NMR-active Nuclei Research Articles

Expression and Purification of Isotopically Enriched MHC Binding Immunogenic Peptides for NMR Studies

Peptides are important naturally occurring ligands of MHC molecules. X-ray crystallographic studies have enabled extensive characterization of such peptide ligands. Yet structural and dynamic changes of these peptides in the MHC bound state are not well understood. These conformational transitions are key to understanding the function of MHC molecules and for the development of peptide-based therapeutics. Employing NMR for such studies can fill this gap but it requires the availability of peptides labeled with NMR-active nuclei. Here we report production of nine-mer MHC-binding peptides for use in high resolution NMR studies. The method utilizes a fusion protein approach of attaching the peptide to an easily expressed bacterial protein. The fusion protein construct design allows for rapid purification of the fusion protein and avoids chemical modification of the peptide as a result of the cleavage reaction. The methods developed here allow for rapid cloning of additional MHC binding peptides without significant molecular biology effort. 8–10 mg of mature freeze dried peptides can be obtained from 1 liter of minimal media, sufficient for NMR experimentation. Six uniformly 15N-labeled peptides have been successfully expressed in bacteria and NMR spectra with the expected number of well-resolved signals were recorded. The results obtained here will make peptide-MHC complexes amenable to structural analysis which has not been possible previously.

Diffusion-Ordered NMR Spectroscopy as a Reliable Alternative to TEM for Determining the Size of Gold Nanoparticles in Organic Solutions

Diffusion-ordered spectroscopy is used to determine gold nanoparticle sizes. Traditional characterization of nanoparticles has centered on imaging by electron microscopy and plasmon resonance absorption in UV−visible electronic spectra. We present a convenient method to characterize gold nanoparticles using diffusion-ordered NMR spectroscopy (DOSY). 2D DOSY NMR is used to calculate diffusion constants and the diameter of solubilized gold nanoparticles capped with 1-dodecanethiol (C12) or 1-octanethiol (C8) in three deuterated solvents. The distributions of nanoparticle sizes strongly correlate with transmission electron microscopy (TEM) image analysis. C12 and C8 capped nanoparticle sizes were found to be 4.6 and 2.7 nm by TEM as compared to estimates of 4.6 ± 0.3 and 2.5 ± 0.1 nm based on 2D DOSY NMR data. This demonstrates that reliable size characterization of nanoparticles with NMR active nuclei (1H in this study) in their protective groups (alkane thiols in this study) can be achieved by a widely ava...

Quantitative Rate Determination by Dynamic Nuclear Polarization Enhanced NMR of a Diels−Alder Reaction

Emerging techniques for hyperpolarization of nuclear spins, foremost dynamic nuclear polarization (DNP), lend unprecedented sensitivity to nuclear magnetic resonance spectroscopy. Sufficient signal can be obtained from a single scan, and reactions even far from equilibrium can be studied in real-time. When following the progress of a reaction by nuclear magnetic resonance, however, spin relaxation occurs concomitantly with the reaction to alter resonance line intensities. Here, we present a model for accounting for spin-relaxation in such reactions studied by hyperpolarized NMR. The model takes into account auto- and cross-relaxation in dipole-dipole coupled spin systems and is therefore applicable to NMR of hyperpolarized protons, the most abundant NMR-active nuclei. Applied to the Diels-Alder reaction of 1,4-dipheneylbutadiene (DPBD) with 4-phenyl-1,2,4-triazole-3,5-dione (PTD), reaction rates could be obtained accurately and reproducibly. Additional parameters available from the same experiment include relaxation rates of the reaction product, which may yield further information about the molecular properties of the product. The method presented is also compatible with an experiment where a single spin in the reactant is labeled in its spin-state by a selective radio frequency pulse for subsequent tracking through the reaction, allowing the unambiguous identification of its position in the product molecule. In this case, the chemical shift specificity of high-resolution NMR can allow for the simultaneous determination of reaction rates and mechanistic information in one experiment.

Determination of Molecular Torsion Angles Using Nuclear Singlet Relaxation

The exponential relaxation time constant, T(S), of a nuclear singlet state is influenced by the proximity of neighboring NMR-active nuclei. For methylene groups in particular this dependence is much stronger than the case for other NMR relaxation constants, including the "conventional" relaxation time constant, T(1), of the longitudinal magnetization. This sensitivity provides a new route for determining torsional angles plus other molecular structural details in the isotropic solution phase.

A novel variable field system for field-cycled dynamic nuclear polarization spectroscopy

Dynamic nuclear polarization (DNP) is an NMR-based technique which enables detection and spectral characterization of endogenous and exogenous paramagnetic substances measured via transfer of polarization from the saturated unpaired electron spin system to the NMR active nuclei. A variable field system capable of performing DNP spectroscopy with NMR detection at any magnetic field in the range 0–0.38 T is described. The system is built around a clinical open-MRI system. To obtain EPR spectra via DNP, partial cancellation of the detection field B 0 NMR is required to alter the evolution field B 0 EPR at which the EPR excitation is achieved. The addition of resistive actively shielded field cancellation coils in the gap of the primary magnet provides this field offset in the range of 0–100 mT. A description of the primary magnet, cancellation coils, power supplies, interfacing hardware, RF electronics and console are included. Performance of the instrument has been evaluated by acquiring DNP spectra of phantoms with aqueous nitroxide solutions (TEMPOL) at three NMR detection fields of 97 G, 200 G and 587 G corresponding to 413 kHz, 851.6 kHz and 2.5 MHz respectively and fixed EPR evolution field of 100 G corresponding to an irradiation frequency of 282.3 MHz. This variable-field DNP system offers great flexibility for the performance of DNP spectroscopy with independent optimum choice of EPR excitation and NMR detection fields.

Synthesis and Characterization of Transition-Metal Complexes Containing 1,1’-Bis(diphenylphosphino)ferrocene

Learning synthetic techniques is an important component of the inorganic laboratory experience. However, if a lab only requires students to prepare a compound, they can be left questioning if the compound they made serves any useful purpose. In this lab, the ligand 1,1'-bis(diphenylphosphino)ferrocene (dppf) can either be prepared as part of a previous laboratory or purchased. A variety of transition-metal complexes are prepared and characterized by NMR and UV–visible spectroscopy. While 1H NMR will be useful in characterizing the complexes, 31P{1H} NMR will be essential for characterization. By varying the metal centers, instructors will be able to introduce crystal field theory, the Evans method, and the effect of NMR active nuclei that are not 100% abundant. In addition, students can examine the electrochemistry of their compounds to determine the effect of the metal on the potential at which oxidation of their ligands occurs.

Intermolecular shielding contributions studied by modeling the (13)C chemical-shift tensors of organic single crystals with plane waves.

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all (13)C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.

Spontaneous Transfer of Parahydrogen Derived Spin Order to Pyridine at Low Magnetic Field

The cationic iridium complex [Ir(COD)(PCy(3))(py)]BF(4) (1) is shown to react with dihydrogen in the presence of pyridine (py) to form the dihydride complex fac,cis-[Ir(PCy(3))(py)(3)(H)(2)]BF(4) (2). Complex 2 undergoes rapid exchange of the two bound pyridine ligands which are trans to hydride with free pyridine; the activation parameters for this process in methanol are DeltaH(double dagger) = 97.4 +/- 9 kJ mol(-1) and DeltaS(double dagger) = 84 +/- 31 J K(-1) mol(-1). When parahydrogen is employed as a source of nuclear spin polarization, spontaneous magnetization transfer proceeds in low magnetic field from the two nascent hydride ligands of 2 to its other NMR active nuclei. Upon interrogation by NMR spectroscopy in a second step, signal enhancements in excess of 100 fold are observed for the (1)H, (13)C and (15)N resonances of free pyridine after ligand exchange. The degree of signal enhancement in the free substrate is increased by employing electronically rich and sterically encumbered phosphine ligands such as PCy(3), PCy(2)Ph, or P(i)Pr(3) and by optimizing the strength of the magnetic field in which polarization transfer occurs.

Searching for Microporous, Strongly Basic Catalysts: Experimental and Calculated 29Si NMR Spectra of Heavily Nitrogen-Doped Y Zeolites

Nitrogen substituted zeolites with high crystallinity and microporosity are obtained by nitrogen substitution for oxygen in zeolite Y. The substitution reaction is performed under ammonia flow by varying the temperature and reaction time. We examine the effect of aluminum content and charge-compensating cation (H(+)/Na(+)/NH(4)(+)) on the degree of nitrogen substitution and on the preference for substitution of Si-O-Al vs Si-O-Si linkages in the FAU zeolite structure. Silicon-29 magic angle spinning (MAS) nuclear magnetic resonance (NMR) and (1)H/(29)Si cross-polarization MAS NMR spectroscopy have been used to probe the different local environments of the nitrogen-substituted zeolites. Experimental data are compared to simulated NMR spectra obtained by constructing a compendium (>100) of zeolite clusters with and without nitrogen, and by performing quantum calculations of chemical shifts for the NMR-active nuclei in each cluster. The simulated NMR spectra, which assume peak intensities predicted by statistical analysis, agree remarkably well with the experimental data. The results show that high levels of nitrogen substitution can be achieved while maintaining porosity, particularly for NaY and low-aluminum HY materials, without significant loss in crystallinity. Experiments performed at lower temperatures (750-800 degrees C) show a preference for substitution at Si-OH-Al sites. No preference is seen for reactions performed at higher temperatures and longer reaction times (e.g., 850 degrees C and 48 h).

NMR spectroscopy explained: simplified theory, applications and examples for organic chemistry and structural biology

NMR spectroscopy explained: simplified theory, applications and examples for organic chemistry and structural biology

Polymer-Supported Reagents and 1H–19F NMR Couplings: The Synthesis of 2-Fluoroacetophenone

We describe an experiment for the undergraduate organic laboratory curriculum in which 2-bromoacetophenone is converted to 2-fluoroacetophenone using a solid-phase nucleophilic fluorine source. The experiment introduces students to the utility of solid-phase reagents in organic synthesis, to NMR-active nuclei other than 1H without the requirement of a special NMR probe, and to the unique uses of fluorine in molecular design.

Endohedral and External Through-Space Shieldings of the Fullerenes C50, C60, C60-6, C70, and C70-6Visualization of (Anti)Aromaticity and Their Effects on the Chemical Shifts of Encapsulated Nuclei

Endohedral and external through-space NMR shieldings (TSNMRS) and the magnetic susceptibilities of the fullerene carbon cages of C50, C60, C60(-6), C70, and C70(-6) were assessed by ab initio molecular orbital calculations. Employing the nucleus-independent chemical shift (NICS) concept, these TSNMRS were visualized as isochemical shielding surfaces (ICSS) and were applied to quantitatively estimate either the aromaticity or the anti-aromaticity on the fullerene surface pertaining to the five- or six-membered ring moieties and the shielding of any nuclei enclosed within the carbon cages. Differences between the NICSs calculated at the center of the fullerene carbon cages and the experimental chemical shifts of encapsulated NMR-active nuclei as well as experimental shieldings observed for different encapsulated nuclei were able to be understood readily for the first time.

Hydrogen Bonds in Ionic Liquids Revisited: 35/37Cl NMR Studies of Deuterium Isotope Effects in 1-n-Butyl-3-Methylimidazolium Chloride

Detailed knowledge of the structure, dynamics, and interionic interactions of ionic liquids (ILs) is critical to understand their physicochemical properties. In this letter, we show that deuterium isotope effects on the chloride ion 35/37Cl NMR signal represent a useful tool in the study of interionic hydrogen bonds in imidazolium chloride ILs. Sizable Delta35/37Cl(H,D) values obtained for the model system 1-n-butyl-3-methylimidazolium chloride ([C4mim]Cl) upon deuteriation of the imidazolium C-2 and C-2,4,5 positions, of nearly 1 and 2 ppm, respectively, show that the approach can readily identify and differentiate Cl...H hydrogen bonds between the anion and cation. Our study is one of a few examples in which hydrogen-bonding in ILs has been investigated using deuterium isotope effects and, to our knowledge, the only one employing 35/37Cl NMR to detect these interactions. The methodology described could be easily extended to the study of other systems bearing NMR-active nuclei.

Electronic structure of theNa16Rb8Si136andK16Rb8Si136clathrates

We have calculated the electronic structure and the equations of state of the ${\mathrm{Na}}_{16}{\mathrm{Rb}}_{8}{\mathrm{Si}}_{136}$ and ${\mathrm{K}}_{16}{\mathrm{Rb}}_{8}{\mathrm{Si}}_{136}$ clathrates. These compounds are based on the type II silicon clathrate structure. The smaller Na (or K) atoms occupy the 20-atom cages, while the Rb atoms occupy the 28-atom cages. Equation of state, electronic band structure, and density of states calculations were performed using density functional theory in the local density approximation (LDA). The ``guest'' impurity atoms inside the cages modify the material electronic structure. Guest atom electrons occupy the ${\mathrm{Si}}_{136}$ conduction band states, resulting in a Fermi level shift into the conduction band of the ``parent'' ${\mathrm{Si}}_{136}$ framework. In qualitative agreement with the rigid-band model, the band structures display no major modifications due to the inclusion of the alkali metal guests. However, the electronic densities of states of the filled clathrates show two sharp peaks and a dip near the Fermi level. This feature may help to qualitatively explain the temperature-dependent Knight shift observed for the NMR-active nuclei in ${\mathrm{Na}}_{16}{\mathrm{Rb}}_{8}{\mathrm{Si}}_{136}$. We compare our calculations with experimental results for ${\mathrm{Na}}_{16}{\mathrm{Rb}}_{8}{\mathrm{Si}}_{136}$.

The embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculations

AbstractThe nuclear magnetic shielding anisotropy of NMR active nuclei is highly sensitive to the nuclear electronic environment. Hence, measurements of the nuclear magnetic shielding anisotropy represent a powerful tool in the elucidation of molecular structure for a wide variety of materials. Quantum mechanical ab initio nuclear magnetic shielding calculations effectively complement the experimental NMR data by revealing additional structural information. The accuracy and capacity of these calculations has been improved considerably in recent years. However, the inherent problem of the limitation in the size of the systems that may be studied due to the relatively demanding computational requirements largely remains. Accordingly, ab initio shielding calculations have been performed predominantly on isolated molecules, neglecting the molecular environment. This approach is sufficient for neutral nonpolar systems, but leads to serious errors in the shielding calculations on polar and ionic systems. Conducting ab initio shielding calculations on clusters of molecules (i.e., including the nearest neighbor interactions) has improved the accuracy of the calculations in many cases. Other methods of simulating crystal lattice effects in shielding calculations that have been developed include the electrostatic representation of the crystal lattice using point charge arrays, full ab initio methods, ab initio methods under periodic boundary conditions, and hybrid ab initio/molecular dynamics methods. The embedded ion method (EIM) discussed here follows the electrostatic approach. The method mimics the intermolecular and interionic interactions experienced by a subject molecule or cluster in a given crystal in quantum mechanical shielding calculations with a large finite, periodic, and self‐consistent array of point charges. The point charge arrays in the EIM are generated using the Ewald summation method and embed the molecule or ion of interest for which the ab initio shielding calculations are performed. The accuracy with which the EIM reproduces experimental nuclear magnetic shift tensor principal values, the sensitivity of the EIM to the parameters defining the point charge arrays, as well as the strengths and limitations of the EIM in comparison with other methods that include crystal lattice effects in chemical shielding calculations, are presented. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 347–368, 2006

Solid‐state NMR characterization of 69Ga and 71Ga in crystalline solids

Gallium model systems containing four- and six-coordinate gallium sites have been investigated using solid-state NMR. Measurement of the isotropic chemical shift and electric field gradient (EFG) have been performed at 9.4 T on alpha-Ga2O3, beta-Ga2O3, LiGaO2, NaGaO2, KGaO2, Ga2(SO4)3, and LaGaO3 using a variety of techniques on both NMR active nuclei (69Ga and 71Ga) including static, high speed magic-angle spinning (MAS), satellite transition (ST) spectroscopy, and rotor-assisted population transfer (RAPT). The chemical shift is found to correlate well with the coordination number, with four-coordinate gallium having values of approximately 50 ppm and six-coordinate gallium having values near 225 ppm (referenced to 1 M gallium nitrate solution). The magnitude of the EFG is found to be correlated to the distortion of the gallium polyhedra, with the strained systems having EFGs of 3 x 10(21) Vm(-2) or more, while the less strained systems have values of 1.5 x 10(21) Vm(-2) or less. A plot of chemical shift versus EFG suggests that solid-state NMR of gallium oxyanions can be more discriminating than liquid state NMR chemical shifts alone.

In-cell NMR for protein-protein interactions (STINT-NMR)

We describe an in-cell NMR-based method for mapping the structural interactions (STINT-NMR) that underlie protein-protein complex formation. This method entails sequentially expressing two (or more) proteins within a single bacterial cell in a time-controlled manner and monitoring their interactions using in-cell NMR spectroscopy. The resulting NMR data provide a complete titration of the interaction and define structural details of the interacting surfaces at atomic resolution. Unlike the case where interacting proteins are simultaneously overexpressed in the labeled medium, in STINT-NMR the spectral complexity is minimized because only the target protein is labeled with NMR-active nuclei, which leaves the interactor protein(s) cryptic. This method can be combined with genetic and molecular screens to provide a structural foundation for proteomic studies. The protocol takes 4 d from the initial transformation of the bacterial cells to the acquisition of the NMR spectra.

3D-NMR Studies of B-Centered n-ad Structures in Poly(ethylene-co-13C-n-butyl acrylate-co-carbon monoxide)

This paper presents the first application of a suite of three-dimensional (3D) NMR techniques for the characterization of complex microstructures in hydrocarbon-based terpolymers. The 3D-NMR experiments are used to disperse and assign the 1H and 13C resonances of 13C-labeled poly(ethylene-co-1,2,3-13C3-n-butyl acrylate-co-carbon monoxide). The one-dimensional (1D) and two-dimensional 2D-NMR spectra of the complex mixture of structures in this polymer are far too complex to interpret. Selective 13C-labeling of all or one carbon in a monomer and use of shaped pulses (which treat the resonances from the labeled 13C as if they were from a third NMR active nucleus) along with 3D-NMR is a solution to this complex problem as it greatly simplifies the spectra by dispersing the resonances into a third dimension and provides atomic connectivity information among three different nuclei. This paper represents the first demonstration of new 3D-NMR methodology for determining structures and resonance assignments of complex hydrocarbon-based structures and mixtures.

New Protonation Microequilibrium Treatment in the Case of Some Amino Acid and Peptide Derivatives Containing a Bis(imidazolyl)methyl Group

We present a microequilibrium analysis of a series of amino acid and peptide derivatives containing the chelating bis(imidazol-2-yl)methyl group (BIP, Gly-BIMA, His-BIMA, alpha-Glu-BIMA, gamma-Glu-BIMA, and Phe-His-BIMA). NMR measurements were performed in D2O to follow the deprotonation steps. The software PSEQUAD and a specialized program written in MATLAB were used to determine the macroscopic and microscopic constants. The method assumes that the effect of pH on the chemical shift of an NMR-active nucleus can be interpreted by adding the independent effects of the protonation of individual sites. For derivatives containing histidine (His-BIMA and Phe-His-BIMA), the deprotonation steps of the second imidazole and the His-imidazole significantly overlap. In the Glu derivatives (alpha-Glu-BIMA and gamma-Glu-BIMA), the amino and the second imidazole pK values are separate; the deprotonation processes of the first imidazole nitrogen and the side-chain carboxyl group, however, significantly overlap. In gamma-Glu-BIMA, the deprotonation sequence is carboxylate-imidazole1-imidazole2-amino, while in the case of alpha-Glu-BIMA, it changes to imidazole1-carboxylate-imidazole2-amino, according to the microscopic pk values. The main advantage of the method is that it does not require the synthesis and NMR microequilibrium analysis of substances modeling the individual parts of the target ligand, in contrast to the methods used by others. The method presented here demands slightly more mathematical and computational power, which is readily available today.

Gas-phase NMR technique for studying the thermolysis of materials: thermal decomposition of ammonium perfluorooctanoate.

The kinetics of the thermal decomposition of ammonium perfluorooctanoate (APFO) has been studied by high-temperature gas-phase nuclear magnetic resonance spectroscopy over the temperature range 196-234 degrees C. We find that APFO cleanly decomposes by first-order kinetics to give the hydrofluorocarbon 1-H-perfluoroheptane and is completely decomposed (>99%) in a matter of minutes at the upper limit of this temperature range. Based on the temperature dependence of the measured rate constants, we find that the enthalpy and entropy of activation are DeltaH++ = 150 +/- 11 kJ mol(-1) and DeltaS++ = 3 +/- 23 J mol(-)(1) deg(-1). These activation parameters may be used to calculate the rate of APFO decomposition at the elevated temperatures (350-400 degrees C) at which fluoropolymers are processed; for example, at 350 degrees C the half-life for APFO is estimated to be less than 0.2 s. Our studies provide the fundamental parameters involved in the decomposition of the ammonium salt of perfluorooctanoic acid and indicate the utility of gas-phase NMR for thermolysis studies of a variety of materials that release compounds that are volatile at the temperature of decomposition and that contain an NMR-active nucleus.