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.

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.

Mycosporine-like Amino Acids and Other Phytochemicals Directly Detected by High-Resolution NMR on Klamath (Aphanizomenon flos-aquae) Blue-Green Algae.

PubMed

Righi, Valeria; Parenti, Francesca; Schenetti, Luisa; Mucci, Adele

2016-09-07

This study describes for the first time the use of high-resolution nuclear magnetic resonance (NMR) on Klamath (Aphanizomenon flos-aquae, AFA) blue-green algae directly on powder suspension. These algae are considered to be a "superfood", due to their complete nutritional profile that has proved to have important therapeutic effects. The main advantage of NMR spectroscopy is that it permits the detection of a number of metabolites all at once. The Klamath alga metabolome was revealed to be quite complex, and the most peculiar phytochemicals that can be detected directly on algae by NMR are mycosporine-like amino acids (porphyra-334, P334; shinorine, Shi) and low molecular weight glycosides (glyceryl β-d-galactopyranoside, GalpG; glyceryl 6-amino-6-deoxy-α-d-glucopyranoside, ADG), all compounds with a high nutraceutical value. The presence of cis-3,4-DhLys was revealed for the first time. This molecule could be involved in the anticancer properties ascribed to AFA.

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

PubMed

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

2017-10-10

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

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.

Stereoselective synthesis, spectral and antimicrobial studies of some cyanoacetyl hydrazones of 3-alkyl-2,6-diarylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Velayutham Pillai, M.; Rajeswari, K.; Vidhyasagar, T.

2014-11-01

A series of novel cyanoacetyl hydrazones of 3-alkyl-2,6-diarylpiperidin-4-ones were synthesized stereoselectively and characterized by IR, Mass, 1H NMR, 13C NMR, 1H-1H COSY and 1H-13C COSY spectra. The stereochemistry of the synthesized compounds was established using NMR spectra. Antimicrobial screening of the synthesized compounds revealed their antibacterial and antifungal potencies. Growth inhibition of Enterobacter Aerogenes by compound 15 was found to be superior to the standard drug.

Electronic properties of GeTe and Ag- or Sb-substituted GeTe studied by low-temperature Te 125 NMR

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

Cui, J.; Levin, E. M.; Lee, Y.

We have carried out 125Te nuclear magnetic resonance (NMR) in a wide temperature range of 1.5–300 K to investigate the electronic properties of Ge 50 Te 50, Ag 2 Ge 48Te 50 , and Sb 2 Ge 48 Te 50 from a microscopic point of view. From the temperature dependence of the NMR shift (K) and nuclear spin lattice relaxation rate (1/T 1), we found that two bands contribute to the physical properties of the materials. One band overlaps the Fermi level providing the metallic state where no strong electron correlations are revealed by Korringa analysis. The other band ismore » separated from the Fermi level by an energy gap of E g/k B ~67 K, which gives rise to semiconductorlike properties. First-principles calculation reveals that the metallic band originates from the Ge vacancy while the semiconductorlike band is related to the fine structure of the density of states near the Fermi level. We find low-temperature Te125 NMR data for the materials studied here clearly show that Ag substitution increases hole concentration while Sb substitution decreases it.« less

Electronic properties of GeTe and Ag- or Sb-substituted GeTe studied by low-temperature Te 125 NMR

DOE PAGES

Cui, J.; Levin, E. M.; Lee, Y.; ...

2016-08-18

We have carried out 125Te nuclear magnetic resonance (NMR) in a wide temperature range of 1.5–300 K to investigate the electronic properties of Ge 50 Te 50, Ag 2 Ge 48Te 50 , and Sb 2 Ge 48 Te 50 from a microscopic point of view. From the temperature dependence of the NMR shift (K) and nuclear spin lattice relaxation rate (1/T 1), we found that two bands contribute to the physical properties of the materials. One band overlaps the Fermi level providing the metallic state where no strong electron correlations are revealed by Korringa analysis. The other band ismore » separated from the Fermi level by an energy gap of E g/k B ~67 K, which gives rise to semiconductorlike properties. First-principles calculation reveals that the metallic band originates from the Ge vacancy while the semiconductorlike band is related to the fine structure of the density of states near the Fermi level. We find low-temperature Te125 NMR data for the materials studied here clearly show that Ag substitution increases hole concentration while Sb substitution decreases it.« less

Effects of varying water adsorption on a Cu3(BTC)2 metal-organic framework (MOF) as studied by 1H and 13C solid-state NMR spectroscopy.

PubMed

Gul-E-Noor, Farhana; Jee, Bettina; Pöppl, Andreas; Hartmann, Martin; Himsl, Dieter; Bertmer, Marko

2011-05-07

The process of water adsorption on a dehydrated Cu(3)(BTC)(2) (copper (II) benzene 1,3,5-tricarboxylate) metal-organic framework (MOF) was studied with (1)H and (13)C solid-state NMR. Different relative amounts of water (0.5, 0.75, 1, 1.5, 2, and 5 mole equivalents with respect to copper) were adsorbed via the gas phase. (1)H and (13)C MAS NMR spectra of dehydrated and water-loaded Cu(3)(BTC)(2) samples gave evidence on the structural changes due to water adsorption within the MOF material as well as information on water dynamics. The analysis of (1)H spinning sideband intensities reveals differences in the (1)H-(63/65)Cu hyperfine coupling between dehydrated and water-loaded samples. The investigation was continued for 60 days to follow the stability of the Cu(3)(BTC)(2) network under humid conditions. NMR data reveal that Cu(3)(BTC)(2) decomposes quite fast with the decomposition being different for different water contents. This journal is © the Owner Societies 2011

Mechanisms of amyloid formation revealed by solution NMR

PubMed Central

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

2015-01-01

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

Dammarane-type triterpenes from the Brazilian medicinal plant Cordia multispicata.

PubMed

Kuroyanagi, Masanori; Kawahara, Nobuo; Sekita, Setsuko; Satake, Motoyoshi; Hayashi, Tatsuo; Takase, Yoichi; Masuda, Kazuo

2003-10-01

From the Brazilian medicinal plant Carucaá (Cordia multispicata), oleanane- and ursane-type triterpenoids were previously reported as anti-androgenic constituents of the plant. In this study, purification of the polar elements of the EtOAc-soluble fraction of the plant revealed nine novel dammarane-type triterpenes, named cordianols A-I (1-9) along with the known compound cordialin A (10). The structures of these new compounds were elucidated by means of spectral methods including HRFABMS, (1)H NMR, (13)C NMR, and 2D NMR (HMQC, HMBC, NOESY). Absolute configuration at C-23 of compound 7 was determined by an excitone chirality method. Some of these new compounds revealed a hemiketal structure on the A ring and a hydroxylated or epoxidated 20(22)-(E)-ene side chain and showed weak anti-androgenic activity.

Calorimetric, FTIR and 1H NMR measurements in combination with DFT calculations for monitoring solid-state changes of dynamics of sibutramine hydrochloride.

PubMed

Pajzderska, Aleksandra; Chudoba, Dorota M; Mielcarek, Jadwiga; Wąsicki, Jan

2012-10-01

Two forms of sibutramine hydrochloride, monohydrate and anhydrous, have been investigated by calorimetric methods, Fourier transform infrared (FTIR) absorption and (1) H nuclear magnetic resonance (NMR) measurements as well as by density functional theory (DFT) of vibrational frequencies and infrared intensities, calculations of steric hindrances and Monte Carlo simulations. The results of FTIR spectra combined with DFT calculations permitted identification of the bands corresponding to the dynamics and vibrations of water molecules. NMR study and Monte Carlo simulations revealed the occurrence of reorientation jumps of the methyl groups in sibutramine cation and also revealed that the reorientation of isopropyl group is possible only in sibutramine monohydrate hydrochloride. The hydration of sibutramine hydrochloride causes a change in the conformation of sibutramine cation. Copyright © 2012 Wiley-Liss, Inc.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

[Derivative spectrophotometric and NMR spectroscopic study in pharmaceutical science].

PubMed

Kitamura, Keisuke

2007-10-01

This review starts with an introduction of derivative spectrophotometry followed by a description on the construction of a personal computer-assisted derivative spectrophotometric (DS) system. An acquisition system for inputting digitalized absorption spectra into personal computers and a BASIC program for calculating derivative spectra were developed. Then, applications of the system to drug analyses that are difficult with traditional absorption methods are described. Following this, studies on the interactions of drugs with biological macromolecules by the DS and NMR methods were discussed. An (1)H NMR study elucidated that the small unilamellar vesicle (SUV) has a single membrane made of a phosphatidylcholine bilayer, and that chlorpromazine interacts with both the outer and inner layers. (13)C NMR revealed a reduction of the dissociation constants of phenothiazine drugs due to their interaction with SUV. The partition coefficients of phenothiazine, benzodiazepine and steroid drugs in an SUV-water system and the effects of cholesterol or amino lipids content on these partition coefficients were examined by the DS method. The binding constants of phenothiazine drugs to bovine serum albumin (BSA) and the influence of Na(+), K(+), Cl(-), Br(-), and I(-) on these binding constants were determined by DS. It was found that I(-), Br(-), Cl(-) reduce the binding constants in this order, and that Na(+) and K(+) have no effect. A (19)F NMR study revealed that triflupromazine binds to BSA and human serum albumin in two regions including Site II with different populations, and that a nonsteroidal anti-inflammatory drug, niflumic acid, binds Sites Ia and Ib.

Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts.

PubMed

Monaco, Serena; Tailford, Louise E; Juge, Nathalie; Angulo, Jesus

2017-11-27

Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP-STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D 2 O/H 2 O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP-STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

NMR-based metabolic study of fruits of Physalis peruviana L. grown in eight different Peruvian ecosystems.

PubMed

Maruenda, Helena; Cabrera, Rodrigo; Cañari-Chumpitaz, Cristhian; Lopez, Juan M; Toubiana, David

2018-10-01

The berry of Physalis peruviana L. (Solanaceae) represents an important socio-economical commodity for Latin America. The absence of a clear phenotype renders it difficult to trace its place of origin. In this study, Cape gooseberries from eight different regions within the Peruvian Andes were profiled for their metabolism implementing a NMR platform. Twenty-four compounds could be unequivocally identified and sixteen quantified. One-way ANOVA and post-hoc Tukey test revealed that all of the quantified metabolites changed significantly among regions: Bambamarca I showed the most accumulated significant differences. The coefficient of variation demonstrated high phenotypic plasticity for amino acids, while sugars displayed low phenotypic plasticity. Correlation analysis highlighted the closely coordinated behavior of the amino acid profile. Finally, PLS-DA revealed a clear separation among the regions based on their metabolic profiles, accentuating the discriminatory capacity of NMR in establishing significant phytochemical differences between producing regions of the fruit of P. peruviana L. Copyright © 2018 Elsevier Ltd. All rights reserved.

73Ge-NMR study on magnetic fluctuations of ferromagnetic superconductor UGe2

NASA Astrophysics Data System (ADS)

Noma, Y.; Kotegawa, H.; Kubo, T.; Tou, H.; Harima, H.; Haga, Y.; Yamamoto, E.; Ōnuki, Y.; Itoh, K. M.; Haller, E. E.; Nakamura, A.; Homma, Y.; Honda, F.; Aoki, D.

2018-05-01

We report 73Ge-NMR measurement on the ferromagnetic superconductor UGe2 at ambient pressure. The observed NMR spectrum supports that the electric field gradient at three inequivalent Ge sites is correctly deduced by a LDA calculation. The temperature dependences of the nuclear spin lattice relaxation rate 1 /T1 for H0 ⊥ a (easy axis) and H0 ∥ a were obtained for the oriented sample. The contrasting behavior in 1 /T1 for H0 ⊥ a and H0 ∥ a reveals that the magnetic fluctuation of UGe2 is highly anisotropic.

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

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.

STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.

PubMed

Gaßmeyer, Sarah Katharina; Yoshikawa, Hiroyuki; Enoki, Junichi; Hülsemann, Nadine; Stoll, Raphael; Miyamoto, Kenji; Kourist, Robert

2015-06-23

Structure-guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation-transfer-difference NMR (STD-NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum memory enhanced nuclear magnetic resonance of nanometer-scale samples with a single spin in diamond

NASA Astrophysics Data System (ADS)

Aslam, Nabeel; Pfender, Matthias; Zaiser, Sebastian; Favaro de Oliveira, Felipe; Momenzadeh, S. Ali; Denisenko, Andrej; Isoya, Junichi; Neumann, Philipp; Wrachtrup, Joerg

Recently nuclear magnetic resonance (NMR) of nanoscale samples at ambient conditions has been achieved with nitrogen-vacancy (NV) centers in diamond. So far the spectral resolution in the NV NMR experiments was limited by the sensor's coherence time, which in turn prohibited revealing the chemical composition and dynamics of the system under investigation. By entangling the NV electron spin sensor with a long-lived memory spin qubit we increase the spectral resolution of NMR measurement sequences for the detection of external nuclear spins. Applying the latter sensor-memory-couple it is particularly easy to track diffusion processes, to identify the molecules under study and to deduce the actual NV center depth inside the diamond. We performed nanoscale NMR on several liquid and solid samples exhibiting unique NMR response. Our method paves the way for nanoscale identification of molecule and protein structures and dynamics of conformational changes.

Study of acute biochemical effects of thallium toxicity in mouse urine by NMR spectroscopy.

PubMed

Tyagi, Ritu; Rana, Poonam; Khan, Ahmad Raza; Bhatnagar, Deepak; Devi, M Memita; Chaturvedi, Shubhra; Tripathi, Rajendra P; Khushu, Subash

2011-10-01

Thallium (Tl) is a toxic heavy metal and its exposure to the human body causes physiological and biochemical changes due to its interference with potassium-dependent biological reactions. A high-resolution (1)H NMR spectroscopy based metabonomic approach has been applied for investigating acute biochemical effects caused by thallium sulfate (Tl(2)SO(4)). Male strain A mice were divided in three groups and received three doses of Tl(2)SO(4) (5, 10 and 20 mg kg(-1) b.w., i.p.). Urine samples collected at 3, 24, 72 and 96 h post-dose time points were analyzed by (1)H NMR spectroscopy. NMR spectral data were processed and analyzed using principal components analysis to represent biochemical variations induced by Tl(2)SO(4). Results showed Tl-exposed mice urine to have distinct metabonomic phenotypes and revealed dose- and time-dependent clustering of treated groups. The metabolic signature of urine analysis from Tl(2)SO(4)-treated animals exhibited an increase in the levels of creatinine, taurine, hippurate and β-hydroxybutyrate along with a decrease in energy metabolites trimethylamine and choline. These findings revealed Tl-induced disturbed gut flora, membrane metabolite, energy and protein metabolism, representing physiological dysfunction of vital organs. The present study indicates the great potential of NMR-based metabonomics in mapping metabolic response for toxicology, which could ultimately lead to identification of potential markers for Tl toxicity. Copyright © 2011 John Wiley & Sons, Ltd.

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.

Coexistence of antiferromagnetic and ferromagnetic spin correlations in SrCo 2As 2 revealed by 59Co and 75As NMR

DOE PAGES

Wiecki, P.; Ogloblichev, V.; Pandey, Abhishek; ...

2015-06-15

In nonsuperconducting, metallic paramagnetic SrCo 2As 2, inelastic neutron scattering measurements have revealed strong stripe-type q=(π,0) antiferromagnetic (AFM) spin correlations. Using nuclear magnetic resonance (NMR) measurements on 59Co and 75As nuclei, we demonstrate that stronger ferromagnetic (FM) spin correlations coexist in SrCo 2As 2. Our NMR data are consistent with density functional theory (DFT) calculations which show enhancements at both q=(π,0) and the in-plane FM q=0 wave vectors in static magnetic susceptibility χ(q). We suggest that the strong FM fluctuations prevent superconductivity in SrCo 2As 2, despite the presence of stripe-type AFM fluctuations. Since DFT calculations have consistently revealed similarmore » enhancements of the χ(q) at both q=(π,0) and q=0 in the iron-based superconductors and parent compounds, our observation of FM correlations in SrCo 2As 2 calls for detailed studies of FM correlations in the iron-based superconductors.« less

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...

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

DOE PAGES

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

2016-03-21

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

Cytotoxic Effects of Sarcophyton sp. Soft Corals—Is There a Correlation to Their NMR Fingerprints?

PubMed Central

Farag, Mohamed A.; Fekry, Mostafa I.; Al-Hammady, Montasser A.; Khalil, Mohamed N.; El-Seedi, Hesham R.; Meyer, Achim; Westphal, Hildegard; Wessjohann, Ludger A.

2017-01-01

Sarcophyton sp. soft corals are rich in cembranoid diterpenes, which represent the main chemical defense of corals against their natural predators in addition to their myriad biological effects in humans. Quantitative NMR (qNMR) was applied for assessing the diterpene variation in 16 soft coral specimens in the context of their genotype, origin, and growing habitat. qNMR revealed high diterpene levels in Sarcophyton sp. compared to Sinularia and Lobophyton, with (ent)sarcophines as major components (17–100 µg/mg) of the coral tissues. Multivariate data analysis was employed to classify samples based on the quantified level of diterpenes, and compared to the untargeted NMR approach. Results revealed that qNMR provided a stronger classification model of Sarcophyton sp. than untargeted NMR fingerprinting. Additionally, cytotoxicity of soft coral crude extracts was assessed against androgen-dependent prostate cancer cell lines (PC3) and androgen-independent colon cancer cell lines (HT-29), with IC50 values ranging from 10–60 µg/mL. No obvious correlation between the extracts’ IC50 values and their diterpene levels was found using either Spearman or Pearson correlations. This suggests that this type of bioactivity may not be easily predicted by NMR metabolomics in soft corals, or is not strongly correlated to measured diterpene levels. PMID:28677625

Cytotoxic Effects of Sarcophyton sp. Soft Corals-Is There a Correlation to Their NMR Fingerprints?

PubMed

Farag, Mohamed A; Fekry, Mostafa I; Al-Hammady, Montasser A; Khalil, Mohamed N; El-Seedi, Hesham R; Meyer, Achim; Porzel, Andrea; Westphal, Hildegard; Wessjohann, Ludger A

2017-07-04

Sarcophyton sp. soft corals are rich in cembranoid diterpenes, which represent the main chemical defense of corals against their natural predators in addition to their myriad biological effects in humans. Quantitative NMR (qNMR) was applied for assessing the diterpene variation in 16 soft coral specimens in the context of their genotype, origin, and growing habitat. qNMR revealed high diterpene levels in Sarcophyton sp. compared to Sinularia and Lobophyton , with (ent)sarcophines as major components (17-100 µg/mg) of the coral tissues. Multivariate data analysis was employed to classify samples based on the quantified level of diterpenes, and compared to the untargeted NMR approach. Results revealed that qNMR provided a stronger classification model of Sarcophyton sp. than untargeted NMR fingerprinting. Additionally, cytotoxicity of soft coral crude extracts was assessed against androgen-dependent prostate cancer cell lines (PC3) and androgen-independent colon cancer cell lines (HT-29), with IC 50 values ranging from 10-60 µg/mL. No obvious correlation between the extracts' IC 50 values and their diterpene levels was found using either Spearman or Pearson correlations. This suggests that this type of bioactivity may not be easily predicted by NMR metabolomics in soft corals, or is not strongly correlated to measured diterpene levels.

NMR and TRLFS studies of Ln(iii) and An(iii) C5-BPP complexes.

PubMed

Adam, Christian; Beele, Björn B; Geist, Andreas; Müllich, Udo; Kaden, Peter; Panak, Petra J

2015-02-01

C5-BPP is a highly efficient N-donor ligand for the separation of trivalent actinides, An(iii), from trivalent lanthanides, Ln(iii). The molecular origin of the selectivity of C5-BPP and many other N-donor ligands of the BTP-type is still not entirely understood. We present here the first NMR studies on C5-BPP Ln(iii) and An(iii) complexes. C5-BPP is synthesized with 10% 15 N labeling and characterized by NMR and LIFDI-MS methods. 15 N NMR spectroscopy gives a detailed insight into the bonding of C5-BPP with lanthanides and Am(iii) as a representative for trivalent actinide cations, revealing significant differences in 15 N chemical shift for coordinating nitrogen atoms compared to Ln(iii) complexes. The temperature dependence of NMR chemical shifts observed for the Am(iii) complex indicates a weak paramagnetism. This as well as the observed large chemical shift for coordinating nitrogen atoms show that metal-ligand bonding in Am(C5-BPP) 3 has a larger share of covalence than in lanthanide complexes, confirming earlier studies. The Am(C5-BPP) 3 NMR sample is furthermore spiked with Cm(iii) and characterized by time-resolved laser fluorescence spectroscopy (TRLFS), yielding important information on the speciation of trace amounts of minor complex species.

Colloidal 3-Mercaptopropionic Acid Capped Lead Sulfide Quantum Dots in a Low Boiling Point Solvent.

PubMed

Reinhart, Chase C; Johansson, Erik

2017-04-26

Colloidal 3-mercaptopropionic acid (3-MPA) capped lead sulfide quantum dots were prepared in a variety of organic solvents stabilized with a quaternary ammonium halide salt. The stabilized colloids' optical properties were studied through optical absorption and emission spectroscopy and found to be dependent on both the concentration of a new ligand and stabilizer, and sample age. Nanocrystal ligand chemistry was studied through a combination of 1 H NMR and two-dimensional Nuclear Overhauser Effect Spectroscopy (NOESY) which revealed full displacement of the original oleate ligand to form a dynamically exchanging ligand shell. The colloids were studied optically and via NMR as they aged and revealed a quantitative conversion of monomeric 3-mercaptopropionic acid to its dimer, dithiodipropionic acid (dTdPA).

Ammonia fixation by humic substances: A nitrogen-15 and carbon-13 NMR study

USGS Publications Warehouse

Thorn, K.A.; Mikita, M.A.

1992-01-01

The process of ammonia fixation has been studied in three well characterized and structurally diverse fulvic and humic acid samples. The Suwannee River fulvic acid, and the IHSS peat and leonardite humic acids, were reacted with 15N-labelled ammonium hydroxide, and analyzed by liquid phase 15N NMR spectrometry. Elemental analyses and liquid phase 13C NMR spectra also were recorded on the samples before and after reaction with ammonium hydroxide. The largest increase in percent nitrogen occurred with the Suwannee River fulvic acid, which had a nitrogen content of 0.88% before fixation and 3.17% after fixation. The 15N NMR spectra revealed that ammonia reacted similarly with all three samples, indicating that the functional groups which react with ammonia exist in structural configurations common to all three samples. The majority of nitrogcn incorporated into the samples appears to be in the form of indole and pyrrole nitrogen, followed by pyridine, pyrazine, amide and aminohydroquinone nitrogen. Chemical changes in the individual samples upon fixation could not be discerned from the 13C NMR spectra.

Internally stabilized selenocysteine derivatives: syntheses, 77Se NMR and biomimetic studies.

PubMed

Phadnis, Prasad P; Mugesh, G

2005-07-07

Selenocystine ([Sec]2) and aryl-substituted selenocysteine (Sec) derivatives are synthesized, starting from commercially available amino acid l-serine. These compounds are characterized by a number of analytical techniques such as NMR (1H, 13C and 77Se) and TOF mass spectroscopy. This study reveals that the introduction of amino/imino substituents capable of interacting with selenium may stabilize the Sec derivatives. This study further suggests that the oxidation-elimination reactions in Sec derivatives could be used for the generation of biologically active selenols having internally stabilizing substituents.

Heterogeneous Coordination Environments in Lithium-Neutralized Ionomers Identified Using 1H and 7Li MAS NMR

PubMed Central

Alam, Todd M.; Jenkins, Janelle E.; Bolintineanu, Dan S.; Stevens, Mark J.; Frischknecht, Amalie L.; Buitrago, C. Francisco; Winey, Karen I.; Opper, Kathleen L.; Wagener, Kenneth B.

2012-01-01

The carboxylic acid proton and the lithium coordination environments for precise and random Li-neutralized polyethylene acrylic acid P(E-AA) ionomers were explored using high speed solid-state 1H and 7Li MAS NMR. While the 7Li NMR revealed only a single Li coordination environment, the chemical shift temperature variation was dependent on the precise or random nature of the P(E-AA) ionomer. The 1H MAS NMR revealed two different carboxylic acid proton environments in these materials. By utilizing 1H-7Li rotational echo double resonance (REDOR) MAS NMR experiments, it was demonstrated that the proton environments correspond to different average 1H-7Li distances, with the majority of the protonated carboxylic acids having a close through space contact with the Li. Molecular dynamics simulations suggest that the shortest 1H-7Li distance corresponds to un-neutralized carboxylic acids directly involved in the coordination environment of Li clusters. These solid-state NMR results show that heterogeneous structural motifs need to be included when developing descriptions of these ionomer materials.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Significance of histopathology in pulsed NMR studies on cancer.

PubMed

Ranade, S S; Bharade, S H; Talwalkar, G V; Sujata, G K; Shrinivasan, V T; Singh, B B

1985-04-01

Characterization of tissue by pulsed nuclear magnetic resonance spectrometry opened a new area of research. The differences in the NMR parameters T1 and T2 of normal and malignant tissues constitute the basis for their distinction by pulsed NMR spectrometry and also by NMR imaging in vivo. The present studies were undertaken to correlate the role of constituent histological elements encountered in various malignancy-associated changes and T1 variations and are based on evaluation of samples taken from surgically resected specimens of carcinoma of the esophagus, comprising the uninvolved portions of the esophagus and the gastric end on gross examination. The uninvolved and involved regions showed low and high T1 values, respectively. High T1 values were also encountered in the zones of samples of uninvolved esophagus which histologically revealed areas with dysplasia. This feature, viz., dysplasia representing malignancy-associated changes, has been found to recur in many samples. Detailed histological studies provided further evidence confirming that areas with dysplasia contribute to an increase in T1 values whereas in zones at the gastric end metaplasia and hyperplasia are more common. The results are of value for demarcation of tumor area by in vivo NMR imaging.

High-pressure autoclave for multipurpose nuclear magnetic resonance measurements up to 10 MPa

NASA Astrophysics Data System (ADS)

Behr, W.; Haase, A.; Reichenauer, G.; Fricke, J.

1999-05-01

High-pressure nuclear magnetic resonance (NMR) is an established method in NMR spectroscopy: on-line coupling of high-performance liquid chromatography with NMR, for example, reveals structural information which cannot be obtained with any other method. However, applications has been focused solely on high-pressure NMR spectroscopy, even though high-pressure NMR imaging allows in situ studies of processes such as the fluid exchange in porous media. A versatile high-pressure autoclave for NMR imaging is described in this article. The autoclave allows measurements in any horizontal NMR imager using magnetic field coil systems with an inside diameter of more than 70 mm. Any sample with a diameter up to 28 mm and a length of about 200 mm can be investigated. The autoclave is constructed for operating pressures up to 10 MPa and is temperature controlled between 10 and 60 °C. The materials of the high-pressure cell which are the thermoplastic polyetheretherketon (PEEK) for the pressure tube and brass (63% Cu, 37% Zn) for the caps also permit investigations with aggressive fluids such as supercritical carbon dioxide. Inlet and outlet valves allow replacement of fluids and pressure variations in the autoclave during the NMR measurement. FLASH NMR images of the fluid exchange of methanol for liquid carbon dioxide in silica alcogels at 6.5 MPa are presented in order to demonstrate possible applications.

NMR and TRLFS studies of Ln(iii) and An(iii) C5-BPP complexes† †Electronic supplementary information (ESI) available: LIFDI-MS spectra and additional NMR spectra. See DOI: 10.1039/c4sc03103b

PubMed Central

Beele, Björn B.; Geist, Andreas; Müllich, Udo; Kaden, Peter; Panak, Petra J.

2015-01-01

C5-BPP is a highly efficient N-donor ligand for the separation of trivalent actinides, An(iii), from trivalent lanthanides, Ln(iii). The molecular origin of the selectivity of C5-BPP and many other N-donor ligands of the BTP-type is still not entirely understood. We present here the first NMR studies on C5-BPP Ln(iii) and An(iii) complexes. C5-BPP is synthesized with 10% 15N labeling and characterized by NMR and LIFDI-MS methods. 15N NMR spectroscopy gives a detailed insight into the bonding of C5-BPP with lanthanides and Am(iii) as a representative for trivalent actinide cations, revealing significant differences in 15N chemical shift for coordinating nitrogen atoms compared to Ln(iii) complexes. The temperature dependence of NMR chemical shifts observed for the Am(iii) complex indicates a weak paramagnetism. This as well as the observed large chemical shift for coordinating nitrogen atoms show that metal–ligand bonding in Am(C5-BPP)3 has a larger share of covalence than in lanthanide complexes, confirming earlier studies. The Am(C5-BPP)3 NMR sample is furthermore spiked with Cm(iii) and characterized by time-resolved laser fluorescence spectroscopy (TRLFS), yielding important information on the speciation of trace amounts of minor complex species. PMID:29560242

A structural study of epoxidized natural rubber (ENR-50) and its cyclic dithiocarbonate derivative using NMR spectroscopy techniques.

PubMed

Hamzah, Rosniza; Bakar, Mohamad Abu; Khairuddean, Melati; Mohammed, Issam Ahmed; Adnan, Rohana

2012-09-12

A structural study of epoxidized natural rubber (ENR-50) and its cyclic dithiocarbonate derivative was carried out using NMR spectroscopy techniques. The overlapping (1)H-NMR signals of ENR-50 at δ 1.56, 1.68-1.70, 2.06, 2.15-2.17 ppm were successfully assigned. In this work, the <(13)C-NMR chemical shift assignments of ENR-50 were consistent to the previously reported work. A cyclic dithiocarbonate derivative of ENR-50 was synthesized from the reaction of purified ENR-50 with carbon disulfide (CS(2)), in the presence of 4-dimethylaminopyridine (DMAP) as catalyst at reflux temperature. The cyclic dithiocarbonate formation involved the epoxide ring opening of the ENR-50. This was followed by insertion of the C-S moiety of CS(2) at the oxygen attached to the quaternary carbon and methine carbon of epoxidized isoprene unit, respectively. The bands due to the C=S and C-O were clearly observed in the FTIR spectrum while the (1)H-NMR spectrum of the derivative revealed the peak attributed to the methylene protons had split. The (13)C-NMR spectrum of the derivative further indicates two new carbon peaks arising from the >C=S and quaternary carbon of cyclic dithiocarbonate. All other (1)H- and (13)C-NMR chemical shifts of the derivative remain unchanged with respect to the ENR-50.

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.

Validated ¹H and 13C Nuclear Magnetic Resonance Methods for the Quantitative Determination of Glycerol in Drug Injections.

PubMed

Lu, Jiaxi; Wang, Pengli; Wang, Qiuying; Wang, Yanan; Jiang, Miaomiao

2018-05-15

In the current study, we employed high-resolution proton and carbon nuclear magnetic resonance spectroscopy (¹H and 13 C NMR) for quantitative analysis of glycerol in drug injections without any complex pre-treatment or derivatization on samples. The established methods were validated with good specificity, linearity, accuracy, precision, stability, and repeatability. Our results revealed that the contents of glycerol were convenient to calculate directly via the integration ratios of peak areas with an internal standard in ¹H NMR spectra, while the integration of peak heights were proper for 13 C NMR in combination with an external calibration of glycerol. The developed methods were both successfully applied in drug injections. Quantitative NMR methods showed an extensive prospect for glycerol determination in various liquid samples.

Interfacial Ca2+ environments in nanocrystalline apatites revealed by dynamic nuclear polarization enhanced 43Ca NMR spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Daniel; Leroy, César; Crevant, Charlène; Bonhomme-Coury, Laure; Babonneau, Florence; Laurencin, Danielle; Bonhomme, Christian; de Paëpe, Gaël

2017-01-01

The interfaces within bones, teeth and other hybrid biomaterials are of paramount importance but remain particularly difficult to characterize at the molecular level because both sensitive and selective techniques are mandatory. Here, it is demonstrated that unprecedented insights into calcium environments, for example the differentiation of surface and core species of hydroxyapatite nanoparticles, can be obtained using solid-state NMR, when combined with dynamic nuclear polarization. Although calcium represents an ideal NMR target here (and de facto for a large variety of calcium-derived materials), its stable NMR-active isotope, calcium-43, is a highly unreceptive probe. Using the sensitivity gains from dynamic nuclear polarization, not only could calcium-43 NMR spectra be obtained easily, but natural isotopic abundance 2D correlation experiments could be recorded for calcium-43 in short experimental time. This opens perspectives for the detailed study of interfaces in nanostructured materials of the highest biological interest as well as calcium-based nanosystems in general.

Mechanical, structural, and dynamical modifications of cholesterol exposed porcine aortic elastin.

PubMed

Bilici, Kubra; Morgan, Steven W; Silverstein, Moshe C; Wang, Yunjie; Sun, Hyung Jin; Zhang, Yanhang; Boutis, Gregory S

2016-11-01

Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2 H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13 C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin is more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanical, Structural, and Dynamical Modifications of Cholesterol Exposed Porcine Aortic Elastin

PubMed Central

Bilici, Kubra; Morgan, Steven W.; Silverstein, Moshe C.; Wang, Yunjie; Sun, Hyung Jin; Zhang, Katherine; Boutis, Gregory S.

2016-01-01

Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin appears more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. PMID:27648754

Non-Catalyzed Click Reactions of ADIBO Derivatives with 5-Methyluridine Azides and Conformational Study of the Resulting Triazoles

PubMed Central

Smyslova, Petra; Popa, Igor; Lyčka, Antonín; Tejral, Gracian; Hlavac, Jan

2015-01-01

Copper-free click reactions between a dibenzoazocine derivative and azides derived from 5-methyluridine were investigated. The non-catalyzed reaction yielded both regioisomers in an approximately equivalent ratio. The NMR spectra of each regioisomer revealed conformational isomery. The ratio of isomers was dependent on the type of regioisomer and the type of solvent. The synthesis of various analogs, a detailed NMR study and computational modeling provided evidence that the isomery was dependent on the interaction of the azocine and pyrimidine parts. PMID:26673606

Genetic transformation of rare Verbascum eriophorum Godr. plants and metabolic alterations revealed by NMR-based metabolomics.

PubMed

Marchev, Andrey; Yordanova, Zhenya; Alipieva, Kalina; Zahmanov, Georgi; Rusinova-Videva, Snezhana; Kapchina-Toteva, Veneta; Simova, Svetlana; Popova, Milena; Georgiev, Milen I

2016-09-01

To develop a protocol to transform Verbascum eriophorum and to study the metabolic differences between mother plants and hairy root culture by applying NMR and processing the datasets with chemometric tools. Verbascum eriophorum is a rare species with restricted distribution, which is poorly studied. Agrobacterium rhizogenes-mediated genetic transformation of V. eriophorum and hairy root culture induction are reported for the first time. To determine metabolic alterations, V. eriophorum mother plants and relevant hairy root culture were subjected to comprehensive metabolomic analyses, using NMR (1D and 2D). Metabolomics data, processed using chemometric tools (and principal component analysis in particular) allowed exploration of V. eriophorum metabolome and have enabled identification of verbascoside (by means of 2D-TOCSY NMR) as the most abundant compound in hairy root culture. Metabolomics data contribute to the elucidation of metabolic alterations after T-DNA transfer to the host V. eriophorum genome and the development of hairy root culture for sustainable bioproduction of high value verbascoside.

Polymer mobilization and drug release during tablet swelling. A 1H NMR and NMR microimaging study.

PubMed

Dahlberg, Carina; Fureby, Anna; Schuleit, Michael; Dvinskikh, Sergey V; Furó, István

2007-09-26

The objective of this study was to investigate the swelling characteristics of a hydroxypropyl methylcellulose (HPMC) matrix incorporating the hydrophilic drug antipyrine. We have used this matrix to introduce a novel analytical method, which allows us to obtain within one experimental setup information about the molecular processes of the polymer carrier and its impact on drug release. Nuclear magnetic resonance (NMR) imaging revealed in situ the swelling behavior of tablets when exposed to water. By using deuterated water, the spatial distribution and molecular dynamics of HPMC and their kinetics during swelling could be observed selectively. In parallel, NMR spectroscopy provided the concentration of the drug released into the aqueous phase. We find that both swelling and release are diffusion controlled. The ability of monitoring those two processes using the same experimental setup enables mapping their interconnection, which points on the importance and potential of this analytical technique for further application in other drug delivery forms.

In-pore exchange and diffusion of carbonate solvent mixtures in nanoporous carbon

DOE PAGES

Alam, Todd M.; Osborn Popp, Thomas M.

2016-06-04

High resolution magic angle spinning (HRMAS) 1H NMR spectroscopy has been used to resolve different surface and in-pore solvent environments of ethylene carbonate (EC) and dimethyl carbonate (DMC) mixtures absorbed within nanoporous carbon (NPC). Two dimensional (2D) 1H HRMAS NMR exchange measurements revealed that the inhomogeneous broadened in-pore resonances have pore-to-pore exchange rates on the millisecond timescale. Pulsed-field gradient (PFG) NMR diffusometry revealed the in-pore self-diffusion constants for both EC and DMC were reduced by up to a factor of five with respect to the diffusion in the non-absorbed solvent mixtures.

Synthesis, stereochemistry, crystal structure, docking study and biological evaluation of some new N-benzylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Ponnuswamy, S.; Kayalvizhi, R.; Sethuvasan, S.; Sugumar, P.; Ponnuswamy, M. N.

2018-03-01

Two new N-benzylpiperidin-4-ones 3 and 4 have been synthesized and characterized using IR, 1D and 2D NMR spectral studies. The NMR data of N-benzylpiperidin-4-ones 3 and 4 reveal that the compounds prefer to exist in chair conformation with equatorial orientation of the bulky substituents and the single crystal X-ray structure of compound 4 also reveals a similar conformation in solid state. Furthermore, the antimicrobial studies carried out for the compounds 1-4 indicate moderate activities with the selected strains. The antioxidant potency of 3 is superior whereas 4 exhibits moderate activity when compared to that of standard drug. The results of molecular docking studies with the AmpC β-lactamase enzyme indicate that compound 3 shows better docking score and binding energy than the co-crystal ligand.

(1)H NMR-based metabonomics revealed protective effect of Naodesheng bioactive extract on ischemic stroke rats.

PubMed

Luo, Lan; Zhen, Lifeng; Xu, Yatao; Yang, Yongxia; Feng, Suxiang; Wang, Shumei; Liang, Shengwang

2016-06-20

Stroke is a leading cause of death and disability in the world. However, current therapies are limited. Naodesheng, a widely used traditional Chinese medicine prescription, has shown a good clinical curative effect on ischemic stroke. Also, Naodesheng has been suggested to have neuroprotective effect on focal cerebral ischemia rats, but the underlying molecular mechanism remains unclear. The present study was designed to evaluate the effect of Naodesheng bioactive extract on the metabolic changes in brain tissue, plasma and urine induced by cerebral ischemia perfusion injury, and explore the possible metabolic mechanisms by using a (1)H NMR-based metabonomics approach. A middle cerebral artery occlusion rat model was established and confirmed by the experiments of neurobehavioral abnormality evaluation, brain tissue TTC staining and pathological examination. The metabolic changes in brain tissue, plasma and urine were then assessed by a (1)H NMR technique combined with multivariate statistical analysis method. These NMR data showed that cerebral ischemia reperfusion induced great metabolic disorders in brain tissue, plasma and urine metabolisms. However, Naodesheng bioactive extract could reverse most of the imbalanced metabolites. Meanwhile, it was found that both the medium and high dosages of Naodesheng bioactive extract were more effective on the metabolic changes than the low dosage, consistent with histopathological assessments. These results revealed that Naodesheng had protective effect on ischemic stroke rats and the underlying mechanisms involved multiple metabolic pathways, including energy metabolism, amino acid metabolism, oxidative stress and inflammatory injury. The present study could provide evidence that metabonomics revealed its capacity to evaluate the holistic efficacy of traditional Chinese medicine and explore the underlying mechanisms. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Analyzing the adsorption of blood plasma components by means of fullerene-containing silica gels and NMR spectroscopy in solids

NASA Astrophysics Data System (ADS)

Melenevskaya, E. Yu.; Mokeev, M. V.; Nasonova, K. V.; Podosenova, N. G.; Sharonova, L. V.; Gribanov, A. V.

2012-10-01

The results from studying the adsorption of blood plasma components (e.g., protein, triglycerides, cholesterol, and lipoproteins of low and high density) using silica gels modified with fullerene molecules (in the form of C60 or the hydroxylated form of C60(OH) x ) and subjected to hydration (or, alternatively, dehydration) are presented. The conditions for preparing adsorbents that allow us to control the adsorption capacity of silica gel and the selectivity of adsorption toward the components of blood plasma, are revealed. The nature and strength of the interactions of the introduced components (fullerene molecules and water) with functional groups on the silica surface are studied by means of solid state NMR spectroscopy (NMR-SS). Conclusions regarding the nature of the centers that control adsorption are drawn on the basis of NMR-SS spectra in combination with direct measurements of adsorption. The interaction of the oxygen of the hydroxyl group of silica gel with fullerene, leading to the formation of electron-donor complexes of C60-H, C60-OH, or C60-OSi type, is demonstrated by the observed changes in the NMR-SS spectra of silica gels in the presence of fullerene.

Crocus sativus Petals: Waste or Valuable Resource? The Answer of High-Resolution and High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance.

PubMed

Righi, Valeria; Parenti, Francesca; Tugnoli, Vitaliano; Schenetti, Luisa; Mucci, Adele

2015-09-30

Intact Crocus sativus petals were studied for the first time by high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy, revealing the presence of kinsenoside (2) and goodyeroside A (3), together with 3-hydroxy-γ-butyrolactone (4). These findings were confirmed by HR-NMR analysis of the ethanol extract of fresh petals and showed that, even though carried out rapidly, partial hydrolysis of glucopyranosyloxybutanolides occurs during extraction. On the other hand, kaempferol 3-O-sophoroside (1), which is "NMR-silent" in intact petals, is present in extracts. These results suggest to evaluate the utilization of saffron petals for phytopharmaceutical and nutraceutical purposes to exploit a waste product of massive production of commercial saffron and point to the application of HR-MAS NMR for monitoring bioactive compounds directly on intact petals, avoiding the extraction procedure and the consequent hydrolysis reaction.

Defects in doped LaGaO3 anionic conductors: linking NMR spectral features, local environments, and defect thermodynamics.

PubMed

Blanc, Frédéric; Middlemiss, Derek S; Gan, Zhehong; Grey, Clare P

2011-11-09

Doped lanthanum gallate perovskites (LaGaO(3)) constitute some of the most promising electrolyte materials for solid oxide fuel cells operating in the intermediate temperature regime. Here, an approach combining experimental multinuclear NMR spectroscopy with density functional theory total energy and GIPAW NMR calculations yields a comprehensive understanding of the structural and defect chemistries of Sr- and Mg-doped LaGaO(3) anionic conductors. The DFT energetics demonstrate that Ga-V(O)-Ga (V(O) = oxygen vacancy) environments are favored (vs Ga-V(O)-Mg, Mg-V(O)-Mg and Mg-O-Mg-V(O)-Ga) across a range y = 0.0625, 0.125, and 0.25 of fractional Mg contents in LaGa(1-y)Mg(y)O(3-y/2). The results are interpreted in terms of doping and mean phase formation energies (relative to binary oxides) and are compared with previous calculations and experimental calorimetry data. Experimental multinuclear NMR data reveal that while Mg sites remain six-fold coordinated across the range of phase stoichiometries, albeit with significant structural disorder, a stoichiometry-dependent minority of the Ga sites resonate at a shift consistent with Ga(V) coordination, demonstrating that O vacancies preferentially locate in the first anion coordination shell of Ga. The strong Mg-V(O) binding inferred by previous studies is not observed here. The (17)O NMR spectra reveal distinct resonances that can be assigned by using the GIPAW NMR calculations to anions occupying equatorial and axial positions with respect to the Ga(V)-V(O) axis. The disparate shifts displayed by these sites are due to the nature and extent of the structural distortions caused by the O vacancies.

Complex Mixture Analysis of Organic Compounds in Yogurt by NMR Spectroscopy

PubMed Central

Lu, Yi; Hu, Fangyu; Miyakawa, Takuya; Tanokura, Masaru

2016-01-01

NMR measurements do not require separation and chemical modification of samples and therefore rapidly and directly provide non-targeted information on chemical components in complex mixtures. In this study, one-dimensional (1H, 13C, and 31P) and two-dimensional (1H-13C and 1H-31P) NMR spectroscopy were conducted to analyze yogurt without any pretreatment. 1H, 13C, and 31P NMR signals were assigned to 10 types of compounds. The signals of α/β-lactose and α/β-galactose were separately observed in the 1H NMR spectra. In addition, the signals from the acyl chains of milk fats were also successfully identified but overlapped with many other signals. Quantitative difference spectra were obtained by subtracting the diffusion ordered spectroscopy (DOSY) spectra from the quantitative 1H NMR spectra. This method allowed us to eliminate interference on the overlaps; therefore, the correct intensities of signals overlapped with those from the acyl chains of milk fat could be determined directly without separation. Moreover, the 1H-31P HMBC spectra revealed for the first time that N-acetyl-d-glucosamine-1-phosphate is contained in yogurt. PMID:27322339

Insight into the local environment of magnesium and calcium in low-coordination-number organo-complexes using 25Mg and 43Ca solid-state NMR: a DFT study.

PubMed

Gervais, Christel; Jones, Cameron; Bonhomme, Christian; Laurencin, Danielle

2017-03-01

With the increasing number of organocalcium and organomagnesium complexes under development, there is a real need to be able to characterize in detail their local environment in order to fully rationalize their reactivity. For crystalline structures, in cases when diffraction techniques are insufficient, additional local spectroscopies like 25 Mg and 43 Ca solid-state NMR may provide valuable information to help fully establish the local environment of the metal ions. In this current work, a prospective DFT investigation on crystalline magnesium and calcium complexes involving low-coordination numbers and N-bearing organic ligands was carried out, in which the 25 Mg and 43 Ca NMR parameters [isotropic chemical shift, chemical shift anisotropy (CSA) and quadrupolar parameters] were calculated for each structure. The analysis of the calculated parameters in relation to the local environment of the metal ions revealed that they are highly sensitive to very small changes in geometry/distances, and hence that they could be used to assist in the refinement of crystal structures. Moreover, such calculations provide a guideline as to how the NMR measurements will need to be performed, revealing that these will be very challenging.

Physicochemical properties of liposomes as potential anticancer drugs carriers. Interaction of etoposide and cytarabine with the membrane: Spectroscopic studies

NASA Astrophysics Data System (ADS)

Pentak, Danuta

2014-03-01

The interactions between etoposide, cytarabine and 1,2-dihexadecanoyl-sn-glycerol-3-phosphocholine bilayers were studied using differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR). These techniques have proven to be a very powerful tool in studying the structure and dynamics of phospholipid bilayers. In particular, DSC can provide information on the phase transition temperature and cooperativity of the lipid molecules in the absence and presence of the drug. Vibrational spectroscopy is well suited to the study of drug-lipid interactions, since it allows for an investigation of the conformation of phospholipid molecules at different levels in lipid bilayers and follows structural changes that occur during the gel to liquid-crystalline phase transition. NMR supported the determination of the main phase transition temperatures (TC) of 1,2-dihexadecanoyl-sn-glycerol-3-phosphocholine (DPPC). The main phase transition temperature (TC) determined by 1H NMR is comparable with values obtained by DSC for all studied liposomes. The location of cytarabine and etoposide in liposomes was also determined by NMR. Atomic force microscopy (AFM) images, acquired immediately after sample deposition on a mica surface, revealed the spherical shape of lipid vesicles.

Evidence for cis Amide Bonds in Peptoid Nanosheets.

PubMed

Hudson, Benjamin C; Battigelli, Alessia; Connolly, Michael D; Edison, John; Spencer, Ryan K; Whitelam, Stephen; Zuckermann, Ronald N; Paravastu, Anant K

2018-05-17

Peptoid nanosheets are supramolecular protein-mimetic materials that form from amphiphilic polypeptoids with aromatic and ionic side chains. Nanosheets have been studied at the nanometer scale, but the molecular structure has been difficult to probe. We report the use of 13 C- 13 C dipolar recoupling solid-state NMR measurements to reveal the configuration of backbone amide bonds selected by 13 C isotopic labeling of adjacent α-carbons. Measurements on the same molecules in the amorphous state and in nanosheets revealed that amide bonds in the center of the amino block of peptoid (NaeNpe) 7 -(NceNpe) 7 (B28) favor the trans configuration in the amorphous state and the cis configuration in the nanosheet. This unexpected result contrasts with previous NMR and theoretical studies of short solvated peptoids. Furthermore, examination of the amide bond at the junction of the two charged blocks within B28 revealed a mixture of both cis and trans configurational states, consistent with the previously predicted brickwork-like intermolecular organization.

DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline.

PubMed

Gowda, Vasantha; Laitinen, Risto S; Telkki, Ville-Veikko; Larsson, Anna-Carin; Antzutkin, Oleg N; Lantto, Perttu

2016-12-06

The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state 13 C and 15 N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and 13 C and 15 N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P2 1 /n. Both 13 C and 15 N CP-MAS NMR revealed the presence of six structurally different dithiocarbamate groups in the asymmetric unit cell, implying a non-centrosymmetric packing arrangement of molecules. This was supported by single-crystal X-ray crystallography showing that the title compound crystallised in the triclinic space group P1[combining macron]. In addition, the crystal structure also revealed that one of the dithiocarbamate ligands has a conformational disorder. NMR chemical shift calculations employing the periodic gauge including projector augmented wave (GIPAW) approach supported the assignment of the experimental 13 C and 15 N NMR spectra. However, the best correspondences were obtained with the structure where the atomic positions in the X-ray unit cell were optimised at the DFT level. The roles of the scalar and spin-orbit relativistic effects on NMR shielding were investigated using the zeroth-order regular approximation (ZORA) method with the outcome that already the scalar relativistic level qualitatively reproduces the experimental chemical shifts. The electronic properties of the complex were evaluated based on the results of the natural bond orbital (NBO) and topology of the electron density analyses. Overall, we apply a multidisciplinary approach acquiring comprehensive information about the solid-state structure and the metal-ligand bonding of the heteroleptic lanthanum complex.

Palladium(II) complexes bearing di-(2-picolyl)amine functionalized chrysin fragments. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

González-Montiel, Simplicio; Valdez-Calderón, Alejandro; Vásquez-Pérez, J. Manuel; Torres-Valencia, J. Martín; Martínez-Otero, Diego; López, Jorge A.; Cruz-Borbolla, Julián

2017-10-01

A new series of chrysin derivatives containing the di-(2-picolyl)amine (2a-d) moiety have been designed, synthesized, and treated with PdCl2·2CH3CN allowing the preparation of new cationic Palladium(II) complexes (3a-d). Solution-phase studies by 1H NMR spectroscopy of 3a-d revealed that the protons of the methylene groups of the di(2-picolyl)amine fragment are diasterotopic. GIAO/DFT studies were performed to predict the molecular structures of 3a-d by comparing the experimental and theoretical 1H-NMR chemical shifts. The molecular structure of 3c was determined by X-ray crystallographic analysis revealing that di-(2-picolyl)amine fragment is coordinated to the palladium center in a κ3-N,N,N-tridentate fashion in an overall square-planar geometry completed with a chloride atom.

NMR approach for monitoring post-mortem changes in Atlantic salmon fillets stored at 0 and 4°C.

PubMed

Shumilina, Elena; Ciampa, Alessandra; Capozzi, Francesco; Rustad, Turid; Dikiy, Alexander

2015-10-01

High resolution NMR technique has been used to monitor post-mortem changes in salmon (Salmo salar) fillets upon storage at 4 and 0°C. Thirty-one different fish metabolites influencing freshness and taste properties have been unequivocally assigned by NMR using either available standard compounds or ad hoc acquired 2D (1)H-(1)H TOCSY and (1)H-(13)С HSQC spectra. The monitored fish metabolites include amino acids, dipeptides, sugars, vitamins, biogenic amines, as well as different products of the ATP degradation. The detection and monitoring of biogenic amines by NMR, upon fish storage, is information of interest for consumers, since some of these compounds are toxic. The data from this study shows that NMR spectroscopy also provides the amount of all metabolites necessary for the calculation of the K-index used to express fish freshness. A good correlation was found between the K-index increase and the formation of the undesired biogenic amines. The metabolite concentrations and the K-index found in this work were compared and found coherent with literature data. The performed study reveals the strengths and the suitability of the NMR approach to monitor different biochemical processes occurring during fish storage and qualitatively and quantitatively characterise fish metabolites determining fish quality. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

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

Qu, Yi; Feng, Ju; Deng, Shuang

2014-11-19

Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis ofmore » the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.« less

MAS-NMR studies of lithium aluminum silicate (LAS) glasses and glass-ceramics having different Li 2O/Al 2O 3 ratio

NASA Astrophysics Data System (ADS)

Ananthanarayanan, A.; Kothiyal, G. P.; Montagne, L.; Revel, B.

2010-01-01

Emergence of phases in lithium aluminum silicate (LAS) glasses of composition (wt%) xLi 2O-71.7SiO 2-(17.7- x)Al 2O 3-4.9K 2O-3.2B 2O 3-2.5P 2O 5 (5.1≤ x≤12.6) upon heat treatment were studied. 29Si, 27Al, 31P and 11B MAS-NMR were employed for structural characterization of both LAS glasses and glass-ceramics. In glass samples, Al is found in tetrahedral coordination, while P exists mainly in the form of orthophosphate units. B exists as BO 3 and BO 4 units. 27Al NMR spectra show no change with crystallization, ruling out the presence of any Al containing phase. Contrary to X-ray diffraction studies carried out, 11B (high field 18.8 T) and 29Si NMR spectra clearly indicate the unexpected crystallization of a borosilicate phase (Li,K)BSi 2O 6, whose structure is similar to the aluminosilicate virgilite. Also, lithium disilicate (Li 2Si 2O 5), lithium metasilicate (Li 2SiO 3) and quartz (SiO 2) were identified in the 29Si NMR spectra of the glass-ceramics. 31P NMR spectra of the glass-ceramics revealed the presence of Li 3PO 4 and a mixed phase (Li,K) 3PO 4 at low alkali concentrations.

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.

(13)C and (15)N solid-state NMR studies on albendazole and cyclodextrin albendazole complexes.

PubMed

Ferreira, M João G; García, A; Leonardi, D; Salomon, Claudio J; Lamas, M Celina; Nunes, Teresa G

2015-06-05

(13)C and (15)N solid-state nuclear magnetic resonance (NMR) spectra were recorded from albendazole (ABZ) and from ABZ:β-cyclodextrin, ABZ:methyl-β-cyclodextrin, ABZ:hydroxypropyl-β-cyclodextrin and ABZ:citrate-β-cyclodextrin, which were prepared by the spray-drying technique. ABZ signals were typical of a crystalline solid for the pure drug and of an amorphous compound obtained from ABZ:cyclodextrin samples. Relevant spectral differences were correlated with chemical interaction between ABZ and cyclodextrins. The number and type of complexes revealed a strong dependence on the cyclodextrin group substituent. Solid-state NMR data were consistent with the presence of stable inclusion complexes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Coenzyme Q10-Loaded Fish Oil-Based Bigel System: Probing the Delivery Across Porcine Skin and Possible Interaction with Fish Oil Fatty Acids.

PubMed

Zulfakar, Mohd Hanif; Chan, Lee Mei; Rehman, Khurram; Wai, Lam Kok; Heard, Charles M

2018-04-01

Coenzyme Q10 (CoQ10) is a vitamin-like oil-soluble molecule that has anti-oxidant and anti-ageing effects. To determine the most optimal CoQ10 delivery vehicle, CoQ10 was solubilised in both water and fish oil, and formulated into hydrogel, oleogel and bigel. Permeability of CoQ10 from each formulation across porcine ear skin was then evaluated. Furthermore, the effects of the omega-3 fatty eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids from fish oil on skin permeation were investigated by means of nuclear magnetic resonance (NMR) and computerised molecular modelling docking experiments. The highest drug permeation was achieved with the bigel formulation that proved to be the most effective vehicle in delivering CoQ10 across the skin membrane due to a combination of its adhesive, viscous and lipophilic properties. Furthermore, the interactions between CoQ10 and fatty acids revealed by NMR and molecular modelling experiments likely accounted for skin permeability of CoQ10. NMR data showed dose-dependent changes in proton chemical shifts in EPA and DHA. Molecular modelling revealed complex formation and large binding energies between fatty acids and CoQ10. This study advances the knowledge about bigels as drug delivery vehicles and highlights the use of NMR and molecular docking studies for the prediction of the influence of drug-excipient relationships at the molecular level.

NMR evidence for static local nematicity and its cooperative interplay with low-energy magnetic fluctuations in FeSe under pressure

DOE PAGES

Wiecki, P.; Nandi, M.; Bohmer, Anna; ...

2017-11-13

Here, we present 77Se -NMR measurements on single-crystalline FeSe under pressures up to 2 GPa. Based on the observation of the splitting and broadening of the NMR spectrum due to structural twin domains, we discovered that static, local nematic ordering exists well above the bulk nematic ordering temperature, T s. The static, local nematic order and the low-energy stripe-type antiferromagnetic spin fluctuations, as revealed by NMR spin-lattice relaxation rate measurements, are both insensitive to pressure application. Our NMR results provide clear evidence for the microscopic cooperation between magnetism and local nematicity in FeSe.

NMR evidence for static local nematicity and its cooperative interplay with low-energy magnetic fluctuations in FeSe under pressure

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

Wiecki, P.; Nandi, M.; Bohmer, Anna

Here, we present 77Se -NMR measurements on single-crystalline FeSe under pressures up to 2 GPa. Based on the observation of the splitting and broadening of the NMR spectrum due to structural twin domains, we discovered that static, local nematic ordering exists well above the bulk nematic ordering temperature, T s. The static, local nematic order and the low-energy stripe-type antiferromagnetic spin fluctuations, as revealed by NMR spin-lattice relaxation rate measurements, are both insensitive to pressure application. Our NMR results provide clear evidence for the microscopic cooperation between magnetism and local nematicity in FeSe.

Genome-wide association study of a nicotine metabolism biomarker in African American smokers: impact of chromosome 19 genetic influences.

PubMed

Chenoweth, Meghan J; Ware, Jennifer J; Zhu, Andy Z X; Cole, Christopher B; Cox, Lisa Sanderson; Nollen, Nikki; Ahluwalia, Jasjit S; Benowitz, Neal L; Schnoll, Robert A; Hawk, Larry W; Cinciripini, Paul M; George, Tony P; Lerman, Caryn; Knight, Joanne; Tyndale, Rachel F

2018-03-01

The activity of CYP2A6, the major nicotine-inactivating enzyme, is measurable in smokers using the nicotine metabolite ratio (NMR; 3'hydroxycotinine/cotinine). Due to its role in nicotine clearance, the NMR is associated with smoking behaviours and response to pharmacotherapies. The NMR is highly heritable (~80%), and on average lower in African Americans (AA) versus whites. We previously identified several reduce and loss-of-function CYP2A6 variants common in individuals of African descent. Our current aim was to identify novel genetic influences on the NMR in AA smokers using genome-wide approaches. Genome-wide association study (GWAS). Multiple sites within Canada and the United States. AA smokers from two clinical trials: Pharmacogenetics of Nicotine Addiction Treatment (PNAT)-2 (NCT01314001; n = 504) and Kick-it-at-Swope (KIS)-3 (NCT00666978; n = 450). Genome-wide SNP genotyping, the NMR (phenotype) and population substructure and NMR covariates. Meta-analysis revealed three independent chromosome 19 signals (rs12459249, rs111645190 and rs185430475) associated with the NMR. The top overall hit, rs12459249 (P = 1.47e-39; beta = 0.59 per C (versus T) allele, SE = 0.045), located ~9.5 kb 3' of CYP2A6, remained genome-wide significant after controlling for the common (~10% in AA) non-functional CYP2A6*17 allele. In contrast, rs111645190 and rs185430475 were not genome-wide significant when controlling for CYP2A6*17. In total, 96 signals associated with the NMR were identified; many were not found in prior NMR GWASs in individuals of European descent. The top hits were also associated with the NMR in a third cohort of AA (KIS2; n = 480). None of the hits were in UGT or OCT2 genes. Three independent chromosome 19 signals account for ~20% of the variability in the nicotine metabolite ratio in African American smokers. The hits identified may contribute to inter-ethnic variability in nicotine metabolism, smoking behaviours and tobacco-related disease risk. © 2017 Society for the Study of Addiction.

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

PubMed

Summers, Samantha R; Sprenger, K G; Pfaendtner, Jim; Marchant, Jan; Summers, Michael F; Kaar, Joel L

2017-12-07

The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). Enzymatic studies revealed that [BMIM][Cl] inactivates E1 in a biphasic manner that involves rapid, reversible inhibition, followed by slow, irreversible deactivation. Backbone NMR signals of the 40.5 kDa E1 were assigned by triple resonance NMR methods, enabling monitoring of residue-specific perturbations. 1 H- 15 N NMR titration experiments revealed that [BMIM][Cl] binds reversibly to the E1 active site, indicating that reversible deactivation is due to competitive inhibition of substrate binding. Prolonged incubation with [BMIM][Cl] led to substantial global changes in the 1 H- 15 N heteronuclear single quantum coherence NMR and CD spectra of E1 indicative of protein denaturation. Notably, weak interactions between [BMIM][Cl] and residues at the termini of several helices were also observed, which, together with MD simulations, suggest that E1 denaturation is promoted by [BMIM][Cl]-induced destabilization of helix capping structures. In addition to identifying determinants of E1 inactivation, our findings establish a molecular framework for engineering cellulases with improved IL compatibility.

The metabolic profile of lemon juice by proton HR-MAS NMR: the case of the PGI Interdonato Lemon of Messina.

PubMed

Cicero, Nicola; Corsaro, Carmelo; Salvo, Andrea; Vasi, Sebastiano; Giofré, Salvatore V; Ferrantelli, Vincenzo; Di Stefano, Vita; Mallamace, Domenico; Dugo, Giacomo

2015-01-01

We have studied by means of High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) the metabolic profile of the famous Sicilian lemon known as 'Interdonato Lemon of Messina PGI'. The PGI Interdonato Lemon of Messina possesses high organoleptic and healthy properties and is recognised as one of the most nutrient fruits. In particular, some of its constituents are actively studied for their chemo-preventive and therapeutic properties. In this paper, we have determined by means of HR-MAS NMR spectroscopy the molar concentration of the main metabolites constituent the juice of PGI Interdonato Lemon of Messina in comparison with that of the not-PGI Interdonato Lemon of Turkey. Our aim is to develop an analytical technique, in order to determine a metabolic fingerprint able to reveal commercial frauds in national and international markets.

Practical aspects of NMR signal assignment in larger and challenging proteins

PubMed Central

Frueh, Dominique P.

2014-01-01

NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins. PMID:24534088

Fingerprinting analysis of Saposhnikovia divaricata using 1H nuclear magnetic resonance spectroscopy and high performance liquid chromatography.

PubMed

Xin, Yue-Yang; Deng, An-Jun; Du, Guan-Hua; Zhang, Jin-Lan; Qin, Hai-Lin

2010-09-01

The (1)H nuclear magnetic resonance ((1)H NMR) fingerprints of fractionated non-polar and polar extracts (control substance for plant drug [CSPD] A and B) from the roots of 12 specimens of Saposhnikovia divaricata (Turcz.) Schischk were achieved with Fourier Transform (FT)-NMR spectrometer and assigned by comparison to each other and to the (1)H NMR spectra of the isolated individual compounds. These fingerprints were found to be uniform in terms of the specificity for the implication of all 12 specimens being systematically of the same origin. The uniformity was further affirmed by high performance liquid chromatography (HPLC), which also revealed exactly identical specificity for the identified S. divaricata species with the (1)H NMR appearances of corresponding CSPD on the part of the composition of characteristic constituents when comparing to corresponding individual compounds. This investigation unambiguously shows that the specific signals from the chemotaxonomically significant compounds of chromones and coumarins in S. divaricata are exhibited distinctively in the composite features of both (1)H NMR fingerprints and HPLC profiles. The (1)H NMR and HPLC profiles established can successfully be used as reference for the authentication of the origin of S. divaricata species as well as for chemotaxonomic studies.

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.

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

Metabolites Re-programming and Physiological Changes Induced in Scenedesmus regularis under Nitrate Treatment.

PubMed

Ma, Nyuk-Ling; Aziz, Ahmad; Teh, Kit-Yinn; Lam, Su Shiung; Cha, Thye-San

2018-06-27

Nitrate is required to maintain the growth and metabolism of plant and animals. Nevertheless, in excess amount such as polluted water, its concentration can be harmful to living organisms such as microalgae. Recently, studies on microalgae response towards nutrient fluctuation are usually limited to lipid accumulation for the production of biofuels, disregarding the other potential of microalgae to be used in wastewater treatments and as source of important metabolites. Our study therefore captures the need to investigate overall metabolite changes via NMR spectroscopy approach coupled with multivariate data to understand the complex molecular process under high (4X) and low (1/4X) concentrations of nitrate ([Formula: see text]). NMR spectra with the aid of chemometric analysis revealed contrasting metabolites makeup under abundance and limited nitrate treatment. By using NMR technique, 43 types of metabolites and 8 types of fatty acid chains were detected. Nevertheless, only 20 key changes were observed and 16 were down regulated in limited nitrate condition. This paper has demonstrated the feasibility of NMR-based metabolomics approach to study the physiological impact of changing environment such as pollution to the implications for growth and productivity of microalgae population.

Ultraviolet radiation induces stress in etiolated Landoltia punctata, as evidenced by the presence of alanine, a universal stress signal: a ¹⁵N NMR study.

PubMed

Monselise, E B-I; Levkovitz, A; Kost, D

2015-01-01

Analysis with (15) N NMR revealed that alanine, a universal cellular stress signal, accumulates in etiolated duckweed plants exposed to 15-min pulsed UV light, but not in the absence of UV irradiation. The addition of 10 mm vitamin C, a radical scavenger, reduced alanine levels to zero, indicating the involvement of free radicals. Free D-alanine was detected in (15) N NMR analysis of the chiral amino acid content, using D-tartaric acid as solvent. The accumulation of D-alanine under stress conditions presents a new perspective on the biochemical processes taking place in prokaryote and eukaryote cells. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Mechanical Insight into Resistance of Betaine to Urea-Induced Protein Denaturation.

PubMed

Chen, Jiantao; Gong, Xiangjun; Zeng, Chaoxi; Wang, Yonghua; Zhang, Guangzhao

2016-12-08

It is known that urea can induce protein denaturation that can be inhibited by osmolytes. Yet, experimental explorations on this mechanism at the molecular level are still lacking. We have investigated the resistance of betaine to the urea-induced denaturation of lysozyme in aqueous solutions using low-field NMR. Our study demonstrates that urea molecules directly interact with lysozyme, leading to denaturation. However, betaine molecules interacting with urea more strongly than lysozyme can pull the bound urea molecules from lysozyme so that the protein is protected from denaturation. The number of urea molecules bound to a betaine molecule is given under different conditions. Proton NMR spectroscopy ( 1 H-NMR) and Fourier transform infrared spectroscopy reveal that the interaction between betaine and urea is through hydrogen bonding.

Metabolic fingerprint of Brazilian maize landraces silk (stigma/styles) using NMR spectroscopy and chemometric methods.

PubMed

Kuhnen, Shirley; Bernardi Ogliari, Juliana; Dias, Paulo Fernando; da Silva Santos, Maiara; Ferreira, Antônio Gilberto; Bonham, Connie C; Wood, Karl Vernon; Maraschin, Marcelo

2010-02-24

Aqueous extract from maize silks is used by traditional medicine for the treatment of several ailments, mainly related to the urinary system. This work focuses on the application of NMR spectroscopy and chemometric analysis for the determination of metabolic fingerprint and pattern recognition of silk extracts from seven maize landraces cultivated in southern Brazil. Principal component analysis (PCA) of the (1)H NMR data set showed clear discrimination among the maize varieties by PC1 and PC2, pointing out three distinct metabolic profiles. Target compounds analysis showed significant differences (p < 0.05) in the contents of protocatechuic acid, gallic acid, t-cinnamic acid, and anthocyanins, corroborating the discrimination of the genotypes in this study as revealed by PCA analysis. Thus the combination of (1)H NMR and PCA is a useful tool for the discrimination of maize silks in respect to their chemical composition, including rapid authentication of the raw material of current pharmacological interest.

Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy.

PubMed

Zhao, Bo; Hansen, Alexandar L; Zhang, Qi

2014-01-08

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1ρ) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1ρ) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).

Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-Lock Field R1ρ NMR Spectroscopy

PubMed Central

Zhao, Bo; Hansen, Alexandar L.; Zhang, Qi

2016-01-01

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R1ρ relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R1ρ RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR “invisible” state. The utility of CEST and low spin-lock field R1ρ RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s−1. PMID:24299272

Use of qNMR for speciation of flaxseeds (Linum usitatissimum) and quantification of cyanogenic glycosides.

PubMed

Roulard, Romain; Fontaine, Jean-Xavier; Jamali, Arash; Cailleu, Dominique; Tavernier, Reynald; Guillot, Xavier; Rhazi, Larbi; Petit, Emmanuel; Molinie, Roland; Mesnard, François

2017-12-01

This report describes a routine method taking less than 20 min to quantify cyanogenic glycosides such as linustatin and neolinustatin from flaxseeds (Linum usitatissimum L.) using 1 H nuclear magnetic resonance. After manual dehulling, a higher linustatin content was shown in the almond fraction, while neolinustatin and total cyanogenic glycoside contents were significantly higher in hulls. Linustatin and neolinustatin were quantified in seven cultivars grown in two locations in three different years. Linustatin, neolinustatin, and total cyanogenic glycosides ranged between 91 and 267 mg/100 g, 78-272 mg/100 g, and 198-513 mg/100 g dry weight flaxseeds, respectively. NMR revealed differences of up to 70% between samples with standard deviation variations lower than 6%. This study shows that NMR is a very suitable tool to perform flaxseed varietal selection for the cyanogenic glycoside content. Graphical abstract qNMR can be used to perform flaxseed varietal selection for the cyanogenic glycoside content.

Facilitated Visual Interpretation of Scores in Principal Component Analysis by Bioactivity-Labeling of 1H-NMR Spectra-Metabolomics Investigation and Identification of a New α-Glucosidase Inhibitor in Radix Astragali.

PubMed

Liu, Yueqiu; Nyberg, Nils T; Jäger, Anna K; Staerk, Dan

2017-03-06

Radix Astragali is a component of several traditional medicines used for the treatment of type 2 diabetes in China. Radix Astragali is known to contain isoflavones, which inhibit α-glucosidase in the small intestines, and thus lowers the blood glucose levels. In this study, 21 samples obtained from different regions of China were extracted with ethyl acetate, then the IC50-values were determined, and the crude extracts were analyzed by 1H-NMR spectroscopy. A principal component analysis of the 1H-NMR spectra labeled with their IC50-values, that is, bioactivity-labeled 1H-NMR spectra, showed a clear correlation between spectral profiles and the α-glucosidase inhibitory activity. The loading plot and LC-HRMS/NMR of microfractions indicated that previously unknown long chain ferulates could be partly responsible for the observed antidiabetic activity of Radix Astragali. Subsequent preparative scale isolation revealed a compound not previously reported, linoleyl ferulate (1), showing α-glucosidase inhibitory activity (IC50 0.5 mM) at a level comparable to the previously studied isoflavones. A closely related analogue, hexadecyl ferulate (2), did not show significant inhibitory activity, and the double bonds in the alcohol part of 1 seem to be important structural features for the α-glucosidase inhibitory activity. This proof of concept study demonstrates that bioactivity-labeling of the 1H-NMR spectral data of crude extracts allows global and nonselective identification of individual constituents contributing to the crude extract's bioactivity.

Crossover from Commensurate to Incommensurate Antiferromagnetism in Stoichiometric NaFeAs Revealed by Single-Crystal 23Na,75As-NMR Experiments

NASA Astrophysics Data System (ADS)

Kitagawa, Kentaro; Mezaki, Yuji; Matsubayashi, Kazuyuki; Uwatoko, Yoshiya; Takigawa, Masashi

2011-03-01

We report the results of 23Na and 75As nuclear magnetic resonance (NMR) experiments on a self-flux grown high-quality single crystal of stoichiometric NaFeAs. The NMR spectra reveal a tetragonal to twinned-orthorhombic structural phase transition at TO = 57 K and an antiferromagnetic (AF) transition at TAF = 45 K. The divergent behavior of nuclear relaxation rate near TAF shows significant anisotropy, indicating that the critical slowing down of stripe-type AF fluctuations are strongly anisotropic in spin space. The NMR spectra at sufficiently low temperatures consist of sharp peaks showing a commensurate stripe AF order with a small moment of ˜0.3 μB. However, the spectra just below TAF exhibit a highly asymmetric broadening pointing to an incommensurate modulation. The commensurate-incommensurate crossover in NaFeAs shows a certain similarity to the behavior of SrFe2As2 under high pressure.

MAS-NMR investigations of the crystallization behaviour of lithium aluminum silicate (LAS) glasses containing P 2O 5 and TiO 2 nucleants

NASA Astrophysics Data System (ADS)

Ananthanarayanan, A.; Kothiyal, G. P.; Montagne, L.; Revel, B.

2010-06-01

Lithium aluminum silicate (LAS) glass of composition (mol%) 20.4Li 2O-4.0Al 2O 3-68.6SiO 2-3.0K 2O-2.6B 2O 3-0.5P 2O 5-0.9TiO 2 was prepared by melt quenching. The glass was then nucleated and crystallized based on differential thermal analysis (DTA) data and was characterized by 29Si, 31P, 11B and 27Al MAS-NMR. XRD and 29Si NMR showed that lithium metasilicate (Li 2SiO 3) is the first phase to c form followed by cristobalite (SiO 2) and lithium disilicate (Li 2Si 2O 5). 29Si MAS-NMR revealed a change in the network structure already for the glasses nucleated at 550 °C. Since crystalline Li 3PO 4, as observed by 31P MAS-NMR, forms concurrently with the silicate phases, we conclude that crystalline Li 3PO 4 does not act as a nucleating agent for lithium silicate phases. Moreover, 31P NMR indicates the formation of M-PO 4 ( M=B, Al or Ti) complexes. The presence of BO 3 and BO 4 structural units in all the glass/glass-ceramic samples is revealed through 11B MAS-NMR. B remains in the residual glass and the crystallization of silicate phases causes a reduction in the number of alkali ions available for charge compensation. As a result, the number of trigonally coordinated B (BO 3) increases at the expense of tetrahedrally coordinated B (BO 4). The 27Al MAS-NMR spectra indicate the presence of tetrahedrally coordinated Al species, which are only slightly perturbed by the crystallization.

Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat

PubMed Central

2013-01-01

Background The naked mole rats (NMRs) are small-sized underground rodents with plenty of unusual traits. Their life expectancy can be up to thirty years, more than seven times longer than laboratory rat. Furthermore, they are resistant to both congenital and experimentally induced cancer genesis. These peculiar physiological and pathological characteristics allow them to become a suitable model for cancer and aging research. Results In this paper, we carried out a genome-wide comparative analysis of rat and NMR using the recently published genome sequence of NMR. First, we identified all the rat-NMR orthologous genes and specific genes within each of them. The expanded and contracted numbers of protein families in NMR were also analyzed when compared to rat. Seven cancer-related protein families appeared to be significantly expanded, whereas several receptor families were found to be contracted in NMR. We then chose those rat genes that were inexistent in NMR and adopted KEGG pathway database to investigate the metabolic processes in which their proteins may be involved. These genes were significantly enriched in two rat cancer pathways, "Pathway in cancer" and "Bladder cancer". In the rat "Pathway in cancer", 9 out of 14 paths leading to evading apoptosis appeared to be affected in NMR. In addition, a significant number of other NMR-missing genes enriched in several cancer-related pathways have been known to be related to a variety of cancers, implying that many of them may be also related to tumorigenesis in mammals. Finally, investigation of sequence variations among orthologous proteins between rat and NMR revealed that significant fragment insertions/deletions within important functional domains were present in some NMR proteins, which might lead to expressional and/or functional changes of these genes in different species. Conclusions Overall, this study provides insights into understanding the possible anti-cancer mechanisms of NMR as well as searching for new cancer-related candidate genes. PMID:24565050

Low-temperature methyl group dynamics of hexamethylbenzene in crystalline and glassy matrices as studied by 2H NMR

NASA Astrophysics Data System (ADS)

Börner, K.; Diezemann, G.; Rössler, E.; Vieth, H. M.

1991-07-01

2H NMR spectra of hexamethylbenzene (HMB) in protonated crystalline and amorphous matrices at low temperatures are presented. All spectra reveal lineshape changes which can be attributed to methyl group tunnelling. Compared to neat HMB, a drastic increase of the tunnelling frequency is found for all systems. This indicates that the hindering potential originates predominantly from intermolecular forces. We studied the temperature dependence of these spectra and the spin-lattice relaxation in order to exclude a distribution of motional correlation times describing a thermally activated process. In addition, we find a distortion of the methyl tetrahedron.

Insight into hydrogen bonding of uranyl hydroxide layers and capsules by use of 1H magic-angle spinning NMR spectroscopy [Insight into the hydrogen bonding for uranyl hydroxides using 1H MAS NMR spectroscopy

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

Alam, Todd M.; Liao, Zuolei; Nyman, May

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO 2(OH) 2] (α-UOH) and hydrated uranyl hydroxide [(UO 2) 4O(OH) 6·5H 2O (metaschoepite). For the metaschoepite material, proton resonances of the μ 2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H– 1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization ofmore » local hydrogen-bond environments in uranyl U 24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

Insight into hydrogen bonding of uranyl hydroxide layers and capsules by use of 1H magic-angle spinning NMR spectroscopy [Insight into the hydrogen bonding for uranyl hydroxides using 1H MAS NMR spectroscopy

DOE PAGES

Alam, Todd M.; Liao, Zuolei; Nyman, May; ...

2016-04-27

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO 2(OH) 2] (α-UOH) and hydrated uranyl hydroxide [(UO 2) 4O(OH) 6·5H 2O (metaschoepite). For the metaschoepite material, proton resonances of the μ 2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H– 1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization ofmore » local hydrogen-bond environments in uranyl U 24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

Communication between Tandem cAMP Binding Domains in the Regulatory Subunit of Protein Kinase A-Iα as Revealed by Domain-silencing Mutations*

PubMed Central

McNicholl, E. Tyler; Das, Rahul; SilDas, Soumita; Taylor, Susan S.; Melacini, Giuseppe

2010-01-01

Protein kinase A (PKA) is the main receptor for the universal cAMP second messenger. PKA is a tetramer with two catalytic (C) and two regulatory (R) subunits, each including two tandem cAMP binding domains, i.e. CBD-A and -B. Structural investigations of RIα have revealed that although CBD-A plays a pivotal role in the cAMP-dependent inhibition of C, the main function of CBD-B is to regulate the access of cAMP to site A. To further understand the mechanism underlying the cross-talk between CBD-A and -B, we report here the NMR investigation of a construct of R, RIα-(119–379), which unlike previous fragments characterized by NMR, spans in full both CBDs. Our NMR studies were also extended to two mutants, R209K and the corresponding R333K, which severely reduce the affinity of cAMP for CBD-A and -B, respectively. The comparative NMR analysis of wild-type RIα-(119–379) and of the two domain silencing mutations has led to the definition at an unprecedented level of detail of both intra- and interdomain allosteric networks, revealing several striking differences between the two CBDs. First, the two domains, although homologous in sequence and structure, exhibit remarkably different responses to the R/K mutations especially at the β2-3 allosteric “hot spot.” Second, although the two CBDs are reciprocally coupled at the level of local unfolding of the hinge, the A-to-B and B-to-A pathways are dramatically asymmetrical at the level of global unfolding. Such an asymmetric interdomain cross-talk ensures efficiency and robustness in both the activation and de-activation of PKA. PMID:20202931

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

NASA Astrophysics Data System (ADS)

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

Recombinant expression of Ixolaris, a Kunitz-type inhibitor from the tick salivary gland, for NMR studies.

PubMed

De Paula, V S; Silva, F H S; Francischetti, I M B; Monteiro, R Q; Valente, A P

2017-11-01

Ixolaris is an anticoagulant protein identified in the tick saliva of Ixodes scapularis. Ixolaris contains 2 Kunitz like domains and binds to Factor Xa or Factor X as a scaffold for inhibition of the Tissue Factor (TF)/Factor VIIa (FVIIa). In contrast to tissue factor pathway inhibitor (TFPI), however, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite. Due to its potent and long-lasting antithrombotic activity, Ixolaris is a promising agent for anticoagulant therapy. Although numerous functional studies of Ixolaris exist, three-dimensional structure of Ixolaris has not been obtained at atomic resolution. Using the pET32 vector, we successfully expressed a TRX-His 6 -Ixolaris fusion protein. By combining Ni-NTA chromatography, enterokinase protease cleavage, and reverse phase HPLC (RP-HPLC), we purified isotopically labeled Ixolaris for NMR studies. 1D 1 H and 2D 15 N- 1 H NMR analysis yielded high quality 2D 15 N- 1 H HSQC spectra revealing that the recombinant protein is folded. These studies represent the first steps in obtaining high-resolution structural information by NMR for Ixolaris enabling the investigation of the molecular basis for Ixolaris-coagulation factors interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

NMR crystallography of α-poly(L-lactide).

PubMed

Pawlak, Tomasz; Jaworska, Magdalena; Potrzebowski, Marek J

2013-03-07

A complementary approach that combines NMR measurements, analysis of X-ray and neutron powder diffraction data and advanced quantum mechanical calculations was employed to study the α-polymorph of L-polylactide. Such a strategy, which is known as NMR crystallography, to the best of our knowledge, is used here for the first time for the fine refinement of the crystal structure of a synthetic polymer. The GIPAW method was used to compute the NMR shielding parameters for the different models, which included the α-PLLA structure obtained by 2-dimensional wide-angle X-ray diffraction (WAXD) at -150 °C (model M1) and at 25 °C (model M2), neutron diffraction (WAND) measurements (model M3) and the fully optimized geometry of the PLLA chains in the unit cell with defined size (model M4). The influence of changes in the chain conformation on the (13)C σ(ii) NMR shielding parameters is shown. The correlation between the σ(ii) and δ(ii) values for the M1-M4 models revealed that the M4 model provided the best fit. Moreover, a comparison of the experimental (13)C NMR spectra with the spectra calculated using the M1-M4 models strongly supports the data for the M4 model. The GIPAW method, via verification using NMR measurements, was shown to be capable of the fine refinement of the crystal structures of polymers when coarse X-ray diffraction data for powdered samples are available.

Experimental (13C NMR, 1H NMR, FT-IR, single-crystal X-ray diffraction) and DFT studies on 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione.

PubMed

Süleymanoğlu, Nevin; Ustabaş, Reşat; Alpaslan, Yelda Bingöl; Eyduran, Fatih; Ozyürek, Cengiz; Iskeleli, Nazan Ocak

2011-12-01

In this work, 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione C(10)H(16)N(2)O(2) (I), was synthesized and characterized by (13)C NMR, (1)H NMR, FT-IR, UV-vis spectroscopy and single-crystal X-ray diffraction. DFT method with 6-31G(d,p) basis set has been used to calculate the optimized geometrical parameters, atomic charges, vibrational frequencies and chemical shift values. The calculated vibrational frequencies and chemical shift values are compared with experimental FT-IR and NMR spectra. The results of the calculation shows good agreement between experimental and calculated values of the compound I. The existence of N-H⋯O type intermolecular ve C-H⋯O type intramolecular hydrogen bonds can be deduced from differences between experimental and calculated results of FT-IR and NMR. In addition, the molecular electrostatic potential map and frontier molecular orbitals and electronic absorption spectra were performed at B3LYP/6-31G(d,p) level of theory. HOMO-LUMO electronic transition of 4.90 eV are derived from the contribution of the bands π→π* and n→π* The spectral results obtained from FT-IR, NMR and X-ray of I revealed that the compound I is in predominantly enamine tautomeric form, which was supported by DFT calculations. Copyright © 2011 Elsevier B.V. All rights reserved.

Probing the calcium and sodium local environment in bones and teeth using multinuclear solid state NMR and X-ray absorption spectroscopy.

PubMed

Laurencin, Danielle; Wong, Alan; Chrzanowski, Wojciech; Knowles, Jonathan C; Qiu, Dong; Pickup, David M; Newport, Robert J; Gan, Zhehong; Duer, Melinda J; Smith, Mark E

2010-02-07

Despite the numerous studies of bone mineral, there are still many questions regarding the exact structure and composition of the mineral phase, and how the mineral crystals become organised with respect to each other and the collagen matrix. Bone mineral is commonly formulated as hydroxyapatite, albeit with numerous substitutions, and has previously been studied by (31)P and (1)H NMR, which has given considerable insight into the complexity of the mineral structure. However, to date, there has been no report of an NMR investigation of the other major component of bone mineral, calcium, nor of common minority cations like sodium. Here, direct analysis of the local environment of calcium in two biological apatites, equine bone (HB) and bovine tooth (CT), was carried out using both (43)Ca solid state NMR and Ca K-edge X-ray absorption spectroscopy, revealing important structural information about the calcium coordination shell. The (43)Ca delta(iso) in HB and CT is found to correlate with the average Ca-O bond distance measured by Ca K-edge EXAFS, and the (43)Ca NMR linewidths show that there is a greater distribution in chemical bonding around calcium in HB and CT, compared to synthetic apatites. In the case of sodium, (23)Na MAS NMR, high resolution 3Q-MAS NMR, as well as (23)Na{(31)P} REDOR and (1)H{(23)Na} R(3)-HMQC correlation experiments give the first direct evidence that some sodium is located inside the apatite phase in HB and CT, but with a greater distribution of environments compared to a synthetic sodium substituted apatite (Na-HA).

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars.

PubMed

Hu, Boran; Yue, Yaqing; Zhu, Yong; Wen, Wen; Zhang, Fengmin; Hardie, Jim W

2015-01-01

Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (1H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although 1H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors. We applied 1H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses. Differences in grape-derived metabolites associated with genetic differences alone are a major source of 1H NMR-based discrimination of wines and 1H NMR has the capacity to discriminate between very closely related cultivars. The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by 1H NMR-PCA/PLS and indicates that 1H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach.

Screening molecular associations with lipid membranes using natural abundance 13C cross-polarization magic-angle spinning NMR and principal component analysis.

PubMed

Middleton, David A; Hughes, Eleri; Madine, Jillian

2004-08-11

We describe an NMR approach for detecting the interactions between phospholipid membranes and proteins, peptides, or small molecules. First, 1H-13C dipolar coupling profiles are obtained from hydrated lipid samples at natural isotope abundance using cross-polarization magic-angle spinning NMR methods. Principal component analysis of dipolar coupling profiles for synthetic lipid membranes in the presence of a range of biologically active additives reveals clusters that relate to different modes of interaction of the additives with the lipid bilayer. Finally, by representing profiles from multiple samples in the form of contour plots, it is possible to reveal statistically significant changes in dipolar couplings, which reflect perturbations in the lipid molecules at the membrane surface or within the hydrophobic interior.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

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.

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.

Homonuclear 1H NMR and circular dichroism study of the HIV-1 Tat Eli variant.

PubMed

Watkins, Jennifer D; Campbell, Grant R; Halimi, Hubert; Loret, Erwann P

2008-09-22

The HIV-1 Tat protein is a promising target to develop AIDS therapies, particularly vaccines, due to its extracellular role that protects HIV-1-infected cells from the immune system. Tat exists in two different lengths, 86 or 87 residues and 99 or 101 residues, with the long form being predominant in clinical isolates. We report here a structural study of the 99 residue Tat Eli variant using 2D liquid-state NMR, molecular modeling and circular dichroism. Tat Eli was obtained from solid-phase peptide synthesis and the purified protein was proven biologically active in a trans-activation assay. Circular dichroism spectra at different temperatures up to 70 degrees C showed that Tat Eli is not a random coil at 20 degrees C. Homonuclear 1H NMR spectra allowed us to identify 1639 NMR distance constraints out of which 264 were interresidual. Molecular modeling satisfying at least 1474 NMR constraints revealed the same folding for different model structures. The Tat Eli model has a core region composed of a part of the N-terminus including the highly conserved Trp 11. The extra residues in the Tat Eli C-terminus protrude from a groove between the basic region and the cysteine-rich region and are well exposed to the solvent. We show that active Tat variants share a similar folding pattern whatever their size, but mutations induce local structural changes.

Nanodisc-Targeted STD NMR Spectroscopy Reveals Atomic Details of Ligand Binding to Lipid Environments.

PubMed

Muñoz-García, Juan C; Inacio Dos Reis, Rosana; Taylor, Richard J; Henry, Alistair J; Watts, Anthony

2018-05-18

Saturation transfer difference (STD) NMR spectroscopy is one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. This is due to its robustness and the fact that it is focused on the signals of the ligand, without any need for NMR information on the macromolecular target. This technique is most commonly applied to systems involving different types of ligands (e.g., small organic molecules, carbohydrates or lipids) and a protein as the target, in which the latter is selectively saturated. However, only a few examples have been reported where membrane mimetics are the macromolecular binding partners. Here, we have employed STD NMR spectroscopy to investigate the interactions of the neurotransmitter dopamine with mimetics of lipid bilayers, such as nanodiscs, by saturation of the latter. In particular, the interactions between dopamine and model lipid nanodiscs formed either from charged or zwitterionic lipids have been resolved at the atomic level. The results, in agreement with previous isothermal titration calorimetry studies, show that dopamine preferentially binds to negatively charged model membranes, but also provide detailed atomic insights into the mode of interaction of dopamine with membrane mimetics. Our findings provide relevant structural information for the design of lipid-based drug carriers of dopamine and its structural analogues and are of general applicability to other systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human metabolic profiles are stably controlled by genetic and environmental variation

PubMed Central

Nicholson, George; Rantalainen, Mattias; Maher, Anthony D; Li, Jia V; Malmodin, Daniel; Ahmadi, Kourosh R; Faber, Johan H; Hallgrímsdóttir, Ingileif B; Barrett, Amy; Toft, Henrik; Krestyaninova, Maria; Viksna, Juris; Neogi, Sudeshna Guha; Dumas, Marc-Emmanuel; Sarkans, Ugis; The MolPAGE Consortium; Silverman, Bernard W; Donnelly, Peter; Nicholson, Jeremy K; Allen, Maxine; Zondervan, Krina T; Lindon, John C; Spector, Tim D; McCarthy, Mark I; Holmes, Elaine; Baunsgaard, Dorrit; Holmes, Chris C

2011-01-01

1H Nuclear Magnetic Resonance spectroscopy (1H NMR) is increasingly used to measure metabolite concentrations in sets of biological samples for top-down systems biology and molecular epidemiology. For such purposes, knowledge of the sources of human variation in metabolite concentrations is valuable, but currently sparse. We conducted and analysed a study to create such a resource. In our unique design, identical and non-identical twin pairs donated plasma and urine samples longitudinally. We acquired 1H NMR spectra on the samples, and statistically decomposed variation in metabolite concentration into familial (genetic and common-environmental), individual-environmental, and longitudinally unstable components. We estimate that stable variation, comprising familial and individual-environmental factors, accounts on average for 60% (plasma) and 47% (urine) of biological variation in 1H NMR-detectable metabolite concentrations. Clinically predictive metabolic variation is likely nested within this stable component, so our results have implications for the effective design of biomarker-discovery studies. We provide a power-calculation method which reveals that sample sizes of a few thousand should offer sufficient statistical precision to detect 1H NMR-based biomarkers quantifying predisposition to disease. PMID:21878913

NMR studies of spin dynamics in cuprates

NASA Astrophysics Data System (ADS)

Takigawa, M.; Mitzi, D. B.

1994-04-01

We report recent NMR results in cuprates. The oxygen Knight shift and the Cu nuclear spin-lattice relaxation rate in Bi2.1Sr1.94Ca0.88Cu2.07O8+δ single crystals revealed a gapless superconducting state, which can be most naturally explained by a d-wave pairing state and the intrinsic disorder in this material. The Cu nuclear spin-spin relaxation rate in underdoped YBa2Cu3O6.63 shows distinct temperature dependence from the spin-lattice relaxation rate, providing direct evidence for a pseudo spin-gap near the antiferromagnetic wave vector.

Dynamics of glass-forming di-n-butyl phthalate as studied by NMR.

PubMed

Szcześniak, E; Głowinkowski, S; Suchański, W; Jurga, S

1997-04-01

Spin-lattice relaxation times T1 and nuclear Overhauser effect (NOE) enhancement factors for the individual ring carbons in di-n-butyl phthalate (DBF) show that the reorientational correlation function corresponding to the global dynamics in supercooled liquid can be described by a Davidson-Cole distribution. Measurements of proton spin-lattice relaxation times T1 and T1p, as well as 1H NMR spectra at temperatures below the glass transition temperature, Tg, reveal that the same distribution holds also for description of local dynamics in glassy DBF. The activation parameters of the motions detected are derived.

Decontamination of 2-chloroethyl ethylsulfide using titanate nanoscrolls

NASA Astrophysics Data System (ADS)

Kleinhammes, Alfred; Wagner, George W.; Kulkarni, Harsha; Jia, Yuanyuan; Zhang, Qi; Qin, Lu-Chang; Wu, Yue

2005-08-01

Titanate nanoscrolls, a recently discovered variant of TiO 2 nanocrystals, are tested as reactive sorbent for chemical warfare agent (CWA) decontamination. The large surface area of the uncapped tubules provides the desired rapid absorption of the contaminant while water molecules, intrinsic constituents of titanate nanoscrolls, provide the necessary chemistry for hydrolytic reaction. In this study the decomposition of 2-chloroethyl ethylsulfide (CEES), a simulant for the CWA mustard, was monitored using 13C NMR. The NMR spectra reveal reaction products as expected from the hydrolysis of CEES. This demonstrates that titanate nanoscrolls could potentially be employed as a decontaminant for CWAs.

Evidence of land plant affinity for the Devonian fossil Protosalvinia (Foerstia)

USGS Publications Warehouse

Romankiw, L.A.; Hatcher, P.G.; Roen, J.B.

1988-01-01

The Devonian plant fossil Protosalvinia (Foerstia) has been examined by solid-state 13C nuclear magnetic resonance spectroscopy (NMR) and pyrolysis-gas chromatography-mass spectrometry (PY-GC-MS). Results of these studies reveal that the chemical structure of Protosalvinia is remarkably similar to that of coalified wood. A well-defined phenolic carbon peak in the NMR spectra and the appearance of phenol and alkylated phenols in pyrolysis products are clearly indicative of lignin-like compounds. These data represent significant new information on the chemical nature of Protosalvinia and provide the first substantial organic geochemical evidence for land plant affinity. -Authors

Hyperpolarized 13C NMR lifetimes in the liquid-state: relating structures and T1 relaxation times

NASA Astrophysics Data System (ADS)

Parish, Christopher; Niedbalski, Peter; Hashami, Zohreh; Fidelino, Leila; Kovacs, Zoltan; Lumata, Lloyd

Among the various attempts to solve the insensitivity problem in nuclear magnetic resonance (NMR), the physics-based technique dissolution dynamic nuclear polarization (DNP) is probably the most successful method of hyperpolarization or amplifying NMR signals. Using this technique, liquid-state NMR signal enhancements of several thousand-fold are expected for low-gamma nuclei such as carbon-13. The lifetimes of these hyperpolarized 13C NMR signals are directly related to their 13C spin-lattice relaxation times T1. Depending upon the 13C isotopic location, the lifetimes of hyperpolarized 13C compounds can range from a few seconds to minutes. In this study, we have investigated the hyperpolarized 13C NMR lifetimes of several 13C compounds with various chemical structures from glucose, acetate, citric acid, naphthalene to tetramethylallene and their deuterated analogs at 9.4 T and 25 deg C. Our results show that the 13C T1s of these compounds can range from a few seconds to more than 60 s at this field. Correlations between the chemical structures and T1 relaxation times will be discussed and corresponding implications of these results on 13C DNP experiments will be revealed. US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

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

PubMed

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

2015-08-15

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

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

Hao, Naijia; Bezerra, Tais Lacerda; Wu, Qiong

Pyrolysis is a promising method for converting biomass to biofuels. However, some of pyrolysis oil's physiochemical properties still limit its commercial applications. Here, the autohydrolysis pretreatment at 175 ± 3 °C for 40 min was conducted to improve the resulting pine pyrolysis oil’s properties as a fuel. During autohydrolysis, deacetylation and decomposition of hemicellulose was observed by ion-exchange chromatography and Fourier transform infrared spectroscopy (FT-IR). Additionally, the cleavage of lignin ether bonds was clearly determined by 13C cross-polarization/magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR). Phosphitylation followed by 31P NMR analysis of the heavy oils gave detailed structural information ofmore » the hydroxyl groups; the results revealed that autohydrolysis pretreatment led to a reduction of carboxyl acids in the heavy oils generated at all three pyrolysis temperatures (400, 500, and 600 °C). The 31P NMR analysis also revealed that autohydrolysis pretreatment led to a reduction of condensed phenolic hydroxyl groups in the heavy oils produced at 600 °C. 1H- 13C heteronuclear single-quantum correlation (HSQC) NMR analysis showed that at a pyrolysis temperature of 600 °C, the pretreated pine produced lower methoxy group constituents. In both 31P and HSQC NMR results indicated that autohydrolysis pretreatment increased levoglucosan yields in the bio-oils.« less

Investigation of ionic mobility in NASICON-type solid electrolytes

NASA Astrophysics Data System (ADS)

Vyalikh, A.; Vizgalov, V.; Itkis, D. M.; Meyer, D. C.

2016-10-01

Impedance spectroscopy and 7Li NMR have been applied to characterize the lithium conducting glass-ceramics membranes of the Li1.5Al0.5Ge1.5(PO4)3 composition with the NASICON-type structure. The 7Li NMR spectra and T1 relaxation times have been compared for the precursor glass and two glass-ceramics annealed for 2 and 6 hours, and analysed with respect to the ionic conductivity in these materials. The 7Li static NMR spectra reveal two components in the glass-ceramics samples: A quadrupole pattern with CQ of 38.7 kHz and 32.5 kHz, and a narrow signal of the Lorentzian or Gaussian lineshape for the samples annealed for 2 and 6 hours, respectively. Variation of the lineshape and the deconvolution parameters point out to the modification of the NASICON framework in the former, which affects the conductivity channels towards improved movement of lithium ions. The NMR data correlate with the conductivity measurements demonstrating enhanced ionic mobility in the glass-ceramics annealed for 2 hours. The 7Li NMR relaxation data seem to be very sensitive to the species with different mobility and reveal the presence of an additional minor component, which can be responsible for decrease of conductivity at longer thermal treatment.

A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum.

PubMed

Tomita, Satoru; Tanaka, Naoto; Okada, Sanae

2017-03-01

The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Combined Application of UHPLC-QTOF/MS, HPLC-ELSD and 1 H-NMR Spectroscopy for Quality Assessment of DA-9801, A Standardised Dioscorea Extract.

PubMed

Kang, Kyo Bin; Ryu, Jayoung; Cho, Youngwoong; Choi, Sang-Zin; Son, Miwon; Sung, Sang Hyun

2017-05-01

DA-9801, a standardised 50% aqueous ethanolic extract of a mixture of Dioscorea japonica and D. nipponica, is a botanical drug candidate for the treatment of diabetic neuropathy, which finished its US phase II clinical trials recently. An advanced quality control method is needed for further development of DA-9801, considering its high contents of both primary and secondary metabolites. Development of a quality assessment strategy for DA-9801, based on the combination of UHPLC-QTOF/MS, HPLC-ELSD, and 1 H-NMR spectroscopy. The method was developed and tested with 15 batch products of DA-9801. The steroidal saponins of DA-9801 were tentatively identified by UHPLC-QTOF/MS and were quantified with the validated HPLC-ELSD method. Primary metabolites of DA-9801 were identified and profiled using 1 H-NMR spectrometry. The batch-to-batch equivalence of DA-9801 was tested with the 1 H-NMR spectra using spectral binning, correlation analysis, and principal component analysis. Six major saponins of DA-9801 were tentatively identified by UHPLC-QTOF/MS. Among them, protodioscin and dioscin were quantified by the validated HPLC-ELSD method. Twenty-six metabolites were identified in 1 H-NMR spectra. The similarity between DA-9801 batches could be evaluated with the NMR spectra of DA-9801. The 1 H-NMR method also revealed that two Dioscorea species contributed distinct amino acids to the contents of DA-9801. This study validates the effectiveness of UHPLC-QTOF/MS, HPLC-ELSD, and 1 H NMR-combined method for quality control of DA-9801 and its crude materials. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars

PubMed Central

Zhu, Yong; Wen, Wen; Zhang, Fengmin; Hardie, Jim W.

2015-01-01

Background and Aims Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (1H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although 1H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors. Methods and Results We applied 1H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses. Conclusions Differences in grape-derived metabolites associated with genetic differences alone are a major source of 1H NMR-based discrimination of wines and 1H NMR has the capacity to discriminate between very closely related cultivars. Significance of the Study The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by 1H NMR-PCA/PLS and indicates that 1H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach. PMID:26658757

Structure of Ancient Glass by 29 Si Magic Angle Spinning NMR Spectroscopy.

PubMed

Bradford, Henry; Ryder, Amy; Henderson, Julian; Titman, Jeremy J

2018-05-23

29 Si magic angle spinning (MAS) NMR spectroscopy has been applied for the first time to the structural analysis of ancient glass samples obtained from archaeological excavations. The results show that it is possible to establish the distribution of Si environments in ancient glass by 29 Si MAS NMR, so long as the concentrations of magnetic impurities, such as Mn and Fe oxides, are low. In general, good agreement has been obtained with compositions determined by means of electron probe microanalysis. In addition, the 29 Si MAS NMR data reveal structural differences between glasses manufactured at separate ancient sites. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metabolic fingerprinting of Leontopodium species (Asteraceae) by means of 1H NMR and HPLC–ESI-MS

PubMed Central

Safer, Stefan; Cicek, Serhat S.; Pieri, Valerio; Schwaiger, Stefan; Schneider, Peter; Wissemann, Volker; Stuppner, Hermann

2011-01-01

The genus Leontopodium, mainly distributed in Central and Eastern Asia, consists of ca. 34–58 different species. The European Leontopodium alpinum, commonly known as Edelweiss, has a long tradition in folk medicine. Recent research has resulted in the identification of prior unknown secondary metabolites, some of them with interesting biological activities. Despite this, nearly nothing is known about the Asian species of the genus. In this study, we applied proton nuclear magnetic resonance (1H NMR) spectroscopy and liquid chromatography–mass spectrometry (LC–MS) metabolic fingerprinting to reveal insights into the metabolic patterns of 11 different Leontopodium species, and to conclude on their taxonomic relationship. Principal component analysis (PCA) of 1H NMR fingerprints revealed two species groups. Discriminators for these groups were identified as fatty acids and sucrose for group A, and ent-kaurenoic acid and derivatives thereof for group B. Five diterpenes together with one sesquiterpene were isolated from Leontopodium franchetii roots; the compounds were described for the first time for L. franchetii: ent-kaur-16-en-19-oic acid, methyl-15α-angeloyloxy-ent-kaur-16-en-19-oate, methyl-ent-kaur-16-en-19-oate, 8-acetoxymodhephene, 19-acetoxy-ent-kaur-16-ene, methyl-15β–angeloyloxy-16,17-epoxy-ent-kauran-19-oate. In addition, differences in the metabolic profile between collected and cultivated species could be observed using a partial least squares-discriminant analysis (PLS-DA). PCA of the LC–MS fingerprints revealed three groups. Discriminating signals were compared to literature data and identified as two bisabolane derivatives responsible for discrimination of group A and C, and one ent-kaurenoic acid derivative, discriminating group B. A taxonomic relationship between a previously unidentified species and L. franchetii and Leontopodium sinense could be determined by comparing NMR fingerprints. This finding supports recent molecular data. Furthermore, Leontopodium dedekensii and L. sinense, two closely related species in terms of morphology and DNA-fingerprints, could be distinguished clearly using 1H NMR and LC–MS metabolic fingerprinting. PMID:21550615

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

Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory.

PubMed

Gupta, Rupal; Stringer, John; Struppe, Jochem; Rehder, Dieter; Polenova, Tatyana

2018-07-01

Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17 O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17 O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates. Copyright © 2018 Elsevier Inc. All rights reserved.

Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae-A 2D NMR Metabolomics Study.

PubMed

Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

2016-09-02

Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of ¹H-(13)C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae.

In Situ Flow MAS NMR Spectroscopy and Synchrotron PDF Analyses of the Local Response of the Brønsted Acidic Site in SAPO-34 during Hydration at Elevated Temperatures.

PubMed

Kalantzopoulos, Georgios N; Lundvall, Fredrik; Checchia, Stefano; Lind, Anna; Wragg, David S; Fjellvåg, Helmer; Arstad, Bjørnar

2018-02-19

In situ flow magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and synchrotron-based pair distribution function (PDF) analyses were applied to study water's interactions with the Brønsted acidic site and the surrounding framework in the SAPO-34 catalyst at temperatures up to 300 °C for NMR spectroscopy and 700 °C for PDF. 29 Si enrichment of the sample enabled detailed NMR spectroscopy investigations of the T-atom generating the Brønsted site. By NMR spectroscopy, we observed dehydration above 100 °C and a coalescence of Si peaks due to local framework adjustments. Towards 300 °C, the NMR spectroscopy data indicated highly mobile acidic protons. In situ total X-ray scattering measurements analyzed by PDF showed clear changes in the Al local environment in the 250-300 °C region, as the Al-O bond lengths showed a sudden change. This fell within the same temperature range as the increased Brønsted proton mobility. We suggest that the active site in this catalyst under industrial conditions comprises not only the Brønsted proton but also SiO 4 . To the best of our knowledge, this is the first work proposing a structural model of a SAPO catalyst by atomic PDF analysis. The combination of synchrotron PDF analysis with in situ NMR spectroscopy is promising in revealing the dynamic features of a working catalyst. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear magnetic resonance probe head design for precision strain control

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

Kissikov, T.; Sarkar, R.; Bush, B. T.

Here, we present the design and construction of an NMR probe to investigate single crystals under strain at cryogenic temperatures. The probe head incorporates a piezoelectric-based apparatus from Razorbill Instruments that enables both compressive and tensile strain tuning up to strain values on the order of 0.3% with a precision of 0.001%. 75As NMR in BaFe 2As 2 reveals large changes to the electric field gradient and indicates that the strain is homogeneous to within 16% over the volume of the NMR coil.

Nuclear magnetic resonance probe head design for precision strain control

DOE PAGES

Kissikov, T.; Sarkar, R.; Bush, B. T.; ...

2017-10-03

Here, we present the design and construction of an NMR probe to investigate single crystals under strain at cryogenic temperatures. The probe head incorporates a piezoelectric-based apparatus from Razorbill Instruments that enables both compressive and tensile strain tuning up to strain values on the order of 0.3% with a precision of 0.001%. 75As NMR in BaFe 2As 2 reveals large changes to the electric field gradient and indicates that the strain is homogeneous to within 16% over the volume of the NMR coil.

Urine metabonomic profiling of a female adolescent with PIT-1 mutation before and during growth hormone therapy: insights into the metabolic effects of growth hormone.

PubMed

Abd Rahman, Shaffinaz; Schirra, Horst Joachim; Lichanska, Agnieszka M; Huynh, Tony; Leong, Gary M

2013-01-01

Growth hormone (GH) is a protein hormone with important roles in growth and metabolism. The objective of this study was to investigate the metabolism of a human subject with severe GH deficiency (GHD) due to a PIT-1 gene mutation and the metabolic effects of GH therapy using Nuclear Magnetic Resonance (NMR)-based metabonomics. NMR-based metabonomics is a platform that allows the metabolic profile of biological fluids such as urine to be recorded, and any alterations in the profile modulated by GH can potentially be detected. Urine samples were collected from a female subject with severe GHD before, during and after GH therapy, and from healthy age- and sex-matched controls and analysed with NMR-based metabonomics. The samples were collected at a hospital and the study was performed at a research facility. We studied a 17 year old female adolescent with severe GHD secondary to PIT-1 gene mutation who had reached final adult height and who had ceased GH therapy for over 3 years. The subject was subsequently followed for 5 years with and without GH therapy. Twelve healthy age-matched female subjects acted as control subjects. The GH-deficient subject re-commenced GH therapy at a dose of 1 mg/day to normalise serum IGF-1 levels. Urine metabolic profiles were recorded using NMR spectroscopy and analysed with multivariate statistics to distinguish the profiles at different time points and identify significant metabolites affected by GH therapy. NMR-based metabonomics revealed that the metabolic profile of the GH-deficient subject altered with GH therapy and that her profile was different from healthy controls before, and during withdrawal of GH therapy. This study illustrates the potential use of NMR-based metabonomics for monitoring the effects of GH therapy on metabolism by profiling the urine of GH-deficient subjects. Further controlled studies in larger numbers of GH-deficient subjects are required to determine the clinical benefits of NMR-based metabonomics in subjects receiving GH therapy. Copyright © 2012 Elsevier Ltd. All rights reserved.

29 Si NMR and SAXS investigation of the hybrid organic–inorganic glasses obtained by consolidation of the melting gels

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

Jitianu, Andrei; Cadars, Sylvian; Zhang, Fan

This study is focused on structural characterization of hybrid glasses obtained by consolidation of melting gels. The melting gels were prepared in molar ratios of methyltriethoxysilane (MTES) and dimethyldiethoxysilane (DMDES) of 75%MTES-25%DMDES and 65%MTES-35%DMDES. Following consolidation, the hybrid glasses were characterized using Raman, 29Si and 13C Nuclear Magnetic Resonance (NMR) spectroscopies, synchrotron Small Angle X-Ray Scattering (SAXS) and scanning electron microscopy (SEM). Raman spectroscopy revealed the presence of Si–C bonds in the hybrid glasses and 8-membered ring structures in the Si–O–Si network. Qualitative NMR spectroscopy identified the main molecular species, while quantitative NMR data showed that the ratio of trimersmore » (T) to dimers (D) varied between 4.6 and 3.8. Two-dimensional 29Si NMR data were used to identify two distinct types of T3 environments. SAXS data showed that the glasses are homogeneous across the nm to micrometer length scales. The scattering cross section was one thousand times lower than what is expected when phase separation occurs. The SEM images show a uniform surface without defects, in agreement with the SAXS results, which further supports that the hybrid glasses are nonporous.« less

29Si NMR and SAXS investigation of the hybrid organic-inorganic glasses obtained by consolidation of the melting gels

PubMed Central

Jitianu, Andrei; Cadars, Sylvian; Zhang, Fan; Rodriguez, Gabriela; Picard, Quentin; Aparicio, Mario; Mosa, Jadra; Klein, Lisa C.

2017-01-01

This study is focused on structural characterization of hybrid glasses obtained by consolidation of melting gels. The melting gels were prepared in molar ratios of methyltriethoxysilane (MTES) and dimethyldiethoxysilane (DMDES) of 75%MTES-25%DMDES and 65%MTES-35%DMDES. Following consolidation, the hybrid glasses were characterized using Raman, 29Si and 13C Nuclear Magnetic Resonance (NMR) spectroscopies, synchrotron Small Angle X-Ray Scattering (SAXS) and scanning electron microscopy (SEM). Raman spectroscopy revealed the presence of Si-C bonds in the hybrid glasses and 8-membered ring structures in the Si-O-Si network. Qualitative NMR spectroscopy identified the main molecular species, while quantitative NMR data showed that the ratio of trimers (T) to dimers (D) varied between 4.6 and 3.8. Two-dimensional 29Si NMR data were used to identify two distinct types of T3 environments. SAXS data showed that the glasses are homogeneous across the nm to micrometer length scales. The scattering cross section was one thousand times lower than what is expected when phase separation occurs. The SEM images show a uniform surface without defects, in agreement with the SAXS results, which further supports that the hybrid glasses are nonporous. PMID:28262904

Measurement and Quantification of Heterogeneity, Flow, and Mass Transfer in Porous Media Using NMR Low-Field Techiques

NASA Astrophysics Data System (ADS)

Paciok, E.; Olaru, A. M.; Haber, A.; van Landeghem, M.; Haber-Pohlmeier, S.; Sucre, O. E.; Perlo, J.; Casanova, F.; Blümich, B.; RWTH Aachen Mobile Low-Field NMR

2011-12-01

Nuclear magnetic resonance (NMR) is renowned for its unique potential to both reveal and correlate spectroscopic, relaxometric, spatial and dynamic properties in a large variety of organic and inorganic systems. NMR has no restrictions regarding sample opacity and is an entirely non-invasive method, which makes it the ideal tool for the investigation of porous media. However, for years NMR research of soils was limited by the use of high-field NMR devices, which necessitated elaborate NMR experiments and were not applicable to bulky samples or on-site field measurements. The evolution of low-field NMR devices during the past 20 years has brought forth portable, small-scale NMR systems with open and closed magnet arrangements specialized to specific NMR applications. In combination with recent advances in 2D-NMR Laplace methodology [1], low-field NMR has opened up the possibility to study real-life microporous systems ranging from granular media to natural soils and oil well boreholes. Thus, information becomes available, which before has not been accessible with high-field NMR. In this work, we present our recent progress in mobile low-field NMR probe design for field measurements of natural soils: a slim-line logging tool, which can be rammed into the soil of interest on-site. The performance of the device is demonstrated in measurements of moisture profiles of model soils [2] and field measurements of relaxometric properties and moisture profiles of natural soils [3]. Moreover, an improved concept of the slim-line logging tool is shown, with a higher excitation volume and a better signal-to-noise due to an improved coil design. Furthermore, we present our recent results in 2D exchange relaxometry and simulation. These include relaxation-relaxation experiments on natural soils with varying degree of moisture saturation, where we could draw a connection between the relaxometric properties of the soil to its pore size-related diffusivity and to its clay content. Also models, simulations and possibilities are discussed to derive from the so obtained information a "characteristic pore shape" that can be used to characterize and to fingerprint natural soils. [1] L. Venkataramanan et al., IEEE Trans. Signal Process. 2002, 50, 1017-26. [2] O. Sucre et al., Open Magn. Reson. J. 2010, 3, 63-68. [3] B. Blümich et al., New J. Phys. 2011, 13, 015003.

Study of the gel films of Acetobacter Xylinum cellulose and its modified samples by {sup 1}H NMR cryoporometry and small-angle X-ray scattering

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

Babushkina, T. A.; Klimova, T. P.; Shtykova, E. V.

2010-03-15

Gel films of Acetobacter Xylinum cellulose and its modified samples have been investigated by 1H nuclear magnetic resonance (NMR) cryoporometry and small-angle X-ray scattering. The joint use of these two methods made it possible to characterize the sizes of aqueous pores in gel films and estimate the sizes of structural inhomogeneities before and after the sorption of polyvinylpyrrolidone and Se{sub 0} nanoparticles (stabilized by polyvinylpyrrolidone) into the films. According to small-angle X-ray scattering data, the sizes of inhomogeneities in a gel film change only slightly upon the sorption of polyvinylpyrrolidone and nanoparticles. The impregnated material is sorbed into water-filled cavitiesmore » that are present in the gel film. {sup 1}H NMR cryoporometry allowed us to reveal the details of changes in the sizes of small aqueous pores during modifications.« less

Structural analysis and biomedical applications of dextran produced by a new isolate Pediococcus pentosaceus screened from biodiversity hot spot Assam.

PubMed

Patel, Seema; Kasoju, Naresh; Bora, Utpal; Goyal, Arun

2010-09-01

Dextran produced by a natural isolate of Pediococcus pentosaceus, screened from Assam, in the Northeastern region of India, was estimated, purified, structure characterised and functionality analysed. The dextran concentration in the cell free supernatant of the isolate P. pentosaceus was 10.2mg/ml. FT-IR analysis revealed the hydroxyl and carboxyl functional groups present in the dextran. (1)H NMR and (13)C NMR spectral data revealed that the dextran has a linear backbone of alpha-(1-->6) linked D-glucose residues. The decrease in viscosity of dextran solution with the increase in shear rate, threw light on its typical non-Newtonian pseudoplastic behaviour. The cytotoxicity tests on human cervical cancer (HeLa) cell line was studied which showed the dextran is non-toxic and biocompatible, rendering it safe for drug delivery, tissue engineering and various other biomedical applications. (c) 2010 Elsevier Ltd. All rights reserved.

Structure and Orientation of Bovine Lactoferrampin in the Mimetic Bacterial Membrane as Revealed by Solid-State NMR and Molecular Dynamics Simulation

PubMed Central

Tsutsumi, Atsushi; Javkhlantugs, Namsrai; Kira, Atsushi; Umeyama, Masako; Kawamura, Izuru; Nishimura, Katsuyuki; Ueda, Kazuyoshi; Naito, Akira

2012-01-01

Bovine lactoferrampin (LFampinB) is a newly discovered antimicrobial peptide found in the N1-domain of bovine lactoferrin (268–284), and consists of 17 amino-acid residues. It is important to determine the orientation and structure of LFampinB in bacterial membranes to reveal the antimicrobial mechanism. We therefore performed 13C and 31P NMR, 13C-31P rotational echo double resonance (REDOR), potassium ion-selective electrode, and quartz-crystal microbalance measurements for LFampinB with mimetic bacterial membrane and molecular-dynamics simulation in acidic membrane. 31P NMR results indicated that LFampinB caused a defect in mimetic bacterial membranes. Ion-selective electrode measurements showed that ion leakage occurred for the mimetic bacterial membrane containing cardiolipin. Quartz-crystal microbalance measurements revealed that LFampinB had greater affinity to acidic phospholipids than that to neutral phospholipids. 13C DD-MAS and static NMR spectra showed that LFampinB formed an α-helix in the N-terminus region and tilted 45° to the bilayer normal. REDOR dephasing patterns between carbonyl carbon nucleus in LFampinB and phosphorus nuclei in lipid phosphate groups were measured by 13C-31P REDOR and the results revealed that LFampinB is located in the interfacial region of the membrane. Molecular-dynamics simulation showed the tilt angle to be 42° and the rotation angle to be 92.5° for Leu3, which are in excellent agreement with the experimental values. PMID:23083717

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.

Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

PubMed

Sborgi, Lorenzo; Verma, Abhinav; Muñoz, Victor; de Alba, Eva

2011-01-01

GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

Compositional and surface characterization of HULIS by UV-Vis, FTIR, NMR and XPS: Wintertime study in Northern India

NASA Astrophysics Data System (ADS)

Kumar, Varun; Goel, Anubha; Rajput, Prashant

2017-09-01

This study (first attempt) characterizes HULIS (Humic Like Substances) in wintertime aerosols (n = 12 during day and nighttime each) from Indo-Gangetic Plain (IGP, at Kanpur) by using various state-of-the art techniques such as UV-VIS, FTIR, 1H NMR and XPS. Based on UV-Vis analysis the absorption coefficient at 365 nm (babs-365) of HULIS was found to average at 13.6 and 28.8 Mm-1 during day and nighttime, respectively. Relatively high babs-365 of HULIS during the nighttime is attributed to influence of fog-processing. However, the power fit of UV-Vis spectrum provided near similar AAE (absorption Angstrom exponent) value of HULIS centering at 4.9 ± 1.4 and 5.1 ± 1.3 during daytime and nighttime, respectively. FTIR spectra and its double derivative revealed the presence of various functional groups viz. alcohols, ketones aldehydes, carboxylic acids as well as unsaturated and saturated carbon bonds. 1H NMR spectroscopy was applied to quantify relative percentage of various types of hydrogen atoms contained in HULIS, whereas XPS technique provided information on surface composition and oxidation states of various elements present. A significantly high abundance of H‒C‒O group has been observed in HULIS (based on 1H NMR); 41.4± 2.7% and 30.9± 2.4% in day and nighttime, respectively. However, aromatic protons (Ar-H) were higher in nighttime samples (19.3± 1.8%) as compared to that in daytime samples (7.5 ± 1.9). XPS studies revealed presence of various species on the surface of HULIS samples. Carbon existed in 7 different chemical states while total nitrogen and sulfur exhibited 3 and 2 different oxidation states (respectively) on the surface of HULIS. This study reports structural information and absorption properties of HULIS which has implications to their role as cloud condensation nuclei and atmospheric direct radiative forcing.

High-field EPR on membrane proteins - crossing the gap to NMR.

PubMed

Möbius, Klaus; Lubitz, Wolfgang; Savitsky, Anton

2013-11-01

In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Review of NMR studies of nanoscale molecular magnets composed of geometrically frustrated antiferromagnetic triangles

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

Furukawa, Yuji

This paper presents a comprehensive review of nuclear magnetic resonance (NMR) studies performed on three nanoscale molecular magnets with different novel configurations of geometrically frustrated antiferromagnetic (AFM) triangles: (1) the isolated single AFM triangle K 6[V 15As 6O 42(H 2O)]·8H 2O (in short V15), (2) the spin ball [Mo 72Fe 30O 252(Mo 2O 7(H 2O)) 2(Mo 2O 8H 2(H 2O)) (CH 3COO) 12(H 2O) 91]·150H 2O (in short Fe30 spin ball), and (3) the twisted triangular spin tube [(CuCl 2tachH) 3Cl]Cl 2 (in short Cu3 spin tube). In V15t, from 51V NMR spectra, the local spin configurations were directly determinedmore » in both the nonfrustrated total spin S T = 3/2 state at higher magnetic fields (H ge; 2.7 T) and the two nearly degenerate S T = 1/2 ground states at lower magnetic fields (H ≤ 2.7 T). The dynamical magnetic properties of V15 were investigated by proton spin-lattice relaxation rate (1/T 1) measurements. In the S T = 3/2 state, 1/T 1 shows thermally activated behaviour as a function of temperature. On the other hand, the temperature independent behaviour of 1/T 1 at very low temperatures is observed in the frustrated S T = 1/2 ground state. Possible origins for the peculiar behaviour of 1/T 1 will be discussed in terms of magnetic fluctuations due to spin frustrations. In Fe30, static and dynamical properties of Fe 3+ (s = 5/2) have been investigated by proton NMR spectra and 1/T 1 measurements. From the temperature dependence of 1/T 1, the fluctuation frequency of the Fe 3+ spins is found to decrease with decreasing temperature, indicating spin freezing at low temperatures. The spin freezing is also evidenced by the observation of a sudden broadening of 1H NMR spectra below 0.6 K. Finally, 1H NMR data in Cu3 will be described. An observation of magnetic broadening of 1H NMR spectra at low temperatures below 1 K directly revealed a gapless ground state. The 1/T 1 measurements revealed a usual slow spin dynamics in the Cu3 spin tube.« less

Review of NMR studies of nanoscale molecular magnets composed of geometrically frustrated antiferromagnetic triangles

DOE PAGES

Furukawa, Yuji

2016-10-01

This paper presents a comprehensive review of nuclear magnetic resonance (NMR) studies performed on three nanoscale molecular magnets with different novel configurations of geometrically frustrated antiferromagnetic (AFM) triangles: (1) the isolated single AFM triangle K 6[V 15As 6O 42(H 2O)]·8H 2O (in short V15), (2) the spin ball [Mo 72Fe 30O 252(Mo 2O 7(H 2O)) 2(Mo 2O 8H 2(H 2O)) (CH 3COO) 12(H 2O) 91]·150H 2O (in short Fe30 spin ball), and (3) the twisted triangular spin tube [(CuCl 2tachH) 3Cl]Cl 2 (in short Cu3 spin tube). In V15t, from 51V NMR spectra, the local spin configurations were directly determinedmore » in both the nonfrustrated total spin S T = 3/2 state at higher magnetic fields (H ge; 2.7 T) and the two nearly degenerate S T = 1/2 ground states at lower magnetic fields (H ≤ 2.7 T). The dynamical magnetic properties of V15 were investigated by proton spin-lattice relaxation rate (1/T 1) measurements. In the S T = 3/2 state, 1/T 1 shows thermally activated behaviour as a function of temperature. On the other hand, the temperature independent behaviour of 1/T 1 at very low temperatures is observed in the frustrated S T = 1/2 ground state. Possible origins for the peculiar behaviour of 1/T 1 will be discussed in terms of magnetic fluctuations due to spin frustrations. In Fe30, static and dynamical properties of Fe 3+ (s = 5/2) have been investigated by proton NMR spectra and 1/T 1 measurements. From the temperature dependence of 1/T 1, the fluctuation frequency of the Fe 3+ spins is found to decrease with decreasing temperature, indicating spin freezing at low temperatures. The spin freezing is also evidenced by the observation of a sudden broadening of 1H NMR spectra below 0.6 K. Finally, 1H NMR data in Cu3 will be described. An observation of magnetic broadening of 1H NMR spectra at low temperatures below 1 K directly revealed a gapless ground state. The 1/T 1 measurements revealed a usual slow spin dynamics in the Cu3 spin tube.« less

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.

NMR-based diffusion pore imaging by double wave vector measurements.

PubMed

Kuder, Tristan Anselm; Laun, Frederik Bernd

2013-09-01

One main interest of nuclear magnetic resonance (NMR) diffusion experiments is the investigation of boundaries such as cell membranes hindering the diffusion process. NMR diffusion measurements allow collecting the signal from the whole sample. This mainly eliminates the problem of vanishing signal at increasing resolution. It has been a longstanding question if, in principle, the exact shape of closed pores can be determined by NMR diffusion measurements. In this work, we present a method using short diffusion gradient pulses only, which is able to reveal the shape of arbitrary closed pores without relying on a priori knowledge. In comparison to former approaches, the method has reduced demands on relaxation times due to faster convergence to the diffusion long-time limit and allows for a more flexible NMR sequence design, because, e.g., stimulated echoes can be used. Copyright © 2012 Wiley Periodicals, Inc.

Nuclear magnetic resonance spectroscopy reveals metabolic changes in living cardiomyocytes after low doses of ionizing radiation.

PubMed

Gramatyka, Michalina; Skorupa, Agnieszka; Sokół, Maria

2018-01-01

Several lines of evidence indicate that exposure of heart to ionizing radiation increases the risk of cardiotoxicity manifested by heart dysfunction and cardiovascular diseases. It was initially believed that the heart is an organ relatively resistant to radiation. Currently, however, it is suspected that even low doses of radiation (< 2 Gy) may have a negative impact on the cardiovascular system. Cardiotoxicity of ionizing radiation is associated with metabolic changes observed in cardiac cells injured by radiation. In this study, we used human cardiomyocytes as a model system, and studied their metabolic response to radiation using high-resolution magic angle spinning nuclear magnetic resonance techniques (HR-MAS NMR). Human cardiomyocytes cultured in vitro were exposed to ionizing radiation and their survival was assessed by clonogenic assay. Changes in apoptosis intensity and cell cycle distribution after the irradiation were measured as well. NMR spectra of cardiomyocytes were acquired using Bruker Avance 400 MHz spectrometer at a spinning rate of 3200 Hz. Survival of cardiomyocytes after NMR experiments was assessed by the Trypan blue exclusion assay. Exposure of cardiomyocytes to small doses of ionizing radiation had no effect on cell proliferation potential and intensity of cell death. However, analysis of metabolic profiles revealed changes in lipids, threonine, glycine, glycerophosphocholine, choline, valine, isoleucine, glutamate, reduced glutathione and taurine metabolism. The results of this study showed that ionizing radiation affects metabolic profiles of cardiomyocytes even at low doses, which potentially have no effect on cell viability.

Crossover of Microscopic Dynamics in Metallic Supercooled Liquid Observed by NMR

NASA Astrophysics Data System (ADS)

Wu, Yue; Li, Lilong

2004-03-01

Nuclear magnetic resonance (NMR) is used to characterize local atomic motions in the glassy and supercooled liquid states of the bulk metallic glass system Pd_43Ni_10Cu_27P_20. It is shown that NMR is very effective in detecting local motions such as vibrations in metallic systems. The temperature dependence of the Knight shift reveals that certain local atomic motion decreases rapidly below a crossover temperature T_c. Above Tc as well as below the glass transition temperature Tg the mean-squared amplitude of local motions is shown to depend linearly on the temperature. The observed rapid decrease below Tc cannot be explained by heterogeneity effects. It reveals that qualitative changes of microscopic properties in the supercooled liquid take place at temperatures significantly above T_g. The observed phenomenon can be explained in terms of a rapid disappearance of certain local motions below Tc as suggested by the mode-coupling theory.

Homonuclear 1H NMR and circular dichroism study of the HIV-1 Tat Eli variant

PubMed Central

Watkins, Jennifer D; Campbell, Grant R; Halimi, Hubert; Loret, Erwann P

2008-01-01

Background The HIV-1 Tat protein is a promising target to develop AIDS therapies, particularly vaccines, due to its extracellular role that protects HIV-1-infected cells from the immune system. Tat exists in two different lengths, 86 or 87 residues and 99 or 101 residues, with the long form being predominant in clinical isolates. We report here a structural study of the 99 residue Tat Eli variant using 2D liquid-state NMR, molecular modeling and circular dichroism. Results Tat Eli was obtained from solid-phase peptide synthesis and the purified protein was proven biologically active in a trans-activation assay. Circular dichroism spectra at different temperatures up to 70°C showed that Tat Eli is not a random coil at 20°C. Homonuclear 1H NMR spectra allowed us to identify 1639 NMR distance constraints out of which 264 were interresidual. Molecular modeling satisfying at least 1474 NMR constraints revealed the same folding for different model structures. The Tat Eli model has a core region composed of a part of the N-terminus including the highly conserved Trp 11. The extra residues in the Tat Eli C-terminus protrude from a groove between the basic region and the cysteine-rich region and are well exposed to the solvent. Conclusion We show that active Tat variants share a similar folding pattern whatever their size, but mutations induce local structural changes. PMID:18808674

Structural Changes in Senescing Oilseed Rape Leaves at Tissue and Subcellular Levels Monitored by Nuclear Magnetic Resonance Relaxometry through Water Status

PubMed Central

Musse, Maja; De Franceschi, Loriane; Cambert, Mireille; Sorin, Clément; Le Caherec, Françoise; Burel, Agnès; Bouchereau, Alain; Mariette, François; Leport, Laurent

2013-01-01

Nitrogen use efficiency is relatively low in oilseed rape (Brassica napus) due to weak nitrogen remobilization during leaf senescence. Monitoring the kinetics of water distribution associated with the reorganization of cell structures, therefore, would be valuable to improve the characterization of nutrient recycling in leaf tissues and the associated senescence processes. In this study, nuclear magnetic resonance (NMR) relaxometry was used to describe water distribution and status at the cellular level in different leaf ranks of well-watered plants. It was shown to be able to detect slight variations in the evolution of senescence. The NMR results were linked to physiological characterization of the leaves and to light and electron micrographs. A relationship between cell hydration and leaf senescence was revealed and associated with changes in the NMR signal. The relative intensities and the transverse relaxation times of the NMR signal components associated with vacuole water were positively correlated with senescence, describing water uptake and vacuole and cell enlargement. Moreover, the relative intensity of the NMR signal that we assigned to the chloroplast water decreased during the senescence process, in agreement with the decrease in relative chloroplast volume estimated from micrographs. The results are discussed on the basis of water flux occurring at the cellular level during senescence. One of the main applications of this study would be for plant phenotyping, especially for plants under environmental stress such as nitrogen starvation. PMID:23903438

Effect of autohydrolysis pretreatment on biomass structure and the resulting bio-oil from a pyrolysis process

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

Hao, Naijia; Bezerra, Tais Lacerda; Wu, Qiong

Pyrolysis is a promising method for converting biomass to biofuels. However, some of pyrolysis oil's physiochemical properties still limit its commercial applications. Here, the autohydrolysis pretreatment at 175 ± 3 °C for 40 min was conducted to improve the resulting pine pyrolysis oil’s properties as a fuel. During autohydrolysis, deacetylation and decomposition of hemicellulose was observed by ion-exchange chromatography and Fourier transform infrared spectroscopy (FT-IR). Additionally, the cleavage of lignin ether bonds was clearly determined by 13C cross-polarization/magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR). Phosphitylation followed by 31P NMR analysis of the heavy oils gave detailed structural information ofmore » the hydroxyl groups; the results revealed that autohydrolysis pretreatment led to a reduction of carboxyl acids in the heavy oils generated at all three pyrolysis temperatures (400, 500, and 600 °C). The 31P NMR analysis also revealed that autohydrolysis pretreatment led to a reduction of condensed phenolic hydroxyl groups in the heavy oils produced at 600 °C. 1H- 13C heteronuclear single-quantum correlation (HSQC) NMR analysis showed that at a pyrolysis temperature of 600 °C, the pretreated pine produced lower methoxy group constituents. In both 31P and HSQC NMR results indicated that autohydrolysis pretreatment increased levoglucosan yields in the bio-oils.« less

Effect of autohydrolysis pretreatment on biomass structure and the resulting bio-oil from a pyrolysis process

DOE PAGES

Hao, Naijia; Bezerra, Tais Lacerda; Wu, Qiong; ...

2017-06-29

Pyrolysis is a promising method for converting biomass to biofuels. However, some of pyrolysis oil's physiochemical properties still limit its commercial applications. Here, the autohydrolysis pretreatment at 175 ± 3 °C for 40 min was conducted to improve the resulting pine pyrolysis oil’s properties as a fuel. During autohydrolysis, deacetylation and decomposition of hemicellulose was observed by ion-exchange chromatography and Fourier transform infrared spectroscopy (FT-IR). Additionally, the cleavage of lignin ether bonds was clearly determined by 13C cross-polarization/magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR). Phosphitylation followed by 31P NMR analysis of the heavy oils gave detailed structural information ofmore » the hydroxyl groups; the results revealed that autohydrolysis pretreatment led to a reduction of carboxyl acids in the heavy oils generated at all three pyrolysis temperatures (400, 500, and 600 °C). The 31P NMR analysis also revealed that autohydrolysis pretreatment led to a reduction of condensed phenolic hydroxyl groups in the heavy oils produced at 600 °C. 1H- 13C heteronuclear single-quantum correlation (HSQC) NMR analysis showed that at a pyrolysis temperature of 600 °C, the pretreated pine produced lower methoxy group constituents. In both 31P and HSQC NMR results indicated that autohydrolysis pretreatment increased levoglucosan yields in the bio-oils.« less

[Hyperfine structure analysis in magnetic resonance spectroscopy: from astrophysical measurements towards endogenous biosensors in human tissue].

PubMed

Schröder, Leif

2007-01-01

The hyperfine interaction of two spins is a well studied effect in atomic systems. Magnetic resonance experiments demonstrate that the detectable dipole transitions are determined by the magnetic moments of the constituents and the external magnetic field. Transferring the corresponding quantum mechanics to molecular bound nuclear spins allows for precise prediction of NMR spectra obtained from metabolites in human tissue. This molecular hyperfine structure has been neglected so far in in vivo NMR spectroscopy but contains useful information, especially when studying molecular dynamics. This contribution represents a review of the concept of applying the Breit-Rabi formalism to coupled nuclear spins and discusses the immobilization of different metabolites in anisotropic tissue revealed by 1H NMR spectra of carnosine, phosphocreatine and taurine. Comparison of atomic and molecular spin systems allows for statements on the biological constraints for direct spin-spin interactions. Moreover, the relevance of hyperfine effects on the line shapes of multiplets of indirectly-coupled spin systems with more than two constituents can be predicted by analyzing quantum mechanical parameters. As an example, the superposition of eigenstates of the A MX system of adenosine 5'-triphosphate and its application for better quantification of 31P-NMR spectra will be discussed.

NMR metabolomics of esca disease-affected Vitis vinifera cv. Alvarinho leaves.

PubMed

Lima, Marta R M; Felgueiras, Mafalda L; Graça, Gonçalo; Rodrigues, João E A; Barros, António; Gil, Ana M; Dias, Alberto C P

2010-09-01

Esca is a destructive disease that affects vineyards leading to important losses in wine production. Information about the response of Vitis vinifera plants to this disease is scarce, particularly concerning changes in plant metabolism. In order to study the metabolic changes in Vitis plants affected by esca, leaves from both infected and non-affected cordons of V. vinifera cv. Alvarinho (collected in the Vinho Verde region, Portugal) were analysed. The metabolite composition of leaves from infected cordons with visible symptoms [diseased leaves (dl)] and from asymptomatic cordons [healthy leaves (hl)] was evaluated by 1D and 2D (1)H-nuclear magnetic resonance (NMR) spectroscopy. Principal component analysis (PCA) of the NMR spectra showed a clear separation between dl and hl leaves, indicating differential compound production due to the esca disease. NMR/PCA analysis allowed the identification of specific compounds characterizing each group, and the corresponding metabolic pathways are discussed. Altogether, the study revealed a significant increase of phenolic compounds in dl, compared with hl, accompanied by a decrease in carbohydrates, suggesting that dl are rerouting carbon and energy from primary to secondary metabolism. Other metabolic alterations detected comprised increased levels of methanol, alanine, and gamma-aminobutyric acid in dl, which might be the result of the activation of other defence mechanisms.

Hyperfine fields and anisotropy of the orbital moment in epitaxial Mn5Ge3 films studied by 55Mn NMR

NASA Astrophysics Data System (ADS)

Kalvig, R.; Jedryka, E.; Wojcik, M.; Allodi, G.; De Renzi, R.; Petit, M.; Michez, L.

2018-05-01

55Mn NMR was used to perform the atomic-scale study of the anisotropic properties of Mn5Ge3 /Ge(111) epitaxial films with thicknesses between 9 and 300 nm. The NMR spectra have been recorded as a function of strong external magnetic field applied in the film plane and perpendicular to it. Two 55Mn NMR resonances have been observed, corresponding to the two manganese sites 4 d and 6 g , in the hexagonal D 88 structure; in zero field their frequency is centered around 207.5 and 428 MHz, respectively. The anisotropy of 55Mn hyperfine fields between the hexagonal c direction and the c plane at both Mn sites was evidenced and attributed to the anisotropic term due to the unquenched Mn orbital momentum. The anisotropy of the orbital contribution to hyperfine fields was determined as 1.52 T in the 4 d site and up to 2.77 T in the 6 g site. The 4 d site reveals a quadrupolar interaction due to the strong electric field gradient: Vz z=5.3 ×1019V/m2 in this site, which is shown to be oriented along the hexagonal c axis.

(1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins.

PubMed

Wu, Chin H; Das, Bibhuti B; Opella, Stanley J

2010-02-01

(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples. Copyright 2009 Elsevier Inc. All rights reserved.

Simultaneous 19F-1H medium resolution NMR spectroscopy for online reaction monitoring

NASA Astrophysics Data System (ADS)

Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Kraume, Matthias; Guthausen, Gisela; Maiwald, Michael

2014-12-01

Medium resolution nuclear magnetic resonance (MR-NMR) spectroscopy is currently a fast developing field, which has an enormous potential to become an important analytical tool for reaction monitoring, in hyphenated techniques, and for systematic investigations of complex mixtures. The recent developments of innovative MR-NMR spectrometers are therefore remarkable due to their possible applications in quality control, education, and process monitoring. MR-NMR spectroscopy can beneficially be applied for fast, non-invasive, and volume integrating analyses under rough environmental conditions. Within this study, a simple 1/16″ fluorinated ethylene propylene (FEP) tube with an ID of 0.04″ (1.02 mm) was used as a flow cell in combination with a 5 mm glass Dewar tube inserted into a benchtop MR-NMR spectrometer with a 1H Larmor frequency of 43.32 MHz and 40.68 MHz for 19F. For the first time, quasi-simultaneous proton and fluorine NMR spectra were recorded with a series of alternating 19F and 1H single scan spectra along the reaction time coordinate of a homogeneously catalysed esterification model reaction containing fluorinated compounds. The results were compared to quantitative NMR spectra from a hyphenated 500 MHz online NMR instrument for validation. Automation of handling, pre-processing, and analysis of NMR data becomes increasingly important for process monitoring applications of online NMR spectroscopy and for its technical and practical acceptance. Thus, NMR spectra were automatically baseline corrected and phased using the minimum entropy method. Data analysis schemes were designed such that they are based on simple direct integration or first principle line fitting, with the aim that the analysis directly revealed molar concentrations from the spectra. Finally, the performance of 1/16″ FEP tube set-up with an ID of 1.02 mm was characterised regarding the limit of detection (LOQ (1H) = 0.335 mol L-1 and LOQ (19F) = 0.130 mol L-1 for trifluoroethanol in D2O (single scan)) and maximum quantitative flow rates up to 0.3 mL min-1. Thus, a series of single scan 19F and 1H NMR spectra acquired with this simple set-up already presents a valuable basis for quantitative reaction monitoring.

Nuclear magnetic resonance (NMR) study of the effect of cisplatin on the metabolic profile of MG-63 osteosarcoma cells.

PubMed

Duarte, Iola F; Lamego, Ines; Marques, Joana; Marques, M Paula M; Blaise, Benjamin J; Gil, Ana M

2010-11-05

In the present study, (1)H HRMAS NMR spectroscopy was used to assess the changes in the intracellular metabolic profile of MG-63 human osteosarcoma (OS) cells induced by the chemotherapy agent cisplatin (CDDP) at different times of exposure. Multivariate analysis was applied to the cells spectra, enabling consistent variation patterns to be detected and drug-specific metabolic effects to be identified. Statistical recoupling of variables (SRV) analysis and spectral integration enabled the most relevant spectral changes to be evaluated, revealing significant time-dependent alterations in lipids, choline-containing compounds, some amino acids, polyalcohols, and nitrogenated bases. The metabolic relevance of these compounds in the response of MG-63 cells to CDDP treatment is discussed.

1H NMR study of the effect of variable ligand on heme oxygenase electronic and molecular structure

PubMed Central

Ma, Li-Hua; Liu, Yangzhong; Zhang, Xuhong; Yoshida, Tadashi; La Mar, Gerd N.

2009-01-01

Heme oxygenase carries out stereospecific catabolism of protohemin to yield iron, CO and biliverdin. Instability of the physiological oxy complex has necessitated the use of model ligands, of which cyanide and azide are amenable to solution NMR characterization. Since cyanide and azide are contrasting models for bound oxygen, it is of interest to characterize differences in their molecular and/or electronic structures. We report on detailed 2D NMR comparison of the azide and cyanide substrate complexes of heme oxygenase from Neisseria meningitidis, which reveals significant and widespread differences in chemical shifts between the two complexes. To differentiate molecular from electronic structural changes between the two complexes, the anisotropy and orientation of the paramagnetic susceptibility tensor were determined for the azide complex for comparison with those for the cyanide complex. Comparison of the predicted and observed dipolar shifts reveals that shift differences are strongly dominated by differences in electronic structure and do not provide any evidence for detectable differences in molecular structure or hydrogen bonding except in the immediate vicinity of the distal ligand. The readily cleaved C-terminus interacts with the active site and saturation-transfer allows difficult heme assignments in the high-spin aquo complex. PMID:18976815

NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors

PubMed Central

Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid; Lens, Piet N. L.; Saikaly, Pascal E.

2015-01-01

Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the 1H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates. PMID:26391984

NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors.

PubMed

Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid; Lens, Piet N L; Saikaly, Pascal E

2015-09-22

Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the (1)H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates.

Separation and analysis of trace degradants in a pharmaceutical formulation using on-line capillary isotachophoresis-NMR.

PubMed

Eldridge, Stacie L; Almeida, Valentino K; Korir, Albert K; Larive, Cynthia K

2007-11-15

NMR spectroscopy is widely used in the pharmaceutical industry for the structure elucidation of pharmaceutical impurities, especially when coupled to a separation method, such as HPLC. However, NMR has relatively poor sensitivity compared with other techniques such as mass spectrometry, limiting its applicability in impurity analyses. This limitation is addressed here through the on-line coupling of microcoil NMR with capillary isotachophoresis (cITP), a separation method that can concentrate dilute components by 2-3 orders of magnitude. With this approach, 1H NMR spectra can be acquired for microgram (nanomole) quantities of trace impurities in a complex sample matrix. cITP-NMR was used in this work to isolate and detect 4-aminophenol (PAP) in an acetaminophen sample spiked at the 0.1% level, with no interference from the parent compound. Analysis of an acetaminophen thermal degradation sample revealed resonances of several degradation products in addition to PAP, confirming the effectiveness of on-line cITP-NMR for trace analyses of pharmaceutical formulations. Subsequent LC-MS/MS analysis provided complementary information for the structure elucidation of the unknown degradation products, which were dimers formed during the degradation process.

Electrochemical Study on Newly Synthesized Chlorocurcumin as an Inhibitor for Mild Steel Corrosion in Hydrochloric Acid.

PubMed

Al-Amiery, Ahmed A; Kadhum, Abdul Amir H; Mohamad, Abu Bakar; Musa, Ahmed Y; Li, Cheong Jiun

2013-11-27

A new curcumin derivative, i.e. , (1E,4Z,6E)-5-chloro-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one (chlorocurcumin), was prepared starting with the natural compound curcumin. The newly synthesized compound was characterized by elemental analysis and spectral studies (IR, ¹H-NMR and 13 C-NMR). The corrosion inhibition of mild steel in 1 M HCl by chlorocurcumin has been studied using potentiodynamic polarization (PDP) measurements and electrochemical impedance spectroscopy (EIS). The inhibition efficiency increases with the concentration of the inhibitor but decreases with increases in temperature. The potentiodynamic polarization reveals that chlorocurcumin is a mixed-type inhibitor. The kinetic parameters for mild steel corrosion were determined and discussed.

Electrochemical Study on Newly Synthesized Chlorocurcumin as an Inhibitor for Mild Steel Corrosion in Hydrochloric Acid

PubMed Central

Al-Amiery, Ahmed A.; Kadhum, Abdul Amir H.; Mohamad, Abu Bakar; Musa, Ahmed Y.; Li, Cheong Jiun

2013-01-01

A new curcumin derivative, i.e., (1E,4Z,6E)-5-chloro-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one (chlorocurcumin), was prepared starting with the natural compound curcumin. The newly synthesized compound was characterized by elemental analysis and spectral studies (IR, 1H-NMR and 13C-NMR). The corrosion inhibition of mild steel in 1 M HCl by chlorocurcumin has been studied using potentiodynamic polarization (PDP) measurements and electrochemical impedance spectroscopy (EIS). The inhibition efficiency increases with the concentration of the inhibitor but decreases with increases in temperature. The potentiodynamic polarization reveals that chlorocurcumin is a mixed-type inhibitor. The kinetic parameters for mild steel corrosion were determined and discussed. PMID:28788402

NMR studies of preimplantation embryo metabolism in human assisted reproductive techniques: a new biomarker for assessment of embryo implantation potential.

PubMed

Pudakalakatti, Shivanand M; Uppangala, Shubhashree; D'Souza, Fiona; Kalthur, Guruprasad; Kumar, Pratap; Adiga, Satish Kumar; Atreya, Hanudatta S

2013-01-01

There has been growing interest in understanding energy metabolism in human embryos generated using assisted reproductive techniques (ART) for improving the overall success rate of the method. Using NMR spectroscopy as a noninvasive tool, we studied human embryo metabolism to identify specific biomarkers to assess the quality of embryos for their implantation potential. The study was based on estimation of pyruvate, lactate and alanine levels in the growth medium, ISM1, used in the culture of embryos. An NMR study involving 127 embryos from 48 couples revealed that embryos transferred on Day 3 (after 72 h in vitro culture) with successful implantation (pregnancy) exhibited significantly (p < 10(-5) ) lower pyruvate/alanine ratios compared to those that failed to implant. Lactate levels in media were similar for all embryos. This implies that in addition to lactate production, successfully implanted embryos use pyruvate to produce alanine and other cellular functions. While pyruvate and alanine individually have been used as biomarkers, the present study highlights the potential of combining them to provide a single parameter that correlates strongly with implantation potential. Copyright © 2012 John Wiley & Sons, Ltd.

Interaction of the replication terminator protein of Bacillus subtilis with DNA probed by NMR spectroscopy

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

Hastings, Adam F.; Otting, Gottfried; Folmer, Rutger H.A.

2005-09-23

Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the dimeric 29 kDa replication terminator protein (RTP) and DNA terminator sites. We have used NMR spectroscopy to probe the changes in {sup 1}H-{sup 15}N correlation spectra of a {sup 15}N-labelled RTP.C110S mutant upon the addition of a 21 base pair symmetrical DNA binding site. Assignment of the {sup 1}H-{sup 15}N correlations was achieved using a suite of triple resonance NMR experiments with {sup 15}N,{sup 13}C,70% {sup 2}H enriched protein recorded at 800 MHz and using TROSY pulse sequences. Perturbationsmore » to {sup 1}H-{sup 15}N spectra revealed that the N-termini, {alpha}3-helices and several loops are affected by the binding interaction. An analysis of this data in light of the crystallographically determined apo- and DNA-bound forms of RTP.C110S revealed that the NMR spectral perturbations correlate more closely to protein structural changes upon complex formation rather than to interactions at the protein-DNA interface.« less

Structural Masquerade of Plesiomonas shigelloides Strain CNCTC 78/89 O-Antigen-High-Resolution Magic Angle Spinning NMR Reveals the Modified d-galactan I of Klebsiella pneumoniae.

PubMed

Ucieklak, Karolina; Koj, Sabina; Pawelczyk, Damian; Niedziela, Tomasz

2017-11-29

The high-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HR-MAS NMR) analysis of Plesiomonas shigelloides 78/89 lipopolysaccharide directly on bacteria revealed the characteristic structural features of the O -acetylated polysaccharide in the NMR spectra. The O -antigen profiles were unique, yet the pattern of signals in the, spectra along with their ¹H, 13 C chemical shift values, resembled these of d-galactan I of Klebsiella pneumoniae . The isolated O- specific polysaccharide (O-PS) of P. shigelloides strain CNCTC 78/89 was investigated by ¹H and 13 C NMR spectroscopy, mass spectrometry and chemical methods. The analyses demonstrated that the P. shigelloides 78/89 O- PS is composed of →3)-α-d-Gal p -(1→3)-β-d-Gal f 2OAc-(1→ disaccharide repeating units. The O- acetylation was incomplete and resulted in a microheterogeneity of the O- antigen. This O- acetylation generates additional antigenic determinants within the O- antigen, forms a new chemotype, and contributes to the epitopes recognized by the O- serotype specific antibodies. The serological cross-reactivities further confirmed the inter-specific structural similarity of these O- antigens.

Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases.

PubMed

Grimm, Lena Lisbeth; Weissbach, Sophie; Flügge, Friedemann; Begemann, Nora; Palcic, Monica M; Peters, Thomas

2017-07-04

Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H, 15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H, 15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[ 13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

NMR spectroscopy of filtered serum of prostate cancer: A new frontier in metabolomics.

PubMed

Kumar, Deepak; Gupta, Ashish; Mandhani, Anil; Sankhwar, Satya Narain

2016-09-01

To address the shortcomings of digital rectal examinations (DRE), serum prostate-specific antigen (PSA), and trans-rectal ultrasound (TRUS) for precise determination of prostate cancer (PC) and differentiation from benign prostatic hyperplasia (BPH), we applied (1) H-nuclear magnetic resonance (NMR) spectroscopy as a surrogate tactic for probing and prediction of PC and BPH. The study comprises 210 filtered sera from suspected PC, BPH, and a healthy subjects' cohort (HC). The filtered serum approach delineates to identify and quantify 52 metabolites using (1) H NMR spectroscopy. All subjects had undergone clinical evaluations (DRE, PSA, and TRUS) followed by biopsy for Gleason score, if needed. NMR-measured metabolites and clinical evaluation data were examined separately using linear multivariate discriminant function analysis (DFA) to probe the signature descriptors for each cohort. DFA indicated that glycine, sarcosine, alanine, creatine, xanthine, and hypoxanthine were able to determine abnormal prostate (BPH + PC). DFA-based classification presented high precision (86.2% by NMR and 68.1% by clinical laboratory method) in discriminating HC from BPH + PC. DFA reveals that alanine, sarcosine, creatinine, glycine, and citrate were able to discriminate PC from BPH. DFA-based categorization exhibited high accuracy (88.3% by NMR and 75.2% by clinical laboratory method) to differentiate PC from BPH. (1) H NMR-based metabolic profiling of filtered-serum sample appears to be assuring, swift, and least-invasive for probing and prediction of PC and BPH with its signature metabolic profile. This novel technique is not only on a par with histopathological evaluation of PC determination but is also comparable to liquid chromatography-based mass spectrometry to identify the metabolites. Prostate 76:1106-1119, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

PubMed

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

2007-12-26

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

Observations using Phosphorus-31 nuclear magnetic resonance (31P-NMR) of structural changes in freeze-thawed hen egg yolk.

PubMed

Wakamatsu, Hiroki; Handa, Akihiro; Chiba, Kazuhiro

2018-04-01

Hen egg yolk (EY) has a complicated structure consisting of lipids and proteins, and its structure is deeply related with its functional properties. 31 P-NMR is an efficient technique to non-destructively detect the dynamic behaviour of phospholipids, the main component of bio-membranes. We determined conditions for measuring the 31 P NMR spectra of EY and identified the components. 31 P-NMR was used to detect phosvitin, inorganic phosphate, and lipoprotein as well as structural changes such as granule collapse and freeze-thaw denaturation as signal changes. Freeze-thaw denaturation generated a new denaturation peak. We separated aggregates of LDL from freeze-thawed plasma using centrifugation. TEM and 31 P-NMR observations revealed that the denaturation peak corresponded to LDL aggregates. The 31 P-NMR spectra suggested the formation of multiple forms of LDL aggregates in which the head groups of phospholipid molecules adopt a face-to-face orientation, similar to that observed following the flocculation of lipoproteins or in the lamellar-like structures of phospholipids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid Identification of Candida Species by Using Nuclear Magnetic Resonance Spectroscopy and a Statistical Classification Strategy

PubMed Central

Himmelreich, Uwe; Somorjai, Ray L.; Dolenko, Brion; Lee, Ok Cha; Daniel, Heide-Marie; Murray, Ronan; Mountford, Carolyn E.; Sorrell, Tania C.

2003-01-01

Nuclear magnetic resonance (NMR) spectra were acquired from suspensions of clinically important yeast species of the genus Candida to characterize the relationship between metabolite profiles and species identification. Major metabolites were identified by using two-dimensional correlation NMR spectroscopy. One-dimensional proton NMR spectra were analyzed by using a staged statistical classification strategy. Analysis of NMR spectra from 442 isolates of Candida albicans, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis resulted in rapid, accurate identification when compared with conventional and DNA-based identification. Spectral regions used for the classification of the five yeast species revealed species-specific differences in relative amounts of lipids, trehalose, polyols, and other metabolites. Isolates of C. parapsilosis and C. glabrata with unusual PCR fingerprinting patterns also generated atypical NMR spectra, suggesting the possibility of intraspecies discontinuity. We conclude that NMR spectroscopy combined with a statistical classification strategy is a rapid, nondestructive, and potentially valuable method for identification and chemotaxonomic characterization that may be broadly applicable to fungi and other microorganisms. PMID:12902244

Insights into reaction mechanisms in heterogeneous catalysis revealed by in situ NMR spectroscopy.

PubMed

Blasco, Teresa

2010-12-01

This tutorial review intends to show the possibilities of in situ solid state NMR spectroscopy in the elucidation of reaction mechanisms and the nature of the active sites in heterogeneous catalysis. After a brief overview of the more usual experimental devices used for in situ solid state NMR spectroscopy measurements, some examples of applications taken from the recent literature will be presented. It will be shown that in situ NMR spectroscopy allows: (i) the identification of stable intermediates and transient species using indirect methods, (ii) to prove shape selectivity in zeolites, (iii) the study of reaction kinetics, and (iv) the determination of the nature and the role played by the active sites in a catalytic reaction. The approaches and methodology used to get this information will be illustrated here summarizing the most relevant contributions on the investigation of the mechanisms of a series of reactions of industrial interest: aromatization of alkanes on bifunctional catalysts, carbonylation reaction of methanol with carbon monoxide, ethylbenzene disproportionation, and the Beckmann rearrangement reaction. Special attention is paid to the research carried out on the role played by carbenium ions and alkoxy as intermediate species in the transformation of hydrocarbon molecules on solid acid catalysts.

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.

NMR insight into myosin-binding subunit coiled-coil structure reveals binding interface with protein kinase G-Iα leucine zipper in vascular function.

PubMed

Sharma, Alok K; Birrane, Gabriel; Anklin, Clemens; Rigby, Alan C; Alper, Seth L

2017-04-28

Nitrovasodilators relax vascular smooth-muscle cells in part by modulating the interaction of the C-terminal coiled-coil domain (CC) and/or the leucine zipper (LZ) domain of the myosin light-chain phosphatase component, myosin-binding subunit (MBS), with the N-terminal LZ domain of protein kinase G (PKG)-Iα. Despite the importance of vasodilation in cardiovascular homeostasis and therapy, our structural understanding of the MBS CC interaction with LZ PKG-1α has remained limited. Here, we report the 3D NMR solution structure of homodimeric CC MBS in which amino acids 932-967 form a coiled-coil of two monomeric α-helices in parallel orientation. We found that the structure is stabilized by non-covalent interactions, with dominant contributions from hydrophobic residues at a and d heptad positions. Using NMR chemical-shift perturbation (CSP) analysis, we identified a subset of hydrophobic and charged residues of CC MBS (localized within and adjacent to the C-terminal region) contributing to the dimer-dimer interaction interface between homodimeric CC MBS and homodimeric LZ PKG-Iα. 15 N backbone relaxation NMR revealed the dynamic features of the CC MBS interface residues identified by NMR CSP. Paramagnetic relaxation enhancement- and CSP-NMR-guided HADDOCK modeling of the dimer-dimer interface of the heterotetrameric complex exhibits the involvement of non-covalent intermolecular interactions that are localized within and adjacent to the C-terminal regions of each homodimer. These results deepen our understanding of the binding restraints of this CC MBS·LZ PKG-Iα low-affinity heterotetrameric complex and allow reevaluation of the role(s) of myosin light-chain phosphatase partner polypeptides in regulation of vascular smooth-muscle cell contractility. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Polymer dynamics under nanoscopic constraints: the "corset effect" as revealed by NMR relaxometry and diffusometry.

PubMed

Fatkullin, Nail; Fischer, Elmar; Mattea, Carlos; Beginn, Uwe; Kimmich, Rainer

2004-06-21

A spinodal demixing technique was employed for the preparation of linear poly(ethylene oxide) (PEO) confined in nanoscopic strands, which in turn are embedded in a quasi-solid methacrylate matrix impenetrable to PEO. Both the molecular weight of the PEO and the mean diameter of the strands are variable to a certain degree. Chain dynamics of the PEO in the molten state were examined with the aid of field-gradient NMR diffusometry and field-cycling NMR relaxometry. The dominating mechanism for translational displacements in the nanoscopic strands is shown to be reptation. A formalism for the evaluation of NMR diffusometry is presented, which permits the estimation of the mean PEO strand diameter. Samples of different composition revealed diameters in the range 9-58 nm, in reasonable agreement with electron micrographs. The time scale of the diffusion measurements was 10-300 ms. On the much shorter time scale of field-cycling NMR relaxometry, 10(-9)-10(-4)s, a frequency dispersion of the spin-lattice relaxation time characteristic for reptation clearly showed up in all samples. An effective tube diameter of only 0.6 nm was found even when the strand diameter was larger than the radius of gyration of the PEO chain random coils. The finding that the tube diameter effective on the short time scale of field-cycling NMR relaxometry is much smaller than the diameter of the confining structure is termed the "corset effect", and is traced back to the lack of local free-volume fluctuation capacity under nanoscale confinements. The order of magnitude of the 'pore' diameter, at which the cross-over from confined to bulk chain dynamics is expected, is estimated.

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.

Isoprene derivatives from the leaves and callus cultures of Vaccinium corymbosum var. bluecrop.

PubMed

Migas, Piotr; Cisowski, Wojciech; Dembińska-Migas, Wanda

2005-01-01

The phytochemical analysis of Vaccinium corymbosum var bluecrop leaves and callus biomass revealed ursolic acid, oleanolic acid, alpha-amyrin and beta-amyrin in both plant materials. Beta-sitosterol was determined only in callus biomass. The structure of isolated compounds was elucidated by TLC co-chromatography with standards and with spectroscopic methods (1H NMR, 13C NMR, EI-MS).

Prediction of carbonate rock type from NMR responses using data mining techniques

NASA Astrophysics Data System (ADS)

Gonçalves, Eduardo Corrêa; da Silva, Pablo Nascimento; Silveira, Carla Semiramis; Carneiro, Giovanna; Domingues, Ana Beatriz; Moss, Adam; Pritchard, Tim; Plastino, Alexandre; Azeredo, Rodrigo Bagueira de Vasconcellos

2017-05-01

Recent studies have indicated that the accurate identification of carbonate rock types in a reservoir can be employed as a preliminary step to enhance the effectiveness of petrophysical property modeling. Furthermore, rock typing activity has been shown to be of key importance in several steps of formation evaluation, such as the study of sedimentary series, reservoir zonation and well-to-well correlation. In this paper, a methodology based exclusively on the analysis of 1H-NMR (Nuclear Magnetic Resonance) relaxation responses - using data mining algorithms - is evaluated to perform the automatic classification of carbonate samples according to their rock type. We analyze the effectiveness of six different classification algorithms (k-NN, Naïve Bayes, C4.5, Random Forest, SMO and Multilayer Perceptron) and two data preprocessing strategies (discretization and feature selection). The dataset used in this evaluation is formed by 78 1H-NMR T2 distributions of fully brine-saturated rock samples from six different rock type classes. The experiments reveal that the combination of preprocessing strategies with classification algorithms is able to achieve a prediction accuracy of 97.4%.

Moisture-Absorption and Water Dynamics in the Powder of Egg Albumen Peptide, Met-Pro-Asp-Ala-His-Leu.

PubMed

Yang, Shuailing; Liu, Xuye; Zhang, Mingdi; Lin, Songyi; Chen, Feng

2017-01-01

Moisture absorbed into the powder of Met-Pro-Asp-Ala-His-Leu (MPDAHL)-a novel egg albumen antioxidant peptide-profoundly affects its properties. In this study, we elucidated water dynamics in MPDAHL using DVS, DSC, and low-field 1 H NMR. Based on the DVS data, we found that MPDAHL sorption kinetics obey a parallel exponential model. DSC results indicated that both water and heating could change the microstructure of MPDAHL. The T 2 parameters of NMR reflected the different phases of moisture absorption revealed that there were 4 categories of water with different states or mobility in the MPDAHL during the moisture absorption process. The fastest fraction T 2b mainly dominated the hygroscopicity of MPDAHL and the absorbed water significantly changed the proton distribution and structure of MPDAHL. Thus, this study shows that DVS, DSC, and low-field 1 H NMR are effective methods for monitoring water mobility and distribution in synthetic peptides. It can be used to improve the quality assurance of functional peptides. © 2016 Institute of Food Technologists®.

High field 27Al MAS NMR and TPD studies of active sites in ethanol dehydration using thermally treated transitional aluminas as catalysts

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

Hu, Jian Zhi; Xu, Suochang; Kwak, Ja Hun

High field quantitative 27Al MAS NMR and temperature programmed desorption (TPD) of ethanol are used to study the surface and phase transformation of gamma-Al2O3 during calcination in the temperature range of 500 to 1300 degrees C. Following ethanol adsorption, ethylene is generated during TPD with a desorption temperature > 200 degrees C. With increasing calcination temperature prior to TPD, the amount of ethylene produced decreases monotonically. Significantly, 27Al MAS NMR reveals that the amount of penta-coordinate Al3+ ions (Lewis acid sites) also decreases with increasing calcination temperature. In fact, a strong correlation between the amount of penta-coordinate Al3+ ions andmore » the amount of strongly adsorbed ethanol molecules (i.e., the ones that convert to ethylene during TPD) is obtained. This result indicates that the penta-coordinate aluminum sites are the catalytic active sites on alumina surfaces during ethanol dehydration reaction across the entire course of gamma- to alpha-Al2O3 phase transformations.« less

Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study

PubMed Central

Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

2016-01-01

Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of 1H-13C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae. PMID:27598144

Screening protein – Single stranded RNA complexes by NMR spectroscopy for structure determination☆

PubMed Central

Foot, Jaelle N.; Feracci, Mikael; Dominguez, Cyril

2014-01-01

In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory roles. Associated with that, the number of identified RNA binding proteins (RBPs) has increased considerably and mutations in RNA molecules or RBP have been shown to cause various diseases, such as cancers. It is therefore crucial to understand at the molecular level how these proteins specifically recognise their RNA targets in order to design new generation drug therapies targeting protein–RNA complexes. Nuclear magnetic resonance (NMR) is a particularly well-suited technique to study such protein–RNA complexes at the atomic level and can provide valuable information for new drug discovery programs. In this article, we describe the NMR strategy that we and other laboratories use for screening optimal conditions necessary for structural studies of protein-single stranded RNA complexes, using two proteins, Sam68 and T-STAR, as examples. PMID:24096002

Probing Metal Carbonation Reactions of CO2 in a Model System Containing Forsterite and H2O Using Si-29, C-13 Magic Angle Sample Spinning NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Hu, J.; Kwak, J.; Hoyt, D. W.; Sears, J. A.; Rosso, K. M.; Felmy, A. R.

2009-12-01

Ex situ solid state NMR have been used for the first time to study fundamental mineral carbonation processes and reaction extent relevant to geologic carbon sequestration using a model silicate mineral forsterite (Mg2SiO4)+scCO2 with and without H2O. Run conditions were 80C and 96 bar. Si-29 NMR clearly shows that in the absence of CO2, the role of H2O is to hydrolyze surface Mg-O-Si bonds to produce Mg2+, and mono- and oligomeric hydroxylated silica species. The surface hydrolysis products contain only Q0 (Si(OH)4) and Q1 (Si(OH)3OSi) species. An equilibrium between Q0, Q1 and Mg2+ with a saturated concentration equivalent to less than 3.2% of the Mg2SiO4 conversion is obtained at a reaction time of up to 7 days. Using scCO2 without H2O, no reaction is observed within 7 days. Using both scCO2 and H2O, the surface reaction products for silica are mainly Q3 (SiOH(OSi)3) species accompanied by a lesser amount of Q2 (Si(OH)2(OSi)2) and Q4 (Si(OSi)4). However, no Q0 and Q1 were detected, indicating the carbonic acid formation/deprotonation and magnesite (MgCO3) precipitation reactions are faster than the forsterite hydrolysis process. Thus it can be concluded that the Mg2SiO4 hydrolysis process is the rate limiting step of the overall mineral carbonation process. Si-29 NMR combined with XRD, TEM, SAED and EDX further reveal that the reaction is a surface reaction with the Mg2SiO4 crystallite in the core and with condensed Q2-Q4 species forming amorphous surface layers. C-13 MAS NMR identified a possible reaction intermediates as (MgCO3)4*Mg(OH)2*5H2O. However, at long reaction times only crystallite magnesite MgCO3 products are observed. This research is part of a broader effort at PNNL to develop experimental tools and fundamental insights into chemical transformations affecting subsurface CO2 reactive transport. Si-29 (left) and C-13 (right) MAS NMR spectra of Mg2SiO4 under various reaction conditions. Si-29 NMR reveals that in scCO2 without H2O, no reaction is observed (b). In H2O without scCO2, only surface hydrolysis products Q0 and Q1 are present (c). In a mixture of both H2O and scCO2, the products are Q2, Q3 and Q4 (d). C-13 NMR (e-f) reveals the formation of MgCO3 at long reaction times with (MgCO3)4*Mg(OH)2*5H2O as a possible reaction intermediate.

NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds

PubMed Central

Yu, Jun-lan; Chen, Tian-tian; Zhou, Chen; Lian, Fu-lin; Tang, Xu-long; Wen, Yi; Shen, Jing-kang; Xu, Ye-chun; Xiong, Bing; Zhang, Nai-xia

2016-01-01

Aim: Fragment-based lead discovery (FBLD) is a complementary approach in drug research and development. In this study, we established an NMR-based FBLD platform that was used to screen novel scaffolds targeting human bromodomain of BRD4, and investigated the binding interactions between hit compounds and the target protein. Methods: 1D NMR techniques were primarily used to generate the fragment library and to screen compounds. The inhibitory activity of hits on the first bromodomain of BRD4 [BRD4(I)] was examined using fluorescence anisotropy binding assay. 2D NMR and X-ray crystallography were applied to characterize the binding interactions between hit compounds and the target protein. Results: An NMR-based fragment library containing 539 compounds was established, which were clustered into 56 groups (8–10 compounds in each group). Eight hits with new scaffolds were found to inhibit BRD4(I). Four out of the 8 hits (compounds 1, 2, 8 and 9) had IC50 values of 100–260 μmol/L, demonstrating their potential for further BRD4-targeted hit-to-lead optimization. Analysis of the binding interactions revealed that compounds 1 and 2 shared a common quinazolin core structure and bound to BRD4(I) in a non-acetylated lysine mimetic mode. Conclusion: An NMR-based platform for FBLD was established and used in discovery of BRD4-targeted compounds. Four potential hit-to-lead optimization candidates have been found, two of them bound to BRD4(I) in a non-acetylated lysine mimetic mode, being selective BRD4(I) inhibitors. PMID:27238211

Magnetic fluctuations and superconducting properties of CaKFe 4 As 4 studied by As 75 NMR

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

Cui, J.; Ding, Q. -P.; Meier, W. R.

In this paper, we report 75As nuclear magnetic resonance (NMR) studies on a new iron-based superconductor, CaKFe 4As 4, with T c = 35 K. 75As NMR spectra show two distinct lines corresponding to the As(1) and As(2) sites close to the K and Ca layers, respectively, revealing that K and Ca layers are well ordered without site inversions. We found that nuclear quadrupole frequencies ν Q of the As(1) and As(2) sites show an opposite temperature T dependence. Nearly T independent behavior of the Knight shifts K is observed in the normal state, and a sudden decrease in Kmore » in the superconducting (SC) state suggests spin-singlet Cooper pairs. 75As spin-lattice relaxation rates 1/T 1 show a power-law T dependence with different exponents for the two As sites. The isotropic antiferromagnetic spin fluctuations characterized by the wave vector q = (π, 0) or (0, π) in the single-iron Brillouin zone notation are revealed by 1/T 1T and K measurements. Such magnetic fluctuations are necessary to explain the observed temperature dependence of the 75As quadrupole frequencies, as evidenced by our first-principles calculations. Finally, in the SC state, 1/T 1 shows a rapid decrease below T c without a Hebel-Slichter peak and decreases exponentially at low T, consistent with an s ± nodeless two-gap superconductor.« less

Magnetic fluctuations and superconducting properties of CaKFe 4 As 4 studied by As 75 NMR

DOE PAGES

Cui, J.; Ding, Q. -P.; Meier, W. R.; ...

2017-09-25

In this paper, we report 75As nuclear magnetic resonance (NMR) studies on a new iron-based superconductor, CaKFe 4As 4, with T c = 35 K. 75As NMR spectra show two distinct lines corresponding to the As(1) and As(2) sites close to the K and Ca layers, respectively, revealing that K and Ca layers are well ordered without site inversions. We found that nuclear quadrupole frequencies ν Q of the As(1) and As(2) sites show an opposite temperature T dependence. Nearly T independent behavior of the Knight shifts K is observed in the normal state, and a sudden decrease in Kmore » in the superconducting (SC) state suggests spin-singlet Cooper pairs. 75As spin-lattice relaxation rates 1/T 1 show a power-law T dependence with different exponents for the two As sites. The isotropic antiferromagnetic spin fluctuations characterized by the wave vector q = (π, 0) or (0, π) in the single-iron Brillouin zone notation are revealed by 1/T 1T and K measurements. Such magnetic fluctuations are necessary to explain the observed temperature dependence of the 75As quadrupole frequencies, as evidenced by our first-principles calculations. Finally, in the SC state, 1/T 1 shows a rapid decrease below T c without a Hebel-Slichter peak and decreases exponentially at low T, consistent with an s ± nodeless two-gap superconductor.« less

Functional Characteristics of the Naked Mole Rat μ-Opioid Receptor

PubMed Central

Roth, Clarisse A.

2013-01-01

While humans and most animals respond to µ-opioid receptor (MOR) agonists with analgesia and decreased aggression, in the naked mole rat (NMR) opioids induce hyperalgesia and severe aggression. Single nucleotide polymorphisms in the human mu-opioid receptor gene (OPRM1) can underlie altered behavioral responses to opioids. Therefore, we hypothesized that the primary structure of the NMR MOR may differ from other species. Sequencing of the NMR oprm1 revealed strong homology to other mammals, but exposed three unique amino acids that might affect receptor-ligand interactions. The NMR and rat oprm1 sequences were cloned into mammalian expression vectors and transfected into HEK293 cells. Radioligand binding and 3'-5'-cyclic adenosine monophosphate (cAMP) enzyme immunoassays were used to compare opioid binding and opioid-mediated cAMP inhibition. At normalized opioid receptor protein levels we detected significantly lower [3H]DAMGO binding to NMR compared to rat MOR, but no significant difference in DAMGO-induced cAMP inhibition. Strong DAMGO-induced MOR internalization was detectable using radioligand binding and confocal imaging in HEK293 cells expressing rat or NMR receptor, while morphine showed weak or no effects. In summary, we found minor functional differences between rat and NMR MOR suggesting that other differences e.g. in anatomical distribution of MOR underlie the NMR's extreme reaction to opioids. PMID:24312175

NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

PubMed Central

Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

2011-01-01

The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

Homeostatic signature of anabolic steroids in cattle using 1H-13C HMBC NMR metabonomics.

PubMed

Dumas, Marc-Emmanuel; Canlet, Cécile; Vercauteren, Joseph; André, François; Paris, Alain

2005-01-01

We used metabonomics to discriminate the urinary signature of different anabolic steroid treatments in cattle having different physiological backgrounds (age, sex, and race). (1)H-(13)C heteronuclear multiple bonding connectivity NMR spectroscopy and multivariate statistical methods reveal that metabolites such as trimethylamine-N-oxide, dimethylamine, hippurate, creatine, creatinine, and citrate characterize the biological fingerprint of anabolic treatment. These urinary biomarkers suggest an overall homeostatic adaptation in nitrogen and energy metabolism. From results obtained in this study, it is now possible to consider metabonomics as a complementary method usable to improve doping control strategies to detect fraudulent anabolic treatment in cattle since the oriented global metabolic response provides helpful discrimination.

N-15 NMR study of the immobilization of 2,4- and 2,6-dinitrotoluene in aerobic compost

USGS Publications Warehouse

Thorn, K.A.; Pennington, J.C.; Kennedy, K.R.; Cox, L.G.; Hayes, C.A.; Porter, B.E.

2008-01-01

Large-scale aerobic windrow composting has been used to bioremediate washout lagoon soils contaminated with the explosives TNT (2,4,6- trinitrotoluene) and RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) at several sites within the United States. We previously used 15N NMR to investigate the reduction and binding of T15NT in aerobic bench -scale reactors simulating the conditions of windrow composting. These studies have been extended to 2,4-dinitrotoluene (2,4DNT) and 2,6-dinitrotoluene (2,6DNT), which, as impurities in TNT, are usually present wherever soils have been contaminated with TNT. Liquid-state 15N NMR analyses of laboratory reactions between 4-methyl-3-nitroaniline-15N, the major monoamine reduction product of 2,4DNT, and the Elliot soil humic acid, both in the presence and absence of horseradish peroxidase, indicated that the amine underwent covalent binding with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and non-heterocyclic condensation products. Liquid-state 15N NMR analyses of the methanol extracts of 20 day aerobic bench-scale composts of 2,4-di-15N-nitrotoluene and 2,6-di-15N-nitrotoluene revealed the presence of nitrite and monoamine, but not diamine, reduction products, indicating the occurrence of both dioxygenase enzyme and reductive degradation pathways. Solid-state CP/MAS 15N NMR analyses of the whole composts, however, suggested that reduction to monoamines followed by covalent binding of the amines to organic matter was the predominant pathway. ?? 2008 American Chemical Society.

Probing the Carbonyl Functionality of a Petroleum Resin and Asphaltene through Oximation and Schiff Base Formation in Conjunction with N-15 NMR

PubMed Central

Thorn, Kevin A.; Cox, Larry G.

2015-01-01

Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected. PMID:26556054

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.

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

PubMed Central

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

2013-01-01

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

Dynamic and organizational studies by SH NMR of polyisoprenols (PIs) in model membranes

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

Troy, F.A.; Knudsen, M.J.

1987-05-01

The objective of the authors studies seeks to understand the molecular details of how undecaprenol (C55) and dolichol (C95) function as chemical carriers of glycosyl residues in the membrane-directed synthesis of glycoconjugates. SH NMR studies provide information on the organization and dynamics of PIs in model membranes. Incorporation of polar or omega-terminus SH-labeled PIs into multilamellar membranes of phosphatidylcholine (PC) give rise to SH-NMR spectra interpretable in terms of quadrupole splittings ( vq), a measure of the degree of orderness of the SH-labeled site, and spin lattice relaxation times (T1's), revealing rates of motion. The authors results show: 1) vqmore » of the PIs increased with increase concentration of label and with lowering of temperature; 2) little difference in T1 or vq values between tail-group or headgroup SH-labeled geraniol (C10), farnesol (C15) or solanesol (C45) was observed; and 3) T1 measurements revealed correlation times close to the fatty acyl CH3 termini in PC. These data indicate that both ends of the esterified PI molecules see similar environments in the bilayer (BL) interior, and suggest that the esterified PIs studied here do not adopt a conventional head-group-at-interface orientation of lipids within the BL. These data support the authors earlier conclusions based on spin label EPR studies. Headgroup labeled dolichol (C95-CD2-OH) and dolichol phosphate (C94-CD2-O-PO3H2) have been synthesized. Surprisingly, no anisotropic quadrupole splitting in PC vesicles were observed. This may indicate an unusual conformation of the long poly-cis prenyl chains.« less

NMR analysis reveals a wealth of metabolites in root-knot nematode resistant roots of Citrullus amarus watermelon plants

USDA-ARS?s Scientific Manuscript database

Citrullus amarus (CA) (previously known as Citrullus lanatus var. citroides) accessions collected in southern Africa are known to have resistance to root-knot nematodes (RKN) and are suitable rootstocks for grafted watermelon. A comparative metabolomics study was performed to identify unique metabol...

Unequivocal glycyrrhizin isomer determination and comparative in vitro bioactivities of root extracts in four Glycyrrhiza species

PubMed Central

Farag, Mohamed A.; Porzel, Andrea; Wessjohann, Ludger A.

2014-01-01

Glycyrrhiza glabra, commonly known as licorice, is a popular herbal supplement used for the treatment of chronic inflammatory conditions and as sweetener in the food industry. This species contains a myriad of phytochemicals including the major saponin glycoside glycyrrhizin (G) of Glycyrrhetinic acid (GA) aglycone. In this study, 2D-ROESY NMR technique was successfully applied for distinguishing 18α and 18β glycyrrhetinic acid (GA). ROESY spectra acquired from G. glabra, Glycyrrhiza uralensis and Glycyrrhiza inflata crude extracts revealed the presence of G in its β-form. Anti-inflammatory activity of four Glycyrrhiza species, G, glabra, G. uralensis, G. inflata, and G. echinata roots was assessed against COX-1 inhibition revealing that phenolics rather than glycyrrhizin are biologically active in this assay. G. inflata exhibits a strong cytotoxic effect against PC3 and HT29 cells lines, whereas other species are inactive. This study presents an effective NMR method for G isomer assignment in licorice extracts that does not require any preliminary chromatography or any other purification step. PMID:25685548

Pharmacological and Toxicological Screening of Novel Benzimidazole-Morpholine Derivatives as Dual-Acting Inhibitors.

PubMed

Can, Nafiz Öncü; Çevik, Ulviye Acar; Sağlık, Begüm Nurpelin; Özkay, Yusuf; Atlı, Özlem; Baysal, Merve; Özkay, Ümide Demir; Can, Özgür Devrim

2017-08-19

The aim of this study was to investigate acetylcholinesterase (AChE), monoamine oxidase A (MAO-A), monoamine oxidase B (MAO-B), cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) enzyme inhibitory, and antimicrobial activities of a new series of 2-(4-substituted phenyl)-1-[2-(morpholin-4-yl)ethyl]-1 H -benzimidazole derivatives, for their possible use as multi-action therapeutic agents. Target compounds ( n = 15) were synthesized under microwave irradiation conditions in two steps, and their structures were elucidated by FT-IR, ¹H-NMR, 13 C-NMR and high resolution mass spectroscopic analyses. Pharmacological screening studies revealed that two of the compounds ( 2b and 2j ) have inhibitory potential on both COX-1 and COX-2 enzymes. In addition, cytotoxic and genotoxic properties of the compounds 2b , 2j and 2m were investigated via the well-known MTT and Ames tests, which revealed that the mentioned compounds are non-cytotoxic and non-genotoxic. As a concise conclusion, two novel compounds were characterized as potential candidates for treatment of frequently encountered inflammatory diseases.

Polarity dependent photoisomerization of ether substituted azodyes: Synthesis and photoswitching behavior.

PubMed

Gan, Siew Mei; Pearl, Zynia Fernandes; Yuvaraj, A R; Lutfor, M R; Gurumurthy, Hegde

2015-10-05

Two new ether substituted azodyes were synthesized and characterized by different spectral analysis such as (1)H NMR, (13)C NMR, FTIR and UV/Vis. Synthesized compounds were used to study the photoisomerization phenomenon by using UV-Vis spectro-photometer. Interesting polarity dependent effect is observed for the first time on these materials. Trans-cis (E-Z) and cis-trans (Z-E) conversion occurred within 41 s and 445 min, respectively for both the compounds in solutions. Polarizing optical microscopy studies revealed that there is no liquid crystal phase for both the compounds. The dramatic variation in the optical property is speculated to be the polarity of the chemical species. These derivatives are useful to fabricate optical data storage devices. Copyright © 2015 Elsevier B.V. All rights reserved.

Spatial distribution of organic functional groups supported on mesoporous silica nanoparticles: A study by conventional and DNP-enhanced 29Si solid-state NMR

DOE PAGES

Kobayashi, Takeshi; Singappuli-Arachchige, Dilini; Wang, Zhuoran; ...

2016-12-23

Solid-state NMR spectroscopy, both conventional and dynamic nuclear polarization (DNP)-enhanced, was employed to study the spatial distribution of organic functional groups attached to the surface of mesoporous silica nanoparticles via co-condensation and grafting. The most revealing information was provided by DNP-enhanced two-dimensional 29Si– 29Si correlation measurements, which unambiguously showed that post-synthesis grafting leads to a more homogeneous dispersion of propyl and mercaptopropyl functionalities than co-condensation. Furthermore, during the anhydrous grafting process, the organosilane precursors do not self-condense and are unlikely to bond to the silica surface in close proximity (less than 4 Å) due to the limited availability of suitablymore » arranged hydroxyl groups.« less

Carbonic anhydrase inhibition of Schiff base derivative of imino-methyl-naphthalen-2-ol: Synthesis, structure elucidation, molecular docking, dynamic simulation and density functional theory calculations

NASA Astrophysics Data System (ADS)

Abbas, Saghir; Nasir, Hafiza Huma; Zaib, Sumera; Ali, Saqib; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz; Iqbal, Jamshed

2018-03-01

In the present study, we have designed and synthesized a Schiff base derivative 3 and characterized by FT-IR, 1H and 13C NMR spectroscopy. Single crystal X-ray diffraction and NMR studies were also performed. The synthetic compound was screened for its inhibitory potential against carbonic anhydrase II. The experimental results were validated by molecular docking and dynamic simulations of compound 3 in the active pocket of enzyme. Important binding interactions with the key residues in the active site of the carbonic anhydrase enzyme were revealed. Moreover, supramolecular assembly of the title compound was analyzed by density functional theory (DFT) calculations. These studies rendered a more clear understanding for the demonstration of novel molecular mechanism involved in CA II inhibition by the synthesized compound.

Behavior of atypical amphiphilic molecules

NASA Astrophysics Data System (ADS)

Ko, John

1997-08-01

The physical behavior of several atypical amphiphilic molecules was studied in various environments including micelles, model bilayer membranes, and emulsions. The molecules under investigation were nor-chenodeoxycholic acid (nor-CDCA), ursodeoxycholic acid (UDCA), sphingosine (Sp), sphingosine hydrochloride (SpċHCl), and tetrahydrolipstatin (THL). The bile acids, nor-CDCA and UDCA, were studied using 13C-Nuclear Magnetic Resonance ([13C) -NMR) in micelles of taurocholate and in bilayers of phosphatidylcholine. The pK a values of the bile acids in each environment were determined by [13C) -NMR and are as follows: 6.08 ±.03 for nor-CDCA and 6.27 ±.01 for UDCA in micelles, and 7.04 ± 12 for nor-CDCA and 6.89 ±.05 for UDCA in vesicles. Using line shape analysis, the transbilayer movement rate at 36oC for nor-CDCA and UDCA was calculated to be 580 sec--1 and 409 sec-1, respectively. [13C) -NMR titration of Sp gave pK a values of 9.09 ±.02 in micelles and 9.69 ±.21 in bilayers. Differential scanning calorimetry (DSC) and X-ray diffraction were used to establish the Spċwater and SpċHClċwater phase diagrams. Anhydrous and hydrated samples ranging from 5- 90% water were analyzed. The DSC thermograms traced out the transition temperatures of each molecule while the X- ray diffraction patterns revealed their chain and crystalline lattice packing structures. In general, sphingosine exists as a hydrated crystal with β packing phase below 43oC and melts into an Lα phase. Sphingosine hydrochloride, however, exists as a gel phase (L_beta or /beta/sp') below 42oC that swells to 61% hydration. At low water concentrations (0-64%), a lamellar liquid crystal phase (L_alpha) is formed above the chain melting transition of 42oC. At medium concentration (65%), a Hexagonal I phase is present, and at high water concentrations (66-90%), a micellar phase is present. THL, a specific inhibitor of lipases, was analyzed with [ 13C) -NMR to study its behavior in various environments, ranging from carbon tetrachloride to water to pure triolein. THL was also incorporated into phosphatidylcholine bilayers and into microemulsions of triolein and phosphatidylcholine. [ 13C) -NMR analysis revealed that THL gets incorporated into the surface of vesicles, and into both the surface and core of microemulsion particles.

Dissociation behavior of methane--ethane mixed gas hydrate coexisting structures I and II.

PubMed

Kida, Masato; Jin, Yusuke; Takahashi, Nobuo; Nagao, Jiro; Narita, Hideo

2010-09-09

Dissociation behavior of methane-ethane mixed gas hydrate coexisting structures I and II at constant temperatures less than 223 K was studied with use of powder X-ray diffraction and solid-state (13)C NMR techniques. The diffraction patterns at temperatures less than 203 K showed both structures I and II simultaneously convert to Ih during the dissociation, but the diffraction pattern at temperatures greater than 208 K showed different dissociation behavior between structures I and II. Although the diffraction peaks from structure II decreased during measurement at constant temperatures greater than 208 K, those from structure I increased at the initial step of dissociation and then disappeared. This anomalous behavior of the methane-ethane mixed gas hydrate coexisting structures I and II was examined by using the (13)C NMR technique. The (13)C NMR spectra revealed that the anomalous behavior results from the formation of ethane-rich structure I. The structure I hydrate formation was associated with the dissociation rate of the initial methane-ethane mixed gas hydrate.

In situ NMR and electrochemical quartz crystal microbalance techniques reveal the structure of the electrical double layer in supercapacitors

NASA Astrophysics Data System (ADS)

Griffin, John M.; Forse, Alexander C.; Tsai, Wan-Yu; Taberna, Pierre-Louis; Simon, Patrice; Grey, Clare P.

2015-08-01

Supercapacitors store charge through the electrosorption of ions on microporous electrodes. Despite major efforts to understand this phenomenon, a molecular-level picture of the electrical double layer in working devices is still lacking as few techniques can selectively observe the ionic species at the electrode/electrolyte interface. Here, we use in situ NMR to directly quantify the populations of anionic and cationic species within a working microporous carbon supercapacitor electrode. Our results show that charge storage mechanisms are different for positively and negatively polarized electrodes for the electrolyte tetraethylphosphonium tetrafluoroborate in acetonitrile; for positive polarization charging proceeds by exchange of the cations for anions, whereas for negative polarization, cation adsorption dominates. In situ electrochemical quartz crystal microbalance measurements support the NMR results and indicate that adsorbed ions are only partially solvated. These results provide new molecular-level insight, with the methodology offering exciting possibilities for the study of pore/ion size, desolvation and other effects on charge storage in supercapacitors.

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.

DNP-enhanced ultrawideline solid-state NMR spectroscopy: Studies of platinum in metal–organic frameworks

DOE PAGES

Kobayashi, Takeshi; Perras, Frederic A.; Goh, Tian Wei; ...

2016-06-06

Ultrawideline dynamic nuclear polarization (DNP)-enhanced 195Pt solid-state NMR (SSNMR) spectroscopy and theoretical calculations are used to determine the coordination of atomic Pt species supported within the pores of metal–organic frameworks (MOFs). The 195Pt SSNMR spectra, with breadths reaching 10,000 ppm, were obtained by combining DNP with broadbanded cross-polarization and CPMG acquisition. Although the DNP enhancements in static samples are lower than those typically observed under magic-angle spinning conditions, the presented measurements would be very challenging using the conventional SSNMR methods. The DNP-enhanced ultrawideline NMR spectra served to separate signals from cis- and trans-coordinated atomic Pt 2+ species supported on themore » UiO-66-NH 2 MOF. Here, the data revealed a dominance of kinetic effects in the formation of Pt 2+ complexes and the thermodynamic effects in their reduction to nanoparticles. A single cis-coordinated Pt 2+ complex was confirmed in MOF-253.« less

NMR, HS-SPME-GC/MS, and HPLC/MSn Analyses of Phytoconstituents and Aroma Profile of Rosmarinus eriocalyx.

PubMed

Bendif, Hamdi; Miara, Mohamed Djamel; Peron, Gregorio; Sut, Stefania; Dall'Acqua, Stefano; Flamini, Guido; Maggi, Filippo

2017-10-01

In this work, a comprehensive study on the chemical constituents of the aerial parts of Rosmarinus eriocalyx (Lamiaceae), an aromatic shrub traditionally consumed as a food and herbal remedy in Algeria, is presented. The aroma profile was analysed by headspace solid phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC/MS), whereas the crude extract constituents were analyzed by 1 H-NMR and by high performance liquid chromatography coupled with mass spectrometry (HPLC/MS n ). Thirty-nine volatile compounds, most of them being monoterpenes, have been identified, with camphor, camphene, and α-pinene as the most abundant constituents. 1 H-NMR analysis revealed the presence of phenolic compounds and betulinic acid while HPLC/MS n allowed the identification of glycosilated and aglyconic flavonoids as well as phenylpropanoid derivatives. Some of these constituents, namely as betulinic acid, rosmanol, and cirsimaritin were reported for the first time in R. eriocalyx. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Structure elucidation of a novel oligosaccharide (Medalose) from camel milk

NASA Astrophysics Data System (ADS)

Gangwar, Lata; Singh, Rinku; Deepak, Desh

2018-02-01

Free oligosaccharides are the third most abundant solid component in milk after lactose and lipids. The study of milk oligosaccharides indicate that nutrients are not only benefits the infant's gut but also perform a number of other functions which include stimulation of growth, receptor analogues to inhibit binding of pathogens and substances that promote postnatal brain development. Surveys reveal that camel milk oligosaccharides possess varied biological activities that help in the treatment of diabetes, asthma, anaemia, piles and also a food supplement to milking mothers. In this research, camel milk was selected for its oligosaccharide contents, which was then processed by Kobata and Ginsburg method followed by the HPLC and CC techniques. Structure elucidation of isolated compound was done by the chemical degradation, chemical transformation and comparison of chemical shift of NMR data of natural and acetylated oligosaccharide structure reporter group theory, the 1H, 13C NMR, 2D-NMR (COSY, TOCSY and HSQC) techniques, and mass spectrometry. The structure was elucidated as under: MEDALOSE

1H NMR and PCA-based analysis revealed variety dependent changes in phenolic contents of apple fruit after drying.

PubMed

Francini, Alessandra; Romeo, Stefania; Cifelli, Mario; Gori, Daniele; Domenici, Valentina; Sebastiani, Luca

2017-04-15

Dry and fresh apples have been studied monitoring their polyphenolic profiles through 1 H NMR, antioxidant capacity and total polyphenol content. Six ancient and underutilized apple varieties (Mantovana, Mora, Nesta, Cipolla, Ruggina, Sassola) and a commercial one (Golden Delicious) were dried with an air-drying system at 45°C for 19h. Although some of their polyphenol constituents were lost during drying, the antioxidant capacity of some apple varieties remained higher compared to Golden Delicious. This result is very important for ancient and underutilized varieties that are not consumed on large scale as fresh product since they have low attractiveness, due to their ugly appearance. Combining quantitative NMR spectroscopy with principal component analysis we have identified and quantified several polyphenols (such as catechin, epicathechin, and chlorogenic acid) that are important to establish the nutraceutical value of the different investigated apple varieties. Copyright © 2016 Elsevier Ltd. All rights reserved.

{sup 13}C chemical shift anisotropies for carbonate ions in cement minerals and the use of {sup 13}C, {sup 27}Al and {sup 29}Si MAS NMR in studies of Portland cement including limestone additions

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

Sevelsted, Tine F.; Herfort, Duncan; Skibsted, Jørgen, E-mail: jskib@chem.au.dk

2013-10-15

{sup 13}C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed {sup 13}C MAS or {sup 13}C({sup 1}H) CP/MAS NMR spectra (9.4 T or 14.1 T) for {sup 13}C in natural abundance. The variation in the {sup 13}C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in {sup 13}C MAS NMR spectra. However, it is shown that by combining {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR carbonate anions in anhydrousmore » and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends {sup 29}Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in {sup 27}Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •{sup 13}C chemical shift anisotropies for inorganic carbonates from {sup 13}C MAS NMR. •Narrow {sup 13}C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase.« less

Antiferromagnetic Ordering in Organic Conductor λ-(BEDT-TTF)2GaCl4 Probed by 13C NMR

NASA Astrophysics Data System (ADS)

Saito, Yohei; Fukuoka, Shuhei; Kobayashi, Takuya; Kawamoto, Atsushi; Mori, Hatsumi

2018-01-01

The ground state of λ-(BEDT-TTF)2GaCl4, which has the same structure as the organic superconductor λ-(BETS)2GaCl4, was investigated by magnetic susceptibility and 13C NMR measurements. The temperature dependence of the magnetic susceptibility revealed an antiferromagnetic (AF) correlation with J/kB ≃ 98 K. NMR spectrum splitting and the divergence of 1/T1 were observed at approximately 13 K, which is associated with the AF transition. We found that the AF structure is commensurate according to discrete NMR peak splitting, suggesting that the ground state of λ-(BEDT-TTF)2GaCl4 is an AF dimer-Mott insulating state. Our results suggest that the superconducting phase of λ-type salts would be located near the AF insulating phase.

'Boomerang'-like insertion of a fusogenic peptide in a lipid membrane revealed by solid-state 19F NMR.

PubMed

Afonin, Sergii; Dürr, Ulrich H N; Glaser, Ralf W; Ulrich, Anne S

2004-02-01

Solid state (19)F NMR revealed the conformation and alignment of the fusogenic peptide sequence B18 from the sea urchin fertilization protein bindin embedded in flat phospholipid bilayers. Single (19)F labels were introduced into nine distinct positions along the wild-type sequence by substituting each hydrophobic amino acid, one by one, with L-4-fluorophenylglycine. Their anisotropic chemical shifts were measured in uniaxially oriented membrane samples and used as orientational constraints to model the peptide structure in the membrane-bound state. Previous (1)H NMR studies of B18 in 30% TFE and in detergent micelles had shown that the peptide structure consists of two alpha-helical segments that are connected by a flexible hinge. This helix-break-helix motif was confirmed here by the solid-state (19)F NMR data, while no other secondary structure (beta-sheet, 3(10)-helix) was compatible with the set of orientational constraints. For both alpha-helical segments we found that the helical conformation extends all the way to the respective N- and C-termini of the peptide. Analysis of the corresponding tilt and azimuthal rotation angles showed that the N-terminal helix of B18 is immersed obliquely into the bilayer (at a tilt angle tau approximately 54 degrees), whereas the C-terminus is peripherally aligned (tau approximately 91 degrees). The azimuthal orientation of the two segments is consistent with the amphiphilic distribution of side-chains. The observed 'boomerang'-like mode of insertion into the membrane may thus explain how peptide binding leads to lipid dehydration and acyl chain perturbation as a prerequisite for bilayer fusion to occur. Copyright 2004 John Wiley & Sons, Ltd.

The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope.

PubMed

Morag, Omry; Sgourakis, Nikolaos G; Baker, David; Goldbourt, Amir

2015-01-27

Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6-16.7 Å and a tilt of 36.1-36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.

Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase.

PubMed

Liu, Dongsheng; Cowburn, David

2016-01-01

The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Synthesis of Novel μ-Star Copolymers with Poly(N-Octyl Benzamide) and Poly(ε-Caprolactone) Miktoarms through Chain-Growth Condensation Polymerization, Styrenics-Assisted Atom Transfer Radical Coupling, and Ring-Opening Polymerization.

PubMed

Huang, Chih-Feng; Aimi, Junko; Lai, Kuan-Yu

2017-02-01

Star copolymers are known to phase separate on the nanoscale, providing useful self-assembled morphologies. In this study, the authors investigate synthesis and assembly behavior of miktoarm star (μ-star) copolymers. The authors employ a new strategy for the synthesis of unprecedented μ-star copolymers presenting poly(N-octyl benzamide) (PBA) and poly(ε-caprolactone) (PCL) arms: a combination of chain-growth condensation polymerization, styrenics-assisted atom transfer radical coupling, and ring-opening polymerization. Gel permeation chromatography, mass-analyzed laser desorption/ionization mass spectrometry, and 1 H NMR spectroscopy reveal the successful synthesis of a well-defined (PBA 11 ) 2 -(PCL 15 ) 4 μ-star copolymer (M n ,NMR ≈ 12 620; Đ = 1.22). Preliminary examination of the PBA 2 PCL 4 μ-star copolymer reveals assembled nanofibers having a uniform diameter of ≈20 nm. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Frustration of square cupola in Sr(TiO)Cu4(PO4)4

NASA Astrophysics Data System (ADS)

Islam, S. S.; Ranjith, K. M.; Baenitz, M.; Skourski, Y.; Tsirlin, A. A.; Nath, R.

2018-05-01

The structural and magnetic properties of the square-cupola antiferromagnet Sr (TiO ) Cu4(PO4)4 are investigated via x-ray diffraction, magnetization, heat capacity, and 31P nuclear magnetic resonance experiments on polycrystalline samples, as well as density-functional band-structure calculations. The temperature-dependent unit-cell volume could be described well using the Debye approximation with a Debye temperature of θD≃ 550 K. Magnetic response reveals a pronounced two-dimensionality with a magnetic long-range order below TN≃6.2 K. High-field magnetization exhibits a kink at about 1 /3 of the saturation magnetization. Asymmetric 31P NMR spectra clearly suggest strong in-plane anisotropy in the magnetic susceptibility, as anticipated from the crystal structure. From the 31P NMR shift versus bulk susceptibility plot, the isotropic and axial parts of the hyperfine coupling between the 31P nuclei and the Cu2 + spins are calculated to be Ahfiso≃6539 and Ahfax≃952 Oe/μB, respectively. The low-temperature and low-field 31P NMR spectra indicate a commensurate antiferromagnetic ordering. The frustrated nature of the compound is inferred from the temperature-dependent 31P NMR spin-lattice relaxation rate and confirmed by our microscopic analysis, which reveals strong frustration of the square cupola by next-nearest-neighbor exchange couplings.

Persistence of urban organic aerosols composition: Decoding their structural complexity and seasonal variability.

PubMed

Matos, João T V; Duarte, Regina M B O; Lopes, Sónia P; Silva, Artur M S; Duarte, Armando C

2017-12-01

Organic Aerosols (OAs) are typically defined as highly complex matrices whose composition changes in time and space. Focusing on time vector, this work uses two-dimensional nuclear magnetic resonance (2D NMR) techniques to examine the structural features of water-soluble (WSOM) and alkaline-soluble organic matter (ASOM) sequentially extracted from fine atmospheric aerosols collected in an urban setting during cold and warm seasons. This study reveals molecular signatures not previously decoded in NMR-related studies of OAs as meaningful source markers. Although the ASOM is less hydrophilic and structurally diverse than its WSOM counterpart, both fractions feature a core with heteroatom-rich branched aliphatics from both primary (natural and anthropogenic) and secondary origin, aromatic secondary organics originated from anthropogenic aromatic precursors, as well as primary saccharides and amino sugar derivatives from biogenic emissions. These common structures represent those 2D NMR spectral signatures that are present in both seasons and can thus be seen as an "annual background" profile of the structural composition of OAs at the urban location. Lignin-derived structures, nitroaromatics, disaccharides, and anhydrosaccharides signatures were also identified in the WSOM samples only from periods identified as smoke impacted, which reflects the influence of biomass-burning sources. The NMR dataset on the H-C molecules backbone was also used to propose a semi-quantitative structural model of urban WSOM, which will aid efforts for more realistic studies relating the chemical properties of OAs with their atmospheric behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

NMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA.

PubMed

Ma, Dejian; Tillman, Tommy S; Tang, Pei; Meirovitch, Eva; Eckenhoff, Roderic; Carnini, Anna; Xu, Yan

2008-10-28

Structural studies of polytopic membrane proteins are often hampered by the vagaries of these proteins in membrane mimetic environments and by the difficulties in handling them with conventional techniques. Designing and creating water-soluble analogues with preserved native structures offer an attractive alternative. We report here solution NMR studies of WSK3, a water-soluble analogue of the potassium channel KcsA. The WSK3 NMR structure (PDB ID code 2K1E) resembles the KcsA crystal structures, validating the approach. By more stringent comparison criteria, however, the introduction of several charged residues aimed at improving water solubility seems to have led to the possible formations of a few salt bridges and hydrogen bonds not present in the native structure, resulting in slight differences in the structure of WSK3 relative to KcsA. NMR dynamics measurements show that WSK3 is highly flexible in the absence of a lipid environment. Reduced spectral density mapping and model-free analyses reveal dynamic characteristics consistent with an isotropically tumbling tetramer experiencing slow (nanosecond) motions with unusually low local ordering. An altered hydrogen-bond network near the selectivity filter and the pore helix, and the intrinsically dynamic nature of the selectivity filter, support the notion that this region is crucial for slow inactivation. Our results have implications not only for the design of water-soluble analogues of membrane proteins but also for our understanding of the basic determinants of intrinsic protein structure and dynamics.

Chirp echo Fourier transform EPR-detected NMR

NASA Astrophysics Data System (ADS)

Wili, Nino; Jeschke, Gunnar

2018-04-01

A new ultra-wide band (UWB) pulse EPR method is introduced for observing all nuclear frequencies of a paramagnetic center in a single shot. It is based on burning spectral holes with a high turning angle (HTA) pulse that excites forbidden transitions and subsequent detection of the hole pattern by a chirp echo. We term this method Chirp Echo Epr SpectroscopY (CHEESY)-detected NMR. The approach is a revival of FT EPR-detected NMR. It yields similar spectra and the same type of information as electron-electron double resonance (ELDOR)-detected NMR, but with a multiplex advantage. We apply CHEESY-detected NMR in Q band to nitroxides and correlate the hyperfine spectrum to the EPR spectrum by varying the frequency of the HTA pulse. Furthermore, a selective π pulse before the HTA pulse allows for detecting hyperfine sublevel correlations between transitions of one nucleus and for elucidating the coupling regime, the same information as revealed by the HYSCORE experiment. This is demonstrated on hexaaquamanganese(II). We expect that CHEESY-detected NMR is generally applicable to disordered systems and that our results further motivate the development of EPR spectrometers capable of coherent UWB excitation and detection, especially at higher fields and frequencies.

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

PubMed Central

Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

2015-01-01

Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix. PMID:25550503

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR.

PubMed

Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

2015-01-13

Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.

Two classes of cholesterol binding sites for the β2AR revealed by thermostability and NMR.

PubMed

Gater, Deborah L; Saurel, Olivier; Iordanov, Iordan; Liu, Wei; Cherezov, Vadim; Milon, Alain

2014-11-18

Cholesterol binding to G protein-coupled receptors (GPCRs) and modulation of their activities in membranes is a fundamental issue for understanding their function. Despite the identification of cholesterol binding sites in high-resolution x-ray structures of the ?2 adrenergic receptor (β2AR) and other GPCRs, the binding affinity of cholesterol for this receptor and exchange rates between the free and bound cholesterol remain unknown. In this study we report the existence of two classes of cholesterol binding sites in β2AR. By analyzing the β2AR unfolding temperature in lipidic cubic phase (LCP) as a function of cholesterol concentration we observed high-affinity cooperative binding of cholesterol with sub-nM affinity constant. In contrast, saturation transfer difference (STD) NMR experiments revealed the existence of a second class of cholesterol binding sites, in fast exchange on the STD NMR timescale. Titration of the STD signal as a function of cholesterol concentration provided a lower limit of 100 mM for their dissociation constant. However, these binding sites are specific for both cholesterol and β2AR, as shown with control experiments using ergosterol and a control membrane protein (KpOmpA). We postulate that this specificity is mediated by the high-affinity bound cholesterol molecules and propose the formation of transient cholesterol clusters around the high-affinity binding sites.

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

PubMed

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

2016-07-14

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

Interactions between cations and peat organic matter monitored with NMR wideline, static and FFC NMR relaxometry

NASA Astrophysics Data System (ADS)

Schaumann, Gabriele E.; Conte, Pellegrino; Jäger, Alexander; Alonzo, Giuseppe; Bertmer, Marko

2010-05-01

The molecular size of humic substances is still under debate and is believed to range up to several hundred thousands Dalton, although a number of recent studies suggest much lower molecular weights. Nowadays an increasing number of authors suggest a model of molecular aggregates. One explanation why results on the molecular mass of humic materials are contradictory, may be that individual OM molecules are linked via intermolecular interactions, by bridges of water molecules or by cations bridging cation exchange sites (Schaumann, 2006a, b). Properties of such cross-linked systems can be similar to macromolecular systems revealing covalent cross-links. In this context, multivalent cations play an important ecological role, serving as reversible cross-linking agent. Formation and disruption of such cation bridges may close or open sorption sites in soil organic matter. Although cross-linking by multivalent cations has been proposed in many studies, the cross-linking effect has not yet been demonstrated on the molecular scale. The objective of this study was to investigate the interactions between cations and peat organic matter using NMR wideline techniques as well as static and fast field cycling (FFC) NMR relaxometry. Peat treated with solutions containing either Na+, Ca2+ or Al3+ was investigated in air-dried state for longitudinal relaxation times (T1) and NMR wideline characteristics. T1 distributions were separated into two Gaussian functions which were interpreted to represent two proton populations belonging to two environments of differing mobility. The relaxation rates (R1 = T1-1) in the cation treated samples spread over a range of 87-123 s-1 (R1a: fast component) and 32-42 s-1 (R1b: slow component). The rates in all treatments are significantly different from each other. and decrease in the order conditioned sample > desalinated sample > Na-treated sample. The treatment with multivalent cations affects R1a and R1b in different ways and needs more detailed explanation. Wideline proton NMR spectra can be used to quantify proton containing material, mainly water, based on their mobility. Spectra were decomposed into a Gaussian and Lorentzian line and changes to mobility after heat treatment indicate the water binding strength. In this study, differences in the various NMR parameters on the cation treatments will be presented and discussed with respect to the crosslinking hypothesis.

The transcription repressor NmrA is subject to proteolysis by three Aspergillus nidulans proteases

PubMed Central

Zhao, Xiao; Hume, Samantha L; Johnson, Christopher; Thompson, Paul; Huang, Junyong; Gray, Joe; Lamb, Heather K; Hawkins, Alastair R

2010-01-01

The role of specific cleavage of transcription repressor proteins by proteases and how this may be related to the emerging theme of dinucleotides as cellular signaling molecules is poorly characterized. The transcription repressor NmrA of Aspergillus nidulans discriminates between oxidized and reduced dinucleotides, however, dinucleotide binding has no effect on its interaction with the zinc finger in the transcription activator AreA. Protease activity in A. nidulans was assayed using NmrA as the substrate, and was absent in mycelium grown under nitrogen sufficient conditions but abundant in mycelium starved of nitrogen. One of the proteases was purified and identified as the protein Q5BAR4 encoded by the gene AN2366.2. Fluorescence confocal microscopy showed that the nuclear levels of NmrA were reduced approximately 38% when mycelium was grown on nitrate compared to ammonium and absent when starved of nitrogen. Proteolysis of NmrA occurred in an ordered manner by preferential digestion within a C-terminal surface exposed loop and subsequent digestion at other sites. NmrA digested at the C-terminal site was unable to bind to the AreA zinc finger. These data reveal a potential new layer of control of nitrogen metabolite repression by the ordered proteolytic cleavage of NmrA. NmrA digested at the C-terminal site retained the ability to bind NAD+ and showed a resistance to further digestion that was enhanced by the presence of NAD+. This is the first time that an effect of dinucleotide binding to NmrA has been demonstrated. PMID:20506376

1H NMR-based metabolic profiling reveals the effects of fluoxetine on lipid and amino acid metabolism in astrocytes.

PubMed

Bai, Shunjie; Zhou, Chanjuan; Cheng, Pengfei; Fu, Yuying; Fang, Liang; Huang, Wen; Yu, Jia; Shao, Weihua; Wang, Xinfa; Liu, Meiling; Zhou, Jingjing; Xie, Peng

2015-04-15

Fluoxetine, a selective serotonin reuptake inhibitor (SSRI), is a prescribed and effective antidepressant and generally used for the treatment of depression. Previous studies have revealed that the antidepressant mechanism of fluoxetine was related to astrocytes. However, the therapeutic mechanism underlying its mode of action in astrocytes remains largely unclear. In this study, primary astrocytes were exposed to 10 µM fluoxetine; 24 h post-treatment, a high-resolution proton nuclear magnetic resonance (1H NMR)-based metabolomic approach coupled with multivariate statistical analysis was used to characterize the metabolic variations of intracellular metabolites. The orthogonal partial least-squares discriminant analysis (OPLS-DA) score plots of the spectra demonstrated that the fluoxetine-treated astrocytes were significantly distinguished from the untreated controls. In total, 17 differential metabolites were identified to discriminate the two groups. These key metabolites were mainly involved in lipids, lipid metabolism-related molecules and amino acids. This is the first study to indicate that fluoxetine may exert antidepressant action by regulating the astrocyte's lipid and amino acid metabolism. These findings should aid our understanding of the biological mechanisms underlying fluoxetine therapy.

1H NMR-Based Metabolic Profiling Reveals the Effects of Fluoxetine on Lipid and Amino Acid Metabolism in Astrocytes

PubMed Central

Bai, Shunjie; Zhou, Chanjuan; Cheng, Pengfei; Fu, Yuying; Fang, Liang; Huang, Wen; Yu, Jia; Shao, Weihua; Wang, Xinfa; Liu, Meiling; Zhou, Jingjing; Xie, Peng

2015-01-01

Fluoxetine, a selective serotonin reuptake inhibitor (SSRI), is a prescribed and effective antidepressant and generally used for the treatment of depression. Previous studies have revealed that the antidepressant mechanism of fluoxetine was related to astrocytes. However, the therapeutic mechanism underlying its mode of action in astrocytes remains largely unclear. In this study, primary astrocytes were exposed to 10 µM fluoxetine; 24 h post-treatment, a high-resolution proton nuclear magnetic resonance (1H NMR)-based metabolomic approach coupled with multivariate statistical analysis was used to characterize the metabolic variations of intracellular metabolites. The orthogonal partial least-squares discriminant analysis (OPLS-DA) score plots of the spectra demonstrated that the fluoxetine-treated astrocytes were significantly distinguished from the untreated controls. In total, 17 differential metabolites were identified to discriminate the two groups. These key metabolites were mainly involved in lipids, lipid metabolism-related molecules and amino acids. This is the first study to indicate that fluoxetine may exert antidepressant action by regulating the astrocyte’s lipid and amino acid metabolism. These findings should aid our understanding of the biological mechanisms underlying fluoxetine therapy. PMID:25884334

1H-NMR and UPLC-MS metabolomics: Functional tools for exploring chemotypic variation in Sceletium tortuosum from two provinces in South Africa.

PubMed

Zhao, Jianping; Khan, Ikhlas A; Combrinck, Sandra; Sandasi, Maxleene; Chen, Weiyang; Viljoen, Alvaro M

2018-05-17

Sceletium tortuosum (Aizoaceae) is widely recognised for the treatment of stress, anxiety and depression, as well as for obsessive compulsive disorders. A comprehensive intraspecies chemotypic variation study, using samples harvested from two distinct regions of South Africa, was done using both proton nuclear magnetic resonance ( 1 H-NMR) spectroscopy of methanol extracts (N = 145) and ultra performance liquid chromatography-mass spectrometry (UPLC-MS) of acid/base extracts (N = 289). Chemometric analysis of the 1 H-NMR data indicated two main clusters that were region-specific (Northern Cape and Western Cape provinces). Two dimensional (2D) NMR was used to identify analytes that contributed to the clustering as revealed by the S-plot. The sceletium alkaloids, pinitol and two alkylamines, herein reported for the first time from S. tortuosum, were identified as markers that distinguished the two groups. Relative quantification of the marker analytes conducted by qNMR indicated that samples from the Northern Cape generally contained higher concentrations of all the markers than samples from the Western Cape. Quantitative analysis of the four mesembrine alkaloids using a validated UPLC-photo diode array (PDA) detection method confirmed the results of qNMR with regard to the total alkaloid concentrations. Samples from the Northern Cape Province were found to contain, on average, very high total alkaloids, ranging from 4938.0 to 9376.8 mg/kg dry w. Regarding the Western Cape samples, the total yields of the four mesembrine alkaloids were substantially lower (averages 16.4-4143.2 mg/kg). Hierarchical cluster analysis of the UPLC-MS data, based on the alkaloid chemistry, revealed three branches, with one branch comprising samples primarily from the Northern Cape that seemed somewhat chemically conserved, while the other two branches represented mainly samples from the Western Cape. The construction of an orthogonal projections to latent structures-discriminant analysis model and subsequent loadings plot, allowed alkaloid markers to be identified for each cluster. The diverse sceletium alkaloid chemistry of samples from the three clusters may facilitate the recognition of alkaloid profiles, rather than individual compounds, that exert targeted effects on various brain receptors involved in stress, anxiety or depression. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effect of oxygen concentration on viability and metabolism in a fluidized-bed bioartificial liver using ³¹P and ¹³C NMR spectroscopy.

PubMed

Jeffries, Rex E; Gamcsik, Michael P; Keshari, Kayvan R; Pediaditakis, Peter; Tikunov, Andrey P; Young, Gregory B; Lee, Haakil; Watkins, Paul B; Macdonald, Jeffrey M

2013-02-01

Many oxygen mass-transfer modeling studies have been performed for various bioartificial liver (BAL) encapsulation types; yet, to our knowledge, there is no experimental study that directly and noninvasively measures viability and metabolism as a function of time and oxygen concentration. We report the effect of oxygen concentration on viability and metabolism in a fluidized-bed NMR-compatible BAL using in vivo ³¹P and ¹³C NMR spectroscopy, respectively, by monitoring nucleotide triphosphate (NTP) and ¹³C-labeled nutrient metabolites, respectively. Fluidized-bed bioreactors eliminate the potential channeling that occurs with packed-bed bioreactors and serve as an ideal experimental model for homogeneous oxygen distribution. Hepatocytes were electrostatically encapsulated in alginate (avg. diameter, 500 μm; 3.5×10⁷ cells/mL) and perfused at 3 mL/min in a 9-cm (inner diameter) cylindrical glass NMR tube. Four oxygen treatments were tested and validated by an in-line oxygen electrode: (1) 95:5 oxygen:carbon dioxide (carbogen), (2) 75:20:5 nitrogen:oxygen:carbon dioxide, (3) 60:35:5 nitrogen:oxygen:carbon dioxide, and (4) 45:50:5 nitrogen:oxygen:carbon dioxide. With 20% oxygen, β-NTP steadily decreased until it was no longer detected at 11 h. The 35%, 50%, and 95% oxygen treatments resulted in steady β-NTP levels throughout the 28-h experimental period. For the 50% and 95% oxygen treatment, a ¹³C NMR time course (∼5 h) revealed 2-¹³C-glycine and 2-¹³C-glucose to be incorporated into [2-¹³C-glycyl]glutathione (GSH) and 2-¹³C-lactate, respectively, with 95% having a lower rate of lactate formation. ³¹P and ¹³C NMR spectroscopy is a noninvasive method for determining viability and metabolic rates. Modifying tissue-engineered devices to be NMR compatible is a relatively easy and inexpensive process depending on the bioreactor shape.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

NASA Astrophysics Data System (ADS)

Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA.

PubMed

Mroue, Kamal H; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H; Morris, Michael D; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans. Copyright © 2014 Elsevier Inc. All rights reserved.

Lignin Composition and Structure in Young versus Adult Eucalyptus globulus Plants1

PubMed Central

Rencoret, Jorge; Gutiérrez, Ana; Nieto, Lidia; Jiménez-Barbero, J.; Faulds, Craig B.; Kim, Hoon; Ralph, John; Martínez, Ángel T.; del Río, José C.

2011-01-01

Lignin changes during plant growth were investigated in a selected Eucalyptus globulus clone. The lignin composition and structure were studied in situ by a new procedure enabling the acquisition of two-dimensional nuclear magnetic resonance (2D-NMR) spectra on wood gels formed in the NMR tube as well as by analytical pyrolysis-gas chromatography-mass spectrometry. In addition, milled-wood lignins were isolated and analyzed by 2D-NMR, pyrolysis-gas chromatography-mass spectrometry, and thioacidolysis. The data indicated that p-hydroxyphenyl and guaiacyl units are deposited at the earlier stages, whereas the woods are enriched in syringyl (S) lignin during late lignification. Wood 2D-NMR showed that β-O-4′ and resinol linkages were predominant in the eucalypt lignin, whereas other substructures were present in much lower amounts. Interestingly, open β-1′ structures could be detected in the isolated lignins. Phenylcoumarans and cinnamyl end groups were depleted with age, spirodienone abundance increased, and the main substructures (β-O-4′ and resinols) were scarcely modified. Thioacidolysis revealed a higher predominance of S units in the ether-linked lignin than in the total lignin and, in agreement with NMR, also indicated that resinols are the most important nonether linkages. Dimer analysis showed that most of the resinol-type structures comprised two S units (syringaresinol), the crossed guaiacyl-S resinol appearing as a minor substructure and pinoresinol being totally absent. Changes in hemicelluloses were also shown by the 2D-NMR spectra of the wood gels without polysaccharide isolation. These include decreases of methyl galacturonosyl, arabinosyl, and galactosyl (anomeric) signals, assigned to pectin and related neutral polysaccharides, and increases of xylosyl (which are approximately 50% acetylated) and 4-O-methylglucuronosyl signals. PMID:21098672

Determination of Diethyl Phthalate and Polyhexamethylene Guanidine in Surrogate Alcohol from Russia

PubMed Central

Monakhova, Yulia B.; Kuballa, Thomas; Leitz, Jenny; Lachenmeier, Dirk W.

2011-01-01

Analytical methods based on spectroscopic techniques were developed and validated for the determination of diethyl phthalate (DEP) and polyhexamethylene guanidine (PHMG), which may occur in unrecorded alcohol. Analysis for PHMG was based on UV-VIS spectrophotometry after derivatization with Eosin Y and 1H NMR spectroscopy of the DMSO extract. Analysis of DEP was performed with direct UV-VIS and 1H NMR methods. Multivariate curve resolution and spectra computation methods were used to confirm the presence of PHMG and DEP in the investigated beverages. Of 22 analysed alcohol samples, two contained DEP or PHMG. 1H NMR analysis also revealed the presence of signals of hawthorn extract in three medicinal alcohols used as surrogate alcohol. The simple and cheap UV-VIS methods can be used for rapid screening of surrogate alcohol samples for impurities, while 1H NMR is recommended for specific confirmatory analysis if required. PMID:21647285

Determination of diethyl phthalate and polyhexamethylene guanidine in surrogate alcohol from Russia.

PubMed

Monakhova, Yulia B; Kuballa, Thomas; Leitz, Jenny; Lachenmeier, Dirk W

2011-01-01

Analytical methods based on spectroscopic techniques were developed and validated for the determination of diethyl phthalate (DEP) and polyhexamethylene guanidine (PHMG), which may occur in unrecorded alcohol. Analysis for PHMG was based on UV-VIS spectrophotometry after derivatization with Eosin Y and (1)H NMR spectroscopy of the DMSO extract. Analysis of DEP was performed with direct UV-VIS and (1)H NMR methods. Multivariate curve resolution and spectra computation methods were used to confirm the presence of PHMG and DEP in the investigated beverages. Of 22 analysed alcohol samples, two contained DEP or PHMG. (1)H NMR analysis also revealed the presence of signals of hawthorn extract in three medicinal alcohols used as surrogate alcohol. The simple and cheap UV-VIS methods can be used for rapid screening of surrogate alcohol samples for impurities, while (1)H NMR is recommended for specific confirmatory analysis if required.

Comprehensive NMR analysis of compositional changes of black garlic during thermal processing.

PubMed

Liang, Tingfu; Wei, Feifei; Lu, Yi; Kodani, Yoshinori; Nakada, Mitsuhiko; Miyakawa, Takuya; Tanokura, Masaru

2015-01-21

Black garlic is a processed food product obtained by subjecting whole raw garlic to thermal processing that causes chemical reactions, such as the Maillard reaction, which change the composition of the garlic. In this paper, we report a nuclear magnetic resonance (NMR)-based comprehensive analysis of raw garlic and black garlic extracts to determine the compositional changes resulting from thermal processing. (1)H NMR spectra with a detailed signal assignment showed that 38 components were altered by thermal processing of raw garlic. For example, the contents of 11 l-amino acids increased during the first step of thermal processing over 5 days and then decreased. Multivariate data analysis revealed changes in the contents of fructose, glucose, acetic acid, formic acid, pyroglutamic acid, cycloalliin, and 5-(hydroxymethyl)furfural (5-HMF). Our results provide comprehensive information on changes in NMR-detectable components during thermal processing of whole garlic.

Relationships between solid dispersion preparation process, particle size and drug release--an NMR and NMR microimaging study.

PubMed

Dahlberg, Carina; Millqvist-Fureby, Anna; Schuleit, Michael; Furó, István

2010-10-01

Solid dispersion tablets prepared by either spray drying or rotoevaporation and exhibiting different grain and pore sizes were investigated under the process of hydration-swelling-gelation. (2)H and (1)H NMR microimaging experiments were used to selectively follow water penetration and polymer mobilization kinetics, respectively, while the drug release kinetics was followed by (1)H NMR spectroscopy. The obtained data, in combination with morphological information by scanning electron microscopy (SEM), reveal a complex process that ultimately leads to release of the drug into the aqueous phase. We find that the rate of water ingress has no direct influence on release kinetics, which also renders air in the tablets a secondary factor. On the other hand, drug release is directly correlated with the polymer mobilization kinetics. Water diffusion into the originally dry polymer grains determines the rate of grain swelling and the hydration within the grains varies strongly with grain size. We propose that this sets the stage for creating homogeneous gels for small grain sizes and heterogeneous gels for large grain sizes. Fast diffusion through water-rich sections of the inhomogeneous gels that exhibit a large mesh size is the factor which yields a faster drug release from tablets prepared by rotoevaporation. Copyright © 2010. Published by Elsevier B.V.

Ammonia Vapor Removal by Cu(3)(BTC)(2) and Its Characterization by MAS NMR.

PubMed

Peterson, Gregory W; Wagner, George W; Balboa, Alex; Mahle, John; Sewell, Tara; Karwacki, Christopher J

2009-07-01

Adsorption equilibria and NMR experiments were performed to study the adsorption and interactions of ammonia with metal-organic framework (MOF) HKUST-1, or Cu(3)(BTC)(2) (BTC = 1,3,5-benzenetricarboxylate). Ammonia capacities determined from chemical breakthrough measurements show significantly higher uptake capacities than from adsorption alone, suggesting a stronger interaction involving a potential reaction with the Cu(3)(BTC)(2) framework. Indeed, (1)H MAS NMR reveals that a major disruption of the relatively simple spectrum of Cu(3)(BTC)(2) occurs to generate a composite spectrum consistent with Cu(OH)(2) and (NH(4))(3)BTC species under humid conditions-the anticipated products of a copper(II) carboxylate reacted with limited ammonia. These species are not detected under dry conditions; however, reaction stoichiometry combined with XRD results suggests the partial formation of an indeterminate diammine copper (II) complex with some residual Cu(3)(BTC)(2) structure retained. Cu(II)-induced paramagnetic shifts exhibited by various species in (1)H and (13)C MAS NMR spectra are consistent with model compounds and previous literature. Although results show extensive ammonia capacity of Cu(3)(BTC)(2), much of the capacity is due to reaction with the structure itself, causing a permanent loss in porosity and structural integrity.

Ammonia Vapor Removal by Cu3(BTC)2 and Its Characterization by MAS NMR

PubMed Central

Peterson, Gregory W.; Wagner, George W.; Balboa, Alex; Mahle, John; Sewell, Tara; Karwacki, Christopher J.

2009-01-01

Adsorption equilibria and NMR experiments were performed to study the adsorption and interactions of ammonia with metal-organic framework (MOF) HKUST-1, or Cu3(BTC)2 (BTC = 1,3,5-benzenetricarboxylate). Ammonia capacities determined from chemical breakthrough measurements show significantly higher uptake capacities than from adsorption alone, suggesting a stronger interaction involving a potential reaction with the Cu3(BTC)2 framework. Indeed, 1H MAS NMR reveals that a major disruption of the relatively simple spectrum of Cu3(BTC)2 occurs to generate a composite spectrum consistent with Cu(OH)2 and (NH4)3BTC species under humid conditions—the anticipated products of a copper(II) carboxylate reacted with limited ammonia. These species are not detected under dry conditions; however, reaction stoichiometry combined with XRD results suggests the partial formation of an indeterminate diammine copper (II) complex with some residual Cu3(BTC)2 structure retained. Cu(II)-induced paramagnetic shifts exhibited by various species in 1H and 13C MAS NMR spectra are consistent with model compounds and previous literature. Although results show extensive ammonia capacity of Cu3(BTC)2, much of the capacity is due to reaction with the structure itself, causing a permanent loss in porosity and structural integrity. PMID:20161144

NMR studies of multiple conformations in complexes of Lactobacillus casei dihydrofolate reductase with analogues of pyrimethamine

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

Birdsall, B.; Tendler, S.J.B.; Feeney, J.

1990-10-01

{sup 1}H and {sup 19}F NMR signals from bound ligands have been assigned in one- and two-dimensional NMR spectra of complexes of Lactobacillus casei dihydrofolate reductase with various pyrimethamine analogues. The signals were identified mainly by correlating signals from bound and free ligands by using 2D exchange experiments. Analogues with symmetrically substituted phenyl rings give rise to {sup 1}H signals from four nonequivalent aromatic protons, clearly indicating the presence of hindered rotation about the pyrimidine-phenyl bond. Analogues with symmetrically substituted phenyl rings give rise to {sup 1}H signals from four nonequivalent aromatic protons, clearly indicating the presence of hindered rotationmore » about the pyrimidine-phenyl bond. Analogues containing asymmetrically substituted aromatic rings exist as mixtures of two rotational isomers (an enantiomeric pair) because of this hindered rotation and the NMR spectra revealed that both isomers (forms A and B) bind to the enzyme with comparable, though unequal, binding energies. In this case two complete sets of bound proton signals were observed. The relative orientations of the two forms have been determined from NOE through-space connections between protons on the ligand and protein. Ternary complexes with NADP{sup {plus}} were also examined.« less

Insights into the distribution of water in a self-humidifying H2/O2 proton-exchange membrane fuel cell using 1H NMR microscopy.

PubMed

Feindel, Kirk W; Bergens, Steven H; Wasylishen, Roderick E

2006-11-01

Proton ((1)H) NMR microscopy is used to investigate in-situ the distribution of water throughout a self-humidifying proton-exchange membrane fuel cell, PEMFC, operating at ambient temperature and pressure on dry H(2)(g) and O(2)(g). The results provide the first experimental images of the in-plane distribution of water within the PEM of a membrane electrode assembly in an operating fuel cell. The effect of gas flow configuration on the distribution of water in the PEM and cathode flow field is investigated, revealing that the counter-flow configurations yield a more uniform distribution of water throughout the PEM. The maximum power output from the PEMFC, while operating under conditions of constant external load, occurs when H(2)O(l) is first visible in the (1)H NMR image of the cathode flow field, and subsequently declines as this H(2)O(l) continues to accumulate. The (1)H NMR microscopy experiments are in qualitative agreement with predictions from several theoretical modeling studies (e.g., Pasaogullari, U.; Wang, C. Y. J. Electrochem. Soc. 2005, 152, A380-A390), suggesting that combined theoretical and experimental approaches will constitute a powerful tool for PEMFC design, diagnosis, and optimization.

Detection of Apoptosis and Necrosis in Normal Human Lung Cells Using 1H NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Shih, Chwen-Ming; Ko, Wun-Chang; Yang, Liang-Yo; Lin, Chien-Ju; Wu, Jui-Sheng; Lo, Tsui-Yun; Wang, Shwu-Huey; Chen, Chien-Tsu

2005-05-01

This study aimed to detect apoptosis and necrosis in MRC-5, a normal human lung cell line, by using noninvasive proton nuclear magnetic resonance (1H NMR). Live MRC-5 cells were processed first for 1H NMR spectroscopy; subsequently their types and the percentage of cell death were assessed on a flow cytometer. Cadmium (Cd) and mercury (Hg) induced apoptosis and necrosis in MRC-5 cells, respectively, as revealed by phosphatidylserine externalization on a flow cytometer. The spectral intensity ratio of methylene (CH2) resonance (at 1.3 ppm) to methyl (CH3) resonance (at 0.9 ppm) was directly proportional to the percentage of apoptosis and strongly and positively correlated with PI staining after Cd treatment (r2 = 0.9868, P < 0.01). In contrast, this ratio only increased slightly within 2-h Hg treatment, and longer Hg exposure failed to produce further increase. Following 2-h Hg exposure, the spectral intensity of choline resonance (at 3.2 ppm) was abolished, but this phenomenon was absent in Cd-induced apoptosis. These findings together demonstrate that 1H NMR is a novel tool with a quantitative potential to distinguish apoptosis from necrosis as early as the onset of cell death in normal human lung cells.

Dissolution mechanism of crystalline cellulose in H3PO4 as assessed by high-field NMR spectroscopy and fast field cycling NMR relaxometry.

PubMed

Conte, Pellegrino; Maccotta, Antonella; De Pasquale, Claudio; Bubici, Salvatore; Alonzo, Giuseppe

2009-10-14

Many processes have been proposed to produce glucose as a substrate for bacterial fermentation to obtain bioethanol. Among others, cellulose degradation appears as the most convenient way to achieve reliable amounts of glucose units. In fact, cellulose is the most widespread biopolymer, and it is considered also as a renewable resource. Due to extended intra- and interchain hydrogen bonds that provide a very efficient packing structure, however, cellulose is also a very stable polymer, the degradation of which is not easily achievable. In the past decade, researchers enhanced cellulose reactivity by increasing its solubility in many solvents, among which concentrated phosphoric acid (H(3)PO(4)) played the major role because of its low volatility and nontoxicity. In the present study, the solubilization mechanism of crystalline cellulose in H(3)PO(4) has been elucidated by using high- and low-field NMR spectroscopy. In particular, high-field NMR spectra showed formation of direct bonding between phosphoric acid and dissolved cellulose. On the other hand, molecular dynamics studies by low-field NMR with a fast field cycling (FFC) setup revealed two different H(3)PO(4) relaxing components. The first component, described by the fastest longitudinal relaxation rate (R(1)), was assigned to the H(3)PO(4) molecules bound to the biopolymer. Conversely, the second component, characterized by the slowest R(1), was attributed to the bulk solvent. The understanding of cellulose dissolution in H(3)PO(4) represents a very important issue because comprehension of chemical mechanisms is fundamental for process ameliorations to produce bioenergy from biomasses.

Probing the carbonyl functionality of a petroleum resin and asphaltene through oximation and schiff base formation in conjunction with N-15 NMR

USGS Publications Warehouse

Thorn, Kevin A.; Cox, Larry G.

2015-01-01

Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

Multiscale approach to (micro)porosity quantification in continental spring carbonate facies: Case study from the Cakmak quarry (Denizli, Turkey)

NASA Astrophysics Data System (ADS)

De Boever, Eva; Foubert, Anneleen; Oligschlaeger, Dirk; Claes, Steven; Soete, Jeroen; Bertier, Pieter; Özkul, Mehmet; Virgone, Aurélien; Swennen, Rudy

2016-07-01

Carbonate spring deposits gained renewed interest as potential contributors to subsurface reservoirs and as continental archives of environmental changes. In contrast to their fabrics, petrophysical characteristics - and especially the importance of microporosity (< 1µm) - are less understood. This study presents the combination of advanced petrophysical and imaging techniques to investigate the pore network characteristics of three, common and widespread spring carbonate facies, as exposed in the Pleistocene Cakmak quarry (Denizli, Turkey): the extended Pond, the dipping crystalline Proximal Slope Facies and the draping Apron and Channel Facies deposits formed by encrustation of biological substrate. Integrating mercury injection capillary pressure, bulk and diffusion Nuclear Magnetic Resonance (NMR), NMR profiling and Brunauer-Emmett-Teller (BET) measurements with microscopy and micro-computer tomography (µ-CT), shows that NMR T2 distributions systematically display a single group of micro-sized pore bodies, making up between 6 and 33% of the pore space (average NMR T2 cut-off value: 62 ms). Micropore bodies are systematically located within cloudy crystal cores of granular and dendritic crystal textures in all facies. The investigated properties therefore do not reveal differences in micropore size or shape with respect to more or less biology-associated facies. The pore network of the travertine facies is distinctive in terms of (i) the percentage of microporosity, (ii) the connectivity of micropores with meso- to macropores, and (ii) the degree of heterogeneity at micro- and macroscale. Results show that an approach involving different NMR experiments provided the most complete view on the 3-D pore network especially when microporosity and connectivity are of interest.

Quadrupolar magic angle spinning NMR spectra fitted using the Pearson IV function.

PubMed

Mironenko, Roman M; Belskaya, Olga B; Talsi, Valentin P; Likholobov, Vladimir A

2014-01-01

The Pearson IV function was used to fit the asymmetric solid-state (27)Al NMR spectra of alumina based catalysts. A high convergence (correlation coefficient is no less than 0.997) between experimental and simulated spectra was achieved. The decomposition of the (27)Al NMR spectra of zinc/aluminum mixed oxides with different Zn/Al molar ratio revealed an increased fraction (6-9%) of pentacoordinated aluminum atoms in these oxides as compared to γ-Al2O3. As the Zn/Al ratio is raised, the fraction of [AlO6] octahedral units decreases, while the fraction of [AlO4] tetrahedra increases. Copyright © 2014 Elsevier Inc. All rights reserved.

How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study.

PubMed

Gonzalez, Miguel A; Barriga, Hanna M G; Richens, Joanna L; Law, Robert V; O'Shea, Paul; Bresme, Fernando

2017-03-29

Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid-protein systems and more recently to study lipid flip-flop in model membrane systems. It is well recognised that lanthanide salts can influence the behaviour of both lipid and protein systems, however a full molecular level description of lipid-lanthanide interactions is still outstanding. Here we present a study of lanthanide-bilayer interactions, using molecular dynamics computer simulations, fluorescence electrostatic potential experiments and nuclear magnetic resonance. Computer simulations reveal the microscopic structure of DMPC lipid bilayers in the presence of Yb 3+ , and a surprising ability of the membranes to adsorb significant concentrations of Yb 3+ without disrupting the overall membrane structure. At concentrations commonly used in NMR experiments, Yb 3+ ions bind strongly to 5 lipids, inducing a small decrease of the area per lipid and a slight increase of the ordering of the aliphatic chains and the bilayer thickness. The area compressibility modulus increases by a factor of two, with respect to the free-salt case, showing that Yb 3+ ions make the bilayer more rigid. These modifications of the bilayer properties should be taken into account in the interpretation of NMR experiments.

A New Method for the Isolation of Ergosterol and Peroxyergosterol as Active Compounds of Hygrophoropsis aurantiaca and in Vitro Antiproliferative Activity of Isolated Ergosterol Peroxide.

PubMed

Nowak, Renata; Drozd, Marta; Mendyk, Ewaryst; Lemieszek, Marta; Krakowiak, Olga; Kisiel, Wanda; Rzeski, Wojciech; Szewczyk, Katarzyna

2016-07-21

In the present study, ergosterol peroxide and ergosterol were isolated for the first time from fresh fruit bodies of Hygrophoropsis aurantiaca (False Chanterelle). The substances were characterized mainly by spectroscopic methods (¹H-NMR, (13)C-NMR, DEPT-45, DEPT-90, DEPT-135, 2D-NMR). In our study, a new specific thin layer chromatographic method was developed for determination of ergosterol and ergosterol peroxide in H. aurantiaca extract. The method is based on the separation of n-hexane extract on silica gel (Silica Gel G) TLC plates using the optimized solvent system toluene/ethyl acetate (3:1; v/v). The main advantages of the developed method are the simplicity of operation and the low cost. The in vitro study results revealed the antiproliferative properties of ergosterol peroxide against LS180 human colon cancer cells. The described effect was attributed both to altered mitochondrial activity and decreased DNA synthesis. Additionally, in the same concentration range the investigated compound was not toxic to CCD 841 CoTr human colon epithelial cells. The present study suggests that fruit bodies of H. aurantiaca have great potential for producing substances and extracts with potential applications in medicine.

Cyclopropenimine superbases: Competitive initiation processes in lactide polymerization

DOE PAGES

Stukenbroeker, Tyler S.; Bandar, Jeffrey S.; Zhang, Xiangyi; ...

2015-07-30

Cyclopropenimine superbases were employed in this study to catalyze the ring-opening polymerization of lactide. Polymerization occurred readily in the presence and absence of alcohol initiators. Polymerizations in the absence of alcohol initiators revealed a competitive initiation mechanism involving deprotonation of lactide by the cyclopropenimine to generate an enolate. NMR and MALDI-TOF analysis of the poly(lactides) generated from cyclopropenimines in the absence of alcohol initiators showed acylated lactide and hydroxyl end groups. Finally, model studies and comparative experiments with guanidine and phosphazene catalysts revealed the subtle influence of the nature of the superbase on competitive initiation processes.

A Kinetic Study of DDGS Hemicellulose Acid Hydrolysis and NMR Characterization of DDGS Hydrolysate.

PubMed

Chen, Hanchi; Liu, Shijie

2015-09-01

Liquid hot water (LHW) extraction was used as a pretreatment method to separate the hemicellulose fraction from dried distiller's grain with solubles (DDGS) into liquid phase. Acid hydrolysis using 3.264 % w/w sulfuric acid at 130 °C was performed to convert polysaccharides in LHW extract to monosaccharides. The structure characterization of DDGS in anomeric carbon region based on proton NMR and heteronuclear single quantum coherence (HSQC) during acid hydrolysis was studied in this work. It reveals that the sugar units in DDGS hemicelluloses are constructed with (1-4)-β-D-xylopyranose and α-L-arabinofuranosyl residues. A kinetic model is included to explain the changing concentration of monomer, oligomer, and sugar units. The model was further tested based on the changing concentration of five carbon sugar units during hydrolysis.

Non-polymeric asymmetric binary glass-formers. II. Secondary relaxation studied by dielectric, 2H NMR, and 31P NMR spectroscopy

NASA Astrophysics Data System (ADS)

Pötzschner, B.; Mohamed, F.; Bächer, C.; Wagner, E.; Lichtinger, A.; Bock, D.; Kreger, K.; Schmidt, H.-W.; Rössler, E. A.

2017-04-01

We investigate the secondary (β-) relaxations of an asymmetric binary glass former consisting of a spirobichroman derivative (SBC; Tg = 356 K) as the high-Tg component and the low-Tg component tripropyl phosphate (TPP; Tg = 134 K). The main relaxations are studied in Paper I [B. Pötzschner et al., J. Chem. Phys. 146, 164503 (2017)]. A high Tg contrast of ΔTg = 222 K is put into effect in a non-polymeric system. Component-selective studies are carried out by combining results from dielectric spectroscopy (DS) for mass concentrations cTPP ≥ 60% and those from different methods of 2H and 31P NMR spectroscopy. In the case of NMR, the full concentration range (10% ≤ cTPP ≤ 100%) is covered. The neat components exhibit a β-relaxation (β1 (SBC) and β2 (TPP)). The latter is rediscovered by DS in the mixtures for all concentrations with unchanged time constants. NMR spectroscopy identifies the β-relaxations as being alike to those in neat glasses. A spatially highly restricted motion with angular displacement below ±10° encompassing all molecules is involved. In the low temperature range, where TPP shows the typical 31P NMR echo spectra of the β2-process, very similar spectral features are observed for the (deuterated) SBC component by 2H NMR, in addition to its "own" β1-process observed at high temperatures. Apparently, the small TPP molecules enslave the large SBC molecules to perform a common hindered reorientation. The temperature dependence of the spin-lattice relaxation time of both components is the same and reveals an angular displacement of the SBC molecules somewhat smaller than that of TPP, though the time constants τβ2 are the same. Furthermore, T1(T) of TPP in the temperature region of the β2-process is absolutely the same as in the mixture TPP/polystyrene investigated previously. It appears that the manifestations of the β-process introduced by one component are essentially independent of the second component. Finally, at cTPP ≤ 20% one finds indications that the β2-process starts to disintegrate. More and more TPP molecules get immobilized upon decreasing cTPP. We conclude that the β-process is a cooperative process.

Metabolic profiling of lung granuloma in Mycobacterium tuberculosis infected guinea pigs: ex vivo 1H magic angle spinning NMR studies.

PubMed

Somashekar, B S; Amin, Anita G; Rithner, Christopher D; Troudt, JoLynn; Basaraba, Randall; Izzo, Angelo; Crick, Dean C; Chatterjee, Delphi

2011-09-02

A crucial and distinctive feature of tuberculosis infection is that Mycobacterium tuberculosis (Mtb) resides in granulomatous lesion at various stages of disease development and necrosis, an aspect that is little understood. We used a novel approach, applying high resolution magic angle spinning nuclear magnetic resonance spectroscopy (HRMAS NMR) directly to infected tissues, allowing us to study the development of tuberculosis granulomas in guinea pigs in an untargeted manner. Significant up-regulation of lactate, alanine, acetate, glutamate, oxidized and the reduced form of glutathione, aspartate, creatine, phosphocholine, glycerophosphocholine, betaine, trimethylamine N-oxide, myo-inositol, scyllo-inositol, and dihydroxyacetone was clearly visualized and was identified as the infection progressed. Concomitantly, phosphatidylcholine was down-regulated. Principal component analysis of NMR data revealed clear group separation between infected and uninfected tissues. These metabolites are suggestive of utilization of alternate energy sources by the infiltrating cells that generate much of the metabolites in the increasingly necrotic and hypoxic developing granuloma through the glycolytic, pentose phosphate, and tricarboxylic acid pathways. The most relevant changes seen are, surprisingly, very similar to metabolic changes seen in cancer during tumor development.

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.

Single ferromagnetic fluctuations in UCoGe revealed by 73Ge- and 59Co-NMR studies

NASA Astrophysics Data System (ADS)

Manago, Masahiro; Ishida, Kenji; Aoki, Dai

2018-02-01

73Ge and 59Co nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR) measurements have been performed on a 73Ge-enriched single-crystalline sample of the ferromagnetic superconductor UCoGe in the paramagnetic state. The 73Ge NQR parameters deduced from NQR and NMR are close to those of another isostructural ferromagnetic superconductor URhGe. The Knight shifts of the Ge and Co sites are well scaled to each other when the magnetic field is parallel to the b or c axis. The hyperfine coupling constants of Ge are estimated to be close to those of Co. The large difference of spin susceptibilities between the a and b axes could lead to the different response of the superconductivity and ferromagnetism with the field parallel to these directions. The temperature dependence of the nuclear spin-lattice relaxation rates 1 /T1 at the two sites is similar to each other above 5 K. These results indicate that the itinerant U-5 f electrons are responsible for the ferromagnetism in this compound, consistent with previous studies. The similarities and differences in the three ferromagnetic superconductors are discussed.

Comparative study of single/combination use of Huang-Lian-Jie-Du decoction and berberine on their protection on sepsis induced acute liver injury by NMR metabolic profiling.

PubMed

Lv, Yan; Wang, Junsong; Xu, Dingqiao; Liao, Shanting; Li, Pei; Zhang, Qian; Yang, Minghua; Kong, Lingyi

2017-10-25

Sepsis is a serious clinical disease with a high mortality rate all around the world. Liver organ dysfunction is an important sign for the severity and outcome of sepsis in patients. In this study, 1 H NMR-based metabolomics approach and biochemical assays were applied to investigate the metabolic profiling for cecal ligation and puncture (CLP) induced acute liver injury, the therapeutical effect of single/combination use of Huang-Lian-Jie-Du decoction (HLJDD) and berberine, and the interaction of them. Metabolomics analysis revealed significant perturbations in livers of septic rats, which could be ameliorated by HLJDD, berberine and their combination treatment. Berberine could better rectified glycolysis and nucleic acid metabolism in the liver. HLJDD had exceptional better anti-inflammatory, antibacterial and antioxidative effects than berberine. The interaction of berberine and HLJDD could further strengthen the anti-inflammation and anti-oxidation, but with poor effect on amino acids metabolism. These findings highlighted the feasibility of the integrated NMR based metabolomics approach to understand the pathogenesis of diseases, the action mechanisms of therapy and the herb-drug interaction. Copyright © 2017 Elsevier B.V. All rights reserved.

Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

PubMed Central

Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John-Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoë

2015-01-01

Human carbonic anhydrase II (HCA II) uses a Zn-bound OH−/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic residues. One of these residues, Tyr7, was previously shown to be deprotonated in the neutron crystal structure at pH 10. This observation indicated that Tyr7 has a perturbed pKa compared with free tyrosine. To further probe the pKa of this residue, NMR spectroscopic measurements of [13C]Tyr-labeled holo HCA II (with active-site Zn present) were preformed to titrate all Tyr residues between pH 5.4–11.0. In addition, neutron studies of apo HCA II (with Zn removed from the active site) at pH 7.5 and holo HCA II at pH 6 were conducted. This detailed interrogation of tyrosines in HCA II by NMR and neutron crystallography revealed a significantly lowered pKa of Tyr7 and how pH and Tyr proximity to Zn affect hydrogen-bonding interactions. PMID:25902526

Changes in dissolved organic matter during the treatment processes of a drinking water plant in Sweden and formation of previously unknown disinfection byproducts.

PubMed

Gonsior, Michael; Schmitt-Kopplin, Philippe; Stavklint, Helena; Richardson, Susan D; Hertkorn, Norbert; Bastviken, David

2014-11-04

The changes in dissolved organic matter (DOM) throughout the treatment processes in a drinking water treatment plant in Sweden and the formation of disinfection byproducts (DBPs) were evaluated by using ultra-high-resolution mass spectrometry (resolution of ∼500,000 at m/z 400) and nuclear magnetic resonance (NMR). Mass spectrometric results revealed that flocculation induced substantial changes in the DOM and caused quantitative removal of DOM constituents that usually are associated with DBP formation. While half of the chromophoric DOM (CDOM) was removed by flocculation, ∼4-5 mg L(-1) total organic carbon remained in the finished water. A conservative approach revealed the formation of ∼800 mass spectrometry ions with unambiguous molecular formula assignments that contained at least one halogen atom. These molecules likely represented new DBPs, which could not be prevented by the flocculation process. The most abundant m/z peaks, associated with formed DBPs, could be assigned to C5HO3Cl3, C5HO3Cl2Br, and C5HO3ClBr2 using isotope simulation patterns. Other halogen-containing formulas suggested the presence of halogenated polyphenolic and aromatic acid-type structures, which was supported by possible structures that matched the lower molecular mass range (maximum of 10 carbon atoms) of these DBPs. 1H NMR before and after disinfection revealed an ∼2% change in the overall 1H NMR signals supporting a significant change in the DOM caused by disinfection. This study underlines the fact that a large and increasing number of people are exposed to a very diverse pool of organohalogens through water, by both drinking and uptake through the skin upon contact. Nontarget analytical approaches are indispensable for revealing the magnitude of this exposure and to test alternative ways to reduce it.

Real time neutron diffraction and NMR of the Empress II glass-ceramic system.

PubMed

O'Donnell, M D; Hill, R G; Karpukhina, N; Law, R V

2011-10-01

This study reports real time neutron diffraction on the Empress II glass-ceramic system. The commercial glass-ceramics was characterized by real time neutron diffraction, ³¹P and ²⁹Si solid-state MAS-NMR, DSC and XRD. On heating, the as-received glass ceramic contained lithium disilicate (Li₂Si₂O₅), which melted with increasing temperature. This was revealed by neutron diffraction which showed the Bragg peaks for this phase had disappeared by 958°C in agreement with thermal analysis. On cooling lithium metasilicate (Li₂SiO₃) started to form at around 916°C and a minor phase of cristobalite at around 852°C. The unit cell volume of both Li-silicate phases increased linearly with temperature at a rate of +17×10⁻³ ų.°C⁻¹. Room temperature powder X-ray diffraction (XRD) of the material after cooling confirms presence of the lithium metasilicate and cristobalite as the main phases and shows, in addition, small amount of lithium disilicate and orthophosphate. ³¹P MAS-NMR reveals presence of the lithiorthophosphate (Li₃PO₄) before and after heat treatment. The melting of lithium disilicate on heating and crystallisation of lithium metasilicate on cooling agree with endothermic and exotermic features respectively observed by DSC. ²⁹Si MAS-NMR shows presence of lithium disilicate phase in the as-received glass-ceramic, though not in the major proportion, and lithium metasilicate in the material after heat treatment. Both phases have significantly long T₁ relaxation time, especially the lithium metasilicate, therefore, a quantitative analysis of the ²⁹Si MAS-NMR spectra was not attempted. Significance. The findings of the present work demonstrate importance of the commercially designed processing parameters in order to preserve desired characteristics of the material. Processing the Empress II at a rate slower than recommended 60°C min⁻¹ or long isothermal hold at the maximal processing temperature 920°C can cause crystallization of lithium metasilicate and cristobalite instead of lithium disilicate as major phase. Copyright © 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

PubMed

Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

2017-12-06

Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 < MoF 3 < MoF 6 before sharply decreasing for MoF 9 , with a similar effect for the supported systems (MoF 0 ≈ MoF 9 < MoF 6 < MoF 3 ). This is consistent with the different kinetic behavior (zeroth order in alkyne for MoF 9 derivatives instead of first order for the others) and the isolation of stable metallacyclobutadiene intermediates of MoF 9 for both molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

(1)H NMR and GC-MS Based Metabolomics Reveal Defense and Detoxification Mechanism of Cucumber Plant under Nano-Cu Stress.

PubMed

Zhao, Lijuan; Huang, Yuxiong; Hu, Jerry; Zhou, Hongjun; Adeleye, Adeyemi S; Keller, Arturo A

2016-02-16

Because copper nanoparticles are being increasingly used in agriculture as pesticides, it is important to assess their potential implications for agriculture. Concerns have been raised about the bioaccumulation of nano-Cu and their toxicity to crop plants. Here, the response of cucumber plants in hydroponic culture at early development stages to two concentrations of nano-Cu (10 and 20 mg/L) was evaluated by proton nuclear magnetic resonance spectroscopy ((1)H NMR) and gas chromatography-mass spectrometry (GC-MS) based metabolomics. Changes in mineral nutrient metabolism induced by nano-Cu were determined by inductively coupled plasma-mass spectrometry (ICP-MS). Results showed that nano-Cu at both concentrations interferes with the uptake of a number of micro- and macro-nutrients, such as Na, P, S, Mo, Zn, and Fe. Metabolomics data revealed that nano-Cu at both levels triggered significant metabolic changes in cucumber leaves and root exudates. The root exudate metabolic changes revealed an active defense mechanism against nano-Cu stress: up-regulation of amino acids to sequester/exclude Cu/nano-Cu; down-regulation of citric acid to reduce the mobilization of Cu ions; ascorbic acid up-regulation to combat reactive oxygen species; and up-regulation of phenolic compounds to improve antioxidant system. Thus, we demonstrate that nontargeted (1)H NMR and GC-MS based metabolomics can successfully identify physiological responses induced by nanoparticles. Root exudates metabolomics revealed important detoxification mechanisms.

Application of metabonomics on an experimental model of fibrosis and cirrhosis induced by thioacetamide in rats

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

Constantinou, Maria A.; Department of Forensic Medicine and Toxicology, Medical School, University of Athens, 75, Mikras Asias str., 11527 Athens; Theocharis, Stamatios E.

2007-01-01

Metabonomics has already been used to discriminate different pathological states in biological fields. The metabolic profiles of chronic experimental fibrosis and cirrhosis induction in rats were investigated using {sup 1}H NMR spectroscopy of liver extracts and serum combined with pattern recognition techniques. Rats were continuously administered with thioacetamide (TAA) in the drinking water (300 mg TAA/L), and sacrificed on 1st, 2nd, and 3rd month of treatment. {sup 1}H NMR spectra of aqueous and lipid liver extracts, together with serum were subjected to Principal Component Analysis (PCA). Liver portions were also subjected to histopathological examination and biochemical determination of malondialdehyde (MDA).more » Liver fibrosis and cirrhosis were progressively induced in TAA-treated rats, verified by the histopathological examination and the alterations of MDA levels. TAA administration revealed a number of changes in the {sup 1}H NMR spectra compared to control samples. The performance of PCA in liver extracts and serum, discriminated the control samples from the fibrotic and cirrhotic ones. Metabolic alterations revealed in NMR spectra during experimental liver fibrosis and cirrhosis induction, characterize the stage of fibrosis and could be illustrated by subsequent PCA of the spectra. Additionally, the PCA plots of the serum samples presented marked clustering during fibrosis progression and could be extended in clinical diagnosis for the management of cirrhotic patients.« less

1H NMR based pharmacometabolomics analysis of urine identifies metabolic phenotype of clopidogrel high on treatment platelets reactivity in coronary artery disease patients.

PubMed

Amin, Arwa M; Sheau Chin, Lim; Teh, Chin-Hoe; Mostafa, Hamza; Mohamed Noor, Dzul Azri; Sk Abdul Kader, Muhamad Ali; Kah Hay, Yuen; Ibrahim, Baharudin

2017-11-30

Clopidogrel high on treatment platelets reactivity (HTPR) has burdened achieving optimum therapeutic outcome. Although there are known genetic and non-genetic factors associated with clopidogrel HTPR, which explain in part clopidogrel HTPR, yet, great portion remains unknown, often hindering personalizing antiplatelet therapy. Nuclear magnetic resonance ( 1 H NMR) pharmacometabolomics analysis is useful technique to phenotype drug response. We investigated using 1 H NMR analysis to phenotype clopidogrel HTPR in urine. Urine samples were collected from 71 coronary artery disease (CAD) patients who were planned for interventional angiographic procedure prior to taking 600mg clopidogrel loading dose (LD) and 6h post LD. Patients' platelets function testing was assessed with the VerifyNow ® P2Y12 assay at 6h after LD. Urine samples were analysed using 1 H NMR. Multivariate statistical analysis was used to identify metabolites associated with clopidogrel HTPR. In pre-dose samples, 16 metabolites were associated with clopidogrel HTPR. However, 18 metabolites were associated with clopidogrel HTPR in post-dose samples. The pathway analysis of the identified biomarkers reflected that multifactorial conditions are associated with clopidogrel HTPR. It also revealed the implicated role of gut microbiota in clopidogrel HTPR. Pharmacometabolomics not only discovered novel biomarkers of clopidogrel HTPR but also revealed implicated pathways and conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

One-dimensional scanning of moisture in heated porous building materials with NMR.

PubMed

van der Heijden, G H A; Huinink, H P; Pel, L; Kopinga, K

2011-02-01

In this paper we present a new dedicated NMR setup which is capable of measuring one-dimensional moisture profiles in heated porous materials. The setup, which is placed in the bore of a 1.5 T whole-body scanner, is capable of reaching temperatures up to 500 °C. Moisture and temperature profiles can be measured quasi simultaneously with a typical time resolution of 2-5 min. A methodology is introduced for correcting temperature effects on NMR measurements at these elevated temperatures. The corrections are based on the Curie law for paramagnetism and the observed temperature dependence of the relaxation mechanisms occurring in porous materials. Both these corrections are used to obtain a moisture content profile from the raw NMR signal profile. To illustrate the methodology, a one-sided heating experiment of concrete with a moisture content in equilibrium with 97% RH is presented. This kind of heating experiment is of particular interest in the research on fire spalling of concrete, since it directly reveals the moisture and heat transport occurring inside the concrete. The obtained moisture profiles reveal a moisture peak building up behind the boiling front, resulting in a saturated layer. To our knowledge the direct proof of the formation of a moisture peak and subsequent moisture clogging has not been reported before. Copyright © 2010 Elsevier Inc. All rights reserved.

Eu(III) Complex with DO3A-amino-phosphonate Ligand as a Concentration-Independent pH-Responsive Contrast Agent for Magnetic Resonance Spectroscopy (MRS).

PubMed

Krchová, Tereza; Herynek, Vít; Gálisová, Andrea; Blahut, Jan; Hermann, Petr; Kotek, Jan

2017-02-20

A new DOTA-like ligand H 5 do3aNP with a 2-[amino(methylphosphonic acid)]ethyl-coordinating pendant arm was prepared, and its coordinating properties were studied by NMR spectroscopy and potentiometry. The study revealed a rare slow exchange (on the 1 H and 31 P NMR time scale) between protonated and unprotonated complex species with a corresponding acidity constant pK A ∼ 8.0. This unusually slow time scale associated with protonation is caused by a significant geometric change from square-antiprismatic (SA) arrangement observed for protonated complex SA-[Eu(Hdo3aNP)] - to twisted-square-antiprismatic (TSA) arrangement found for deprotonated complex TSA-[Eu(do3aNP)] 2- . This behavior results in simultaneous occurrence of the signals of both species in the 31 P NMR spectra at approximately -118 and +70 ppm, respectively. Such an unprecedented difference in the chemical shifts between species differing by a proton is caused by a significant movement of the principal magnetic axis and by a change of phosphorus atom position in the coordination sphere of the central Eu(III) ion (i.e., by relative movement of the phosphorus atom with respect to the principal magnetic axis). It changes the sign of the paramagnetic contribution to the 31 P NMR chemical shift. The properties discovered can be employed in the measurement of pH by MRS techniques as presented by proof-of-principle experiments on phantoms.

Serum profiling of healthy aging identifies phospho- and sphingolipid species as markers of human longevity.

PubMed

Montoliu, Ivan; Scherer, Max; Beguelin, Fiona; DaSilva, Laeticia; Mari, Daniela; Salvioli, Stefano; Martin, Francois-Pierre J; Capri, Miriam; Bucci, Laura; Ostan, Rita; Garagnani, Paolo; Monti, Daniela; Biagi, Elena; Brigidi, Patrizia; Kussmann, Martin; Rezzi, Serge; Franceschi, Claudio; Collino, Sebastiano

2014-01-01

As centenarians well represent the model of healthy aging, there are many important implications in revealing the underlying molecular mechanisms behind such successful aging. By combining NMR metabonomics and shot-gun lipidomics in serum we analyzed metabolome and lipidome composition of a group of centenarians with respect to elderly individuals. Specifically, NMR metabonomics profiling of serum revealed that centenarians are characterized by a metabolic phenotype distinct from that of elderly subjects, in particular regarding amino acids and lipid species. Shot- gun lipidomics approach displays unique changes in lipids biosynthesis in centenarians, with 41 differently abundant lipid species with respect to elderly subjects. These findings reveal phospho/sphingolipids as putative markers and biological modulators of healthy aging, in humans. Considering the particular actions of these metabolites, these data are suggestive of a better counteractive antioxidant capacity and a well-developed membrane lipid remodelling process in the healthy aging phenotype.

Chirp echo Fourier transform EPR-detected NMR.

PubMed

Wili, Nino; Jeschke, Gunnar

2018-04-01

A new ultra-wide band (UWB) pulse EPR method is introduced for observing all nuclear frequencies of a paramagnetic center in a single shot. It is based on burning spectral holes with a high turning angle (HTA) pulse that excites forbidden transitions and subsequent detection of the hole pattern by a chirp echo. We term this method Chirp Echo Epr SpectroscopY (CHEESY)-detected NMR. The approach is a revival of FT EPR-detected NMR. It yields similar spectra and the same type of information as electron-electron double resonance (ELDOR)-detected NMR, but with a multiplex advantage. We apply CHEESY-detected NMR in Q band to nitroxides and correlate the hyperfine spectrum to the EPR spectrum by varying the frequency of the HTA pulse. Furthermore, a selective π pulse before the HTA pulse allows for detecting hyperfine sublevel correlations between transitions of one nucleus and for elucidating the coupling regime, the same information as revealed by the HYSCORE experiment. This is demonstrated on hexaaquamanganese(II). We expect that CHEESY-detected NMR is generally applicable to disordered systems and that our results further motivate the development of EPR spectrometers capable of coherent UWB excitation and detection, especially at higher fields and frequencies. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation

NASA Astrophysics Data System (ADS)

Ruan, Qing-Xia; Zhou, Ping

2008-07-01

In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to β-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil → helix-like → β-sheet-like → β-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of β-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.

Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and 19F-NMR

PubMed Central

Yang, Fan; Yu, Xiao; Liu, Chuan; Qu, Chang-Xiu; Gong, Zheng; Liu, Hong-Da; Li, Fa-Hui; Wang, Hong-Mei; He, Dong-Fang; Yi, Fan; Song, Chen; Tian, Chang-Lin; Xiao, Kun-Hong; Wang, Jiang-Yun; Sun, Jin-Peng

2015-01-01

Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance (19F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 ‘reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by 19F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors. PMID:26347956

Application of metabonomics in a compound ranking study in early drug development revealing drug-induced excretion of choline into urine.

PubMed

Dieterle, Frank; Schlotterbeck, Götz; Ross, Alfred; Niederhauser, Urs; Senn, Hans

2006-09-01

Selecting drug candidates based on toxicity is an important step in early drug development. In this case study, it is shown how metabonomics is applied to a ranking study, in which drug candidates with equal pharmacological activities are selected based on least toxic side effects. The metabonomic analyses were carried out on an animal study that followed an established protocol for pilot toxicology/ranking studies in rats, however, not specifically modified for a metabonomic assessment. It is shown how conditions not specificially adopted for metabonomics investigations can significantly influence the metabolic profiles recorded by NMR. Furthermore, it is shown how the multivariate analysis of the NMR spectra identified an extreme excretion of an endogenous metabolite into urine induced by two out of the five drug candidates. The subsequent structure elucidation by two-dimensional NMR experiments and a subsequent validation by spiking experiments identified the metabolite as choline. The discussion of the mechanistic background for the excretion of choline, which is usually well-conserved in the body, results in two hypotheses of either a massive degradation of cell membranes or an inhibition of the choline oxidation. Although the validation of these hypotheses needs a follow-up study, the finding of a increased excretion of the important metabolite choline warrants exclusion of these two compounds as viable drug candidates from a metabonomics point of view.

Filter paper saturated by urine sample in metabolic disorders detection by proton magnetic resonance spectroscopy.

PubMed

Blasco, Hélène; Garrigue, Marie-Ange; De Vos, Aymeric; Antar, Catherine; Labarthe, François; Maillot, François; Andres, Christian R; Nadal-Desbarats, Lydie

2010-02-01

NMR spectroscopy of urine samples is able to diagnose many inborn errors of metabolism (IEM). However, urinary metabolites have a poor stability, requiring special care for routine analysis (storage of urine at -20 or -80 degrees C, fast transport). The aim of our study was to investigate the reliability of dried urine filter paper for urine storage and transport and to evaluate the ability of NMR to detect several IEM using this method. Urine samples from five healthy subjects were analyzed by (1)H NMR following different storage conditions (-20 vs 4 degrees C vs dried on filter paper) and at different time points (24 h, 48 h, 96 h, and 7 days). Urine pattern of fresh urine was considered as a reference. We analyzed the conservation of some amino acids and organic acids using Bland and Altman plot with intraclass correlation coefficient determination. Then, we evaluated the use of filter paper to detect four different IEM (methylmalonic and isovaleric acidurias, ornithine transcarbamylase deficiency, and cystinuria). Analysis of urine samples from healthy subjects revealed a high stability of studied molecules (ICC > 0.8) even after 7 days of storage on filter paper. Moreover, an excellent preservation of metabolites specifically accumulated in IEM was observed when analysis of dried urine filter paper was compared to fresh urine (coefficient of variation < 15%). This preliminary study demonstrates that storage of dried urine on filter paper is reliable for (1)H NMR spectroscopy analysis. Preservation of urine molecules over time using that method is convenient for routine clinical practice.

J-GFT NMR for precise measurement of mutually correlated nuclear spin-spin couplings.

PubMed

Atreya, Hanudatta S; Garcia, Erwin; Shen, Yang; Szyperski, Thomas

2007-01-24

G-matrix Fourier transform (GFT) NMR spectroscopy is presented for accurate and precise measurement of chemical shifts and nuclear spin-spin couplings correlated according to spin system. The new approach, named "J-GFT NMR", is based on a largely extended GFT NMR formalism and promises to have a broad impact on projection NMR spectroscopy. Specifically, constant-time J-GFT (6,2)D (HA-CA-CO)-N-HN was implemented for simultaneous measurement of five mutually correlated NMR parameters, that is, 15N backbone chemical shifts and the four one-bond spin-spin couplings 13Calpha-1Halpha, 13Calpha-13C', 15N-13C', and 15N-1HNu. The experiment was applied for measuring residual dipolar couplings (RDCs) in an 8 kDa protein Z-domain aligned with Pf1 phages. Comparison with RDC values extracted from conventional NMR experiments reveals that RDCs are measured with high precision and accuracy, which is attributable to the facts that (i) the use of constant time evolution ensures that signals do not broaden whenever multiple RDCs are jointly measured in a single dimension and (ii) RDCs are multiply encoded in the multiplets arising from the joint sampling. This corresponds to measuring the couplings multiple times in a statistically independent manner. A key feature of J-GFT NMR, i.e., the correlation of couplings according to spin systems without reference to sequential resonance assignments, promises to be particularly valuable for rapid identification of backbone conformation and classification of protein fold families on the basis of statistical analysis of dipolar couplings.

Pyrrole and Fused Pyrrole Compounds with Bioactivity against Inflammatory Mediators.

PubMed

Said Fatahala, Samar; Hasabelnaby, Sherifa; Goudah, Ayman; Mahmoud, Ghada I; Helmy Abd-El Hameed, Rania

2017-03-17

A new series of pyrrolopyridines and pyrrolopyridopyrimidines have been synthesized from aminocyanopyrroles. The synthesized compounds have been characterized by FTIR, ¹H-NMR and mass spectroscopy. The final compounds have been screened for in vitro pro-inflammatory cytokine inhibitory and in vivo anti-inflammatory activity. The biological results revealed that among all tested compounds some fused pyrroles, namely the pyrrolopyridines 3i and 3l , show promising activity. A docking study of the active synthesized molecules confirmed the biological results and revealed a new binding pose in the COX-2 binding site.

Synthesis, biological activity and molecular modeling study of new Schiff bases incorporated with indole moiety.

PubMed

Halawa, Ahmed H; El-Gilil, Shimaa Mohamed Abd; Bedair, Ahmed H; Shaaban, Mohamed; Frese, Marcel; Sewald, Norbert; Eliwa, Essam M; El-Agrody, Ahmed M

2017-10-26

A new series of heterocyclic Schiff bases 2-9 containing indole moiety were synthesized by facile and efficient condensation of indole-3/2/5-carboxaldehyde (1a/1b/1c) with different aromatic and heterocyclic primary amines using conventional and/or microwave irradiation methods. The structures of the obtained compounds were assigned by sophisticated spectroscopic and spectrometric techniques (1D-NMR, 2D-NMR and MS). The synthesized compounds were screened for their cytotoxicity and antibacterial activities. In vitro cytotoxicity screening revealed that compound 5 exhibited moderate activity against KB-3-1 cell line (IC50=57.7 μM) while 5-indolylimino derivative 7 indicated close to the activity (IC50=19.6 μM) in comparison with the positive control (+)-Griseofulvin (IC50=19.2 μM), while the tested compounds 5, 6b, 7 and 9 revealed good or moderate antibacterial activity. In addition, molecular docking study of Schiff bases 2-9 was performed by Molecular Operating Environment (MOE 2014.09) program on the matrix metalloproteinase-8 (MMP-8) (Protein Data Bank (PDB) ID: 1MNC) in an attempt to explore their mode of action as anticancer drugs.

Comparison of 13C Nuclear Magnetic Resonance and Fourier Transform Infrared spectroscopy for estimating humification and aromatization of soil organic matter

NASA Astrophysics Data System (ADS)

Rogers, K.; Cooper, W. T.; Hodgkins, S. B.; Verbeke, B. A.; Chanton, J.

2017-12-01

Solid state direct polarization 13C NMR spectroscopy (DP-NMR) is generally considered the most quantitatively reliable method for soil organic matter (SOM) characterization, including determination of the relative abundances of carbon functional groups. These functional abundances can then be used to calculate important soil parameters such as degree of humification and extent of aromaticity that reveal differences in reactivity or compositional changes along gradients (e.g. thaw chronosequence in permafrost). Unfortunately, the 13C NMR DP-NMR experiment is time-consuming, with a single sample often requiring over 24 hours of instrument time. Alternatively, solid state cross polarization 13C NMR (CP-NMR) can circumvent this problem, reducing analyses times to 4-6 hours but with some loss of quantitative reliability. Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) is a quick and relatively inexpensive method for characterizing solid materials, and has been suggested as an alternative to NMR for analysis of soil organic matter and determination of humification (HI) and aromatization (AI) indices. However, the quantitative reliability of ATR-FTIR for SOM analyses has never been verified, nor have any ATR-FTIR data been compared to similar measurements by NMR. In this work we focused on FTIR vibrational bands that correspond to the three functional groups used to calculate HI and AI values: carbohydrates (1030 cm-1), aromatics (1510, 1630 cm-1), and aliphatics (2850, 2920 cm-1). Data from ATR-FTIR measurements were compared to analogous quantitation by DP- and CP-NMR using peat samples from Sweden, Minnesota, and North Carolina. DP- and CP-NMR correlate very strongly, although the correlations are not always 1:1. Direct comparison of relative abundances of the three functional groups determined by NMR and ATR-FTIR yielded satisfactory results for carbohydrates (r2= 0.78) and aliphatics (r2=0.58), but less so for aromatics (r2= 0.395). ATR-FTIR has to this point been used primarily for relative abundance analyses (e.g. calculating HI and AI values), but these results suggest FTIR can provide quantitative reliability that approaches that of NMR.

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

PubMed

Pawlak, Tomasz; Potrzebowski, Marek J

2014-03-27

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.

PubMed

Zook, James; Mo, Gina; Sisco, Nicholas J; Craciunescu, Felicia M; Hansen, Debra T; Baravati, Bobby; Cherry, Brian R; Sykes, Kathryn; Wachter, Rebekka; Van Horn, Wade D; Fromme, Petra

2015-06-02

Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer membrane lipoprotein, Flpp3, has been identified as a virulence determinant as well as a potential subunit template for vaccine development. Here we present the first structure for the soluble domain of Flpp3 from the highly infectious Type A SCHU S4 strain, derived through high-resolution solution nuclear magnetic resonance (NMR) spectroscopy; the first structure of a lipoprotein from the genus Francisella. The Flpp3 structure demonstrates a globular protein with an electrostatically polarized surface containing an internal cavity-a putative binding site based on the structurally homologous Bet v1 protein family of allergens. NMR-based relaxation studies suggest loop regions that potentially modulate access to the internal cavity. The Flpp3 structure may add to the understanding of F. tularensis virulence and contribute to the development of effective vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

13C CPMAS NMR studies and DFT calculations of triterpene xylosides isolated from Actaea racemosa

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Paradowska, Katarzyna; Gliński, Jan A.; Wawer, Iwona

2011-05-01

13C CPMAS NMR spectra of four triterpene glycosides: cimigenol xyloside ( 1), 26-deoxyactein ( 2), cimicifugoside H-1 ( 3) and 24-acethylhydroshengmanol xyloside ( 4) were recorded and analyzed to characterize their solid-state structure. Experimental data were supported by theoretical calculations of NMR shielding constants with the GIAO/6-31G**-su1 approach. A number of methods for the conformational search and a number of functionals for the DFT calculations were applied to ( 1). The best method was proven to be MMFF or MMFFAQ for the conformational search and the PBE1PBE functional for the DFT calculations. Extra calculations simulating C16 dbnd O⋯HOH hydrogen bond yield the isotropic shielding closer to the experimental solid-state value. For all the compounds CP kinetics parameters were calculated using either the I-S or the I-I*-S model. The analysis of CP kinetics data for methyl groups revealed differences in the T2 time constant for two methyl groups (C29 and C30) linked at C4.

Paramagnetic-to-nonmagnetic transition in antiperovskite nitride Cr3GeN studied by 14N-NMR and µSR

NASA Astrophysics Data System (ADS)

Takao, K.; Liu, Z.; Uji, K.; Waki, T.; Tabata, Y.; Watanabe, I.; Nakamura, H.

2017-06-01

The antiperovskite-related nitride Cr3GeN forms a tetragonal structure with the space group P\\bar{4}{2}1m at room temperature. It shows a tetragonal (P\\bar{4}{2}1m) to tetragonal (I4/mcm) structural transition with a large hysteresis at 300-400 K. The magnetic susceptibility of Cr3GeN shows Curie-Weiss type temperature dependence at high temperature, but is almost temperature-independent below room temperature. We carried out µSR and 14N-NMR microscopy measurements to reveal the magnetic ground state of Cr3GeN. Gradual muon spin relaxation, which is nearly temperature-independent below room temperature, was observed, indicating that Cr3GeN is magnetically inactive. In the 14N-NMR measurement, a quadrupole-split spectrum was obtained at around 14 K = 0. The temperature dependence of 14(1/T1) satisfies the Korringa relation. These experimental results indicate that the ground state of Cr3GeN is Pauli paramagnetic, without antiferromagnetic long-range order.

4-hydroxyphenylacetic acid derivatives of inositol from dandelion (Taraxacum officinale) root characterised using LC-SPE-NMR and LC-MS techniques.

PubMed

Kenny, O; Smyth, T J; Hewage, C M; Brunton, N P; McLoughlin, P

2014-02-01

The combination of hyphenated techniques, LC-SPE-NMR and LC-MS, to isolate and identify minor isomeric compounds from an ethyl acetate fraction of Taraxacum officinale root was employed in this study. Two distinct fractions of 4-hydroxyphenylacetic acid derivatives of inositol were isolated and characterised by spectroscopic methods. The (1)H NMR spectra and MS data revealed two groups of compounds, one of which were derivatives of the di-4-hydroxyphenylacetic acid derivative of the inositol compound tetrahydroxy-5-[2-(4-hydroxyphenyl)acetyl] oxycyclohexyl-2-(4-hydroxyphenyl) acetate, while the other group consisted of similar tri-substituted inositol derivatives. For both fractions the derivatives of inositols vary in the number of 4-hydroxyphenylacetic acid groups present and their position and geometry on the inositol ring. In total, three di-substituted and three tri-substituted 4-hydroxyphenylacetic acid inositol derivates were identified for the first time along with a further two previously reported di-substituted inositol derivatives. Copyright © 2013 Elsevier Ltd. All rights reserved.

A NMR study of parasitized Tenebrio molitor and Hymenolepis diminuta cysticercoids.

PubMed

Schoen, J; Modha, A; Maslow, K; Novak, M; Blackburn, B J

1996-07-01

In vivo NMR spectra of uninfected and Hymenolepis diminuta-infected Tenebrio molitor fed D-(1-13C)glucose showed that infected beetles of both sexes had a significantly higher ratio for (glycogen C1/lipid (CH2)n) than the corresponding controls. Quantitative metabolic profiles and the per cent 13C-label in metabolites, based on NMR of perchloric acid extracts, are presented for control and infected beetles fed D-(1-13C)glucose and for H. diminuta cysticercoids. Female beetles, both control and infected, contained more glycogen than their male counterparts and infected beetles of both sexes possessed less glycerophos-phocholine, but more glycogen and a higher percentage label in glucose and trehalose than their respective controls. Label was also incorporated into glycogen, succinate, acetate, alanine and lactate. Extracts of cysticercoids from beetles fed D-(1-13C)glucose contained the following labelled compounds, in order of decreasing per cent 13C label: glucose, trehalose, alanine, succinate, lactate, glycogen and acetate. In vitro cultivation experiments, employing D-(1-13C)glucose, revealed that trehalose found in cysticercoids was of parasite, and not beetle, origin.

CO 2 Dynamics in Pure and Mixed-Metal MOFs with Open Metal Sites

DOE PAGES

Marti, Robert M.; Howe, Joshua D.; Morelock, Cody R.; ...

2017-09-22

Metal–organic frameworks (MOFs), such as MOF-74, can have open metal sites to which adsorbates such as CO 2 preferentially bind. 13C NMR of 13CO 2 is highly informative about the binding sites present in Mg-MOF-74. We used this technique to investigate loadings between ~0.88 and 1.15 molecules of CO 2 per metal in Mg-MOF-74 at 295 K. 13C lineshapes recorded as a function of loading can be understood in terms of the dependence of the CO 2 NMR frequency on the angle (θ) with respect to the CO 2 axis and the channel of the MOF, reflected in the Legendremore » polynomial, P 2. In the fast motion limit, the NMR spectra reveal the time-averaged value of P 2, where θ is the angle between the instantaneous CO 2 axis and the channel axis. DFT calculations were used to determine a weighted average of P 2 in this regime and are in good agreement with experimental data. Static variable temperature 13C NMR from cryogenic temperatures to room temperature was used to investigate 13CO 2 binding in Mg-MOF-74 loaded at two levels (~0.88 and 1.08 molecules of CO 2 per metal), revealing temperature-dependent lineshapes. We have investigated the effect of partial substitution of Cd for Mg in Mg-MOF-74 on the 13CO 2 variable temperature NMR spectra. The chemical shift anisotropy (CSA) that leads to characteristic lineshapes of 13C indicates that incorporation of Cd leads to weaker binding energies for adsorbed CO 2.« less

Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation

PubMed Central

Toraya, Shuichi; Javkhlantugs, Namsrai; Mishima, Daisuke; Nishimura, Katsuyuki; Ueda, Kazuyoshi; Naito, Akira

2010-01-01

Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state 31P and 13C NMR spectroscopy. 31P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (Tc) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the Tc. 13C NMR spectra of site-specifically 13C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers. PMID:21081076

CO 2 Dynamics in Pure and Mixed-Metal MOFs with Open Metal Sites

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

Marti, Robert M.; Howe, Joshua D.; Morelock, Cody R.

Metal–organic frameworks (MOFs), such as MOF-74, can have open metal sites to which adsorbates such as CO 2 preferentially bind. 13C NMR of 13CO 2 is highly informative about the binding sites present in Mg-MOF-74. We used this technique to investigate loadings between ~0.88 and 1.15 molecules of CO 2 per metal in Mg-MOF-74 at 295 K. 13C lineshapes recorded as a function of loading can be understood in terms of the dependence of the CO 2 NMR frequency on the angle (θ) with respect to the CO 2 axis and the channel of the MOF, reflected in the Legendremore » polynomial, P 2. In the fast motion limit, the NMR spectra reveal the time-averaged value of P 2, where θ is the angle between the instantaneous CO 2 axis and the channel axis. DFT calculations were used to determine a weighted average of P 2 in this regime and are in good agreement with experimental data. Static variable temperature 13C NMR from cryogenic temperatures to room temperature was used to investigate 13CO 2 binding in Mg-MOF-74 loaded at two levels (~0.88 and 1.08 molecules of CO 2 per metal), revealing temperature-dependent lineshapes. We have investigated the effect of partial substitution of Cd for Mg in Mg-MOF-74 on the 13CO 2 variable temperature NMR spectra. The chemical shift anisotropy (CSA) that leads to characteristic lineshapes of 13C indicates that incorporation of Cd leads to weaker binding energies for adsorbed CO 2.« less

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution

PubMed Central

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J.; Golovanov, Alexander P.

2016-01-01

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (SosCat) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of SosCat, while SosCat also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos. PMID:27412770

A simple and highly selective 2,2-diferrocenylpropane-based multi-channel ion pair receptor for Pb(2+) and HSO4(-).

PubMed

Wan, Qian; Zhuo, Ji-Bin; Wang, Xiao-Xue; Lin, Cai-Xia; Yuan, Yao-Feng

2015-03-28

A structurally simple, 2,2-diferrocenylpropane-based ion pair receptor 1 was synthesized and characterized by (1)H NMR, (13)C NMR, HRMS, elemental analyses, and single-crystal X-ray diffraction. The ion pair receptor 1 showed excellent selectivity and sensitivity towards Pb(2+) with multi-channel responses: a fluorescence enhancement (more than 42-fold), a notable color change from yellow to red, redox anodic shift (ΔE1/2 = 151 mV), while HSO4(-) promoted fluorescence enhancement when Pb(2+) or Zn(2+) was bonded to the cation binding-site. (1)H NMR titration and density functional theory were performed to reveal the sensing mechanism based on photo-induced electron transfer (PET).

Water speciation in sodium silicate glasses (quenched melts): A comprehensive NMR study

NASA Astrophysics Data System (ADS)

Xue, X.; Kanzaki, M.; Eguchi, J.

2012-12-01

Dissolution mechanism of water is an important factor governing how the dissolved water affects the physical and thermodynamic properties of silicate melts and glasses. Our previous studies have demonstrated that 1H MAS NMR in combination with 29Si-1H and 27Al-1H double-resonance NMR experiments is an effective approach for unambiguously differentiating and quantifying different water species in quenched silicate melts (glasses). Several contrasting dissolution mechanisms have been revealed depending on the melt composition: for relatively polymerized melts, the formation of SiOH/AlOH species (plus molecular H2O) and depolymerization of the network structure dominate; whereas for depolymerized Ca-Mg silicate melts, free OH (e.g. MgOH) become increasingly important (cf. [1]). The proportion of free OH species has been shown to decrease with both increasing melt polymerization (silica content) and decreasing field strength of the network modifying cations (from Mg to Ca). Our previous 1H and 29Si MAS NMR results for hydrous Na silicate glasses of limited compositions (Na2Si4O9 and Na2Si2O5) were consistent with negligible free OH (NaOH) species and depolymerizing effect of water dissolution [2]. On the other hand, there were also other studies that proposed the presence of significant NaOH species in hydrous glasses near the Na2Si2O5 composition. The purpose of this study is apply the approach of combined 1H MAS NMR and double-resonance (29Si-1H and 23Na-1H) NMR to gain unambiguous evidence for the OH speciation in Na silicate glasses (melts) as a function of composition. Hydrous Na silicate glasses containing mostly ≤ 1 wt% H2O for a range of Na/Si ratios from 0.33 to 1.33 have been synthesized by rapidly quenching melts either at 0.2 GPa using an internally heated gas pressure vessel or at 1 GPa using a piston cylinder high-pressure apparatus. NMR spectra have been acquired using a 9.4 T Varian Unity-Inova spectrometer. The 29Si and 1H chemical shifts are reported relative to TMS. The 1H MAS NMR spectra show broad peaks covering a chemical shift range of 1 to 17 ppm, with peak maxima near 4 and 15 ppm for more Si-rich compositions and near 12 ppm for less Si-rich compositions. The 1H-29Si-1H and 23Na-1H cross-polarization (CP) MAS NMR spectra for all the hydrous Na silicate glasses suggest negligible NaOH species, which, if present, should show enhanced relative intensity with 23Na-1H CP and the opposite with 1H-29Si-1H CP. All the observed 1H NMR intensities can be attributed to SiOH species of a range of hydrogen-bonding distances, plus a small amount of molecular H2O for higher water-content samples that contribute to intensities around 6 ppm. In conclusion, our combined 1H MAS NMR and double-resonance (1H-29Si-1H and 23Na-1H CP) MAS NMR study on Na silicate glasses of a range of Na/Si ratios has confirmed that water dissolves predominantly as SiOH and molecular H2O species in Na silicate melts (glasses), consistent with the trend predicted from studies on the Ca-Mg silicate system [1,2]. References:[1] Xue, X. Y.; Kanzaki, M. J. Am. Ceram. Soc. 2009, 92, 2803-2830. [2] Xue, X. Y.; Kanzaki, M. Geochim. Cosmochim. Acta 2004, 68, 5027-5057.

Comparison of diffusivity data derived from electrochemical and NMR investigations of the SeCN¯/(SeCN)2/(SeCN)3¯ system in ionic liquids.

PubMed

Solangi, Amber; Bond, Alan M; Burgar, Iko; Hollenkamp, Anthony F; Horne, Michael D; Rüther, Thomas; Zhao, Chuan

2011-06-02

Electrochemical studies in room temperature ionic liquids are often hampered by their relatively high viscosity. However, in some circumstances, fast exchange between participating electroactive species has provided beneficial enhancement of charge transport. The iodide (I¯)/iodine (I(2))/triiodide (I(3)¯) redox system that introduces exchange via the I¯ + I(2) ⇌ I(3)¯ process is a well documented example because it is used as a redox mediator in dye-sensitized solar cells. To provide enhanced understanding of ion movement in RTIL media, a combined electrochemical and NMR study of diffusion in the {SeCN¯-(SeCN)(2)-(SeCN)(3)¯} system has been undertaken in a selection of commonly used RTILs. In this system, each of the Se, C and N nuclei is NMR active. The electrochemical behavior of the pure ionic liquid, [C(4)mim][SeCN], which is synthesized and characterized here for the first time, also has been investigated. Voltammetric studies, which yield readily interpreted diffusion-limited responses under steady-state conditions by means of a Random Assembly of Microdisks (RAM) microelectrode array, have been used to measure electrochemically based diffusion coefficients, while self-diffusion coefficients were measured by pulsed field gradient NMR methods. The diffusivity data, derived from concentration and field gradients respectively, are in good agreement. The NMR data reveal that exchange processes occur between selenocyanate species, but the voltammetric data show the rates of exchange are too slow to enhance charge transfer. Thus, a comparison of the iodide and selenocyanate systems is somewhat paradoxical in that while the latter give RTILs of low viscosity, sluggish exchange kinetics prevent any significant enhancement of charge transfer through direct electron exchange. In contrast, faster exchange between iodide and its oxidation products leads to substantial electron exchange but this effect does not compensate sufficiently for mass transport limitations imposed by the higher viscosity of iodide RTILs.

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

Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-chloro 4-nitrostilbene (CONS): a potential NLO material.

PubMed

Dinakaran, Paul M; Kalainathan, S

2013-07-01

4-Chloro 4-nitrostilbene (CONS) a new organic nonlinear optical material has been synthesized. Employing slow evaporation method, good optical quality single crystals (dimensions up to 6×2×3 mm(3)) have been grown using ethyl methyl ketone (EMK) as a solvent. The grown crystals have been subjected to various characterizations such as single crystal X-ray diffraction, powder XRD, Fourier Transform Infrared spectroscopy (FTIR), proton NMR, solid UV absorption, SHG studies. Single crystal X-ray diffraction reveals that the crystal system belongs to monoclinic with noncentrosymmetric space group P21. The UV-Vis absorption spectrum has been recorded and found that the cut off wavelength is 380 nm. Functional groups and the structure of the title compound have been confirmed by FTIR and (1)H NMR spectroscopic analyses respectively. Molecular mass of the CONS confirmed by the high resolution mass spectral analysis .The thermal behavior of the grown crystal has been studied by TG/DTA analysis and it shows the melting point is at 188.66 °C. Dislocations and growth pattern present in the grown crystal revealed by the etching study. The mechanical strength of the CONS crystal has been studied by Vicker's hardness measurement. The SHG efficiency of the grown crystal has been determined by Kurtz and Perry powder test which revealed that the CONS crystal (327 mV) has 15 times greater efficiency than that of KDP (21.7 mV). Copyright © 2013 Elsevier B.V. All rights reserved.

N-acetylglyoxylic amide bearing a nitrophenyl group as anion receptors: NMR and X-ray investigations on anion binding and selectivity

NASA Astrophysics Data System (ADS)

Suryanti, Venty; Bhadbhade, Mohan; Black, David StC; Kumar, Naresh

2017-10-01

N-Nitrophenylglyoxylic amides 1 and 2 in presence of tetrabutylammonium cation (TBA) act as receptors for anions HSO4-, Cl-, Br- and NO3- as investigated by NMR studies. The receptors formed 1:1 host-guest complexes in solution. X-ray structure of 1 along with TBA that bind a chloride anion is reported. Molecule 1 showed the highest selectivity for HSO4- anion over others measured. X-ray structure of the bound Cl- revealed a pocket containing the anion making strong (Nsbnd H⋯Cl) and weak hydrogen bonds (Csbnd H⋯Cl) that contribute to the recognition of the chloride anion. Nsbnd H and Csbnd H hydrogen bonds resulted in a relatively strong binding for chloride ions.

[Studies by means of 1H NMR spectroscopy of complex formation of aromatic biologically active compounds with antibiotic topotecan].

PubMed

Mosunov, A A; Kostiukov, V V; Evstigneev, M P

2012-01-01

The analysis of heteroassociation of antibiotic topotecan (TPT) with aromatic biologically active compounds (BAC): caffeine, mutagens ethidium bromide and proflavine, antibiotic daunomycin, vitamins flavin-mononucleotide and nicotinamide, has been carried out in the work using 1H NMR spectroscopy data. The equilibrium constants of heteroassociation and induced chemical shifts of the protons have been obtained in the complexes with BAC. It is found that the complex formation TPT-BAC has the nature of stacking of the chromophores, additionally stabilized in the case of proflavine by intermolecular hydrogen bond. Calculation of the basic components of the Gibbs free energy of the complexation reactions is carried out, and the factors which stabilize and destabilize the heterocomplexes of molecules are revealed.

Phosphorylation-induced conformation of β2-adrenoceptor related to arrestin recruitment revealed by NMR.

PubMed

Shiraishi, Yutaro; Natsume, Mei; Kofuku, Yutaka; Imai, Shunsuke; Nakata, Kunio; Mizukoshi, Toshimi; Ueda, Takumi; Iwaï, Hideo; Shimada, Ichio

2018-01-15

The C-terminal region of G-protein-coupled receptors (GPCRs), stimulated by agonist binding, is phosphorylated by GPCR kinases, and the phosphorylated GPCRs bind to arrestin, leading to the cellular responses. To understand the mechanism underlying the formation of the phosphorylated GPCR-arrestin complex, we performed NMR analyses of the phosphorylated β 2 -adrenoceptor (β 2 AR) and the phosphorylated β 2 AR-β-arrestin 1 complex, in the lipid bilayers of nanodisc. Here we show that the phosphorylated C-terminal region adheres to either the intracellular side of the transmembrane region or lipids, and that the phosphorylation of the C-terminal region allosterically alters the conformation around M215 5.54 and M279 6.41 , located on transemembrane helices 5 and 6, respectively. In addition, we found that the conformation induced by the phosphorylation is similar to that corresponding to the β-arrestin-bound state. The phosphorylation-induced structures revealed in this study propose a conserved structural motif of GPCRs that enables β-arrestin to recognize dozens of GPCRs.

Characterization of textural, rheological, thermal, microstructural, and water mobility in wheat flour dough and bread affected by trehalose.

PubMed

Peng, Bo; Li, Youqian; Ding, Shiyong; Yang, Jun

2017-10-15

The study aims to elucidate the effects of trehalose on the mechanical, thermal, and rheological properties of wheat flour dough and water distribution in bread. Texture profile analysis, DSC, farinograph, extensograph, and frequency sweep were applied in dough. The results from SEM revealed that the gluten film became less notable with the presence of trehalose. The kinetics of staling process, low-field 1 H NMR, and water-binding capacity were employed to characterize physicochemical properties of bread. Trehalose decreased the staling rate constant k, indicating an inhibitory effect on firming process in bread. Trehalose had the ability to retain water by hindering the interaction among water molecules, gluten and starch, thus relatively increasing the immobility of the part of water represented by T 22 in low-field 1 H NMR tests. Trehalose restricted water mobilization during storage, resulting in a better water-holding capacity. Our findings reveal that trehalose could be an improver in dough and bread-making performance, as well as an antistaling agent in bread. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spirocyclic character of ixazomib citrate revealed by comprehensive XRD, NMR and DFT study

NASA Astrophysics Data System (ADS)

Skorepova, Eliska; Čerňa, Igor; Vlasáková, Růžena; Zvoníček, Vít; Tkadlecová, Marcela; Dušek, Michal

2017-11-01

Ixazomib citrate is a very recently approved anti-cancer drug. Until now, to the best of our knowledge, no one has been able to solve any crystal structures of this compound. In this work, we present the crystal structures of two isostructural solvates of ixazomib citrate. In all currently available literature, the molecule is characterized as containing a single optically active carbon atom and a borate cycle formed when ixazomib is reacted with citric acid to form a stabilized ixazomib citrate that can be administered orally. However, the crystal structures revealed that none of the up-to-date presented structural formulas of ixazomib citrate are fully accurate. In addition to the citrate ring, another 5-membered ring is formed. These two rings are connected by the boron atom, making this compound a spirocyclic borate. By spirocyclization, the boron atom becomes tetrahedral and therefore optically active. In the crystal structures, ixazomib citrate was found to be in forms of two RR and RS stereoisomers. The results are supported by solid-state and solution NMR and DFT quantum mechanical calculations.

Structure-based design of potent histatin analogues.

PubMed

Brewer, Dyanne; Lajoie, Gilles

2002-04-30

Conformational studies of human salivary peptide, histatin 3 (Hst3), were performed by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy in a membrane-mimicking environment. The structural information that was obtained was used in the design of peptide analogues with improved antifungal activity. In the presence of increasing concentrations of L-alpha-dimyristoylphosphatidylcholine (L-alpha-DMPC) lipid vesicles, a dramatic increase in a minimum at 198 nm is observed in the CD spectra of Hst3. The NMR data of Hst3 in the presence of L-alpha-DMPC lipid vesicles reveal the proximity of residues Y(10) and S(20), indicating the existence of a more compact structure. Peptide analogues were designed on the basis of this observation, which incorporated a disulfide bond to stabilize an extended loop in this region of the sequence. One of these, peptide 4, was 100 times more potent than Hst5 against Saccharomyces cerevisiae cells. Conformational analysis of peptide 4 revealed a looped structure with charged residues protruding on the outside surface, while a combination of aromatic residues and histidines are packed into an internal core.

Role of internal motions and molecular geometry on the NMR relaxation of hydrocarbons

NASA Astrophysics Data System (ADS)

Singer, P. M.; Asthagiri, D.; Chen, Z.; Valiya Parambathu, A.; Hirasaki, G. J.; Chapman, W. G.

2018-04-01

The role of internal motions and molecular geometry on 1H NMR relaxation rates in liquid-state hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for intramolecular and intermolecular 1H-1H dipole-dipole interactions. The effects of molecular geometry and internal motions on the functional form of the autocorrelation functions are studied by comparing symmetric molecules such as neopentane and benzene to corresponding straight-chain alkanes n-pentane and n-hexane, respectively. Comparison of rigid versus flexible molecules shows that internal motions cause the intramolecular and intermolecular correlation-times to get significantly shorter, and the corresponding relaxation rates to get significantly smaller, especially for longer-chain n-alkanes. Site-by-site simulations of 1H's across the chains indicate significant variations in correlation times and relaxation rates across the molecule, and comparison with measurements reveals insights into cross-relaxation effects. Furthermore, the simulations reveal new insights into the relative strength of intramolecular versus intermolecular relaxation as a function of internal motions, as a function of molecular geometry, and on a site-by-site basis across the chain.

Synthesis and high temperature stability of amorphous Si(B)CN-MWCNT composite nanowires

NASA Astrophysics Data System (ADS)

Bhandavat, Romil; Singh, Gurpreet

2012-02-01

We demonstrate synthesis of a hybrid nanowire structure consisting of an amorphous polymer-derived silicon boron-carbonitride (Si-B-C-N) shell with a multiwalled carbon nanotube core. This was achieved through a novel process involving preparation of a boron-modified liquid polymeric precursor through a reaction of trimethyl borate and polyureasilazane under atmospheric conditions; followed by conversion of polymer to glass-ceramic on carbon nanotube surfaces through controlled heating. Chemical structure of the polymer was studied by liquid-NMR while evolution of various ceramic phases was studied by Raman spectroscopy, solid-NMR, Fourier transform infrared and X-ray photoelectron spectroscopy. Electron microscopy and X-ray diffraction confirms presence of amorphous Si(B)CN coating on individual nanotubes for all specimen processed below 1400 degree C. Thermogravimetric analysis, followed by TEM revealed high temperature stability of the carbon nanotube core in flowing air up to 1300 degree C.

A homologous series of regioselectively tetradeprotonated group 8 metallocenes: new inverse crown ring compounds synthesized via a mixed sodium-magnesium tris(diisopropylamide) synergic base.

PubMed

Andrikopoulos, Prokopis C; Armstrong, David R; Clegg, William; Gilfillan, Carly J; Hevia, Eva; Kennedy, Alan R; Mulvey, Robert E; O'Hara, Charles T; Parkinson, John A; Tooke, Duncan M

2004-09-22

Subjecting ferrocene, ruthenocene, or osmocene to the synergic amide base sodium-magnesium tris(diisopropylamido) affords a unique homologous series of metallocene derivatives of general formula [(M(C(5)H(3))(2))Na(4)Mg(4)(i-Pr(2)N)(8)] (where M = Fe (1), Ru (2), or Os (3)). X-ray crystallographic studies of 1-3 reveal a common molecular "inverse crown" structure comprising a 16-membered [(NaNMgN)(4)](4+) "host" ring and a metallocenetetraide [M(C(5)H(3))(2)](4-) "guest" core, the cleaved protons of which are lost selectively from the 1, 1', 3, and 3'-positions. Variable-temperature NMR spectroscopic studies indicate that 1, 2, and 3 each exist as two distinct interconverting conformers in arene solution, the rates of exchange of which have been calculated using coalescence and EXSY NMR measurements.

NMR signal analysis to characterize solid, aqueous, and lipid phases in baked cakes.

PubMed

Le Grand, F; Cambert, M; Mariette, F

2007-12-26

Proton mobility was studied in molecular fractions of some model systems and of cake using a 1H nuclear magnetic resonance (NMR) relaxation technique. For cake, five spin-spin relaxation times (T2) were obtained from transverse relaxation curves: T2 (1) approximately 20 micros, T2 (2) approximately 0.2 ms, T2 (3) approximately 3 ms, T2 (4) approximately 50 ms, and T2 (2) approximately 165 ms. The faster component was attributed to the solid phase, components 2 and 3 were associated with the aqueous phase, and the two slowest components were linked to the lipid phase. After cooking, the crust contained more fat but less water than the center part of the cake. The amount of gelatinized starch was lower in the crust, and water was more mobile due to less interaction with macromolecules. This preliminary study revealed different effects of storage on the center and crust.

Preparation, crystal structure, vibrational spectral and density functional studies of bis (4-nitrophenol)-2,4,6-triamino-1,3,5-triazine monohydrate

NASA Astrophysics Data System (ADS)

Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Renganathan, N. G.; Gunasekaran, S.; Anbalagan, G.

2013-10-01

An organic-organic salt, bis (4-nitrophenol) 2,4,6-triamino 1,3,5-triazine monohydrate (BNPM) has been prepared by slow evaporation technique at room temperature. Single crystal X-ray diffraction analysis reveals that the compound crystallizes in triclinic system with centrosymmetric space group P-1. IR and Raman spectra of BNPM have been recorded and analyzed. The study has been extended to confocal Raman spectral analysis. Band assignments have been made for the melamine and p-nitrophenol molecules. Vibrational spectra have also been discussed on the basis of quantum chemical density functional theory calculations using Firefly (PC GAMESS) Version 7.1 G. Vibrational frequencies are calculated and scaled values are compared with the experimental one. The Mulliken charges, HOMO-LUMO orbital energies are calculated and analyzed. The chemical structure of the compound was established by 1H NMR and 13C NMR spectra.

Structure of a polysaccharide from Urtica fissa determined by NMR spectra.

PubMed

Wang, Yan-Liang; Li, Li; Cheng, Xiao-Chen; Lu, Yu-Xin; Zhang, Qing-Lin

2012-01-01

A polysaccharide, isolated and purified from the aqueous extract of nettle plant Urtica fissa, was found to consist of D-glucose and D-arabinose. Molecular weight was determined to be Mn 4140. The NMR experiments (¹H, ¹³C, ¹H--¹H COSY, TOCSY, HSQC, NOESY, and HMBC) revealed the structure as the following repeating unit: -->6)-α-D-Glcp-(1-->6)-α-D-Glcp-(1-->6)-β-D-Glcp--(1-->5)-β-D-Araf-(1-->3)-β-D-Glcp-(1-->

NMR measurements in SSC dipole D00001

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

Kuchnir, M.; Schmidt, E.E.; Hanft, R.W.

The first 16.5 m long SSC dipole magnet (D00001) had its field intensity measured as a function of position with a custom made NMR magnetometer. A short description of the probe is presented. The data obtained (most of it near 2 T spaced apart by one inch) shows an average transfer function of 1.02830 T/KA with position dependent values deviating from the average by up to .00130 T/KA revealing contruction inhomogeneities that were measured with a sensitivity of 25 ppM.

Potential antimicrobial agents from triazole-functionalized 2H-benzo[b][1,4]oxazin-3(4H)-ones.

PubMed

Bollu, Rajitha; Banu, Saleha; Bantu, Rajashaker; Reddy, A Gopi; Nagarapu, Lingaiah; Sirisha, K; Kumar, C Ganesh; Gunda, Shravan Kumar; Shaik, Kamal

2017-12-01

A series of substituted triazole functionalized 2H-benzo[b][1,4]oxazin-3(4H)-ones were synthesized by employing click chemistry and further characterized based on 1 H NMR, 13 C NMR, IR and mass spectral studies. All the synthesized derivatives were screened for their in vitro antimicrobial activities. Further, molecular docking studies were accomplished to explore the binding interactions between 1,2,3-triazol-4-yl-2H-benzo[b][1,4]oxazin-3(4H)-one and the active site of Staphylococcus aureus (CrtM) dehydrosqualene synthase (PDB ID: 2ZCS). These docking studies revealed that the synthesized derivatives showed high binding energies and strong H-bond interactions with the dehydrosqualene synthase validating the observed antimicrobial activity data. Based on antimicrobial activity and docking studies, the compounds 9c, 9d and 9e were identified as promising antimicrobial leads. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insight into magnesium coordination environments in benzoate and salicylate complexes through 25Mg solid-state NMR spectroscopy.

PubMed

Burgess, Kevin M N; Xu, Yang; Leclerc, Matthew C; Bryce, David L

2013-08-01

We report on the (25)Mg solid-state nuclear magnetic resonance (NMR) characterization of a series of magnesium complexes featuring Mg(2+) ions in organic coordination environments. Six compounds have been synthesized with benzoate and salicylate ligands, which are typically used as linkers in metal organic frameworks (MOFs). The use of ultrahigh-field solid-state NMR has revealed a relatively large range of values for the (25)Mg quadrupolar coupling constant, CQ((25)Mg), in these compounds. In contrast to some previously studied inorganic Mg(2+) complexes, the values of CQ((25)Mg) in organic Mg(2+) complexes are well rationalized by the degree of octahedral strain of the "MgO6" coordination polyhedra. (13)C and (25)Mg isotropic chemical shifts were also found to be sensitive to the binding mode of the carboxylate ligands. The experimental findings are corroborated by gauge-including projector-augmented-wave (GIPAW) density functional theory (DFT) computations, and these have allowed for an interpretation of the experimentally observed trend in the CQ((25)Mg) values and for the visualization of the EFG tensor principal components with respect to the molecular structure. These new insights may prove to be valuable for the understanding and interpretation of (25)Mg NMR data for Mg(2+) ions in organic binding environments such as those found in MOFs and protein-divalent metal binding sites.

Geophysical monitoring of organic contaminants in sediments

NASA Astrophysics Data System (ADS)

Zhang, C.; Jennings, J.

2016-12-01

Soil and groundwater contamination pose threats to the health of human and the environment. Successful contaminant remediation requires effective in situ monitoring of physical, chemical, and biological processes in the subsurface. Minimally invasive geophysical methods have shown promise in characterizing organic contaminants in soil and groundwater and have been applied to monitor remediation processes. This study examines the sensitivity of low field proton nuclear magnetic resonance (NMR) and complex conductivity to the presence of organic contaminants in sediments. We aim to improve understanding of relationships between NMR and complex conductivity observables and hydrological properties of the sediments, as well as the amount and state of contaminants in porous media. We used toluene as a representative organic contaminant, and pure silica sands and montmorillonite clay as synthetic sediments. Sand-clay mixtures with various sand/clay ratios were prepared and saturated with different concentration of toluene. Relationships between the compositions of porous media, hydrocarbon concentration, and hydrological properties of sediments and geophysical response were investigated. The results from NMR relaxation time (T2) measurements reveal the dominant control of clay content on T2 relaxation, establish minimum toluene detectability, and demonstrate the effect of contaminant concentration on NMR signals. The diffusion-relaxation (D-T2) correlation measurement show toluene can be resolved from toluene-water mixture in sand-clay mixture. The results from ongoing complex conductivity measurements will also be presented and discussed.

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

PubMed Central

Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2012-01-01

Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an A-form-like conformation, with the level of order decreasing toward the terminal ends. An A-to-C mutation within the polyadenine tract alters the observed dynamics consistent with the introduction of a dynamic kink. Pre-ordering of the tail may increase the efficacy of ligand binding above that achieved by a random-coil ssRNA. The REMD simulations recapitulate important trends in the NMR data, but suggest more internal motions than inferred from the NMR analysis. Our study unmasks a previously unappreciated level of complexity in ssRNA, which we believe will also serve as an excellent model system for testing and developing computational force fields. PMID:22009676

Structural mimicry of O-antigen by a peptide revealed in a complex with an antibody raised against Shigella flexneri serotype 2a.

PubMed

Theillet, François-Xavier; Saul, Frederick A; Vulliez-Le Normand, Brigitte; Hoos, Sylviane; Felici, Franco; Weintraub, Andrej; Mulard, Laurence A; Phalipon, Armelle; Delepierre, Muriel; Bentley, Graham A

2009-05-15

The use of carbohydrate-mimicking peptides to induce immune responses against surface polysaccharides of pathogenic bacteria offers a novel approach to vaccine development. Factors governing antigenic and immunogenic mimicry, however, are complex and poorly understood. We have addressed this question using the anti-lipopolysaccharide monoclonal antibody F22-4, which was raised against Shigella flexneri serotype 2a and shown to protect against homologous infection in a mouse model. In a previous crystallographic study, we described F22-4 in complex with two synthetic fragments of the O-antigen, the serotype-specific saccharide moiety of lipopolysaccharide. Here, we present a crystallographic and NMR study of the interaction of F22-4 with a dodecapeptide selected by phage display using the monoclonal antibody. Like the synthetic decasaccharide, the peptide binds to F22-4 with micromolar affinity. Although the peptide and decasaccharide use very similar regions of the antigen-binding site, indicating good antigenic mimicry, immunogenic mimicry by the peptide was not observed. The F22-4-antigen interaction is significantly more hydrophobic with the peptide than with oligosaccharides; nonetheless, all hydrogen bonds formed between the peptide and F22-4 have equivalents in the oligosaccharide complex. Two bridging water molecules are also in common, adding to partial structural mimicry. Whereas the bound peptide is entirely helical, its structure in solution, as shown by NMR, is helical in the central region only. Moreover, docking the NMR structure into the antigen-binding site shows that steric hindrance would occur, revealing poor complementarity between the major solution conformation and the antibody that could contribute to the absence of immunogenic mimicry.

New catalytic roles for serine esterases: a 19F-NMR study of the interaction of 3,3,3-trifluoro-2,2-dihydroxy-1-phenyl-1-propanone with chicken liver carboxylesterase.

PubMed

Bowles, M R; King, G J; Berndt, M C; Zerner, B

1996-12-05

The reactions of 3,3,3-trifluoro-2,2-dihydroxy-1-phenyl-1-propanone (TDPP) with chicken liver carboxylesterase have shown that this ketone hydrate is not only a potent inhibitor of the enzyme, but also a substrate for a number of enzyme-catalyzed reactions. The kinetics of inhibition are consistent with a mechanism in which the bound hydrate is initially dehydrated in a rate-limiting step catalyzed by the enzyme. Nucleophilic attack by the active-site serine on the parent ketone then produces a hemiketal adduct. However, the slow reactivation (by dialysis) of TDPP-inhibited enzyme indicates that the interaction with this inhibitor is more complex. At equilibrium, a dissociation constant of 2.4 pM was obtained for this interaction. 19F-NMR studies of the enzyme-TDPP complex show that after pre-equilibration, the major adduct is not the hemiketal adduct. It is proposed that this final adduct is a cross-linked adduct formed between TDPP, the active-site serine and the active-site histidine. 19F-NMR studies reveal that chicken liver carboxylesterase catalyses the cleavage of TDPP to yield either fluoride ion or trifluoroacetate, and also the benzilic acid rearrangement of TDPP to alpha-trifluoromethylmandelate. These products have also been identified in model studies of the reaction between TDPP and imidazole.

A 93Nb solid-state NMR and density functional theory study of four- and six-coordinate niobate systems.

PubMed

Hanna, John V; Pike, Kevin J; Charpentier, Thibault; Kemp, Thomas F; Smith, Mark E; Lucier, Bryan E G; Schurko, Robert W; Cahill, Lindsay S

2010-03-08

A variable B(0) field static (broadline) NMR study of a large suite of niobate materials has enabled the elucidation of high-precision measurement of (93)Nb NMR interaction parameters such as the isotropic chemical shift (delta(iso)), quadrupole coupling constant and asymmetry parameter (C(Q) and eta(Q)), chemical shift span/anisotropy and skew/asymmetry (Omega/Deltadelta and kappa/eta(delta)) and Euler angles (alpha, beta, gamma) describing the relative orientation of the quadrupolar and chemical shift tensorial frames. These measurements have been augmented with ab initio DFT calculations by using WIEN2k and NMR-CASTEP codes, which corroborate these reported values. Unlike previous assertions made about the inability to detect CSA (chemical shift anisotropy) contributions from Nb(V) in most oxo environments, this study emphasises that a thorough variable B(0) approach coupled with the VOCS (variable offset cumulative spectroscopy) technique for the acquisition of undistorted broad (-1/2<-->+1/2) central transition resonances facilitates the unambiguous observation of both quadrupolar and CSA contributions within these (93)Nb broadline data. These measurements reveal that the (93)Nb electric field gradient tensor is a particularly sensitive measure of the immediate and extended environments of the Nb(V) positions, with C(Q) values in the 0 to >80 MHz range being measured; similarly, the delta(iso) (covering an approximately 250 ppm range) and Omega values (covering a 0 to approximately 800 ppm range) characteristic of these niobate systems are also sensitive to structural disposition. However, their systematic rationalisation in terms of the Nb-O bond angles and distances defining the immediate Nb(V) oxo environment is complicated by longer-range influences that usually involve other heavy elements comprising the structure. It has also been established in this study that the best computational method(s) of analysis for the (93)Nb NMR interaction parameters generated here are the all-electron WIEN2k and the gauge included projector augmented wave (GIPAW) NMR-CASTEP DFT approaches, which account for the short- and long-range symmetries, periodicities and interaction-potential characteristics for all elements (and particularly the heavy elements) in comparison with Gaussian 03 methods, which focus on terminated portions of the total structure.

Development of LC-13C NMR

NASA Technical Reports Server (NTRS)

Dorn, H. C.; Wang, J. S.; Glass, T. E.

1986-01-01

This study involves the development of C-13 nuclear resonance as an on-line detector for liquid chromatography (LC-C-13 NMR) for the chemical characterization of aviation fuels. The initial focus of this study was the development of a high sensitivity flow C-13 NMR probe. Since C-13 NMR sensitivity is of paramount concern, considerable effort during the first year was directed at new NMR probe designs. In particular, various toroid coil designs were examined. In addition, corresponding shim coils for correcting the main magnetic field (B sub 0) homogeneity were examined. Based on these initial probe design studies, an LC-C-13 NMR probe was built and flow C-13 NMR data was obtained for a limited number of samples.

Quantification of taurine in energy drinks using ¹H NMR.

PubMed

Hohmann, Monika; Felbinger, Christine; Christoph, Norbert; Wachter, Helmut; Wiest, Johannes; Holzgrabe, Ulrike

2014-05-01

The consumption of so called energy drinks is increasing, especially among adolescents. These beverages commonly contain considerable amounts of the amino sulfonic acid taurine, which is related to a magnitude of various physiological effects. The customary method to control the legal limit of taurine in energy drinks is LC-UV/vis with postcolumn derivatization using ninhydrin. In this paper we describe the quantification of taurine in energy drinks by (1)H NMR as an alternative to existing methods of quantification. Variation of pH values revealed the separation of a distinct taurine signal in (1)H NMR spectra, which was applied for integration and quantification. Quantification was performed using external calibration (R(2)>0.9999; linearity verified by Mandel's fitting test with a 95% confidence level) and PULCON. Taurine concentrations in 20 different energy drinks were analyzed by both using (1)H NMR and LC-UV/vis. The deviation between (1)H NMR and LC-UV/vis results was always below the expanded measurement uncertainty of 12.2% for the LC-UV/vis method (95% confidence level) and at worst 10.4%. Due to the high accordance to LC-UV/vis data and adequate recovery rates (ranging between 97.1% and 108.2%), (1)H NMR measurement presents a suitable method to quantify taurine in energy drinks. Copyright © 2013 Elsevier B.V. All rights reserved.

Xenon NMR of liquid crystals confined to cylindrical nanocavities: a simulation study.

PubMed

Karjalainen, Jouni; Vaara, Juha; Straka, Michal; Lantto, Perttu

2015-03-21

Applications of liquid crystals (LCs), such as smart windows and the ubiquitous display devices, are based on controlling the orientational and translational order in a small volume of LC medium. Hence, understanding the effects of confinement to the liquid crystal phase behaviour is essential. The NMR shielding of (129)Xe atoms dissolved in LCs constitutes a very sensitive probe to the details of LC environment. Linking the experimental results to microscopic phenomena calls for molecular simulations. In this work, the NMR shielding of atomic (129)Xe dissolved in a uniaxial thermotropic LC confined to nanosized cylindrical cavities is computed from coarse-grained (CG) isobaric Monte Carlo (MC) simulations with a quantum-chemically (QC) pre-parameterised pairwise-additive model for the Xe nuclear shielding tensor. We report the results for the (129)Xe nuclear shielding and its connection to the structure and order of the LC appropriate to two different cavity sizes, as well as a comparison to the results of bulk (non-confined) simulations. We find that the confinement changes the LC phase structure dramatically and gives rise to the coexistence of varying degrees of LC order, which is reflected in the Xe shielding. Furthermore, we qualitatively reproduce the behaviour of the mean (129)Xe chemical shift with respect to temperature for atomic Xe dissolved in LC confined to controlled-pore glass materials. In the small-radius cavity the nematic - paranematic phase transition is revealed only by the anisotropic component of the (129)Xe nuclear shielding. In the larger cavity, the nematic - paranematic - isotropic transition is clearly seen in the Xe shielding. The simulated (129)Xe NMR shielding is insensitive to the smectic-A - nematic transition, since in the smectic-A phase, the Xe atoms largely occupy the imperfect layer structure near the cavity walls. The direct contribution of the cavity wall to (129)Xe nuclear shielding is dependent on the cavity size but independent of temperature. Our results show that the combination of CG simulations and a QC pre-parameterised (129)Xe NMR shielding allows efficient studies of the phase behaviour and structure of complex systems containing thousands of molecules, and brings us closer to the simulation of NMR experiments.

NMR spectroscopic study of organic phosphate esters coprecipitated with calcite

NASA Astrophysics Data System (ADS)

Phillips, Brian L.; Zhang, Zelong; Kubista, Laura; Frisia, Silvia; Borsato, Andrea

2016-06-01

Organic phosphorus incorporated in calcite during laboratory precipitation experiments and in natural cave deposits was investigated by solid-state NMR spectroscopy. For calcite precipitated in the presence of organic phosphoesters of varying size and functionality, solid-state 31P{1H} CP/MAS NMR shows that the phosphoesters were incorporated intact into the solid. Systematic changes in the 31P NMR chemical shift of the phosphate group were observed between the solid phosphoester and that incorporated in the solid precipitate, yielding 31P NMR chemical shifts of the coprecipitates in the range of +1.8 to -2.2 ppm. These chemical shifts are distinct from that of similarly prepared calcite coprecipitated with inorganic phosphate, 3.5 ppm. Only minor changes were noted in the phosphoester 31P chemical shift anisotropy (CSA) which suggests no significant change in the local structure of the phosphate group, which is dominated by C-O-P bonding. Close spatial proximity of the organic phosphate group to calcite structural components was revealed by 31P/13C rotational echo double resonance (REDOR) experiments for coprecipitates prepared with 13C-labeled carbonate. All coprecipitates showed significant 31P dephasing effects upon 13C-irradiation, signaling atomic-scale proximity to carbonate carbon. The dephasing rate for smaller organophosphate molecules is similar to that observed for inorganic phosphate, whereas much slower dephasing was observed for larger molecules having long and/or bulky side-chains. This result suggests that small organic molecules can be tightly enclosed within the calcite structure, whereas significant structural disruption required to accommodate the larger organic molecules leads to longer phosphate-carbonate distances. Comparison of 31P NMR spectroscopic data from the synthetic coprecipitates with those from calcite moonmilk speleothems indicates that phosphorus occurs mainly as inorganic orthophosphate in the natural deposits, although small signals occur with characteristics consistent with phosphate monoesters. The results of this study indicate that trace- to minor concentrations of dissolved organic molecules can be effectively taken up during calcite precipitation and incorporated in the structure, leaving a resilient record of materials present during crystallization.

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 -

Neuronal Tracing with Magnetic Labels: NMR Imaging Methods, Preliminary Results, and New Optimized Coils.

NASA Astrophysics Data System (ADS)

Ghosh, Pratik

1992-01-01

The investigations focussed on in vivo NMR imaging studies of magnetic particles with and within neural cells. NMR imaging methods, both Fourier transform and projection reconstruction, were implemented and new protocols were developed to perform "Neuronal Tracing with Magnetic Labels" on small animal brains. Having performed the preliminary experiments with neuronal tracing, new optimized coils and experimental set-up were devised. A novel gradient coil technology along with new rf-coils were implemented, and optimized for future use with small animals in them. A new magnetic labelling procedure was developed that allowed labelling of billions of cells with ultra -small magnetite particles in a short time. The relationships among the viability of such cells, the amount of label and the contrast in the images were studied as quantitatively as possible. Intracerebral grafting of magnetite labelled fetal rat brain cells made it possible for the first time to attempt monitoring in vivo the survival, differentiation, and possible migration of both host and grafted cells in the host rat brain. This constituted the early steps toward future experiments that may lead to the monitoring of human brain grafts of fetal brain cells. Preliminary experiments with direct injection of horse radish peroxidase-conjugated magnetite particles into neurons, followed by NMR imaging, revealed a possible non-invasive alternative, allowing serial study of the dynamic transport pattern of tracers in single living animals. New gradient coils were built by using parallel solid-conductor ribbon cables that could be wrapped easily and quickly. Rapid rise times provided by these coils allowed implementation of fast imaging methods. Optimized rf-coil circuit development made it possible to understand better the sample-coil properties and the associated trade -offs in cases of small but conducting samples.

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations.

PubMed

Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika

2018-05-30

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Effects of salt and nanoparticles on the segmental motion of poly(ethylene oxide) in its crystalline and amorphous phases: 2H and 7Li NMR studies.

PubMed

Vogel, M; Herbers, C; Koch, B

2008-09-11

We use (2)H NMR to investigate the segmental motion of poly(ethylene oxide) (PEO) in neat and nanocomposite materials that do and do not contain salt. Specifically, in addition to a neat low-molecular-weight PEO, we study mixtures of this polymer with TiO 2 nanoparticles and LiClO 4. To characterize the polymer dynamics over a wide range of time scales, we combine (2)H NMR spin-lattice relaxation, line-shape, and stimulated-echo analyses. The results consistently show that the presence of nanoparticles hardly affects the behavior of the polymer, while addition of salt leads to substantial changes; e.g., it reduces the crystallinity. For neat PEO and a PEO-TiO 2 mixture, stimulated-echo spectroscopy enables measurement of rotational correlation functions for the crystalline phase. Analysis of the decays allows us to determine correlation times, to demonstrate the existence of a nonexponential relaxation, which implies a high complexity of the polymer dynamics in the crystal, and to show that the reorientation can be described as a large-angle jump. For a PEO-TiO 2-LiClO 4 mixture, we use (2)H and (7)Li NMR to study the polymer and the lithium dynamics, respectively. Analysis of the (7)Li spin-lattice relaxation reveals a high lithium ionic mobility in this nanocomposite polymer electrolyte. The (7)Li stimulated-echo decay is well described by a stretched exponential extending over about 6 orders of magnitude, indicating that a broad and continuous distribution of correlation times characterizes the fluctuations of the local lithium ionic environments.

Decoherence and fluctuation dynamics of the quantum dot nuclear spin bath probed by nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Chekhovich, Evgeny A.

2017-06-01

Dynamics of nuclear spin decoherence and nuclear spin flip-flops in self-assembled InGaAs/GaAs quantum dots are studied experimentally using optically detected nuclear magnetic resonance (NMR). Nuclear spin-echo decay times are found to be in the range 1-4 ms. This is a factor of ~3 longer than in strain-free GaAs/AlGaAs structures and is shown to result from strain-induced quadrupolar effects that suppress nuclear spin flip-flops. The correlation times of the flip-flops are examined using a novel frequency-comb NMR technique and are found to exceed 1 s, a factor of ~1000 longer than in strain-free structures. These findings complement recent studies of electron spin coherence and reveal the paradoxical dual role of the quadrupolar effects in self-assembled quantum dots: large increase of the nuclear spin bath coherence and at the same time significant reduction of the electron spin-qubit coherence. Approaches to increasing electron spin coherence are discussed. In particular the nanohole filled GaAs/AlGaAs quantum dots are an attractive option: while their optical quality matches the self-assembled dots the quadrupolar effects measured in NMR spectra are a factor of 1000 smaller.

Metabolic profiling of ob/ob mouse fatty liver using HR-MAS 1H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway.

PubMed

Gogiashvili, Mikheil; Edlund, Karolina; Gianmoena, Kathrin; Marchan, Rosemarie; Brik, Alexander; Andersson, Jan T; Lambert, Jörg; Madjar, Katrin; Hellwig, Birte; Rahnenführer, Jörg; Hengstler, Jan G; Hergenröder, Roland; Cadenas, Cristina

2017-02-01

Metabolic perturbations resulting from excessive hepatic fat accumulation are poorly understood. Thus, in this study, leptin-deficient ob/ob mice, a mouse model of fatty liver disease, were used to investigate metabolic alterations in more detail. Metabolites were quantified in intact liver tissues of ob/ob (n = 8) and control (n = 8) mice using high-resolution magic angle spinning (HR-MAS) 1 H-NMR. In addition, after demonstrating that HR-MAS 1 H-NMR does not affect RNA integrity, transcriptional changes were measured by quantitative real-time PCR on RNA extracted from the same specimens after HR-MAS 1 H-NMR measurements. Importantly, the gene expression changes obtained agreed with those observed by Affymetrix microarray analysis performed on RNA isolated directly from fresh-frozen tissue. In total, 40 metabolites could be assigned in the spectra and subsequently quantified. Quantification of lactate was also possible after applying a lactate-editing pulse sequence that suppresses the lipid signal, which superimposes the lactate methyl resonance at 1.3 ppm. Significant differences were detected for creatinine, glutamate, glycine, glycolate, trimethylamine-N-oxide, dimethylglycine, ADP, AMP, betaine, phenylalanine, and uridine. Furthermore, alterations in one-carbon metabolism, supported by both metabolic and transcriptional changes, were observed. These included reduced demethylation of betaine to dimethylglycine and the reduced expression of genes coding for transsulfuration pathway enzymes, which appears to preserve methionine levels, but may limit glutathione synthesis. Overall, the combined approach is advantageous as it identifies changes not only at the single gene or metabolite level but also deregulated pathways, thus providing critical insight into changes accompanying fatty liver disease. Graphical abstract A Evaluation of RNA integrity before and after HR-MAS 1 H-NMR of intact mouse liver tissue. B Metabolite concentrations and gene expression levels assessed in ob/ob (steatotic) and ob/+ (control) mice using HR-MAS 1 H-NMR and qRT-PCR, respectively.

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.

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

Sequence Effect on the Formation of DNA Minidumbbells.

PubMed

Liu, Yuan; Lam, Sik Lok

2017-11-16

The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.

Structure and Orientation of a Voltage-Sensor Toxin in Lipid Membranes

PubMed Central

Jung, Hyun Ho; Jung, Hoi Jong; Milescu, Mirela; Lee, Chul Won; Lee, Seungkyu; Lee, Ju Yeon; Eu, Young-Jae; Kim, Ha Hyung; Swartz, Kenton J.; Kim, Jae Il

2010-01-01

Abstract Amphipathic protein toxins from tarantula venom inhibit voltage-activated potassium (Kv) channels by binding to a critical helix-turn-helix motif termed the voltage sensor paddle. Although these toxins partition into membranes to bind the paddle motif, their structure and orientation within the membrane are unknown. We investigated the interaction of a tarantula toxin named SGTx with membranes using both fluorescence and NMR spectroscopy. Depth-dependent fluorescence-quenching experiments with brominated lipids suggest that Trp30 in SGTx is positioned ∼9 Å from the center of the bilayer. NMR spectra reveal that the inhibitor cystine knot structure of the toxin does not radically change upon membrane partitioning. Transferred cross-saturation NMR experiments indicate that the toxin's hydrophobic protrusion contacts the hydrophobic core of the membrane, whereas most surrounding polar residues remain at interfacial regions of the bilayer. The inferred orientation of the toxin reveals a twofold symmetry in the arrangement of basic and hydrophobic residues, a feature that is conserved among tarantula toxins. These results have important implications for regions of the toxin involved in recognizing membranes and voltage-sensor paddles, and for the mechanisms by which tarantula toxins alter the activity of different types of ion channels. PMID:20643084

(19)F NMR reveals multiple conformations at the dimer interface of the nonstructural protein 1 effector domain from influenza A virus.

PubMed

Aramini, James M; Hamilton, Keith; Ma, Li-Chung; Swapna, G V T; Leonard, Paul G; Ladbury, John E; Krug, Robert M; Montelione, Gaetano T

2014-04-08

Nonstructural protein 1 of influenza A virus (NS1A) is a conserved virulence factor comprised of an N-terminal double-stranded RNA (dsRNA)-binding domain and a multifunctional C-terminal effector domain (ED), each of which can independently form symmetric homodimers. Here we apply (19)F NMR to NS1A from influenza A/Udorn/307/1972 virus (H3N2) labeled with 5-fluorotryptophan, and we demonstrate that the (19)F signal of Trp187 is a sensitive, direct monitor of the ED helix:helix dimer interface. (19)F relaxation dispersion data reveal the presence of conformational dynamics within this functionally important protein:protein interface, whose rate is more than three orders of magnitude faster than the kinetics of ED dimerization. (19)F NMR also affords direct spectroscopic evidence that Trp187, which mediates intermolecular ED:ED interactions required for cooperative dsRNA binding, is solvent exposed in full-length NS1A at concentrations below aggregation. These results have important implications for the diverse roles of this NS1A epitope during influenza virus infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

Self-assembly of Zn(salphen) complexes: steric regulation, stability studies and crystallographic analysis revealing an unexpected dimeric 3,3'-t-Bu-substituted Zn(salphen) complex.

PubMed

Martínez Belmonte, Marta; Wezenberg, Sander J; Haak, Robert M; Anselmo, Daniele; Escudero-Adán, Eduardo C; Benet-Buchholz, Jordi; Kleij, Arjan W

2010-05-21

The self-assembly features of a series of (non)symmetrical Zn(salphen) complexes have been studied in detail by X-ray crystallography, NMR and UV-vis techniques. The combined data demonstrate that the stability of these dimeric assemblies and the relative position of each monomeric unit within the dinuclear structure depend on the location and combination of the aromatic ring substituents.

NMR-based metabonomic analysis of the hepatotoxicity induced by combined exposure to PCBs and TCDD in rats

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

Lu Chunfeng; Department of Pharmacology, Basic Medical College, Jiamusi University, Jiamusi 154007; Wang Yimei

2010-11-01

A metabonomic approach using {sup 1}H NMR spectroscopy was adopted to investigate the metabonomic pattern of rat urine after oral administration of environmental endocrine disruptors (EDs) polychlorinated biphenyls (PCBs) and 2,3,7,8-tetrachlorodibenzo- p-dioxin (TCDD) alone or in combination and to explore the possible hepatotoxic mechanisms of combined exposure to PCBs and TCDD. {sup 1}H NMR spectra of urines collected 24 h before and after exposure were analyzed via pattern recognition by using principal component analysis (PCA). Serum biochemistry and liver histopathology indicated significant hepatotoxicity in the rats of the combined group. The PCA scores plots of urinary {sup 1}H NMR datamore » showed that all the treatment groups could be easily distinguished from the control group, so could the PCBs or TCDD group and the combined group. The loadings plots of the PCA revealed remarkable increases in the levels of lactate, glucose, taurine, creatine, and 2-hydroxy-isovaleric acid and reductions in the levels of 2-oxoglutarate, citrate, succinate, hippurate, and trimethylamine-N-oxide in rat urine after exposure. These changes were more striking in the combined group. The changed metabolites may be considered possible biomarker for the hepatotoxicity. The present study demonstrates that combined exposure to PCBs and TCDD induced significant hepatotoxicity in rats, and mitochondrial dysfunction and fatty acid metabolism perturbations might contribute to the hepatotoxicity. There was good conformity between changes in the urine metabonomic pattern and those in serum biochemistry and liver histopathology. These results showed that the NMR-based metabonomic approach may provide a promising technique for the evaluation of the combined toxicity of EDs.« less

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.

Soft Corals Biodiversity in the Egyptian Red Sea: A Comparative MS and NMR Metabolomics Approach of Wild and Aquarium Grown Species.

PubMed

Farag, Mohamed A; Porzel, Andrea; Al-Hammady, Montasser A; Hegazy, Mohamed-Elamir F; Meyer, Achim; Mohamed, Tarik A; Westphal, Hildegard; Wessjohann, Ludger A

2016-04-01

Marine life has developed unique metabolic and physiologic capabilities and advanced symbiotic relationships to survive in the varied and complex marine ecosystems. Herein, metabolite composition of the soft coral genus Sarcophyton was profiled with respect to its species and different habitats along the coastal Egyptian Red Sea via (1)H NMR and ultra performance liquid chromatography-mass spectrometry (UPLC-MS) large-scale metabolomics analyses. The current study extends the application of comparative secondary metabolite profiling from plants to corals revealing for metabolite compositional differences among its species via a comparative MS and NMR approach. This was applied for the first time to investigate the metabolism of 16 Sarcophyton species in the context of their genetic diversity or growth habitat. Under optimized conditions, we were able to simultaneously identify 120 metabolites including 65 diterpenes, 8 sesquiterpenes, 18 sterols, and 15 oxylipids. Principal component analysis (PCA) and orthogonal projection to latent structures-discriminant analysis (OPLS) were used to define both similarities and differences among samples. For a compound based classification of coral species, UPLC-MS was found to be more effective than NMR. The main differentiations emanate from cembranoids and oxylipids. The specific metabolites that contribute to discrimination between soft corals of S. ehrenbergi from the three different growing habitats also belonged to cembrane type diterpenes, with aquarium S. ehrenbergi corals being less enriched in cembranoids compared to sea corals. PCA using either NMR or UPLC-MS data sets was found equally effective in predicting the species origin of unknown Sarcophyton. Cyclopropane containing sterols observed in abundance in corals may act as cellular membrane protectant against the action of coral toxins, that is, cembranoids.

Transformations of the chemical compositions of high molecular weight DOM along a salinity transect: Using two dimensional correlation spectroscopy and principal component analysis approaches

NASA Astrophysics Data System (ADS)

Abdulla, Hussain A. N.; Minor, Elizabeth C.; Dias, Robert F.; Hatcher, Patrick G.

2013-10-01

In a study of chemical transformations of estuarine high-molecular-weight (HMW, >1000 Da) dissolved organic matter (DOM) collected over a period of two years along a transect through the Elizabeth River/Chesapeake Bay system to the coastal Atlantic Ocean off Virginia, USA, δ13C values, N/C ratios, and principal component analysis (PCA) of the solid-state 13C NMR (nuclear magnetic resonance) spectra of HMW-DOM show an abrupt change in both its sources and chemical structural composition occurring around salinity 20. HMW-DOM in the lower salinity region had lighter isotopic values, higher aromatic and lower carbohydrate contents relative to that in the higher salinity region. These changes around a salinity of 20 are possibly due to introduction of a significant amount of new carbon (autotrophic DOM) to the transect. PC-1 loadings plot shows that spatially differing DOM components are similar to previously reported 13C NMR spectra of heteropolysaccharides (HPS) and carboxyl-rich alicyclic molecules (CRAM). Applying two dimensional correlation spectroscopy techniques to 1H NMR spectra from the same samples reveals increases in the contribution of N-acetyl amino sugars, 6-deoxy sugars, and sulfated polysaccharides to HPS components along the salinity transect, which suggests a transition from plant derived carbohydrates to marine produced carbohydrates within the HMW-DOM pool. In contrast to what has been suggested previously, our combined results from 13C NMR, 1H NMR, and FTIR indicate that CRAM consists of at least two different classes of compounds (aliphatic polycarboxyl compounds and lignin-like compounds).

Chemical Exchange Saturation Transfer in Chemical Reactions: A Mechanistic Tool for NMR Detection and Characterization of Transient Intermediates.

PubMed

Lokesh, N; Seegerer, Andreas; Hioe, Johnny; Gschwind, Ruth M

2018-02-07

The low sensitivity of NMR and transient key intermediates below detection limit are the central problems studying reaction mechanisms by NMR. Sensitivity can be enhanced by hyperpolarization techniques such as dynamic nuclear polarization or the incorporation/interaction of special hyperpolarized molecules. However, all of these techniques require special equipment, are restricted to selective reactions, or undesirably influence the reaction pathways. Here, we apply the chemical exchange saturation transfer (CEST) technique for the first time to NMR detect and characterize previously unobserved transient reaction intermediates in organocatalysis. The higher sensitivity of CEST and chemical equilibria present in the reaction pathway are exploited to access population and kinetics information on low populated intermediates. The potential of the method is demonstrated on the proline-catalyzed enamine formation for unprecedented in situ detection of a DPU stabilized zwitterionic iminium species, the elusive key intermediate between enamine and oxazolidinones. The quantitative analysis of CEST data at 250 K revealed the population ratio of [Z-iminium]/[exo-oxazolidinone] 0.02, relative free energy +8.1 kJ/mol (calculated +7.3 kJ/mol), and free energy barrier of +45.9 kJ/mol (ΔG ⧧ calc. (268 K) = +42.2 kJ/mol) for Z-iminium → exo-oxazolidinone. The findings underpin the iminium ion participation in enamine formation pathway corroborating our earlier theoretical prediction and help in better understanding. The reliability of CEST is validated using 1D EXSY-build-up techniques at low temperature (213 K). The CEST method thus serves as a new tool for mechanistic investigations in organocatalysis to access key information, such as chemical shifts, populations, and reaction kinetics of intermediates below the standard NMR detection limit.

High-resolution NMR spectroscopic trends and assignment rules of metal-free, metallated and substituted corroles.

PubMed

Balazs, Yael S; Saltsman, Irena; Mahammed, Atif; Tkachenko, Elena; Golubkov, Galina; Levine, Joshua; Gross, Zeev

2004-07-01

Major advances over the last few years have facilitated the synthesis of a large variety of meso-only substituted corroles that display interesting catalytic, therapeutic and photophysical properties. This work is the first to study extensively the NMR spectral characteristics of both metallated and non-metallated triarylcorroles in various organic solvents and provide guidelines for easy and reliable assignments of 1D 1H spectra from trends of J coupling constants and chemical shifts. An excellent correlation is found between C=C bond lengths derived from 3J(H,H) values and experimental lengths determined by x-ray crystallography of the same molecules. The nuclear Overhauser effect provides a robust 1D 1H NMR tool for determining the selectivity of electrophilic substitutions. Variable-temperature NMR and isotopic labelling reveal a single preferred tautomerization state and unsymmetric ring orientations at -70 degrees C. The beta-pyrrole protons demonstrate long-range heteronuclear couplings with the coordination core (15N) and with the ortho-19F nuclei of the meso-carbon aryl rings. In sum, application of multinuclear magnetic resonance to corroles and their metal complexes, through the compilation of chemical shifts and J couplings and the recognition of trends therein, provides basic information essential to reliable spectral assignments. Additionally, the conclusions drawn about the structures of corroles and the electron densities at various positions of the corrole macrocycle resulting from the application of high-resolution NMR techniques are of importance to an in-depth understanding of the molecular interactions and processes of this relatively new and rapidly expanding class of compounds. Copyright 2004 John Wiley & Sons, Ltd.

ACETYL CHOLINESTERASE AND BUTYRYL CHOLINESTERASE INhIBITORY ACTIVITIES OF ZALEYA PENTANDRA.

PubMed

Afzal, Samina; Chaudhry, Bashir Ahmad; Afzal, Khurram; Saeed, Javeria; Akash, Sajd Hamid; Qadir, Muhammad Imran

2017-05-01

The aim of this study was to reveal acetyl cholinesterase (AchE) and butyryl cholinesterase (BchE) inhibitory activities of Zaleya pentandra. The aerial parts of the plant were air, freeze-dried and powdered. The extraction was carried out with methanol at room temperature for 24 h. The extract was concentrated on rotavapor and fractioned by column chromatography. The isolation and purification afforded amorphous solid which was subjected to physical, chemical and spectroscopic techniques i.e., UV, IR, H-NMR, "C-NMR and HREI-MS for the structure elucidation of the isolated compound. The compound was concluded as "Pentandradione" a novel compound. AchE and BchE inhibitory activities were estimated. The result showed that the isolated extract possessed significant activity against butyryl cholinesterase as compared to standard eserine while the extract lacks acetyl cholinesterase inhibitory activity.

Study on the inclusion behavior of p-sulfonatocalix[6]arene with propranolol by spectrofluorometry

NASA Astrophysics Data System (ADS)

Li, Hui; Song, Jin-Ping; Chao, Jian-Bin; Shuang, Shao-Min; Dong, Chuan

2012-11-01

The inclusion interaction between propranolol (PPL) and p-sulfonatocalix[6]arene (SCX6) was investigated by fluorescence and 1H NMR spectroscopy. Influences of pH, temperature, ionic strength and the concentration of SCX6 were examined in detail. In phosphate buffer solution with pH 7.5, the fluorescence of PPL dramatically quenched upon addition of SCX6 revealing the formation of inclusion complexes between PPL and SCX6. The stoichiometric ratio was verified to be 1:1 by the continuous variation method. The inclusion constant of PPL-SCX6 complexes was calculated as 2.2 × 104 L/mol by the nonlinear curve fitting method. 1H NMR titration spectra testified that the aliphatic chain of PPL may be partially penetrated into the hydrophobic cavity of SCX6. This was confirmed by molecular dynamics calculations.

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques.

PubMed

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-03-30

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 10 5  M -1 ) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

PubMed Central

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-01-01

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M−1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA. PMID:28358124

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.

A Metabolomic Approach (1H HRMAS NMR Spectroscopy) Supported by Histology to Study Early Post-transplantation Responses in Islet-transplanted Livers.

PubMed

Vivot, Kevin; Benahmed, Malika A; Seyfritz, Elodie; Bietiger, William; Elbayed, Karim; Ruhland, Elisa; Langlois, Allan; Maillard, Elisa; Pinget, Michel; Jeandidier, Nathalie; Gies, Jean-Pierre; Namer, Izzie-Jacques; Sigrist, Séverine; Reix, Nathalie

2016-01-01

Intrahepatic transplantation of islets requires a lot of islets because more than 50% of the graft is lost during the 24 hours following transplantation. We analyzed, in a rat model, early post-transplantation inflammation using systemic inflammatory markers, or directly in islet-transplanted livers by immunohistochemistry. 1 H HRMAS NMR was employed to investigate metabolic responses associated with the transplantation. Inflammatory markers (Interleukin-6, α2-macroglobulin) are not suitable to follow islet reactions as they are not islet specific. To study islet specific inflammatory events, immunohistochemistry was performed on sections of islet transplanted livers for thrombin (indicator of the instant blood-mediated inflammatory reaction (IBMIR)) and granulocytes and macrophages. We observed a specific correlation between IBMIR and granulocyte and macrophage infiltration after 12 h. In parallel, we identified a metabolic response associated with transplantation: after 12 h, glucose, alanine, aspartate, glutamate and glutathione were significantly increased. An increase of glucose is a marker of tissue degradation, and could be explained by immune cell infiltration. Alanine, aspartate and glutamate are inter-connected in a common metabolic pathway known to be activated during hypoxia. An increase of glutathione revealed the presence of antioxidant protection. In this study, IBMIR visualization combined with 1 H HRMAS NMR facilitated the characterization of cellular and molecular pathways recruited following islet transplantation.

A Metabolomic Approach (1H HRMAS NMR Spectroscopy) Supported by Histology to Study Early Post-transplantation Responses in Islet-transplanted Livers

PubMed Central

Vivot, Kevin; Benahmed, Malika A.; Seyfritz, Elodie; Bietiger, William; Elbayed, Karim; Ruhland, Elisa; Langlois, Allan; Maillard, Elisa; Pinget, Michel; Jeandidier, Nathalie; Gies, Jean-Pierre; Namer, Izzie-Jacques; Sigrist, Séverine; Reix, Nathalie

2016-01-01

Intrahepatic transplantation of islets requires a lot of islets because more than 50% of the graft is lost during the 24 hours following transplantation. We analyzed, in a rat model, early post-transplantation inflammation using systemic inflammatory markers, or directly in islet-transplanted livers by immunohistochemistry. 1H HRMAS NMR was employed to investigate metabolic responses associated with the transplantation. Inflammatory markers (Interleukin-6, α2-macroglobulin) are not suitable to follow islet reactions as they are not islet specific. To study islet specific inflammatory events, immunohistochemistry was performed on sections of islet transplanted livers for thrombin (indicator of the instant blood-mediated inflammatory reaction (IBMIR)) and granulocytes and macrophages. We observed a specific correlation between IBMIR and granulocyte and macrophage infiltration after 12 h. In parallel, we identified a metabolic response associated with transplantation: after 12 h, glucose, alanine, aspartate, glutamate and glutathione were significantly increased. An increase of glucose is a marker of tissue degradation, and could be explained by immune cell infiltration. Alanine, aspartate and glutamate are inter-connected in a common metabolic pathway known to be activated during hypoxia. An increase of glutathione revealed the presence of antioxidant protection. In this study, IBMIR visualization combined with 1H HRMAS NMR facilitated the characterization of cellular and molecular pathways recruited following islet transplantation. PMID:27766032

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

NASA Astrophysics Data System (ADS)

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-03-01

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M-1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

Nuclear magnetic resonance diagnosis of an anaplastic astrocytoma.

PubMed

Jackson, J A; Derman, H S; Harper, R L; Willcott, M R; Ford, J J; Schneiders, N J; McCrary, J A; Kelly, A; Bryan, R N

1984-01-01

A patient presented with an 8-month history of a progressive left homonymous visual field deficit, left hemiparesis, and a left thalamocortical sensory deficit that was not detectable by repeated conventional neurodiagnostic evaluations. Proton nuclear magnetic resonance (NMR) imaging revealed a right parietal lesion characterized by a prolonged T2 (spin-spin relaxation time). At surgery, the mass proved to be an anaplastic astrocytoma. NMR appears to be more sensitive than x-ray computerized tomography scanning in some patients with malignant gliomas and offers the clinician an additional probe with which to evaluate these patients.

Theory and Applications of Solid-State NMR Spectroscopy to Biomembrane Structure and Dynamics

NASA Astrophysics Data System (ADS)

Xu, Xiaolin

Solid-state Nuclear Magnetic Resonance (NMR) is one of the premiere biophysical methods that can be applied for addressing the structure and dynamics of biomolecules, including proteins, lipids, and nucleic acids. It illustrates the general problem of determining the average biomolecular structure, including the motional mean-square amplitudes and rates of the fluctuations. Lineshape and relaxtion studies give us a view into the molecular properties under different environments. To help the understanding of NMR theory, both lineshape and relaxation experiments are conducted with hexamethylbezene (HMB). This chemical compound with a simple structure serves as a perfect test molecule. Because of its highly symmetric structure, its motions are not very difficult to understand. The results for HMB set benchmarks for other more complicated systems like membrane proteins. After accumulating a large data set on HMB, we also proceed to develop a completely new method of data analysis, which yields the spectral densities in a body-fixed frame revealing internal motions of the system. Among the possible applications of solid-state NMR spectroscopy, we study the light activation mechanism of visual rhodopsin in lipid membranes. As a prototype of G-protein-coupled receptors, which are a large class of membrane proteins, the cofactor isomerization is triggered by photon absorption, and the local structural change is then propagated to a large-scale conformational change of the protein. Facilitation of the binding of transducin then passes along the visual signal to downstream effector proteins like transducin. To study this process, we introduce 2H labels into the rhodopsin chromophore retinal and the C-terminal peptide of transducin to probe the local structure and dynamics of these two hotspots of the rhodopsin activation process. In addition to the examination of local sites with solid-state 2H NMR spectroscopy, wide angle X-ray scattering (WAXS) provides us the chance of looking at the overall conformational changes through difference scattering profiles. Although the resolution of this method is not as high as NMR spectroscopy, which gives information on atomic scale, the early activation probing is possible because of the short duration of the optical pump and X-ray probe lasers. We can thus visualize the energy dissipation process by observing and comparing the difference scattering profiles at different times after the light activation moments.

Synthesis, Characterization, Antimicrobial Studies and Corrosion Inhibition Potential of 1,8-dimethyl-1,3,6,8,10,13-hexaazacyclotetradecane: Experimental and Quantum Chemical Studies

PubMed Central

Nwankwo, Henry U.; Ateba, Collins N.; Olasunkanmi, Lukman O.; Adekunle, Abolanle S.; Isabirye, David A.; Onwudiwe, Damian C.; Ebenso, Eno E.

2016-01-01

The macrocylic ligand, 1,8-dimethyl-1,3,6,8,10,13-hexaazacyclotetradecane (MHACD) was synthesized by the demetallation of its freshly synthesized Ni(II) complex (NiMHACD). Successful synthesis of NiMHACD and the free ligand (MHACD) was confirmed by various characterization techniques, including Fourier transform infra-red (FT-IR), proton nuclear magnetic resonance (1H-NMR), carbon-13 nuclear magnetic resonance (13C-NMR), ultraviolet-visible (UV-vis), and energy dispersive X-ray (EDX) spectroscopic techniques. The anti-bacteria activities of MHACD were investigated against Staphylococcus aureus and Enterococcus species and the results showed that MHACD possesses a spectrum of activity against the two bacteria. The electrochemical cyclic voltammetry study on MHACD revealed that it is a redox active compound with promising catalytic properties in electrochemical applications. The inhibition potential of MHACD for mild steel corrosion in 1 M HCl was investigated using potentiodynamic polarization method. The results showed that MHACD inhibits steel corrosion as a mixed-type inhibitor, and the inhibition efficiency increases with increasing concentration of MHACD. The adsorption of MHACD obeys the Langmuir adsorption isotherm; it is spontaneous and involves competitive physisorption and chemisorption mechanisms. Quantum chemical calculations revealed that the energy of the highest occupied molecular orbital (HOMO) of MHACD is high enough to favor forward donation of charges to the metal during adsorption and corrosion inhibition. Natural bond orbital (NBO) analysis revealed the presence of various orbitals in the MHACD that are capable of donating or accepting electrons under favorable conditions. PMID:28787909

Hepatitis B virus X protein (HBx)-induced abnormalities of nucleic acid metabolism revealed by (1)H-NMR-based metabonomics.

PubMed

Dan Yue; Zhang, Yuwei; Cheng, Liuliu; Ma, Jinhu; Xi, Yufeng; Yang, Liping; Su, Chao; Shao, Bin; Huang, Anliang; Xiang, Rong; Cheng, Ping

2016-04-14

Hepatitis B virus X protein (HBx) plays an important role in HBV-related hepatocarcinogenesis; however, mechanisms underlying HBx-mediated carcinogenesis remain unclear. In this study, an NMR-based metabolomics approach was applied to systematically investigate the effects of HBx on cell metabolism. EdU incorporation assay was conducted to examine the effects of HBx on DNA synthesis, an important feature of nucleic acid metabolism. The results revealed that HBx disrupted metabolism of glucose, lipids, and amino acids, especially nucleic acids. To understand the potential mechanism of HBx-induced abnormalities of nucleic acid metabolism, gene expression profiles of HepG2 cells expressing HBx were investigated. The results showed that 29 genes involved in DNA damage and DNA repair were differentially expressed in HBx-expressing HepG2 cells. HBx-induced DNA damage was further demonstrated by karyotyping, comet assay, Western blotting, immunofluorescence and immunohistochemistry analyses. Many studies have previously reported that DNA damage can induce abnormalities of nucleic acid metabolism. Thus, our results implied that HBx initially induces DNA damage, and then disrupts nucleic acid metabolism, which in turn blocks DNA repair and induces the occurrence of hepatocellular carcinoma (HCC). These findings further contribute to our understanding of the occurrence of HCC.

NMR spectroscopy reveals the presence and association of lipids and keratin in adhesive gecko setae

PubMed Central

Jain, Dharamdeep; Stark, Alyssa Y.; Niewiarowski, Peter H.; Miyoshi, Toshikazu; Dhinojwala, Ali

2015-01-01

Lipid and protein aggregates are one of the fundamental materials of biological systems. Examples include cell membranes, insect cuticle, vertebrate epidermis, feathers, hair and adhesive structures known as ‘setae’ on gecko toes. Until recently gecko setae were assumed to be composed entirely of keratin, but analysis of footprints left behind by geckos walking on surfaces revealed that setae include various kinds of lipids. However, the arrangement and molecular-level behavior of lipids and keratin in the setae is still not known. In the present study we demonstrate, for the first time, the use of Nuclear Magnetic Resonance (NMR) spectroscopy techniques to confirm the presence of lipids and investigate their association with keratin in ‘pristine' sheds, or natural molts of the adhesive toe pad and non-adhesive regions of the skin. Analysis was also carried on the sheds after they were ‘delipidized’ to remove surface lipids. Our results show a distribution of similar lipids in both the skin and toe shed but with different dynamics at a molecular level. The present study can help us understand the gecko system both biologically and for design of synthetic adhesives, but the findings may be relevant to the characteristics of lipid-protein interactions in other biological systems. PMID:25902194

Spectroscopic characterization of metal bound phytochelatin analogue (Glu-Cys)4-Gly.

PubMed

Cheng, Yongsheng; Yan, Yong-Bin; Liu, Jinyuan

2005-10-01

The metal ion binding properties of a phytochelatin (PC) analogue, (Glu-Cys)4-Gly (named as EC4), have been studied by a divalent metal ion binding assay monitored by UV-visible spectroscopy, circular dichroism and NMR spectroscopy. Spectro- photometric titration with different divalent metal ions have revealed that the stiochoimetry of metal-bound EC4 was 1:1, and its metal binding affinities with different divalent metal ions in the order of Cd(II)>Cu(II)>Zn(II)>Pb(II)>Ni(II)>Co(II). UV-visible spectroscopic analysis of metal complexes indicated that four sulfur atoms in cysteine residues are attributable to ligand-to-metal charge transfer (LMCT) between divalent metal ions and EC4, and further confirmed by 1D H1 NMR study and Circular Dichroism. In addition, Circular Dichroism spectra of both free and metal-bound forms of EC4 revealed that metal coordination drives the nonapeptide chain to fold into a turned conformation. The comprehensive analysis of spectroscopic properties of the nonapeptide complexed with metal ions not only provides a fundamental description of the metal ion binding properties of PC analogue, but also shows a correlation between metal binding affinity of PC analogue and the induction activity of metal ions.

Using nuclear magnetic resonance and transient electromagnetics to characterise water distribution beneath an ice covered volcanic crater: the case of Sherman Crater Mt. Baker Washington.

USGS Publications Warehouse

Irons, Trevor P.; Martin, Kathryn; Finn, Carol A.; Bloss, Benjamin; Horton, Robert J.

2014-01-01

Surface and laboratory Nuclear Magnetic Resonance (NMR) measurements combined with transient electromagnetic (TEM) data are powerful tools for subsurface water detection. Surface NMR (sNMR) and TEM soundings, laboratory NMR, complex resistivity, and X-Ray Diffraction (XRD) analysis were all conducted to characterise the distribution of water within Sherman Crater on Mt. Baker, WA. Clay rich rocks, particularly if water saturated, can weaken volcanoes, thereby increasing the potential for catastrophic sector collapses that can lead to far-travelled, destructive debris flows. Detecting the presence and volume of shallow groundwater is critical for evaluating these landslide hazards. The TEM data identified a low resistivity layer (<10 ohm-m), under 60 m of glacial ice related to water saturated clays. The TEM struggles to resolve the presence or absence of a plausible thin layer of bulk liquid water on top of the clay. The sNMR measurements did not produce any observable signal, indicating the lack of substantial accumulated bulk water below the ice. Laboratory analysis on a sample from the crater wall that likely represented the clays beneath the ice confirmed that the controlling factor for the lack of sNMR signal was the fine-grained nature of the media. The laboratory measurements further indicated that small pores in clays detected by the XRD contain as much as 50% water, establishing an upper bound on the water content in the clay layer. Forward modelling of geologic scenarios revealed that bulk water layers as thin as ½ m between the ice and clay layer would have been detectable using sNMR. The instrumentation conditions which would allow for sNMR detection of the clay layer are investigated. Using current instrumentation the combined analysis of the TEM and sNMR data allow for valuable characterisation of the groundwater system in the crater. The sNMR is able to reduce the uncertainty of the TEM in regards to the presence of a bulk water layer, a valuable piece of information in hazard assessment.

Design, synthesis, structural characterization by IR, (1) H, (13) C, (15) N, 2D-NMR, X-ray diffraction and evaluation of a new class of phenylaminoacetic acid benzylidene hydrazines as pfENR inhibitors.

PubMed

Samal, Ramanuj P; Khedkar, Vijay M; Pissurlenkar, Raghuvir R S; Bwalya, Angela Gono; Tasdemir, Deniz; Joshi, Ramesh A; Rajamohanan, P R; Puranik, Vedavati G; Coutinho, Evans C

2013-06-01

Recent studies have revealed that plasmodial enoyl-ACP reductase (pfENR, FabI), one of the crucial enzymes in the plasmodial type II fatty acid synthesis II (FAS II) pathway, is a promising target for liver stage malaria infections. Hence, pfENR inhibitors have the potential to be used as causal malarial prophylactic agents. In this study, we report the design, synthesis, structural characterization and evaluation of a new class of pfENR inhibitors. The search for inhibitors began with a virtual screen of the iResearch database by molecular docking. Hits obtained from the virtual screen were ranked according to their Glide score. One hit was selected as a lead and modified to improve its binding to pfENR; from this, a series of phenylamino acetic acid benzylidene hydrazides were designed and synthesized. These molecules were thoroughly characterized by IR, (1) H, (13) C, (15) N, 2D-NMR (COSY, NOESY, (1) H-(13) C, (1) H-(15) N HSQC and HMBC), and X-ray diffraction. NMR studies revealed the existence of conformational/configurational isomers around the amide and imine functionalities. The major species in DMSO solution is the E, E form, which is in dynamic equilibrium with the Z, E isomer. In the solid state, the molecule has a completely extended conformation and forms helical structures that are stabilized by strong hydrogen bond interactions, forming a helical structure stabilized by N-H…O interactions, a feature unique to this class of compounds. Furthermore, detailed investigation of the NMR spectra indicated the presence of a minor impurity in most compounds. The structure of this impurity was deduced as an imidazoline-4-one derivative based on (1) H-(13) C and (1) H-(15) H HMBC spectra and was confirmed from the NOESY spectra. The molecules were screened for in vitro activity against recombinant pfENR enzyme by a spectrophotometric assay. Four molecules, viz. 17, 7, 10, and 12 were found to be active at 7, 8, 10, and 12 μm concentration, respectively, showing promising pfENR inhibitory potential. A classification model was derived based on a binary QSAR approach termed recursive partitioning (RP) to highlight structural characteristics that could be tuned to improve activity. © 2013 John Wiley & Sons A/S.

Amorphous surface layer versus transient amorphous precursor phase in bone - A case study investigated by solid-state NMR spectroscopy.

PubMed

Von Euw, Stanislas; Ajili, Widad; Chan-Chang, Tsou-Hsi-Camille; Delices, Annette; Laurent, Guillaume; Babonneau, Florence; Nassif, Nadine; Azaïs, Thierry

2017-09-01

The presence of an amorphous surface layer that coats a crystalline core has been proposed for many biominerals, including bone mineral. In parallel, transient amorphous precursor phases have been proposed in various biomineralization processes, including bone biomineralization. Here we propose a methodology to investigate the origin of these amorphous environments taking the bone tissue as a key example. This study relies on the investigation of a bone tissue sample and its comparison with synthetic calcium phosphate samples, including a stoichiometric apatite, an amorphous calcium phosphate sample, and two different biomimetic apatites. To reveal if the amorphous environments in bone originate from an amorphous surface layer or a transient amorphous precursor phase, a combined solid-state nuclear magnetic resonance (NMR) experiment has been used. The latter consists of a double cross polarization 1 H→ 31 P→ 1 H pulse sequence followed by a 1 H magnetization exchange pulse sequence. The presence of an amorphous surface layer has been investigated through the study of the biomimetic apatites; while the presence of a transient amorphous precursor phase in the form of amorphous calcium phosphate particles has been mimicked with the help of a physical mixture of stoichiometric apatite and amorphous calcium phosphate. The NMR results show that the amorphous and the crystalline environments detected in our bone tissue sample belong to the same particle. The presence of an amorphous surface layer that coats the apatitic core of bone apatite particles has been unambiguously confirmed, and it is certain that this amorphous surface layer has strong implication on bone tissue biogenesis and regeneration. Questions still persist on the structural organization of bone and biomimetic apatites. The existing model proposes a core/shell structure, with an amorphous surface layer coating a crystalline bulk. The accuracy of this model is still debated because amorphous calcium phosphate (ACP) environments could also arise from a transient amorphous precursor phase of apatite. Here, we provide an NMR spectroscopy methodology to reveal the origin of these ACP environments in bone mineral or in biomimetic apatite. The 1 H magnetization exchange between protons arising from amorphous and crystalline domains shows unambiguously that an ACP layer coats the apatitic crystalline core of bone et biomimetic apatite platelets. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

NMR studies reveal the role of biomembranes in modulating ligand binding and release by intracellular bile acid binding proteins.

PubMed

Pedò, Massimo; Löhr, Frank; D'Onofrio, Mariapina; Assfalg, Michael; Dötsch, Volker; Molinari, Henriette

2009-12-18

Bile acid molecules are transferred vectorially between basolateral and apical membranes of hepatocytes and enterocytes in the context of the enterohepatic circulation, a process regulating whole body lipid homeostasis. This work addresses the role of the cytosolic lipid binding proteins in the intracellular transfer of bile acids between different membrane compartments. We present nuclear magnetic resonance (NMR) data describing the ternary system composed of the bile acid binding protein, bile acids, and membrane mimetic systems, such as anionic liposomes. This work provides evidence that the investigated liver bile acid binding protein undergoes association with the anionic membrane and binding-induced partial unfolding. The addition of the physiological ligand to the protein-liposome mixture is capable of modulating this interaction, shifting the equilibrium towards the free folded holo protein. An ensemble of NMR titration experiments, based on nitrogen-15 protein and ligand observation, confirm that the membrane and the ligand establish competing binding equilibria, modulating the cytoplasmic permeability of bile acids. These results support a mechanism of ligand binding and release controlled by the onset of a bile salt concentration gradient within the polarized cell. The location of a specific protein region interacting with liposomes is highlighted.

Revisiting the formation of cyclic clusters in liquid ethanol

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

Balanay, Mannix P.; Fan, Haiyan, E-mail: haiyan.fan@nu.edu.kz; Kim, Dong Hee

2016-04-21

The liquid phase of ethanol in pure and in non-polar solvents was studied at room temperature using Fourier transform infrared (FT-IR) and {sup 1}H nuclear magnetic resonance (NMR) spectroscopies together with theoretical approach. The FT-IR spectra for pure ethanol and solution in cyclohexane at different dilution stages are consistent with {sup 1}H NMR results. The results from both methods were best explained by the results of the density functional theory based on a multimeric model. It is suggested that cyclic trimers and tetramers are dominated in the solution of cyclohexane/hexane with the concentration greater than 0.5M at room temperature. Inmore » liquid ethanol, while the primary components at room temperature are cyclic trimers and tetramers, there is a certain amount (∼14%) of open hydroxide group representing the existence of chain like structures in the equilibria. The cyclic cluster model in the liquid and concentrated solution phase (>0.5M) can be used to explain the anomalously lower freezing point of ethanol (159 K) than that of water (273 K) at ambient conditions. In addition, {sup 1}H NMR at various dilution stages reveals the dynamics for the formation of cyclic clusters.« less

NMR-Based Metabolomic Study on Isatis tinctoria: Comparison of Different Accessions, Harvesting Dates, and the Effect of Repeated Harvesting.

PubMed

Guldbrandsen, Niels; Kostidis, Sarantos; Schäfer, Hartmut; De Mieri, Maria; Spraul, Manfred; Skaltsounis, Alexios-Leandros; Mikros, Emmanuel; Hamburger, Matthias

2015-05-22

Isatis tinctoria is an ancient dye and medicinal plant with potent anti-inflammatory and antiallergic properties. Metabolic differences were investigated by NMR spectroscopy of accessions from different origins that were grown under identical conditions on experimental plots. For these accessions, metabolite profiles at different harvesting dates were analyzed, and single and repeatedly harvested plants were compared. Leaf samples were shock-frozen in liquid N2 immediately after being harvested, freeze-dried, and cryomilled prior to extraction. Extracts were prepared by pressurized liquid extraction with ethyl acetate and 70% aqueous methanol. NMR spectra were analyzed using a combination of different methods of multivariate data analysis such as principal component analysis (PCA), canonical analysis (CA), and k-nearest neighbor concept (k-NN). Accessions and harvesting dates were well separated in the PCA/CA/k-NN analysis in both extracts. Pairwise statistical total correlation spectroscopy (STOCSY) revealed unsaturated fatty acids, porphyrins, carbohydrates, indole derivatives, isoprenoids, phenylpropanoids, and minor aromatic compounds as the cause of these differences. In addition, the metabolite profile was affected by the repeated harvest regime, causing a decrease of 1,5-anhydroglucitol, sucrose, unsaturated fatty acids, porphyrins, isoprenoids, and a flavonoid.

Magnetic resonance studies of inorganic oxides and a new pulse programming system for pulsed EMR

NASA Astrophysics Data System (ADS)

Schwartz, Dwight Allen

We have investigated several inorganic oxide systems using nuclear and electron magnetic resonance spectroscopies and also report a new pulse programming system for a pulsed S-band EMR spectrometer. We show in a study of simple perovskites (Ca,Sr,Ba)(Ti,Zr) Osb3 that magic-angle spinning O-17 NMR provides unique, highly-resolved spectra in these materials and gives evidence of being useful as a diagnostic tool in mixed phase materials (Asb{x}Asbsp{1-x}{'})BOsb3. Various used NMR and EMR techniques to study of the commercial borosilicate glasses CGW-3320, CGW-7502, CGW-7740 (Pyrex) and GSC-4, and T-08 (pure silica glass) which had received 5-10 gigarad doses of Co-60 gamma-radiation in the presence and absence of hydrogen gas. We show that B-11, Al-27 and Si-29 MAS NMR spectra contain indications of structural changes in these glasses as a result of large doses of radiation. We also observed the reduction of trace Ti(IV) to Ti(III) when Hsb2 gas was present during irradiation of glass samples. Static NMR and EMR studies in the (Na,Li)POsb3 system indicate a possible mixed alkali effect in the spin-lattice relaxation of Na-23 in NaPOsb3 and Lisb{0.4}Nasb{0.6}POsb3. Static Na-23 NMR studies of NaPOsb3 reveal the presence of different structural or dynamical environments as a function of temperatures between 23-566 C. We have investigated glass and glass fibers of Lisb{0.6}Nasb{0.4}POsb3 and Na(Psb{0.99},Vsb{0.01})Osb3, and show P-31 NMR and EMR evidence that these materials remained structurally isotropic when pulled into fibers. We show that vanadium (in Na(Psb{0.99},Vsb{0.01})Osb3) appears to suppress radiolytic unpaired electron and hole defect production which does take place in nominally vanadium-free NaPOsb3 during small doses of gamma-radiation. We describe hardware and software developed for a pulse programming system for a pulsed S-band EMR spectrometer. This system supports user-programmable automatic independent control of all pulse sequence parameters (pulse and delay durations, and pulse phases). We demonstrate the capabilities of this new system in 2-, 3-, and 4-pulse EMR experiments, and also demonstrate a new software suite for interactive simulation and simulation optimization of electron spin echo envelope modulation (ESEEM) patterns using a genetic algorithm.

Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

USGS Publications Warehouse

Leenheer, J.A.; Brown, G.K.; MacCarthy, P.; Cabaniss, S.E.

1998-01-01

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The 'metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-1R spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short- chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The `metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.

1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

PubMed Central

Lankadurai, Brian P.; Furdui, Vasile I.; Reiner, Eric J.; Simpson, André J.; Simpson, Myrna J.

2013-01-01

1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined. PMID:24958147

Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l-arabinofuranosidase from Thermobacillus xylanilyticus.

PubMed

Arab-Jaziri, Faten; Bissaro, Bastien; Barbe, Sophie; Saurel, Olivier; Débat, Hélène; Dumon, Claire; Gervais, Virginie; Milon, Alain; André, Isabelle; Fauré, Régis; O'Donohue, Michael J

2012-10-01

This study is focused on the elucidation of the functional role of the mobile β2α2 loop in the α-L-arabinofuranosidase from Thermobacillus xylanilyticus, and particularly on the roles of loop residues H98 and W99. Using site-directed mutagenesis, coupled to characterization methods including isothermal titration calorimetry (ITC) and saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, and molecular dynamics simulations, it has been possible to provide a molecular level view of interactions and the consequences of mutations. Binding of para-nitrophenyl α-L-arabinofuranoside (pNP-α-l-Araf) to the wild-type arabinofuranosidase was characterized by K(d) values (0.32 and 0.16 mm, from ITC and STD-NMR respectively) that highly resembled that of the arabinoxylo-oligosaccharide XA(3)XX (0.21 mm), and determination of the thermodynamic parameters of enzyme : pNP-α-L-Araf binding revealed that this process is driven by favourable entropy, which is linked to the movement of the β2α2 loop. Loop closure relocates the solvent-exposed W99 into a buried location, allowing its involvement in substrate binding and in the formation of a functional active site. Similarly, the data underline the role of H98 in the ‘dynamic’ formation and definition of a catalytically operational active site, which may be a specific feature of a subset of GH51 arabinofuranosidases. Substitution of H98 and W99 by alanine or phenylalanine revealed that mutations affected K(M) and/or k(cat). Molecular dynamics performed on W99A implied that this mutation causes the loss of a hydrogen bond and leads to an alternative binding mode that is detrimental for catalysis. STD-NMR experiments revealed altered binding of the aglycon motif in the active site, combined with reduced STD intensities of the α-L-arabinofuranosyl moiety for W99 substitutions. © 2012 The Authors Journal compilation © 2012 FEBS.

High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States.

PubMed

Zhang, Yi; Kitazawa, Soichiro; Peran, Ivan; Stenzoski, Natalie; McCallum, Scott A; Raleigh, Daniel P; Royer, Catherine A

2016-11-23

Understanding protein folding mechanisms and their sequence dependence requires the determination of residue-specific apparent kinetic rate constants for the folding and unfolding reactions. Conventional two-dimensional NMR, such as HSQC experiments, can provide residue-specific information for proteins. However, folding is generally too fast for such experiments. ZZ-exchange NMR spectroscopy allows determination of folding and unfolding rates on much faster time scales, yet even this regime is not fast enough for many protein folding reactions. The application of high hydrostatic pressure slows folding by orders of magnitude due to positive activation volumes for the folding reaction. We combined high pressure perturbation with ZZ-exchange spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9. We obtained residue-specific apparent rates at 2500 bar for the N-terminal domain of L9 (NTL9), and rates at atmospheric pressure for a mutant of the C-terminal domain (CTL9) from pressure dependent ZZ-exchange measurements. Our results revealed that NTL9 folding is almost perfectly two-state, while small deviations from two-state behavior were observed for CTL9. Both domains exhibited large positive activation volumes for folding. The volumetric properties of these domains reveal that their transition states contain most of the internal solvent excluded voids that are found in the hydrophobic cores of the respective native states. These results demonstrate that by coupling it with high pressure, ZZ-exchange can be extended to investigate a large number of protein conformational transitions.

In situ NMR spectroscopy: inulin biomass conversion in ZnCl₂ molten salt hydrate medium-SnCl₄ addition controls product distribution.

PubMed

Wang, Yingxiong; Pedersen, Christian Marcus; Qiao, Yan; Deng, Tiansheng; Shi, Jing; Hou, Xianglin

2015-01-22

The dehydration of inulin biomass to the platform chemicals, 5-hydroxymethylfurfural (5-HMF) and levulinic acid (LA), in ZnCl2 molten salt hydrate medium was investigated. The influence of the Lewis acid catalyst, SnCl4, on the product distribution was examined. An in situ(1)H NMR technique was employed to follow the reaction at the molecular level. The experimental results revealed that only 5-HMF was obtained from degradation of inulin biomass in ZnCl2 molten salt hydrate medium, while the LA was gradually becoming the main product when the reaction temperature was increased in the presence of the Lewis acid catalyst SnCl4. In situ NMR spectroscopy could monitor the reaction and give valuable insight. Copyright © 2014 Elsevier Ltd. All rights reserved.

Antibacterial colorants: characterization of prodiginines and their applications on textile materials.

PubMed

Alihosseini, Farzaneh; Ju, Kou-San; Lango, Jozsef; Hammock, Bruce D; Sun, Gang

2008-01-01

A strain of Vibrio sp. isolated from marine sediments produced large quantities of bright red pigments that could be used to dye many fibers including wool, nylon, acrylics, and silk. Characterization of the pigments by electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) revealed three prodiginine-like structures with nonpolar characteristics and low molecular mass. UV-visible spectra of the major constituent in methanol solution showed absorbance at lambda max 530 nm wavelength. The accurate mass result showed that the main isolated product has a molecular mass of m/z 323.1997. Further analysis using mass fragmentation (MS/MS), 1H NMR, COSY, HMQC NMR and DEPT confirmed the detailed structure of the pigment with an elementary composition of C20H25N3O. Fabrics dyed with the microbial prodiginines demonstrated antibacterial activity.

Long-range Li+ dynamics in the lithium argyrodite Li7PSe6 as probed by rotating-frame spin-lattice relaxation NMR.

PubMed

Epp, V; Gün, O; Deiseroth, H-J; Wilkening, M

2013-05-21

Lithium-rich argyrodites belong to a relatively new group of fast ion conducting solids. They might serve as powerful electrolytes in all-solid-state lithium-ion batteries being, from a medium-term point of view, the key technology when safe energy storage systems have to be developed. Spin-lattice relaxation (SLR) nuclear magnetic resonance (NMR) measurements carried out in the rotating frame of reference turned out to be the method of choice to study Li dynamics in argyrodites. When plotted as a function of the inverse temperature, the SLR rates log10(R1ρ) reveal an asymmetric diffusion-induced rate peak. The rate peak contains information on the Li jump rate, the activation energy of the hopping process as well as correlation effects. In particular, considering the high-temperature flank of the SLR NMR rate peak recorded in the rotating frame of reference, an activation energy of approximately 0.49 eV is found. This value represents long-range lithium jump diffusion in crystalline Li7PSe6. As an example, at 325 K the Li jump rate determined from SLR NMR is in the order of 1.4 × 10(5) s(-1). The pronounced asymmetry of the rate peak R1ρ(1/T) points to correlated Li motion. It is comparable to that which is typically found for structurally disordered materials showing a broad range of correlation times.

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

PubMed Central

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

2013-01-01

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

Studies on interaction of norbixin with DNA: Multispectroscopic and in silico analysis

NASA Astrophysics Data System (ADS)

Anantharaman, Amrita; Priya, Rajendra Rao; Hemachandran, Hridya; Sivaramakrishna, Akella; Babu, Subramanian; Siva, Ramamoorthy

2015-06-01

The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08 × 105 Mol-1 L. FTIR and CD studies were coupled with 1H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

PubMed

Havrila, Marek; Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Krepl, Miroslav; Otyepka, Michal; Šponer, Jiří

2015-12-10

We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.

Polymeric proanthocyanidins 13C NMR studies of procyanidins

Treesearch

Lawrence J. Porter; Roger H. Newman; Lai Yeap Foo; Herbert Wong; Richard W. Hemingway

1982-01-01

Proanthocyanidin polymers have been shown to consist entirely of flavan-3-ol units by a combination of techniques including 13C n.m.r. spectroscopy. The 13C n.m.r. spectra of the polymers and related molecules are now considered in more detail. Prior to this study UC n.m.r. data has been published of procyanidins and...

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

NMR evidence of charge fluctuations in multiferroic CuBr2

NASA Astrophysics Data System (ADS)

Wang, Rui-Qi; Zheng, Jia-Cheng; Chen, Tao; Wang, Peng-Shuai; Zhang, Jin-Shan; Cui, Yi; Wang, Chao; Li, Yuan; Xu, Sheng; Yuan, Feng; Yu, Wei-Qiang

2018-03-01

We report combined magnetic susceptibility, dielectric constant, nuclear quadruple resonance (NQR), and zero-field nuclear magnetic resonance (NMR) measurements on single crystals of multiferroics CuBr2. High quality of the sample is demonstrated by the sharp magnetic and magnetic-driven ferroelectric transition at {T}{{N}}={T}{{C}}≈ 74 K. The zero-field 79Br and 81Br NMR are resolved below T N. The spin-lattice relaxation rates reveal charge fluctuations when cooled below 60 K. Evidences of an increase of NMR linewidth, a reduction of dielectric constant, and an increase of magnetic susceptibility are also seen at low temperatures. These data suggest an emergent instability which competes with the spiral magnetic ordering and the ferroelectricity. Candidate mechanisms are discussed based on the quasi-one-dimensional nature of the magnetic system. Project supported by the Ministry of Science and Technology of China (Grant No. 2016YFA0300504), the National Natural Science Foundation of China (Grant No. 11374364), the Fundamental Research Funds for the Central Universities of China, and the Research Funds of Renmin University, China (Grant No. 14XNLF08).

5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy

PubMed Central

Puffer, Barbara; Kreutz, Christoph; Rieder, Ulrike; Ebert, Marc-Olivier; Konrat, Robert; Micura, Ronald

2009-01-01

19F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D 19F and 1H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis. PMID:19843610

5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.

PubMed

Puffer, Barbara; Kreutz, Christoph; Rieder, Ulrike; Ebert, Marc-Olivier; Konrat, Robert; Micura, Ronald

2009-12-01

(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D (19)F and (1)H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis.

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

NASA Astrophysics Data System (ADS)

Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Kumar Vasa, Suresh; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G.

2014-09-01

We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

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.

Growth of large zeolite crystals in space

NASA Technical Reports Server (NTRS)

Sacco, A., Jr.; Dixon, A.; Thompson, R.; Scott, G.; Ditr, J.

1988-01-01

Synthesis studies performed using close analogs of triethanolamine (TEA) have shown that all three hydroxyl groups and the amine group in this molecule are necessary to provide nucleation suppression. Studies using C-13 nuclear magnetic resonance (NMR) revealed that the hydroxyl ions and the amine group are involved in the formation of an aluminum complex. It was also shown that silicate species fo not interact this way with TEA in an alkaline solution. These results suggest that successful aluminum complexation leads to nucleation in zeolite-A crystallization.

NMR binding and crystal structure reveal that intrinsically-unstructured regulatory domain auto-inhibits PAK4 by a mechanism different from that of PAK1.

PubMed

Wang, Wei; Lim, Liangzhong; Baskaran, Yohendran; Manser, Ed; Song, Jianxing

2013-08-16

Six human PAK members are classified into groups I (PAKs 1-3) and II (PAK4-6). Previously, only group I PAKs were thought to be auto-inhibited but very recently PAK4, the prototype of group II PAKs, has also been shown to be auto-inhibited by its N-terminal regulatory domain. However, the complete auto-inhibitory domain (AID) sequence remains undefined and the mechanism underlying its auto-inhibition is largely elusive. Here, the N-terminal regulatory domain of PAK4 sufficient for auto-inhibiting and binding Cdc42/Rac was characterized to be intrinsically unstructured, but nevertheless we identified the entire AID sequence by NMR. Strikingly, an AID peptide was derived by deleting the binding-unnecessary residues, which has a Kd of 320 nM to the PAK4 catalytic domain. Consequently, the PAK4 crystal structure complexed with the entire AID has been determined, which reveals that the complete kinase cleft is occupied by 20 AID residuescomposed of an N-terminal α-helix and a previously-identified pseudosubstrate motif, thus achieving auto-inhibition. Our study reveals that PAK4 is auto-inhibited by a novel mechanism which is completely different from that for PAK1, thus bearing critical implications for design of inhibitors specific for group II PAKs. Copyright © 2013 Elsevier Inc. All rights reserved.

Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

PubMed Central

Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

2017-01-01

Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

Nuclear Magnetic Resonance Reveals Disordered Level-Crossing Physics in the Bose-Glass Regime of the Br-Doped Ni(Cl_{1-x}Br_{x})_{2}-4SC(NH_{2})_{2} Compound at a High Magnetic Field.

PubMed

Orlova, Anna; Blinder, Rémi; Kermarrec, Edwin; Dupont, Maxime; Laflorencie, Nicolas; Capponi, Sylvain; Mayaffre, Hadrien; Berthier, Claude; Paduan-Filho, Armando; Horvatić, Mladen

2017-02-10

By measuring the nuclear magnetic resonance (NMR) T_{1}^{-1} relaxation rate in the Br (bond) doped DTN compound, Ni(Cl_{1-x}Br_{x})_{2}-4SC(NH_{2})_{2}(DTNX), we show that the low-energy spin dynamics of its high magnetic field "Bose-glass" regime is dominated by a strong peak of spin fluctuations found at the nearly doping-independent position H^{*}≅13.6  T. From its temperature and field dependence, we conclude that this corresponds to a level crossing of the energy levels related to the doping-induced impurity states. Observation of the local NMR signal from the spin adjacent to the doped Br allowed us to fully characterize this impurity state. We have thus quantified a microscopic theoretical model that paves the way to better understanding of the Bose-glass physics in DTNX, as revealed in the related theoretical study [M. Dupont, S. Capponi, and N. Laflorencie, Phys. Rev. Lett. 118, 067204 (2017).PRLTAO0031-900710.1103/PhysRevLett.118.067204].

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

Successful Sampling Strategy Advances Laboratory Studies of NMR Logging in Unconsolidated Aquifers

NASA Astrophysics Data System (ADS)

Behroozmand, Ahmad A.; Knight, Rosemary; Müller-Petke, Mike; Auken, Esben; Barfod, Adrian A. S.; Ferré, Ty P. A.; Vilhelmsen, Troels N.; Johnson, Carole D.; Christiansen, Anders V.

2017-11-01

The nuclear magnetic resonance (NMR) technique has become popular in groundwater studies because it responds directly to the presence and mobility of water in a porous medium. There is a need to conduct laboratory experiments to aid in the development of NMR hydraulic conductivity models, as is typically done in the petroleum industry. However, the challenge has been obtaining high-quality laboratory samples from unconsolidated aquifers. At a study site in Denmark, we employed sonic drilling, which minimizes the disturbance of the surrounding material, and extracted twelve 7.6 cm diameter samples for laboratory measurements. We present a detailed comparison of the acquired laboratory and logging NMR data. The agreement observed between the laboratory and logging data suggests that the methodologies proposed in this study provide good conditions for studying NMR measurements of unconsolidated near-surface aquifers. Finally, we show how laboratory sample size and condition impact the NMR measurements.

Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma

PubMed Central

2013-01-01

Nuclear magnetic resonance spectroscopy (NMR) provides robust readouts of many metabolic parameters in one experiment. However, identification of clinically relevant markers in 1H NMR spectra is a major challenge. Association of NMR-derived quantities with genetic variants can uncover biologically relevant metabolic traits. Using NMR data of plasma samples from 1,757 individuals from the KORA study together with 655,658 genetic variants, we show that ratios between NMR intensities at two chemical shift positions can provide informative and robust biomarkers. We report seven loci of genetic association with NMR-derived traits (APOA1, CETP, CPS1, GCKR, FADS1, LIPC, PYROXD2) and characterize these traits biochemically using mass spectrometry. These ratios may now be used in clinical studies. PMID:23414815

FT-IR, FT-Raman, UV-visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol.

PubMed

Chain, Fernando E; Leyton, Patricio; Paipa, Carolina; Fortuna, Mario; Brandán, Silvia A

2015-03-05

In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G(∗) basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated (1)H NMR and (13)C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations. Copyright © 2014 Elsevier B.V. All rights reserved.

Multi-platform metabolomics assays for human lung lavage fluids in an air pollution exposure study.

PubMed

Surowiec, Izabella; Karimpour, Masoumeh; Gouveia-Figueira, Sandra; Wu, Junfang; Unosson, Jon; Bosson, Jenny A; Blomberg, Anders; Pourazar, Jamshid; Sandström, Thomas; Behndig, Annelie F; Trygg, Johan; Nording, Malin L

2016-07-01

Metabolomics protocols are used to comprehensively characterize the metabolite content of biological samples by exploiting cutting-edge analytical platforms, such as gas chromatography (GC) or liquid chromatography (LC) coupled to mass spectrometry (MS) assays, as well as nuclear magnetic resonance (NMR) assays. We have developed novel sample preparation procedures combined with GC-MS, LC-MS, and NMR metabolomics profiling for analyzing bronchial wash (BW) and bronchoalveolar lavage (BAL) fluid from 15 healthy volunteers following exposure to biodiesel exhaust and filtered air. Our aim was to investigate the responsiveness of metabolite profiles in the human lung to air pollution exposure derived from combustion of biofuels, such as rapeseed methyl ester biodiesel, which are increasingly being promoted as alternatives to conventional fossil fuels. Our multi-platform approach enabled us to detect the greatest number of unique metabolites yet reported in BW and BAL fluid (82 in total). All of the metabolomics assays indicated that the metabolite profiles of the BW and BAL fluids differed appreciably, with 46 metabolites showing significantly different levels in the corresponding lung compartments. Furthermore, the GC-MS assay revealed an effect of biodiesel exhaust exposure on the levels of 1-monostearylglycerol, sucrose, inosine, nonanoic acid, and ethanolamine (in BAL) and pentadecanoic acid (in BW), whereas the LC-MS assay indicated a shift in the levels of niacinamide (in BAL). The NMR assay only identified lactic acid (in BW) as being responsive to biodiesel exhaust exposure. Our findings demonstrate that the proposed multi-platform approach is useful for wide metabolomics screening of BW and BAL fluids and can facilitate elucidation of metabolites responsive to biodiesel exhaust exposure. Graphical Abstract Graphical abstract illustrating the study workflow. NMR Nuclear Magnetic Resonance, LC-TOFMS Liquid chromatography-Time Of Flight Mass Spectrometry, GC Gas Chromatography-Mass spectrometry.

Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

PubMed Central

Barthelmes, Katja; Reynolds, Anne M.; Peisach, Ezra; Jonker, Hendrik R. A.; DeNunzio, Nicholas J.; Allen, Karen N.; Imperiali, Barbara; Schwalbe, Harald

2011-01-01

Lanthanide-binding-tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β and varied the length of the spacer between the LBT and the protein (denoted 1-3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing 1H-15N-HSQC NMR spectra with wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop-constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated based on RDCs and pseudocontact shifts (PCSs). A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modelling. PMID:21182275

Structural characterization of lignin from grape stalks (Vitis vinifera L.).

PubMed

Prozil, Sónia O; Evtuguin, Dmitry V; Silva, Artur M S; Lopes, Luísa P C

2014-06-18

The chemical structure of lignin from grape stalks, an abundant waste of winemaking, has been studied. The dioxane lignin was isolated from extractive- and protein-free grape stalks (Vitis vinifera L.) by modified acidolytic procedure and submitted to a structural analysis by wet chemistry (nitrobenzene and permanganate oxidation (PO)) and spectroscopic techniques. The results obtained suggest that grape stalk lignin is an HGS type with molar proportions of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units of 3:71:26. Structural analysis by (1)H and (13)C NMR spectroscopy and PO indicates the predominance of β-O-4' structures (39% mol) in grape stalk lignin together with moderate amounts of β-5', β-β, β-1', 5-5', and 4-O-5' structures. NMR studies also revealed that grape lignin should be structurally associated with tannins. The condensation degree of grape stalks lignin is higher than that of conventional wood lignins and lignins from other agricultural residues.

A newly developed highly selective ratiometric fluoride ion sensor: spectroscopic, NMR and density functional studies.

PubMed

Mallick, Arabinda; Roy, Ujjal Kanti; Haldar, Basudeb; Pratihar, Sanjay

2012-03-07

A new easy-to-synthesize chemosensor, 3,3'-bis(indolyl)-4-chlorophenylmethane (hereafter S), was designed, synthesized and employed as a selective optical chemosensor for fluoride ions.(1)H NMR and density functional studies on the system have been carried out to determine the nature of the interaction between S and X(-) (X = inorganic anions) responsible for the significant fluoride-induced changes in the absorption properties of S. The experimental results reveal that abstraction of an acidic proton of S by the fluoride ion, leading to the formation of anionic species, is responsible for the spectral changes. These changes allow signaling for the fluoride ion to detect and estimate the concentration of fluoride ion present even at the submicromolar level, accurate up to 2 μM. Calculations of the transition energies of S, S(-), and S···F(-) (hydrogen bonded complex) show that only S(-) is responsible for the long-wavelength absorption band in the presence of F(-).

Low-temperature 1H NMR spectroscopic study of hydration properties of a hybrid system based on nanosilica, DNA and doxorubicin in the presence of C60 fullerene

NASA Astrophysics Data System (ADS)

Turov, V. V.; Prylutskyy, Yu. I.; Ugnivenko, A. P.; Barvinchenko, V. N.; Krupskaya, T. V.; Tsierkezos, N. G.; Ritter, U.

2014-03-01

The structure of hydrate cover layers of SiO2-DNA-Dox (where Dox: doxorubicin) and SiO2-DNA-Dox-C60 fullerene hybrids was studied by means of low-temperature 1H NMR spectroscopy in tetrachloromethane. The hydration properties of SiO2-DNA-Dox nanomaterials combined with fullerenes and their derivatives are extremely important for their further use as therapeutics in cancer treatment and for safety reasons. The findings reveal that the hydration properties of the hybrids differ from those of the solid DNA particulates or SiO2-DNA systems due to the existence of different types of water clusters, namely the weakly (WAW) and strongly associated water (SAW) clusters. For SAW clusters the radial distributions as well as the distributions of change in Gibbs free energy due to adsorptive interactions at the surfaces of the investigated systems were obtained.

Nematic biaxiality in a bent-core material

NASA Astrophysics Data System (ADS)

Yoon, Hyung Guen; Kang, Shin-Woong; Dong, Ronald Y.; Marini, Alberto; Suresh, Kattera A.; Srinivasarao, Mohan; Kumar, Satyendra

2010-05-01

The results of a recent investigation of the nematic biaxiality in a bent-core mesogen (A131) are in apparent disagreement with earlier claims. Samples of mesogen A131 used in the two studies were investigated with polarized optical microscopy, conoscopy, carbon-13 NMR, and crossover frequency measurements. The results demonstrate that textural changes associated with the growth of biaxial nematic order appear at ˜149°C . The Maltese cross observed in the conoscopic figure gradually splits into two isogyres at lower temperatures indicating phase biaxiality. Presence of the uniaxial to biaxial nematic phase transition is further confirmed by temperature trends of local order parameters based on C13 chemical shifts in NMR experiments. Frequency switching measurements also clearly reveal a transition at 149°C . Differences between the two reports appear to be related to the presence of solvent, impurities, and/or adsorbed gases in samples of A131 used in the study of Van Le [Phys. Rev. E 79, 030701 (2009)].

[Study of the stability of pyrimido-[5,4-e]-1,2,4-triazine antibiotics in acid-base media by NMR spectroscopy].

PubMed

Esipov, S E; Chernyshev, A I; Shorshnev, S V; Iakushkina, N I; Antonovskiĭ, V L

1985-02-01

A comparative study of the NMR 1H and 13C spectra of reumycin, fervenulin and xanthothricin in aqueous acid-base media showed that at pH or pD ranging from 8.0 to 1.0 the antibiotics were chemically stable. By the ratio of the 1H and 13C chemical shifts of reumycin at pH 4.0-10.0 the pKa values of this antibiotic were determined: 6.7 in aqueous (D2O) solution and 8.76 in dimethylsulfoxide media. Alkalization of the solutions of reumycin (pH 12.0), fervenulin (pH 9.0) and xanthothricin (pH 8.0) resulted in irreversible chemical transformation of the antibiotics. The analysis of the chemical shifts in the PMR spectra of the transformation products revealed transformation of the uracil ring in reumycin and uracil and triazine rings in fervenulin and xanthothricin. Alkalization of the xanthothricin solutions resulted also in demethylation with formation of reumycin.

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

PubMed

Borkar, Aditi N; Vallurupalli, Pramodh; Camilloni, Carlo; Kay, Lewis E; Vendruscolo, Michele

2017-01-25

RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.

Revealing lithium-silicide phase transformations in nano-structured silicon-based lithium ion batteries via in situ NMR spectroscopy.

PubMed

Ogata, K; Salager, E; Kerr, C J; Fraser, A E; Ducati, C; Morris, A J; Hofmann, S; Grey, C P

2014-01-01

Nano-structured silicon anodes are attractive alternatives to graphitic carbons in rechargeable Li-ion batteries, owing to their extremely high capacities. Despite their advantages, numerous issues remain to be addressed, the most basic being to understand the complex kinetics and thermodynamics that control the reactions and structural rearrangements. Elucidating this necessitates real-time in situ metrologies, which are highly challenging, if the whole electrode structure is studied at an atomistic level for multiple cycles under realistic cycling conditions. Here we report that Si nanowires grown on a conducting carbon-fibre support provide a robust model battery system that can be studied by (7)Li in situ NMR spectroscopy. The method allows the (de)alloying reactions of the amorphous silicides to be followed in the 2nd cycle and beyond. In combination with density-functional theory calculations, the results provide insight into the amorphous and amorphous-to-crystalline lithium-silicide transformations, particularly those at low voltages, which are highly relevant to practical cycling strategies.

Effect of pressure on the short-range structure and speciation of carbon in alkali silicate and aluminosilicate glasses and melts at high pressure up to 8 GPa: 13C, 27Al, 17O and 29Si solid-state NMR study

NASA Astrophysics Data System (ADS)

Kim, Eun Jeong; Fei, Yingwei; Lee, Sung Keun

2018-03-01

Despite the pioneering efforts to explore the nature of carbon in carbon-bearing silicate melts under compression, experimental data for the speciation and the solubility of carbon in silicate melts above 4 GPa have not been reported. Here, we explore the speciation of carbon and pressure-induced changes in network structures of carbon-bearing silicate (Na2O-3SiO2, NS3) and sodium aluminosilicate (NaAlSi3O8, albite) glasses quenched from melts at high pressure up to 8 GPa using multi-nuclear solid-state NMR. The 27Al triple quantum (3Q) MAS NMR spectra for carbon-bearing albite melts revealed the pressure-induced increase in the topological disorder around 4 coordinated Al ([4]Al) without forming [5,6]Al. These structural changes are similar to those in volatile-free albite melts at high pressure, indicating that the addition of CO2 in silicate melts may not induce any additional increase in the topological disorder around Al at high pressure. 13C MAS NMR spectra for carbon-bearing albite melts show multiple carbonate species, including [4]Si(CO3)[4]Si, [4]Si(CO3)[4]Al, [4]Al(CO3)[4]Al, and free CO32-. The fraction of [4]Si(CO3)[4]Al increases with increasing pressure, while those of other bridging carbonate species decrease, indicating that the addition of CO2 may enhance mixing of Si and Al at high pressure. A noticeable change is not observed for 29Si NMR spectra for the carbon-bearing albite glasses with varying pressure at 1.5-6 GPa. These NMR results confirm that the densification mechanisms established for fluid-free, polymerized aluminosilicate melts can be applied to the carbon-bearing albite melts at high pressure. In contrast, the 29Si MAS NMR spectra for partially depolymerized, carbon-bearing NS3 glasses show that the fraction of [5,6]Si increases with increasing pressure at the expense of Q3 species ([4]Si species with one non-bridging oxygen as the nearest neighbor). The pressure-induced increase in topological disorder around Si is evident from an increase in peak width of [4]Si with pressure. 17O NMR spectrum shows that the fraction of Na⋯Osbnd [5]Si in carbon-bearing NS3 glasses is less than that of carbon-free NS3 glasses at 6 GPa potentially due to the formation of bridging carbonate species. While its presence is not evident from the 17O NMR spectrum primarily due to low carbon concentration, 13C MAS NMR results imply the formation of bridging carbonates, [4]Si(CO3)[4]Si, above 6 GPa. The spin-lattice relaxation time (T1) of CO2 in albite melts increases with increasing pressure from 42 s (at 1.5 GPa) to 149 s (at 6 GPa). Taking the pressure-induced change in T1 of carbon species into consideration, total carbon content in carbon-bearing albite melts increases with pressure from ∼1 wt% at 1.5 GPa to ∼4.1 wt% at 6 GPa. The results also reveal a noticeable drop in the peak intensity of free carbonates in carbon-bearing NS3 melts at 6 GPa, implying a potential non-linear change in the carbon solubility with pressure. The current results of carbon speciation in the silicate melts above 4 GPa provide an improved link among the atomic configurations around carbon species, their carbon contents, and isotope composition of carbon-bearing melts in the upper mantle.

Host-Guest Interaction of Cucurbit[8]uril with N-(3-Aminopropyl)cyclohexylamine: Cyclohexyl Encapsulation Triggered Ternary Complex.

PubMed

Xia, Yu; Wang, Chuan-Zeng; Tian, Mengkui; Tao, Zhu; Ni, Xin-Long; Prior, Timothy J; Redshaw, Carl

2018-01-15

The host-guest interaction of a series of cyclohexyl-appended guests with cucurbit[8]uril (Q[8]) was studied by ¹H NMR spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography. The X-ray structure revealed that two cycloalkane moieties can be simultaneously encapsulated in the hydrophobic cavity of the Q[8] host to form a ternary complex for the first time.

DNA cleavage, antibacterial, antifungal and anthelmintic studies of Co(II), Ni(II) and Cu(II) complexes of coumarin Schiff bases: Synthesis and spectral approach

NASA Astrophysics Data System (ADS)

Patil, Sangamesh A.; Prabhakara, Chetan T.; Halasangi, Bhimashankar M.; Toragalmath, Shivakumar S.; Badami, Prema S.

2015-02-01

The metal complexes of Co(II), Ni(II) and Cu(II) have been synthesized from 6-formyl-7,8-dihydroxy-4-methylcoumarin with o-toluidine/3-aminobenzotrifluoride. The synthesized Schiff bases and their metal complexes were structurally characterized based on IR, 1H NMR, 13C NMR, UV-visible, ESR, magnetic, thermal, fluorescence, mass and ESI-MS studies. The molar conductance values indicate that complexes are non-electrolytic in nature. Elemental analysis reveals ML2·2H2O [M = Co(II), Ni(II) and Cu(II)] stoichiometry, where 'L' stands for a singly deprotonated ligand. The presence of co-ordinated water molecules were confirmed by thermal studies. The spectroscopic studies suggest the octahedral geometry. Redox behavior of the complexes were confirmed by cyclic voltammetry. All the synthesized compounds were screened for their antibacterial (Escherichia coli, Pseudomonas auregenosa, klebsiella, Proteus, Staphylococcus aureus and salmonella) antifungal (Candida, Aspergillus niger and Rhizopus), anthelmintic (Pheretima posthuma) and DNA cleavage (Calf Thymus DNA) activity.

DNA cleavage, antibacterial, antifungal and anthelmintic studies of Co(II), Ni(II) and Cu(II) complexes of coumarin Schiff bases: synthesis and spectral approach.

PubMed

Patil, Sangamesh A; Prabhakara, Chetan T; Halasangi, Bhimashankar M; Toragalmath, Shivakumar S; Badami, Prema S

2015-02-25

The metal complexes of Co(II), Ni(II) and Cu(II) have been synthesized from 6-formyl-7,8-dihydroxy-4-methylcoumarin with o-toluidine/3-aminobenzotrifluoride. The synthesized Schiff bases and their metal complexes were structurally characterized based on IR, (1)H NMR, (13)C NMR, UV-visible, ESR, magnetic, thermal, fluorescence, mass and ESI-MS studies. The molar conductance values indicate that complexes are non-electrolytic in nature. Elemental analysis reveals ML2·2H2O [M = Co(II), Ni(II) and Cu(II)] stoichiometry, where 'L' stands for a singly deprotonated ligand. The presence of co-ordinated water molecules were confirmed by thermal studies. The spectroscopic studies suggest the octahedral geometry. Redox behavior of the complexes were confirmed by cyclic voltammetry. All the synthesized compounds were screened for their antibacterial (Escherichia coli, Pseudomonas auregenosa, klebsiella, Proteus, Staphylococcus aureus and salmonella) antifungal (Candida, Aspergillus niger and Rhizopus), anthelmintic (Pheretima posthuma) and DNA cleavage (Calf Thymus DNA) activity. Copyright © 2014 Elsevier B.V. All rights reserved.

Coordination Polymer: Synthesis, Spectral Characterization and Thermal Behaviour of Starch-Urea Based Biodegradable Polymer and Its Polymer Metal Complexes

PubMed Central

Malik, Ashraf; Parveen, Shadma; Ahamad, Tansir; Alshehri, Saad M.; Singh, Prabal Kumar; Nishat, Nahid

2010-01-01

A starch-urea-based biodegradable coordination polymer modified by transition metal Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) was prepared by polycondensation of starch and urea. All the synthesized polymeric compounds were characterized by Fourier transform-infrared spectroscopy (FT-IR), 1H-NMR spectroscopy, 13C-NMR spectroscopy, UV-visible spectra, magnetic moment measurements, differential scanning calorimeter (DSC), and thermogravimetric analysis (TGA). The results of electronic spectra and magnetic moment measurements indicate that Mn(II), Co(II), and Ni(II) complexes show octahedral geometry, while Cu(II) and Zn(II) complexes show square planar and tetrahedral geometry, respectively. The thermogravimetric analysis revealed that all the polymeric metal complexes are more thermally stable than the parental ligand. In addition, biodegradable studies of all the polymeric compounds were also carried out through ASTM standards of biodegradable polymers by CO2 evolution method. PMID:20414461

A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure.

PubMed

Pellach, Michal; Mondal, Sudipta; Harlos, Karl; Mance, Deni; Baldus, Marc; Gazit, Ehud; Shimon, Linda J W

2017-03-13

The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rational Design of Glycomimetic Compounds Targeting the Saccharomyces cerevisiae Transglycosylase Gas2.

PubMed

Delso, Ignacio; Valero-González, Jessika; Marca, Eduardo; Tejero, Tomás; Hurtado-Guerrero, Ramón; Merino, Pedro

2016-02-01

The transglycosylase Saccharomyces cerevisiae Gas2 (ScGas2) belongs to a large family of enzymes that are key players in yeast cell wall remodeling. Despite its biologic importance, no studies on the synthesis of substrate-based compounds as potential inhibitors have been reported. We have synthesized a series of docking-guided glycomimetics that were evaluated by fluorescence spectroscopy and saturation-transfer difference (STD) NMR experiments, revealing that a minimum of three glucose units linked via a β-(1,3) linkage are required for achieving molecular recognition at the binding donor site. The binding mode of our compounds is further supported by STD-NMR experiments using the active site-mutants Y107Q and Y244Q. Our results are important for both understanding of ScGas2-substrate interactions and setting up the basis for future design of glycomimetics as new antifungal agents. © 2015 John Wiley & Sons A/S.

Mechanistic insights into lithium ion battery electrolyte degradation - a quantitative NMR study.

PubMed

Wiemers-Meyer, S; Winter, M; Nowak, S

2016-09-29

The changes in electrolyte composition on the molecular level and the reaction mechanisms of electrolyte degradation upon thermal aging are monitored by quantitative NMR spectroscopy, revealing similar rates of degradation for pristine and already aged electrolytes. The data analysis is not in favor of an autocatalytic reaction mechanism based on OPF 3 but rather indicates that the degradation of LiPF 6 in carbonate based solvents proceeds via a complex sequence of "linear" reactions rather than a cyclic reaction pattern which is determined by the amount of water present in the samples. All investigated electrolytes are reasonably stable at temperatures of up to 60 °C in the presence of minor amounts or absence of water hence indicating that chemical instability of electrolyte components against water is decisive for degradation and an increase in temperature ("thermal aging") just accelerates the degradation impact of water.

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.

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

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

ERIC Educational Resources Information Center

Chesick, John P.

1989-01-01

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

Solution NMR 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.

A more detailed picture of the interactions between virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and ITC studies.

PubMed

Trotta, Roberta; De Tito, Stefano; Lauri, Ilaria; La Pietra, Valeria; Marinelli, Luciana; Cosconati, Sandro; Martino, Luigi; Conte, Maria R; Mayol, Luciano; Novellino, Ettore; Randazzo, Antonio

2011-08-01

The growing amount of literature about G-quadruplex DNA clearly demonstrates that such a structure is no longer viewed as just a biophysical strangeness but it is instead being considered as an important target for the treatment of various human disorders such as cancers or venous thrombosis. In this scenario, with the aim of finding brand new molecular scaffolds able to interact with the groove of the DNA quadruplex [d(TGGGGT)](4), we recently performed a successful structure-based virtual screening (VS) campaign. As a result, six molecules were found to be somehow groove binders. Herein, we report the results of novel NMR titration experiments of these VS-derived ligands with modified quadruplexes, namely [d(TGG(Br)GGT)](4) and [d(TGGGG(Br)T)](4). The novel NMR spectroscopy experiments combined with molecular modelling studies, allow for a more detailed picture of the interaction between each binder and the quadruplex DNA. Noteworthy, isothermal titration calorimetry (ITC) measurements on the above-mentioned compounds revealed that 2, 4, and 6 besides their relatively small dimensions bind the DNA quadruplex [d(TGGGGT)](4) with higher affinity than distamycin A, to the best of our knowledge, the most potent groove binder identified thus far. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Study of the interactions between a proline-rich protein and a flavan-3-ol by NMR: residual structures in the natively unfolded protein provides anchorage points for the ligands.

PubMed

Pascal, Christine; Paté, Franck; Cheynier, Véronique; Delsuc, Marc-André

2009-09-01

Astringency is one of the major organoleptic properties of food and beverages that are made from plants, such as tea, chocolate, beer, or red wine. This sensation is thought to be due to interactions between tannins and salivary proline-rich proteins, which are natively unfolded proteins. A human salivary proline-rich protein, namely IB-5, was produced by the recombinant method. Its interactions with a model tannin, epigallocatechin gallate (EGCG), the major flavan-3-ol in green tea, were studied here. Circular dichroism experiments showed that IB-5 presents residual structures (PPII helices) when the ionic strength is close to that in saliva. In the presence of these residual structures, IB-5 undergoes an increase in structural content upon binding to EGCG. NMR data corroborated the presence of preformed structural elements within the protein prior to binding and a partial assignment was proposed, showing partial structuration. TOCSY experiments showed that amino acids that are involved in PPII helices are more likely to interact with EGCG than those in random coil regions, as if they were anchorage points for the ligand. The signal from IB-5 in the DOSY NMR spectrum revealed an increase in polydispersity upon addition of EGCG while the mean hydrodynamic radius remained unchanged. This strongly suggests the formation of IB-5/EGCG aggregates.

Synthesis, single crystal X-ray, spectroscopic (FT-IR, UV-vis, fluorescence, 1H &13C NMR), computational (DFT/B3LYP) studies of some imidazole based picrates

NASA Astrophysics Data System (ADS)

Arockia doss, M.; Rajarajan, G.; Thanikachalam, V.; Selvanayagam, S.; Sridhar, B.

2018-04-01

2,4,5-triphenyl-1H-imidazol-3-ium picrate (1), 2-(4-fluorophenyl)-4,5-diphenyl-1H-imidazol-3-ium picrate (2), 2-(4-methylphenyl)-4,5-diphenyl-1H-imidazol-3-ium picrate (3) were synthesised. These compounds 1-3 were characterized by elemental, FT-IR, 1H NMR and 13C NMR analyses. The structure of compound 3 was further confirmed by single crystal X-ray diffraction. The studies reveal that the molecule is associated with weak Nsbnd H⋯O and Csbnd H⋯N and van der Waals interactions which are responsible for the formation and strengthening of supramolecular assembly. The nature of the interactions and their importance are explored using the Hirshfeld surface method. The physicochemical properties of the compounds 1-3 were evaluated by UV-vis spectroscopy, fluorescence spectroscopy, and thermogravimetric analysis. According to thermal data the salts possess excellent thermal stabilities with decomposition temperatures ranging from 220 to 280 °C. Second-harmonic generation (SHG) results exposed that the picrates 1-3 were about 1.13-1.50 times greater than potassium dihydrogen phosphate (KDP). Here we also used Density functional theory (DFT) calculations in order to investigate the opto-electronic properties. The obtained theoretical results validate with available experimental data.

Toxic responses of Perna viridis hepatopancreas exposed to DDT, benzo(a)pyrene and their mixture uncovered by iTRAQ-based proteomics and NMR-based metabolomics.

PubMed

Song, Qinqin; Zhou, Hailong; Han, Qian; Diao, Xiaoping

2017-11-01

Dichlorodiphenyltrichloroethane (DDT) and benzo(a)pyrene (BaP) are environmental estrogens (EEs) that are ubiquitous in the marine environment. In the present study, we integrated isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic and nuclear magnetic resonance (NMR)-based metabolomic approaches to explore the toxic responses of green mussel hepatopancreas exposed to DDT (10μg/L), BaP (10μg/L) and their mixture. The metabolic responses indicated that BaP primarily disturbed energy metabolism and osmotic regulation in the hepatopancreas of the male green mussel P. viridis. Both DDT and the mixture of DDT and BaP perturbed the energy metabolism and osmotic regulation in P. viridis. The proteomic responses revealed that BaP affected the proteins involved in energy metabolism, material transformation, cytoskeleton, stress responses, reproduction and development in green mussels. DDT exposure could change the proteins involved in primary metabolism, stress responses, cytoskeleton and signal transduction. However, the mixture of DDT and BaP altered proteins associated with material and energy metabolism, stress responses, signal transduction, reproduction and development, cytoskeleton and apoptosis. This study showed that iTRAQ-based proteomic and NMR-based metabolomic approaches could effectively elucidate the essential molecular mechanism of disturbances in hepatopancreas function of green mussels exposed to environmental estrogens. Copyright © 2017 Elsevier B.V. All rights reserved.

Immobilization of radioactive iodine in silver aluminophosphate glasses.

PubMed

Lemesle, Thomas; Méar, François O; Campayo, Lionel; Pinet, Olivier; Revel, Bertrand; Montagne, Lionel

2014-01-15

Silver aluminophosphate glasses have been investigated as matrices for the immobilization of radioactive iodine. In this study, up to 28mol% AgI have been incorporated without volatilization thanks to a low temperature synthesis protocol. Alumina was added in the composition in order to increase the glass transition temperature for a better thermal stability in a repository conditions. Two series of glasses have been investigated, based on AgPO3 and Ag5P3O10 compositions, and with 0-5mol% Al2O3. We report (31)P, (27)Al and (109)Ag NMR study of these glasses, including advanced measurement of the connectivities through {(27)Al}-(31)P cross-polarization and (31)P-(31)P double-quantum correlation. We confirm that AgI is inserted in the aluminophosphate glasses and does not form clusters. AgI does not induce any modification of the glass polymerization but only an expansion of the network. Despite no evidence for crystallization could be obtained from XRD, NMR revealed that the introduction of AgI induces an exclusion of alumina from the network, leading to the crystallization of aluminophosphate phases such as Al(PO3)3 or AlPO4. As a consequence, despite NMR gives evidence for the presence of aluminophosphate bonds, only a limited effect of alumina addition on thermal properties is observed. Copyright © 2013 Elsevier B.V. All rights reserved.

Low temperature FTIR, Raman, NMR spectroscopic and theoretical study of hydroxyethylammonium picrate

NASA Astrophysics Data System (ADS)

Sudharsana, N.; Sharma, A.; Kuş, N.; Fausto, R.; Luísa Ramos, M.; Krishnakumar, V.; Pal, R.; Guru Row, T. N.; Nagalakshmi, R.

2016-01-01

A combined experimental (infrared, Raman and NMR) and theoretical quantum chemical study is performed on the charge-transfer complex hydroxyethylammonium picrate (HEAP). The infrared (IR) spectra for HEAP were recorded at various temperatures, ranging from 16 K to 299 K, and the Raman spectrum was recorded at room temperature. A comparison of the experimental IR and Raman spectra with the corresponding calculated spectra was done, in order to facilitate interpretation of the experimental data. Formation of the HEAP complex is evidenced by the presence of the most prominent characteristic bands of the constituting groups of the charge-transfer complex [e.g., NH3+, CO- and NO2]. Vibrational spectroscopic analysis, together with natural bond orbital (NBO) and theoretical charge density analysis in the crystalline phase, was used to shed light on relevant structural details of HEAP resulting from deprotonation of picric acid followed by formation of a hydrogen bond of the N-H⋯OC type between the hydroxyethylammonium cation and the picrate. 13C and 1H NMR spectroscopic analysis are also presented for the DMSO-d6 solution of the compound revealing that in that medium the HEAP crystal dissolves forming the free picrate and hydroxyethylammonium ions. Finally, the electron excitation analysis of HEAP was performed in an attempt to determine the nature of the most important excited states responsible for the NLO properties exhibited by the compound.

Secondary Structures in a Freeze-Dried Lignite Humic Acid Fraction Caused by Hydrogen-Bonding of Acidic Protons with Aromatic Rings.

PubMed

Cao, Xiaoyan; Drosos, Marios; Leenheer, Jerry A; Mao, Jingdong

2016-02-16

A lignite humic acid (HA) was separated from inorganic and non-HA impurities (i.e., aluminosilicates, metals) and fractionated by a combination of dialysis and XAD-8 resin. Fractionation revealed a more homogeneous structure of lignite HA. New and more specific structural information on the main lignite HA fraction is obtained by solid-state nuclear magnetic resonance (NMR) spectroscopy. Quantitative (13)C multiple cross-polarization (multiCP) NMR indicated oxidized phenyl propane structures derived from lignin. MultiCP experiments, conducted on potassium HA salts titrated to pH 10 and pH 12, revealed shifts consistent with carboxylate and phenolate formation, but structural changes associated with enolate formation from aromatic beta keto acids were not detected. Two-dimensional (1)H-(13)C heteronuclear correlation (2D HETCOR) NMR indicated aryl-aliphatic ketones, aliphatic and aromatic carboxyl groups, phenol, and methoxy phenyl ethers. Acidic protons from carboxyl groups in both the lignite HA fraction and a synthetic HA-like polycondensate were found to be hydrogen-bonded with electron-rich aromatic rings. Our results coupled with published infrared spectra provide evidence for the preferential hydrogen bonding of acidic hydrogens with electron-rich aromatic rings rather than adjacent carbonyl groups. These hydrogen-bonding interactions likely result from stereochemical arrangements in primary structures and folding.

Chemical Equilibrium in Supramolecular Systems as Studied by NMR Spectrometry

ERIC Educational Resources Information Center

Gonzalez-Gaitano, Gustavo; Tardajos, Gloria

2004-01-01

Undergraduate students are required to study the chemical balance in supramolecular assemblies constituting two or more interacting species, by using proton NMR spectrometry. A good knowledge of physical chemistry, fundamentals of chemical balance, and NMR are pre-requisites for conducting this study.

Monitoring of fluid motion in a micromixer by dynamic NMR microscopy.

PubMed

Ahola, Susanna; Casanova, Federico; Perlo, Juan; Münnemann, Kerstin; Blümich, Bernhard; Stapf, Siegfried

2006-01-01

The velocity distribution of liquid flowing in a commercial micromixer has been determined directly by using pulsed-field gradient NMR. Velocity maps with a spatial resolution of 29 microm x 43 microm were obtained by combining standard imaging gradient units with a homebuilt rectangular surface coil matching the mixer geometry. The technique provides access to mixers and reactors of arbitrary shape regardless of optical transparency. Local heterogeneities in the signal intensity and the velocity pattern were found and serve to investigate the quality and functionality of a micromixer, revealing clogging and inhomogeneous flow distributions.

Ultra-slow dynamics in low density amorphous ice revealed by deuteron NMR: indication of a glass transition.

PubMed

Löw, Florian; Amann-Winkel, Katrin; Loerting, Thomas; Fujara, Franz; Geil, Burkhard

2013-06-21

The postulated glass-liquid transition of low density amorphous ice (LDA) is investigated with deuteron NMR stimulated echo experiments. Such experiments give access to ultra-slow reorientations of water molecules on time scales expected for structural relaxation of glass formers close to the glass-liquid transition temperature. An involved data analysis is necessary to account for signal contributions originating from a gradual crystallization to cubic ice. Even if some ambiguities remain, our findings support the view that pressure amorphized LDA ices are of glassy nature and undergo a glass-liquid transition before crystallization.

HPLC, NMR and MALDI-TOF MS analysis of condensed tannins from Lithocarpus glaber leaves with potent free radical scavenging activity.

PubMed

Zhang, Liang Liang; Lin, Yi Ming

2008-12-04

Using acid-catalyzed degradation in the presence of cysteamine, the condensed tannins from Lithocarpus glaber leaves were characterized, following thiolysis, by means of reversed-phase HPLC, 13C-NMR and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analyses. The thiolysis reaction products showed the presence of the procyanidin (PC) and prodelphinidin (PD) structures. The 13C-NMR spectrum revealed that the condensed tannins were comprised of PD (72.4%) and PC (27.6%), and with a greater content of cis configuration rather than the trans configuration of C2-C3. The MALDI-TOF MS analysis proved the presence of PD units, and the maximum degree of polymerization (DP) was an undecamer. The antioxidant activity of condensed tannins from L. glaber leaves was evaluated by using a free radical scavenging activity assay.

Velocity distributions in a micromixer measured by NMR imaging.

PubMed

Ahola, Susanna; Telkki, Ville-Veikko; Stapf, Siegfried

2012-04-24

Velocity distributions (so-called propagators) with two-dimensional spatial resolution inside a chemical micromixer were measured by pulsed-field-gradient spin-echo (PGSE) nuclear magnetic resonance (NMR). A surface coil matching the volume of interest was built to enhance the signal-to-noise ratio. This enabled the acquisition of velocity maps with a very high spatial resolution of 29 μm × 39 μm. The measured propagators are compared with theoretical distributions and a good agreement is found. The results show that the propagator data provide much richer information about flow behaviour than conventional NMR velocity imaging and the information is essential for understanding the performance of a micromixer. It reveals, for example, deviations in the shape and size of the channel structures and multicomponent flow velocity distribution of overlapping channels. Propagator data efficiently compensate lost information caused by insufficient 3D resolution in conventional velocity imaging.

NMR-based metabolomic analysis of spatial variation in soft corals.

PubMed

He, Qing; Sun, Ruiqi; Liu, Huijuan; Geng, Zhufeng; Chen, Dawei; Li, Yinping; Han, Jiao; Lin, Wenhan; Du, Shushan; Deng, Zhiwei

2014-03-28

Soft corals are common marine organisms that inhabit tropical and subtropical oceans. They are shown to be rich source of secondary metabolites with biological activities. In this work, soft corals from two geographical locations were investigated using ¹H-NMR spectroscopy coupled with multivariate statistical analysis at the metabolic level. A partial least-squares discriminant analysis showed clear separation among extracts of soft corals grown in Sanya Bay and Weizhou Island. The specific markers that contributed to discrimination between soft corals in two origins belonged to terpenes, sterols and N-containing compounds. The satisfied precision of classification obtained indicates this approach using combined ¹H-NMR and chemometrics is effective to discriminate soft corals collected in different geographical locations. The results revealed that metabolites of soft corals evidently depended on living environmental condition, which would provide valuable information for further relevant coastal marine environment evaluation.

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

NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy

ERIC Educational Resources Information Center

Alonso, David E.; Warren, Steven E.

2005-01-01

A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…

Exploring high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for metabonomic analysis of apples.

PubMed

Vermathen, Martina; Marzorati, Mattia; Vermathen, Peter

2012-01-01

Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

Hypothesis driven assessment of an NMR curriculum

NASA Astrophysics Data System (ADS)

Cossey, Kimberly

The goal of this project was to develop a battery of assessments to evaluate an undergraduate NMR curriculum at Penn State University. As a chemical education project, we sought to approach the problem of curriculum assessment from a scientific perspective, while remaining grounded in the education research literature and practices. We chose the phrase hypothesis driven assessment to convey this process of relating the scientific method to the study of educational methods, modules, and curricula. We began from a hypothesis, that deeper understanding of one particular analytical technique (NMR) will increase undergraduate students' abilities to solve chemical problems. We designed an experiment to investigate this hypothesis, and data collected were analyzed and interpreted in light of the hypothesis and several related research questions. The expansion of the NMR curriculum at Penn State was funded through the NSF's Course, Curriculum, and Laboratory Improvement (CCLI) program, and assessment was required. The goal of this project, as stated in the grant proposal, was to provide NMR content in greater depth by integrating NMR modules throughout the curriculum in physical chemistry, instrumental, and organic chemistry laboratory courses. Hands-on contact with the NMR spectrometer and NMR data and repeated exposure of the analytical technique within different contexts (courses) were unique factors of this curriculum. Therefore, we maintained a focus on these aspects throughout the evaluation process. The most challenging and time-consuming aspect of any assessment is the development of testing instruments and methods to provide useful data. After key variables were defined, testing instruments were designed to measure these variables based on educational literature (Chapter 2). The primary variables measured in this assessment were: depth of understanding of NMR, basic NMR knowledge, problem solving skills (HETCOR problem), confidence for skills used in class (within the hands-on NMR modules), confidence for NMR tasks (not practiced), and confidence for general science tasks. Detailed discussion of the instruments, testing methods and experimental design used in this assessment are provided (Chapter 3). All data were analyzed quantitatively using methods adapted from the educational literature (Chapter 4). Data were analyzed and the descriptive statistics, independent t-tests between the experimental and control groups, and correlation statistics were calculated for each variable. In addition, for those variables included on the pretest, dependent t-tests between pretest and posttest scores were also calculated. The results of study 1 and study 2 were used to draw conclusions based on the hypothesis and research questions proposed in this work (Chapter 4). Data collected in this assessment were used to answer the following research questions: (1) Primary research question: Is depth of understanding of NMR linked to problem solving skills? (2) Are the NMR modules working as intended? Do they promote depth of understanding of NMR? (a) Will students who complete NMR modules have a greater depth of understanding of NMR than students who do not complete the modules? (b) Is depth of understanding increasing over the course of the experiment? (3) Is confidence an intermediary between depth of understanding and problem solving skills? Is it linked to both variables? (4) What levels of confidence are affected by the NMR modules? (a) Will confidence for the NMR class skills used in the modules themselves be greater for those who have completed the modules? (b) Will confidence for NMR tasks not practiced in the course be affected? (c) Will confidence for general science tasks be affected? (d) Are different levels of confidence (class skills, NMR tasks, general science tasks) linked to each other? Results from this NMR curriculum assessment could also have implications outside of the courses studied, and so there is potential to impact the chemical education community (section 5.2.1). In addition to providing reliable testing instruments/measures that could be used outside the university, the results of this research contribute to the study of problem solving in chemistry, learner characteristics within the context of chemical education studies, and NMR specific educational evaluations. Valuable information was gathered through the current method of evaluation for the NMR curriculum. However, improvements could be made to the existing assessment, and an alternate assessment that could supplement the information found in this study has been proposed (Chapter 5).

Metabolic phenotyping of urine for discriminating alcohol-dependent from social drinkers and alcohol-naive subjects.

PubMed

Mostafa, Hamza; Amin, Arwa M; Teh, Chin-Hoe; Murugaiyah, Vikneswaran; Arif, Nor Hayati; Ibrahim, Baharudin

2016-12-01

Alcohol-dependence (AD) is a ravaging public health and social problem. AD diagnosis depends on questionnaires and some biomarkers, which lack specificity and sensitivity, however, often leading to less precise diagnosis, as well as delaying treatment. This represents a great burden, not only on AD individuals but also on their families. Metabolomics using nuclear magnetic resonance spectroscopy (NMR) can provide novel techniques for the identification of novel biomarkers of AD. These putative biomarkers can facilitate early diagnosis of AD. To identify novel biomarkers able to discriminate between alcohol-dependent, non-AD alcohol drinkers and controls using metabolomics. Urine samples were collected from 30 alcohol-dependent persons who did not yet start AD treatment, 54 social drinkers and 60 controls, who were then analysed using NMR. Data analysis was done using multivariate analysis including principal component analysis (PCA) and orthogonal partial least square-discriminate analysis (OPLS-DA), followed by univariate and multivariate logistic regression to develop the discriminatory model. The reproducibility was done using intraclass correlation coefficient (ICC). The OPLS-DA revealed significant discrimination between AD and other groups with sensitivity 86.21%, specificity 97.25% and accuracy 94.93%. Six biomarkers were significantly associated with AD in the multivariate logistic regression model. These biomarkers were cis-aconitic acid, citric acid, alanine, lactic acid, 1,2-propanediol and 2-hydroxyisovaleric acid. The reproducibility of all biomarkers was excellent (0.81-1.0). This study revealed that metabolomics analysis of urine using NMR identified AD novel biomarkers which can discriminate AD from social drinkers and controls with high accuracy. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Ion counting in supercapacitor electrodes using NMR spectroscopy.

PubMed

Griffin, John M; Forse, Alexander C; Wang, Hao; Trease, Nicole M; Taberna, Pierre-Louis; Simon, Patrice; Grey, Clare P

2014-01-01

(19)F NMR spectroscopy has been used to study the local environments of anions in supercapacitor electrodes and to quantify changes in the populations of adsorbed species during charging. In the absence of an applied potential, anionic species adsorbed within carbon micropores (in-pore) are distinguished from those in large mesopores and spaces between particles (ex-pore) by a characteristic nucleus-independent chemical shift (NICS). Adsorption experiments and two-dimensional exchange experiments confirm that anions are in dynamic equilibrium between the in- and ex-pore environments with an exchange rate in the order of tens of Hz. (19)F in situ NMR spectra recorded at different charge states reveal changes in the intensity and NICS of the in-pore resonances, which are interpreted in term of changes in the population and local environments of the adsorbed anions that arise due to the charge-storage process. A comparison of the results obtained for a range of electrolytes reveals that several factors influence the charging mechanism. For a tetraethylammonium tetrafluoroborate electrolyte, positive polarisation of the electrode is found to proceed by anion adsorption at a low concentration, whereas increased ion exchange plays a more important role for a high concentration electrolyte. In contrast, negative polarization of the electrode proceeds by cation adsorption for both concentrations. For a tetrabutylammonium tetrafluoroborate electrolyte, anion expulsion is observed in the negative charging regime; this is attributed to the reduced mobility and/or access of the larger cations inside the pores, which forces the expulsion of anions in order to build up ionic charge. Significant anion expulsion is also observed in the negative charging regime for alkali metal bis(trifluoromethane)sulfonimide electrolytes, suggesting that more subtle factors also affect the charging mechanism.

Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Cawley, K. M.; Schmitt-Kopplin, P.; Jaffé, R.

2015-08-01

Wetlands provide quintessential ecosystem services such as maintenance of water quality, water supply and biodiversity, among others; however, wetlands are also among the most threatened ecosystems worldwide. They are usually characterized by high levels of natural dissolved organic matter (DOM), representing a critical component in wetland biogeochemistry. This study describes the first detailed, comparative, molecular characterization of DOM in sub-tropical, pulsed, wetlands, namely the Everglades (USA), the Pantanal (Brazil) and the Okavango Delta (Botswana), using optical properties, high field nuclear magnetic resonance (NMR) and ultrahigh resolution mass spectrometry (FT-ICRMS), and compares compositional features to variations in organic matter sources and flooding characteristics (i.e. differences in hydroperiod). While optical properties showed both similarities and differences between these ecosystems, these differences were mainly based on the degree of aromaticity of the DOM. Analogies were such that an established excitation emission matrix fluorescence parallel factor analysis (EEM-PARAFAC) model for the Everglades was perfectly applicable to the other two wetlands. High-field (500 and 800 MHz) NMR spectra with cryogenic detection provided exceptional coverage and chemical description of wetland solid phase extracted (SPE) DOM. Area-normalized 1H NMR spectra of selected samples revealed clear distinctions of samples along with pronounced congruence within the three pairs of wetland DOM. Within sample pairs (long vs. short hydroperiod sites), internal differences mainly referred to intensity variations (denoting variable abundance) rather than to alterations of NMR resonances positioning (denoting diversity of molecules). The relative disparity was largest between the Everglades long and short hydroperiod samples, whereas Pantanal and Okavango samples were more alike among themselves. Otherwise, molecular divergence was most obvious in the case of unsaturated protons (δH > 5 ppm). The larger discrimination observed between 1H NMR spectra of DOM from different wetlands in comparison with the intrinsic variance among DOM within each wetland readily suggests the presence of an individual molecular signature, characteristic of each particular wetland. 2-D NMR spectroscopy for a particular sample revealed a large richness of aliphatic and unsaturated substructures, likely derived from microbial sources such as periphyton in the Everglades. In contrast, the chemical diversity of aromatic wetland DOM likely originates from a combination of higher plant sources, progressive microbial and photochemical oxidation, and contributions from combustion-derived products (e.g. black carbon). In addition, FT-ICRMS spectra allowed far-reaching classifications of wetland DOM. While DOM of both Okavango and Pantanal showed near 57 ± 2 % CHO, 8 ± 2 % CHOS, 33 ± 2 CHNO, and < 1 % CHNOS molecules, the mass spectra of Everglades samples were fundamentally different compared to those as well as among long and short hydroperiod samples, as they were markedly enriched in CHOS and CHNOS at the expense of CHO and CHNO compounds. Here, four groups of CHOS molecules were differentiated as (a) saturated sulfolipids, (b) unsaturated sulfolipids, (c) molecularly diverse DOM-type CHOS molecules, (d) and particularly enriched in the Everglades short hydroperiod site, a large set of aromatic and oxygen-deficient "black sulphur" compounds. The significantly higher proportion of CHOS compounds in general for the Everglades samples is likely the result of higher inputs of agriculture-derived and sea spray derived sulphate to this wetland compared to the others. Although wetland DOM samples were found to share many molecular features, each sample was unique in its composition, which reflected specific environmental drivers and/or specific biogeochemical processes.

Investigation of local environments in Nafion-SiO(2) composite membranes used in vanadium redox flow batteries.

PubMed

Vijayakumar, M; Schwenzer, Birgit; Kim, Soowhan; Yang, Zhenguo; Thevuthasan, S; Liu, Jun; Graff, Gordon L; Hu, Jianzhi

2012-04-01

Proton conducting polymer composite membranes are of technological interest in many energy devices such as fuel cells and redox flow batteries. In particular, polymer composite membranes, such as SiO(2) incorporated Nafion membranes, are recently reported as highly promising for the use in redox flow batteries. However, there is conflicting reports regarding the performance of this type of Nafion-SiO(2) composite membrane in the redox flow cell. This paper presents results of the analysis of the Nafion-SiO(2) composite membrane used in a vanadium redox flow battery by nuclear magnetic resonance (NMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier Transform Infra Red (FTIR) spectroscopy, and ultraviolet-visible spectroscopy. The XPS study reveals the chemical identity and environment of vanadium cations accumulated at the surface. On the other hand, the (19)F and (29)Si NMR measurement explores the nature of the interaction between the silica particles, Nafion side chains and diffused vanadium cations. The (29)Si NMR shows that the silica particles interact via hydrogen bonds with the sulfonic groups of Nafion and the diffused vanadium cations. Based on these spectroscopic studies, the chemical environment of the silica particles inside the Nafion membrane and their interaction with diffusing vanadium cations during flow cell operations are discussed. This study discusses the origin of performance degradation of the Nafion-SiO(2) composite membrane materials in vanadium redox flow batteries. Copyright © 2011 Elsevier Inc. All rights reserved.

Structural study of Al2O3-Na2O-CaO-P2O5 bioactive glasses as a function of aluminium content.

PubMed

Smith, J M; King, S P; Barney, E R; Hanna, J V; Newport, R J; Pickup, D M

2013-01-21

Calcium phosphate based biomaterials are extensively used in the context of tissue engineering: small changes in composition can lead to significant changes in properties allowing their use in a wide range of applications. Samples of composition (Al(2)O(3))(x)(Na(2)O)(0.11-x)(CaO)(0.445)(P(2)O(5))(0.445), where x = 0, 0.03, 0.05, and 0.08, were prepared by melt quenching. The atomic-scale structure has been studied using neutron diffraction and solid state (27)Al MAS NMR, and these data have been rationalised with the determined density of the final glass product. With increasing aluminium concentration the density increases initially, but beyond about 3 mol. % Al(2)O(3) the density starts to decrease. Neutron diffraction data show a concomitant change in the aluminium speciation, which is confirmed by (27)Al MAS NMR studies. The NMR data reveal that aluminium is present in 4, 5, and 6-fold coordination and that the relative concentrations of these environments change with increasing aluminium concentration. Materials containing aluminium in 6-fold coordination tend to have higher densities than analogous materials with the aluminium found in 4-fold coordination. Thus, the density changes may readily be explained in terms of an increase in the relative concentration of 4-coordinated aluminium at the expense of 6-fold aluminium as the Al(2)O(3) content is increased beyond 3 mol. %.

Investigation of Local Environments in Nafion-SiO2 Composite Membranes used in Vanadium Redox Flow Batteries

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

Vijayakumar, M.; Schwenzer, Birgit; Kim, Soowhan

2012-04-01

The proton conducting polymer composite membranes are of technological interest in many energy devices such as fuel cells and redox flow batteries. In particular, the polymer composite membranes such as SiO2 incorporated Nafion membranes are recently reported as highly promising for the redox flow batteries. However, there is conflicting reports regarding the performance of this Nafion-SiO2 composite membrane in the redox flow cell. This paper presents results of the analysis of the Nafion-SiO2 composite membrane used in a vanadium redox flow battery by nuclear magnetic resonance (NMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier Transformed Infra Red (FTIR) spectroscopy, and ultravioletmore » visible spectroscopy. The XPS study reveals the chemical identity and environment of vanadium cations accumulated at the surface. On the other hand, the 19F and 29Si NMR measurement explores the nature of the interaction between the silica particles, Nafion side chains and diffused vanadium cations. The 29Si NMR shows that the silica particles interaction via hydrogen bonds to the sulfonic groups of Nafion and diffused vanadium cations. Based on these spectroscopic studies, the chemical environment of the silica particles inside the Nafion membrane and their interaction with diffusing vanadium cations during flow cell operations are discussed. This study discusses the origin of performance degradation of the Nafion-SiO2 composite membrane materials in vanadium redox flow batteries.« less

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

PubMed

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

2016-09-15

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

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

Spectroscopic Study of the Interaction between Horse Heart Myoglobin and Zirconium(IV)-Substituted Polyoxometalates as Artificial Proteases.

PubMed

Ly, Hong Giang T; Parac-Vogt, Tatjana N

2017-09-20

A recent study [Angew. Chem. Int. Ed. 2015, 54, 7391-7394] has shown that horse heart myoglobin (HHM) is selectively hydrolyzed by a range of zirconium(IV)-substituted polyoxometalates (POMs) under mild conditions. In this study, the molecular interactions between the Zr-POM catalysts and HHM are investigated by using a range of complementary techniques, including circular dichroism (CD), UV/Vis spectroscopy, tryptophan fluorescence spectroscopy, and 1 H and 31 P NMR spectroscopy. A tryptophan fluorescence quenching study reveals that, among all examined Zr-POMs, the most reactive POM, 2:2 Zr IV -Keggin, exhibits the strongest interaction with HHM. 31 P NMR spectroscopy studies show that this POM dissociates in solution, resulting in the formation of a monomeric 1:1 Zr IV -Keggin structure, which is likely to be a catalytically active species. In the presence of Zr IV -POMs, HHM does not undergo complete denaturation, as evidenced by CD, UV/Vis, tryptophan fluorescence, and 1 H NMR spectroscopy. CD spectroscopy shows a gradual decrease in the α-helical content of HHM upon addition of Zr IV -POMs. The largest effect is observed in the presence of a large Zr IV -Wells-Dawson structure, whereas small Zr IV -Lindqvist POM has the least influence on the decrease in the α-helical content of HHM. In all cases, the Soret band at λ=409 nm is maintained in the presence of all examined Zr-POMs, which indicates that no conformational changes in the protein occur near the heme group. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

NMR-Metabolic Methodology in the Study of GM Foods

USDA-ARS?s Scientific Manuscript database

The 1H NMR methodology used in the study of genetically modified (GM) foodstuff is discussed. The study of transgenic lettuce (Lactuca sativa cv "Luxor") over-expressing the KNAT1 gene from Arabidopsis is presented as a novel study-case. The 1H NMR metabolic profiling was carried out. Twenty-two wat...

Structural characterisation of the Li argyrodites Li7PS6 and Li7PSe6 and their solid solutions: quantification of site preferences by MAS-NMR spectroscopy.

PubMed

Kong, Shiao Tong; Gün, Ozgül; Koch, Barbara; Deiseroth, Hans Jörg; Eckert, Hellmut; Reiner, Christof

2010-05-03

Li(7)PS(6) and Li(7)PSe(6) belong to a class of new solids that exhibit high Li(+) mobility. A series of quaternary solid solutions Li(7)PS(6-x)Se(x) (0 < or = x < or = 6) were characterised by X-ray crystallography and magic-angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. The high-temperature (HT) modifications were studied by single-crystal investigations (both F43m, Z=4, Li(7)PS(6): a=9.993(1) A, Li(7)PSe(6): a=10.475(1) A) and show the typical argyrodite structures with strongly disordered Li atoms. HT-Li(7)PS(6) and HT-Li(7)PSe(6) transform reversibly into low-temperature (LT) modifications with ordered Li atoms. X-ray powder diagrams show the structures of LT-Li(7)PS(6) and LT-Li(7)PSe(6) to be closely related to orthorhombic LT-alpha-Cu(7)PSe(6). Single crystals of the LT modifications are not available due to multiple twinning and formation of antiphase domains. The gradual substitution of S by Se shows characteristic site preferences closely connected to the functionalities of the different types of chalcogen atoms (S, Se). High-resolution solid-state (31)P NMR is a powerful method to differentiate quantitatively between the distinct (PS(4-n)Se(n))(3-) local environments. Their population distribution differs significantly from a statistical scenario, revealing a pronounced preference for P-S over P-Se bonding. This preference, shown for the series of LT samples, can be quantified in terms of an equilibrium constant specifying the melt reaction Se(P)+S(2-) <==>S(P)+Se(2-), prior to crystallisation. The (77)Se MAS-NMR spectra reveal that the chalcogen distributions in the second and third coordination sphere of the P atoms are essentially statistical. The number of crystallographically independent Li atoms in both LT modifications was analysed by means of (6)Li{(7)Li} cross polarisation magic angle spinning (CPMAS).

Structural Elucidation of Poloxamer 237 and Poloxamer 237/Praziquantel Solid Dispersions: Impact of Poly(Vinylpyrrolidone) over Drug Recrystallization and Dissolution.

PubMed

Orlandi, Silvina; Priotti, Josefina; Diogo, Hermínio P; Leonardi, Dario; Salomon, Claudio J; Nunes, Teresa G

2018-04-01

Praziquantel (PZQ) is the recommended, effective, and safe treatment against all forms of schistosomiasis. Solid dispersions (SDs) in water-soluble polymers have been reported to increase solubility and bioavailability of poorly water-soluble drugs like PZQ, generally due to the amorphous form stabilization. In this work, poloxamer (PLX) 237 and poly(vinylpyrrolidone) (PVP) K30 were evaluated as potential carriers to revert PZQ crystallization. Binary and ternary SDs were prepared by the solvent evaporation method. PZQ solubility increased similarly with PLX either as binary physical mixtures or SDs. Such unpredicted data correlated well with crystalline PZQ and PLX as detected by solid-state NMR (ssNMR) and differential scanning calorimetry in those samples. Ternary PVP/PLX/PZQ SDs showed both ssNMR broad and narrow superimposed signals, thus revealing the presence of amorphous and crystalline PZQ, respectively, and exhibited the highest PZQ dissolution efficiency (up to 82% at 180 min). SDs with PVP provided a promising way to enhance solubility and dissolution rate of PZQ since PLX alone did not prevent recrystallization of amorphous PZQ. Based on ssNMR data, novel evidences on PLX structure and molecular dynamics were also obtained. As shown for the first time using ssNMR, propylene glycol and ethylene glycol constitute the PLX amorphous and crystalline components, respectively.

Comparative analysis of Hibiscus sabdariffa (roselle) hot and cold extracts in respect to their potential for α-glucosidase inhibition.

PubMed

Rasheed, Dalia M; Porzel, Andrea; Frolov, Andrei; El Seedi, Hesham R; Wessjohann, Ludger A; Farag, Mohamed A

2018-06-01

Roselle (Hibiscus sabdariffa) is a functional food with potential health benefits, consumed either as hot or cold beverage. To ensure quality control of its various products, accurate measurement of active metabolites is warranted. Herein, we propose a combination of ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and nuclear magnetic resonance (NMR) analytical platforms for the untargeted characterization of metabolites in two roselle cultivars, Aswan and Sudan-1. The analyses revealed 33 metabolites, including sugars, flavonoids, anthocyanins, phenolic and aliphatic organic acids. Their relative contents in cultivars were assessed via principle component analysis (PCA) and orthogonal projection to latent structures analysis (OPLS). Impact of the different extraction methods (decoction, infusion and maceration) was compared by quantitative 1 H NMR spectroscopy, revealing cold maceration to be optimal for preserving anthocyanins, whereas infusion was more suited for recovering organic acids. The metabolite pattern revealed by the different extraction methods was found in good correlation for their ability to inhibit α-glucosidase enzyme. Copyright © 2018 Elsevier Ltd. All rights reserved.

Methanol incorporation in clathrate hydrates and the implications for oil and gas pipeline flow assurance and icy planetary bodies

PubMed Central

Shin, Kyuchul; Udachin, Konstantin A.; Moudrakovski, Igor L.; Leek, Donald M.; Alavi, Saman; Ratcliffe, Christopher I.; Ripmeester, John A.

2013-01-01

One of the best-known uses of methanol is as antifreeze. Methanol is used in large quantities in industrial applications to prevent methane clathrate hydrate blockages from forming in oil and gas pipelines. Methanol is also assigned a major role as antifreeze in giving icy planetary bodies (e.g., Titan) a liquid subsurface ocean and/or an atmosphere containing significant quantities of methane. In this work, we reveal a previously unverified role for methanol as a guest in clathrate hydrate cages. X-ray diffraction (XRD) and NMR experiments showed that at temperatures near 273 K, methanol is incorporated in the hydrate lattice along with other guest molecules. The amount of included methanol depends on the preparative method used. For instance, single-crystal XRD shows that at low temperatures, the methanol molecules are hydrogen-bonded in 4.4% of the small cages of tetrahydrofuran cubic structure II hydrate. At higher temperatures, NMR spectroscopy reveals a number of methanol species incorporated in hydrocarbon hydrate lattices. At temperatures characteristic of icy planetary bodies, vapor deposits of methanol, water, and methane or xenon show that the presence of methanol accelerates hydrate formation on annealing and that there is unusually complex phase behavior as revealed by powder XRD and NMR spectroscopy. The presence of cubic structure I hydrate was confirmed and a unique hydrate phase was postulated to account for the data. Molecular dynamics calculations confirmed the possibility of methanol incorporation into the hydrate lattice and show that methanol can favorably replace a number of methane guests. PMID:23661058

Methanol incorporation in clathrate hydrates and the implications for oil and gas pipeline flow assurance and icy planetary bodies.

PubMed

Shin, Kyuchul; Udachin, Konstantin A; Moudrakovski, Igor L; Leek, Donald M; Alavi, Saman; Ratcliffe, Christopher I; Ripmeester, John A

2013-05-21

One of the best-known uses of methanol is as antifreeze. Methanol is used in large quantities in industrial applications to prevent methane clathrate hydrate blockages from forming in oil and gas pipelines. Methanol is also assigned a major role as antifreeze in giving icy planetary bodies (e.g., Titan) a liquid subsurface ocean and/or an atmosphere containing significant quantities of methane. In this work, we reveal a previously unverified role for methanol as a guest in clathrate hydrate cages. X-ray diffraction (XRD) and NMR experiments showed that at temperatures near 273 K, methanol is incorporated in the hydrate lattice along with other guest molecules. The amount of included methanol depends on the preparative method used. For instance, single-crystal XRD shows that at low temperatures, the methanol molecules are hydrogen-bonded in 4.4% of the small cages of tetrahydrofuran cubic structure II hydrate. At higher temperatures, NMR spectroscopy reveals a number of methanol species incorporated in hydrocarbon hydrate lattices. At temperatures characteristic of icy planetary bodies, vapor deposits of methanol, water, and methane or xenon show that the presence of methanol accelerates hydrate formation on annealing and that there is unusually complex phase behavior as revealed by powder XRD and NMR spectroscopy. The presence of cubic structure I hydrate was confirmed and a unique hydrate phase was postulated to account for the data. Molecular dynamics calculations confirmed the possibility of methanol incorporation into the hydrate lattice and show that methanol can favorably replace a number of methane guests.

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.

Biodiversity in targeted metabolomics analysis of filamentous fungal pathogens by 1H NMR-based studies.

PubMed

Ząbek, Adam; Klimek-Ochab, Magdalena; Jawień, Ewa; Młynarz, Piotr

2017-07-01

The taxonomical classification among fungi kingdom in the last decades was evolved. In this work the targeted metabolomics study based on 1 H NMR spectroscopy combined with chemometrics tools was reported to be useful for differentiation of three model of fungal strains, which represent various genus of Ascomycota (Aspergillus pallidofulvus, Fusarium oxysporum, Geotrichum candidum) were selected in order to perform metabolomics studies. Each tested species, revealed specific metabolic profile of primary endo-metabolites. The species of A. pallidofulvus is represented by the highest concentration of glycerol, glucitol and Unk5. While, F. oxysporum species is characterised by increased level of propylene glycol, ethanol, 4-aminobutyrate, succinate, xylose, Unk1 and Unk4. In G. candidum, 3-methyl-2-oxovalerate, glutamate, pyruvate, glutamine and citrate were elevated. Additionally, a detailed analysis of metabolic changes among A. pallidofulvus, F. oxysporum and G. candidum showed that A. pallidofulvus seems to be the most pathogenic fungi. The obtained results demonstrated that targeted metabolomics analysis could be utilized in the future as a supporting taxonomical tool for currently methods.

Investigation of Local Structures in Cation-ordered Microwave Dielectric A Solid-state NMR and First Principle Calculation Study

NASA Astrophysics Data System (ADS)

Kalfarisi, Rony G.

Solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy has proven to be a powerful method to probe the local structure and dynamics of a system. In powdered solids, the nuclear spins experience various anisotropic interactions which depend on the molecular orientation. These anisotropic interactions make ssNMR very useful as they give a specific appearance to the resonance lines of the spectra. The position and shape of these resonance lines can be related to local structure and dynamics of the system under study. My research interest has focused around studying local structures and dynamics of quadrupolar nuclei in materials using ssNMR spectroscopy. 7Li and 93Nb ssNMR magic angle spinning (MAS) spectra, acquired at 17.6 and 7.06 T, have been used to evaluate the structural and dynamical properties of cation-ordered microwave dielectric materials. Microwave dielectric materials are essential in the application of wireless telecommunication, biomedical engineering, and other scientific and industrial implementations that use radio and microwave signals. The study of the local environment with respect to average structure, such as X-ray diffraction study, is essential for the better understanding of the correlations between structures and properties of these materials. The investigation for short and medium range can be performed with the use of ssNMR techniques. Even though XRD results show cationic ordering at the B-site (third coordination sphere), NMR spectra show a presence of disorder materials. This was indicated by the observation of a distribution in NMR parameters derived from experimental . {93}Nb NMR spectraand supported by theoretical calculations.

Polymorphic phase transitions and molecular motion in pyridinium chlorochromate

NASA Astrophysics Data System (ADS)

Pajaķ, Z.; Szafrańska, B.; Czarnecki, P.; Mayer, J.; Kozak, A.

1997-08-01

DTA, DSC, NMR and dielectric studies have been performed for pyridinium chlorochromate over a wide temperature range. A sequence of four solid-solid phase transitions was discovered. The in-plane complex reorientation of the cation is described by a three-well potential model with two correlation times. At higher temperatures one observes simultaneous cation tumbling and diffusion. Thus existence of a new ionic plastic phase is revealed. The domain structure observed suggests ferroelastic properties of the compound.

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

Sun, S.-W., E-mail: sunsw0819@163.com; Zhang, X., E-mail: zhangx@hit.edu.cn; Wang, G.-F.

A series of 2-arylidenebenzocycloalkanones containing heterocyclic rings 1–8 were prepared and characterized by IR, {sup 1}H NMR and elemental analyses. X-ray diffraction study of 6 reveals that the cyclohexyl ring of the 3,4-dihydronaphthalen-1(2H)-one adopts a chair conformation with a maximum deviation of 0.547(3) Å and makes dihedral angles of 52.24(17)° and 11.23(16)°, respectively, with the benzene plane and the mean plane of the benzimidazole ring.

Ion dynamics in a new class of materials: nanoglassy lithium alumosilicates

NASA Astrophysics Data System (ADS)

Stanje, B.; Bottke, P.; Breuer, S.; Hanzu, I.; Heitjans, P.; Wilkening, M.

2018-03-01

In many cases nanocrystalline materials, prepared through high-energy ball milling, reveal enhanced ion dynamics when compared to the situation in the coarse-grained analogues. This effect, which has particularly been seen for lithium alumosilicates, has been ascribed to structural disorder, i.e., the introduction of defect sites during mechanical treatment. Much less is, however, known about ion transport in nanostructured amorphous materials, e.g., nanoglassy compounds, which are regarded as a new class of functional materials. Following earlier studies on nanoglassy lithium alumosilicates and borates, here we studied ion dynamics in nanoglassy petalite LiAlSi4O10. While conductivity spectroscopy unequivocally reveals that long-range ion dynamics in nanoglassy LiAlSi4O10 decreases upon milling, local dynamics, sensed by 7Li nuclear magnetic resonance (NMR) spin-lattice relaxation, points to enhanced Li ion mobility compared to the non-treated glass. Most likely, as for nanocrystalline ceramics also for nanoglassy samples a heterogeneous structure, consisting of bulk and interfacial regions, is formed. For LiAlSi4O10 these interfacial regions, characterized by a higher degree of free volume, might act as hosts for spins experiencing fast longitudinal NMR relaxation. Obviously, these regions do not form a through-going network, which would allow the ions to move over long distances as quickly as in the unmilled glass.

Comprehensive analysis of commercial willow bark extracts by new technology platform: combined use of metabolomics, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy and high-resolution radical scavenging assay.

PubMed

Agnolet, Sara; Wiese, Stefanie; Verpoorte, Robert; Staerk, Dan

2012-11-02

Here, proof-of-concept of a new analytical platform used for the comprehensive analysis of a small set of commercial willow bark products is presented, and compared with a traditional standardization solely based on analysis of salicin and salicin derivatives. The platform combines principal component analysis (PCA) of two chemical fingerprints, i.e., HPLC and (1)H NMR data, and a pharmacological fingerprint, i.e., high-resolution 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS(+)) reduction profile, with targeted identification of constituents of interest by hyphenated HPLC-solid-phase extraction-tube transfer NMR, i.e., HPLC-SPE-ttNMR. Score plots from PCA of HPLC and (1)H NMR fingerprints showed the same distinct grouping of preparations formulated as capsules of Salix alba bark and separation of S. alba cortex. Loading plots revealed this to be due to high amount of salicin in capsules and ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba cortex, respectively. PCA of high-resolution radical scavenging profiles revealed clear separation of preparations along principal component 1 due to the major radical scavengers (+)-catechin and ampelopsin. The new analytical platform allowed identification of 16 compounds in commercial willow bark extracts, and identification of ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba bark extract is reported for the first time. The detection of the novel compound, ethyl 1-hydroxy-6-oxocyclohex-2-enecarboxylate, is also described. Copyright © 2012 Elsevier B.V. All rights reserved.

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

Cr{sub 2}O{sub 5} as new cathode for rechargeable sodium ion batteries

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

Feng, Xu-Yong; Chien, Po-Hsiu; Rose, Alyssa M.

2016-10-15

Chromium oxide, Cr{sub 2}O{sub 5}, was synthesized by pyrolyzing CrO{sub 3} at 350 °C and employed as a new cathode in rechargeable sodium ion batteries. Cr{sub 2}O{sub 5}/Na rechargeable batteries delivered high specific capacities up to 310 mAh/g at a current density of C/16 (or 20 mA/g). High-resolution solid-state {sup 23}Na NMR both qualitatively and quantitatively revealed the reversible intercalation of Na ions into the bulk electrode and participation of Na ions in the formation of the solid-electrolyte interphase largely at low potentials. Amorphization of the electrode structure occurred during the first discharge revealed by both NMR and X-ray diffractionmore » data. CrO{sub 3}-catalyzed electrolyte degradation and loss in electronic conductivity led to gradual capacity fading. The specific capacity stabilized at >120 mAh/g after 50 charge-discharge cycles. Further improvement in electrochemical performance is possible via electrode surface modification, polymer binder incorporation, or designs of new morphologies. - Graphical abstract: Electrochemical profile of a Cr{sub 2}O{sub 5}/Na battery cell and high-resolution solid-state {sup 23}Na MAS NMR spectrum of a Cr{sub 2}O{sub 5} electrode discharged to 2 V. - Highlights: • Cr{sub 2}O{sub 5} was synthesized and used as a new cathode in rechargeable Na ion batteries. • A high capacity of 310 mAh/g and an energy density of 564 Wh/kg were achieved. • High-resolution solid-state {sup 23}Na NMR was employed to follow the reaction mechanisms.« less

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

PubMed

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

2016-09-15

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

Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS

NASA Astrophysics Data System (ADS)

Hertkorn, Norbert; Harir, Mourad; Cawley, Kaelin M.; Schmitt-Kopplin, Philippe; Jaffé, Rudolf

2016-04-01

Wetlands provide quintessential ecosystem services such as maintenance of water quality, water supply and biodiversity, among others; however, wetlands are also among the most threatened ecosystems worldwide. Natural dissolved organic matter (DOM) is an abundant and critical component in wetland biogeochemistry. This study describes the first detailed, comparative, molecular characterization of DOM in subtropical, pulsed, wetlands, namely the Everglades (USA), the Pantanal (Brazil) and the Okavango Delta (Botswana), using optical properties, high-field nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (FT-ICRMS), and compares compositional features to variations in organic matter sources and flooding characteristics (i.e., differences in hydroperiod). While optical properties showed a high degree of variability within and between the three wetlands, analogies in DOM fluorescence properties were such that an established excitation emission matrix fluorescence parallel factor analysis (EEM-PARAFAC) model for the Everglades was perfectly applicable to the other two wetlands. Area-normalized 1H NMR spectra of selected samples revealed clear distinctions of samples while a pronounced congruence within the three pairs of wetland DOM readily suggested the presence of an individual wetland-specific molecular signature. Within sample pairs (long- vs. short-hydroperiod sites), internal differences mainly referred to intensity variations (denoting variable abundance) rather than to alterations of NMR resonances positioning (denoting diversity of molecules). The relative disparity was largest between the Everglades long- and short-hydroperiod samples, whereas Pantanal and Okavango samples were more alike among themselves. Otherwise, molecular divergence was most obvious in the case of unsaturated protons (δH > 5 ppm). 2-D NMR spectroscopy for a particular sample revealed a large richness of aliphatic and unsaturated substructures, likely derived from microbial sources such as periphyton in the Everglades. In contrast, the chemical diversity of aromatic wetland DOM likely originates from a combination of higher plant sources, progressive microbial and photochemical oxidation, and contributions from combustion-derived products (e.g., black carbon). FT-ICRMS spectra of both Okavango and Pantanal showed near 57 ± 2 % CHO, 8 ± 2 % CHOS, 33 ± 2 % CHNO and < 1 % CHNOS molecules, whereas those of Everglades samples were markedly enriched in CHOS and CHNOS at the expense of CHO and CHNO compounds. In particular, the Everglades short-hydroperiod site showed a large set of aromatic and oxygen-deficient "black sulfur" compounds whereas the long-hydroperiod site contained oxygenated sulfur attached to fused-ring polyphenols. The elevated abundance of CHOS compounds for the Everglades samples likely results from higher inputs of agriculture-derived and sea-spray-derived sulfate. Although wetland DOM samples were found to share many molecular features, each sample was unique in its composition, which reflected specific environmental drivers and/or specific biogeochemical processes.

Analysis of salivary phenotypes of generalized aggressive and chronic periodontitis through nuclear magnetic resonance-based metabolomics.

PubMed

Romano, Federica; Meoni, Gaia; Manavella, Valeria; Baima, Giacomo; Tenori, Leonardo; Cacciatore, Stefano; Aimetti, Mario

2018-06-07

Recent findings about the differential gene expression signature of periodontal lesions have raised the hypothesis of distinctive biological phenotypes expressed by generalized chronic periodontitis (GCP) and generalized aggressive periodontitis (GAgP) patients. Therefore, this cross-sectional investigation was planned, primarily, to determine the ability of nuclear magnetic resonance (NMR) spectroscopic analysis of unstimulated whole saliva to discriminate GCP and GAgP disease-specific metabolomic fingerprint and, secondarily, to assess potential metabolites discriminating periodontitis patients from periodontally healthy individuals (HI). NMR-metabolomics spectra were acquired from salivary samples of patients with a clinical diagnosis of GCP (n = 33) or GAgP (n = 28) and from HI (n = 39). The clustering of HI, GCP and GAgP patients was achieved by using a combination of the Principal Component Analysis and Canonical Correlation Analysis on the NMR profiles. These analyses revealed a significant predictive accuracy discriminating HI from GCP, and discriminating HI from GAgP patients (both 81%). In contrast, the GAgP and GCP saliva samples seem to belong to the same metabolic space (60% predictive accuracy). Significantly lower levels (P < 0.05) of pyruvate, N-acetyl groups and lactate and higher levels (P < 0.05) of proline, phenylalanine, and tyrosine were found in GCP and GAgP patients compared with HI. Within the limitations of this study, CGP and GAgP metabolomic profiles were not unequivocally discriminated through a NMR-based spectroscopic analysis of saliva. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Resolving the Magnetic Asymmetry of the Inner Space in Self-assembled Dimeric Capsules Based on Tetraurea-calix[4]pyrrole Components.

PubMed

Espelt, Mónica; Aragay, Gemma; Ballester, Pablo

2015-01-01

The encapsulation of N,N, N',N'-tetramethyl-1,5-pentanediamine-N,N'-dioxide 2 in a non-chiral capsular assembly formed by dimerization of tetraurea-calix[4]pyrrole 1a produced the observation of the N-methyl groups of the encapsulated guest as two separated singlets resonating highly upfield in the (1)H NMR spectrum. In order to clarify the origin of the observed signal splitting we assembled and studied a series of structurally related dimeric capsules. We used the tetraurea-calix[4]pyrrole 1a , the enantiomerically pure tetraurea-calix[4] pyrrole R-1b and the tetraurea-bisloop calix[4]pyrrole 1c as components of the produced assemblies. The (1)H NMR spectra of the assembled encapsulation complexes with bis-N-oxide 2 evidenced diverse splitting patterns of the N-methyl groups. In addition, 2D EXSY/ROESY NMR experiments revealed the existence of chemical exchange processes involving the separated methyl signals of the encapsulated guest. The capsular assemblies were mainly stabilized by a belt of eight head-to-tail hydrogen-bonded urea groups. The interconversion between the two senses of rotation of the unidirectionally oriented urea groups was slow on the (1)H NMR timescale. These characteristics determined the appearance of a new asymmetry element (supramolecular conformational chirality) in the assemblies that accounted for some of the magnetic asymmetries featured by the capsule's inner space. The racemization of the supramolecular chirality element was fast on the EXSY timescale and produced the chemical exchange processes detected for the encapsulation complexes.

Water dynamics in different biochar fractions.

PubMed

Conte, Pellegrino; Nestle, Nikolaus

2015-09-01

Biochar is a carbonaceous porous material deliberately applied to soil to improve its fertility. The mechanisms through which biochar acts on fertility are still poorly understood. The effect of biochar texture size on water dynamics was investigated here in order to provide information to address future research on nutrient mobility towards plant roots as biochar is applied as soil amendment. A poplar biochar has been stainless steel fractionated in three different textured fractions (1.0-2.0 mm, 0.3-1.0 mm and <0.3 mm, respectively). Water-saturated fractions were analyzed by fast field cycling (FFC) NMR relaxometry. Results proved that 3D exchange between bound and bulk water predominantly occurred in the coarsest fraction. However, as porosity decreased, water motion was mainly associated to a restricted 2D diffusion among the surface-site pores and the bulk-site ones. The X-ray μ-CT imaging analyses on the dry fractions revealed the lowest surface/volume ratio for the coarsest fraction, thereby corroborating the 3D water exchange mechanism hypothesized by FFC NMR relaxometry. However, multi-micrometer porosity was evidenced in all the samples. The latter finding suggested that the 3D exchange mechanism cannot even be neglected in the finest fraction as previously excluded only on the basis of NMR relaxometry results. X-ray μ-CT imaging showed heterogeneous distribution of inorganic materials inside all the fractions. The mineral components may contribute to the water relaxation mechanisms by FFC NMR relaxometry. Further studies are needed to understand the role of the inorganic particles on water dynamics. Copyright © 2015 John Wiley & Sons, Ltd.

NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1.

PubMed

Lyukmanova, Ekaterina N; Shenkarev, Zakhar O; Shulepko, Mikhail A; Mineev, Konstantin S; D'Hoedt, Dieter; Kasheverov, Igor E; Filkin, Sergey Yu; Krivolapova, Alexandra P; Janickova, Helena; Dolezal, Vladimir; Dolgikh, Dmitry A; Arseniev, Alexander S; Bertrand, Daniel; Tsetlin, Victor I; Kirpichnikov, Mikhail P

2011-03-25

Discovery of proteins expressed in the central nervous system sharing the three-finger structure with snake α-neurotoxins provoked much interest to their role in brain functions. Prototoxin LYNX1, having homology both to Ly6 proteins and three-finger neurotoxins, is the first identified member of this family membrane-tethered by a GPI anchor, which considerably complicates in vitro studies. We report for the first time the NMR spatial structure for the water-soluble domain of human LYNX1 lacking a GPI anchor (ws-LYNX1) and its concentration-dependent activity on nicotinic acetylcholine receptors (nAChRs). At 5-30 μM, ws-LYNX1 competed with (125)I-α-bungarotoxin for binding to the acetylcholine-binding proteins (AChBPs) and to Torpedo nAChR. Exposure of Xenopus oocytes expressing α7 nAChRs to 1 μM ws-LYNX1 enhanced the response to acetylcholine, but no effect was detected on α4β2 and α3β2 nAChRs. Increasing ws-LYNX1 concentration to 10 μM caused a modest inhibition of these three nAChR subtypes. A common feature for ws-LYNX1 and LYNX1 is a decrease of nAChR sensitivity to high concentrations of acetylcholine. NMR and functional analysis both demonstrate that ws-LYNX1 is an appropriate model to shed light on the mechanism of LYNX1 action. Computer modeling, based on ws-LYNX1 NMR structure and AChBP x-ray structure, revealed a possible mode of ws-LYNX1 binding.

Long-term normal-appearing brain tissue monitoring after irradiation using proton magnetic resonance spectroscopy in vivo: Statistical analysis of a large group of patients

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

Matulewicz, Lukasz; Sokol, Maria; Michnik, Anna

2006-11-01

Purpose: The aim of this study was to detect the non-neoplastic white-matter changes vs. time after irradiation using {sup 1}H nuclear magnetic resonance (NMR) spectroscopy in vivo. Methods and Materials: A total of 394 {sup 1}H MR spectra were acquired from 100 patients (age 19-74 years; mean and median age, 43 years) before and during 2 years after radiation therapy (the mean absorbed doses calculated for the averaged spectroscopy voxels are similar and close to 20 Gy). Results: Ocilations were observed in choline-containing compounds (Cho)/creatine and phosphocreatine (Cr), Cho/N-acetylaspartate (NAA), and center of gravity (CG) of the lipid band inmore » the range of 0.7-1.5 ppm changes over time reveal oscillations. The parameters have the same 8-month cycle period; however the CG changes precede the other by 2 months. Conclusions: The results indicate the oscillative nature of the brain response to irradiation, which may be caused by the blood-brain barrier disruption and repair processes. These oscillations may influence the NMR results, depending on the cycle phase in which the NMR measurements are performed in. The earliest manifestation of radiation injury detected by magnetic resonance spectroscopy is the CG shift.« less

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.

Novel and unusual triterpene from Black Cohosh. Determination of structure of 9,10-seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations.

PubMed

Jamróz, Marta K; Jamróz, Michał H; Dobrowolski, Jan Cz; Gliński, Jan A; Davey, Matthew H; Wawer, Iwona

2011-01-01

A new triterpene xyloside, designated cimipodocarpaside was isolated from a Black Cohosh (Actea racemosa L.) extract and its structure was elucidated by means of 1H, 13C NMR, IR and Raman spectroscopy supported by B3LYP/6-31G** calculations. The vibrational spectra were interpreted using the PED analysis of 273 fundamentals. Its structure comprises four condensed rings A-D which are 6, 7, 6, and 5-membered, respectively. An oxiirane ring is located in the side chain and a xylose moiety is attached to the A-ring. Comparison of the experimental 13C NMR data with the theoretical chemical shifts of 24S- and 24R-cimipodocarpaside isomers revealed that the isolated compound has the 24S-configuration. Combined spectroscopic and computational studies enabled the determination of the structure of cimipodocarpaside as (24S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10-seco-9,19-cyclolanost-7(8),9(11),10(19)-trien-3-O-β-D-xylopyranoside. Triterpenes with 7-membered ring were thus far isolated from only Actea podocarpa DC. plants. This is the first report on the isolation of such a compound from Black Cohosh. Copyright © 2010 Elsevier B.V. All rights reserved.

Monitoring mechanistic details in the synthesis of pyrimidines via real-time, ultrafast multidimensional NMR spectroscopy

PubMed Central

Pardo, Zulay D.; Olsen, Greg; Fernández-Valle, María Encarnación; Frydman, Lucio; Martínez-Álvarez, Roberto; Herrera, Antonio

2016-01-01

Recent years have witnessed unprecedented advances in the development of fast multidimensional NMR acquisition techniques. This progress could open valuable new opportunities for the elucidation of chemical and biochemical processes. This study demonstrates one such capability, with the first real-time 2D dynamic analysis of a complex organic reaction relying on unlabeled substrates. Implementing such measurements required the development of new ultrafast 2D methods, capable of monitoring multiple spectral regions of interest as the reaction progressed. The alternate application of these acquisitions in an interleaved, excitation-optimized fashion, allowed us to extract new structural and dynamic insight concerning the reaction between aliphatic ketones and triflic anhydride in the presence of nitriles to yield alkylpyrimidines. Up to 2500 2D NMR data sets were thus collected over the course of this nearly 100 min long reaction, in an approach resembling that used in functional magnetic resonance imaging. With the aid of these new frequency-selective low-gradient-strength experiments, supplemented by chemical shift calculations of the spectral coordinates observed in the 2D heteronuclear correlations, previously postulated intermediates involved in the alkylpyrimidine formation process could be confirmed, and hitherto undetected ones were revealed. The potential and limitations of the resulting methods are discussed. PMID:22283498

Isolation and structural characterization of the milled wood lignin, dioxane lignin, and cellulolytic lignin preparations from brewer's spent grain.

PubMed

Rencoret, Jorge; Prinsen, Pepijn; Gutiérrez, Ana; Martínez, Ángel T; Del Río, José C

2015-01-21

The structure of the lignin from brewer's spent grain (BSG) has been studied in detail. Three different lignin preparations, the so-called "milled-wood" lignin (MWL), dioxane lignin (DL), and cellulolytic lignin (CEL), were isolated from BSG and then thoroughly characterized by pyrolysis GC/MS, 2D-NMR, and derivatization followed by reductive cleavage (DFRC). The data indicated that BSG lignin presents a predominance of guaiacyl units (syringyl/guaiacyl ratio of 0.4-0.5) with significant amounts of associated p-coumarates and ferulates. The flavone tricin was also present in the lignin from BSG, as also occurred in other grasses. 2D-NMR (HSQC) revealed that the main substructures present are β-O-4' alkyl-aryl ethers (77-79%) followed by β-5' phenylcoumarans (11-13%) and lower amounts of β-β' resinols (5-6%) and 5-5' dibenzodioxocins (3-5%). The results from 2D-NMR (HMBC) and DFRC indicated that p-coumarates are acylating the γ-carbon of lignin side chains and are mostly involved in condensed structures. DFRC analyses also indicated a minor degree of γ-acylation with acetate groups, which takes place preferentially on S lignin (6% of S units are acetylated) over G lignin (only 1% of G units are acetylated).

A comparative study between para-aminophenyl and ortho-aminophenyl benzothiazoles using NMR and DFT calculations.

PubMed

Pierens, G K; Venkatachalam, T K; Reutens, D

2014-08-01

Ortho-substituted and para-substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho-substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho-substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o-aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the (1)H, (13)C and (15)N NMR chemical shifts and density functional theory calculated structures of the compounds are described. Copyright © 2014 John Wiley & Sons, Ltd.

Comparative Investigation of the Ionicity of Aprotic and Protic Ionic Liquids in Molecular Solvents by using Conductometry and NMR Spectroscopy.

PubMed

Thawarkar, Sachin; Khupse, Nageshwar D; Kumar, Anil

2016-04-04

Electrical conductivity (σ), viscosity (η), and self-diffusion coefficient (D) measurements of binary mixtures of aprotic and protic imidazolium-based ionic liquids with water, dimethyl sulfoxide, and ethylene glycol were measured from 293.15 to 323.15 K. The temperature dependence study reveals typical Arrhenius behavior. The ionicities of aprotic ionic liquids were observed to be higher than those of protic ionic liquids in these solvents. The aprotic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate, [bmIm][BF4 ], displays 100 % ionicity in both water and ethylene glycol. The protic ionic liquids in both water and ethylene glycol are classed as good ionic candidates, whereas in DMSO they are classed as having a poor ionic nature. The solvation dynamics of the ionic species of the ionic liquids are illustrated on the basis of the (1) H NMR chemical shifts of the ionic liquids. The self-diffusion coefficients D of the cation and anion of [HmIm][CH3 COO] in D2 O and in [D6 ]DMSO are determined by using (1) H nuclei with pulsed field gradient spin-echo NMR spectroscopy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14

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

Albright, Seth; Chen Bin; Holbrook, Kristen

CD14 functions as a key pattern recognition receptor for a diverse array of Gram-negative and Gram-positive cell-wall components in the host innate immune response by binding to pathogen-associated molecular patterns (PAMPs) at partially overlapping binding site(s). To determine the potential contribution of CD14 residues in this pattern recognition, we have examined using solution NMR spectroscopy, the binding of three different endotoxin ligands, lipopolysaccharide, lipoteichoic acid, and a PGN-derived compound, muramyl dipeptide to a {sup 15}N isotopically labeled 152-residue N-terminal fragment of sCD14 expressed in Pichia pastoris. Mapping of NMR spectral changes upon addition of ligands revealed that the pattern ofmore » residues affected by binding of each ligand is partially similar and partially different. This first direct structural observation of the ability of specific residue combinations of CD14 to differentially affect endotoxin binding may help explain the broad specificity of CD14 in ligand recognition and provide a structural basis for pattern recognition. Another interesting finding from the observed spectral changes is that the mode of binding may be dynamically modulated and could provide a mechanism for binding endotoxins with structural diversity through a common binding site.« less

Novel and unusual triterpene from Black Cohosh. Determination of structure of 9,10- seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Jamróz, Michał H.; Dobrowolski, Jan Cz.; Gliński, Jan A.; Davey, Matthew H.; Wawer, Iwona

2011-01-01

A new triterpene xyloside, designated cimipodocarpaside was isolated from a Black Cohosh ( Actea racemosa L.) extract and its structure was elucidated by means of 1H, 13C NMR, IR and Raman spectroscopy supported by B3LYP/6-31G** calculations. The vibrational spectra were interpreted using the PED analysis of 273 fundamentals. Its structure comprises four condensed rings A-D which are 6, 7, 6, and 5-membered, respectively. An oxiirane ring is located in the side chain and a xylose moiety is attached to the A-ring. Comparison of the experimental 13C NMR data with the theoretical chemical shifts of 24 S- and 24 R-cimipodocarpaside isomers revealed that the isolated compound has the 24 S-configuration. Combined spectroscopic and computational studies enabled the determination of the structure of cimipodocarpaside as (24 S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10- seco-9,19-cyclolanost-7(8),9(11),10(19)-trien-3-O-β- D-xylopyranoside. Triterpenes with 7-membered ring were thus far isolated from only Actea podocarpa DC. plants. This is the first report on the isolation of such a compound from Black Cohosh.

Quantitative determinations of levofloxacin and rifampicin in pharmaceutical and urine samples using nuclear magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Salem, A. A.; Mossa, H. A.; Barsoum, B. N.

2005-11-01

Rapid, specific and simple methods for determining levofloxacin and rifampicin antibiotic drugs in pharmaceutical and human urine samples were developed. The methods are based on 1H NMR spectroscopy using maleic acid as an internal standard and DMSO-d6 as NMR solvent. Integration of NMR signals at 8.9 and 8.2 ppm were, respectively, used for calculating the concentration of levofloxacin and rifampicin drugs per unit dose. Maleic acid signal at 6.2 ppm was used as the reference signal. Recoveries of (97.0-99.4) ± 0.5 and (98.3-99.7) ± 1.08% were obtained for pure levofloxacin and rifampicin, respectively. Corresponding recoveries of 98.5-100.3 and 96.8-100.0 were, respectively, obtained in pharmaceutical capsules and urine samples. Relative standard deviations (R.S.D.) values ≤2.7 were obtained for analyzed drugs in pure, pharmaceutical and urine samples. Statistical Student's t-test gave t-values ≤2.87 indicating insignificant difference between the real and the experimental values at the 95% confidence level. F-test revealed insignificant difference in precisions between the developed NMR methods and each of fluorimetric and HPLC methods for analyzing levofloxacin and rifampicin.

“Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations

PubMed Central

Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

2015-01-01

Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide-rich protein. In addition, sensitive 15N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. PMID:25676351

Binding Isotherms and Time Courses Readily from Magnetic Resonance.

PubMed

Xu, Jia; Van Doren, Steven R

2016-08-16

Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins. Although the sigmoidal shifts and line broadening of intermediate exchange distorts binding isotherms constructed conventionally, applying PCA directly to these spectra along with Pareto scaling overcomes the distortion. Applying PCA to time-domain NMR data also yields binding isotherms from titrations in fast or slow exchange. The algorithm readily extracts from magnetic resonance imaging movie time courses such as breathing and heart rate in chest imaging. Similarly, two-step binding processes detected by NMR are easily captured by principal components 1 and 2. PCA obviates the customary focus on specific peaks or regions of images. Applying it directly to a series of complex data will easily delineate binding isotherms, equilibrium shifts, and time courses of reactions or fluctuations.

Unraveling the active hypoglycemic agent trigonelline in Balanites aegyptiaca date fruit using metabolite fingerprinting by NMR.

PubMed

Farag, Mohamed A; Porzel, Andrea; Wessjohann, Ludger A

2015-11-10

Trigonelline (3-carboxy-1-methyl pyridinium) was identified as a relevant bioactivity and taste imparting component in Balanites aegyptiaca fruit, using (1)H NMR of crude extracts without any fractionation or isolation step. The structural integrity of trigonelline was established within the extract matrix via(1)H NMR, (1)H-(1)H COSY, HMQC and HMBC and by comparison with authentic standard. A quantitative (1)H NMR method (qHNMR) was used to determine trigonelline concentrations in the peel and pulp of B. aegyptiaca fruit of 8 and 13mgg(-1), respectively. Trigonelline so far has not been reported from B. aegyptiaca or its genus as it easily escapes LC-MS based detection. Its discovery provides novel insight into the balanite fruits antidiabetic properties as the compound is known for a pronounced hypoglycemic effect. In addition, it is likely to impart the perceptible bitter taste portion to balanites sweet bitter taste. UPLC-MS of the crude extract additionally revealed the fruit flavonoid pattern showing quercetin/isorhamnetin flavonol conjugates in addition to epicatechin, the latter being present at much lower levels. Copyright © 2015 Elsevier B.V. All rights reserved.

Towards Using NMR to Screen for Spoiled Tomatoes Stored in 1,000 L, Aseptically Sealed, Metal-Lined Totes

PubMed Central

Pinter, Michael D.; Harter, Tod; McCarthy, Michael J.; Augustine, Matthew P.

2014-01-01

Nuclear magnetic resonance (NMR) spectroscopy is used to track factory relevant tomato paste spoilage. It was found that spoilage in tomato paste test samples leads to longer spin lattice relaxation times T1 using a conventional low magnetic field NMR system. The increase in T1 value for contaminated samples over a five day room temperature exposure period prompted the work to be extended to the study of industry standard, 1,000 L, non-ferrous, metal-lined totes. NMR signals and T1 values were recovered from a large format container with a single-sided NMR sensor. The results of this work suggest that a handheld NMR device can be used to study tomato paste spoilage in factory process environments. PMID:24594611

Towards using NMR to screen for spoiled tomatoes stored in 1,000 L, aseptically sealed, metal-lined totes.

PubMed

Pinter, Michael D; Harter, Tod; McCarthy, Michael J; Augustine, Matthew P

2014-03-03

Nuclear magnetic resonance (NMR) spectroscopy is used to track factory relevant tomato paste spoilage. It was found that spoilage in tomato paste test samples leads to longer spin lattice relaxation times T1 using a conventional low magnetic field NMR system. The increase in T1 value for contaminated samples over a five day room temperature exposure period prompted the work to be extended to the study of industry standard, 1,000 L, non-ferrous, metal-lined totes. NMR signals and T1 values were recovered from a large format container with a single-sided NMR sensor. The results of this work suggest that a handheld NMR device can be used to study tomato paste spoilage in factory process environments.

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

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.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba 2In 2O 4(OH) 2 Structure and Dynamics

DOE PAGES

Dervisoglu, Riza; Middlemiss, Derek S.; Blanc, Frederic; ...

2015-05-01

Here, a structural characterization of the hydrated form of the brownmillerite-type phase Ba 2In 2O 5, Ba 2In 2O 4(OH) 2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics 2004, 170, 25–32) using X-ray and neutron studies. Calculationsmore » of possible proton arrangements within the partially occupied layer of Ba 2In 2O 4(OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H– 17O double resonance experiments.« less

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics.

PubMed

Dervişoğlu, Rıza; Middlemiss, Derek S; Blanc, Frédéric; Lee, Yueh-Lin; Morgan, Dane; Grey, Clare P

2015-06-09

A structural characterization of the hydrated form of the brownmillerite-type phase Ba 2 In 2 O 5 , Ba 2 In 2 O 4 (OH) 2 , is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2 O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25-32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba 2 In 2 O 4 (OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1 H and 17 O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1 H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1 H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17 O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1 H- 17 O double resonance experiments.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics

PubMed Central

2015-01-01

A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments. PMID:26321789

Proton NMR spectral study of UV treated live Escherichia coli Bacteria

NASA Astrophysics Data System (ADS)

Sorokopud, Michael

The lethal effects of ultraviolet radiation on microorganisms have been known and utilized for many years. In sufficiently high photon fluences, light and in particular, UV light, is an effective and subtle means of killing or at least immobilizing most, if not all cells and micro-organisms. Because of their small size, light can penetrate the enclosing protective walls and enter the inner volumes where it can break organic bonds in components that are vital to cell function. Despite the fact that a very low dose of UV light (1-9 mJ/cm2) has been shown to inactivate many micro-organisms, there remains a dearth of biological information about light induced effects in molecules and their interactions within living microbial systems. The use of 1H NMR as a spectroscopic tool was chosen to undertake an examination of the possible effects resulting from exposing E. coli to lethal fluencies of UV radiation. Once sample preparation, treatment, and NMR mounting methods were optimized, the high sensitivity and high resolution capabilities of the method produced reproducible results for a series of experiments. These results reveal significant changes in the ratio of the 1H NMR spectra of the treated to untreated E.coli samples when the treated sample was exposed to a lethal fluence of 275nm light. Photons at the 275nm wavelength, used in this study, have enough energy to break all of the principle bonds in an organic molecule. The difference spectrum between treated to untreated samples appears to be fitted well using specific component spectra from these groups of compounds. Increases in NMR peak amplitudes are observed and appear to be correlated with the spectral locations of several amino acids, membrane components and several sugars/saccharides. Increases in peak intensities of 4-8% were observed in the 0.8-1.1 ppm chemical shift region, characteristic of lipid and amino acid groups. A 3.5-4% increase was observed in the 2 ppm and 3.4-4 ppm region characteristic of various sugars and possibly amino acid components.

Spectral, thermal, and molecular modeling studies on the encapsulation of selected sulfonamide drugs in β-cyclodextrin nano-cavity

NASA Astrophysics Data System (ADS)

Bani-Yaseen, Abdulilah Dawoud; Mo'ala, Abeer

2014-10-01

In the present work the inclusion complexation of three sulfonamide (SA) drugs, namely sulfisoxazole (SSX), sulfamethizole (SMZ), and Sulfamethazine (STM) with β-cyclodextrin (β-CD) has been investigated using UV-Vis spectroscopy, DSC, 1H NMR spectroscopy, and molecular modeling methods. The binding constant (Kb) of SA:β-CD inclusion complexation was determined via applying the modified form of Benesi-Hildebrand equation employing the changes in absorbance at λmax. Obtained results revealed that SA drugs form 1:1 inclusion complex with β-CD with Kb of 650, 1532, 714 M-1 at 25 °C for SSX, SMZ, and STM, respectively. The UV-Vis absorption spectra displayed solvatochromic behavior of bathochromic shift with decreasing solvent polarity that in turn is good agreement with their behavior in the presence of β-CD in terms of environment polarity dependency. The inclusion complex formation between β-CD and tested SA drugs in liquid and solid states was confirmed by 1H NMR and DSC, respectively. Using semi-empirical quantum chemistry methods at PM3 theoretical level, inclusion complexes' structures as well as energetic and thermodynamic parameters of encapsulation were elucidated. Obtained results revealed that the encapsulation is favorably energetic and enthalpic in nature with the inclusion of the aniline moiety through the wide rim side of β-CD nano-cavity. Further, molecular modeling revealed that β-CD encapsulation of SA drugs reduced their (EHOMO - ELUMO) gap.

NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

PubMed Central

Konrat, Robert

2014-01-01

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

NMR crystallography: structure and properties of materials from solid-state nuclear magnetic resonance observables

PubMed Central

Bryce, David L.

2017-01-01

This topical review provides a brief overview of recent developments in NMR crystallography and related NMR approaches to studying the properties of molecular and ionic solids. Areas of complementarity with diffraction-based methods are underscored. These include the study of disordered systems, of dynamic systems, and other selected examples where NMR can provide unique insights. Highlights from the literature as well as recent work from my own group are discussed. PMID:28875022

Interfaces in polymer nanocomposites – An NMR study

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

Böhme, Ute; Scheler, Ulrich, E-mail: scheler@ipfdd.de

Nuclear Magnetic Resonance (NMR) is applied for the investigation of polymer nanocomposites. Solid-state NMR is applied to study the modification steps to compatibilize layered double hydroxides with non-polar polymers. {sup 1}H relaxation NMR gives insight on the polymer dynamics over a wide range of correlation times. For the polymer chain dynamics the transverse relaxation time T{sub 2} is most suited. In this presentation we report on two applications of T{sub 2} measurements under external mechanical stress. In a low-field system relaxation NMR studies are performed in-situ under uniaxial stress. High-temperature experiments in a Couette cell permit the investigation of themore » polymer dynamics in the melt under shear flow.« less

NMR Studies of Protein Hydration and Protein-Ligand Interactions

NASA Astrophysics Data System (ADS)

Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be facilitated by hydration. On the other hand, alcohols can bind to many nonspecific sites on the protein. In dry proteins, this type of binding only occurs above a threshold of alcohol vapor pressure. Such a threshold is gradually reduced by increasing the hydration level and can be removed above a critical hydration level. Hydration also shifts the nonspecific alcohol binding from an entropy-driven to an enthalpy-driven process. This dissertation reveals the mechanism of protein hydration and the detailed roles of hydration in ligand binding, with important implications for the understanding of protein functions.

Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions.

PubMed

Hattori, Yoshikazu; Heidenreich, David; Ono, Yuki; Sugiki, Toshihiko; Yokoyama, Kei-Ichi; Suzuki, Ei-Ichiro; Fujiwara, Toshimichi; Kojima, Chojiro

2017-08-01

The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic 15 N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. 19 F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility. Here, 19 F-labeling of glutamine side chains using TGase and 2,2,2-trifluoroethylamine hydrochloride was established for use in an NMR study. This enzymatic 19 F-labeling readily provided NMR detection of protein-drug and protein-protein interactions with complexes of about 100 kDa since the surface residues provided a good substrate for TGase. The 19 F-labeling method was 3.5-fold more sensitive than 15 N-labeling, and could be combined with other chemical modification techniques such as lysine 13 C-methylation. 13 C-dimethylated- 19 F-labeled FKBP12 provided more accurate information concerning the FK506 binding site.

Hydrogen bonding pattern in N-benzoyl(- DL-)- L-phenylalanines as revealed by solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Potrzebowski, M. J.; Schneider, C.; Tekely, P.

1999-11-01

The nature of the hydrogen bonding pattern has been investigated in N-benzoyl- DL-phenylalanine ( 1) and N-benzoyl- L-phenylalanine ( 2) polymorphes by solid-state NMR spectroscopy. It has been shown that the multiple resonances of carboxyl carbon in 2 are directly connected to different types of hydrogen bonding. The differences in intermolecular distances of carboxyl groups involved in different types of hydrogen bonding have been visualized by the 2D exchange and 1D ODESSA experiments. Potential applications of such a new approach include the exploration of intermolecular distances in hydrogen bonded compounds with singly labeled biomolecules.

Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-16000.

PubMed

Fontana, Carolina; Zaccheus, Mona; Weintraub, Andrej; Ansaruzzaman, Mohammad; Widmalm, Göran

2016-09-02

The structure of a polysaccharide from Vibrio parahaemolyticus strain AN-16000 has been investigated. The sugar and absolute configuration analysis revealed d-Glc, d-GalN, d-QuiN and l-FucN as major components. The PS was subjected to dephosphorylation with aqueous 40% HF to obtain an oligosaccharide that was analyzed by (1)H and (13)C NMR spectroscopy. The HR-MS spectrum of the oligosaccharide revealed a pentasaccharide composed of two Glc residues, one QuiNAc and one GalNAc, one FucNAc, as well as a glycerol moiety. The structure of the PS was determined using (1)H, (13)C, (15)N and (31)P NMR spectroscopy; inter-residue correlations were identified by (1)H,(13)C-heteronuclear multiple-bond correlation, (1)H,(1)H-NOESY and (1)H,(31)P-hetero-TOCSY experiments. The PS backbone has the following teichoic acid-like structure: →3)-d-Gro-(1-P-6)-β-d-Glcp-(1→4)-α-l-FucpNAc-(1→3)-β-d-QuipNAc-(1→ with a side-chain consisting of α-d-Glcp-(1→6)-α-d-GalpNAc-(1→ linked to the O3 position of the FucNAc residue. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metabolite signatures in hydrophilic extracts of mouse lungs exposed to cigarette smoke revealed by 1H NMR metabolomics investigation

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

Hu, Jian Z.; Wang, Xuan; Feng, Ju

Herein, 1H-NMR metabolomics are carried out to evaluate the changes of metabolites in lungs of mice exposed to cigarette smoke. It is found that the concentrations of adenosine derivatives (i.e. ATP, ADP and AMP), inosine and uridine are significantly fluctuated in the lungs of mice exposed to cigarette smoke compared with those of controls regardless the mouse is obese or regular weight. The decreased ATP, ADP, AMP and elevated inosine predict that the deaminases in charge of adenosine derivatives to inosine derivatives conversion are altered in lungs of mice exposed to cigarette smoke. Transcriptional analysis reveals that the concentrations ofmore » adenosine monophosphate deaminase and adenosine deaminase are different in the lungs of mice exposed to cigarette smoke, confirming the prediction from metabolomics studies. We also found, for the first time, that the ratio of glycerophosphocholine (GPC) to phosphocholine (PC) is significantly increased in the lungs of obese mice compared with regular weight mice. The ratio of GPC/PC is further elevated in the lungs of obese group by cigarette smoke exposure. Since GPC/PC ratio is a known biomarker for cancer, these results may suggest that obese group is more susceptible to lung cancer when exposed to cigarette smoke.« less

Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome.

PubMed

Galera-Prat, Albert; Pantoja-Uceda, David; Laurents, Douglas V; Carrión-Vázquez, Mariano

2018-04-15

Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1 H, 13 C and 15 N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode. Copyright © 2018 Elsevier Inc. All rights reserved.

Metabolite signatures in hydrophilic extracts of mouse lungs exposed to cigarette smoke revealed by 1H NMR metabolomics investigation

DOE PAGES

Hu, Jian Z.; Wang, Xuan; Feng, Ju; ...

2015-05-12

Herein, 1H-NMR metabolomics are carried out to evaluate the changes of metabolites in lungs of mice exposed to cigarette smoke. It is found that the concentrations of adenosine derivatives (i.e. ATP, ADP and AMP), inosine and uridine are significantly fluctuated in the lungs of mice exposed to cigarette smoke compared with those of controls regardless the mouse is obese or regular weight. The decreased ATP, ADP, AMP and elevated inosine predict that the deaminases in charge of adenosine derivatives to inosine derivatives conversion are altered in lungs of mice exposed to cigarette smoke. Transcriptional analysis reveals that the concentrations ofmore » adenosine monophosphate deaminase and adenosine deaminase are different in the lungs of mice exposed to cigarette smoke, confirming the prediction from metabolomics studies. We also found, for the first time, that the ratio of glycerophosphocholine (GPC) to phosphocholine (PC) is significantly increased in the lungs of obese mice compared with regular weight mice. The ratio of GPC/PC is further elevated in the lungs of obese group by cigarette smoke exposure. Since GPC/PC ratio is a known biomarker for cancer, these results may suggest that obese group is more susceptible to lung cancer when exposed to cigarette smoke.« less

Lipoprotein particle concentration measured by nuclear magnetic resonance spectroscopy is associated with gestational age at delivery: a prospective cohort study.

PubMed

Grace, M R; Vladutiu, C J; Nethery, R C; Siega-Riz, A M; Manuck, T A; Herring, A H; Savitz, D; Thorp, J T

2018-06-01

To estimate the association between lipoprotein particle concentrations in pregnancy and gestational age at delivery. Prospective cohort study. The study was conducted in the USA at the University of North Carolina. We assessed 715 women enrolled in the Pregnancy, Infection, and Nutrition study from 2001 to 2005. Fasting blood was collected at two time points (<20 and 24-29 weeks of gestation). Nuclear magnetic resonance (NMR) quantified lipoprotein particle concentrations [low-density lipoprotein (LDL), high-density lipoprotein (HDL), very-low density lipoprotein (VLDL)] and 10 subclasses of lipoproteins. Concentrations were assessed as continuous measures, with the exception of medium HDL which was classified as any or no detectable level, given its distribution. Cox proportional hazards models estimated hazard ratios (HR) for gestational age at delivery adjusting for covariates. Gestational age at delivery, preterm birth (<37 weeks of gestation), and spontaneous preterm birth. At <20 weeks of gestation, three lipoproteins were associated with later gestational ages at delivery [large LDL NMR (HR 0.78, 95% CI 0.64-0.96), total VLDL NMR (HR 0.77, 95% CI 0.61-0.98), and small VLDL NMR (HR 0.78, 95% CI 0.62-0.98], whereas large VLDL NMR (HR 1.19, 95% CI 1.01-1.41) was associated with a greater hazard of earlier delivery. At 24-28 weeks of gestation, average VLDL NMR (HR 1.25, 95% CI 1.03-1.51) and a detectable level of medium HDL NMR (HR 1.90, 95% CI 1.19-3.02) were associated with earlier gestational ages at delivery. In this sample of pregnant women, particle concentrations of VLDL NMR , LDL NMR , IDL NMR , and HDL NMR were each independently associated with gestational age at delivery for all deliveries or spontaneous deliveries <37 weeks of gestation. These findings may help formulate hypotheses for future studies of the complex relationship between maternal lipoproteins and preterm birth. Nuclear magnetic resonance spectroscopy may identify lipoprotein particles associated with preterm delivery. © 2017 Royal College of Obstetricians and Gynaecologists.

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.

Proton Environments in Biomimetic Calcium Phosphates Formed from Mesoporous Bioactive CaO-SiO2-P2O5 Glasses in Vitro: Insights from Solid-State NMR.

PubMed

Mathew, Renny; Turdean-Ionescu, Claudia; Yu, Yang; Stevensson, Baltzar; Izquierdo-Barba, Isabel; García, Ana; Arcos, Daniel; Vallet-Regí, María; Edén, Mattias

2017-06-22

When exposed to body fluids, mesoporous bioactive glasses (MBGs) of the CaO-SiO 2 -P 2 O 5 system develop a bone-bonding surface layer that initially consists of amorphous calcium phosphate (ACP), which transforms into hydroxy-carbonate apatite (HCA) with a very similar composition as bone/dentin mineral. Information from various 1 H-based solid-state nuclear magnetic resonance (NMR) experiments was combined to elucidate the evolution of the proton speciations both at the MBG surface and within each ACP/HCA constituent of the biomimetic phosphate layer formed when each of three MBGs with distinct Ca, Si, and P contents was immersed in a simulated body fluid (SBF) for variable periods between 15 min and 30 days. Directly excited magic-angle-spinning (MAS) 1 H NMR spectra mainly reflect the MBG component, whose surface is rich in water and silanol (SiOH) moieties. Double-quantum-single-quantum correlation 1 H NMR experimentation at fast MAS revealed their interatomic proximities. The comparatively minor H species of each ACP and HCA component were probed selectively by heteronuclear 1 H- 31 P NMR experimentation. The initially prevailing ACP phase comprises H 2 O and "nonapatitic" HPO 4 2- /PO 4 3- groups, whereas for prolonged MBG soaking over days, a well-progressed ACP → HCA transformation was evidenced by a dominating O 1 H resonance from HCA. We show that 1 H-detected 1 H → 31 P cross-polarization NMR is markedly more sensitive than utilizing powder X-ray diffraction or 31 P NMR for detecting the onset of HCA formation, notably so for P-bearing (M)BGs. In relation to the long-standing controversy as to whether bone mineral comprises ACP and/or forms via an ACP precursor, we discuss a recently accepted structural core-shell picture of both synthetic and biological HCA, highlighting the close relationship between the disordered surface layer and ACP.

NMR Studies of Low-Gamma Nuclei in Solids

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

Wasylishen, Roderick E.; Forgeron, Michelle A.; Siegel, Renee

2006-07-24

Over the past five years we have devoted considerable time to solid-state NMR investigaitons of nuclei, which are traditionally known as "difficult" because of their small magnetic moments. These include quadrupolar nuclei such as 35Cl, 53 Cr, 91Zr, 95Mo, 99Ru, 131 Xe, as well as spin-1/2 nuclei such as 109Ag. While NMR studies of such isotopes remain challenging, the use of moderate to high magnetic field strengths together with a variety of enhancement techniques is leading to many interesting applications. In this talk some of our successes in studying these isotopes will be presented. For example, we will present preliminarymore » results of 131Xe NMR studies of solid sodium perxenate, as well as 109Ag NMR studies of silver dialkylphosphites. Our experience using population enhancement techniques that utilize hyperbolic secant pulses will also be discussed.« less

Certified Reference Material for Use in 1H, 31P, and 19F Quantitative NMR, Ensuring Traceability to the International System of Units.

PubMed

Rigger, Romana; Rück, Alexander; Hellriegel, Christine; Sauermoser, Robert; Morf, Fabienne; Breitruck, KathrinBreitruck; Obkircher, Markus

2017-09-01

In recent years, quantitative NMR (qNMR) spectroscopy has become one of the most important tools for content determination of organic substances and quantitative evaluation of impurities. Using Certified Reference Materials (CRMs) as internal or external standards, the extensively used qNMR method can be applied for purity determination, including unbroken traceability to the International System of Units (SI). The implementation of qNMR toward new application fields, e.g., metabolomics, environmental analysis, and physiological pathway studies, brings along more complex molecules and systems, thus making use of 1H qNMR challenging. A smart workaround is possible by the use of other NMR active nuclei, namely 31P and 19F. This article presents the development of three classes of qNMR CRMs based on different NMR active nuclei (1H, 31P, and 19F), and the corresponding approaches to establish traceability to the SI through primary CRMs from the National Institute of Standards and Technology and the National Metrology Institute of Japan. These TraceCERT® qNMR CRMs are produced under ISO/IEC 17025 and ISO Guide 34 using high-performance qNMR.

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

PubMed

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

2017-10-01

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

Induced secondary structure and polymorphism in an intrinsically disordered structural linker of the CNS: solid-state NMR and FTIR spectroscopy of myelin basic protein bound to actin.

PubMed

Ahmed, Mumdooh A M; Bamm, Vladimir V; Shi, Lichi; Steiner-Mosonyi, Marta; Dawson, John F; Brown, Leonid; Harauz, George; Ladizhansky, Vladimir

2009-01-01

The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully (13)C,(15)N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in beta-sheet content in actin, and increases in both alpha-helix and beta-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both alpha-helical and beta-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub.

Coupling HPLC-SPE-NMR with a microplate-based high-resolution antioxidant assay for efficient analysis of antioxidants in food--validation and proof-of-concept study with caper buds.

PubMed

Wiese, Stefanie; Wubshet, Sileshi G; Nielsen, John; Staerk, Dan

2013-12-15

This work describes the coupling of a microplate-based antioxidant assay with a hyphenated system consisting of high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy, i.e., HPLC-SPE-NMR/high-resolution antioxidant assay, for the analysis of complex food extracts. The applicability of the microplate-based antioxidant assay for high-resolution screening of common food phenolics as well as parameters related to their trapping efficiency, elution behavior, and recovery on/from SPE cartridges are described. It was found that the microplate-based high-resolution antioxidant assay is an attractive and easy implementable alternative to direct on-line screening methods. Furthermore, it was shown that Resin SH and Resin GP SPE material are superior to RP C18HD for trapping of phenolic compounds. Proof-of-concept study was performed with caper bud extract, revealing the most important antioxidants to be quercetin, kaempferol, rutin, kaempferol-3-O-β-rutinoside and N(1),N(5),N(10)-triphenylpropenoyl spermidine amides. Targeted isolation of the latter, and comprehensive NMR experiments showed them to be N(1),N(10)-di-(E)-caffeoyl-N(5)-p-(E)-coumaroyl spermidine, N(1)-(E)-caffeoyl-N(5),N(10)-di-p-(E)-coumaroyl spermidine, N(10)-(E)-caffeoyl-N(1),N(5)-di-p-(E)-coumaroyl spermidine, and N(1),N(5),N(10)-tri-p-(E)-coumaroyl spermidine amides. Copyright © 2013 Elsevier Ltd. All rights reserved.