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.

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.

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.

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 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.

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.

Solution state NMR of lignins

Treesearch

John Ralph; Jane M. Marita; Sally A. Ralph; Ronald D. Hatfield; Fachuang Lu; Richard M. Ede; Junpeng Peng; Larry L. Landucci

1999-01-01

Despite the rather random and heterogeneous nature of isolated lignins, many of their intimate structural details are revealed by diagnostic NMR experiments. 13C-NMR was recognized early-on as a high-resolution method for detailed structural characterization, aided by the almost exact agreement between chemical shifts of carbons in good low-molecular...

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.

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.

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.

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.

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

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.

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...

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

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

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

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.

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.

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.

Solid state NMR: The essential technology for helical membrane protein structural characterization

PubMed Central

Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

2014-01-01

NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed – neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. PMID:24412099

Solid state NMR: The essential technology for helical membrane protein structural characterization

NASA Astrophysics Data System (ADS)

Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

2014-02-01

NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

Stabilization of a supersaturated solution of mefenamic acid from a solid dispersion with EUDRAGIT(®) EPO.

PubMed

Kojima, Taro; Higashi, Kenjirou; Suzuki, Toyofumi; Tomono, Kazuo; Moribe, Kunikazu; Yamamoto, Keiji

2012-10-01

The stabilization mechanism of a supersaturated solution of mefenamic acid (MFA) from a solid dispersion with EUDRAGIT(®) EPO (EPO) was investigated. The solid dispersions were prepared by cryogenic grinding method. Powder X-ray diffractometry, in vitro dissolution test, in vivo oral absorption study, infrared spectroscopy, and solid- and solution-state NMR spectroscopies were used to characterize the solid dispersions. Dissolution tests in acetate buffer (pH 5.5) revealed that solid dispersion showed > 200-fold higher concentration of MFA. Supersaturated solution was stable over 1 month and exhibited improved oral bioavailability of MFA in rats, with a 7.8-fold higher area under the plasma concentration-versus-time curve. Solid-state (1)H spin-lattice relaxation time (T(1)) measurement showed that MFA was almost monomolecularly dispersed in the EPO polymer matrix. Intermolecular interaction between MFA and EPO was indicated by solid-state infrared and (13)C-T(1) measurements. Solution-state (1)H-NMR measurement demonstrated that MFA existed in monomolecular state in supersaturated solution. (1)H-T(1) and difference nuclear Overhauser effect measurements indicated that cross relaxation occurred between MFA and EPO due to the small distance between them. The formation and high stability of the supersaturated solution were attributable to the specifically formed intermolecular interactions between MFA and EPO.

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...

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

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

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

PubMed

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

2016-07-19

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.

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

Solid-state NMR and IR for the analysis of pharmaceutical solids: polymorphs of fosinopril sodium.

PubMed

Brittain, H G; Morris, K R; Bugay, D E; Thakur, A B; Serajuddin, A T

1993-01-01

The two polymorphic modifications of fosinopril sodium have been characterized as to their differences in melting behaviour, powder X-ray diffraction patterns, Fourier transform infrared spectra (FTIR), and solid-state 31P- and 13C-NMR spectra. The polymorphs were found to be enantiotropically related based upon melting point, heat of fusion, and solution mediated transformation data. Analysis of the solid-state FTIR and 13C-NMR data indicated that the environment of the acetal side chain of fosinopril sodium differed in two polymorphs, and that there might be cis-trans isomerization about the C6-N peptide bond. These conformational differences are postulated as the origin of the observed polymorphism.

Structural investigation of Titan tholins by solution-state 1H, 13C, and 15N NMR: one-dimensional and decoupling experiments.

PubMed

He, Chao; Lin, Guangxin; Upton, Kathleen T; Imanaka, Hiroshi; Smith, Mark A

2012-05-17

Titan, the largest moon of Saturn, is enveloped in a reddish brown organic haze. Titan haze is presumed to be formed from methane and nitrogen (CH(4) and N(2)) in Titan's upper atmosphere through energetic photochemistry and particle bombardment. Though Titan haze has been directly investigated using methods including the Cassini mission, its formation mechanism and the contributing chemical structures and prebiotic potential are still not well developed. We report here the structural investigation of the (13)C and (15)N labeled, simulated Titan haze aerosol (tholin) by solution-state NMR. The one-dimensional (1)H, (13)C, and (15)N NMR spectra and decoupling experiments indicate that the tholin sample contains amine, nitrile, imine, and N-heteroaromatic compounds of tremendous import in understanding complex organic chemistry in anaerobic, extraterrestrial environments.

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

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.

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.

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...

Equilibrium state at supersaturated drug concentration achieved by hydroxypropyl methylcellulose acetate succinate: molecular characterization using (1)H NMR technique.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Yamamoto, Keiji; Moribe, Kunikazu

2015-04-06

The maintenance mechanism of the supersaturated state of poorly water-soluble drugs, glibenclamide (GLB) and chlorthalidone (CLT), in hydroxypropyl methylcellulose acetate succinate (HPMC-AS) solution was investigated at a molecular level. HPMC-AS suppressed drug crystallization from supersaturated drug solution and maintained high supersaturated level of drugs with small amount of HPMC-AS for 24 h. However, the dissolution of crystalline GLB into HPMC-AS solution failed to produce supersaturated concentrations, although supersaturated concentrations were achieved by adding amorphous GLB to HPMC-AS solution. HPMC-AS did not improve drug dissolution and/or solubility but efficiently inhibited drug crystallization from supersaturated drug solutions. Such an inhibiting effect led to the long-term maintenance of the amorphous state of GLB in HPMC-AS solution. NMR measurements showed that HPMC-AS suppressed the molecular mobility of CLT depending on their supersaturation level. Highly supersaturated CLT in HPMC-AS solution formed a gel-like structure with HPMC-AS in which the molecular mobility of the CLT was strongly suppressed. The gel-like structure of HPMC-AS could inhibit the reorganization from drug prenuclear aggregates to the crystal nuclei and delay the formation of drug crystals. The prolongation subsequently led to the redissolution of the aggregated drugs in aqueous solution and formed the equilibrium state at the supersaturated drug concentration in HPMC-AS solution. The equilibrium state formation of supersaturated drugs by HPMC-AS should be an essential mechanism underlying the marked drug concentration improvement.

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

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…

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

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.

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...

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

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

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.

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

Kim, Y.W.; Labouriau, A.; Taylor, C.M.

Dynamics and structure of tri-n-butyltin fluoride in n-hexane solutions were probed using (tin-119) nuclear magnetic resonance spin relaxation methodologies. Significant relaxation-induced polarization transfer effects were observed and exploited. The experimental observations indicate that the tri-n-butyl fluoride exists in a polymeric form in solution. For a 0.10% (w/w) solution at 25 [degree]C, NMR reveals significant orientational/exchange relaxation on both the microsecond and nanosecond time scales. Solution-state and solid-state parameters are compared and contrasted. 26 refs., 3 figs., 1 tab.

Solid state nuclear magnetic resonance studies of prion peptides and proteins

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

Heller, Jonathan

1997-08-01

High-resolution structural studies using x-ray diffraction and solution nuclear magnetic resonance (NMR) are not feasible for proteins of low volubility and high tendency to aggregate. Solid state NMR (SSNMR) is in principle capable of providing structural information in such systems, however to do this efficiently and accurately, further SSNMR tools must be developed This dissertation describes the development of three new methods and their application to a biological system of interest, the priori protein (PrP).

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 ...

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.

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

A 13C NMR study of the structure of four cinnamic acids and their methyl esters

NASA Astrophysics Data System (ADS)

Silva, A. M. S.; Alkorta, I.; Elguero, J.; Silva, V. L. M.

2001-09-01

The 13C NMR spectra, both in DMSO solution and in the solid state of four cinnamic acids (p-methoxy, p-hydroxy, p-methyl, p-chloro) and their corresponding methyl esters have been recorded. The two main results in the solid state are: (i) the only significant difference between acids and esters chemical shifts concerns the Cdbnd O group which, on average, appears at 173 ppm in the acids and 168 ppm in the esters; (ii) the signals of the ortho and meta carbons both in the acids and the esters are splitted. The two 'anomalies' disappear in DMSO solution. These observations can be rationalized using simple GIAO/B3LYP/6-31G∗ calculations.

NMR at Low and Ultra-Low Temperatures

PubMed Central

Tycko, Robert

2017-01-01

Conspectus Solid state nuclear magnetic resonance (NMR) measurements at low temperatures have been common in physical sciences for many years, and are becoming increasingly important in studies of biomolecular systems. This article reviews a diverse set of projects from my laboratory, dating back to the early 1990s, that illustrate the motivations for low-temperature solid state NMR, the types of information that are available from the measurements, and likely directions for future research. These projects include NMR studies of both physical and biological systems, performed at low (cooled with nitrogen, down to 77 K) and very low (cooled with helium, below 77 K) temperatures, and performed with and without magic-angle spinning (MAS). In NMR studies of physical systems, the main motivation is to study phenomena that occur only at low temperatures. Two examples from my laboratory are studies of molecular rotation and an orientational ordering in solid C60 at low temperatures and studies of unusual electronic states, called skyrmions, in two-dimensionally confined electron systems within semiconductor quantum wells. NMR measurements on quantum wells were facilitated by optical pumping of nuclear spin polarizations, a signal enhancement phenomenon that exists at very low temperatures. In studies of biomolecular systems, motivations for low-temperature NMR include suppression of molecular tumbling (thereby permitting solid state NMR measurements on soluble proteins), suppression of conformational exchange (thereby permitting quantitation of conformational distributions), and trapping of transient intermediate states in a non-equilibrium kinetic process (by rapid freeze-quenching). Solid state NMR measurements on AIDS-related peptide/antibody complexes, chemically denatured states of the model protein HP35, and a transient intermediate in the rapid folding pathway of HP35 illustrate these motivations. NMR sensitivity generally increases with decreasing sample temperature. It is therefore advantageous to go as cold as possible, particularly in studies of biomolecular systems in frozen solutions. However, solid state NMR studies of biomolecular systems generally require rapid MAS. A novel MAS NMR probe design that uses nitrogen gas for sample spinning and cold helium only for sample cooling allows a wide variety of solid state NMR measurements to be performed on biomolecular systems at 20-25 K, where signals are enhanced by factors of 12-15 relative to measurements at room temperature. MAS NMR at very low temperatures also facilitates dynamic nuclear polarization (DNP), allowing sizeable additional signal enhancements and large absolute NMR signal amplitudes to be achieved with relatively low microwave powers. Current research in my laboratory seeks to develop and exploit DNP-enhanced MAS NMR at very low temperatures, for example in studies of transient intermediates in protein folding and aggregation processes and studies of peptide/protein complexes that can be prepared only at low concentrations. PMID:23470028

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

DOE PAGES

Zinke, Maximilian; Fricke, Pascal; Samson, Camille; ...

2017-07-07

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

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

Zinke, Maximilian; Fricke, Pascal; Samson, Camille

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

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.

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.

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.

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.

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.

Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

PubMed

Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

2018-02-01

A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. 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.

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.

Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR.

PubMed

Skotnicki, Marcin; Apperley, David C; Aguilar, Juan A; Milanowski, Bartłomiej; Pyda, Marek; Hodgkinson, Paul

2016-01-04

Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material.

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.

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.

The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.

PubMed

Takashima, S

2001-04-05

The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments.

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.

1H- 14N HSQC detection of choline-containing compounds in solutions

NASA Astrophysics Data System (ADS)

Mao, Jiezhen; Jiang, Ling; Jiang, Bin; Liu, Maili; Mao, Xi-an

2010-09-01

Choline nitrogen ( 14N) has a long relaxation time (seconds) which is due to the highly symmetric chemical environments. 14N in choline also has coupling constants with protons (0.6 Hz to methyl protons, 2.7 Hz to CH 2O protons and 0.2 Hz to NCH 2 protons). Based on these properties, we introduce a two-dimensional NMR method to detect choline and its derivatives in solutions. This method is the 1H- 14N hetero-nuclear single-quantum correlation (HSQC) experiment which has been developed in solid-state NMR in recent years. Experiments have demonstrated that the 1H- 14N HSQC technique is a sensitive method for detection of choline-containing compounds in solutions. From 1 mM choline solution in 16 min on a 500 MHz NMR spectrometer, a 1H- 14N HSQC spectrum has been recorded with a signal-to-noise ratio of 1700. Free choline, phosphocholine and glycerophosphocholine in milk can be well separated in 1H- 14N HSQC spectra. This technique would become a promising analytical approach to mixture analyses where choline-containing compounds are of interest, such as tissue extracts, body fluids and food solutions.

15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores.

PubMed

Chekmenev, Eduard Y; Hu, Jun; Gor'kov, Peter L; Brey, William W; Cross, Timothy A; Ruuge, Andres; Smirnov, Alex I

2005-04-01

This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

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

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.

In situ molecular NMR picture of bioavailable calcium stabilized as amorphous CaCO3 biomineral in crayfish gastroliths

PubMed Central

Akiva-Tal, Anat; Kababya, Shifi; Balazs, Yael S.; Glazer, Lilah; Berman, Amir; Sagi, Amir; Schmidt, Asher

2011-01-01

Bioavailable calcium is maintained by some crustaceans, in particular freshwater crayfish, by stabilizing amorphous calcium carbonate (ACC) within reservoir organs—gastroliths, readily providing the Ca2+ needed to build a new exoskeleton. Despite the key scientific and biomedical importance of the in situ molecular-level picture of biogenic ACC and its stabilization in a bioavailable form, its description has eluded efforts to date. Herein, using multinuclear NMR, we accomplish in situ molecular-level characterization of ACC within intact gastroliths of the crayfish Cherax quadricarinatus. In addition to the known CaCO3, chitin scaffold and inorganic phosphate (Pi), we identify within the gastrolith two primary metabolites, citrate and phosphoenolpyruvate (PEP) and quantify their abundance by applying solution NMR techniques to the gastrolith “soluble matrix.” The long-standing question on the physico-chemical state of ACC stabilizing, P-bearing moieties within the gastrolith is answered directly by the application of solid state rotational-echo double-resonance (REDOR) and transferred-echo double-resonance (TEDOR) NMR to the intact gastroliths: Pi and PEP are found molecularly dispersed throughout the ACC as a solid solution. Citrate carboxylates are found < 5 Å from a phosphate (intermolecular C⋯P distance), an interaction that must be mediated by Ca2+. The high abundance and extensive interactions of these molecules with the ACC matrix identify them as the central constituents stabilizing the bioavailable form of calcium. This study further emphasizes that it is imperative to characterize the intact biogenic CaCO3. Solid state NMR spectroscopy is shown to be a robust and accessible means of determining composition, internal structure, and molecular functionality in situ. PMID:21873244

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

PubMed

Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

2017-09-13

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group.

PubMed

Brouwer, Darren H

2013-01-01

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information. Copyright © 2013 Elsevier Inc. All rights reserved.

Non-Invasive Nanodiagnostics of Cancer (NINOC)

DTIC Science & Technology

2008-04-01

context. Since the delivery and detection principles are universal, the same nanocarriers can be used with different contrast reporter moieties such...conventional solution-state 1H NMR allowed us only to estimate the changes in the extent of cross-linking upon the synthesis (Figure 9 2). As expected...time of Gd-loaded nanogels was estimated from 1H NMR spectra acquired using a Varian INOVA 500MHz spectrometer and relaxivity (R1) was calculated. In

Easy-Going On-Spectrometer Optimisation of Phase Modulated Homonuclear Decoupling Sequences in Solid-State NMR

NASA Astrophysics Data System (ADS)

Grimminck, Dennis L. A. G.; Vasa, Suresh K.; Meerts, W. Leo; Kentgens, P. M.

2011-06-01

A global optimisation scheme for phase modulated proton homonuclear decoupling sequences in solid-state NMR is presented. Phase modulations, parameterised by DUMBO Fourier coefficients, were optimized using a Covariance Matrix Adaptation Evolution Strategies algorithm. Our method, denoted EASY-GOING homonuclear decoupling, starts with featureless spectra and optimises proton-proton decoupling, during either proton or carbon signal detection. On the one hand, our solutions closely resemble (e)DUMBO for moderate sample spinning frequencies and medium radio-frequency (rf) field strengths. On the other hand, the EASY-GOING approach resulted in a superior solution, achieving significantly better resolved proton spectra at very high 680 kHz rf field strength. N. Hansen, and A. Ostermeier. Evol. Comput. 9 (2001) 159-195 B. Elena, G. de Paepe, L. Emsley. Chem. Phys. Lett. 398 (2004) 532-538

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

Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR

NASA Astrophysics Data System (ADS)

Lange, Adam; Giller, Karin; Hornig, Sönke; Martin-Eauclaire, Marie-France; Pongs, Olaf; Becker, Stefan; Baldus, Marc

2006-04-01

The active site of potassium (K+) channels catalyses the transport of K+ ions across the plasma membrane-similar to the catalytic function of the active site of an enzyme-and is inhibited by toxins from scorpion venom. On the basis of the conserved structures of K+ pore regions and scorpion toxins, detailed structures for the K+ channel-scorpion toxin binding interface have been proposed. In these models and in previous solution-state nuclear magnetic resonance (NMR) studies using detergent-solubilized membrane proteins, scorpion toxins were docked to the extracellular entrance of the K+ channel pore assuming rigid, preformed binding sites. Using high-resolution solid-state NMR spectroscopy, here we show that high-affinity binding of the scorpion toxin kaliotoxin to a chimaeric K+ channel (KcsA-Kv1.3) is associated with significant structural rearrangements in both molecules. Our approach involves a combined analysis of chemical shifts and proton-proton distances and demonstrates that solid-state NMR is a sensitive method for analysing the structure of a membrane protein-inhibitor complex. We propose that structural flexibility of the K+ channel and the toxin represents an important determinant for the high specificity of toxin-K+ channel interactions.

Structure determination of helical filaments by solid-state NMR spectroscopy

PubMed Central

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

NMR implementation of adiabatic SAT algorithm using strongly modulated pulses.

PubMed

Mitra, Avik; Mahesh, T S; Kumar, Anil

2008-03-28

NMR implementation of adiabatic algorithms face severe problems in homonuclear spin systems since the qubit selective pulses are long and during this period, evolution under the Hamiltonian and decoherence cause errors. The decoherence destroys the answer as it causes the final state to evolve to mixed state and in homonuclear systems, evolution under the internal Hamiltonian causes phase errors preventing the initial state to converge to the solution state. The resolution of these issues is necessary before one can proceed to implement an adiabatic algorithm in a large system where homonuclear coupled spins will become a necessity. In the present work, we demonstrate that by using "strongly modulated pulses" (SMPs) for the creation of interpolating Hamiltonian, one can circumvent both the problems and successfully implement the adiabatic SAT algorithm in a homonuclear three qubit system. This work also demonstrates that the SMPs tremendously reduce the time taken for the implementation of the algorithm, can overcome problems associated with decoherence, and will be the modality in future implementation of quantum information processing by NMR.

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.

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.

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

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.

Field-cycling NMR with high-resolution detection under magic-angle spinning: determination of field-window for nuclear hyperpolarization in a photosynthetic reaction center.

PubMed

Gräsing, Daniel; Bielytskyi, Pavlo; Céspedes-Camacho, Isaac F; Alia, A; Marquardsen, Thorsten; Engelke, Frank; Matysik, Jörg

2017-09-21

Several parameters in NMR depend on the magnetic field strength. Field-cycling NMR is an elegant way to explore the field dependence of these properties. The technique is well developed for solution state and in relaxometry. Here, a shuttle system with magic-angle spinning (MAS) detection is presented to allow for field-dependent studies on solids. The function of this system is demonstrated by exploring the magnetic field dependence of the solid-state photochemically induced nuclear polarization (photo-CIDNP) effect. The effect allows for strong nuclear spin-hyperpolarization in light-induced spin-correlated radical pairs (SCRPs) under solid-state conditions. To this end, 13 C MAS NMR is applied to a photosynthetic reaction center (RC) of the purple bacterium Rhodobacter (R.) sphaeroides wildtype (WT). For induction of the effect in the stray field of the magnet and its subsequent observation at 9.4 T under MAS NMR conditions, the sample is shuttled by the use of an aerodynamically driven sample transfer technique. In the RC, we observe the effect down to 0.25 T allowing to determine the window for the occurrence of the effect to be between about 0.2 and 20 T.

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.

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

Determining the Orientation and Localization of Membrane-Bound Peptides

PubMed Central

Hohlweg, Walter; Kosol, Simone; Zangger, Klaus

2012-01-01

Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance. PMID:22044140

Dithallium(III)-Containing 30-Tungsto-4-phosphate, [Tl2Na2(H2O)2(P2W15O56)2]16-: Synthesis, Structural Characterization, and Biological Studies.

PubMed

Ayass, Wassim W; Fodor, Tamás; Farkas, Edit; Lin, Zhengguo; Qasim, Hafiz M; Bhattacharya, Saurav; Mougharbel, Ali S; Abdallah, Khaled; Ullrich, Matthias S; Zaib, Sumera; Iqbal, Jamshed; Harangi, Sándor; Szalontai, Gábor; Bányai, István; Zékány, László; Tóth, Imre; Kortz, Ulrich

2018-06-18

Here we report on the synthesis and structural characterization of the dithallium(III)-containing 30-tungsto -4-phosphate [Tl 2 Na 2 (H 2 O) 2 {P 2 W 15 O 56 } 2 ] 16- (1) by a multitude of solid-state and solution techniques. Polyanion 1 comprises two octahedrally coordinated Tl 3+ ions sandwiched between two trilacunary {P 2 W 15 } Wells-Dawson fragments and represents only the second structurally characterized, discrete thallium-containing polyoxometalate to date. The two outer positions of the central rhombus are occupied by sodium ions. The title polyanion is solution-stable as shown by 31 P and 203/205 Tl NMR. This was also supported by Tl NMR spectra simulations including several spin systems of isotopologues with half-spin nuclei ( 203 Tl, 205 Tl, 31 P, 183 W). 23 Na NMR showed a time-averaged signal of the Na + counter cations and the structurally bonded Na + ions. 203/205 Tl NMR spectra also showed a minor signal tentatively attributed to the trithallium-containing derivative [Tl 3 Na(H 2 O) 2 (P 2 W 15 O 56 ) 2 ] 14- , which could also be identified in the solid state by single-crystal X-ray diffraction. The bioactivity of polyanion 1 was also tested against bacteria and Leishmania.

Solid-State Characterization of Novel Propylene Glycol Ester Solvates Isolated from Lipid Formulations.

PubMed

Chakravarty, Paroma; Kothari, Sanjeev; Deese, Alan; Lubach, Joseph W

2015-07-06

The purpose of this study was to identify and characterize precipitates obtained from a liquid formulation of GNE068.HCl, a Genentech developmental compound, and lipophilic excipients, such as propylene glycol monocaprylate, and monolaurate. Precipitates were characterized using powder X-ray diffractometry (PXRD), differential scanning calorimetry, thermogravimetry, microscopy, nuclear magnetic resonance spectroscopy (NMR; solution and solid-state) and water sorption analysis. PXRD and NMR revealed the precipitates to be crystalline solvates of propylene glycol esters. The solvates (capryolate and lauroglycolate) were isomorphic and stable up to 70 °C, beyond which melting of the lattice occurred with subsequent dissolution of the active ingredient in the melt (microscopy and variable temperature PXRD). They were found to be mechanically stable (no change in PXRD pattern upon compression) and were nonhygroscopic up to ∼70% RH (25 °C). Our results highlight the outcome of inadvertent drug-excipient interactions in two separate lipid solution formulations with good solid-state properties and, thus, potential for further development.

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.

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.

Resolving Confined 7Li Dynamics of Uranyl Peroxide Capsule U 24

DOE PAGES

Xie, Jing; Neal, Harrison A.; Szymanowski, Jennifer; ...

2018-04-18

Here, we obtained a kerosene-soluble form of the lithium salt [UO 2(O 2)(OH) 2] 24 phase (Li-U 24), by adding cetyltrimethylammonium bromide surfactant to aqueous Li-U 24. Interestingly, its variable-temperature solution 7Li NMR spectroscopy resolves two narrowly spaced resonances down to –10 °C, which shift upfield with increasing temperature, and finally coalesce at temperatures > 85 °C. Comparison with solid-state NMR demonstrates that the Li dynamics in the Li-U 24-CTA phase involves only exchange between different local encapsulated environments. This behavior is distinct from the rapid Li exchange dynamics observed between encapsulated and external Li environments for Li-U 24 inmore » both the aqueous and the solid-state phases. Density functional theory calculations suggest that the two experimental 7Li NMR chemical shifts are due to Li cations coordinated within the square and hexagonal faces of the U 24 cage, and they can undergo exchange within the confined environment, as the solution is heated. Very different than U 24 in aqueous media, there is no evidence that the Li cations exit the cage, and therefore, this represents a truly confined space.« less

Resolving Confined 7Li Dynamics of Uranyl Peroxide Capsule U 24

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

Xie, Jing; Neal, Harrison A.; Szymanowski, Jennifer

Here, we obtained a kerosene-soluble form of the lithium salt [UO 2(O 2)(OH) 2] 24 phase (Li-U 24), by adding cetyltrimethylammonium bromide surfactant to aqueous Li-U 24. Interestingly, its variable-temperature solution 7Li NMR spectroscopy resolves two narrowly spaced resonances down to –10 °C, which shift upfield with increasing temperature, and finally coalesce at temperatures > 85 °C. Comparison with solid-state NMR demonstrates that the Li dynamics in the Li-U 24-CTA phase involves only exchange between different local encapsulated environments. This behavior is distinct from the rapid Li exchange dynamics observed between encapsulated and external Li environments for Li-U 24 inmore » both the aqueous and the solid-state phases. Density functional theory calculations suggest that the two experimental 7Li NMR chemical shifts are due to Li cations coordinated within the square and hexagonal faces of the U 24 cage, and they can undergo exchange within the confined environment, as the solution is heated. Very different than U 24 in aqueous media, there is no evidence that the Li cations exit the cage, and therefore, this represents a truly confined space.« less

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

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.

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

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.

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.

Solution Structures of Mycobacterium tuberculosis Thioredoxin C and Models of the Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

PubMed Central

Olson, Andrew L.; Neumann, Terrence S.; Cai, Sheng; Sem, Daniel S.

2012-01-01

Here we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared to the solution structure. Based on these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function. PMID:23229911

The effects of soy on freezable bread dough: a magnetic resonance study.

PubMed

Simmons, Amber L; Vodovotz, Yael

2012-11-15

Hygroscopic soy ingredients were hypothesised to slow the rate of water migration in unleavened bread dough during frozen storage. Thawed soy (18% dry weight) and wheat dough samples were assessed using non-destructive nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) for up to 8 wks frozen storage time. MRI suggested a spatially homogeneous, net increase in proton mobility with frozen storage and, with solution state proton NMR, distinct "free" and "bound" states were discerned. T(2) relaxation times of the majority proton population suggested increased mobility with frozen storage time, and statistical difference from the fresh sample was seen later for the soy samples than the wheat samples. As seen by (13)C-solid state NMR, the crystallinity of the starch was not affected by either soy addition or frozen storage. In conclusion, addition of soy to bakery products led to slightly enhanced preservation of "fresh" characteristics of the dough during frozen storage. Copyright © 2012 Elsevier Ltd. All rights reserved.

C-shaped diastereomers containing cofacial thiophene-substituted quinoxaline rings: synthesis, photophysical properties, and X-ray crystallography.

PubMed

DeBlase, Catherine R; Finke, Ryan T; Porras, Jonathan A; Tanski, Joseph M; Nadeau, Jocelyn M

2014-05-16

Synthesis and characterization of two diastereomeric C-shaped molecules containing cofacial thiophene-substituted quinoxaline rings are described. A previously known bis-α-diketone was condensed with an excess of 4-bromo-1,2-diaminobenzene in the presence of zinc acetate to give a mixture of two C-shaped diastereomers with cofacial bromine-substituted quinoxaline rings. After chromatographic separation, thiophene rings were installed by a microwave-assisted Suzuki coupling reaction, resulting in highly emissive diastereomeric compounds that were studied by UV-vis, fluorescence, and NMR spectroscopy, as well as X-ray crystallography. The unique symmetry of each diastereomer was confirmed by NMR spectroscopy. NMR data indicated that the syn isomer has restricted rotation about the bond connecting the thiophene and quinoxaline rings, which was also observed in the solid state. The spectroscopic properties of the C-shaped diastereomers were compared to a model compound containing only a single thiophene-substituted quinoxaline ring. Ground state intramolecular π-π interactions in solution were detected by NMR and UV-vis spectroscopy. Red-shifted emission bands, band broadening, and large Stokes shifts were observed, which collectively suggest excited state π-π interactions that produce excimer-like emissions, as well as a remarkable positive emission solvatochromism, indicating charge-transfer character in the excited state.

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

Magnetic field sensors using 13-spin cat states

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

Simmons, Stephanie; Karlen, Steven D.; Jones, Jonathan A.

2010-08-15

Measurement devices could benefit from entangled correlations to yield a measurement sensitivity approaching the physical Heisenberg limit. Building upon previous magnetometric work using pseudoentangled spin states in solution-state NMR, we present two conceptual advancements to better prepare and interpret the pseudoentanglement resource. We apply these to a 13-spin cat state to measure the local magnetic field with a 12.2 sensitivity increase over an equivalent number of isolated spins.

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.

Structural investigations of Pu{sup III} phosphate by X-ray diffraction, MAS-NMR and XANES spectroscopy

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

Popa, Karin; Raison, Philippe E., E-mail: philippe.raison@ec.europa.eu; Martel, Laura

2015-10-15

PuPO{sub 4} was prepared by a solid state reaction method and its crystal structure at room temperature was solved by powder X-ray diffraction combined with Rietveld refinement. High resolution XANES measurements confirm the +III valence state of plutonium, in agreement with valence bond derivation. The presence of the americium (as β{sup −} decay product of plutonium) in the +III oxidation state was determined based on XANES spectroscopy. High resolution solid state {sup 31}P NMR agrees with the XANES results and the presence of a solid-solution. - Graphical abstract: A full structural analysis of PuPO{sub 4} based on Rietveld analysis ofmore » room temperature X-ray diffraction data, XANES and MAS NMR measurements was performed. - Highlights: • The crystal structure of PuPO{sub 4} monazite is solved. • In PuPO{sub 4} plutonium is strictly trivalent. • The presence of a minute amount of Am{sup III} is highlighted. • We propose PuPO{sub 4} as a potential reference material for spectroscopic and microscopic studies.« less

On the Observation of Discrete Fluorine NMR Spectra for Uridine 5′-β,γ-Fluoromethylenetriphosphate Diastereomers at Basic pH

PubMed Central

2015-01-01

Jakeman et al. recently reported the inability to distinguish the diastereomers of uridine 5′-β,γ-fluoromethylenetriphosphate (β,γ-CHF-UTP, 1) by 19F NMR under conditions we previously prescribed for the resolution of the corresponding β,γ-CHF-dGTP spectra, stating further that 1 decomposed under these basic conditions. Here we show that the 19F NMR spectra of 1 (∼1:1 diastereomer mixture prepared by coupling of UMP-morpholidate with fluoromethylenebis(phosphonic acid)) in D2O at pH 10 are indeed readily distinguishable. 1 in this solution was stable for 24 h at rt. PMID:24819695

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.

Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5†

PubMed Central

Ralph, John

2014-01-01

NMR fingerprinting of the components of finely divided plant cell walls swelled in DMSO has been recently described. Cell wall gels, produced directly in the NMR tube with perdeutero-dimethylsulfoxide, allowed the acquisition of well resolved/dispersed 2D 13C–1H correlated solution-state NMR spectra of the entire array of wall polymers, without the need for component fractionation. That is, without actual solubilization, and without apparent structural modification beyond that inflicted by the ball milling and ultrasonication steps, satisfactorily interpretable spectra can be acquired that reveal compositional and structural details regarding the polysaccharide and lignin components in the wall. Here, the profiling method has been improved by using a mixture of perdeuterated DMSO and pyridine (4:1, v/v). Adding pyridine provided not only easier sample handling because of the better mobility compared to the DMSO-d6-only system but also considerably elevated intensities and improved resolution of the NMR spectra due to the enhanced swelling of the cell walls. This modification therefore provides a more rapid method for comparative structural evaluation of plant cell walls than is currently available. We examined loblolly pine (Pinus taeda, a gymnosperm), aspen (Populus tremuloides, an angiosperm), kenaf (Hibiscus cannabinus, an herbaceous plant), and corn (Zea mays L., a grass, i.e., from the Poaceae family). In principle, lignin composition (notably, the syringyl : guaiacyl : p-hydroxyphenyl ratio) can be quantified without the need for lignin isolation. Correlations for p-coumarate units in the corn sample are readily seen, and a variety of the ferulate correlations are also well resolved; ferulates are important components responsible for cell wall cross-linking in grasses. Polysaccharide anomeric correlations were tentatively assigned for each plant sample based on standard samples and various literature data. With the new potential for chemometric analysis using the 2D NMR fingerprint, this gel-state method may provide the basis for an attractive approach to providing a secondary screen for selecting biomass lines and for optimizing biomass processing and conversion efficiencies. PMID:20090974

Enhanced hydrogen release by catalyzed hydrolysis of sodium borohydride-ammonia borane mixtures: a solution-state 11B NMR study.

PubMed

Hannauer, J; Demirci, U B; Geantet, C; Herrmann, J M; Miele, P

2011-03-07

Hydrolysis of mixtures consisting of sodium borohydride NaBH(4) (SB) and ammonia borane NH(3)BH(3) (AB) was studied in the absence/presence of a Co catalyst. The kinetics of the H(2) evolutions was measured. The reactions were followed in situ by solution-state (11)B NMR and the hydrolysis by-products characterized by NMR, XRD and IR. It is demonstrated that the combination of the two compounds gives a synergetic effect. SB rapidly reduces the Co catalyst precursor and the NH(4)(+) ions from AB contribute in the dispersion of the in situ formed Co nanoparticles. As a result, the kinetics of H(2) evolution is greatly improved. For instance, a hydrogen generation rate of 29.6 L min(-1) g(-1)(Co) was found for a mixture consisting of 81 wt% NH(3)BH(3), 9 wt% NaBH(4) and 10 wt% CoCl(2). By (11)B NMR, it was showed that the reaction mechanisms are quite trivial. As soon as the Co catalyst forms in situ, SB, rather than AB, hydrolyzes until it is totally converted. Then, the overall hydrolysis continues with that of AB. Both reactions follow a bimolecular Langmuir-Hinshelwood mechanism; no reaction intermediates were observed during the process. In fact, SB and AB convert directly into B(OH)(4)(-), which comes in equilibrium with a polyborate compound identified as B(3)O(3)(OH)(4)(-). All of these results are discussed herein.

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.

Visualising substrate-fingermark interactions: Solid-state NMR spectroscopy of amino acid reagent development on cellulose substrates.

PubMed

Spindler, Xanthe; Shimmon, Ronald; Roux, Claude; Lennard, Chris

2015-05-01

Most spectroscopic studies of the reaction products formed by ninhydrin, 1,2-indanedione-zinc (Ind-Zn) and 1,8-diazafluoren-9-one (DFO) when reacted with amino acids or latent fingermarks on paper substrates are focused on visible absorption or luminescence spectroscopy. In addition, structural elucidation studies are typically limited to solution-based mass spectrometry or liquid nuclear magnetic resonance (NMR) spectroscopy, which does not provide an accurate representation of the fingermark development process on common paper substrates. The research presented in this article demonstrates that solid-state carbon-13 magic angle spinning NMR ((13)C-MAS-NMR) is a technique that can not only be utilised for structural studies of fingermark enhancement reagents, but is a promising technique for characterising the effect of paper chemistry on fingermark deposition and enhancement. The latter opens up a research area that has been under-explored to date but has the potential to improve our understanding of how fingermark secretions and enhancement reagents interact with paper substrates. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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.

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.

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

Unexpected Solubility Enhancement of Drug Bases in the Presence of a Dimethylaminoethyl Methacrylate Copolymer.

PubMed

Saal, Wiebke; Ross, Alfred; Wyttenbach, Nicole; Alsenz, Jochem; Kuentz, Martin

2018-01-02

The methacrylate copolymer Eudragit EPO (EPO) has previously shown to greatly enhance solubilization of acidic drugs via ionic interactions and by multiple hydrophobic contacts with polymeric side chains. The latter type of interaction could also play a role for solubilization of other compounds than acids. The aim of this study was therefore to investigate the solubility of six poorly soluble bases in presence and absence of EPO by quantitative ultrapressure liquid chromatography with concomitant X-ray powder diffraction analysis of the solid state. For a better mechanistic understanding, spectra and diffusion data were obtained by 1 H nuclear magnetic resonance (NMR) spectroscopy. Unexpected high solubility enhancement (up to 360-fold) was evidenced in the presence of EPO despite the fact that bases and polymer were both carrying positive charges. This exceptional and unexpected solubilization was not due to a change in the crystalline solid state. NMR spectra and measured diffusion coefficients indicated both strong drug-polymer interactions in the bulk solution, and diffusion data suggested conformational changes of the polymer in solution. Such conformational changes may have increased the accessibility and extent of hydrophobic contacts thereby leading to increased overall molecular interactions. These initially surprising solubilization results demonstrate that excipient selection should not be based solely on simple considerations of, for example, opposite charges of drug and excipient, but it requires a more refined molecular view. Different solution NMR techniques are especially promising tools to gain such mechanistic insights.

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

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.

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

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

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure.

PubMed

Fuglestad, Brian; Stetz, Matthew A; Belnavis, Zachary; Wand, A Joshua

2017-12-01

Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately -115mlmol -1 and an average pressure dependent change in compressibility of approximately 30mlmol -1 kbar -1 . In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state. Copyright © 2017 Elsevier B.V. All rights reserved.

The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media.

PubMed

Planchard, Noelya; Point, Élodie; Dahmane, Tassadite; Giusti, Fabrice; Renault, Marie; Le Bon, Christel; Durand, Grégory; Milon, Alain; Guittet, Éric; Zoonens, Manuela; Popot, Jean-Luc; Catoire, Laurent J

2014-10-01

Solution-state nuclear magnetic resonance studies of membrane proteins are facilitated by the increased stability that trapping with amphipols confers to most of them as compared to detergent solutions. They have yielded information on the state of folding of the proteins, their areas of contact with the polymer, their dynamics, water accessibility, and the structure of protein-bound ligands. They benefit from the diversification of amphipol chemical structures and the availability of deuterated amphipols. The advantages and constraints of working with amphipols are discussed and compared to those associated with other non-conventional environments, such as bicelles and nanodiscs.

Direct evidence of photochemical α-cleavage of benzoin in fluid solutions

NASA Astrophysics Data System (ADS)

Koyanagi, Motohiko; Futami, Hiroshi; Mukai, Masahiro; Yamauchi, Seigo

1989-02-01

By means of optical absorption, 1 NMR, and transient EPR techniques, the fate of diluted benzoin upon light irradiation to its S 1 (nπ*) state has been investigated in methylcyclohexane and benzene solutions at room temperature. The CIDEP spectrum of benzoin is observed for the first time, and the intermediate radicals involved are assigned. The overall results show that the main scheme of the photochemical reactions is the α-cleavage occurring in the excited triplet state of benzoin, as proved in the almost net emission pattern of the CIDEP spectra. A stoichiometric reaction leading to effective benzaldehyde formation is established for the benzoin solutions.

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

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

PubMed

Courtney, Joseph M; Ye, Qing; Nesbitt, Anna E; Tang, Ming; Tuttle, Marcus D; Watt, Eric D; Nuzzio, Kristin M; Sperling, Lindsay J; Comellas, Gemma; Peterson, Joseph R; Morrissey, James H; Rienstra, Chad M

2015-10-06

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum

PubMed Central

Courtney, Joseph M.; Ye, Qing; Nesbitt, Anna E.; Tang, Ming; Tuttle, Marcus D.; Watt, Eric D.; Nuzzio, Kristin M.; Sperling, Lindsay J.; Comellas, Gemma; Peterson, Joseph R.; Morrissey, James H.; Rienstra, Chad M.

2016-01-01

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D 13C-13C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins—GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor—and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. PMID:26365800

Investigations of the structure and "interfacial" surface chemistry of Bioglass (RTM) materials by solid-state multinuclear NMR spectroscopy

NASA Astrophysics Data System (ADS)

Sarkar, Gautam

Bioactive materials such as BioglassRTM 45S5 (45% SiO 2, 24.5% CaO, 24.5% Na2O, and 6% P2O5 by weight) are sodium-phosphosilicate glasses containing independent three-dimensional silicate and phosphate networks and Na+ and Ca2+ ions as modifying cations. Due to their bioactivity, these materials are currently used as implants and for other surgical and clinical applications. The bioactivity of BioglassesRTM is due to their unique capability to form chemical bonds to tissues through an octacalciumphosphate (OCP)- and/or hydroxyapatite-like (HA) "interfacial" matrix. The formation of OCP and/or HA is preceded by the formation of a silica-rich surface layer and the subsequent growth of an amorphous calcium phosphate (a-CP) layer. Structural characterization of a series of commercial and synthesized Bioglass materials 45S5 52S, 55S, 60S, and synthesized 17O-labelled "Bioglass materials 45S, 52S, 55S and 60S" have been obtained using solid-state single-pulse magic-angle spinning (SP/MAS) 17O, 23Na, 29Si and 31P NMR. The 17O NMR isotropic chemical shifts and estimates of the quadrupole coupling constants (Cq) [at fixed asymmetry parameter ( hQ ) values of zero] have been obtained from solid-state spin-echo 17O SP/MAS NMR spectra of 17O-labelled "Bioglasses". The simulation results of these spectra reveal the presence of both bridging-oxygens (BO, i.e. ≡ Si-17OSi ≡ ) and non-bridging oxygens (NBO, i.e. ≡ Si-17O-Na+/Ca2+ ) in the silicate networks in these materials. 17O NMR spectra of these Bioglass materials do not show any direct evidence for the presence of BO and NBO atoms in the phosphate units; however, they are expected to be present in small amounts. In vitro reactions of BioglassRTM 45S5, 60S and 77S powders have been used to study the "interfacial" surface chemistry of these materials in simulated body-fluid (SBF, Kyoto or K9 solution) and/or 17O-enriched tris-buffer solution. 29Si and 31P SP/MAS NMR have been used to identify and quantify the extent of formation of surface silica species and follow the formation of phosphate species, respectively, while cross-polarization magic-angle spinning (CP/MAS) 29Si and 31P NMR have provided information about low intensity NMR peaks due to various silicon- and phosphorus-species present in the vicinity of associated protons on the surface of in vitro reacted BioglassRTM materials. The solid-state NMR investigations of the "interfacial" surface reactions of BioglassRTM materials are discussed in the context of the structure of these materials and the influence of this structure on the kinetics and the mechanism of their "interfacial" surface chemistry. (Abstract shortened by UMI.) BioglassRTM, trademark, University of Florida, Gainesville, FL, 32611.

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...

Sequence-defined oligo(ortho-arylene) foldamers derived from the benzannulation of ortho(arylene ethynylene)s† †Electronic supplementary information (ESI) available. CCDC 1483959–1483967. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc02520j Click here for additional data file. Click here for additional data file.

PubMed Central

Lehnherr, Dan; Chen, Chen; Pedramrazi, Zahra; DeBlase, Catherine R.; Alzola, Joaquin M.; Keresztes, Ivan; Lobkovsky, Emil B.

2016-01-01

A Cu-catalyzed benzannulation reaction transforms ortho(arylene ethynylene) oligomers into ortho-arylenes. This approach circumvents iterative Suzuki cross-coupling reactions previously used to assemble hindered ortho-arylene backbones. These derivatives form helical folded structures in the solid-state and in solution, as demonstrated by X-ray crystallography and solution-state NMR analysis. DFT calculations of misfolded conformations are correlated with variable-temperature 1H and EXSY NMR to reveal that folding is cooperative and more favorable in halide-substituted naphthalenes. Helical ortho-arylene foldamers with specific aromatic sequences organize functional π-electron systems into arrangements ideal for ambipolar charge transport and show preliminary promise for the surface-mediated synthesis of structurally defined graphene nanoribbons. PMID:28567248

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

Solution conformation of carbohydrates: a view by using NMR assisted by modeling.

PubMed

Díaz, Dolores; Canales-Mayordomo, Angeles; Cañada, F Javier; Jiménez-Barbero, Jesús

2015-01-01

Structural elucidation of complex carbohydrates in solution is not a trivial task. From the NMR view point, the limited chemical shift dispersion of sugar NMR spectra demands the combination of a variety of NMR techniques as well as the employment of molecular modeling methods. Herein, a general protocol for assignment of resonances and determination of inter-proton distances within the saccharides by homonuclear and heteronuclear experiments (i.e., (1)H and (13)C) is described. In addition, several computational tools and procedures for getting a final ensemble of geometries that represent the structure in solution are presented.

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.

High-Field Liquid-State Dynamic Nuclear Polarization in Microliter Samples.

PubMed

Yoon, Dongyoung; Dimitriadis, Alexandros I; Soundararajan, Murari; Caspers, Christian; Genoud, Jeremy; Alberti, Stefano; de Rijk, Emile; Ansermet, Jean-Philippe

2018-05-01

Nuclear hyperpolarization in the liquid state by dynamic nuclear polarization (DNP) has been of great interest because of its potential use in NMR spectroscopy of small samples of biological and chemical compounds in aqueous media. Liquid state DNP generally requires microwave resonators in order to generate an alternating magnetic field strong enough to saturate electron spins in the solution. As a consequence, the sample size is limited to dimensions of the order of the wavelength, and this restricts the sample volume to less than 100 nL for DNP at 9 T (∼260 GHz). We show here a new approach that overcomes this sample size limitation. Large saturation of electron spins was obtained with a high-power (∼150 W) gyrotron without microwave resonators. Since high power microwaves can cause serious dielectric heating in polar solutions, we designed a planar probe which effectively alleviates dielectric heating. A thin liquid sample of 100 μm of thickness is placed on a block of high thermal conductivity aluminum nitride, with a gold coating that serves both as a ground plane and as a heat sink. A meander or a coil were used for NMR. We performed 1 H DNP at 9.2 T (∼260 GHz) and at room temperature with 10 μL of water, a volume that is more than 100× larger than reported so far. The 1 H NMR signal is enhanced by a factor of about -10 with 70 W of microwave power. We also demonstrated the liquid state of 31 P DNP in fluorobenzene containing triphenylphosphine and obtained an enhancement of ∼200.

Supramolecular architectures with π-acidic 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine cavities: role of anion-π interactions in the remarkable stability of Fe(II) metallacycles in solution.

PubMed

Chifotides, Helen T; Giles, Ian D; Dunbar, Kim R

2013-02-27

The comprehensive investigation reported herein provides compelling evidence that anion-π interactions are the main driving force in the formation of self-assembled Fe(II)-templated metallacycles with bptz [3,6-bis(2-pyridyl)-1,2,4,5-tetrazine] in high yields. It was demonstrated by X-ray crystallography, (1)H NMR, solution and solid-state MAS (19)F NMR spectroscopies, CV and MS studies that the anions [X](-) = [BF(4)](-), [ClO(4)](-) and the anions [Y](-) = [SbF(6)](-), [AsF(6)](-), [PF(6)](-) template molecular squares [Fe(4)(bptz)(4)(CH(3)CN)(8)][X](8) and pentagons [Fe(5)(bptz)(5)(CH(3)CN)(10)][Y](10), respectively. The X-ray structures of [{Fe(4)(bptz)(4)(CH(3)CN)(8)}⊂BF(4)][BF(4)](7) and [{Fe(5)(bptz)(5)(CH(3)CN)(10)}⊂2SbF(6)][SbF(6)](8) revealed that the [BF(4)](-) and [SbF(6)](-) anions occupy the π-acidic cavities, establishing close directional F···C(tetrazine) contacts with the tetrazine rings that are by ~0.4 Å shorter than the sum of the F···C van der Waals radii (ΣR(vdW) F···C = 3.17 Å). The number and strength of F···C(tetrazine) contacts are maximized; the F···C(tetrazine) distances and anion positioning versus the polygon opposing tetrazine rings are in agreement with DFT calculations for C(2)N(4)R(2)···[X](-)···C(2)N(4)R(2) (R = F, CN; [X](-) = [BF(4)](-), [PF(6)](-)). In unprecedented solid-state (19)F MAS NMR studies, the templating anions, engaged in anion-π interactions in the solid state, exhibit downfield chemical shifts Δδ((19)F) ≈ 3.5-4.0 ppm versus peripheral anions. NMR, CV, and MS studies also establish that the Fe(II) metallacycles remain intact in solution. Additionally, interconversion studies between the Fe(II) metallacycles in solution, monitored by (1)H NMR spectroscopy, underscore the remarkable stability of the metallapentacycles [Fe(5)(bptz)(5)(CH(3)CN)(10)][PF(6)](10) ≪ [Fe(5)(bptz)(5)(CH(3)CN)(10)][SbF(6)](10) < [Fe(5)(bptz)(5)(CH(3)CN)(10)][AsF(6)](10) versus [Fe(4)(bptz)(4)(CH(3)CN)(8)][BF(4)](8), given the inherent angle strain in five-membered rings. Finally, the low anion activation energies of encapsulation (ΔG(‡) ≈ 50 kJ/mol), determined from variable-temperature (19)F NMR studies for [Fe(5)(bptz)(5)(CH(3)CN)(10)][PF(6)](10) and [Zn(4)(bptz)(4)(CH(3)CN)(8)][BF(4)](8), confirm anion encapsulation in the π-acidic cavities by anion-π contacts (~20-70 kJ/mol).

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.

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

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.

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.

Quantitative analysis of Bordeaux red wine precipitates by solid-state NMR: Role of tartrates and polyphenols.

PubMed

Prakash, Shipra; Iturmendi, Nerea; Grelard, Axelle; Moine, Virginie; Dufourc, Erick

2016-05-15

Stability of wines is of great importance in oenology matters. Quantitative estimation of dark red precipitates formed in Merlot and Cabernet Sauvignon wine from Bordeaux region for vintages 2012 and 2013 was performed during the oak barrel ageing process. Precipitates were obtained by placing wine at -4°C or 4°C for 2-6 days and monitored by periodic sampling during a one-year period. Spectroscopic identification of the main families of components present in the precipitate powder was performed with (13)C solid-state CPMAS NMR and 1D and 2D solution NMR of partially water re-solubilized precipitates. The study revealed that the amount of precipitate obtained is dependent on vintage, temperature and grape variety. Major components identified include potassium bitartrate, polyphenols, polysaccharides, organic acids and free amino acids. No evidence was found for the presence of proteins. The influence of main compounds found in the precipitates is discussed in relation to wine stability. Copyright © 2016. Published by Elsevier Ltd.

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.

Shape-dependent hydrogen-storage properties in Pd nanocrystals: which does hydrogen prefer, octahedron (111) or cube (100)?

PubMed

Li, Guangqin; Kobayashi, Hirokazu; Dekura, Shun; Ikeda, Ryuichi; Kubota, Yoshiki; Kato, Kenichi; Takata, Masaki; Yamamoto, Tomokazu; Matsumura, Syo; Kitagawa, Hiroshi

2014-07-23

Pd octahedrons and cubes enclosed by {111} and {100} facets, respectively, have been synthesized for investigation of the shape effect on hydrogen-absorption properties. Hydrogen-storage properties were investigated using in situ powder X-ray diffraction, in situ solid-state (2)H NMR and hydrogen pressure-composition isotherm measurements. With these measurements, it was found that the exposed facets do not affect hydrogen-storage capacity; however, they significantly affect the absorption speed, with octahedral nanocrystals showing the faster response. The heat of adsorption of hydrogen and the hydrogen diffusion pathway were suggested to be dominant factors for hydrogen-absorption speed. Furthermore, in situ solid-state (2)H NMR detected for the first time the state of (2)H in a solid-solution (Pd + H) phase of Pd nanocrystals at rt.

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.

Self-assembly behavior of tail-to-tail superstructure formed by mono-6-O-(4-carbamoylmethoxy-benzoyl)-β-cyclodextrin in solution and the solid state.

PubMed

Xu, Zhe; Chen, Xin; Liu, Jing; Yan, Dong-Qing; Diao, Chun-Hua; Guo, Min-Jie; Fan, Zhi

2014-07-01

A novel mono-modified β-cyclodextrin (β-CD) consisting of 4-carbamoylmethoxy-benzoyl unit at the primary side was synthesized and its self-assembly behavior was determined by X-ray crystallography and NMR spectroscopy. The crystal structure shows a 'Yin-Yang'-like packing mode, in which the modified β-CD exhibits a channel superstructure formed by a tail-to-tail dimer as the repeating motif with the substituted group embedded within the hydrophobic cavity of the facing β-CD. The geometry of the substituted group is determined by the inclusion of the cavity and is further stabilized by two intermolecular hydrogen bonds between the carbonyl O atom and phenyl group. Furthermore, NMR ROESY investigation indicates that the self-assembly behavior of the substituted group within the β-CD cavity is retained in aqueous solution, and the effective binding constant Ka was calculated to be 1330 M(-1) by means of (1)H NMR titration according to iterative determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phosphorus Speciation of Sequential Extracts of Organic Amendments using NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Akinremi, O.

2009-04-01

O.O. 1Akinremi Babasola Ajiboye and Donald N. Flaten 1Department of Soil Science, University of Manitoba, Winnipeg, R3T 2NT, Canada We carried out this study in order to determine the forms of phosphorus in various organic amendments using state-of-the art spectroscopic technique. Anaerobically digested biosolids (BIO), hog (HOG), dairy (DAIRY), beef (BEEF) and poultry (POULTRY) manures were subjected to sequential extraction. The extracts were analyzed by solution 31P nuclear magnetic resonance (NMR) spectroscopy. Most of the total P analysed by inductively coupled plasma-optical emission spectroscopy (ICP-OES) in the sequential extracts of organic amendments were orthophosphate, except POULTRY, which was dominated by organic P. The labile P fraction in all the organic amendments, excluding POULTRY, was mainly orthophosphate P from readily soluble calcium and some aluminum phosphates. In the poultry litter, however, Ca phytate was the main P species controlling P solubility. Such knowledge of the differences in the chemical forms of phosphorus in organic amendments are essential for proper management of these amendments for agro-environmental purposes Key words: organic amendments, solution NMR, sequential fractionation, labile phosphorus

Chemical Modification of Kraft Lignin: Effect on Chemical and Thermal Properties

Treesearch

Yao Chen; Nicole M. Stark; Zhiyong Cai; Charles R. Frihart; Linda F. Lorenz; Rebecca E. Ibach

2014-01-01

Esterified kraft lignins (KL) were prepared by reaction with maleic anhydride (MA), succinic anhydride (SA), and phthalic anhydride (PA) in acetone solutions. The esterified lignins were characterized using ATR-FTIR, solid state CP-MAS 13C NMR spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). PA...

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.

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.

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

Relative affinities of divalent polyamines and of their N-methylated analogues for helical DNA determined by sup 23 Na NMR

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

Padmanabhan, S.; Brushaber, V.M.; Anderson, C.F.

1991-07-30

Interactions of divalent polyamines with double-helical DNA in aqueous solution are investigated by monitoring the decrease in {sup 23}Na NMR relaxation rates as NaDNA is titrated with H{sub 3}N{sup +}-(CH{sub 2}){sub m}-{sup +}NH{sup 3}, where m = 3, 4, 5, or 6. Analogous measurements are made for the same homologous series of methylated polyamines (methonium ions). The dependence of the {sup 23}Na relaxation rates on the amount of added divalent cation (M{sup 2+}) is analyzes quantitatively in terms of a two-state model. The sodium ions are assumed to be in rapid exchange between a bound state, where they are closemore » enough to DNA so that it affects their relaxation rate, and a free state in bulk solution, where their relaxation rate is the same as in solutions containing no DNA. (1) For polyamines and methonium ions of the same m, D{sub H} exceeds D{sub Me} by factors that are significantly larger for m = 3 and 4 than for m = 5 and 6. (2) D{sub H} for m = 3 and 4 is larger than D{sub H} for m = 5 and 6. (3) D{sub Me} for m = 3 and 4 is smaller than D{sub Me} for m = 5 and 6.« less

Protein folding on the ribosome studied using NMR spectroscopy

PubMed Central

Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

2013-01-01

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

Gelation of Na-alginate aqueous solution: A study of sodium ion dynamics via NMR relaxometry.

PubMed

Zhao, Congxian; Zhang, Chao; Kang, Hongliang; Xia, Yanzhi; Sui, Kunyan; Liu, Ruigang

2017-08-01

Sodium alginate (SA) hydrogels have a wide range of applications including tissue engineering, drug delivery and formulations for preventing gastric reflux. The dynamics of sodium ions during the gelation process of SA solution is critical for clarification of the gelation procedure. In this work, nuclear magnetic resonance (NMR) relaxometry and pulsed-field-gradient (PFG) NMR diffusometry were used to investigate the dynamics of the sodium ions during the gelation of SA alginate. We find that sodium ions are in two different states with the addition of divalent calcium ions, corresponding to Ca 2+ crosslinked and un-crosslinked regions in the hydrogels. The sodium ions within the un-crosslinked regions are those released from the alginate chains without Ca 2+ crosslinking. The relative content of sodium ions within the Ca 2+ crosslinked regions decreased with the increase in the content of calcium ions in the system. The relaxation time T 2 of sodium ions within the Ca 2+ crosslinked and un-crosslinked regions shift to shorter and longer relaxation time with the increase in concentration of calcium ion, which indicates the closer package of SA chains and the larger space for the diffusion of free sodium ions. This work clarifies the dynamics of 23 Na + in a calcium alginate gel at the equilibrium state. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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.

Experimental Determination of pK[subscript a] Values by Use of NMR Chemical Shifts, Revisited

ERIC Educational Resources Information Center

Gift, Alan D.; Stewart, Sarah M.; Bokashanga, Patrick Kwete

2012-01-01

This laboratory experiment, using proton NMR spectroscopy to determine the dissociation constant for heterocyclic bases, has been modified from a previously described experiment. A solution of a substituted pyridine is prepared using deuterium oxide (D[subscript 2]O) as the solvent. The pH of the solution is adjusted and proton NMR spectra are…

Pyrolysis temperature affects phosphorus transformation in biochar: Chemical fractionation and (31)P NMR analysis.

PubMed

Xu, Gang; Zhang, You; Shao, Hongbo; Sun, Junna

2016-11-01

Phosphorus (P) recycling or reuse by pyrolyzing crop residue has recently elicited increased research interest. However, the effects of feedstock and pyrolysis conditions on P species have not been fully understood. Such knowledge is important in identifying the agronomic and environmental uses of biochar. Residues of three main Chinese agricultural crops and the biochars (produced at 300°C-600°C) derived from these crops were used to determine P transformations during pyrolysis. Hedley sequential fractionation and (31)P NMR analyses were used in the investigation. Our results showed that P transformation in biochar was significantly affected by pyrolysis temperature regardless of feedstock (Wheat straw, maize straw and peanut husk). Pyrolysis treatment transformed water soluble P into a labile (NaHCO3-Pi) or semi-labile pool (NaOH-Pi) and into a stable pool (Dil. HCl P and residual-P). At the same time, organic P was transformed into inorganic P fractions which was identified by the rapid decomposition of organic P detected with solution (31)P NMR. The P transformation during pyrolysis process suggested more stable P was formed at a higher pyrolysis temperature. This result was also evidenced by the presence of less soluble or stable P species, such as such as poly-P, crandallite (CaAl3(OH)5(PO4)2) and Wavellite (Al3(OH)3(PO4)2·5H2O), as detected by solid-state (31)P NMR in biochars formed at a higher pyrolysis temperature. Furthermore, a significant proportion of less soluble pyrophosphate was identified by solution (2%-35%) and solid-state (8%-53%) (31)P NMR, which was also responsible for the stable P forms at higher pyrolysis temperature although their solubility or stability requires further investigation. Results suggested that a relatively lower pyrolysis temperature retains P availability regardless of feedstock during pyrolysis process. Copyright © 2016. Published by Elsevier B.V.

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.

Light-induced yellowing of selectively 13C-enriched dehydrogenation polymers (DHPs). Part 1, Side-chain 13C-enriched DHP ([alpha], [beta], and [gamma]-13C)

Treesearch

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

2004-01-01

Light-induced yellowing has been studied using side-chain ([alpha], [beta], and [gamma]) 13C-enriched DHP (dehydrogenation polymer) and quantitative solution state 13C NMR spectroscopy. The DHP was formed from 13C-enriched coniferin using an enzymatic system consisting of [beta]-glucosidase, glucose oxidase, and peroxidase in a pH 6 buffer solution. The DHP was applied...

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

Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state 13C NMR and solution 31P NMR spectroscopy

NASA Astrophysics Data System (ADS)

LIU, S. S.; Zhu, Y.; Meng, W.; Wu, F.

2016-12-01

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 and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state 13C NMR and solution 31P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O-C-O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH3 and COO/N-C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH3 and COO/N-C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes.

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.

Structure of N-(5-ethyl-[1,3,4]-thiadiazole-2-yl)toluenesulfonamide by combined X-ray powder diffraction, 13C solid-state NMR and molecular modelling.

PubMed

Hangan, Adriana; Borodi, Gheorghe; Filip, Xenia; Tripon, Carmen; Morari, Cristian; Oprean, Luminita; Filip, Claudiu

2010-12-01

The crystal structure solution of the title compound is determined from microcrystalline powder using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct-space methods with information from (13)C solid-state NMR (SSNMR), and molecular modelling using the GIPAW (gauge including projector augmented-wave) method. The space group is Pbca with one molecule in the asymmetric unit. The proposed methodology proves very useful for unambiguously characterizing the supramolecular arrangement adopted by the N-(5-ethyl-[1,3,4]-thiadiazole-2-yl)toluenesulfonamide molecules in the crystal, which consists of extended double strands held together by C-H···π non-covalent interactions.

Insights into the nature of DNA binding of AbrB-like transcription factors

PubMed Central

Sullivan, Daniel M.; Bobay, Benjamin G.; Kojetin, Douglas J.; Thompson, Richele J.; Rance, Mark; Strauch, Mark A.; Cavanagh, John

2008-01-01

Summary Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these ‘transition-state regulator’ proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel shift assays, mutagenic and NMR studies to generate a structural model of the complex between AbrBN55 and its cognate promoter, abrB8. These investigations have enabled us to generate the first model for the specific nature of the transition-state regulator-DNA interaction. PMID:19000822

Conformational state of β-hydroxynaphthylamides: Barriers for the rotation of the amide group around CN bond and dynamics of the morpholine ring

NASA Astrophysics Data System (ADS)

Kozlecki, Tomasz; Tolstoy, Peter M.; Kwocz, Agnieszka; Vovk, Mikhail A.; Kochel, Andrzej; Polowczyk, Izabela; Tretyakov, Peter Yu.; Filarowski, Aleksander

2015-10-01

Three β-hydroxynaphthylamides (morpholine, pyrrolidine and dimethylamine derivatives) have been synthesized and their conformational state was analyzed by NMR, X-ray and DFT calculations. In aprotic solution the molecules contain intramolecular OHO hydrogen bonds, which change into intermolecular ones in solid state. The energy barriers for the amide group rotation around the CN bond were estimated from the line shape analysis of 1H and 13C NMR signals. A tentative correlation between the barrier height and the strength of OHO bond was proposed. Calculations of the potential energy profiles for the rotations around CC and CN bonds were done. In case of morpholine derivative experimental indications of additional dynamics: chair-chair 'ring flip' in combination with the twisting around CC bond were obtained and confirmed by quantum chemistry calculations.

Phenol-formaldehyde reactivity with lignin in the wood cell wall

Treesearch

Daniel J. Yelle; John Ralph

2016-01-01

Latewood from Pinus taeda was reacted with alkaline phenol–formaldehyde (PF) adhesive and characterised using two-dimensional 1H–13C solution-state nuclear magnetic resonance (NMR) spectroscopy so that chemical modification of the wood cell wall polymers, after PF resol curing, could be elucidated. The...

CHEMICAL CHARACTERIZATION OF A CHELATOR-TREATED SOIL HUMATE BY SOLUTION-STATE MULTINUCLEAR TWO-DIMENSIONAL NMR WITH FTIR AND PYROLYSIS-GCMS. (R825433C007)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Detergent/Nanodisc Screening for High-Resolution NMR Studies of an Integral Membrane Protein Containing a Cytoplasmic Domain

PubMed Central

Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland

2013-01-01

Because membrane proteins need to be extracted from their natural environment and reconstituted in artificial milieus for the 3D structure determination by X-ray crystallography or NMR, the search for membrane mimetic that conserve the native structure and functional activities remains challenging. We demonstrate here a detergent/nanodisc screening study by NMR of the bacterial α-helical membrane protein YgaP containing a cytoplasmic rhodanese domain. The analysis of 2D [15N,1H]-TROSY spectra shows that only a careful usage of low amounts of mixed detergents did not perturb the cytoplasmic domain while solubilizing in parallel the transmembrane segments with good spectral quality. In contrast, the incorporation of YgaP into nanodiscs appeared to be straightforward and yielded a surprisingly high quality [15N,1H]-TROSY spectrum opening an avenue for the structural studies of a helical membrane protein in a bilayer system by solution state NMR. PMID:23349867

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

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

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE PAGES

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; ...

2016-02-04

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Association of 2-acylaminopyridines and benzoic acids. Steric and electronic substituent effect studied by XRD, solution and solid-state NMR and calculations

NASA Astrophysics Data System (ADS)

Ośmiałowski, Borys; Kolehmainen, Erkki; Ejsmont, Krzysztof; Ikonen, Satu; Valkonen, Arto; Rissanen, Kari; Nonappa

2013-12-01

Eight single crystal X-ray structures, solid-state NMR spectroscopic, and theoretical studies utilizing QTAIM methodology were used to characterize the 2-acyl (alkyl in acyl = methyl, ethyl, t-butyl, and 1-adamantyl) amino-6-R-pyridine/4-R‧-benzoic acid (R,R‧ = H or Me) cocrystals. As expected among alkyl groups 1-adamantyl due to its bulkiness has the most significant effect on the relative positions of molecules in cocrystals. In addition, the subtle electronic and steric effects by the methyl substituents were observed. The theoretical calculations with full geometry optimizations are in agreement with the experimental findings (geometry, energy of hydrogen bonds). Based on the crystal structures and calculations it is concluded that p-methyl substituent in benzoic acid increase the hydrogen bond accepting ability of the CO oxygen and decreases the hydrogen bond donating ability of OH proton. The 15N solid-state (CP MAS) NMR chemical shifts prove that molecules in cocrystal are held together by hydrogen bonding. The biggest variation in the 15N chemical shift of acylamino nitrogen can be related with the size of the alkyl group in acyl moiety.

Proline isomerization in the C-terminal region of HSP27.

PubMed

Alderson, T Reid; Benesch, Justin L P; Baldwin, Andrew J

2017-07-01

In mammals, small heat-shock proteins (sHSPs) typically assemble into interconverting, polydisperse oligomers. The dynamic exchange of sHSP oligomers is regulated, at least in part, by molecular interactions between the α-crystallin domain and the C-terminal region (CTR). Here we report solution-state nuclear magnetic resonance (NMR) spectroscopy investigations of the conformation and dynamics of the disordered and flexible CTR of human HSP27, a systemically expressed sHSP. We observed multiple NMR signals for residues in the vicinity of proline 194, and we determined that, while all observed forms are highly disordered, the extra resonances arise from cis-trans peptidyl-prolyl isomerization about the G193-P194 peptide bond. The cis-P194 state is populated to near 15% at physiological temperatures, and, although both cis- and trans-P194 forms of the CTR are flexible and dynamic, both states show a residual but differing tendency to adopt β-strand conformations. In NMR spectra of an isolated CTR peptide, we observed similar evidence for isomerization involving proline 182, found within the IPI/V motif. Collectively, these data indicate a potential role for cis-trans proline isomerization in regulating the oligomerization of sHSPs.

Conformation of kainic acid in solution from molecular modelling and NMR spectra.

PubMed

Falk, M; Sidhu, P; Walter, J A

1998-01-01

Conformational behaviour of kainic acid in aqueous solution was elucidated by molecular mechanics and dynamics. The pucker of the five-membered ring in kainic acid was examined and compared with that of model compounds. In cyclopentane there is no barrier to pseudorotation, so that all puckered states coexist. In pyrrolidinium, the presence of a hetero-atom in the ring introduces a small barrier (about 0.6 kcal mol(-1)) to pseudorotation, separating two stable regions, A and B, which are equivalent by symmetry. In proline, the presence of the carboxylate group on C2 removes the symmetry but two stable conformational minima, A and B, remain. In kainic acid, the presence of side-chains on C3 and C4 introduces complications resulting in additional sub-minima in both regions, A and B. In solution, kainic acid is a complex mixture of conformers with comparable energies, because of the combination of several stable states of the pyrrolidinium ring with the torsional degrees of freedom arising from the two side-chains. The individual geometries, energies, and estimates of relative populations of these conformers were obtained from molecular dynamics simulations. The calculations were validated by a comparison of predicted inter-proton distances and vicinal proton coupling constants with the experimental quantities derived from NMR spectra.

Recent advances in the structure elucidation of small organic molecules by the LSD software.

PubMed

Plainchont, Bertrand; de Paulo Emerenciano, Vicente; Nuzillard, Jean-Marc

2013-08-01

The LSD software proposes the structures of small organic molecules that fit with structural constraints from 1D and 2D NMR spectroscopy. Its initial design introduced limits that needed to be eliminated to extend its scope and help its users choose the most likely structure among those proposed. The LSD software code has been improved, so that it recognizes a wider set of atom types to build molecules. More flexibility has been given in the interpretation of 2D NMR data, including the automatic detection of very long-range correlations. A program named pyLSD was written to deal with problems in which atom types are ambiguously defined. It also provides a (13)C NMR chemical shift-based solution ranking algorithm. PyLSD was able to propose the correct structure of hexacyclinol, a natural product whose structure determination has been highly controversal. The solution was ranked first within a list of ten structures that were produced by pyLSD from the literature NMR data. The structure of an aporphin natural product was determined by pyLSD, taking advantage of the possibility of handling electrically charged atoms. The structure generation of the insect antifeedant azadirachtin by LSD was reinvestigated by pyLSD, considering that three (13)C resonances did not lead to univocal hybridization states. Copyright © 2013 John Wiley & Sons, Ltd.

Synthesis and characterization of silver nanoparticles from (bis)alkylamine silver carboxylate precursors

NASA Astrophysics Data System (ADS)

Uznanski, Pawel; Zakrzewska, Joanna; Favier, Frederic; Kazmierski, Slawomir; Bryszewska, Ewa

2017-03-01

A comparative study of amine and silver carboxylate adducts [R1COOAg-2(R2NH2)] (R1 = 1, 7, 11; R2 = 8, 12) as a key intermediate in NPs synthesis is carried out via differential scanning calorimetry, solid-state FT-infrared spectroscopy, 13C CP MAS NMR, powder X-ray diffraction and X-ray photoelectron spectroscopy, and various solution NMR spectroscopies (1H and 13C 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.

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.

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.

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.

The U.S. Dairy Forage Research Center (USDFRC) Condensed Tannin NMR Database.

PubMed

Zeller, Wayne E; Schatz, Paul F

2017-06-28

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, and 1 H and 13 C chemical shifts of the condensed tannins. Citations for all literature references are provided and should serve as valuable resource for scientists working in the field of condensed tannin research. The database will be periodically updated as additional information becomes available, typically on a yearly basis and is available for use, free of charge, from the U.S. Dairy Forage Research Center (USDFRC) Website.

The conformation of cyclo(-D-Pro-Ala4-) as a model for cyclic pentapeptides of the DL4 type.

PubMed

Heller, Markus; Sukopp, Martin; Tsomaia, Natia; John, Michael; Mierke, Dale F; Reif, Bernd; Kessler, Horst

2006-10-25

The conformation of the cyclic pentapeptide cyclo(-D-Pro-Ala(4)-) in solution and in the solid state was reinvestigated using modern NMR techniques. To allow unequivocal characterization of hydrogen bonds, relaxation behavior, and intramolecular distances, differently labeled isotopomers were synthesized. The NMR results, supported by extensive MD simulations, demonstrate unambiguously that the preferred conformation previously described by us, but recently questioned, is indeed correct. The validation of the conformational preferences of this cyclic peptide is important given that this system is a template for several bioactive compounds and for controlled "spatial screening" for the search of bioactive conformations.

Restricted amide rotation with steric hindrance induced multiple conformations

NASA Astrophysics Data System (ADS)

Krishnan, V. V.; Vazquez, Salvador; Maitra, Kalyani; Maitra, Santanu

2017-12-01

The Csbnd N bond character is dependent directly upon the resonance-contributor structure population driven by the delocalized nitrogen lone-pair of electrons. In the case of N, N-dibenzyl-ortho-toluamide (o-DBET), the molecule adopts subpopulations of conformers with distinct NMR spectral features, particularly at low temperatures. This conformational adaptation is unique to o-DBET, while the corresponding meta- and para- forms do not show such behavior. Variable-temperature (VT) NMR, two-dimensional exchange spectroscopy (EXSY), and qualitative molecular modeling studies are used to demonstrate how multiple competing interactions such as restricted amide rotation and steric hindrance effects can lead to versatile molecular adaptations in the solution state.

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.

Structure and dynamics of the influenza A M2 channel: a comparison of three structures.

PubMed

Leonov, Hadas; Arkin, Isaiah T

2009-11-01

The M2 protein is an essential component of the Influenza virus' infectivity cycle. It is a homo-tetrameric bundle forming a pH-gated H(+) channel. The structure of M2 was solved by three different groups, using different techniques, protein sequences and pH environment. For example, solid-state NMR spectroscopy was used on a protein in lipid bilayers, while X-ray crystallography and solution NMR spectroscopy were applied on a protein in detergent micelles. The resulting structures from the above efforts are rather distinct. Herein, we examine the different structures under uniform conditions such as a lipid bilayer and specified protonation state. We employ extensive molecular dynamics simulations, in several protonation states, representing both closed and open forms of the channel. Exploring the properties of each of these structures has shown that the X-ray structure is more stable than the other structures according to various criteria, although its water conductance and water-wire formation do not correlate to the protonation state of the channel.

Correlation of soil and sediment organic matter polarity to aqueous sorption of nonionic compounds

USGS Publications Warehouse

Kile, D.E.; Wershaw, R. L.; Chiou, C.T.

1999-01-01

Polarities of the soiL/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment sam pies were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (K(oc)) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxylamide-ester carbons. A plot of the measured partition coefficients (K(oc)) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of K(oc) values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in K(oc) between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with K(oc) illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.Polarities of the soil/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment samples were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (Koc) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxyl-amide-ester carbons. A plot of the measured partition coefficients (Koc) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of Koc values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in Koc between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with Koc illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.

Structure and physicochemical characterization of a naproxen–picolinamide cocrystal

PubMed Central

Kerr, Hannah E.; Softley, Lorna K.; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-01-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-meth­oxy­naphthalen-2-yl)propanoic acid–pyridine-2-carbox­amide (1/1), C14H14O3·C6H6N2O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH–CONH hydrogen-bonded dimers. 1H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations. PMID:28257010

Structure and physicochemical characterization of a naproxen-picolinamide cocrystal.

PubMed

Kerr, Hannah E; Softley, Lorna K; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-03-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-methoxynaphthalen-2-yl)propanoic acid-pyridine-2-carboxamide (1/1), C 14 H 14 O 3 ·C 6 H 6 N 2 O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH-CONH hydrogen-bonded dimers. 1 H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations.

Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology.

PubMed

Horst, Reto; Wüthrich, Kurt

2015-07-20

Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [ 2 H, 15 N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al ., 2013). 2D [ 15 N, 1 H]-correlation maps are used as "fingerprints" to assess the foldedness of the IMP in solution. For promising samples, these "inexpensive" data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer.

The short-lived signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes.

PubMed

Ramachandran, Pradeep L; Lovett, Janet E; Carl, Patrick J; Cammarata, Marco; Lee, Jae Hyuk; Jung, Yang Ouk; Ihee, Hyotcherl; Timmel, Christiane R; van Thor, Jasper J

2011-06-22

The signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 Å upon illumination. The SAXS/WAXS difference signal for the signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I(2)' state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I(2)' state, which is structurally modeled by dynamical annealing and refinement calculations.

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.

Synthesis, structural, conformational and pharmacological study of some amides derived from 3 -methyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9α-amine

NASA Astrophysics Data System (ADS)

Iriepa, I.; Bellanato, J.; Gálvez, E.; Gil-Alberdi, B.

2010-07-01

Some mono-substituted amides ( 2- 5) derived from 3-methyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9α-amine were synthesized and studied by IR, 1H and 13C NMR spectroscopy. The crystal structure of 3-methyl-2,4-diphenyl-9α-(3,5-dichlorobenzamido)-3-azabicyclo[3.3.1]nonane ( 3) was determined by X-ray diffraction. NMR data showed that all compounds adopt in CDCl 3 a preferred flattened chair-chair conformation with the N-CH 3 group in equatorial disposition. X-ray data agreed with this conformation in the case of compound 3. IR data revealed that compounds 2 and 3 present a C dbnd O⋯HN intermolecular bond in the solid state. This conclusion was also confirmed by X-ray data of compound 3. In the case of compound 5, IR results suggested intermolecular NH⋯N-heterocyclic bonding. On the contrary, in the pyrazine derivative ( 4), IR, 1H and 13C NMR data showed the presence of an intramolecular NH⋯N1″-heterocyclic hydrogen bond in the solid state and solution. Moreover, NMR and IR data showed a preferred trans disposition for the NH-C dbnd O group. NMR also revealed free rotation of the -NH-CO-R group around C9-NH bond. Pharmacological assays on mice were drawn to evaluate analgesic activity.

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.

Concurrent display of both α- and β-turns in a model peptide.

PubMed

Srinivas, Deekonda; Vijayadas, Kuruppanthara N; Gonnade, Rajesh; Phalgune, Usha D; Rajamohanan, Pattuparambil R; Sanjayan, Gangadhar J

2011-08-21

This article describes a model peptide that concurrently displays both α- and β-turns, as demonstrated by structural investigations using single crystal X-ray crystallography and solution-state NMR studies. The motif reported herein has the potential for the design of novel conformationally ordered synthetic oligomers with structural architectures distinct from those classically observed.

Solution-state NMR analysis of hydroxymethylated resorcinol cured in the presence of crude milled-wood lignin from Acer saccharum

Treesearch

Daniel J. Yelle

2017-01-01

Resorcinol-formaldehyde adhesives can reinforce stress fractures that appear from wood surface preparation. Researchers have found that applying the resorcinol-formaldehyde prepolymer, hydroxymethylated resorcinol is thought to plasticize lignin components and stabilize stress fractures through reactions with lignin subunits and hemicelluloses in wood. In this study, a...

Characterization of manure from conventional and phytase transgenic pigs by advanced solid-state NMR spectroscopy

USDA-ARS?s Scientific Manuscript database

Non-point phosphorus (P) pollution from animal manure is becoming a serious global problem. The current solution for the swine industry is including the enzyme phytase as a component of the cereal grain diet. A very real possibility in the future is the production of transgenic pigs that express phy...

Aryl C—H···Cl– Hydrogen Bonding in a Fluorescent Anion Sensor

PubMed Central

Tresca, Blakely W.; Zakharov, Lev N.; Carroll, Calden N.; Johnson, Darren W.; Haley, Michael M.

2014-01-01

A new phenyl-acetylene receptor containing a carbonaceous hydrogen bond donor activates anion binding in conjunction with two stabilizing ureas. The unusual CH···Cl– hydrogen bond is apparent in solution by large 1H NMR chemical shifts and by a short, linear contact in the solid state. PMID:23843050

Glycerol derivatives of cutin and suberin monomers: synthesis and self-assembly.

PubMed

Douliez, Jean-Paul; Barrault, Joël; Jerome, François; Heredia, Antonio; Navailles, Laurence; Nallet, Frédéric

2005-01-01

Glycerol derivatives of cutin and suberin monomers were synthesized by acid catalysis. Their dispersion in an aqueous solution was examined by phase contrast microscopy, neutron scattering, and solid state NMR. It is shown that the phase behavior strongly depends on the nature of the derivatives forming either lumps of aggregated membranes or well dispersed membranes.

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

PubMed

Sekhar, Ashok; Kay, Lewis E

2013-08-06

The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

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

Molecular-level elucidation of saccharin-assisted rapid dissolution and high supersaturation level of drug from Eudragit® E solid dispersion.

PubMed

Ueda, Keisuke; Kanaya, Harunobu; Higashi, Kenjirou; Yamamoto, Keiji; Moribe, Kunikazu

2018-03-01

In this work, the effect of saccharin (SAC) addition on the dissolution and supersaturation level of phenytoin (PHT)/Eudragit® E (EUD-E) solid dispersion (SD) at neutral pH was examined. The PHT/EUD-E SD showed a much slower dissolution of PHT compared to the PHT/EUD-E/SAC SD. EUD-E formed a gel layer after the dispersion of the PHT/EUD-E SD into an aqueous medium, resulting in a slow dissolution of PHT. Pre-dissolving SAC in the aqueous medium significantly improved the dissolution of the PHT/EUD-E SD. Solid-state 13 C NMR measurements showed an ionic interaction between the tertiary amino group of EUD-E and the amide group of SAC in the EUD-E gel layer. Consequently, the ionized EUD-E could easily dissolve from the gel layer, promoting PHT dissolution. Solution-state 1 H NMR measurements revealed the presence of ionic interactions between SAC and the amino group of EUD-E in the PHT/EUD-E/SAC solution. In contrast, interactions between PHT and the hydrophobic group of EUD-E strongly inhibited the crystallization of the former from its supersaturated solution. The PHT supersaturated solution was formed from the PHT/EUD-E/SAC SD by the fast dissolution of PHT and the strong crystallization inhibition effect of EUD-E after aqueous dissolution. Copyright © 2018 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.

Characterizing RNA ensembles from NMR data with kinematic models

PubMed Central

Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

2014-01-01

Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

Fractionation of bamboo culms by autohydrolysis, organosolv delignification and extended delignification: understanding the fundamental chemistry of the lignin during the integrated process.

PubMed

Wen, Jia-Long; Sun, Shao-Ni; Yuan, Tong-Qi; Xu, Feng; Sun, Run-Cang

2013-12-01

Bamboo (Phyllostachys pubescens) was successfully fractionated using a three-step integrated process: (1) autohydrolysis pretreatment facilitating xylooligosaccharide (XOS) production (2) organosolv delignification with organic acids to obtain high-purity lignin, and (3) extended delignification with alkaline hydrogen peroxide (AHP) to produce purified pulp. The integrated process was comprehensively evaluated by component analysis, SEM, XRD, and CP-MAS NMR techniques. Emphatically, the fundamental chemistry of the lignin fragments obtained from the integrated process was thoroughly investigated by gel permeation chromatography and solution-state NMR techniques (quantitative (13)C, 2D-HSQC, and (31)P-NMR spectroscopies). It is believed that the integrated process facilitate the production of XOS, high-purity lignin, and purified pulp. Moreover, the enhanced understanding of structural features and chemical reactivity of lignin polymers will maximize their utilizations in a future biorefinery industry. Copyright © 2013 Elsevier Ltd. 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.

[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

PubMed

Abaturov, L V; Nosova, N G

2013-01-01

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the solution of the crystalline structure of crambin the essential changes of the backbone conformation are caused by the intermolecular contacts absence, but partly masked by the structure changes owing to the nonpolar H atoms absence on the simulated structure. The intermolecular contact absence is partly manifested upon the molecular dynamics simulation of the crambin crystal with one protein molecule. Compared to the crystal structure the lengths of the interpeptide hydrogen bonds and other interresidue contacts in an average solution NMR structure are somewhat shorter and accordingly the energy of the interpeptide hydrogen bonds is better. This length shortening can occur at the stage of the refinement of the NMR structures of the crambin and other proteins by its energy minimizations in the vacuum surroundings and not exist in the solution protein structures.

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.

New insights into the coordination chemistry of Schiff bases derived from amino acids: Planar [Ni4] complexes with tyrosine side-chains

NASA Astrophysics Data System (ADS)

Muche, Simon; Hołyńska, Małgorzata

2017-08-01

Structure and properties of a rare metal complex of the chiral Schiff base ligand derived from ortho-vanillin and L-tyrosine are presented. This study is a continuation of research on ligands containing biologically compatible moieties. The ligand is also fully characterized in form of a sodium salt, in particular in solution, for the first time. The metal complex contains a unique bowl-shaped [Ni4] core. Its structure is investigated both in solution (ESI-MS, NMR) and in solid state (X-ray diffraction studies). Under certain conditions the complex can be isolated as crystalline DMF solvate which is studied in solid state.

CHEMICAL CHARACTERIZATION OF A CHELATOR-TREATED SOIL HUMATE BY SOLUTION-STATE MULTINUCLEAR TWO-DIMENSIONAL NMR WITH FTIR AND PYROLYSIS-GCMS. (R825960)

EPA Science Inventory

A California forest soil used for contaminant bioavailability
studies was extracted for humic substances (HS) and
then treated with 4,5-dihydroxy-1,3-benzene disulfonate
("Tiron") to remove exchangeable metal ions. This yielded
HS that was readily water-soluble at ...

The effect of sample hydration on 13C CPMAS NMR spectra of fulvic acids

USGS Publications Warehouse

Hatcher, P.G.; Wilson, M.A.

1991-01-01

Three fulvic acids, two of which have been well studied by a number of other groups (Armadale and Suwannee river fulvic acids) have been examined by high resolution solid-state 13C-NMR techniques to delineate the effect of absorbed water. Two main effects of absorbed water were observed: (1) changes in spin lattice relaxation times in the rotating frame and cross polarization times and (2) total loss of signal so that some fulvic acid is effectively in solution. These results suggest that discrepancies in the literature concerning observed relative signal intensities from different structural groups are due to absorbed water and emphasize the necessity for proper precautionary drying before spectroscopic analysis. ?? 1991.

Chevrel-phase solid solution Mo 6Se 8- xTe x. Study of its superconducting, magnetic and NMR properties

NASA Astrophysics Data System (ADS)

Hamard1a, C.; Auffret, V.; Peña, O.; Le Floch, M.; Nowak, B.; Wojakowski, A.

2000-09-01

The Chevrel-phase solid solution Mo 6Se 8-Mo 6Te 8 was studied by X-ray diffraction, AC and DC magnetic susceptibility and 77Se and 125Te NMR spectroscopy. From the smooth evolution of the lattice parameters and superconducting critical temperatures, a progressive substitution of selenium atoms by tellurium is shown, on the whole range of composition 0⩽ x⩽8, in the formulation Mo 6Se 8- xTe x: the unit-cell volume increases linearly because of the larger ionic size of tellurium, while Tc decreases rapidly (from 6.45 down to 0 K) because of the different formal oxidation states of the anions and a probable evolution of the Fermi level in the density of states. Results of magnetic susceptibility support this model and suggest the inhibition of the intrinsic metallic behavior with increasing x. The NMR spectra of the binaries Mo 6Se 8 and Mo 6Te 8 reveal two significant features, attributed to two different chalcogen positions in the R 3¯ symmetry. At low Se contents in Mo 6Se 8- xTe x ( x=7.5, 7 and 6), selenium first fills the two X(2) sites along the three-fold axis (2c positions), and then it becomes statistically distributed over the general 6f positions, leading to broad 77Se NMR lines. On the other hand, substitution of Te atoms in Mo 6Se 8 seems to occur in a random way, creating large perturbations on the 125Te NMR spectra, over the whole range of x. Theoretical analysis based on the presence of two anisotropic lines (of axial and non-axial symmetries, respectively) allowed us to estimate their anisotropy factors and to perfectly simulate the frequency response of both Mo 6Se 8 and Mo 6Te 8 binaries. Analysis of the Knight shift anisotropy leads us to conclude about the importance of the molybdenum z 2 molecular orbital contribution which controls the Mo-X dipolar interactions.

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

Bridging the gap between homogeneous and heterogeneous catalysis: ortho/para H(2) conversion, hydrogen isotope scrambling, and hydrogenation of olefins by Ir(CO)Cl(PPh(3))(2).

PubMed

Matthes, Jochen; Pery, Tal; Gründemann, Stephan; Buntkowsky, Gerd; Sabo-Etienne, Sylviane; Chaudret, Bruno; Limbach, Hans-Heinrich

2004-07-14

Some transition metal complexes are known to catalyze ortho/para hydrogen conversion, hydrogen isotope scrambling, and hydrogenation reactions in liquid solution. Using the example of Vaska's complex, we present here evidence by NMR that the solvent is not necessary for these reactions to occur. Thus, solid frozen solutions or polycrystalline powdered samples of homogeneous catalysts may become heterogeneous catalysts. Comparative liquid- and solid-state studies provide novel insight into the reaction mechanisms.

On the problem of resonance assignments in solid state NMR of uniformly 15N, 13C-labeled proteins

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic 15N and 13C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

Development and Application of a Low-Volume Flow System for Solution-State in Vivo NMR.

PubMed

Tabatabaei Anaraki, Maryam; Dutta Majumdar, Rudraksha; Wagner, Nicole; Soong, Ronald; Kovacevic, Vera; Reiner, Eric J; Bhavsar, Satyendra P; Ortiz Almirall, Xavier; Lane, Daniel; Simpson, Myrna J; Heumann, Hermann; Schmidt, Sebastian; Simpson, André J

2018-06-18

In vivo nuclear magnetic resonance (NMR) spectroscopy is a particularly powerful technique, since it allows samples to be analyzed in their natural, unaltered state, criteria paramount for living organisms. In this study, a novel continuous low-volume flow system, suitable for in vivo NMR metabolomics studies, is demonstrated. The system allows improved locking, shimming, and water suppression, as well as allowing the use of trace amounts of expensive toxic contaminants or low volumes of precious natural environmental samples as stressors. The use of a double pump design with a sump slurry pump return allows algal food suspensions to be continually supplied without the need for filters, eliminating the possibility of clogging and leaks. Using the flow system, the living organism can be kept alive without stress indefinitely. To evaluate the feasibility and applicability of the flow system, changes in the metabolite profile of 13 C enriched Daphnia magna over a 24-h period are compared when feeding laboratory food vs exposing them to a natural algal bloom sample. Clear metabolic changes are observed over a range of metabolites including carbohydrates, lipids, amino acids, and a nucleotide demonstrating in vivo NMR as a powerful tool to monitor environmental stress. The particular bloom used here was low in microcystins, and the metabolic stress impacts are consistent with the bloom being a poor food source forcing the Daphnia to utilize their own energy reserves.

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

Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains

PubMed Central

Hora, Manuel; Carballo-Pacheco, Martin; Weber, Benedikt; Morris, Vanessa K.; Wittkopf, Antje; Buchner, Johannes; Strodel, Birgit; Reif, Bernd

2017-01-01

Antibody light chain amyloidosis is a rare disease caused by fibril formation of secreted immunoglobulin light chains (LCs). The huge variety of antibody sequences puts a serious challenge to drug discovery. The green tea polyphenol epigallocatechin-3-gallate (EGCG) is known to interfere with fibril formation in general. Here we present solution- and solid-state NMR studies as well as MD simulations to characterise the interaction of EGCG with LC variable domains. We identified two distinct EGCG binding sites, both of which include a proline as an important recognition element. The binding sites were confirmed by site-directed mutagenesis and solid-state NMR analysis. The EGCG-induced protein complexes are unstructured. We propose a general mechanistic model for EGCG binding to a conserved site in LCs. We find that EGCG reacts selectively with amyloidogenic mutants. This makes this compound a promising lead structure, that can handle the immense sequence variability of antibody LCs. PMID:28128355

Lead(II) binding to the chelating agent d-penicillamine in aqueous solution

DOE PAGES

Sisombath, Natalie S.; Jalilehvand, Farideh; Schell, Adam C.; ...

2014-11-11

Here, a spectroscopic investigation of the complexes formed between the Pb(II) ion and d-penicillamine (H 2Pen), a chelating agent used in the treatment of lead poisoning, was carried out on two sets of alkaline aqueous solutions with C Pb(II) ≈ 10 and 100 mM, varying the H 2Pen/Pb(II) molar ratio (2.0, 3.0, 4.0, 10.0). Ultraviolet–visible (UV-vis) spectra of the 10 mM Pb(II) solutions consistently showed an absorption peak at 298 nm for S – → Pb(II) ligand-to-metal charge-transfer. The downfield 13C NMR chemical shift for the penicillamine COO – group confirmed Pb(II) coordination. The 207Pb NMR chemical shifts were confinedmore » to a narrow range between 1806 ppm and 1873 ppm for all Pb(II)-penicillamine solutions, indicating only small variations in the speciation, even in large penicillamine excess. Those chemical shifts are considerably deshielded, relative to the solid-state 207Pb NMR isotropic chemical shift of 909 ppm obtained for crystalline penicillaminatolead(II) with Pb(S,N,O-Pen) coordination. The Pb L III-edge extended X-ray absorption fine structure (EXAFS) spectra obtained for these solutions were well-modeled with two Pb–S and two Pb-(N/O) bonds with mean distances 2.64 ± 0.04 Å and 2.45 ± 0.04 Å, respectively. The combined spectroscopic results, reporting δ( 207Pb) ≈ 1870 ppm and λ max ≈ 298 nm for a Pb IIS 2NO site, are consistent with a dominating 1:2 lead(II):penicillamine complex with [Pb(S,N,O-Pen)(S-H nPen)] 2–n (n = 0–1) coordination in alkaline solutions, and provide useful structural information on how penicillamine can function as an antidote against lead toxicity in vivo.« less

Lead(II) Binding to the Chelating Agent d-Penicillamine in Aqueous Solution

PubMed Central

2015-01-01

A spectroscopic investigation of the complexes formed between the Pb(II) ion and d-penicillamine (H2Pen), a chelating agent used in the treatment of lead poisoning, was carried out on two sets of alkaline aqueous solutions with CPb(II) ≈ 10 and 100 mM, varying the H2Pen/Pb(II) molar ratio (2.0, 3.0, 4.0, 10.0). Ultraviolet–visible (UV-vis) spectra of the 10 mM Pb(II) solutions consistently showed an absorption peak at 298 nm for S– → Pb(II) ligand-to-metal charge-transfer. The downfield 13C NMR chemical shift for the penicillamine COO– group confirmed Pb(II) coordination. The 207Pb NMR chemical shifts were confined to a narrow range between 1806 ppm and 1873 ppm for all Pb(II)-penicillamine solutions, indicating only small variations in the speciation, even in large penicillamine excess. Those chemical shifts are considerably deshielded, relative to the solid-state 207Pb NMR isotropic chemical shift of 909 ppm obtained for crystalline penicillaminatolead(II) with Pb(S,N,O-Pen) coordination. The Pb LIII-edge extended X-ray absorption fine structure (EXAFS) spectra obtained for these solutions were well-modeled with two Pb–S and two Pb-(N/O) bonds with mean distances 2.64 ± 0.04 Å and 2.45 ± 0.04 Å, respectively. The combined spectroscopic results, reporting δ(207Pb) ≈ 1870 ppm and λmax ≈ 298 nm for a PbIIS2NO site, are consistent with a dominating 1:2 lead(II):penicillamine complex with [Pb(S,N,O-Pen)(S-HnPen)]2–n (n = 0–1) coordination in alkaline solutions, and provide useful structural information on how penicillamine can function as an antidote against lead toxicity in vivo. PMID:25385465

Developing advanced X-ray scattering methods combined with crystallography and computation.

PubMed

Perry, J Jefferson P; Tainer, John A

2013-03-01

The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one's repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography*

PubMed Central

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N.; Nishida, Clinton R.; de Montellano, Paul R. Ortiz

2015-01-01

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. PMID:25670859

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

Monometallic Ni(0) and Heterobimetallic Ni(0) /Au(I) Complexes of Tripodal Phosphine Ligands: Characterization in Solution and in the Solid State and Catalysis.

PubMed

Cluff, Kyle J; Bhuvanesh, Nattamai; Blümel, Janet

2015-07-06

The tridentate chelate nickel complexes [(CO)Ni{(PPh2 CH2 )3 CMe}] (2), [(CO)Ni{(PPh2 CH2 CH2 )3 SiMe}] (6), and [Ph3 PNi{(PPh2 CH2 CH2 )3 SiMe}] (7), as well as the bidentate complex [(CO)2 Ni{(PPh2 CH2 )2 CMeCH2 PPh2 }] (3) and the heterobimetallic complex [(CO)2 Ni{(PPh2 CH2 )2 CMeCH2 Ph2 PAuCl}] (4), have been synthesized and fully characterized in solution. All (1) H and (13) C NMR signal assignments are based on 2D-NMR methods. Single crystal X-ray structures have been obtained for all complexes. Their (31) P CP/MAS (cross polarization with magic angle spinning) NMR spectra have been recorded and the isotropic lines identified. The signals were assigned with the help of their chemical shift anisotropy (CSA) data. All complexes have been tested regarding their catalytic activity for the cyclotrimerization of phenylacetylene. Whereas complexes 2-4 display low catalytic activity, complex 7 leads to quantitative conversion of the substrate within four hours and is highly selective throughout the catalytic reaction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

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.

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.

Measurement of Solution Viscosity via Diffusion-Ordered NMR Spectroscopy (DOSY)

ERIC Educational Resources Information Center

Li, Weibin; Kagan, Gerald; Hopson, Russell; Williard, Paul G.

2011-01-01

Increasingly, the undergraduate chemistry curriculum includes nuclear magnetic resonance (NMR) spectroscopy. Advanced NMR techniques are often taught including two-dimensional gradient-based experiments. An investigation of intermolecular forces including viscosity, by a variety of methods, is often integrated in the undergraduate physical and…

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.

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.

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.

Elucidating How Wood Adhesives Bond to Wood Cell Walls using High-Resolution Solution-State NMR Spectroscopy

Treesearch

Daniel J. Yelle

2013-01-01

Some extensively used wood adhesives, such as pMDI (polymeric methylene diphenyl diisocyanate) and PF (phenol formaldehyde) have shown excellent adhesion properties with wood. However, distinguishing whether the strength is due to physical bonds (i.e., van der Waals, London, or hydrogen bond forces) or covalent bonds between the adherend and the adhesive is not fully...

White light generation by carbonyl based indole derivatives due to proton transfer: an efficient fluorescence sensor.

PubMed

Singla, Nidhi; Bhadram, Venkata Srinu; Narayana, Chandrabhas; Chowdhury, Papia

2013-04-04

The motivation of the present work is to understand the optical, chemical, and electrical aspects of the proton transfer mechanism of indole (I) and some carbonyl based indole derivatives: indole-3-carboxaldehyde (I3C) and indole-7-carboxaldehyde (I7C) for both powder form and their liquid solution. Structural information for indole derivatives (isolated molecule and in solution) is obtained with density functional theory (DFT) and time dependent DFT (TD-DFT) methods. Calculated transition energies are used to generate UV-vis, FTIR, Raman, and NMR spectra which are later verified with the experimental spectra. The occurrence of different conformers [cis (N(c)), trans (N(t)), and zwitterion (Z*)] have been interpreted by Mulliken charge, natural bond orbital (NBO) analysis, and polarization versus electric field (P-E loop) studies. (1)H and (13)C NMR and molecular vibrational frequencies of the fundamental modes established the stability of Nc due to the presence of intramolecular hydrogen bonding (IHB) in the ground state (S0). Computed/experimental UV-vis absorption/emission studies reveal the creation of new species: zwitterion (Z*) and anion (A*) in the excited state (S1) due to excited state intramolecular and intermolecular proton transfer (ESI(ra)PT and ESI(er)PT). Increased electrical conductivity (σ(ac)) with temperature and increased ferroelectric polarization at higher field verifies proton conduction in I7C.

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 ...

NMR solution structure study of one saturated sulphur-containing amides from Glycosmis lucida.

PubMed

Geng, Zhu-Feng; Yang, Kai; Li, Yin-Ping; Guo, Shan-Shan; You, Chun-Xue; Zhang, Wen-Juan; Zhang, Zhe; Du, Shu-Shan

2017-04-01

One sulphur-containing amide (N-[2-(4-Hydroxyphenyl)-ethyl]-3-methanesulfonyl-N-methyl-propionamide) which was isolated from Glycosmis lucida Wall ex Huang had a different NMR profile with this kind of compounds' normal case. Based on the information obtained by nuclear magnetic resonance pectroscopy (NMR) and mass spectrometry (MS), its configurations in solution were investigated. The results indicated that the compound would have two stable configurations in solution as the double bond switched between C-N and C-O in an appropriate rate. This phenomenon was clearly exposed by the one dimension selective NOE (1D-NOE) experiments. This conclusion would play an active role in the structure analysis work of this kind of compounds.

Preparation, Characterization, and Antimicrobial Activities of Bimetallic Complexes of Sarcosine with Zn(II) and Sn(IV)

PubMed Central

Arafat, Yasir; Ali, Saqib; Shahzadi, Saira; Shahid, Muhammad

2013-01-01

Heterobimetallic complexes of Zn(II) and Sn(IV) with sarcosine have been synthesized at room temperature under stirring conditions by the reaction of sarcosine and zinc acetate in 2 : 1 molar ratio followed by the stepwise addition of CS2 and organotin(IV) halides, where R = Me, n-Bu, and Ph. The complexes were characterized by elemental analysis, FT-IR and NMR (1H, 13C) spectroscopy. IR data showed that the ligand acts in a bidentate manner. NMR data revealed the four coordinate geometry in solution state. In vitro antimicrobial activities data showed that complexes (3) and (4) were effective against bacterial and fungal strains with few exceptions. PMID:24235910

Three-Dimensional Conformation of Folded Polymers in Single Crystals

NASA Astrophysics Data System (ADS)

Hong, You-lee; Yuan, Shichen; Li, Zhen; Ke, Yutian; Nozaki, Koji; Miyoshi, Toshikazu

2015-10-01

The chain-folding mechanism and structure of semicrystalline polymers have long been controversial. Solid-state NMR was applied to determine the chain trajectory of 13C CH3 -labeled isotactic poly(1-butene) (i PB 1 ) in form III chiral single crystals blended with nonlabeled i PB 1 crystallized in dilute solutions under low supercooling. An advanced 13C - 13C double-quantum NMR technique probing the spatial proximity pattern of labeled 13C nuclei revealed that the chains adopt a three-dimensional (3D) conformation in single crystals. The determined results indicate a two-step crystallization process of (i) cluster formation via self-folding in the precrystallization stage and (ii) deposition of the nanoclusters as a building block at the growth front in single crystals.

Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy.

PubMed

Grondin, Julie M; Langelaan, David N; Smith, Steven P

2017-01-01

Solution-state nuclear magnetic resonance (NMR) spectroscopy can be used to monitor protein-carbohydrate interactions. Two-dimensional 1 H- 15 N heteronuclear single quantum coherence (HSQC)-based techniques described in this chapter can be used quickly and effectively to screen a set of possible carbohydrate binding partners, to quantify the dissociation constant (K d ) of any identified interactions, and to map the carbohydrate binding site on the structure of the protein. Here, we describe the titration of a family 32 carbohydrate binding module from Clostridium perfringens (CpCBM32) with the monosaccharide N-acetylgalactosamine (GalNAc), in which we calculate the apparent dissociation of the interaction, and map the GalNAc binding site onto the structure of CpCBM32.

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 -

Revisiting HgCl 2: A solution- and solid-state 199Hg NMR and ZORA-DFT computational study

NASA Astrophysics Data System (ADS)

Taylor, R. E.; Carver, Colin T.; Larsen, Ross E.; Dmitrenko, Olga; Bai, Shi; Dybowski, C.

2009-07-01

The 199Hg chemical-shift tensor of solid HgCl 2 was determined from spectra of polycrystalline materials, using static and magic-angle spinning (MAS) techniques at multiple spinning frequencies and field strengths. The chemical-shift tensor of solid HgCl 2 is axially symmetric ( η = 0) within experimental error. The 199Hg chemical-shift anisotropy (CSA) of HgCl 2 in a frozen solution in dimethylsulfoxide (DMSO) is significantly smaller than that of the solid, implying that the local electronic structure in the solid is different from that of the material in solution. The experimental chemical-shift results (solution and solid state) are compared with those predicted by density functional theory (DFT) calculations using the zeroth-order regular approximation (ZORA) to account for relativistic effects. 199Hg spin-lattice relaxation of HgCl 2 dissolved in DMSO is dominated by a CSA mechanism, but a second contribution to relaxation arises from ligand exchange. Relaxation in the solid state is independent of temperature, suggesting relaxation by paramagnetic impurities or defects.

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.

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.

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.

Spectroscopic and structural studies of the first complex formed between salinomycin and organic amine

NASA Astrophysics Data System (ADS)

Antoszczak, Michał; Janczak, Jan; Brzezinski, Bogumił; Huczyński, Adam

2017-02-01

For the first time, the crystalline complex of salinomycin with benzylamine was obtained and its molecular structure was studied using single crystal X-ray diffraction, FT-IR, 1H NMR, 13C NMR, 2D NMR and ESI MS methods. These studies provided evidence that the proton from the carboxylic group of salinomycin (SAL) is transferred to the amine group of benzylamine (BnA) forming the host-guest complex (SAL-BnA). It was shown that the SAL-BnA complex both in solid state and in chloroform solution is stabilized by the intramolecular O-H⋯O hydrogen bonds and also by the intermolecular hydrogen bonding interactions of the carboxylate, ketone and/or hydroxyl groups of SAL with water molecules present in the investigated system. The solvated acetonitrile molecules are additionally located in the voids between the SAL-BnA complex molecules in the crystal structure, while water molecules involved in the dihydrated crystalline SAL-BnA complex partially move into the solvent upon dissolution in chloroform.

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.

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

Characterization of molecular disorder in vapor-deposited thin films of aluminum tris(quinoline-8-olate) by one-dimensional 27Al NMR under magic angle spinning.

PubMed

Utz, Marcel; Nandagopal, Magesh; Mathai, Mathew; Papadimitrakopoulos, Fotios

2006-01-21

Aluminum tris (quinoline-8-olate) (Alq3) is used as an electron-transport layer in organic light-emitting diodes. The material can be obtained in a wide range of different solid phases, both crystalline and amorphous, by deposition from the vapor phase or from solution under controlled conditions. While the structure of the crystalline polymorphs of Alq3 has been investigated thoroughly by x-ray diffraction as well as solid-state NMR, very little information is currently available on the amount of structural disorder in the amorphous forms of Alq3. In the present contribution, we report the use of 27Al NMR spectroscopy in the solid state under magic angle spinning to extract such information from amorphous vapor deposits of Alq3. The NMR spectra obtained from these samples exhibit different degrees of broadening, reflecting distributions of the electric-field gradient tensor at the site of the aluminum ion. These distributions can be obtained from the NMR spectra by solving the corresponding inverse problem. From these results, the magnitude of structural disorder in terms of molecular geometry has been estimated by density-functional theory calculations. It was found that the electric-field gradient anisotropy delta follows a bimodal distribution. Its majority component is centered around delta values comparable to the meridianal alpha crystal polymorph and has a width of about 10%, corresponding to distortions of the molecular geometry of a few degrees in the orientation of the ligands. Alq3 samples obtained at higher deposition rates exhibit higher degrees of disorder. The minor component, present at about 7%, has a much smaller anisotropy, suggesting that it may be due to the facial isomer of Alq3.

Investigation of Phase Mixing in Amorphous Solid Dispersions of AMG 517 in HPMC-AS Using DSC, Solid-State NMR, and Solution Calorimetry.

PubMed

Calahan, Julie L; Azali, Stephanie C; Munson, Eric J; Nagapudi, Karthik

2015-11-02

Intimate phase mixing between the drug and the polymer is considered a prerequisite to achieve good physical stability for amorphous solid dispersions. In this article, spray dried amorphous dispersions (ASDs) of AMG 517 and HPMC-as were studied by differential scanning calorimetry (DSC), solid-state NMR (SSNMR), and solution calorimetry. DSC analysis showed a weakly asymmetric (ΔTg ≈ 13.5) system with a single glass transition for blends of different compositions indicating phase mixing. The Tg-composition data was modeled using the BKCV equation to accommodate the observed negative deviation from ideality. Proton spin-lattice relaxation times in the laboratory and rotating frames ((1)H T1 and T1ρ), as measured by SSNMR, were consistent with the observation that the components of the dispersion were in intimate contact over a 10-20 nm length scale. Based on the heat of mixing calculated from solution calorimetry and the entropy of mixing calculated from the Flory-Huggins theory, the free energy of mixing was calculated. The free energy of mixing was found to be positive for all ASDs, indicating that the drug and polymer are thermodynamically predisposed to phase separation at 25 °C. This suggests that miscibility measured by DSC and SSNMR is achieved kinetically as the result of intimate mixing between drug and polymer during the spray drying process. This kinetic phase mixing is responsible for the physical stability of the ASD.

Novel solution-phase structures of gallium-containing pyrogallol[4]arene scaffolds**

PubMed Central

Kumari, Harshita; Kline, Steven R.; Wycoff, Wei G.; Paul, Rick L.; Mossine, Andrew V.; Deakyne, Carol A.; Atwood, Jerry L.

2012-01-01

The variations in architecture of gallium-seamed (PgC4Ga) and gallium-zinc-seamed (PgC4GaZn) C-butylpyrogallol[4]arene nanoassemblies in solution (SANS/NMR) versus the solid state (XRD) have been investigated. Rearrangement from the solid-state spheroidal to the solution-phase toroidal shape differentiates the gallium-containing pyrogallol[4]arene nanoassemblies from all other PgCnM nanocapsules studied thus far. Different structural arrangements of the metals and arenes of PgC4Ga versus PgC4GaZn have been deduced from the different toroidal dimensions, C–H proton environments and guest encapsulation of the two toroids. PGAA of mixed-metal hexamers reveals a decrease in gallium-to-metal ratio as the second metal varies from cobalt to zinc. Overall, the combined study demonstrates the versatility of gallium in directing the self-assembly of pyrogallol[4]arenes into novel nanoarchitectures. PMID:22511521

Spider Silk: From Protein-Rich Gland Fluids to Diverse Biopolymer Fibers

DTIC Science & Technology

2016-01-06

characterize the protein-rich fluid in the various spider silk producing glands. We have been using a battery of magnetic resonance methods including...solution and solid-state nuclear magnetic resonance (NMR) and micro imaging (MRI) in combination with wide angle and small angle X-ray diffraction...range of magnetic resonance methods. We successfully developed magnetic resonance imaging (MRI) techniques with localized spectroscopy to probe the silk

Correlating the chemical and spectroscopic characteristics of natural organic matter with the photodegradation of sulfamerazine.

PubMed

Batista, Ana Paula S; Teixeira, Antonio Carlos S C; Cooper, William J; Cottrell, Barbara A

2016-04-15

The role of aquatic natural organic matter (NOM) in the removal of contaminants of emerging concern has been widely studied. Sulfamerazine (SMR), a sulfonamide antibiotic detected in aquatic environments, is implicated in environmental toxicity and may contribute to the resistance of bacteria to antibiotics. In aquatic systems sulfonamides may undergo direct photodegradation, and, indirect photodegradation through the generation of reactive species. Because some forms of NOM inhibit the photodegradation there is an increasing interest in correlating the spectroscopic parameters of NOM as potential indicators of its degradation in natural waters. Under the conditions used in this study, SMR hydrolysis was shown to be negligible; however, direct photolysis is a significant in most of the solutions studied. Photodegradation was investigated using standard solutions of NOM: Suwannee River natural organic matter (SRNOM), Suwannee River humic acid (SRHA), Suwannee River fulvic acid (SRFA), and Aldrich humic acid (AHA). The steady-state concentrations and formation rates of the reactive species and the SMR degradation rate constants (k1) were correlated with NOM spectroscopic parameters determined using UV-vis absorption, excitation-emission matrix (EEM) fluorescence spectroscopy, and proton nuclear magnetic resonance ((1)H NMR). SMR degradation rate constants (k1) were correlated with steady-state concentrations of NOM triplet-excited state ([(3)NOM(∗)]ss) and the corresponding formation rates ((3)NOM*) for SRNOM, SRHA, and AHA. The efficiency of SMR degradation was highest in AHA solution and was inhibited in solutions of SRFA. The steady-state concentrations of singlet oxygen ([(1)O2]ss) and the SMR degradation rate constants with singlet oxygen (k1O2) were linearly correlated with the total fluorescence and inversely correlated with the carbohydrate/protein content ((1)H NMR) for all forms of NOM. The total fluorescence and EEMs Peak A were confirmed as indicators of (1)O2 formation. Specific ultraviolet absorbance at 254 nm (SUVA254) and aromaticity showed potential correlations with the steady-state concentrations of hydroxyl radical ([HO]ss) and the corresponding formation rates (HO). Copyright © 2015 Elsevier Ltd. All rights reserved.

Solid-state NMR characterization of copolymers of nylon 11 and nylon 12.

PubMed

Johnson, C G; Mathias, L J

1997-05-01

Solid-state 13C and 15N NMR spectroscopy, in conjunction with differential scanning calorimetry, wide-angle X-ray diffraction and infrared spectroscopy, were used to characterize a series of nylon 11 and 12 copolymers with mole percentages of nylon 12 monomer of 0, 15, 35, 50, 65, 85, and 100%. Monotonic melting point (Tm) and heat of fusion depressions were observed for the copolymer series with the 65 mol% nylon 12 copolymer having the lowest apparent crystallinity and Tm at 148 degrees C. Solid-state 15N NMR spectra showed a smooth shift of the main peak position for the as-prepared copolymers from 84 ppm for the alpha-form of pure nylon 11 to 89 ppm for the gamma-form of pure nylon 12. Similar behavior was seen for FTIR amide V and VI modes which are also sensitive to the alpha- and gamma-crystal forms. 13C NMR T1 measurements showed that the overall most mobile sample was the 65:35 copolymer. The amide group of the 1:1 copolymer was labelled using 15N-labelled amino acids available through the Gabriel synthesis; an annealed, solution-cast film of this sample showed a T1N value of 349 s, similar to values seen for annealed nylon 11 and nylon 12 homopolymers. The WAXS pattern for the 65 mol% nylon 12 sample showed a sharp peak at 2 theta = 21.3, overlapping a broad peak centered at 2 theta = 21.0. These are consistent with the values seen for gamma-form nylon 12. The 1:1 copolymer (15N labelled) was shown to be polymorphic, like the homopolymers after specific treatments, with a gamma-like phase formed upon solvent casting, and an alpha-like phase dominating for as-polymerized material and precipitated flakes.

Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

PubMed

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N; Nishida, Clinton R; de Montellano, Paul R Ortiz

2015-04-17

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE PAGES

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; ...

2015-02-10

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

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

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Advanced solid-state NMR spectroscopy of natural organic matter.

PubMed

Mao, Jingdong; Cao, Xiaoyan; Olk, Dan C; Chu, Wenying; Schmidt-Rohr, Klaus

2017-05-01

Solid-state NMR is essential for the characterization of natural organic matter (NOM) and is gaining importance in geosciences and environmental sciences. This review is intended to highlight advanced solid-state NMR techniques, especially a systematic approach to NOM characterization, and their applications to the study of NOM. We discuss some basics of how to acquire high-quality and quantitative solid-state 13 C NMR spectra, and address some common technical mistakes that lead to unreliable spectra of NOM. The identification of specific functional groups in NOM, primarily based on 13 C spectral-editing techniques, is described and the theoretical background of some recently-developed spectral-editing techniques is provided. Applications of solid-state NMR to investigating nitrogen (N) in NOM are described, focusing on limitations of the widely used 15 N CP/MAS experiment and the potential of improved advanced NMR techniques for characterizing N forms in NOM. Then techniques used for identifying proximities, heterogeneities and domains are reviewed, and some examples provided. In addition, NMR techniques for studying segmental dynamics in NOM are reviewed. We also briefly discuss applications of solid-state NMR to NOM from various sources, including soil organic matter, aquatic organic matter, organic matter in atmospheric particulate matter, carbonaceous meteoritic organic matter, and fossil fuels. Finally, examples of NMR-based structural models and an outlook are provided. Copyright © 2016 Elsevier B.V. All rights reserved.

31P Solid-state NMR based monitoring of permeation of cell penetrating peptides into skin

PubMed Central

Desai, Pinaki R.; Cormier, Ashley R.; Shah, Punit P.; Patlolla, Ram R.; Paravastu, Anant K.; Singh, Mandip

2013-01-01

The main objective of the current study was to investigate penetration of cell penetrating peptides (CPPs: TAT, R8, R11 and YKA) through skin intercellular lipids using 31P magic angle spinning (MAS) solid-state NMR. In vitro skin permeation studies were performed on rat skin, sections (0–60, 61–120 and 121–180 µm) were collected and analyzed for 31P NMR signal. The concentration dependent shift of 0, 25, 50, 100 and 200 mg/ml of TAT on skin layers, diffusion of TAT, R8, R11 and YKA in the skin and time dependent permeation of R11 was measured on various skin sections using 31P solid-state NMR. Further, CPPs and CPP-tagged fluorescent dye encapsulate liposomes (FLip) in skin layers were tagged using confocal microscopy. The change in 31P NMR chemical shift was found to depend monotonically on the amount of CPP applied on skin, with saturation behavior above 100 mg/ml CPP concentration. R11 and TAT caused more shift in solid-state NMR peaks compared to other peptides. Furthermore, NMR spectra showed R11 penetration up to 180 µm within 30 min. The results of the solid-state NMR study were in agreement with confocal microscopy studies. Thus, 31P solid-state NMR can be used to track CPP penetration into different skin layers. PMID:23702274

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. ...

Advanced solid-state NMR spectroscopy of natural organic matter

USDA-ARS?s Scientific Manuscript database

Solid-state NMR is essential for the characterization of natural organic matter (NOM) and is gaining importance in geosciences and environmental sciences. This review is intended to highlight advanced solid-state NMR techniques, especially the systematic approach to NOM characterization, and their ...

A prototype hybrid 7π quinone-fused 1,3,2-dithiazolyl radical.

PubMed

Decken, A; Mailman, A; Passmore, J; Rautiainen, J M; Scherer, W; Scheidt, E-W

2011-01-28

Reaction of 1,4-naphthoquinone and SNSMF(6) (M = As, Sb) in SO(2) solution in a 1 : 2 molar ratio led to the naphthoquinone fused 1,3,2-dithiazolylium salts, 3MF(6) quantitatively by multinuclear NMR (87% isolated yield of 3SbF(6)) via the cycloaddition and oxidative dehydrogenation chemistry of SNS(+) with formation of NH(4)SbF(6) and S(8). The product 3SbF(6) was fully characterized by IR, Raman, multinuclear {(1)H, (13)C, (14)N} NMR, elemental analysis, cyclic voltammetry and single crystal X-ray crystallography. The reduction of 3SbF(6) with ferrocene (Cp(2)Fe) in refluxing acetonitrile (CH(3)CN) led to the first isolation of a fused quinone-thiazyl radical, 3˙ in 73% yield. The prototype hybrid quinone-thiazyl radical 3˙ was fully characterized by IR, Raman microscopy, EI-MS, elemental analysis, solution and solid state EPR, magnetic susceptibility (2-370 K) and was found to form π*-π* dimers in the solid state as determined by single crystal X-ray crystallography. Furthermore, the thermal decomposition of 3˙ led to a novel quinone-fused 1,2,3,4-tetrathiine, 10 (x = 2) and the known 1,2,5-thiadiazole, 11. The energetics of the cycloadditon and oxidative dehydrogenation chemistry of SNS(+) and 1,4-naphthoquinone leading to 3SbF(6) were estimated in the gas phase and SO(2) solution by DFT calculations (PBE0/6-311G(d)) and lattice enthalpies obtained by the volume based thermodynamic (VBT) approach in the solid state. The gas phase ion energetics (ionization potential (IP) and electron affinity (EA)) of 3˙ are compared to related 1,3,2- and 1,2,3-dithiazolyl radicals.

Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications.

PubMed

Hiruma-Shimizu, Kazumi; Shimizu, Hiroki; Thompson, Gary S; Kalverda, Arnout P; Patching, Simon G

2015-01-01

Detergents are amphiphilic compounds that have crucial roles in the extraction, purification and stabilization of integral membrane proteins and in experimental studies of their structure and function. One technique that is highly dependent on detergents for solubilization of membrane proteins is solution-state NMR spectroscopy, where detergent micelles often serve as the best membrane mimetic for achieving particle sizes that tumble fast enough to produce high-resolution and high-sensitivity spectra, although not necessarily the best mimetic for a biomembrane. For achieving the best quality NMR spectra, detergents with partial or complete deuteration can be used, which eliminate interfering proton signals coming from the detergent itself and also eliminate potential proton relaxation pathways and strong dipole-dipole interactions that contribute line broadening effects. Deuterated detergents have also been used to solubilize membrane proteins for other experimental techniques including small angle neutron scattering and single-crystal neutron diffraction and for studying membrane proteins immobilized on gold electrodes. This is a review of the properties, chemical synthesis and applications of detergents that are currently commercially available and/or that have been synthesized with partial or complete deuteration. Specifically, the detergents are sodium dodecyl sulphate (SDS), lauryldimethylamine-oxide (LDAO), n-octyl-β-D-glucoside (β-OG), n-dodecyl-β-D-maltoside (DDM) and fos-cholines including dodecylphosphocholine (DPC). The review also considers effects of deuteration, detergent screening and guidelines for detergent selection. Although deuterated detergents are relatively expensive and not always commercially available due to challenges associated with their chemical synthesis, they will continue to play important roles in structural and functional studies of membrane proteins, especially using solution-state NMR.

Possible 6-qubit NMR quantum computer device material; simulator of the NMR line width

NASA Astrophysics Data System (ADS)

Hashi, K.; Kitazawa, H.; Shimizu, T.; Goto, A.; Eguchi, S.; Ohki, S.

2002-12-01

For an NMR quantum computer, splitting of an NMR spectrum must be larger than a line width. In order to find a best device material for a solid-state NMR quantum computer, we have made a simulation program to calculate the NMR line width due to the nuclear dipole field by the 2nd moment method. The program utilizes the lattice information prepared by commercial software to draw a crystal structure. By applying this program, we can estimate the NMR line width due to the nuclear dipole field without measurements and find a candidate material for a 6-qubit solid-state NMR quantum computer device.

NMR studies of the protonation states of pyridoxal-5‧-phosphate in water

NASA Astrophysics Data System (ADS)

Chan-Huot, Monique; Niether, Christiane; Sharif, Shasad; Tolstoy, Peter M.; Toney, Michael D.; Limbach, Hans-Heinrich

2010-07-01

We have measured the 13C NMR spectra of the cofactor pyridoxal-5'-phosphate (vitamin B 6, PLP) at 278 K in aqueous solution as a function of pH. By 13C enrichment of PLP in the C-4' and C-5' positions we were able to measure spectra down to pH 1. From the dependence of the 13C chemical shifts on pH, the p Ka values of PLP could be determined. In particular, the heretofore uncharacterized protonation state of PLP, in which the phosphate group as well as the pyridine ring and the phenolic groups are fully protonated, has been analyzed. The corresponding p Ka value of 2.4 indicates that the phosphate group is solely involved in the first deprotonation step. The 15N chemical shifts of the pyridine ring of PLP published previously are in good agreement with the new results. These shifts contain information about the tautomerism of the different protonation states of PLP. The implications of these findings for the biological function of PLP are discussed.

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.

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.

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

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...

An extrapolation scheme for solid-state NMR chemical shift calculations

NASA Astrophysics Data System (ADS)

Nakajima, Takahito

2017-06-01

Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

Dithia[3.3]paracyclophane-based monometal ruthenium acetylide complexes: synthesis, characterization and substituent effects.

PubMed

Zhu, Xingxun; Ou, Yaping; Zhang, Jing; Xia, Jian-Long; Yin, Jun; Yu, Guang-Ao; Liu, Sheng Hua

2013-05-21

A series of dithia[3.3]metaparacyclophane-based monometal ruthenium acetylide complexes have been synthesized. All of the complexes have been fully characterised by NMR spectrometry, X-ray crystallography and elemental analyses. At the same time, their basic optical properties, such as UV/Vis absorption spectra, and electrochemical properties have been determined. (1)H NMR and X-ray crystal structure studies reveal that there are intramolecular C-H···π interactions in these ruthenium complexes, in both solution and solid states. Electrochemical studies reveal that the substituted groups on the dithia[3.3]paracyclophane ring can clearly affect the oxidation activities of the ruthenium center by way of the intramolecular C-H···π interaction. In addition, electron-donating groups facilitate the oxidation of the ruthenium center compared with electron-deficient groups. UV/Vis absorption and IR spectra of some complexes in neutral and oxidized states also have been studied. IR spectra studies indicated that the substituents in the cyclophane have some effects on the ν(C≡C) bands of these complexes in the neutral state and little effect on ν(C≡C) of these complexes in the oxidized state.

Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling.

PubMed

Filip, Xenia; Borodi, Gheorghe; Filip, Claudiu

2011-10-28

A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data. This journal is © the Owner Societies 2011

Synthesis, crystal structure, and spectral studies of 10-(2-Benzothiazolylazo)-9-phenanthrol

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

Davydov, V. V.; Sokol, V. I.; Polyanskaya, N. A.

2012-03-15

10-(2-Benzothiazolylazo)-9-phenanthrol (L) is prepared by a reaction of 2-hydrazinobenzothiazol with 9,10-phenanthrenequinone. The crystal and molecular structure of the L{center_dot}CHCl{sub 3} solvate is determined by X-ray diffraction. The data of the X-ray diffraction study, as well as IR, {sup 1}H NMR, and electronic absorption spectra, indicate that in the crystal state and solutions the L molecule exists in the form of a quinohydrazone tautomer (b) (s-trans, cis) stabilized by the intramolecular N{sub 2}-HN{sub 2} Horizontal-Ellipsis O1 hydrogen bond. The 'mobile' H atom is located at the N2 atom of the azo group. The benzothiazolyl and phenanthrenequinone fragments are nearly coplanar. Spectroscopicmore » criteria for the state of L in various media are determined based on the data of IR, {sup 1}H NMR, and electronic absorption spectroscopy and the results of the Pariser-Parr-Pople quantum-chemical calculations.« less

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

Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR

NASA Astrophysics Data System (ADS)

Simmons, Thomas J.; Mortimer, Jenny C.; Bernardinelli, Oigres D.; Pöppler, Ann-Christin; Brown, Steven P.; Deazevedo, Eduardo R.; Dupree, Ray; Dupree, Paul

2016-12-01

Exploitation of plant lignocellulosic biomass is hampered by our ignorance of the molecular basis for its properties such as strength and digestibility. Xylan, the most prevalent non-cellulosic polysaccharide, binds to cellulose microfibrils. The nature of this interaction remains unclear, despite its importance. Here we show that the majority of xylan, which forms a threefold helical screw in solution, flattens into a twofold helical screw ribbon to bind intimately to cellulose microfibrils in the cell wall. 13C solid-state magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, supported by in silico predictions of chemical shifts, shows both two- and threefold screw xylan conformations are present in fresh Arabidopsis stems. The twofold screw xylan is spatially close to cellulose, and has similar rigidity to the cellulose microfibrils, but reverts to the threefold screw conformation in the cellulose-deficient irx3 mutant. The discovery that induced polysaccharide conformation underlies cell wall assembly provides new principles to understand biomass properties.

Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR.

PubMed

Simmons, Thomas J; Mortimer, Jenny C; Bernardinelli, Oigres D; Pöppler, Ann-Christin; Brown, Steven P; deAzevedo, Eduardo R; Dupree, Ray; Dupree, Paul

2016-12-21

Exploitation of plant lignocellulosic biomass is hampered by our ignorance of the molecular basis for its properties such as strength and digestibility. Xylan, the most prevalent non-cellulosic polysaccharide, binds to cellulose microfibrils. The nature of this interaction remains unclear, despite its importance. Here we show that the majority of xylan, which forms a threefold helical screw in solution, flattens into a twofold helical screw ribbon to bind intimately to cellulose microfibrils in the cell wall. 13 C solid-state magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, supported by in silico predictions of chemical shifts, shows both two- and threefold screw xylan conformations are present in fresh Arabidopsis stems. The twofold screw xylan is spatially close to cellulose, and has similar rigidity to the cellulose microfibrils, but reverts to the threefold screw conformation in the cellulose-deficient irx3 mutant. The discovery that induced polysaccharide conformation underlies cell wall assembly provides new principles to understand biomass properties.

Silica nanoparticles carrying boron-containing polymer brushes

NASA Astrophysics Data System (ADS)

Brozek, Eric M.; Mollard, Alexis H.; Zharov, Ilya

2014-05-01

A new class of surface-modified silica nanoparticles has been developed for potential applications in boron neutron capture therapy. Sub-50 nm silica particles were synthesized using a modified Stöber method and used in surface-initiated atom transfer radical polymerization of two biocompatible polymers, poly(2-(hydroxyethyl)methacrylate) and poly(2-(methacryloyloxy)ethyl succinate). The carboxylic acid and hydroxyl functionalities of the polymeric side chains were functionalized with carboranyl clusters in high yields. The resulting particles were characterized using DLS, TEM, solution 1H NMR, solid state 11B NMR and thermogravimetric analysis. The particles contain between 13 and 18 % of boron atoms by weight, which would provide a high amount of 10B nuclides for BNCT, while the polymer chains are suitable for further modification with cell targeting ligands.

Synthesis, spectroscopic, and molecular structure characterizations of some azo derivatives of 2-hydroxyacetophenone

NASA Astrophysics Data System (ADS)

Albayrak, Çiğdem; Gümrükçüoğlu, İsmail E.; Odabaşoğlu, Mustafa; İskeleli, Nazan Ocak; Ağar, Erbil

2009-08-01

Some novel azo compounds were prepared by the reaction of 2-hydroxyacetophenone with aniline and its substituted derivatives. The structures of synthesized azo compounds were determined by IR, UV-Vis, 1H NMR and 13C NMR spectroscopic techniques and the structures of some of these compounds were also determined by X-ray diffraction studies. Structural analysis using IR in solid state shows that the azo form is favoured in the azo compounds whereas UV-Vis analysis of the azo compounds in solution has shown that there is a azo and ionic form. The azo compounds in the basic solvents dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are both azo and ionic form while these compounds in ethyl alcohol (EtOH) and chloroform (CHCl 3) are only azo form.

Host-guest inclusion system of ferulic acid with p-Sulfonatocalix[n]arenes: Preparation, characterization and antioxidant activity

NASA Astrophysics Data System (ADS)

Chao, Jianbin; Wang, Huijuan; Song, Kailun; Wang, Yongzhao; Zuo, Ying; Zhang, Liwei; Zhang, Bingtai

2017-02-01

The inclusion complexes of ferulic acid (FA) with p-Sulfonatocalix[n]arenes (SCXn, n = 4, 6, 8) were prepared and characterized both in the solid state and in solution using fluorescence spectroscopy, 1H nuclear magnetic resonance (1H NMR), attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR), atomic force microscopy (AFM) and differential scanning calorimetry (DSC). The results show that FA is able to form inclusion complexes with SCXn in a molar ratio of 1:1, causing a significant decrease in the fluorescence intensity of FA. The association constant of the inclusion complexes was calculated from the fluorescence titration data. 1H NMR spectroscopy analysis demonstrates that the aromatic ring and methoxy group of FA are partially covered by SCXn.

Degree of Biomimicry of Artificial Spider Silk Spinning Assessed by NMR Spectroscopy.

PubMed

Otikovs, Martins; Andersson, Marlene; Jia, Qiupin; Nordling, Kerstin; Meng, Qing; Andreas, Loren B; Pintacuda, Guido; Johansson, Jan; Rising, Anna; Jaudzems, Kristaps

2017-10-02

Biomimetic spinning of artificial spider silk requires that the terminal domains of designed minispidroins undergo specific structural changes in concert with the β-sheet conversion of the repetitive region. Herein, we combine solution and solid-state NMR methods to probe domain-specific structural changes in the NT2RepCT minispidroin, which allows us to assess the degree of biomimicry of artificial silk spinning. In addition, we show that the structural effects of post-spinning procedures can be examined. By studying the impact of NT2RepCT fiber drying, we observed a reversible beta-to-alpha conversion. We think that this approach will be useful for guiding the optimization of artificial spider silk fibers. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions.

PubMed

Pendrill, Robert; Engström, Olof; Volpato, Andrea; Zerbetto, Mirco; Polimeno, Antonino; Widmalm, Göran

2016-01-28

The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

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.

Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

NASA Astrophysics Data System (ADS)

Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E.; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K.

2015-06-01

Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable “beads-on-a-string” concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.

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.

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.

Applications of solid-state NMR to membrane proteins.

PubMed

Ladizhansky, Vladimir

2017-11-01

Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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.

Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR.

PubMed

Thompson, Matthew K; Ehlinger, Aaron C; Chazin, Walter J

2017-01-01

Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples. © 2017 Elsevier Inc. All rights reserved.

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

CO2 Responsive Imidazolium-Type Poly(Ionic Liquid) Gels.

PubMed

Zhang, Jing; Xu, Dan; Guo, Jiangna; Sun, Zhe; Qian, Wenjing; Zhang, Ye; Yan, Feng

2016-07-01

Poly(ionic liquid) (PIL) gels with CO2 stimulus responsiveness have been synthesized through the copolymerization of an imidazolium-type ionic liquid monomer with 2-(dimethyl amino) ethyl methacrylate. Upon bubbling with CO2 gas, the prepared PIL solution is converted to a transparent and stable gel, which can be turned back to the initial solution state after N2 bubbling. The reversible sol-gel phase transition behavior is proved by the reversible values of viscosity and ionic conductivity. The possible mechanism for such a reversible sol-gel phase transition is demonstrated by NMR, conductivity, and rheological measurements. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A "special perspectives" issue: Recent achievements and new directions in biomolecular solid state NMR

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

Twenty years ago, applications of solid state nuclear magnetic resonance (NMR) methods to real problems involving biological systems or biological materials were few and far between. Starting in the 1980s, a small number of research groups had begun to explore the possibility of obtaining structural and dynamical information about peptides, proteins, and other biopolymers from solid state NMR spectra. Progress was initially slow due to the relatively primitive state of solid state NMR probes, spectrometers, sample preparation methods, and pulse sequence techniques, coupled with the small number of people contributing to this research area. By the early 1990s, with the advent of new ideas about pulse sequence techniques such as dipolar recoupling, improvements in techniques for orienting membrane proteins and in technology for magic-angle spinning (MAS), improvements in the capabilities of commercial NMR spectrometers, and general developments in multidimensional spectroscopy, it began to appear that biomolecular solid state NMR might have a viable future. It was not until 1993 that the annual number of publications in this area crept above twenty.

Contrasting coordination behavior of Group 12 perchlorate salts with an acyclic N3O2 donor ligand by X-ray crystallography and (1)H NMR.

PubMed

Tice, Daniel B; Pike, Robert D; Bebout, Deborah C

2016-08-09

An unbranched N3O2 ligand 2,6-bis[((2-pyridinylmethyl)oxy)methyl]pyridine (L1) was used to prepare new mononuclear heteroleptic Group 12 perchlorate complexes characterized by IR, (1)H NMR and X-ray crystallography. Racemic complexes with pentadentate L1 and one to four oxygens from either water or perchlorate bound to a metal ion were structurally characterized. Octahedral [Zn(L1)(OH2)](ClO4)2 (1) and pentagonal bipyramidal [Cd(L1)(OH2)(OClO3)]ClO4 (2) structures were found with lighter congeners. The polymorphic forms of [Hg(L1)(ClO4)2] characterized (3 in P1[combining macron] and 4 in P21/c) had a mix of monodentate, anisobidentate and bidentate perchlorates, providing the first examples of a tricapped trigonal prismatic Hg(ii) coordination geometry, as well as additional examples of a rare square antiprismatic Hg(ii) coordination geometry. Solution state (1)H NMR characterization of the Group 12 complexes in CD3CN indicated intramolecular reorganization remained rapid under conditions where intermolecular M-L1 exchange was slow on the chemical shift time scale for Zn(ii) and on the J(M(1)H) time scale for Cd(ii) and Hg(ii). Solution studies with more than one equivalent of ligand also suggested that a complex with a 1 : 2 ratio of M : L1 contributed significantly to solution equilibria with Hg(ii) but not the other metal ions. The behavior of related linear pentadentate ligands with Group 12 perchlorate salts is discussed.

Determination of Molecular Self-Diffusion Coefficients Using Pulsed-Field-Gradient NMR: An Experiment for Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Harmon, Jennifer; Coffman, Cierra; Villarrial, Spring; Chabolla, Steven; Heisel, Kurt A.; Krishnan, Viswanathan V.

2012-01-01

NMR spectroscopy has become one of the primary tools that chemists utilize to characterize a range of chemical species in the solution phase, from small organic molecules to medium-sized proteins. A discussion of NMR spectroscopy is an essential component of physical and biophysical chemistry lecture courses, and a number of instructional…

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.

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.

Monomeric and dimeric structures analysis and spectroscopic characterization of 3,5-difluorophenylboronic acid with experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV) techniques and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Karabacak, Mehmet; Kose, Etem; Atac, Ahmet; Asiri, Abdullah M.; Kurt, Mustafa

2014-01-01

The spectroscopic properties of 3,5-difluorophenylboronic acid (3,5-DFPBA, C6H3F2B(OH)2) were investigated by FT-IR, FT-Raman UV-Vis, 1H and 13C NMR spectroscopic techniques. FT-IR (4000-400 cm-1) and FT-Raman spectra (3500-10 cm-1) in the solid phase and 1H and 13C NMR spectra in DMSO solution were recorded. The UV spectra that dissolved in ethanol and water were recorded in the range of 200-400 nm for each solution. The structural and spectroscopic data of the molecule have been obtained for possible three conformers from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Hydrogen-bonded dimer of title molecule, optimized by counterpoise correction, was also studied B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. 1H and 13C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. The effects due to the substitutions of boric acid group and halogen were investigated. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), nonlinear optical properties (NLO) and thermodynamic features were performed.

Analytical Applications of NMR: Summer Symposium on Analytical Chemistry.

ERIC Educational Resources Information Center

Borman, Stuart A.

1982-01-01

Highlights a symposium on analytical applications of nuclear magnetic resonance spectroscopy (NMR), discussing pulse Fourier transformation technique, two-dimensional NMR, solid state NMR, and multinuclear NMR. Includes description of ORACLE, an NMR data processing system at Syracuse University using real-time color graphics, and algorithms for…

Synthesis, characterization, and photophysical properties of a thiophene-functionalized bis(pyrazolyl) pyridine (BPP) tricarbonyl rhenium(I) complex.

PubMed

Lytwak, Lauren A; Stanley, Julie M; Mejía, Michelle L; Holliday, Bradley J

2010-09-07

A bromo tricarbonyl rhenium(I) complex with a thiophene-functionalized bis(pyrazolyl) pyridine ligand (L), ReBr(L)(CO)(3) (1), has been synthesized and characterized by variable temperature and COSY 2-D (1)H NMR spectroscopy, single-crystal X-ray diffraction, and photophysical methods. Complex 1 is highly luminescent in both solution and solid-state, consistent with phosphorescence from an emissive (3)MLCT excited state with an additional contribution from a LC (3)(pi-->pi*) transition. The single-crystal X-ray diffraction structure of the title ligand is also reported.

NMR Studies of Dynamic Biomolecular Conformational Ensembles

PubMed Central

Torchia, Dennis A.

2015-01-01

Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. PMID:25669739

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.

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.

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.

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

Experimental and Theoretical Study of Molecular Response of Amine Bases in Organic Solvents

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

Kathmann, Shawn M.; Cho, Herman M.; Chang, Tsun-Mei

2014-05-08

Reorientational correlation times of various amine bases (viz., pyridine, 2,6-lutidene, 2,2,6,6-tetramethylpiperidine) and organic solvents (dichloromethane, toluene) were determined by solution-state NMR relaxation time measurements and compared with predictions from molecular dynamics (MD) simulations. The bases and solvents are reagents in complex reactions involving Frustrated Lewis Pairs (FLP), which display remarkable catalytic activity in metal-free H2 scission. The comparison of measured and simulated correlation times is a key test of the ability of recent MD and quantum electronic structure calculations to elucidate the mechanism of FLP activity. Correla- tion times were found to be in the range 1.4-3.4 ps (NMR) andmore » 1.23-5.28 ps (MD) for the amines, and 0.9-2.3 ps (NMR) and 0.2-1.7 ps (MD) for the solvent molecules. This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacic Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

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

Atomic substitutions in synthetic apatite; Insights from solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Vaughn, John S.

Apatite, Ca5(PO4)3X (where X = F, Cl, or OH), is a unique mineral group capable of atomic substitutions for cations and anions of varied size and charge. Accommodation of differing substituents requires some kind of structural adaptation, e.g. new atomic positions, vacancies, or coupled substitutions. These structural adaptations often give rise to important physicochemical properties relevant to a range of scientific disciplines. Examples include volatile trapping during apatite crystallization, substitution for large radionuclides for long-term storage of nuclear fission waste, substitution for fluoride to improve acid resistivity in dental enamel composed dominantly of hydroxylapatite, and the development of novel biomaterials with enhanced biocompatibility. Despite the importance and ubiquity of atomic substitutions in apatite materials, many of the mechanisms by which these reactions occur are poorly understood. Presence of substituents at dilute concentration and occupancy of disordered atomic positions hinder detection by bulk characterization methods such as X-ray diffraction (XRD) and infrared (IR) spectroscopy. Solid-state nuclear magnetic resonance (NMR) spectroscopy is an isotope-specific structural characterization technique that does not require ordered atomic arrangements, and is therefore well suited to investigate atomic substitutions and structural adaptations in apatite. In the present work, solid-state NMR is utilized to investigate structural adaptations in three different types of apatite materials; a series of near-binary F, Cl apatite, carbonate-hydroxylapatite compositions prepared under various synthesis conditions, and a heat-treated hydroxylapatite enriched in 17O. The results indicate that hydroxyl groups in low-H, near binary F,Cl apatite facilitate solid-solution between F and Cl via column reversals, which result in average hexagonal symmetry despite very dilute OH concentration ( 2 mol percent). In addition, 19F NMR spectra indicate that fluorine occupies a complex distribution of atomic positions, which give rise to complex 19F peak shapes owing to varied F-Ca distance. 13C NMR analysis of carbonate-hydroxylapatite indicates that AB-type carbonate hydroxylapatite can be prepared without the presence of sodium or heat treatment. Isotopic 17O enrichment of hydroxylapatite and 17O NMR analysis reveals distinct signals corresponding to phosphate and hydroxyl oxygens, and heat treatment under vacuum results in loss of hydroxyl signal due to decomposition to tricalcium phosphate, which was observed by powder X-Ray diffraction (PXRD).

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.

Towards Tailored Interphase Formation Utilizing Surface-Active Benzylsulfonium Salts as Cationic Initiators

DTIC Science & Technology

1994-07-15

34,AR V3 APR edrtion may be ved until eha uv’ed. CURITY" Sf ’’ NO F G .. Towsrds Talared lnterphae F .- wmon qjdM to 0 Surfzce-Actlve BenzyWM*irn Sa, -l...min with nltrog, purge. Solution "C NMR were preformed on a Bruker AC-200 wle so state ’C CPMAS, A b f • and "Sl CPMAS were run on a Bnker \\4SL.-400

Green Perylene Bisimide Dyes: Synthesis, Photophysical and Electrochemical Properties

PubMed Central

Chang, Che-Wei; Tsai, Hsing-Yang; Chen, Kew-Yu

2014-01-01

Three asymmetric amino-substituted perylene bisimide dyes with different n-alkyl chain lengths (n = 6, 12, or 18), 1-(N,N-dialkylamino)perylene bisimides (1a–1c), were synthesized under mild condition in high yields and were characterized by 1H NMR, 13C NMR (nuclear magnetic resonance), HRMS (High Resolution Mass Spectrometer), UV-Vis and fluorescence spectra, as well as cyclic voltammetry (CV). These molecules show intense green color in both solution and solid state and are highly soluble in dichloromethane and even in nonpolar solvents, such as hexane. The shapes of the absorption spectra of 1a–1c in solid state and in solution were found to be virtually the same, indicating that the long alkyl chains could efficiently prevent aggregation. They exhibit a unique charge transfer emission in the near-infrared region, of which the peak wavelengths show strong solvatochromism. The dipole moments of the compounds have been estimated using the Lippert-Mataga equation, and upon excitation, they show larger dipole moment changes than that of 1-aminoperylene bisimide (2). Furthermore, all of the compounds exhibit two quasi-reversible one-electron oxidations and two quasi-reversible one-electron reductions in dichloromethane at modest potentials. Complementary density functional theory (DFT) calculations performed on these dyes are reported in order to rationalize their molecular structures and electronic properties. PMID:28788140

1,7-Bis-(N,N-dialkylamino)perylene Bisimides: Facile Synthesis and Characterization as Near-Infrared Fluorescent Dyes

PubMed Central

Chen, Kew-Yu; Chang, Che-Wei

2014-01-01

Three symmetric alkylamino-substituted perylene bisimides with different n-alkyl chain lengths (n = 6, 12, or 18), 1,7-bis-(N,N-dialkylamino)perylene bisimides (1a–1c), were synthesized under mild condition and were characterized by 1H NMR, 13C NMR and high resolution mass spectroscopy. Their optical and electrochemical properties were measured using UV-Vis and emission spectroscopic techniques as well as cyclic voltammetry (CV). These compounds show deep green color in both solution and solid state, and are highly soluble in dichloromethane and even in nonpolar solvents such as hexane. The shapes of the absorption spectra of 1a–1c in the solution and solid state were found to be almost the same, indicating that the long alkyl chains could efficiently prevent intermolecular contact and aggregation. They show a unique charge transfer emission in the near-infrared region, of which the peak wavelengths exhibit strong solvatochromism. The dipole moments of the molecules have been estimated using the Lippert–Mataga equation, and upon excitation, they show larger dipole moment changes than that of 1,7-diaminoperylene bisimide (2). Moreover, all the dyes exhibit two irreversible one-electron oxidations and two quasi-reversible one-electron reductions in dichloromethane at modest potentials. Complementary density functional theory calculations performed on these chromophores are reported in order to rationalize their electronic structure and optical properties. PMID:28788262

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

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

Determining pH at elevated pressure and temperature using in situ ¹³C NMR.

PubMed

Surface, J Andrew; Wang, Fei; Zhu, Yanzhe; Hayes, Sophia E; Giammar, Daniel E; Conradi, Mark S

2015-02-03

We have developed an approach for determining pH at elevated pressures and temperatures by using (13)C NMR measurements of inorganic carbon species together with a geochemical equilibrium model. The approach can determine in situ pH with precision better than 0.1 pH units at pressures, temperatures, and ionic strengths typical of geologic carbon sequestration systems. A custom-built high pressure NMR probe was used to collect (13)C NMR spectra of (13)C-labeled CO2 reactions with NaOH solutions and Mg(OH)2 suspensions at pressures up to 107 bar and temperatures of 80 °C. The quantitative nature of NMR spectroscopy allows the concentration ratio [CO2]/[HCO3(-)] to be experimentally determined. This ratio is then used with equilibrium constants calculated for the specific pressure and temperature conditions and appropriate activity coefficients for the solutes to calculate the in situ pH. The experimentally determined [CO2]/[HCO3(-)] ratios agree well with the predicted values for experiments performed with three different concentrations of NaOH and equilibration with multiple pressures of CO2. The approach was then applied to experiments with Mg(OH)2 slurries in which the change in pH could track the dissolution of CO2 into solution, rapid initial Mg(OH)2 dissolution, and onset of magnesium carbonate precipitation.

Metal Substitution in Keggin-Type Tridecameric Aluminum-Oxo-Hydroxy Clusters.

PubMed

Parker, Wallace O'Neil; Millini, Roberto; Kiricsi, Imre

1997-02-12

The species resulting from a typical preparation for metal-substituted hybrids of the Keggin tridecamer, Al 13 or [AlO 4 Al 12 (OH) 24 (OH 2 ) 12 ] 7+ , were examined by performing 27 Al NMR on the solutions during aging and by studying the precipitated sulfate salts via solid state 27 Al NMR and powder X-ray diffraction (XRD). Aqueous mixtures (0.25 mol L -1 ) of AlCl 3 and another metal ion (M), in a 12:1 mole ratio (Al:M), where M = Fe 3+ , Zn 2+ , Ga 3+ , In 3+ , Sn 2+ , La 3+ , and Bi 3+ , were subjected to forced hydrolysis by addition of NaOH (1.0 mol L -1 ) until OH/(Al + M) = 2.25, and the kinetics of Al 13 formation and disappearance with aging at 80 °C was monitored by 27 Al NMR spectroscopy. Al 13 units polymerize on aging with an apparent rate constant (k) of 4.8(8) × 10 -2 h -1 to form a species referred to as AlP 2 . Only the solutions containing Ga 3+ and Sn 2+ exhibited faster Al 13 conversion rates. GaAl 12 forms quickly at 80 °C (k = 0.54 h -1 ) and is more stable than AlP 2 . Sn 2+ apparently promotes AlP 2 formation (k = 0.38 h -1 ). XRD and solid state NMR reveal that only the Ga hybrid can be prepared by this method. No hybrid formation was evidenced using M = Mg 2+ , Fe 3+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , In 3+ , La 3+ , or Ce 3+ at 25 °C or M = Co 2+ or La 3+ under reflux conditions. Isostructural (cubic symmetry) single crystals were obtained for the sulfate salts of Al 13 and GaAl 12 . Single-crystal XRD analysis of these two polyoxocations provides the first rigorous comparison between them and shows they have very similar structures. The main crystallographic data for Al 13 and GaAl 12 are as follows:  Na[AlO 4 Al 12 (OH) 24 (H 2 O) 12 ](SO 4 ) 4 ·10H 2 O, cubic, F4̄3m, a = 17.856(2) Å, Z = 4; Na[GaO 4 Al 12 (OH) 24 (H 2 O) 12 ](SO 4 ) 4 ·10H 2 O, cubic, F4̄3m, a = 17.869(3) Å, Z = 4. Thus, the greater thermal stability of GaAl 12 cannot be rationalized in terms of the overall geometric considerations, as suggested by others. Solid state NMR also shows the coordination symmetries of the outer 12 Al nuclei in both clusters to be similar.

Structure of 1,5-benzodiazepinones in the solid state and in solution: Effect of the fluorination in the six-membered ring

PubMed Central

Pérez-Torralba, Marta; Ángeles García, M; López, Concepción; Torralba, M Carmen; Rosario Torres, M; Alkorta, Ibon; Elguero, José

2013-01-01

Summary Two novel tetrafluorinated 1,5-benzodiazepinones were synthesized and their X-ray structures determined. 6,7,8,9-Tetrafluoro-4-methyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one crystallizes in the monoclinic P21/c space group and 6,7,8,9-tetrafluoro-1,4-dimethyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one in the triclinic P−1 space group. Density functional theory studies at the B3LYP/6-311++G(d,p) level were carried out on these compounds and on four non-fluorinated derivatives, allowing to calculate geometries, tautomeric energies and ring-inversion barriers, that were compared with the experimental results obtained by static and dynamic NMR in solution and in solid state. PMID:24204428

Conformation of flexibly linked triterpene dimers by using RDC-enhanced NMR spectroscopy

NASA Astrophysics Data System (ADS)

Lakshmi, Jerripothula K.; Pattnaik, Banita; Kavitha, Rachineni; Mallavadhani, Uppuluri V.; Jagadeesh, Bharatam

2018-06-01

Dimers of flexibly linked pentacyclic triterpene ursolic acid (UA) and its related frameworks such as asiatic acid (AA) and oleanolic acid (OA) have recently attracted significant attention due to their enhanced anti-cancer and anti-HCV activity compared to their respective monomers. Determination of conformation/inter-monomer orientation of these molecules is very important to understand their structure-activity relationship and to develop new scaffolds, which, however, is difficult through conventional NOE based solution-state NMR spectroscopy, due to lack of long-range NOEs. In the present work, we report a precise determination of conformation of two 1,2,3-triazole-linked triterpene dimer molecules, UA-AA and UA-OA, by employing one-bond Csbnd H residual dipolar couplings (RDCs) as additional long-range orientational restraints, measured in anisotropic PDMS/CDCl3 solvent medium.

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.

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.

1H NMR spectra dataset and solid-state NMR data of cowpea (Vigna unguiculata).

PubMed

Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

2017-04-01

In this article the NMR data from chemical shifts, coupling constants, and structures of all the characterized compounds were provided, beyond a complementary PCA evaluation for the corresponding manuscript (E.G. Alves Filho, L.M.A. Silva, E.M. Teofilo, F.H. Larsen, E.S. de Brito, 2017) [3]. In addition, a complementary assessment from solid-state NMR data was provided. For further chemometric analysis, numerical matrices from the raw 1 H NMR data were made available in Microsoft Excel workbook format (.xls).

Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation.

PubMed

Kametani, Shunsuke; Tasei, Yugo; Nishimura, Akio; Asakura, Tetsuo

2017-08-09

Polyalanine (polyA) sequences are well known as the simplest sequence that naturally forms anti-parallel β-sheets and constitute a key element in the structure of spider and wild silkworm silk fibers. We have carried out a systematic analysis of the packing of anti-parallel β-sheets for (Ala) n , n = 5, 6, 7 and 12, using primarily 13 C solid-state NMR and MD simulation. HFIP and TFA are frequently used as the dope solvents for recombinant silks, and polyA was solidified from both HFIP and TFA solutions by drying. An analysis of Ala Cβ peaks in the 13 C CP/MAS NMR spectra indicated that polyA from HFIP was mainly rectangular but polyA from TFA was mainly staggered. The transition from the rectangular to the staggered arrangement in (Ala) 6 was observed for the first time from the change in the Ala Cβ peak through heat treatment at 200 °C for 4 h. The removal of the bound water was confirmed by thermal analysis. This transition could be reproduced by MD simulation of (Ala) 6 molecules at 200 °C after removal of the bound water molecules. In this way, the origin of the stability of the different packing arrangements of polyA was clarified.

Investigating the Vanadium Environments in Hydroxylamido V(V) Dipicolinate Complexes Using 51V NMR Spectroscopy and Density Functional Theory

PubMed Central

Ooms, Kristopher J.; Bolte, Stephanie E.; Smee, Jason J.; Baruah, Bharat; Crans, Debbie C.; Polenova, Tatyana

2014-01-01

Using 51V magic angle spinning solid-state NMR, SSNMR, spectroscopy and quantum chemical DFT calculations we have characterized the chemical shift and quadrupolar coupling parameters of a series of 8 hydroxylamido vanadium(V) dipicolinate complexes of the general formula VO(dipic)(ONR1R2)(H2O) where R1 and R2 can be H, CH3, or CH2CH3. This class of vanadium compounds was chosen for investigation because of their seven coordinate vanadium atom, a geometry for which there is limited 51V SSNMR data. Furthermore, a systematic series of compounds with different electronic properties are available and allows for the effects of ligand substitution on the NMR parameters to be studied. The quadrupolar coupling constants, CQ, are small, 3.0 to 3.9 MHz, but exhibit variations as a function of the ligand substitution. The chemical shift tensors in the solid state are sensitive to changes in both the hydroxylamide substituent and the dipic ligand, a sensitivity which is not observed for isotropic chemical shifts in solution. The chemical shift tensors span approximately 1000 ppm, and are nearly axially symmetric. Based on DFT calculations of the chemical shift tensors, one of the largest contributors to the magnetic shielding anisotropy is an occupied molecular orbital with significant vanadium dz2 character along the V=O bond. PMID:17902653

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.

31P and 1H NMR Studies of the Molecular Organization of Lipids in the Parallel Artificial Membrane Permeability Assay.

PubMed

Assmus, Frauke; Ross, Alfred; Fischer, Holger; Seelig, Joachim; Seelig, Anna

2017-01-03

The parallel artificial membrane permeability assay (PAMPA) has emerged as a widely used primary in vitro screen for passive permeability of potential drug candidates. However, the molecular structure of the permeation barrier (consisting of a filter-supported dodecane-egg lecithin mixture) has never been characterized. Here, we investigated the long-range order of phospholipids in the PAMPA barrier by means of 31 P static solid-state NMR. Diffusion constants of PAMPA membrane components were derived from liquid state NMR and, in addition, drug distribution between the PAMPA lipid phase and buffer (log D PAMPA at pH 7.4) was systematically investigated. Increasing concentration of n-dodecane to the system egg lecithin-water (lamellar phase, L α ) induces formation of inverted hexagonal (H ii ) and isotropic phases. At n-dodecane concentrations matching those used in PAMPA (9%, w/v) a purely "isotropic" phase was observed corresponding to lipid aggregates with a diameter in the range 4-7 nm. Drug distribution studies indicate that these reverse micelles facilitate the binding to, and in turn the permeation across, the PAMPA dodecane barrier, in particular for amphiphilic solutes. The proposed model for the molecular architecture and function of the PAMPA barrier provides a fundamental, hitherto missing framework to evaluate the scope but also limitations of PAMPA for the prediction of in vivo membrane permeability.

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.

Molecular Characterization of Cryoconite Organic Matter from the Athabasca Glacier, Canadian Rocky Mountains

NASA Astrophysics Data System (ADS)

Xu, Y.; Simpson, M. J.; Eyles, N.; Simpson, A.; Baer, A. J.

2009-05-01

Cryoconite is a dark-colored, dust-like material found on the surfaces of glaciers. Cryoconite holes, which are produced by accelerated ice melt due to more solar radiation absorption by cryoconite than bare ice, act as habitats for microbial life and biologically mediated chemical reactions on otherwise relatively inert glacier surfaces. Cryoconite holes may behave as bacterial shelters during "Snowball Earth" events postulated for the Neoproterozoic Earth. In this study organic matter (OM) biomarkers and a host of one- and two-dimensional NMR techniques were used to characterize cryoconite organic matter (COM) collected from the Athabasca Glacier in the Canadian Rocky Mountains. Solvent extracts contain large quantities of fatty acids, n-alkanols, n- alkanes, wax esters and sterols. A large contribution of C23 and C25 relative to C29 and C31 n-alkanes ([C23/(C23+C29)] = 0.51) suggests that allochthonous COM is derived mainly from lower order plants such as mosses and lichens. This is confirmed by the absence of lignin-derived phenols, a biomarker of terrestrial vascular plants, after copper (II) oxidation in extracts and NMR analyses of COM. Solution-state 1H NMR reveals prominent peptide/protein structures which are characteristic of microbial inputs, while solid-state 13C CP/MAS NMR analysis shows a very high alkyl/O-alkyl ratio (2.16), suggesting that COM is unique compared to organic matter found in nearby soils which have alkyl/O-alkyl ratio of ~0.39. Our NMR results suggest that COM is dominated by microbial-derived compounds, which is also confirmed by phospholipid fatty acid results (6,950µg/gOC) which show significant microbial contributions to COM primarily from bacteria and minor microeukaryotes. Both biomarker and NMR data suggest that COM likely supports active microbial communities on the Athabasca Glacier. Given that such material is incorporated within the glacier in the accumulation zone or flushed by meltwaters into subglacial environments, reworked COM may provide nutrient sources for active microbial communities found within and under glaciers.

Experimental Determination of pK[subscript a] Values and Metal Binding for Biomolecular Compounds Using [superscript 31]P NMR Spectroscopy

ERIC Educational Resources Information Center

Swartz, Mason A.; Tubergen, Philip J.; Tatko, Chad D.; Baker, Rachael A.

2018-01-01

This lab experiment uses [superscript 31]P NMR spectroscopy of biomolecules to determine pK[subscript a] values and the binding energies of metal/biomolecule complexes. Solutions of adenosine nucleotides are prepared, and a series of [superscript 31]P NMR spectra are collected as a function of pH and in the absence and presence of magnesium or…

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…

Solution and solid state NMR approaches to draw iron pathways in the ferritin nanocage.

PubMed

Lalli, Daniela; Turano, Paola

2013-11-19

Ferritins are intracellular proteins that can store thousands of iron(III) ions as a solid mineral. These structures autoassemble from four-helix bundle subunits to form a hollow sphere and are a prototypical example of protein nanocages. The protein acts as a reservoir, encapsulating iron as ferric oxide in its central cavity in a nontoxic and bioavailable form. Scientists have long known the structural details of the protein shell, owing to very high resolution X-ray structures of the apoform. However, the atomic level mechanism governing the multistep biomineralization process remained largely elusive. Through analysis of the chemical behavior of ferritin mutants, chemists have found the role of some residues in key reaction steps. Using Mössbauer and XAS, they have identified some di-iron intermediates of the catalytic reaction trapped by rapid freeze quench. However, structural information about the iron interaction sites remains scarce. The entire process is governed by a number of specific, but weak, interactions between the protein shell and the iron species moving across the cage. While this situation may constitute a major problem for crystallography, NMR spectroscopy represents an optimal tool to detect and characterize transient species involving soluble proteins. Regardless, NMR analysis of the 480 kDa ferritin represents a real challenge. Our interest in ferritin chemistry inspired us to use an original combination of solution and solid state approaches. While the highly symmetric structure of the homo-24-mer frog ferritin greatly simplifies the spectra, the large protein size hinders the efficient coherence transfer in solution, thus preventing the sequence specific assignments. In contrast, extensive (13)C-spin diffusion makes the solution (13)C-(13)C NOESY experiment our gold standard to monitor protein side chains both in the apoprotein alone and in its interaction with paramagnetic iron species, inducing line broadening on the resonances of nearby residues. We could retrieve the structural information embedded in the (13)C-(13)C NOESY due to a partial sequence specific assignment of protein backbone and side chains we obtained from solid state MAS NMR of ferritin microcrystals. We used the 59 assigned amino acids (∼33% of the total) as probes to locate paramagnetic ferric species in the protein cage. Through this approach, we could identify ferric dimers at the ferroxidase site and on their pathway towards the nanocage. Comparison with existing data on bacterioferritins and bacterial ferritins, as well as with eukaryotic ferritins loaded with various nonfunctional divalent ions, allowed us to reinterpret the available information. The resulting picture of the ferroxidase site is slightly different with various ferritins but is designed to provide multiple and generally weak iron ligands. The latter assist binding of two incoming iron(II) ions in two proximal positions to facilitate coupling with oxygen. Subsequent oxidation is accompanied by a decrease in the metal-metal distance (consistent with XAS/Mössbauer) and in the number of protein residues involved in metal coordination, facilitating the release of products as di-iron clusters under the effect of new incoming iron(II) ions.

Supramolecular self-assemblies of beta-cyclodextrins with aromatic tethers: factors governing the helical columnar versus linear channel superstructures.

PubMed

Liu, Yu; Fan, Zhi; Zhang, Heng-Yi; Yang, Ying-Wei; Ding, Fei; Liu, Shuang-Xi; Wu, Xue; Wada, Takehiko; Inoue, Yoshihisa

2003-10-31

A series of 6-O-(p-substituted phenyl)-modified beta-cyclodextrin derivatives, i.e., 6-O-(4-bromophenyl)-beta-CD (1), 6-O-(4-nitrophenyl)-beta-CD (2), 6-O-(4-formylphenyl)-beta-CD (3), 6-phenylselenyl-6-deoxy-beta-CD (4), and 6-O-(4-hydroxybenzoyl)-beta-CD (5), were synthesized, and their inclusion complexation behavior in aqueous solution and self-assembling behavior in the solid state were comparatively studied by NMR spectroscopy, microcalorimetry, crystallography, and scanning tunneling microscopy. Interestingly, (seleno)ethers 1-4 and ester 5 displayed distinctly different self-assembling behavior in the solid state, affording a successively threading head-to-tail polymeric helical structure for the (seleno)ethers or a mutually penetrating tail-to-tail dimeric columnar channel structure for the ester. Combining the present and previous structures reported for the relevant beta-CD derivatives, we further deduce that the pivot heteroatom, through which the aromatic substituent is tethered to beta-CD, plays a critical role in determining the helix structure, endowing the 2-fold and 4-fold axes to the N/O- and S/Se-pivoted beta-CD aggregates, respectively. This means that one can control the self-assembling orientation, alignment, and helicity in the solid state by finely tuning the pivot atom and the tether length. Further NMR and calorimetric studies on the self-assembling behavior in aqueous solution revealed that the dimerization step is the key to the formation of linear polymeric supramolecular architecture, which is driven by favorable entropic contributions.

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

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.

PubMed

Delaforge, Elise; Milles, Sigrid; Huang, Jie-Rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J; Blackledge, Martin

2016-01-01

Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

PubMed Central

Delaforge, Elise; Milles, Sigrid; Huang, Jie-rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J.; Blackledge, Martin

2016-01-01

Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales. PMID:27679800

Facile Conversion of Red Phosphorus into Soluble Polyphosphide Anions by Reaction with Potassium Ethoxide.

PubMed

Dragulescu-Andrasi, Alina; Miller, L Zane; Chen, Banghao; McQuade, D Tyler; Shatruk, Michael

2016-03-14

Soluble polyphosphide anions were successfully generated in a number of organic solvents by the reaction between shelf-stable red phosphorus and potassium ethoxide. The species were identified by (31)P NMR spectroscopy in solution and by X-ray crystal-structure determination of (Bu4N)2P16 in the solid state. The reaction was scaled up to gram quantities by using a flow-chemistry process. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solid-state NMR studies of form I of atorvastatin calcium.

PubMed

Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

2012-03-22

Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

FT-IR, UV-vis, 1H and 13C NMR spectra and the equilibrium structure of organic dye molecule disperse red 1 acrylate: a combined experimental and theoretical analysis.

PubMed

Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet

2011-12-01

This study reports the characterization of disperse red 1 acrylate compound by spectral techniques and quantum chemical calculations. The spectroscopic properties were analyzed by FT-IR, UV-vis, (1)H NMR and (13)C NMR techniques. FT-IR spectrum in solid state was recorded in the region 4000-400 cm(-1). The UV-vis absorption spectrum of the compound that dissolved in methanol was recorded in the range of 200-800 nm. The (1)H and (13)C NMR spectra were recorded in CDCl(3) solution. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP exchange correlation and the 6-311++G(d,p) basis set. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. A satisfactory consistency between the experimental and theoretical spectra was obtained and it shows that the hybrid DFT method is very useful in predicting accurate vibrational structure, especially for high-frequency region. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. A study on the electronic properties were performed by timedependent DFT (TD-DFT) and CIS(D) approach. To investigate non linear optical properties, the electric dipole moment μ, polarizability α, anisotropy of polarizability Δα and molecular first hyperpolarizability β were computed. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the compound can be a good candidate of nonlinear optical materials. Copyright © 2011 Elsevier B.V. All rights reserved.

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

Petersen, Line Boisen; Lipton, Andrew S.; Zorin, Vadim

Ordering of gallium(III) in a series of magnesium gallium (MgGa) layered double hydroxides (LDHs), [Mg{sub 1−x}Ga{sub x}(OH){sub 2}(NO{sub 3}){sub x}·yH{sub 2}O] was investigated using solid-state {sup 1}H and {sup 71}Ga NMR spectroscopy as well as powder X-ray diffraction. Three different proton environments from Mg{sub 3}-OH, Mg{sub 2}Ga-OH and intergallery water molecules were assigned and quantified using ({sup 1}H,{sup 71}Ga) HETCOR and {sup 1}H MAS NMR. A single {sup 71}Ga site originating from the unique Ga site in the MgGa LDH's was observed in {sup 71}Ga MAS and 3QMAS NMR spectra. Both {sup 1}H MAS NMR spectra recorded at 21.1 Tmore » (900 MHz) and elemental analysis show that the synthesized MgGa LDH's had a lower Mg:Ga ratio than that of the starting reactant solution. The origin of this is the formation of soluble [Ga(OH){sub 4}]{sup −} complexes formed during synthesis, and not due to formation of insoluble gallium (oxy)hydroxides. No sign of Ga-O-Ga connectivities or defects were detected for the MgGa LDH's. - Graphical abstract: Two types of hydroxides groups are observed in magnesium gallium layered double hydroxides revealing an ordering of Ga in the cation layer. - Highlights: • Ga is ordered in our magnesium gallium layered double hydroxides. • Ga depletion due to formation of soluble Ga complexes during synthesis. • No sign of Ga rich regions in magnesium gallium LDHs. • Solid state {sup 1}H and {sup 71}Ga give detailed insight into the structure.« less

Spectroscopic and electrochemical properties of organic framework of macrocylic OONNOO-donor ligand with its metal organic framework: host/guest stability measurements.

PubMed

Kumar, Rajiv; Singh, R P; Singh, R P

2008-11-15

In this study, we synthesized 1,2-di(o-aminophenoxy)ethane, as the starting material, used in the preparation of a novel hexadentate OONNOO-donor macrocyclic ligand-1,4,11,14-tetraoxo-7,8-diaza-5,6:9,10;15,16:19,20-terabezocyclododeca-8,17-iene. It has twenty membered organic framework (OF), which has been designed, synthesized and characterized. Our main findings of this paper are related to the organic framework of ligand, its capacity to digest the metal ions and the stability of metal organic framework (MOFs) with cobalt(II), nickel(II) and manganese(II). The authenticity of the used organic framework and its metal complexes have been detected and observed in solid state as well as in aqueous solutions. The main observations were made on the basis of physiochemical measurements viz.: elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, 1H NMR, 13C NMR, mass spectroscopy, electronic, ESR spectroscopy. In addition, the magnetic susceptibility and electrochemistry measurements have been made. The 1H NMR spectra suggest stereochemistry and proton movement interaction. Considering the used organic framework there are a lot of carbon atoms in the molecule reflected by the 13C NMR spectrum. All these observations gave a clear view to confirming the encapsulation; arrive at the composition, structure and geometry of encapsulated complexes. In simple words, it confirms the host/guest coordination and its stability. Electrochemical properties of the complexes have been investigated to confirm the various changes in oxidation state of metals with change in potentials with respect to current at different scan rate.

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

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

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

PubMed Central

Tuszynski, Jack A.; Gallo, Diego; Morbiducci, Umberto; Danani, Andrea

2016-01-01

The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water. PMID:26745628

Fluorination Effects on NOS Inhibitory Activity of Pyrazoles Related to Curcumin.

PubMed

Nieto, Carla I; Cabildo, María Pilar; Cornago, María Pilar; Sanz, Dionisia; Claramunt, Rosa M; Torralba, María Carmen; Torres, María Rosario; Elguero, José; García, José A; López, Ana; Acuña-Castroviejo, Darío

2015-08-28

A series of new (E)-3(5)-[β-(aryl)-ethenyl]-5(3)-phenyl-1H-pyrazoles bearing fluorine atoms at different positions of the aryl group have been synthesized starting from the corresponding β-diketones. All compounds have been characterized by elemental analysis, DSC as well as NMR (¹H, (13)C, (19)F and (15)N) spectroscopy in solution and in solid state. Three structures have been solved by X-ray diffraction analysis, confirming the tautomeric forms detected by solid state NMR. The in vitro study of their inhibitory potency and selectivity on the activity of nNOS and eNOS (calcium-calmodulin dependent) as well as iNOS (calcium-calmodulin independent) isoenzymes is presented. A qualitative structure-activity analysis allowed the establishment of a correlation between the presence/ absence of different substituents with the inhibition data proving that fluorine groups enhance the biological activity. (E)-3(5)-[β-(3-Fluoro-4-hydroxyphenyl)-ethenyl]-5(3)-phenyl-1H-pyrazole (13), is the best inhibitor of iNOS, being also more selective towards the other two isoforms.

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.

Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression

PubMed Central

Ishima, Rieko

2016-01-01

Abundant solvent nuclear spins, such as water protons in aqueous solution, cause radiation damping in NMR experiments. It is important to know how the effect of radiation damping appears in high-resolution protein NMR because macromolecular studies always require very high magnetic field strengths with a highly sensitive NMR probe that can easily cause radiation damping. Here, we show the behavior of water magnetization after a pulsed-field gradient (PFG) using nutation experiments at 900 MHz with a cryogenic probe: when water magnetization is located in the upper hemisphere (having +Z component, parallel to the external magnetic field), dephasing of the magnetization by a PFG effectively suppresses residual water magnetization in the transverse plane. In contrast, when magnetization is located in the lower hemisphere (having −Z component), the small residual transverse component remaining after a PFG is still sufficient to induce radiation damping. Based on this observation, we designed 1H-15N HSQC experiments in which water magnetization is maintained in the upper hemisphere, but not necessarily along Z, and compared them with the conventional experiments, in which water magnetization is inverted during the t1 period. The result demonstrates moderate gain of signal-to-noise ratio, 0–28%. Designing the experiments such that water magnetization is maintained in the upper hemisphere allows shorter pulses to be used compared to the complete water flip-back and, thereby, is useful as a building block of protein NMR pulse programs in solution. PMID:27524944

Interactions of poly(amidoamine) dendrimers with human serum albumin: binding constants and mechanisms.

PubMed

Giri, Jyotsnendu; Diallo, Mamadou S; Simpson, André J; Liu, Yi; Goddard, William A; Kumar, Rajeev; Woods, Gwen C

2011-05-24

The interactions of nanomaterials with plasma proteins have a significant impact on their in vivo transport and fate in biological fluids. This article discusses the binding of human serum albumin (HSA) to poly(amidoamine) [PAMAM] dendrimers. We use protein-coated silica particles to measure the HSA binding constants (K(b)) of a homologous series of 19 PAMAM dendrimers in aqueous solutions at physiological pH (7.4) as a function of dendrimer generation, terminal group, and core chemistry. To gain insight into the mechanisms of HSA binding to PAMAM dendrimers, we combined (1)H NMR, saturation transfer difference (STD) NMR, and NMR diffusion ordered spectroscopy (DOSY) of dendrimer-HSA complexes with atomistic molecular dynamics (MD) simulations of dendrimer conformation in aqueous solutions. The binding measurements show that the HSA binding constants (K(b)) of PAMAM dendrimers depend on dendrimer size and terminal group chemistry. The NMR (1)H and DOSY experiments indicate that the interactions between HSA and PAMAM dendrimers are relatively weak. The (1)H NMR STD experiments and MD simulations suggest that the inner shell protons of the dendrimers groups interact more strongly with HSA proteins. These interactions, which are consistently observed for different dendrimer generations (G0-NH(2)vs G4-NH(2)) and terminal groups (G4-NH(2)vs G4-OH with amidoethanol groups), suggest that PAMAM dendrimers adopt backfolded configurations as they form weak complexes with HSA proteins in aqueous solutions at physiological pH (7.4).

Backbone resonance assignment of an insect arylalkylamine N-acetyltransferase from Bombyx mori reveals conformational heterogeneity.

PubMed

Aboalroub, Adam A; Zhang, Ziming; Keramisanou, Dimitra; Gelis, Ioannis

2017-04-01

Arylalkylamine N-acetyltransferases (AANATs) catalyze the transfer of an acetyl group from the acetyl-group donor, acetyl-CoA, to an arylalkylamine acceptor. Although a single AANAT has been identified in mammals, insects utilize multiple AANATs in a diverse array of biological processes. AANATs belong to the GCN5-related acetyltransferase (GNAT) superfamily of enzymes, which despite their overall very low sequence homology, are characterized by a well conserved catalytic core domain. The structural properties of many GNATs have been extensively studied by X-ray crystallography that revealed common features during the catalytic cycle. Here we report the 1 H, 13 C and 15 N backbone NMR resonance assignment of the 24 kDa AANAT3 from Bombyx mori (bmAANAT3) as a first step towards understanding the role of protein dynamics in the catalytic properties of AANATs. Our preliminary solution NMR studies reveal that bmAANAT3 is well-folded in solution. The P-loop, which is responsible for cofactor binding, is flexible in the free-state, while a large region of the enzyme interconverts between two distinct conformations in the slow exchange regime.

[Physicochemical properties of suplatast tosilate racemate and enantiomers].

PubMed

Ushio, T; Endo, K; Yamamoto, K

1996-11-01

The physicochemical properties of the enantiomer and racemates of suplatast tosilate (ST) were investigated by means of infrared spectroscopy, solid-state 13C CP/MAS NMR spectroscopy, thermal analysis, and X-ray diffraction analysis, and by measuring the solubility and hygroscopy. The infrared and NMR spectra and X-ray diffraction pattern of the enantiomer were distinctly different from those of the racemate. The melting point of the enantiomer was lower than that of the racemate by 5 degrees C, while the solubility of the enantiomer was 1.3 times higher than that of the racemate. The hygroscopic rate of the enantiomer was greater than that of the racemate. These results suggested that ST was classified into a racemic compound crystal. Furthermore, by comparing the relative peak intensity ratios on X-ray diffraction patterns of the crystals with various optical purities prepared by recrystallization, it was found that a mixture of racemic compound crystals and either of racemic mixture crystals or racemic solid solutions was obtained by recrystallization of ST in the content of 0 to 64%ee, while the recrystallization of ST in the content of more than 64%ee led to the formation of racemic mixture crystals or racemic solid solutions.

NMR doesn't lie or how solid-state NMR spectroscopy contributed to a better understanding of the nature and function of soil organic matter (Philippe Duchaufour Medal Lecture)

NASA Astrophysics Data System (ADS)

Knicker, Heike

2016-04-01

"Nuclear magnetic resonance (NMR) does not lie". More than anything else, this statement of a former colleague and friend has shaped my relation to solid-state NMR spectroscopy. Indeed, if this technique leads to results which contradict the expectations, it is because i) some parts of the instrument are broken, ii) maladjustment of the acquisition parameters or iii) wrong preparation or confusion of samples. However, it may be even simpler, namely that the expectations were wrong. Of course, for researchers, the latter is the most interesting possibility since it forces to reassess accepted views and to search for new explanations. As my major analytical tool, NMR spectroscopy has confronted me with this challenge often enough to turn this issue into the main subject of my talk and to share with the audience how it formed my understanding of function and nature of soil organic matter (SOM). Already shortly after its introduction into soil science in the 1980's, the data obtained with solid-state 13C NMR spectroscopy opened the stage for ongoing discussions, since they showed that in humified SOM aromatic carbon is considerably less important than previously thought. This finding had major implications regarding the understanding of the origin of SOM and the mechanisms by which it is formed. Certainly, the discrepancy between the new results and previous paradigms contributed to mistrust in the reliability of solid-state NMR techniques. The respective discussion has survived up to our days, although already in the 1980's and 1990's fundamental studies could demonstrate that quantitative solid-state NMR data can be obtained if i) correct acquisition parameters are chosen, ii) the impact of paramagnetic compounds is reduced and iii) the presence of soot in soils can be excluded. On the other hand, this mistrust led to a detailed analysis of the impact of paramagnetics on the NMR behavior of C groups which then improved our understanding of the role of carbohydrates for organo-mineral interactions. Since decent solid-state NMR spectra cannot be obtained from graphenic components, the successful acquisition of solid-state 13C and 15N NMR spectra of charcoals challenged the well accepted model of their chemical nature. Application of advanced 2D NMR approaches confirmed the new view of charcoal as a heterogeneous material, the composition of which depends upon the feedstock and charring condition. The respective consequences of this alternative for the understanding of C sequestration are still matter of ongoing debates. Although the sensitivity of 15N for NMR spectroscopy is 50 times lower than that of 13C, first solid-state 15N NMR spectra of soils with natural 15N abundance were already published in the 1990's. They clearly identified peptide-like structures as the main organic N form in unburnt soils. However, in spite of their high contribution to SOM, the role of peptides in soils is far from understood. Considering the new technological developments in the field of NMR spectroscopy, this technique will certainly not stop to contribute to unexpected results.

Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

PubMed

Barakat, Assem; Al-Najjar, Hany J; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-05

The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580

Characterization of Three Venom Peptides from the Spitting Spider Scytodes thoracica

PubMed Central

Ariki, Nathanial K.; Muñoz, Lisa E.; Armitage, Elizabeth L.; Goodstein, Francesca R.; George, Kathryn G.; Smith, Vanessa L.; Vetter, Irina; Herzig, Volker; King, Glenn F.; Loening, Nikolaus M.

2016-01-01

We present the solution-state NMR structures and preliminary functional characterizations of three venom peptides identified from the spitting spider Scytodes thoracica. Despite little sequence identity to other venom peptides, structural characterization reveals that these peptides contain an inhibitor cystine knot motif common to many venom peptides. These are the first structures for any peptide or protein from spiders of the Scytodidae family. Many venom peptides target neuronal ion channels or receptors. However, we have not been able to determine the target of these Scytodes peptides so we can only state with certainty the channels and receptors that they do not target. PMID:27227898

Laponite as carrier for controlled in vitro delivery of dexamethasone in vitreous humor models.

PubMed

Fraile, José M; Garcia-Martin, Elena; Gil, Cristina; Mayoral, José A; Pablo, Luis E; Polo, Vicente; Prieto, Esther; Vispe, Eugenio

2016-11-01

Laponite clay is able to retain dexamethasone by simple physisorption, presumably accomplished by hydrogen bonding formation and/or complexation with sodium counterions, as shown by solid state NMR. The physisorption can be somehow modulated by changing the solvent in the adsorption process. This simple system is able to deliver dexamethasone in a controlled manner to solutions used as models for vitreous humor. The proven biocompatibility of laponite as well as its transparency in the gel state, together with the simplicity of the preparation method, makes this system suitable for future in vivo tests of ophthalmic treatment. Copyright © 2016 Elsevier B.V. All rights reserved.

Modeling an in-register, parallel "iowa" aβ fibril structure using solid-state NMR data from labeled samples with rosetta.

PubMed

Sgourakis, Nikolaos G; Yau, Wai-Ming; Qiang, Wei

2015-01-06

Determining the structures of amyloid fibrils is an important first step toward understanding the molecular basis of neurodegenerative diseases. For β-amyloid (Aβ) fibrils, conventional solid-state NMR structure determination using uniform labeling is limited by extensive peak overlap. We describe the characterization of a distinct structural polymorph of Aβ using solid-state NMR, transmission electron microscopy (TEM), and Rosetta model building. First, the overall fibril arrangement is established using mass-per-length measurements from TEM. Then, the fibril backbone arrangement, stacking registry, and "steric zipper" core interactions are determined using a number of solid-state NMR techniques on sparsely (13)C-labeled samples. Finally, we perform Rosetta structure calculations with an explicitly symmetric representation of the system. We demonstrate the power of the hybrid Rosetta/NMR approach by modeling the in-register, parallel "Iowa" mutant (D23N) at high resolution (1.2Å backbone rmsd). The final models are validated using an independent set of NMR experiments that confirm key features. Copyright © 2015 Elsevier Ltd. All rights reserved.

Imidazole as a pH Probe: An NMR Experiment for the General Chemistry Laboratory

ERIC Educational Resources Information Center

Hagan, William J., Jr.; Edie, Dennis L.; Cooley, Linda B.

2007-01-01

The analysis describes an NMR experiment for the general chemistry laboratory, which employs an unknown imidazole solution to measure the pH values. The described mechanism can also be used for measuring the acidity within the isolated cells.

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.

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.

Study of an efficient conversion of 1,3-dimethyl-5-(Arylazo)-6-Amino-Uracils to 1,3-dimethyl-8-(Aryl)-Azapurin-2,6-Diones

NASA Astrophysics Data System (ADS)

Debnath, Diptanu; Purkayastha, Atanu; Kirillov, Alexander; Ganguly, Rakesh; Misra, Tarun Kumar

2017-12-01

6-Aminouracils have extensively been used as precursors for synthesizing numerous uracil derivatives of biological and pharmaceutical significance. This study describes an application of 1,3-dimethyl-5-(arylazo)-6-aminouracils (Uazo: Uazo1-Uazo4, precursors) for an efficient synthesis of a series of 8-substituted-azapurins (AP), namely 1,3-dimethyl-8-(aryl)-azapurin-2,6-diones (aryl = p-HC6H4 (AP1), -MeC6H4 (AP2), sbnd ClC6H4 (AP3), and sbnd SO2NH2C6H4 (AP4)) following an oxidation method in the presence of copper (II) nitrate and in alkaline medium. The obtained compounds were isolated in good yields as crystalline air-stable products and have been fully characterized in the solution by UV-vis and NMR spectroscopy, as well as in the solid state by FT-IR spectroscopy, elemental analysis, and single-crystal X-ray diffraction (for AP2 and AP4). UV-vis study evidences that the conversion of the 6-aminouracil precursors occurs via an intermediate, Cu(II)-complex and a plausible mechanism for the formation of AP1-AP4 has been proposed. Unlike AP2 the crystal structure of AP4 reveals the formation of interdigitated 1D H-bonded chains that has been topologically classified within the 2C1 type. The 1H NMR spectra of the products have proton signals that completely devoid of hydrazone (sbnd NHsbnd) and imine (=NH) signals of their parent Uazo derivatives, thus confirming their full conversion and a stability of the AP1-AP4 in solution. The excitation and emission spectra of AP1-AP4 were also recorded in solution, revealing electronic transitions between similar vibrational energy levels of S0 (singlet ground state) and S1 (singlet first excited state).

Speeding up NMR by in Situ Photo-Induced Reversible Acceleration of T1 -Relaxation (PIRAT).

PubMed

Stadler, Eduard; Dommaschk, Marcel; Frühwirt, Philipp; Herges, Rainer; Gescheidt, Georg

2018-03-05

Increasing the signal-to-noise ratio is one of the major goals in the field of NMR spectroscopy. In this proof of concept, we accelerate relaxation during an NMR pulse sequence using photo-generated paramagnetic states of an inert sensitizer. For the follow-up acquisition period, the system is converted to a diamagnetic state. The reversibility of the photo-induced switching allows extensive repetition required for multidimensional NMR. We thus eliminate the obstacle of line-broadening by the presence of paramagnetic species. In this contribution, we show how cycling of synchronized light/pulse sequences leads to an enhanced efficiency in multidimensional NMR. Our approach utilizes a molecular spin switch reversibly altering between a paramagnetic and diamagnetic state. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A nuclear magnetic resonance spectrometer concept for hermetically sealed magic angle spinning investigations on highly toxic, radiotoxic, or air sensitive materials.

PubMed

Martel, L; Somers, J; Berkmann, C; Koepp, F; Rothermel, A; Pauvert, O; Selfslag, C; Farnan, I

2013-05-01

A concept to integrate a commercial high-resolution, magic angle spinning nuclear magnetic resonance (MAS-NMR) probe capable of very rapid rotation rates (70 kHz) in a hermetically sealed enclosure for the study of highly radiotoxic materials has been developed and successfully demonstrated. The concept centres on a conventional wide bore (89 mm) solid-state NMR magnet operating with industry standard 54 mm diameter probes designed for narrow bore magnets. Rotor insertion and probe tuning take place within a hermetically enclosed glovebox, which extends into the bore of the magnet, in the space between the probe and the magnet shim system. Oxygen-17 MAS-NMR measurements demonstrate the possibility of obtaining high quality spectra from small sample masses (~10 mg) of highly radiotoxic material and the need for high spinning speeds to improve the spectral resolution when working with actinides. The large paramagnetic susceptibility arising from actinide paramagnetism in (Th(1-x)U(x))O2 solid solutions gives rise to extensive spinning sidebands and poor resolution at 15 kHz, which is dramatically improved at 55 kHz. The first (17)O MAS-NMR measurements on NpO(2+x) samples spinning at 55 kHz are also reported. The glovebox approach developed here for radiotoxic materials can be easily adapted to work with other hazardous or even air sensitive materials.

Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT-GIAO calculations

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Bąk, Joanna; Gliński, Jan A.; Koczorowska, Agnieszka; Wawer, Iwona

2009-09-01

Actein is a prominent triterpene glycoside occurring in Actaea racemosa. The triterpene glycosides are believed to be responsible for the estrogenic activity of an extract prepared from this herb. We determined in the crystal structure of actein by X-ray crystallography to be monoclinic P2(1) chiral space group. Refining the disorder, we determined 70% and 30% of contributions of ( S)- and ( R)-actein, respectively. The IR and Raman spectra suggest that actein forms at least four different types of hydrogen bonds. The 13C NMR spectra of actein were recorded both in solution and solid state. The 13C CPMAS spectrum of actein displays multiplet signals, in agreement with the crystallographic data. The NMR shielding constants were calculated for actein using GIAO approach and a variety of basis sets: 6-31G**, 6-311G**, 6-31+G**, cc-pVDZ, cc-pVDZ-su1 and 6-31G**-su1, as well as IGLO approach combined with the IGLO II basis set. The best results (RMSD of 1.6 ppm and maximum error of 3.4 ppm) were obtained with the 6-31G**-su1 basis set. The calculations of the shielding constants are helpful in the interpretation of the 13C CPMAS NMR spectra of actein and actein's analogues.

Synthesis, spectroscopy and computational studies of some biologically important hydroxyhaloquinolines and their novel derivatives

NASA Astrophysics Data System (ADS)

Malecki, Grzegorz; Nycz, Jacek E.; Ryrych, Ewa; Ponikiewski, Lukasz; Nowak, Maria; Kusz, Joachim; Pikies, Jerzy

2010-04-01

A series crystalline compounds of methyl and phosphinyl derivatives of 2-methylquinolin-8-ol ( 1a) and related 5,7-dichloro-2-methylquinolin-8-ol ( 1b) were quantitatively prepared and characterized by microanalysis, IR, UV-vis and multinuclear NMR spectroscopy. Five of them have been characterized by single crystal X-ray diffraction method. The known compounds, 8-methoxy-2-methylquinoline ( 2a) and 8-methoxyquinoline ( 2d), were synthesised by a new route. NMR solution spectra at ambient temperature, showed readily diagnostic H-1 and C-13 signals from methyl groups. The geometries of the studied compounds were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. In general, the predicted bond lengths and angles are in a good agreement with the values based on the X-ray crystal structure data. Electronic spectra were calculated by TDDFT method.

NMR Studies on the Aqueous Phase Photochemical Degradation of TNT

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

Thorn, Kevin A.; Cox, Larry G.

2008-04-06

Aqueous phase photochemical degradation of 2,4,6-trinitrotoluene (TNT) is an important pathway in several environments, including washout lagoon soils, impact craters from partially detonated munitions that fill with rain or groundwater, and shallow marine environments containing unexploded munitions that have corroded. Knowledge of the degradation products is necessary for compliance issues on military firing ranges and formerly used defense sites. Previous laboratory studies have indicated that UV irradiation of aqueous TNT solutions results in a multicomponent product mixture, including polymerization compounds, that has been only partially resolved by mass spectrometric analyses. This study illustrates how a combination of solid and liquidmore » state 1H, 13C, and 15N NMR spectroscopy, including two dimensional analyses, provides complementary information on the total product mixture from aqueous photolysis of TNT, and the effect of reaction conditions. Among the degradation products detected were amine, amide, azoxy, azo, and carboxylic acid compounds.« less

Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism

PubMed Central

Hughes, Travis S.; Chalmers, Michael J.; Novick, Scott; Kuruvilla, Dana S.; Chang, Mi Ra; Kamenecka, Theodore M.; Rance, Mark; Johnson, Bruce A.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.

2011-01-01

SUMMARY Ligand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution NMR studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators. PMID:22244763

Matching multiple rigid domain decompositions of proteins

PubMed Central

Flynn, Emily; Streinu, Ileana

2017-01-01

We describe efficient methods for consistently coloring and visualizing collections of rigid cluster decompositions obtained from variations of a protein structure, and lay the foundation for more complex setups that may involve different computational and experimental methods. The focus here is on three biological applications: the conceptually simpler problems of visualizing results of dilution and mutation analyses, and the more complex task of matching decompositions of multiple NMR models of the same protein. Implemented into the KINARI web server application, the improved visualization techniques give useful information about protein folding cores, help examining the effect of mutations on protein flexibility and function, and provide insights into the structural motions of PDB proteins solved with solution NMR. These tools have been developed with the goal of improving and validating rigidity analysis as a credible coarse-grained model capturing essential information about a protein’s slow motions near the native state. PMID:28141528

InP/ZnS nanocrystals: coupling NMR and XPS for fine surface and interface description.

PubMed

Virieux, Héloïse; Le Troedec, Marianne; Cros-Gagneux, Arnaud; Ojo, Wilfried-Solo; Delpech, Fabien; Nayral, Céline; Martinez, Hervé; Chaudret, Bruno

2012-12-05

Advanced (1)H, (13)C, and (31)P solution- and solid-state NMR studies combined with XPS were used to probe, at the molecular scale, the composition (of the core, the shell, and the interface) and the surface chemistry of InP/ZnS core/shell quantum dots prepared via a non-coordinating solvent strategy. The interface between the mismatched InP and ZnS phases is composed of an amorphous mixed oxide phase incorporating InPO(x) (with x = 3 and predominantly 4), In(2)O(3), and InO(y)(OH)(3-2y) (y = 0, 1). Thanks to the analysis of the underlying reaction mechanisms, we demonstrate that the oxidation of the upper part of the InP core is the consequence of oxidative conditions brought by decarboxylative coupling reactions (ketonization). These reactions occur during both the core preparation and the coating process, but according to different mechanisms.

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.

Full analytical solution of the bloch equation when using a hyperbolic-secant driving function.

PubMed

Zhang, Jinjin; Garwood, Michael; Park, Jang-Yeon

2017-04-01

The frequency-swept pulse known as the hyperbolic-secant (HS) pulse is popular in NMR for achieving adiabatic spin inversion. The HS pulse has also shown utility for achieving excitation and refocusing in gradient-echo and spin-echo sequences, including new ultrashort echo-time imaging (e.g., Sweep Imaging with Fourier Transform, SWIFT) and B 1 mapping techniques. To facilitate the analysis of these techniques, the complete theoretical solution of the Bloch equation, as driven by the HS pulse, was derived for an arbitrary state of initial magnetization. The solution of the Bloch-Riccati equation for transverse and longitudinal magnetization for an arbitrary initial state was derived analytically in terms of HS pulse parameters. The analytical solution was compared with the solutions using both the Runge-Kutta method and the small-tip approximation. The analytical solution was demonstrated on different initial states at different frequency offsets with/without a combination of HS pulses. Evolution of the transverse magnetization was influenced significantly by the choice of HS pulse parameters. The deviation of the magnitude of the transverse magnetization, as obtained by comparing the small-tip approximation to the analytical solution, was < 5% for flip angles < 30 °, but > 10% for the flip angles > 40 °. The derived analytical solution provides insights into the influence of HS pulse parameters on the magnetization evolution. Magn Reson Med 77:1630-1638, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

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.

Rapid acquisition of data dense solid-state CPMG NMR spectral sets using multi-dimensional statistical analysis

DOE PAGES

Mason, H. E.; Uribe, E. C.; Shusterman, J. A.

2018-01-01

Tensor-rank decomposition methods have been applied to variable contact time 29 Si{ 1 H} CP/CPMG NMR data sets to extract NMR dynamics information and dramatically decrease conventional NMR acquisition times.

Rapid acquisition of data dense solid-state CPMG NMR spectral sets using multi-dimensional statistical analysis

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

Mason, H. E.; Uribe, E. C.; Shusterman, J. A.

Tensor-rank decomposition methods have been applied to variable contact time 29 Si{ 1 H} CP/CPMG NMR data sets to extract NMR dynamics information and dramatically decrease conventional NMR acquisition times.

Photo-CIDNP NMR spectroscopy of amino acids and proteins.

PubMed

Kuhn, Lars T

2013-01-01

Photo-chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance (NMR) phenomenon which, among other things, is exploited to extract information on biomolecular structure via probing solvent-accessibilities of tryptophan (Trp), tyrosine (Tyr), and histidine (His) amino acid side chains both in polypeptides and proteins in solution. The effect, normally triggered by a (laser) light-induced photochemical reaction in situ, yields both positive and/or negative signal enhancements in the resulting NMR spectra which reflect the solvent exposure of these residues both in equilibrium and during structural transformations in "real time". As such, the method can offer - qualitatively and, to a certain extent, quantitatively - residue-specific structural and kinetic information on both the native and, in particular, the non-native states of proteins which, often, is not readily available from more routine NMR techniques. In this review, basic experimental procedures of the photo-CIDNP technique as applied to amino acids and proteins are discussed, recent improvements to the method highlighted, and future perspectives presented. First, the basic principles of the phenomenon based on the theory of the radical pair mechanism (RPM) are outlined. Second, a description of standard photo-CIDNP applications is given and it is shown how the effect can be exploited to extract residue-specific structural information on the conformational space sampled by unfolded or partially folded proteins on their "path" to the natively folded form. Last, recent methodological advances in the field are highlighted, modern applications of photo-CIDNP in the context of biological NMR evaluated, and an outlook into future perspectives of the method is given.

Using liquid and solid state NMR and photoluminescence to study the synthesis and solubility properties of amine capped silicon nanoparticles.

PubMed

Giuliani, J R; Harley, S J; Carter, R S; Power, P P; Augustine, M P

2007-08-01

Water soluble silicon nanoparticles were prepared by the reaction of bromine terminated silicon nanoparticles with 3-(dimethylamino)propyl lithium and characterized with liquid and solid state nuclear magnetic resonance (NMR) and photoluminescence (PL) spectroscopies. The surface site dependent 29Si chemical shifts and the nuclear spin relaxation rates from an assortment of 1H-29Si heteronuclear solid state NMR experiments for the amine coated reaction product are consistent with both the 1H and 13C liquid state NMR results and routine transmission electron microscopy, ultra-violet/visible, and Fourier transform infrared measurements. PL was used to demonstrate the pH dependent solubility properties of the amine passivated silicon nanoparticles.

Solution equilibrium behind the room-temperature synthesis of nanocrystalline titanium dioxide

NASA Astrophysics Data System (ADS)

Seisenbaeva, Gulaim A.; Daniel, Geoffrey; Nedelec, Jean-Marie; Kessler, Vadim G.

2013-03-01

Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions.Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions. Electronic supplementary information (ESI) available: Crystallographic data in cif and table format, detailed description of hydrogen bonding in (NH4)2[Ti(l-Lactate)3].3H2O, additional TEM images, DLS data on particle size in solutions and NanoSight data on particle size distribution, photos of produced TiO2 colloids, details of NMR experiments and a real-time movie demonstrating the equilibrium leading to TiO2 formation and re-dissolution in pH-neutral ammonium lactate solutions. CCDC 915222. For ESI and crystallographic data in CIF or other electronic format. see DOI: 10.1039/c3nr34068f

In situ molecular elucidation of drug supersaturation achieved by nano-sizing and amorphization of poorly water-soluble drug.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Yamamoto, Keiji; Moribe, Kunikazu

2015-09-18

Quantitative evaluation of drug supersaturation and nanoparticle formation was conducted using in situ evaluation techniques, including nuclear magnetic resonance (NMR) spectroscopy. We prepared a ternary complex of carbamazepine (CBZ) with hydroxypropyl methylcellulose (HPMC) and sodium dodecyl sulfate (SDS) to improve the drug concentration. Different preparation methods, including grinding and spray drying, were performed to prepare the ternary component products, ground mixture (GM) and spray-dried sample (SD), respectively. Although CBZ was completely amorphized in the ternary SD, CBZ was partially amorphized with the remaining CBZ crystals in the ternary GM. Aqueous dispersion of the ternary GM formed nanoparticles of around 150 nm, originating from the CBZ crystals in the ternary GM. In contrast, the ternary SD formed transparent solutions without a precipitate. The molecular-level evaluation using NMR measurements revealed that approximately half a dose of CBZ in the ternary GM dispersion was present as nanoparticles; however, CBZ in the ternary SD was completely dissolved in the aqueous solution. The characteristic difference between the solid states, followed by different preparation methods, induced different solution characteristics in the ternary GM and SD. The permeation study, using a dialysis membrane, showed that the CBZ concentration dissolved in the bulk water phase rapidly reduced in the ternary SD dispersion compared to the ternary GM dispersion; this demonstrated the advantage of ternary GM dispersion in the maintenance of CBZ supersaturation. Long-term maintenance of a supersaturated state of CBZ observed in the ternary GM dispersion rather than in the ternary SD dispersion was achieved by the inhibition of CBZ crystallization owing to the existence of CBZ nanoparticles in the ternary GM dispersion. Nanoparticle formation, combined with drug amorphization, could be a promising approach to improve drug concentrations. The detailed elucidation of solution characteristics using in situ evaluation techniques will lead to the formation of useful solid dispersion and nanoparticle formulations, resulting in improved drug absorption. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Fluxional σ-Bonds of the 2,5,8-Trimethylphenalenyl Dimer: Direct Observation of the Sixfold σ-Bond Shift via a π-Dimer.

PubMed

Uchida, Kazuyuki; Mou, Zhongyu; Kertesz, Miklos; Kubo, Takashi

2016-04-06

Direct evidence for σ-bond fluxionality in a phenalenyl σ-dimer was successfully obtained by a detailed investigation of the solution-state dynamics of 2,5,8-trimethylphenalenyl (TMPLY) using both experimental and theoretical approaches. TMPLY formed three diamagnetic dimers, namely, the σ-dimer (RR/SS), σ-dimer (RS), and π-dimer, which were fully characterized by (1)H NMR spectroscopy and electronic absorption measurements. The experimental findings gave the first quantitative insights into the essential preference of these competitive and unusual dimerization modes. The spectroscopic analyses suggested that the σ-dimer (RR/SS) is the most stable in terms of energy, whereas the others are metastable; the energy differences between these three isomers are less than 1 kcal mol(-1). Furthermore, the intriguing dynamics of the TMPLY dimers in the solution state were fully revealed by means of (1)H-(1)H exchange spectroscopy (EXSY) measurements and variable-temperature (1)H NMR studies. Surprisingly, the σ-dimer (RR/SS) demonstrated a sixfold σ-bond shift between the six sets of α-carbon pairs. This unusual σ-bond fluxionality is ascribed to the presence of a direct interconversion pathway between the σ-dimer (RR/SS) and the π-dimer, which was unambiguously corroborated by the EXSY measurements. The proposed mechanism of the sixfold σ-bond shift based on the experimental findings was well-supported by theoretical calculations.

Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR

PubMed Central

Teramura, Hiroshi; Sasaki, Kengo; Oshima, Tomoko; Aikawa, Shimpei; Matsuda, Fumio; Okamoto, Mami; Shirai, Tomokazu; Kawaguchi, Hideo; Ogino, Chiaki; Yamasaki, Masanori; Kikuchi, Jun; Kondo, Akihiko

2015-01-01

A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45–0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = –0.95 to –0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate. PMID:26083431

Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota

PubMed Central

Ogura, Tatsuki; Date, Yasuhiro; Kikuchi, Jun

2013-01-01

Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an “ECOMICS” web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation. PMID:23840554

A comparative experimental and quantum chemical study on monomeric and dimeric structures of 3,5-dibromoanthranilic acid.

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-10-01

This study presents the structural and spectroscopic characterization of 3,5-dibromoanthranilic acid with help of experimental techniques (FT-IR, FT-Raman, UV, NMR) and quantum chemical calculations. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 and 4000-50 cm(-1), respectively. The vibrational frequencies were also computed using B3LYP method of DFT with 6-311++G(d,p) basis set. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The (1)H, (13)C and DEPT NMR spectra were recorded in DMSO solution and calculated by gauge-invariant atomic orbitals (GIAO) method. The UV absorption spectra of the compound were recorded in the range of 200-400 nm in ethanol, water and DMSO solutions. Solvent effects were calculated using time-dependent density functional theory and CIS method. The ground state geometrical structure of compound was predicted by B3LYP method and compared with the crystallographic structure of similar compounds. All calculations were made for monomeric and dimeric structure of compound. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken atomic charges of neutral and anionic form of the molecule were computed and compared with anthranilic acid. Copyright © 2012 Elsevier B.V. All rights reserved.

Solution NMR investigation of the CD95/FADD homotypic death domain complex suggests lack of engagement of the CD95 C terminus.

PubMed

Esposito, Diego; Sankar, Andrew; Morgner, Nina; Robinson, Carol V; Rittinger, Katrin; Driscoll, Paul C

2010-10-13

We have addressed complex formation between the death domain (DD) of the death receptor CD95 (Fas/APO-1) with the DD of immediate adaptor protein FADD using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and size-exclusion chromatography with in-line light scattering. We find complexation to be independent of the C-terminal 12 residues of CD95 and insensitive to mutation of residues that engage in the high-order clustering of CD95-DD molecules in a recently reported crystal structure obtained at pH 4. Differential NMR linewidths indicate that the C-terminal region of the CD95 chains remains in a disordered state and (13)C-methyl TROSY data are consistent with a lack of high degree of symmetry for the complex. The overall molecular mass of the complex is inconsistent with that in the crystal structure, and the complex dissociates at pH 4. We discuss these findings using sequence analysis of CD95 orthologs and the effect of FADD mutations on the interaction with CD95. Copyright © 2010 Elsevier Ltd. All rights reserved.

Transient α-helices in the disordered RPEL motifs of the serum response factor coactivator MKL1

NASA Astrophysics Data System (ADS)

Mizuguchi, Mineyuki; Fuju, Takahiro; Obita, Takayuki; Ishikawa, Mitsuru; Tsuda, Masaaki; Tabuchi, Akiko

2014-06-01

The megakaryoblastic leukemia 1 (MKL1) protein functions as a transcriptional coactivator of the serum response factor. MKL1 has three RPEL motifs (RPEL1, RPEL2, and RPEL3) in its N-terminal region. MKL1 binds to monomeric G-actin through RPEL motifs, and the dissociation of MKL1 from G-actin promotes the translocation of MKL1 to the nucleus. Although structural data are available for RPEL motifs of MKL1 in complex with G-actin, the structural characteristics of RPEL motifs in the free state have been poorly defined. Here we characterized the structures of free RPEL motifs using NMR and CD spectroscopy. NMR and CD measurements showed that free RPEL motifs are largely unstructured in solution. However, NMR analysis identified transient α-helices in the regions where helices α1 and α2 are induced upon binding to G-actin. Proline mutagenesis showed that the transient α-helices are locally formed without helix-helix interactions. The helix content is higher in the order of RPEL1, RPEL2, and RPEL3. The amount of preformed structure may correlate with the binding affinity between the intrinsically disordered protein and its target molecule.

Editorial: The Sackler International Prize in Biophysical Sciences

NASA Astrophysics Data System (ADS)

Frydman, Lucio

2018-02-01

The Raymond and Beverly Sackler International Prize is awarded alternatively in the fields of Biophysics, Chemistry and Physics on a yearly basis, by Tel Aviv University. The price is intended to encourage dedication to science, originality and excellence, by rewarding outstanding scientists under 45 years of age, with a total purse of 100,000. The 2016 Raymond and Beverly Sackler Prize was awarded in the field of Magnetic Resonance last February in a festive symposium, to three excellent researchers: Professor John Morton (University College London), Professor Guido Pintacuda (Ecole Normale Supérieure de Lyon and CNRS), and Professor Charalampos Kalodimos (at the time at the University of Minnesota). John was recognized for his novel contributions to quantum information processing, by means of a range of highly elegant physical phenomena involving both NMR and EPR. Guido was recognized for his methodological advances in solid state NMR spectroscopy, including advances in proton detection under ultrafast MAS at ultrahigh magnetic field, and for his insightful applications to challenging biological systems. While Charalampos (Babis) was recognized for beautifully detailed characterizations of structure, function, and dynamics in challenging and important biological systems through solution NMR spectroscopy.

Synthesis, spectroscopic and computational characterization of the tautomerism of pyrazoline derivatives from chalcones

NASA Astrophysics Data System (ADS)

Miguel, Fábio Balbino; Dantas, Juliana Arantes; Amorim, Stefany; Andrade, Gustavo F. S.; Costa, Luiz Antônio Sodré; Couri, Mara Rubia Costa

2016-01-01

In the present study a series of novel pyrazolines derivatives has been synthesized, and their structures assigned on the basis of FT-Raman, 1H and 13C NMR spectral data and computational DFT calculations. A joint computational study using B3LYP/6-311G(2d,2p) density functional theory and FT-Raman investigation on the tautomerism of 3-(4-substituted-phenyl)-4,5-dihydro-5-(4-substituted-phenyl)pyrazole-1-carbothioamide and 3-(4-substituted-phenyl)-4,5-dihydro-5-(4-substituted-phenyl)pyrazole-1-carboxamide are presented. The structures were characterized as a minimum in the potential energy surface using DFT. The calculated Raman and NMR spectra were of such remarkable agreement to the experimental results that the equilibrium between tautomeric forms has been discussed in detail. Our study suggests the existence of tautomers, the carboxamide/carbothioamide group may tautomerize, in the solid state or in solution. Thermodynamic data calculated suggests that the R(Cdbnd S)NH2 and R(Cdbnd O)NH2 species are more stable than the R(Cdbnd NH)SH and R(Cdbnd NH)OH species. Additionally, results found for the 1H NMR shifting, pointed out to which structure is present.

Promising applications in drug delivery systems of a novel β-cyclodextrin derivative obtained by green synthesis.

PubMed

García, Agustina; Leonardi, Darío; Lamas, María C

2016-01-15

An efficient and green method has been developed for the synthesis of succinyl-β-cyclodextrin in aqueous media obtaining very good yield. Acidic groups have been introduced in the synthesized carrier molecule to improve the guest-host affinity. To evaluate the suitability of the novel excipient focused to develop oral dosage forms, albendazole, a BSC class II compound, was chosen as a model drug. The β-cyclodextrin derivative and the inclusion complex were thoroughly characterized in solution and solid state by phase solubility studies, FT-IR spectroscopy, SEM, XRD, ESI-MS, DSC, 1D (1)H NMR, 1D (13)C NMR, selective 1D TOCSY, 2D COSY, 2D HSQC, 2D HMBC and ROESY NMR spectroscopy. Phase solubility studies indicated that both of them β-cyclodextrin and succinyl-β-cyclodextrin formed 1:1 inclusion complexes with albendazole, and the stability constants were 68M(-1) (β-cyclodextrin), 437M(-1) (succinyl-β-cyclodextrin), respectively. Water solubility and dissolution rate of albendazole were significantly improved in complex forms. Thus, the succinyl-β-cyclodextrin derivative could be a promising excipient to design oral dosage forms. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Persistent dopants and phase segregation in organolead mixed-halide perovskites

DOE PAGES

Rosales, Bryan A.; Men, Long; Cady, Sarah D.; ...

2016-07-25

Organolead mixed-halide perovskites such as CH 3NH 3PbX 3–aX' a (X, X' = I, Br, Cl) are interesting semiconductors because of their low cost, high photovoltaic power conversion efficiencies, enhanced moisture stability, and band gap tunability. Using a combination of optical absorption spectroscopy, powder X-ray diffraction (XRD), and, for the first time, 207Pb solid state nuclear magnetic resonance (ssNMR), we probe the extent of alloying and phase segregation in these materials. Because 207Pb ssNMR chemical shifts are highly sensitive to local coordination and electronic structure, and vary linearly with halogen electronegativity and band gap, this technique can provide the truemore » chemical speciation and composition of organolead mixed-halide perovskites. We specifically investigate samples made by three different preparative methods: solution phase synthesis, thermal annealing, and solid phase synthesis. 207Pb ssNMR reveals that nonstoichiometric dopants and semicrystalline phases are prevalent in samples made by solution phase synthesis. We show that these nanodomains are persistent after thermal annealing up to 200 °C. Further, a novel solid phase synthesis that starts from the parent, single-halide perovskites can suppress phase segregation but not the formation of dopants. Our observations are consistent with the presence of miscibility gaps and spontaneous spinodal decomposition of the mixed-halide perovskites at room temperature. This underscores how strongly different synthetic procedures impact the nanostructuring and composition of organolead halide perovskites. In conclusion, better optoelectronic properties and improved device stability and performance may be achieved through careful manipulation of the different phases and nanodomains present in these materials.« less

Persistent dopants and phase segregation in organolead mixed-halide perovskites

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

Rosales, Bryan A.; Men, Long; Cady, Sarah D.

Organolead mixed-halide perovskites such as CH 3NH 3PbX 3–aX' a (X, X' = I, Br, Cl) are interesting semiconductors because of their low cost, high photovoltaic power conversion efficiencies, enhanced moisture stability, and band gap tunability. Using a combination of optical absorption spectroscopy, powder X-ray diffraction (XRD), and, for the first time, 207Pb solid state nuclear magnetic resonance (ssNMR), we probe the extent of alloying and phase segregation in these materials. Because 207Pb ssNMR chemical shifts are highly sensitive to local coordination and electronic structure, and vary linearly with halogen electronegativity and band gap, this technique can provide the truemore » chemical speciation and composition of organolead mixed-halide perovskites. We specifically investigate samples made by three different preparative methods: solution phase synthesis, thermal annealing, and solid phase synthesis. 207Pb ssNMR reveals that nonstoichiometric dopants and semicrystalline phases are prevalent in samples made by solution phase synthesis. We show that these nanodomains are persistent after thermal annealing up to 200 °C. Further, a novel solid phase synthesis that starts from the parent, single-halide perovskites can suppress phase segregation but not the formation of dopants. Our observations are consistent with the presence of miscibility gaps and spontaneous spinodal decomposition of the mixed-halide perovskites at room temperature. This underscores how strongly different synthetic procedures impact the nanostructuring and composition of organolead halide perovskites. In conclusion, better optoelectronic properties and improved device stability and performance may be achieved through careful manipulation of the different phases and nanodomains present in these materials.« less

Structures in solutions from joint experimental-computational analysis: applications to cyclic molecules and studies of noncovalent interactions.

PubMed

Aliev, Abil E; Mia, Zakirin A; Khaneja, Harmeet S; King, Frank D

2012-01-26

The potential of an approach combining nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations for full structural characterizations in solution is assessed using cyclic organic compounds, namely, benzazocinone derivatives 1-3 with fused five- and eight-membered aliphatic rings, camphoric anhydride 4, and bullvalene 5. Various MD simulations were considered, using force field and semiempirical QM treatments, implicit and explicit solvation, and high-temperature MD calculations for selecting plausible molecular geometries for subsequent QM geometry optimizations using mainly B3LYP, M062X, and MP2 methods. The QM-predicted values of NMR parameters were compared to their experimental values for verification of the final structures derived from the MD/QM analysis. From these comparisons, initial estimates of quality thresholds (calculated as rms deviations) were 0.7-0.9 Hz for (3)J(HH) couplings, 0.07-0.11 Å for interproton distances, 0.05-0.08 ppm for (1)H chemical shifts, and 1.0-2.1 ppm for (13)C chemical shifts. The obtained results suggest that the accuracy of the MD analysis in predicting geometries and relative conformational energies is not critical and that the final geometry refinements of the structures selected from the MD simulations using QM methods are sufficient for correcting for the expected inaccuracy of the MD analysis. A unique example of C(sp(3))-H···N(sp(3)) intramolecular noncovalent interaction is also identified using the NMR/MD/QM and the natural bond orbital analyses. As the NMR/MD/QM approach relies on the final QM geometry optimization, comparisons of geometric characteristics predicted by different QM methods and those from X-ray and neutron diffraction measurements were undertaken using rigid and flexible cyclic systems. The joint analysis shows that intermolecular noncovalent interactions present in the solid state alter molecular geometries significantly compared to the geometries of isolated molecules from QM calculations.

Synthetic routes to a nanoscale inorganic cluster [Ga{sub 13}(μ{sub 3}-OH){sub 6}(μ{sub 2}-OH){sub 18}(H{sub 2}O)](NO{sub 3}){sub 15} evaluated by solid-state {sup 71}Ga NMR

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

Hammann, Blake A.; Marsh, David A.; Ma, Zayd L.

Solid-state {sup 71}Ga NMR was used to characterize a series of [Ga{sub 13}(μ{sub 3}-OH){sub 6}(μ{sub 2}-OH){sub 18}(H{sub 2}O)](NO{sub 3}){sub 15} “Ga{sub 13}” molecular clusters synthesized by multiple methods. These molecular clusters are precursors to thin film electronics and may be employed in energy applications. The synthetic routes provide varying levels of impurities in the solid phase, and these impurities often elude traditional characterization techniques such as powder X-ray diffraction and Raman spectroscopy. Solid-state NMR can provide a window into the gallium species even in amorphous phases. This information is vital in order to prevent the impurities from causing defect sitesmore » in the corresponding thin films upon gelation and condensation (polymerization) of the Ga{sub 13} clusters. This work demonstrates the resolving power of solid-state NMR to evaluate structure and synthetic quality in the solid state, and the application of high-field NMR to study quadrupolar species, such as {sup 71}Ga. - Graphical abstract: The various synthetic routes and {sup 71}Ga solid-state NMR spectra of the nanoscale inorganic cluster [Ga{sub 13}(μ{sub 3}-OH){sub 6}(μ{sub 2}-OH){sub 18}(H{sub 2}O)](NO{sub 3}){sub 15}. - Highlights: • Solid-state {sup 71}Ga NMR of hydroxo-aquo metal clusters and the impurities present. • High-field NMR capability allows for quadrupolar species, such as {sup 71}Ga, to be routinely studied. • Efficient and environmentally friendly synthetic routes have been developed to prepare hydroxo-aquo metal clusters.« less

Natural abundance (25)Mg solid-state NMR of mg oxyanion systems: a combined experimental and computational study.

PubMed

Cahill, Lindsay S; Hanna, John V; Wong, Alan; Freitas, Jair C C; Yates, Jonathan R; Harris, Robin K; Smith, Mark E

2009-09-28

Solid-state (25)Mg magic angle spinning nuclear magnetic resonance (MAS NMR) data are reported from a range of organic and inorganic magnesium-oxyanion compounds at natural abundance. To constrain the determination of the NMR interaction parameters (delta(iso), chi(Q), eta(Q)) data have been collected at three external magnetic fields (11.7, 14.1 and 18.8 T). Corresponding NMR parameters have also been calculated by using density functional theory (DFT) methods using the GIPAW approach, with good correlations being established between experimental and calculated values of both chi(Q) and delta(iso). These correlations demonstrate that the (25)Mg NMR parameters are very sensitive to the structure, with small changes in the local Mg(2+) environment and the overall hydration state profoundly affecting the observed spectra. The observations suggest that (25)Mg NMR spectroscopy is a potentially potent probe for addressing some key problems in inorganic materials and of metal centres in biologically relevant molecules.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

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

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.

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.

Visualization and processing of computed solid-state NMR parameters: MagresView and MagresPython.

PubMed

Sturniolo, Simone; Green, Timothy F G; Hanson, Robert M; Zilka, Miri; Refson, Keith; Hodgkinson, Paul; Brown, Steven P; Yates, Jonathan R

2016-09-01

We introduce two open source tools to aid the processing and visualisation of ab-initio computed solid-state NMR parameters. The Magres file format for computed NMR parameters (as implemented in CASTEP v8.0 and QuantumEspresso v5.0.0) is implemented. MagresView is built upon the widely used Jmol crystal viewer, and provides an intuitive environment to display computed NMR parameters. It can provide simple pictorial representation of one- and two-dimensional NMR spectra as well as output a selected spin-system for exact simulations with dedicated spin-dynamics software. MagresPython provides a simple scripting environment to manipulate large numbers of computed NMR parameters to search for structural correlations. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

{sup 45}Sc Solid State NMR studies of the silicides ScTSi (T=Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt)

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

Harmening, Thomas; Eckert, Hellmut, E-mail: eckerth@uni-muenster.de; Fehse, Constanze M.

The silicides ScTSi (T=Fe, Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt) were synthesized by arc-melting and characterized by X-ray powder diffraction. The structures of ScCoSi, ScRuSi, ScPdSi, and ScIrSi were refined from single crystal diffractometer data. These silicides crystallize with the TiNiSi type, space group Pnma. No systematic influences of the {sup 45}Sc isotropic magnetic shift and nuclear electric quadrupolar coupling parameters on various structural distortion parameters calculated from the crystal structure data can be detected. {sup 45}Sc MAS-NMR data suggest systematic trends in the local electronic structure probed by the scandium atoms: both the electric field gradients andmore » the isotropic magnetic shifts relative to a 0.2 M aqueous Sc(NO{sub 3}){sub 3} solution decrease with increasing valence electron concentration and within each T group the isotropic magnetic shift decreases monotonically with increasing atomic number. The {sup 45}Sc nuclear electric quadrupolar coupling constants are generally well reproduced by quantum mechanical electric field gradient calculations using the WIEN2k code. Highlights: Black-Right-Pointing-Pointer Arc-melting synthesis of silicides ScTSi. Black-Right-Pointing-Pointer Single crystal X-ray data of ScCoSi, ScRuSi, ScPdSi, and ScIrSi. Black-Right-Pointing-Pointer {sup 45}Sc solid state NMR of silicides ScTSi.« less

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.

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,…

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.

[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.

Palladium complexes with simple iminopyridines as catalysts for polyketone synthesis.

PubMed

Rosar, V; Dedeic, D; Nobile, T; Fini, F; Balducci, G; Alessio, E; Carfagna, C; Milani, B

2016-10-07

Four iminopyridines (N-N') differing in the nature of the substituents on the iminic carbon and on the ortho positions of the aryl ring (H or CH3) on the iminic nitrogen were used for the synthesis of neutral and monocationic palladium(ii) complexes of general formulae [Pd(CH3)Cl(N-N')] and [Pd(CH3)(NCCH3)(N-N')][PF6]. The detailed NMR characterization in solution highlighted that: (i) for both series of complexes, the Pd-CH3 signal is progressively shifted to a lower frequency on increasing the number of methyl groups on the ligand skeleton; (ii) for the neutral derivatives, the chemical shift of the (15)N NMR signals, determined through {(1)H,(15)N}-HMBC spectra, is significantly affected by the coordination to palladium; (iii) the coordination induced shift (CIS) of the nitrogen atom trans to the CH3 ligand is smaller than the other. The structure in the solid state for the neutral derivatives with all the four ligands was solved, pointing out that: (iv) the Pd-C bond distance increases with the basicity of the nitrogen-donor ligand; (v) the Pd-N bond distance correlates well with the CIS value. The combining of the solution and solid state structural features allows stating that: (vi) the Pd-CH3 singlet is a good probe for the electron donor capability of the ligand; (vii) the CIS value might be used as a probe for the strength of the Pd-N bond. All monocationic complexes generated active catalysts for the CO/vinyl arene copolymerization, leading to prevailingly syndiotactic polyketones. The catalyst performances, both in terms of catalyst productivity and polymer molecular weight, correlate well with the precatalyst structural features.

13C CP MAS NMR and GIAO-CHF calculations of coumarins.

PubMed

Zolek, Teresa; Paradowska, Katarzyna; Wawer, Iwona

2003-01-01

13C cross-polarization magic-angle spinning NMR spectra were recorded for a series of solid coumarins. Ab initio calculations of shielding constants were performed with the use of GIAO-CHF method. The combined CPMAS NMR and theoretical approach was successful in characterizing solid-state conformations of coumarins; a relationship sigma (ppm) = -1.032 xdelta + 205.28 (R(2) = 0.9845) can be used to obtain structural information for coumarins, for which solid-state NMR or crystal structure data are not available. Copyright 2002 Elsevier Science (USA)

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

Structural study of human growth hormone-releasing factor fragment (1?29) by vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Carmona, P.; Molina, M.; Lasagabaster, A.

1995-05-01

The conformational structure of fragment 1-29 of human growth hormone releasing factor, hGHRF (1-29), in aqueous solution and in the solid state is investigated by infrared and Raman spectroscopy. The polypeptide backbone is found to be unordered in the solid state. However, the spectra of the peptide prepared as 5% (w/w) aqueous solutions show that approximately 28% of the peptide is involved in intermolecular β-sheet aggregation. The remainder of the peptide exists largely as disordered and β-sheet conformations with a small portion of α-helices. Tyrosine residues are found to be exposed to the solvent. The secondary structures are quantitatively examined through infrared spectroscopy, the conformational percentages being near those obtained by HONDAet al. [ Biopolymers31, 869 (1991)] using circular dichroism. The fast hydrogen/deuterium exchange in peptide groups and the absence of any NMR sign indicative of ordered structure [ G. M. CLOREet al., J. Molec. Biol.191, 553 (1986)] support that the solution conformations of the non-aggregated peptide interconvert in dynamic equilibrium. Some physiological advantages that may derive from this conformational flexibility are also discussed

Oxothiomolybdenum derivatives of the superlacunary crown heteropolyanion {P8W48}: structure of [K4{Mo4O4S4(H2O)3(OH)2}2(WO2)(P8W48O184)]30– and studies in solution.

PubMed

Korenev, Vladimir S; Floquet, Sébastien; Marrot, Jérôme; Haouas, Mohamed; Mbomekallé, Israël-Martyr; Taulelle, Francis; Sokolov, Maxim N; Fedin, Vladimir P; Cadot, Emmanuel

2012-02-20

Reaction of the cyclic lacunary [H(7)P(8)W(48)O(184)](33-) anion (noted P(8)W(48)) with the [Mo(2)S(2)O(2)(H(2)O)(6)](2+) oxothiocation led to two compounds, namely, [K(4){Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(WO(2))(P(8)W(48)O(184))](30-) (denoted 1) and [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(P(8)W(48)O(184))](36-) (denoted 2), which were characterized in the solid state and solution. In the solid state, the structure of [K(4){Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(WO(2))(P(8)W(48)O(184))](30-) reveals the presence of two disordered {Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2+) "handles" connected on both sides of the P(8)W(48) ring. Such a disorder is consistent with the presence of two geometrical isomers where the relative disposition of the two {Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2+) handles are arranged in a perpendicular or parallel mode. Such an interpretation is fully supported by (31)P and (183)W NMR solution studies. The relative stability of both geometrical isomers appears to be dependent upon the nature of the internal alkali cations, i.e., Na(+) vs K(+), and increased lability of the two {Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2+) handles, compared to the oxo analogous, was clearly identified by significant broadening of the (31)P and (183)W NMR lines. Solution studies carried out by UV-vis spectroscopy showed that formation of the adduct [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(P(8)W(48)O(184))](36-) occurs in the 1.5-4.7 pH range and corresponds to a fast and quantitative condensation process. Furthermore, (31)P NMR titrations in solution reveal formation of the "monohandle" derivative [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(P(8)W(48)O(184))](38-) as an intermediate prior to formation of the "bishandle" derivatives. Furthermore, the electrochemical behavior of [{Mo(4)O(4)S(4)(H(2)O)(3)(OH)(2)}(2)(P(8)W(48)O(184))](36-) was studied in aqueous medium and compared with the parent anion P(8)W(48).

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.

Nuclear magnetic resonance of laser-polarized noble gases in molecules, materials and organisms

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

Goodson, Boyd McLean

1999-12-01

Conventional nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are fundamentally challenged by the insensitivity that stems from the ordinarily low spin polarization achievable in even the strongest NMR magnets. However, by transferring angular momentum from laser light to electronic and nuclear spins, optical pumping methods can increase the nuclear spin polarization of noble gases by several orders of magnitude, thereby greatly enhancing their NMR sensitivity. This dissertation is primarily concerned with the principles and practice of optically pumped nuclear magnetic resonance (OPNMR). The enormous sensitivity enhancement afforded by optical pumping noble gases can be exploited to permitmore » a variety of novel NMR experiments across many disciplines. Many such experiments are reviewed, including the void-space imaging of organisms and materials, NMR and MRI of living tissues, probing structure and dynamics of molecules in solution and on surfaces, and zero-field NMR and MRI.« less

High-resolution magnetic resonance spectroscopy using a solid-state spin sensor

NASA Astrophysics Data System (ADS)

Glenn, David R.; Bucher, Dominik B.; Lee, Junghyun; Lukin, Mikhail D.; Park, Hongkun; Walsworth, Ronald L.

2018-03-01

Quantum systems that consist of solid-state electronic spins can be sensitive detectors of nuclear magnetic resonance (NMR) signals, particularly from very small samples. For example, nitrogen–vacancy centres in diamond have been used to record NMR signals from nanometre-scale samples, with sensitivity sufficient to detect the magnetic field produced by a single protein. However, the best reported spectral resolution for NMR of molecules using nitrogen–vacancy centres is about 100 hertz. This is insufficient to resolve the key spectral identifiers of molecular structure that are critical to NMR applications in chemistry, structural biology and materials research, such as scalar couplings (which require a resolution of less than ten hertz) and small chemical shifts (which require a resolution of around one part per million of the nuclear Larmor frequency). Conventional, inductively detected NMR can provide the necessary high spectral resolution, but its limited sensitivity typically requires millimetre-scale samples, precluding applications that involve smaller samples, such as picolitre-volume chemical analysis or correlated optical and NMR microscopy. Here we demonstrate a measurement technique that uses a solid-state spin sensor (a magnetometer) consisting of an ensemble of nitrogen–vacancy centres in combination with a narrowband synchronized readout protocol to obtain NMR spectral resolution of about one hertz. We use this technique to observe NMR scalar couplings in a micrometre-scale sample volume of approximately ten picolitres. We also use the ensemble of nitrogen–vacancy centres to apply NMR to thermally polarized nuclear spins and resolve chemical-shift spectra from small molecules. Our technique enables analytical NMR spectroscopy at the scale of single cells.

Application of Solid-State NMR Relaxometry for Characterization and Formulation Optimization of Grinding-Induced Drug Nanoparticle.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Moribe, Kunikazu

2016-03-07

The formation mechanism of drug nanoparticles was investigated using solid-state nuclear magnetic resonance (NMR) techniques for the efficient discovery of an optimized nanoparticle formulation. The cogrinding of nifedipine (NIF) with polymers, including hydroxypropyl methylcellulose (HPMC) and polyvinylpyrrolidone (PVP), and sodium dodecyl sulfate (SDS) was performed to prepare the NIF nanoparticle formulations. Then, solid-state NMR relaxometry was used for the nanometer-order characterization of NIF in the polymer matrix. Solid-state NMR measurements revealed that the crystal size of NIF was reduced to several tens of nanometers with amorphization of NIF by cogrinding with HPMC and SDS for 100 min. Similarly, the size of the NIF crystal was reduced to less than 90 nm in the 40 min ground mixture of NIF/PVP/SDS. Furthermore, 100 min grinding of NIF/PVP/SDS induced amorphization of almost all the NIF crystals followed by nanosizing. The hydrogen bond between NIF and PVP led to the efficient amorphization of NIF in the NIF/PVP/SDS system compared with NIF/HPMC/SDS system. The efficient nanosizing of the NIF crystal in the solid state, revealed by the solid-state NMR relaxation time measurements, enabled the formation of large amounts of NIF nanoparticles in water followed by the polymer dissolution. In contrast, excess amorphization of the NIF crystals failed to efficiently prepare the NIF nanoparticles. The solid-state characterization of the crystalline NIF revealed good correlation with the NIF nanoparticles formation during aqueous dispersion. Furthermore, the solid-state NMR measurements including relaxometry successfully elucidated the nanometer-order dispersion state of NIF in polymer matrix, leading to the discovery of optimized conditions for the preparation of suitable drug nanoparticles.

Synthesis, Crystal Structures and Properties of Ferrocenyl Bis-Amide Derivatives Yielded via the Ugi Four-Component Reaction.

PubMed

Zhao, Mei; Shao, Guang-Kui; Huang, Dan-Dan; Lv, Xue-Xin; Guo, Dian-Shun

2017-05-04

Ten ferrocenyl bis-amide derivatives were successfully synthesized via the Ugi four-component reaction by treating ferrocenecarboxylic acid with diverse aldehydes, amines, and isocyanides in methanol solution. Their chemical structures were fully characterized by IR, NMR, HR-MS, and X-ray diffraction analyses. They feature unique molecular morphologies and create a 14-membered ring motif in the centro-symmetric dimers generated in the solid state. Moreover, the electrochemical behavior of these ferrocenyl bis-amides was assessed by cyclic voltammetry.

pH Dependent Spin State Population and 19F NMR Chemical Shift via Remote Ligand Protonation in an Iron(II) Complex (Postprint)

DTIC Science & Technology

2017-12-11

AFRL-RX-WP-JA-2017-0501 pH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL SHIFT VIA REMOTE LIGAND PROTONATION IN AN IRON(II...From - To) 16 November 2017 Interim 24 January 2014 – 16 October 2017 4. TITLE AND SUBTITLE PH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL...dx.doi.org/10.1039/C7CC08099A 14. ABSTRACT (Maximum 200 words) An FeII complex that features a pH- dependent spin state population, by virtue of a

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.

A novel low-molecular-mass gelator with a redox active ferrocenyl group: tuning gel formation by oxidation.

PubMed

Liu, Jing; Yan, Junlin; Yuan, Xuanwei; Liu, Kaiqiang; Peng, Junxia; Fang, Yu

2008-02-15

A novel low-molecular-mass gelator containing a redox-active ferrocenyl group, cholesteryl glycinate ferrocenoylamide (CGF), was intentionally designed and prepared. It was demonstrated that the gelator gels 13 out of the 45 solvents tested. Scanning electron microscopy (SEM) measurements revealed that the gelator self-assembled into different supramolecular network structures in different gels. Chemical oxidation of the ferrocenyl residue resulted in phase transition of the gel from gel state to solution state. FTIR and (1)H NMR spectroscopy studies revealed that hydrogen bonding between the gelator molecules in the gel was one of the main driving forces for the formation of the gels.

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

Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

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

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

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less

Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

DOE PAGES

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

2016-09-02

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less

Chemical disorder and 207Pb hyperfine fields in the magnetoelectric multiferroic Pb (F e1 /2S b1 /2 ) O3 and its solid solution with Pb (F e1 /2N b1 /2) O3

NASA Astrophysics Data System (ADS)

Zagorodniy, Yu. O.; Kuzian, R. O.; Kondakova, I. V.; Maryško, M.; Chlan, V.; Štěpánková, H.; Olekhnovich, N. M.; Pushkarev, A. V.; Radyush, Yu. V.; Raevski, I. P.; Zalar, B.; Laguta, V. V.; Stephanovich, V. A.

2018-01-01

We report on the results of magnetic susceptibility, electron paramagnetic resonance, and 207Pb nuclear magnetic resonance (NMR) studies of the magnetoelectric multiferroic Pb (F e1 /2S b1 /2 ) O3 (PFS) ceramic, as well as its solid solution with Pb (F e1 /2N b1 /2) O3 (PFN) of different degrees of the 1:1 ordering of magnetic F e3 + and nonmagnetic S b5 + ions. The ordering has been studied by x-ray diffraction (XRD) and NMR methods. In particular, two spectral lines, originating from the ordered and disordered regions, respectively, are resolved in the 207Pb NMR spectra. This demonstrates the presence of spatially heterogeneous ordering where ordered regions are embedded into a disordered matrix. Combining XRD and NMR data, we have determined both the long-range order parameter s and the volume fraction of ordered regions s' for all investigated samples. The values vary in the range s =0 -0.93 and s'=0 -1 . We have found that the 207Pb Fermi contact interaction strongly depends on the disorder in the Fe/Sb positions: whereas it reaches 7.08 MHz in the ordered lattice, it is almost zero in the disordered environment. These results are further supported by the studies of PFS-PFN solid solutions. The analysis of experimental data in terms of density functional theory reveals a noticeably higher hybridization between Pb 6s and Fe 3d orbitals in the ordered case. The ordering of magnetic and nonmagnetic ions has a strong impact on the magnetic properties of PFS, leading to a transformation of the long-range ordered antiferromagnetic phase in chemically ordered samples to the spin glass state already in partially (s =0.35 ) disordered specimens. In our opinion, the difference in the magnetic properties of PFN and PFS is related to the fact that PFN is completely disordered, in contrast to PFS, which is only partially disordered, with small ordered regions existing in the disordered matrix that prevent the percolation of the nearest-neighbor Fe-Fe exchange interaction across the lattice.

Solution XAS Analysis for Exploring the Active Species in Homogeneous Vanadium Complex Catalysis

NASA Astrophysics Data System (ADS)

Nomura, Kotohiro; Mitsudome, Takato; Tsutsumi, Ken; Yamazoe, Seiji

2018-06-01

Selected examples in V K-edge X-ray Absorption Near Edge Structure (XANES) analysis of a series of vanadium complexes containing imido ligands (possessing metal-nitrogen double bond) in toluene solution have been introduced, and their pre-edge and the edge were affected by their structures and nature of ligands. Selected results in exploring the oxidation states of the active species in ethylene dimerization/polymerization using homogeneous vanadium catalysts [consisting of (imido)vanadium(V) complexes and Al cocatalysts] by X-ray absorption spectroscopy (XAS) analyses have been introduced. It has been demonstrated that the method should provide more clear information concerning the active species in situ, especially by combination with the other methods (NMR and ESR spectra, X-ray crystallographic analysis, and reaction chemistry), and should be powerful tool for study of catalysis mechanism as well as for the structural analysis in solution.

Is organic matter found in glaciers similar to soil organic matter? A detailed molecular-level investigation of organic matter found in cryoconite holes on the Athabasca Glacier

NASA Astrophysics Data System (ADS)

Simpson, M. J.; Xu, Y.; Eyles, N.; Simpson, A. J.; Baer, A.

2009-04-01

Cryoconite is a dark-coloured, dust-like material found on the surfaces of glaciers. Cryoconite has received much interest recently because cryoconite holes, which are produced by accelerated ice melt, act as habitats for microbes on glacier surfaces and accelerate ice melt. To the best of our knowledge, cyroconite organic matter (COM) has not yet been chemically characterized at the molecular level. In this study, organic matter biomarkers and a host of Nuclear Magnetic Resonance (NMR) techniques were used to characterize COM from the Athabasca Glacier in the Canadian Rocky Mountains. The research questions that were targeted by this study include: 1) what are the sources of COM on the Athabasca Glacier; 2) are there any biomarker and/or NMR evidence for microbial community activity in the cryoconite holes; and 3) is the COM structurally similar to terrestrial OM? Solvent extracts contained large quantities of fatty acids, n-alkanols, n-alkanes, wax esters and sterols. A large contribution of C23, C25 and C27 relative to C29 and C31 n-alkanes suggests that allochthonous COM is mainly from lower order plants (mosses, lichens). This is confirmed by the absence of lignin phenols (after copper (II) oxidation) in extracts and NMR analyses of COM. Solution-state 1H NMR reveals prominent signals from microbial components, while solid-state 13C Cross Polarization Magic Angle Spinning NMR analysis shows an atypically high alkyl/O-alkyl ratio, suggesting that COM is unique compared to organic matter found in nearby soils. The NMR results suggest that COM is dominated by microbial-derived compounds which were confirmed by phospholipid fatty acid analysis, which showed a significant microbial contribution, primarily from bacteria and minor microeukaryotes. Both biomarker and NMR data suggest that COM likely supports active microbial communities on the Athabasca Glacier and that COM composition is uniquely different than that found in terrestrial environments. Our data indicate that windblown or meltwater fluvial OM rich materials from adjacent peatlands or mosses and lichens developed on tundra soils can be trapped and preserved in cryoconite holes in glaciers and may be an important mechanism for promoting active bacterial colonies in glacial environments both modern and ancient. Given that such material is incorporated within the glacier in the accumulation zone or flushed by meltwaters into subglacial environments, reworked COM may provide nutrient sources for active microbial communities found within and under glaciers.

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

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.

Conformational polymorphism and thermochemical analysis of 5,5' ''-bis[(2,2,5,5-tetramethyl-1-aza-2,5-disila-1-cyclopentyl)ethyl]-2,2':5',2' ':5' ',2' ''-quaterthiophene.

PubMed

Muguruma, Hitoshi; Hotta, Shu

2006-11-23

The titled compound exists as two polymorphic solid phases (denoted form-I and form-II). Form-I obtained by as-synthesized material is a more stable phase. Form-II is a less stable phase. Spontaneous solid-solid transformation from form-II to form-I is observed in the temperature range between room temperature and the melting point of form-I (Tm = 156.5 degrees C), and its activation energy is estimated to be 96 kJ mol-1 by Arrhenius plot. The solid-solute-solid transformation (recrystallization from solution) from form-II to form-I is also observed. In contrast, form-II is obtained only by a solid-melt-solid transformation from form-I. Therefore, the system of two polymorphs is monotropic. The solid-state NMR measurement shows that form-I has the molecular conformation of complete S-syn-anti-syn in the oligothiophene backbone, whereas form-II has that of S-all-anti. With the solution NMR data, the polymorphism could not be observed. Therefore, the polymorphs originate from the different molecular packing involving the conformational change of the molecule. This unique property is attributed to the extra bulky terminal groups of the compounds. However, despite the extra bulky terminal groups, the mentioned polymorphism is not observed in the titled compound analogue which has S-all-anti conformation (like form-II).

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.

Dissolution DNP-NMR spectroscopy using galvinoxyl as a polarizing agent

NASA Astrophysics Data System (ADS)

Lumata, Lloyd L.; Merritt, Matthew E.; Malloy, Craig R.; Sherry, A. Dean; van Tol, Johan; Song, Likai; Kovacs, Zoltan

2013-02-01

The goal of this work was to test feasibility of using galvinoxyl (2,6-di-tert-butyl-α-(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)-p-tolyloxy) as a polarizing agent for dissolution dynamic nuclear polarization (DNP) NMR spectroscopy. We have found that galvinoxyl is reasonably soluble in ethyl acetate, chloroform, or acetone and the solutions formed good glasses when mixed together or with other solvents such as dimethyl sulfoxide. W-band electron spin resonance (ESR) measurements revealed that galvinoxyl has an ESR linewidth D intermediate between that of carbon-centered free radical trityl OX063 and the nitroxide-based 4-oxo-TEMPO, thus the DNP with galvinoxyl for nuclei with low gyromagnetic ratio γ such as 13C and 15N is expected to proceed predominantly via the thermal mixing process. The optimum radical concentration that would afford the highest 13C nuclear polarization (approximately 6% for [1-13C]ethyl acetate) at 3.35 T and 1.4 K was found to be around 40 mM. After dissolution, large liquid-state NMR enhancements were achieved for a number of 13C and 15N compounds with long spin-lattice relaxation time T1. In addition, the hydrophobic galvinoxyl free radical can be easily filtered out from the dissolution liquid when water is used as the solvent. These results indicate that galvinoxyl can be considered as an easily available free radical polarizing agent for routine dissolution DNP-NMR spectroscopy.

NMR crystallography of zeolites: How far can we go without diffraction data?

PubMed

Brouwer, Darren H; Van Huizen, Jared

2018-05-10

Nuclear magnetic resonance (NMR) crystallography-an approach to structure determination that seeks to integrate solid-state NMR spectroscopy, diffraction, and computation methods-has emerged as an effective strategy to determine structures of difficult-to-characterize materials, including zeolites and related network materials. This paper explores how far it is possible to go in determining the structure of a zeolite framework from a minimal amount of input information derived only from solid-state NMR spectroscopy. It is shown that the framework structure of the fluoride-containing and tetramethylammonium-templated octadecasil clathrasil material can be solved from the 1D 29 Si NMR spectrum and a single 2D 29 Si NMR correlation spectrum alone, without the space group and unit cell parameters normally obtained from diffraction data. The resulting NMR-solved structure is in excellent agreement with the structures determined previously by diffraction methods. It is anticipated that NMR crystallography strategies like this will be useful for structure determination of other materials, which cannot be solved from diffraction methods alone. Copyright © 2018 John Wiley & Sons, Ltd.

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids

PubMed Central

2013-01-01

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1H and 13C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1H and 13C chemical shifts for directly bonded 13C–1H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure. PMID:24386493

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids.

PubMed

Dudenko, Dmytro V; Williams, P Andrew; Hughes, Colan E; Antzutkin, Oleg N; Velaga, Sitaram P; Brown, Steven P; Harris, Kenneth D M

2013-06-13

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1 H and 13 C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1 H and 13 C chemical shifts for directly bonded 13 C- 1 H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure.

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.

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.

Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

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

Jacques, David A.; Streamer, Margaret; Rowland, Susan L.

2009-09-02

The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB. The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomericmore » or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations.« less

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

PubMed

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid for organic light-emitting devices.

PubMed

Saş, E Babur; Kurt, M; Can, M; Okur, S; İçli, S; Demiç, S

2014-12-10

The molecular structure and vibrations of 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid (MePIFA) were investigated by infrared and Raman spectroscopies, UV-Vis, (1)H and (13)C NMR spectroscopic techniques and NBO analysis. FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. (1)H and (13)C NMR spectra and UV-Vis spectrum were recorded in DMSO solution. HOMO-LUMO analysis and molecular electrostatic potential (MEP) analysis were performed. The theoretical calculations for the molecular structure and spectroscopies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After the geometry of the molecule was optimized, vibration wavenumbers and fundamental vibration wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The total (TDOS), partial (PDOS) density of state and overlap population density of state (OPDOS) diagrams analysis were made using GaussSum 2.2 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid for organic light-emitting devices

NASA Astrophysics Data System (ADS)

Saş, E. Babur; Kurt, M.; Can, M.; Okur, S.; İçli, S.; Demiç, S.

2014-12-01

The molecular structure and vibrations of 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid (MePIFA) were investigated by infrared and Raman spectroscopies, UV-Vis, 1H and 13C NMR spectroscopic techniques and NBO analysis. FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. 1H and 13C NMR spectra and UV-Vis spectrum were recorded in DMSO solution. HOMO-LUMO analysis and molecular electrostatic potential (MEP) analysis were performed. The theoretical calculations for the molecular structure and spectroscopies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After the geometry of the molecule was optimized, vibration wavenumbers and fundamental vibration wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The total (TDOS), partial (PDOS) density of state and overlap population density of state (OPDOS) diagrams analysis were made using GaussSum 2.2 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra.

Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

PubMed

Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

2012-07-10

We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

New thermoresistant polymorph from CO2 recrystallization of minocycline hydrochloride.

PubMed

Rodrigues, Miguel A; Tiago, João M; Padrela, Luis; Matos, Henrique A; Nunes, Teresa G; Pinheiro, Lídia; Almeida, António J; de Azevedo, Edmundo Gomes

2014-11-01

To prepare and thoroughly characterize a new polymorph of the broad-spectrum antibiotic minocycline from its hydrochloride dehydrate salts. The new minocycline hydrochloride polymorph was prepared by means of the antisolvent effect caused by carbon dioxide. Minocycline recrystallized as a red crystalline hydrochloride salt, starting from solutions or suspensions containing CO2 and ethanol under defined conditions of temperature, pressure and composition. This novel polymorph (β-minocycline) revealed characteristic PXRD and FTIR patterns and a high melting point (of 247 ºC) compared to the initial minocycline hydrochloride hydrates (α-minocycline). Upon dissolution the new polymorph showed full anti-microbial activity. Solid-state NMR and DSC studies evidenced the higher chemical stability and crystalline homogeneity of β-minocycline compared to the commercial chlorohydrate powders. Molecular structures of both minocyclines present relevant differences as shown by multinuclear solid-state NMR. This work describes a new crystalline structure of minocycline and evidences the ability of ethanol-CO2 system in removing water molecules from the crystalline structure of this API, at modest pressure, temperature and relatively short time (2 h), while controlling the crystal habit. This process has therefore the potential to become a consistent alternative towards the control of the solid form of APIs.

Structural study of the membrane protein MscL using cell-free expression and solid-state NMR

NASA Astrophysics Data System (ADS)

Abdine, Alaa; Verhoeven, Michiel A.; Park, Kyu-Ho; Ghazi, Alexandre; Guittet, Eric; Berrier, Catherine; Van Heijenoort, Carine; Warschawski, Dror E.

2010-05-01

High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75 kDa pentameric α-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR.

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

PubMed Central

Tian, Ye; Schwieters, Charles D.; Opella, Stanley J.; Marassi, Francesca M.

2011-01-01

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes. PMID:22036904

Solid-state NMR adiabatic TOBSY sequences provide enhanced sensitivity for multidimensional high-resolution magic-angle-spinning 1H MR spectroscopy

NASA Astrophysics Data System (ADS)

Andronesi, Ovidiu C.; Mintzopoulos, Dionyssios; Struppe, Jochem; Black, Peter M.; Tzika, A. Aria

2008-08-01

We propose a solid-state NMR method that maximizes the advantages of high-resolution magic-angle-spinning (HRMAS) applied to intact biopsies when compared to more conventional liquid-state NMR approaches. Theoretical treatment, numerical simulations and experimental results on intact human brain biopsies are presented. Experimentally, it is proven that an optimized adiabatic TOBSY (TOtal through Bond correlation SpectroscopY) solid-state NMR pulse sequence for two-dimensional 1H- 1H homonuclear scalar-coupling longitudinal isotropic mixing provides a 20%-50% improvement in signal-to-noise ratio relative to its liquid-state analogue TOCSY (TOtal Correlation SpectroscopY). For this purpose we have refined the C9151 symmetry-based 13C TOBSY pulse sequence for 1H MRS use and compared it to MLEV-16 TOCSY sequence. Both sequences were rotor-synchronized and implemented using WURST-8 adiabatic inversion pulses. As discussed theoretically and shown in simulations, the improved magnetization-transfer comes from actively removing residual dipolar couplings from the average Hamiltonian. Importantly, the solid-state NMR techniques are tailored to perform measurements at low temperatures where sample degradation is reduced. This is the first demonstration of such a concept for HRMAS metabolic profiling of disease processes, including cancer, from biopsies requiring reduced sample degradation for further genomic analysis.

Synthesis, structure characterization and biological studies on a new aromatic hydrazone, 5-(2-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)hydrazono)-2,2-dimethyl-1,3-dioxane-4,6-dione, and its transition metal complexes

NASA Astrophysics Data System (ADS)

Kumar, Shubha S.; Biju, S.; Sadasivan, V.

2018-03-01

A new aromatic hydrazone 5-(2-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)hydrazono)-2,2-dimethyl-1,3-dioxane-4,6-dione has been synthesized by Japp-Klingemann reaction from diazotized 4-aminoantipyrine and Meldrum's acid. A few 3d-metal ion complexes of this hydrazone were synthesized. The compound and its complexes were characterized by UV-Visible, 1H NMR, ESR, Mass spectral, molar conductance and magnetic susceptibility measurements. The compound was found to exist in hydrazone form in solid state and solution from SXRD and 1H NMR study. The influence of pH on the molecule was studied and found that it shows azo/enol-hydrazone tautomerism in solution. This molecule act as a univalent tridentate ligand and the complexes were assigned to have a 1:2 stoichiometry (M:L). The antioxidant properties of the compounds were explored by DPPH assay and found that the ligand possesses better free radical scavenging effect than the complexes. Antimicrobial activities of these compounds were investigated and were found to be active.

Bioactivity of Sodium Free Fluoride Containing Glasses and Glass-Ceramics

PubMed Central

Chen, Xiaojing; Chen, Xiaohui; Brauer, Delia S.; Wilson, Rory M.; Hill, Robert G.; Karpukhina, Natalia

2014-01-01

The bioactivity of a series of fluoride-containing sodium-free calcium and strontium phosphosilicate glasses has been tested in vitro. Glasses with high fluoride content were partially crystallised to apatite and other fluoride-containing phases. The bioactivity study was carried out in Tris and SBF buffers, and apatite formation was monitored by XRD, FTIR and solid state NMR. Ion release in solutions has been measured using ICP-OES and fluoride-ion selective electrode. The results show that glasses with low amounts of fluoride that were initially amorphous degraded rapidly in Tris buffer and formed apatite as early as 3 h after immersion. The apatite was identified as fluorapatite by 19F MAS-NMR after 6 h of immersion. Glass degradation and apatite formation was significantly slower in SBF solution compared to Tris. On immersion of the partially crystallised glasses, the fraction of apatite increased at 3 h compared to the amount of apatite prior to the treatment. Thus, partial crystallisation of the glasses has not affected bioactivity significantly. Fast dissolution of the amorphous phase was also indicated. There was no difference in kinetics between Tris and SBF studies when the glass was partially crystallised to apatite before immersion. Two different mechanisms of apatite formation for amorphous or partially crystallised glasses are discussed. PMID:28788139

High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

PubMed

Tian, Ye; Schwieters, Charles D; Opella, Stanley J; Marassi, Francesca M

2017-01-01

Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision, and conformation, and that structure refinement can be obtained by short relaxation with EEFx to obtain improvements in these key metrics. These developments broaden the range of biomolecular structures that can be calculated with high fidelity from NMR restraints.

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

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Crystallographic structure refinement with quadrupolar nuclei: a combined solid-state NMR and GIPAW DFT example using MgBr(2).

PubMed

Widdifield, Cory M; Bryce, David L

2009-09-07

Solid-state NMR spectroscopy and GIPAW DFT calculations reveal the pronounced sensitivity of (79/81)Br and (25)Mg quadrupolar coupling constants to subtle aspects of solid state structure which were not previously detected by pXRD methods.

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.

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.

Reassessment of MxiH subunit orientation and fold within native Shigella T3SS needles using surface labelling and solid-state NMR.

PubMed

Verasdonck, Joeri; Shen, Da-Kang; Treadgold, Alexander; Arthur, Christopher; Böckmann, Anja; Meier, Beat H; Blocker, Ariel J

2015-12-01

T3SSs are essential virulence determinants of many Gram-negative bacteria, used to inject bacterial effectors of virulence into eukaryotic host cells. Their major extracellular portion, a ∼50 nm hollow, needle-like structure, is essential to host cell sensing and the conduit for effector secretion. It is formed of a small, conserved subunit arranged as a helical polymer. The structure of the subunit has been studied by electron cryomicroscopy within native polymers and by solid-state NMR in recombinant polymers, yielding two incompatible atomic models. To resolve this controversy, we re-examined the native polymer used for electron cryomicroscopy via surface labelling and solid-state NMR. Our data show the orientation and overall fold of the subunit within this polymer is as established by solid-state NMR for recombinant polymers. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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.