Spectral separation of gaseous fluorocarbon mixtures and measurement of diffusion constants by 19F gas phase DOSY NMR.

PubMed

Marchione, Alexander A; McCord, Elizabeth F

2009-11-01

Diffusion-ordered (DOSY) NMR techniques have for the first time been applied to the spectral separation of mixtures of fluorinated gases by diffusion rates. A mixture of linear perfluoroalkanes from methane to hexane was readily separated at 25 degrees C in an ordinary experimental setup with standard DOSY pulse sequences. Partial separation of variously fluorinated ethanes was also achieved. The constants of self-diffusion of a set of pure perfluoroalkanes were obtained at pressures from 0.25 to 1.34 atm and temperatures from 20 to 122 degrees C. Under all conditions there was agreement within 20% of experimental self-diffusion constant D and values calculated by the semiempirical Fuller method.

Evaluation of 1H NMR metabolic profiling using biofluid mixture design.

PubMed

Athersuch, Toby J; Malik, Shahid; Weljie, Aalim; Newton, Jack; Keun, Hector C

2013-07-16

A strategy for evaluating the performance of quantitative spectral analysis tools in conditions that better approximate background variation in a metabonomics experiment is presented. Three different urine samples were mixed in known proportions according to a {3, 3} simplex lattice experimental design and analyzed in triplicate by 1D (1)H NMR spectroscopy. Fifty-four urinary metabolites were subsequently quantified from the sample spectra using two methods common in metabolic profiling studies: (1) targeted spectral fitting and (2) targeted spectral integration. Multivariate analysis using partial least-squares (PLS) regression showed the latent structure of the spectral set recapitulated the experimental mixture design. The goodness-of-prediction statistic (Q(2)) of each metabolite variable in a PLS model was calculated as a metric for the reliability of measurement, across the sample compositional space. Several metabolites were observed to have low Q(2) values, largely as a consequence of their spectral resonances having low s/n or strong overlap with other sample components. This strategy has the potential to allow evaluation of spectral features obtained from metabolic profiling platforms in the context of the compositional background found in real biological sample sets, which may be subject to considerable variation. We suggest that it be incorporated into metabolic profiling studies to improve the estimation of matrix effects that confound accurate metabolite measurement. This novel method provides a rational basis for exploiting information from several samples in an efficient manner and avoids the use of multiple spike-in authentic standards, which may be difficult to obtain.

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

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

PubMed

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

2003-02-15

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

Integrated Geophysical Measurements for Bioremediation Monitoring: Combining Spectral Induced Polarization, Nuclear Magnetic Resonance and Magnetic Methods

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

Keating, Kristina; Slater, Lee; Ntarlagiannis, Dimitris

2015-02-24

This documents contains the final report for the project "Integrated Geophysical Measurements for Bioremediation Monitoring: Combining Spectral Induced Polarization, Nuclear Magnetic Resonance and Magnetic Methods" (DE-SC0007049) Executive Summary: Our research aimed to develop borehole measurement techniques capable of monitoring subsurface processes, such as changes in pore geometry and iron/sulfur geochemistry, associated with remediation of heavy metals and radionuclides. Previous work has demonstrated that geophysical method spectral induced polarization (SIP) can be used to assess subsurface contaminant remediation; however, SIP signals can be generated from multiple sources limiting their interpretation value. Integrating multiple geophysical methods, such as nuclear magnetic resonance (NMR)more » and magnetic susceptibility (MS), with SIP, could reduce the ambiguity of interpretation that might result from a single method. Our research efforts entails combining measurements from these methods, each sensitive to different mineral forms and/or mineral-fluid interfaces, providing better constraints on changes in subsurface biogeochemical processes and pore geometries significantly improving our understanding of processes impacting contaminant remediation. The Rifle Integrated Field Research Challenge (IFRC) site was used as a test location for our measurements. The Rifle IFRC site is located at a former uranium ore-processing facility in Rifle, Colorado. Leachate from spent mill tailings has resulted in residual uranium contamination of both groundwater and sediments within the local aquifer. Studies at the site include an ongoing acetate amendment strategy, native microbial populations are stimulated by introduction of carbon intended to alter redox conditions and immobilize uranium. To test the geophysical methods in the field, NMR and MS logging measurements were collected before, during, and after acetate amendment. Next, laboratory NMR, MS, and SIP measurements were collected on columns of Rifle sediments during acetate amendment. The laboratory experiments were designed to simulate the field experiments; changes in geophysical signals were expected to correlate with changes in redox conditions and iron speciation. Field MS logging measurements revealed vertically stratified magnetic mineralization, likely the result of detrital magnetic fraction within the bulk alluvium. Little to no change was observed in the MS data suggesting negligible production of magnetic phases (e.g. magnetite, pyrrhotite) as a result of sulfidogenesis. Borehole NMR measurements contained high levels of noise contamination requiring significant signal processing, and analysis suggests that any changes may be difficult to differentiate from simultaneous changes in water content. Laboratory MS and NMR measurements remained relatively stable throughout the course of the acetate amendment experiment, consistent with field measurements. However, SIP measurements changed during the acetate amendment associated with the formation of iron-sulfide mineral phases; a finding that is consistent with chemical analysis of the solid phase materials in the columns.« less

Complete 13C NMR chemical shifts assignment for cholesterol crystals by combined CP-MAS spectral editing and ab initio GIPAW calculations with dispersion forces.

PubMed

Küçükbenli, Emine; Sonkar, Kanchan; Sinha, Neeraj; de Gironcoli, Stefano

2012-04-12

We report here the first fully ab initio determination of (13)C NMR spectra for several crystal structures of cholesterol, observed in various biomaterials. We combine Gauge-Including Projector Augmented Waves (GIPAW) calculations at relaxed structures, fully including dispersion forces, with Magic Angle Spinning Solid State NMR experiments and spectral editing to achieve a detailed interpretation of the complex NMR spectra of cholesterol crystals. By introducing an environment-dependent secondary referencing scheme in our calculations, not only do we reproduce the characteristic spectral features of the different crystalline polymorphs, thus clearly discriminating among them, but also closely represent the spectrum in the region of several highly overlapping peaks. This, in combination with spectral editing, allows us to provide a complete peak assignment for monohydrate (ChM) and low-temperature anhydrous (ChAl) crystal polymorphs. Our results show that the synergy between ab initio calculations and refined experimental techniques can be exploited for an accurate and efficient NMR crystallography of complex systems of great interest for biomaterial studies. The method is general in nature and can be applied for studies of various complex biomaterials.

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

DOE PAGES

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

2018-01-01

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

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

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

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

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

High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification

NASA Astrophysics Data System (ADS)

Kotler, Samuel A.; Brender, Jeffrey R.; Vivekanandan, Subramanian; Suzuki, Yuta; Yamamoto, Kazutoshi; Monette, Martine; Krishnamoorthy, Janarthanan; Walsh, Patrick; Cauble, Meagan; Holl, Mark M. Banaszak; Marsh, E. Neil. G.; Ramamoorthy, Ayyalusamy

2015-07-01

Alzheimer’s disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling 1H-1H NMR experiments to overcome many of these limitations. Using 1H-1H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time 1H-1H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5-15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils.

High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification

PubMed Central

Kotler, Samuel A.; Brender, Jeffrey R.; Vivekanandan, Subramanian; Suzuki, Yuta; Yamamoto, Kazutoshi; Monette, Martine; Krishnamoorthy, Janarthanan; Walsh, Patrick; Cauble, Meagan; Holl, Mark M. Banaszak; Marsh, E. Neil. G.; Ramamoorthy, Ayyalusamy

2015-01-01

Alzheimer’s disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling 1H-1H NMR experiments to overcome many of these limitations. Using 1H-1H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time 1H-1H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5–15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils. PMID:26138908

High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification.

PubMed

Kotler, Samuel A; Brender, Jeffrey R; Vivekanandan, Subramanian; Suzuki, Yuta; Yamamoto, Kazutoshi; Monette, Martine; Krishnamoorthy, Janarthanan; Walsh, Patrick; Cauble, Meagan; Holl, Mark M Banaszak; Marsh, E Neil G; Ramamoorthy, Ayyalusamy

2015-07-03

Alzheimer's disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling (1)H-(1)H NMR experiments to overcome many of these limitations. Using (1)H-(1)H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time (1)H-(1)H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5-15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils.

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

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

Huang, Yuqing; Cai, Shuhui; Yang, Yu

2016-03-14

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

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Earth field NMR with chemical shift spectral resolution: theory and proof of concept.

PubMed

Katz, Itai; Shtirberg, Lazar; Shakour, Gubrail; Blank, Aharon

2012-06-01

A new method for obtaining an NMR signal in the Earth's magnetic field (EF) is presented. The method makes use of a simple pulse sequence with only DC fields which is much less demanding than previous approaches in terms of the pulses' rise and fall times. Furthermore, it offers the possibility of obtaining NMR data with enough spectral resolution to allow retrieving high resolution molecular chemical shift (CS) information - a capability that was not considered possible in EF NMR until now. Details of the pulse sequence, the experimental system, and our specially tailored EF NMR probe are provided. The experimental results demonstrate the capability to differentiate between three types of samples made of common fluorine compounds, based on their CS data. Copyright © 2012 Elsevier Inc. All rights reserved.

Robust and transferable quantification of NMR spectral quality using IROC analysis

NASA Astrophysics Data System (ADS)

Zambrello, Matthew A.; Maciejewski, Mark W.; Schuyler, Adam D.; Weatherby, Gerard; Hoch, Jeffrey C.

2017-12-01

Non-Fourier methods are increasingly utilized in NMR spectroscopy because of their ability to handle nonuniformly-sampled data. However, non-Fourier methods present unique challenges due to their nonlinearity, which can produce nonrandom noise and render conventional metrics for spectral quality such as signal-to-noise ratio unreliable. The lack of robust and transferable metrics (i.e. applicable to methods exhibiting different nonlinearities) has hampered comparison of non-Fourier methods and nonuniform sampling schemes, preventing the identification of best practices. We describe a novel method, in situ receiver operating characteristic analysis (IROC), for characterizing spectral quality based on the Receiver Operating Characteristic curve. IROC utilizes synthetic signals added to empirical data as "ground truth", and provides several robust scalar-valued metrics for spectral quality. This approach avoids problems posed by nonlinear spectral estimates, and provides a versatile quantitative means of characterizing many aspects of spectral quality. We demonstrate applications to parameter optimization in Fourier and non-Fourier spectral estimation, critical comparison of different methods for spectrum analysis, and optimization of nonuniform sampling schemes. The approach will accelerate the discovery of optimal approaches to nonuniform sampling experiment design and non-Fourier spectrum analysis for multidimensional NMR.

Mononuclear Pd(II) complex as a new therapeutic agent: Synthesis, characterization, biological activity, spectral and DNA binding approaches

NASA Astrophysics Data System (ADS)

Saeidifar, Maryam; Mirzaei, Hamidreza; Ahmadi Nasab, Navid; Mansouri-Torshizi, Hassan

2017-11-01

The binding ability between a new water-soluble palladium(II) complex [Pd(bpy)(bez-dtc)]Cl (where bpy is 2,2‧-bipyridine and bez-dtc is benzyl dithiocarbamate), as an antitumor agent, and calf thymus DNA was evaluated using various physicochemical methods, such as UV-Vis absorption, Competitive fluorescence studies, viscosity measurement, zeta potential and circular dichroism (CD) spectroscopy. The Pd(II) complex was synthesized and characterized using elemental analysis, molar conductivity measurements, FT-IR, 1H NMR, 13C NMR and electronic spectra studies. The anticancer activity against HeLa cell lines demonstrated lower cytotoxicity than cisplatin. The binding constants and the thermodynamic parameters were determined at different temperatures (300 K, 310 K and 320 K) and shown that the complex can bind to DNA via electrostatic forces. Furthermore, this result was confirmed by the viscosity and zeta potential measurements. The CD spectral results demonstrated that the binding of Pd(II) complex to DNA induced conformational changes in DNA. We hope that these results will provide a basis for further studies and practical clinical use of anticancer drugs.

Structural basis of sodium–potassium exchange of a human telomeric DNA quadruplex without topological conversion

PubMed Central

Wang, Zi-Fu; Li, Ming-Hao; Hsu, Shang-Te Danny; Chang, Ta-Chau

2014-01-01

Understanding the mechanism of Na+/K+-dependent spectral conversion of human telomeric G-quadruplex (G4) sequences has been limited not only because of the structural polymorphism but also the lack of sufficient structural information at different stages along the conversion process for one given oligonucleotide. In this work, we have determined the topology of the Na+ form of Tel23 G4, which is the same hybrid form as the K+ form of Tel23 G4 despite the distinct spectral patterns in their respective nuclear magnetic resonance (NMR) and circular dichroism spectra. The spectral difference, particularly the well-resolved imino proton NMR signals, allows us to monitor the structural conversion from Na+ form to K+ form during Na+/K+ exchange. Time-resolved NMR experiments of hydrogen–deuterium exchange and hybridization clearly exclude involvement of the global unfolding for the fast Na+/K+ spectral conversion. In addition, the K+ titration monitored by NMR reveals that the Na+/K+ exchange in Tel23 G4 is a two-step process. The addition of K+ significantly stabilizes the unfolding kinetics of Tel23 G4. These results offer a possible explanation of rapid spectral conversion of Na+/K+ exchange and insight into the mechanism of Na+/K+ structural conversion in human telomeric G4s. PMID:24476914

Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

NASA Astrophysics Data System (ADS)

McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M. Banaszak; Tecklenburg, Mary M. J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

2013-10-01

Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43-ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO32- range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

PubMed

MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

2013-01-01

Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Copyright © 2012 Elsevier Inc. All rights reserved.

Combination of 1H nuclear magnetic resonance spectroscopy and principal component analysis to evaluate the lipid fluidity of flutamide-encapsulated lipid nanoemulsions.

PubMed

Takegami, Shigehiko; Ueyama, Keita; Konishi, Atsuko; Kitade, Tatsuya

2018-06-06

The lipid fluidity of various lipid nanoemulsions (LNEs) without and with flutamide (FT) and containing one of two neutral lipids, one of four phosphatidylcholines as a surfactant, and sodium palmitate as a cosurfactant was investigated by the combination of 1 H nuclear magnetic resonance (NMR) spectroscopy and principal component analysis (PCA). In the 1 H NMR spectra, the peaks from the methylene groups of the neutral lipids and surfactants for all LNE preparations showed downfield shifts with increasing temperature from 20 to 60 °C. PCA was applied to the 1 H NMR spectral data obtained for the LNEs. The PCA resulted in a model in which the first two principal components (PCs) extracted 88% of the total spectral variation; the first PC (PC-1) axis and second PC (PC-2) axis accounted for 73 and 15%, respectively, of the total spectral variation. The Score-1 values for PC-1 plotted against temperature revealed the existence of two clusters, which were defined by the neutral lipid of the LNE preparations. Meanwhile, the Score-2 values decreased with rising temperature and reflected the increase in lipid fluidity of each LNE preparation, consistent with fluorescence anisotropy measurements. In addition, the changes of Score-2 values with temperature for LNE preparations with FT were smaller than those for LNE preparations without FT. This indicates that FT encapsulated in LNE particles markedly suppressed the increase in lipid fluidity of LNE particles with rising temperature. Thus, PCA of 1 H NMR spectra will become a powerful tool to analyze the lipid fluidity of lipid nanoparticles. Graphical abstract ᅟ.

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.

Implementation of picoSpin Benchtop NMR Instruments into Organic Chemistry Teaching Laboratories through Spectral Analysis of Fischer Esterification Products

ERIC Educational Resources Information Center

Yearty, Kasey L.; Sharp, Joseph T.; Meehan, Emma K.; Wallace, Doyle R.; Jackson, Douglas M.; Morrison, Richard W.

2017-01-01

[Superscript 1]H NMR analysis is an important analytical technique presented in introductory organic chemistry courses. NMR instrument access is limited for undergraduate organic chemistry students due to the size of the instrument, price of NMR solvents, and the maintenance level required for instrument upkeep. The University of Georgia Chemistry…

A scoring metric for multivariate data for reproducibility analysis using chemometric methods

PubMed Central

Sheen, David A.; de Carvalho Rocha, Werickson Fortunato; Lippa, Katrice A.; Bearden, Daniel W.

2017-01-01

Process quality control and reproducibility in emerging measurement fields such as metabolomics is normally assured by interlaboratory comparison testing. As a part of this testing process, spectral features from a spectroscopic method such as nuclear magnetic resonance (NMR) spectroscopy are attributed to particular analytes within a mixture, and it is the metabolite concentrations that are returned for comparison between laboratories. However, data quality may also be assessed directly by using binned spectral data before the time-consuming identification and quantification. Use of the binned spectra has some advantages, including preserving information about trace constituents and enabling identification of process difficulties. In this paper, we demonstrate the use of binned NMR spectra to conduct a detailed interlaboratory comparison and composition analysis. Spectra of synthetic and biologically-obtained metabolite mixtures, taken from a previous interlaboratory study, are compared with cluster analysis using a variety of distance and entropy metrics. The individual measurements are then evaluated based on where they fall within their clusters, and a laboratory-level scoring metric is developed, which provides an assessment of each laboratory’s individual performance. PMID:28694553

NMR resonance splitting of urea in stretched hydrogels: proton exchange and (1)H/(2)H isotopologues.

PubMed

Kuchel, Philip W; Naumann, Christoph; Chapman, Bogdan E; Shishmarev, Dmitry; Håkansson, Pär; Bacskay, George; Hush, Noel S

2014-10-01

Urea at ∼12 M in concentrated gelatin gel, that was stretched, gave (1)H and (2)H NMR spectral splitting patterns that varied in a predictable way with changes in the relative proportions of (1)H2O and (2)H2O in the medium. This required consideration of the combinatorics of the two amide groups in urea that have a total of four protonation/deuteration sites giving rise to 16 different isotopologues, if all the atoms were separately identifiable. The rate constant that characterized the exchange of the protons with water was estimated by back-transformation analysis of 2D-EXSY spectra. There was no (1)H NMR spectral evidence that the chiral gelatin medium had caused in-equivalence in the protons bonded to each amide nitrogen atom. The spectral splitting patterns in (1)H and (2)H NMR spectra were accounted for by intra-molecular scalar and dipolar interactions, and quadrupolar interactions with the electric field gradients of the gelatin matrix, respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

PubMed

Nowling, Ronald J; Vyas, Jay; Weatherby, Gerard; Fenwick, Matthew W; Ellis, Heidi J C; Gryk, Michael R

2011-05-01

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

Experimental aspects in acquisition of wide bandwidth solid-state MAS NMR spectra of low-γ nuclei with different opportunities on two commercial NMR spectrometers

NASA Astrophysics Data System (ADS)

Jakobsen, Hans J.; Bildsøe, Henrik; Gan, Zhehong; Brey, William W.

2011-08-01

The acquisition and different appearances observed for wide bandwidth solid-state MAS NMR spectra of low-γ nuclei, using 14N as an illustrative nucleus and employing two different commercial spectrometers (Varian, 14.1 T and Bruker, 19.6 T), have been compared/evaluated and optimized from an experimental NMR and an electronic engineering point of view, to account for the huge differences in these spectra. The large differences in their spectral appearances, employing the recommended/standard experimental set-up for the two different spectrometers, are shown to be associated with quite large differences in the electronic design of the two types of preamplifiers, which are connected to their respective probes through a 50 Ω cable, and are here completely accounted for. This has led to different opportunities for optimum performances in the acquisition of nearly ideal wide bandwidth spectra for low-γ nuclei on the two spectrometers by careful evaluation of the length for the 50 Ω probe-to-preamp cable for the Varian system and appropriate changes to the bandwidth ( Q) of the NMR probe used on the Bruker spectrometer. Earlier, we reported quite distorted spectra obtained with Varian Unity INOVA spectrometers (at 11.4 and 14.1 T) in several exploratory wide bandwidth 14N MAS NMR studies of inorganic nitrates and amino acids. These spectra have now been compared/evaluated with fully analyzed 14N MAS spectra correspondingly acquired at 19.6 T on a Bruker spectrometer. It is shown that our upgraded version of the STARS simulation/iterative-fitting software is capable of providing identical sets for the molecular spectral parameters and corresponding fits to the experimental spectra, which fully agree with the electronic measurements, despite the highly different appearances for the MAS NMR spectra acquired on the Varian and Bruker spectrometers.

Relationship between pore geometric characteristics and SIP/NMR parameters observed for mudstones

NASA Astrophysics Data System (ADS)

Robinson, J.; Slater, L. D.; Keating, K.; Parker, B. L.; Robinson, T.

2017-12-01

The reliable estimation of permeability remains one of the most challenging problems in hydrogeological characterization. Cost effective, non-invasive geophysical methods such as spectral induced polarization (SIP) and nuclear magnetic resonance (NMR) offer an alternative to traditional sampling methods as they are sensitive to the mineral surfaces and pore spaces that control permeability. We performed extensive physical characterization, SIP and NMR geophysical measurements on fractured rock cores extracted from a mudstone site in an effort to compare 1) the pore size characterization determined from traditional and geophysical methods and 2) the performance of permeability models based on these methods. We focus on two physical characterizations that are well-correlated with hydraulic properties: the pore volume normalized surface area (Spor) and an interconnected pore diameter (Λ). We find the SIP polarization magnitude and relaxation time are better correlated with Spor than Λ, the best correlation of these SIP measures for our sample dataset was found with Spor divided by the electrical formation factor (F). NMR parameters are, similarly, better correlated with Spor than Λ. We implement previously proposed mechanistic and empirical permeability models using SIP and NMR parameters. A sandstone-calibrated SIP model using a polarization magnitude does not perform well while a SIP model using a mean relaxation time performs better in part by more sufficiently accounting for the effects of fluid chemistry. A sandstone-calibrated NMR permeability model using an average measure of the relaxation time does not perform well, presumably due to small pore sizes which are either not connected or contain water of limited mobility. An NMR model based on the laboratory determined portions of the bound versus mobile portions of the relaxation distribution performed reasonably well. While limitations exist, there are many opportunities to use geophysical data to predict permeability in mudstone formations.

NMR studies of the helical antiferromagnetic compound EuCo2P2

NASA Astrophysics Data System (ADS)

Higa, N.; Ding, Q.-P.; Kubota, F.; Uehara, H.; Yogi, M.; Furukawa, Y.; Sangeetha, N. S.; Johnston, D. C.; Nakamura, A.; Hedo, M.; Nakama, T.; Ōnuki, Y.

2018-05-01

In EuCo2P2, 4f electron spins of Eu2+ ions order antiferromagnetically below a Néel temperature TN = 66.5 K . The magnetic structure below TN was reported to be helical with the helix axis along the c-axis from the neutron diffraction study. We report the results of 153Eu, 59Co and 31P nuclear magnetic resonance (NMR) measurements on EuCo2P2 using a single crystal and a powdered sample. In the antiferromagnetic (AFM) state, we succeeded in observing 153Eu, 59Co and 31P NMR spectra in zero magnetic field. The sharp 153Eu zero field NMR (ZF NMR) lines indicate homogeneous Eu ordered moment. The 59Co and 31P ZF NMR spectra showed an asymmetric spectral shape, indicating a distribution of the internal magnetic induction at each nuclear position. The AFM propagation vector k characterizing the helical AFM state can be determined from the internal magnetic induction at Co site. We have determined the model-independent value of the AFM propagation vector k distributed from (0, 0, 0.86)2π/c to (0, 0, 0.73)2π/c, where c is the lattice parameter.

27 Al MAS NMR Studies of HBEA Zeolite at Low to High Magnetic Fields

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

Hu, Jian Zhi; Wan, Chuan; Vjunov, Aleksei

27Al single pulse (SP) MAS NMR spectra of HBEA zeolites with high Si/Al ratios of 71 and 75 were obtained at three magnetic field strengths of 7.05, 11.75 and 19.97 T. High field 27Al MAS NMR spectra acquired at 19.97 T show significantly improved spectral resolution, resulting in at least two well-resolved tetrahedral-Al NMR peaks. Based on the results obtained from 27Al MAS and MQMAS NMR acquired at 19.97 T, four different quadrupole peaks are used to deconvolute the 27Al SP MAS spectra acquired at vari-ous fields by using the same set of quadrupole coupling constants, asymmetric parameters and relativemore » integrated peak intensities for the tetrahedral Al peaks. The line shapes of individual peaks change from typical quadrupole line shape at low field to essentially symmetrical line shapes at high field. We demonstrate that for fully hydrated HBEA zeolites the effect of second order quadrupole interaction can be ignored and quantitative spectral analysis can be performed by directly fitting the high field spectra using mixed Gaussian/Lorentzian line shapes. Also, the analytical steps described in our work allow direct assignment of spectral intensity to individual Al tetrahedral sites (T-sites) of zeolite HBEA. Finally, the proposed concept is suggested generally applicable to other zeo-lite framework types, thus, allowing a direct probing of Al distributions by NMR spectroscopic methods in zeolites with high confi-dence.« less

PSYCHE Pure Shift NMR Spectroscopy.

PubMed

Foroozandeh, Mohammadali; Morris, Gareth; Nilsson, Mathias

2018-03-13

Broadband homodecoupling techniques in NMR, also known as "pure shift" methods, aim to enhance spectral resolution by suppressing the effects of homonuclear coupling interactions to turn multiplet signals into singlets. Such techniques typically work by selecting a subset of "active" nuclear spins to observe, and selectively inverting the remaining, "passive", spins to reverse the effects of coupling. Pure Shift Yielded by Chirp Excitation (PSYCHE) is one such method; it is relatively recent, but has already been successfully implemented in a range of different NMR experiments. Paradoxically, PSYCHE is one of the trickiest of pure shift NMR techniques to understand but one of the easiest to use. Here we offer some insights into theoretical and practical aspects of the method, and into the effects and importance of the experimental parameters. Some recent improvements that enhance the spectral purity of PSYCHE spectra will be presented, and some experimental frameworks including examples in 1D and 2D NMR spectroscopy, for the implementation of PSYCHE will be introduced. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced solid-state NMR spectroscopy of natural organic matter.

PubMed

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

2017-05-01

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

A highly versatile automatized setup for quantitative measurements of PHIP enhancements

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

PubMed

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

2012-09-27

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

On the predictions of the 11B solid state NMR parameters

NASA Astrophysics Data System (ADS)

Czernek, Jiří; Brus, Jiří

2016-07-01

The set of boron containing compounds has been subject to the prediction of the 11B solid state NMR spectral parameters using DFT-GIPAW methods properly treating the solid phase effects. The quantification of the differences between measured and theoretical values has been presented, which is directly applicable in structural studies involving 11B nuclei. In particular, a simple scheme has been proposed, which is expected to provide for an estimate of the 11B chemical shift within ±2.0 ppm from the experimental value. The computer program, INFOR, enabling the visualization of concomitant Euler rotations related to the tensorial transformations has been presented.

Quick, sensitive serial NMR experiments with Radon transform.

PubMed

Dass, Rupashree; Kasprzak, Paweł; Kazimierczuk, Krzysztof

2017-09-01

The Radon transform is a potentially powerful tool for processing the data from serial spectroscopic experiments. It makes it possible to decode the rate at which frequencies of spectral peaks shift under the effect of changing conditions, such as temperature, pH, or solvent. In this paper we show how it also improves speed and sensitivity, especially in multidimensional experiments. This is particularly important in the case of low-sensitivity techniques, such as NMR spectroscopy. As an example, we demonstrate how Radon transform processing allows serial measurements of 15 N-HSQC spectra of unlabelled peptides that would otherwise be infeasible. Copyright © 2017 Elsevier Inc. All rights reserved.

Exotic phases of frustrated antiferromagnet LiCu2O2

NASA Astrophysics Data System (ADS)

Bush, A. A.; Büttgen, N.; Gippius, A. A.; Horvatić, M.; Jeong, M.; Kraetschmer, W.; Marchenko, V. I.; Sakhratov, Yu. A.; Svistov, L. E.

2018-02-01

7Li NMR spectra were measured in a magnetic field up to 17 T at temperatures 5-30 K on single crystalline LiCu2O2 . Earlier reported anomalies on magnetization curves correspond to magnetic field values where we observe changes of the NMR spectral shape. For the interpretation of the field and temperature evolutions of our NMR spectra, the magnetic structures were analyzed in the frame of the phenomenological theoretical approach of the Dzyaloshinskii-Landau theory. A set of possible planar and collinear structures was obtained. Most of these structures have an unusual configuration; they are characterized by a two-component order parameter and their magnetic moments vary harmonically not only in direction, but also in size. From the modeling of the observed spectra, a possible scenario of magnetic structure transformations is obtained.

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

Structure elucidation of organic compounds aided by the computer program system SCANNET

NASA Astrophysics Data System (ADS)

Guzowska-Swider, B.; Hippe, Z. S.

1992-12-01

Recognition of chemical structure is a very important problem currently solved by molecular spectroscopy, particularly IR, UV, NMR and Raman spectroscopy, and mass spectrometry. Nowadays, solution of the problem is frequently aided by the computer. SCANNET is a computer program system for structure elucidation of organic compounds, developed by our group. The structure recognition of an unknown substance is made by comparing its spectrum with successive reference spectra of standard compounds, i.e. chemical compounds of known chemical structure, stored in a spectral database. The computer program system SCANNET consists of six different spectral databases for following the analytical methods: IR, UV, 13C-NMR, 1H-NMR and Raman spectroscopy, and mass spectrometry. A chemist, to elucidate a structure, can use one of these spectral methods or a combination of them and search the appropriate databases. As the result of searching each spectral database, the user obtains a list of chemical substances whose spectra are identical and/or similar to the spectrum input into the computer. The final information obtained from searching the spectral databases is in the form of a list of chemical substances having all the examined spectra, for each type of spectroscopy, identical or simlar to those of the unknown compound.

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

Focus: a robust workflow for one-dimensional NMR spectral analysis.

PubMed

Alonso, Arnald; Rodríguez, Miguel A; Vinaixa, Maria; Tortosa, Raül; Correig, Xavier; Julià, Antonio; Marsal, Sara

2014-01-21

One-dimensional (1)H NMR represents one of the most commonly used analytical techniques in metabolomic studies. The increase in the number of samples analyzed as well as the technical improvements involving instrumentation and spectral acquisition demand increasingly accurate and efficient high-throughput data processing workflows. We present FOCUS, an integrated and innovative methodology that provides a complete data analysis workflow for one-dimensional NMR-based metabolomics. This tool will allow users to easily obtain a NMR peak feature matrix ready for chemometric analysis as well as metabolite identification scores for each peak that greatly simplify the biological interpretation of the results. The algorithm development has been focused on solving the critical difficulties that appear at each data processing step and that can dramatically affect the quality of the results. As well as method integration, simplicity has been one of the main objectives in FOCUS development, requiring very little user input to perform accurate peak alignment, peak picking, and metabolite identification. The new spectral alignment algorithm, RUNAS, allows peak alignment with no need of a reference spectrum, and therefore, it reduces the bias introduced by other alignment approaches. Spectral alignment has been tested against previous methodologies obtaining substantial improvements in the case of moderate or highly unaligned spectra. Metabolite identification has also been significantly improved, using the positional and correlation peak patterns in contrast to a reference metabolite panel. Furthermore, the complete workflow has been tested using NMR data sets from 60 human urine samples and 120 aqueous liver extracts, reaching a successful identification of 42 metabolites from the two data sets. The open-source software implementation of this methodology is available at http://www.urr.cat/FOCUS.

DNA Binding, Cleavage and Antibacterial Activity of Mononuclear Cu(II), Ni(II) and Co(II) Complexes Derived from Novel Benzothiazole Schiff Bases.

PubMed

Vamsikrishna, Narendrula; Kumar, Marri Pradeep; Tejaswi, Somapangu; Rambabu, Aveli; Shivaraj

2016-07-01

A series of novel bivalent metal complexes M(L1)2 and M(L2)2 where M = Cu(II), Ni(II), Co(II) and L1 = 2-((benzo [d] thiazol-6-ylimino)methyl)-4-bromophenol [BTEMBP], L2 = 1-((benzo [d] thiazol-6-ylimino)methyl) naphthalen-2-ol [BTEMNAPP] were synthesized. All the compounds have been characterized by elemental analysis, SEM, Mass, (1)H NMR, (13)C NMR, UV-Vis, IR, ESR, spectral data and magnetic susceptibility measurements. Based on the analytical and spectral data four-coordinated square planar geometry is assigned to all the complexes. DNA binding properties of these complexes have been investigated by electronic absorption spectroscopy, fluorescence and viscosity measurements. It is observed that these binary complexes strongly bind to calf thymus DNA by an intercalation mode. DNA cleavage efficacy of these complexes was tested in presence of H2O2 and UV light by gel electrophoresis and found that all the complexes showed better nuclease activity. Finally the compounds were screened for antibacterial activity against few pathogens and found that the complexes have potent biocidal activity than their free ligands.

An Introduction to Biological NMR Spectroscopy*

PubMed Central

Marion, Dominique

2013-01-01

NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

Synthesis, spectral and quantum chemical studies on NO-chelating sulfamonomethoxine-cyclophosph(V)azane and its Er(III) complex.

PubMed

Alaghaz, Abdel-Nasser M A; Ammar, Reda A A; Koehler, Gottfried; Wolschann, Karl Peter; El-Gogary, Tarek M

2014-07-15

Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of novel ethane-1,2-diol-dichlorocyclophosph(V)azane of sulfamonomethoxine (L), and its binuclear Er(III) complex. Different tautomers of the ligand were optimized at the ab initio DFT level. Keto-form structure is about 15.8 kcal/mol more stable than the enol form (taking zpe correction into account). Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which show good agreement with measured electronic spectra. The structures of the novel isolated products are proposed based on elemental analyses, IR, UV-VIS, (1)H NMR, (31)P NMR, SEM, XRD spectra, effective magnetic susceptibility measurements and thermogravimetric analysis (TGA). Copyright © 2014 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

NMR studies of the helical antiferromagnetic compound EuCo 2P 2

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

Higa, N.; Ding, Q. -P.; Johnston, D. C.

In EuCo 2P 2, 4 f electron spins of Eu 2+ ions order antiferromagnetically below a Neel temperature T N = 66.5K. The magnetic structure below T N was reported to be helical with the helix axis along the c-axis from the neutron diffraction study. We report the results of 153Eu, 59Co and 31P nuclear magnetic resonance (NMR) measurements on EuCo 2P 2 using a single crystal and a powdered sample. In the antiferromagnetic (AFM) state, we succeeded in observing 153Eu, 59Co and 31P NMR spectra in zero magnetic field. The sharp 153Eu zero field NMR (ZF NMR) lines indicatemore » homogeneous Eu ordered moment. The 59Co and 31P ZF NMR spectra showed an asymmetric spectral shape, indicating a distribution of the internal magnetic induction at each nuclear position. The AFM propagation vector k characterizing the helical AFM state can be determined from the internal magnetic induction at Co site. In conclusion, we have determined the model-independent value of the AFM propagation vector k distributed from (0, 0, 0.86)2π/c to (0, 0, 0.73)2π/c, where c is the lattice parameter.« less

NMR studies of the helical antiferromagnetic compound EuCo 2P 2

DOE PAGES

Higa, N.; Ding, Q. -P.; Johnston, D. C.; ...

2017-09-18

In EuCo 2P 2, 4 f electron spins of Eu 2+ ions order antiferromagnetically below a Neel temperature T N = 66.5K. The magnetic structure below T N was reported to be helical with the helix axis along the c-axis from the neutron diffraction study. We report the results of 153Eu, 59Co and 31P nuclear magnetic resonance (NMR) measurements on EuCo 2P 2 using a single crystal and a powdered sample. In the antiferromagnetic (AFM) state, we succeeded in observing 153Eu, 59Co and 31P NMR spectra in zero magnetic field. The sharp 153Eu zero field NMR (ZF NMR) lines indicatemore » homogeneous Eu ordered moment. The 59Co and 31P ZF NMR spectra showed an asymmetric spectral shape, indicating a distribution of the internal magnetic induction at each nuclear position. The AFM propagation vector k characterizing the helical AFM state can be determined from the internal magnetic induction at Co site. In conclusion, we have determined the model-independent value of the AFM propagation vector k distributed from (0, 0, 0.86)2π/c to (0, 0, 0.73)2π/c, where c is the lattice parameter.« less

Video Toroid Cavity Imager

DOEpatents

Gerald, II, Rex E.; Sanchez, Jairo; Rathke, Jerome W.

2004-08-10

A video toroid cavity imager for in situ measurement of electrochemical properties of an electrolytic material sample includes a cylindrical toroid cavity resonator containing the sample and employs NMR and video imaging for providing high-resolution spectral and visual information of molecular characteristics of the sample on a real-time basis. A large magnetic field is applied to the sample under controlled temperature and pressure conditions to simultaneously provide NMR spectroscopy and video imaging capabilities for investigating electrochemical transformations of materials or the evolution of long-range molecular aggregation during cooling of hydrocarbon melts. The video toroid cavity imager includes a miniature commercial video camera with an adjustable lens, a modified compression coin cell imager with a fiat circular principal detector element, and a sample mounted on a transparent circular glass disk, and provides NMR information as well as a video image of a sample, such as a polymer film, with micrometer resolution.

Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR

NASA Astrophysics Data System (ADS)

Beger, Richard D.; Buzatu, Dan A.; Wilkes, Jon G.

2002-10-01

A three-dimensional quantitative spectrometric data-activity relationship (3D-QSDAR) modeling technique which uses NMR spectral and structural information that is combined in a 3D-connectivity matrix has been developed. A 3D-connectivity matrix was built by displaying all possible assigned carbon NMR chemical shifts, carbon-to-carbon connections, and distances between the carbons. Two-dimensional 13C-13C COSY and 2D slices from the distance dimension of the 3D-connectivity matrix were used to produce a relationship among the 2D spectral patterns for polychlorinated dibenzofurans, dibenzodioxins, and biphenyls (PCDFs, PCDDs, and PCBs respectively) binding to the aryl hydrocarbon receptor (AhR). We refer to this technique as comparative structural connectivity spectral analysis (CoSCoSA) modeling. All CoSCoSA models were developed using forward multiple linear regression analysis of the predicted 13C NMR structure-connectivity spectral bins. A CoSCoSA model for 26 PCDFs had an explained variance (r2) of 0.93 and an average leave-four-out cross-validated variance (q4 2) of 0.89. A CoSCoSA model for 14 PCDDs produced an r2 of 0.90 and an average leave-two-out cross-validated variance (q2 2) of 0.79. One CoSCoSA model for 12 PCBs gave an r2 of 0.91 and an average q2 2 of 0.80. Another CoSCoSA model for all 52 compounds had an r2 of 0.85 and an average q4 2 of 0.52. Major benefits of CoSCoSA modeling include ease of development since the technique does not use molecular docking routines.

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

PubMed Central

2013-01-01

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

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

PubMed

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

2013-06-13

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

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR

PubMed Central

Mobli, Mehdi; Hoch, Jeffrey C.

2017-01-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. PMID:25456315

Glycerol dehydration of native and diabetic animal tissues studied by THz-TDS and NMR methods

PubMed Central

Smolyanskaya, O. A.; Schelkanova, I. J.; Kulya, M. S.; Odlyanitskiy, E. L.; Goryachev, I. S.; Tcypkin, A. N.; Grachev, Ya. V.; Toropova, Ya. G.; Tuchin, V. V.

2018-01-01

The optical clearing method has been widely used for different spectral ranges where it provides tissue transparency. In this work, we observed the enhanced penetration of the terahertz waves inside biological samples (skin, kidney, and cornea) treated with glycerol solutions inducing changes of optical and dielectric properties. It was supported by the observed trend of free-to-bound water ratio measured by the nuclear magnetic resonance (NMR) method. The terahertz clearing efficiency was found to be less for diabetic samples than for normal ones. Results of the numerical simulation proved that pulse deformation is due to bigger penetration depth caused by the reduction of absorption and refraction at optical clearing. PMID:29541513

Structural and Biological Behaviour of Co(II), Cu(II) and Ni(II) Metal Complexes of Some Amino Acid Derived Schiff-Bases

PubMed Central

Chohan, Zahid H.; Praveen, M.; Ghaffar, A.

1997-01-01

Biologically active tridentate amino acid (Alanine, Glycine & Tyrosine) derived Schiff-bases and their Co(II), Cu(II) & Ni(II) complexes have been synthesised and characterised on the basis of their conductance and magnetic measurements, elemental analysis and 13C-NMR, 1H-NMR, IR and electronic spectral data. These Schiff-bases and their complexes have been evaluated for their antibacterial activity against bacterial species such as Staphylococcus aureus, Escherichia coli, Klebsiella pneumonae, Proteus vulgarus and Pseudomonas aeruginosa and this activity data show the metal complexes to be more antibacterial than the Schiff-bases against one or more bacterial species. PMID:18475798

Synthesis and spectral studies of platinum metal complexes of benzoin thiosemicarbazone

NASA Astrophysics Data System (ADS)

Offiong, Offiong E.

1994-11-01

The platinum metal chelates of benzoin thiosemicarbazone obtained with Ru(III), Rh(III), Ir(III), Pd(II) and Pt(II) were prepared from their corresponding halide salts. The complexes were characterized by elemental analysis, conductance measurement, IR, Raman, 1H-NMR, 13C-NMR and UV-visible spectra studies. Various ligand field parameters and nephelauxetic parameters were also calculated. The mode of bonding and the geometry of the ligand environment around the metal ion have been discussed in the light of the available data obtained. Complexes of Ru(III), Rh(III) and Ir(III) are six-coordinate octahedral, while Pd(II) and Pt(II) halide complexes are four-coordinated with halides bridging.

The spectroscopic properties of anticancer drug Apigenin investigated by using DFT calculations, FT-IR, FT-Raman and NMR analysis

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.; Manoharan, S.

2012-09-01

The FT-Raman and FT-Infrared spectra of solid Apigenin sample were measured in order to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm-1 and 4000-400 cm-1, respectively. The recorded FT-IR and FT-Raman spectral measurements favor the calculated (by B3LYP/6-31G(d,p) method) structural parameters which are further supported by spectral simulation. Additional support is given by the collected 1H and 13C NMR spectra recorded with the sample dissolved in DMSO. The predicted chemical shifts at the B3LYP/6-31G(d) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. The UV-visible absorption spectra of the compound that dissolved in Ethanol, Methanol and DMSO were recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and atomic charges of the title compound were investigated using theoretical calculations. The results are discussed herein and compared with similar molecules whenever appropriate.

Spectral and quantum chemical studies on 1,3-bis(N(1)-4-amino-6-methoxypyrimidinebenzenesulfonamide-2,2,4,4-ethane-1,2-dithiol)-2,4-dichlorocyclodiphosph(V)azane and its erbium complex.

PubMed

Al-Mogren, Muneerah M; Alaghaz, Abdel-Nasser M A; El-Gogary, Tarek M

2014-01-24

Novel 1,3-bis(N(1)-4-amino-6-methoxypyrimidine-benzenesulfonamide-2,2,4,4-ethane-1,2-dithiol)-2,4-dichlorocyclodiphosph(V)azane (L), was prepared and their coordinating behavior towards the lanthanide ion Er(III) was studied. The structures of the isolated products are proposed based on elemental analyses, IR, UV-VIS., (1)H NMR, (13)C NMR, (31)P NMR, SEM, XRD, mass spectra, effective magnetic susceptibility measurements and thermogravimetric analysis (TGA). Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of L and its binuclear Er(III) complex. Different tautomers of the ligand were optimized at the ab initio DFT level. Keto-form structure is about 17.7 kcal/mol more stable than the enol form (taking zpe correction into account). Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which compared by the measured electronic spectra. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed

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

2018-04-11

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

Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.

PubMed

Barnwal, Ravi Pratap; Rout, Ashok K; Chary, Kandala V R; Atreya, Hanudatta S

2007-12-01

We present two NMR experiments, (3,2)D HNHA and (3,2)D HNHB, for rapid and accurate measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides based on the principle of G-matrix Fourier transform NMR spectroscopy and quantitative J-correlation. These experiments, which facilitate fast acquisition of three-dimensional data with high spectral/digital resolution and chemical shift dispersion, will provide renewed opportunities to utilize them for sequence specific resonance assignments, estimation/characterization of secondary structure with/without prior knowledge of resonance assignments, stereospecific assignment of prochiral groups and 3D structure determination, refinement and validation. Taken together, these experiments have a wide range of applications from structural genomics projects to studying structure and folding in polypeptides.

Spectral studies of 2-pyrazoline derivatives: structural elucidation through single crystal XRD and DFT calculations.

PubMed

Chinnaraja, D; Rajalakshmi, R; Srinivasan, T; Velmurugan, D; Jayabharathi, J

2014-04-24

A series of biologically active N-thiocarbamoyl pyrazoline derivatives have been synthesized using anhydrous potassium carbonate as the catalyst. All the synthesized compounds were characterized by FT-IR, (1)H NMR, (13)C NMR spectral studies, LCMS, CHN Analysis and X-ray diffraction analysis (compound 7). In order to supplement the XRD parameters, molecular modelling was carried out by Gaussian 03W. From the optimized structure, the energy, dipolemoment and HOMO-LUMO energies of all the systems were calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

In vivo1H NMR spectroscopy of the human brain at 9.4 T: Initial results

NASA Astrophysics Data System (ADS)

Deelchand, Dinesh Kumar; Moortele, Pierre-François Van de; Adriany, Gregor; Iltis, Isabelle; Andersen, Peter; Strupp, John P.; Thomas Vaughan, J.; Uğurbil, Kâmil; Henry, Pierre-Gilles

2010-09-01

In vivo proton NMR spectroscopy allows non-invasive detection and quantification of a wide range of biochemical compounds in the brain. Higher field strength is generally considered advantageous for spectroscopy due to increased signal-to-noise and increased spectral dispersion. So far 1H NMR spectra have been reported in the human brain up to 7 T. In this study we show that excellent quality short echo time STEAM and LASER 1H NMR spectra can be measured in the human brain at 9.4 T. The information content of the human brain spectra appears very similar to that measured in the past decade in rodent brains at the same field strength, in spite of broader linewidth in human brain. Compared to lower fields, the T1 relaxation times of metabolites were slightly longer while T2 relaxation values of metabolites were shorter (<100 ms) at 9.4 T. The linewidth of the total creatine (tCr) resonance at 3.03 ppm increased linearly with magnetic field (1.35 Hz/T from 1.5 T to 9.4 T), with a minimum achievable tCr linewidth of around 12.5 Hz at 9.4 T. At very high field, B0 microsusceptibility effects are the main contributor to the minimum achievable linewidth.

(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.

Synthesis, characterization stereochemistry and anti-bacterial evaluation of certain N-acyl-c-3,t-3-dimethyl-r-2,c-6-diphenylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Ponnuswamy, S.; Kayalvizhi, R.; Jamesh, M.; Uma Maheswari, J.; Thenmozhi, M.; Ponnuswamy, M. N.

2016-09-01

A new series of N-acyl-c-3,t-3-dimethyl-r-2,c-6-diphenylpiperidin-4-ones 2-6 has been synthesized and characterized using IR, mass, 1H, 13C, DEPT and 2D (COSY and HSQC) NMR spectral techniques. The NMR spectral data indicate that the N-acylpiperidin-4-ones 2-6 prefer to exist in a distorted boat conformation B1 with coplanar orientation of N-C=O moiety. The stereodynamics of these systems have been studied by recording the dynamic 1H NMR spectra of compound 4, and the energy barrier for N-CO rotation is determined to be 52.75 kJ/mol. Furthermore the compounds 1-5 show significant antibacterial activity.

Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy.

PubMed

Kurimoto, Eiji; Nishi, Yohei; Yamaguchi, Yoshiki; Zako, Tamotsu; Iizuka, Ryo; Ide, Naoki; Yohda, Masafumi; Kato, Koichi

2008-03-01

Group II chaperonin (CPN) cooperates with prefoldin (PFD), which forms a jellyfish-shaped heterohexameric complex with a molecular mass of 87 kDa. PFD captures an unfolded protein with the tentacles and transfers it to the cavity of CPN. Although X-ray crystal structures of CPN and PFD have been reported, no structural information has been so far available for the terminal regions of the PFD tentacles nor for the C-terminal segments of CPNs, which were regarded to be functionally significant in the previous studies. Here we report 13C NMR analyses on archaeal PFD, CPN, and their complex, focusing on those structurally uncharacterized regions. The PFD and CPN complexes selectively labeled with 13C at methionyl carbonyl carbons were separately and jointly subjected to NMR measurements. 13C NMR spectral data demonstrated that the N-terminal segment of the alpha and beta subunits of PFD as well as the C-terminal segments of the CPN hexadecamer retain significant degrees of freedom in internal motion even in the complex with a molecular mass of 1.1 MDa. 2007 Wiley-Liss, Inc.

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.

PubMed

Kuhn, Stefan; Egert, Björn; Neumann, Steffen; Steinbeck, Christoph

2008-09-25

Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.

Sequence-specific sup 1 H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

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

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-08-07

On the basis of an analysis of two-dimensional {sup 1}H NMR spectra, the complete sequence-specific {sup 1}H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four {beta}-strands that form a single antiparallel {beta}-sheet and two well-defined {alpha}-helices. There are two stretchesmore » of extended backbone structure, one of which contains the active site His{sub 15}. The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies.« less

Convex Accelerated Maximum Entropy Reconstruction

PubMed Central

Worley, Bradley

2016-01-01

Maximum entropy (MaxEnt) spectral reconstruction methods provide a powerful framework for spectral estimation of nonuniformly sampled datasets. Many methods exist within this framework, usually defined based on the magnitude of a Lagrange multiplier in the MaxEnt objective function. An algorithm is presented here that utilizes accelerated first-order convex optimization techniques to rapidly and reliably reconstruct nonuniformly sampled NMR datasets using the principle of maximum entropy. This algorithm – called CAMERA for Convex Accelerated Maximum Entropy Reconstruction Algorithm – is a new approach to spectral reconstruction that exhibits fast, tunable convergence in both constant-aim and constant-lambda modes. A high-performance, open source NMR data processing tool is described that implements CAMERA, and brief comparisons to existing reconstruction methods are made on several example spectra. PMID:26894476

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

PubMed

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

2017-04-18

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

Spectral, coordination and thermal properties of 5-arylidene thiobarbituric acids

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; El-Marghany, Adel; Orabi, Adel; Ali, Alaa E.; Sayed, Reham

2013-04-01

Synthesis of 5-arylidine thiobarbituric acids containing different functional groups with variable electronic characters were described and their Co2+, Ni2+ and Cu2+ complexes. The stereochemistry and mode of bonding of 5-(substituted benzylidine)-2-TBA complexes were achieved based on elemental analysis, spectral (UV-VIS, IR, 1H NMR, MS), magnetic susceptibility and conductivity measurements. The ligands were of bidentate and tridentate bonding through S, N and O of pyrimidine nucleolus. All complexes were of octahedral configuration. The thermal data of the complexes pointed to their stability. The mechanism of the thermal decomposition is discussed. The thermodynamic parameters of the dissociation steps were evaluated and discussed.

New phenylpropanoid glycosides from Juniperus communis var. depressa.

PubMed

Iida, Naoki; Inatomi, Yuka; Murata, Hiroko; Murata, Jin; Lang, Frank A; Tanaka, Toshiyuki; Nakanishi, Tsutomu; Inada, Akira

2010-05-01

Two new phenylpropanoid glycosides were isolated from the leaves and stems of Juniperus communis var. depressa (Cupressaceae) along with 14 known compounds. Their structures were determined by spectral analyses, in particular by 2D-NMR spectral evidence.

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

PubMed

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

2017-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Peak picking NMR spectral data using non-negative matrix factorization.

PubMed

Tikole, Suhas; Jaravine, Victor; Rogov, Vladimir; Dötsch, Volker; Güntert, Peter

2014-02-11

Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap.

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

NASA Astrophysics Data System (ADS)

Savorani, F.; Tomasi, G.; Engelsen, S. B.

2010-02-01

The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can affect the absolute and the relative position of an NMR signal and it is not always possible or desirable to eliminate these effects a priori. To remove misalignment of NMR signals a posteriori, several algorithms have been proposed in the literature. The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis. The icoshift algorithm is based on correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously. The algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries. The algorithm is made open source and the Matlab code including documentation can be downloaded from www.models.life.ku.dk.

"Ersatz" and "hybrid" NMR spectral estimates using the filter diagonalization method.

PubMed

Ridge, Clark D; Shaka, A J

2009-03-12

The filter diagonalization method (FDM) is an efficient and elegant way to make a spectral estimate purely in terms of Lorentzian peaks. As NMR spectral peaks of liquids conform quite well to this model, the FDM spectral estimate can be accurate with far fewer time domain points than conventional discrete Fourier transform (DFT) processing. However, noise is not efficiently characterized by a finite number of Lorentzian peaks, or by any other analytical form, for that matter. As a result, noise can affect the FDM spectrum in different ways than it does the DFT spectrum, and the effect depends on the dimensionality of the spectrum. Regularization to suppress (or control) the influence of noise to give an "ersatz", or EFDM, spectrum is shown to sometimes miss weak features, prompting a more conservative implementation of filter diagonalization. The spectra obtained, called "hybrid" or HFDM spectra, are acquired by using regularized FDM to obtain an "infinite time" spectral estimate and then adding to it the difference between the DFT of the data and the finite time FDM estimate, over the same time interval. HFDM has a number of advantages compared to the EFDM spectra, where all features must be Lorentzian. They also show better resolution than DFT spectra. The HFDM spectrum is a reliable and robust way to try to extract more information from noisy, truncated data records and is less sensitive to the choice of regularization parameter. In multidimensional NMR of liquids, HFDM is a conservative way to handle the problems of noise, truncation, and spectral peaks that depart significantly from the model of a multidimensional Lorentzian peak.

Monovacancy paramagnetism in neutron-irradiated graphite probed by 13C NMR

NASA Astrophysics Data System (ADS)

Zhang, Z. T.; Xu, C.; Dmytriieva, D.; Molatta, S.; Wosnitza, J.; Wang, Y. T.; Helm, M.; Zhou, Shengqiang; Kühne, H.

2017-11-01

We report on the magnetic properties of monovacancy defects in neutron-irradiated graphite, probed by 13C nuclear magnetic resonance spectroscopy. The bulk paramagnetism of the defect moments is revealed by the temperature dependence of the NMR frequency shift and spectral linewidth, both of which follow a Curie behavior, in agreement with measurements of the macroscopic magnetization. Compared to pristine graphite, the fluctuating hyperfine fields generated by the defect moments lead to an enhancement of the 13C nuclear spin-lattice relaxation rate 1/T1 by about two orders of magnitude. With an applied magnetic field of 7.1 T, the temperature dependence of 1/T1 below about 10 K can well be described by a thermally activated form, \

Solid-state NMR spectroscopy and first-principles calculations: a powerful combination of tools for the investigation of polymorphism of indomethacin.

PubMed

Ukmar, Tina; Kaučič, Venčeslav; Mali, Gregor

2011-09-01

Two polymorphs of indomethacin were investigated by 1H MAS and CRAMPS, and 1H-13C CPMAS and HETCOR NMR techniques. The obtained spectra clearly elucidated the structural differences between the polymorphs, especially the different numbers of indomethacin molecules within the crystallographic asymmetric units and the different schemes of hydrogen bonding among the molecules. Known structure of indomethacin gamma was used in first-principles DFT/GIPAW calculations of 1H and 13C isotropic chemical shifts. Two packages, freely available Quantum Espresso and commercially available CASTEP, were employed. They both provided values that excellently agreed with the measured values, and thus allowed unambiguous assignment of 1H and 13C spectral lines.

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

Non-invasive analysis of swelling in polymer dispersions by means of time-domain(TD)-NMR.

PubMed

Nestle, Nikolaus; Häberle, Karl

2009-11-03

In this contribution, we discuss the potential of low-field time-domain(TD)-NMR to study the swelling of (aqueous) polymer dispersions by a volatile solvent. Due to the sensitivity of transverse relaxation times (T2) to swelling-induced changes in the molecular dynamics of the polymer component, the effects of swelling can be measured without spectral resolution. The measurement is performed on polymer dispersions in native state with solids contents around 50% in a non-invasive way without separating the polymeric phase and the water phase from each other. Using acetone in two polyurethane (PU) dispersions with different hard phase contents, we explore the sensitivity of the method and present a data evaluation strategy based on multicomponent fitting and proton balancing. Furthermore, we report exchange continualization as a further effect that needs to be taken into account for correct interpretation of the data.

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

PubMed

Mobli, Mehdi; Hoch, Jeffrey C

2014-11-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis of metal complexes involving Schiff base ligand with methylenedioxy moiety: spectral, thermal, XRD and antimicrobial studies.

PubMed

Sundararajan, M L; Jeyakumar, T; Anandakumaran, J; Karpanai Selvan, B

2014-10-15

Metal complexes of Zn(II), Cd(II), Ni(II), Cu(II), Fe(III), Co(II), Mn(II) Hg(II), and Ag(I) have been synthesized from Schiff base ligand, prepared by the condensation of 3,4-(methylenedioxy)aniline and 5-bromo salicylaldehyde. All the compounds have been characterized by using elemental analysis, molar conductance, FT-IR, UV-Vis, (1)H NMR, (13)C NMR, mass spectra, powder XRD and thermal analysis (TG/DTA) technique. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectral data suggest that the ligand coordinate to the metal atom by imino nitrogen and phenolic oxygen as bidentate manner. Mass spectral data further support the molecular mass of the compounds and their structure. Powder XRD indicates the crystalline state and morphology of the ligand and its metal complexes. The thermal behaviors of the complexes prove the presence of lattice as well as coordinated water molecules in the complexes. Melting point supports the thermal stability of all the compounds. The in vitro antimicrobial effects of the synthesized compounds were tested against five bacterial and three fungal species by well diffusion method. Antioxidant activities have also been performed for all the compounds. Metal complexes show more biological activity than the Schiff base. Copyright © 2014 Elsevier B.V. All rights reserved.

Differentiating and characterizing geminal silanols in silicas by (29)Si NMR spectroscopy.

PubMed

Murray, David K

2010-12-01

Single and geminal hydroxyl species in silicas have been characterized using solid-state (29)Si NMR spectroscopy. Differentiating hydroxyl types is important in understanding their roles in chemical toxicity mechanisms for inhaled crystalline silicas responsible for silicosis. (1)H-(29)Si cross polarization NMR spectroscopy has been employed to obtain (29)Si NMR chemical shift data and signal accrual and relaxation characteristics. Spectral deconvolution is used to examine relative single and geminal hydroxyl resonance areas for a series of representative silicas and silica gels. Silicon-containing materials examined include 1878a quartz, and 1879a cristobalite from the National Institute for Science and Technology, kaolin, and several widely used respirable silicas and silica gels. Geminal hydroxyls were observed in every case, with relative resonance areas accounting for 21-65% of total hydroxyl signals. Factors affecting relative areas measured as a function of contact time, relaxation, and surface area are discussed. Subsequent (29)Si and (31)P NMR studies of a silica coated with various sodium hydrogen phosphates show preferential single silanol-phosphate interaction for basic phosphates, and oligomerization products for acidic phosphates. Geminal hydroxyl resonance areas displayed significant error (4-17%) for low surface area silicas, limiting this method to studies exhibiting major changes in chemical or spectroscopic properties. Published by Elsevier Inc.

1H NMR Detection of superparamagnetic nanoparticles at 1 T using a microcoil and novel tuning circuit

NASA Astrophysics Data System (ADS)

Sillerud, Laurel O.; McDowell, Andrew F.; Adolphi, Natalie L.; Serda, Rita E.; Adams, David P.; Vasile, Michael J.; Alam, Todd M.

2006-08-01

Magnetic beads containing superparamagnetic iron oxide nanoparticles (SPIONs) have been shown to measurably change the nuclear magnetic resonance (NMR) relaxation properties of nearby protons in aqueous solution at distances up to ˜50 μm. Therefore, the NMR sensitivity for the in vitro detection of single cells or biomolecules labeled with magnetic beads will be maximized with microcoils of this dimension. We have constructed a prototype 550 μm diameter solenoidal microcoil using focused gallium ion milling of a gold/chromium layer. The NMR coil was brought to resonance by means of a novel auxiliary tuning circuit, and used to detect water with a spectral resolution of 2.5 Hz in a 1.04 T (44.2 MHz) permanent magnet. The single-scan SNR for water was 137, for a 200 μs π/2 pulse produced with an RF power of 0.25 mW. The nutation performance of the microcoil was sufficiently good so that the effects of magnetic beads on the relaxation characteristics of the surrounding water could be accurately measured. A solution of magnetic beads (Dynabeads MyOne Streptavidin) in deionized water at a concentration of 1000 beads per nL lowered the T1 from 1.0 to 0.64 s and the T2∗ from 110 to 0.91 ms. Lower concentrations (100 and 10 beads/nL) also resulted in measurable reductions in T2∗, suggesting that low-field, microcoil NMR detection using permanent magnets can serve as a high-sensitivity, miniaturizable detection mechanism for very low concentrations of magnetic beads in biological fluids.

Structural confirmation of regioisomers of Lopinavir impurities using MS and gradient COSY (1H and 13C NMR assignment of Lopinavir impurities).

PubMed

Siva Lakshmi Devi, A; Srinivasa Rao, Y; Suresh, Y; Yogeswar Reddy, M; Jyothi, G; Rajababu, B; Prasad, V S R; Umamaheswar Rao, V

2007-05-01

We report the complete (1)H and (13)C NMR assignment of impurities of six Lopinavir (2S)-N-[(2S, 4S, 5S)-5-{[2-(2,6-dimethylphenoxy)acetyl]amino}-4-hydroxy-1,6-diphenyl hexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butan- amide. Two of the impurities are regioisomers and GCOSY used to differentiate the two structures. The spectral assignments for all six impurities were achieved by concerted application of one and two-dimensional NMR techniques ((1)H NMR, (13)C NMR, DEPT, GCOSY, GHSQC and GHMBC). Copyright (c) 2007 John Wiley & Sons, Ltd.

Diester-containing Zwitterionic Gemini Surfactants with Different Spacer and Its Impact on Micellization Properties and Viscosity of Aqueous Micellar Solution.

PubMed

Patil, Sachin Vasant; Patil, Sanyukta Arun; Pratap, Amit Prabhakar

2016-09-01

A series of diester containing zwitterionic gemini surfactants, N,N-dimethyl-N-alkyl-2-[[hydroxy (alkoxy) phosphinyl]oxy]-alkylammonium designated as C8(-)-S-Cn(+), S = 2 and 3, n = 12, 14 and 16, were synthesized and characterized by instrumental techniques namely FT-IR, (1)H NMR, (13)C NMR, (31)P NMR and Mass spectral studies. These new gemini surfactants further investigated for their various surfactant properties. The critical micelle concentration (cmc) and the effectiveness of surface tension reduction (Πcmc) were determined as a function of surfactant concentration by means of surface tension measurement. Micellization and viscosity properties were investigated by surface tension, electrical conductivity, dye micellization and rheology techniques. The findings of the aqueous surfactant system obtained were impacted by polarity, size and the nature of zwitterions as the surface. The thermodynamic and viscosity properties of these surfactants found to be based on the structures of gemini surfactants.

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

PubMed

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

2013-05-01

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

LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

PubMed

Mund, Markus; Overbeck, Jan H; Ullmann, Janina; Sprangers, Remco

2013-10-18

Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies. © 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of Creative Commons the Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Synthesis and characterization of copper complexes of Schiff base derived from isatin and salicylic hydrazide

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

Lekshmy, R. K., E-mail: lekshmyulloor@gmail.com, E-mail: tharapradeepkumar@yahoo.com; Thara, G. S., E-mail: lekshmyulloor@gmail.com, E-mail: tharapradeepkumar@yahoo.com

A series of novel metal complexes of Schiff base have been prepared by the interaction of Cu(II) with isatin salicylic hydrazide. All the new compounds were characterized by elemental analysis, conductance measurement, magnetic moment determination, IR, UV, NMR, Mass and EPR spectral studies, thermal studies and microbial activities. The results indicate that the ligand acts as a tridentate chelating ligand coordinating through nitrogen and oxygen atoms. The ligand and complexes show inactive against Escherichia coli and active against Staphylococcus aureus and B.substilis. By analyzing the results of spectral, thermal and elemental analysis square planar geometry is proposed for all themore » complexes.« less

Origin and Correction of Magnetic Field Inhomogeneity at the Interface in Biphasic NMR Samples

PubMed Central

Martin, Bryan T.; Chingas, G. C.

2012-01-01

The use of susceptibility matching to minimize spectral distortion of biphasic samples layered in a standard 5 mm NMR tube is described. The approach uses magic angle spinning (MAS) to first extract chemical shift differences by suppressing bulk magnetization. Then, using biphasic coaxial samples, magnetic susceptibilities are matched by titration with a paramagnetic salt. The matched phases are then layered in a standard NMR tube where they can be shimmed and examined. Line widths of two distinct spectral lines, selected to characterize homogeneity in each phase, are simultaneously optimized. Two-dimensional distortion-free, slice-resolved spectra of an octanol/water system illustrate the method. These data are obtained using a 2D stepped-gradient pulse sequence devised for this application. Advantages of this sequence over slice-selective methods are that acquisition efficiency is increased and processing requires only conventional software. PMID:22459062

Nuclear magnetic resonance study of the conformation and dynamics of beta-casein at the oil/water interface in emulsions.

PubMed Central

ter Beek, L C; Ketelaars, M; McCain, D C; Smulders, P E; Walstra, P; Hemminga, M A

1996-01-01

A (13)C and (31)P nuclear magnetic resonance (NMR) study has been carried out on beta-casein adsorbed at the interface of a tetradecane/water emulsion. (13)C NMR spectra show signals from the carbonyl, carboxyl, aromatic, and C alpha carbons in beta-casein, well resolved from solvent resonances. Only a small fraction of all carbon atoms in beta-casein contribute to detectable signals; intensity measurements show that the observable spectrum is derived from about 30 to 40 amino acid residues.(31)P NMR spectra show signals from the five phosphoserines on the hydrophilic N-terminal part of the protein. Analysis of T(1) relaxation times of these nuclei, using the model free approach for the spectral density function and the line shape of the alpha-carbon region, indicates that a large part of the protein is in a random coil conformation with restricted motion and a relatively long internal correlation time. The NMR results show that the conformation and dynamics of the N-terminal part of beta-casein are not strongly altered at the oil/water interface, as compared to beta-casein in micelle-like aggregates in aqueous solution. PMID:9172765

1H NMR Metabolomics Study of Spleen from C57BL/6 Mice Exposed to Gamma Radiation

PubMed Central

Xiao, X; Hu, M; Liu, M; Hu, JZ

2016-01-01

Due to the potential risk of accidental exposure to gamma radiation, it’s critical to identify the biomarkers of radiation exposed creatures. In the present study, NMR based metabolomics combined with multivariate data analysis to evaluate the metabolites changed in the C57BL/6 mouse spleen after 4 days whole body exposure to 3.0 Gy and 7.8 Gy gamma radiations. Principal component analysis (PCA) and orthogonal projection to latent structures analysis (OPLS) are employed for classification and identification potential biomarkers associated with gamma irradiation. Two different strategies for NMR spectral data reduction (i.e., spectral binning and spectral deconvolution) are combined with normalize to constant sum and unit weight before multivariate data analysis, respectively. The combination of spectral deconvolution and normalization to unit weight is the best way for identifying discriminatory metabolites between the irradiation and control groups. Normalized to the constant sum may achieve some pseudo biomarkers. PCA and OPLS results shown that the exposed groups can be well separated from the control group. Leucine, 2-aminobutyrate, valine, lactate, arginine, glutathione, 2-oxoglutarate, creatine, tyrosine, phenylalanine, π-methylhistidine, taurine, myoinositol, glycerol and uracil are significantly elevated while ADP is decreased significantly. These significantly changed metabolites are associated with multiple metabolic pathways and may be potential biomarkers in the spleen exposed to gamma irradiation. PMID:27019763

1H NMR metabolomics study of spleen from C57BL/6 mice exposed to gamma radiation

DOE PAGES

Xiao, Xiongjie; Hu, M.; Liu, M.; ...

2016-01-27

Due to the potential risk of accidental exposure to gamma radiation, it’s critical to identify the biomarkers of radiation exposed creatures. In the present study, NMR based metabolomics combined with multivariate data analysis to evaluate the metabolites changed in the C57BL/6 mouse spleen after 4 days whole body exposure to 3.0 Gy and 7.8 Gy gamma radiations. Principal component analysis (PCA) and orthogonal projection to latent structures analysis (OPLS) are employed for classification and identification potential biomarkers associated with gamma irradiation. Two different strategies for NMR spectral data reduction (i.e., spectral binning and spectral deconvolution) are combined with normalize tomore » constant sum and unit weight before multivariate data analysis, respectively. The combination of spectral deconvolution and normalization to unit weight is the best way for identifying discriminatory metabolites between the irradiation and control groups. Normalized to the constant sum may achieve some pseudo biomarkers. PCA and OPLS results shown that the exposed groups can be well separated from the control group. Leucine, 2-aminobutyrate, valine, lactate, arginine, glutathione, 2-oxoglutarate, creatine, tyrosine, phenylalanine, π-methylhistidine, taurine, myoinositol, glycerol and uracil are significantly elevated while ADP is decreased significantly. As a result, these significantly changed metabolites are associated with multiple metabolic pathways and may be potential biomarkers in the spleen exposed to gamma irradiation.« less

Complete NMR assignment of a bisecting hybrid-type oligosaccharide transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase.

PubMed

Yamanoi, Takashi; Oda, Yoshiki; Katsuraya, Kaname; Inazu, Toshiyuki; Yamamoto, Kenji

2016-06-02

This study describes the complete nuclear magnetic resonance (NMR) spectral assignment of a bisecting hybrid-type oligosaccharide 1, transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase (Endo-M). Through (1)H- and (13)C-NMR, DQF-COSY, HSQC, HMBC, TOCSY, and NOESY experiments, we determine the structure of the glycoside linkage formed by the Endo-M transglycosylation, i.e., the connection between GlcNAc and GlcNAc in oligosaccharide 1. Copyright © 2016 Elsevier Ltd. All rights reserved.

A simple and low-cost permanent magnet system for NMR

NASA Astrophysics Data System (ADS)

Chonlathep, K.; Sakamoto, T.; Sugahara, K.; Kondo, Y.

2017-02-01

We have developed a simple, easy to build, and low-cost magnet system for NMR, of which homogeneity is about 4 ×10-4 at 57 mT, with a pair of two commercially available ferrite magnets. This homogeneity corresponds to about 90 Hz spectral resolution at 2.45 MHz of the hydrogen Larmor frequency. The material cost of this NMR magnet system is little more than 100. The components can be printed by a 3D printer.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Antibacterial activity and spectral studies of trivalent chromium, manganese, iron macrocyclic complexes derived from oxalyldihydrazide and glyoxal.

PubMed

Singh, D P; Kumar, Ramesh; Singh, Jitender

2009-06-01

A new series of complexes is synthesized by template condensation of oxalyldihydrazide and glyoxal in methanolic medium in the presence of trivalent chromium, manganese and iron salts forming complexes of the type: [M(C(8)H(8)N(8)O(4))X]X(2) where M = Cr(III), Mn(III), Fe(III) and X = Cl(-1), NO(-1)(3), CH(3)COO(-1). The complexes have been characterized with the help of elemental analyses, conductance measurements, magnetic susceptibility measurements, electronic, NMR, infrared and far infrared spectral studies. On the basis of these studies, a five coordinate square pyramidal geometry for these complexes has been proposed. The biological activities of the metal complexes were tested in vitro against a number of pathogenic bacteria and some of the complexes exhibited remarkable antibacterial activities.

Peak picking NMR spectral data using non-negative matrix factorization

PubMed Central

2014-01-01

Background Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. Results To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Conclusions Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap. PMID:24511909

A comprehensive NMR methodology to assess the composition of biobased and biodegradable polymers in contact with food.

PubMed

Gratia, Audrey; Merlet, Denis; Ducruet, Violette; Lyathaud, Cédric

2015-01-01

A nuclear magnetic resonance (NMR) methodology was assessed regarding the identification and quantification of additives in three types of polylactide (PLA) intended as food contact materials. Additives were identified using the LNE/NMR database which clusters NMR datasets on more than 130 substances authorized by European Regulation No. 10/2011. Of the 12 additives spiked in the three types of PLA pellets, 10 were rapidly identified by the database and correlated with spectral comparison. The levels of the 12 additives were estimated using quantitative NMR combined with graphical computation. A comparison with chromatographic methods tended to prove the sensitivity of NMR by demonstrating an analytical difference of less than 15%. Our results therefore demonstrated the efficiency of the proposed NMR methodology for rapid assessment of the composition of PLA. Copyright © 2014 Elsevier B.V. All rights reserved.

Solid-state 11B and 13C NMR, IR, and X-ray crystallographic characterization of selected arylboronic acids and their catechol cyclic esters.

PubMed

Oh, Se-Woung; Weiss, Joseph W E; Kerneghan, Phillip A; Korobkov, Ilia; Maly, Kenneth E; Bryce, David L

2012-05-01

Nine arylboronic acids, seven arylboronic catechol cyclic esters, and two trimeric arylboronic anhydrides (boroxines) are investigated using (11)B solid-state NMR spectroscopy at three different magnetic field strengths (9.4, 11.7, and 21.1 T). Through the analysis of spectra of static and magic-angle spinning samples, the (11)B electric field gradient and chemical shift tensors are determined. The effects of relaxation anisotropy and nutation field strength on the (11)B NMR line shapes are investigated. Infrared spectroscopy was also used to help identify peaks in the NMR spectra as being due to the anhydride form in some of the arylboronic acid samples. Seven new X-ray crystallographic structures are reported. Calculations of the (11)B NMR parameters are performed using cluster model and periodic gauge-including projector-augmented wave (GIPAW) density functional theory (DFT) approaches, and the results are compared with the experimental values. Carbon-13 solid-state NMR experiments and spectral simulations are applied to determine the chemical shifts of the ipso carbons of the samples. One bond indirect (13)C-(11)B spin-spin (J) coupling constants are also measured experimentally and compared with calculated values. The (11)B/(10)B isotope effect on the (13)C chemical shift of the ipso carbons of arylboronic acids and their catechol esters, as well as residual dipolar coupling, is discussed. Overall, this combined X-ray, NMR, IR, and computational study provides valuable new insights into the relationship between NMR parameters and the structure of boronic acids and esters. Copyright © 2012 John Wiley & Sons, Ltd.

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

Spectral relative standard deviation: a practical benchmark in metabolomics.

PubMed

Parsons, Helen M; Ekman, Drew R; Collette, Timothy W; Viant, Mark R

2009-03-01

Metabolomics datasets, by definition, comprise of measurements of large numbers of metabolites. Both technical (analytical) and biological factors will induce variation within these measurements that is not consistent across all metabolites. Consequently, criteria are required to assess the reproducibility of metabolomics datasets that are derived from all the detected metabolites. Here we calculate spectrum-wide relative standard deviations (RSDs; also termed coefficient of variation, CV) for ten metabolomics datasets, spanning a variety of sample types from mammals, fish, invertebrates and a cell line, and display them succinctly as boxplots. We demonstrate multiple applications of spectral RSDs for characterising technical as well as inter-individual biological variation: for optimising metabolite extractions, comparing analytical techniques, investigating matrix effects, and comparing biofluids and tissue extracts from single and multiple species for optimising experimental design. Technical variation within metabolomics datasets, recorded using one- and two-dimensional NMR and mass spectrometry, ranges from 1.6 to 20.6% (reported as the median spectral RSD). Inter-individual biological variation is typically larger, ranging from as low as 7.2% for tissue extracts from laboratory-housed rats to 58.4% for fish plasma. In addition, for some of the datasets we confirm that the spectral RSD values are largely invariant across different spectral processing methods, such as baseline correction, normalisation and binning resolution. In conclusion, we propose spectral RSDs and their median values contained herein as practical benchmarks for metabolomics studies.

Synthesis, spectral behaviour and photophysics of donor-acceptor kind of chalcones: Excited state intramolecular charge transfer and fluorescence quenching studies

NASA Astrophysics Data System (ADS)

Pannipara, Mehboobali; Asiri, Abdullah M.; Alamry, Khalid A.; Arshad, Muhammad N.; El-Daly, Samy A.

2015-02-01

The spectral and photophysical properties of two chalcones containing electron donating and accepting groups with intramolecular charge transfer characteristics were synthesized and characterized by 1H NMR, 13C NMR and X-ray crystallography. Both compounds show very strong solvent polarity dependent changes in their photophysical characteristics, namely, remarkable red shift in the emission spectra with increasing solvent polarity, large change in Stokes shift, significant reduction in the fluorescence quantum yield; indicating that the fluorescence states of these compounds are of intramolecular charge transfer (ICT) character. The solvent effect on the photophysical parameters such as singlet absorption, molar absorptivity, oscillator strength, dipole moment, fluorescence spectra, and fluorescence quantum yield of both compounds have been investigated comprehensively. For both dyes, Lippert-Mataga and Reichardt's correlations were used to estimate the difference between the excited and ground state dipole moments (Δμ). The interactions of dyes with colloidal silver nanoparticles (Ag NPs) were also studied in ethanol using steady state fluorescence quenching measurements. The fluorescence quenching data reveal that dynamic quenching and energy transfer play a major role in the fluorescence quenching of dyes by Ag NPs.

Synthesis and characterization of tin(II) complexes of fluorinated Schiff bases derived from amino acids.

PubMed

Singh, Har Lal

2010-07-01

New tin(II) complexes of general formula Sn(L)(2) (L=monoanion of 3-methyl-4-fluoro-acetophenone phenylalanine L(1)H, 3-methyl-4-fluoro-acetophenone alanine L(2)H, 3-methyl-4-fluoro acetophenone tryptophan L(3)H, 3-methyl-4-fluoro-acetophenone valine L(4)H, 3-methyl-4-fluoro-acetophenone isoleucine L(5)H and 3-methyl-4-fluoro-acetophenone glycine L(6)H) have been prepared. It is characterized by elemental analyses, molar conductance measurements and molecular weight determinations. Bonding of these complexes is discussed in terms of their UV-visible, infrared, and nuclear magnetic resonance ((1)H, (13)C, (19)F and (119)Sn NMR) spectral studies. The ligands act as bidentate towards metal ions, via the azomethine nitrogen and deprotonated oxygen of the respective amino acid. Elemental analyses and NMR spectral data of the ligands with their tin(II) complexes agree with their proposed square pyramidal structures. A few representative ligands and their tin complexes have been screened for their antibacterial activities and found to be quite active in this respect. Copyright 2010 Elsevier B.V. All rights reserved.

Revisiting Cu 63 NMR evidence for charge order in superconducting La 1.885 Sr 0.115 CuO 4

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

Imai, T.; Takahashi, S. K.; Arsenault, A.

Here, the presence of charge and spin stripe order in the La 2CuO 4-based family of superconductors continues to lead to new insight on the unusual ground-state properties of high- T c cuprates. Soon after the discovery of charge stripe order at T charge≃65 K in Nd 3+ co-doped La 1.48Nd 0.4Sr 0.12CuO 4( Tc≃6 K), Hunt et al. demonstrated that La 1.48Nd 0.4Sr 0.12CuO 4 and superconducting La 2–xSr xCuO 4 with x~1/8( Tc≃30 K) share nearly identical NMR anomalies near Tcharge of the former. Their inevitable conclusion that La 1.885Sr 0.115CuO 4 also undergoes charge order at amore » comparable temperature became controversial, because diffraction measurements at the time were unable to detect Bragg peaks associated with charge order. Recent advances in x-ray diffraction techniques finally led to definitive confirmations of the charge order Bragg peaks in La 1.885Sr 0.115CuO 4 with an onset at as high as Tcharge≃80 K. Meanwhile, improved instrumental technology has enabled routine NMR measurements that were not feasible two decades ago. Motivated by these new developments, we revisit the charge order transition of a La 1.885Sr 0.115CuO 4 single crystal based on 63Cu NMR techniques. We demonstrate that 63Cu NMR properties of the nuclear spin I z=–1/2 to +1/2 central transition below Tcharge exhibit unprecedentedly strong dependence on the measurement time scale set by the separation time τ between the 90° and 180° radio-frequency pulses; a new kind of anomalous, very broad winglike 63Cu NMR signals gradually emerge below Tcharge only for extremely short τ≲4μs, while the spectral weight I Normal of the normal NMR signals is progressively wiped out. The NMR linewidth and relaxation rates depend strongly on τ below Tcharge, and their enhancement in the charge ordered state indicates that charge order turns on strong but inhomogeneous growth of Cu spin-spin correlations.« less

Revisiting Cu 63 NMR evidence for charge order in superconducting La 1.885 Sr 0.115 CuO 4

DOE PAGES

Imai, T.; Takahashi, S. K.; Arsenault, A.; ...

2017-12-26

Here, the presence of charge and spin stripe order in the La 2CuO 4-based family of superconductors continues to lead to new insight on the unusual ground-state properties of high- T c cuprates. Soon after the discovery of charge stripe order at T charge≃65 K in Nd 3+ co-doped La 1.48Nd 0.4Sr 0.12CuO 4( Tc≃6 K), Hunt et al. demonstrated that La 1.48Nd 0.4Sr 0.12CuO 4 and superconducting La 2–xSr xCuO 4 with x~1/8( Tc≃30 K) share nearly identical NMR anomalies near Tcharge of the former. Their inevitable conclusion that La 1.885Sr 0.115CuO 4 also undergoes charge order at amore » comparable temperature became controversial, because diffraction measurements at the time were unable to detect Bragg peaks associated with charge order. Recent advances in x-ray diffraction techniques finally led to definitive confirmations of the charge order Bragg peaks in La 1.885Sr 0.115CuO 4 with an onset at as high as Tcharge≃80 K. Meanwhile, improved instrumental technology has enabled routine NMR measurements that were not feasible two decades ago. Motivated by these new developments, we revisit the charge order transition of a La 1.885Sr 0.115CuO 4 single crystal based on 63Cu NMR techniques. We demonstrate that 63Cu NMR properties of the nuclear spin I z=–1/2 to +1/2 central transition below Tcharge exhibit unprecedentedly strong dependence on the measurement time scale set by the separation time τ between the 90° and 180° radio-frequency pulses; a new kind of anomalous, very broad winglike 63Cu NMR signals gradually emerge below Tcharge only for extremely short τ≲4μs, while the spectral weight I Normal of the normal NMR signals is progressively wiped out. The NMR linewidth and relaxation rates depend strongly on τ below Tcharge, and their enhancement in the charge ordered state indicates that charge order turns on strong but inhomogeneous growth of Cu spin-spin correlations.« less

Revisiting 63Cu NMR evidence for charge order in superconducting La1.885Sr0.115CuO4

NASA Astrophysics Data System (ADS)

Imai, T.; Takahashi, S. K.; Arsenault, A.; Acton, A. W.; Lee, D.; He, W.; Lee, Y. S.; Fujita, M.

2017-12-01

The presence of charge and spin stripe order in the La2CuO4 -based family of superconductors continues to lead to new insight on the unusual ground-state properties of high-Tc cuprates. Soon after the discovery of charge stripe order at Tcharge≃65 K in Nd3 + co-doped La1.48Nd0.4Sr0.12CuO4 (Tc≃6 K) [Tranquada et al., Nature (London) 375, 561 (1995), 10.1038/375561a0], Hunt et al. demonstrated that La1.48Nd0.4Sr0.12CuO4 and superconducting La2 -xSrxCuO4 with x ˜1 /8 (Tc≃30 K) share nearly identical NMR anomalies near Tcharge of the former [Phys. Rev. Lett. 82, 4300 (1999), 10.1103/PhysRevLett.82.4300]. Their inevitable conclusion that La1.885Sr0.115CuO4 also undergoes charge order at a comparable temperature became controversial, because diffraction measurements at the time were unable to detect Bragg peaks associated with charge order. Recent advances in x-ray diffraction techniques finally led to definitive confirmations of the charge order Bragg peaks in La1.885Sr0.115CuO4 with an onset at as high as Tcharge≃80 K. Meanwhile, improved instrumental technology has enabled routine NMR measurements that were not feasible two decades ago. Motivated by these new developments, we revisit the charge order transition of a La1.885Sr0.115CuO4 single crystal based on 63Cu NMR techniques. We demonstrate that 63Cu NMR properties of the nuclear spin Iz=-1/2 to +1/2 central transition below Tcharge exhibit unprecedentedly strong dependence on the measurement time scale set by the separation time τ between the 90∘ and 180∘ radio-frequency pulses; a new kind of anomalous, very broad winglike 63Cu NMR signals gradually emerge below Tcharge only for extremely short τ ≲4 μ s , while the spectral weight INormal of the normal NMR signals is progressively wiped out. The NMR linewidth and relaxation rates depend strongly on τ below Tcharge, and their enhancement in the charge ordered state indicates that charge order turns on strong but inhomogeneous growth of Cu spin-spin correlations.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

[Spectral characteristics of decomposition of incorporated straw in compound polluted arid loess].

PubMed

Fan, Chun-Hui; Zhang, Ying-Chao; Xu, Ji-Ting; Wang, Jia-Hong

2014-04-01

The original loess from western China was used as soil sample, the spectral methods of scanning electron microscope-energy dispersive X-ray spectroscopy (SEM-EDS), elemental analysis, Fourier transform infrared spectroscopy (FT-IR) and 13C nuclear magnetic resonance (13C NMR) were used to investigate the characteristics of decomposed straw and formed humic acids in compound polluted arid loess. The SEM micrographs show the variation from dense to decomposed surface, and finally to damaged structure, and the EDS data reveal the phenomenon of element transfer. The newly-formed humic acids are of low aromaticity, helpful for increasing the activity of organic matters in loess. The FTIR spectra in the whole process are similar, indicating the complexity of transformation dynamics of humic acids. The molecular structure of humic acids becomes simpler, shown from 13C NMR spectra. The spectral methods are useful for humic acids identification in loess region in straw incorporation process.

1H and 13C NMR spectral assignments of four dammarane triterpenoids from carnauba wax.

PubMed

Cysne, Juliana de Brito; Braz-Filho, Raimundo; Assunção, Marcus Vinícius; Uchoa, Daniel E de Andrade; Silveira, Edilberto R; Pessoa, Otília Deusdênia L

2006-06-01

The phytochemical investigation of carnauba wax led to the isolation of three new dammarane triterpenoids 1, 2 and 4, together with the known triterpene 3. The structures of the new compounds were determined by 1D and 2D NMR spectroscopy and by comparison with published data for closely related compounds. 2006 John Wiley & Sons, Ltd.

A simple and low-cost permanent magnet system for NMR.

PubMed

Chonlathep, K; Sakamoto, T; Sugahara, K; Kondo, Y

2017-02-01

We have developed a simple, easy to build, and low-cost magnet system for NMR, of which homogeneity is about 4×10 -4 at 57mT, with a pair of two commercially available ferrite magnets. This homogeneity corresponds to about 90Hz spectral resolution at 2.45MHz of the hydrogen Larmor frequency. The material cost of this NMR magnet system is little more than $100. The components can be printed by a 3D printer. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Spectral characterization and antibacterial activity of an isolated compound from Memecylon edule leaves.

PubMed

Srinivasan, R; Natarajan, D; Shivakumar, M S

2017-03-01

Memecylon edule Roxb. (Melastamataceae family) is a small evergreen tree reported as having ethnobotanical and pharmacological properties. The present study was aimed to investigate the spectral characterization and antibacterial activity of isolated pure compound (3β-hydroxyurs-12-en-28-oic acid (ursolic acid)) from Memecylon edule leaves by performing bioassay guided isolation method. The structure derivation of isolated compound was done by different spectral studies like UV, FT-IR, LC-MS, CHNS analysis, 1D ( 1 H, 13 C and DEPT-135) and 2D-NMR (HSQC and HMBC), respectively. About 99.29% purity of the compound was found in LC analysis. 1 H NMR spectrum results of compound shown 48 protons appear at different shielded region and most of the protons were present in aliphatic region. Whereas, 13 C NMR spectral data resulted seven methyl carbons (CH3), nine methylene carbons (CH2), seven methine carbons (CH) and six non-hydrogenated carbons (C) which are characteristic of pentacyclic triterpene. The isolated pure compound was tested for its antibacterial properties against targeted human pathogens by performing agar well diffusion, MIC and MBC assays and the result exhibits better growth inhibitory effects against S. epidermidis and S. pneumoniae, with the MIC values of 1.56 and 3.15μg/ml. The outcome of this study suggests that the bioactive compound is used for development of plant based drugs in pharmaceutical industry for combating microbial mediated diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

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

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

DOE PAGES

Li, Mi; Yoo, Chang Geun; Pu, Yunqiao; ...

2017-12-05

The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

AQuA: An Automated Quantification Algorithm for High-Throughput NMR-Based Metabolomics and Its Application in Human Plasma.

PubMed

Röhnisch, Hanna E; Eriksson, Jan; Müllner, Elisabeth; Agback, Peter; Sandström, Corine; Moazzami, Ali A

2018-02-06

A key limiting step for high-throughput NMR-based metabolomics is the lack of rapid and accurate tools for absolute quantification of many metabolites. We developed, implemented, and evaluated an algorithm, AQuA (Automated Quantification Algorithm), for targeted metabolite quantification from complex 1 H NMR spectra. AQuA operates based on spectral data extracted from a library consisting of one standard calibration spectrum for each metabolite. It uses one preselected NMR signal per metabolite for determining absolute concentrations and does so by effectively accounting for interferences caused by other metabolites. AQuA was implemented and evaluated using experimental NMR spectra from human plasma. The accuracy of AQuA was tested and confirmed in comparison with a manual spectral fitting approach using the ChenomX software, in which 61 out of 67 metabolites quantified in 30 human plasma spectra showed a goodness-of-fit (r 2 ) close to or exceeding 0.9 between the two approaches. In addition, three quality indicators generated by AQuA, namely, occurrence, interference, and positional deviation, were studied. These quality indicators permit evaluation of the results each time the algorithm is operated. The efficiency was tested and confirmed by implementing AQuA for quantification of 67 metabolites in a large data set comprising 1342 experimental spectra from human plasma, in which the whole computation took less than 1 s.

Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

PubMed

Shrot, Yoav; Frydman, Lucio

2011-04-01

A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called "ultrafast" methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR's simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains - often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method's performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%. Copyright © 2011 Elsevier Inc. All rights reserved.

High-resolution solid-state 13C NMR spectroscopy of the paramagnetic metal-organic frameworks, STAM-1 and HKUST-1.

PubMed

Dawson, Daniel M; Jamieson, Lauren E; Mohideen, M Infas H; McKinlay, Alistair C; Smellie, Iain A; Cadou, Romain; Keddie, Neil S; Morris, Russell E; Ashbrook, Sharon E

2013-01-21

Solid-state (13)C magic-angle spinning (MAS) NMR spectroscopy is used to investigate the structure of the Cu(II)-based metal-organic frameworks (MOFs), HKUST-1 and STAM-1, and the structural changes occurring within these MOFs upon activation (dehydration). NMR spectroscopy is an attractive technique for the investigation of these materials, owing to its high sensitivity to local structure, without any requirement for longer-range order. However, interactions between nuclei and unpaired electrons in paramagnetic systems (e.g., Cu(II)-based MOFs) pose a considerable challenge, not only for spectral acquisition, but also in the assignment and interpretation of the spectral resonances. Here, we exploit the rapid T(1) relaxation of these materials to obtain (13)C NMR spectra using a spin-echo pulse sequence at natural abundance levels, and employ frequency-stepped acquisition to ensure uniform excitation of resonances over a wide frequency range. We then utilise selective (13)C isotopic labelling of the organic linker molecules to enable an unambiguous assignment of NMR spectra of both MOFs for the first time. We show that the monomethylated linker can be recovered from STAM-1 intact, demonstrating not only the interesting use of this MOF as a protecting group, but also the ability (for both STAM-1 and HKUST-1) to recover isotopically-enriched linkers, thereby reducing significantly the overall cost of the approach.

Spectral and structural studies of the anti-cancer drug Flutamide by density functional theoretical method

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.

2014-01-01

A comprehensive screening of the more recent DFT theoretical approach to structural analysis is presented in this section of theoretical structural analysis. The chemical name of 2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-propanamide is usually called as Flutamide (In the present study it is abbreviated as FLT) and is an important and efficacious drug in the treatment of anti-cancer resistant. The molecular geometry, vibrational spectra, electronic and NMR spectral interpretation of Flutamide have been studied with the aid of density functional theory method (DFT). The vibrational assignments of the normal modes were performed on the basis of the PED calculations using the VEDA 4 program. Comparison of computational results with X-ray diffraction results of Flutamide allowed the evaluation of structure predictions and confirmed B3LYP/6-31G(d,p) as accurate for structure determination. Application of scaling factors for IR and Raman frequency predictions showed good agreement with experimental values. This is supported the assignment of the major contributors of the vibration modes of the title compound. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The comparison of measured FTIR, FT-Raman, and UV-Visible data to calculated values allowed assignment of major spectral features of the title molecule. Besides, Frontier molecular orbital analyze was also investigated using theoretical calculations.

Water confinement in faujasite cages: a deuteron NMR investigation in a wide temperature range. 1. Low temperature spectra.

PubMed

Szymocha, A M; Birczyński, A; Lalowicz, Z T; Stoch, G; Krzystyniak, M; Góra-Marek, K

2014-07-24

Deuteron NMR spectra were measured for D2O confined in NaX, NaY, and DY faujasites with various D2O loadings at temperatures ranging from T = 70 K to T = 200 K with the aim to study the molecular mobility of confined water as a function of Si/Al ratio and loading. The recorded spectra were fitted with linear combinations of representative spectral components. At low loading, with the number of water molecules per unit cell close to the abundance of sodium cations, a component related to π-jumps of water deuterons about the 2-fold symmetry axis dominated. For loadings at levels 3 times and 5 times higher than the initial loading level, Pake dublets due to rigid water deuterons dominated the recorded spectra. A set of the quadrupole coupling constant values of localized water deuterons was derived from the analysis of the Pake dublets. Their values were attributed to deuteron positions corresponding to the locations at oxygen atoms in the faujasite framework and locations within hydrogen-bonded water clusters inside faujasite cages. The contributions of the different spectral components were observed to change with increasing temperature according to the Arrhenius law with a characteristic dynamic crossover point at T = 165 K. Below T = 165 K a spectral component was observed whose contribution changed with temperature, yielding the activation energy of about 2 kJ/mol, characteristic for jumps between inversion-related water positions in clusters.

Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

PubMed Central

2015-01-01

The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

Using 31P NMR spectroscopy at 14.1 Tesla to investigate PARP-1 associated energy failure and metabolic rescue in cerebrocortical slices.

PubMed

Zeng, Jianying; Hirai, Kiyoshi; Yang, Guo-Yuan; Ying, Weihai; Swanson, Raymond A; Kelly, Mark; Mayer, Moriz; James, Thomas L; Litt, Lawrence

2004-08-01

PARP-1 activation by H(2)O(2) in an acute preparation of superfused, respiring, neonatal cerebrocortical slices was assessed from PAR-polymer formation detected with immunohistochemistry and Western blotting. (31)P NMR spectroscopy at 14.1 Tesla of perchloric acid slice extracts was used to assess energy failure in a 1-h H(2)O(2) exposure as well as in a subsequent 4-h recovery period where the superfusate had no H(2)O(2) and specifically chosen metabolic substrates. Although more data are needed to fully characterize different bioenergetic responses, a high NMR spectral resolution (PCr full-width at half-max approximately.01 ppm) and narrow widths for most metabolites (<.2 ppm) permitted accurate quantifications of spectrally resolved resonances for ADP, ATP, NAD(+)/NADH, and other high energy phosphates. It appears possible to use brain slices to quantitatively study PARP-related, NAD-associated energy failure, and rescue with TCA metabolites.

CP/MAS ¹³C NMR study of pulp hornification using nanocrystalline cellulose as a model system.

PubMed

Idström, Alexander; Brelid, Harald; Nydén, Magnus; Nordstierna, Lars

2013-01-30

The hornification process of paper pulp was investigated using solid-state (13)C NMR spectroscopy. Nanocrystalline cellulose was used to serve as a model system of the crystalline parts of the fibrils in pulp fibers. Characterization of the nanocrystalline cellulose dimensions was carried out using scanning electron microscopy. The samples were treated by drying and wetting cycles prior to NMR analysis where the hornification phenomenon was recorded by spectral changes of the cellulose C-4 carbon signals. An increase of the crystalline signal and a decrease of the signals corresponding to the accessible amorphous domains were found for both paper pulp and nanocrystalline cellulose. These spectral changes grew stronger with repeating drying and wetting cycles. The results show that cellulose co-crystallization contribute to hornification. Another conclusion is that the surfaces of higher hydrophobicity in cellulose fibrils have an increased preference for aggregation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Two-dimensional NMR spectroscopy of 13C methanol at less than 5 μT

NASA Astrophysics Data System (ADS)

Shim, Jeong Hyun; Lee, Seong-Joo; Hwang, Seong-min; Yu, Kwon-Kyu; Kim, Kiwoong

2014-09-01

Two-dimensional (2D) spectroscopy is one of the most significant applications of nuclear magnetic resonance (NMR). Here, we demonstrate that the 2D NMR can be performed even at a low magnetic field of less than 5 μT, which is ten times less than the Earth’s magnetic field. The pulses used in the experiment were composed of circularly polarized fields for coherent as well as wideband excitations. Since the excitation band covers the entire spectral range, the simplest two-pulse sequence delivered the full 2D spectrum. At 5 μT, methanol with 13C enriched up to 99% belongs to a strongly coupled regime, and thus its 2D spectrum exhibits complicated spectral correlations, which can be exploited as a fingerprint in chemical analysis. In addition, we show that, with compressive sensing, the acquisition of the 2D spectrum can be accelerated to take only 45% of the overall duration.

Purpurediolin and purpurenin, two new cytotoxic adjacent bis-tetrahydrofuran annonaceous acetogenins from the seeds of Annona purpurea.

PubMed

Chávez, D; Mata, R

1998-05-01

Two novel cytotoxic acetogenins, purpurediolin (1) and purpurenin (2), were isolated from the seeds of Annona purpurea. Their structures were elucidated by a combination of chemical and spectral methods including MS and NMR measurements. In addition, six known acetogenins were obtained, namely, bullatacin, squamocin (annonin I), motrilin (squamocin C), annoglaucin, xylomatenin, and annonacin A. Compounds 1 and 2 exhibited potent cytotoxic activity in vitro against six human solid tumor cell lines.

17O solid-state NMR spectroscopy of A2B2O7 oxides: quantitative isotopic enrichment and spectral acquisition?

PubMed

Fernandes, Arantxa; Moran, Robert F; Sneddon, Scott; Dawson, Daniel M; McKay, David; Bignami, Giulia P M; Blanc, Frédéric; Whittle, Karl R; Ashbrook, Sharon E

2018-02-13

The potential of 17 O NMR spectroscopy for the investigation of A 2 B 2 O 7 ceramic oxides important in the encapsulation of radioactive waste is demonstrated, with post-synthetic enrichment by exchange with 17 O 2 gas. For Y 2 Sn 2 O 7 , Y 2 Ti 2 O 7 and La 2 Sn 2 O 7 pyrochlores, enrichment of the two distinct O species is clearly non quantitative at lower temperatures (∼700 °C and below) and at shorter times, despite these being used in prior work, with preferential enrichment of OA 2 B 2 favoured over that of OA 4 . At higher temperatures, the 17 O NMR spectra suggest that quantitative enrichment has been achieved, but the integrated signal intensities do not reflect the crystallographic 1 : 6 (O1 : O2) ratio until corrected for differences in T 1 relaxation rates and, more importantly, the contribution of the satellite transitions. 17 O NMR spectra of Y 2 Zr 2 O 7 and Y 2 Hf 2 O 7 defect fluorites showed little difference with any variation in enrichment temperature or time, although an increase in the absolute level of enrichment (up to ∼7.5%) was observed at higher temperature. DFT calculations show that the six distinct resonances observed cannot be assigned unambiguously, as each has contributions from more than one of the five possible next nearest neighbour environments. For La 2 Ti 2 O 7 , which adopts a layered perovskite-like structure, little difference in the spectral intensities is observed with enrichment time or temperature, although the highest absolute levels of enrichment (∼13%) were obtained at higher temperature. This work demonstrates that 17 O NMR has the potential to be a powerful probe of local structure and disorder in oxides, but that considerable care must be taken both in choosing the conditions for 17 O enrichment and the experimental acquisition parameters if the necessary quantitative measurements are to be obtained for more complex systems.

Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures.

PubMed

Dass, Rupashree; Grudzia Ż, Katarzyna; Ishikawa, Takao; Nowakowski, Michał; Dȩbowska, Renata; Kazimierczuk, Krzysztof

2017-01-01

The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1 H experiments have been reported in studies of bacterial metabolism monitored in situ . However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes , an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13 C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.

Process spectroscopy in microemulsions—setup and multi-spectral approach for reaction monitoring of a homogeneous hydroformylation process

NASA Astrophysics Data System (ADS)

Meyer, K.; Ruiken, J.-P.; Illner, M.; Paul, A.; Müller, D.; Esche, E.; Wozny, G.; Maiwald, M.

2017-03-01

Reaction monitoring in disperse systems, such as emulsions, is of significant technical importance in various disciplines like biotechnological engineering, chemical industry, food science, and a growing number other technical fields. These systems pose several challenges when it comes to process analytics, such as heterogeneity of mixtures, changes in optical behavior, and low optical activity. Concerning this, online nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for process monitoring in complex reaction mixtures due to its unique direct comparison abilities, while at the same time being non-invasive and independent of optical properties of the sample. In this study the applicability of online-spectroscopic methods on the homogeneously catalyzed hydroformylation system of 1-dodecene to tridecanal is investigated, which is operated in a mini-plant scale at Technische Universität Berlin. The design of a laboratory setup for process-like calibration experiments is presented, including a 500 MHz online NMR spectrometer, a benchtop NMR device with 43 MHz proton frequency as well as two Raman probes and a flow cell assembly for an ultraviolet and visible light (UV/VIS) spectrometer. Results of high-resolution online NMR spectroscopy are shown and technical as well as process-specific problems observed during the measurements are discussed.

Antiandrogen and Antimicrobial Aspects of Coordination Compounds of Palladium(II), Platinum(II) and Lead(II)

PubMed Central

Joshi, S. C.; Kulshrestha, Shalini; Nagpal, Pooja; Bansal, Anil

2001-01-01

Synthesis, characterization and antimicrobial activities of an interesting class of biologically potent macrocyclic complexes have been carried out. All the complexes have been evaluated for their antimicrobial effects on different species of pathogenic fungi and bacteria. The testicular sperm density, testicular sperm morphology, sperm motility, density of cauda epididymal spermatozoa and fertility in mating trails and biochemical parameters of reproductive organs have been examined and discussed. The resulting biologically active [M(MaLn)(R2)]Cl2 and [Pb(MaLn)(R2)X2] (where, M = PdII or PtII and X = Cl or NO3) type of complexes have been synthesized by the reactions of macrocyclic ligands (MaLn) with metal salts and different diamines in 1:1:1 molar ratio in methanol. Initially the complexes were characterized by elemental analyses, molecular weight determinations and conductivity measurements. The mode of bonding was established on the basis of IR, 1H NMR, 13C NMR, 195Pt NMR, 207Pb NMR, XRD and electronic spectral studies. The macrocyclic ligand coordinates through the four azomethine nitrogen atoms which are bridged by benzil moieties. IR spectra suggest that the pyridine nitrogen is not coordinating. The palladium and platinum complexes exhibit tetracoordinated square-planar geometry, whereas a hexacoordinated octahedral geometry is suggested for lead complexes. PMID:18475989

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics

PubMed Central

Rist, Manuela J.; Muhle-Goll, Claudia; Görling, Benjamin; Bub, Achim; Heissler, Stefan; Watzl, Bernhard; Luy, Burkhard

2013-01-01

It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at −20 °C, on dry ice, at −80 °C or in liquid nitrogen and then stored at −20 °C, −80 °C or in liquid nitrogen vapor phase for 1–5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at −20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol. PMID:24957990

Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics.

PubMed

Rist, Manuela J; Muhle-Goll, Claudia; Görling, Benjamin; Bub, Achim; Heissler, Stefan; Watzl, Bernhard; Luy, Burkhard

2013-04-09

It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at -20 °C, on dry ice, at -80 °C or in liquid nitrogen and then stored at -20 °C, -80 °C or in liquid nitrogen vapor phase for 1-5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at -20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol.

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

PubMed

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

2015-11-01

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

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.

In vivo high-resolution magic angle spinning magnetic and electron paramagnetic resonance spectroscopic analysis of mitochondria-targeted peptide in Drosophila melanogaster with trauma-induced thoracic injury.

PubMed

Constantinou, Caterina; Apidianakis, Yiorgos; Psychogios, Nikolaos; Righi, Valeria; Mindrinos, Michael N; Khan, Nadeem; Swartz, Harold M; Szeto, Hazel H; Tompkins, Ronald G; Rahme, Laurence G; Tzika, A Aria

2016-02-01

Trauma is the most common cause of mortality among individuals aged between 1 and 44 years and the third leading cause of mortality overall in the US. In this study, we examined the effects of trauma on the expression of genes in Drosophila melanogaster, a useful model for investigating genetics and physiology. After trauma was induced by a non-lethal needle puncture of the thorax, we observed the differential expression of genes encoding for mitochondrial uncoupling proteins, as well as those encoding for apoptosis-related and insulin signaling-related proteins, thus indicating muscle functional dysregulation. These results prompted us to examine the link between insulin signaling and mitochondrial dysfunction using in vivo nuclear magnetic resonance (NMR) with complementary electron paramagnetic resonance (EPR) spectroscopy. Trauma significantly increased insulin resistance biomarkers, and the NMR spectral profile of the aged flies with trauma-induced thoracic injury resembled that of insulin-resistant chico mutant flies. In addition, the mitochondrial redox status, as measured by EPR, was significantly altered following trauma, indicating mitochondrial uncoupling. A mitochondria-targeted compound, Szeto-Schiller (SS)-31 that promotes adenosine triphosphate (ATP) synthesis normalized the NMR spectral profile, as well as the mitochondrial redox status of the flies with trauma-induced thoracic injury, as assessed by EPR. Based on these findings, we propose a molecular mechanism responsible for trauma-related mortality and also propose that trauma sequelae in aging are linked to insulin signaling and mitochondrial dysfunction. Our findings further suggest that SS-31 attenuates trauma-associated pathological changes.

NMR and mass spectrometric characterization of vinblastine, vincristine and some new related impurities - part I.

PubMed

Dubrovay, Zsófia; Háda, Viktor; Béni, Zoltán; Szántay, Csaba

2013-10-01

In the course of exploring the possibilities of developing a new, improved process at Gedeon Richter for the production of the "bisindole" alkaloids vinblastine (VLB) and vincristine (VCR), some novel VLB/VCR-related trace impurities were detected by analytical HPLC. Following isolation by preparative HPLC, a combination of 1D and 2D ultra high-field NMR and high-resolution (HR) (LC-)MS/MS studies allowed the structural identification and complete spectral characterization of several hitherto unpublished VLB/VCR-analogue impurities. Since the impurities could not be isolated in entirely pure forms and were available only in minute, mass-limited quantities, accessing the spectral information needed for their ab initio structure determination was met with various practical difficulties. Successful structure determination therefore relied heavily on the availability and use of detailed and definitive spectral data for both VLB and VCR. In particular, the utilization of detailed (1)H, (13)C, and (15)N NMR assignments as well as (1)H-(1)H, (1)H-(13)C and (1)H-(15)N spin-spin connectivities pertaining to different solvents for VLB/VCR base and sulphate salt was required. Although NMR studies on VLB base and other bisindoles were reported earlier in the literature, an NMR characterization of VLB and VCR under the above-mentioned circumstances and using ultra-high field instrumentation is either scarcely available or entirely lacking, therefore the necessary data had to be obtained in-house. Likewise, a modern tandem HR-ESI-MS/MS(n) fragmentation study of VLB and VCR has not been published yet. In the present paper we therefore give a thorough NMR and MS characterization of VLB and VCR specifically with a view to filling this void and to provide sufficiently extensive and solid reference data for the structural investigation of the aforementioned VLB/VCR impurities. Besides being scientifically relevant in its own right, the disclosed data should be useful for anyone interested in VLB/VCR-related molecules at a structural level. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantitative Study of Longitudinal Relaxation (T 1) Contrast Mechanisms in Brain MRI

NASA Astrophysics Data System (ADS)

Jiang, Xu

Longitudinal relaxation (T1) contrast in MRI is important for studying brain morphology and is widely used in clinical applications. Although MRI only detects signals from water hydrogen ( 1H) protons (WPs), T1 contrast is known to be influenced by other species of 1H protons, including those in macromolecules (MPs), such as lipids and proteins, through magnetization transfer (MT) between WPs and MPs. This complicates the use and quantification of T1 contrast for studying the underlying tissue composition and the physiology of the brain. MT contributes to T1 contrast to an extent that is generally dependent on MT kinetics, as well as the concentration and NMR spectral properties of MPs. However, the MP spectral properties and MT kinetics are both difficult to measure directly, as the signal from MPs is generally invisible to MRI. Therefore, to investigate MT kinetics and further quantify T1 contrast, we first developed a reliable way to indirectly measure the MP fraction and their exchange rate with WPs, with minimal dependence on the spectral properties of MPs. For this purpose, we used brief, highpower radiofrequency (RF) NMR excitation pulses to almost completely saturate the magnetization of MPs. Based on this, both MT kinetics and the contribution of MPs to T1 contrast through MT were studied. The thus obtained knowledge allowed us to subsequently infer the spectral properties of MPs by applying low-power, frequencyselective off-resonance RF pulses and measuring the offset-frequency dependent effect of MPs on the WP MRI signal. A two-pool exchange model was used in both cases to account for direct effects of the RF pulse on WP magnetization. Consistent with earlier works using MRI at low-field and post-mortem analysis of brain tissue, our novel measurement approach found that MPs constitute an up to 27% fraction of the total 1H protons in human brain white matter, and their spectrum follows a super-Lorentzian line with a T2 of 9.6+/-0.6 mus and a resonance frequency centered at -2.58+/-0.05 ppm, at 7 T. T1 contrast was found to be dominated by MP fraction, with iron only modestly contributing even in the iron-rich regions of brain.

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

pH optimization for a reliable quantification of brain tumor cell and tissue extracts with (1)H NMR: focus on choline-containing compounds and taurine.

PubMed

Robert, O; Sabatier, J; Desoubzdanne, D; Lalande, J; Balayssac, S; Gilard, V; Martino, R; Malet-Martino, M

2011-01-01

The aim of this study was to define the optimal pH for (1)H nuclear magnetic resonance (NMR) spectroscopy analysis of perchloric acid or methanol-chloroform-water extracts from brain tumor cells and tissues. The systematic study of the proton chemical shift variations as a function of pH of 13 brain metabolites in model solutions demonstrated that recording (1)H NMR spectra at pH 10 allowed resolving resonances that are overlapped at pH 7, especially in the 3.2-3.3 ppm choline-containing-compounds region. (1)H NMR analysis of extracts at pH 7 or 10 showed that quantitative measurements of lactate, alanine, glutamate, glutamine (Gln), creatine + phosphocreatine and myo-inositol (m-Ino) can be readily performed at both pHs. The concentrations of glycerophosphocholine, phosphocholine and choline that are crucial metabolites for tumor brain malignancy grading were accurately measured at pH 10 only. Indeed, the resonances of their trimethylammonium moieties are cleared of any overlapping signal, especially those of taurine (Tau) and phosphoethanolamine. The four non-ionizable Tau protons resonating as a singlet in a non-congested spectral region permits an easier and more accurate quantitation of this apoptosis marker at pH 10 than at pH 7 where the triplet at 3.43 ppm can be overlapped with the signals of glucose or have an intensity too low to be measured. Glycine concentration was determined indirectly at both pHs after subtracting the contribution of the overlapped signals of m-Ino at pH 7 or Gln at pH 10.

Scalable NMR spectroscopy with semiconductor chips

PubMed Central

Ha, Dongwan; Paulsen, Jeffrey; Sun, Nan; Song, Yi-Qiao; Ham, Donhee

2014-01-01

State-of-the-art NMR spectrometers using superconducting magnets have enabled, with their ultrafine spectral resolution, the determination of the structure of large molecules such as proteins, which is one of the most profound applications of modern NMR spectroscopy. Many chemical and biotechnological applications, however, involve only small-to-medium size molecules, for which the ultrafine resolution of the bulky, expensive, and high-maintenance NMR spectrometers is not required. For these applications, there is a critical need for portable, affordable, and low-maintenance NMR spectrometers to enable in-field, on-demand, or online applications (e.g., quality control, chemical reaction monitoring) and co-use of NMR with other analytical methods (e.g., chromatography, electrophoresis). As a critical step toward NMR spectrometer miniaturization, small permanent magnets with high field homogeneity have been developed. In contrast, NMR spectrometer electronics capable of modern multidimensional spectroscopy have thus far remained bulky. Complementing the magnet miniaturization, here we integrate the NMR spectrometer electronics into 4-mm2 silicon chips. Furthermore, we perform various multidimensional NMR spectroscopies by operating these spectrometer electronics chips together with a compact permanent magnet. This combination of the spectrometer-electronics-on-a-chip with a permanent magnet represents a useful step toward miniaturization of the overall NMR spectrometer into a portable platform. PMID:25092330

Online low-field NMR spectroscopy for process control of an industrial lithiation reaction-automated data analysis.

PubMed

Kern, Simon; Meyer, Klas; Guhl, Svetlana; Gräßer, Patrick; Paul, Andrea; King, Rudibert; Maiwald, Michael

2018-05-01

Monitoring specific chemical properties is the key to chemical process control. Today, mainly optical online methods are applied, which require time- and cost-intensive calibration effort. NMR spectroscopy, with its advantage being a direct comparison method without need for calibration, has a high potential for enabling closed-loop process control while exhibiting short set-up times. Compact NMR instruments make NMR spectroscopy accessible in industrial and rough environments for process monitoring and advanced process control strategies. We present a fully automated data analysis approach which is completely based on physically motivated spectral models as first principles information (indirect hard modeling-IHM) and applied it to a given pharmaceutical lithiation reaction in the framework of the European Union's Horizon 2020 project CONSENS. Online low-field NMR (LF NMR) data was analyzed by IHM with low calibration effort, compared to a multivariate PLS-R (partial least squares regression) approach, and both validated using online high-field NMR (HF NMR) spectroscopy. Graphical abstract NMR sensor module for monitoring of the aromatic coupling of 1-fluoro-2-nitrobenzene (FNB) with aniline to 2-nitrodiphenylamine (NDPA) using lithium-bis(trimethylsilyl) amide (Li-HMDS) in continuous operation. Online 43.5 MHz low-field NMR (LF) was compared to 500 MHz high-field NMR spectroscopy (HF) as reference method.

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.

Synthesis, spectroscopic characterization, electrochemical behaviour, reactivity and antibacterial activity of some transition metal complexes with 2-(N-salicylideneamino)-3-carboxyethyl-4,5-dimethylthiophene.

PubMed

Daniel, Varughese P; Murukan, B; Kumari, B Sindhu; Mohanan, K

2008-07-01

Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes with a potentially tridentate Schiff base, formed by condensation of 2-amino-3-carboxyethyl-4,5-dimethylthiophene with salicylaldehyde were synthesized and characterized on the basis of elemental analyses, molar conductance values, magnetic susceptibility measurements, UV-vis, IR, EPR and NMR spectral data, wherever possible and applicable. Spectral studies reveal that the free ligand exists in a bifunctionally hydrogen bonded manner and coordinates to the metal ion in a tridentate fashion through the deprotonated phenolate oxygen, azomethine nitrogen and ester carbonyl group. On the basis of electronic spectral data and magnetic susceptibility measurements, suitable geometry has been proposed for each complex. The EPR spectral data of the Cu(II) complex showed that the metal-ligand bonds have considerable covalent character. The Ni(II) complex has undergone facile transesterification reaction when refluxed in methanol for a lengthy period. X-ray diffraction studies of Cu(II) complex showed that the complex has an orthorhombic crystal lattice. In view of the biological activity of thiophene derivatives, the ligand and the complexes were subjected to antibacterial screening. It has been observed that the antibacterial activity of the ligand increased on chelation with metal ion.

Raman bandshape analysis of the symmetric bending vibration in liquid chloroform

NASA Astrophysics Data System (ADS)

Yuan, P.; Schwartz, M.

In order to determine whether accurate rotational diffusion coefficients in liquids may be determined from the bandshapes of isotopically broadened vibrational peaks, we have investigated the isotropic and anisotropic Raman spectra of the ν 3( A1), CCl 3 symmetric bending, vibration in CHCl 3 as a function of temperature in the liquid phase. The spectral lineshapes were fitted by a model containing four Lorentzian/Gaussian summation bands with relative peak intensities equal to the relative abundances of the four isotopic combinations and frequency displacements constrained to values measured in the matrix infrared spectrum. The calculated room temperature perpendicular diffusion coefficient, D⊥ (25°C) = 8.310 10 s -1, was within the range of values reported from Raman measurements on the ν 1, symmetric carbon-hydrogen stretching, vibration, but was somewhat lower than published results from NMR relaxation time measurements, T1( 2D), on CDCl 3, and from dielectric relaxation. The activation energy, Ea( D⊥), determined from the ν 3 bandshape measurements was 30% higher than the average value from the NMR and dielectric studies. The deviation is believed to result from the sensitivity of this quantity to the fractional Lorentzian character of the fitting functions.

Combining 7Li NMR field-cycling relaxometry and stimulated-echo experiments: a powerful approach to lithium ion dynamics in solid-state electrolytes.

PubMed

Graf, Magnus; Kresse, Benjamin; Privalov, Alexei F; Vogel, Michael

2013-01-01

We use (7)Li NMR to study lithium ion dynamics in a (Li2S)-(P2S5) glass. In particular, it is shown that a combination of (7)Li field-cycling relaxometry and (7)Li stimulated-echo experiments allows us to cover a time window extending over 10 orders of magnitude without any gaps. While the (7)Li stimulated-echo method proved suitable to measure correlation functions F2(t) of lithium ion dynamics in solids in recent years, we establish the (7)Li field-cycling technique as a versatile tool to ascertain the spectral density J2(ω) of the lithium ionic motion in this contribution. It is found that the dynamic range of (7)Li field-cycling relaxometry is 10(-9)-10(-5)s and, hence, it complements in an ideal way that of (7)Li stimulated-echo experiments, which amounts to 10(-5)-10(1)s. Transformations between time and frequency domains reveal that the field-cycling and stimulated-echo approaches yield results for the translational motion of the lithium ions that are consistent both with each other and with findings for the motional narrowing of (7)Li NMR spectra of the studied (Li2S)-(P2S5) glass. In the (7)Li field-cycling studies of the (Li2S)-(P2S5) glass, we observe the translational ionic motion at higher temperatures and the nearly constant loss at lower temperatures. For the former motion, the frequency dependence of the measured spectral density is well described by a Cole-Davidson function. For the latter phenomenon, which was considered as an universal phenomenon of disordered solids in the literature, we find an exponential temperature dependence. Copyright © 2013 Elsevier Inc. All rights reserved.

Novel axially carborane-cage substituted silicon phthalocyanine photosensitizer; synthesis, characterization and photophysicochemical properties

NASA Astrophysics Data System (ADS)

Atmaca, Göknur Yaşa; Dizman, Cemil; Eren, Tarık; Erdoğmuş, Ali

2015-02-01

The novel axially dicarborane substituted silicon (IV) (SiPc-DC) phthalocyanine was synthesized by treating silicon phthalocyanine dichloride SiPc(Cl)2 (SiPc) with o-Carborane monool. The compound was characterized by mass spectrometry, UV-Vis, FT-IR, 1H and 11B Nuclear Magnetic Resonance Spectroscopy (NMR). Spectral, photophysical (fluorescence quantum yield) and photochemical (singlet oxygen (ΦΔ) and photodegradation quantum yield (Φd)) properties of the complex were reported in different solutions (Dimethyl sulfoxide (DMSO), Dimethylformamide (DMF) and Toluene). The results of spectral measurements showed that both SiPc and carborane cage can have potential to be used as sensitizers in photodynamic therapy (PDT) and boron neutron capture therapy (BNCT) by their singlet oxygen efficiencies (ΦΔ = 0.41, 0.39).

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.

Reconstruction of full high-resolution HSQC using signal split in aliased spectra.

PubMed

Foroozandeh, Mohammadali; Jeannerat, Damien

2015-11-01

Resolution enhancement is a long-sought goal in NMR spectroscopy. In conventional multidimensional NMR experiments, such as the (1) H-(13) C HSQC, the resolution in the indirect dimensions is typically 100 times lower as in 1D spectra because it is limited by the experimental time. Reducing the spectral window can significantly increase the resolution but at the cost of ambiguities in frequencies as a result of spectral aliasing. Fortunately, this information is not completely lost and can be retrieved using methods in which chemical shifts are encoded in the aliased spectra and decoded after processing to reconstruct high-resolution (1) H-(13) C HSQC spectrum with full spectral width and a resolution similar to that of 1D spectra. We applied a new reconstruction method, RHUMBA (reconstruction of high-resolution using multiplet built on aliased spectra), to spectra obtained from the differential evolution for non-ambiguous aliasing-HSQC and the new AMNA (additional modulation for non-ambiguous aliasing)-HSQC experiments. The reconstructed spectra significantly facilitate both manual and automated spectral analyses and structure elucidation based on heteronuclear 2D experiments. The resolution is enhanced by two orders of magnitudes without the usual complications due to spectral aliasing. Copyright © 2015 John Wiley & Sons, Ltd.

Spectroscopic characterizations of a mixed surfactant mesophase and its application in materials synthesis

NASA Astrophysics Data System (ADS)

Liu, Limin

A viscous lyotropic crystalline mesophase containing bis (2-ethylhexyl) sodium sulfosuccinate (AOT), alpha-phosphatidylcholine (lecithin), with comparable volume fractions of isooctane and water was characterized by Fourier-transform 31P and 1H nuclear magnetic resonance (NMR) spectroscopy. Shear alignment on the reverse hexagonal mesophase was reflected through both 31P NMR and 1H NMR spectra. A complicated 31P spectrum was observed as a result of superposition of chemical shifts according to the distribution of crystalline domains prior to shear. The initially disordered samples with polydomain structures became macroscopically aligned after Couette shear and the alignment retained for a long period of time. 31P NMR chemical shift anisotropy characteristics were used to elucidate orientation of the hexagonal phase. Interestingly, 1H NMR of the water, methyl and methylene groups exhibited spectral changes upon shear alignment closely corresponding with that of 31P NMR spectra. A reverse hexagonal to lamellar phase transition was manifested as an expanding of the expressed 31P NMR chemical shift anisotropy and an apparent reversal of the powder pattern with increasing water content and/or temperature. Correspondingly, 1H NMR spectra also experienced a spectral pattern transition as the water content or temperature was increased. These observations complement the findings of mesophase alignment obtained using small angle neutron scattering (SANS) and imply that 31P and 1H NMR spectroscopy can be used as probes to define microstructure and monitor orientation changes in this binary surfactant system. This is especially beneficial if these mesophases are used as templates for materials synthesis. The mesophase retains its alignment for extended periods allowing materials synthesis to be decoupled from the application of shear. Highly aligned string-like silica nanostructures were obtained through templated synthesis in the columnar hexagonal structure of the viscous lyotropic crystalline mesophase. A two-step procedure was used to first shear-align the surfactant mesophase, and then conduct synthesis under quiescent conditions in the mesophase. Polystyrene was post-grafted to the silica surface without disturbing its nanostring morphology. The coupling of materials synthesis in surfactant mesophases with processing techniques (e.g. extrusion) may result in functional materials, such as new catalyst support and membrane nanoarchitectures.

Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR.

PubMed

Gupta, Sebanti; Tycko, Robert

2018-02-01

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15 N, 13 C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies

NASA Astrophysics Data System (ADS)

Fasshuber, Hannes Klaus; Demers, Jean-Philippe; Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

2015-03-01

Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively 13C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved.

Monovacancy paramagnetism in neutron-irradiated graphite probed by 13C NMR.

PubMed

Zhang, Z T; Xu, C; Dmytriieva, D; Molatta, S; Wosnitza, J; Wang, Y T; Helm, M; Zhou, Shengqiang; Kühne, H

2017-10-20

We report on the magnetic properties of monovacancy defects in neutron-irradiated graphite, probed by 13 C nuclear magnetic resonance spectroscopy. The bulk paramagnetism of the defect moments is revealed by the temperature dependence of the NMR frequency shift and spectral linewidth, both of which follow a Curie behavior, in agreement with measurements of the macroscopic magnetization. Compared to pristine graphite, the fluctuating hyperfine fields generated by the defect moments lead to an enhancement of the 13 C nuclear spin-lattice relaxation rate [Formula: see text] by about two orders of magnitude. With an applied magnetic field of 7.1 T, the temperature dependence of [Formula: see text] below about 10 K can well be described by a thermally activated form, [Formula: see text], yielding a singular Zeeman energy of ([Formula: see text]) meV, in excellent agreement with the sole presence of polarized, non-interacting defect moments.

Synthesis, characterization and theoretical studies of 5-(benzylthio)-1-cylopentyl-1H-tetrazole

NASA Astrophysics Data System (ADS)

Saglam, S.; Disli, A.; Erdogdu, Y.; Marchewka, M. K.; Kanagathara, N.; Bay, B.; Güllüoğlu, M. T.

2015-01-01

In this study, 5-(benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized. Boiling points of the obtained compound have been determined and it has been characterized by FT-IR, 1H NMR, 13C-APT and LC-MS spectroscopy techniques. The FT-IR, 1H NMR and 13C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the vibrational bands observed in spectra has been discussed. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on Density Functional Theory (DFT) at 6-311++G**, cc-pVDZ and cc-pVTZ basis sets. The optimized geometry with 6-311++G** basis sets were used to determine the total energy distribution, harmonic vibrational frequencies, IR intensities.

Synthesis, characterization and theoretical studies of 5-(benzylthio)-1-cylopentyl-1H-tetrazole.

PubMed

Saglam, S; Disli, A; Erdogdu, Y; Marchewka, M K; Kanagathara, N; Bay, B; Güllüoğlu, M T

2015-01-25

In this study, 5-(benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized. Boiling points of the obtained compound have been determined and it has been characterized by FT-IR, (1)H NMR, (13)C-APT and LC-MS spectroscopy techniques. The FT-IR, (1)H NMR and (13)C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the vibrational bands observed in spectra has been discussed. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on Density Functional Theory (DFT) at 6-311++G(**), cc-pVDZ and cc-pVTZ basis sets. The optimized geometry with 6-311++G(**) basis sets were used to determine the total energy distribution, harmonic vibrational frequencies, IR intensities. Copyright © 2014 Elsevier B.V. All rights reserved.

Structures of glycans bound to receptors from saturation transfer difference (STD) NMR spectroscopy: quantitative analysis by using CORCEMA-ST.

PubMed

Enríquez-Navas, Pedro M; Guzzi, Cinzia; Muñoz-García, Juan C; Nieto, Pedro M; Angulo, Jesús

2015-01-01

Glycan-receptor interactions are of fundamental relevance for a large number of biological processes, and their kinetics properties (medium/weak binding affinities) make them appropriated to be studied by ligand observed NMR techniques, among which saturation transfer difference (STD) NMR spectroscopy has been shown to be a very robust and powerful approach. The quantitative analysis of the results from a STD NMR study of a glycan-receptor interaction is essential to be able to translate the resulting spectral intensities into a 3D molecular model of the complex. This chapter describes how to carry out such a quantitative analysis by means of the Complete Relaxation and Conformational Exchange Matrix Approach for STD NMR (CORCEMA-ST), in general terms, and an example of a previous work on an antibody-glycan interaction is also shown.

Continuous-wave Submillimeter-wave Gyrotrons

PubMed Central

Han, Seong-Tae; Griffin, Robert G.; Hu, Kan-Nian; Joo, Chan-Gyu; Joye, Colin D.; Mastovsky, Ivan; Shapiro, Michael A.; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Torrezan, Antonio C.; Woskov, Paul P.

2007-01-01

Recently, dynamic nuclear polarization enhanced nuclear magnetic resonance (DNP/NMR) has emerged as a powerful technique to obtain significant enhancements in spin spectra from biological samples. For DNP in modern NMR systems, a high power continuous-wave source in the submillimeter wavelength range is necessary. Gyrotrons can deliver tens of watts of CW power at submillimeter wavelengths and are well suited for use in DNP/NMR spectrometers. To date, 140 GHz and 250 GHz gyrotrons are being employed in DNP spectrometer experiments at 200 MHz and 380 MHz at MIT. A 460 GHz gyrotron, which has operated with 8 W of CW output power, will soon be installed in a 700 MHz NMR spectrometer. High power radiation with good spectral and spatial resolution from these gyrotrons should provide NMR spectrometers with high signal enhancement through DNP. Also, these tubes operating at submillimeter wavelengths should have important applications in research in physics, chemistry, biology, materials science and medicine. PMID:17404605

The FAQUIRE Approach: FAst, QUantitative, hIghly Resolved and sEnsitivity Enhanced 1H, 13C Data.

PubMed

Farjon, Jonathan; Milande, Clément; Martineau, Estelle; Akoka, Serge; Giraudeau, Patrick

2018-02-06

The targeted analysis of metabolites in complex mixtures is a challenging issue. NMR is one of the major tools in this field, but there is a strong need for more sensitive, better-resolved, and faster quantitative methods. In this framework, we introduce the concept of FAst, QUantitative, hIghly Resolved and sEnsitivity enhanced (FAQUIRE) NMR to push forward the limits of metabolite NMR analysis. 2D 1 H, 13 C 2D quantitative maps are promising alternatives for enhancing the spectral resolution but are highly time-consuming because of (i) the intrinsic nature of 2D, (ii) the longer recycling times required for quantitative conditions, and (iii) the higher number of scans needed to reduce the level of detection/quantification to access low concentrated metabolites. To reach this aim, speeding up the recently developed QUantItative Perfected and pUre shifted HSQC (QUIPU HSQC) is an interesting attempt to develop the FAQUIRE concept. Thanks to the combination of spectral aliasing, nonuniform sampling, and variable repetition time, the acquisition time of 2D quantitative maps is reduced by a factor 6 to 9, while conserving a high spectral resolution thanks to a pure shift approach. The analytical potential of the new Quick QUIPU HSQC (Q QUIPU HSQC) is evaluated on a model metabolite sample, and its potential is shown on breast-cell extracts embedding metabolites at millimolar to submillimolar concentrations.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Spectral and structural studies of the anti-cancer drug Flutamide by density functional theoretical method.

PubMed

Mariappan, G; Sundaraganesan, N

2014-01-03

A comprehensive screening of the more recent DFT theoretical approach to structural analysis is presented in this section of theoretical structural analysis. The chemical name of 2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-propanamide is usually called as Flutamide (In the present study it is abbreviated as FLT) and is an important and efficacious drug in the treatment of anti-cancer resistant. The molecular geometry, vibrational spectra, electronic and NMR spectral interpretation of Flutamide have been studied with the aid of density functional theory method (DFT). The vibrational assignments of the normal modes were performed on the basis of the PED calculations using the VEDA 4 program. Comparison of computational results with X-ray diffraction results of Flutamide allowed the evaluation of structure predictions and confirmed B3LYP/6-31G(d,p) as accurate for structure determination. Application of scaling factors for IR and Raman frequency predictions showed good agreement with experimental values. This is supported the assignment of the major contributors of the vibration modes of the title compound. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The comparison of measured FTIR, FT-Raman, and UV-Visible data to calculated values allowed assignment of major spectral features of the title molecule. Besides, Frontier molecular orbital analyze was also investigated using theoretical calculations. Copyright © 2013 Elsevier B.V. All rights reserved.

Spectrally edited 2D 13Csbnd 13C NMR spectra without diagonal ridge for characterizing 13C-enriched low-temperature carbon materials

NASA Astrophysics Data System (ADS)

Johnson, Robert L.; Anderson, Jason M.; Shanks, Brent H.; Fang, Xiaowen; Hong, Mei; Schmidt-Rohr, Klaus

2013-09-01

Two robust combinations of spectral editing techniques with 2D 13Csbnd 13C NMR have been developed for characterizing the aromatic components of 13C-enriched low-temperature carbon materials. One method (exchange with protonated and nonprotonated spectral editing, EXPANSE) selects cross peaks of protonated and nearby nonprotonated carbons, while the other technique, dipolar-dephased double-quantum/single-quantum (DQ/SQ) NMR, selects signals of bonded nonprotonated carbons. Both spectra are free of a diagonal ridge, which has many advantages: Cross peaks on the diagonal or of small intensity can be detected, and residual spinning sidebands or truncation artifacts associated with the diagonal ridge are avoided. In the DQ/SQ experiment, dipolar dephasing of the double-quantum coherence removes protonated-carbon signals; this approach also eliminates the need for high-power proton decoupling. The initial magnetization is generated with minimal fluctuation by combining direct polarization, cross polarization, and equilibration by 13C spin diffusion. The dipolar dephased DQ/SQ spectrum shows signals from all linkages between aromatic rings, including a distinctive peak from polycondensed aromatics. In EXPANSE NMR, signals of protonated carbons are selected in the first spectral dimension by short cross polarization combined with dipolar dephasing difference. This removes ambiguities of peak assignment to overlapping signals of nonprotonated and protonated aromatic carbons, e.g. near 125 ppm. Spin diffusion is enhanced by dipolar-assisted rotational resonance. Before detection, Csbnd H dipolar dephasing by gated decoupling is applied, which selects signals of nonprotonated carbons. Thus, only cross peaks due to magnetization originating from protonated C and ending on nearby nonprotonated C are retained. Combined with the chemical shifts deduced from the cross-peak position, this double spectral editing defines the bonding environment of aromatic, COO, and Cdbnd O carbons, which is particularly useful for identifying furan and arene rings. The Cdbnd O carbons, whose chemical shifts vary strongly (between 212 and 165 ppm) and systematically depend on their two bonding partners, show particularly informative cross peaks, given that one bonding partner is defined by the other frequency coordinate of the cross peak. The new techniques and the information content of the resulting spectra are validated on sulfuric-acid treated low-temperature carbon materials and on products of the Maillard reaction. The crucial need for spectral editing for correct peak assignment is demonstrated in an example.

Synthesis, spectroscopy, X-ray crystallography, DFT calculations, DNA binding and molecular docking of a propargyl arms containing Schiff base.

PubMed

Balakrishnan, C; Subha, L; Neelakantan, M A; Mariappan, S S

2015-11-05

A propargyl arms containing Schiff base (L) was synthesized by the condensation of 1-[2-hydroxy-4-(prop-2-yn-1-yloxy)phenyl]ethanone with trans-1,2-diaminocyclohexane. The structure of L was characterized by IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by single crystal X-ray diffraction analysis. The UV-Visible spectral behavior of L in different solvents exhibits positive solvatochromism. Density functional calculation of the L in gas phase was performed by using DFT (B3LYP) method with 6-31G basis set. The computed vibrational frequencies and NMR signals of L were compared with the experimental data. Tautomeric stability study inferred that the enolimine is more stable than the ketoamine form. The charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Electronic absorption and emission spectral studies were used to study the binding of L with CT-DNA. The molecular docking was done to identify the interaction of L with A-DNA and B-DNA. Copyright © 2015 Elsevier B.V. All rights reserved.

Discrete decoding based ultrafast multidimensional nuclear magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Wei, Zhiliang; Lin, Liangjie; Ye, Qimiao; Li, Jing; Cai, Shuhui; Chen, Zhong

2015-07-01

The three-dimensional (3D) nuclear magnetic resonance (NMR) spectroscopy constitutes an important and powerful tool in analyzing chemical and biological systems. However, the abundant 3D information arrives at the expense of long acquisition times lasting hours or even days. Therefore, there has been a continuous interest in developing techniques to accelerate recordings of 3D NMR spectra, among which the ultrafast spatiotemporal encoding technique supplies impressive acquisition speed by compressing a multidimensional spectrum in a single scan. However, it tends to suffer from tradeoffs among spectral widths in different dimensions, which deteriorates in cases of NMR spectroscopy with more dimensions. In this study, the discrete decoding is proposed to liberate the ultrafast technique from tradeoffs among spectral widths in different dimensions by focusing decoding on signal-bearing sites. For verifying its feasibility and effectiveness, we utilized the method to generate two different types of 3D spectra. The proposed method is also applicable to cases with more than three dimensions, which, based on the experimental results, may widen applications of the ultrafast technique.

Optimized Spectral Editing of 13C MAS NMR Spectra of Rigid Solids Using Cross-Polarization Methods

NASA Astrophysics Data System (ADS)

Sangill, R.; Rastrupandersen, N.; Bildsoe, H.; Jakobsen, H. J.; Nielsen, N. C.

Combinations of 13C magic-angle spinning (MAS) NMR experiments employing cross polarization (CP), cross polarization-depolarization (CPD), and cross polarization-depolarization-repolarization are analyzed quantitatively to derive simple and general procedures for optimized spectral editing of 13C CP/MAS NMR spectra of rigid solids by separation of the 13C resonances into CH n subspectra ( n = 0, 1, 2, and 3). Special attention is devoted to a differentiation by CPD/MAS of CH and CH 2 resonances since these groups behave quite similarly during spin lock under Hartmann-Hahn match and are therefore generally difficult to distinguish unambiguously. A general procedure for the design of subexperiments and linear combinations of their spectra to provide optimized signal-to-noise ratios for the edited subspectra is described. The technique is illustrated by a series of edited 13C CP/MAS spectra for a number of rigid solids ranging from simple organic compounds (sucrose and l-menthol) to complex pharmaceutical products (calcipotriol monohydrate and vitamin D 3) and polymers (polypropylene, polyvinyl alcohol, polyvinyl chloride, and polystyrene).

Spectroscopic characterization of natural calcite minerals.

PubMed

Gunasekaran, S; Anbalagan, G

2007-11-01

The FT-IR, FT-Raman, NMR spectral data of ten different limestone samples have been compared. FT-IR and FT-Raman spectral data show that calcium carbonate in limestone, principally in the form of calcite, as identified by its main absorption bands at 1426, 1092, 876 and 712 cm(-1). The sharp diffractions at the d-spacings, 3.0348, 1.9166 and 1.8796 confirm the presence of calcite structure and the calculated lattice parameters are: a=4.9781 A, c=17.1188 A. The range of 13C chemical shifts for different limestone samples is very small, varying from 198.38 to 198.42 ppm. The observed chemical shifts are consistent with the identical C-O bonding in different limestone samples. 27Al MAS NMR spectra of the samples exhibit a central line at 1 ppm and another line at 60 ppm corresponding to octahedral and tetrahedral Al ions, respectively. The five component resonances were observed in 29Si MAS NMR spectrum of limestone and these resonances were assigned to Si (4 Al), Si (3 Al), Si (2 Al), Si (1 Al) and Si (0 Al) from low field to high field.

Structural analysis and characterization of dextran produced by wild and mutant strains of Leuconostoc mesenteroides.

PubMed

Siddiqui, Nadir Naveed; Aman, Afsheen; Silipo, Alba; Qader, Shah Ali Ul; Molinaro, Antonio

2014-01-01

An exopolysaccharide known as dextran was produced by Leuconostoc mesenteroides KIBGE-IB22 (wild) and L. mesenteroides KIBGE-IB22M20 (mutant). The structure was characterized using FTIR, (1)H NMR, (13)C NMR and 2D NMR spectroscopic techniques, whereas surface morphology was analyzed using SEM. A clear difference in the spectral chemical shift patterns was observed in both samples. All the spectral data indicated that the exopolysaccharide produced by KIBGE-IB22 is a mixture of two biopolymers. One was dextran in α-(1 → 6) configuration with a small proportion of α-(1 → 3) branching and the other was levan containing β-(2 → 6) fructan fructofuranosyl linkages. However, remarkably the mutant only produced dextran without any concomitant production of levan. Study suggested that the property of KIBGE-IB22M20, regarding improved production of high molecular weight dextran in a shorter period of fermentation time without any contamination of other exopolysaccharide, could be employed to make the downstream process more feasible and cost effective on large scale. Copyright © 2013 Elsevier Ltd. All rights reserved.

7-epi-griffonilide, a new lactone from Bauhinia pentandra: complete 1H and 13C chemical shift assignments.

PubMed

Almeida, Macia C S DE; Souza, Luciana G S; Ferreira, Daniele A; Pinto, Francisco C L; Oliveira, Débora R DE; Santiago, Gilvandete M P; Monte, Francisco J Q; Braz-Filho, Raimundo; Lemos, Telma L G DE

2017-01-01

A new lactone, 7-epi-griffonilide (1), and six known compounds, 2, 3a - 3c, 4a and 4b, were isolated from the leaves of Bauhinia pentandra (Fabaceae). The structures elucidation of 1 and 2 were based on detailed 2D NMR techniques and spectral comparison with related compounds, leading to complete assignment of the 1H and 13C NMR spectra.

Time domain para hydrogen induced polarization.

PubMed

Ratajczyk, Tomasz; Gutmann, Torsten; Dillenberger, Sonja; Abdulhussaein, Safaa; Frydel, Jaroslaw; Breitzke, Hergen; Bommerich, Ute; Trantzschel, Thomas; Bernarding, Johannes; Magusin, Pieter C M M; Buntkowsky, Gerd

2012-01-01

Para hydrogen induced polarization (PHIP) is a powerful hyperpolarization technique, which increases the NMR sensitivity by several orders of magnitude. However the hyperpolarized signal is created as an anti-phase signal, which necessitates high magnetic field homogeneity and spectral resolution in the conventional PHIP schemes. This hampers the application of PHIP enhancement in many fields, as for example in food science, materials science or MRI, where low B(0)-fields or low B(0)-homogeneity do decrease spectral resolution, leading to potential extinction if in-phase and anti-phase hyperpolarization signals cannot be resolved. Herein, we demonstrate that the echo sequence (45°-τ-180°-τ) enables the acquisition of low resolution PHIP enhanced liquid state NMR signals of phenylpropiolic acid derivatives and phenylacetylene at a low cost low-resolution 0.54 T spectrometer. As low field TD-spectrometers are commonly used in industry or biomedicine for the relaxometry of oil-water mixtures, food, nano-particles, or other systems, we compare two variants of para-hydrogen induced polarization with data-evaluation in the time domain (TD-PHIP). In both TD-ALTADENA and the TD-PASADENA strong spin echoes could be detected under conditions when usually no anti-phase signals can be measured due to the lack of resolution. The results suggest that the time-domain detection of PHIP-enhanced signals opens up new application areas for low-field PHIP-hyperpolarization, such as non-invasive compound detection or new contrast agents and biomarkers in low-field Magnetic Resonance Imaging (MRI). Finally, solid-state NMR calculations are presented, which show that the solid echo (90y-τ-90x-τ) version of the TD-ALTADENA experiment is able to convert up to 10% of the PHIP signal into visible magnetization. Copyright © 2012 Elsevier Inc. All rights reserved.

The plane-wave DFT investigations into the structure and the 11B solid-state NMR parameters of lithium fluorooxoborates

NASA Astrophysics Data System (ADS)

Czernek, Jiří; Brus, Jiří

2016-12-01

The strategy for an application of the first-principles calculations on crystalline systems to predict the 11B solid-state NMR powder-patterns is described, and its efficacy is demonstrated for two novel lithium-containing fluorooxborates, Li2B3O4F3 and Li2B6O9F2. This strategy involves the plane-wave DFT computations of the NMR parameters, whose values are then scaled and used in the spectral simulations, and are supposed to be directly applicable in the NMR crystallography studies of boron-containing systems. In particular, the GIPAW method and the PBE, PW91, and RPBE functionals are applied. Issues specific to the signal-assignment of the two compounds are also discussed.

Enhanced detection of aldehydes in Extra-Virgin Olive Oil by means of band selective NMR spectroscopy

NASA Astrophysics Data System (ADS)

Dugo, Giacomo; Rotondo, Archimede; Mallamace, Domenico; Cicero, Nicola; Salvo, Andrea; Rotondo, Enrico; Corsaro, Carmelo

2015-02-01

High resolution Nuclear Magnetic Resonance (NMR) spectroscopy is a very powerful tool for comprehensive food analyses and especially for Extra-Virgin Olive Oils (EVOOs). We use the NMR technique to study the spectral region of aldehydes (8-10 ppm) for EVOOs coming from the south part of Italy. We perform novel experiments by using mono and bidimensional band selective spin-echo pulse sequences and identify four structural classes of aldehydes in EVOOs. For the first time such species are identified in EVOOs without any chemical treatment; only dilution with CDCl3 is employed. This would allow the discrimination of different EVOOs for the aldehydes content increasing the potentiality of the NMR technique in the screening of metabolites for geographical characterization of EVOOs.

High-Throughput Nuclear Magnetic Resonance Metabolomic Footprinting for Tissue Engineering

PubMed Central

Seagle, Christopher; Christie, Megan A.; Winnike, Jason H.; McClelland, Randall E.; Ludlow, John W.; O'Connell, Thomas M.; Gamcsik, Michael P.

2008-01-01

Abstract We report a high-throughput (HTP) nuclear magnetic resonance (NMR) method for analysis of media components and a metabolic schematic to help easily interpret the data. Spin-lattice relaxation values and concentrations were measured for 19 components and 2 internal referencing agents in pure and 2-day conditioned, hormonally defined media from a 3-dimensional (3D) multicoaxial human bioartificial liver (BAL). The 1H NMR spectral signal-to-noise ratio is 21 for 0.16 mM alanine in medium and is obtained in 12 min using a 400 MHz NMR spectrometer. For comparison, 2D gel cultures and 3D multicoaxial BALs were batch cultured, with medium changed every day for 15 days after inoculation with human liver cells in Matrigel–collagen type 1 gels. Glutamine consumption was higher by day 8 in the BAL than in 2D culture; lactate production was lower through the 15-day culture period. Alanine was the primary amino acid produced and tracked with lactate or urea production. Glucose and pyruvate consumption were similar in the BAL and 2D cultures. NMR analysis permits quality assurance of the bioreactor by identifying contaminants. Ethanol was observed because of a bioreactor membrane “wetting” procedure. A biochemical scheme is presented illustrating bioreactor metabolomic footprint results and demonstrating how this can be translated to modify bioreactor operational parameters or quality assurance issues. PMID:18544027

Automatic differential analysis of NMR experiments in complex samples.

PubMed

Margueritte, Laure; Markov, Petar; Chiron, Lionel; Starck, Jean-Philippe; Vonthron-Sénécheau, Catherine; Bourjot, Mélanie; Delsuc, Marc-André

2018-06-01

Liquid state nuclear magnetic resonance (NMR) is a powerful tool for the analysis of complex mixtures of unknown molecules. This capacity has been used in many analytical approaches: metabolomics, identification of active compounds in natural extracts, and characterization of species, and such studies require the acquisition of many diverse NMR measurements on series of samples. Although acquisition can easily be performed automatically, the number of NMR experiments involved in these studies increases very rapidly, and this data avalanche requires to resort to automatic processing and analysis. We present here a program that allows the autonomous, unsupervised processing of a large corpus of 1D, 2D, and diffusion-ordered spectroscopy experiments from a series of samples acquired in different conditions. The program provides all the signal processing steps, as well as peak-picking and bucketing of 1D and 2D spectra, the program and its components are fully available. In an experiment mimicking the search of a bioactive species in a natural extract, we use it for the automatic detection of small amounts of artemisinin added to a series of plant extracts and for the generation of the spectral fingerprint of this molecule. This program called Plasmodesma is a novel tool that should be useful to decipher complex mixtures, particularly in the discovery of biologically active natural products from plants extracts but can also in drug discovery or metabolomics studies. Copyright © 2017 John Wiley & Sons, Ltd.

Synthesis, spectral characterization and DNA binding of Schiff-base metal complexes derived from 2-amino-3-hydroxyprobanoic acid and acetylacetone

NASA Astrophysics Data System (ADS)

Hosny, Nasser Mohammed; Hussien, Mostafa A.; Radwan, Fatima M.; Nawar, Nagwa

2014-11-01

Four new metal complexes derived from the reaction of Cu(II), Co(II), Ni(II) and Zn(II) acetates with the Schiff-base ligand (H3L) resulted from the condensation of the amino acid 2-amino-3-hydroxyprobanoic acid (serine) and acetylacetone have been synthesized and characterized by, elemental analyses, ES-MS, IR, UV-Vis., 1H NMR, 13C NMR, ESR, thermal analyses (TGA and DTG) and magnetic measurements. The results showed that the Schiff-base ligand acts as bi-negative tridentate through the azomethine nitrogen, the deprotonated carboxylate oxygen and the enolic carbonyl oxygen. The optical band gaps measurements indicated the semi-conducting nature of these complexes. Molecular docking was used to predict the binding between the Schiff base ligand with the receptor of prostate cancer mutant H874Y. The interactions between the Cu(II) complex and calf thymus DNA (CT-DNA) have been studied by UV spectra. The results confirm that the Cu(II) complex binds to CT-DNA in an intercalative mode.

High-resolution diffusion and relaxation-edited magic angle spinning 1H NMR spectroscopy of intact liver tissue.

PubMed

Rooney, O M; Troke, J; Nicholson, J K; Griffin, J L

2003-11-01

High-resolution magic angle spinning (HRMAS) (1)H NMR spectroscopy is ideal for monitoring the metabolic environment within tissues, particularly when spectra are weighted by physical properties such as T(1) and T(2) relaxation times and apparent diffusion coefficients (ADCs). In this study, spectral-editing using T(1) and T(2) relaxation times and ADCs at variable diffusion times was used in conjunction with HRMAS (1)H NMR spectroscopy at 14.1 T in liver tissue. To enhance the sensitivity of ADC measurements to low molecular weight metabolites a T(2) spin echo was included in a standard stimulated gradient spin-echo sequence. Fatty liver induced in rats by chronic orotic acid feeding was investigated using this modified sequence. An increase in the combined ADC for the co-resonant peaks glucose, betaine, and TMAO during fatty liver disease was detected (ADCs = 0.60 +/- 0.11 and 0.35 +/- 0.1 * 10(-9) m(2)s(-1) (n = 3) for rats fed with and without orotic acid), indicative of a reduction in glucose and betaine and an increase in TMAO. Copyright 2003 Wiley-Liss, Inc.

Optical, mechanical and thermal behaviors of Nitrilotriacetic acid single crystal

NASA Astrophysics Data System (ADS)

Deepa, B.; Philominathan, P.

2017-11-01

An organic nonlinear single crystal of Nitrilotriacetic acid (NTAA) was grown for the first time by employing a simple slow evaporation technique. Single crystal X-ray diffraction (XRD) analysis reveals that the grown crystal belongs to the monoclinic system with noncentrosymmetric space group CC. Fourier transform infrared (FTIR) spectral study ascertains the presence of functional groups in NTAA. The molecular structure of the grown crystal was confirmed by Nuclear Magnetic Resonance (NMR) spectral analysis. The optical parameters such as transmittance, absorption coefficient and band gap were calculated from UV-Visible and fluorescence studies. Dielectric measurements were carried out for different frequency and temperature. The mechanical strength of the grown crystal was measured using Vickers microhardness test. The high thermal stability and the melting point of the grown crystal were also estimated using thermogravimetric (TGA) and differential thermal analyses (DTA). The confirmation of the grown crystals belonging to nonlinear optical crystals was performed by Kurtz-Perry technique and found as suitable candidate for optoelectronics applications.

Modeling of temperature-induced near-infrared and low-field time-domain nuclear magnetic resonance spectral variation: chemometric prediction of limonene and water content in spray-dried delivery systems.

PubMed

Andrade, Letícia; Farhat, Imad A; Aeberhardt, Kasia; Bro, Rasmus; Engelsen, Søren Balling

2009-02-01

The influence of temperature on near-infrared (NIR) and nuclear magnetic resonance (NMR) spectroscopy complicates the industrial applications of both spectroscopic methods. The focus of this study is to analyze and model the effect of temperature variation on NIR spectra and NMR relaxation data. Different multivariate methods were tested for constructing robust prediction models based on NIR and NMR data acquired at various temperatures. Data were acquired on model spray-dried limonene systems at five temperatures in the range from 20 degrees C to 60 degrees C and partial least squares (PLS) regression models were computed for limonene and water predictions. The predictive ability of the models computed on the NIR spectra (acquired at various temperatures) improved significantly when data were preprocessed using extended inverted signal correction (EISC). The average PLS regression prediction error was reduced to 0.2%, corresponding to 1.9% and 3.4% of the full range of limonene and water reference values, respectively. The removal of variation induced by temperature prior to calibration, by direct orthogonalization (DO), slightly enhanced the predictive ability of the models based on NMR data. Bilinear PLS models, with implicit inclusion of the temperature, enabled limonene and water predictions by NMR with an error of 0.3% (corresponding to 2.8% and 7.0% of the full range of limonene and water). For NMR, and in contrast to the NIR results, modeling the data using multi-way N-PLS improved the models' performance. N-PLS models, in which temperature was included as an extra variable, enabled more accurate prediction, especially for limonene (prediction error was reduced to 0.2%). Overall, this study proved that it is possible to develop models for limonene and water content prediction based on NIR and NMR data, independent of the measurement temperature.

Identifying metabolites related to nitrogen mineralisation using 1H NMR spectroscopy

NASA Astrophysics Data System (ADS)

. T McDonald, Noeleen; Graham, Stewart; Watson, Catherine; Gordon, Alan; Lalor, Stan; Laughlin, Ronnie; Elliott, Chris; . P Wall, David

2015-04-01

Exploring new analysis techniques to enhance our knowledge of the various metabolites within our soil systems is imperative. Principally, this knowledge would allow us to link key metabolites with functional influences on critical nutrient processes, such as the nitrogen (N) mineralisation in soils. Currently there are few studies that utilize proton nuclear magnetic resonance spectroscopy (1H NMR) to characterize multiple metabolites within a soil sample. The aim of this research study was to examine the effectiveness of 1H NMR for isolating multiple metabolites that are related to the mineralizable N (MN) capacity across a range of 35 Irish grassland soils. Soils were measured for MN using the standard seven day anaerobic incubation (AI-7). Additionally, soils were also analysed for a range of physio-chemical properties [e.g. total N, total C, mineral N, texture and soil organic matter (SOM)]. Proton NMR analysis was carried on these soils by extracting with 40% methanol:water, lyophilizing and reconstituting in deuterium oxide and recording the NMR spectra on a 400MHz Bruker AVANCE III spectrometer. Once the NMR data were spectrally processed and analysed using multivariate statistical analysis, seven metabolites were identified as having significant relationships with MN (glucose, trimethylamine, glutamic acid, serine, aspartic acid, 4-aminohippuirc acid and citric acid). Following quantification, glucose was shown to explain the largest percentage variability in MN (72%). These outcomes suggest that sources of labile carbon are essential in regulating N mineralisation and the capacity of plant available N derived from SOM-N pools in these soils. Although, smaller in concentration, the amino acids; 4-aminohippuirc acid, glutamic acid and serine also significantly (P<0.05) explained 43%, 27% and 19% of the variability in MN, respectively. This novel study highlights the effectiveness of using 1H NMR as a practical approach to profile multiple metabolites in soils simultaneously, and increasing the potential to identify those related to various soil processes.

Spectroscopic, thermal analysis and DFT computational studies of salen-type Schiff base complexes.

PubMed

Ebrahimi, Hossein Pasha; Hadi, Jabbar S; Abdulnabi, Zuhair A; Bolandnazar, Zeinab

2014-01-03

A new series of metal(II) complexes of Co(II), Ni(II), Cu(II), Zn(II), and Pb(II) have been synthesized from a salen-type Schiff base ligand derived from o-vanillin and 4-methyl-1,2-phenylenediamine and characterized by elemental analysis, spectral (IR, UV-Vis, (1)H NMR, (13)C NMR and EI-mass), molar conductance measurements and thermal analysis techniques. Coats-Redfern method has been utilized to calculate the kinetic and thermodynamic parameters of the metal complexes. The molecular geometry, Mulliken atomic charges of the studied compounds were investigated theoretically by performing density functional theory (DFT) to access reliable results to the experimental values. The theoretical (13)C chemical shift results of the studied compounds have been calculated at the B3LYP, PBEPBE and PW91PW91 methods and standard 6-311+G(d,p) basis set starting from optimized geometry. The comparison of the results indicates that B3LYP/6-311+G(d,p) yields good agreement with the observed chemical shifts. The measured low molar conductance values in DMF indicate that the metal complexes are non-electrolytes. The spectral and thermal analysis reveals that all complexes have octahedral geometry except Cu(II) complex which can attain the square planner arrangement. The presence of lattice and coordinated water molecules are indicated by thermograms of the complexes. The thermogravimetric (TG/DTG) analyses confirm high stability for all complexes followed by thermal decomposition in different steps. Copyright © 2013 Elsevier B.V. All rights reserved.

NMR Investigations of Structure and Dynamics in Polymers for Energy Storage Applications

NASA Astrophysics Data System (ADS)

Greenbaum, Steven

Materials innovation is needed to realize major progress in energy storage capacity for lithium batteries and capacitors. Polymers hold considerable promise as ion conducting media in batteries and electrochemical capacitors and as dielectrics in thin film capacitors. Structural studies of materials utilized in lithium battery technology are hampered by the lack of long-range order found in well-defined crystalline phases. Powder x-ray diffraction yields structural parameters that have been averaged over hundreds of lattice sites, and is unable to provide structural information about amorphous phases. Our laboratory uses solid state nuclear magnetic resonance (NMR) methods to investigate structural and chemical aspects of lithium ion cathodes, anodes, electrolytes, interfaces and interphases. NMR is element- (nuclear-) specific and sensitive to small variations in the immediate environment of the ions being probed, for example Li+, and in most cases is a reliably quantitative spectroscopy in that the integrated intensity of a particular spectral component is directly proportional to the number of nuclei in the corresponding material phase. NMR is also a powerful tool for probing ionic and molecular motion in lithium battery electrolytes with a dynamic range spanning some ten orders of magnitude through spin-lattice relaxation and self-diffusion measurements. Broadband relaxometry based on Fast Field Cycling NMR (FFCNMR) methods can span three to four of these orders of magnitude in a single set of measurements. Results of several recent NMR investigations performed on our lab will be presented. We explore the ion transport mechanism in polyether-based and lithium polymer electrolytes and those based on other base polymers, in particular, the extent to which ionic motion is coupled to polymer segmental motion. Polycarbonates are being considered as a possible replacement for polypropylene in high power thin film capacitors due to their favorable dielectric properties. We investigate the effects of incorporation of two types of additives in the polymer film on the ring-flip motions corresponding to the γ relaxation: (i) high dielectric constant ceramic particles; (ii) polar organic diluent molecules, The low frequency realm of broadband relaxometry allows meaningful comparison with dielectric relaxation studies of these samples performed by collaborators. Work Supported in part by the U.S. Office of Naval Research.

EASY: a simple tool for simultaneously removing background, deadtime and acoustic ringing in quantitative NMR spectroscopy--part I: basic principle and applications.

PubMed

Jaeger, Christian; Hemmann, Felix

2014-01-01

Elimination of Artifacts in NMR SpectroscopY (EASY) is a simple but very effective tool to remove simultaneously any real NMR probe background signal, any spectral distortions due to deadtime ringdown effects and -specifically- severe acoustic ringing artifacts in NMR spectra of low-gamma nuclei. EASY enables and maintains quantitative NMR (qNMR) as only a single pulse (preferably 90°) is used for data acquisition. After the acquisition of the first scan (it contains the wanted NMR signal and the background/deadtime/ringing artifacts) the same experiment is repeated immediately afterwards before the T1 waiting delay. This second scan contains only the background/deadtime/ringing parts. Hence, the simple difference of both yields clean NMR line shapes free of artefacts. In this Part I various examples for complete (1)H, (11)B, (13)C, (19)F probe background removal due to construction parts of the NMR probes are presented. Furthermore, (25)Mg EASY of Mg(OH)2 is presented and this example shows how extremely strong acoustic ringing can be suppressed (more than a factor of 200) such that phase and baseline correction for spectra acquired with a single pulse is no longer a problem. EASY is also a step towards deadtime-free data acquisition as these effects are also canceled completely. EASY can be combined with any other NMR experiment, including 2D NMR, if baseline distortions are a big problem. © 2013 Published by Elsevier Inc.

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

PubMed

Pupier, Marion; Nuzillard, Jean-Marc; Wist, Julien; Schlörer, Nils E; Kuhn, Stefan; Erdelyi, Mate; Steinbeck, Christoph; Williams, Antony J; Butts, Craig; Claridge, Tim D W; Mikhova, Bozhana; Robien, Wolfgang; Dashti, Hesam; Eghbalnia, Hamid R; Farès, Christophe; Adam, Christian; Kessler, Pavel; Moriaud, Fabrice; Elyashberg, Mikhail; Argyropoulos, Dimitris; Pérez, Manuel; Giraudeau, Patrick; Gil, Roberto R; Trevorrow, Paul; Jeannerat, Damien

2018-04-14

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases. Copyright © 2018 John Wiley & Sons, Ltd.

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

Study on structural and spectral properties of isobavachalcone and 4-hydroxyderricin by computational method

NASA Astrophysics Data System (ADS)

Rong, Yuzhi; Wu, Jinhong; Liu, Xing; Zhao, Bo; Wang, Zhengwu

Isobavachalcone and 4-hydroxyderricin, two major chalcone constituents isolated from the roots of Angelica keiskei KOIDZUMI, exhibit numerous biological activities. Quantum chemical methods have been employed to investigate their structural and spectral properties. The ground state structures were optimized using density functional B3LYP method with 6-311G (d, p) basis set in both gas and solvent phases. Based on the optimized geometries, the harmonic vibrational frequency, the 1H and 13C nuclear magnetic resonance (NMR) chemical shift using the GIAO method were calculated at the same level of theory, with the aim of verifying the experimental values. Results reveal that B3LYP has been a good method to study their vibrational spectroscopic and NMR spectral properties of the two chalcones. The electronic absorption spectra were calculated using the time-dependent density functional theory (TDDFT) method. The solvent polarity effects were considered and calculated using the polarizable continuum model (PCM). Results also show that substitutions of different electron donating groups can alter the absorption properties and shift the spectra to a higher wavelength region.

The influence of sulfur configuration in 1 H NMR chemical shifts of diasteromeric five-membered cyclic sulfites.

PubMed

Obregón-Mendoza, Marco A; Sánchez-Castellanos, Mariano; Cuevas, Gabriel; Gnecco, Dino; Cassani, Julia; Poveda-Jaramillo, Juan C; Reynolds, William F; Enríquez, Raúl G

2017-03-01

The effect of the stereochemistry of the sulfur atom on 1 H chemical shifts of the diasteromeric pair of cyclic sulfites of 4-[methoxy(4-nitrophenyl)methyl]-5-phenyl-1,3,2-dioxathiolan-2-oxide was investigated. The complete 1 H and 13 C NMR spectral assignment was achieved by the use of one-dimensional and two-dimensional NMR techniques in combination with X-ray data. A correlation of experimental data with theoretical calculations of chemical shift tensors using density functional theory and topological theory of atoms in molecules was made. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers.

PubMed

Clos, Lawrence J; Jofre, M Fransisca; Ellinger, James J; Westler, William M; Markley, John L

2013-06-01

To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin ™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.

Automatic 1H-NMR Screening of Fatty Acid Composition in Edible Oils

PubMed Central

Castejón, David; Fricke, Pascal; Cambero, María Isabel; Herrera, Antonio

2016-01-01

In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC). To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual) was determined by 1H-NMR spectroscopy according to this protocol. PMID:26891323

Non-invasive grading of astrocytic tumours from the relative contents of myo-inositol and glycine measured by in vivo MRS.

PubMed

Candiota, A P; Majós, C; Julià-Sapé, M; Cabañas, M; Acebes, J J; Moreno-Torres, A; Griffiths, J R; Arús, C

2011-01-01

MRI and MRS are established methodologies for evaluating intracranial lesions. One MR spectral feature suggested for in vivo grading of astrocytic tumours is the apparent myo-lnositol (ml) intensity (ca 3.55 ppm) at short echo times, although glycine (gly) may also contribute in vivo to this resonance. The purpose of this study was to quantitatively evaluate the ml + gly contribution to the recorded spectral pattern in vivo and correlate it with in vitro data obtained from perchloric acid extraction of tumour biopsies. Patient spectra (n = 95) at 1.5T at short (20-31 ms) and long (135-136 ms) echo times were obtained from the INTERPRET MRS database (http://gabrmn.uab.eslinterpretvalidateddbl). Phantom spectra were acquired with a comparable protocol. Spectra were automatically processed and the ratios of the (ml + gly) to Cr peak heights ((ml + gly)/Cr) calculated. Perchloric acid extracts of brain tumour biopsies were analysed by high-resolution NMR at 9.4T. The ratio (ml + gly)/Cr decreased significantly with astrocytic grade in vivo between low-grade astrocytoma (A2) and glioblastoma multiforme (GBM). In vitro results displayed a somewhat different tendency, with anaplastic astrocytomas having significantly higher (ml + gly)/Cr than A2 and GBM. The discrepancy between in vivo and in vitro data suggests that the NMR visibility of glycine in glial brain tumours is restricted in vivo.

Resolution Improvements in in Vivo1H NMR Spectra with Increased Magnetic Field Strength

NASA Astrophysics Data System (ADS)

Gruetter, Rolf; Weisdorf, Sally A.; Rajanayagan, Vasantham; Terpstra, Melissa; Merkle, Hellmut; Truwit, Charles L.; Garwood, Michael; Nyberg, Scott L.; Ugurbil, Kâmil

1998-11-01

The measurement of cerebral metabolites using highly homologous localization techniques and similar shimming methods was performed in the human brain at 1.5 and 4 T as well as in the dog and rat brain at 9.4 T. In rat brain, improved resolution was achieved by shimming all first- and second-order shim coils using a fully adiabatic FASTMAP sequence. The spectra showed a clear improvement in spectral resolution for all metabolite resonances with increased field strength. Changes in cerebral glutamine content were clearly observed at 4 T compared to 1.5 T in patients with hepatic encephalopathy. At 9.4 T, glutamine H4 at 2.46 ppm was fully resolved from glutamate H4 at 2.37 ppm, as was the potential resonance from γ-amino-butyric acid at 2.30 ppm and N-acetyl-aspartyl-glutamate at 2.05 ppm. Singlet linewidths were found to be as low as 6 Hz (0.015 ppm) at 9.4 T, indicating a substantial decrease in ppm linewidth with field strength. Furthermore, the methylene peak of creatine was partially resolved from phosphocreatine, indicating a close to 1:1 relationship in gray matter. We conclude that increasing the magnetic field strength increases spectral resolution also for1H NMR, which can lead to more than linear sensitivity gains.

Photophysical Behavior and Computational Investigation of Novel 1,4-Bis(2-(2-Phenylpyrimido[1,2-a]Benzimidazol-4-Yl)Phenoxy)Butan (BPPB) Macromolecule.

PubMed

Saleh, Tamer S; Hussein, Mahmoud A; Osman, Osman I; Alamry, Khalid A; Mekky, Ahmed E M; Asiri, Abdullah M; El-Daly, Samy A

2016-09-01

A new macromolecule pyrimido[l,2-a]benzimidazole derivative named 1,4-bis(2-(2-phenylpyrimido[1,2-a]benzimidazol-4-yl)phenoxy)butan (BPPB) has been synthesized in accepted yield using microwave assistance. The new compound BPPB has been formed by the interaction of 3,3'-((butane-1,4-diylbis(oxy))bis(2,1-phenylene))bis(1-phenylprop-2-en-1-one) (3) with 2- aminobenzimidazole (4) in the presence of potassium hydroxide as a basic catalyst in dimethylformamide (DMF) under microwave radiation for 20 min. The chemical structure of this novel compound was elucidated by elemental and spectral techniques including: FT-IR, (1)H-NMR, (13)C-NMR and mass spectra. The electronic absorption and emission spectra of BPPB were measured in different solvents. BPPB displayed a solvatochromic effect of the emission spectrum that is reflected by red shifts of its fluorescence emission maxima on increasing the solvent polarity, indicating a change of electronic charge distribution upon excitation. BPPB crystalline solids gave excimer-like emission at 535 nm with a bandwidth of ca. 60 nm. Ground and excited states electronic geometry optimizations using density functional theory (DFT) and time-dependent density functional theory (TD-DFT), respectively, complemented these spectral findings. The intramolecular charge transfer was investigated by natural bond orbital (NBO) technique.

A new rearranged dolabellane diterpene from the soft coral Clavularia inflata.

PubMed

Alea, Glenn V; Bowden, Bruce F; Ragasa, Consolacion Y

2008-06-15

A new dolabellane type diterpene 1 has been isolated through its acetate 1a. The structure of 1a was elucidated by extensive 1D and 2D NMR spectroscopy and confirmed by mass spectrometry. The structure of 1 was deduced by comparison of its NMR spectral data with those of 1a, while its relative stereochemistry was deduced by NOESY. The absolute stereochemistry of C-7 was determined by analyses of 1 separately esterified with R and S O-mandelic acids.

The photolysis of NH3 in the presence of substituted acetylenes - A possible source of oligomers and HCN on Jupiter

NASA Technical Reports Server (NTRS)

Ferris, James P.; Jacobson, Richard R.; Guillemin, Jean C.

1992-01-01

An NMR spectral study is presently conducted of NH3 photolysis in the presence of substituted acetylenes with NMR spectra and gas chromatography. Quantum yields and percentage conversions to products are reported. It is shown that acetylenic hydrocarbons generated during methane photolysis in Jupiter's stratosphere can react with radicals formed by NH3 photolysis to yield nonvolatile, yellow-brown polymers, alkylnitriles, and in due course, HCN, as observed on Jupiter.

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.

PubMed

Jayaseelan, Kalai Vanii; Steinbeck, Christoph

2014-07-05

In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structural identities of unknown compounds. It is generally accepted that a single 1D NMR spectrum or mass spectrum is usually not sufficient to establish the identity of a hitherto unknown compound. When a suite of spectra from 1D and 2D NMR experiments supplemented with a molecular formula are available, the successful elucidation of the chemical structure for candidates with up to 30 heavy atoms has been reported previously by one of the authors. In high-throughput metabolomics, usually 1D NMR or mass spectrometry experiments alone are conducted for rapid analysis of samples. This method subsequently requires that the spectral patterns are analyzed automatically to quickly identify known and unknown structures. In this study, we investigated whether additional existing knowledge, such as the fact that the unknown compound is a natural product, can be used to improve the ranking of the correct structure in the result list after the structure elucidation process. To identify unknowns using as little spectroscopic information as possible, we implemented an evolutionary algorithm-based CASE mechanism to elucidate candidates in a fully automated fashion, with input of the molecular formula and 13C NMR spectrum of the isolated compound. We also tested how filters like natural product-likeness, a measure that calculates the similarity of the compounds to known natural product space, might enhance the performance and quality of the structure elucidation. The evolutionary algorithm is implemented within the SENECA package for CASE reported previously, and is available for free download under artistic license at http://sourceforge.net/projects/seneca/. The natural product-likeness calculator is incorporated as a plugin within SENECA and is available as a GUI client and command-line executable. Significant improvements in candidate ranking were demonstrated for 41 small test molecules when the CASE system was supplemented by a natural product-likeness filter. In spectroscopically underdetermined structure elucidation problems, natural product-likeness can contribute to a better ranking of the correct structure in the results list.

Detecting gas hydrate behavior in crude oil using NMR.

PubMed

Gao, Shuqiang; House, Waylon; Chapman, Walter G

2006-04-06

Because of the associated experimental difficulties, natural gas hydrate behavior in black oil is poorly understood despite its grave importance in deep-water flow assurance. Since the hydrate cannot be visually observed in black oil, traditional methods often rely on gas pressure changes to monitor hydrate formation and dissociation. Because gases have to diffuse through the liquid phase for hydrate behavior to create pressure responses, the complication of gas mass transfer is involved and hydrate behavior is only indirectly observed. This pressure monitoring technique encounters difficulties when the oil phase is too viscous, the amount of water is too small, or the gas phase is absent. In this work we employ proton nuclear magnetic resonance (NMR) spectroscopy to observe directly the liquid-to-solid conversion of the water component in black oil emulsions. The technique relies on two facts. The first, well-known, is that water becomes essentially invisible to liquid state NMR as it becomes immobile, as in hydrate or ice formation. The second, our recent finding, is that in high magnetic fields of sufficient homogeneity, it is possible to distinguish water from black oil spectrally by their chemical shifts. By following changes in the area of the water peak, the process of hydrate conversion can be measured, and, at lower temperatures, the formation of ice. Taking only seconds to accomplish, this measurement is nearly direct in contrast to conventional techniques that measure the pressure changes of the whole system and assume these changes represent formation or dissociation of hydrates - rather than simply changes in solubility. This new technique clearly can provide accurate hydrate thermodynamic data in black oils. Because the technique measures the total mobile water with rapidity, extensions should prove valuable in studying the dynamics of phase transitions in emulsions.

Multi-objective optimization for an automated and simultaneous phase and baseline correction of NMR spectral data

NASA Astrophysics Data System (ADS)

Sawall, Mathias; von Harbou, Erik; Moog, Annekathrin; Behrens, Richard; Schröder, Henning; Simoneau, Joël; Steimers, Ellen; Neymeyr, Klaus

2018-04-01

Spectral data preprocessing is an integral and sometimes inevitable part of chemometric analyses. For Nuclear Magnetic Resonance (NMR) spectra a possible first preprocessing step is a phase correction which is applied to the Fourier transformed free induction decay (FID) signal. This preprocessing step can be followed by a separate baseline correction step. Especially if series of high-resolution spectra are considered, then automated and computationally fast preprocessing routines are desirable. A new method is suggested that applies the phase and the baseline corrections simultaneously in an automated form without manual input, which distinguishes this work from other approaches. The underlying multi-objective optimization or Pareto optimization provides improved results compared to consecutively applied correction steps. The optimization process uses an objective function which applies strong penalty constraints and weaker regularization conditions. The new method includes an approach for the detection of zero baseline regions. The baseline correction uses a modified Whittaker smoother. The functionality of the new method is demonstrated for experimental NMR spectra. The results are verified against gravimetric data. The method is compared to alternative preprocessing tools. Additionally, the simultaneous correction method is compared to a consecutive application of the two correction steps.

Norcyanine dyes with benzo[c,d]indolium moiety: Spectral sensitivity with pH change for fluorescence pH imaging in living cells.

PubMed

Guan, Li; Liu, Qi; Zhang, Borui; Wang, Lanying

2017-01-01

Fluorescence pH imaging in living cells is a rapidly expanding research direction, however, it relies on the development of pH-sensitive fluorescent imaging agents. Here four norcyanine dyes with benzo[c,d]indolium moiety, exhibiting high spectral sensitivity with pH changes, were synthesized for fluorescence pH imaging in living cells, and characterized by 1 H NMR, 13 C NMR, IR, UV-Vis and HRMS. The investigation of their spectral properties in methanol and water showed that the absorption and emission maxima were in the region 488-618nm and 583-651nm, respectively, and four dyes exhibited high photostability. The pH spectral titrations showed that selective dye D1 had pH-dependent absorption spectral changes within the pH range of 2.4 to 9.4, and high fluorescent spectral sensitivity at pH5.0-8.0, with a pK a of 5.0. A cell association study indicated that dye D1 exhibited no or mild cytotoxicity at the application dose and duration, and could be accumulated in cells and mainly distributed in the cytoplasm, giving red fluorescence imaging. In particular, dye D1 could achieve pH-dependent fluorescence imaging in living cells with the increase of pH from 3.0 to 8.0, at excitation wavelength of 543nm and receiving wavelength of 655-755nm, which was valuable for studying the weak acidic, neutral and weak alkaline biological tissue compartments. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2007-12-01

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

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

Gamma-, sigma- and theta-Al2O3 are well known metastable “transitional” alumina structural polymorphs. Upon heating, Al2O3 transitions to the so-called and Al2O3 polymorphs and finally forms the thermally stable Al2O3. The poorly developed crystallinity and co-existence of the , , and Al2O3 prior to forming all Al2O3, making it difficult to characterize the structures as well as to quantify the various phases of the transition alumina. As a result, there are significant controversies in the literatures. In this work, a detailed NMR analysis was carried out at high magnetic field on three special aluminum oxide samples where the, , , Al2O3more » phases are made dominant, respectively, by controlling the synthesis conditions. The goal is to simplify, including making unambiguous, spectral assignments in 27Al MAS NMR spectra of transition alumina that have not yet been commonly agreed previously. Specifically, quantitative 1D 27Al MAS NMR was used to quantify the ratios of the different alumina structural units, 2D MQMAS 27Al MAS was used for obtaining the highest spectral resolution to guide the analysis of the 1D spectrum, and a saturation pulse sequence was integrated into the 1D NMR to select the amorphous structures, including obtain spectra where the penta-coordinate sites are observed with enhanced relative intensity. Collectively, this study uniquely assigns Al-peaks (both octahedral and tetrahedral) to the Al2O3 and the Al2O3 phases and offers a new way of understanding, including quantifying, the different structural units and sites in transition alumina samples.« less

Peptidoglycan and Teichoic Acid Levels and Alterations in Staphylococcus aureus by Cell-Wall and Whole-Cell Nuclear Magnetic Resonance.

PubMed

Romaniuk, Joseph A H; Cegelski, Lynette

2018-06-11

Gram-positive bacteria surround themselves with a multilayered macromolecular cell wall that is essential to cell survival and serves as a major target for antibiotics. The cell wall of Staphylococcus aureus is composed of two major structural components, peptidoglycan (PG) and wall teichoic acid (WTA), together creating a heterogeneous and insoluble matrix that poses a challenge to quantitative compositional analysis. Here, we present 13 C cross polarization magic angle spinning solid-state nuclear magnetic resonance (NMR) spectra of intact cell walls, purified PG, and purified WTA. The spectra reveal the clear molecular differences in the two polymers and enable quantification of PG and WTA in isolated cell walls, an attractive alternative to estimating teichoic acid content from a phosphate analysis of completely pyrolyzed cell walls. Furthermore, we discovered that unique PG and WTA spectral signatures could be identified in whole-cell NMR spectra and used to compare PG and WTA levels among intact bacterial cell samples. The distinguishing whole-cell 13 C NMR contributions associated with PG include the GlcNAc-MurNAc sugar carbons and glycyl α-carbons. WTA contributes carbons from the phosphoribitol backbone. Distinguishing 15 N spectral signatures include glycyl amide nitrogens in PG and the esterified d-alanyl amine nitrogens in WTA. 13 C NMR analysis was performed with samples at natural abundance and included 10 whole-cell sample comparisons. Changes consistent with altered PG and WTA content were detected in whole-cell spectra of bacteria harvested at different growth times and in cells treated with tunicamycin. This use of whole-cell NMR provides quantitative parameters of composition in the context of whole-cell activity.

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.

Quantum-mechanical calculations of magnesium aspartate arginine structure and spectroscopic characteristics

NASA Astrophysics Data System (ADS)

Marcoin, W.; Pasterny, K.; Wrzalik, R.

2005-05-01

Theoretical calculations of magnesium aspartate-arginine (Mg[Asp-Arg]) structure and spectroscopic characteristics have been performed in the gas phase with the GAUSSIAN 98 software package using density functional theory (DFT) at the B3PW91 level. The 6-31+G* basis set was selected due to their reasonable quality and size. The comparison with corresponding results for magnesium aspartate-glycine (Mg[Asp-Gly]) is presented. NMR and IR measurements were carried out and obtained experimental 1H and 13C chemical shifts and IR spectra are compared with calculated spectral parameters.

Precise and rapid isotopomic analysis by (1)H-(13)C 2D NMR: Application to triacylglycerol matrices.

PubMed

Merchak, Noelle; Silvestre, Virginie; Rouger, Laetitia; Giraudeau, Patrick; Rizk, Toufic; Bejjani, Joseph; Akoka, Serge

2016-08-15

An optimized HSQC sequence was tested and applied to triacylglycerol matrices to determine their isotopic and metabolomic profiles. Spectral aliasing and non-uniform sampling approaches were used to decrease the experimental time and to improve the resolution, respectively. An excellent long-term repeatability of signal integrals was achieved enabling to perform isotopic measurements. Thirty-two commercial vegetable oils were analyzed by this methodology. The results show that this method can be used to classify oil samples according to their geographical and botanical origins. Copyright © 2016 Elsevier B.V. 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.

(13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens.

PubMed

Veeraprakash, B; Lobo, Nitin P; Narasimhaswamy, T

2015-12-03

Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate.

Ultra-low field nuclear magnetic resonance and magnetic resonance imaging to discriminate and identify materials

DOEpatents

Matlashov, Andrei Nikolaevich; Urbaitis, Algis V.; Savukov, Igor Mykhaylovich; Espy, Michelle A.; Volegov, Petr Lvovich; Kraus, Jr., Robert Henry

2013-03-05

Method comprising obtaining an NMR measurement from a sample wherein an ultra-low field NMR system probes the sample and produces the NMR measurement and wherein a sampling temperature, prepolarizing field, and measurement field are known; detecting the NMR measurement by means of inductive coils; analyzing the NMR measurement to obtain at least one measurement feature wherein the measurement feature comprises T1, T2, T1.rho., or the frequency dependence thereof; and, searching for the at least one measurement feature within a database comprising NMR reference data for at least one material to determine if the sample comprises a material of interest.

Molecular structure and spectroscopic investigation of sodium(E)-2-hydroxy-5-((4-sulfonatophenyl)diazenyl)benzoate: A DFT study

NASA Astrophysics Data System (ADS)

Shahab, Siyamak; Kumar, Rakesh; Darroudi, Mahdieh; Yousefzadeh Borzehandani, Mostafa

2015-03-01

Quantum-chemical calculations using the Density Functional Theory (DFT) approach for structural analysis of new azodye sodium(E)-2-hydroxy-5-((4-sulfonatophenyl)diazenyl) (trans isomer) is carried out using B3LYP methods with 6-31G∗ basis set. The comparison of measured UV-Vis data, IR and NMR spectra of the molecule with the experimental data were also described which allowed assignment of major spectral features of title molecule. The optimized geometrical parameters obtained by B3LYP methods show a good agreement with experimental data. On the basis of polyvinyl alcohol (PVA) and the dichroic synthesized dye polarizer absorbing in the UV region of the spectrum (λmax = 353 nm) with the effect of polarization in the absorption maximum 96% was developed. The spectral-polarization parameters of stretched PVA-films were calculated.

DNA binding, anti-inflammatory and analgesic evaluation of metal complexes of N/S/O donor ligands; Synthesis, spectral characterization

NASA Astrophysics Data System (ADS)

Kumar Naik, K. H.; Ashok, B.; Naik, Nagaraja; Mulla, Jameel Ahmed S.; Prakasha, Avinash

2015-04-01

Transition metal complexes containing tri-dentate NSN donor ligands i.e., 5-((1(aminomethyl)cyclohexyl)methyl)-1,3,4-thiadiazol-2-amine (AMTA) (2) and 5-(2-aminophenyl)-1,3,4-thiadiazol-2-amine (ATA) (4i-ii) have been synthesized. The newly synthesized ligands and their respective complexes were characterized by elemental analysis, molar conductance measurement and various spectral studies [infrared (IR), electronic, and NMR (for ligands only)]. Metal complexes are like [M(AMTA)2], [M(ATA)2] type, where M = Mn(II), Co(II) and Cu(II). The proposed geometries of the complexes are octahedral in nature. The synthesized ligands and their complexes were exhibits effective anti-inflammatory, analgesic and DNA binding activities. All the tested compounds exhibited significant analgesic activity, whereas the compound 4i, 4(ia) and 4(iib) is equipotent with Diclofenac sodium.

New mixed ligand palladium(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands: Synthesis, structural characterization, binding interactions with DNA and BSA, in vitro cytotoxicity studies and DFT calculations

NASA Astrophysics Data System (ADS)

Tabrizi, Leila; Chiniforoshan, Hossein; Tavakol, Hossein

2015-04-01

The complexes [Pd(valp)2(imidazole)2] (1), [Pd(valp)2(pyrazine)2] (2) (valp is sodium valproate) have been synthesized and characterized using IR, 1H NMR, 13C{1H} NMR and UV-Vis spectrometry. The interaction of complexes with CT-DNA has been investigated using spectroscopic tools and viscosity measurement. In each case, the association constant (Kb) was deduced from the absorption spectral study and the number of binding sites (n) and the binding constant (K) were calculated from relevant fluorescence quenching data. As a result, a non-covalent interaction between the metal complex and DNA was suggested, which could be assigned to an intercalative binding. In addition, the interaction of 1 and 2 was ventured with bovine serum albumin (BSA) with the help of absorption and fluorescence spectroscopy measurements. Through these techniques, the apparent association constant (Kapp) and the binding constant (K) could be calculated for each complex. Evaluation of cytotoxic activity of the complexes against four different cancer cell lines proved that the complexes exhibited cytotoxic specificity and significant cancer cell inhibitory rate. Moreover, density functional theory (DFT) calculations were employed to provide more evidence about the observed data. The majority of trans isomers were supported not only by energies, but also by the similarity of its calculated IR frequencies, UV adsorptions and NMR chemical shifts to the experimental values.

Antifungal activity and isomerization of octadecyl p-coumarates from Ipomoea carnea subsp. fistulosa.

PubMed

Nidiry, Eugene Sebastian J; Ganeshan, Girija; Lokesha, Ankanahalli N

2011-12-01

Bioassay monitored HPLC assisted isolation and purification of the chief antifungal fraction of the leaves of Ipomoea carnea subsp. fistulosa (Convulvulaceae) were achieved using Colletotrichum gloeosporioides and Cladosporium cucumerinum as test organisms. The activity of the purified fraction was further confirmed by the dose dependent inhibition of the spore germination of Alternaria alternata and A. porri. The active fraction was identified as a mixture of (E)-octadecyl p-coumarate and (Z)-octadecyl p-coumarate. The two isomers were detected on an HPLC column with substantially different retention times, but once eluted from the column, one form was partly converted to the other in daylight. Conclusive evidence for the structures and their isomerization were obtained from the HPLC behavior, IR, UV, HRESIMS, CIMS and and NMR spectral data. Important 1H NMR and 13C NMR signals could be separately assigned for the isomers using 2D NMR techniques.

Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies.

PubMed

Fasshuber, Hannes Klaus; Demers, Jean-Philippe; Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

2015-03-01

Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively (13)C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved. Copyright © 2015 Elsevier Inc. All rights reserved.

Monovacancy paramagnetism in neutron-irradiated graphite probed by ¹³C NMR.

PubMed

Zhang, Zhi Tao; Xu, C; Dmytriieva, Daryna; Molatta, Sebastian; Wosnitza, J; Wang, Y T; Helm, Manfred; Zhou, Shengqiang; Kuehne, Hannes

2017-09-18

We report on the magnetic properties of monovacancy defects in neutron-irradiated graphite, probed by $^{13}$C nuclear magnetic resonance spectroscopy. The bulk paramagnetism of the defect moments is revealed by the temperature dependence of the NMR frequency shift and spectral linewidth, both of which follow a Curie behavior, in agreement with measurements of the macroscopic magnetization. Compared to pristine graphite, the fluctuating hyperfine fields generated by the defect moments lead to an enhancement of the $^{13}$C nuclear spin-lattice relaxation rate $1/T_{1}$ by about two orders of magnitude. With an applied magnetic field of 7.1 T, the temperature dependence of $1/T_{1}$ below about 10 K can well be described by a thermally activated form, $1/T_{1}\\propto\\exp(-\\Delta/k_{B}T)$, yielding a singular Zeeman energy of ($0.41\\pm0.01$) meV, in excellent agreement with the sole presence of polarized, non-interacting defect moments. © 2017 IOP Publishing Ltd.

Spectral, optical and cytotoxicity studies on 2-isonicotinoyl-N-phenylhydrazine-1-carboxamide(H3L) and some of its metal complexes

NASA Astrophysics Data System (ADS)

Hosny, Nasser M.; Hassan, Nader Y.; Mahmoud, Heba M.; Abdel-Rhman, Mohamed H.

2018-03-01

The ligand 2-isonicotinoyl-N-phenylhydrazine-1-carboxamide (H3L) and its metal complexes with Co(II), Ni(II), Cu(II) and Zn(II) acetates have been synthesized. The isolated compounds have been characterized by elemental analyses, FT-IR, 1H NMR, 13C NMR, ESR, mass, electronic spectra, electrical conductivity, effective magnetic moments and thermal analyses. The free organic ligand exists in the keto form, but in the metal complexes, it coordinates in the enol form. Four coordinated species were suggested for all the isolated metal complexes. The measured optical band gap values confirmed the presence of direct electronic transition and the semi-conductivity of the compounds. The ligand and its Zn(II) complex were examined as cytotoxic agent against HCT-116 and HePG-2. The ligand showed very strong cytotoxic effect against HePG-2, but moderate cytotoxicity against HCT-116. Zn(II) complex showed weak cytotoxicity against the two cell lines.

New 15-membered tetraaza (N4) macrocyclic ligand and its transition metal complexes: Spectral, magnetic, thermal and anticancer activity

NASA Astrophysics Data System (ADS)

El-Boraey, Hanaa A.; EL-Gammal, Ohyla A.

2015-03-01

Novel tetraamidemacrocyclic 15-membered ligand [L] i.e. naphthyl-dibenzo[1,5,9,12]tetraazacyclopentadecine-6,10,11,15-tetraoneand its transition metal complexes with Fe(II), Co(II), Ni(II), Cu(II), Ru(III) and Pd(II) have been synthesized and characterized by elemental analysis, spectral, thermal as well as magnetic and molar conductivity measurements. On the basis of analytical, spectral (IR, MS, UV-Vis, 1H NMR and EPR) and thermal studies distorted octahedral or square planar geometry has been proposed for the complexes. The antitumor activity of the synthesized ligand and some complexes against human breast cancer cell lines (MCF-7) and human hepatocarcinoma cell lines (HepG2) has been studied. The complexes (IC50 = 2.27-2.7, 8.33-31.1 μg/mL, respectively) showed potent antitumor activity, towards the former cell lines comparable with their ligand (IC50 = 13, 26 μg/mL, respectively). The results show that the activity of the ligand towards breast cancer cell line becomes more pronounced and significant when coordinated to the metal ion.

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/.

The Spectral Game: leveraging Open Data and crowdsourcing for education

PubMed Central

2009-01-01

We report on the implementation of the Spectral Game, a web-based game where players try to match molecules to various forms of interactive spectra including 1D/2D NMR, Mass Spectrometry and Infrared spectra. Each correct selection earns the player one point and play continues until the player supplies an incorrect answer. The game is usually played using a web browser interface, although a version has been developed in the virtual 3D environment of Second Life. Spectra uploaded as Open Data to ChemSpider in JCAMP-DX format are used for the problem sets together with structures extracted from the website. The spectra are displayed using JSpecView, an Open Source spectrum viewing applet which affords zooming and integration. The application of the game to the teaching of proton NMR spectroscopy in an undergraduate organic chemistry class and a 2D Spectrum Viewer are also presented. PMID:20298527

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.

Synthesis, Characterization and Antifertility Activity of New Unsymmetrical Macrocyclic Complexes of Tin(II)

PubMed Central

Sharma, Kripa; Joshi, S. C.

2000-01-01

A new series of unsymmetrical macrocyclic complexes of tin(ll) has been prepared by the template process using bis(3-oxo-2-butylidene)propane-1,3-diamine as precursor. This affords a method to synthesize these complexes with various ring sizes. The tetradentate macrocyclic precursor [N4mL] reacts with SnCl2 and different diamines in a 1:1:1 molar ratio in refluxing methanol to give complexes of the type [Sn(N4mL)Cl2]. The ring expansion has been achieved by varying the diamine between the two diacetyl amino nitrogen atoms. The macrocyclic precursor and its metal complexes have been characterized on the basis of elemental analysis, molar conductance, molecular weight determinations, IR, 1H NMR,13C NMR, 119Sn NMR and electronic spectral studies. An octahedral geometry around the metal ion is suggested for these complexes. On the basis of molecular weights and conductivity measurements, their monomeric and non-electrolytic nature has been confirmed. The precursor and complexes have been screened in vitro against a number of pathogenic fungi and bacteria to assess their growth inhibiting potential. The testicular sperm density and testicular sperm morphology, sperm motility, density of cauda epididymal spermatozoa and fertility in mating trails and biochemicals parameters of reproductive organs have been examined and discussed. PMID:18475951

Lithium ion dynamics in Li2S+GeS2+GeO2 glasses studied using (7)Li NMR field-cycling relaxometry and line-shape analysis.

PubMed

Gabriel, Jan; Petrov, Oleg V; Kim, Youngsik; Martin, Steve W; Vogel, Michael

2015-09-01

We use (7)Li NMR to study the ionic jump motion in ternary 0.5Li2S+0.5[(1-x)GeS2+xGeO2] glassy lithium ion conductors. Exploring the "mixed glass former effect" in this system led to the assumption of a homogeneous and random variation of diffusion barriers in this system. We exploit that combining traditional line-shape analysis with novel field-cycling relaxometry, it is possible to measure the spectral density of the ionic jump motion in broad frequency and temperature ranges and, thus, to determine the distribution of activation energies. Two models are employed to parameterize the (7)Li NMR data, namely, the multi-exponential autocorrelation function model and the power-law waiting times model. Careful evaluation of both of these models indicates a broadly inhomogeneous energy landscape for both the single (x=0.0) and the mixed (x=0.1) network former glasses. The multi-exponential autocorrelation function model can be well described by a Gaussian distribution of activation barriers. Applicability of the methods used and their sensitivity to microscopic details of ionic motion are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Spectral analysis, vibrational assignments, NBO analysis, NMR, UV-Vis, hyperpolarizability analysis of 2-aminofluorene by density functional theory.

PubMed

Jone Pradeepa, S; Sundaraganesan, N

2014-05-05

In this present investigation, the collective experimental and theoretical study on molecular structure, vibrational analysis and NBO analysis has been reported for 2-aminofluorene. FT-IR spectrum was recorded in the range 4000-400 cm(-1). FT-Raman spectrum was recorded in the range 4000-50 cm(-1). The molecular geometry, vibrational spectra, and natural bond orbital analysis (NBO) were calculated for 2-aminofluorene using Density Functional Theory (DFT) based on B3LYP/6-31G(d,p) model chemistry. (13)C and (1)H NMR chemical shifts of 2-aminofluorene were calculated using GIAO method. The computed vibrational and NMR spectra were compared with the experimental results. The total energy distribution (TED) was derived to deepen the understanding of different modes of vibrations contributed by respective wavenumber. The experimental UV-Vis spectra was recorded in the region of 400-200 nm and correlated with simulated spectra by suitably solvated B3LYP/6-31G(d,p) model. The HOMO-LUMO energies were measured with time dependent DFT approach. The nonlinearity of the title compound was confirmed by hyperpolarizabilty examination. Using theoretical calculation Molecular Electrostatic Potential (MEP) was investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

Total NMR assignments of new [C7-O-C7'']-biflavones from leaves of the limonene-carvone chemotype of Lippia alba (Mill) N. E. Brown.

PubMed

Barbosa, Francisco Geraldo; Lima, Mary Anne Sousa; Silveira, Edilberto Rocha

2005-04-01

Phytochemical analysis of leaves of the limonene-carvone chemotype of Lippia alba led to the isolation of two biflavonoids with a new structural pattern with an ether linkage: 5,5''-dihydroxy-6,4',6'',3''',4'''-pentamethoxy-[C(7)--O--C(7'')]-biflavone (1) and 4',4,5,5''-tetrahydroxy-6,6'',3'''-trimethoxy-[C(7)--O--C(7'')]-biflavone (2). Structural elucidation of the new compounds was established on the basis of spectral data, through the use of 1D NMR and several 2D shift correlated NMR pulse sequences (COSY, HMQC, HMBC and NOESY). Copyright (c) 2005 John Wiley & Sons, Ltd

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.

Development of a superconducting bulk magnet for NMR and MRI.

PubMed

Nakamura, Takashi; Tamada, Daiki; Yanagi, Yousuke; Itoh, Yoshitaka; Nemoto, Takahiro; Utumi, Hiroaki; Kose, Katsumi

2015-10-01

A superconducting bulk magnet composed of six vertically stacked annular single-domain c-axis-oriented Eu-Ba-Cu-O crystals was energized to 4.74 T using a conventional superconducting magnet for high-resolution NMR spectroscopy. Shim coils, gradient coils, and radio frequency coils for high resolution NMR and MRI were installed in the 23 mm-diameter room-temperature bore of the bulk magnet. A 6.9 ppm peak-to-peak homogeneous region suitable for MRI was achieved in the central cylindrical region (6.2 mm diameter, 9.1 mm length) of the bulk magnet by using a single layer shim coil. A 21 Hz spectral resolution that can be used for high resolution NMR spectroscopy was obtained in the central cylindrical region (1.3 mm diameter, 4 mm length) of the bulk magnet by using a multichannel shim coil. A clear 3D MR image dataset of a chemically fixed mouse fetus with (50 μm)(3) voxel resolution was obtained in 5.5 h. We therefore concluded that the cryogen-free superconducting bulk magnet developed in this study is useful for high-resolution desktop NMR, MRI and mobile NMR device. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Quantitative analysis of sitagliptin using the (19)F-NMR method: a universal technique for fluorinated compound detection.

PubMed

Zhang, Fen-Fen; Jiang, Meng-Hong; Sun, Lin-Lin; Zheng, Feng; Dong, Lei; Shah, Vishva; Shen, Wen-Bin; Ding, Ya

2015-01-07

To expand the application scope of nuclear magnetic resonance (NMR) technology in quantitative analysis of pharmaceutical ingredients, (19)F nuclear magnetic resonance ((19)F-NMR) spectroscopy has been employed as a simple, rapid, and reproducible approach for the detection of a fluorine-containing model drug, sitagliptin phosphate monohydrate (STG). ciprofloxacin (Cipro) has been used as the internal standard (IS). Influential factors, including the relaxation delay time (d1) and pulse angle, impacting the accuracy and precision of spectral data are systematically optimized. Method validation has been carried out in terms of precision and intermediate precision, linearity, limit of detection (LOD) and limit of quantification (LOQ), robustness, and stability. To validate the reliability and feasibility of the (19)F-NMR technology in quantitative analysis of pharmaceutical analytes, the assay result has been compared with that of (1)H-NMR. The statistical F-test and student t-test at 95% confidence level indicate that there is no significant difference between these two methods. Due to the advantages of (19)F-NMR, such as higher resolution and suitability for biological samples, it can be used as a universal technology for the quantitative analysis of other fluorine-containing pharmaceuticals and analytes.

Further refinement of 17O TRAPDOR NMR methods for determining oxygen speciation in multi-component oxide glasses

NASA Astrophysics Data System (ADS)

LaComb, M.; Stebbins, J. F.

2017-12-01

Solid state nuclear magnetic resonance (NMR) spectroscopy has often been utilized to determine network speciation in oxide glasses, typically using NMR-active nuclides such as 11B, 27Al and 17O. High field strength magnets allow for visible separation between bridging (BO) and non-bridging oxygens (NBO) in 17O magic-angle spinning (MAS) NMR spectra, but many questions remain due to limited ability to directly observe NBO associated with silicon, boron or aluminum in ternary glass systems with MAS NMR techniques. Recent studies have utilized the combination of 17O{27Al} and 17O{11B} TRAnsfer of Population in DOuble-Resonance (TRAPDOR) NMR to attempt to separate out resonances for these different bridging and non-bridging oxygen species in multicomponent calcium aluminosilicate and aluminoborosilicate glasses and rare-earth aluminoborosilicates. With improved technology and better resolution of spectral components we were able to expand this study to a wider range of calcium aluminosilicate, aluminoborate and aluminoborosilicate glasses and further separate out resonances for both bridging and non-bridging oxygens coordinated with aluminum, boron and/or silicon cations in these glasses.

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.

PubMed

Beirnaert, Charlie; Meysman, Pieter; Vu, Trung Nghia; Hermans, Nina; Apers, Sandra; Pieters, Luc; Covaci, Adrian; Laukens, Kris

2018-03-01

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq).

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

PubMed Central

Pieters, Luc; Covaci, Adrian

2018-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq). PMID:29494588

Ligational behavior of clioquinol antifungal drug towards Ag(I), Hg(II), Cr(III) and Fe(III) metal ions: Synthesis, spectroscopic, thermal, morphological and antimicrobial studies

NASA Astrophysics Data System (ADS)

El-Megharbel, Samy M.; Refat, Moamen S.

2015-04-01

This article presents a synthesis, characterization, theoretical and biological (anti-bacterial, and anti-fugal) evaluation studies of Ag(I), Hg(II), Cr(III) and Fe(III) complexes of clioquinol (CQ) drug ligand. Structures of the titled complexes cited herein were discussed using elemental analyses and spectral measurements e.g., IR, 1H NMR, and electronic studies. The results confirmed the formation of the clioquinol complexes by three molar ratios (1:1) for Ag(I), (1:2) for Hg(II) and (1:3) for both Cr(III) and Fe(III) metal ions. The clioquinol reacts as a bidentate chelate bound to all respected metal ions through the oxygen and nitrogen of quinoline-8-ol. The metal(II) ions coordinated to clioquinol ligand through deprotonation of sbnd OH terminal group. Infrared and 1H NMR spectral data confirm that coordination is via the oxygen of phenolic group and nitrogen atom of quinoline moiety. The molar conductance measurements of the CQ complexes in DMSO correspond to be non-electrolyte nature. Thus, these complexes may be formulated as [Ag(CQ)(H2O)2] H2O, [Hg(CQ)2]ṡ2H2O, [Cr(CQ)3] and [Fe(CQ)3]H2O. The Coats-Redfern method, the kinetic thermodynamic parameters like activation energies (E∗), entropies (ΔS∗), enthalpies (ΔH∗), and Gibbs free energies (ΔG∗) of the thermal decomposition reactions have been deduced from thermogravimetric curves (TG) with helpful of differential thermo gravimetric (DTG) curves. The narrow size distribution in nano-scale range for the clioquinol complexes have been discussed using X-ray powder diffraction (XRD), scanning electron microscope (SEM), and X-ray energy dispersive spectrometer (EDX) analyzer.

FTIR, magnetic, 1H NMR spectral and thermal studies of some chelates of caproic acid: inhibitory effect on different kinds of bacteria.

PubMed

Refat, Moamen S; El-Korashy, Sabry A; Kumar, Deo Nandan; Ahmed, Ahmed S

2008-06-01

A convenient method for the preparation of complexes of the Cr3+, Mn2+, Fe3+, Co2+, Ni2+, Zn2+, ZrO2+, UO2(2+), Zr4+ and Th4+ ions with caproic acid (Hcap) is reported and this has enabled 10 complexes of caproate anion to be formulated: [Cr(cap)3].5H2O, [Mn(cap)2(H2O)2], [Fe(cap)3].12H2O, [Co(cap)2(H2O)2].4H2O, [Ni(cap)2(H2O)2].3H2O, [Zn(cap)2], [ZrO(cap)2].3H2O, [UO2(cap)(NO3)], [Zr(cap)2(Cl)2] and [Th(cap)4]. These new complexes were synthesized and characterized by elemental analysis, molar conductivity, magnetic measurements, spectral methods (mid infrared, 1H NMR and UV-vis spectra) and simultaneous thermal analysis (TG and DTG) techniques. It has been found from the elemental analysis as well as thermal studies that the caproate ligand behaves as bidentate ligand and forming chelates with 1:1 (metal:ligand) stoichiometry for UO2(2+), 1:2 for (Mn2+, Co2+, Ni2+, Zn2+, ZrO2+ and Zr4+), 1:3 stoichiometry for (Cr3+ and Fe3+) and 1:4 for Th4+ caproate complexes, respectively, as bidentate chelating. The molar conductance measurements proved that the caproate complexes are non-electrolytes. The kinetic thermodynamic parameters such as: E*, DeltaH*, DeltaS* and DeltaG* are estimated from the DTG curves. The antibacterial activity of the caproic acid and their complexes was evaluated against some gram positive/negative bacteria.

Phytochemical investigation and hair growth studies on the rhizomes of Nardostachys jatamansi DC

PubMed Central

Gottumukkala, Venkateswara Rao; Annamalai, Tiruganasambandham; Mukhopadhyay, Triptikumar

2011-01-01

Nardostachys jatamansi DC rhizomes were subjected to extraction, fractionation, and isolation of terpenoid compounds. Three terpenoid compounds were isolated which are nardal, jatamansic acid, and nardin. These compounds were identified based on physical and spectral data (UV, IR,1H and13C NMR, 2D NMR, Mass) and comparison with authentic compounds. The crude extract, fractions, and two of the isolated compounds were tested for their hair growth activity. The hair growth studies showed good activities for the extract, fraction, and the isolated compounds. PMID:21716625

Influence of pH on the cis- trans isomerization of Valine-Proline dipeptide: An integrated NMR and theoretical investigation

NASA Astrophysics Data System (ADS)

Ivanova, Galya; Yakimova, Boryana; Angelova, Silvia; Stoineva, Ivanka; Enchev, Venelin

2010-06-01

The pH influence on the cis- trans isomerization of the Valine-Proline dipeptide was investigated by means of NMR spectral techniques and quantum chemical calculations at different computational levels. It was found that the process of isomerization is strongly pH dependent. The trans-isomer of Val-Pro is the more abundant isomer when the amino group is protonated, while an approximately equal distribution between the cis and trans-isomers for the neutral and anion forms of the dipeptide was confirmed.

SAIL--stereo-array isotope labeling.

PubMed

Kainosho, Masatsune; Güntert, Peter

2009-11-01

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

New milbemycin metabolites from the genetically engineered strain Streptomyces bingchenggensis BCJ60.

PubMed

Li, Jian-Song; Du, Min-Na; Zhang, Hui; Zhang, Ji; Zhang, Shao-Yong; Wang, Hai-Yan; Chen, An-Liang; Wang, Ji-Dong; Xiang, Wen-Sheng

2017-04-01

Two new milbemycin derivatives, 27-methoxylmilbemycin α 31 (1) and 27-oxomilbemycin α 31 (2), were isolated from the genetically engineered strain Streptomyces bingchenggensis BCJ60. Their structures were determined by 1D NMR, 2D NMR and HR-ESI-MS spectral analysis, and comparison with previous reports. The acaricidal and nematocidal capacities of compounds 1 and 2 were evaluated against Tetranychus cinnabarinus and Bursaphelenchus xylophilus, respectively. The results showed that the two new macrocyclic lactones 1 and 2 possessed potent acaricidal and nematocidal activities.

Owariensisone: a new iridolactone from the whole plant of Brillantaisia owariensis P. Beauv.

PubMed

Foning Tebou, Perrin Lanversin; Mabou, Florence Déclaire; Ngnokam, David; Harakat, Dominique; Voutquenne-Nazabadioko, Laurence

2016-07-01

From the whole plant of Brillantaisia owariensis P. Beauv, a new iridolactone, owariensisone (1) together with six known compounds (nepetin-7-O-glucoside, choline, sucrose, mannitol, xylitol, 1-O-palmitoyl-2-eicosanoyl-3-O-(6-amino-6-deoxy)-β-d-glucopyranosyl-glycerol) were isolated. Structures of these compounds were established by direct interpretation of their spectral data, mainly HR-TOFESIMS, 1-D NMR ((1)H and (13)C) and 2-D NMR ((1)H-(1)H COSY, HSQC, HMBC, NOESY, TOCSY and DOCSY) and by comparison with the literature.

A new isocoumarin from Cajanus cajan (Fabaceae).

PubMed

Rodrigues, Virginia F; Oliveira, Rodrigo R; Vega, Maria Raquel G

2014-04-01

A new isocoumarin, 3-phenyl-8-hydroxy-6-methoxy-5-gamma,gamma-dimethylallyl-isocoumarin, named cajavilmina (1) and eight known compounds: a-amirenone (2), beta-amirenone (3), lupenone (4), 5-hydroxy-7-methoxydihydroflavone (5), longistilin C (6), 3-hydroxy-5-methoxystilbene (7), beta-sitosterol (8) and stigmasterol (9) were identified in a dichloromethane fraction from Cajanus cajan leaves. Structures were elucidated by analysis of spectral data, mainly those afforded by 1H, NOEDIFF and 13C NMR (1D and 2D NMR HMQC, HMBC and COSY) and mass spectra.

1H and 13C NMR spectral data of new saponins from Cordia piauhiensis.

PubMed

Santos, Renata P; Silveira, Edilberto R; Uchôa, Daniel Esdras de A; Pessoa, Otília Deusdênia L; Viana, Francisco Arnaldo; Braz-Filho, Raimundo

2007-08-01

Two new bidesmoside triterpenoid saponins were isolated from stems of Cordia piauhiensis. Their structures, characterized as 3-O-alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl pomolic acid 28-O-beta-D-glucopyranosyl ester (1) and 3-O-alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl oleanolic acid 28-O-beta-D-glucopyranosyl-(1 --> 6)-beta-D-glucopyranosyl ester (2), were unequivocally established after extensive NMR (1H, 13C, DEPT 135 degrees, COSY, HSQC, HMBC, TOCSY, and NOESY) studies. Copyright 2007 John Wiley & Sons, Ltd.

A compact spin-exchange optical pumping system for 3He polarization based on a solenoid coil, a VBG laser diode, and a cosine theta RF coil

NASA Astrophysics Data System (ADS)

Lee, Sungman; Kim, Jongyul; Moon, Myung Kook; Lee, Kye Hong; Lee, Seung Wook; Ino, Takashi; Skoy, Vadim R.; Lee, Manwoo; Kim, Guinyun

2013-02-01

For use as a neutron spin polarizer or analyzer in the neutron beam lines of the HANARO (High-flux Advanced Neutron Application ReactOr) nuclear research reactor, a 3He polarizer was designed based on both a compact solenoid coil and a VBG (volume Bragg grating) diode laser with a narrow spectral linewidth of 25 GHz. The nuclear magnetic resonance (NMR) signal was measured and analyzed using both a built-in cosine radio-frequency (RF) coil and a pick-up coil. Using a neutron transmission measurement, we estimated the polarization ratio of the 3He cell as 18% for an optical pumping time of 8 hours.

New 14-membered octaazamacrocyclic complexes of divalent transition metal ions with their antimicrobial and spectral studies

NASA Astrophysics Data System (ADS)

Singh, D. P.; Kumar, Krishan; Sharma, Chetan

2010-01-01

A novel series of macrocyclic complexes of the type [M(C 18H 14N 10S 2)X 2]; where M = Co(II), Ni(II), Cu(II), Zn(II) and Cd(II); X = Cl -, NO 3-, CH 3COO - has been synthesized by [2+2] condensation of thiocarbohydrazide and isatin in the presence of divalent metal salts in methanolic medium. The complexes have been characterized with the help of elemental analyses, conductance measurements, magnetic measurements, electronic, NMR and infrared spectral studies. The low value of molar conductance indicates them to be non-electrolytes. On the basis of various studies a distorted octahedral geometry may be proposed for all of these complexes. These metal complexes were also tested for their in vitro antimicrobial activities against some Gram-positive bacteria viz. Staphylococcus aureus, Bacillus subtilis, and some Gram-negative bacteria Escherichia coli, Pseudomonas aeruginosa and some fungal strains Aspergillus niger, Aspergillus flavus (molds), Candida albicans, Saccharomyces cerevisiae (yeasts). The results obtained were compared with standard antibiotic: Ciprofloxacin and the standard antifungal drug: Amphotericin-B.

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Segmental Isotopic Labeling of Proteins for Nuclear Magnetic Resonance

PubMed Central

Dongsheng, Liu; Xu, Rong; Cowburn, David

2009-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as one of the principle techniques of structural biology. It is not only a powerful method for elucidating the 3D structures under near physiological conditions, but also a convenient method for studying protein-ligand interactions and protein dynamics. A major drawback of macromolecular NMR is its size limitation caused by slower tumbling rates and greater complexity of the spectra as size increases. Segmental isotopic labeling allows specific segment(s) within a protein to be selectively examined by NMR thus significantly reducing the spectral complexity for large proteins and allowing a variety of solution-based NMR strategies to be applied. Two related approaches are generally used in the segmental isotopic labeling of proteins: expressed protein ligation and protein trans-splicing. Here we describe the methodology and recent application of expressed protein ligation and protein trans-splicing for NMR structural studies of proteins and protein complexes. We also describe the protocol used in our lab for the segmental isotopic labeling of a 50 kDa protein Csk (C-terminal Src Kinase) using expressed protein ligation methods. PMID:19632474

Automatic alignment of individual peaks in large high-resolution spectral data sets

NASA Astrophysics Data System (ADS)

Stoyanova, Radka; Nicholls, Andrew W.; Nicholson, Jeremy K.; Lindon, John C.; Brown, Truman R.

2004-10-01

Pattern recognition techniques are effective tools for reducing the information contained in large spectral data sets to a much smaller number of significant features which can then be used to make interpretations about the chemical or biochemical system under study. Often the effectiveness of such approaches is impeded by experimental and instrument induced variations in the position, phase, and line width of the spectral peaks. Although characterizing the cause and magnitude of these fluctuations could be important in its own right (pH-induced NMR chemical shift changes, for example) in general they obscure the process of pattern discovery. One major area of application is the use of large databases of 1H NMR spectra of biofluids such as urine for investigating perturbations in metabolic profiles caused by drugs or disease, a process now termed metabonomics. Frequency shifts of individual peaks are the dominant source of such unwanted variations in this type of data. In this paper, an automatic procedure for aligning the individual peaks in the data set is described and evaluated. The proposed method will be vital for the efficient and automatic analysis of large metabonomic data sets and should also be applicable to other types of data.

Prediction of physical-chemical properties of crude oils by 1H NMR analysis of neat samples and chemometrics.

PubMed

Masili, Alice; Puligheddu, Sonia; Sassu, Lorenzo; Scano, Paola; Lai, Adolfo

2012-11-01

In this work, we report the feasibility study to predict the properties of neat crude oil samples from 300-MHz NMR spectral data and partial least squares (PLS) regression models. The study was carried out on 64 crude oil samples obtained from 28 different extraction fields and aims at developing a rapid and reliable method for characterizing the crude oil in a fast and cost-effective way. The main properties generally employed for evaluating crudes' quality and behavior during refining were measured and used for calibration and testing of the PLS models. Among these, the UOP characterization factor K (K(UOP)) used to classify crude oils in terms of composition, density (D), total acidity number (TAN), sulfur content (S), and true boiling point (TBP) distillation yields were investigated. Test set validation with an independent set of data was used to evaluate model performance on the basis of standard error of prediction (SEP) statistics. Model performances are particularly good for K(UOP) factor, TAN, and TPB distillation yields, whose standard error of calibration and SEP values match the analytical method precision, while the results obtained for D and S are less accurate but still useful for predictions. Furthermore, a strategy that reduces spectral data preprocessing and sample preparation procedures has been adopted. The models developed with such an ample crude oil set demonstrate that this methodology can be applied with success to modern refining process requirements. Copyright © 2012 John Wiley & Sons, Ltd.

Mixed ligand complexes of Cu(II)/Zn(II) ions containing (m-)/(p-) carboxylato phenyl azo pentane 2,4-dione and 2,2‧-bipyridine/1,10 phenanthroline: Synthesis, characterization, DNA binding, nuclease and topoisomerase I inhibitory activity

NASA Astrophysics Data System (ADS)

Hasan, Md. Amin; Kumari, Niraj; Singh, Kanhaiya; Singh, Kiran; Mishra, Lallan

2016-01-01

Metal complexes of type [Cu(L1H)2(bpy)] (1), [Zn(L1H)2(bpy)] (2), [Cu(L2H)2(bpy)] (3) and [Cu(L2H)2(Phen)] (4) (L1H2 = 3-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, L2H2 = 4-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, bpy = 2,2‧-bipyridine, Phen = 1,10 phenanthroline) are synthesized and characterized using spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, electronic absorption and emission) and elemental analysis data. The assembly of the complexes involving intramolecular H-bonding is displayed using corresponding crystal structure. Binding of the complexes separately with Calf Thymus DNA is monitored using UV-vis spectral titrations. The displacement of ethidium bromide (EB) bound to DNA by the complexes, in phosphate buffer solution (pH ∼ 7.2) is monitored using fluorescence spectral titrations. Nuclease activity of the complexes follow the order 4 > 3 > 1 > 2. The gel electrophoretic mobility assay measurement in presence of minor groove binder 4‧,6-diamidino-2-phenylindole (DAPI), suggests that complexes preferably bind with the minor groove of DNA. Topoisomerase I inhibitory activity of the complexes 3 and 4 inhibit topoisomerase I activity with IC50 values of 112 and 87 μM respectively.

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling.

PubMed

Castagné, Raphaële; Boulangé, Claire Laurence; Karaman, Ibrahim; Campanella, Gianluca; Santos Ferreira, Diana L; Kaluarachchi, Manuja R; Lehne, Benjamin; Moayyeri, Alireza; Lewis, Matthew R; Spagou, Konstantina; Dona, Anthony C; Evangelos, Vangelis; Tracy, Russell; Greenland, Philip; Lindon, John C; Herrington, David; Ebbels, Timothy M D; Elliott, Paul; Tzoulaki, Ioanna; Chadeau-Hyam, Marc

2017-10-06

1 H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1 H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies.

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling

PubMed Central

2017-01-01

1H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies. PMID:28823158

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

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

NASA Astrophysics Data System (ADS)

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

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

Ligand-receptor binding affinities from saturation transfer difference (STD) NMR spectroscopy: the binding isotherm of STD initial growth rates.

PubMed

Angulo, Jesús; Enríquez-Navas, Pedro M; Nieto, Pedro M

2010-07-12

The direct evaluation of dissociation constants (K(D)) from the variation of saturation transfer difference (STD) NMR spectroscopy values with the receptor-ligand ratio is not feasible due to the complex dependence of STD intensities on the spectral properties of the observed signals. Indirect evaluation, by competition experiments, allows the determination of K(D), as long as a ligand of known affinity is available for the protein under study. Herein, we present a novel protocol based on STD NMR spectroscopy for the direct measurements of receptor-ligand dissociation constants (K(D)) from single-ligand titration experiments. The influence of several experimental factors on STD values has been studied in detail, confirming the marked impact on standard determinations of protein-ligand affinities by STD NMR spectroscopy. These factors, namely, STD saturation time, ligand residence time in the complex, and the intensity of the signal, affect the accumulation of saturation in the free ligand by processes closely related to fast protein-ligand rebinding and longitudinal relaxation of the ligand signals. The proposed method avoids the dependence of the magnitudes of ligand STD signals at a given saturation time on spurious factors by constructing the binding isotherms using the initial growth rates of the STD amplification factors, in a similar way to the use of NOE growing rates to estimate cross relaxation rates for distance evaluations. Herein, it is demonstrated that the effects of these factors are cancelled out by analyzing the protein-ligand association curve using STD values at the limit of zero saturation time, when virtually no ligand rebinding or relaxation takes place. The approach is validated for two well-studied protein-ligand systems: the binding of the saccharides GlcNAc and GlcNAcbeta1,4GlcNAc (chitobiose) to the wheat germ agglutinin (WGA) lectin, and the interaction of the amino acid L-tryptophan to bovine serum albumin (BSA). In all cases, the experimental K(D) measured under different experimental conditions converged to the thermodynamic values. The proposed protocol allows accurate determinations of protein-ligand dissociation constants, extending the applicability of the STD NMR spectroscopy for affinity measurements, which is of particular relevance for those proteins for which a ligand of known affinity is not available.

250 GHz CW Gyrotron Oscillator for Dynamic Nuclear Polarization in Biological Solid State NMR

PubMed Central

Bajaj, Vikram S.; Hornstein, Melissa K.; Kreischer, Kenneth E.; Sirigiri, Jagadishwar R.; Woskov, Paul P.; Mak-Jurkauskas, Melody L.; Herzfeld, Judith; Temkin, Richard J.; Griffin, Robert G.

2009-01-01

In this paper, we describe a 250 GHz gyrotron oscillator, a critical component of an integrated system for magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments at 9T, corresponding to 380 MHz 1H frequency. The 250 GHz gyrotron is the first gyro-device designed with the goal of seamless integration with an NMR spectrometer for routine DNP-enhanced NMR spectroscopy and has operated under computer control for periods of up to 21 days with a 100% duty cycle. Following a brief historical review of the field, we present studies of the membrane protein bacteriorhodopsin (bR) using DNP-enhanced multidimensional NMR. These results include assignment of active site resonances in [U-13C,15N]-bR and demonstrate the utility of DNP for studies of membrane proteins. Next, we review the theory of gyro-devices from quantum mechanical and classical viewpoints and discuss the unique considerations that apply to gyrotron oscillators designed for DNP experiments. We then characterize the operation of the 250 GHz gyrotron in detail, including its long-term stability and controllability. We have measured the spectral purity of the gyrotron emission using both homodyne and heterodyne techniques. Radiation intensity patterns from the corrugated waveguide that delivers power to the NMR probe were measured using two new techniques to confirm pure mode content: a thermometric approach based on the temperature-dependent color of liquid crystalline media applied to a substrate and imaging with a pyroelectric camera. We next present a detailed study of the mode excitation characteristics of the gyrotron. Exploration of the operating characteristics of several fundamental modes reveals broadband continuous frequency tuning of up to 1.8 GHz as a function of the magnetic field alone, a feature that may be exploited in future tunable gyrotron designs. Oscillation of the 250 GHz gyrotron at the second harmonic of cyclotron resonance begins at extremely low beam currents (as low 12 mA) at frequencies between 320–365 GHz, suggesting an efficient route for the generation of even higher frequency radiation. The low starting currents were attributed to an elevated cavity Q, which is confirmed by cavity thermal load measurements. We conclude with an appendix containing a detailed description of the control system that safely automates all aspects of the gyrotron operation. PMID:17942352

Spectral density mapping at multiple magnetic fields suitable for 13C NMR relaxation studies

NASA Astrophysics Data System (ADS)

Kadeřávek, Pavel; Zapletal, Vojtěch; Fiala, Radovan; Srb, Pavel; Padrta, Petr; Přecechtělová, Jana Pavlíková; Šoltésová, Mária; Kowalewski, Jozef; Widmalm, Göran; Chmelík, Josef; Sklenář, Vladimír; Žídek, Lukáš

2016-05-01

Standard spectral density mapping protocols, well suited for the analysis of 15N relaxation rates, introduce significant systematic errors when applied to 13C relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and 13C frequencies can be obtained from data acquired at three magnetic fields for uniformly 13C -labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

Ergosterol in POPC membranes: physical properties and comparison with structurally similar sterols.

PubMed

Hsueh, Ya-Wei; Chen, Mei-Ting; Patty, Philipus J; Code, Christian; Cheng, John; Frisken, Barbara J; Zuckermann, Martin; Thewalt, Jenifer

2007-03-01

The physical properties of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/ergosterol bilayers in the liquid-crystalline phase were determined using deuterium nuclear magnetic resonance ((2)H NMR) and vesicle extrusion. For the (2)H NMR experiments, the sn-1 chain of POPC was perdeuterated, and spectra were taken as a function of ergosterol concentration and temperature. Analysis of the liquid-crystalline spectra provides clear evidence that two types of liquid-crystalline domains, neither of which is a liquid-ordered phase, having distinct average chain conformations coexist in 80:20 and 75:25 POPC/ergosterol membranes over a wide temperature range (from -2 to at least 31 degrees C). Adding ergosterol to a concentration of 25 mol % increases POPC-d(31) chain ordering as measured by the NMR spectral first moment M(1) and also increases the membrane lysis tension, obtained from vesicle extrusion. Further addition of ergosterol had no effect on either chain order or lysis tension. This behavior is in marked contrast to the effect of cholesterol on POPC membranes: POPC/cholesterol membranes have a linear dependence of chain order on sterol concentration to at least 40 mol %. To investigate further we compared the dependence on sterol structure and concentration of the NMR spectra and lysis tension for several POPC/sterol membranes at 25 degrees C. For all POPC/sterol membranes investigated in this study, we observed a universal linear relation between lysis tension and M(1). This suggests that changes in acyl chain ordering directly affect the tensile properties of the membrane.

Ergosterol in POPC Membranes: Physical Properties and Comparison with Structurally Similar Sterols

PubMed Central

Hsueh, Ya-Wei; Chen, Mei-Ting; Patty, Philipus J.; Code, Christian; Cheng, John; Frisken, Barbara J.; Zuckermann, Martin; Thewalt, Jenifer

2007-01-01

The physical properties of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/ergosterol bilayers in the liquid-crystalline phase were determined using deuterium nuclear magnetic resonance (2H NMR) and vesicle extrusion. For the 2H NMR experiments, the sn-1 chain of POPC was perdeuterated, and spectra were taken as a function of ergosterol concentration and temperature. Analysis of the liquid-crystalline spectra provides clear evidence that two types of liquid-crystalline domains, neither of which is a liquid-ordered phase, having distinct average chain conformations coexist in 80:20 and 75:25 POPC/ergosterol membranes over a wide temperature range (from −2 to at least 31°C). Adding ergosterol to a concentration of 25 mol % increases POPC-d31 chain ordering as measured by the NMR spectral first moment M1 and also increases the membrane lysis tension, obtained from vesicle extrusion. Further addition of ergosterol had no effect on either chain order or lysis tension. This behavior is in marked contrast to the effect of cholesterol on POPC membranes: POPC/cholesterol membranes have a linear dependence of chain order on sterol concentration to at least 40 mol %. To investigate further we compared the dependence on sterol structure and concentration of the NMR spectra and lysis tension for several POPC/sterol membranes at 25°C. For all POPC/sterol membranes investigated in this study, we observed a universal linear relation between lysis tension and M1. This suggests that changes in acyl chain ordering directly affect the tensile properties of the membrane. PMID:17142279

A biologically active fructan from the roots of Arctium lappa L., var. Herkules.

PubMed

Kardosová, A; Ebringerová, A; Alföldi, J; Nosál'ová, G; Franová, S; Hríbalová, V

2003-11-01

From the roots of Arctium lappa L., var. Herkules a low-molecular-weight fructofuranan of the inulin-type has been isolated by water extraction and ethanol precipitation, followed by ion-exchange chromatography and gel filtration of the crude precipitate. The methods employed in structural determination were methylation analysis and 1H and 13C NMR spectral measurements. In tests for antitussive activity in cats the fructan was found to be equally active as some non-narcotic, synthetic preparations used in clinical practice to treat coughing, and in mitogenic and comitogenic tests its biological response was comparable to that of the commercial Zymosan immunomodulator.

(14)N overtone transition in double rotation solid-state NMR.

PubMed

Haies, Ibraheem M; Jarvis, James A; Brown, Lynda J; Kuprov, Ilya; Williamson, Philip T F; Carravetta, Marina

2015-10-07

Solid-state NMR transitions involving outer energy levels of the spin-1 (14)N nucleus are immune, to first order in perturbation theory, to the broadening caused by the nuclear quadrupole interaction. The corresponding overtone spectra, when acquired in conjunction with magic-angle sample spinning, result in lines, which are just a few kHz wide, permitting the direct detection of nitrogen compounds without the need for labeling. Despite the success of this technique, "overtone" resonances are still broadened due to indirect, second order effects arising from the large quadrupolar interaction. Here we demonstrate that another order of magnitude in spectral resolution may be gained by using double rotation. This brings the width of the (14)N solid-state NMR lines much closer to the region commonly associated with high-resolution solid-state NMR spectroscopy of (15)N and demonstrates the improvements in resolution that may be possible through the development of pulsed methodologies to suppress these second order effects.

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

DOE PAGES

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

2017-07-07

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

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

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

Zinke, Maximilian; Fricke, Pascal; Samson, Camille

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

Isolation and Characterization of a Novel Rebaudioside M Isomer from a Bioconversion Reaction of Rebaudioside A and NMR Comparison Studies of Rebaudioside M Isolated from Stevia rebaudiana Bertoni and Stevia rebaudiana Morita

PubMed Central

Prakash, Indra; Bunders, Cynthia; Devkota, Krishna P.; Charan, Romila D.; Ramirez, Catherine; Priedemann, Christopher; Markosyan, Avetik

2014-01-01

A minor product, rebaudioside M2 (2), from the bioconversion reaction of rebaudioside A (4) to rebaudioside D (3), was isolated and the complete structure of the novel steviol glycoside was determined. Rebaudioside M2 (2) is considered an isomer of rebaudioside M (1) and contains a relatively rare 1→6 sugar linkage. It was isolated and characterized with NMR (1H, 13C, COSY, HSQC-DEPT, HMBC, 1D-TOCSY, and NOESY) and mass spectral data. Additionally, we emphasize the importance of 1D and 2D NMR techniques when identifying complex steviol glycosides. Numerous NMR spectroscopy studies of rebaudioside M (1), rebaudioside D (3), and mixture of 1 and 3 led to the discovery that SG17 which was previously reported in literature, is a mixture of rebaudioside D (3), rebaudioside M (1), and possibly other related steviol glycosides. PMID:24970220

Synthesis, spectral, structural prediction and computational studies of octylcarbazole ornamented 3-phenothiazinal

NASA Astrophysics Data System (ADS)

Karuppasamy, Ayyanar; Udhaya kumar, Chandran; Karthikeyan, Subramanian; Velayutham Pillai, Muthiah Pillai; Ramalingan, Chennan

2017-11-01

A novel conjugated octylcarbazole ornamented 3-phenothiazinal, 10-(9-octyl-9H-carbazol-3-yl)-10H-phenothiazine-3-carbaldehyde (OCPTC) was synthesized and fully characterized by 1H-NMR, 13C-NMR, elemental and single crystal XRD analyses. The optimized geometrical structure, vibrational frequencies and NMR have been computed with M06-2X method using 6-31+G(d,p) basis set. Total electronic energies and HOMO-LUMO energy gaps in gas phase are discussed. The geometrical parameters of the title compound obtained from single crystal XRD studies have been found in accord with the calculated (DFT) values. The experimental and theoretical FT-IR and NMR results of the title molecule have been investigated. The experimentally observed vibrational frequencies have been compared with the calculated ones, which are in good agreement with each other. Single crystal X-ray structural analysis of OCPTC, evidences the ''butterfly conformation'' of phenothiazine ring with nearly perpendicular orientation of the carbazole structural motif to the phenothiazine moiety.

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

PubMed Central

Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland

2013-01-01

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

{sup 1}H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis

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

Zhang, Ying; Lin, Lianjie; Xu, Yanbin

2013-04-19

Highlights: •Twenty ulcerative colitis patients and nineteen healthy controls were enrolled. •Increased 3-hydroxybutyrate, glucose, phenylalanine, and decreased lipid were found. •We report early stage diagnosis of ulcerative colitis using NMR-based metabolomics. -- Abstract: Ulcerative colitis (UC) has seriously impaired the health of citizens. Accurate diagnosis of UC at an early stage is crucial to improve the efficiency of treatment and prognosis. In this study, proton nuclear magnetic resonance ({sup 1}H NMR)-based metabolomic analysis was performed on serum samples collected from active UC patients (n = 20) and healthy controls (n = 19), respectively. The obtained spectral profiles were subjected tomore » multivariate data analysis. Our results showed that consistent metabolic alterations were present between the two groups. Compared to healthy controls, UC patients displayed increased 3-hydroxybutyrate, β-glucose, α-glucose, and phenylalanine, but decreased lipid in serum. These findings highlight the possibilities of NMR-based metabolomics as a non-invasive diagnostic tool for UC.« less

Communication: molecular dynamics and (1)H NMR of n-hexane in liquid crystals.

PubMed

Weber, Adrian C J; Burnell, E Elliott; Meerts, W Leo; de Lange, Cornelis A; Dong, Ronald Y; Muccioli, Luca; Pizzirusso, Antonio; Zannoni, Claudio

2015-07-07

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

Communication: Molecular dynamics and {sup 1}H NMR of n-hexane in liquid crystals

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

Weber, Adrian C. J., E-mail: WeberA@BrandonU.CA; Burnell, E. Elliott, E-mail: elliott.burnell@ubc.ca; Meerts, W. Leo, E-mail: leo.meerts@science.ru.nl

The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings.more » In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.« less

The Time-Domain Matched Filter and the Spectral-Domain Matched Filter in 1-Dimensional NMR Spectroscopy.

PubMed

Spencer, Richard G

2010-09-01

A type of "matched filter" (MF), used extensively in the processing of one-dimensional spectra, is defined by multiplication of a free-induction decay (FID) by a decaying exponential with the same time constant as that of the FID. This maximizes, in a sense to be defined, the signal-to-noise ratio (SNR) in the spectrum obtained after Fourier transformation. However, a different entity known also as the matched filter was introduced by van Vleck in the context of pulse detection in the 1940's and has become widely integrated into signal processing practice. These two types of matched filters appear to be quite distinct. In the NMR case, the "filter", that is, the exponential multiplication, is defined by the characteristics of, and applied to, a time domain signal in order to achieve improved SNR in the spectral domain. In signal processing, the filter is defined by the characteristics of a signal in the spectral domain, and applied in order to improve the SNR in the temporal (pulse) domain. We reconcile these two distinct implementations of the matched filter, demonstrating that the NMR "matched filter" is a special case of the matched filter more rigorously defined in the signal processing literature. In addition, two limitations in the use of the MF are highlighted. First, application of the MF distorts resonance ratios as defined by amplitudes, although not as defined by areas. Second, the MF maximizes SNR with respect to resonance amplitude, while intensities are often more appropriately defined by areas. Maximizing the SNR with respect to area requires a somewhat different approach to matched filtering.

Calibration of NMR well logs from carbonate reservoirs with laboratory NMR measurements and μXRCT

DOE PAGES

Mason, Harris E.; Smith, Megan M.; Hao, Yue; ...

2014-12-31

The use of nuclear magnetic resonance (NMR) well log data has the potential to provide in-situ porosity, pore size distributions, and permeability of target carbonate CO₂ storage reservoirs. However, these methods which have been successfully applied to sandstones have yet to be completely validated for carbonate reservoirs. Here, we have taken an approach to validate NMR measurements of carbonate rock cores with independent measurements of permeability and pore surface area to volume (S/V) distributions using differential pressure measurements and micro X-ray computed tomography (μXRCT) imaging methods, respectively. We observe that using standard methods for determining permeability from NMR data incorrectlymore » predicts these values by orders of magnitude. However, we do observe promise that NMR measurements provide reasonable estimates of pore S/V distributions, and with further independent measurements of the carbonate rock properties that universally applicable relationships between NMR measured properties may be developed for in-situ well logging applications of carbonate reservoirs.« less

Calibration of NMR well logs from carbonate reservoirs with laboratory NMR measurements and μXRCT

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

Mason, Harris E.; Smith, Megan M.; Hao, Yue

The use of nuclear magnetic resonance (NMR) well log data has the potential to provide in-situ porosity, pore size distributions, and permeability of target carbonate CO₂ storage reservoirs. However, these methods which have been successfully applied to sandstones have yet to be completely validated for carbonate reservoirs. Here, we have taken an approach to validate NMR measurements of carbonate rock cores with independent measurements of permeability and pore surface area to volume (S/V) distributions using differential pressure measurements and micro X-ray computed tomography (μXRCT) imaging methods, respectively. We observe that using standard methods for determining permeability from NMR data incorrectlymore » predicts these values by orders of magnitude. However, we do observe promise that NMR measurements provide reasonable estimates of pore S/V distributions, and with further independent measurements of the carbonate rock properties that universally applicable relationships between NMR measured properties may be developed for in-situ well logging applications of carbonate reservoirs.« less

NMR Methods, Applications and Trends for Groundwater Evaluation and Management

NASA Astrophysics Data System (ADS)

Walsh, D. O.; Grunewald, E. D.

2011-12-01

Nuclear magnetic resonance (NMR) measurements have a tremendous potential for improving groundwater characterization, as they provide direct detection and measurement of groundwater and unique information about pore-scale properties. NMR measurements, commonly used in chemistry and medicine, are utilized in geophysical investigations through non-invasive surface NMR (SNMR) or downhole NMR logging measurements. Our recent and ongoing research has focused on improving the performance and interpretation of NMR field measurements for groundwater characterization. Engineering advancements have addressed several key technical challenges associated with SNMR measurements. Susceptibility of SNMR measurements to environmental noise has been dramatically reduced through the development of multi-channel acquisition hardware and noise-cancellation software. Multi-channel instrumentation (up to 12 channels) has also enabled more efficient 2D and 3D imaging. Previous limitations in measuring NMR signals from water in silt, clay and magnetic geology have been addressed by shortening the instrument dead-time from 40 ms to 4 ms, and increasing the power output. Improved pulse sequences have been developed to more accurately estimate NMR relaxation times and their distributions, which are sensitive to pore size distributions. Cumulatively, these advancements have vastly expanded the range of environments in which SNMR measurements can be obtained, enabling detection of groundwater in smaller pores, in magnetic geology, in the unsaturated zone, and nearby to infrastructure (presented here in case studies). NMR logging can provide high-resolution estimates of bound and mobile water content and pore size distributions. While NMR logging has been utilized in oil and gas applications for decades, its use in groundwater investigations has been limited by the large size and high cost of oilfield NMR logging tools and services. Recently, engineering efforts funded by the US Department of Energy have produced an NMR logging tool that is much smaller and less costly than comparable oilfield NMR logging tools. This system is specifically designed for near surface groundwater investigations, incorporates small diameter probes (as small as 1.67 inches diameter) and man-portable surface stations, and provides NMR data and information content on par with oilfield NMR logging tools. A direct-push variant of this logging tool has also been developed. Key challenges associated with small diameter tools include inherently lower SNR and logging speeds, the desire to extend the sensitive zone as far as possible into unconsolidated formations, and simultaneously maintaining high power and signal fidelity. Our ongoing research in groundwater NMR aims to integrating surface and borehole measurements for regional-scale permeability mapping, and to develop in-place NMR sensors for long term monitoring of contaminant and remediation processes. In addition to groundwater resource characterization, promising new applications of NMR include assessing water content in ice and permafrost, management of groundwater in mining operations, and evaluation and management of groundwater in civil engineering applications.

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.

Automated Control of the Organic and Inorganic Composition of Aloe vera Extracts Using (1)H NMR Spectroscopy.

PubMed

Monakhova, Yulia B; Randel, Gabriele; Diehl, Bernd W K

2016-09-01

Recent classification of Aloe vera whole-leaf extract by the International Agency for Research and Cancer as a possible carcinogen to humans as well as the continuous adulteration of A. vera's authentic material have generated renewed interest in controlling A. vera. The existing NMR spectroscopic method for the analysis of A. vera, which is based on a routine developed at Spectral Service, was extended. Apart from aloverose, glucose, malic acid, lactic acid, citric acid, whole-leaf material (WLM), acetic acid, fumaric acid, sodium benzoate, and potassium sorbate, the quantification of Mg(2+), Ca(2+), and fructose is possible with the addition of a Cs-EDTA solution to sample. The proposed methodology was automated, which includes phasing, baseline-correction, deconvolution (based on the Lorentzian function), integration, quantification, and reporting. The NMR method was applied to 41 A. vera preparations in the form of liquid A. vera juice and solid A. vera powder. The advantages of the new NMR methodology over the previous method were discussed. Correlation between the new and standard NMR methodologies was significant for aloverose, glucose, malic acid, lactic acid, citric acid, and WLM (P < 0.0001, R(2) = 0.99). NMR was found to be suitable for the automated simultaneous quantitative determination of 13 parameters in A. vera.

Sesterterpenes from a common marine sponge, Hyrtios erecta.

PubMed

Crews, P; Bescansa, P

1986-01-01

Eleven sesterterpenes have been characterized from the biotoxic extracts of Hyrtios erecta. Their structures and stereochemistry were established by spectral properties or results from chemical interconversions. Especially valuable for establishing stereochemical features were 13C-nmr methyl shift correlations and analysis of 1H-nmr couplings and chemical shifts. The new scalarane sesterterpenes included 2, 3, 7, 9, and 10a (but 9 and 10a might be artifacts), and they were accompanied by five previously described scalaranes, 1, 4, 5a, 6, and 8, along with hyrtial (11), a novel norsesterterpene. Many of these sesterterpenes exhibited interesting biological activity.

Sesquiterpenes from the Formosan stolonifer Tubipora musica.

PubMed

Duh, C Y; Chen, K J; El-Gamal, A A; Dai, C F

2001-11-01

Eight new sesquiterpenes, tubipolides A-G (1-7) and tubiporone (8) (novel carbon skeleton), and a known sesquiterpene, spirotubipolide, have been isolated from the Formosan stolonifer Tubipora musica. The structures of compounds 1-8 were determined by 1D and 2D NMR spectral analysis.

Synthesis, spectral characterization, molecular modeling, biological activity and potentiometric studies of 4-amino-5-mercapto-3-methyl-S-triazole Schiff's base complexes

NASA Astrophysics Data System (ADS)

Alaghaz, Abdel-Nasser M. A.; Zayed, Mohamed E.; Alharbi, Suliman A.

2015-03-01

The Schiff's base derived from condensation of s-triazole (4-amino-5-mercapto-3-methyl-S-triazole) with pyridine-2-aldehyde and their corresponding Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes have been synthesized. The isolated solid complexes were characterized by elemental analyses, molar conductance, spectral (IR, UV-Vis, 1H NMR, mass), magnetic moment and thermal measurements. The IR spectral data suggest that the ligand coordinate in a tridentate manner (SNN) via the one thiol (SH), one pyridine ring and the azomethine (Cdbnd N) groups. The data show that the complexes have composition of ML2 type. The activation of thermodynamic parameters are calculated using Coats-Redfern, Horowitz-Metzger (HM), and Piloyan-Novikova (PN). The octahedral geometry of the complexes is confirmed using DFT method from DMOL3 calculations and ligand field parameters. Protonation constants of Schiff base and stability constants of their binary metal complexes have been determined potentiometrically in 50% DMSO-water media at 25 °C and ionic strength 0.10 M potassium nitrate. The biological activity of these compounds against various fungi has been investigated.

Theoretical study of homonuclear J coupling between quadrupolar spins: single-crystal, DOR, and J-resolved NMR.

PubMed

Perras, Frédéric A; Bryce, David L

2014-05-01

The theory describing homonuclear indirect nuclear spin-spin coupling (J) interactions between pairs of quadrupolar nuclei is outlined and supported by numerical calculations. The expected first-order multiplets for pairs of magnetically equivalent (A2), chemically equivalent (AA'), and non-equivalent (AX) quadrupolar nuclei are given. The various spectral changeovers from one first-order multiplet to another are investigated with numerical simulations using the SIMPSON program and the various thresholds defining each situation are given. The effects of chemical equivalence, as well as quadrupolar coupling, chemical shift differences, and dipolar coupling on double-rotation (DOR) and J-resolved NMR experiments for measuring homonuclear J coupling constants are investigated. The simulated J coupling multiplets under DOR conditions largely resemble the ideal multiplets predicted for single crystals, and a characteristic multiplet is expected for each of the A2, AA', and AX cases. The simulations demonstrate that it should be straightforward to distinguish between magnetic inequivalence and equivalence using J-resolved NMR, as was speculated previously. Additionally, it is shown that the second-order quadrupolar-dipolar cross-term does not affect the splittings in J-resolved experiments. Overall, the homonuclear J-resolved experiment for half-integer quadrupolar nuclei is demonstrated to be robust with respect to the effects of first- and second-order quadrupolar coupling, dipolar coupling, and chemical shift differences. Copyright © 2014 Elsevier Inc. All rights reserved.

Overview of the development of high-resolution 920 MHz NMR in NIMS

NASA Astrophysics Data System (ADS)

Shimizu, Tadashi; Hashi, Kenjiro; Goto, Atsushi; Tansyo, Masataka; Kiyoshi, Tsukasa; Matsumoto, Shinji; Wada, Hitoshi; Fujito, Teruaki; Hasegawa, Ken-ichi; Kirihara, Noriaki; Suematsu, Hiroto; Kida, Yoshiki; Yoshikawa, Masatoshi; Miki, Takashi; Ito, Satoshi; Hamada, Mamoru; Hayashi, Seiji

2004-04-01

We have developed a 920 MHz NMR system and performed the proton NMR measurement of ethylbenzene and water using the superconducting magnet operating at 21.6 T ( 920 MHz for proton), which is the highest field produced by a superconducting NMR magnet in the persistent mode. From the NMR measurements, it is verified that both homogeneity and stability of the magnet have a specification sufficient for a high-resolution NMR. The sensitivity has been examined by 1H NMR of 0.1% ethylbenzene in Wilmad 555 tube and obtained the signal-to-noise ratio as S/ N=2981, which is the highest record, to our knowledge, among the room temperature measurements.

Achievement of a 920-MHz High Resolution NMR

NASA Astrophysics Data System (ADS)

Hashi, Kenjiro; Shimizu, Tadashi; Goto, Atsushi; Kiyoshi, Tsukasa; Matsumoto, Shinji; Wada, Hitoshi; Fujito, Teruaki; Hasegawa, Ken-ichi; Yoshikawa, Masatoshi; Miki, Takashi; Ito, Satoshi; Hamada, Mamoru; Hayashi, Seiji

2002-06-01

We have developed a 920-MHz NMR system and performed the proton NMR measurement of H 2O and ethylbenzene using the superconducting magnet operating at 21.6 T (920 MHz for proton), which is the highest field produced by a superconducting NMR magnet in the persistent mode. From the NMR measurements, it is verified that both homogeneity and stability of the magnet have a specification sufficient for a high resolution NMR.

Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

PubMed

Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

2016-04-01

A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Novel menadione hybrids: Synthesis, anticancer activity, and cell-based studies.

PubMed

Prasad, Chakka Vara; Nayak, Vadithe Lakshma; Ramakrishna, Sistla; Mallavadhani, Uppuluri Venkata

2018-01-01

A series of novel menadione-based triazole hybrids were designed and synthesized by employing copper-catalyzed azide-alkyne cycloaddition (CuAAC). All the synthesized hybrids were characterized by their spectral data ( 1 H NMR, 13 C NMR, IR, and HRMS). The synthesized compounds were evaluated for their anticancer activity against five selected cancer cell lines including lung (A549), prostate (DU-145), cervical (Hela), breast (MCF-7), and mouse melanoma (B-16) using MTT assay. The screening results showed that majority of the synthesized compounds displayed significant anticancer activity. Among the tested compounds, the triazoles 5 and 6 exhibited potent activity against all cell lines. In particular, compound 6 showed higher potency than the standard tamoxifen and parent menadione against MCF-7 cell line. Flow cytometric analysis revealed that compound 6 arrested cell cycle at G0/G1 phase and induced apoptotic cell death which was further confirmed by Hoechst staining, measurement of mitochondrial membrane potential (ΔΨm) and Annexin-V-FITC assay. Thus, compound 6 can be considered as lead molecule for further development as potent anticancer therapeutic agent. © 2017 John Wiley & Sons A/S.

Enhancing the detection of edges and non-differentiable points in an NMR spectrum using delayed-acquisition.

PubMed

Gong, Zhaoyuan; Walls, Jamie D

2018-02-01

Delayed-acquisition, which is a common technique for improving spectral resolution in Fourier transform based spectroscopies, typically relies upon differences in T 2 relaxation rates that are often due to underlying differences in dynamics and/or complexities of the spin systems being studied. After an acquisition delay, the broad signals from fast T 2 -relaxing species are more suppressed relative to the sharp signals from slow T 2 -relaxing species. In this paper, an alternative source of differential "dephasing" under delayed-acquisition is demonstrated that is based solely upon the mathematical properties of the line shape and is independent of the underlying spin dynamics and/or complexity. Signals associated with frequencies where the line shape either changes sharply and/or is non-differentiable at some finite order dephase at a much slower rate than those signals associated with frequencies where the line shape is smooth. Experiments employing delayed-acquisition to study interfaces in biphasic samples, to measure spatially-dependent longitudinal relaxation, and to highlight sharp features in NMR spectra are presented. Copyright © 2017 Elsevier Inc. All rights reserved.

Enhancing the detection of edges and non-differentiable points in an NMR spectrum using delayed-acquisition

NASA Astrophysics Data System (ADS)

Gong, Zhaoyuan; Walls, Jamie D.

2018-02-01

Delayed-acquisition, which is a common technique for improving spectral resolution in Fourier transform based spectroscopies, typically relies upon differences in T2 relaxation rates that are often due to underlying differences in dynamics and/or complexities of the spin systems being studied. After an acquisition delay, the broad signals from fast T2 -relaxing species are more suppressed relative to the sharp signals from slow T2 -relaxing species. In this paper, an alternative source of differential "dephasing" under delayed-acquisition is demonstrated that is based solely upon the mathematical properties of the line shape and is independent of the underlying spin dynamics and/or complexity. Signals associated with frequencies where the line shape either changes sharply and/or is non-differentiable at some finite order dephase at a much slower rate than those signals associated with frequencies where the line shape is smooth. Experiments employing delayed-acquisition to study interfaces in biphasic samples, to measure spatially-dependent longitudinal relaxation, and to highlight sharp features in NMR spectra are presented.

Suppression of Protonated Organic Solvents in NMR Spectroscopy Using a Perfect Echo Low-Pass Filtration Pulse Sequence.

PubMed

Howe, Peter W A

2018-04-03

Proton NMR spectra are usually acquired using deuterated solvents, but in many cases it is necessary to obtain spectra on samples in protonated solvents. In these cases, the intense resonances of the protonated solvents need to be suppressed to maximize sensitivity and spectral quality. A wide range of highly effective solvent suppression methods have been developed, but additional measures are needed to suppress the 13 C satellites of the solvent. Because the satellites represent 1.1% of the original solvent signal, they remain problematic if unsuppressed. The recently proposed DISPEL pulse sequences suppress 13 C satellites extremely effectively, and this Technical Note demonstrates that combining DISPEL and presaturation results in exceptionally effective solvent suppression. An important element in the effectiveness is volume selection, which is inherent within the DISPEL sequence. Spectra acquired in protonated dimethlysulfoxide and tetrahydrofuran show that optimum results are obtained by modifying the phase cycle, cycling the pulse-field gradients, and using broadband 13 C inversion pulses to reduce the effects of radiofrequency offset and inhomogeneity.

UV-visible-DAD and 1H-NMR spectroscopy data fusion for studying the photodegradation process of azo-dyes using MCR-ALS.

PubMed

Fernández, Cristina; Pilar Callao, M; Larrechi, M Soledad

2013-12-15

The photodegradation process of three azo-dyes - Acid Orange 61, Acid Red 97 and Acid Brown 425 - was monitored simultaneously by ultraviolet-visible spectroscopy with diode array detector (UV-vis-DAD) and (1)H-nuclear magnetic resonance ((1)H-NMR). Multivariate curve resolution-alternating least squares (MCR-ALS) was applied to obtain the concentration and spectral profile of the chemical compounds involved in the process. The analysis of the H-NMR data suggests there are more intermediate compounds than those obtained with the UV-vis-DAD data. The fusion of UV-vis-DAD and the (1)H-NMR signal before the multivariate analysis provides better results than when only one of the two detector signals was used. It was concluded that three degradation products were present in the medium when the three azo-dyes had practically degraded. This study is the first application of UV-vis-DAD and (1)H-NMR spectroscopy data fusion in this field and illustrates its potential as a quick method for evaluating the evolution of the azo-dye photodegradation process. © 2013 Elsevier B.V. All rights reserved.

Synthesis, NMR data and theoretical study of semi-synthetic derivatives from trans-dehydrocrotonin

NASA Astrophysics Data System (ADS)

Soares, Breno Almeida; Medeiros Maciel, Maria Aparecida; Castro, Rosane Nora; Kaiser, Carlos R.; Firme, Caio Lima

2016-03-01

In this work, the 19-nor-diterpenoid clerodane-type dehydrocrotonin (t-DCTN) was a primary source for a two-step synthetic procedure. The catalytic hydrogenation of t-DCTN afforded the semi-synthetic trans-crotonin (t-CTN) in a highly stereospecific reaction confirmed by DFT calculations. The unsaturated carbonyl group of t-DCTN was reduced by NaBH4/EtOH providing an epimeric α-OH and β-OH mixture named t-CTN-OL. Both epimeric compound structures t-CTN-α-OL and t-CTN-β-OL were elucidated by 1D and 2D NMR spectral data. Comparison of NMR data from natural source of t-CTN was done to confirm the stereochemical authenticity of semi-synthetic t-CTN. Calculated NMR data for all described derivatives (semi-synthetic t-CTN and its t-CTN-OL epimeric mixture) were performed using B3LYP/6-311G++(d,p) level of theory which validated our previously developed NMR theoretical protocol for structural analyses of organic molecules. Topological data using Quantum Theory of Atoms in Molecules (QTAIM) of t-CTN quantified and qualified intramolecular interactions of its most stable conformer.

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.

Studies on synthesis, growth, structural, thermal, linear and nonlinear optical properties of organic picolinium maleate single crystals.

PubMed

Pandi, P; Peramaiyan, G; Sudhahar, S; Chakkaravarthi, G; Mohan Kumar, R; Bhagavannarayana, G; Jayavel, R

2012-12-01

Picolinium maleate (PM), an organic material has been synthesised and single crystals were grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. PM crystal belongs to the monoclinic crystallographic system with space group P2(1)/c. The crystalline perfection of the grown crystals was analyzed by high-resolution X-ray diffraction rocking curve measurements. The presence of functional groups in PM was identified by FTIR and FT-NMR spectral analyses. Thermal behaviour and stability of picolinium maleate were studied by TGA/DTA analyses. UV-Vis spectral studies reveal that PM crystals are transparent in the wavelength region 327-1100 nm. The laser damage threshold value of PM crystal was found to be 4.3 GW/cm(2) using Nd:YAG laser. The Kurtz and Perry powder second harmonic generation technique confirms the nonlinear optical property of the grown crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

Leaf flavonoids of Albizia lebbeck.

PubMed

el-Mousallamy, A M

1998-06-01

Two new tri-O-glycoside flavonols: kaempferol and quercetin 3-O-alpha-rhamnopyranosyl(1-->6)-beta-glucopyranosyl(1-->6)-beta- galactopyranosides, were identified from the leaves of Albizia lebbeck. Structures were established by conventional methods of analysis and confirmed by ESI-MS, 1H and 13C-NMR spectral analysis.

A new biflavonyloxymethane from Pongamia pinnata.

PubMed

Ghosh, Anindita; Mandal, Suvra; Banerji, Avijit; Banerji, Julie

2010-08-01

The root bark of Pongamia pinnata Pierre Syn Pongamia glabra (Family: Fabaceae) has afforded a new biflavonyloxymethane, karanjabiflavone, along with a known furanoflavone, pongapin. The structure of this new biflavonyloxymethane was elucidated from extensive spectral studies including 2D-NMR experiments. Both of these compounds possess antioxidant activity.

FTIR, FT-Raman, FT-NMR, UV-visible and quantum chemical investigations of 2-amino-4-methylbenzothiazole.

PubMed

Arjunan, V; Sakiladevi, S; Rani, T; Mythili, C V; Mohan, S

2012-03-01

The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectral measurements and complete assignments of the observed spectra of 2-amino-4-methylbenzothiazole (2A4MBT) have been proposed. Ab initio and DFT calculations have been performed and the structural parameters of the compound were determined from the optimised geometry with 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO, LUMO and band gap energies were measured by time-dependent DFT (TD-DFT) approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman activities chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. The influences of methyl and amino groups on the skeletal modes and on the proton chemical shifts have been investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Accelerated 2D magnetic resonance spectroscopy of single spins using matrix completion

NASA Astrophysics Data System (ADS)

Scheuer, Jochen; Stark, Alexander; Kost, Matthias; Plenio, Martin B.; Naydenov, Boris; Jelezko, Fedor

2015-12-01

Two dimensional nuclear magnetic resonance (NMR) spectroscopy is one of the major tools for analysing the chemical structure of organic molecules and proteins. Despite its power, this technique requires long measurement times, which, particularly in the recently emerging diamond based single molecule NMR, limits its application to stable samples. Here we demonstrate a method which allows to obtain the spectrum by collecting only a small fraction of the experimental data. Our method is based on matrix completion which can recover the full spectral information from randomly sampled data points. We confirm experimentally the applicability of this technique by performing two dimensional electron spin echo envelope modulation (ESEEM) experiments on a two spin system consisting of a single nitrogen vacancy (NV) centre in diamond coupled to a single 13C nuclear spin. The signal to noise ratio of the recovered 2D spectrum is compared to the Fourier transform of randomly subsampled data, where we observe a strong suppression of the noise when the matrix completion algorithm is applied. We show that the peaks in the spectrum can be obtained with only 10% of the total number of the data points. We believe that our results reported here can find an application in all types of two dimensional spectroscopy, as long as the measured matrices have a low rank.

Development of high resolution NMR spectroscopy as a structural tool

NASA Astrophysics Data System (ADS)

Feeney, James

1992-06-01

The discovery of the nuclear magnetic resonance (NMR) phenomenon and its development and exploitation as a scientific tool provide an excellent basis for a case-study for examining the factors which control the evolution of scientific techniques. Since the detection of the NMR phenomenon and the subsequent rapid discovery of all the important NMR spectral parameters in the late 1940s, the method has emerged as one of the most powerful techniques for determining structures of molecules in solution and for analysis of complex mixtures. The method has made a dramatic impact on the development of structural chemistry over the last 30 years and is now one of the key techniques in this area. Support for NMR instrumentation attracts a dominant slice of public funding in most scientifically developed countries. The technique is an excellent example of how instrumentation and technology have revolutionised structural chemistry and it is worth exploring how it has been developed so successfully. Clearly its wide range of application and the relatively direct connection between the NMR data and molecular structure has created a major market for the instrumentation. This has provided several competing manufacturers with the incentive to develop better and better instruments. Understanding the complexity of the basics of NMR spectroscopy has been an ongoing challenge attracting the attention of physicists. The well-organised specialist NMR literature and regular scientific meetings have ensured rapid exploitation of any theoretical advances that have a practical relevance. In parallel, the commercial development of the technology has allowed the fruits of such theoretical advances to be enjoyed by the wider scientific community.

Accelerating two-dimensional nuclear magnetic resonance correlation spectroscopy via selective coherence transfer

NASA Astrophysics Data System (ADS)

Ye, Qimiao; Chen, Lin; Qiu, Wenqi; Lin, Liangjie; Sun, Huijun; Cai, Shuhui; Wei, Zhiliang; Chen, Zhong

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool for both qualitative and quantitative analyses of various systems in chemistry, biology, and medicine. However, applications of one-dimensional 1H NMR are often restrained by the presence of severe overlap among different resonances. The advent of two-dimensional (2D) 1H NMR constitutes a promising alternative by extending the crowded resonances into a plane and thereby alleviating the spectral congestions. However, the enhanced ability in discriminating resonances is achieved at the cost of extended experimental duration due to necessity of various scans with progressive delays to construct the indirect dimension. Therefore, in this study, we propose a selective coherence transfer (SECOT) method to accelerate acquisitions of 2D correlation spectroscopy by converting chemical shifts into spatial positions within the effective sample length and then performing an echo planar spectroscopic imaging module to record the spatial and spectral information, which generates 2D correlation spectrum after 2D Fourier transformation. The feasibility and effectiveness of SECOT have been verified by a set of experiments under both homogeneous and inhomogeneous magnetic fields. Moreover, evaluations of SECOT for quantitative analyses are carried out on samples with a series of different concentrations. Based on these experimental results, the SECOT may open important perspectives for fast, accurate, and stable investigations of various chemical systems both qualitatively and quantitatively.

Antimicrobial Applications of Transition Metal Complexes of Benzothiazole Based Terpolymer: Synthesis, Characterization, and Effect on Bacterial and Fungal Strains

PubMed Central

Riswan Ahamed, Mohamed A.; Azarudeen, Raja S.; Kani, N. Mujafar

2014-01-01

Terpolymer of 2-amino-6-nitro-benzothiazole-ethylenediamine-formaldehyde (BEF) has been synthesized and characterized by elemental analysis and various spectral techniques like FTIR, UV-Visible, and 1H and 13C-NMR. The terpolymer metal complexes were prepared with Cu2+, Ni2+, and Zn2+ metal ions using BEF terpolymer as a ligand. The complexes have been characterized by elemental analysis and IR, UV-Visible, ESR, 1H-NMR, and 13C-NMR spectral studies. Gel permeation chromatography was used to determine the molecular weight of the ligand. The surface features and crystalline behavior of the ligand and its complexes were analyzed by scanning electron microscope and X-ray diffraction methods. Thermogravimetric analysis was used to analyze the thermal stability of the ligand and its metal complexes. Kinetic parameters such as activation energy (E a) and order of reaction (n) and thermodynamic parameters, namely, ΔS, ΔF, S*, and Z, were calculated using Freeman-Carroll (FC), Sharp-Wentworth (SW), and Phadnis-Deshpande (PD) methods. Thermal degradation model of the terpolymer and its metal complexes was also proposed using PD method. Biological activities of the ligand and its complexes were tested against Shigella sonnei, Escherichia coli, Klebsiella species, Staphylococcus aureus, Bacillus subtilis, and Salmonella typhimurium bacteria and Aspergillus flavus, Aspergillus niger, Penicillium species, Candida albicans, Cryptococcus neoformans, Mucor species fungi. PMID:25298760

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.

Humic acids from particulate organic matter in the Saguenay Fjord and the St. Lawrence Estuary investigated by advanced solid-state NMR

NASA Astrophysics Data System (ADS)

Mao, J.-D.; Tremblay, L.; Gagné, J.-P.; Kohl, S.; Rice, J.; Schmidt-Rohr, K.

2007-11-01

Detailed structural information on two humic acids extracted from two sinking particulate matter samples at a water depth of 20 m in the Saguenay Fjord (F-20-HA) and the St. Lawrence Estuary (E-20-HA) (Canada), was obtained by advanced solid-state NMR. Spectral-editing analyses provided numerous structural details rarely reported in geochemical studies. The NMR data account almost quantitatively for the elemental compositions. The two humic acids were found to be quite similar, consisting of four main structural components: peptides (ca. 39 ± 3% vs. 34 ± 3% of all C for E-20-HA and F-20-HA, respectively); aliphatic chains, 14-20 carbons long (ca. 25 ± 5% vs. 17 ± 5% of all C); aromatic structures (ca. 17 ± 2% vs. 26 ± 2% of all C); and sugar rings (14 ± 2% vs. 15 ± 2% of all C). Peptides were identified by 13C{ 14N} SPIDER NMR, which selects signals of carbons bonded to nitrogen, and by dipolar DEPT, which selects CH-group signals, in particular the NCH band of peptides. The SPIDER spectra also indicate that heterocycles constitute a significant fraction of the aromatic structures. The aliphatic (CH 2) n chains, which are highly mobile, contain at least one double bond per two chains and end in methyl groups. 1H spin diffusion NMR experiments showed that these mobile aliphatic chains are in close (<10 nm) proximity to the other structural components. A major bacterial contribution to these two samples could explain why the samples, which have different dominant organic matter sources (terrestrial vs. marine), are similar to each other as well as to degraded algae and particles from other waters. The NMR data suggest structures containing mobile lipids in close proximity to peptides and carbohydrates (e.g., peptidoglycan) as found in bacterial cell walls. Measured yields of muramic acid and D-amino acids confirmed the presence of bacterial cell wall components in the studied samples.

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.

Efficient DNP NMR of Membrane Proteins: Sample Preparation Protocols, Sensitivity, and Radical Location

PubMed Central

Liao, Shu Y.; Lee, Myungwoon; Wang, Tuo; Sergeyev, Ivan V.; Hong, Mei

2016-01-01

Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~4 fold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105–160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes. PMID:26873390

The structural and spectroscopic investigation of 2-chloro-3-methylquinoline by DFT method and UV-Vis, NMR and vibrational spectral techniques combined with molecular docking analysis

NASA Astrophysics Data System (ADS)

Kose, Etem; Atac, Ahmet; Bardak, Fehmi

2018-07-01

This study comprises the structural and spectroscopic evaluation of a quinoline derivative, 2-chloro-3-methylquinoline (2Cl3MQ), via UV-Vis, 1H and 13C NMR, FT-IR and FT-Raman techniques experimentally, theoretically with DFT and TD-DFT quantum chemical calculations at B3LYP/6-311++G (d, p) level of theory, and investigation of the in silico pharmaceutical potent of 2Cl3MQ in comparison to 2ClnMQ (n = 3,4,7,8,9,10) substituted quinolines. The experimental measurements were recorded as follows; UV-vis spectra were obtained in the range of 200-400 nm in the water and ethanol solvents. 1H and 13C NMR spectra were recorded in CDCl3. Vibrational spectra were obtained in the region of 4000-400 cm-1 and 3500-10 cm-1 for FT-IR and FT-Raman spectra, respectively. Structural and spectroscopic features obtained through theoretical evaluations include: electrostatic features, atomic charges and molecular electrostatic potential surface, the frontier molecular orbital characteristics, the density of states and their overlapping nature, the electronic transition properties, thermodynamical and nonlinear optical characteristics, and predicted UV-Vis, 1H and 13C NMR, FT-IR and FT-Raman spectra. Ligand-enzyme interactions of 2ClnMQ (n = 3,4,7,8,9,10) substituted quinolines with Malate Synthase from Mycobacterium Tuberculosis (MtbMS) were investigated via molecular docking. The role of position of methyl substitution on the inhibitor character of the ligands was discussed on the basis of noncovalent interaction profiles.

The Influence of Plant Litter on Soil Water Repellency: Insight from 13C NMR Spectroscopy.

PubMed

Cesarano, Gaspare; Incerti, Guido; Bonanomi, Giuliano

2016-01-01

Soil water repellency (SWR, i.e. reduced affinity for water owing to the presence of organic hydrophobic coatings on soil particles) has relevant hydrological implications because low rates of infiltration enhance water runoff, and untargeted diffusion of fertilizers and pesticides. Previous studies investigated the occurrence of SWR in ecosystems with different vegetation cover but did not clarify its relationships with litter biochemical quality. Here, we investigated the capability of different plant litter types to induce SWR by using fresh and decomposed leaf materials from 12 species, to amend a model sandy soil over a year-long microcosm experiment. Water repellency, measured by the Molarity of an Ethanol Droplet (MED) test, was tested for the effects of litter species and age, and compared with litter quality assessed by 13C-CPMAS NMR in solid state and elemental chemical parameters. All litter types were highly water repellent, with MED values of 18% or higher. In contrast, when litter was incorporated into the soil, only undecomposed materials induced SWR, but with a large variability of onset and peak dynamics among litter types. Surprisingly, SWR induced by litter addition was unrelated to the aliphatic fraction of litter. In contrast, lignin-poor but labile C-rich litter, as defined by O-alkyl C and N-alkyl and methoxyl C of 13C-CPMAS NMR spectral regions, respectively, induced a stronger SWR. This study suggests that biochemical quality of plant litter is a major controlling factor of SWR and, by defining litter quality with 13C-CPMAS NMR, our results provide a significant novel contribution towards a full understanding of the relationships between plant litter biochemistry and SWR.

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.

DNA interaction studies of new nano metal based anticancer agent: validation by spectroscopic methods

NASA Astrophysics Data System (ADS)

Tabassum, Sartaj; Sharma, Girish Chandra; Arjmand, Farukh; Azam, Ameer

2010-05-01

A new nano dimensional heterobimetallic Cu-Sn containing complex as a potential drug candidate was designed, synthesized and characterized by analytical and spectral methods. The electronic absorption and electron paramagnetic resonance parameters of the complex revealed that the Cu(II) ion exhibits a square pyramidal geometry with the two pyrazole nitrogen atoms, the amine nitrogen atom and the carboxylate oxygen of the phenyl glycine chloride ligand located at the equatorial sites and the coordinated chloride ion occupying an apical position. 119Sn NMR spectral data showed a hexa-coordinated environment around the Sn(IV) metal ion. TEM, AFM and XRD measurements illustrate that the complex could induce the condensation of CT-DNA to a particulate nanostructure. The interaction of the Cu-Sn complex with CT-DNA was investigated by UV-vis absorption and emission spectroscopy, as well as cyclic voltammetric measurements. The results indicated that the complex interacts with DNA through an electrostatic mode of binding with an intrinsic binding constant Kb = 8.42 × 104 M - 1. The Cu-Sn complex exhibits effective cleavage of pBR322 plasmid DNA by an oxidative cleavage mechanism, monitored at different concentrations both in the absence and in the presence of reducing agents.

Antimicrobial Evaluation of Mangiferin Analogues

PubMed Central

Singh, S. K.; Kumar, Y.; Kumar, S. Sadish; Sharma, V. K.; Dua, K.; Samad, A.

2009-01-01

The naturally occurring xanthone glycoside mangiferin has been isolated by column chromatography from the ethanol extract of stem bark of Mangifera indica. Mangiferin was further converted to 5-(N-phenylaminomethyleno)mangiferin, 5-(N-p-chlorophenylaminomethyleno) mangiferin, 5-(N-2-methylphenylaminomethyleno) mangiferin, 5-(N-p-methoxyphenylaminomethyleno) mangiferin, 5-(N, N-diphenylaminomethyleno) mangiferin, 5-(N--napthylaminomethyleno) mangiferin and 5-(N-4-methylphenylaminomethyleno) mangiferin. Mangiferin and its analogues were characterized by melting point and Rf value determination and through spectral technique like UV, IR, and NMR spectral analysis. The synthesized compounds were screened for antimicrobial activity. PMID:20490307

Author Correction: Biochemical phosphates observed using hyperpolarized 31P in physiological aqueous solutions.

PubMed

Nardi-Schreiber, Atara; Gamliel, Ayelet; Harris, Talia; Sapir, Gal; Sosna, Jacob; Gomori, J Moshe; Katz-Brull, Rachel

2018-05-22

The original version of the Supplementary Information associated with this Article contained an error in Supplementary Figure 2 and Supplementary Figure 5 in which the 31 P NMR spectral lines were missing. The HTML has been updated to include a corrected version of the Supplementary Information.

Effect of Temperature on Electrical Conductivity of Guaiacol-Guanidine Hydrochloride-Formaldehyde Copolymer Resin

NASA Astrophysics Data System (ADS)

Kukade, S. D.; Bawankar, S. V.

2018-02-01

The purpose of the present paper is to report temperature dependence of electrical conductivity on Guaiacol-guanidine hydrochloride-formaldehyde copolymer resin. By using a microwave irradiation technique, various ratios of copolymer resin were synthesized from the reacting monomers, i.e., guaiacol, guanidine hydrochloride and formaldehyde. The characterization of the copolymer resins has been fulfilled by spectral methods viz. ultraviolet visible (UV visible), infrared and proton nuclear magnetic spectroscopy (1H-NMR). The solid state direct current electrical conductivity of synthesized copolymer resins has been measured as a function of temperature. The electrical conductivity values of all the copolymers have been found in the range of a semiconductor.

Dye Foils With Increased Durability For Passive Q-Switching In A 1064 Nm Laser.

NASA Astrophysics Data System (ADS)

Mierczyk, Z.; Kwasny, M.; Czeszko, J.

1987-10-01

The results of spectral (IR, UV-VIS, H NMR) , gel permeation chromatography and differential thermal analysis investigations of structures of dye foils consisting of bis-(4-dimethyl-amino-dithio-benzil)-nickel dye suspended in polymethylmethacrylate matrix, to be used for passive Q-switching in a 1064 nm laser, are reported. Results of experimental measurements and of numerical calculations of thermal and generating properties, and of the endurance of passive foil type Q-switches in the resona-tor of YAG:Nd3+ laser are also presented. Optimization of polymerization conditions has enabled the production of dye foils with high thermal and photochemical resistance, which give stable operation of a giant pulsed laser.

The spectroscopy of singlets and triplets excites electronic states, spatial and electronic structure of hydrocarbons and quantum classifications in chemmotology

NASA Astrophysics Data System (ADS)

Obukhov, A. E.

2017-01-01

In this work we demonstrate the physical foundations of the spectroscopy of the grounds states: E- and X-ray, (RR) Raman scattering the NMR 1H and 13C and IR-, EPR- absorption and the singlets and triplets electronic excited states in the multinuclear hydrocarbons in chemmotology. The parameters of UV-absorption, RR-Raman scattering of light, the fluorescence and the phosphorescence and day-lasers at the pumping laser and lamp, OLEDs and OTETs- are measurements. The spectral-energy properties are briefly studied. The quantum-chemical LCAO-MO SCF expanded-CI PPP/S and INDO/S methods in the electronic and spatial structure hidrocarbons are considered.

Nicotine Metabolite Ratio (3-hydroxycotinine/cotinine) in Plasma and Urine by Different Analytical Methods and Laboratories: Implications for Clinical Implementation

PubMed Central

Tanner, Julie-Anne; Novalen, Maria; Jatlow, Peter; Huestis, Marilyn A.; Murphy, Sharon E.; Kaprio, Jaakko; Kankaanpää, Aino; Galanti, Laurence; Stefan, Cristiana; George, Tony P.; Benowitz, Neal L.; Lerman, Caryn; Tyndale, Rachel F.

2015-01-01

Background The highly genetically variable enzyme CYP2A6 metabolizes nicotine to cotinine (COT) and COT to trans-3′-hydroxycotinine (3HC). The nicotine metabolite ratio (NMR, 3HC/COT) is commonly used as a biomarker of CYP2A6 enzymatic activity, rate of nicotine metabolism, and total nicotine clearance; NMR is associated with numerous smoking phenotypes, including smoking cessation. Our objective was to investigate the impact of different measurement methods, at different sites, on plasma and urinary NMR measures from ad libitum smokers. Methods Plasma (n=35) and urine (n=35) samples were sent to eight different laboratories, which employed similar and different methods of COT and 3HC measurements to derive the NMR. We used Bland-Altman analysis to assess agreement, and Pearson correlations to evaluate associations, between NMR measured by different methods. Results Measures of plasma NMR were in strong agreement between methods according to Bland-Altman analysis (ratios 0.82–1.16) and were highly correlated (all Pearson r>0.96, P<0.0001). Measures of urinary NMR were in relatively weaker agreement (ratios 0.62–1.71) and less strongly correlated (Pearson r values of 0.66–0.98, P<0.0001) between different methods. Plasma and urinary COT and 3HC concentrations, while weaker than NMR, also showed good agreement in plasma, which was better than in urine, as was observed for NMR. Conclusions Plasma is a very reliable biological source for the determination of NMR, robust to differences in these analytical protocols or assessment site. Impact Together this indicates a reduced need for differential interpretation of plasma NMR results based on the approach used, allowing for direct comparison of different studies. PMID:26014804

Structure determination of two new indole-diterpenoids from Penicillium sp. CM-7 by NMR spectroscopy.

PubMed

Zhang, Yu-Hong; Huang, Sheng-Dong; Pan, Hua-Qi; Bian, Xi-Qing; Wang, Zai-Ying; Han, Ai-Hong; Bai, Jiao

2014-06-01

Two new indole-diterpenoids 4b-deoxy-1'-O-acetylpaxilline (1) and 4b-deoxypenijanthine A (2) were isolated from the fermentation broth and the mycelia of the soil fungus Penicillium sp. CM-7, along with three known structurally related compounds, 1'-O-acetylpaxilline (3), paspaline (4) and 3-deoxo-4b-deoxypaxilline (5). The structures of compounds 1 and 2 were elucidated by extensive spectroscopic methods, especially 2D NMR, and their absolute configurations were suggested on the basis of the circular dichroism spectral analysis and the NOESY data. Copyright © 2014 John Wiley & Sons, Ltd.

New Naphthoquinone Terpenoids from Marine Actinobacterium, Streptomyces sp. CNQ-509

PubMed Central

Kwon, Hak Cheol

2018-01-01

A member of the marine streptomycete clade MAR4, Streptomyces sp. CNQ-509, has genetic potential for the biosynthesis of hybrid isoprenoids and produces several meroterpenoids such as naphterpin, nitropyrrolin and marinophenazine. Our research on the strain CNQ-509 led to the isolation of two new naphterpin derivatives (1 and 2) comprised of naphthoquinone and geranyl moieties along with the known terpenoid, debromomarinone. The two-dimensional structure of these compounds was determined through spectral data analysis using data from NMR, MS and UV spectroscopy. Furthermore, the full structures of 1 and 2 including absolute configurations were unequivocally established by a combination of NMR experiments and chemical modifications. PMID:29534540

Restricted amide rotation with steric hindrance induced multiple conformations

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Multiple biological activities and molecular docking studies of newly synthesized 3-(pyridin-4-yl)-1H-pyrazole-5-carboxamide chalcone hybrids.

PubMed

Sribalan, Rajendran; Banuppriya, Govindharasu; Kirubavathi, Maruthan; Jayachitra, A; Padmini, Vediappen

2016-12-01

A series of fifteen new chemical entities, 3-(pyridin-4-yl)-1H-pyrazole-5-carboxamide chalcones (6a-o), were synthesized as new hybrids with enriched biological activities compared to their parent molecules. The compounds were characterized by 1 H NMR, 13 C NMR, Mass and IR spectral studies. Their antibacterial, anti-inflammatory and antioxidant activities have been evaluated. These compounds showed moderate to good antibacterial, anti-inflammatory and antioxidant activities. The molecular docking analysis was performed with cyclooxygenase enzyme to ascertain the probable binding model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Band selective small flip angle COSY: a simple experiment for the analyses of 1H NMR spectra of small chiral molecules.

PubMed

Prabhu, Uday Ramesh; Suryaprakash, N

2008-12-01

The NMR spectroscopic discrimination of enantiomers in the chiral liquid crystalline solvent is more often carried out using (2)H detection in its natural abundance. The employment of (1)H detection for such a purpose is severely hampered due to significant loss of resolution in addition to indistinguishable overlap of the spectra from the two enantiomers. This study demonstrates that the band selected small flip angle homonuclear correlation experiment is a simple and robust technique that provides unambiguous discrimination, very high spectral resolution, reduced multiplicity of transitions, relative signs of the couplings and enormous saving of instrument time.

Differential Attenuation of NMR Signals by Complementary Ion-Exchange Resin Beads for De Novo Analysis of Complex Metabolomics Mixtures.

PubMed

Zhang, Bo; Yuan, Jiaqi; Brüschweiler, Rafael

2017-07-12

A primary goal of metabolomics is the characterization of a potentially very large number of metabolites that are part of complex mixtures. Application to biofluids and tissue samples offers insights into biochemical metabolic pathways and their role in health and disease. 1D 1 H and 2D 13 C- 1 H HSQC NMR spectra are most commonly used for this purpose. They yield quantitative information about each proton of the mixture, but do not tell which protons belong to the same molecule. Interpretation requires the use of NMR spectral databases, which naturally limits these investigations to known metabolites. Here, a new method is presented that uses complementary ion exchange resin beads to differentially attenuate 2D NMR cross-peaks that belong to different metabolites. Based on their characteristic attenuation patterns, cross-peaks could be clustered and assigned to individual molecules, including unknown metabolites with multiple spin systems, as demonstrated for a metabolite model mixture and E. coli cell lysate. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

2017-07-19

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

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

PubMed

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

2009-11-02

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

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Photochemical Degradation of the Anticancer Drug Bortezomib by V-UV/UV (185/254 nm) Investigated by (1)H NMR Fingerprinting: A Way to Follow Aromaticity Evolution.

PubMed

Martignac, Marion; Balayssac, Stéphane; Gilard, Véronique; Benoit-Marquié, Florence

2015-06-18

We have investigated the removal of bortezomib, an anticancer drug prescribed in multiple myeloma, using the photochemical advanced oxidation process of V-UV/UV (185/254 nm). We used two complementary analytical techniques to follow the removal rate of bortezomib. Nuclear magnetic resonance (NMR) is a nonselective method requiring no prior knowledge of the structures of the byproducts and permits us to provide a spectral signature (fingerprinting approach). This untargeted method provides clues to the molecular structure changes and information on the degradation of the parent drug during the irradiation process. This holistic NMR approach could provide information for monitoring aromaticity evolution. We use liquid chromatography, coupled with high-resolution mass spectrometry (LC-MS), to correlate results obtained by (1)H NMR and for accurate identification of the byproducts, in order to understand the mechanistic degradation pathways of bortezomib. The results show that primary byproducts come from photoassisted deboronation of bortezomib at 254 nm. A secondary byproduct of pyrazinecarboxamide was also identified. We obtained a reliable correlation between these two analytical techniques.

13C and 1H NMR (Nuclear Magnetic Resonance) studies of solid polyolefines

NASA Technical Reports Server (NTRS)

Cudby, M. E. A.; Harris, R. K.; Metcalfe, K.; Packer, K. J.; Smith, P. W. R.

1983-01-01

The basis of H-1 and C-13 high-resolution NMR investigations of solid polymers is outlined. The C-13 NMR spectra of solid syndiotactic and isotactic polypropene are discussed and their interpretation in terms of conformation and chain-packing effects are reviewed. The effects of decreasing temperature on the C-13 high-resolution spectrum of an annealed sample of isotactic polypropene is described and interpreted in terms of the crystal structure. The question of the proportion of the sample giving rise to C-13 signals is addressed and some results reported. The main cause for observing only part of the total sample is shown to be the H-1 rotating frame spin-lattice relaxation behavior. The H-1 spin-lattice relaxation and spectral characteristics of a number of polyolefin samples are summarized and the role of spin-diffusion discussed.

Characterization of two minor saponins from Cordia piauhiensis by 1H and 13C NMR spectroscopy.

PubMed

Santos, Renata P; Silveira, Edilberto R; Lemos, Telma Leda G; Viana, Francisco Arnaldo; Braz-Filho, Raimundo; Pessoa, Otília Deusdênia L

2005-06-01

A careful NMR analysis with full assignment of the 1H and 13C spectral data for two minor saponins isolated from stems of Cordia piauhiensis is reported. These saponins were isolated by high-performance liquid chromatography and characterized as 3beta-O-[alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl]pomolic acid 28-O-[beta-D-glucopyranosyl-(1 --> 6)-beta-D-glucopyranosyl] ester (1) and 3beta-O-[alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl]oleanolic acid 28-O-[beta-D-xylopyranosyl-(1 --> 2)-beta-D-glucopyranosyl-(1 --> 6)-beta-D-glucopyranosyl] ester (2). Their structures were established using a combination of 1D and 2D (1H, 1H-COSY, TOCSY, NOESY, gs-HMQC and gs-HMBC) NMR techniques, electrospray ionization mass spectrometry and chemical evidence. Copyright 2005 John Wiley & Sons, Ltd.

CD and 31P NMR studies of tachykinin and MSH neuropeptides in SDS and DPC micelles

NASA Astrophysics Data System (ADS)

Schneider, Sydney C.; Brown, Taylor C.; Gonzalez, Javier D.; Levonyak, Nicholas S.; Rush, Lydia A.; Cremeens, Matthew E.

2016-02-01

Secondary structural characteristics of substance P (SP), neurokinin A (NKA), neurokinin B (NKB), α-melanocyte stimulating hormone peptide (α-MSH), γ1-MSH, γ2-MSH, and melittin were evaluated with circular dichroism in phosphite buffer, DPC micelles, and SDS micelles. CD spectral properties of γ1-MSH and γ2-MSH as well as 31P NMR of DPC micelles with all the peptides are reported for the first time. Although, a trend in the neuropeptide/micelle CD data appears to show increased α-helix content for the tachykinin peptides (SP, NKA, NKB) and increased β-sheet content for the MSH peptides (α-MSH, γ1-MSH, γ2-MSH) with increasing peptide charge, the lack of perturbed 31P NMR signals for all neuropeptides could suggest that the reported antimicrobial activity of SP and α-MSH might not be related to a membrane disruption mode of action.

Enhanced NMR-based profiling of polyphenols in commercially available grape juices using solid-phase extraction.

PubMed

Savage, Angela K; van Duynhoven, John P M; Tucker, Gregory; Daykin, Clare A

2011-12-01

Grapes and related products, such as juices, and in particular, their polyphenols, have previously been associated with many health benefits, such as protection against cardiovascular disease. Within grapes, a large range of structurally diverse polyphenols can be present, and their characterisation stands as a challenge. (1)H NMR spectroscopy in principle would provide a rapid, nondestructive and straightforward method for profiling of polyphenols. However, polyphenol profiling and identification in grape juices is hindered because of signals of prevailing carbohydrates causing spectral overlap and compromising dynamic range. This study describes the development of an extraction method prior to analysis using (1)H NMR spectroscopy, which can, potentially, significantly increase the number of detectable polyphenols and aid their identification, by reduction of signal overlap and selective removal of heavily dominating compounds such as sugars. Copyright © 2012 John Wiley & Sons, Ltd.

Cell-free synthesis of membrane subunits of ATP synthase in phospholipid bicelles: NMR shows subunit a fold similar to the protein in the cell membrane

PubMed Central

Uhlemann, Eva-Maria E; Pierson, Hannah E; Fillingame, Robert H; Dmitriev, Oleg Y

2012-01-01

NMR structure determination of large membrane proteins is hampered by broad spectral lines, overlap, and ambiguity of signal assignment. Chemical shift and NOE assignment can be facilitated by amino acid selective isotope labeling in cell-free protein synthesis system. However, many biological detergents are incompatible with the cell-free synthesis, and membrane proteins often have to be synthesized in an insoluble form. We report cell-free synthesis of subunits a and c of the proton channel of Escherichia coli ATP synthase in a soluble form in a mixture of phosphatidylcholine derivatives. In comparison, subunit a was purified from the cell-free system and from the bacterial cell membranes. NMR spectra of both preparations were similar, indicating that our procedure for cell-free synthesis produces protein structurally similar to that prepared from the cell membranes. PMID:22162071

Identification of polymethoxylated flavones from green tangerine peel (Pericarpium Citri Reticulatae Viride) by chromatographic and spectroscopic techniques.

PubMed

Wang, Dandan; Wang, Jian; Huang, Xuehui; Tu, Ying; Ni, Kunyi

2007-05-09

Polymethoxylated flavones (PMFs) were extracted from Pericarpium Citri Reticulatae Viride using a procedure that obtained a consistent mixture of PMFs both in identity and proportion. The mixture consisted of isosinensetin (0.2%) (1), sinensetin (1.7%) (4), tetramethyl-o-isoscutellarein (0.3%) (5), nobiletin (40.5%) (6), tetramethyl-o-scutellarein (1.2%) (7), tangeretin (45.6%) (10), 5-demethylnobiletin (8.7%) (12), 5-demethyl tangeretin (0.8%) (14) and other flavonoids including heptamethoxyflavone (1.0%) (9), among which, compounds 1, 4, 5, 7 and 9 were identified based on their UV spectra, MS data and elution order described in the literature while compounds 6, 10, 12 and 14 were isolated and identified by UV, IR, MS, (1)H NMR, (13)C NMR and 2D NMR spectral studies. In addition, compound 14 was isolated and identified for the first time from Citrus.

Complexation of nitrogen and sulphur donor Schiff's base ligand to Cr(III) and Ni(II) metal ions: Synthesis, spectroscopic and antipathogenic studies

NASA Astrophysics Data System (ADS)

Sharma, Amit Kumar; Chandra, Sulekh

2011-01-01

2,6-Diacetyl pyridine based ligand was synthesized by the reaction of 2,6-diacetyl pyridine with thiocarbohydrazide in presence of acetic acid. The coordination compounds with Cr(III) and Ni(II) metal ions having [Cr(L)X]X 2 and [Ni(L)X]X compositions (where L = ligand and X = NO 3-, Cl - and CH 3COO -) were synthesized and characterized by physicochemical and spectral studies. The studies like elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV-Vis, NMR, mass and EPR reveal that the complexes are octahedral. The compounds were examined against the pathogenic fungal and bacterial strains like Alternaria brassicae, Aspergillus niger, Fusarium oxysporum, Xanthomonas compestris and Pseudomonas aeruginosa. A. niger causes the diseases Apergillosis and Otomycosis in humans.

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.

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes.

PubMed

Romer, Frederik H; Underwood, Andrew P; Senekal, Nadine D; Bonnet, Susan L; Duer, Melinda J; Reid, David G; van der Westhuizen, Jan H

2011-01-28

Solid state ¹³C-NMR spectra of pure tannin powders from four different sources--mimosa, quebracho, chestnut and tara--are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The ²⁷Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

Structural features of a bituminous coal and their changes during low-temperature oxidation and loss of volatiles investigated by advanced solid-state NMR spectroscopy

USGS Publications Warehouse

Mao, J.-D.; Schimmelmann, A.; Mastalerz, Maria; Hatcher, P.G.; Li, Y.

2010-01-01

Quantitative and advanced 13C solid-state NMR techniques were employed to investigate (i) the chemical structure of a high volatile bituminous coal, as well as (ii) chemical structural changes of this coal after evacuation of adsorbed gases, (iii) during oxidative air exposure at room temperature, and (iv) after oxidative heating in air at 75 ??C. The solid-state NMR techniques employed in this study included quantitative direct polarization/magic angle spinning (DP/MAS) at a high spinning speed of 14 kHz, cross polarization/total sideband suppression (CP/TOSS), dipolar dephasing, CH, CH2, and CHn selection, 13C chemical shift anisotropy (CSA) filtering, two-dimensional (2D) 1H-13C heteronuclear correlation NMR (HETCOR), and 2D HETCOR with 1H spin diffusion. With spectral editing techniques, we identified methyl CCH 3, rigid and mobile methylene CCH2C, methine CCH, quaternary Cq, aromatic CH, aromatic carbons bonded to alkyls, small-sized condensed aromatic moieties, and aromatic C-O groups. With direct polarization combined with spectral-editing techniques, we quantified 11 different types of functional groups. 1H-13C 2D HETCOR NMR experiments indicated spatial proximity of aromatic and alkyl moieties in cross-linked structures. The proton spin diffusion experiments indicated that the magnetization was not equilibrated at a 1H spin diffusion time of 5 ms. Therefore, the heterogeneity in spatial distribution of different functional groups should be above 2 nm. Recoupled C-H long-range dipolar dephasing showed that the fraction of large charcoal-like clusters of polycondensed aromatic rings was relatively small. The exposure of this coal to atmospheric oxygen at room temperature for 6 months did not result in obvious chemical structural changes of the coal, whereas heating at 75 ??C in air for 10 days led to oxidation of coal and generated some COO groups. Evacuation removed most volatiles and caused a significant reduction in aliphatic signals in its DP/MAS spectrum. DP/MAS, but not CP/MAS, allowed us to detect the changes during low-temperature oxidation and loss of volatiles. These results demonstrate the applicability of advanced solid-state NMR techniques in chemical characterization of coal. ?? 2010 American Chemical Society.

GC-MS and /sup 17/O NMR tracer studies of Et/sub 3/PO formation from auranofin and H/sub 2//sup 17/O in the presence of bovine serum albumin: an in vitro model for auranofin metabolism

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

Isab, A.A.; Shaw, C.F. III; Locke, J.

1988-09-21

/sup 17/O NMR spectroscopy and gas chromatographic-mass spectral analysis have been used to monitor the source of oxygen in the triethylphosphine oxide formed by the reaction of the antiarthritic drug auranofin ((2,3,4,6-tetra-O-acetyl-..beta..-D-1-glucopyranosato)(triethylphosphine)gold(I)) and bovine serum albumin (BSA) in the presence of reduced glutathione (GtSH). A procedure to extract Et/sub 3/PO from aqueous solutions and concentrate it for subsequent analyses was developed. When the in vitro reaction is carried out aerobically in /sup 17/O-enriched water, Et/sub 3/P/sup 17/O is generated. The chemical ionization (CH/sub 4/) mass measurement, (m + 1)/z = 135, and the /sup 17/O NMR parameters (delta/sub O/ =more » 40.6 and /sup 1/J/sub PO/ = 156 /plus minus/ 5 Hz) unambiguously establish its identity. The SH titer of the albumin (mole ratio of protein SH groups to BSA) increases during the reaction, confirming that albumin disulfide bonds are reduced in the reaction. Under aerobic conditions, the enriched Et/sub 3/PO accounts for at least 60% of the Et/sub 3/PO formed. The significance of these results for the in vivo formation of Et/sub 3/PO, an auranofin metabolite, is discussed. 25 references, 2 figures.« less

Biopolymer nanocomposite films reinforced with nanocellulose whiskers

Treesearch

Amit Saxena; Marcus Foston; Mohamad Kassaee; Thomas J. Elder; Arthur J. Ragauskas

2011-01-01

A xylan nanocomposite film with improved strength and barrier properties was prepared by a solution casting using nanocellulose whiskers as a reinforcing agent. The 13C cross-polarization magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR) analysis of the spectral data obtained for the NCW/xylan nanocomposite films indicated the signal intensity originating...

Spectral Study of Modified Humic Acids from Lignite

NASA Astrophysics Data System (ADS)

Zherebtsov, Sergey; Malyshenko, Natalya; Bryukhovetskaya, Ludmila; Ismagilov, Zinfer

2017-11-01

The IR-Fourier, ESR and solid-state 13C NMR analysis are used for investigation of unmodified and modified humic acids obtained from Tisul lignite (the Kansko-Achinsk Basin). Treatment with Hydrogen peroxide used for modification of humic acids and it changes the functionalgroup composition of the humic acids and increases the sorptional capacity

Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

NASA Astrophysics Data System (ADS)

Karthigha, S.; Krishnamoorthi, C.

2018-03-01

An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

Growth, density functional theory (DFT) and spectral studies on L-2-aminobutyric acid -biologically active material

NASA Astrophysics Data System (ADS)

Usha, C.; Santhakumari, R.; Meenakshi, R.; Jayasree, R.; Bhuvaneswari, M.

2017-12-01

Single crystal of L-2-aminobutyric acid (ABA) was grown from water by slow evaporation at room temperature. The crystalline nature of the grown crystal was confirmed using powder X-ray diffraction studies. The grown crystal was subjected to FT-IR, FT-Raman, 1H NMR and 13C NMR spectral analyses to confirm the presence of functional group and molecular structure respectively. Thermal properties were investigated by thermogravimetric and differential thermal analyses. The range and percentage of optical transmission was ascertained by recording UV-vis-NIR spectrum. The electronic charge distribution and reactivity of the molecules within the crystal were studied by HOMO and LUMO analysis and the molecular electrostatic potential (MEP) of the grown crystal was performed using the B3LYP method. The anti-bacterial activities of the crystal were performed by disk diffusion method against the standard bacteria E. coli. The crystal exhibits good anti-bacterial activity. Second harmonic generation efficiency of the powdered ABA crystal was tested using Nd:YAG laser and it is found to be ∼3.3 times that of potassium dihydrogen orthophosphate.

NMR of (133)Cs(+) in stretched hydrogels: One-dimensional, z- and NOESY spectra, and probing the ion's environment in erythrocytes.

PubMed

Kuchel, Philip W; Shishmarev, Dmitry; Puckeridge, Max; Levitt, Malcolm H; Naumann, Christoph; Chapman, Bogdan E

2015-12-01

(133)Cs nuclear magnetic resonance (NMR) spectroscopy was conducted on (133)Cs(+) in gelatin hydrogels that were either relaxed or stretched. Stretching generated a septet from this spin-7/2 nucleus, and its nuclear magnetic relaxation was studied via z-spectra, and two-dimensional nuclear Overhauser (NOESY) spectroscopy. Various spectral features were well simulated by using Mathematica and the software package SpinDynamica. Spectra of CsCl in suspensions of human erythrocytes embedded in gelatin gel showed separation of the resonances from the cation inside and outside the cells. Upon stretching the sample, the extracellular (133)Cs(+) signal split into a septet, while the intracellular peak was unchanged, revealing different alignment/ordering properties of the environment inside and around the cells. Differential interference contrast light microscopy confirmed that the cells were stretched when the overall sample was elongated. Analysis of the various spectral features of (133)Cs(+) reported here opens up applications of this K(+) congener for studies of cation-handling by metabolically-active cells and tissues in aligned states. Copyright © 2015 Elsevier Inc. All rights reserved.

Spectral characterization of novel ternary zinc(II) complexes containing 1,10-phenanthroline and Schiff bases derived from amino acids and salicylaldehyde-5-sulfonates

NASA Astrophysics Data System (ADS)

Boghaei, Davar M.; Gharagozlou, Mehrnaz

2007-07-01

A series of new ternary zinc(II) complexes [Zn(L 1-10)(phen)], where phen is 1,10-phenanthroline and H 2L 1-10 = tridentate Schiff base ligands derived from the condensation of amino acids (glycine, L-phenylalanine, L-valine, L-alanine, and L-leucine) and salicylaldehyde-5-sulfonates (sodium salicylaldehyde-5-sulfonate and sodium 3-methoxy-salicylaldehyde-5-sulfonate), have been synthesized. The complexes were characterized by elemental analysis, IR, UV-vis, 1H NMR, and 13C NMR spectra. The IR spectra of the complexes showed large differences between νas(COO) and νs(COO), Δ ν ( νas(COO) - νs(COO)) of 191-225 cm -1, indicating a monodentate coordination of the carboxylate group. Spectral data showed that in these ternary complexes the zinc atom is coordinated with the Schiff base ligand acts as a tridentate ONO moiety, coordinating to the metal through its phenolic oxygen, imine nitrogen, and carboxyl oxygen, and also with the neutral planar chelating ligand, 1,10-phenanthroline, coordinating through nitrogens.

Synthesis, characterization, stereochemistry and biological investigation of certain N-dichloroacetyl-bis(2-chlorophenyl)piperidin-4-ones

NASA Astrophysics Data System (ADS)

Kayalvizhi, R.; Ponnuswamy, S.; Gomathi, K.; Ezhilarasi, K. S.; Usha, G.

2018-02-01

A new series of N-dichloroacetyl-bis(2-chlorophenyl)piperidin-4-ones 4-6 has been synthesized and characterized using IR, 1H, 13C, DEPT and 2D (COSY and HSQC) NMR spectral techniques. The NMR spectral data indicate that the N-acylpiperidin-4-ones 4-6 prefer to exist in an equilibrium between the twist boat conformations with coplanar orientation of Nsbnd Cdbnd O moiety. Furthermore, the antibacterial and antifungal studies have been carried out for compounds 1-6 and the results show that they possess significant activity towards the bacterial organisms Staphylococcus aureus and Salmoneela paratyphi and better activity against the remaining bacterial organisms. All the compounds 1-6 possess moderate antifungal activity. The compounds 4-6 have been docked with the structure of MRSA and the results demonstrate that the compounds 4-6 have similar docking score and glide energy when compared to each other and thus having equal binding affinity. The antioxidant studies show greater activity for compound 4 and poor activity for compounds 5 &6 when compared to the standard drug.

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

PubMed Central

2011-01-01

Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php. PMID:21668943

Online monitoring of fermentation processes via non-invasive low-field NMR.

PubMed

Kreyenschulte, Dirk; Paciok, Eva; Regestein, Lars; Blümich, Bernhard; Büchs, Jochen

2015-09-01

For the development of biotechnological processes in academia as well as in industry new techniques are required which enable online monitoring for process characterization and control. Nuclear magnetic resonance (NMR) spectroscopy is a promising analytical tool, which has already found broad applications in offline process analysis. The use of online monitoring, however, is oftentimes constrained by high complexity of custom-made NMR bioreactors and considerable costs for high-field NMR instruments (>US$200,000). Therefore, low-field (1) H NMR was investigated in this study in a bypass system for real-time observation of fermentation processes. The new technique was validated with two microbial systems. For the yeast Hansenula polymorpha glycerol consumption could accurately be assessed in spite of the presence of high amounts of complex constituents in the medium. During cultivation of the fungal strain Ustilago maydis, which is accompanied by the formation of several by-products, the concentrations of glucose, itaconic acid, and the relative amount of glycolipids could be quantified. While low-field spectra are characterized by reduced spectral resolution compared to high-field NMR, the compact design combined with the high temporal resolution (15 s-8 min) of spectra acquisition allowed online monitoring of the respective processes. Both applications clearly demonstrate that the investigated technique is well suited for reaction monitoring in opaque media while at the same time it is highly robust and chemically specific. It can thus be concluded that low-field NMR spectroscopy has a great potential for non-invasive online monitoring of biotechnological processes at the research and practical industrial scales. © 2015 Wiley Periodicals, Inc.

Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins

NASA Astrophysics Data System (ADS)

Koroloff, Sophie N.; Nevzorov, Alexander A.

2017-01-01

Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the 1H-15N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the 15N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins.

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

NASA Astrophysics Data System (ADS)

Li, Wei

2017-12-01

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

Transition metal complexes of a new 15-membered [N5] penta-azamacrocyclic ligand with their spectral and anticancer studies

NASA Astrophysics Data System (ADS)

El-Boraey, Hanaa A.; Serag El-Din, Azza A.

2014-11-01

Novel penta-azamacrocyclic 15-membered [N5] ligand [L] i.e. 1,5,8,12-tetetraaza-3,4: 9,10-dibenzo-6-ethyl-7-methyl-1,12-(2,6-pyrido)cyclopentadecan-5,7 diene-2,11-dione and its transition metal complexes with Co(II), Ni(II), Cu(II), Ru(III) and Pd(II) have been synthesized and structurally characterized by elemental analysis, spectral, thermal as well as magnetic and molar conductivity measurements. On basis of IR, MS, UV-Vis 1H NMR and EPR spectral studies an octahedral geometry has been proposed for all complexes except Co(II), Cu(II) nitrate complexes and Pd(II) chloride complex that adopt tetrahedral, square pyramidal and square planar geometries, respectively. The antitumor activity of the synthesized ligand and some complexes against human breast cancer cell lines (MCF-7) and human hepatocarcinoma cell lines (HepG2) has been studied. The complexes (IC50 = 2.04-9.7, 2.5-3.7 μg/mL) showed potent antitumor activity comparable with their ligand (IC50 = 11.7, 3.45 μg/mL) against the above mentioned cell lines, respectively. The results evidently show that the activity of the ligand becomes more pronounced and significant when coordinated to the metal ion.

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

A theoretical perspective on the accuracy of rotational resonance (R 2)-based distance measurements in solid-state NMR

NASA Astrophysics Data System (ADS)

Pandey, Manoj Kumar; Ramachandran, Ramesh

2010-03-01

The application of solid-state NMR methodology for bio-molecular structure determination requires the measurement of constraints in the form of 13C-13C and 13C-15N distances, torsion angles and, in some cases, correlation of the anisotropic interactions. Since the availability of structurally important constraints in the solid state is limited due to lack of sufficient spectral resolution, the accuracy of the measured constraints become vital in studies relating the three-dimensional structure of proteins to its biological functions. Consequently, the theoretical methods employed to quantify the experimental data become important. To accentuate this aspect, we re-examine analytical two-spin models currently employed in the estimation of 13C-13C distances based on the rotational resonance (R 2) phenomenon. Although the error bars for the estimated distances tend to be in the range 0.5-1.0 Å, R 2 experiments are routinely employed in a variety of systems ranging from simple peptides to more complex amyloidogenic proteins. In this article we address this aspect by highlighting the systematic errors introduced by analytical models employing phenomenological damping terms to describe multi-spin effects. Specifically, the spin dynamics in R 2 experiments is described using Floquet theory employing two different operator formalisms. The systematic errors introduced by the phenomenological damping terms and their limitations are elucidated in two analytical models and analysed by comparing the results with rigorous numerical simulations.

Chemical Analysis of a "Miller-Type" Complex Prebiotic Broth. Part II: Gas, Oil, Water and the Oil/Water-Interface

NASA Astrophysics Data System (ADS)

Scherer, Sabrina; Wollrab, Eva; Codutti, Luca; Carlomagno, Teresa; da Costa, Stefan Gomes; Volkmer, Andreas; Bronja, Amela; Schmitz, Oliver J.; Ott, Albrecht

2017-12-01

We have analyzed the chemical variety obtained by Miller-Urey-type experiments using nuclear magnetic resonance (NMR) spectroscopy and coherent anti-Stokes Raman scattering (CARS) spectroscopy, gas chromatography followed by mass spectrometry (GC/MS) and two-dimensional gas chromatography followed by mass spectrometry (GCxGC/MS). In the course of a running Miller-Urey-type experiment, a hydrophobic organic layer emerged besides the hydrophilic aqueous phase and the gaseous phase that were initially present. The gas phase mainly consisted of aromatic compounds and molecules containing C≡ C or C≡ N triple bonds. The hydrophilic phase contained at least a few thousands of different molecules, primarily distributed in a range of 50 and 500 Da. The hydrophobic phase is characterized by carbon-rich, oil-like compounds and their amphiphilic derivatives containing oxygen with tensioactive properties. The presence of a wide range of oxidized molecules hints to the availability of oxygen radicals. We suggest that they intervene in the formation of alkylated polyethylene glycol (PEG) in the oil/water interface. CARS spectroscopy revealed distinct vibrational molecular signatures. In particular, characteristic spectral bands for cyanide compounds were observed if the broth was prepared with electric discharges in the gaseous phase. The characteristic spectral bands were absent if discharges were released onto the water surface. NMR spectroscopy on the same set of samples independently confirmed the observation. In addition, NMR spectroscopy revealed overall high chemical variability that suggests strong non-linearities due to interdependent, sequential reaction steps.

Chemical Analysis of a "Miller-Type" Complex Prebiotic Broth : Part II: Gas, Oil, Water and the Oil/Water-Interface.

PubMed

Scherer, Sabrina; Wollrab, Eva; Codutti, Luca; Carlomagno, Teresa; da Costa, Stefan Gomes; Volkmer, Andreas; Bronja, Amela; Schmitz, Oliver J; Ott, Albrecht

2017-12-01

We have analyzed the chemical variety obtained by Miller-Urey-type experiments using nuclear magnetic resonance (NMR) spectroscopy and coherent anti-Stokes Raman scattering (CARS) spectroscopy, gas chromatography followed by mass spectrometry (GC/MS) and two-dimensional gas chromatography followed by mass spectrometry (GCxGC/MS). In the course of a running Miller-Urey-type experiment, a hydrophobic organic layer emerged besides the hydrophilic aqueous phase and the gaseous phase that were initially present. The gas phase mainly consisted of aromatic compounds and molecules containing C≡C or C≡N triple bonds. The hydrophilic phase contained at least a few thousands of different molecules, primarily distributed in a range of 50 and 500 Da. The hydrophobic phase is characterized by carbon-rich, oil-like compounds and their amphiphilic derivatives containing oxygen with tensioactive properties. The presence of a wide range of oxidized molecules hints to the availability of oxygen radicals. We suggest that they intervene in the formation of alkylated polyethylene glycol (PEG) in the oil/water interface. CARS spectroscopy revealed distinct vibrational molecular signatures. In particular, characteristic spectral bands for cyanide compounds were observed if the broth was prepared with electric discharges in the gaseous phase. The characteristic spectral bands were absent if discharges were released onto the water surface. NMR spectroscopy on the same set of samples independently confirmed the observation. In addition, NMR spectroscopy revealed overall high chemical variability that suggests strong non-linearities due to interdependent, sequential reaction steps.

Second-order quadrupolar line shapes under molecular dynamics: An additional transition in the extremely fast regime.

PubMed

Hung, Ivan; Wu, Gang; Gan, Zhehong

NMR spectroscopy is a powerful tool for probing molecular dynamics. For the classic case of two-site exchange, NMR spectra go through the transition from exchange broadening through coalescence and then motional narrowing as the exchange rate increases passing through the difference between the resonance frequencies of the two sites. For central-transition spectra of half-integer quadrupolar nuclei in solids, line shape change due to molecular dynamics occurs in two stages. The first stage occurs when the exchange rate is comparable to the second-order quadrupolar interaction. The second spectral transition comes at a faster exchange rate which approaches the Larmor frequency and generally reduces the isotropic quadrupolar shift. Such a two-stage transition phenomenon is unique to half-integer quadrupolar nuclei. A quantum mechanical formalism in full Liouville space is presented to explain the physical origin of the two-stage phenomenon and for use in spectral simulations. Variable-temperature 17 O NMR of solid NaNO 3 in which the NO 3 - ion undergoes 3-fold jumps confirms the two-stage transition process. The spectra of NaNO 3 acquired in the temperature range of 173-413K agree well with simulations using the quantum mechanical formalism. The rate constants for the 3-fold NO 3 - ion jumps span eight orders of magnitude (10 2 -10 10 s -1 ) covering both transitions of the dynamic 17 O line shape. Copyright © 2016 Elsevier Inc. All rights reserved.

Fast experiments for structure elucidation of small molecules: Hadamard NMR with multiple receivers.

PubMed

Gierth, Peter; Codina, Anna; Schumann, Frank; Kovacs, Helena; Kupče, Ēriks

2015-11-01

We propose several significant improvements to the PANSY (Parallel NMR SpectroscopY) experiments-PANSY COSY and PANSY-TOCSY. The improved versions of these experiments provide sufficient spectral information for structure elucidation of small organic molecules from just two 2D experiments. The PANSY-TOCSY-Q experiment has been modified to allow for simultaneous acquisition of three different types of NMR spectra-1D C-13 of non-protonated carbon sites, 2D TOCSY and multiplicity edited 2D HETCOR. In addition the J-filtered 2D PANSY-gCOSY experiment records a 2D HH gCOSY spectrum in parallel with a (1) J-filtered HC long-range HETCOR spectrum as well as offers a simplified data processing. In addition to parallel acquisition, further time savings are feasible because of significantly smaller F1 spectral windows as compared to the indirect detection experiments. Use of cryoprobes and multiple receivers can significantly alleviate the sensitivity issues that are usually associated with the so called direct detection experiments. In cases where experiments are sampling limited rather than sensitivity limited further reduction of experiment time is achieved by using Hadamard encoding. In favorable cases the total recording time for the two PANSY experiments can be reduced to just 40 s. The proposed PANSY experiments provide sufficient information to allow the CMCse software package (Bruker) to solve structures of small organic molecules. Copyright © 2015 John Wiley & Sons, Ltd.

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

PubMed

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to uncover large consistent sets of interactions. Our algorithm has been implemented in the platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

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.

Characterization of KCNE1 inside Lipodisq Nanoparticles for EPR Spectroscopic Studies of Membrane Proteins.

PubMed

Sahu, Indra D; Zhang, Rongfu; Dunagan, Megan M; Craig, Andrew F; Lorigan, Gary A

2017-06-01

EPR spectroscopic studies of membrane proteins in a physiologically relevant native membrane-bound state are extremely challenging due to the complexity observed in inhomogeneity sample preparation and dynamic motion of the spin-label. Traditionally, detergent micelles are the most widely used membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is often difficult to examine whether the protein structure in a micelle environment is the same as that of the respective membrane-bound state. Recently, lipodisq nanoparticles have been introduced as a potentially good membrane mimetic system for structural studies of membrane proteins. However, a detailed characterization of a spin-labeled membrane protein incorporated into lipodisq nanoparticles is still lacking. In this work, lipodisq nanoparticles were used as a membrane mimic system for probing the structural and dynamic properties of the integral membrane protein KCNE1 using site-directed spin labeling EPR spectroscopy. The characterization of spin-labeled KCNE1 incorporated into lipodisq nanoparticles was carried out using CW-EPR titration experiments for the EPR spectral line shape analysis and pulsed EPR titration experiment for the phase memory time (T m ) measurements. The CW-EPR titration experiment indicated an increase in spectral line broadening with the addition of the SMA polymer which approaches close to the rigid limit at a lipid to polymer weight ratio of 1:1, providing a clear solubilization of the protein-lipid complex. Similarly, the T m titration experiment indicated an increase in T m values with the addition of SMA polymer and approaches ∼2 μs at a lipid to polymer weight ratio of 1:2. Additionally, CW-EPR spectral line shape analysis was performed on six inside and six outside the membrane spin-label probes of KCNE1 in lipodisq nanoparticles. The results indicated significant differences in EPR spectral line broadening and a corresponding inverse central line width between spin-labeled KCNE1 residues located inside and outside of the membrane for lipodisq nanoparticle samples when compared to lipid vesicle samples. These results are consistent with the solution NMR structure of KCNE1. This study will be beneficial for researchers working on studying the structural and dynamic properties of membrane proteins.

On the exactness of effective Floquet Hamiltonians employed in solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Garg, Rajat; Ramachandran, Ramesh

2017-05-01

Development of theoretical models based on analytic theory has remained an active pursuit in molecular spectroscopy for its utility both in the design of experiments as well as in the interpretation of spectroscopic data. In particular, the role of "Effective Hamiltonians" in the evolution of theoretical frameworks is well known across all forms of spectroscopy. Nevertheless, a constant revalidation of the approximations employed in the theoretical frameworks is necessitated by the constant improvements on the experimental front in addition to the complexity posed by the systems under study. Here in this article, we confine our discussion to the derivation of effective Floquet Hamiltonians based on the contact transformation procedure. While the importance of the effective Floquet Hamiltonians in the qualitative description of NMR experiments has been realized in simpler cases, its extension in quantifying spectral data deserves a cautious approach. With this objective, the validity of the approximations employed in the derivation of the effective Floquet Hamiltonians is re-examined through a comparison with exact numerical methods under differing experimental conditions. The limitations arising from the existing analytic methods are outlined along with remedial measures for improving the accuracy of the derived effective Floquet Hamiltonians.

Self-sorted photoconductive xerogels† †Electronic supplementary information (ESI) available: Full experimental details, rheological data, pK a titrations, further NMR data, full details of the photoconductivity set-up, further photoconductivity measurements. See DOI: 10.1039/c6sc02644c Click here for additional data file.

PubMed Central

Draper, Emily R.; Lee, Jonathan R.; Wallace, Matthew; Jäckel, Frank; Cowan, Alexander J.

2016-01-01

We show that a perylene bisimide (PBI)-based gelator forms self-sorted mixtures with a stilbene-based gelator. To form the self-sorted gels, we use a slow pH change induced by the hydrolysis of glucono-δ-lactone (GdL) to gluconic acid. We prove that self-sorting occurs using NMR spectroscopy, UV-Vis spectroscopy, rheology, and viscometry. The corresponding xerogels are photoconductive. Importantly, the wavelength dependence of the photoconductive films is different to that of the films formed from the perylene bisimide alone. Transient absorption spectroscopy of the xerogels reveals changes in the spectrum of the PBI on the picosecond timescale in the presence of stilbene with a PBI radical anion being formed within 10 ps when the stilbene is present. The ability to form the PBI radical anion under visible light leads to the enhanced spectral response of the multicomponent gels. These systems therefore have potential as useful visible-active optoelectronics. PMID:28451108

1H nuclear magnetic resonance studies of sarcoplasmic oxygenation in the red cell-perfused rat heart.

PubMed

Jelicks, L A; Wittenberg, B A

1995-05-01

The proximal histidine N delta H proton of deoxymyoglobin experiences a large hyperfine shift resulting in its 1H nuclear magnetic resonance (NMR) signal appearing at approximately 76 ppm (at 35 degrees C), downfield of the diamagnetic spectral region. 1H NMR of this proton is used to monitor sarcoplasmic oxygen pressure in isolated perfused rat heart. This method monitors intracellular oxygenation in the whole heart and does not reflect oxygenation in a limited region. The deoxymyoglobin resonance intensity is reduced upon conversion of myoglobin to the ferric form by sodium nitrite. 1H resonances of the N delta H protons of the alpha and beta subunits of bovine deoxyhemoglobin do not interfere with the measurement of myoglobin deoxygenation in blood-perfused rat heart. We find that steady-state myoglobin deoxygenation is increased progressively (and reversibly) as oxygenation of the perfusing medium is decreased in both saline and red blood cell-perfused hearts at constant work output. An eightfold increase in the heart rate of the blood-perfused heart resulted in no change in the deoxymyoglobin signal intensity. Intracellular PO2 of myoglobin-containing cells is maintained remarkably constant in changing work states.

Synthesis, characterization and anti-microbial activity of phenylurea-formaldehyde resin (PUF) and its polymer metal complexes (PUF-Mn(II)

NASA Astrophysics Data System (ADS)

Ahamad, Tansir; Alshehri, Saad M.

2012-10-01

Phenylurea-formaldehyde polymer (PUF) was synthesized via polycondensation of phenylurea and formaldehyde in basic medium, its polymer-metal complexes [PUF-M(II)] were prepared with Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) ions. PUF and PUF-M(II) were characterized with magnetic moment measurements, elemental and spectral (UV-visible, FTIR, 1H-NMR, 13C-NMR and ESR) analysis. The thermal behaviors of all the synthesized polymers were carried out using thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The thermal data revealed that all of the PUF-M(II) showed higher thermal stabilities than the PUF and also ascribed that the PUF-Cu(II) showed better thermal stability than the other PUF-M(II). The kinetic parameters such as activation energy, pre-exponential factor etc., were evaluated for these polymer metal complexes using Coats-Redfern equation. In addition, the antimicrobial activity of the synthesized polymers was tested against several microorganisms using agar well diffusion methods. Among all of the PUF-M(II), the antimicrobial activity of the PUF-Cu(II) showed the highest zone of inhibition because of its higher stability constant and may be used in biomedical applications.

Assessment of 1H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

PubMed

Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

2017-01-01

Proton nuclear magnetic resonance ( 1 H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R 2 =0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R 2 =0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative proton magnetic resonance spectroscopy without water suppression

NASA Astrophysics Data System (ADS)

Özdemir, M. S.; DeDeene, Y.; Fieremans, E.; Lemahieu, I.

2009-06-01

The suppression of the abundant water signal has been traditionally employed to decrease the dynamic range of the NMR signal in proton MRS (1H MRS) in vivo. When using this approach, if the intent is to utilize the water signal as an internal reference for the absolute quantification of metabolites, additional measurements are required for the acquisition of the water signal. This can be prohibitively time-consuming and is not desired clinically. Additionally, traditional water suppression can lead to metabolite alterations. This can be overcome by performing quantitative 1H MRS without water suppression. However, the non-water-suppressed spectra suffer from gradient-induced frequency modulations, resulting in sidebands in the spectrum. Sidebands may overlap with the metabolites, which renders the spectral analysis and quantification problematic. In this paper, we performed absolute quantification of metabolites without water suppression. Sidebands were removed by utilizing the phase of an external reference signal of single resonance to observe the time-varying the static field fluctuations induced by gradient-vibration and deconvolving this phase contamination from the desired NMR signal. The quantification of metabolites was determined after sideband correction by calibrating the metabolite signal intensities against the recorded water signal. The method was evaluated by phantom and in vivo measurements in human brain. The maximum systematic error for the quantified metabolite concentrations was found to be 10.8%, showing the feasibility of the quantification after sideband correction.

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate.

PubMed

Bagno, Alessandro; Rastrelli, Federico; Saielli, Giacomo

2008-06-01

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems. Copyright (c) 2008 John Wiley & Sons, Ltd

H-1 NMR study of ternary ammonia-alkali metal-graphite intercalation compounds

NASA Technical Reports Server (NTRS)

Tsang, T.; Fronko, R. M.; Resing, H. A.; Qian, X. W.; Solin, S. A.

1987-01-01

For the first-stage ternary ammonia-alkali metal-graphite intercalation compounds M(NH3)(x)C24(x of about 4, M = K, Rb, Cs), three sets of triplet H-1 NMR spectral lines have been observed at various temperatures and orientations due to the H-1 - H-1 and N-14 - H-1 dipolar interactions. The structures of these compounds have been inferred as mobile (liquid-like) intercalant layers of planar M(NH3)4 ions in between the carbon layers. For the intercalated ammonia molecules, the potential barrier is about 0.2 eV and the molecular geometry is very close to the free NH3 in gas phase.

Revisiting NMR composite pulses for broadband 2H excitation

PubMed Central

Shen, Ming; Roopchand, Rabia; Mananga, Eugene S.; Amoureux, Jean-Paul; Chen, Qun; Boutis, Gregory S.; Hu, Bingwen

2014-01-01

Quadrupolar echo NMR spectroscopy of static solids often requires RF excitation that covers spectral widths exceeding 100 kHz, which is difficult to obtain due to instrumental limitations. In this work we revisit four well-known composite pulses (COM-I, II, III and IV) for broadband excitation in deuterium quadrupolar echo spectroscopy. These composite pulses are combined with several phase cycling schemes that were previously shown to decrease finite pulse width distortions in deuterium solid-echo experiments performed with two single pulses. The simulations and experiments show that COM-II and IV composite pulses combined with an 8-step phase cycling aid in achieving broadband excitation with limited pulse width distortions. PMID:25583576

Gamma ray degradation of electrolytes containing alkylcarbonate solvents and a lithium salt

NASA Astrophysics Data System (ADS)

Caillon-Caravanier, Magaly; Jones, Jennifer; Anouti, Mérièm; Montigny, Frédéric; Willmann, Patrick; David, Jean-Pierre; Soonckindt, Sabine; Lemordant, Daniel

Lithium-ion batteries for space applications, such as satellites, are subjected to cosmic radiations, in particular, γ-irradiation. In this study, the effects of this radiation on electrolytes and their components used in the lithium-ion batteries are investigated. The conductivity and viscosity of the samples have been measured before and after the irradiation. The modifications are evaluated by spectral analyses such as Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (1H and 13C NMR), solid phase microextraction-gas chromatography (SPME-GC) and gas chromatography-mass spectroscopy (GC-MS). The experimental results show that only the samples containing vinylene carbonate and/or the lithium salt LiPF 6 are degraded by γ-radiation.

Molecular dynamics in aluminum layered double hydroxides as studied by 1H T1ρ NMR measurements

NASA Astrophysics Data System (ADS)

Vyalikh, Anastasia; Wang, De-Yi; Wagenknecht, Udo; Heinrich, Gert; Scheler, Ulrich

2011-06-01

Proton dynamics in pristine and organically-modified layered double hydroxide has been studied by 1H T1ρ. Inverse Laplace transform with spectral resolution results in a correlation of T1ρ and chemical shift. In LDH two contributions are resolved. They are assigned to the metal hydroxides, forming the LDH sheets (4-8 ms), and mobile interlayer water (2 ms). Apparent T1ρ values of OH-protons in surfactant-modified LDH are different in dodecylbenzenesulfonate- (SDBS) and sodium octasulfonate- (C8) modified LDH. This difference is explained by the presence of water in LDH-SDBS. The effects of spin diffusion have been studied by performing 2D 1H RFDR in the LDH-SDBS.

Coordinated Noninvasive Studies (CNS) Project

NASA Astrophysics Data System (ADS)

Lauter, Judith

1988-11-01

Research activities during this period include: data collection related to the interface between complex-sound production and perception, specifically, studies on speech acoustics including two experiments on voice-onset-time variability in productions by speakers of several languages, and a series on acoustical characteristics of emotional expression; data collection regarding individual differences in the effect of stimulus characteristic on relative ear advantages; continuing data analysis and new collections documenting individual differences in auditory evoked potentials, with details related to auditory-systems asymmetries preliminary tests regarding the match between behavioral measures of relative ear advantages and quantitative-electroencephalographic asymmetries observed during auditory stimulation; pilot testing using a combination of Nuclear Magnetic Resonance's (NMR) anatomical-imaging and chemical-spectral-analysis capabilities to study physiological activation in the human brain.

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

PubMed

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

2015-08-05

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

The relationship between the nicotine metabolite ratio and three self-report measures of nicotine dependence across sex and race.

PubMed

Schnoll, Robert A; George, Tony P; Hawk, Larry; Cinciripini, Paul; Wileyto, Paul; Tyndale, Rachel F

2014-06-01

Variability in the rate of nicotine metabolism, measured by the nicotine metabolite ratio (NMR), is associated with smoking behavior. However, data linking the NMR with nicotine dependence measured by the Fagerström test for nicotine dependence (FTND) are mixed. Few past studies have examined alternative measures of nicotine dependence and how this relationship may vary by sex and race. Using data from smokers undergoing eligibility evaluation for a smoking cessation clinical trial (n = 833), this study examined variability in the relationship between NMR and nicotine dependence across sex and race and using three measures of nicotine dependence: FTND, time-to-first-cigarette (TTFC), and the heaviness of smoking index (HSI). Controlling for sex and race, nicotine metabolism was associated with nicotine dependence only when using the HSI (p < 0.05). Male normal metabolizers of nicotine were more likely to have high nicotine dependence based on the FTND and HSI (p < 0.05), but NMR was not related to measures of nicotine dependence in women. For African Americans, the NMR was associated with nicotine dependence only for the TTFC (p < 0.05), but NMR was not associated with nicotine dependence among Caucasians. Post hoc analyses indicated that the NMR was associated with cigarettes per day, overall, and among men and Caucasians (p < 0.05). While there was some variation in the relationship between nicotine metabolism and nicotine dependence across measures and sex and race, the results indicate that this relationship may be more attributable to the association between NMR and cigarettes per day.

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.

NMR measurements on the triumf polarized deuterium target

NASA Astrophysics Data System (ADS)

Wait, G. D.; Delheij, P. P. J.; Healey, D. C.

1989-01-01

The NMR system and the polarization measurements of the TRIUMF polarized deuterium target are described. The NMR tuned circuit is kept resonant at all frequencies to allow for a high gain in the rf amplifiers and to permit the measurement of the real part of the NMR signal. A Starburst (J-11) and an LSI-11 are used to process the NMR signal at a high sample rate. A synthesizer under the control of an 8085 based microprocessor (TRIMAC) provides the rf sweep. Vector polarizations between -0.33 and -0.40 were routinely achieved during a four week run in the TRIUMF M11 pion beamline with a statistical uncertainty of 3.4% and a systematic uncertainty of 5%.

Synthesis, structural and spectral characterization of a novel NLO crystal N,N‧-diphenylguanidinium picrate: diacetone solvate

NASA Astrophysics Data System (ADS)

Shanmugavadivu, T.; Dhandapani, M.; Naveen, S.; Lokanath, N. K.

2017-09-01

An organic NLO active material N,N‧-diphenylguanidinium picrate: diacetone solvate (C13H14N3+. C6H2N3O7-. 2C3H6O) (DPGPD) was synthesized and single crystals were grown by slow evaporation-solution growth technique at room temperature. DPGPD crystallizes in monoclinic crystal system with noncentrosymmetric space group, Cc confirmed by single crystal X-ray diffraction analysis. The presence of various functional groups was identified from FT-IR spectral analysis and the proton transfer during the formation of compound was confirmed by NMR spectroscopic techniques. The thermal stability was investigated by TG/DTA analyses. Optical transmittance was measured by UV-Vis-NIR spectroscopy and band gap energy was calculated. Photoluminescence spectrum was used to explore its applicability towards laser diodes. Dielectric property of the material was ascertained at different temperatures and it is found that the grown crystal has higher dielectric constant in low frequencies. Photoconductivity study revealed that DPGPD exhibits positive photoconductivity. SHG property was found to be 0.6 times higher than that of KDP.

Fertility Inhibitor Heterobimetallic Complexes of Platinum(II) and Palladium(II): Synthetic, Spectroscopic and Antimicrobial Aspects

PubMed Central

Sharma, Kripa; Joshi, S. C.

2000-01-01

Synthetic, spectroscopic and antimicrobial aspects of some fertility inhibitor heterobimetallic complexes have been carried out. These heterobimetallic chelates [M(C5H5N3)2M2'(R)4]Cl2 (M = Pd or Pt and M' = Si, Sn, Ti and Zr) have been successfully synthesinzed via the reaction of M(C5H7N3)2Cl2 with group four or fourteen dichlorides in 1:2 stoichiometric proportions. The products were characterized by elemental analyses, molecular weight determinations, magnetic susceptibility measurements, conductance, and IR multinuclear NMR and electronic spectral studies. A square planar geometry has been suggested for all the complexes with the help of spectral data. Conductivity data strongly suggest that chlorine atoms are ionic in nature due to which complexes behave as electrolytes. All the complexes have been evaluated for their antmicrobial effects on different species of pathogenic fungi and bacteria. The testicular sperm density, testicular sperm morphology, sperm motility, density of cauda epididymal spermatozoa and fertility in mating trails and biochemical parameters of reproductive organs have been examined and discussed. PMID:18475932

A new polyoxygenated farnesylcyclohexenone from Fungus Penicillium sp.

PubMed

Yang, Yabin; Yang, Fangfang; Zhao, Lixing; Duang, Rongting; Chen, Guangyi; Li, Xiaozhan; Li, Qiling; Qin, Shaohuan; Ding, Zhongtao

2016-01-01

A new polyoxygenated farnesylcyclohexenone, peniginsengin A (1), was isolated from the fermentation of Penicillium sp. YIM PH30003, an endophytic fungus associated with Panax notoginseng (Burk.) F. H. Chen. The structure was assigned based on a combination of 1 D and 2 D NMR and mass spectral data. The cytotoxicity and antimicrobial activities of compound 1 were investigated.

Synthesis, characterization and biological studies of substituted quinozoline-4-(3H)-ones containing diazepine moiety.

PubMed

Narayana Rao, D V; Raghavendra Guru Prasad, A; Spoorthy, Y N; Pariplavi, M; Ravindranath, L K

2014-01-01

The synthesis and characterization of new series of 1,4-benzodiazepine derivatives have been presented. The structures were confirmed by elemental analyses, IR spectral, (1)H NMR spectral and mass spectral data. All the compounds were screened for in vitro antimicrobial and anthelmintic activities. The antibacterial activity was tested against Staphylococcus aureus (Gram positive), Bacillus cereus (Gram positive), Escherichia coli (Gram negative) and Pseudomonas aeruginosa (Gram negative). The antifungal activity was tested against Aspergillus niger and Candida albicans. All the compounds showed considerable antimicrobial activity against the microorganism studied. The significant anthelmintic activity of all novel compounds was demonstrated against Pheretima posthuma. Based on the nature of substituent present, the structure-activity correlation of novel compounds was discussed. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

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

Structure and dynamics of [3.3]paracyclophane as studied by nuclear magnetic resonance and density functional theory calculations.

PubMed

Dodziuk, Helena; Szymański, Sławomir; Jaźwiński, Jarosław; Marchwiany, Maciej E; Hopf, Henning

2010-09-30

Strained cyclophanes with small (-CH(2)-)(n) bridges connecting two benzene rings are interesting objects of basic research, mostly because of the nonplanarity of the rings and of interference of π-electrons of the latter. For title [3.3]paracyclophane, in solutions occurring in two interconverting cis and trans conformers, the published nuclear magnetic resonance (NMR) data are incomplete and involve its partially deuterated isotopomers. In this paper, variable-temperature NMR studies of its perprotio isotopomer combined with DFT quantum chemical calculations provide a complete characterization of the solution structure, NMR parameters, and interconversion of the cis and trans isomers of the title compound. Using advanced methods of spectral analysis, total quantitative interpretation of its proton NMR spectra in both the static and dynamic regimes is conducted. In particular, not only the geminal but also all of the vicinal J(HH) values for the bridge protons are determined, and for the first time, complete Arrhenius data for the interconversion process are reported. The experimental proton and carbon chemical shifts and the (n)J(HH), (1)J(CH), and (1)J(CC) coupling constants are satisfactorily reproduced theoretically by the values obtained from the density functional theory calculations.

Complexation of nitrogen and sulphur donor Schiff's base ligand to Cr(III) and Ni(II) metal ions: synthesis, spectroscopic and antipathogenic studies.

PubMed

Sharma, Amit Kumar; Chandra, Sulekh

2011-01-01

2,6-diacetyl pyridine based ligand was synthesized by the reaction of 2,6-diacetyl pyridine with thiocarbohydrazide in presence of acetic acid. The coordination compounds with Cr(III) and Ni(II) metal ions having [Cr(L)X]X2 and [Ni(L)X]X compositions (where L=ligand and X=NO3-, Cl- and CH3COO-) were synthesized and characterized by physicochemical and spectral studies. The studies like elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV-Vis, NMR, mass and EPR reveal that the complexes are octahedral. The compounds were examined against the pathogenic fungal and bacterial strains like Alternaria brassicae, Aspergillus niger, Fusarium oxysporum, Xanthomonas compestris and Pseudomonas aeruginosa. A. niger causes the diseases Apergillosis and Otomycosis in humans. Copyright © 2010. Published by Elsevier B.V.

Synthesis and spectroscopic studies of biologically active compounds derived from oxalyldihydrazide and benzil, and their Cr(III), Fe(III) and Mn(III) complexes.

PubMed

Singh, D P; Kumar, Ramesh; Singh, Jitender

2009-04-01

A new series of complexes have been synthesized by template condensation of oxalyldihydrazide and benzil in methanolic medium in the presence of trivalent chromium, manganese and iron salts forming complexes of the type [M(C(32)H(24)N(8)O(4))X]X(2) where M = Cr(III), Mn(III), Fe(III) and X = Cl(-1), NO(3)(-1), CH(3)COO(-1). The complexes have been characterized with the help of elemental analyses, conductance measurements, magnetic susceptibility measurements, electronic, NMR, infrared and far infrared spectral studies. On the basis of these studies, a five coordinate square pyramidal geometry has been proposed for all these complexes. The biological activities of the metal complexes have been tested in vitro against a number of pathogenic bacteria to assess their inhibiting potential. Some of these complexes have been found to exhibit remarkable antibacterial activities.

Syntheses and characterization of Ru(III) with chelating containing ONNO donor quadridentate Schiff bases.

PubMed

Refat, Moamen S; El-Korashy, Sabry A; Kumar, Deo Nandan; Ahmed, Ahmed S

2008-09-01

Complexes of ruthenium(III) with N,N'-disalicylidene-l,2-phenylenediamine (H2dsp), N,N'-disalicylidene-3,4-diaminotoluene (H2dst), 4-nitro-N,N'-disalicylidene-1,2-phenylenediamine (H2ndsp) and N,N'-disalicylidene ethylenediamine (H2salen) have been prepared and characterized by elemental analysis, molar conductivity, spectral methods (mid-infrared, 1H NMR and UV-vis spectra) and simultaneous thermal analysis (TG and DTG) techniques. The molar conductance measurements proved that all these complexes are non-electrolytes. The electronic spectra measurements were used to infer the structures. The IR spectra of the ligands and their complexes are used to identify the type of bonding. The kinetic thermodynamic parameters such as: E*, DeltaH*, DeltaS* and DeltaG* are estimated from the DTG curves. The four ligands and their complexes have been studied for their possible biological antifungal activity.

Phase-sensitive spectral estimation by the hybrid filter diagonalization method.

PubMed

Celik, Hasan; Ridge, Clark D; Shaka, A J

2012-01-01

A more robust way to obtain a high-resolution multidimensional NMR spectrum from limited data sets is described. The Filter Diagonalization Method (FDM) is used to analyze phase-modulated data and cast the spectrum in terms of phase-sensitive Lorentzian "phase-twist" peaks. These spectra are then used to obtain absorption-mode phase-sensitive spectra. In contrast to earlier implementations of multidimensional FDM, the absolute phase of the data need not be known beforehand, and linear phase corrections in each frequency dimension are possible, if they are required. Regularization is employed to improve the conditioning of the linear algebra problems that must be solved to obtain the spectral estimate. While regularization smoothes away noise and small peaks, a hybrid method allows the true noise floor to be correctly represented in the final result. Line shape transformation to a Gaussian-like shape improves the clarity of the spectra, and is achieved by a conventional Lorentzian-to-Gaussian transformation in the time-domain, after inverse Fourier transformation of the FDM spectra. The results obtained highlight the danger of not using proper phase-sensitive line shapes in the spectral estimate. The advantages of the new method for the spectral estimate are the following: (i) the spectrum can be phased by conventional means after it is obtained; (ii) there is a true and accurate noise floor; and (iii) there is some indication of the quality of fit in each local region of the spectrum. The method is illustrated with 2D NMR data for the first time, but is applicable to n-dimensional data without any restriction on the number of time/frequency dimensions. Copyright © 2011. Published by Elsevier Inc.

Contact replacement for NMR resonance assignment.

PubMed

Xiong, Fei; Pandurangan, Gopal; Bailey-Kellogg, Chris

2008-07-01

Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein-protein and protein-ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments. We formulate contact replacement for resonance assignment as the problem of computing correspondences between a contact graph representing the structure and an NMR graph representing the data; the NMR graph is a significantly corrupted, ambiguous version of the contact graph. We first show that by combining connectivity and amino acid type information, and exploiting the random structure of the noise, one can provably determine unique correspondences in polynomial time with high probability, even in the presence of significant noise (a constant number of noisy edges per vertex). We then detail an efficient randomized algorithm and show that, over a variety of experimental and synthetic datasets, it is robust to typical levels of structural variation (1-2 AA), noise (250-600%) and missings (10-40%). Our algorithm achieves very good overall assignment accuracy, above 80% in alpha-helices, 70% in beta-sheets and 60% in loop regions. Our contact replacement algorithm is implemented in platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

Nuclear magnetic resonance relaxation and diffusion measurements as a proxy for soil properties

NASA Astrophysics Data System (ADS)

Duschl, Markus; Pohlmeier, Andreas; Galvosas, Petrik; Vereecken, Harry

2013-04-01

Nuclear Magnetic Resonance (NMR) relaxation and NMR diffusion measurements are two of a series of fast and non-invasive NMR applications widely used e.g. as well logging tools in petroleum exploration [1]. For experiments with water, NMR relaxation measures the relaxation behaviour of former excited water molecules, and NMR diffusion evaluates the self-diffusion of water. Applied in porous media, both relaxation and diffusion measurements depend on intrinsic properties of the media like pore size distribution, connectivity and tortuosity of the pores, and water saturation [2, 3]. Thus, NMR can be used to characterise the pore space of porous media not only in consolidated sediments but also in soil. The physical principle behind is the relaxation of water molecules in an external magnetic field after excitation. In porous media water molecules in a surface layer of the pores relax faster than the molecules in bulk water because of interactions with the pore wall. Thus, the relaxation in smaller pores is generally faster than in bigger pores resulting in a relaxation time distribution for porous media with a range of pore sizes like soil [4]. In NMR diffusion experiments, there is an additional encoding of water molecules by application of a magnetic field gradient. Subsequent storage of the magnetization and decoding enables the determination of the mean square displacement and therefore of the self-diffusion of the water molecules [5]. Employing various relaxation and diffusion experiments, we get a measure of the surface to volume ratio of the pores and the tortuosity of the media. In this work, we show the characterisation of a set of sand and soil samples covering a wide range of textural classes by NMR methods. Relaxation times were monitored by the Carr-Purcell-Meiboom-Gill sequence and analysed using inverse Laplace transformation. Apparent self-diffusion constants were detected by a 13-intervall pulse sequence and variation of the storage time. We correlated the results with various soil properties like texture, water retention parameters, and hydraulic conductivity. This way we show that we can predict soil properties by NMR measurements and that we are able use results of NMR measurements as a proxy without the need of direct measurements. [1] Song, Y.-Q., Vadose Zone Journal, 9 (2010) [2] Stingaciu, L. R., et al., Water Resources Research, 46 (2010) [3] Vogt, C., et al., Journal of Applied Geophysics, 50 (2002) [4] Barrie, P. J., Annual Reports on NMR Spectroscopy, 41 (2000) [5] Stallmach, F., Galvosas, P., Annual Reports on NMR Spectroscopy, 61 (2007)

Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

NASA Astrophysics Data System (ADS)

Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

2018-04-01

A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

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.

Ameliorating effects of Mango (Mangifera indica L.) fruit on plasma ethanol level in a mouse model assessed with 1H-NMR based metabolic profiling

PubMed Central

Kim, So-Hyun; K. Cho, Somi; Min, Tae-Sun; Kim, Yujin; Yang, Seung-Ok; Kim, Hee-Su; Hyun, Sun-Hee; Kim, Hana; Kim, Young-Suk; Choi, Hyung-Kyoon

2011-01-01

The ameliorating effects of Mango (Mangifera indica L.) flesh and peel samples on plasma ethanol level were investigated using a mouse model. Mango fruit samples remarkably decreased mouse plasma ethanol levels and increased the activities of alcohol dehydrogenase and acetaldehyde dehydrogenase. The 1H-NMR-based metabolomic technique was employed to investigate the differences in metabolic profiles of mango fruits, and mouse plasma samples fed with mango fruit samples. The partial least squares-discriminate analysis of 1H-NMR spectral data of mouse plasma demonstrated that there were clear separations among plasma samples from mice fed with buffer, mango flesh and peel. A loading plot demonstrated that metabolites from mango fruit, such as fructose and aspartate, might stimulate alcohol degradation enzymes. This study suggests that mango flesh and peel could be used as resources for functional foods intended to decrease plasma ethanol level after ethanol uptake. PMID:21562641

Tannins and terpenoids as major precursors of Suwannee River fulvic acid

USGS Publications Warehouse

Leenheer, Jerry A.; Rostad, Colleen E.

2004-01-01

Suwannee River fulvic acid (SRFA) was fractionated into 7 fractions by normal-phase chromatography on silica gel followed by reverse-phase fractionation on XAD-8 resin that produced 18 subfractions. Selected major subfractions were characterized by 13C-nuclear magnetic resonance (NMR), infrared spectrometry, and elemental analyses. 13C-NMR spectra of the subfractions were more indicative of precursor structures than unfractionated SRFA, and gave spectral profiles that indicated SRFA mass was about equally split between tannin precursors and terpenoid precursors. Lignin precursors were minor components. Synthesis of 13C-NMR data with elemental data for subfractions derived from both tannin and terpenoid precursors revealed high ring contents and low numbers of carbon per rings which is indicative of fused ring structures that are extensively substituted with carboxyl and methyl groups. These results ruled out extended chain structures for SRFA. This information is useful for determining sources and properties of fulvic acid in drinking water supplies as tannins are more reactive with chlorine to produce undesirable disinfection by-products than are terpenoids.

Si-29 NMR spectroscopy of naturally-shocked quartz from Meteor Crater, Arizona: Correlation to Kieffer's classification scheme

NASA Technical Reports Server (NTRS)

Boslough, M. B.; Cygan, R. T.; Kirkpatrick, R. J.

1993-01-01

We have applied solid state Si-29 nuclear magnetic resonance (NMR) spectroscopy to five naturally-shocked Coconino Sandstone samples from Meteor Crater, Arizona, with the goal of examining possible correlations between NMR spectral characteristics and shock level. This work follows our observation of a strong correlation between the width of a Si-29 resonance and peak shock pressure for experimentally shocked quartz powders. The peak width increase is due to the shock-induced formation of amorphous silica, which increases as a function of shock pressure over the range that we studied (7.5 to 22 GPa). The Coconino Sandstone spectra are in excellent agreement with the classification scheme of Kieffer in terms of presence and approximate abundances of quartz, coesite, stishovite, and glass. We also observe a new resonance in two moderately shocked samples that we have tentatively identified with silicon in tetrahedra with one hydroxyl group in a densified form of amorphous silica.

Cell-free expressed bacteriorhodopsin in different soluble membrane mimetics: biophysical properties and NMR accessibility.

PubMed

Etzkorn, Manuel; Raschle, Thomas; Hagn, Franz; Gelev, Vladimir; Rice, Amanda J; Walz, Thomas; Wagner, Gerhard

2013-03-05

Selecting a suitable membrane-mimicking environment is of fundamental importance for the investigation of membrane proteins. Nonconventional surfactants, such as amphipathic polymers (amphipols) and lipid bilayer nanodiscs, have been introduced as promising environments that may overcome intrinsic disadvantages of detergent micelle systems. However, structural insights into the effects of different environments on the embedded protein are limited. Here, we present a comparative study of the heptahelical membrane protein bacteriorhodopsin in detergent micelles, amphipols, and nanodiscs. Our results confirm that nonconventional environments can increase stability of functional bacteriorhodopsin, and demonstrate that well-folded heptahelical membrane proteins are, in principle, accessible by solution-NMR methods in amphipols and phospholipid nanodiscs. Our data distinguish regions of bacteriorhodopsin that mediate membrane/solvent contacts in the tested environments, whereas the protein's functional inner core remains almost unperturbed. The presented data allow comparing the investigated membrane mimetics in terms of NMR spectral quality and thermal stability required for structural studies. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

1993-12-01

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

Automated structure determination of proteins with the SAIL-FLYA NMR method.

PubMed

Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

2007-01-01

The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

Experimental and DFT studies of (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline: electronic and vibrational properties.

PubMed

Sun, Wenqi; Yuan, Guozan; Liu, Jingxin; Ma, Li; Liu, Chengbu

2013-04-01

The title molecule (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline (DPEQ) was synthesized and characterized by FT-IR, UV-vis, NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results indicate that the theoretical vibrational frequencies, 1H and 13C NMR chemical shift values show good agreement with experimental data. The electronic properties like UV-vis spectral analysis and HOMO-LUMO analysis of DPEQ have been reported and compared with experimental data. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP). Copyright © 2013 Elsevier B.V. All rights reserved.

Experimental and DFT studies of (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline: Electronic and vibrational properties

NASA Astrophysics Data System (ADS)

Sun, Wenqi; Yuan, Guozan; Liu, Jingxin; Ma, Li; Liu, Chengbu

2013-04-01

The title molecule (E)-2-[2-(2,6-dichlorophenyl)ethenyl]-8-hydroxyquinoline (DPEQ) was synthesized and characterized by FT-IR, UV-vis, NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results indicate that the theoretical vibrational frequencies, 1H and 13C NMR chemical shift values show good agreement with experimental data. The electronic properties like UV-vis spectral analysis and HOMO-LUMO analysis of DPEQ have been reported and compared with experimental data. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP).

Experimental and theoretical NMR and IR studies of the side-chain orientation effects on the backbone conformation of dehydrophenylalanine residue.

PubMed

Buczek, Aneta M; Ptak, Tomasz; Kupka, Teobald; Broda, Małgorzata A

2011-06-01

Conformation of N-acetyl-(E)-dehydrophenylalanine N', N'-dimethylamide (Ac-(E)-ΔPhe-NMe(2)) in solution, a member of (E)-α, β-dehydroamino acids, was studied by NMR and infrared spectroscopy and the results were compared with those obtained for (Z) isomer. To support the spectroscopic interpretation, the Φ, Ψ potential energy surfaces were calculated at the MP2/6-31 + G(d,p) level of theory in chloroform solution modeled by the self-consistent reaction field-polarizable continuum model method. All minima were fully optimized by the MP2 method and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds and dipole interactions between carbonyl groups. The obtained NMR spectral features were compared with theoretical nuclear magnetic shieldings, calculated using Gauge Independent Atomic Orbitals (GIAO) approach and rescaled to theoretical chemical shifts using benzene as reference. The calculated indirect nuclear spin-spin coupling constants were compared with available experimental parameters. Copyright © 2011 John Wiley & Sons, Ltd.

Optimization of homonuclear 2D NMR for fast quantitative analysis: application to tropine-nortropine mixtures.

PubMed

Giraudeau, Patrick; Guignard, Nadia; Hillion, Emilie; Baguet, Evelyne; Akoka, Serge

2007-03-12

Quantitative analysis by (1)H NMR is often hampered by heavily overlapping signals that may occur for complex mixtures, especially those containing similar compounds. Bidimensional homonuclear NMR spectroscopy can overcome this difficulty. A thorough review of acquisition and post-processing parameters was carried out to obtain accurate and precise, quantitative 2D J-resolved and DQF-COSY spectra in a much reduced time, thus limiting the spectrometer instabilities in the course of time. The number of t(1) increments was reduced as much as possible, and standard deviation was improved by optimization of spectral width, number of transients, phase cycling and apodization function. Localized polynomial baseline corrections were applied to the relevant chemical shift areas. Our method was applied to tropine-nortropine mixtures. Quantitative J-resolved spectra were obtained in less than 3 min and quantitative DQF-COSY spectra in 12 min, with an accuracy of 3% for J-spectroscopy and 2% for DQF-COSY, and a standard deviation smaller than 1%.

A combined experimental and DFT investigation of disazo dye having pyrazole skeleton

NASA Astrophysics Data System (ADS)

Şener, Nesrin; Bayrakdar, Alpaslan; Kart, Hasan Hüseyin; Şener, İzzet

2017-02-01

Disazo dye containing pyrazole skeleton has been synthesized. The structure of the dye has been confirmed by using FT-IR, 1H NMR, 13C NMR, HRMS spectral technique and elemental analysis. The molecular geometry and infrared spectrum are also calculated by the Density Functional Theory (DFT) employing B3LYP level with 6-311G (d,p) basis set. The chemical shifts calculation for 1H NMR of the title molecule is done by using by Gauge-Invariant Atomic Orbital (GIAO) method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via Gauss Sum 3.0 program. Frontier molecular orbitals such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and molecular electrostatic potential surface on the title molecule are predicted for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical values have been compared.

Fast and global authenticity screening of honey using ¹H-NMR profiling.

PubMed

Spiteri, Marc; Jamin, Eric; Thomas, Freddy; Rebours, Agathe; Lees, Michèle; Rogers, Karyne M; Rutledge, Douglas N

2015-12-15

An innovative analytical approach was developed to tackle the most common adulterations and quality deviations in honey. Using proton-NMR profiling coupled to suitable quantification procedures and statistical models, analytical criteria were defined to check the authenticity of both mono- and multi-floral honey. The reference data set used was a worldwide collection of more than 800 honeys, covering most of the economically significant botanical and geographical origins. Typical plant nectar markers can be used to check monofloral honey labeling. Spectral patterns and natural variability were established for multifloral honeys, and marker signals for sugar syrups were identified by statistical comparison with a commercial dataset of ca. 200 honeys. Although the results are qualitative, spiking experiments have confirmed the ability of the method to detect sugar addition down to 10% levels in favorable cases. Within the same NMR experiments, quantification of glucose, fructose, sucrose and 5-HMF (regulated parameters) was performed. Finally markers showing the onset of fermentation are described. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-10-25

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

Quantitative measurement of regional blood flow with gadolinium diethylenetriaminepentaacetate bolus track NMR imaging in cerebral infarcts in rats: validation with the iodo[14C]antipyrine technique.

PubMed Central

Wittlich, F; Kohno, K; Mies, G; Norris, D G; Hoehn-Berlage, M

1995-01-01

NMR bolus track measurements were correlated with autoradiographically determined regional cerebral blood flow (rCBF). The NMR method is based on bolus infusion of the contrast agent gadolinium diethylenetriaminepentaacetate and high-speed T*2-sensitive NMR imaging. The first pass of the contrast agent through the image plane causes a transient decrease of the signal intensity. This time course of the signal intensity is transformed into relative concentrations of the contrast agent in each pixel. The mean transit time and relative blood flow and volume are calculated from such indicator dilution curves. We investigated whether this NMR technique correctly expresses the relative rCBF. The relative blood flow data, calculated from NMR bolus track experiments, and the absolute values of iodo[14C]antipyrine autoradiography were compared. A linear relationship was observed, indicating the proportionality of the transient NMR signal change with CBF. Excellent interindividual reproducibility of calibration constants is observed (r = 0.963). For a given NMR protocol, bolus track measurements calibrated with autoradiography after the experiment allow determination of absolute values for rCBF and regional blood volume. Images Fig. 2 Fig. 3 PMID:7892189

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease.

PubMed

Widdifield, Cory M; Nilsson Lill, Sten O; Broo, Anders; Lindkvist, Maria; Pettersen, Anna; Svensk Ankarberg, Anna; Aldred, Peter; Schantz, Staffan; Emsley, Lyndon

2017-06-28

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured 13 C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR ( 1 H, 13 C, 15 N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct 13 C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental 13 C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of 13 C shift tensors and the observation of residual dipolar coupling between 13 C and 14 N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD 16 = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD 16 = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

Synthesis, spectroscopic and DNA binding ability of CoII, NiII, CuII and ZnII complexes of Schiff base ligand (E)-1-(((1H-benzo[d]imidazol-2-yl)methylimino)methyl)naphthalen-2-ol. X-ray crystal structure determination of cobalt (II) complex.

PubMed

Yarkandi, Naeema H; El-Ghamry, Hoda A; Gaber, Mohamed

2017-06-01

A novel Schiff base ligand, (E)-1-(((1H-benzo[d]imidazol-2-yl)methylimino)methyl)naphthalen-2-ol (HL), has been designed and synthesized in addition to its metal chelates [Co(L) 2 ]·l2H 2 O, [Ni(L)Cl·(H 2 O) 2 ].5H 2 O, [Cu(L)Cl] and [Zn(L)(CH 3 COO)]. The structures of the isolated compounds have been confirmed and identified by means of different spectral and physicochemical techniques including CHN analysis, 1 H & 13 C NMR, mass spectral analysis, molar conductivity measurement, UV-Vis, infrared, magnetic moment in addition to TGA technique. The infrared spectral results ascertained that the ligand acts as monobasic tridentate binding to the metal centers via deprotonated hydroxyl oxygen, azomethine and imidazole nitrogen atoms. The UV-Vis, magnetic susceptibility and molar conductivity data implied octahedral geometry for Co(II) & Ni(II) complexes, tetrahedral for Zn(II) complex and square planar for Cu(II) complex. X-ray structural analysis of Co(II) complex 1 has been reported and discussed. Moreover, the type of interaction between the ligand & its complexes towards salmon sperm DNA (SS-DNA) has been examined by the measurement of absorption spectra and viscosity which confirmed that the ligand and its complexes interact with DNA via intercalation interaction as concluded from the values of binding constants (K b ). Copyright © 2017 Elsevier B.V. All rights reserved.

Low-field nuclear magnetic resonance characterization of organic content in shales

USGS Publications Warehouse

Washburn, Kathryn E.; Birdwell, Justin E.; Seymour, Joseph D.; Kirkland, Catherine; Vogt, Sarah J.

2013-01-01

Low-field nuclear magnetic resonance (LF-NMR) relaxometry is a non-invasive technique commonly used to assess hydrogen-bearing fluids in petroleum reservoir rocks. Longitudinal T1 and transverse T2 relaxation time measurements made using LF-NMR on conventional reservoir systems provides information on rock porosity, pore size distributions, and fluid types and saturations in some cases. Recent improvements in LF-SNMR instrument electronics have made it possible to apply these methods to assess highly viscous and even solid organic phases within reservoir rocks. T1 and T2 relaxation responses behave very differently in solids and liquids, therefore the relationship between these two modes of relaxation can be used to differentiate organic phases in rock samples or to characterize extracted organic materials. Using T1-T2 correlation data, organic components present in shales, such as kerogen and bitumen, can be examined in laboratory relaxometry measurements. In addition, implementation of a solid-echo pulse sequence to refocus some types of T2 relaxation during correlation measurements allows for improved resolution of solid phase photons. LF-NMR measurements of T1 and T2 relaxation time correlations were carried out on raw oil shale samples from resources around the world. These shales vary widely in mineralogy, total organic carbon (TOC) content and kerogen type. NMR results were correlcated with Leco TOC and geochemical data obtained from Rock-Eval. There is excellent correlation between NMR data and programmed pyrolysis parameters, particularly TOC and S2, and predictive capability is also good. To better understand the NMR response, the 2D NMR spectra were compared to similar NMR measurements made using high-field (HF) NMR equipment.

In vivo two-dimensional NMR correlation spectroscopy

NASA Astrophysics Data System (ADS)

Kraft, Robert A.

1999-10-01

The poor resolution of in-vivo one- dimensional nuclear magnetic resonance spectroscopy (NMR) has limited its clinical potential. Currently, only the large singlet methyl resonances arising from N-acetyl aspartate (NAA), choline, and creatine are quantitated in a clinical setting. Other metabolites such as myo- inositol, glutamine, glutamate, lactate, and γ- amino butyric acid (GABA) are of clinical interest but quantitation is difficult due to the overlapping resonances and limited spectral resolution. To improve the spectral resolution and distinguish between overlapping resonances, a series of two- dimensional chemical shift correlation spectroscopy experiments were developed for a 1.5 Tesla clinical imaging magnet. Two-dimensional methods are attractive for in vivo spectroscopy due to their ability to unravel overlapping resonances with the second dimension, simplifying the interpretation and quantitation of low field NMR spectra. Two-dimensional experiments acquired with mix-mode line shape negate the advantages of the second dimension. For this reason, a new experiment, REVOLT, was developed to achieve absorptive mode line shape in both dimensions. Absorptive mode experiments were compared to mixed mode experiments with respect to sensitivity, resolution, and water suppression. Detailed theoretical and experimental calculations of the optimum spin lock and radio frequency power deposition were performed. Two-dimensional spectra were acquired from human bone marrow and human brain tissue. The human brain tissue spectra clearly reveal correlations among the coupled spins of NAA, glutamine, glutamate, lactate, GABA, aspartate and myo-inositol obtained from a single experiment of 23 minutes from a volume of 59 mL. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

Structural and spectroscopic (UV-Vis, IR, Raman, and NMR) characteristics of anisaldehydes that are flavoring food additives: A density functional study in comparison with experiments

NASA Astrophysics Data System (ADS)

Altun, Ahmet; Swesi, O. A. A.; Alhatab, B. S. S.

2017-01-01

The molecular structures, vibrational spectra (IR and Raman), electronic spectra (UV-Vis and DOS), and NMR spectra (13C and 1H) of p-anisaldehyde, m-anisaldehyde, and o-anisaldehyde have been studied by using the B3LYP density functional and the 6-311++G** basis set. While p-anisaldehyde has been found to contain two stable conformers at room temperature, m-anisaldehyde and o-anisaldehyde contain four stable conformers. In agreement with the calculated ground-state energetics and small transition barriers, the comparison of the experimental and calculated spectra of the anisaldehydes indicates equilibrium between all conformers at room temperature. However, the two conformers of o-anisaldehyde, in which the methoxy group lies out of the ring plane, are too rare at the equilibrium. The equilibrium conditions of the conformers of the anisaldehyde isomers have been shown readily accessible through UV-Vis and 13C NMR spectral studies but requiring very detailed vibrational analyses. The effect of the solvent has been found to red-shift the electronic absorption bands and to make the anisaldehydes more reactive and soft. Molecular electrostatic potential maps of the anisaldehydes show that their oxygen atoms are the sites for nucleophilic reactivity. Compared with the most sophisticated NBO method, ESP charges have been found mostly reliable while Mulliken charges fail badly with the present large 6-311++G** basis set. The present calculations reproduce not only the experimental spectral characteristics of the anisaldehydes but also reveal their several structural features.

H-1 Nuclear Magnetic Resonance Metabolomics Analysis Identifies Novel Urinary Biomarkers for Lung Function

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

MCClay, Joseph L.; Adkins, Daniel E.; Isern, Nancy G.

2010-06-04

Chronic obstructive pulmonary disease (COPD), characterized by chronic airflow limitation, is a serious and growing public health concern. The major environmental risk factor for COPD is tobacco smoking, but the biological mechanisms underlying COPD are not well understood. In this study, we used proton nuclear magnetic resonance (1H-NMR) spectroscopy to identify and quantify metabolites associated with lung function in COPD. Plasma and urine were collected from 197 adults with COPD and from 195 adults without COPD. Samples were assayed using a 600 MHz NMR spectrometer, and the resulting spectra were analyzed against quantitative spirometric measures of lung function. After correctingmore » for false discoveries and adjusting for covariates (sex, age, smoking) several spectral regions in urine were found to be significantly associated with baseline lung function. These regions correspond to the metabolites trigonelline, hippurate and formate. Concentrations of each metabolite, standardized to urinary creatinine, were associated with baseline lung function (minimum p-value = 0.0002 for trigonelline). No significant associations were found with plasma metabolites. Two of the three urinary metabolites positively associated with baseline lung function, i.e. hippurate and formate, are often related to gut microflora. This suggests that the microbiome composition is variable between individuals with different lung function. Alternatively, the nature and origins of all three associated metabolites may reflect lifestyle differences affecting overall health. Our results will require replication and validation, but demonstrate the utility of NMR metabolomics as a screening tool for identifying novel biomarkers of lung disease or disease risk.« less

Ab initio calculation of Ti NMR shieldings for titanium oxides and halides

NASA Astrophysics Data System (ADS)

Tossell, J. A.

Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.

Increased mean aliphatic lipid chain length in left ventricular hypertrophy secondary to arterial hypertension: A cross-sectional study.

PubMed

Evaristi, Maria Francesca; Caubère, Céline; Harmancey, Romain; Desmoulin, Franck; Peacock, William Frank; Berry, Matthieu; Turkieh, Annie; Barutaut, Manon; Galinier, Michel; Dambrin, Camille; Polidori, Carlo; Miceli, Cristina; Chamontin, Bernard; Koukoui, François; Roncalli, Jerôme; Massabuau, Pierre; Smih, Fatima; Rouet, Philippe

2016-11-01

About 77.9 million (1 in 4) American adults have high blood pressure. High blood pressure is the primary cause of left ventricular hypertrophy (LVH), which represents a strong predictor of future heart failure and cardiovascular mortality. Previous studies have shown an altered metabolic profile in hypertensive patients with LVH. The goal of this study was to identify blood metabolomic LVH biomarkers by H NMR to provide novel diagnostic tools for rapid LVH detection in populations of hypertensive individuals. This cross-sectional study included 48 hypertensive patients with LVH matched with 48 hypertensive patients with normal LV size, and 24 healthy controls. Two-dimensional targeted M-mode echocardiography was performed to measure left ventricular mass index. Partial least squares discriminant analysis was used for the multivariate analysis of the H NMR spectral data. From the H NMR-based metabolomic profiling, signals coming from methylene (-CH2-) and methyl (-CH3) moieties of aliphatic chains from plasma lipids were identified as discriminant variables. The -CH2-/-CH3 ratio, an indicator of the mean length of the aliphatic lipid chains, was significantly higher (P < 0.001) in the LVH group than in the hypertensive group without LVH and controls. Receiver operating characteristic curve showed that a cutoff of 2.34 provided a 52.08% sensitivity and 85.42% specificity for discriminating LVH (AUC = 0.703, P-value < 0.001). We propose the -CH2-/-CH3 ratio from plasma aliphatic lipid chains as a biomarker for the diagnosis of left ventricular remodeling in hypertension.

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.

Near-Infrared (NIR) Spectroscopy of Synthetic Hydroxyapatites and Human Dental Tissues.

PubMed

Kolmas, Joanna; Marek, Dariusz; Kolodziejski, Waclaw

2015-08-01

Near-infrared spectroscopy (NIR) was used to analyze synthetic hydroxyapatite calcined at various temperatures, synthetic carbonated hydroxyapatite, and human hard dental tissues (enamel and dentin). The NIR bands of those materials in the combination, first-overtone, and second-overtone spectral regions were assigned and evaluated for structural characterization. They were attributed to adsorbed and structural water, structural hydroxyl (OH) groups and surface P-OH groups. The NIR spectral features were quantitatively discussed in view of proton solid-state magic-angle spinning nuclear magnetic resonance ((1)H MAS NMR) results. We conclude that the NIR spectra of apatites are useful in the structural characterization of synthetic and biogenic apatites.

Functionalized xenon as a biosensor

PubMed Central

Spence, Megan M.; Rubin, Seth M.; Dimitrov, Ivan E.; Ruiz, E. Janette; Wemmer, David E.; Pines, Alexander; Yao, Shao Qin; Tian, Feng; Schultz, Peter G.

2001-01-01

The detection of biological molecules and their interactions is a significant component of modern biomedical research. In current biosensor technologies, simultaneous detection is limited to a small number of analytes by the spectral overlap of their signals. We have developed an NMR-based xenon biosensor that capitalizes on the enhanced signal-to-noise, spectral simplicity, and chemical-shift sensitivity of laser-polarized xenon to detect specific biomolecules at the level of tens of nanomoles. We present results using xenon “functionalized” by a biotin-modified supramolecular cage to detect biotin–avidin binding. This biosensor methodology can be extended to a multiplexing assay for multiple analytes. PMID:11535830

Neolignan and flavonoid glycosides in Juniperus communis var. depressa.

PubMed

Nakanishi, Tsutomu; Iida, Naoki; Inatomi, Yuka; Murata, Hiroko; Inada, Akira; Murata, Jin; Lang, Frank A; Iinuma, Munekazu; Tanaka, Toshiyuki

2004-01-01

Two neolignan glycosides (junipercomnosides A and B) were isolated from aerial parts of Juniperus communis var. depressa along with two known neolignan glycosides and seven flavonoid glycosides. The structures of the isolated compounds were determined by spectral analysis, in particular by 2D-NMR analysis. The significance of distribution of flavonoids in the chemotaxonomy of genus Juniperus was also discussed.

Flavonoids and terpenoids from Helichrysum forskahlii.

PubMed

Al-Rehaily, Adnan J; Albishi, Omar A; El-Olemy, Mahmoud M; Mossa, Jaber S

2008-06-01

Three new flavonoids, namely helichrysone A (1), helichrysone B (2) and helichrysone C (3) were isolated from the aerial parts of Helichrysum forskahlii, together with 10 known flavonoids, three triterpenes, and one sesquiterpene. The structures of the new flavonoids 1-3 were established by 1D and 2D NMR spectral data. In addition, the antimicrobial activities of the isolated compounds were determined.

Synthesis and insect antifeedant activities of some substituted styryl 3,4-dichlorophenyl ketones

NASA Astrophysics Data System (ADS)

Thirunarayanan, G.; Surya, S.; Srinivasan, S.; Vanangamudi, G.; Sathiyendiran, V.

2010-01-01

Sixteen substituted styryl 3,4-dichlorophenyl ketones [ (2E)-1-(3,4-dichlorophenyl)-3-phenyl-2-propen-1-ones] were synthesized using eco-friendly benign stereoselective crossed-aldol reaction. They are characterized by their analytical, infrared, NMR and mass spectral data. The insect antifeedant activities of these chalcones were evaluated using Caster semilooper and Achoea janata L.

The Synthesis of "N"-Benzyl-2-Azanorbornene via Aqueous Hetero Diels-Alder Reaction: An Undergraduate Project in Organic Synthesis and Structural Analysis

ERIC Educational Resources Information Center

Sauvage, Xavier; Delaude, Lionel

2008-01-01

The synthesis of "N"-benzyl-2-azanorbornene via aqueous hetero Diels-Alder reaction of cyclopentadiene and benzyliminium chloride formed in situ from benzylamine hydrochloride and formaldehyde is described. Characterization of the product was achieved by IR and NMR spectroscopies. The spectral data acquired are thoroughly discussed. Numerous…

Synthesis, spectral characterization, crystal structure and molecular docking study of 2,7-diaryl-1,4-diazepan-5-ones

NASA Astrophysics Data System (ADS)

Sethuvasan, S.; Sugumar, P.; Maheshwaran, V.; Ponnuswamy, M. N.; Ponnuswamy, S.

2016-07-01

In this study, a series of variously substituted r-2,c-7-diaryl-1,4-diazepan-5-ones 9-16 have been synthesized using Schmidt rearrangement and are characterized by IR, mass and 1D & 2D NMR spectral data. The proton NMR coupling constant and estimated dihedral angles reveal that the compounds 9-16 prefer a chair conformation with equatorial orientation of alkyl and aryl groups. Single crystal X-ray structure has been solved for compounds 9 and 11 which also indicates the preference for distorted chair conformation with equatorial orientation of substituents. The compounds 9-16 have been docked with the structure of Methicillin-resistant Staphylococcus aureus (MRSA) and the results demonstrate that compound 10 is having better docking score and glide energy than others and it is comparable to co-crystal ligand. Furthermore, all the compounds have been evaluated for their antibacterial and antioxidant activities. All the compounds show moderate antibacterial activity and only 11 exhibits better activity against S. aures and Escherichia coli. The compounds 11, 13 and 14 exhibit half of the antioxidant power when compared to the BHT and the remaining compounds show moderate activity.

Crystal structure, spectral property, antimicrobial activity and DFT calculation of N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea

NASA Astrophysics Data System (ADS)

Zhang, Hong-Song; Zhang, Kong-Yan; Chen, Li-Chuan; Li, Yao-Xin; Chai, Lan-Qin

2017-10-01

N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea was synthesized and characterized by elemental analysis, IR, 1H NMR, 13C NMR, UV-Vis and emission spectroscopy, as well as by single-crystal X-ray diffraction. X-ray crystallographic analyses have indicated that the crystal structure consists of two dimethyl sulfoxide (DMSO) solvent molecules and the structural geometry of DMSO is a trigonal pyramid in shape. In the crystal structure, a self-assembling two-dimensional (2-D) layer supramolecular architecture is formed through intermolecular hydrogen bonds, Cdbnd O···π (thiadiazole ring) and π···π stacking interactions. The geometry of the compound has been optimized by the DFT method and the results are compared with the X-ray diffraction data. The electronic transitions and spectral features of the compound were carried out by using DFT/B3LYP method. In addition, the antimicrobial activity was also studied, and the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and HOMO-LUMO gap were also calculated.

Interactions of praseodymium and neodymium with nucleosides and nucleotides: absorption difference and comparative absorption spectral study.

PubMed

Misra, S N; Anjaiah, K; Joseph, G; Abdi, S H

1992-02-01

The interactions of praseodymium(III) and neodymium(III) with nucleosides and nucleotides have been studied in different stoichiometry in water and water-DMF mixtures by employing absorption difference and comparative absorption spectrophotometry. The 4f-4f bands were analysed by linear curve analysis followed by gaussian curve analysis, and various spectral parameters were computed, using partial and multiple regression method. The magnitude of changes in both energy interaction and intensity were used to explore the degree of outer and inner sphere coordination, incidence of covalency and the extent of metal 4f-orbital involvement in chemical bonding. Crystalline complexes of the type [Ln(nucleotide)2(H2O)2]- (where nucleotide--GMP or IMP) were characterized by IR, 1H NMR, 31P NMR data. These studies indicated that the binding of the nucleotide is through phosphate oxygen in a bidentate manner and the complexes undergo substantial ionisation in aqueous medium, thereby supporting the observed weak 4f-4f bands and lower values for nephelauxetic effect (1-beta), bonding (b) and covalency (delta) parameters derived from coulombic and spin orbit interaction parameters.

Green coffee oil analysis by high-resolution nuclear magnetic resonance spectroscopy.

PubMed

D'Amelio, Nicola; De Angelis, Elisabetta; Navarini, Luciano; Schievano, Elisabetta; Mammi, Stefano

2013-06-15

In this work, we show how an extensive and fast quantification of the main components in green coffee oil can be achieved by NMR, with minimal sample manipulation and use of organic solvents. The approach is based on the integration of characteristic NMR signals, selected because of their similar relaxation properties and because they fall in similar spectral regions, which minimizes offset effects. Quantification of glycerides, together with their fatty acid components (oleic, linoleic, linolenic and saturated) and minor species (caffeine, cafestol, kahweol and 16-O-methylcafestol), is achieved in less than 1h making use of (1)H and (13)C spectroscopy. The compositional data obtained are in reasonable agreement with classical chromatographic analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

Independent valine and leucine isotope labeling in Escherichia coli protein overexpression systems.

PubMed

Lichtenecker, Roman J; Weinhäupl, Katharina; Reuther, Lukas; Schörghuber, Julia; Schmid, Walther; Konrat, Robert

2013-11-01

The addition of labeled α-ketoisovalerate to the growth medium of a protein-expressing host organism has evolved into a versatile tool to achieve concomitant incorporation of specific isotopes into valine- and leucine- residues. The resulting target proteins represent excellent probes for protein NMR analysis. However, as the sidechain resonances of these residues emerge in a narrow spectral range, signal overlap represents a severe limitation in the case of high-molecular-weight NMR probes. We present a protocol to eliminate leucine labeling by supplying the medium with unlabeled α-ketoisocaproate. The resulting spectra of a model protein exclusively feature valine signals of increased intensity, confirming the method to be a first example of independent valine and leucine labeling employing α-ketoacid precursor compounds.

Androgen Receptor Antagonists and Anti-Prostate Cancer Activities of Some Newly Synthesized Substituted Fused Pyrazolo-, Triazolo- and Thiazolo-Pyrimidine Derivatives

PubMed Central

Bahashwan, Saleh A.; Fayed, Ahmed A.; Ramadan, Mohamed A.; Amr, Abd El-Galil E.; Al-Harbi, Naif O.

2014-01-01

A series of substituted pyrazole, triazole and thiazole derivatives (2–13) were synthesized from 1-(naphtho[1,2-d]thiazol-2-yl)hydrazine as starting material and evaluated as androgen receptor antagonists and anti-prostate cancer agents. The newly synthesized compounds showed potent androgen receptor antagonists and anti-prostate cancer activities with low toxicity (lethal dose 50 (LD50)) comparable to Bicalutamide as reference drug. The structures of newly synthesized compounds were confirmed by IR, 1H-NMR, 13C-NMR, and MS spectral data and elemental analysis. The detailed synthesis, spectroscopic data, LD50 values and pharmacological activities of the synthesized compounds are reported. PMID:25421248

Synthesis, spectral features and biological activity of some novel hetarylazo dyes derived from 6-amino-1,3-dimethyluracil

NASA Astrophysics Data System (ADS)

Yousefi, Hessamoddin; Yahyazadeh, Asieh; Yazdanbakhsh, Mohammad Reza; Rassa, Mehdi; Moradi-e-Rufchahi, Enayat O.'llah

2012-05-01

A series of hetarylazoaminouracil dyes were prepared by coupling of 6-amino-1,3-dimethyluracil with eight diazotized heterocyclic amines in nitrosyl sulphuric acid. The prepared azo dyes were characterized by UV-Vis, FT-IR, 13C NMR, 1H NMR spectroscopic techniques and elemental analysis. The solvatochromism of dyes was evaluated with respect to wavelength of maximum absorption (λmax) in seven solvents with different polarities: acetic acid, methanol, water, chloroform, acetonitrile, dimethyl sulfoxide and dimethyl formamide. The effects of acid, base and concentration of the dye on the visible absorption spectra were also reported. In addition, the antimicrobial activity of the synthesized dyes was evaluated on Escherichia coli, Bacillus subtilis, Micrococcus leuteus and Pseudomonas aeruginosa.

Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

NASA Astrophysics Data System (ADS)

Cao, Xiaoyan; Aiken, George R.; Spencer, Robert G. M.; Butler, Kenna; Mao, Jingdong; Schmidt-Rohr, Klaus

2016-05-01

Seasonal (spring freshet, summer-autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV-visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64-74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63-77%) and TPIA (54-78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OCnp, OCnpO and Cq, 13-17% of HPOA and 15-20% of TPIA) and isolated O-CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (∼5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C-O and O-C-O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

USGS Publications Warehouse

Cao, Xiaoyan; Aiken, George R.; Spencer, Robert G. M.; Butler, Kenna D.; Mao, Jingdong; Schmidt-Rohr, Klaus

2016-01-01

Seasonal (spring freshet, summer–autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV–visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64–74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63–77%) and TPIA (54–78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OCnp, OCnpO and Cq, 13–17% of HPOA and 15–20% of TPIA) and isolated O–CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (∼5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C–O and O–C–O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

Structural Changes and Proapoptotic Peroxidase Activity of Cardiolipin-Bound Mitochondrial Cytochrome c

PubMed Central

Mandal, Abhishek; Hoop, Cody L.; DeLucia, Maria; Kodali, Ravindra; Kagan, Valerian E.; Ahn, Jinwoo; van der Wel, Patrick C.A.

2015-01-01

The cellular process of intrinsic apoptosis relies on the peroxidation of mitochondrial lipids as a critical molecular signal. Lipid peroxidation is connected to increases in mitochondrial reactive oxygen species, but there is also a required role for mitochondrial cytochrome c (cyt-c). In apoptotic mitochondria, cyt-c gains a new function as a lipid peroxidase that catalyzes the reactive oxygen species-mediated chemical modification of the mitochondrial lipid cardiolipin (CL). This peroxidase activity is caused by a conformational change in the protein, resulting from interactions between cyt-c and CL. The nature of the conformational change and how it causes this gain-of-function remain uncertain. Via a combination of functional, structural, and biophysical experiments we investigate the structure and peroxidase activity of cyt-c in its membrane-bound state. We reconstituted cyt-c with CL-containing lipid vesicles, and determined the increase in peroxidase activity resulting from membrane binding. We combined these assays of CL-induced proapoptotic activity with structural and dynamic studies of the membrane-bound protein via solid-state NMR and optical spectroscopy. Multidimensional magic angle spinning (MAS) solid-state NMR of uniformly 13C,15N-labeled protein was used to detect site-specific conformational changes in oxidized and reduced horse heart cyt-c bound to CL-containing lipid bilayers. MAS NMR and Fourier transform infrared measurements show that the peripherally membrane-bound cyt-c experiences significant dynamics, but also retains most or all of its secondary structure. Moreover, in two-dimensional and three-dimensional MAS NMR spectra the CL-bound cyt-c displays a spectral resolution, and thus structural homogeneity, that is inconsistent with extensive membrane-induced unfolding. Cyt-c is found to interact primarily with the membrane interface, without significantly disrupting the lipid bilayer. Thus, membrane binding results in cyt-c gaining the increased peroxidase activity that represents its pivotal proapoptotic function, but we do not observe evidence for large-scale unfolding or penetration into the membrane core. PMID:26536264

NMR measurement system including two synchronized ring buffers, with 128 rf coils for in situ water monitoring in a polymer electrolyte fuel cell

NASA Astrophysics Data System (ADS)

Ogawa, Kuniyasu; Haishi, Tomoyuki; Aoki, Masaru; Hasegawa, Hiroshi; Morisaka, Shinichi; Hashimoto, Seitaro

2017-01-01

A small radio-frequency (rf) coil inserted into a polymer electrolyte fuel cell (PEFC) can be used to acquire nuclear magnetic resonance (NMR) signals from the water in a membrane electrode assembly (MEA) or in oxygen gas channels in the PEFC. Measuring the spatial distribution of the water in a large PEFC requires using many rf probes, so an NMR measurement system which acquires NMR signals from 128 rf probes at intervals of 0.5 s was manufactured. The system has eight rf transceiver units with a field-programmable gate array (FPGA) for modulation of the excitation pulse and quadrature phase detection of the NMR signal, and one control unit with two ring buffers for data control. The sequence data required for the NMR measurement were written into one ring buffer. The acquired NMR signal data were then written temporarily into the other ring buffer and then were transmitted to a personal computer (PC). A total of 98 rf probes were inserted into the PEFC that had an electrical generation area of 16 cm × 14 cm, and the water generated in the PEFC was measured when the PEFC operated at 100 A. As a result, time-dependent changes in the spatial distribution of the water content in the MEA and the water in the oxygen gas channels were obtained.

Geophysical Parameter Estimation of Near Surface Materials Using Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Keating, K.

2017-12-01

Proton nuclear magnetic resonance (NMR), a mature geophysical technology used in petroleum applications, has recently emerged as a promising tool for hydrogeophysicists. The NMR measurement, which can be made in the laboratory, in boreholes, and using a surface based instrument, are unique in that it is directly sensitive to water, via the initial signal magnitude, and thus provides a robust estimate of water content. In the petroleum industry rock physics models have been established that relate NMR relaxation times to pore size distributions and permeability. These models are often applied directly for hydrogeophysical applications, despite differences in the material in these two environments (e.g., unconsolidated versus consolidated, and mineral content). Furthermore, the rock physics models linking NMR relaxation times to pore size distributions do not account for partially saturated systems that are important for understanding flow in the vadose zone. In our research, we are developing and refining quantitative rock physics models that relate NMR parameters to hydrogeological parameters. Here we highlight the limitations of directly applying established rock physics models to estimate hydrogeological parameters from NMR measurements, and show some of the successes we have had in model improvement. Using examples drawn from both laboratory and field measurements, we focus on the use of NMR in partial saturated systems to estimate water content, pore-size distributions, and the water retention curve. Despite the challenges in interpreting the measurements, valuable information about hydrogeological parameters can be obtained from NMR relaxation data, and we conclude by outlining pathways for improving the interpretation of NMR data for hydrogeophysical investigations.

Ultra-Low Field SQUID-NMR using LN2 Cooled Cu Polarizing Field coil

NASA Astrophysics Data System (ADS)

Demachi, K.; Kawagoe, S.; Ariyoshi, S.; Tanaka, S.

2017-07-01

We are developing an Ultra-Low Field (ULF) Magnetic Resonance Imaging (MRI) system using a High-Temperature Superconductor superconducting quantum interference device (HTS rf-SQUID) for food inspection. The advantages of the ULF-NMR (Nuclear Magnetic Resonance) / MRI as compared with a conventional high field MRI are that they are compact and of low cost. In this study, we developed a ULF SQUID-NMR system using a polarizing coil to measure fat of which relaxation time T1 is shorter. The handmade polarizing coil was cooled by liquid nitrogen to reduce the resistance and accordingly increase the allowable current. The measured decay time of the polarizing field was 40 ms. The measurement system consisted of the liquid nitrogen cooled polarizing coil, a SQUID, a Cu wound flux transformer, a measurement field coil for the field of 47 μT, and an AC pulse coil for a 90°pulse field. The NMR measurements were performed in a magnetically shielded room to reduce the environmental magnetic field. The size of the sample was ϕ35 mm × L80 mm. After applying a polarizing field and a 90°pulse, an NMR signal was detected by the SQUID through the flux transformer. As a result, the NMR spectra of fat samples were obtained at 2.0 kHz corresponding to the measurement field Bm of 47 μT. The T1 relaxation time of the mineral oil measured in Bm was 45 ms. These results suggested that the ULF-NMR/MRI system has potential for food inspection.

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.

31P-NMR measurements of ATP, ADP, 2,3-diphosphoglycerate and Mg2+ in human erythrocytes.

PubMed

Petersen, A; Kristensen, S R; Jacobsen, J P; Hørder, M

1990-08-17

Absolute 31P-NMR measurements of ATP, ADP and 2,3-diphosphoglycerate (2,3-DPG) in oxygenated and partly deoxygenated human erythrocytes, compared to measurements by standard assays after acid extraction, show that ATP is only 65% NMR visible, ADP measured by NMR is unexpectedly 400% higher than the enzymatic measurement and 2,3-DPG is fully NMR visible, regardless of the degree of oxygenation. These results show that binding to hemoglobin is unlikely to cause the decreased visibility of ATP in human erythrocytes as deoxyhemoglobin binds the phosphorylated metabolites more tightly than oxyhemoglobin. The high ADP visibility is unexplained. The levels of free Mg2+ [( Mg2+]free) in human erythrocytes are 225 mumol/l at an oxygen saturation of 98.6% and instead of the expected increase, the level decreased to 196 mumol/l at an oxygen saturation of 38.1% based on the separation between the alpha- and beta-ATP peaks. [Mg2+]free in the erythrocytes decreased to 104 mumol/l at a high 2,3-DPG concentration of 25.4 mmol/l red blood cells (RBC) and a normal ATP concentration of 2.05 mmol/l RBC. By increasing the ATP concentration to 3.57 mmol/l RBC, and with a high 2,3-DPG concentration of 24.7 mmol/l RBC, the 31P-NMR measured [Mg2+]free decreased to 61 mumol/l. These results indicate, that the 31P-NMR determined [Mg2+]free in human erythrocytes, based solely on the separation of the alpha- and beta-ATP peaks, does not give a true measure of intracellular free Mg2+ changes with different oxygen saturation levels. Furthermore the measurement is influenced by the concentration of the Mg2+ binding metabolites ATP and 2,3-DPG. Failure to take these factors into account when interpreting 31P-NMR data from human erythrocytes may explain some discrepancies in the literature regarding [Mg2+]free.

Application of the double relaxation oscillation superconducting quantum interference device sensor to micro-tesla 1H nuclear magnetic resonance experiments

NASA Astrophysics Data System (ADS)

Kang, Chan Seok; Kim, Kiwoong; Lee, Seong-Joo; Hwang, Seong-min; Kim, Jin-Mok; Yu, Kwon Kyu; Kwon, Hyukchan; Lee, Sang Kil; Lee, Yong-Ho

2011-09-01

We developed an ultra-low field (ULF)-nuclear magnetic resonance (NMR) measurement system capable of working with a measurement field (Bm) of several micro-tesla and performed basic NMR studies with a double relaxation oscillation superconducting quantum interference device (DROS) instead of conventional dc-SQUIDs. DROS is a SQUID sensor utilizing a relaxation oscillation between a dc-SQUID and a relaxation circuit; the new unit consists of an inductor and a resistor, and is connected in parallel with the SQUID. DROS has a 10 times larger flux-to-voltage transfer coefficient (˜mV/ϕ0) than that of the dc-SQUID, and this large transfer coefficient enables the acquisition of the SQUID signal with a simple flux-locked-loop (FLL) circuit using room temperature pre-amplifiers. The DROS second-order gradiometer showed average field noise of 9.2 μϕ0/√Hz in a magnetically shielded room (MSR). In addition, a current limiter formed of a Josephson junction array was put in a flux-transformer of DROS to prevent excessive currents that can be generated from the high pre-polarization field (Bp). Using this system, we measured an 1H NMR signal in water under 2.8 μT Bm field and reconstructed a one-dimensional MR image from the 1H NMR signal under a gradient field BG of 4.09 nT/mm. In addition, we confirmed that the ULF-NMR system can measure the NMR signal in the presence of metal without any distortion by measuring the NMR signal of a sample wrapped with metal. Lastly, we have measured the scalar J-coupling of trimethylphosphate and were able to confirm a clear doublet NMR signal with the coupling strength J3[P,H] = 10.4 ± 0.8 Hz. Finally, because the existing ULF-NMR/MRI studies were almost all performed with dc-SQUID based systems, we constructed a dc-SQUID-based ULF-NMR system in addition to the DROS based system and compared the characteristics of the two different systems by operating the two systems under identical experimental conditions.

Spectral study on conformation switchable cationic calix[4]carbazole serving as curcumin container, stabilizer and sustained-delivery carrier

NASA Astrophysics Data System (ADS)

Zhao, Liang; Kang, Le; Chen, Yan; Li, Gang; Wang, Lan; Hu, Chun; Yang, Peng

2018-03-01

A fluorescent 2,7-dimethoxy-substituted calix[4]carbazole (1) is facilely synthesized. The spectral behaviors of both the guest-induced switchable conformation of 1 and its abilities serving as the stabilizer and molecular carrier of curcumin are investigated. UV-vis, fluorescence and NMR spectral results show that upon binding to curcumin, the 1,3-alternate conformation of 1 is converted to be the cone one. The relative high association constant (6.4 × 106 M- 1) of 1 binding to curcumin enables it to stabilize the curcumin, to suppress its degradation, and to sustainably deliver it into the EYPC vesicles within 20 h. Moreover, the cytotoxicity assay shows that 1 does not interfere the antiproliferative activities of curcumin. All these properties endow 1 the potential capability of serving as the molecular drug carrier. Our current result may pave the way looking for more efficient fluorescent calixcarbazoles and thereof spectral utilities.

Measurement of Lipid Accumulation in Chlorella vulgaris via Flow Cytometry and Liquid-State ¹H NMR Spectroscopy for Development of an NMR-Traceable Flow Cytometry Protocol

PubMed Central

Bono Jr., Michael S.; Garcia, Ravi D.; Sri-Jayantha, Dylan V.; Ahner, Beth A.; Kirby, Brian J.

2015-01-01

In this study, we cultured Chlorella vulgaris cells with a range of lipid contents, induced via nitrogen starvation, and characterized them via flow cytometry, with BODIPY 505/515 as a fluorescent lipid label, and liquid-state 1H NMR spectroscopy. In doing so, we demonstrate the utility of calibrating flow cytometric measurements of algal lipid content using triacylglyceride (TAG, also known as triacylglycerol or triglyceride) content per cell as measured via quantitative 1H NMR. Ensemble-averaged fluorescence of BODIPY-labeled cells was highly correlated with average TAG content per cell measured by bulk NMR, with a linear regression yielding a linear fit with r 2 = 0.9974. This correlation compares favorably to previous calibrations of flow cytometry protocols to lipid content measured via extraction, and calibration by NMR avoids the time and complexity that is generally required for lipid quantitation via extraction. Flow cytometry calibrated to a direct measurement of TAG content can be used to investigate the distribution of lipid contents for cells within a culture. Our flow cytometry measurements showed that Chlorella vulgaris cells subjected to nitrogen limitation exhibited higher mean lipid content but a wider distribution of lipid content that overlapped the relatively narrow distribution of lipid content for replete cells, suggesting that nitrogen limitation induces lipid accumulation in only a subset of cells. Calibration of flow cytometry protocols using direct in situ measurement of TAG content via NMR will facilitate rapid development of more precise flow cytometry protocols, enabling investigation of algal lipid accumulation for development of more productive algal biofuel feedstocks and cultivation protocols. PMID:26267664

Measurement of lipid accumulation in Chlorella vulgaris via flow cytometry and liquid-state ¹H NMR spectroscopy for development of an NMR-traceable flow cytometry protocol.

PubMed

Bono, Michael S; Garcia, Ravi D; Sri-Jayantha, Dylan V; Ahner, Beth A; Kirby, Brian J

2015-01-01

In this study, we cultured Chlorella vulgaris cells with a range of lipid contents, induced via nitrogen starvation, and characterized them via flow cytometry, with BODIPY 505/515 as a fluorescent lipid label, and liquid-state 1H NMR spectroscopy. In doing so, we demonstrate the utility of calibrating flow cytometric measurements of algal lipid content using triacylglyceride (TAG, also known as triacylglycerol or triglyceride) content per cell as measured via quantitative 1H NMR. Ensemble-averaged fluorescence of BODIPY-labeled cells was highly correlated with average TAG content per cell measured by bulk NMR, with a linear regression yielding a linear fit with r2 = 0.9974. This correlation compares favorably to previous calibrations of flow cytometry protocols to lipid content measured via extraction, and calibration by NMR avoids the time and complexity that is generally required for lipid quantitation via extraction. Flow cytometry calibrated to a direct measurement of TAG content can be used to investigate the distribution of lipid contents for cells within a culture. Our flow cytometry measurements showed that Chlorella vulgaris cells subjected to nitrogen limitation exhibited higher mean lipid content but a wider distribution of lipid content that overlapped the relatively narrow distribution of lipid content for replete cells, suggesting that nitrogen limitation induces lipid accumulation in only a subset of cells. Calibration of flow cytometry protocols using direct in situ measurement of TAG content via NMR will facilitate rapid development of more precise flow cytometry protocols, enabling investigation of algal lipid accumulation for development of more productive algal biofuel feedstocks and cultivation protocols.

Method and apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise oreintationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions is zero.

Topological superfluids confined in a nanoscale slab geometry

NASA Astrophysics Data System (ADS)

Saunders, John

2013-03-01

Nanofluidic samples of superfluid 3He provide a route to explore odd-parity topological superfluids and their surface, edge and defect-bound excitations under well controlled conditions. We have cooled superfluid 3He confined in a precisely defined nano-fabricated cavity to well below 1 mK for the first time. We fingerprint the order parameter by nuclear magnetic resonance, exploiting a SQUID NMR spectrometer of exquisite sensitivity. We demonstrate that dimensional confinement, at length scales comparable to the superfluid Cooper-pair diameter, has a profound influence on the superfluid order of 3He. The chiral A-phase is stabilized at low pressures, in a cavity of height 650 nm. At higher pressures we observe 3He-B with a surface induced planar distortion. 3He-B is a time-reversal invariant topological superfluid, supporting gapless Majorana surface states. In the presence of the small symmetry breaking NMR static magnetic field we observe two possible B-phase states of the order parameter manifold, which can coexist as domains. Non-linear NMR on these states enables a measurement of the surface induced planar distortion, which determines the spectral weight of the surface excitations. The expected structure of the domain walls is such that, at the cavity surface, the line separating the two domains is predicted to host fermion zero modes, protected by symmetry and topology. Increasing confinement should stabilize new p-wave superfluid states of matter, such as the quasi-2D gapped A phase, which breaks time reversal symmetry, has a protected chiral edge mode, and may host half-quantum vortices with a Majorana zero-mode at the core. We discuss experimental progress toward this phase, through measurements on a 100 nm cavity. On the other hand, a cavity height of 1000 nm may stabilize a novel ``striped'' superfluid with spatially modulated order parameter. Supported by EPSRC (UK) GR/J022004/1 and European Microkelvin Consortium, FP7 grant 228464

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

NASA Astrophysics Data System (ADS)

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

2002-12-01

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

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.

Use of proline mutants to help solve the NMR solution structure of type III antifreeze protein.

PubMed Central

Chao, H.; Davies, P. L.; Sykes, B. D.; Sönnichsen, F. D.

1993-01-01

To help understand the structure/function relationships in antifreeze proteins (AFP), and to define the motifs required for ice binding, a Type III AFP suitable for two-dimensional (2D) NMR studies was produced in Escherichia coli. A synthetic gene for one of the Type III AFP isoforms was assembled in a T7 polymerase-directed expression vector. The 67-amino acid-long gene product differed from the natural AFP by inclusion of an N-terminal methionine but was indistinguishable in activity. The NMR spectra of this AFP were complicated by cis-trans proline isomerization from the C-terminal sequence YPPA. Substitution of this sequence by YAA eliminated isomer signals without altering the activity or structure of the mutant AFP. This variant (rQAE m1.1) was selected for sequential assignment and the secondary structure determination using 2D 1H NMR spectroscopy. Nine beta-strands are paired to form two triple-stranded antiparallel sheets and one double-stranded antiparallel sheet. Two further proline replacements, P29A and P33A, were made to delineate the role of conserved prolines in Type III AFP. These mutants were valuable in clarifying ambiguous NMR spectral assignments amongst the remaining six prolines of rQAE m1.1. In contrast to the replacement of the C-terminal prolyl residues, the exchange of P29 and P33 caused some structural changes and significantly decreased protein solubility and antifreeze activity. PMID:8401227

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and "hidden" dimensions.

PubMed

Meng, Xi; Nguyen, Bao D; Ridge, Clark; Shaka, A J

2009-01-01

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to "reduced-dimensionality" strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the filter diagonalization method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra-dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths.

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and “hidden” dimensions

PubMed Central

Meng, Xi; Nguyen, Bao D.; Ridge, Clark; Shaka, A. J.

2009-01-01

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to “reduced-dimensionality” strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the Filter Diagonalization Method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths. PMID:18926747

Synthesis, biological evaluation and molecular modeling of novel series of pyridine derivatives as anticancer, anti-inflammatory and analgesic agents

NASA Astrophysics Data System (ADS)

Helal, M. H.; El-Awdan, S. A.; Salem, M. A.; Abd-elaziz, T. A.; Moahamed, Y. A.; El-Sherif, A. A.; Mohamed, G. A. M.

2015-01-01

This paper presents a combined synthesis; characterization, computational and biological activity studies of novel series of pyridines heterocyclic compounds. The compounds have been characterized by elemental analyses and spectral like IR, 1H NMR, 13C NMR and MS studies. Michael addition of substituted-2-methoxycarbonylacetanilide 2a,b on the α-substituted cinnamonitriles 3a-d gave the corresponding 2-pyridone derivatives 5-10. Structures of the titled compounds cited in this article were elucidated by spectrometric data (IR, 1H NMR, 13C NMR and MS). The molecular modeling of the synthesized compounds has been drawn and their molecular parameters were calculated. Also, valuable information is obtained from the calculation of molecular parameters including electronegativity, net dipole moment of the compounds, total energy, electronic energy, binding energy, HOMO and LUMO energy. Various in vitro antitumor as well as in vivo anti-inflammatory and analgesic activities of the synthesized compounds were investigated. Evaluation of anti-inflammatory activity of test compounds was performed using carrageenan induced paw edema in rats. All the tested compounds showed moderate to good activity. The SAR results indicate that all compounds showed moderate to good activity, among these 7 and 10 compounds having -N(CH3)2 group are most effective.

High-Resolution Magic-Angle-Spinning NMR and Magnetic Resonance Imaging Spectroscopies Distinguish Metabolome and Structural Properties of Maize Seeds from Plants Treated with Different Fertilizers and Arbuscular mycorrhizal fungi.

PubMed

Mazzei, Pierluigi; Cozzolino, Vincenza; Piccolo, Alessandro

2018-03-21

Both high-resolution magic-angle-spinning (HRMAS) and magnetic resonance imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology, and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by arbuscular mycorrhizal fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI. Principal component analysis (PCA) was applied to evaluate 1 H CPMG (Carr-Purcel-Meiboom-Gill) HRMAS spectra as well as several MRI-derived parameters ( T 1 , T 2 , and self-diffusion coefficients) of intact maize caryopses. PCA score-plots from spectral results indicated that both seeds metabolome and structural properties depended on the specific field treatment undergone by maize plants. Our findings show that a combination of multivariate statistical analyses with advanced and nondestructive NMR techniques, such as HRMAS and MRI, enables the evaluation of the effects induced on maize caryopses by different fertilization and management practices at field level. The spectroscopic approach adopted here may become useful for the objective appraisal of the quality of seeds produced under a sustainable agriculture.

Dynamic pictures of membrane proteins in two-dimensional crystal, lipid bilayer and detergent as revealed by site-directed solid-state 13C NMR.

PubMed

Saitô, Hazime

2004-11-01

We have compared site-directed 13C solid-state NMR spectra of [3-13C]Ala- and/or [1-13C]Val-labeled membrane proteins, including bacteriorhodopsin (bR), pharaonis phoborhodopin (ppR), its cognate transducer (pHtrII) and Escherichia coli diacylglycerol kinase (DGK), in two-dimensional (2D) crystal, lipid bilayers, and detergent. Restricted fluctuation motions of these membrane proteins due to oligomerization of bR by specific protein-protein interactions in the 2D crystalline lattice or protein complex between ppR and pHtrII provide the most favorable environment to yield well-resolved, fully visible 13C NMR signals for [3-13C]Ala-labeled proteins. In contrast, several signals from such membrane proteins were broadened or lost owing to interference of inherent fluctuation frequencies (10(4)-10(5)Hz) with frequency of either proton decoupling or magic angle spinning, if their 13C NMR spectra were recorded as a monomer in lipid bilayers at ambient temperature. The presence of such protein dynamics is essential for the respective proteins to achieve their own biological functions. Finally, spectral broadening found for bR and DGK in detergents were discussed.

Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization.

PubMed

Takahashi, Hiroki; Ayala, Isabel; Bardet, Michel; De Paëpe, Gaël; Simorre, Jean-Pierre; Hediger, Sabine

2013-04-03

Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool.

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.

Quantification of left to right atrial shunts with velocity-encoded cine nuclear magnetic resonance imaging.

PubMed

Brenner, L D; Caputo, G R; Mostbeck, G; Steiman, D; Dulce, M; Cheitlin, M D; O'Sullivan, M; Higgins, C B

1992-11-01

The purpose of this study was to evaluate the ability of velocity-encoded nuclear magnetic resonance (NMR) imaging to quantify left to right intracardiac shunts in patients with an atrial septal defect. Quantification of intracardiac shunts is clinically important in planning therapy. Velocity-encoded NMR imaging was used to quantify stroke flow in the aorta and in the main pulmonary artery in a group of patients who were known to have an increased pulmonary to systemic flow ratio (Qp/Qs). The velocity-encoded NMR flow data were used to calculate Qp/Qs, and these values were compared with measurements of Qp/Qs obtained with oximetric data derived from cardiac catheterization and from stroke volume measurements of the two ventricles by using volumetric data from biphasic spin echo and cine NMR images obtained at end-diastole and end-systole. Two independent observers measured Qp/Qs by using velocity-encoded NMR imaging in 11 patients and found Qp/Qs ranging from 1.4:1 to 3.9:1. These measurements correlated well with both oximetric data (r = 0.91, SEE = 0.35) and ventricular volumetric data (r = 0.94, SEE = 0.30). Interobserver reproducibility for Qp/Qs by velocity-encoded NMR imaging was good (r = 0.97, SEE = 0.20). Velocity-encoded NMR imaging is an accurate and reproducible method for measuring Qp/Qs in left to right shunts. Because it is completely noninvasive, it can be used to monitor shunt volume over time.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Structure of indazole N1-oxide derivatives studied by X-ray, theoretical methods, 1H, 13C, 15N NMR and EI/MS

NASA Astrophysics Data System (ADS)

Gerpe, Alejandra; Piro, Oscar E.; Cerecetto, Hugo; González, Mercedes

2007-12-01

A series of indazole N1-oxide derivatives has been spectroscopically studied in solution using 1H, 13C, and 15N NMR based on pulsed field gradient selected PFG 1H sbnd X (X = 13C and 15N) gHMQC and gHMBC experiments. Some indazoles were prepared using a new methodology to compare its spectral and structural data with the indazole N1-oxide parent compounds. The 13C resonances of the indazole N1-oxide carbon 3 and 7a demonstrate the N-oxide push-electron capability. The 15N resonances of the indazole N-oxide, nitrogen 1, are near to 30 ppm more shielded than the corresponding values in the indazole heterocycle (deoxygenated form). Moreover, the structures of one indazole and one indazole N-oxide were unambiguously confirmed by X-ray crystallography. The solid state structures were contrasted with the theoretical ones obtained in vacuo at different calculus level. The aromaticity of the derivatives was studied analyzing the H sbnd H coupling constants of indazole's aromatic hydrogens and measuring C sbnd C distances in the solid state. The fragmentation that takes place in EI/MS was gathered for all the indazole N-oxide derivatives and the general fragmentation pattern analyzed.

Synthesis, characterization and anti-microbial activity of phenylurea-formaldehyde resin (PUF) and its polymer metal complexes (PUF-Mn(II).

PubMed

Ahamad, Tansir; Alshehri, Saad M

2012-10-01

Phenylurea-formaldehyde polymer (PUF) was synthesized via polycondensation of phenylurea and formaldehyde in basic medium, its polymer-metal complexes [PUF-M(II)] were prepared with Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) ions. PUF and PUF-M(II) were characterized with magnetic moment measurements, elemental and spectral (UV-visible, FTIR, 1H-NMR, 13C-NMR and ESR) analysis. The thermal behaviors of all the synthesized polymers were carried out using thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The thermal data revealed that all of the PUF-M(II) showed higher thermal stabilities than the PUF and also ascribed that the PUF-Cu(II) showed better thermal stability than the other PUF-M(II). The kinetic parameters such as activation energy, pre-exponential factor etc., were evaluated for these polymer metal complexes using Coats-Redfern equation. In addition, the antimicrobial activity of the synthesized polymers was tested against several microorganisms using agar well diffusion methods. Among all of the PUF-M(II), the antimicrobial activity of the PUF-Cu(II) showed the highest zone of inhibition because of its higher stability constant and may be used in biomedical applications. Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis and characterization of an anticoagulant 4-hydroxy-1-thiocoumarin by FTIR, FT-Raman, NMR, DFT, NBO and HOMO-LUMO analysis

NASA Astrophysics Data System (ADS)

Arjunan, V.; Santhanam, R.; Sakiladevi, S.; Marchewka, M. K.; Mohan, S.

2013-04-01

Experimental and theoretical investigations on the molecular structural, electronic and the vibrational characteristics of 4-hydroxy-1-thiocoumarin are presented. Conformational analysis was carried out to obtain the more stable configuration of the compound. The vibrational frequencies were obtained by DFT/B3LYP calculations employing 6-311++G(d,p), 6-31G(d,p), cc-pVTZ basic sets and B3PW91 method with 6-311++G(d,p) basis set and are compared with FTIR and FT-Raman spectral data recorded in the region of 4000-400 and 4000-100 cm-1, respectively. The total electron density and molecular electrostatic potential surfaces of the molecule were constructed to display electrostatic potential (electron + nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. 1H and 13C NMR spectra were recorded and 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated by using the Gauge-Independent Atomic Orbital (GIAO) method and analyzed. The picture of localized bonds and lone pairs, stabilization energy of the delocalization of electrons, the charge and hybridisation of the atoms of 4-hydroxy-1-thiocoumarin were clearly explained by NBO analysis.

Triterpenoid glycosides from Bacopa monnieri.

PubMed

Sivaramakrishna, Chillara; Rao, Chirravuri V; Trimurtulu, Golakoti; Vanisree, Mulabagal; Subbaraju, Gottumukkala V

2005-12-01

Two triterpenoid glycosides have been isolated along with 10 known saponins from Bacopa monnieri. Structures of the compounds have been elucidated as 3-O-[beta-D-glucopyranosyl-(1-->3)-beta-D-glucopyranosyl] jujubogenin (1) and 3-O-[beta-D-glucopyranosyl-(1-->3)-beta-D-glucopyranosyl] pseudojujubogenin (2) by high resolution NMR spectral data and chemical correlations. Further, the chemical compositions of bacosides A and B have been delineated.

Structure and biological activity of a new rotenoid from Pongamia pinnata.

PubMed

Simin, K; Ali, Zulfiqar; Khaliq-Uz-Zaman, Syed Muhammad; Ahmad, Viqar Uddin

2002-10-01

Pongarotene (1), a new rotenoid and karanjin (2), a known flavonol, were isolated from the seeds of Pongamia pinnata. The structure determination of these compounds were based on spectral analyses including 2D-NMR. The antifungal, antibacterial and phytotoxicity results of pure compounds 1 and 2 as well as of the methanol (M) and ethyl acetate (E) crude extracts are also being reported.

Noninvasive Detection of Lactate as a Biomarker of Response Using Spectral-Selective Multiple Quantum Editing Sequence (SS-SelMQC)

DTIC Science & Technology

2010-05-01

for attending ISMRM conference B. Selected Publication Annarao, S., Sidhu, O.P., Roy, R., Tuli , R. and Khetrapal, C.L. (2008). Lipid profiling of... Tuli Rakesh. And Khetrapal, C.L. (2010). Metabolic and Histopathological alterations of Jatropha Mosoic begamovirus infected Jatropha Curcus L. by HR-MAS NMR Spectroscopy and Magnetic Resonace Imaging. Planta. 232: 85-93

Probing porous media with gas diffusion NMR

NASA Technical Reports Server (NTRS)

Mair, R. W.; Wong, G. P.; Hoffmann, D.; Hurlimann, M. D.; Patz, S.; Schwartz, L. M.; Walsworth, R. L.

1999-01-01

We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks.

Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

DOE PAGES

Perras, Frederic A.

2015-12-15

Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

SBIR Phase II Final Report: Low cost Autonomous NMR and Multi-sensor Soil Monitoring Instrument

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

Walsh, David O.

In this 32-month SBIR Phase 2 program, Vista Clara designed, assembled and successfully tested four new NMR instruments for soil moisture measurement and monitoring: An enhanced performance man-portable Dart NMR logging probe and control unit for rapid, mobile measurement in core holes and 2” PVC access wells; A prototype 4-level Dart NMR monitoring probe and prototype multi-sensor soil monitoring control unit for long-term unattended monitoring of soil moisture and other measurements in-situ; A non-invasive 1m x 1m Discus NMR soil moisture sensor with surface based magnet/coil array for rapid measurement of soil moisture in the top 50 cm of themore » subsurface; A non-invasive, ultra-lightweight Earth’s field surface NMR instrument for non-invasive measurement and mapping of soil moisture in the top 3 meters of the subsurface. The Phase 2 research and development achieved most, but not all of our technical objectives. The single-coil Dart in-situ sensor and control unit were fully developed, demonstrated and successfully commercialized within the Phase 2 period of performance. The multi-level version of the Dart probe was designed, assembled and demonstrated in Phase 2, but its final assembly and testing were delayed until close to the end of the Phase 2 performance period, which limited our opportunities for demonstration in field settings. Likewise, the multi-sensor version of the Dart control unit was designed and assembled, but not in time for it to be deployed for any long-term monitoring demonstrations. The prototype ultra-lightweight surface NMR instrument was developed and demonstrated, and this result will be carried forward into the development of a new flexible surface NMR instrument and commercial product in 2018.« less

Method and sample spinning apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR apparatus and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus spins the sample about an axis. The angle of the axis is mechanically varied such that the time average of two or more Legendre polynomials are zero.

Measurement of untruncated nuclear spin interactions via zero- to ultralow-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Blanchard, J. W.; Sjolander, T. F.; King, J. P.; Ledbetter, M. P.; Levine, E. H.; Bajaj, V. S.; Budker, D.; Pines, A.

2015-12-01

Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) provides a new regime for the measurement of nuclear spin-spin interactions free from the effects of large magnetic fields, such as truncation of terms that do not commute with the Zeeman Hamiltonian. One such interaction, the magnetic dipole-dipole coupling, is a valuable source of spatial information in NMR, though many terms are unobservable in high-field NMR, and the coupling averages to zero under isotropic molecular tumbling. Under partial alignment, this information is retained in the form of so-called residual dipolar couplings. We report zero- to ultralow-field NMR measurements of residual dipolar couplings in acetonitrile-2-13C aligned in stretched polyvinyl acetate gels. This permits the investigation of dipolar couplings as a perturbation on the indirect spin-spin J coupling in the absence of an applied magnetic field. As a consequence of working at zero magnetic field, we observe terms of the dipole-dipole coupling Hamiltonian that are invisible in conventional high-field NMR. This technique expands the capabilities of zero- to ultralow-field NMR and has potential applications in precision measurement of subtle physical interactions, chemical analysis, and characterization of local mesoscale structure in materials.

A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.

PubMed

Rozentur-Shkop, Eva; Goobes, Gil; Chill, Jordan H

2016-12-01

Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J( 15 N, 13 Cα) couplings. This concept was realized using a unidirectional (H)NCO 13 C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J( 15 N, 13 Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP 2-65 conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are a useful measureable in characterizing structural ensembles in IDPs, and that the proposed experiment provides a practical method for accurately performing such measurements, once again emphasizing the power of NMR in studying IDP behavior.

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.

Characterization of the fluid and solid components of cyanogel systems during the gelation process

NASA Astrophysics Data System (ADS)

Fortmeyer, Ivy Camille

The work in this thesis concerns the sol-gel transformation in cyanogel systems comprised of d8 square planar chlorometalates (M=Pd(II), Pt(II)) and d6 octahedral hexacyanometalates (M=Fe(II), Co(III), Ru(II)). The body of this thesis is split into two chapters. The first chapter examines the physical changes in the solvent phase of the sol-gel network, and the second focuses on the polymer backbone of the gel. Studies on the water component of cyanogel systems during the gelation process were carried out with a variety of in situ spectroscopic techniques. The use of high resolution-magic angle spinning nuclear magnetic resonance (HR-MAS NMR) to identify and characterize different water environments was explored, but was ultimately found to disrupt gelation. Standard solution-phase 1H NMR proved sufficient for calculation and qualitative modeling of spin-spin and spin-lattice relaxations, providing distinct spectral markers of the gelation point and subsequent aging process. Vibrational spectroscopy was used to explore the hydrogen bonding environment of the water during gelation. The kinetics of polymerization of the cyanogel backbone was explored using both in situ and ex situ techniques. Data collected by 13C NMR and 195Pt NMR primarily demonstrated first order kinetics, implying a dissociative substitution mechanism at the chlorometalate center. Rate constants for gelation in the presence of various added monopotassium and nitrate salts were calculated. Added chloride was found to significantly slow gelation and was further explored using NMR and vibrational spectroscopy. A mechanism was proposed for the polymerization taking into account the dissociative substitution and the bridging geometries implied by 13C NMR.

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.

High-sensitivity NMR beyond 200,000 atmospheres of pressure

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Synthesis, characterization and spectroscopic properties of the hydrazodye and new hydrazodye-metal complexes

NASA Astrophysics Data System (ADS)

Bouhdada, M.; EL Amane, M.

2017-12-01

The hydrazodye (L) [disodium (7-hydroxyl-8-phenylazo-1,3-naphthalenedisulfonate)] is prepared and characterized by infrared 1H,13C, NMR and UV-visible spectra. The spectral data of the ligand (L) existing predominantly in the hydrazones form. Reaction of the hydrazodye (L) with Cd2+, Ni2+, Cu2+ and Zn2+ chloride gave two series of metal complexes with general formula [ML2 (OH2)2]2Cl and [ML2 (caf)2]2Cl. Their complexes were identified by FTIR, UV-visible spectra, 1H, 13C, NMR, EPR, XRD and molar conductance. The molar conductance reveals that the new series of metal complexes are non-electrolytes. The postulated octahedral structure of the obtained complexes is also proposed on spectroscopic data analysis.

Composition and Antioxidant Activity of Geopropolis Collected by Melipona subnitida (Jandaíra) Bees

PubMed Central

Alves de Souza, Silvana; Camara, Celso Amorim; Monica Sarmento da Silva, Eva; Silva, Tania Maria Sarmento

2013-01-01

An investigation of the geopropolis collected by Melipona subnitida (jandaíra) stingless bee led to the isolation and characterization of two phenylpropanoids, 6-O-p-coumaroyl-D-galactopyranose (1) and 6-O-cinnamoyl-1-O-p-coumaroyl-β-D-glucopyranose (2), and seven flavonoids, 7-O-methyl-naringenin (3), 7-O-methyl aromadendrin (4), 7,4′-di-O-methyl aromadendrin (5), 4′-O-methyl kaempferol (6), 3-O-methyl quercetin (7), 5-O-methyl aromadendrin (8), and 5-O-methyl kaempferol (9). The structure of the new phenylpropanoid (1) was established from IR, LC-ESI-MS, and NMR spectral data, including 2D NMR experiments. The extract and fractions demonstrated significant antioxidant activity in DPPH, ABTS, and β-carotene/linoleic acid tests. PMID:23935683

Composition and Antioxidant Activity of Geopropolis Collected by Melipona subnitida (Jandaíra) Bees.

PubMed

Alves de Souza, Silvana; Camara, Celso Amorim; Monica Sarmento da Silva, Eva; Silva, Tania Maria Sarmento

2013-01-01

An investigation of the geopropolis collected by Melipona subnitida (jandaíra) stingless bee led to the isolation and characterization of two phenylpropanoids, 6-O-p-coumaroyl-D-galactopyranose (1) and 6-O-cinnamoyl-1-O-p-coumaroyl- β -D-glucopyranose (2), and seven flavonoids, 7-O-methyl-naringenin (3), 7-O-methyl aromadendrin (4), 7,4'-di-O-methyl aromadendrin (5), 4'-O-methyl kaempferol (6), 3-O-methyl quercetin (7), 5-O-methyl aromadendrin (8), and 5-O-methyl kaempferol (9). The structure of the new phenylpropanoid (1) was established from IR, LC-ESI-MS, and NMR spectral data, including 2D NMR experiments. The extract and fractions demonstrated significant antioxidant activity in DPPH, ABTS, and β -carotene/linoleic acid tests.

Pegylation of Magnetically Oriented Lipid Bilayers

NASA Astrophysics Data System (ADS)

King, Valencia; Parker, Margaret; Howard, Kathleen P.

2000-01-01

We report NMR data for magnetically oriented phospholipid bilayers which have been doped with a lipid derivatized with a polyethylene glycol polymer headgroup to stabilize samples against aggregation. 13C, 31P, and 2H NMR data indicate that the incorporation of PEG2000-PE (1% molar to DMPC) does not interfere with the orientation properties of bicelles prepared at 25% w/v with or without the presence of lanthanide. Bicelles prepared at 10% w/v are also shown to orient when PEG2000-PE is added. The addition of PEG2000-PE to cholesterol-containing, lanthanide-flipped bicelles is shown to inhibit sample phase separation and improve spectral quality. Furthermore, the addition of PEG2000-PE to high w/v bicelles (40% w/v) is demonstrated to lead to an increase in overall sample order.

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.

Catalytic reduction of pralidoxime in pharmaceuticals by macrocyclic Ni(II) compounds derived from orthophthalaldehyde.

PubMed

Reddy, P Muralidhar; Prasad, Adapa V S S; Rohini, Rondla; Ravinder, Vadde

2008-08-01

Efficient catalytic method for the reduction of pralidoxime to its amine derivative by macrocyclic Ni(II) compounds has been developed. Ten macrocyclic Schiff base Ni(II) compounds were synthesized via non-template synthesis by treating the corresponding macrocycles with nickel chloride in 1:1 ratio. The resulting compounds were characterized by elemental, IR, (1)H NMR, (13)C NMR, mass, electronic spectra, conductance, magnetic, thermal studies and their structures have been proposed. These compounds were used as catalysts for the reduction of pralidoxime to its amino derivative. The reduced pralidoxime was also characterized by spectral analysis and catalytic cycle has been established. The reduced product was determined spectrophotometrically by treating with ninhydrin reagent and the percent yields were found to be in the range of 75.12-82.36%.

Phytochemical Investigations on Chemical Constituents of Achillea tenuifolia Lam

PubMed Central

Moradkhani, Shirin; Kobarfard, Farzad; Ayatollahi, Seyed Abdol Majid

2014-01-01

Achillea tenuifolia Lam. (Asteraceae) afforded a methanolic extract from which after fractionation in solvents with different polarities, two known flavones 3’, 5- dihydroxy- 4’, 6, 7- trimethoxy flavone (eupatorine, compound 3), 5- hydroxy- 3’,4’, 6, 7- tetramethoxyflavone (compound 4), besides stearic acid (compound 1), lupeol (compound 2), daucosterol (β- sitosterol 3-O- β- D- glucopyranoside, compound 5), 2, 4- dihydroxy methyl benzoate (compound 6) were isolated for the first time. The structure of isolated compounds was elucidated by means of different spectroscopic methods such as UV, IR, Mass and 1H- NMR (1D and 2D) and 13C-NMR. For further confirming the structures of isolated compounds, comparison of the spectral data of them with those reported in the litratures have been done. PMID:25276207

[Chemical constituents of Swertia macrosperma].

PubMed

Wang, Hongling; Geng, Changan; Zhang, Xuemei; Ma, Yunbao; Jiang, Zhiyong; Chen, Jijun

2010-12-01

To study the chemical constituents of Swertia macrosperma. The air-dried whole plants of Swertia macrosperma were extracted with boiling water. The extract was concentrated to a small amount of volume and extracted with petroleum ether, EtOAc and n-BuOH, successively. The compounds were isolated and purified by column chromatography from the EtOAc fraction, and identified based on spectral analyses (MS, 1H-NMR, 13C-NMR). Thirteen compounds were isolated from S. macrosperma, and were characterized as norbellidifolin (1), 1-hydroxy-3,7, 8-trimethoxy-xanthone (2), norswertianolin (3), swertianolin (4), 1,3,7,8-tetrahydroxyxanthone-8-O-beta-D-glucopyranoside (5), swertiamatin (6), decentapicrin (7), coniferl aldehyde (8), sinapaldehyde (9), balanophonin (10), together with beta-sitosterol, daucosterol, and oleanolic acid . Compounds 2, 4-10 were obtained from Swertia macrosperma for the first time.

UV-vis, IR and 1H NMR spectroscopic studies of some mono- and bis-azo-compounds based on 2,7-dihydroxynaphthalene and aniline derivatives

NASA Astrophysics Data System (ADS)

Issa, Raafat M.; Fayed, Tarek A.; Awad, Mohammed K.; El-Kony, Sanaa M.

2005-12-01

The absorption spectra of mono- and bis-azo-derivatives obtained by coupling the diazonium salts of aromatic amines and 2,7-dihydroxynaphthalene have been studied in six organic solvents. The different absorption bands have been assigned and the effect of solvents on the charge transfer band is also discussed. The diagnostic IR spectral bands and 1H NMR signals are assigned and discussed in relation to molecular structure. Also, semi-empirical molecular orbital calculations using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory have been performed to investigate the molecular and electronic structures of these compounds. According to these calculations, an intramolecular hydrogen bonding is essential for stabilization of such molecules.

Structural characterisation of some vanillic Mannich bases: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Petrović, Vladimir P.; Simijonović, Dušica; Novaković, Sladjana B.; Bogdanović, Goran A.; Marković, Svetlana; Petrović, Zorica D.

2015-10-01

In this paper, synthesis and structural determination of 2-[1-(N-4-fluorophenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-F) is presented. To determine the structure of this new compound, IR and NMR spectral characterisation was performed experimentally and theoretically. Simulation of spectral data was carried out using three functionals: B3LYP, B3LYP-D2, and M06-2X. The results obtained for MB-F were compared to those attained for similar, known compound 2-[1-(N-phenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-H), whose crystal structure is presented here. Taking into account all experimental and theoretical findings, the structure of MB-F was proposed.

Structural characterization of constituents with molecular diversity in fractions from Lysidice brevicalyx by liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry and liquid chromatography/nuclear magnetic resonance.

PubMed

Qu, Jing; Hu, You-cai; Li, Jian-bei; Wang, Ying-hong; Zhang, Jin-lan; Abliz, Zeper; Yu, Shi-shan; Liu, Yun-bao

2008-01-01

A combination of electrospray ionization tandem mass spectrometry with high-performance liquid chromatography (HPLC/ESI-MSn), and hyphenation of liquid chromatography to nuclear magnetic resonance spectroscopy (HPLC/NMR), have been extensively utilized for on-line analysis of natural products, analyzing metabolite and drug impurity. In our last paper, we reported an on-line analytical method for structural identification of trace alkaloids in the same class. However, the structural types of the constituents in plants were various, such as flavanoids, terpenoids and steroids. It is important to establish an effective analytical method for on-line structural identification of constituents with molecular diversity in extracts of plants. So, in the present study, the fragmentation patterns of some isolated stilbenes, phloroglucinols and flavanoids from Lysidice rhodostegia were investigated by ESI-MSn. Their fragmentation rules and UV characteristics are summarized, and the relationship between the spectral characteristics, rules and the structures is described. According to the fragmentation rules, NMR and UV spectral characteristics, 24 constituents of different types in the fractions from L. brevicalyx of the same genus were structurally characterized on the basis of HPLC/HRMS, HPLC-UV/ESI-MSn, HPLC/1H NMR and HPLC/1H-1H COSY rapidly. Of these, six (10, 13, 14, 16, 17 and 23) are new compounds and all of them are reported from L. brevicalyx for the first time. The aim is to develop an effective analytical method for on-line structural identification of natural products with molecular diversity in plants, and to guide the rapid and direct isolation of novel compounds by chemical screening.

An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV-Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure

NASA Astrophysics Data System (ADS)

Uludağ, Nesimi; Serdaroğlu, Goncagül

2018-03-01

This study examines the synthesis of azocino[4,3-b]indole structure, which constitutes the tetracyclic framework of uleine, dasycarpidoneand tubifolidineas well as ABDE substructure of the strychnosalkaloid family. It has been synthesized by Fischer indolization of 2 and through the cylization of 4 by 2,3-dichlor-5-6-dicyanobenzoquinone (DDQ). 1H and 1C NMR chemical shifts have been predicted with GIAO approach and the calculated chemical shifts show very good agreement with observed shifts. FT-IR spectroscopy is important for the analysis of functional groups of synthesized compounds and we also supported FT-IR vibrational analysis with computational IR analysis. The vibrational spectral analysis was performed at B3LYP level of the theory in both the gas and the water phases and it was compared with the observed IR values for the important functional groups. The DFT calculations have been conducted to determine the most stable structure of the 1,2,3,4,5,6,7-Hexahydro-1,5-methanoazocino [4,3-b] indole (5). The Frontier Molecular Orbital Analysis, quantum chemical parameters, physicochemical properties have been predicted by using the same theory of level in both gas phase and the water phase, at 631 + g** and 6311++g** basis sets. TD- DFT calculations have been performed to predict the UV- Vis spectral analysis for this synthesized molecule. The Natural Bond Orbital (NBO) analysis have been performed at B3LYP level of theory to elucidate the intra-molecular interactions such as electron delocalization and conjugative interactions. NLO calculations were conducted to obtain the electric dipole moment and polarizability of the title compound.

Effects of styrene unit on molecular conformation and spectral properties of CNsbnd PhCHdbnd NPhCHdbnd CHPhsbnd CN

NASA Astrophysics Data System (ADS)

Fang, Zhengjun; Wu, Feng; Jiao, Yingchun; Wang, Nanfang; Au, Chaktong; Cao, Chenzhong; Yi, Bing

2018-05-01

Compound CN-PhCH=NPhCH=CHPh-CN with both stilbene and benzylidene aniline units was synthesized, and studied from the viewpoint of molecular conformation and spectroscopic property by a combined use of experimental and computational methods. The maximum UV absorption wavelength (λmax) of the compound in ethanol, acetonitrile, chloroform and cyclohexane solvents were measured, and the 13C NMR chemical shift value δC(Cdbnd N) in chloroform-d was determined. The crystal structure of the compound was determined by X-ray diffraction. The frontier molecular orbital was calculated by density functional theory method. The results show that the UV absorption spectrum of the titled compound is similar to those of Schiff bases, while there is a larger red shift of λmax comparing to that of CN-PhCH=NPh-CN. Moreover, the molecular configuration of the titled compound relative to Cdbnd N is anti-form, having a more obvious twisted structure. The spectral and structural behaviors are further supported by the results of frontier molecular orbital analyses, NBO, electrostatic potentials and TD-DFT calculations. The study provides deeper insights into the molecular conformation of Schiff bases.

Pd (II) complexes of bidentate chalcone ligands: Synthesis, spectral, thermal, antitumor, antioxidant, antimicrobial, DFT and SAR studies

NASA Astrophysics Data System (ADS)

Gaber, Mohamed; Awad, Mohamed K.; Atlam, Faten M.

2018-05-01

The ligation behavior of two chalcone ligands namely, (E)-3-(4-chlorophenyl)-1-(pyridin-2-yl)prop-2-en-1-one (L1) and (E)-3-(4-methoxyphenyl)-1-(pyridin-2-yl)prop-2-en-1-one (L2), towards the Pd(II) ion is determined. The structures of the complexes are elucidated by elemental analysis, spectral methods (IR, electronic and NMR spectra) as well as the conductance measurements and thermal analysis. The metal complexes exhibit a square planar geometrical arrangement. The kinetic and thermodynamic parameters for some selected decomposition steps have been calculated. The antimicrobial, antioxidant and anticancer activities of the chalcones and their Pd(II) complexes have been evaluated. Molecular orbital computations are performed using DFT at B3LYP level with 6-31 + G(d) and LANL2DZ basis sets to access reliable results to the experimental values. The calculations are performed to obtain the optimized molecular geometry, charge density distribution, extent of distortion from regular geometry. Thermodynamic parameters for the investigated compounds are also studied. The calculations confirm that the investigated complexes have square planner geometry, which is in a good agreement with the experimental observation.

Novel mixed ligand complexes of bioactive Schiff base (E)-4-(phenyl (phenylimino) methyl) benzene-1,3-diol and 2-aminophenol/2-aminobenzoic acid: Synthesis, spectral characterization, antimicrobial and nuclease studies

NASA Astrophysics Data System (ADS)

Subbaraj, P.; Ramu, A.; Raman, N.; Dharmaraja, J.

2014-01-01

A novel bidentate Schiff base ligand has been synthesized using 2,4-dihydroxybenzophenone and aniline. Its mixed ligand complexes of MAB type [M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II); HA = Schiff base and B = 2-aminophenol/2-aminobenzoic acid] have been synthesized and characterized on the basis of spectral data UV-Vis, IR, 1H NMR, FAB-Mass, EPR, SEM and magnetic studies. All the complexes were soluble in DMF and DMSO. Elemental analysis and molar conductance values indicate that the complexes are non-electrolytes. HA binds with M(II) ions through azomethine and deprotonated phenolic group and B binds through the primary amine group and deprotonated phenolic/carboxylic groups. Using FAB-Mass the cleavage pattern of the ligand (HA) has been established. All the complexes adopt octahedral geometry around the metal ions. It has been confirmed with the help of UV-Vis, IR, 1H NMR and FAB-Mass spectral data. DNA binding activities of the complexes 1d and 2d are studied by UV-Vis spectroscopy and cleavage studies of Schiff base ligand and its complexes 1d and 2d have been by agarose gel electrophoresis method. In vitro biological activities of the free ligand (HA) and their metal complexes (1a-1e and 2a-2e) were screened against few bacteria, Escherichia coli, Staphylococcus saphyphiticus, Staphylococcus aureus, Pseudomonas aeruginosa and fungi Aspergillus niger, Enterobacter species, Candida albicans by well diffusion technique.

Synthesis and Spectral Evaluation of Some Unsymmetrical Mesoporphyrinic Complexes

PubMed Central

Boscencu, Rica; Oliveira, Anabela Sousa; Ferreira, Diana P.; Ferreira, Luís Filipe Vieira

2012-01-01

Synthesis and spectral evaluation of new zinc and copper unsymmetrical mesoporphyrinic complexes are reported. Zn(II)-5-(4-acetoxy-3-methoxyphenyl)-10,15,20- tris-(4-carboxymethylphenyl)porphyrin, Zn(II)-5-[(3,4-methylenedioxy)phenyl]-10,15,20- tris-(4-carboxymethylphenyl)porphyrin, Cu(II)-5-(4-acetoxy-3-methoxyphenyl)-10,15,20- tris-(4-carboxymethylphenyl)porphyrin and Cu(II)-5-[(3,4-methylenedioxy)phenyl]-10,15,20- tris-(4-carboxymethylphenyl)porphyrin were synthesized using microwave-assisted synthesis. The complexes were characterized by elemental analysis, FT-IR, UV-Vis, EPR and NMR spectroscopy, which fully confirmed their structure. The spectral absorption properties of the porphyrinic complexes were studied in solvents with different polarities. Fluorescence emission and singlet oxygen formation quantum yields were evaluated for the compounds under study, revealing high yields for the zinc derivatives. The copper complexes are not emissive and only display residual capacity for singlet oxygen formation. PMID:22942693

The extended Fourier transform for 2D spectral estimation.

PubMed

Armstrong, G S; Mandelshtam, V A

2001-11-01

We present a linear algebraic method, named the eXtended Fourier Transform (XFT), for spectral estimation from truncated time signals. The method is a hybrid of the discrete Fourier transform (DFT) and the regularized resolvent transform (RRT) (J. Chen et al., J. Magn. Reson. 147, 129-137 (2000)). Namely, it estimates the remainder of a finite DFT by RRT. The RRT estimation corresponds to solution of an ill-conditioned problem, which requires regularization. The regularization depends on a parameter, q, that essentially controls the resolution. By varying q from 0 to infinity one can "tune" the spectrum between a high-resolution spectral estimate and the finite DFT. The optimal value of q is chosen according to how well the data fits the form of a sum of complex sinusoids and, in particular, the signal-to-noise ratio. Both 1D and 2D XFT are presented with applications to experimental NMR signals. Copyright 2001 Academic Press.

The Influences of Riverine Dissolved Organic Matter in the Gulf of Maine

NASA Astrophysics Data System (ADS)

Aiken, G.; Cao, X.; Mao, J.; Spencer, R. G.; Balch, W. M.; Huntington, T. G.

2014-12-01

Dissolved organic matter (DOM) exported from the Gulf of St. Lawrence and by rivers in Maine, Nova Scotia, and New Brunswick is being studied to quantify and characterize optical proxies in the receiving waters of the Gulf of Maine (GoM). Measurements of DOC concentrations, absorption coefficients (254nm, 350 nm and 412 nm), specific ultraviolet absorbance (SUVA254), spectral slope, and fluorescence, and DOC fractionation and isotopic analyses were used to determine the amount and nature of DOM from major inflowing rivers, marine waters, and the GoM. In addition, lignin phenols, 14C-age, 13C-NMR and FTICR-MS analyses were performed on the hydrophobic (HPOA) and transphilic organic acid fractions of the DOM isolated using XAD resins for a smaller subset of samples from the Penobscot River, Penobscot Bay, GoM waters in the Eastern Maine Coastal Current (EMCC), a sample from the eastern portion of the GoM (Scotian Shelf waters), and the Pacific Ocean. These samples provide detailed DOM compositional data in support of the more easily collected concentration and optical data obtained from discrete samples, optical data obtained by in situ glider, and remotely sensed satellite observations. Optical measurements, 13C-NMR, and lignin phenol analyses showed that DOM associated with inflowing rivers to the GoM is rich in aromatic compounds resulting in a large flux of terrestrially derived chromophoric DOM (CDOM). As a result, GoM DOM is more aromatic and younger than open ocean samples collected from the Sargasso Sea and from the Pacific Ocean near Hawaii. This observation is consistent with isotopic data that indicated δ 13C values for the HPOA fractions from the Gulf samples (δ 13C= -27‰ and -25‰) were considerably depleted in comparison to the whole DOM sample (δ 13C = -19‰; which also includes algal-produced DOM) and are more similar to those from the terrestrial sources. Samples from the EMCC were the most heavily influenced by terrestrial sources. While NMR analyses indicated decreases in the aromaticity of the HPOA fractions moving from the rivers to the open ocean, NMR signals associated with carboxyl-rich alicyclic organic matter were observed for all samples. Results from this study are being used to develop relationships for predicting DOC concentration in the GoM from remotely sensed, satellite optical data.

Spectroscopic analysis of cinnamic acid using quantum chemical calculations

NASA Astrophysics Data System (ADS)

Vinod, K. S.; Periandy, S.; Govindarajan, M.

2015-02-01

In this present study, FT-IR, FT-Raman, 13C NMR and 1H NMR spectra for cinnamic acid have been recorded for the vibrational and spectroscopic analysis. The observed fundamental frequencies (IR and Raman) were assigned according to their distinctiveness region. The computed frequencies and optimized parameters have been calculated by using HF and DFT (B3LYP) methods and the corresponding results are tabulated. On the basis of the comparison between computed and experimental results assignments of the fundamental vibrational modes are examined. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The alternation of the vibration pattern of the pedestal molecule related to the substitutions was analyzed. The 13C and 1H NMR spectra have been recorded and the chemical shifts have been calculated using the gauge independent atomic orbital (GIAO) method. The Mulliken charges, UV spectral analysis and HOMO-LUMO analysis of have been calculated and reported. The molecular electrostatic potential (MEP) was constructed.

Development and Validation of Quantitative (1)H NMR Spectroscopy for the Determination of Total Phytosterols in the Marine Seaweed Sargassum.

PubMed

Zhang, Xiu-Li; Wang, Cong; Chen, Zhen; Zhang, Pei-Yu; Liu, Hong-Bing

2016-08-10

Knowledge of phytosterol (PS) contents in marine algae is currently lacking compared to those in terrestrial plants. The present studies developed a quantitative (1)H NMR method for the determination of the total PSs in Sargassum. The characteristic proton signal H-3α in PSs was used for quantification, and 2,3,4,5-tetrachloro-nitrobenzene was used as an internal standard. Seaweed samples could be recorded directly after total lipid extraction and saponification. The results showed that the PS contents in Sargassum fusiforme (788.89-2878.67 mg/kg) were significantly higher than those in Sargassum pallidum (585.33-1596.00 mg/kg). The variable contents in both species suggested that fixed raw materials are very important for future research and development. Orthogonal projection to latent structures discriminant analysis was carried out in the spectral region of δ 3.00-6.50 in the (1)H NMR spectrum. S. fusiforme and S. pallidum could be separated well, and the key sterol marker was fucosterol.

Change of translational-rotational coupling in liquids revealed by field-cycling {sup 1}H NMR

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

Meier, R.; Schneider, E.; Rössler, E. A.

2015-01-21

Applying the field-cycling nuclear magnetic resonance technique, the frequency dependence of the {sup 1}H spin-lattice relaxation rate, R{sub 1}(ω)=T{sub 1}{sup −1}(ω), is measured for propylene glycol (PG) which is increasingly diluted with deuterated chloroform. A frequency range of 10 kHz–20 MHz and a broad temperature interval from 220 to about 100 K are covered. The results are compared to those of experiments, where glycerol and o-terphenyl are diluted with their deuterated counter-part. Reflecting intra- as well as intermolecular relaxation, the dispersion curves R{sub 1}(ω,x) (x denotes mole fraction PG) allow to extract the rotational time constant τ{sub rot}(T, x) andmore » the self-diffusion coefficient D(T, x) in a single experiment. The Stokes-Einstein-Debye (SED) relation is tested in terms of the quantity D(T, x) τ{sub rot}(T, x) which provides a measure of an effective hydrodynamic radius or equivalently of the spectral separation of the translational and the rotational relaxation contribution. In contrast to o-terphenyl, glycerol and PG show a spectral separation much larger than suggested by the SED relation. In the case of PG/chloroform mixtures, not only an acceleration of the PG dynamics is observed with increasing dilution but also the spectral separation of rotational and translational relaxation contributions continuously decreases. Finally, following a behavior similar to that of o-terphenyl already at about x = 0.6; i.e., while D(T, x) τ{sub rot}(T, x) in the mixture is essentially temperature independent, it strongly increases with x signaling thus a change of translational-rotational coupling. This directly reflects the dissolution of the hydrogen-bond network and thus a change of solution structure.« less

Validation of a low field Rheo-NMR instrument and application to shear-induced migration of suspended non-colloidal particles in Couette flow

NASA Astrophysics Data System (ADS)

Colbourne, A. A.; Blythe, T. W.; Barua, R.; Lovett, S.; Mitchell, J.; Sederman, A. J.; Gladden, L. F.

2018-01-01

Nuclear magnetic resonance rheology (Rheo-NMR) is a valuable tool for studying the transport of suspended non-colloidal particles, important in many commercial processes. The Rheo-NMR imaging technique directly and quantitatively measures fluid displacement as a function of radial position. However, the high field magnets typically used in these experiments are unsuitable for the industrial environment and significantly hinder the measurement of shear stress. We introduce a low field Rheo-NMR instrument (1 H resonance frequency of 10.7MHz), which is portable and suitable as a process monitoring tool. This system is applied to the measurement of steady-state velocity profiles of a Newtonian carrier fluid suspending neutrally-buoyant non-colloidal particles at a range of concentrations. The large particle size (diameter > 200 μm) in the system studied requires a wide-gap Couette geometry and the local rheology was expected to be controlled by shear-induced particle migration. The low-field results are validated against high field Rheo-NMR measurements of consistent samples at matched shear rates. Additionally, it is demonstrated that existing models for particle migration fail to adequately describe the solid volume fractions measured in these systems, highlighting the need for improvement. The low field implementation of Rheo-NMR is complementary to shear stress rheology, such that the two techniques could be combined in a single instrument.

Microscale determination of the spectral characteristics and carbon-isotopic compositions of porphyrins

NASA Technical Reports Server (NTRS)

Popp, B. N.; Hayes, J. M.; Boreham, C. J.

1993-01-01

Molar extinction coefficients for band III of Ni porphyrins are calculated from results of spectrophotometric and manometric analyses of individual etioporphyrins, DPEP, cyclic, and diDPEP porphyrins known to initially be pure from mass spectrometry, 1H NMR, and analytical HPLC studies. A method for determining carbon-isotopic compositions and purity of micromolar quantities of individual porphyrins using combined spectrophotometric and manometric techniques is presented.