Interpretation Of Nuclear Magnetic Resonance Research Articles

A proposed NMR solution for multi-phase flow fluid detection

In the petroleum industry, detection of multi-phase fluid flow is very important in both surface and down-hole measurements. Accurate measurement of high rate of water or gas multi-phase flow has always been an academic and industrial focus. NMR is an efficient and accurate technique for the detection of fluids; it is widely used in the determination of fluid compositions and properties. This paper is aimed to quantitatively detect multi-phase flow in oil and gas wells and pipelines and to propose an innovative method for online nuclear magnetic resonance (NMR) detection. The online NMR data acquisition, processing and interpretation methods are proposed to fill the blank of traditional methods. A full-bore straight tube design without pressure drop, a Halbach magnet structure design with zero magnetic leakage outside the probe, a separate antenna structure design without flowing effects on NMR measurement and automatic control technology will achieve unattended operation. Through the innovation of this work, the application of NMR for the real-time and quantitative detection of multi-phase flow in oil and gas wells and pipelines can be implemented.

Numerical simulations of NMR relaxation in chalk using local Robin boundary conditions.

The interpretation of nuclear magnetic resonance (NMR) data is of interest in a number of fields. In Ögren (2014) local boundary conditions for random walk simulations of NMR relaxation in digital domains were presented. Here, we have applied those boundary conditions to large, three-dimensional (3D) porous media samples. We compared the random walk results with known solutions and then applied them to highly structured 3D domains, from images derived using synchrotron radiation CT scanning of North Sea chalk samples. As expected, there were systematic errors caused by digitalization of the pore surfaces so we quantified those errors, and by using linear local boundary conditions, we were able to significantly improve the output. We also present a technique for treating numerical data prior to input into the ESPRIT algorithm for retrieving Laplace components of time series from NMR data (commonly called T-inversion).

Identification of Facet-Dependent Coordination Structures of Carboxylate Ligands on CdSe Nanocrystals.

Aliphatic carboxylates are the most common class of surface ligands to stabilize colloidal nanocrystals. The widely used approach to identify the coordination modes between surface cationic sites and carboxylate ligands is based on the empirical infrared (IR) spectroscopic assignment, which is often ambiguous and thus hampers the practical control of surface structures. In this report, multiple techniques based on nuclear magnetic resonance (NMR) and IR spectra are applied to distinguish the different coordination structures in a series of zinc-blende CdSe nanocrystals with unique facet structures, including nanoplatelets dominated with {100} basal planes, hexahedrons with only three types of low-index facets (i.e., {100}, {110}, and {111}), and spheroidal dots without well-defined facets. Interpretation and assignment of NMR and IR signals were assisted by density functional theory (DFT) calculations. In addition to the identification of facet-sensitive bonding modes, the present methods also allow a nondestructive quantification of mixed ligands.

Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation.

Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET‐s(218‐289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale‐specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross‐correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer‐range correlated motion. Similar trends on ns‐ and μs‐timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.

Allosteres to regulate neurotransmitter sulfonation

Catecholamine neurotransmitter levels in the synapses of the brain shape human disposition-cognitive flexibility, aggression, depression, and reward seeking-and manipulating these levels is a major objective of the pharmaceutical industry. Certain neurotransmitters are extensively sulfonated and inactivated by human sulfotransferase 1A3 (SULT1A3). To our knowledge, sulfonation as a therapeutic means of regulating transmitter activity has not been explored. Here, we describe the discovery of a SULT1A3 allosteric site that can be used to inhibit the enzyme. The structure of the new site is determined using spin-label-triangulation NMR. The site forms a cleft at the edge of a conserved ∼30-residue active-site cap that must open and close during the catalytic cycle. Allosteres anchor into the site via π-stacking interactions with two residues that sandwich the planar core of the allostere and inhibit the enzyme through cap-stabilizing interactions with substituents attached to the core. Changes in cap free energy were calculated ab initio as a function of core substituents and used to design and synthesize a series of inhibitors intended to progressively stabilize the cap and slow turnover. The inhibitors bound tightly (34 nm to 7.4 μm) and exhibited progressive inhibition. The cap-stabilizing effects of the inhibitors were experimentally determined and agreed remarkably well with the theoretical predictions. These studies establish a reliable heuristic for the design of SULT1A3 allosteric inhibitors and demonstrate that the free-energy changes of a small, dynamic loop that is critical for SULT substrate selection and turnover can be calculated accurately.

Computation and structural elucidation of compounds formed via epoxide alcoholysis.

Isobenzofuranones are known for their wide range of biological activities such as fungicide, insecticide, and anticancer. The search for novel bioactive compounds was performed by reaction of epoxide 2 with methanol, ethanol, propan-1-ol, propan-2-ol, and butan-1-ol. The mechanism for the stereoselective and stereospecific epoxide opening with methanol was reasoned by calculating the transition states for the two putative structures (rac)-3a and (rac)-3b. The compound (rac)-3a is the kinetic product as inferred from the lower energies of its transition state (TS1). The 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts for these two candidate structures were calculated and compared with the experimental data using mean absolute error (MAE) and DP4 analyses. Therefore, the relative stereochemistry of (rac)-3a was established by the mechanism, MAE, and DP4 approaches. The hydroxyl group was acetylated to surpass the problem of signal overlapping of H5 and H6 in the 1 H NMR. The relative stereochemistry of the corresponding ester determined by NMR interpretation was in agreement with the structure of (rac)-3a.

Bacillus methylotrophicus ASWU-C2, a strain inhabiting hot desert soil, a new source for antibacterial bacillopyrone, pyrophen, and cyclopeptides.

A strain of Bacillus methylotrophicus was isolated from a soil sample collected in Aswan eastern desert, which is known for its extremely arid climate. After fermentation of the strain in liquid culture and subsequent extraction, a bioassay-guided isolation procedure yielded five compounds: 2-benzyl-4H-pyran-4-one, named bacillopyrone (1), pyrophen (2), macrolactin A (3) and the cyclopeptides malformin A1 (4), and bacillopeptin A (5). The structures were determined by interpretation of nuclear magnetic resonance (NMR) spectroscopy and high resolution mass spectrometry (HR-MS) data. This is the first report on the isolation of compounds 1 and 2 from Bacillus species; compound 1 was reported previously as synthetic product. Bacillopyrone (1) exhibited moderate activity against the Gram-negative Chromobacterium violaceum with minimum inhibitory concentration 266.6 μg/mL, while macrolactin A (3) and malformin A1 (4) inhibited Staphylococcus aureus (minimum inhibitory concentrations 13.3 and 133.3 μg/mL, respectively).

Potential Antiviral Xanthones from a Coastal Saline Soil Fungus Aspergillus iizukae

Five new (1–5) and two known xanthones (6 and 7), one of the latter (6) obtained for the first time as a natural product, together with three known anthraquinones, questin, penipurdin A, and questinol, were isolated from the coastal saline soil-derived Aspergillus iizukae by application of an OSMAC (one strain many compounds) approach. Their structures were determined by interpretation of nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectroscopy (HRESIMS) data, as well as comparison of these data with those of related known compounds. Antiviral activity of xanthones 1−7 was evaluated through the cytopathic effect (CPE) inhibition assay, and compound 2 exhibited distinctly strong activity towards influenza virus (H1N1), herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) with IC50 values of 44.6, 21.4, and 76.7 μM, respectively, which indicated that it was worth to further investigate it as a potential lead compound. The preliminary structure-activity relationship of the xanthones is discussed.

Hydrocarbon saturation in Bakken Petroleum System based on joint inversion of resistivity and dielectric dispersion logs

Bakken Petroleum System (BPS) is composed of both conventional and unconventional units, which exhibits significant variations in lithology, rock texture, clay content, total organic carbon, accompanied by high connate water salinity, presence of disseminated pyrite grains, and low values of porosity. These petrophysical attributes of the BPS lead to inconsistency in the oil-in-place estimates for those obtained from Electromagnetic (EM) induction log, Nuclear Magnetic Resonance (NMR) log, dielectric dispersion log measured by Array Dielectric Tool (ADT), and Dean-Stark core measurements. For purposes of improved hydrocarbon saturation estimation and petrophysical characterization in the BPS, a joint-inversion-based interpretation was performed on dispersive electrical conductivity and dielectric permittivity measurements at 4 dielectric-log-acquisition frequencies and 1 induction resistivity acquired at 20 kHz. This analysis was performed across a 350-ft depth interval in one of the science wells intersecting the BPS. Three geo-electromagnetic mixing models, namely Complex Refractive Index model, Stroud-Milton-De model, and Waxman Smits model are integrated and coupled to the inversion scheme to simultaneously estimate water saturation, formation brine conductivity, cementation exponent and saturation exponent in BPS.Water saturation estimates obtained using the proposed interpretation method were compared against those obtained from NMR log, Dean-Stark core measurements and service company’s dielectric inversion. In Middle Bakken from depth XX720 to XX750 ft, our estimates of water saturation are in better agreement with those estimated by service company’s mineral inversion method and service company’s dielectric interpretation as compared to those obtained from NMR interpretation and Dean Stark core measurement. Water saturation and formation brine conductivity estimates in Middle Bakken are in the ranges of 0.5–1 and 25–45 S/m, respectively. Inversion-derived brine conductivity and saturation exponent estimates are most uncertain in Lodgepole and Three Forks 2 formations, which exhibit a wide range of pore size distribution. Average relative errors in matching the 1 induction resistivity and 8 dielectric dispersion logs using the inversion-derived estimates are 33% and 20%, respectively, in the 350-ft depth interval of BPS. The proposed inversion achieves high certainty for the estimates when the formation has low clay content, low electrical anisotropy, and high porosity.

Integrated Workflow to Estimate Permeability Through Quantification of Rock Fabric Using Joint Interpretation of Nuclear Magnetic Resonance and Electric Measurements

Integrated Workflow to Estimate Permeability Through Quantification of Rock Fabric Using Joint Interpretation of Nuclear Magnetic Resonance and Electric Measurements

New Aromatic Compounds from the Fruiting Body of Sparassis crispa (Wulf.) and Their Inhibitory Activities on Proprotein Convertase Subtilisin/Kexin Type 9 mRNA Expression.

Successive chromatography of EtOAc-soluble extracts of the fruiting body of Sparassis crispa (Wulf.) resulted in isolation of four new aromatic compounds, sparoside A (1) and sparalides A-C (3-5), two new naturally occurring compounds, 2 and 6, and eight known compounds, 7-14. The chemical structures were determined by interpretation of nuclear magnetic resonance and mass spectrometry spectroscopic data. Extract, solvent-soluble fractions of the extract, and all of the pure compounds isolated from the fractions were subjected to the mRNA expression assay for proprotein convertase subtilisin/kexin type 9 (PCSK9). Among them, sparoside A (1), hanabiratakelide A (8), adenosine (11), and 5α,6α-epoxy-(22E,24R)-ergosta-8(14),22-diene-3β,7β-diol (14) exhibited potent inhibitory activities on PCSK9 mRNA expression, with IC50 values of 20.07, 7.18, 18.46, and 8.23 μM, respectively (berberine, positive control, IC50 = 8.04 μM), suggesting that compounds 1, 8, 11, and 14 are suitable for use in supplements to the statins for hyperlipidemia treatments.

Combined interpretation of NMR and TGA measurements to quantify the impact of relative humidity on hydration of clay minerals

Reliability of core measurement and analysis can be highly dependent on the humidity of measurement environment. However, impact of humidity on core measurements is often assumed to be negligible. This paper quantified the influence of relative humidity on the hydration of clay minerals (i.e., montmorillonite, illite, chlorite, and kaolinite) using nuclear magnetic resonance (NMR) and thermogravimetric analysis (TGA). The influence of clay hydration on the assessment of fluid volume in organic-rich mudrocks was also investigated. The NMR T2 (spin-spin relaxation) magnetic decay of the clay samples showed existence of water even after the samples were dried in an oven at 95°C. The TGA measurements in clay minerals confirmed the weight loss between 95°C and dehydroxylation temperature, which is approximately the same volume as that recorded by NMR measurement in dried samples. This recorded water volume corresponded to desorption of water molecules bound to interlayer cations (i.e., interlayer water). In the case of the hydration water, the NMR-based water vapor adsorption experiments showed that the volume of water accumulated on the surface of clay minerals increased significantly as the relative humidity increased. The cation exchange capacity (CEC) measurements of clay minerals demonstrated that the volume of hydration water was strongly related to the CEC. The volume of interlayer water was, however, not related to the CEC. In the case of organic-rich mudrocks, water vapor adsorption experiments showed >250% change in water volume when relative humidity varies in the range of 0% to 95%, which further verified the significant impact of humidity on core measurements and the necessity of applying corrections for such an impact.

Temperature-Dependent Oxygen Effect on NMR D-[Formula: see text] Relaxation-Diffusion Correlation of n-Alkanes.

Nuclear magnetic resonance (NMR) diffusion-relaxation correlation experiments (D-T_2) are widely used for the petrophysical characterisation of rocks saturated with petroleum fluids both in situ and for laboratory analyses. The encoding for both diffusion and relaxation offers increased fluid typing contrast by discriminating fluids based on their self-diffusion coefficients, while relaxation times provide information about the interaction of solid and fluid phases and associated confinement geometry (if NMR responses of pure fluids at particular temperature and pressure are known). Petrophysical interpretation of D-T_2 correlation maps is typically assisted by the “standard alkane line”—a relaxation-diffusion correlation valid for pure normal alkanes and their mixtures in the absence of restrictions to diffusing molecules and effects of internal gradients. This correlation assumes fluids are free from paramagnetic impurities. In situations where fluid samples cannot be maintained at air-free state the diffusion-relaxation response of fluids shift towards shorter relaxation times due to oxygen paramagnetic relaxation enhancement. Interpretation of such a response using the “standard alkane line” would be erroneous and is further complicated by the temperature-dependence of oxygen solubility for each component of the alkane mixture. We propose a diffusion-relaxation correlation suitable for interpretation of low-field NMR D-T_2 responses of normal alkanes and their mixtures saturating rocks over a broad temperature range, in equilibrium with atmospheric air. We review and where necessary revise existing viscosity-relaxation correlations. Findings are applied to diffusion-relaxation dependencies taking into account the temperature dependence of oxygen solubility and solvent vapour pressure. The effect is demonstrated on a partially saturated carbonate rock.

울릉 마가목의 클로로겐산 이성체의 최종당화산물의 생성 저해 및 라디칼 소거 활성

Advanced glycation end product (AGE) formation and reactive oxygen species are potential therapeutic targets for the prevention of diabetic nephropathy and other pathogenic complications. Activity-guided isolation of an ethylacetate-soluble portion of 80% methanolic extract from fruits of Sorbus commixta of the Ulleung Island origin using AGE formation inhibition assay led to the isolation and identification of three caffeoylquinic acid derivatives of a previously known structure, 3-O-caffeoylquinic acid (neochlorogenic acid; 1), 4-O-caffeoylquinic acid (cryptochlorogenic acid; 2), and 5-O-caffeoylquinic acid (chlorogenic acid; 3). The structures of these compounds were confirmed by interpretation of nuclear magnetic resonance and mass spectrometry data. Among the isolates, the major metabolite, neochlorogenic acid (1) showed the most potent inhibitory effect against AGE formation with an IC50 value of 167.5±3.5 μM. Furthermore, all isolated chlorogenic acid isomers were evaluated for their radical scavenging activity against peroxynitrite, and structurally related isomers 1, 2, and 3 exhibited potent inhibitory effects in this radical scavenging assay. This result suggests that the monocaffeoyl quinic acid derivatives isolated from S. commixta might be beneficial for the regulation of diabetic complications and related diseases.

Polyprenylated acylphloroglucinols from the fruits of Hypericum henryi

Hyphenrones R–X (1–7), seven new polyprenylated acylphloroglucinols derivatives, were isolated from the fruits of Hypericum henryi, together with eight know analogues. Compounds 1 and 2 were elucidated to possess complex caged skeleton, while compounds 3–6 shared a common 3,9-epoxy moiety deriving from the normal polyprenylated acylphloroglucinols with a bicyclo[3.3.1]nonane-2,4,9-trione core. The new structures were elucidated on the basis of the interpretation of nuclear magnetic resonance (NMR) data, circular dichroism (CD) comparison, and single-crystal X-ray diffraction. In the bioassay, several compounds exhibited inhibitory activities against human tumor cell lines in vitro.

Isolation, Stereochemical Study, and Antioxidant Activity of Benzofuranone Derivatives from a Mangrove-derived Fungus Eurotium rubrum MA-150.

Enantiomers of a 2-benzofuran-1(3H)-one derivative [(-)- and (+)-] and four known analogs () were isolated and identified from the culture extract of Eurotium rubrum MA-150, a fungus obtained from the mangrove-derived rizospheric soil. Their structures were established by detailed interpretation of nuclear magnetic resonance (NMR) data and the structure of (±)- was confirmed by single-crystal X-ray diffraction analysis. The absolute configuration of the enantiomers (-)- and (+)- was determined by means of online high-performance liquid chromatography - electronic circular dichroism (HPLC-ECD) measurements and time-dependent Density Functional Theory - electronic circular dichroism (TDDFT-ECD) calculations. Compounds (±)- as well as and exhibited potent DPPH radical scavenging activities with IC50 values of 1.23, 2.26, and 3.99 μg/mL, respectively. Chirality 28:581-584, 2016. © 2016 Wiley Periodicals, Inc.

Tight Reservoir Properties Derived by Nuclear Magnetic Resonance, Mercury Porosimetry and Computed Microtomography Laboratory Techniques. Case Study of Palaeozoic Clastic Rocks

Results of the nuclear magnetic resonance (NMR) investigations, mercury porosimetry measurements (MP) and computed microtomography (micro-CT), applied to the tight Palaeozoic rocks from the depths lower than 3000 m, were presented to estimate their reservoir potential. NMR signal analysis and interpretation were performed. Based on NMR driven models, permeability and Free Fluid Index were calculated for data sets divided into homogeneous clusters. Computerized mercury porosimetry results visualization and processing provided useful information, as the automatically determined Swanson parameter is correlated with petrophysical properties of rocks. Micro-CT enriched the image of porous space in qualitative and quantitative ways. Homogeneity of pore space structure was discussed using micro-CT approach. Integration of the results in the frame of reservoir parameters from standard laboratory methods and the modern ones resulted in the improvement of methodology for determining the old, deep-seated, hard sedimentary rocks reservoir potential.

Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems

Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol quinonoid intermediate formed in the β active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van der Waals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size.

Nuclear magnetic resonance characterization of shallow marine sediments from the Nankai Trough, Integrated Ocean Drilling Program Expedition 333

AbstractWe measured nuclear magnetic resonance (NMR) relaxation times on samples from Integrated Ocean Drilling Program Expedition 333 Sites C0011, C0012, and C0018. We compared our results to permeability, grain size, and specific surface measurements, pore size distributions from mercury injection capillary pressure, and mineralogy from X‐ray fluorescence. We found that permeability could be predicted from NMR measurements by including grain size and specific surface to quantify pore networks and that grain size is the most important factor in relating NMR response to permeability. Samples within zones of anomalously high porosity from Sites C0011 and C0012 were found to have different NMR‐permeability relationships than samples from outside these zones, suggesting that the porosity anomaly is related to a fundamental difference in pore structure. We additionally estimated the size of paramagnetic sites that cause proton relaxation and found that in most of our samples, paramagnetic material is present mainly as discrete, clay‐sized grains. This distribution of paramagnetic material may cause pronounced heterogeneity in NMR properties at the pore scale that is not accounted for in most NMR interpretation techniques. Our results provide important insight into the microstructure of marine sediments in the Nankai Trough.

Rapid measurements of heterogeneity in sandstones using low-field nuclear magnetic resonance

Sandstone rocks can contain microscopic variations in composition that complicate interpretation of nuclear magnetic resonance (NMR) relaxation time measurements. In this work, methods for assessing the degree of sample heterogeneity are demonstrated in three sandstones. A two-dimensional T1–Δχapp correlation (where Δχapp is the apparent solid/liquid magnetic susceptibility contrast) reveals the microscopic heterogeneity in composition, whilst a spatially resolved T1 profile reveals the macroscopic structural heterogeneity. To perform these measurements efficiently, a rapid measure of longitudinal T1 relaxation time has been implemented on a low-field NMR spectrometer with a magnetic field strength B0=0.3T. The “double-shot” T1 pulse sequence is appropriate for analysis of porous materials in general. Example relaxation time distributions are presented for doped water phantoms to validate the method. The acquisition time of the double-shot T1 sequence is equivalent to the single-shot Carr–Purcell Meiboom–Gill (CPMG) sequence used routinely in petrophysics to measure transverse T2 relaxation. Rapid T1 measurements enable practical studies of core plugs at magnetic field strengths previously considered inappropriate, as T1 is independent of molecular diffusion through pore-scale (internal) magnetic field gradients.