Nuclear Magnetic Resonance Coupling Research Articles

Tight gas charging and accumulation mechanisms and mathematical model

The gas-water distribution and production heterogeneity of tight gas reservoirs have been summarized from experimental and geological observations, but the charging and accumulation mechanisms have not been examined quantitatively by mathematical model. The tight gas charging and accumulation mechanisms were revealed from a combination of physical simulation of nuclear magnetic resonance coupling displacement, numerical simulation considering material and mechanical equilibria, as well as actual geological observation. The results show that gas migrates into tight rocks to preferentially form a gas saturation stabilization zone near the source-reservoir interface. When the gas source is insufficient, gas saturation reduction zone and uncharged zone are formed in sequence from the source-reservoir interface. The better the source rock conditions with more gas expulsion volume and higher overpressure, the thicker the gas saturation stabilization and reduction zones, and the higher the overall gas saturation. When the source rock conditions are limited, the better the tight reservoir conditions with higher porosity and permeability as well as larger pore throat, the thinner the gas saturation stabilization and reduction zones, but the gas saturation is high. The sweet spot of tight gas is developed in the high-quality reservoir near the source rock, which often corresponds to the gas saturation stabilization zone. The numerical simulation results by mathematical model agree well with the physical simulation results by nuclear magnetic resonance coupling displacement, and reasonably explain the gas-water distribution and production pattern of deep reservoirs in the Xujiaweizi fault depression of the Songliao Basin and tight gas reservoirs in the Linxing−Huangfu area of the Ordos Basin.

A local hybrid exchange functional approximation from first principles.

Local hybrid functionals are a more flexible class of density functional approximations, allowing for a position-dependent admixture of exact exchange. This additional flexibility, however, comes with a more involved mathematical form and a more complicated design. A common denominator for previously constructed local hybrid functionals is the usage of thermochemical benchmark data to construct these functionals. Herein, we design a local hybrid functional without relying on benchmark data. Instead, we construct it in a more ab initio manner, following the principles of modern meta-generalized gradient approximations and considering theoretical constraints. To achieve this, we make use of the density matrix expansion and a local mixing function based on an approximate correlation length. The accuracy of the developed density functional approximation is assessed for thermochemistry, excitation energies, polarizabilities, magnetizabilities, nuclear magnetic resonance (NMR) spin-spin coupling constants, NMR shieldings, and shifts, as well as EPR g-tensors and hyperfine coupling constants. Here, the new exchange functional shows a robust performance and is especially well suited for atomization energies, barrier heights, excitation energies, NMR coupling constants, and EPR properties, whereas it loses some ground for the NMR shifts. Therefore, the designed functional is a major step forward for functionals that have been designed from first principles.

NMR Coupling Constants Based on the Bethe–Salpeter Equation in the GW Approximation

We present the first steps to extend the Green's function GW method and the Bethe-Salpeter equation (BSE) to molecular response properties such as nuclear magnetic resonance (NMR) indirect spin-spin coupling constants. We discuss both a nonrelativistic one-component and a quasi-relativistic two-component formalism. The latter describes scalar-relativistic and spin-orbit effects and allows us to study heavy-element systems with reasonable accuracy. Efficiency is maintained by the application of the resolution of the identity approximation throughout. The performance is demonstrated using conventional central processing units (CPUs) and modern graphics processing units (GPUs) for molecules involving several thousand basis functions. Our results show that a large amount of Hartree-Fock exchange is vital to provide a sufficient Kohn-Sham starting point to compute the GW quasi-particle energies. As the GW-BSE approach is generally less accurate for triplet excitations or related properties such as the Fermi-contact interaction, the admixture of the Kohn-Sham correlation kernel through the contracted BSE (cBSE) method improves the results for NMR coupling constants. This leads to remarkable results when combined with the eigenvalue-only self-consistent variant (evGW) and Becke's half and half functional (BH&HLYP) or the CAM-QTP family. The developed methodology is used to calculate the Karplus curve of tin molecules, illustrating its applicability to extended chemically relevant molecules. Here, the GW-cBSE method improves upon the chosen BH&HLYP Kohn-Sham starting points.

Nuclear Spin Relaxation in Viscous Liquids: Relaxation Stretching of Single-Particle Probes.

Spin-lattice relaxation rates R1(ω,T), probed via high-field and field-cycling nuclear magnetic resonance (NMR), are used to test the validity of frequency-temperature superposition (FTS) for the reorientation dynamics in viscous liquids. For several liquids, FTS is found to apply so that master curves can be generated. The susceptibility spectra are highly similar to those obtained from depolarized light scattering (DLS) and reveal an excess wing. Where FTS works, two approaches are suggested to access the susceptibility: (i) a plot of deuteron R1(T) vs the spin-spin relaxation rate R2(T) and (ii) a plot of R1(T) vs an independently measured reference time τref(T). Using single-frequency scans, (i) allows one to extract the relaxation stretching as well as the NMR coupling constant. Surveying 26 data sets, we find Kohlrausch functions with exponents 0.39 < βK ≤ 0.67. Plots of the spin-spin relaxation rate R2─rescaled by the NMR coupling constant─as a function of temperature allow one to test how well site-specific NMR relaxations couple to a given reference process. Upon cooling of flexible molecule liquids, the site-specific dynamics is found to merge, suggesting that near Tg the molecules reorient essentially as a rigid entity. This presents a possible resolution for the much lower stretching parameters reported here at high temperatures that contrast with the ones that were reported to be universal in a recent DLS study close to Tg. Our analysis underlines that deuteron relaxation is a uniquely powerful tool to probe single-particle reorientation.

Revisiting the structure of Heliannuol L: A computational approach.

Recently, structural elucidation of natural products has undergone a revolution. The combined use of different modern spectroscopic methods has allowed obtaining a complete structural assignment of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially when the substance presents several stereogenic centers. The misinterpretation of nuclear magnetic resonance (NMR) data has resulted in frequent reports addressing structural reassignment. In this context, a great effort has been devoted to developing quantum chemical calculations that simulate NMR parameters accurately, allowing to achieve a more precise spectral interpretation. In this work, we employed a protocol for theoretical calculations of 1 H NMR chemical shifts and coupling constants using density functional theory (DFT), followed by the application of the DP4+ method to revisit the structure of Heliannuol L, a member of the Heliannuol class, isolated from Helianthus annuus. Our results indicate that the originally proposed structure of Heliannuol L needs a stereochemical reassignment, placing the hydroxyl bonded to C10 in the opposite side of the methyl and hydroxyl groups bonded to C7 and C8, respectively.

Oil charging model and controlling factors revealed by an online nuclear magnetic resonance (NMR) system

It is very difficult to simulate the charging process of crude oil under experimental conditions due to the low porosity and permeability of tight sandstone. However, simulations are important for revealing the mechanism of formation of tight oil and the oil-water distribution characteristics, as well as for enhancing the oil recovery efficiency. In this study, we established a new method, called nuclear magnetic resonance coupling displacement (NMR-DP), to simulate the tight oil charging process online. The NMR-DP method has the advantages of high precision, velocity, recyclability, and the ability to reflect the distribution of fluids in the micropores of a tight rock.We conducted a simulation experiment, involving the charging of crude oil into eight sandstone samples from Gaotaizi (in the Qijia-Longhupao area of the Songliao Basin). The results of this experiment were combined with those of microscopic measurements conducted on the pore structure (i.e., nuclear magnetic resonance, nitrogen adsorption, high-pressure and rate-controlled mercury injections, and micron-computed tomography). In this way, we clarified the charging process and its controlling factors (e.g., physical properties and wettability) and established a tight oil charging model. The results indicate that the oil charging saturation was controlled by several factors, including the charging pressure, physical properties, pore throat structure, and mineral composition of the rock. A smaller radius of the pore throat corresponded to a lower oil charging saturation and higher starting pressure gradient. The lower the content of clay and carbonate minerals, and the higher the content of feldspar mineral, the higher the oil saturation. Oil mainly occurred in the larger pores, while residual water mainly occurred in the smaller pores. The charging process was divided into four stages: an exponential rapid growth stage, a logarithmic slow-growth stage, a linear slow-growth stage, and a quasi-stationary stage. The method established in this paper is expected to be helpful for analyzing the distribution law of oil and water in tight sandstone areas, thereby aiding in the prediction of sweet spots and development of tight oil.

Concomitant disorder and high-affinity zinc binding in the human zinc- and iron-regulated transport protein 4 intracellular loop.

The human zinc- and iron-regulated transport protein 4 (hZIP4) protein is the major plasma membrane protein responsible for the uptake of zinc in the body, and as such it plays a key role in cellular zinc homeostasis. hZIP4 plasma membrane levels are regulated through post-translational modification of its large, disordered, histidine-rich cytosolic loop (ICL2) in response to intracellular zinc concentrations. Here, structural characteristics of the isolated disordered loop region, both in the absence and presence of zinc, were investigated using nuclear magnetic resonance (NMR) spectroscopy. NMR chemical shifts, coupling constants and temperature coefficients of the apoprotein, are consistent with a random coil with minor propensities for transient polyproline Type II helices and β-strand in regions implicated in post-translational modifications. The ICL2 protein remains disordered upon zinc binding, which induces exchange broadening. Paramagnetic relaxation enhancement experiments reveal that the histidine-rich region in the apoprotein makes transient tertiary contacts with predicted post-translational modification sites. The residue-specific data presented here strengthen the relationship between hZIP4 post-translational modifications, which impact its role in cellular zinc homeostasis, and zinc sensing by the intracellular loop. Furthermore, the zinc sensing mechanism employed by the ICL2 protein demonstrates that high-affinity interactions can occur in the presence of conformational disorder.

Dissection of the Structural Features of a Fungicidal Antibody-Derived Peptide.

The synthetic peptide T11F (TCRVDHRGLTF), derived from the constant region of human IgM antibodies, proved to exert a significant activity in vitro against yeast strains, including multidrug resistant isolates. Alanine substitution of positively charged residues led to a decrease in candidacidal activity. A more dramatic reduction in activity resulted from cysteine replacement. Here, we investigated the conformational properties of T11F and its alanine-substituted derivatives by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Peptide interaction with Candida albicans cells was studied by confocal and scanning electron microscopy. T11F and most of its derivatives exhibited CD spectra with a negative band around 200 nm and a weaker positive band around 218 nm suggesting, together with NMR coupling constants, the presence of a polyproline II (PPII) helix, a conformational motif involved in a number of biological functions. Analysis of CD spectra revealed a critical role for phenylalanine in preserving the PPII helix. In fact, only the F11A derivative presented a random coil conformation. Interestingly, the loss of secondary structure influenced the rate of killing, which turned out to be significantly reduced. Overall, the obtained results suggest that the PPII conformation contributes in characterising the cell penetrating and fungicidal properties of the investigated peptides.

13C-1H coupling constants as a conformational tool for structural assignment of quinic and octulosonic acid

A complete set of NMR coupling constants (1JC-H, 2JC-H, 3JC-H, and 3JH-H) were calculated for the eight stereoisomers of quinic acid, at the B3LYP/6-311G(d,p)/PCM(methanol) level of theory. The Fermi contact term of the coupling constants was computed with a modified, uncontracted, version of the 6-311G(d,p) basis set, with additional tight polarization functions. 1H and 13C NMR chemical shifts were determined at the same level using the gauge-invariant atomic orbital (GIAO) method. The magnitude of the spin-spin coupling constants was found to be affected by the orientation (axial or equatorial) of the coupling proton and the orientation of the hydroxy group on the coupling carbon, whereas the chemical shifts depend on the presence or absence of electron-withdrawing hydroxy groups attached to the carbon atoms involved.Graphical Nuclear magnetic resonance coupling constants, computed with density functional theory, can be used to differentiate and identify the different stereoisomers of quinic acid.

Nuclear Magnetic Resonance and Pore Coupling in Clay-Coated Sandstones With Anomalous Porosity Preservation, Agua Grande Formation, Reconcavo Basin, Brazil

Nuclear Magnetic Resonance and Pore Coupling in Clay-Coated Sandstones With Anomalous Porosity Preservation, Agua Grande Formation, Reconcavo Basin, Brazil

Identification of a New Interaction Mode between the Src Homology 2 Domain of C-terminal Src Kinase (Csk) and Csk-binding Protein/Phosphoprotein Associated with Glycosphingolipid Microdomains

Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp binding and Csk activation that arises from residues in the βB/βC loop of the SH2 domain.

Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: A basis set and correlation study

In this article, we present the so far most extended investigation of the calculation of the coupling constant polarizability of a molecule. The components of the coupling constant polarizability are derivatives of the nuclear magnetic resonance (NMR) indirect nuclear spin-spin coupling constant with respect to an external electric field and play an important role for both chiral discrimination and solvation effects on NMR coupling constants. In this study, we illustrate the effects of one-electron basis sets and electron correlation both at the level of density functional theory as well as second-order polarization propagator approximation for the small molecule hydrogen peroxide, which allowed us to perform calculations with the largest available basis sets optimized for the calculation of NMR coupling constants. We find a systematic but rather slow convergence with the one-electron basis set and that augmentation functions are required. We observe also large and nonsystematic correlation effects with significant differences between the density functional and wave function theory methods.

Synthesis, Crystal Structure and Chemical Bonding of the Zintl Phase Rb7NaSi8

AbstractAbstract. The Zintl phase Rb7NaSi8 was synthesized as single‐phase material. Powder and single‐crystal X‐ray diffraction, thermal analysis, chemical analysis, measurement of the magnetic susceptibility, and 23Na, 29Si, and 87Rb nuclear magnetic resonance (NMR) spectroscopy were employed to characterize the material. Rb7NaSi8 crystallizes in the Rb7NaGe8 type of structure forming trigonal pyramidal anions Si44–. Two unique environments of the cations are observed, the linear arrangement [Na(Si4)2]7– with short Na–Si distances of 2.94 Å and the Rb2 atom coordinated by six Si44– anions with long Rb–Si distances of 4.09 Å. The environment of the Rb1 atom is similar to the coordination of the rubidium atoms in Rb4Si4. The chemical bonding was investigated by quantum mechanical calculations of the electron localizability indicator (ELI), the electronic density of states (DOS), and NMR coupling parameters. Good agreement of theoretically calculated and experimentally determined NMR coupling parameters was obtained for both chemical shielding and quadrupole coupling. The anisotropy of chemical shielding (CSA) indicates an anisotropic bonding situation of the silicon atoms. This is confirmed by the observation of a lone‐pair‐like feature and three two‐center Si–Si bonds for each silicon atom using the ELI. The electric field gradients (EFG) of 23Na and 87Rb indicate the anisotropy of the charge distribution of the cations. In particular, the linear arrangement [Na(Si4)2]7– and the Rb1 atom feature anisotropic charge distributions of the cations. This is confirmed by calculating the anisotropy ratio defined as Δnp = n(pz)/(½[n(px)+n(py)]) with n(pi) corresponding to the integrated DOS of the respective state. The long distances of Rb2 to the six coordinating Si44– ions are reflected by the small EFG.

On the Configuration of Five‐Membered Rings: A Spin–Spin Coupling Constant Approach

Five-membered rings are clearly among the most common structural motifs found in chemistry and biology. Nevertheless, the configuration of conformationally mobile five-membered rings is often difficult to assign from nuclear magnetic resonance (NMR) data. A simple, reliable, and efficient approach for the stereochemical analysis of five-membered rings based on the measurement of NMR coupling constants is presented. Density functional theory calculations using representative conformations of the full conformational space available to rings with different substitution patterns were used to identify differences between the accessible coupling constant values for cis and trans relative orientations of the substituents. The calculations were assessed experimentally using NMR data obtained from a number of models. This approach can be easily used to analyze different five-membered rings, such as oxolanes, cyclopentanes, furanosides and pyrrolidines, and their relative configuration can be determined without the need for making further conformational considerations.

Approximating correlation effects in multiconfigurational self-consistent field calculations of spin-spin coupling constants

The multiconfigurational self-consistent field (MCSCF) method in their approximations restricted and complete active spaces (RAS and CAS) provides a theoretically accurate description of the coupling constants of a wide range of molecules. To obtain accurate results, however, very large basis sets and large configuration spaces must be used. Nuclear magnetic resonance coupling constants for the equilibrium geometry have been calculated for a series of small molecules using approximated correlation contributions. The four contributions to the coupling constants (Fermi contact, spin dipolar, orbital paramagnetic, and orbital diamagnetic) have been calculated at the CAS and RAS MCSCF and second-order polarization propagator approximation levels using a large basis set. An additive model that considers the effect on the coupling constants from excitation of more than two electrons and from core-electron correlation is used to estimate the coupling constants. Compared with the experimental couplings, the best calculated values, which correspond to the MCSCF results, present a mean absolute error of 3.6 Hz and a maximum absolute deviation of 13.4 Hz. A detailed analysis of the different contributions and of the effects of the additive contributions on the coupling constants is carried out.

Application of high-performance liquid chromatography–nuclear magnetic resonance coupling to the identification of limonoids from mahogany tree ( Switenia macrophylla, Meliaceae) by stopped-flow 1D and 2D NMR spectroscopy

Separation and characterization of limonoids from Switenia macrophylla (Meliaceae) by HPLC–NMR technique has been described. Analyses were carried out using reversed-phase gradient HPLC elution coupled to NMR (600 MHz) spectrometer in stopped-flow mode. Separated peaks were collected into an interface unit prior to NMR measurements, which were performed with suppression of solvent signals by shaped pulses sequences. Structure elucidation of the limonoids was attained by data obtained from 1H NMR, TOCSY, gHSQC and gHMBC spectra without conventional isolation that is usually applied in natural products studies.

LC–NMR coupling technology: recent advancements and applications in natural products analysis

An overview of recent advances in nuclear magnetic resonance (NMR) coupled with separation technologies and their application in natural product analysis is given and discussed. The different modes of LC-NMR operation are described, as well as how technical improvements assist in establishing LC-NMR as an important tool in the analysis of plant-derived compounds. On-flow, stopped-flow and loop-storage procedures are mentioned, together with the new LC-SPE-NMR configuration. The implementation of mass spectrometry in LC-NMR is also useful on account of the molecular weight and fragmentation information that it provides, especially when new plant species are studied. Cryogenic technology and capillary LC-NMR are the other important recent developments. Since the plant kingdom is endless in producing potential drug candidates, development and optimization of LC-NMR techniques convert the study of natural products to a less-time-consuming task, speeding up identification.

Structure-activity study of thiazides by magnetic resonance methods (NQR, NMR, EPR) and DFT calculations

The paper presents a comprehensive analysis of the relationship between the electronic structure of thiazides and their biological activity. The compounds of interest were studied in solid state by the resonance methods nuclear quadrupole resonance (NQR), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) and quantum chemistry (ab inito and DFT) methods. Detailed parallel analysis of the spectroscopic parameters such as quadrupole coupling constant (QCC) NQR chemical shift ( δ), chemical shift anisotropy (CSA), asymmetry parameter ( η), NMR and hyperfine coupling constant (A), EPR was performed and the electronic effects (polarisation and delocalisation) were revealed and compared. Biological activity of thiazides has been found to depend on many factors, but mainly on the physico-chemical properties whose assessment was possible on the basis of electron density determination in the molecules performed by experimental and theoretical methods.

Vicinal fluorine-fluorine coupling constants: Fourier analysis.

Stereochemical dependences of vicinal fluorine-fluorine nuclear magnetic resonance coupling constants (3JFF) have been studied with the multiconfigurational self-consistent field in the restricted active space approach, with the second-order polarization propagator approximation (SOPPA), and with density functional theory. The SOPPA results show the best overall agreement with experimental couplings. The relationship with the dihedral angle between the coupled fluorines has been studied by Fourier analysis, the result is very different from that of proton-proton couplings. The Fourier coefficients do not resemble those of a typical Karplus equation. The four nonrelativistic contributions to the coupling constants of 1,2-difluoroethane configurations have been studied separately showing that up to six Fourier coefficients are required to reproduce the calculated values satisfactorily. Comparison with Fourier coefficients for matching hydrogen fluoride dimer configurations suggests that the higher order Fourier coefficients (Cn> or =3) originate mainly from through-space Fermi contact interaction. The through-space interaction is the main reason 3JFF do not follow the Karplus equation.

Nuclear spin–spin coupling density functions and the Fermi hole

Nuclear spin–spin coupling density functions yield a three-dimensional picture of the interaction between two nuclear dipole moments mediated by electron spin density. A physical interpretation of the Fermi contact coupling density maps can be readily arrived at on account of the Fermi correlation between same-spin electrons as the mechanism whereby the spin polarization induced about one nucleus is transmitted to another nucleus coupled to it. It is shown that the Fermi hole density function, evaluated by an opportune choice of the reference electron, is characterized by morphological aspects very similar to those appearing in the plots of one- and two-bonds Fermi contact density functions. A comparison has been made for hydrogen fluoride, water, ammonia, and methane molecules at the Hartree–Fock level of theory. The results confirm the role of the Fermi correlation as the fundamental vehicle propagating nuclear-spin/electron-spin contact interaction, i.e., the process mainly responsible for nuclear spin–spin coupling. The plots of Fermi hole density show that the geminal H–H coupling would not be possible without the essential contribution of the spin density in the vicinity of the heavier nucleus. The combined use of Fermi contact density functions and Fermi hole distributions yields a very promising approach to the study of nuclear magnetic resonance coupling constants, and provides a sound physical basis for their interpretation.