-separated NIF compared with HPMC. Furthermore, HPMC-AS stabilized NIF supersaturation more effectively in acidic conditions. Solution 1 H NMR measurements of NIF-supersaturated solution revealed that HPMC derivatives distributed into the NIF-rich phase during the phase separation of NIF from the aqueous solution. The hydrophobicity of HPMC derivative strongly affected its distribution into the NIF-rich phase. Moreover, the distribution of HPMC-AS into the NIF-rich phase was promoted at lower pH due to the lower aqueous solubility of HPMC-AS. The distribution of a large amount of HPMC derivatives into NIF-rich phase induced the strong inhibition of NIF crystallization from the NIF-rich phase. Polymer distribution into the drug-rich phase directly monitored by solution NMR technique can be a useful index for the stabilization efficiency of drug-supersaturated solution containing a drug-rich phase.

SAIL--stereo-array isotope labeling.

PubMed

Kainosho, Masatsune; Güntert, Peter

2009-11-01

Optimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.

NMR spectroscopy of single sub-nL ova with inductive ultra-compact single-chip probes

PubMed Central

Grisi, Marco; Vincent, Franck; Volpe, Beatrice; Guidetti, Roberto; Harris, Nicola; Beck, Armin; Boero, Giovanni

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy enables non-invasive chemical studies of intact living matter. However, the use of NMR at the volume scale typical of microorganisms is hindered by sensitivity limitations, and experiments on single intact organisms have so far been limited to entities having volumes larger than 5 nL. Here we show NMR spectroscopy experiments conducted on single intact ova of 0.1 and 0.5 nL (i.e. 10 to 50 times smaller than previously achieved), thereby reaching the relevant volume scale where life development begins for a broad variety of organisms, humans included. Performing experiments with inductive ultra-compact (1 mm2) single-chip NMR probes, consisting of a low noise transceiver and a multilayer 150 μm planar microcoil, we demonstrate that the achieved limit of detection (about 5 pmol of 1H nuclei) is sufficient to detect endogenous compounds. Our findings suggest that single-chip probes are promising candidates to enable NMR-based study and selection of microscopic entities at biologically relevant volume scales. PMID:28317887

Using solid 13C NMR coupled with solution 31P NMR spectroscopy to investigate molecular species and lability of organic carbon and phosphorus from aquatic plants in Tai Lake, China.

PubMed

Liu, Shasha; Zhu, Yuanrong; Wu, Fengchang; Meng, Wei; Wang, Hao; He, Zhongqi; Guo, Wenjing; Song, Fanhao; Giesy, John P

2017-01-01

Forms and labilities of plant-derived organic matters (OMs) including carbon (C) and phosphorus (P) were fundamental for understanding their release, degradation and environmental behaviour in lake ecosystems. Thus, solid 13 C and solution 31 P nuclear magnetic resonance (NMR) spectroscopy were used to characterize biomass of six aquatic plants in Tai Lake, China. The results showed that carbohydrates (61.2% of the total C) were predominant C functional group in the solid 13 C NMR spectra of plant biomass, which may indicate high lability and bioavailability of aquatic plants-derived organic matter in lakes. There was 72.6-103.7% of the total P in aquatic plant biomass extracted by NaOH-EDTA extracts. Solution 31 P NMR analysis of these NaOH-EDTA extracts further identified several molecular species of P including orthophosphate (50.1%), orthophosphate monoesters (46.8%), DNA (1.6%) and pyrophosphate (1.4%). Orthophosphate monoesters included β-glycerophosphate (17.7%), hydrolysis products of RNA (11.7%), α-glycerophosphate (9.2%) and other unknown monoesters (2.1%). Additionally, phytate, the major form of organic P in many lake sediments, was detected in floating plant water poppy. These inorganic P (e.g. orthophosphate and pyrophosphate) and organic P (e.g. diester and its degradation products) identified in plant biomass were all labile and bioavailable P, which would play an important role in recycling of P in lakes. These results increased knowledge of chemical composition and bioavailability of OMs derived from aquatic plants in lakes.

Enhanced efficiency of solid-state NMR investigations of energy materials using an external automatic tuning/matching (eATM) robot.

PubMed

Pecher, Oliver; Halat, David M; Lee, Jeongjae; Liu, Zigeng; Griffith, Kent J; Braun, Marco; Grey, Clare P

2017-02-01

We have developed and explored an external automatic tuning/matching (eATM) robot that can be attached to commercial and/or home-built magic angle spinning (MAS) or static nuclear magnetic resonance (NMR) probeheads. Complete synchronization and automation with Bruker and Tecmag spectrometers is ensured via transistor-transistor-logic (TTL) signals. The eATM robot enables an automated "on-the-fly" re-calibration of the radio frequency (rf) carrier frequency, which is beneficial whenever tuning/matching of the resonance circuit is required, e.g. variable temperature (VT) NMR, spin-echo mapping (variable offset cumulative spectroscopy, VOCS) and/or in situ NMR experiments of batteries. This allows a significant increase in efficiency for NMR experiments outside regular working hours (e.g. overnight) and, furthermore, enables measurements of quadrupolar nuclei which would not be possible in reasonable timeframes due to excessively large spectral widths. Additionally, different tuning/matching capacitor (and/or coil) settings for desired frequencies (e.g. 7 Li and 31 P at 117 and 122MHz, respectively, at 7.05 T) can be saved and made directly accessible before automatic tuning/matching, thus enabling automated measurements of multiple nuclei for one sample with no manual adjustment required by the user. We have applied this new eATM approach in static and MAS spin-echo mapping NMR experiments in different magnetic fields on four energy storage materials, namely: (1) paramagnetic 7 Li and 31 P MAS NMR (without manual recalibration) of the Li-ion battery cathode material LiFePO 4 ; (2) paramagnetic 17 O VT-NMR of the solid oxide fuel cell cathode material La 2 NiO 4+δ ; (3) broadband 93 Nb static NMR of the Li-ion battery material BNb 2 O 5 ; and (4) broadband static 127 I NMR of a potential Li-air battery product LiIO 3 . In each case, insight into local atomic structure and dynamics arises primarily from the highly broadened (1-25MHz) NMR lineshapes that the eATM robot is uniquely suited to collect. These new developments in automation of NMR experiments are likely to advance the application of in and ex situ NMR investigations to an ever-increasing range of energy storage materials and systems. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Enhanced efficiency of solid-state NMR investigations of energy materials using an external automatic tuning/matching (eATM) robot

NASA Astrophysics Data System (ADS)

Pecher, Oliver; Halat, David M.; Lee, Jeongjae; Liu, Zigeng; Griffith, Kent J.; Braun, Marco; Grey, Clare P.

2017-02-01

We have developed and explored an external automatic tuning/matching (eATM) robot that can be attached to commercial and/or home-built magic angle spinning (MAS) or static nuclear magnetic resonance (NMR) probeheads. Complete synchronization and automation with Bruker and Tecmag spectrometers is ensured via transistor-transistor-logic (TTL) signals. The eATM robot enables an automated "on-the-fly" re-calibration of the radio frequency (rf) carrier frequency, which is beneficial whenever tuning/matching of the resonance circuit is required, e.g. variable temperature (VT) NMR, spin-echo mapping (variable offset cumulative spectroscopy, VOCS) and/or in situ NMR experiments of batteries. This allows a significant increase in efficiency for NMR experiments outside regular working hours (e.g. overnight) and, furthermore, enables measurements of quadrupolar nuclei which would not be possible in reasonable timeframes due to excessively large spectral widths. Additionally, different tuning/matching capacitor (and/or coil) settings for desired frequencies (e.g.7Li and 31P at 117 and 122 MHz, respectively, at 7.05 T) can be saved and made directly accessible before automatic tuning/matching, thus enabling automated measurements of multiple nuclei for one sample with no manual adjustment required by the user. We have applied this new eATM approach in static and MAS spin-echo mapping NMR experiments in different magnetic fields on four energy storage materials, namely: (1) paramagnetic 7Li and 31P MAS NMR (without manual recalibration) of the Li-ion battery cathode material LiFePO4; (2) paramagnetic 17O VT-NMR of the solid oxide fuel cell cathode material La2NiO4+δ; (3) broadband 93Nb static NMR of the Li-ion battery material BNb2O5; and (4) broadband static 127I NMR of a potential Li-air battery product LiIO3. In each case, insight into local atomic structure and dynamics arises primarily from the highly broadened (1-25 MHz) NMR lineshapes that the eATM robot is uniquely suited to collect. These new developments in automation of NMR experiments are likely to advance the application of in and ex situ NMR investigations to an ever-increasing range of energy storage materials and systems.

[Effect of Tween 80 on yuxingcao injection and volatile oils from Houttuynia cordata].

PubMed

Tan, Zhigao; Chao, Zhimao; Sui, Yu; Liu, Haiping; Wu, Xiaoyi; Sun, Jian; Yan, Han

2011-01-01

To research the effect of polysorbate 80 (Tween 80) on Yuxingcao injection and volatile oils from Houttuynia cordata. 1H-NMR spectra of aldehydic and new matter in Yuxingcao injection, volatile oils of H. cordata, and solutions of Tween 80 and volatile oil of H. cordata are determined and compared from various angles of growing origin, storage temperature, and storage time. Three aldehydic singlets in 1H-NMR spectra of every volatile oil from 4 aerial part of H. cordata were observed. These aldehydic peaks were basically disappeared and a new peak at delta 8.30 was found in 1H-NMR spectra of the volatile oil solutions in tween 80. Any obvious aldehydic peak in 1H-NMR spectra did not be observed in Yuxincao injection. A weak peak at 8 8.30 was found in 1H-NMR spectra in Yuxincao injection, and the peak high of delta 8.30 was remarked gone up when the injection was stored in 40 degrees C for 1 to 3 months. Tween 80 might cause the obvious reduce of aldehydic compounds contents and the production of a novel singal at delta 8.30 in 1H-NMR spectra when it was mixed with the volatile oil from the aerial part of H. cordata. The novel signal at delta 8.30 in 1H-NMR spectra existed in Yuxincao injection and was very small, but was increased remarkably when the Yuxincao injection was stored at 40 degrees C for 1 month at least.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Zhange; Higa, Kenneth; Han, Kee Sung

The presence of lithium hexafluorophosphate (LiPF 6) ion pairs in carbonate-based electrolyte solutions is widely accepted in the field of battery electrolyte research and is expected to affect solution transport properties. No existing techniques are capable of directly quantifying salt dissociation in these solutions. Previous publications by others have provided estimates of dissociation degrees using dilute solution theory and pulsed field gradient nuclear magnetic resonance spectroscopy (PFG-NMR) measurements of self-diffusivity. However, the behavior of a concentrated electrolyte solution can deviate significantly from dilute solution theory predictions. This paper, for the first time, instead uses Onsager–Stefan–Maxwell concentrated solution theory and themore » generalized Darken relation with PFG-NMR measurements to quantify the degrees of dissociation in electrolyte solutions (LiPF 6 in ethylene carbonate/diethyl carbonate, 1:1 by weight). At LiPF 6 concentrations ranging from 0.1 M to 1.5 M, the salt dissociation degree is found to range from 61% to 37%. Finally, transport properties are then calculated through concentrated solution theory with corrections for these significant levels of ion pairing.« less

Evaluating Transport Properties and Ionic Dissociation of LiPF 6 in Concentrated Electrolyte

DOE PAGES

Feng, Zhange; Higa, Kenneth; Han, Kee Sung; ...

2017-08-17

The presence of lithium hexafluorophosphate (LiPF 6) ion pairs in carbonate-based electrolyte solutions is widely accepted in the field of battery electrolyte research and is expected to affect solution transport properties. No existing techniques are capable of directly quantifying salt dissociation in these solutions. Previous publications by others have provided estimates of dissociation degrees using dilute solution theory and pulsed field gradient nuclear magnetic resonance spectroscopy (PFG-NMR) measurements of self-diffusivity. However, the behavior of a concentrated electrolyte solution can deviate significantly from dilute solution theory predictions. This paper, for the first time, instead uses Onsager–Stefan–Maxwell concentrated solution theory and themore » generalized Darken relation with PFG-NMR measurements to quantify the degrees of dissociation in electrolyte solutions (LiPF 6 in ethylene carbonate/diethyl carbonate, 1:1 by weight). At LiPF 6 concentrations ranging from 0.1 M to 1.5 M, the salt dissociation degree is found to range from 61% to 37%. Finally, transport properties are then calculated through concentrated solution theory with corrections for these significant levels of ion pairing.« less

Evaluating Transport Properties and Ionic Dissociation of LiPF 6 in Concentrated Electrolyte

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Zhange; Higa, Kenneth; Han, Kee Sung

2017-01-01

The presence of lithium hexafluorophosphate (LiPF6) ion pairs in carbonate-based electrolyte solutions is widely accepted in the field of battery electrolyte research and is expected to affect solution transport properties. No existing techniques are capable of directly quantifying salt dissociation in these solutions. Previous publications by others have provided estimates of dissociation degrees using dilute solution theory and pulsed field gradient nuclear magnetic resonance spectroscopy (PFG-NMR) measurements of self-diffusivity. However, the behavior of a concentrated electrolyte solution can deviate significantly from dilute solution theory predictions. This work, for the first time, instead uses Onsager–Stefan–Maxwell concentrated solution theory and the generalized.more » Darken relation with PFG-NMR measurements to quantify the degrees of dissociation in electrolyte solutions (LiPF6 in ethylene carbonate/diethyl carbonate, 1:1 by weight). At LiPF6 concentrations ranging from 0.1 M to 1.5 M, the salt dissociation degree is found to range from 61% to 37%. Transport properties are then calculated through concentrated solution theory with corrections for these significant levels of ion pairing.« less

Superoxygenated Water as an Experimental Sample for NMR Relaxometry

ERIC Educational Resources Information Center

Nestle, Nikolaus; Dakkouri, Marwan; Rauscher, Hubert

2004-01-01

The increase in NMR relaxation rates as a result of dissolved paramagnetic species on the sample of superoxygenated drinking water is demonstrated. It is concluded that oxygen content in NMR samples is an important issue and can give rise to various problems in the interpretation of both spectroscopic and NMR imaging or relaxation experiments.

Numerical simulation of NQR/NMR: Applications in quantum computing.

PubMed

Possa, Denimar; Gaudio, Anderson C; Freitas, Jair C C

2011-04-01

A numerical simulation program able to simulate nuclear quadrupole resonance (NQR) as well as nuclear magnetic resonance (NMR) experiments is presented, written using the Mathematica package, aiming especially applications in quantum computing. The program makes use of the interaction picture to compute the effect of the relevant nuclear spin interactions, without any assumption about the relative size of each interaction. This makes the program flexible and versatile, being useful in a wide range of experimental situations, going from NQR (at zero or under small applied magnetic field) to high-field NMR experiments. Some conditions specifically required for quantum computing applications are implemented in the program, such as the possibility of use of elliptically polarized radiofrequency and the inclusion of first- and second-order terms in the average Hamiltonian expansion. A number of examples dealing with simple NQR and quadrupole-perturbed NMR experiments are presented, along with the proposal of experiments to create quantum pseudopure states and logic gates using NQR. The program and the various application examples are freely available through the link http://www.profanderson.net/files/nmr_nqr.php. Copyright © 2011 Elsevier Inc. All rights reserved.

High-sensitivity NMR beyond 200,000 atmospheres of pressure

NASA Astrophysics Data System (ADS)

Meier, T.; Reichardt, S.; Haase, J.

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. 1 H NMR of water shows sensitivity and resolution obtained with the cells, and 63 Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. 115 In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry.

1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

NASA Astrophysics Data System (ADS)

Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

2004-07-01

NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

The Protonation Site of para-Dimethylaminobenzoic Acid Using Atmospheric Pressure Ionization Methods

NASA Astrophysics Data System (ADS)

Chai, Yunfeng; Weng, Guofeng; Shen, Shanshan; Sun, Cuirong; Pan, Yuanjiang

2015-04-01

The protonation site of para-dimethylaminobenzoic acid ( p-DMABA) was investigated using atmospheric pressure ionization methods (ESI and APCI) coupled with collision-induced dissociation (CID), nuclear magnetic resonance (NMR), and computational chemistry. Theoretical calculations and NMR experiments indicate that the dimethyl amino group is the preferred site of protonation both in the gas phase and aqueous solution. Protonation of p-DMABA occurs at the nitrogen atom by ESI independent of the solvents and other operation conditions under typical thermodynamic control. However, APCI produces a mixture of the nitrogen- and carbonyl oxygen-protonated p-DMABA when aprotic organic solvents (acetonitrile, acetone, and tetrahydrofuran) are used, exhibiting evident kinetic characteristics of protonation. But using protic organic solvents (methanol, ethanol, and isopropanol) in APCI still leads to the formation of thermodynamically stable N-protonated p-DMABA. These structural assignments were based on the different CID behavior of the N- and O-protonated p-DMABA. The losses of methyl radical and water are the diagnostic fragmentations of the N- and O-protonated p-DMABA, respectively. In addition, the N-protonated p-DMABA is more stable than the O-protonated p-DMABA in CID revealed by energy resolved experiments and theoretical calculations.

Lysine N[superscript zeta]-Decarboxylation Switch and Activation of the [beta]-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borbulevych, Oleg; Kumarasiri, Malika; Wilson, Brian

The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of {beta}-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N{sup {zeta}}-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N{sup {zeta}}-decarboxylation. This unique process, termed themore » lysine N{sup {zeta}}-decarboxylation switch, arrests the sensor domain in the activated ('on') state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.« less

Multiple acquisitions via sequential transfer of orphan spin polarization (MAeSTOSO): How far can we push residual spin polarization in solid-state NMR?

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2016-06-01

Conventional multidimensional magic angle spinning (MAS) solid-state NMR (ssNMR) experiments detect the signal arising from the decay of a single coherence transfer pathway (FID), resulting in one spectrum per acquisition time. Recently, we introduced two new strategies, namely DUMAS (DUal acquisition Magic Angle Spinning) and MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), that enable the simultaneous acquisitions of multidimensional ssNMR experiments using multiple coherence transfer pathways. Here, we combined the main elements of DUMAS and MEIOSIS to harness both orphan spin operators and residual polarization and increase the number of simultaneous acquisitions. We show that it is possible to acquire up to eight two-dimensional experiments using four acquisition periods per each scan. This new suite of pulse sequences, called MAeSTOSO for Multiple Acquisitions via Sequential Transfer of Orphan Spin pOlarization, relies on residual polarization of both 13C and 15N pathways and combines low- and high-sensitivity experiments into a single pulse sequence using one receiver and commercial ssNMR probes. The acquisition of multiple experiments does not affect the sensitivity of the main experiment; rather it recovers the lost coherences that are discarded, resulting in a significant gain in experimental time. Both merits and limitations of this approach are discussed.

Solution structure of the chick TGFbeta type II receptor ligand-binding domain.

PubMed

Marlow, Michael S; Brown, Christopher B; Barnett, Joey V; Krezel, Andrzej M

2003-02-28

The transforming growth factor beta (TGFbeta) signaling pathway influences cell proliferation, immune responses, and extracellular matrix reorganization throughout the vertebrate life cycle. The signaling cascade is initiated by ligand-binding to its cognate type II receptor. Here, we present the structure of the chick type II TGFbeta receptor determined by solution NMR methods. Distance and angular constraints were derived from 15N and 13C edited NMR experiments. Torsion angle dynamics was used throughout the structure calculations and refinement. The 20 final structures were energy minimized using the generalized Born solvent model. For these 20 structures, the average backbone root-mean-square distance from the average structure is below 0.6A. The overall fold of this 109-residue domain is conserved within the superfamily of these receptors. Chick receptors fully recognize and respond to human TGFbeta ligands despite only 60% identity at the sequence level. Comparison with the human TGFbeta receptor determined by X-ray crystallography reveals different conformations in several regions. Sequence divergence and crystal packing interactions under low pH conditions are likely causes. This solution structure identifies regions were structural changes, however subtle, may occur upon ligand-binding. We also identified two very well conserved molecular surfaces. One was found to bind ligand in the crystallized human TGFbeta3:TGFbeta type II receptor complex. The other, newly identified area can be the interaction site with type I and/or type III receptors of the TGFbeta signaling complex.

Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

PubMed Central

Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

2017-01-01

Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

NMR determination of the global structure of the 113Cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center.

PubMed Central

Goodfellow, B. J.; Rusnak, F.; Moura, I.; Domke, T.; Moura, J. J.

1998-01-01

Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H-bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this derivative was initially compared with the NMR solution structure of the Zn form (Goodfellow BJ et al., 1996, J Biol Inorg Chem 1:341-353). Backbone amide protons for G4, D5, G13, L11 NH, and the Q14 NH side-chain protons, H-bonded in the X-ray structure, were readily exchanged with solvent. Chemical shift differences observed for amide protons near the metal center confirm the H-bonding pattern seen in the X-ray model (Archer M et al., 1995, J Mol Biol 251:690-702) and also suggest that H-bond lengths may vary between the Fe, Zn, and 113Cd forms. The H-bonding pattern was further probed using a heteronuclear spin echo difference (HSED) experiment; the results confirm the presence of NH-S H-bonds inferred from D2O exchange data and observed in the NMR family of structures. The presence of "H-bond mediated" coupling in Dx indicates that the NH-S H-bonds at the metal center have significant covalent character. The HSED experiment also identified an intermonomer "through space" coupling for one of the L26 methyl groups, indicating its proximity to the 113Cd center in the opposing monomer. This is the first example of an intermonomer "through space" coupling. Initial structure calculations produced subsets of NMR families with the S of C28 pointing away from or toward the L26 methyl: only the subset with the C28 sulfur pointing toward the L26 methyl could result in a "through space" coupling. The HSED result was therefore included in the structure calculations. Comparison of the Fe, Zn, and 113Cd forms of Dx suggests that the geometry of the metal center and the global fold of the protein does not vary to any great extent, although the H-bond network varies slightly when Cd is introduced. The similarity between the H-bonding pattern seen at the metal center in Dx, Rd (including H-bonded and through space-mediated coupling), and many zinc-finger proteins suggests that these H-bonds are structurally vital for stabilization of the metal centers in these proteins. PMID:9568899

NMR determination of the global structure of the 113Cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center.

PubMed

Goodfellow, B J; Rusnak, F; Moura, I; Domke, T; Moura, J J

1998-04-01

Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H-bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this derivative was initially compared with the NMR solution structure of the Zn form (Goodfellow BJ et al., 1996, J Biol Inorg Chem 1:341-353). Backbone amide protons for G4, D5, G13, L11 NH, and the Q14 NH side-chain protons, H-bonded in the X-ray structure, were readily exchanged with solvent. Chemical shift differences observed for amide protons near the metal center confirm the H-bonding pattern seen in the X-ray model (Archer M et al., 1995, J Mol Biol 251:690-702) and also suggest that H-bond lengths may vary between the Fe, Zn, and 113Cd forms. The H-bonding pattern was further probed using a heteronuclear spin echo difference (HSED) experiment; the results confirm the presence of NH-S H-bonds inferred from D2O exchange data and observed in the NMR family of structures. The presence of "H-bond mediated" coupling in Dx indicates that the NH-S H-bonds at the metal center have significant covalent character. The HSED experiment also identified an intermonomer "through space" coupling for one of the L26 methyl groups, indicating its proximity to the 113Cd center in the opposing monomer. This is the first example of an intermonomer "through space" coupling. Initial structure calculations produced subsets of NMR families with the S of C28 pointing away from or toward the L26 methyl: only the subset with the C28 sulfur pointing toward the L26 methyl could result in a "through space" coupling. The HSED result was therefore included in the structure calculations. Comparison of the Fe, Zn, and 113Cd forms of Dx suggests that the geometry of the metal center and the global fold of the protein does not vary to any great extent, although the H-bond network varies slightly when Cd is introduced. The similarity between the H-bonding pattern seen at the metal center in Dx, Rd (including H-bonded and through space-mediated coupling), and many zinc-finger proteins suggests that these H-bonds are structurally vital for stabilization of the metal centers in these proteins.

Chemical effects induced by gamma-irradiation in solid and in aqueous methanol solutions of 4-iodophenol

NASA Astrophysics Data System (ADS)

Mahfouz, R. M.; Siddiqui, M. R. H.; Al-Wassil, A. I.; Al-Resayes, S. I.; Al-Otaibi, A. M.

2005-05-01

The present work is a study on radiolyses of 4-iodophenol in aqueous methanol solutions. The radiolysis products are separated and identified using spectrophotometric and chromatographic techniques. The radiolytic products (I-2, I- and IO3-) formed in aerated solutions at room temperature were identified and the yields are investigated as a function of absorbed gamma-ray dose. The formation of I-2 is mainly dependent on the acidity of solution and produced via the pathway of secondary free radical reactions. Aromatic products of lower and higher molecular weight than the corresponding investigated compound were analysed and separated by HPLC. The results have been discussed in view of mechanisms based on free radicals and ion-molecule interactions. The chemical effects induced by gamma-irradiation in solid 4-iodophenol have also been investigated and the degradation products were identified in solid state by NMR, GC/MS experiments and HPLC after dissolution in aqueous methanol. The results were evaluated and compared with radiolysis data.

Alternating current circuit theory and pulsed NMR (Nuclear Magnetic Resonance)

NASA Astrophysics Data System (ADS)

Gerstein, B. C.

1987-06-01

Pulsed NMR, by definition, deals with time varying excitations. These excitations, supplied by resonant circuits which provide a pulse of radiofrequency (frequencies in the megahertz region) power to a resonant circuit containing, among other things, a coil of wire, or inductor, in which a sample under investigation is placed for purposes of the nuclear magnetic resonance experiment. There are therefore two features of the pulse NMR experiment. First is the fact that we have available a source of continuous wave (CW) alternating current at some angular frequency, omega, measured in radians per second. This source is generally supplied by an ultrastable device called a frequency synthesizer. The second feature of the pulsed NMR experiment is that the sample is not continuously irradiated, but a pulse of radiofrequency oscillation is applied to the sample. This report discusses alternating current theory, resonant circuits and the equipment used in this experiment.

A fast field-cycling device for high-resolution NMR: Design and application to spin relaxation and hyperpolarization experiments

NASA Astrophysics Data System (ADS)

Kiryutin, Alexey S.; Pravdivtsev, Andrey N.; Ivanov, Konstantin L.; Grishin, Yuri A.; Vieth, Hans-Martin; Yurkovskaya, Alexandra V.

2016-02-01

A device for performing fast magnetic field-cycling NMR experiments is described. A key feature of this setup is that it combines fast switching of the external magnetic field and high-resolution NMR detection. The field-cycling method is based on precise mechanical positioning of the NMR probe with the mounted sample in the inhomogeneous fringe field of the spectrometer magnet. The device enables field variation over several decades (from 100 μT up to 7 T) within less than 0.3 s; progress in NMR probe design provides NMR linewidths of about 10-3 ppm. The experimental method is very versatile and enables site-specific studies of spin relaxation (NMRD, LLSs) and spin hyperpolarization (DNP, CIDNP, and SABRE) at variable magnetic field and at variable temperature. Experimental examples of such studies are demonstrated; advantages of the experimental method are described and existing challenges in the field are outlined.

Comparative Study of the Structure of Hydroproducts Derived from Loblolly Pine and Straw Grass

DOE PAGES

Wu, Qiong; Huang, Lang; Yu, Shitao; ...

2017-05-26

We investigated the structural characteristics of products derived from the hydrothermal carbonization (HTC) of loblolly pine (LP) and straw grass (SG) via solid-state cross-polarization/magic angle spinning nuclear magnetic resonance (CP/MAS 13C NMR), heteronuclear single-quantum correlation nuclear magnetic resonance (HSQC-NMR), and solution 13C NMR and 31P NMR techniques. Our results revealed that after HTC, hydrochars from both LP and SG mainly consisted of a combination of lignin, furfural, and condensed polyaromatic structures with a high level of fixed carbon content and higher heating value (HHV). Hydrochar from LP exhibited a higher aryl to furan ratio, and those from SG contained moremore » aliphatic functional groups. Solution 13C NMR and HSQC revealed that both liquid chemicals were condensed polyphenolic structures with aliphatic groups that exist mainly in the form of side chains. Although the LP products exhibited a higher proportion of aromatic structures, the types of polyphenol and aliphatic C–H were more diverse in the SG products. Results also indicated that reactions such as chain scission and condensation occurred during hydrothermal carbonization processes. Overall, HTC was found to be an effective refinery treatment for converting different waste biomass into valuable energy materials and chemicals.« less

Comparative Study of the Structure of Hydroproducts Derived from Loblolly Pine and Straw Grass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Qiong; Huang, Lang; Yu, Shitao

We investigated the structural characteristics of products derived from the hydrothermal carbonization (HTC) of loblolly pine (LP) and straw grass (SG) via solid-state cross-polarization/magic angle spinning nuclear magnetic resonance (CP/MAS 13C NMR), heteronuclear single-quantum correlation nuclear magnetic resonance (HSQC-NMR), and solution 13C NMR and 31P NMR techniques. Our results revealed that after HTC, hydrochars from both LP and SG mainly consisted of a combination of lignin, furfural, and condensed polyaromatic structures with a high level of fixed carbon content and higher heating value (HHV). Hydrochar from LP exhibited a higher aryl to furan ratio, and those from SG contained moremore » aliphatic functional groups. Solution 13C NMR and HSQC revealed that both liquid chemicals were condensed polyphenolic structures with aliphatic groups that exist mainly in the form of side chains. Although the LP products exhibited a higher proportion of aromatic structures, the types of polyphenol and aliphatic C–H were more diverse in the SG products. Results also indicated that reactions such as chain scission and condensation occurred during hydrothermal carbonization processes. Overall, HTC was found to be an effective refinery treatment for converting different waste biomass into valuable energy materials and chemicals.« less

Solid state nuclear magnetic resonance with magic-angle spinning and dynamic nuclear polarization below 25 K

PubMed Central

Thurber, Kent R.; Potapov, Alexey; Yau, Wai-Ming; Tycko, Robert

2012-01-01

We describe an apparatus for solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS) at 20–25 K and 9.4 Tesla. The MAS NMR probe uses helium to cool the sample space and nitrogen gas for MAS drive and bearings, as described earlier (Thurber et al., J. Magn. Reson. 2008) [1], but also includes a corrugated waveguide for transmission of microwaves from below the probe to the sample. With a 30 mW circularly polarized microwave source at 264 GHz, MAS at 6.8 kHz, and 21 K sample temperature, greater than 25-fold enhancements of cross-polarized 13C NMR signals are observed in spectra of frozen glycerol/water solutions containing the triradical dopant DOTOPA-TEMPO when microwaves are applied. As demonstrations, we present DNP-enhanced one-dimensional and two-dimensional 13C MAS NMR spectra of frozen solutions of uniformly 13C-labeled L-alanine and melittin, a 26-residue helical peptide that we have synthesized with four uniformly 13C-labeled amino acids. PMID:23238592

Structure and Membrane Interactions of the Antibiotic Peptide Dermadistinctin K by Multidimensional Solution and Oriented 15N and 31P Solid-State NMR Spectroscopy

PubMed Central

Verly, Rodrigo M.; Moraes, Cléria Mendonça de; Resende, Jarbas M.; Aisenbrey, Christopher; Bemquerer, Marcelo Porto; Piló-Veloso, Dorila; Valente, Ana Paula; Almeida, Fábio C.L.; Bechinger, Burkhard

2009-01-01

DD K, a peptide first isolated from the skin secretion of the Phyllomedusa distincta frog, has been prepared by solid-phase chemical peptide synthesis and its conformation was studied in trifluoroethanol/water as well as in the presence of sodium dodecyl sulfate and dodecylphosphocholine micelles or small unilamellar vesicles. Multidimensional solution NMR spectroscopy indicates an α-helical conformation in membrane environments starting at residue 7 and extending to the C-terminal carboxyamide. Furthermore, DD K has been labeled with 15N at a single alanine position that is located within the helical core region of the sequence. When reconstituted into oriented phosphatidylcholine membranes the resulting 15N solid-state NMR spectrum shows a well-defined helix alignment parallel to the membrane surface in excellent agreement with the amphipathic character of DD K. Proton-decoupled 31P solid-state NMR spectroscopy indicates that the peptide creates a high level of disorder at the level of the phospholipid headgroup suggesting that DD K partitions into the bilayer where it severely disrupts membrane packing. PMID:19289046

Solid state nuclear magnetic resonance with magic-angle spinning and dynamic nuclear polarization below 25 K.

PubMed

Thurber, Kent R; Potapov, Alexey; Yau, Wai-Ming; Tycko, Robert

2013-01-01

We describe an apparatus for solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS) at 20-25 K and 9.4 Tesla. The MAS NMR probe uses helium to cool the sample space and nitrogen gas for MAS drive and bearings, as described earlier, but also includes a corrugated waveguide for transmission of microwaves from below the probe to the sample. With a 30 mW circularly polarized microwave source at 264 GHz, MAS at 6.8 kHz, and 21 K sample temperature, greater than 25-fold enhancements of cross-polarized (13)C NMR signals are observed in spectra of frozen glycerol/water solutions containing the triradical dopant DOTOPA-TEMPO when microwaves are applied. As demonstrations, we present DNP-enhanced one-dimensional and two-dimensional (13)C MAS NMR spectra of frozen solutions of uniformly (13)C-labeled l-alanine and melittin, a 26-residue helical peptide that we have synthesized with four uniformly (13)C-labeled amino acids. Published by Elsevier Inc.

Solution state nuclear magnetic resonance spectroscopy for biological metabolism and pathway intermediate analysis.

PubMed

Nealon, Gareth L; Howard, Mark J

2016-12-15

Using nuclear magnetic resonance (NMR) spectroscopy in the study of metabolism has been immensely popular in medical- and health-related research but has yet to be widely applied to more fundamental biological problems. This review provides some NMR background relevant to metabolism, describes why 1 H NMR spectra are complex as well as introducing relevant terminology and definitions. The applications and practical considerations of NMR metabolic profiling and 13 C NMR-based flux analyses are discussed together with the elegant 'enzyme trap' approach for identifying novel metabolic pathway intermediates. The importance of sample preparation and data analysis are also described and explained with reference to data precision and multivariate analysis to introduce researchers unfamiliar with NMR and metabolism to consider this technique for their research interests. Finally, a brief glance into the future suggests NMR-based metabolism has room to expand in the 21st century through new isotope labels, and NMR technologies and methodologies. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

CONNJUR R: An annotation strategy for fostering reproducibility in bio-NMR: protein spectral assignment

PubMed Central

Fenwick, Matthew; Hoch, Jeffrey C.; Ulrich, Eldon; Gryk, Michael R.

2015-01-01

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata. PMID:26253947

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imai, Mizue; Saio, Tomohide; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810

2016-01-22

Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23–28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction sitemore » for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO. - Highlights: • Solution structure and dynamics analysis for human Cyt c by NMR. • Structural changes responsible for the discrimination of the redox state in Cyt c. • Conformational exchange in the region outside of the interaction site for CcO. • Less flexibility and rigid structure of the interaction site on Cyt c for CcO.« less

Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

ERIC Educational Resources Information Center

Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

2009-01-01

A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

NASA Astrophysics Data System (ADS)

Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA.

PubMed

Mroue, Kamal H; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H; Morris, Michael D; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans. Copyright © 2014 Elsevier Inc. All rights reserved.

Spectroscopic studies of the intramolecular hydrogen bonding in o-hydroxy Schiff bases, derived from diaminomaleonitrile, and their deprotonation reaction products

NASA Astrophysics Data System (ADS)

Szady-Chełmieniecka, Anna; Kołodziej, Beata; Morawiak, Maja; Kamieński, Bohdan; Schilf, Wojciech

2018-01-01

The structural study of five Schiff bases derived from diaminomaleonitrile (DAMN) and 2-hydroxy carbonyl compounds was performed using 1H, 13C and 15N NMR methods in solution and in the solid state as well. ATR-FTIR and X-Ray spectroscopies were used for confirmation of the results obtained by NMR method. The imine obtained from DAMN and benzaldehyde was synthesized as a model compound which lacks intramolecular hydrogen bond. Deprotonation of all synthesized compounds was done by treating with tetramethylguanidine (TMG). NMR data revealed that salicylidene Schiff bases in DMSO solution exist as OH forms without intramolecular hydrogen bonds and independent on the substituents in aromatic ring. In the case of 2-hydroxy naphthyl derivative, the OH proton is engaged into weak intramolecular hydrogen bond. Two of imines (salDAMN and 5-BrsalDAMN) exist in DMSO solution as equilibrium mixtures of two isomers (A and B). The structures of equilibrium mixture in the solid state have been studied by NMR, ATR-FTIR and X-Ray methods. The deprotonation of three studied compounds (salDAMN, 5-BrsalDAMN, and 5-CH3salDAMN) proceeded in two different ways: deprotonation of oxygen atom (X form) or of nitrogen atom of free primary amine group of DAMN moiety (Y form). For 5-NO2salDAMN and naphDAMN only one form (X) was observed.

Kinetics of de-N-acetylation of the chitin disaccharide in aqueous sodium hydroxide solution.

PubMed

Khong, Thang Trung; Aachmann, Finn L; Vårum, Kjell M

2012-05-01

Chitosan is prepared from chitin, a process which is carried out at highly alkaline conditions, and that can be performed either on chitin in solution (homogeneous deacetylation) or heterogeneously with the chitin as a solid throughout the reaction. We report here a study of the de-N-acetylation reaction of the chitin dimer (GlcNAc-GlcNAc) in solution. The reaction was followed by (1)H NMR spectroscopy in deuterated aqueous sodium hydroxide solution as a function of time, sodium-hydroxide concentration and temperature. The (1)H NMR spectrum of GlcNAc-GlcNAc in 2.77 M deuterated aqueous sodium hydroxide solution was assigned. The interpretation of the (1)H NMR spectra allowed us to determine the rates of de-N-acetylation of the reducing and non-reducing ends, showing that the reaction rate at the reducing end is twice the rate at the non-reducing end. The total deacetylation reaction rate was determined as a function of the hydroxide ion concentration, showing for the first time that this de-N-acetylation reaction is second order with respect to hydroxide ion concentration. No significant difference in the deacetylation rates in deuterated water compared to water was observed. The activation energy for the reaction (26-54 °C) was determined to 114.4 and 98.6 kJ/mol at 2.77 and 5.5 M in deuterated aqueous sodium hydroxide solution, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry

PubMed Central

Walker, Peter

2017-01-01

Abstract The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. PMID:28108663

X-ray and 1H-NMR spectroscopic studies of the structures and conformations of the new nootropic agents RU-35929, RU-47010 and RU-35965

NASA Astrophysics Data System (ADS)

Amato, Maria E.; Bandoli, Giuliano; Casellato, Umberto; Pappalardo, Giuseppe C.; Toja, Emilio

1990-10-01

The crystal and molecular structures of the nootropics (±)1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine ( 1), (±)1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine ( 2) and (±)1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine ( 3) have been determined by X-ray analysis. The solution conformation of 1, 2 and 3 has been investigated by 1H NMR spectroscopy. In the solid state, the main feature consists of the similar structural parameters and conformations, with the exception of the conformation adopted by the 5-ethoxy moiety which changes on passing from 1 to 2. The solid state overall enveloped conformation of the 2-pyrrolidinone ring for the three nootropics is found to be retained in solution on the basis of NMR evidence. Comparison between calculated and experimental coupling constant values shows that one of the two possible puckered opposite conformational isomers (half-chair shapes) occurs in solution. The relative pharmacological potencies of 1, 2 and 3 cannot therefore be interpreted in terms of the different conformation features presently detectable by available experimental methods.

Selective observation of charge storing ions in supercapacitor electrode materials.

PubMed

Forse, Alexander C; Griffin, John M; Grey, Clare P

2018-02-01

Nuclear magnetic resonance (NMR) spectroscopy has emerged as a useful technique for probing the structure and dynamics of the electrode-electrolyte interface in supercapacitors, as ions inside the pores of the carbon electrodes can be studied separately from bulk electrolyte. However, in some cases spectral resolution can limit the information that can be obtained. In this study we address this issue by showing how cross polarisation (CP) NMR experiments can be used to selectively observe the in-pore ions in supercapacitor electrode materials. We do this by transferring magnetisation from 13 C nuclei in porous carbons to nearby nuclei in the cations ( 1 H) or anions ( 19 F) of an ionic liquid. Two-dimensional NMR experiments and CP kinetics measurements confirm that in-pore ions are located within Ångströms of sp 2 -hybridised carbon surfaces. Multinuclear NMR experiments hold promise for future NMR studies of supercapacitor systems where spectral resolution is limited. Copyright © 2017 University of Cambridge. Published by Elsevier Inc. All rights reserved.

Gallium(III) chelates of mixed phosphonate-carboxylate triazamacrocyclic ligands relevant to nuclear medicine: Structural, stability and in vivo studies.

PubMed

Prata, Maria I M; André, João P; Kovács, Zoltán; Takács, Anett I; Tircsó, Gyula; Tóth, Imre; Geraldes, Carlos F G C

2017-12-01

Three triaza macrocyclic ligands, H 6 NOTP (1,4,7-triazacyclononane-N,N',N″-trimethylene phosphonic acid), H 4 NO2AP (1,4,7-triazacyclononane-N-methylenephosphonic acid-N',N″-dimethylenecarboxylic acid), and H 5 NOA2P (1,4,7-triazacyclononane-N,N'-bis(methylenephosphonic acid)-N″-methylene carboxylic acid), and their gallium(III) chelates were studied in view of their potential interest as scintigraphic and PET (Positron Emission Tomography) imaging agents. A 1 H, 31 P and 71 Ga multinuclear NMR study gave an insight on the structure, internal dynamics and stability of the chelates in aqueous solution. In particular, the analysis of 71 Ga NMR spectra gave information on the symmetry of the Ga 3+ coordination sphere and the stability of the chelates towards hydrolysis. The 31 P NMR spectra afforded information on the protonation of the non-coordinated oxygen atoms from the pendant phosphonate groups and on the number of species in solution. The 1 H NMR spectra allowed the analysis of the structure and the number of species in solution. 31 P and 1 H NMR titrations combined with potentiometry afforded the measurement of the protonation constants (log K Hi ) and the microscopic protonation scheme of the triaza macrocyclic ligands. The remarkably high thermodynamic stability constant (log K GaL =34.44 (0.04) and stepwise protonation constants of Ga(NOA2P) 2- were determined by potentiometry and 69 Ga and 31 P NMR titrations. Biodistribution and gamma imaging studies have been performed on Wistar rats using the radiolabeled 67 Ga(NO2AP) - and 67 Ga(NOA2P) 2- chelates, having both demonstrated to have renal excretion. The correlation of the molecular properties of the chelates with their pharmacokinetic properties has been analysed. Copyright © 2017 Elsevier Inc. All rights reserved.

Inhibitory effect of hydroxypropyl methylcellulose acetate succinate on drug recrystallization from a supersaturated solution assessed using nuclear magnetic resonance measurements.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Yamamoto, Keiji; Moribe, Kunikazu

2013-10-07

We examined the inhibitory effect of hydroxypropyl methylcellulose acetate succinate (HPMC-AS) on drug recrystallization from a supersaturated solution using carbamazepine (CBZ) and phenytoin (PHT) as model drugs. HPMC-AS HF grade (HF) inhibited the recrystallization of CBZ more strongly than that by HPMC-AS LF grade (LF). 1D-1H NMR measurements showed that the molecular mobility of CBZ was clearly suppressed in the HF solution compared to that in the LF solution. Interaction between CBZ and HF in a supersaturated solution was directly detected using nuclear Overhauser effect spectroscopy (NOESY). The cross-peak intensity obtained using NOESY of HF protons with CBZ aromatic protons was greater than that with the amide proton, which indicated that CBZ had hydrophobic interactions with HF in a supersaturated solution. In contrast, no interaction was observed between CBZ and LF in the LF solution. Saturation transfer difference NMR measurement was used to determine the interaction sites between CBZ and HF. Strong interaction with CBZ was observed with the acetyl substituent of HPMC-AS although the interaction with the succinoyl substituent was quite small. The acetyl groups played an important role in the hydrophobic interaction between HF and CBZ. In addition, HF appeared to be more hydrophobic than LF because of the smaller ratio of the succinoyl substituent. This might be responsible for the strong hydrophobic interaction between HF and CBZ. The intermolecular interactions between CBZ and HPMC-AS shown by using NMR spectroscopy clearly explained the strength of inhibition of HPMC-AS on drug recrystallization.

An alternative NMR method to determine nuclear shielding anisotropies for molecules in liquid-crystalline solutions with (13)C shielding anisotropy of methyl iodide as an example.

PubMed

Tallavaara, Pekka; Jokisaari, Jukka

2008-03-28

An alternative NMR method for determining nuclear shielding anisotropies in molecules is proposed. The method is quite simple, linear and particularly applicable for heteronuclear spin systems. In the technique, molecules of interest are dissolved in a thermotropic liquid crystal (LC) which is confined in a mesoporous material, such as controlled pore glass (CPG) used in this study. CPG materials consist of roughly spherical particles with a randomly oriented and connected pore network inside. LC Merck Phase 4 was confined in the pores of average diameter from 81 to 375 A and LC Merck ZLI 1115 in the pores of average diameter 81 A. In order to demonstrate the functionality of the method, the (13)C shielding anisotropy of (13)C-enriched methyl iodide, (13)CH(3)I, was determined as a function of temperature using one dimensional (13)C NMR spectroscopy. Methane gas, (13)CH(4), was used as an internal chemical shift reference. It appeared that methyl iodide molecules experience on average an isotropic environment in LCs inside the smallest pores within the whole temperature range studied, ranging from bulk solid to isotropic phase. In contrast, in the spaces in between the particles, whose diameter is approximately 150 microm, LCs behave as in the bulk. Consequently, isotropic values of the shielding tensor can be determined from spectra arising from molecules inside the pores at exactly the same temperature as the anisotropic ones from molecules outside the pores. Thus, for the first time in the solution state, shielding anisotropies can easily be determined as a function of temperature. The effects of pore size as well as of different LC media on the shielding anisotropy are examined and discussed.

The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

PubMed Central

Liebold, Christoph; List, Felix; Kalbitzer, Hans Robert; Sterner, Reinhard; Brunner, Eike

2010-01-01

The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5-aminoimidazole-4-carboxamideribotide. Solution NMR spectroscopy of ammonium chloride-titrated samples was used to study the interaction of NH3 with amino acids inside this channel. Although numerous residues showed 15N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78—which is located in the central channel—shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using 1H-15N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon-induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N′-[(5′-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central β-barrel of HisF and overlaps with the putative ammonia transport channel. PMID:20665694

Solution structure of the DNA-binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy.

PubMed Central

Damberger, F. F.; Pelton, J. G.; Harrison, C. J.; Nelson, H. C.; Wemmer, D. E.

1994-01-01

The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces lactis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, 1H-13C-13C-1H total correlation spectroscopy, and 15N-separated total correlation spectroscopy-heteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain 1H, 15N, and 13C resonances. Five-hundred eighty-three NOE constraints identified in 3D 13C- and 15N-separated NOE spectroscopy (NOESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional 13C/13C-edited NOESY spectrum, along with 35 phi, 9 chi 1, and 30 hydrogen bond constraints, were used to calculate 30 structures by hybrid distance geometry/stimulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel beta-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 +/- 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNA-binding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 +/- 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal. PMID:7849597

Ultrafast-based projection-reconstruction three-dimensional nuclear magnetic resonance spectroscopy.

PubMed

Mishkovsky, Mor; Kupce, Eriks; Frydman, Lucio

2007-07-21

Recent years have witnessed increased efforts toward the accelerated acquisition of multidimensional nuclear magnetic resonance (nD NMR) spectra. Among the methods proposed to speed up these NMR experiments is "projection reconstruction," a scheme based on the acquisition of a reduced number of two-dimensional (2D) NMR data sets constituting cross sections of the nD time domain being sought. Another proposition involves "ultrafast" spectroscopy, capable of completing nD NMR acquisitions within a single scan. Potential limitations of these approaches include the need for a relatively slow 2D-type serial data collection procedure in the former case, and a need for at least n high-performance, linearly independent gradients and a sufficiently high sensitivity in the latter. The present study introduces a new scheme that comes to address these limitations, by combining the basic features of the projection reconstruction and the ultrafast approaches into a single, unified nD NMR experiment. In the resulting method each member within the series of 2D cross sections required by projection reconstruction to deliver the nD NMR spectrum being sought, is acquired within a single scan with the aid of the 2D ultrafast protocol. Full nD NMR spectra can thus become available by backprojecting a small number of 2D sets, collected using a minimum number of scans. Principles, opportunities, and limitations of the resulting approach, together with demonstrations of its practical advantages, are here discussed and illustrated with a series of three-dimensional homo- and heteronuclear NMR correlation experiments.

An advanced NMR protocol for the structural characterization of aluminophosphate glasses.

PubMed

van Wüllen, Leo; Tricot, Grégory; Wegner, Sebastian

2007-10-01

In this work a combination of complementary advanced solid-state nuclear magnetic resonance (NMR) strategies is employed to analyse the network organization in aluminophosphate glasses to an unprecedented level of detailed insight. The combined results from MAS, MQMAS and (31)P-{(27)Al}-CP-heteronuclear correlation spectroscopy (HETCOR) NMR experiments allow for a detailed speciation of the different phosphate and aluminate species present in the glass. The interconnection of these local building units to an extended three-dimensional network is explored employing heteronuclear dipolar and scalar NMR approaches to quantify P-O-Al connectivity by (31)P{(27)Al}-heteronuclear multiple quantum coherence (HMQC), -rotational echo adiabatic passage double resonance (REAPDOR) and -HETCOR NMR as well as (27)Al{(31)P}-rotational echo double resonance (REDOR) NMR experiments, complemented by (31)P-2D-J-RESolved MAS NMR experiments to probe P-O-P connectivity utilizing the through bond scalar J-coupling. The combination of the results from the various NMR approaches enables us to not only quantify the phosphate units present in the glass but also to identify their respective structural environments within the three-dimensional network on a medium length scale employing a modified Q notation, Q(n)(m),(AlO)(x), where n denotes the number of connected tetrahedral phosphate, m gives the number of aluminate species connected to a central phosphate unit and x specifies the nature of the bonded aluminate species (i.e. 4, 5 or 6 coordinate aluminium).

Superstatistics model for T₂ distribution in NMR experiments on porous media.

PubMed

Correia, M D; Souza, A M; Sinnecker, J P; Sarthour, R S; Santos, B C C; Trevizan, W; Oliveira, I S

2014-07-01

We propose analytical functions for T2 distribution to describe transverse relaxation in high- and low-fields NMR experiments on porous media. The method is based on a superstatistics theory, and allows to find the mean and standard deviation of T2, directly from measurements. It is an alternative to multiexponential models for data decay inversion in NMR experiments. We exemplify the method with q-exponential functions and χ(2)-distributions to describe, respectively, data decay and T2 distribution on high-field experiments of fully water saturated glass microspheres bed packs, sedimentary rocks from outcrop and noisy low-field experiment on rocks. The method is general and can also be applied to biological systems. Copyright © 2014 Elsevier Inc. All rights reserved.

A highly selective colorimetric and fluorescent chemosensor for Al(III) based-on simple naphthol in aqueous solution

NASA Astrophysics Data System (ADS)

Liu, Zhaodi; Xu, Huajie; Sheng, Liangquan; Chen, Shuisheng; Huang, Deqian; Liu, Jie

2016-03-01

A colorimetric and fluorescent chemosensor (L) for Al(III) was synthesized and fully characterized. L could be both used as a colorimetric and fluorescent chemosensor for the detection of Al3 + ions with low detection limit (8.87 × 10- 7 M) in CH3CN-H2O (1:1, v/v) solution. The binding ratio of L-Al3 + was determined from the Job plot (absorption and fluorescence spectra) and MALDI-TOF MS data to be 1:1. The binding constant (Ka) of Al3 + binding to L was calculated to be 4.8 × 105 M- 1 from a Benesi-Hildebrand plot. Moreover, the binding site of L with Al3 + was determined by 1H NMR titration experiment.

Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements.

PubMed

Yasaka, Yoshiro; Klein, Michael L; Nakahara, Masaru; Matubayasi, Nobuyuki

2012-02-21

The rotational dynamics of benzene and water in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride are studied using molecular dynamics (MD) simulation and NMR T(1) measurements. MD trajectories based on an effective potential are used to calculate the (2)H NMR relaxation time, T(1) via Fourier transform of the relevant rotational time correlation function, C(2R)(t). To compensate for the lack of polarization in the standard fixed-charge modeling of the IL, an effective ionic charge, which is smaller than the elementary charge is employed. The simulation results are in closest agreement with NMR experiments with respect to the temperature and Larmor frequency dependencies of T(1) when an effective charge of ±0.5e is used for the anion and the cation, respectively. The computed C(2R)(t) of both solutes shows a bi-modal nature, comprised of an initial non-diffusive ps relaxation plus a long-time ns tail extending to the diffusive regime. Due to the latter component, the solute dynamics is not under the motional narrowing condition with respect to the prevalent Larmor frequency. It is shown that the diffusive tail of the C(2R)(t) is most important to understand frequency and temperature dependencies of T(1) in ILs. On the other hand, the effect of the initial ps relaxation is an increase of T(1) by a constant factor. This is equivalent to an "effective" reduction of the quadrupolar coupling constant (QCC). Thus, in the NMR T(1) analysis, the rotational time correlation function can be modeled analytically in the form of aexp (-t/τ) (Lipari-Szabo model), where the constant a, the Lipari-Szabo factor, contains the integrated contribution of the short-time relaxation and τ represents the relaxation time of the exponential (diffusive) tail. The Debye model is a special case of the Lipari-Szabo model with a = 1, and turns out to be inappropriate to represent benzene and water dynamics in ILs since a is as small as 0.1. The use of the Debye model would result in an underestimation of the QCC by a factor of 2-3 as a compensation for the neglect of the Lipari-Szabo factor. © 2012 American Institute of Physics

Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements

NASA Astrophysics Data System (ADS)

Yasaka, Yoshiro; Klein, Michael L.; Nakahara, Masaru; Matubayasi, Nobuyuki

2012-02-01

The rotational dynamics of benzene and water in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride are studied using molecular dynamics (MD) simulation and NMR T1 measurements. MD trajectories based on an effective potential are used to calculate the 2H NMR relaxation time, T1 via Fourier transform of the relevant rotational time correlation function, C2R(t). To compensate for the lack of polarization in the standard fixed-charge modeling of the IL, an effective ionic charge, which is smaller than the elementary charge is employed. The simulation results are in closest agreement with NMR experiments with respect to the temperature and Larmor frequency dependencies of T1 when an effective charge of ±0.5e is used for the anion and the cation, respectively. The computed C2R(t) of both solutes shows a bi-modal nature, comprised of an initial non-diffusive ps relaxation plus a long-time ns tail extending to the diffusive regime. Due to the latter component, the solute dynamics is not under the motional narrowing condition with respect to the prevalent Larmor frequency. It is shown that the diffusive tail of the C2R(t) is most important to understand frequency and temperature dependencies of T1 in ILs. On the other hand, the effect of the initial ps relaxation is an increase of T1 by a constant factor. This is equivalent to an "effective" reduction of the quadrupolar coupling constant (QCC). Thus, in the NMR T1 analysis, the rotational time correlation function can be modeled analytically in the form of aexp (-t/τ) (Lipari-Szabo model), where the constant a, the Lipari-Szabo factor, contains the integrated contribution of the short-time relaxation and τ represents the relaxation time of the exponential (diffusive) tail. The Debye model is a special case of the Lipari-Szabo model with a = 1, and turns out to be inappropriate to represent benzene and water dynamics in ILs since a is as small as 0.1. The use of the Debye model would result in an underestimation of the QCC by a factor of 2-3 as a compensation for the neglect of the Lipari-Szabo factor.

Assigning the NMR Spectrum of Glycidol: An Advanced Organic Chemistry Exercise

ERIC Educational Resources Information Center

Helms, Eric; Arpaia, Nicholas; Widener, Melissa

2007-01-01

Various one- and two-dimensional NMR experiments have been found to be extremely useful for assigning the proton and carbon NMR spectra of glycidol. The technique provides extremely valuable information aiding in the complete assignment of the peaks.

Simultaneous acquisition for T2 -T2 Exchange and T1 -T2 correlation NMR experiments

NASA Astrophysics Data System (ADS)

Montrazi, Elton T.; Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G.; Barsi-Andreeta, Mariane; Bonagamba, Tito J.

2018-04-01

The NMR measurements of longitudinal and transverse relaxation times and its multidimensional correlations provide useful information about molecular dynamics. However, these experiments are very time-consuming, and many researchers proposed faster experiments to reduce this issue. This paper presents a new way to simultaneously perform T2 -T2 Exchange and T1 -T2 correlation experiments by taking the advantage of the storage time and the two steps phase cycling used for running the relaxation exchange experiment. The data corresponding to each step is either summed or subtracted to produce the T2 -T2 and T1 -T2 data, enhancing the information obtained while maintaining the experiment duration. Comparing the results from this technique with traditional NMR experiments it was possible to validate the method.

NMR spectroscopy of the ligand binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists

PubMed Central

Fenwick, Michael K.; Oswald, Robert E.

2008-01-01

Glutamate receptors mediate neuronal intercommunication in the central nervous system by coupling extracellular neurotransmitter-receptor interactions to ion channel conductivity. To gain insight into structural and dynamical factors that underlie this coupling, solution NMR experiments were performed on the bi-lobed ligand-binding core of glutamate receptor 2 in complexes with a set of willardiine partial agonists. These agonists are valuable for studying structure-function relationships because their 5-position substituent size is correlated with ligand efficacy and extent of receptor desensitization whereas the substituent electronegativity is correlated with ligand potency. NMR results show that the protein backbone amide chemical shift deviations correlate mainly with efficacy and extent of desensitization. Pronounced deviations occur at specific residues in the ligand-binding site and in the two helical segments that join the lobes by a disulfide bond. Experiments detecting conformational exchange show that micro- to millisecond timescale motions also occur near the disulfide bond and vary largely with efficacy and extent of desensitization. These results thus identify regions displaying structural and dynamical dissimilarity arising from differences in ligand-protein interactions and lobe closure which may play a critical role in receptor response. Furthermore, measures of line broadening and conformational exchange for a portion of the ligand-binding site correlate with ligand EC50 data. These results do not have any correlate in the currently available crystal structures and thus provide a novel view of ligand-binding events that may be associated with agonist potency differences. PMID:18387631

Oxygen-17 NMR Shifts Caused by Cr{Sup ++} in Aqueous Solutions

DOE R&D Accomplishments Database

Jackson, J. A.; Lemons, J. F.; Taube, H.

1962-01-01

Cr{sup ++} in solution produces a paramagnetic shift in the NMR absorption of O{sup 17} in ClO{sub 4}{sup -}, as well as the expected paramagnetic shift for O{sup 17} in H{sub 2}O. As the concentration of ClO{sub 4}{sup -} increases, the shift in the H{sub 2}O{sup 17} absorption is diminished, and eventually changes sign. The effects are ascribed to preferential replacement by ClO{sub 4}{sup -} of water molecules from the axial positions in the first coordination sphere about Cr{sup ++}.

Structural characterization of NRAS isoform 5

PubMed Central

Mal, Tapas K.; Yuan, Chunhua; Courtney, Nicholas B.; Patel, Mitra; Stiff, Andrew R.; Blachly, James; Walker, Christopher; Eisfeld, Ann‐Kathrin; de la Chapelle, Albert

2016-01-01

Abstract It was recently discovered that the NRAS isoform 5 (20 amino acids) is expressed in melanoma and results in a more aggressive cell phenotype. This novel isoform is responsible for increased phosphorylation of downstream targets such as AKT, MEK, and ERK as well as increased cellular proliferation. This structure report describes the NMR solution structure of NRAS isoform 5 to be used as a starting point to understand its biophysical interactions. The isoform is highly flexible in aqueous solution, but forms a helix‐turn‐coil structure in the presence of trifluoroethanol as determined by NMR and CD spectroscopy. PMID:26947772

Structure of a Double Transmembrane Fragment of a G-Protein-Coupled Receptor in Micelles

PubMed Central

Neumoin, Alexey; Cohen, Leah S.; Arshava, Boris; Tantry, Subramanyam; Becker, Jeffrey M.; Zerbe, Oliver; Naider, Fred

2009-01-01

Abstract The structure and dynamic properties of an 80-residue fragment of Ste2p, the G-protein-coupled receptor for α-factor of Saccharomyces cerevisiae, was studied in LPPG micelles with the use of solution NMR spectroscopy. The fragment Ste2p(G31-T110) (TM1-TM2) consisted of 19 residues from the N-terminal domain, the first TM helix (TM1), the first cytoplasmic loop, the second TM helix (TM2), and seven residues from the first extracellular loop. Multidimensional NMR experiments on [15N], [15N, 13C], [15N, 13C, 2H]-labeled TM1-TM2 and on protein fragments selectively labeled at specific amino acid residues or protonated at selected methyl groups resulted in >95% assignment of backbone and side-chain nuclei. The NMR investigation revealed the secondary structure of specific residues of TM1-TM2. TALOS constraints and NOE connectivities were used to calculate a structure for TM1-TM2 that was highlighted by the presence of three α-helices encompassing residues 39–47, 49–72, and 80–103, with higher flexibility around the internal Arg58 site of TM1. RMSD values of individually superimposed helical segments 39–47, 49–72, and 80–103 were 0.25 ± 0.10 Å, 0.40 ± 0.13 Å, and 0.57 ± 0.19 Å, respectively. Several long-range interhelical connectivities supported the folding of TM1-TM2 into a tertiary structure typified by a crossed helix that splays apart toward the extracellular regions and contains considerable flexibility in the G56VRSG60 region. 15N-relaxation and hydrogen-deuterium exchange data support a stable fold for the TM parts of TM1-TM2, whereas the solvent-exposed segments are more flexible. The NMR structure is consistent with the results of biochemical experiments that identified the ligand-binding site within this region of the receptor. PMID:19383463

Cyclometalated products of [(COE)(2)RhCl](2) and 1,3-(RSCH(2))(2)C(6)H(4) (R = (t)Bu, (i)Pr) Are Dimeric. Synthesis, molecular structures, and solution dynamics of [mu-ClRh(H)(RSCH(2))(2)C(6)H(3)-2,6](2).

PubMed

Evans, Daniel R; Huang, Mingsheng; Seganish, W Michael; Chege, Esther W; Lam, Yiu-Fai; Fettinger, James C; Williams, Tracie L

2002-05-20

Two tridentate thioether pincer ligands, 1,3-(RSCH(2))(2)C(6)H(4) (R = (t)()Bu, 1a; R = (i)()Pr, 1b) underwent cyclometalation using [(COE)(2)RhCl](2) in air/moisture-free benzene at room temperature. The resultant complexes, [mu-ClRh(H)(RSCH(2))(2)C(6)H(3)-2,6](2) (R = (t)Bu, 2a; R = (i)Pr, 2b) are dimeric both in the solid state and in solution. A battery of variable-temperature one- and two-dimensional (1)H NMR experiments showed conclusively that both complexes undergo dynamic exchange in solution. Exchange between two dimeric diastereomers of 2a in solution occurred via rotation about the Rh-C(ipso) bond. The dynamic exchange of 2b was significantly more complex as an additional exchange mechanism, sulfur inversion, occurred, which resulted in the exchange between several diastereomers in solution.

Quartz Crystal Temperature Sensor for MAS NMR

NASA Astrophysics Data System (ADS)

Simon, Gerald

1997-10-01

Quartz crystal temperature sensors (QCTS) were tested for the first time as wireless thermometers in NMR MAS rotors utilizing the NMR RF technique itself for exiting and receiving electro-mechanical quartz resonances. This new tool in MAS NMR has a high sensitivity, linearity, and precision. When compared to the frequently used calibration of the variable temperature in the NMR system by a solid state NMR chemical shift thermometer (CST), such as lead nitrate, QCTS shows a number of advantages. It is an inert thermometer in close contact with solid samples operating parallel to the NMR experiment. QCTS can be manufactured for any frequency to be near a NMR frequency of interest (typically 1 to 2 MHz below or above). Due to the strong response of the crystal, signal detection is possible without changing the tuning of the MAS probe. The NMR signal is not influenced due to the relative sharp crystal resonance, restricted excitation by finite pulses, high probeQvalues, and commonly used audio filters. The quadratic dependence of the temperature increase on spinning speed is the same for the QCTS and for the CST lead nitrate and is discussed in terms of frictional heat in accordance with the literature about lead nitrate and with the results of a simple rotor speed jump experiment with differently radial located lead nitrate in the rotor.

Rapid convergence of optimal control in NMR using numerically-constructed toggling frames

NASA Astrophysics Data System (ADS)

Coote, Paul; Anklin, Clemens; Massefski, Walter; Wagner, Gerhard; Arthanari, Haribabu

2017-08-01

We present a numerical method for rapidly solving the Bloch equation for an arbitrary time-varying spin-1/2 Hamiltonian. The method relies on fast, vectorized computations such as summation and quaternion multiplication, rather than slow computations such as matrix exponentiation. A toggling frame is constructed in which the Hamiltonian is time-invariant, and therefore has a simple analytical solution. The key insight is that constructing this frame is faster than solving the system dynamics in the original frame. Rapidly solving the Bloch equations for an arbitrary Hamiltonian is particularly useful in the context of NMR optimal control. Optimal control theory can be used to design pulse shapes for a range of tasks in NMR spectroscopy. However, it requires multiple simulations of the Bloch equations at each stage of the algorithm, and for each relevant set of parameters (e.g. chemical shift frequencies). This is typically time consuming. We demonstrate that by working in an appropriate toggling frame, optimal control pulses can be generated much faster. We present a new alternative to the well-known GRAPE algorithm to continuously update the toggling-frame as the optimal pulse is generated, and demonstrate that this approach is extremely fast. The use and benefit of rapid optimal pulse generation is demonstrated for 19F fragment screening experiments.

Solution conformation of a peptide fragment representing a proposed RNA-binding site of a viral coat protein studied by two-dimensional NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

van der Graaf, M.; van Mierlo, C.P.M.; Hemminga, M.A.

1991-06-11

The first 25 amino acids of the coat protein of cowpea chlorotic mottle virus are essential for binding the encapsidated RNA. Although an {alpha}-helical conformation has been predicted for this highly positively charged N-terminal region. No experimental evidence for this conformation has been presented so far. In this study, two-dimensional proton NMR experiments were performed on a chemically synthesized pentacosapeptide containing the first 25 amino acids of this coat protein. All resonances could be assigned by a combined use of two-dimensional correlated spectroscopy and nuclear Overhauser enhancement spectroscopy carried out at four different temperatures. Various NMR parameters indicate the presencemore » of a conformational ensemble consisting of helical structures rapidly converting into more extended states. Differences in chemical shifts and nuclear Overhauser effects indicate that lowering the temperature induces a shift of the dynamic equilibrium toward more helical structures. At 10{degrees}C, a perceptible fraction of the conformational ensemble consists of structures with an {alpha}-helical conformation between residues 9 and 17, likely starting with a turnlike structure around Thr9 and Arg10. Both the conformation and the position of this helical region agree well with the secondary structure predictions mentioned above.« less

Maximum entropy analysis of NMR data of flexible multirotor molecules partially oriented in nematic solution: 2,2':5',2″-terthiophene, 2,2'- and 3,3'-dithiophene

NASA Astrophysics Data System (ADS)

Caldarelli, Stefano; Catalano, Donata; Di Bari, Lorenzo; Lumetti, Marco; Ciofalo, Maurizio; Alberto Veracini, Carlo

1994-07-01

The dipolar couplings observed by NMR spectroscopy of solutes in nematic solvents (LX-NMR) are used to build up the maximum entropy (ME) probability distribution function of the variables describing the orientational and internal motion of the molecule. The ME conformational distributions of 2,2'- and 3,3'-dithiophene and 2,2':5',2″-terthiophene (α-terthienyl)thus obtained are compared with the results of previous studies. The 2,2'- and 3,3'-dithiophene molecules exhibit equilibria among cisoid and transoid forms; the probability maxima correspond to planar and twisted conformers for 2,2'- or 3,3'-dithiophene, respectively, 2,2':5',2″-Terthiophene has two internal degrees of freedom; the ME approach indicates that the trans, trans and cis, trans planar conformations are the most probable. The correlation between the two intramolecular rotations is also discussed.

Overestimation of organic phosphorus in wetland soils by alkaline extraction and molybdate colorimetry.

PubMed

Turner, Benjamin L; Newman, Susan; Reddy, K Ramesh

2006-05-15

Accurate information on the chemical nature of soil phosphorus is essential for understanding its bioavailability and fate in wetland ecosystems. Solution phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy was used to assess the conventional colorimetric procedure for phosphorus speciation in alkaline extracts of organic soils from the Florida Everglades. Molybdate colorimetry markedly overestimated organic phosphorus by between 30 and 54% compared to NMR spectroscopy. This was due in large part to the association of inorganic phosphate with organic matter, although the error was exacerbated in some samples by the presence of pyrophosphate, an inorganic polyphosphate that is not detected by colorimetry. The results have important implications for our understanding of phosphorus biogeochemistry in wetlands and suggest that alkaline extraction and solution 31p NMR spectroscopy is the only accurate method for quantifying organic phosphorus in wetland soils.

NMR analyses of complex d-glucose anomerization.

PubMed

Kaufmann, Martin; Mügge, Clemens; Kroh, Lothar W

2018-11-01

Analyzing the 1 H NMR spectrum of d-glucose, the resonance frequencies of the anomeric protons of five d-glucose anomers could be determined in dependence on temperature. Besides, the relative concentrations of all cyclic d-glucose anomers could be quantified. Based on that, thermodynamic parameters were calculated. In addition, ring opening rate constants of all cyclic d-glucose anomers were measured for the first time using 1 H selective blind saturation transfer NMR spectroscopy. The results presented here give rise to the assumption that furanoid anomers highly influence the reactivity of total d-glucose. Finally, the complex anomeric equilibration curves for a freshly prepared solution of crystalline α-d-glucopyranose are presented. Based on that, it is hypothesized that the reactivity of a solution of a reducing sugar in general and d-glucose in particular depends on time until the thermodynamic equilibrium state is reached. Copyright © 2018 Elsevier Ltd. All rights reserved.

Solution structure and interactions of the Escherichia coli cell division activator protein CedA.

PubMed

Chen, Ho An; Simpson, Peter; Huyton, Trevor; Roper, David; Matthews, Stephen

2005-05-10

CedA is a protein that is postulated to be involved in the regulation of cell division in Escherichia coli and related organisms; however, little biological data about its possible mode of action are available. Here we present a three-dimensional structure of this protein as determined by NMR spectroscopy. The protein is made up of four antiparallel beta-strands, an alpha-helix, and a large unstructured stretch of residues at the N-terminus. It shows structural similarity to a family of DNA-binding proteins which interact with dsDNA via a three-stranded beta-sheet, suggesting that CedA may be a DNA-binding protein. The putative binding surface of CedA is predominantly positively charged with a number of basic residues surrounding a groove largely dominated by aromatic residues. NMR chemical shift perturbations and gel-shift experiments performed with CedA confirm that the protein binds dsDNA, and its interaction is mediated primarily via the beta-sheet.

Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR

PubMed Central

Camilloni, Carlo; Schaal, Daniel; Schweimer, Kristian; Schwarzinger, Stephan; De Simone, Alfonso

2012-01-01

The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalopathies. Our combined approach allowed us to dissect the factors that govern the conformational states of PrP-H1 in solution, and the implications of these factors for prion protein misfolding and aggregation. The results underline the importance of adopting novel integrated approaches that take advantage of experiments and theory to achieve a comprehensive characterization of the structure and dynamics of biological macromolecules. PMID:22225810

Ionic Borate-Based Covalent Organic Frameworks: Lightweight Porous Materials for Lithium-Stable Solid State Electrolytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Black, Hayden T.; Harrison, Katharine Lee

2016-10-01

The synthesis and characterization of the first polyelectrolyte of intrinsic microporosity (PEIM) is described. The novel material was synthesized via reaction between the nitrile group in the polymer backbone and n-butyl lithium, effectively anchoring an imine anion to the porous framework while introducing a mobile lithium counterion. The PEIM was characterized by 13C, 1H, and 7Li NMR experiments, revealing quantitative conversion of the nitrile functionality to the anionic imine. Variable temperature 7Li NMR analysis of the dry PEIM and the electrolyteswollen PEIM revealed that lithium ion transport within the dry PEIM was largely due to interchain hopping of the Limore » + ions, and that the mobility of polymer associated Li + was reduced after swelling in electrolyte solution. Meanwhile, the swollen PEIM supported efficient transport of dissolved Li + within the expanded pores. These results are discussed in the context of developing novel solid or solid-like lithium ion electrolytes using the new PEIM material.« less

Cell tracking with caged xenon: using cryptophanes as MRI reporters upon cellular internalization.

PubMed

Klippel, Stefan; Döpfert, Jörg; Jayapaul, Jabadurai; Kunth, Martin; Rossella, Federica; Schnurr, Matthias; Witte, Christopher; Freund, Christian; Schröder, Leif

2014-01-07

Caged xenon has great potential in overcoming sensitivity limitations for solution-state NMR detection of dilute molecules. However, no application of such a system as a magnetic resonance imaging (MRI) contrast agent has yet been performed with live cells. We demonstrate MRI localization of cells labeled with caged xenon in a packed-bed bioreactor working under perfusion with hyperpolarized-xenon-saturated medium. Xenon hosts enable NMR/MRI experiments with switchable contrast and selectivity for cell-associated versus unbound cages. We present MR images with 10(3) -fold sensitivity enhancement for cell-internalized, dual-mode (fluorescence/MRI) xenon hosts at low micromolar concentrations. Our results illustrate the capability of functionalized xenon to act as a highly sensitive cell tracer for MRI detection even without signal averaging. The method will bridge the challenging gap for translation to in vivo studies for the optimization of targeted biosensors and their multiplexing applications. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative measurement of regional blood flow with gadolinium diethylenetriaminepentaacetate bolus track NMR imaging in cerebral infarcts in rats: validation with the iodo[14C]antipyrine technique.

PubMed Central

Wittlich, F; Kohno, K; Mies, G; Norris, D G; Hoehn-Berlage, M

1995-01-01

NMR bolus track measurements were correlated with autoradiographically determined regional cerebral blood flow (rCBF). The NMR method is based on bolus infusion of the contrast agent gadolinium diethylenetriaminepentaacetate and high-speed T*2-sensitive NMR imaging. The first pass of the contrast agent through the image plane causes a transient decrease of the signal intensity. This time course of the signal intensity is transformed into relative concentrations of the contrast agent in each pixel. The mean transit time and relative blood flow and volume are calculated from such indicator dilution curves. We investigated whether this NMR technique correctly expresses the relative rCBF. The relative blood flow data, calculated from NMR bolus track experiments, and the absolute values of iodo[14C]antipyrine autoradiography were compared. A linear relationship was observed, indicating the proportionality of the transient NMR signal change with CBF. Excellent interindividual reproducibility of calibration constants is observed (r = 0.963). For a given NMR protocol, bolus track measurements calibrated with autoradiography after the experiment allow determination of absolute values for rCBF and regional blood volume. Images Fig. 2 Fig. 3 PMID:7892189

Solution structure of leptospiral LigA4 Big domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Song; Zhang, Jiahai; Zhang, Xuecheng

Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Bigmore » domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.« less

Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants.

PubMed

Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

2015-09-01

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Speciation of platinum(IV) in nitric acid solutions.

PubMed

Vasilchenko, Danila; Tkachev, Sergey; Baidina, Iraida; Korenev, Sergey

2013-09-16

The speciation of platinum(IV) ions in nitric acid (6-15.8 M) solutions of H2[Pt(OH)6] has been studied by (195)Pt NMR and Raman spectroscopy. Series of aqua-hydroxo-nitrato complexes [Pt(L)(x)(NO3)(6-x)] (L = H2O or OH(-); x = 0, ..., 6) were found to exist in such solutions. The pair additivity model of chemical shifts and statistical theory were used to assign signals in NMR spectra to particular [Pt(L)(x)(NO3)(6-x)] species. Mononuclear hexanitratoplatinates(IV) have been isolated in solid state in substantial yield as pyridinium salt (PyH)2[Pt(NO3)6] and characterized by single-crystal X-ray diffraction. Aging of the platinum nitric acid solutions for more than 5-6 h results in oligomerization of [Pt(L)(x)(NO3)(6-x)] species and the formation of oligonuclear aqua-hydroxo-nitrato complexes with OH(-) and NO3(-) bridging ligands. Oligomeric platinum(IV) complexes with two and four nuclei were unambiguously detected by NMR on (195)Pt -enriched samples. Oligomers with even higher nuclearity were also detected. Dimeric anions [Pt2(μ-OH)2(NO3)8](2-) have been isolated as single crystals of tetramethylammonium salt and characterized by X-ray diffraction.

EASY: a simple tool for simultaneously removing background, deadtime and acoustic ringing in quantitative NMR spectroscopy--part I: basic principle and applications.

PubMed

Jaeger, Christian; Hemmann, Felix

2014-01-01

Elimination of Artifacts in NMR SpectroscopY (EASY) is a simple but very effective tool to remove simultaneously any real NMR probe background signal, any spectral distortions due to deadtime ringdown effects and -specifically- severe acoustic ringing artifacts in NMR spectra of low-gamma nuclei. EASY enables and maintains quantitative NMR (qNMR) as only a single pulse (preferably 90°) is used for data acquisition. After the acquisition of the first scan (it contains the wanted NMR signal and the background/deadtime/ringing artifacts) the same experiment is repeated immediately afterwards before the T1 waiting delay. This second scan contains only the background/deadtime/ringing parts. Hence, the simple difference of both yields clean NMR line shapes free of artefacts. In this Part I various examples for complete (1)H, (11)B, (13)C, (19)F probe background removal due to construction parts of the NMR probes are presented. Furthermore, (25)Mg EASY of Mg(OH)2 is presented and this example shows how extremely strong acoustic ringing can be suppressed (more than a factor of 200) such that phase and baseline correction for spectra acquired with a single pulse is no longer a problem. EASY is also a step towards deadtime-free data acquisition as these effects are also canceled completely. EASY can be combined with any other NMR experiment, including 2D NMR, if baseline distortions are a big problem. © 2013 Published by Elsevier Inc.

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: insights from solid-state 13C NMR and solution 31P NMR spectroscopy

USDA-ARS?s Scientific Manuscript database

Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions...

Analysis of ethanol-soluble extractives in southern pine wood by low-field proton NMR

Treesearch

Thomas L. Eberhardt; Thomas Elder; Nicole Labbe

2007-01-01

Low-field portion NMR was evaluated as a nondestructive and rapid technique for measuring ethanol-soluble extractives in southern pine wood. Matchstick-sized wood specimens were steeped in extractive-containing solutions to generate extractive-enriched samples for analysis. decay curves obtained by the Carr-Purcell-Meiboom-gill (CPMG) pulse sequence were analyzed with...

"Cooking the sample": radiofrequency induced heating during solid-state NMR experiments.

PubMed

d'Espinose de Lacaillerie, Jean-Baptiste; Jarry, Benjamin; Pascui, Ovidiu; Reichert, Detlef

2005-09-01

Dissipation of radiofrequency (RF) energy as heat during continuous wave decoupling in solid-state NMR experiment was examined outside the conventional realm of such phenomena. A significant temperature increase could occur while performing dynamic NMR measurements provided the sample contains polar molecules and the sequence calls for relatively long applications of RF power. It was shown that the methyl flip motion in dimethylsulfone (DMS) is activated by the decoupling RF energy conversion to heat during a CODEX pulse sequence. This introduced a significant bias in the correlation time-temperature dependency measurement used to obtain the activation energy of the motion. By investigating the dependency of the temperature increase in hydrated lead nitrate on experimental parameters during high-power decoupling one-pulse experiments, the mechanisms for the RF energy deposition was identified. The samples were heated due to dissipation of the energy absorbed by dielectric losses, a phenomenon commonly known as "microwave" heating. It was thus established that during solid-state NMR experiments at moderate B0 fields, RF heating could lead to the heating of samples containing polar molecules such as hydrated polymers and inorganic solids. In particular, this could result in systematic errors for slow dynamics measurements by solid-state NMR.

1H, 13C, 15N NMR analysis of sildenafil base and citrate (Viagra) in solution, solid state and pharmaceutical dosage forms.

PubMed

Wawer, Iwona; Pisklak, Maciej; Chilmonczyk, Zdzisław

2005-08-10

Sildenafil citrate (SC) (Viagra) and sildenafil base in pure form are easily and unequivocally characterized by multinuclear NMR spectroscopy. Analysis of chemical shifts indicates that: (i) N6-H forms intramolecular hydrogen bonds, (ii) N25 is protonated in the salt and (iii) intermolecular OH...N hydrogen bonds involving N2 and N4 are present in the solid sildenafil citrate. 13C CPMAS NMR method has been proposed for the identification and quantitation of Viagra in its pharmaceutical formulations.

Photoreactive “Nanorulers” Detect a Novel Conformation of Full length HDAC3-SMRT Complex in Solution

PubMed Central

Abdelkarim, Hazem; Brunsteiner, Michael; Neelarapu, Raghupathi; Bai, He; Madriaga, Antonett; van Breemen, Richard B.; Blond, Sylvie Y.; Gaponenko, Vadim; Petukhov, Pavel A.

2013-01-01

Histone deacetylase 3 (HDAC3) is a promising epigenetic drug target for multiple therapeutic applications. Direct interaction between the Deacetylase Activating Domain of the silencing mediator for retinoid or thyroid hormone receptors (SMRT-DAD) is required for activation of enzymatic activity of HDAC3. The structure of this complex and the nature of interactions with HDAC inhibitors in solution are unknown. Using novel photoreactive HDAC probes – “nanorulers”, we determined the distance between the catalytic site of the full-length HDAC3 and SMRT-DAD in solution at physiologically relevant conditions and found it to be substantially different from that predicted by the X-ray model with a Δ379-428aa truncated HDAC3. Further experiments indicated that in solution this distance might change in response to chemical stimuli, while the enzymatic activity remained unaffected. These observations were further validated by Saturation Transfer Difference (STD) NMR experiments. We propose that the observed changes in the distance are an important part of the histone code that remains to be explored. Mapping direct interactions and distances between macromolecules with such “nanorulers” as a function of cellular events facilitates better understanding of basic biology and ways for its manipulation in cell and tissue specific manner. PMID:24010878

Amplifying Dynamic Nuclear Polarization of Frozen Solutions by Incorporating Dielectric Particles

PubMed Central

2014-01-01

There is currently great interest in understanding the limits on NMR signal enhancements provided by dynamic nuclear polarization (DNP), and in particular if the theoretical maximum enhancements can be achieved. We show that over a 2-fold improvement in cross-effect DNP enhancements can be achieved in MAS experiments on frozen solutions by simply incorporating solid particles into the sample. At 9.4 T and ∼105 K, enhancements up to εH = 515 are obtained in this way, corresponding to 78% of the theoretical maximum. We also underline that degassing of the sample is important to achieve highest enhancements. We link the amplification effect to the dielectric properties of the solid material, which probably gives rise to scattering, diffraction, and amplification of the microwave field in the sample. This is substantiated by simulations of microwave propagation. A reduction in sample heating at a given microwave power also likely occurs due to reduced dielectric loss. Simulations indicate that the microwave field (and thus the DNP enhancement) is inhomogeneous in the sample, and we deduce that in these experiments between 5 and 10% of the solution actually yields the theoretical maximum signal enhancement of 658. The effect is demonstrated for a variety of particles added to both aqueous and organic biradical solutions. PMID:25285480

High-sensitivity NMR beyond 200,000 atmospheres of pressure.

PubMed

Meier, T; Reichardt, S; Haase, J

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. (1)H NMR of water shows sensitivity and resolution obtained with the cells, and (63)Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. (115)In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry. Copyright © 2015 Elsevier Inc. All rights reserved.

An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange

PubMed Central

Baldwin, Andrew J.

2014-01-01

The Carr–Purcell–Meiboom–Gill (CPMG) experiment is widely used to quantitatively analyse the effects of chemical exchange on NMR spectra. In a CPMG experiment, the effective transverse relaxation rate, R2,eff, is typically measured as a function of the pulse frequency, νCPMG. Here, an exact expression for how R2,eff varies with νCPMG is derived for the commonly encountered scenario of two-site chemical exchange of in-phase magnetisation. This result, summarised in Appendix A, generalises a frequently used equation derived by Carver and Richards, published in 1972. The expression enables more rapid analysis of CPMG data by both speeding up calculation of R2,eff over numerical methods by a factor of ca. 130, and yields exact derivatives for use in data analysis. Moreover, the derivation provides insight into the physical principles behind the experiment. PMID:24852115

Fractional motion model for characterization of anomalous diffusion from NMR signals.

PubMed

Fan, Yang; Gao, Jia-Hong

2015-07-01

Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

Fractional motion model for characterization of anomalous diffusion from NMR signals

NASA Astrophysics Data System (ADS)

Fan, Yang; Gao, Jia-Hong

2015-07-01

Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

Is Buffer a Good Proxy for a Crowded Cell-Like Environment? A Comparative NMR Study of Calmodulin Side-Chain Dynamics in Buffer and E. coli Lysate

PubMed Central

Latham, Michael P.; Kay, Lewis E.

2012-01-01

Biophysical studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s) of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomolecules, ions and metabolites. Recently, solution NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded “cell-like” environments. Here we extend these studies through a comparative analysis of Ile, Leu, Val and Met methyl side-chain motions in apo, Ca2+-bound and Ca2+, peptide-bound calmodulin dissolved in aqueous buffer or in E. coli lysate. Deuterium spin relaxation experiments, sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed “test-tube” studies, experiments performed under conditions that are “cell-like” are critical for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function. PMID:23118958

Time-Domain Nuclear Magnetic Resonance Investigation of Water Dynamics in Different Ginger Cultivars.

PubMed

Huang, Chongyang; Zhou, Qi; Gao, Shan; Bao, Qingjia; Chen, Fang; Liu, Chaoyang

2016-01-20

Different ginger cultivars may contain different nutritional and medicinal values. In this study, a time-domain nuclear magnetic resonance method was employed to study water dynamics in different ginger cultivars. Significant differences in transverse relaxation time T2 values assigned to the distribution of water in different parts of the plant were observed between Henan ginger and four other ginger cultivars. Ion concentration and metabolic analysis showed similar differences in Mn ion concentrations and organic solutes among the different ginger cultivars, respectively. On the basis of Pearson's correlation analysis, many organic solutes and 6-gingerol, the main active substance of ginger, exhibited significant correlations with water distribution as determined by NMR T2 relaxation, suggesting that the organic solute differences may impact water distribution. Our work demonstrates that low-field NMR relaxometry provides useful information about water dynamics in different ginger cultivars as affected by the presence of different organic solutes.

Single-Scan Multidimensional NMR Analysis of Mixtures at Sub-Millimolar Concentrations by using SABRE Hyperpolarization.

PubMed

Daniele, Valeria; Legrand, François-Xavier; Berthault, Patrick; Dumez, Jean-Nicolas; Huber, Gaspard

2015-11-16

Signal amplification by reversible exchange (SABRE) is a promising method to increase the sensitivity of nuclear magnetic resonance (NMR) experiments. However, SABRE-enhanced (1)H NMR signals are short lived, and SABRE is often used to record 1D NMR spectra only. When the sample of interest is a complex mixture, this results in severe overlaps for (1)H spectra. In addition, the use of a co-substrate, whose signals may obscure the (1) H spectra, is currently the most efficient way to lower the detection limit of SABRE experiments. Here, we describe an approach to obtain clean, SABRE-hyperpolarized 2D (1)H NMR spectra of mixtures of small molecules at sub-millimolar concentrations in a single scan. The method relies on the use of para-hydrogen together with a deuterated co-substrate for hyperpolarization and ultrafast 2D NMR for acquisition. It is applicable to all substrates that can be polarized with SABRE. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Challenge of representing entropy at different levels of resolution in molecular simulation.

PubMed

Huang, Wei; van Gunsteren, Wilfred F

2015-01-22

The role of entropic contributions in processes involving biomolecules is illustrated using the process of vaporization or condensation of the solvents water and methanol and the process of polypeptide folding in solution using molecular models at different levels of resolution: subatomic, atomic, supra-atomic, and supramolecular. For the folding process, a β-hexapeptide that adopts, as inferred from NMR experiments, both a right-handed 2.710/12-helical fold and a left-handed 314-helical fold in methanol, is used to illustrate the challenge of modeling thermodynamically driven processes at different levels of resolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Xuchu; Hu, Mary; Wei, Xiaoliang

Understanding the solvation structures of electrolytes is important for developing nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivative ferrocene compounds, ferrocenylmethyl dimethyl ethyl ammonium bis (triflyoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C1H and 17O NMR investigations were carried out using solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergo line width broadening, indicating interactions between solute and solvent molecules

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

NASA Astrophysics Data System (ADS)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Cation Hydration Constants by Proton NMR: A Physical Chemistry Experiment.

ERIC Educational Resources Information Center

Smith, Robert L.; And Others

1988-01-01

Studies the polarization effect on water by cations and anions. Describes an experiment to illustrate the polarization effect of sodium, lithium, calcium, and strontium ions on the water molecule in the hydration spheres of the ions. Analysis is performed by proton NMR. (MVL)

ODIN-object-oriented development interface for NMR.

PubMed

Jochimsen, Thies H; von Mengershausen, Michael

2004-09-01

A cross-platform development environment for nuclear magnetic resonance (NMR) experiments is presented. It allows rapid prototyping of new pulse sequences and provides a common programming interface for different system types. With this object-oriented interface implemented in C++, the programmer is capable of writing applications to control an experiment that can be executed on different measurement devices, even from different manufacturers, without the need to modify the source code. Due to the clear design of the software, new pulse sequences can be created, tested, and executed within a short time. To post-process the acquired data, an interface to well-known numerical libraries is part of the framework. This allows a transparent integration of the data processing instructions into the measurement module. The software focuses mainly on NMR imaging, but can also be used with limitations for spectroscopic experiments. To demonstrate the capabilities of the framework, results of the same experiment, carried out on two NMR imaging systems from different manufacturers are shown and compared with the results of a simulation.

Enhanced picture of protein-folding intermediates using organic solvents in H/D exchange and quench-flow experiments

PubMed Central

Nishimura, Chiaki; Dyson, H. Jane; Wright, Peter E.

2005-01-01

Hydrogen/deuterium exchange followed by trapping of the labeled species in the aprotic solvent DMSO has been used to elucidate structure in both the burst-phase molten globule-folding intermediate of apomyoglobin and in an equilibrium intermediate that models the kinetic intermediate. Precise estimates can be made of exchange times in an interrupted exchange-out experiment at pH 4 followed by analysis in DMSO solution, giving extensive sequence-specific information about the structure of the equilibrium intermediate. In addition, the use of DMSO as a solvent for NMR measurements after quench-flow pH-pulse labeling experiments gives a greatly increased data set for the elucidation of the kinetic folding pathway. Interestingly, differences are observed in some regions of apomyoglobin between the equilibrium and kinetic intermediates. These differences are quantitative rather than qualitative; that is, the overall patterns of labeling and secondary structure formation remain similar between the two species. However, local differences are observed, which probably reflect the difference in the solution conditions for the equilibrium experiment (pH 4) vs. the kinetic experiment (pH 6) and the change in the status of the stabilizing hydrogen bond between the side chains of His-24 and His-119. PMID:15769860

Enantiodiscrimination of flexible cyclic solutes using NMR spectroscopy in polypeptide chiral mesophases: investigation of cis-decalin and THF.

PubMed

Aroulanda, Christie; Lafon, Olivier; Lesot, Philippe

2009-08-06

The conformational dynamics and orientational behavior of two model cyclic molecules, cis-decalin (cis-dec) and tetrahydrofurane (THF), dissolved in weakly ordering, polypeptidic chiral liquid crystals (CLCs) are theoretically discussed and experimentally investigated using deuterium and carbon-13 NMR spectroscopies. The analysis of enantiomeric and enantiotopic discriminations in these compounds is shown to depend on the rate of conformational exchange regime, slow or fast. The slow exchange regime is illustrated through the case of cis-dec at low temperature (243 K). We show that the deuterium NMR spectra in this regime can be qualitatively and quantitatively interpreted by restricting the conformational pathway of cis-dec to two enantiomeric conformers of C(2)-symmetry. The orientational order parameters of these interconverting enantiomers are calculated by matching the (2)H quadrupolar splittings with calculated conformer structures. The fast exchange regime is investigated through the examples of cis-dec at high temperature (356 K) and THF at room temperature (300 K). The (2)H NMR spectra above the coalescence temperature are analyzed by introducing the concept of "average molecular structure". This fictitious structure allows easily identifying NMR equivalences of solutes dissolved in CLC. However, it cannot be applied to determine consistent orientational order parameters. This study emphasizes that enantiotopic discriminations observed for flexible molecules in the fast exchange regime can be quantitatively interpreted only by considering the orientational order of each conformer.

Challenges in analysis of high-molar mass dextrans: comparison of HPSEC, AsFlFFF and DOSY NMR spectroscopy.

PubMed

Maina, Ndegwa Henry; Pitkänen, Leena; Heikkinen, Sami; Tuomainen, Päivi; Virkki, Liisa; Tenkanen, Maija

2014-01-01

Dilute solutions of various dextran standards, a high-molar mass (HMM) commercial dextran from Leuconostoc spp., and HMM dextrans isolated from Weissella confusa and Leuconostoc citreum were analyzed with high-performance size-exclusion chromatography (HPSEC), asymmetric flow field-flow fractionation (AsFlFFF), and diffusion-ordered NMR spectroscopy (DOSY). HPSEC analyses were performed in aqueous and dimethyl sulfoxide (DMSO) solutions, while only aqueous solutions were utilized in AsFlFFF and DOSY. The study showed that all methods were applicable to dextran analysis, but differences between the aqueous and DMSO-based solutions were obtained for HMM samples. These differences were attributed to the presence of aggregates in aqueous solution that were less prevalent in DMSO. The study showed that DOSY provides an estimate of the size of HMM dextrans, though calibration standards may be required for each experimental set-up. To our knowledge, this is the first study utilizing these three methods in analyzing HMM dextrans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun

In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO- d 6) and hexamethylphosphoramide (HMPA- d 18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO- d 6/HMPA-d 18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass,more » facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

DOE PAGES

Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; ...

2016-04-26

In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO- d 6) and hexamethylphosphoramide (HMPA- d 18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO- d 6/HMPA-d 18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass,more » facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

A reactor for high-throughput high-pressure nuclear magnetic resonance spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beach, N. J.; Knapp, S. M. M.; Landis, C. R., E-mail: landis@chem.wisc.edu

The design of a reactor for operando nuclear magnetic resonance (NMR) monitoring of high-pressure gas-liquid reactions is described. The Wisconsin High Pressure NMR Reactor (WiHP-NMRR) design comprises four modules: a sapphire NMR tube with titanium tube holder rated for pressures as high as 1000 psig (68 atm) and temperatures ranging from −90 to 90 °C, a gas circulation system that maintains equilibrium concentrations of dissolved gases during gas-consuming or gas-releasing reactions, a liquid injection apparatus that is capable of adding measured amounts of solutions to the reactor under high pressure conditions, and a rapid wash system that enables the reactor tomore » be cleaned without removal from the NMR instrument. The WiHP-NMRR is compatible with commercial 10 mm NMR probes. Reactions performed in the WiHP-NMRR yield high quality, information-rich, and multinuclear NMR data over the entire reaction time course with rapid experimental turnaround.« less

Elucidating Structural Characteristics of Biomass using Solution-State 2 D NMR with a Mixture of Deuterated Dimethylsulfoxide and Hexamethylphosphoramide.

PubMed

Yoo, Chang Geun; Pu, Yunqiao; Li, Mi; Ragauskas, Arthur J

2016-05-23

Recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6 ) and hexamethylphosphoramide (HMPA-d18 ). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. The structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6 /HMPA-d18 ; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. It also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, N.S.K.

In aqueous lysine-sucrose model systems, the effects of reaction time, pH and molar ratio were studied on the formation of non-enzymatic browning reaction (NBR) products. The extent of sucrose hydrolysis was measured and the antioxidant effect of NBR products on linoleic acid emulsions was examined. Nuclear magnetic resonance (NMR) spectra were obtained at various stages of browning. Sucrose produced NMR produces with lysine in an aqueous system at 100/sup 0/C. The C-13 NMR spectra indicated that the NBR started when sucrose and lysine were dissolved in water. The C-13 NMR spectra also showed that heating did not have an effectmore » on the gross composition of polymeric species. The absorbance at 480 nm of 0.75 M lysine-sucrose solution heated up to 6 hours increased with reaction times. The pH values of heated lysine-sucrose solution gradually decreased with reaction time. When 0.75 M sucrose or lysine solution was heated separately up to 6 hours, there were no changes in absorbance in pH. In the pH range of 3.52-6.35, higher absorbance was obtained from heated lysine-sucrose solution at acidic pH levels than at neutral pH levels. As the concentration of lysine and sucrose solution was increased, the absorbance increased. At longer reaction times or acidic pH levels, enhanced hydrolysis of sucrose to reducing sugars resulted in more NBR products. NBR products obtained at a longer reaction time, an acidic pH, and higher concentration of reactants showed a darker brown color and were effective in preventing the formation of peroxides. The oxygen uptake of linoleic acid emulsion having NBR products was smaller than that of linoleic acid emulsion without NBR products. Based on these results, it was concluded that sucrose may act as an antioxidant in processed foods containing both amino acids and lipids.« less

RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case

NASA Astrophysics Data System (ADS)

Beckman, Robert A.; Moreland, David; Louise-May, Shirley; Humblet, Christine

2006-05-01

Nuclear magnetic resonance (NMR) provides structural and dynamic information reflecting an average, often non-linear, of multiple solution-state conformations. Therefore, a single optimized structure derived from NMR refinement may be misleading if the NMR data actually result from averaging of distinct conformers. It is hypothesized that a conformational ensemble generated by a valid molecular dynamics (MD) simulation should be able to improve agreement with the NMR data set compared with the single optimized starting structure. Using a model system consisting of two sequence-related self-complementary ribonucleotide octamers for which NMR data was available, 0.3 ns particle mesh Ewald MD simulations were performed in the AMBER force field in the presence of explicit water and counterions. Agreement of the averaged properties of the molecular dynamics ensembles with NMR data such as homonuclear proton nuclear Overhauser effect (NOE)-based distance constraints, homonuclear proton and heteronuclear 1H-31P coupling constant ( J) data, and qualitative NMR information on hydrogen bond occupancy, was systematically assessed. Despite the short length of the simulation, the ensemble generated from it agreed with the NMR experimental constraints more completely than the single optimized NMR structure. This suggests that short unrestrained MD simulations may be of utility in interpreting NMR results. As expected, a 0.5 ns simulation utilizing a distance dependent dielectric did not improve agreement with the NMR data, consistent with its inferior exploration of conformational space as assessed by 2-D RMSD plots. Thus, ability to rapidly improve agreement with NMR constraints may be a sensitive diagnostic of the MD methods themselves.

Bringing NMR and IR Spectroscopy to High Schools

ERIC Educational Resources Information Center

Bonjour, Jessica L.; Hass, Alisa L.; Pollock, David W.; Huebner, Aaron; Frost, John A.

2017-01-01

Development of benchtop, portable Fourier transform nuclear magnetic resonance (NMR) and infrared (IR) spectrometers has opened up opportunities for creating university-high school partnerships that provide high school students with hands-on experience with NMR and IR instruments. With recent changes to the international baccalaureate chemistry…

Spectroscopic studies of the intramolecular hydrogen bonding in o-hydroxy Schiff bases, derived from diaminomaleonitrile, and their deprotonation reaction products.

PubMed

Szady-Chełmieniecka, Anna; Kołodziej, Beata; Morawiak, Maja; Kamieński, Bohdan; Schilf, Wojciech

2018-01-15

The structural study of five Schiff bases derived from diaminomaleonitrile (DAMN) and 2-hydroxy carbonyl compounds was performed using 1 H, 13 C and 15 N NMR methods in solution and in the solid state as well. ATR-FTIR and X-Ray spectroscopies were used for confirmation of the results obtained by NMR method. The imine obtained from DAMN and benzaldehyde was synthesized as a model compound which lacks intramolecular hydrogen bond. Deprotonation of all synthesized compounds was done by treating with tetramethylguanidine (TMG). NMR data revealed that salicylidene Schiff bases in DMSO solution exist as OH forms without intramolecular hydrogen bonds and independent on the substituents in aromatic ring. In the case of 2-hydroxy naphthyl derivative, the OH proton is engaged into weak intramolecular hydrogen bond. Two of imines (salDAMN and 5-BrsalDAMN) exist in DMSO solution as equilibrium mixtures of two isomers (A and B). The structures of equilibrium mixture in the solid state have been studied by NMR, ATR-FTIR and X-Ray methods. The deprotonation of three studied compounds (salDAMN, 5-BrsalDAMN, and 5-CH 3 salDAMN) proceeded in two different ways: deprotonation of oxygen atom (X form) or of nitrogen atom of free primary amine group of DAMN moiety (Y form). For 5-NO 2 salDAMN and naphDAMN only one form (X) was observed. Copyright © 2017 Elsevier B.V. All rights reserved.

Conformational Plasticity of the Cell-Penetrating Peptide SAP As Revealed by Solid-State 19F-NMR and Circular Dichroism Spectroscopies.

PubMed

Afonin, Sergii; Kubyshkin, Vladimir; Mykhailiuk, Pavel K; Komarov, Igor V; Ulrich, Anne S

2017-07-13

The cell-penetrating peptide SAP, which was designed as an amphipathic poly-l-proline helix II (PPII), was suggested to self-assemble into regular fibrils that are relevant for its internalization. Herein we have analyzed the structure of SAP in the membrane-bound state by solid-state 19 F-NMR, which revealed other structural states, in addition to the expected surface-aligned PPII. Trifluoromethyl-bicyclopentyl-glycine (CF 3 -Bpg) and two rigid isomers of trifluoromethyl-4,5-methanoprolines (CF 3 -MePro) were used as labels for 19 F-NMR analysis. The equilibria between different conformations of SAP were studied and were found to be shifted by the substituents at Pro-11. Synchrotron-CD results suggested that substituting Pro-11 by CF 3 -MePro governed the coil-to-PPII equilibrium in solution and in the presence of a lipid bilayer. Using CD and 19 F-NMR, we examined the slow kinetics of the association of SAP with membranes and the dependence of the SAP conformational dynamics on the lipid composition. The peptide did not bind to lipids in the solid ordered phase and aggregated only in the liquid ordered "raft"-like bilayers. Self-association could not be detected in solution or in the presence of liquid disordered membranes. Surface-bound amphipathic SAP in a nonaggregated state was structured as a mixture of nonideal extended conformations reflecting the equilibrium already present in solution, i.e., before binding to the membrane.

Structure and dynamics of [3.3]paracyclophane as studied by nuclear magnetic resonance and density functional theory calculations.

PubMed

Dodziuk, Helena; Szymański, Sławomir; Jaźwiński, Jarosław; Marchwiany, Maciej E; Hopf, Henning

2010-09-30

Strained cyclophanes with small (-CH(2)-)(n) bridges connecting two benzene rings are interesting objects of basic research, mostly because of the nonplanarity of the rings and of interference of π-electrons of the latter. For title [3.3]paracyclophane, in solutions occurring in two interconverting cis and trans conformers, the published nuclear magnetic resonance (NMR) data are incomplete and involve its partially deuterated isotopomers. In this paper, variable-temperature NMR studies of its perprotio isotopomer combined with DFT quantum chemical calculations provide a complete characterization of the solution structure, NMR parameters, and interconversion of the cis and trans isomers of the title compound. Using advanced methods of spectral analysis, total quantitative interpretation of its proton NMR spectra in both the static and dynamic regimes is conducted. In particular, not only the geminal but also all of the vicinal J(HH) values for the bridge protons are determined, and for the first time, complete Arrhenius data for the interconversion process are reported. The experimental proton and carbon chemical shifts and the (n)J(HH), (1)J(CH), and (1)J(CC) coupling constants are satisfactorily reproduced theoretically by the values obtained from the density functional theory calculations.

Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.

Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, themore » 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.« less

NMR spectroscopy and molecular modelling studies of nitrosylcobalamin: further evidence that the deprotonated, base-off form is important for nitrosylcobalamin in solution†

PubMed Central

Hassanin, Hanaa A.; Hannibal, Luciana; Jacobsen, Donald W.; Brown, Kenneth L.

2009-01-01

The structure of nitrosylcobalamin (NOCbl) in solution has been studied by NMR spectroscopy and the 1H and 13C NMR spectra have been assigned. 13C and 31P NMR chemical shifts, the UV-vis spectrum of NOCbl and the observed pK base-off value of ~5.1 for NOCbl provide evidence that a significant fraction of NOCbl is present in the base-off, 5,6-dimethylbenzimidazole (DMB) deprotonated, form in solution. NOE-restrained molecular mechanics modelling of base-on NOCbl gave annealed structures with minor conformational differences in the flexible side chains and the nucleotide loop position compared with the X-ray structure. A molecular dynamics simulation at 300 K showed that DMB remains in close proximity to the α face of the corrin in the base-off form of NOCbl. Simulated annealing calculations produced two major conformations of base-off NOCbl. In the first, the DMB is perpendicular to the corrin and its B3 nitrogen is about 3.1 Å away from and pointing directly at the metal ion; in the second the DMB is parallel to and tucked beneath the D ring of the corrin. PMID:19122899

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

PubMed Central

Jang, Richard; Wang, Yan

2015-01-01

NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement. PMID:25737244

Novel method for the determination of average molecular weight of natural polymers based on 2D DOSY NMR and chemometrics: Example of heparin.

PubMed

Monakhova, Yulia B; Diehl, Bernd W K; Do, Tung X; Schulze, Margit; Witzleben, Steffen

2018-02-05

Apart from the characterization of impurities, the full characterization of heparin and low molecular weight heparin (LMWH) also requires the determination of average molecular weight, which is closely related to the pharmaceutical properties of anticoagulant drugs. To determine average molecular weight of these animal-derived polymer products, partial least squares regression (PLS) was utilized for modelling of diffused-ordered spectroscopy NMR data (DOSY) of a representative set of heparin (n=32) and LMWH (n=30) samples. The same sets of samples were measured by gel permeation chromatography (GPC) to obtain reference data. The application of PLS to the data led to calibration models with root mean square error of prediction of 498Da and 179Da for heparin and LMWH, respectively. The average coefficients of variation (CVs) did not exceed 2.1% excluding sample preparation (by successive measuring one solution, n=5) and 2.5% including sample preparation (by preparing and analyzing separate samples, n=5). An advantage of the method is that the sample after standard 1D NMR characterization can be used for the molecular weight determination without further manipulation. The accuracy of multivariate models is better than the previous results for other matrices employing internal standards. Therefore, DOSY experiment is recommended to be employed for the calculation of molecular weight of heparin products as a complementary measurement to standard 1D NMR quality control. The method can be easily transferred to other matrices as well. Copyright © 2017 Elsevier B.V. All rights reserved.

A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins.

PubMed

Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G

2014-01-01

A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.

Solid and solution NMR studies of the complexation of Ag + with the trans isomer of captopril: Biological activities of this high blood pressure drug along with its Ag + complex

NASA Astrophysics Data System (ADS)

Isab, Anvarhusein A.; Wazeer, Mohamed I. M.

2006-09-01

Complexation of Ag + with captopril, 1-[(2 S)-3-mercapto-2-methylpropionyl]- L-proline, has been studied by 1H and 13C-NMR spectroscopy. The equilibrium constants for the trans to cis isomers of captopril bound to Ag + were measured by 1H NMR spectroscopy. It is observed that the trans isomer of the drug binds more strongly to Ag + between pH 5 and 8, as shown by the broadening of the trans isomer's resonances in 13C NMR spectra on complexation. A monodentate complexation of the trans captopril with Ag + via the thiol site is proposed based on the solid-state NMR and IR data. A superior antimicrobial activity is exhibited by the Cap-Ag(I) complex compared to captopril ligand itself against Heterotrotropic Plate Counts (HPC), Pseudomonas aeruginosa and Fecal streptococcus bacteria.

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

Assessment of chemical exchange in tryptophan-albumin solution through (19)F multicomponent transverse relaxation dispersion analysis.

PubMed

Lin, Ping-Chang

2015-06-01

A number of NMR methods possess the capability of probing chemical exchange dynamics in solution. However, certain drawbacks limit the applications of these NMR approaches, particularly, to a complex system. Here, we propose a procedure that integrates the regularized nonnegative least squares (NNLS) analysis of multiexponential T2 relaxation into Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments to probe chemical exchange in a multicompartmental system. The proposed procedure was validated through analysis of (19)F T2 relaxation data of 6-fluoro-DL-tryptophan in a two-compartment solution with and without bovine serum albumin. Given the regularized NNLS analysis of a T2 relaxation curve acquired, for example, at the CPMG frequency υ CPMG  = 125, the nature of two distinct peaks in the associated T2 distribution spectrum indicated 6-fluoro-DL-tryptophan either retaining the free state, with geometric mean */multiplicative standard deviation (MSD) = 1851.2 ms */1.51, or undergoing free/albumin-bound interconversion, with geometric mean */MSD = 236.8 ms */1.54, in the two-compartment system. Quantities of the individual tryptophan species were accurately reflected by the associated T2 peak areas, with an interconversion state-to-free state ratio of 0.45 ± 0.11. Furthermore, the CPMG relaxation dispersion analysis estimated the exchange rate between the free and albumin-bound states in this fluorinated tryptophan analog and the corresponding dissociation constant of the fluorinated tryptophan-albumin complex in the chemical-exchanging, two-compartment system.

Monitoring an Induced Permafrost Warming Experiment Using ERT, Temperature, and NMR in Fairbanks, Alaska

NASA Astrophysics Data System (ADS)

Ulrich, C.; Ajo Franklin, J. B.; Ekblaw, I.; Lindsey, N.; Wagner, A. M.; Saari, S.; Daley, T. M.; Freifeld, B. M.

2016-12-01

As global temperatures continue to rise, permafrost landscapes will experience more rapid changes than other global climate zones. Permafrost thaw is a result of increased temperatures in arctic settings resulting in surface deformation and subsurface hydrology changes. From an engineering perspective, surface deformation poses a threat to the stability of existing infrastructure such as roads, utility piping, and building structures. Preemptively detecting or monitoring subsurface thaw dynamics presents a difficult challenge due to the long time scales as deformation occurs. Increased subsurface moisture content results from permafrost thaw of which electrical resistivity tomography (ERT), soil temperature, and nuclear magnetic resonance (NMR) are directly sensitive. In this experiment we evaluate spatial and temporal changes in subsurface permafrost conditions (moisture content and temperature) at a experimental heating plot in Fairbanks, AK. This study focuses on monitoring thaw signatures using multiple collocated electrical resistivity (ERT), borehole temperature, and borehole nuclear magnetic resonance (NMR) measurements. Timelapse ERT (sensitive to changes in moisture content) was inverted using collocated temperature and NMR to constrain ERT inversions. Subsurface thermal state was monitored with timelapse thermistors, sensitive to soil ice content. NMR was collected in multiple boreholes and is sensitive to changes in moisture content and pore scale distribution. As permafrost thaws more hydrogen, in the form of water, is available resulting in a changing NMR response. NMR requires the availability of liquid water in order to induce spin of the hydrogen molecule, hence, if frozen water molecules will be undetectable. In this study, the permafrost is poised close to 0oC and is mainly silt with small pore dimensions; this combination makes NMR particularly useful due to the possibility of sub-zero thaw conditions within the soil column. Overall this experiment presents a complementary suite of methods that provides feedback on subsurface permafrost state even in cases where soil texture might control unfrozen water content.

NMR studies of water dynamics during sol-to-gel transition of poly (N-isopropylacrylamide) in concentrated aqueous solution

USDA-ARS?s Scientific Manuscript database

The thermo-sensitive polymer, poly(N-isopropylacrylamide) (PNIPAM) undergoes a coil-to-globule transition in an aqueous solution as the temperature is raised through the lower critical solution temperature. Thus far, little is known about the dynamical states of the water molecules that contribute ...

Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

PubMed Central

Bothe, Jameson R.; Nikolova, Evgenia N.; Eichhorn, Catherine D.; Chugh, Jeetender; Hansen, Alexandar L.; Al-Hashimi, Hashim M.

2012-01-01

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering. PMID:22036746

A Study of the Structure-Activity Relationship of GABAA-Benzodiazepine Receptor Bivalent Ligands by Conformational Analysis with Low Temperature NMR and X-ray Analysis

PubMed Central

Han, Dongmei; Försterling, F. Holger; Li, Xiaoyan; Deschamps, Jeffrey R.; Parrish, Damon; Cao, Hui; Rallapalli, Sundari; Clayton, Terry; Teng, Yun; Majumder, Samarpan; Sankar, Subramaniam; Roth, Bryan L.; Sieghart, Werner; Furtmuller, Roman; Rowlett, James; Weed, Mike R.; Cook, James M.

2013-01-01

The stable conformations of GABAA-benzodiazepine receptor bivalent ligands were determined by low temperature NMR spectroscopy and confirmed by single crystal X-ray analysis. The stable conformations in solution correlated well with those in the solid state. The linear conformation was important for these dimers to access the binding site and exhibit potent in vitro affinity and was illustrated for α5 subtype selective ligands. Bivalent ligands with an oxygen-containing linker folded back upon themselves both in solution and the solid state. Dimers which are folded do not bind to Bz receptors. PMID:18790643

Revisiting the formation of cyclic clusters in liquid ethanol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balanay, Mannix P.; Fan, Haiyan, E-mail: haiyan.fan@nu.edu.kz; Kim, Dong Hee

2016-04-21

The liquid phase of ethanol in pure and in non-polar solvents was studied at room temperature using Fourier transform infrared (FT-IR) and {sup 1}H nuclear magnetic resonance (NMR) spectroscopies together with theoretical approach. The FT-IR spectra for pure ethanol and solution in cyclohexane at different dilution stages are consistent with {sup 1}H NMR results. The results from both methods were best explained by the results of the density functional theory based on a multimeric model. It is suggested that cyclic trimers and tetramers are dominated in the solution of cyclohexane/hexane with the concentration greater than 0.5M at room temperature. Inmore » liquid ethanol, while the primary components at room temperature are cyclic trimers and tetramers, there is a certain amount (∼14%) of open hydroxide group representing the existence of chain like structures in the equilibria. The cyclic cluster model in the liquid and concentrated solution phase (>0.5M) can be used to explain the anomalously lower freezing point of ethanol (159 K) than that of water (273 K) at ambient conditions. In addition, {sup 1}H NMR at various dilution stages reveals the dynamics for the formation of cyclic clusters.« less

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

PubMed

Shi, Xuesong; Walker, Peter; Harbury, Pehr B; Herschlag, Daniel

2017-05-05

The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Aromatic hydrazones derived from nicotinic acid hydrazide as fluorimetric pH sensing molecules: Structural analysis by computational and spectroscopic methods in solid phase and in solution

NASA Astrophysics Data System (ADS)

Benković, T.; Kenđel, A.; Parlov-Vuković, J.; Kontrec, D.; Chiş, V.; Miljanić, S.; Galić, N.

2018-02-01

Structural analyses of aroylhydrazones were performed by computational and spectroscopic methods (solid state NMR, 1 and 2D NMR spectroscopy, FT-IR (ATR) spectroscopy, Raman spectroscopy, UV-Vis spectrometry and spectrofluorimetry) in solid state and in solution. The studied compounds were N‧-(2,3-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (1), N‧-(2,5-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (2), N‧-(3-chloro-2-hydroxy-phenylmethylidene)-3-pyridinecarbohydrazide (3), and N‧-(2-hydroxy-4-methoxyphenyl-methylidene)-3-pyridinecarbohydrazide (4). Both in solid state and in solution, all compounds were in ketoamine form (form I, sbnd COsbnd NHsbnd Ndbnd Csbnd), stabilized by intramolecular H-bond between hydroxyl proton and nitrogen atom of the Cdbnd N group. In solid state, the Cdbnd O group of 1-4 were involved in additional intermolecular H-bond between closely packed molecules. Among hydrazones studied, the chloro- and methoxy-derivatives have shown pH dependent and reversible fluorescence emission connected to deprotonation/protonation of salicylidene part of the molecules. All findings acquired by experimental methods (NMR, IR, Raman, and UV-Vis spectra) were in excellent agreement with those obtained by computational methods.

Chemical analysis of bleach and hydroxide-based solutions after decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX).

PubMed

Hopkins, F B; Gravett, M R; Self, A J; Wang, M; Chua, Hoe-Chee; Hoe-Chee, C; Lee, H S Nancy; Sim, N Lee Hoi; Jones, J T A; Timperley, C M; Riches, J R

2014-08-01

Detailed chemical analysis of solutions used to decontaminate chemical warfare agents can be used to support verification and forensic attribution. Decontamination solutions are amongst the most difficult matrices for chemical analysis because of their corrosive and potentially emulsion-based nature. Consequently, there are relatively few publications that report their detailed chemical analysis. This paper describes the application of modern analytical techniques to the analysis of decontamination solutions following decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX). We confirm the formation of N,N-diisopropylformamide and N,N-diisopropylamine following decontamination of VX with hypochlorite-based solution, whereas they were not detected in extracts of hydroxide-based decontamination solutions by nuclear magnetic resonance (NMR) spectroscopy or gas chromatography-mass spectrometry. We report the electron ionisation and chemical ionisation mass spectroscopic details, retention indices, and NMR spectra of N,N-diisopropylformamide and N,N-diisopropylamine, as well as analytical methods suitable for their analysis and identification in solvent extracts and decontamination residues.

Effect of clathrate hydrate formation and decomposition on NMR parameters in THF-D2O solution.

PubMed

Rousina-Webb, Alexander; Leek, Donald M; Ripmeester, John

2012-06-28

The NMR spin-lattice relaxation time (T(1)), spin-spin relaxation time (T(2)) and the diffusion coefficient D were measured for (1)H in a 1:17 mol % solution of tetrahydrofuran (THF) in D(2)O. The aim of the work was to clarify some earlier points raised regarding the utility of these measurements to convey structural information on hydrate formation and reformation. A number of irregularities in T(1) and T(2) measurements during hydrate processes reported earlier are explained in terms of the presence of interfaces and possible temperature gradients. We observe that T(1) and T(2) in solution are exactly the same before and after hydrate formation, thus confirming that the solution is isotropic. This is inconsistent with the presence of memory effects, at least those that may affect the dynamics to which T(1) and T(2) are sensitive. The measurement of the diffusion coefficient for a number of hours in the subcooled solution before nucleation proved invariant with time, again suggesting that the solution remains isotropic without affecting the guest dynamics and diffusion.

Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

ERIC Educational Resources Information Center

Wright, Nathan T.

2016-01-01

Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

Using NMR to Expand Chemistry Research and Educational Experiences at North Carolina Central University, an Historically Black University

DTIC Science & Technology

analytical chemistry . Most students do not get hands-on training with an NMR within their classroom or laboratory courses. The NMR will provide...unique opportunities to our students as they train to become the next generation of scientists, doctors, and engineers .

An Integrated Laboratory Project in NMR Spectroscopy.

ERIC Educational Resources Information Center

Hudson, Reggie L.; Pendley, Bradford D.

1988-01-01

Describes an advanced NMR project that can be done with a 60-MHz continuous-wave proton spectrometer. Points out the main purposes are to give students experience in second-order NMR analysis, the simplification of spectra by raising the frequency, and the effect of non-hydrogen nuclei on proton resonances. (MVL)

On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR

PubMed Central

Mandal, Abhishek; Boatz, Jennifer C.; Wheeler, Travis; van der Wel, Patrick C. A.

2017-01-01

A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation. PMID:28229262

Lithium Polymer Electrolytes and Solid State NMR

NASA Technical Reports Server (NTRS)

Berkeley, Emily R.

2004-01-01

Research is being done at the Glenn Research Center (GRC) developing new kinds of batteries that do not depend on a solution. Currently, batteries use liquid electrolytes containing lithium. Problems with the liquid electrolyte are (1) solvents used can leak out of the battery, so larger, more restrictive, packages have to be made, inhibiting the diversity of application and decreasing the power density; (2) the liquid is incompatible with the lithium metal anode, so alternative, less efficient, anodes are required. The Materials Department at GRC has been working to synthesize polymer electrolytes that can replace the liquid electrolytes. The advantages are that polymer electrolytes do not have the potential to leak so they can be used for a variety of tasks, small or large, including in the space rover or in space suits. The polymers generated by Dr. Mary Ann Meador's group are in the form of rod -coil structures. The rod aspect gives the polymer structural integrity, while the coil makes it flexible. Lithium ions are used in these polymers because of their high mobility. The coils have repeating units of oxygen which stabilize the positive lithium by donating electron density. This aids in the movement of the lithium within the polymer, which contributes to higher conductivity. In addition to conductivity testing, these polymers are characterized using DSC, TGA, FTIR, and solid state NMR. Solid state NMR is used in classifying materials that are not soluble in solvents, such as polymers. The NMR spins the sample at a magic angle (54.7') allowing the significant peaks to emerge. Although solid state NMR is a helpful technique in determining bonding, the process of preparing the sample and tuning it properly are intricate jobs that require patience; especially since each run takes about six hours. The NMR allows for the advancement of polymer synthesis by showing if the expected results were achieved. Using the NMR, in addition to looking at polymers, allows for participation on a variety of other projects, including aero-gels and carbon graphite mat en als. The goals of the polymer electrolyte research are to improve the physical properties of the polymers. This includes improving conductivity, durability, and expanding the temperature range over which it is effective. Currently, good conductivity is only present at high temperatures. My goals are to experiment with different arrangements of rods and coils to achieve these desirable properties. Some of my experiments include changing the number of repeat units in the polymer, the size of the diamines, and the types of coil. Analysis of these new polymers indicates improvement in some properties, such as lower glass transition temperature; however, they are not as flexible as desired. With further research we hope to produce polymers that encompass all of these properties to a high degree.

Trispyrazolylborate Complexes: An Advanced Synthesis Experiment Using Paramagnetic NMR, Variable-Temperature NMR, and EPR Spectroscopies

ERIC Educational Resources Information Center

Abell, Timothy N.; McCarrick, Robert M.; Bretz, Stacey Lowery; Tierney, David L.

2017-01-01

A structured inquiry experiment for inorganic synthesis has been developed to introduce undergraduate students to advanced spectroscopic techniques including paramagnetic nuclear magnetic resonance and electron paramagnetic resonance. Students synthesize multiple complexes with unknown first row transition metals and identify the unknown metals by…

A complete 1H and 13C NMR data assignment for the diterpene methyl (-)-zanzibarate by 2D spectroscopy and NOE experiments.

PubMed

Imamura, P M; Miranda, P C M L; Giacomini, R A

2004-06-01

The 1H and 13C NMR spectra of methyl (-)-zanzibarate (1), an ent-labdanic diterpene isolated from the epicarp of Hymenaea courbaril var. altissima (Leguminosaea, Cesalpinoideae, Detariae), was fully assigned by COSY experiments, 13C/1H shift correlation diagrams and NOE experiments. Copyright 2004 John Wiley & Sons, Ltd.

Diels-Alder Cycloadditions: A MORE Experiment in the Organic Laboratory Including a Diene Identification Exercise Involving NMR Spectroscopy and Molecular Modeling

ERIC Educational Resources Information Center

Shaw, Roosevelt; Severin, Ashika; Balfour, Miguel; Nettles, Columbus

2005-01-01

Two Diels-Alder reactions are described that are suitable for a MORE (microwave-induced organic reaction enhanced) experiment in the organic chemistry laboratory course. A second experiment in which the splitting patterns of the vinyl protons in the nuclear magnetic resonance (NMR) spectra of two MORE adducts are used in conjunction with molecular…

Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data.

PubMed

Teixeira, João M C; Skinner, Simon P; Arbesú, Miguel; Breeze, Alexander L; Pons, Miquel

2018-05-11

We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems' responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.

NMR properties of 3He-A in biaxially anisotropic aerogel

NASA Astrophysics Data System (ADS)

Dmitriev, V. V.; Krasnikhin, D. A.; Senin, A. A.; Yudin, A. N.

2012-12-01

Theoretical model of G.E. Volovik for A-like phase of 3He in aerogel suggests formation of Larkin-Imry-Ma state of Anderson-Brinkmann-Morel order parameter. Most of results of NMR studies of A-like phase are in a good agreement with this model in assumption of uniaxial anisotropy, except for some of experiments in weakly anisotropic aerogel samples. We demonstrate that these results can be described in frames of the same model in assumption of biaxial anisotropy. Parameters of anisotropy in these experiments can be determined from the NMR data.

Vanadate complexes bearing an imidazolidine-bridged bis(aryloxido) ligand: synthesis and solid state and solution structure.

PubMed

Kober, Ewa; Nerkowski, Tomasz; Janas, Zofia; Jerzykiewicz, Lucjan B

2012-05-07

A new imidazolidine-bridged bis(aryloxido) ligand precursor (H(2)L) [H(2)L = 2,2'-(imidazolidine-1,3-diylbis(methylene))bis(4-(1,1,3,3-tetramethylbutyl-2-yl)phenol)] was prepared in a relatively high yield (∼60%) via a single-step Mannich condensation of 4-(1,1,3,3-tetramethylbutyl)phenol, ethylenediamine and paraformaldehyde at 2:1:3 molar ratio and characterized by chemical and physical techniques including X-ray crystallography. Reactions of H(2)L with [VO(OEt)(3)] at 1:1 and 1:2 molar ratios in toluene afforded [V(L-κ(3)O,N,N,O)(O)(OEt)] (1) and [V(2)(μ-L-κ(4)O,N,N,O)(μ-OEt)(2)(O)(2)(OEt)(2)] (2), respectively. Alcoholysis of 1 with EtOH enables elimination of one molecule of H(2)L and the formation of 2. Compounds 1 and 2 were characterized by IR and NMR spectroscopy as well as ES-MS experiments. The definitive molecular structure of 2 was provided by a single-crystal analysis and revealed its dinuclear nature, featuring two octahedral vanadium centres bridged by both OEt groups and the L ligand. The (51)V, (1)H and (13)C NMR spectra as well as ES-MS showed that 2 does not stay intact in solution and undergoes dissociation to give 1 and [VO(OEt)(3)].

Calculation of UV, IR, and NMR Spectra of Diethyl 2,2'-[(1,1'-Biphenyl)-4,4'-Diylbis(Azanediyl)]Diacetate

NASA Astrophysics Data System (ADS)

Almodarresiyeh, H. A.; Shahab, S. N.; Zelenkovsky, V. M.; Ariko, N. G.; Filippovich, L. N.; Agabekov, V. E.

2014-03-01

The new substance diethyl 2,2'-[(1,1'-biphenyl)-4,4'-diylbis(azanediyl)]diacetate (M13) was modeled using the Hartree-Fock and density functional theory methods and then synthesized. The electronic absorption spectrum of M13 in dimethylformamide solution was calculated. The UV, IR, and NMR spectra of M13 were presented.

Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, James M.; Korzhnev, Dmitry M.; Ceccarelli, Derek F.

2012-10-23

The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studiesmore » of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.« less

An Oil Spill in a Tube: An Accessible Approach for Teaching Environmental NMR Spectroscopy

ERIC Educational Resources Information Center

Simpson, Andre´ J.; Mitchell, Perry J.; Masoom, Hussain; Mobarhan, Yalda Liaghati; Adamo, Antonio; Dicks, Andrew P.

2015-01-01

NMR spectroscopy has great potential as an instrumental method for environmental chemistry research and monitoring but may be underused in teaching laboratories because of its complexity and the level of expertise required in operating the instrument and interpreting data. This laboratory experiment introduces environmental NMR spectroscopy to…

An NMR Experiment Based on Off-the-Shelf Digital Data-Acquisition Equipment

ERIC Educational Resources Information Center

Hilty, Christian; Bowen, Sean

2010-01-01

Nuclear magnetic resonance (NMR) poses significant challenges for teaching in the context of an undergraduate laboratory, foremost because of high equipment cost. Current off-the-shelf data-acquisition hardware, however, is sufficiently powerful to constitute the core of a fully digital NMR spectrometer operating at the earth's field. We present…

13C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall.

PubMed

Foston, Marcus; Samuel, Reichel; Ragauskas, Arthur J

2012-09-07

The ability to accurately and rapidly measure plant cell wall composition, relative monolignol content and lignin-hemicellulose inter-unit linkage distributions has become essential to efforts centered on reducing the recalcitrance of biomass by genetic engineering. Growing (13)C enriched transgenic plants is a viable route to achieve the high-throughput, detailed chemical analysis of whole plant cell wall before and after pretreatment and microbial or enzymatic utilization by (13)C nuclear magnetic resonance (NMR) in a perdeuterated ionic liquid solvent system not requiring component isolation. 1D (13)C whole cell wall ionic liquid NMR of natural abundant and (13)C enriched corn stover stem samples suggest that a high level of uniform labeling (>97%) can significantly reduce the total NMR experiment times up to ~220 times. Similarly, significant reduction in total NMR experiment time (~39 times) of the (13)C enriched corn stover stem samples for 2D (13)C-(1)H heteronuclear single quantum coherence NMR was found.

A ferromagnetic shim insert for NMR magnets - Towards an integrated gyrotron for DNP-NMR spectroscopy.

PubMed

Ryan, Herbert; van Bentum, Jan; Maly, Thorsten

2017-04-01

In recent years high-field Dynamic Nuclear Polarization (DNP) enhanced NMR spectroscopy has gained significant interest. In high-field DNP-NMR experiments (⩾400MHz 1 H NMR, ⩾9.4T) often a stand-alone gyrotron is used to generate high microwave/THz power to produce sufficiently high microwave induced B 1e fields at the position of the NMR sample. These devices typically require a second, stand-alone superconducting magnet to operate. Here we present the design and realization of a ferroshim insert, to create two iso-centers inside a commercially available wide-bore NMR magnet. This work is part of a larger project to integrate a gyrotron into NMR magnets, effectively eliminating the need for a second, stand-alone superconducting magnet. Copyright © 2017 Elsevier Inc. All rights reserved.

Automated structure determination of proteins with the SAIL-FLYA NMR method.

PubMed

Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

2007-01-01

The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

Production and physicochemical assessment of new stevia amino acid sweeteners from the natural stevioside.

PubMed

Khattab, Sherine N; Massoud, Mona I; Jad, Yahya El-Sayed; Bekhit, Adnan A; El-Faham, Ayman

2015-04-15

New stevia amino acid sweeteners, stevia glycine ethyl ester (ST-GL) and stevia l-alanine methyl ester (ST-GL), were synthesised and characterised by IR, NMR ((1)H NMR and (13)C NMR) and elemental analysis. The purity of the new sweeteners was determined by HPLC and their sensory properties were evaluated relative to sucrose in an aqueous system. Furthermore, the stevia derivatives (ST-GL and ST-AL) were evaluated for their acute toxicity, melting point, solubility and heat stability. The novel sweeteners were stable in acidic, neutral or basic aqueous solutions maintained at 100 °C for 2 h. The sweetness intensity rate of the novel sweeteners was higher than sucrose. Stevia amino acid (ST-GL and ST-AL) solutions had a clean sweetness taste without bitterness when compared to stevioside. The novel sweeteners can be utilised as non-caloric sweeteners in the production of low-calorie food. Copyright © 2014 Elsevier Ltd. All rights reserved.

Experimental and theoretical NMR and IR studies of the side-chain orientation effects on the backbone conformation of dehydrophenylalanine residue.

PubMed

Buczek, Aneta M; Ptak, Tomasz; Kupka, Teobald; Broda, Małgorzata A

2011-06-01

Conformation of N-acetyl-(E)-dehydrophenylalanine N', N'-dimethylamide (Ac-(E)-ΔPhe-NMe(2)) in solution, a member of (E)-α, β-dehydroamino acids, was studied by NMR and infrared spectroscopy and the results were compared with those obtained for (Z) isomer. To support the spectroscopic interpretation, the Φ, Ψ potential energy surfaces were calculated at the MP2/6-31 + G(d,p) level of theory in chloroform solution modeled by the self-consistent reaction field-polarizable continuum model method. All minima were fully optimized by the MP2 method and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds and dipole interactions between carbonyl groups. The obtained NMR spectral features were compared with theoretical nuclear magnetic shieldings, calculated using Gauge Independent Atomic Orbitals (GIAO) approach and rescaled to theoretical chemical shifts using benzene as reference. The calculated indirect nuclear spin-spin coupling constants were compared with available experimental parameters. Copyright © 2011 John Wiley & Sons, Ltd.

Studies related to primitive chemistry. A proton and nitrogen-14 nuclear magnetic resonance amino acid and nucleic acid constituents and a and their possible relation to prebiotic

NASA Technical Reports Server (NTRS)

Manatt, S. L.; Cohen, E. A.; Shiller, A. M.; Chan, S. I.

1973-01-01

Preliminary proton nuclear magnetic resonance (NMR) studies were made to determine the applicability of this technique for the study of interactions between monomeric and polymeric amino acids with monomeric nucleic acid bases and nucleotides. Proton NMR results for aqueous solutions (D2O) demonstrated interactions between the bases cytosine and adenine and acidic and aromatic amino acids. Solutions of 5'-AMP admixed with amino acids exhibited more complex behavior but stacking between aromatic rings and destacking at high amino acids concentration was evident. The multisite nature of 5'-AMP was pointed out. Chemical shift changes for adenine and 5'-AMP with three water soluble polypeptides demonstrated that significant interactions exist. It was found that the linewidth-pH profile of each amino acid is unique. It is concluded that NMR techniques can give significant and quantitative data on the association of amino acid and nucleic acid constituents.

Preparation of Some Homologous TEMPO Nitroxides and Oxoammonium Salts; Notes on the NMR Spectroscopy of Nitroxide Free Radicals; Observed Radical Nature of Oxoammonium Salt Solutions Containing Trace Amounts of Corresponding Nitroxides in an Equilibrium Relationship.

PubMed

Bobbitt, James M; Eddy, Nicholas A; Cady, Clyde X; Jin, Jing; Gascon, Jose A; Gelpí-Dominguez, Svetlana; Zakrzewski, Jerzy; Morton, Martha D

2017-09-15

Three new homologous TEMPO oxoammonium salts and three homologous nitroxide radicals have been prepared and characterized. The oxidation properties of the salts have been explored. The direct 13 C NMR and EPR spectra of the nitroxide free radicals and the oxoammonium salts, along with TEMPO and its oxoammonium salt, have been successfully measured with little peak broadening of the NMR signals. In the spectra of all ten compounds (nitroxides and corresponding oxoammonium salts), the carbons in the 2,2,6,6-tetramethylpiperidine core do not appear, implying paramagnetic properties. This unpredicted overall paramagnetism in the oxoammonium salt solutions is explained by a redox equilibrium as shown between oxoammonium salts and trace amounts of corresponding nitroxide. This equilibrium is confirmed by electron interchange reactions between nitroxides with an N-acetyl substituent and oxoammonium salts with longer acyl side chains.

Methods for measuring exchangeable protons in glycosaminoglycans.

PubMed

Beecher, Consuelo N; Larive, Cynthia K

2015-01-01

Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds, providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.

An NMR Study of Isotope Effect on Keto-Enol Tautomerization: A Physical Organic Chemistry Experiment

ERIC Educational Resources Information Center

Atkinson, D.; Chechik, V.

2004-01-01

Isotope substitution often affects the rate of an organic reaction and can be used to reveal the underlying mechanism. A series of experiments that use (super 1)H NMR to determine primary and secondary isotope effects, activation parameters, and the regioselectivity of butanone enolization are described.

NMR Determination of Hydrogen Bond Thermodynamics in a Simple Diamide: A Physical Chemistry Experiment

ERIC Educational Resources Information Center

Morton, Janine G.; Joe, Candice L.; Stolla, Massiel C.; Koshland, Sophia R.; Londergan, Casey H.; Schofield, Mark H.

2015-01-01

Variable temperature NMR spectroscopy is used to determine the ?H° and ?S° of hydrogen bond formation in a simple diamide. In this two- or three-day experiment, students synthesize N,N'-dimethylmalonamide, dimethylsuccinamide, dimethylglutaramide, or dimethyladipamide from methylamine and the corresponding diester (typically in 50% recrystallized…

The Complexation of the Na(super +) by 18-Crown-6 Studied via Nuclear Magnetic Resonance

ERIC Educational Resources Information Center

Peters, Steven J.; Stevenson, Cheryl D.

2004-01-01

A student friendly experiment that teaches several important concepts of modern nuclear magnetic resonance (NMR), like multinuclear capabilities, the NMR time scale, and time-averaged signals, is described along with some important concepts of thermo chemical equilibria. The mentioned experiment involves safe and inexpensive compounds, such as…

Using Nuclear Magnetic Resonance Spectroscopy for Measuring Ternary Phase Diagrams

ERIC Educational Resources Information Center

Woodworth, Jennifer K.; Terrance, Jacob C.; Hoffmann, Markus M.

2006-01-01

A laboratory experiment is presented for the upper-level undergraduate physical chemistry curriculum in which the ternary phase diagram of water, 1-propanol and n-heptane is measured using proton nuclear magnetic resonance (NMR) spectroscopy. The experiment builds upon basic concepts of NMR spectral analysis, typically taught in the undergraduate…

Theoretical Modeling of (99)Tc NMR Chemical Shifts.

PubMed

Hall, Gabriel B; Andersen, Amity; Washton, Nancy M; Chatterjee, Sayandev; Levitskaia, Tatiana G

2016-09-06

Technetium-99 (Tc) displays a rich chemistry due to its wide range of accessible oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and (99)Tc nuclear magnetic resonance (NMR) spectroscopy is widely used to probe chemical environments of Tc in odd oxidation states. However, interpretation of (99)Tc NMR data is hindered by the lack of reference compounds. Density functional theory (DFT) calculations can help to fill this gap, but to date few computational studies have focused on (99)Tc NMR of compounds and complexes. This work evaluates the effectiveness of both pure generalized gradient approximation and their corresponding hybrid functionals, both with and without the inclusion of scalar relativistic effects, to model the (99)Tc NMR spectra of Tc(I) carbonyl compounds. With the exception of BLYP, which performed exceptionally well overall, hybrid functionals with inclusion of scalar relativistic effects are found to be necessary to accurately calculate (99)Tc NMR spectra. The computational method developed was used to tentatively assign an experimentally observed (99)Tc NMR peak at -1204 ppm to fac-Tc(CO)3(OH)3(2-). This study examines the effectiveness of DFT computations for interpretation of the (99)Tc NMR spectra of Tc(I) coordination compounds in high salt alkaline solutions.

NMR-based investigations into target DNA search processes of proteins.

PubMed

Iwahara, Junji; Zandarashvili, Levani; Kemme, Catherine A; Esadze, Alexandre

2018-05-10

To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR spectroscopy provides unique atomic-level insights into the dynamic DNA-scanning processes, which are difficult to gain by any other experimental means. In this review, we provide an introductory overview on the NMR methods for the structural, dynamic, and kinetic investigations of target DNA search by proteins. We also discuss advantages and disadvantages of these NMR methods over other methods such as single-molecule techniques and biochemical approaches. Copyright © 2018 Elsevier Inc. All rights reserved.

Proton NMR study of α-MnH 0.06

NASA Astrophysics Data System (ADS)

Soloninin, A. V.; Skripov, A. V.; Buzlukov, A. L.; Antonov, V. E.; Antonova, T. E.

2004-07-01

Proton nuclear magnetic resonance (NMR) spectra and spin-lattice relaxation rates for the solid solution α-MnH 0.06 have been measured over the temperature range 11-297 K and the resonance frequency range 20-90 MHz. A considerable shift and broadening of the proton NMR line and a sharp peak of the spin-lattice relaxation rate are observed near 130 K. These effects are attributed to the onset of antiferromagnetic ordering below the Néel temperature TN≈130 K. The proton NMR line does not disappear in the antiferromagnetic phase; this suggests a small magnitude of the local magnetic fields at H-sites in α-MnH 0.06. The spin-lattice relaxation rate in the paramagnetic phase is dominated by the effects of spin fluctuations.

The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database.

PubMed

Takashima, S; Yamaoka, K

1999-08-30

Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein-DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein databases. The dipole moments of globular proteins have hitherto been calculated with X-ray databases and NMR data have never been used before. The advantages of NMR databases are: (a) NMR data are obtained, unlike X-ray databases, using protein solutions. Accordingly, this method eliminates the bothersome question as to the possible alteration of the protein structure due to the transition from the crystalline state to the solution state. This question is particularly important for proteins such as HU protein which has some degree of internal flexibility; (b) the three-dimensional coordinates of hydrogen atoms in protein molecules can be determined with a sufficient resolution and this enables the N-H as well as C = O bond moments to be calculated. Since the NMR database of HU protein from Bacillus stearothermophilus consists of 25 models, the surface charge as well as the core dipole moments were computed for each of these structures. The results of these calculations show that the net permanent dipole moments of HU protein homodimer is approximately 500-530 D (1 D = 3.33 x 10(-30) Cm) at pH 7.5 and 600-630 D at the isoelectric point (pH 10.5). These permanent dipole moments are unusually large for a small protein of the size of 19.5 kDa. Nevertheless, the result of numerical calculations is compatible with the electro-optical observation, confirming a very large dipole moment in this protein.

In Situ Natural Abundance 17 O and 25 Mg NMR Investigation of Aqueous Mg(OH) 2 Dissolution in the Presence of Supercritical CO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Mary Y.; Deng, Xuchu; Thanthiriwatte, K. Sahan

We report the development of an in situ high pressure NMR capability that permits natural abundance 17O and 25Mg NMR characterization of dissolved species in aqueous solution and in the presence of supercritical CO 2 fluid (scCO 2). The dissolution of Mg(OH) 2 (brucite) in a multiphase water/scCO 2 fluid at 90 atm pressure and 50 C was studied in situ, with relevance to geological carbon sequestration. 17O NMR spectra allowed identification and distinction of various fluid species including dissolved CO 2 in the H 2O-rich phase, scCO 2, aqueous H 2O, and HCO 3 -. The widely separated spectralmore » peaks for various species can all be observed both dynamically and quantitatively at concentrations of as low as 20 mM. Measurement of the concentrations of these individual species also allows an in situ estimate of the hydrogen ion concentration, or pCH + values, of the reacting solutions. The concentration of Mg 2+ can be observed by natural abundance 25Mg NMR at a concentration as low as 10 mM. Quantum chemistry calculations of the NMR chemical shifts on cluster models aided in the interpretation of the experimental results. Evidence for the formation of polymeric Mg 2+ clusters at high concentrations in the H 2O-rich phase, a possible critical step needed for magnesium carbonate formation, was found. The approach and findings enable insight into metal carbonation reactions associated with geological carbon sequestration that cannot be probed by ex situ methods.« less

Curie-type paramagnetic NMR relaxation in the aqueous solution of Ni(II).

PubMed

Mareš, Jiří; Hanni, Matti; Lantto, Perttu; Lounila, Juhani; Vaara, Juha

2014-04-21

Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.

Lanthanide paramagnetic probes for NMR spectroscopic studies of fast molecular conformational dynamics and temperature control. Effective six-site proton exchange in 18-crown-6 by exchange spectroscopy.

PubMed

Babailov, Sergey P

2012-02-06

(1)H and (13)C NMR measurements are reported for the CDCl(3) and CD(2)Cl(2) solutions of [La(18-crown-6)(NO(3))(3)] (I), [Pr(18-crown-6) (NO(3))(3)] (II), [Ce(18-crown-6)(NO(3))(3)] (III), and [Nd(18-crown-6)(NO(3))(3)] (IV) complexes. Temperature dependencies of the (1)H NMR spectra of paramagnetic II-IV have been analyzed using the dynamic NMR (DNMR) methods for six-site exchange. Two types of conformational dynamic processes were identified (the first one is conditioned by interconversion of complex enantiomeric forms and pseudorotation of a macrocycle molecule upon the C(2) symmetry axis; the second one is conditioned by macrocycle molecule inversion). Application of exchange spectroscopy (2D-EXSY) of DNMR for investigation of this dynamic system (II-IV) simplifies the assignment of the NMR signals and represents the first experimental study of multisite exchange. In the present work, the methodology of paramagnetic 4f (Ce, Pr, and Nd) probe applications for the study of free-energy, enthalpy, and entropy changes in chemical exchange processes, as well as the advantages of this method in a comparison with DNMR studies of diamagnetic substances, is discussed. In particular, as a result of paramagnetic chemical shifts in 4f complexes, the range of measurable rate constants expands considerably compared to the analogous range in diamagnetic compounds. Coordination compounds investigated in the paper represent new types of thermometric NMR sensors and lanthanide paramagnetic probes for in situ temperature control in solution.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

PubMed

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time. Copyright © 2018 Elsevier Inc. All rights reserved.

[Characterization and optimization of the NaOH-EDTA extracts for solution 31P-NMR analysis of organic phosphorus in river sediments].

PubMed

Zhang, Wen-Qiang; Shan, Bao-Qing; Zhang, Hong; Tang, Wen-Zhong

2014-01-01

Optimization and mechanism of NaOH-EDTA extraction solutions were studied in phosphorus (P) pollution river sediments, which were Fe, Al-rich sediment, by solution 31P nuclear magnetic resonance spectroscopy (31P-NMR). Different proportions of NaOH and EDTA showed different extraction efficiency on total P (TP) and organic P (Po) in the sediment. The concentration of Po in NaOH + EDTA extract was higher than that in NaOH extract. The mechanism was that the TP and Po were released under the conditions of EDTA chelating with Fe and Al. The concentration of TP and Po were the highest in 1.00 mol x L(-1) NaOH +75 mmol x L(-1) EDTA extract and 0.25 mol x L(-1) NaOH + 50 mmol x L(-1) EDTA extract, which were 3.88 mg x g(-1) and 0.24 mg x g(-1), respectively. The extractions of Fe, Mn, Ca, Mg, Al were increasing as the EDTA increased under the same NaOH concentration. Extraction efficiency of Fe, Mn, Ca showed negative correlation with the pH of the extracting solution (P < 0.01). Exponential relationship was found between the extraction of Al and the pH of the extraction solution (P < 0.01) because of the AlO2- and EDTA-Al complex. The quality of spectra of NaOH-EDTA extract was better than that of NaOH extract. Six P species were detected in different extractions, including phosphonates, orthophosphate, pyrophosphate, orthophosphate monoesters, phospholipids and deoxyribonucleic acids. Therefore, 0. 25 mol x L(-1) NaOH + 50 mmol x L(-1) EDTA was the optimization extraction solution for Po analysis in Fe and Al-rich river sediment by 31P-NMR.

Synthesis of 18-hydroxy-19-norcorticosterone and 18-deoxy-19-noraldosterone. Structure determination of related 19-nor steroids by means of 2-D 1H nmr.

PubMed

Harnik, M; Kashman, Y; Carmely, S; Cojocaru, M; Dale, S L; Holbrook, M M; Melby, J C

1986-01-01

The compounds named in the title have been synthesized from the di-(ethylene ketal) of 21-hydroxy-3,20-dioxo-19-norpregn-5-ene-18, 11 beta-lactone and its 5(10)-ene isomer. Reduction of this mixture 1 with sodium aluminum bis-(methoxyethoxy)hydride furnished the 11 beta, 18, 21-triol 2a. Conversion to the 18,21-diacetate 2b, followed by deketalization to the free dione 3 and hydrolysis, afforded 18-hydroxy-19-norcorticosterone 4a which, in the solid state and probably in solution, has the 18,20-hemiacetal structure. Periodate oxidation of 4a gave 11 beta-hydroxy-3-oxo-19-norandrost-4-ene-17 beta, 18-carbolactone 5a, and acid treatment of 4a or its precursor 2a yielded 18-deoxy-19-noraldosterone 6a. The structure of 5a was confirmed by mass spectrometry and 1H nmr, and compared with that of its C-19 methyl homolog 5b and 19-noraldosterone-gamma-etiolactone 8. In particular, 2-D nmr COSY 45 experiments, affording full 1H line assignments, have rigorously established the "natural" beta (axial) configuration of the C-10 hydrogen in the 19-nor lactones 5a and 8, and therefore also in the related 4a, 6a and 19-noraldosterone 7.

In-situ molecular-level elucidation of organofluorine binding sites in a whole peat soil.

PubMed

Longstaffe, James G; Courtier-Murias, Denis; Soong, Ronald; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Hutchins, Howard; Krishnamurthy, Sridevi; Struppe, Jochem; Alaee, Mehran; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, André J

2012-10-02

The chemical nature of xenobiotic binding sites in soils is of vital importance to environmental biogeochemistry. Interactions between xenobiotics and the naturally occurring organic constituents of soils are strongly correlated to environmental persistence, bioaccessibility, and ecotoxicity. Nevertheless, because of the complex structural and chemical heterogeneity of soils, studies of these interactions are most commonly performed indirectly, using correlative methods, fractionation, or chemical modification. Here we identify the organic components of an unmodified peat soil where some organofluorine xenobiotic compounds interact using direct molecular-level methods. Using (19)F→(1)H cross-polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, the (19)F nuclei of organofluorine compounds are used to induce observable transverse magnetization in the (1)H nuclei of organic components of the soil with which they interact after sorption. The observed (19)F→(1)H CP-MAS spectra and dynamics are compared to those produced using model soil organic compounds, lignin and albumin. It is found that lignin-like components can account for the interactions observed in this soil for heptafluoronaphthol (HFNap) while protein structures can account for the interactions observed for perfluorooctanoic acid (PFOA). This study employs novel comprehensive multi-phase (CMP) NMR technology that permits the application of solution-, gel-, and solid-state NMR experiments on intact soil samples in their swollen state.

In vitro mutagenicity, NMR metabolite characterization of azo and triphenylmethanes dyes by adherents bacteria and the role of the "cna" adhesion gene in activated sludge.

PubMed

Ayed, Lamia; Bakir, Karima; Ben Mansour, Hedi; Hammami, Saousen; Cheref, Abdelkrim; Bakhrouf, Amina

2017-02-01

Staphylococcus aureus, showing the greatest decolorization ability, was further investigated for Methyl Red (MR) Congo Red (CR), Crystal Violet (CV) and Malachite Green (MG) decolorization using response surface methodology (RSM). The chemometric methods use, based on statistical design of experiments (DOEs) such as RSM is becoming increasingly widespread in several sciences such as analytical chemistry, engineering and environmental chemistry. Stapphylococcus aureus ATCC 25923, Stapphylococcus aureus (S1) and Stapphylococcus aureus (S2), were isolated from textile wastewater plant located in KsarHellal, Tunisia and were tested for their decolorization capacity. PCR technique was utilized to identify the 3 bacterial strains and to detect the adhesin gene "cna". Biodegradation of MR, CR, CV and MG (750 ppm), were investigated under shaking condition in Mineral Salt Medium (MSM) solution at pH 7.5 and temperature 30 °C, using a 3.7 × 10 5  CFU/ml as inoculum size. Our results showed that Staphylococcus aureus had a high decolorization capacity. Nuclear magnetic resonance (NMR) spectroscopy analysis confirmed the biodegradation of dyes. The four dyes mutagenicity with the S9 metabolizing system decreased significantly after biodegradation and totally disappeared. Nuclear magnetic resonance (NMR) spectroscopy analysis confirmed the biodegradation of dyes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Determination of Solvent Effects on Keto-Enol Equilibria of 1,3-Dicarbonyl Compounds Using NMR: Revisiting a Classic Physical Chemistry Experiment

ERIC Educational Resources Information Center

Cook, A. Gilbert; Feltman, Paul M.

2007-01-01

The use of proton NMR to determine the equilibrium position of tautomeric 1,3-dicarbonyl compounds in various solvents has been a classic physical chemistry experiment. We are presenting an expansion of the excellent description of this experiment by Garland, Shoemaker, and Nibler. Often the assumption is made that the keto tautomer is always the…

A novel method for the investigation of liquid/liquid distribution coefficients and interface permeabilities applied to the water-octanol-drug system.

PubMed

Stein, Paul C; di Cagno, Massimiliano; Bauer-Brandl, Annette

2011-09-01

In this work a new, accurate and convenient technique for the measurement of distribution coefficients and membrane permeabilities based on nuclear magnetic resonance (NMR) is described. This method is a novel implementation of localized NMR spectroscopy and enables the simultaneous analysis of the drug content in the octanol and in the water phase without separation. For validation of the method, the distribution coefficients at pH = 7.4 of four active pharmaceutical ingredients (APIs), namely ibuprofen, ketoprofen, nadolol, and paracetamol (acetaminophen), were determined using a classical approach. These results were compared to the NMR experiments which are described in this work. For all substances, the respective distribution coefficients found with the two techniques coincided very well. Furthermore, the NMR experiments make it possible to follow the distribution of the drug between the phases as a function of position and time. Our results show that the technique, which is available on any modern NMR spectrometer, is well suited to the measurement of distribution coefficients. The experiments present also new insight into the dynamics of the water-octanol interface itself and permit measurement of the interface permeability.

Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR

PubMed Central

Chung, Wai Keen; Freed, Alexander S.; Holstein, Melissa A.; McCallum, Scott A.; Cramer, Steven M.

2010-01-01

NMR titration experiments with labeled human ubiquitin were employed in concert with chromatographic data obtained with a library of ubiquitin mutants to study the nature of protein adsorption in multimodal (MM) chromatography. The elution order of the mutants on the MM resin was significantly different from that obtained by ion-exchange chromatography. Further, the chromatographic results with the protein library indicated that mutations in a defined region induced greater changes in protein affinity to the solid support. Chemical shift mapping and determination of dissociation constants from NMR titration experiments with the MM ligand and isotopically enriched ubiquitin were used to determine and rank the relative binding affinities of interaction sites on the protein surface. The results with NMR confirmed that the protein possessed a distinct preferred binding region for the MM ligand in agreement with the chromatographic results. Finally, coarse-grained ligand docking simulations were employed to study the modes of interaction between the MM ligand and ubiquitin. The use of NMR titration experiments in concert with chromatographic data obtained with protein libraries represents a previously undescribed approach for elucidating the structural basis of protein binding affinity in MM chromatographic systems. PMID:20837551

Observation of NMR noise from solid samples.

PubMed

Schlagnitweit, Judith; Dumez, Jean-Nicolas; Nausner, Martin; Jerschow, Alexej; Elena-Herrmann, Bénédicte; Müller, Norbert

2010-11-01

We demonstrate that proton NMR noise signals, i.e. NMR spectra without excitation by radio frequency, can be obtained from solid samples. Experimental results are shown for static and magic-angle spinning conditions. In addition, a tuning procedure based on the probes' NMR noise characteristics and similar to the one described previously for liquids probes can also be used to optimize signal-to-noise ratios in ¹H-MAS experiments. Copyright © 2010 Elsevier Inc. All rights reserved.

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

PubMed Central

Ferro, Monica; Pastori, Nadia; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco

2017-01-01

Two different formulations of cyclodextrin nanosponges (CDNS), obtained by polycondensation of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn), were treated with aqueous solutions of ibuprofen sodium salt (IbuNa) affording hydrogels that, after lyophilisation, gave two solid CDNS-drug formulations. 1H fast MAS NMR and 13C CP-MAS NMR spectra showed that IbuNa was converted in situ into its acidic and dimeric form (IbuH) after freeze-drying. 13C CP-MAS NMR spectra also indicated that the structure of the nanosponge did not undergo changes upon drug loading compared to the unloaded system. However, the 13C NMR spectra collected under variable contact time cross-polarization (VCT-CP) conditions showed that the polymeric scaffold CDNS changed significantly its dynamic regime on passing from the empty CDNS to the drug-loaded CDNS, thus showing that the drug encapsulation can be seen as the formation of a real supramolecular aggregate rather than a conglomerate of two solid components. Finally, the structural features obtained from the different solid-state NMR approaches reported matched the information from powder X-ray diffraction profiles. PMID:28228859

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy.

PubMed

Ferro, Monica; Castiglione, Franca; Pastori, Nadia; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco; Mele, Andrea

2017-01-01

Two different formulations of cyclodextrin nanosponges (CDNS), obtained by polycondensation of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn), were treated with aqueous solutions of ibuprofen sodium salt (IbuNa) affording hydrogels that, after lyophilisation, gave two solid CDNS-drug formulations. 1 H fast MAS NMR and 13 C CP-MAS NMR spectra showed that IbuNa was converted in situ into its acidic and dimeric form (IbuH) after freeze-drying. 13 C CP-MAS NMR spectra also indicated that the structure of the nanosponge did not undergo changes upon drug loading compared to the unloaded system. However, the 13 C NMR spectra collected under variable contact time cross-polarization (VCT-CP) conditions showed that the polymeric scaffold CDNS changed significantly its dynamic regime on passing from the empty CDNS to the drug-loaded CDNS, thus showing that the drug encapsulation can be seen as the formation of a real supramolecular aggregate rather than a conglomerate of two solid components. Finally, the structural features obtained from the different solid-state NMR approaches reported matched the information from powder X-ray diffraction profiles.

Signal Enhancement in HPLC/Micro-Coil NMR Using Automated Column Trapping

PubMed Central

Djukovic, Danijel; Liu, Shuhui; Henry, Ian; Tobias, Brian; Raftery, Daniel

2008-01-01

A new HPLC-NMR system is described that performs analytical separation, pre-concentration, and NMR spectroscopy in rapid succession. The central component of our method is the online pre-concentration sequence that improves the match between post-column analyte peak volume and the micro-coil NMR detection volume. Separated samples are collected on to a C18 guard column with a mobile phase composed of 90% D2O/10% acetonitrile-D3, and back-flashed to the NMR micro-coil probe with 90% acetonitrile-D3/10% D2O. In order to assess the performance of our unit, we separated a standard mixture of 1 mM ibuprofen, naproxen, and phenylbutazone using a commercially available C18 analytical column. The S/N measurements from the NMR acquisitions indicated that we achieved signal enhancement factors up to 10.4 (±1.2)-fold. Furthermore, we observed that pre-concentration factors increased as the injected amount of analyte decreased. The highest concentration enrichment of 14.7 (±2.2)-fold was attained injecting 100 μL solution of 0.2 mM (~4 μg) ibuprofen. PMID:17037915

Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA.

PubMed

Kotaka, Masayo; Johnson, Christopher; Lamb, Heather K; Hawkins, Alastair R; Ren, Jingshan; Stammers, David K

2008-08-29

Amongst the most common protein motifs in eukaryotes are zinc fingers (ZFs), which, although largely known as DNA binding modules, also can have additional important regulatory roles in forming protein:protein interactions. AreA is a transcriptional activator central to nitrogen metabolism in Aspergillus nidulans. AreA contains a GATA-type ZF that has a competing dual recognition function, binding either DNA or the negative regulator NmrA. We report the crystal structures of three AreA ZF-NmrA complexes including two with bound NAD(+) or NADP(+). The molecular recognition of AreA ZF-NmrA involves binding of the ZF to NmrA via hydrophobic and hydrogen bonding interactions through helices alpha1, alpha6 and alpha11. Comparison with an earlier NMR solution structure of AreA ZF-DNA complex by overlap of the AreA ZFs shows that parts of helices alpha6 and alpha11 of NmrA are positioned close to the GATA motif of the DNA, mimicking the major groove of DNA. The extensive overlap of DNA with NmrA explains their mutually exclusive binding to the AreA ZF. The presence of bound NAD(+)/NADP(+) in the NmrA-AreaA ZF complex, however, causes minimal structural changes. Thus, any regulatory effects on AreA function mediated by the binding of oxidised nicotinamide dinucleotides to NmrA in the NmrA-AreA ZF complex appear not to be modulated via protein conformational rearrangements.

Characterisation of indomethacin and nifedipine using variable-temperature solid-state NMR.

PubMed

Apperley, David C; Forster, Angus H; Fournier, Romain; Harris, Robin K; Hodgkinson, Paul; Lancaster, Robert W; Rades, Thomas

2005-11-01

We have characterised the stable polymorphic forms of two drug molecules, indomethacin (1) and nifedipine (2) by 13C CPMAS NMR and the resonances have been assigned. The signal for the C-Cl carbon of indomethacin has been studied as a function of applied magnetic field, and the observed bandshapes have been simulated. Variable-temperature 1H relaxation measurements of static samples have revealed a T1rho minimum for indomethacin at 17.8 degrees C. The associated activation energy is 38 kJ mol(-1). The relevant motion is probably an internal rotation and it is suggested that this involves the C-OCH3 group. Since the two drug compounds are potential candidates for formulation in the amorphous state, we have examined quench-cooled melts in detail by variable-temperature 13C and 1H NMR. There is a change in slope for T1H and T1rhoH at the glass transition temperature (Tg) for indomethacin, but this occurs a few degrees below Tg for nifedipine, which is perhaps relevant to the lower real-time stability of the amorphous form for the latter compound. Comparison of relaxation time data for the crystalline and amorphous forms of each compound reveals a greater difference for nifedipine than for indomethacin, which again probably relates to real-time stabilities. Recrystallisation of the two drugs has been followed by proton bandshape measurements at higher temperatures. It is shown that, under the conditions of the experiments, recrystallisation of nifedipine can be detected already at 70 degrees C, whereas this does not occur until 110 degrees C for indomethacin. The effect of crushing the amorphous samples has been studied by 13C NMR; nifedipine recrystallises but indomethacin does not. The results were supported by DSC, powder XRD, FTIR and solution-state NMR measurements. Copyright (c) 2005 John Wiley & Sons, Ltd.

Mechanistic insight into formation and changes of nanoparticles in MgF2 sols evidenced by liquid and solid state NMR.

PubMed

Karg, M; Scholz, G; König, R; Kemnitz, E

2012-02-28

The fluorolytic sol-gel reaction of magnesium methoxide with HF in methanol was studied by (19)F, (1)H and (13)C liquid and solid state NMR. In (19)F NMR five different species were identified, three of which belong to magnesium fluoride nanoparticles, i.e. NMR gave access to local structures of solid particles in suspensions. The long-term evolution of (19)F signals was followed and along with (19)F MAS NMR experiments of sols rotating at 13 kHz mechanistic insights into the ageing processes were obtained.

The periplasmic domain of Escherichia coli outer membrane protein A can undergo a localized temperature dependent structural transition.

PubMed

Ishida, Hiroaki; Garcia-Herrero, Alicia; Vogel, Hans J

2014-12-01

Gram-negative bacteria such as Escherichia coli are surrounded by two membranes with a thin peptidoglycan (PG)-layer located in between them in the periplasmic space. The outer membrane protein A (OmpA) is a 325-residue protein and it is the major protein component of the outer membrane of E. coli. Previous structure determinations have focused on the N-terminal fragment (residues 1-171) of OmpA, which forms an eight stranded transmembrane β-barrel in the outer membrane. Consequently it was suggested that OmpA is composed of two independently folded domains in which the N-terminal β-barrel traverses the outer membrane and the C-terminal domain (residues 180-325) adopts a folded structure in the periplasmic space. However, some reports have proposed that full-length OmpA can instead refold in a temperature dependent manner into a single domain forming a larger transmembrane pore. Here, we have determined the NMR solution structure of the C-terminal periplasmic domain of E. coli OmpA (OmpA(180-325)). Our structure reveals that the C-terminal domain folds independently into a stable globular structure that is homologous to the previously reported PG-associated domain of Neisseria meningitides RmpM. Our results lend credence to the two domain structure model and a PG-binding function for OmpA, and we could indeed localize the PG-binding site on the protein through NMR chemical shift perturbation experiments. On the other hand, we found no evidence for binding of OmpA(180-325) with the TonB protein. In addition, we have also expressed and purified full-length OmpA (OmpA(1-325)) to study the structure of the full-length protein in micelles and nanodiscs by NMR spectroscopy. In both membrane mimetic environments, the recombinant OmpA maintains its two domain structure that is connected through a flexible linker. A series of temperature-dependent HSQC experiments and relaxation dispersion NMR experiments detected structural destabilization in the bulge region of the periplasmic domain of OmpA above physiological temperatures, which may induce dimerization and play a role in triggering the previously reported larger pore formation. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis and characterization of silver nanoparticles from (bis)alkylamine silver carboxylate precursors.

PubMed

Uznanski, Pawel; Zakrzewska, Joanna; Favier, Frederic; Kazmierski, Slawomir; Bryszewska, Ewa

2017-01-01

A comparative study of amine and silver carboxylate adducts [R 1 COOAg-2(R 2 NH 2 )] (R 1  = 1, 7, 11; R 2  = 8, 12) as a key intermediate in NPs synthesis is carried out via differential scanning calorimetry, solid-state FT-infrared spectroscopy, 13 C CP MAS NMR, powder X-ray diffraction and X-ray photoelectron spectroscopy, and various solution NMR spectroscopies ( 1 H and 13 C NMR, pulsed field gradient spin-echo NMR, and ROESY). It is proposed that carboxyl moieties in the presence of amine ligands are bound to silver ions via chelating bidentate type of coordination as opposed to bridging bidentate coordination of pure silver carboxylates resulting from the formation of dimeric units. All complexes are packed as lamellar bilayer structures. Silver carboxylate/amine complexes show one first-order melting transition. The evidence presented in this study shows that phase behavior of monovalent metal carboxylates are controlled, mainly, by head group bonding. In solution, insoluble silver salt is stabilized by amine molecules which exist in dynamic equilibrium. Using (bis)amine-silver carboxylate complex as precursor, silver nanoparticles were fabricated. During high-temperature thermolysis, the (bis)amine-carboxylate adduct decomposes to produce silver nanoparticles of small size. NPs are stabilized by strongly interacting carboxylate and trace amounts of amine derived from the silver precursor interacting with carboxylic acid. A corresponding aliphatic amide obtained from silver precursor at high-temperature reaction conditions is not taking part in the stabilization. Combining NMR techniques with FTIR, it was possible to follow an original stabilization mechanism. Graphical abstractThe synthesis of a series (bis)alkylamine silver(I) carboxylate complexes in nonpolar solvents were carried out and fully characterized both in the solid and solution. Carboxyl moieties in the presence of amine ligands are bound to silver ions via chelating bidentate type of coordination. The complexes form layered structures which thermally decompose forming nanoparticles stabilized only by aliphatic carboxylates.

Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma

PubMed Central

2013-01-01

Nuclear magnetic resonance spectroscopy (NMR) provides robust readouts of many metabolic parameters in one experiment. However, identification of clinically relevant markers in 1H NMR spectra is a major challenge. Association of NMR-derived quantities with genetic variants can uncover biologically relevant metabolic traits. Using NMR data of plasma samples from 1,757 individuals from the KORA study together with 655,658 genetic variants, we show that ratios between NMR intensities at two chemical shift positions can provide informative and robust biomarkers. We report seven loci of genetic association with NMR-derived traits (APOA1, CETP, CPS1, GCKR, FADS1, LIPC, PYROXD2) and characterize these traits biochemically using mass spectrometry. These ratios may now be used in clinical studies. PMID:23414815

1H NMR quantification in very dilute toxin solutions: application to anatoxin-a analysis.

PubMed

Dagnino, Denise; Schripsema, Jan

2005-08-01

A complete procedure is described for the extraction, detection and quantification of anatoxin-a in biological samples. Anatoxin-a is extracted from biomass by a routine acid base extraction. The extract is analysed by GC-MS, without the need of derivatization, with a detection limit of 0.5 ng. A method was developed for the accurate quantification of anatoxin-a in the standard solution to be used for the calibration of the GC analysis. 1H NMR allowed the accurate quantification of microgram quantities of anatoxin-a. The accurate quantification of compounds in standard solutions is rarely discussed, but for compounds like anatoxin-a (toxins with prices in the range of a million dollar a gram), of which generally only milligram quantities or less are available, this factor in the quantitative analysis is certainly not trivial. The method that was developed can easily be adapted for the accurate quantification of other toxins in very dilute solutions.

NMR Water Self–Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions

PubMed Central

Bai, Ruiliang; Basser, Peter J.; Briber, Robert M.; Horkay, Ferenc

2013-01-01

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced. PMID:24409001

NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions.

PubMed

Bai, Ruiliang; Basser, Peter J; Briber, Robert M; Horkay, Ferenc

2014-03-15

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca 2+ and Na + . Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na + on the mobility of water molecules was practically undetectable. By contrast, addition of Ca 2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.

Calcium and ascorbic acid affect cellular structure and water mobility in apple tissue during osmotic dehydration in sucrose solutions.

PubMed

Mauro, Maria A; Dellarosa, Nicolò; Tylewicz, Urszula; Tappi, Silvia; Laghi, Luca; Rocculi, Pietro; Rosa, Marco Dalla

2016-03-15

The effects of the addition of calcium lactate and ascorbic acid to sucrose osmotic solutions on cell viability and microstructure of apple tissue were studied. In addition, water distribution and mobility modification of the different cellular compartments were observed. Fluorescence microscopy, light microscopy and time domain nuclear magnetic resonance (TD-NMR) were respectively used to evaluate cell viability and microstructural changes during osmotic dehydration. Tissues treated in a sucrose-calcium lactate-ascorbic acid solution did not show viability. Calcium lactate had some effects on cell walls and membranes. Sucrose solution visibly preserved the protoplast viability and slightly influenced the water distribution within the apple tissue, as highlighted by TD-NMR, which showed higher proton intensity in the vacuoles and lower intensity in cytoplasm-free spaces compared to other treatments. The presence of ascorbic acid enhanced calcium impregnation, which was associated with permeability changes of the cellular wall and membranes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate.

PubMed

Bagno, Alessandro; Rastrelli, Federico; Saielli, Giacomo

2008-06-01

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems. Copyright (c) 2008 John Wiley & Sons, Ltd

Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy.

PubMed

Zhao, Bo; Hansen, Alexandar L; Zhang, Qi

2014-01-08

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1ρ) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1ρ) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).

Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-Lock Field R1ρ NMR Spectroscopy

PubMed Central

Zhao, Bo; Hansen, Alexandar L.; Zhang, Qi

2016-01-01

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R1ρ relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R1ρ RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR “invisible” state. The utility of CEST and low spin-lock field R1ρ RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s−1. PMID:24299272

Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2013-05-01

We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

Changes in NMR relaxation times of adjacent muscle after implantation of malignant and normal tissue.

PubMed Central

Ling, C. R.; Foster, M. A.; Mallard, J. R.

1979-01-01

In separate experiments, normal foreign tissue and malignant tumour were implanted s.c. into the rat thigh. NMR T1 values of the adjacent normal muscle, resulting from local inflammatory reactions or from malignant invasion, were measured. Elevations in T1 of the underlying muscle occurred within 24 h in both experiments, and it is believed these were caused by rapid inflammatory and immunological reactions to the implants. However the T1 values of muscle samples adjacent to the non-malignant implants decreased during the 11 days after implantation, dropping to values within the normal range. In the second experiment there was progressive malignant invasion into the normal adjacent tissue and the elevated T1 values were maintained throughout the 12-day period. The effects of the implantation on tissue water content are discussed in relation to NMR T1 relaxation times, and the relevance to whole-body NMR imaging of elevated T1 values due to nonmalignant pathological states is considered. PMID:526431

Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning.

PubMed

Jaudzems, Kristaps; Bertarello, Andrea; Chaudhari, Sachin R; Pica, Andrea; Cala-De Paepe, Diane; Barbet-Massin, Emeline; Pell, Andrew J; Akopjana, Inara; Kotelovica, Svetlana; Gajan, David; Ouari, Olivier; Tars, Kaspars; Pintacuda, Guido; Lesage, Anne

2018-06-18

Dynamic nuclear polarization (DNP) is a powerful way to overcome the sensitivity limitation of magic-angle-spinning (MAS) NMR experiments. However, the resolution of the DNP NMR spectra of proteins is compromised by severe line broadening associated with the necessity to perform experiments at cryogenic temperatures and in the presence of paramagnetic radicals. High-quality DNP-enhanced NMR spectra of the Acinetobacter phage 205 (AP205) nucleocapsid can be obtained by combining high magnetic field (800 MHz) and fast MAS (40 kHz). These conditions yield enhanced resolution and long coherence lifetimes allowing the acquisition of resolved 2D correlation spectra and of previously unfeasible scalar-based experiments. This enables the assignment of aromatic resonances of the AP205 coat protein and its packaged RNA, as well as the detection of long-range contacts, which are not observed at room temperature, opening new possibilities for structure determination. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

qHNMR Analysis of Purity of Common Organic Solvents--An Undergraduate Quantitative Analysis Laboratory Experiment

ERIC Educational Resources Information Center

Bell, Peter T.; Whaley, W. Lance; Tochterman, Alyssa D.; Mueller, Karl S.; Schultz, Linda D.

2017-01-01

NMR spectroscopy is currently a premier technique for structural elucidation of organic molecules. Quantitative NMR (qNMR) methodology has developed more slowly but is now widely accepted, especially in the areas of natural product and medicinal chemistry. However, many undergraduate students are not routinely exposed to this important concept.…

2D-NMR (HSQC) difference spectra between specifically 13C-enriched and unenriched protolignin of Ginkgo biloba obtained in the solution state of whole cell wall material

Treesearch

Noritsugu Terashima; Takuya Akiyama; Sally Ralph; Dmitry Evtuguin; Carlos Neto Pascoal; Jim Parkas; Magnus Paulsson; Ulla Westermark; John Ralph

2009-01-01

In the structural analysis of lignins by 13C-NMR, signal overlap limits definitive assignment and accurate intensity measurement. Selective labeling by 13C-enrichment of a specific carbon in lignin enhances its signal intensity in the spectrum. Further enhancement of the specifically labeled carbons can be realized via...

Synergic Investigation Of The Self-Assembly Structure And Mechanism Of Retroviral Capsid Proteins By Solid State NMR, Transmission Electron Microscopy And Multiscale simulation

DTIC Science & Technology

2017-03-29

310 helix. Green: this work. Cyans: solution NMR RSV CA structure in PDB entry 1D1D.[18] Magentas: X-ray crystallography structure of flat hexameric...to combine cryo-electron microscopy and X-ray crystallography , Methods, 49 (2009) 174-180. [8] K.Y. Chan, J. Gumbart, R. McGreevy, J.M. Watermeyer

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2′-deoxycytidine† †Electronic supplementary information (ESI) available: Including relevant preliminary results as well as illustrations and geometrical parameters of selected structures. See DOI: 10.1039/c4sc03761h Click here for additional data file.

PubMed Central

Campos, Jesús; Šponer, Judit E.; Šponer, Jiří

2015-01-01

Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebiotically plausible conditions. In this contribution, we present UV-irradiation experiments of β-2′-deoxycytidine in aqueous solution involving H–D exchange followed by NMR spectroscopic analysis of the photoproducts. We further elucidate the outcome of these experiments by means of high-level quantum chemical calculations. In particular, we show that prolonged UV-irradiation of cytidine may lead to H–C1′ hydrogen atom abstraction by the carbonyl oxygen atom of cytosine. This process may enable photoanomerisation and nucleobase loss, two previously unexplained photoreactions observed in pyrimidine nucleotides. PMID:27182431

The use of 1H-NMR spectroscopy and refractometry for investigation of the distribution of nonelectrolytes of N-alcohol series between human red blood cells and extracellular medium.

PubMed

Kucherenko, Y U; Moiseev, V A

2000-01-01

Comparative analysis of 1H NMR spectroscopy and refractometry with respect to their application for investigating the distribution of nonelectrolytes of n-alcohol series (ethanol, 1,2-propanediol, glycerol) and polyethylene glycols (PEGs) with molecular masses of 400, 600, 1500 between human erythrocytes and extracellular medium was performed. The distribution coefficients (Q) for solutions of ethanol, 1,2-propanediol, glycerol, PEG-400, PEG-600 and PEG-1500 were obtained. The Q values decreased with the increase in the nonelectrolyte molecular mass from 1.23+/-0.12 for ethanol to 0.40+/-0.08 for PEG-1500 (1H NMR spectroscopy) and from 2.6+/-0.12 for ethanol to 0.23+/-0.03 for PEG-1500 (refractometry). It was shown that 1H-NMR high-resolution spectroscopy ensures more precise determination of Q values for nonelectrolytes with low molecular masses; for PEGs with high molecular masses, the accuracy of Q value calculation by this method was about 20%. On the contrary, refractometry can be used for investigating substances with high molecular masses; the error of Q value determination for solution of low-refractive substances, such as ethanol, may be more than 50%.

Synthesis, characterization and optical properties of novel star azo-oligomers containing well-defined oligo(ethylene glycol) segments

NASA Astrophysics Data System (ADS)

González-Gómez, Roberto; Vonlanthen, Mireille; Ortíz-Palacios, Jesús; Ruiu, Andrea; Valderrama-García, Bianca X.; Rivera, Ernesto

2018-05-01

In this work, the synthesis and characterization of a series of star azo-oligomers bearing amino, amino-methoxy, amino-nitro and amino-cyano substituted azobenzene units and oligo(ethylene glycol) segments is reported. The full characterization of the obtained compounds was achieved by FTIR, 1H and 13C NMR spectroscopies, and their molecular weights were determined by MALDI-TOF mass spectrometry. The optical properties of these compounds were studied by absorption spectroscopy in solution. Finally, light polarized microscopy experiments as a function of the temperature were performed in order to study the liquid-crystalline behavior of these star azo-oligomers.

High-field dynamic nuclear polarization in aqueous solutions.

PubMed

Prandolini, M J; Denysenkov, V P; Gafurov, M; Endeward, B; Prisner, T F

2009-05-06

Unexpected high DNP enhancements of more than 10 have been achieved in liquid water samples at room temperature and magnetic fields of 9.2 T (corresponding to 400 MHz (1)H NMR frequency and 260 GHz EPR frequency). The liquid samples were polarized in situ using a double-resonance structure, which allows simultaneous excitation of NMR and EPR transitions and achieves significant DNP enhancements at very low incident microwave power of only 45 mW. These results demonstrate the first important step toward the application of DNP to high-resolution NMR, increasing the sensitivity on biomolecules with small sample volumes and at physiologically low concentrations.