Friday, January 31, 2014

Rationalizing Overhauser DNP of nitroxide radicals in water through MD simulations

Sezer, D., Rationalizing Overhauser DNP of nitroxide radicals in water through MD simulations. Phys Chem Chem Phys, 2014. 16(3): p. 1022-32.

The recently introduced methodology (Sezer, Phys. Chem. Chem. Phys., 2013, 15, 526) for calculating dynamic nuclear polarization (DNP) coupling factors through synergistic use of molecular dynamics (MD) simulations and the analytical model of diffusing hard spheres with spins at their centers (HSCS) is applied to several nitroxides in water. Computations with one TEMPONE and one TEMPOL in water agree with experiments at 0.35 T and 3.4 T, respectively. At 9.2 T the predicted coupling factors are larger by about 50% than the experimental numbers obtained with 1 M TEMPOL solution. MD simulations at this elevated concentration reveal nanoscopic TEMPOL clusters and qualitatively explain the lower experimental values. Comparing the dynamics from the MD simulations with those of the HSCS model, the assumption of centered spins is shown to be too limiting even for small molecules like TEMPOL and water. Using the available extension of the HSCS model to off-centered spins, the current procedure for analyzing hydration water dynamics from Overhauser DNP measurements on spin-labeled proteins is revisited.

Wednesday, January 29, 2014

Probing (27)Al-(13)C proximities in metal-organic frameworks using dynamic nuclear polarization enhanced NMR spectroscopy

Pourpoint, F., et al., Probing (27)Al-(13)C proximities in metal-organic frameworks using dynamic nuclear polarization enhanced NMR spectroscopy. Chem Commun (Camb), 2013. 50(8): p. 933-5.

We show how (27)Al-(13)C proximities in the microporous metal-organic framework MIL-100(Al) can be probed using advanced (27)Al-(13)C NMR methods boosted by Dynamic Nuclear Polarization.

Monday, January 27, 2014

Higher Order Amyloid Fibril Structure by MAS NMR and DNP Spectroscopy

Debelouchina, G.T., et al., Higher Order Amyloid Fibril Structure by MAS NMR and DNP Spectroscopy. J Am Chem Soc, 2013. 135(51): p. 19237-47.

Protein magic angle spinning (MAS) NMR spectroscopy has generated structural models of several amyloid fibril systems, thus providing valuable information regarding the forces and interactions that confer the extraordinary stability of the amyloid architecture. Despite these advances, however, obtaining atomic resolution information describing the higher levels of structural organization within the fibrils remains a significant challenge. Here, we detail MAS NMR experiments and sample labeling schemes designed specifically to probe such higher order amyloid structure, and we have applied them to the fibrils formed by an eleven-residue segment of the amyloidogenic protein transthyretin (TTR(105-115)). These experiments have allowed us to define unambiguously not only the arrangement of the peptide beta-strands into beta-sheets but also the beta-sheet interfaces within each protofilament, and in addition to identify the nature of the protofilament-to-protofilament contacts that lead to the formation of the complete fibril. Our efforts have resulted in 111 quantitative distance and torsion angle restraints (10 per residue) that describe the various levels of structure organization. The experiments benefited extensively from the use of dynamic nuclear polarization (DNP), which in some cases allowed us to shorten the data acquisition time from days to hours and to improve significantly the signal-to-noise ratios of the spectra. The beta-sheet interface and protofilament interactions identified here revealed local variations in the structure that result in multiple peaks for the exposed N- and C-termini of the peptide and in inhomogeneous line-broadening for the residues buried within the interior of the fibrils.

Friday, January 24, 2014

Highly Efficient, Water-Soluble Polarizing Agents for Dynamic Nuclear Polarization at High Frequency

Sauvee, C., et al., Highly Efficient, Water-Soluble Polarizing Agents for Dynamic Nuclear Polarization at High Frequency. Angew Chem Int Ed Engl, 2013. 52(41): p. 10858-10861.

Well polarized: Two new polarizing agents PyPol and AMUPol soluble in glycerol/water mixtures are used for dynamic nuclear polarization (DNP) NMR spectroscopy. The enhancement factors (epsilon) are about 3.5 to 4 times larger than for the established agent TOTAPOL at 263 and 395 GHz. For AMUPol, the temperature dependence of epsilon allows DNP experiments to be performed at temperatures significantly higher than for typical high-field DNP NMR experiments.

Wednesday, January 22, 2014

Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control

Sakaguchi, S., et al., Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2013. 317(0): p. 679-684.

Proton polarization at room temperature, produced in a p-terphenyl crystal by using electron population difference in a photo-excited triplet state of pentacene, was enhanced by utilizing an intense laser with an average power of 1.5 W. It was shown that keeping the sample temperature below 300 K is critically important to prevent the rise of the spin–lattice relaxation rate caused by the laser heating. It is also reported that the magnitude of proton polarization strongly depends on the time structure of the laser pulse such as its width and the time interval between them.

Monday, January 20, 2014

A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range

Reynolds, S., et al., A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range. J Magn Reson, 2013. 239C(0): p. 1-8.

Over recent years hyperpolarization by dissolution dynamic nuclear polarization has become an established technique for studying metabolism in vivo in animal models. Temporal signal plots obtained from the injected metabolite and daughter products, e.g. pyruvate and lactate, can be fitted to compartmental models to estimate kinetic rate constants. Modeling and physiological parameter estimation can be made more robust by consistent and reproducible injections through automation. An injection system previously developed by us was limited in the injectable volume to between 0.6 and 2.4ml and injection was delayed due to a required syringe filling step. An improved MR-compatible injector system has been developed that measures the pH of injected substrate, uses flow control to reduce dead volume within the injection cannula and can be operated over a larger volume range. The delay time to injection has been minimized by removing the syringe filling step by use of a peristaltic pump. For 100mul to 10.000ml, the volume range typically used for mice to rabbits, the average delivered volume was 97.8% of the demand volume. The standard deviation of delivered volumes was 7mul for 100mul and 20mul for 10.000ml demand volumes (mean S.D. was 9 ul in this range). In three repeat injections through a fixed 0.96mm O.D. tube the coefficient of variation for the area under the curve was 2%. For in vivo injections of hyperpolarized pyruvate in tumor-bearing rats, signal was first detected in the input femoral vein cannula at 3-4s post-injection trigger signal and at 9-12s in tumor tissue. The pH of the injected pyruvate was 7.1+/-0.3 (mean+/-S.D., n=10). For small injection volumes, e.g. less than 100mul, the internal diameter of the tubing contained within the peristaltic pump could be reduced to improve accuracy. Larger injection volumes are limited only by the size of the receiving vessel connected to the pump.

Friday, January 17, 2014

Asymmetric Collapse in Biomimetic Complex Coacervates Revealed by Local Polymer and Water Dynamics

Ortony, J.H., et al., Asymmetric collapse in biomimetic complex coacervates revealed by local polymer and water dynamics. Biomacromolecules, 2013. 14(5): p. 1395-402.

Complex coacervation is a phenomenon characterized by the association of oppositely charged polyelectrolytes into micrometer-scale liquid condensates. This process is the purported first step in the formation of underwater adhesives by sessile marine organisms, as well as the process harnessed for the formation of new synthetic and protein-based contemporary materials. Efforts to understand the physical nature of complex coacervates are important for developing robust adhesives, injectable materials, or novel drug delivery vehicles for biomedical applications; however, their internal fluidity necessitates the use of in situ characterization strategies of their local dynamic properties, capabilities not offered by conventional techniques such as X-ray scattering, microscopy, or bulk rheological measurements. Herein, we employ the novel magnetic resonance technique Overhauser dynamic nuclear polarization enhanced nuclear magnetic resonance (DNP), together with electron paramagnetic resonance (EPR) line shape analysis, to concurrently quantify local molecular and hydration dynamics, with species- and site-specificity. We observe striking differences in the structure and dynamics of the protein-based biomimetic complex coacervates from their synthetic analogues, which is an asymmetric collapse of the polyelectrolyte constituents. From this study we suggest charge heterogeneity within a given polyelectrolyte chain to be an important parameter by which the internal structure of complex coacervates may be tuned. Acquiring molecular-level insight to the internal structure and dynamics of dynamic polymer complexes in water through the in situ characterization of site- and species-specific local polymer and hydration dynamics should be a promising general approach that has not been widely employed for materials characterization.

Open position: Post Doc specialist in MM and SUB-­‐MMW technologies (M/F)

Open position: Post Doc specialist in MM and SUB-MMW technologies (M/F)

EPFL/LPMN and SWISSto12 SA are now opening a position for Research and Development activities focused on Terahertz Technologies. The project funded by CTI/KTI aims at developing a new family of Planar Probes for Dynamic Nuclear Polarization Enhanced Nuclear Magnetic Resonance.

Introduction to the field of the project:
Nuclear Magnetic Resonance (NMR) is a widespread tool used for research in Chemistry, Physics and
Biology. NMR Spectroscopy performances are greatly enhanced by Dynamic Nuclear Polarization (DNP). This technique involves irradiating samples with terahertz waves in order to excite the electron spin resonance. An innovative DNP-°©‐NMR probe based on a planar geometry has been recently patented by EPFL and CNR(I). Among other unprecedented features, this new piece of instrumentation (the probe) will allow the study of biological samples at room temperature.

Introduction to the commercial partner:
SWISSto12 is a private start‐up company, spin‐off of the Swiss Federal Institute of Technology in Lausanne, (EPFL). It aims at becoming a leading supplier of components and systems for Terahertz (THz) signal transmission. SWISSto12 holds exclusive licenses for patent applications owned by the EPFL, of which the company founders are the inventors. These patent applications cover manufacturing techniques that are the first ones to enable the production of efficient THz signal transmission components over the full THz frequency range. The strategic market position of SWISSto12 can only be developed and sustained through a strong and continuous R&D effort, allowing it to stay in tune with the latest developments. This effort is currently distributed over different projects aiming at reducing production costs, increasing product performances, seeking new solutions for THz signal transmission, as well as developing new products in the domain of Terahertz transmission and probing. Through collaborations with various companies and research institutions around the world SWISSto12 interacts with the key stakeholders for the development of future THz systems and components. The company is currently increasing its team to support its diverse R&D projects. 

Tasks :
  • Design and Numerical characterization of the probe.
  • Cold Tests on Sub‐Components on a brand‐new THz lab at LPMN
  • Probe Assembly
  • Experimental Validation.
  • Gyrotron DNP experiments for benchmark and training with an existing saddle‐coil probe
  • Interface with industrial partners and research institutions for R&D projects and collaborations.

Profile required for this position:
  • A PhD in physics, electrical engineering or electronics covering research on applied electromagnetism, or demonstrated equivalent experience;
  • Proven experience in laboratory tests and instrumentation development at a scientific R&D level, preferably targeting industrial applications;
  • Proven ability to perform high‐level analytical calculations and simulations using scientific software applications like Comsol, Matlab, Mathematica or equivalent;
  • Experience with dedicated electromagnetic or thermo‐mechanical simulation software is considered an advantage; 
  • Experience with supporting software applications for equipment design or laboratory tests, e.g. SolidWorks, Labview etc. is considered an advantage;
  • Interested, inquiring and innovative approach towards cutting edge R&D in electromagnetism;
  • Autonomous and proactive working style.
  • Communicating effectively, excellent relational skills and ability to work in a team;
  • Languages: Fluent in English and possibly in French.
  • Ability to coordinate working groups with different professional and cultural backgrounds.

Contract :
EPFL/LPMN offers a  three (3) contract to be started asap. An application containing a CV, a motivation letter, two reference letters and a copy of your diplomas and grades can be sent by mail to: jean‐

Wednesday, January 15, 2014

Detecting substrates bound to the secondary multidrug efflux pump EmrE by DNP-enhanced solid-state NMR

Ong, Y.S., et al., Detecting substrates bound to the secondary multidrug efflux pump EmrE by DNP-enhanced solid-state NMR. J Am Chem Soc, 2013. 135(42): p. 15754-62.

Escherichia coli EmrE, a homodimeric multidrug antiporter, has been suggested to offer a convenient paradigm for secondary transporters due to its small size. It contains four transmembrane helices and forms a functional dimer. We have probed the specific binding of substrates TPP(+) and MTP(+) to EmrE reconstituted into 1,2-dimyristoyl-sn-glycero-3-phosphocholine liposomes by (31)P MAS NMR. Our NMR data show that both substrates occupy the same binding pocket but also indicate some degree of heterogeneity of the bound ligand population, reflecting the promiscuous nature of ligand binding by multidrug efflux pumps. Direct interaction between (13)C-labeled TPP(+) and key residues within the EmrE dimer has been probed by through-space (13)C-(13)C correlation spectroscopy. This was made possible by the use of solid-state NMR enhanced by dynamic nuclear polarization (DNP) through which a 19-fold signal enhancement was achieved. Our data provide clear evidence for the long assumed direct interaction between substrates such as TPP(+) and the essential residue E14 in transmembrane helix 1. Our work also demonstrates the power of DNP-enhanced solid-state NMR at low temperatures for the study for secondary transporters, which are highly challenging for conventional NMR detection.

Monday, January 13, 2014

A comparative study of 1H and 19F Overhauser DNP in fluorinated benzenes

Neudert, O., et al., A comparative study of 1H and 19F Overhauser DNP in fluorinated benzenes. Phys Chem Chem Phys, 2013. 15(47): p. 20717-26.

Hyperpolarization techniques, such as Overhauser dynamic nuclear polarization (DNP), can provide a dramatic increase in the signal obtained from nuclear magnetic resonance experiments and may therefore enable new applications where sensitivity is a limiting factor. In this contribution, studies of the (1)H and (19)F Overhauser dynamic nuclear polarization enhancements at 345 mT are presented for three different aromatic solvents with the TEMPO radical for a range of radical concentrations. Furthermore, nuclear magnetic relaxation dispersion measurements of the same solutions are analyzed, showing contributions from dipolar and scalar coupling modulated by translational diffusion and different coupling efficiency for different solvents and nuclei. Measurements of the electron paramagnetic resonance linewidth are included to support the analysis of the DNP saturation factor for varying radical concentration. The results of our study give an insight into the characteristics of nitroxide radicals as polarizing agents for (19)F Overhauser DNP of aromatic fluorinated solvents. Furthermore, we compare our results with the findings of the extensive research on Overhauser DNP that was conducted in the past for a large variety of other radicals.

Friday, January 10, 2014

Host-Guest Complexes as Water-Soluble High-Performance DNP Polarizing Agents

Mao, J., et al., Host-Guest Complexes as Water-Soluble High-Performance DNP Polarizing Agents. J Am Chem Soc, 2013. 135(51): p. 19275-81.

Dynamic nuclear polarization (DNP) enhances the sensitivity of solid-state NMR (SSNMR) spectroscopy by orders of magnitude and, therefore, opens possibilities for novel applications from biology to materials science. This multitude of opportunities implicates a need for high-performance polarizing agents, which integrate specific physical and chemical features tailored for various applications. Here, we demonstrate that for the biradical bTbK in complex with captisol (CAP), a beta-cyclodextrin derivative, host-guest assembling offers a new and easily accessible approach for the development of new polarizing agents. In contrast to bTbK, the CAP-bTbK complex is water-soluble and shows significantly improved DNP performance compared to the commonly used DNP agent TOTAPOL. Furthermore, NMR and EPR data reveal improved electron and nuclear spin relaxation properties for bTbK within the host molecule. The numerous possibilities to functionalize host molecules will permit designing novel radical complexes targeting diverse applications.

Wednesday, January 8, 2014

Measurements of short distances between trityl spin labels with CW EPR, DQC and PELDOR

This article does not describe any DNP-NMR experiments. However, in the light of biradicals as polarizing agents for DNP experiments it is still very interesting. Especially since trityl radicals have very narrow EPR lines and these biradicals could be more efficient to polarize low-gamma nuclei such as 13C, 29Si or 15N.

Kunjir, N.C., et al., Measurements of short distances between trityl spin labels with CW EPR, DQC and PELDOR. Phys Chem Chem Phys, 2013. 15(45): p. 19673-85.

Trityl based spin labels are emerging as a complement to nitroxides in nanometer distance measurements using EPR methods. The narrow spectral width of the trityl radicals prompts us to ask the question at which distance between these spin centers, the pseudo-secular part of the dipolar coupling and spin density delocalization have to be taken into account. For this, two trityl-trityl and one trityl-nitroxide model compounds were synthesized with well-defined interspin distances. Continuous wave (CW) EPR, double quantum coherence (DQC) and pulsed electron-electron double resonance (PELDOR) spectra were acquired from these compounds at commercial X-band frequencies. The data analysis shows that two of the compounds, with distances of up to 25 A, fall into the strong coupling regime and that precise distances can only be obtained if both the spin density delocalization and the pseudo-secular part of the dipolar coupling are included in the analysis.

Monday, January 6, 2014

Dynamic nuclear polarization using frequency modulation at 3.34T

Hovav, Y., et al., Dynamic nuclear polarization using frequency modulation at 3.34T. J Magn Reson, 2013. 238C(0): p. 94-105.

During dynamic nuclear polarization (DNP) experiments polarization is transferred from unpaired electrons to their neighboring nuclear spins, resulting in dramatic enhancement of the NMR signals. While in most cases this is achieved by continuous wave (cw) irradiation applied to samples in fixed external magnetic fields, here we show that DNP enhancement of static samples can improve by modulating the microwave (MW) frequency at a constant field of 3.34T. The efficiency of triangular shaped modulation is explored by monitoring the 1H signal enhancement in frozen solutions containing different TEMPOL radical concentrations at different temperatures. The optimal modulation parameters are examined experimentally and under the most favorable conditions a threefold enhancement is obtained with respect to constant frequency DNP in samples with low radical concentrations. The results are interpreted using numerical simulations on small spin systems. In particular, it is shown experimentally and explained theoretically that: (i) The optimal modulation frequency is higher than the electron spin-lattice relaxation rate. (ii) The optimal modulation amplitude must be smaller than the nuclear Larmor frequency and the EPR line-width, as expected. (iii) The MW frequencies corresponding to the enhancement maxima and minima are shifted away from one another when using frequency modulation, relative to the constant frequency experiments.

Friday, January 3, 2014

Solid-phase polarization matrixes for dynamic nuclear polarization from homogeneously distributed radicals in mesostructured hybrid silica materials

Gajan, D., et al., Solid-phase polarization matrixes for dynamic nuclear polarization from homogeneously distributed radicals in mesostructured hybrid silica materials. J Am Chem Soc, 2013. 135(41): p. 15459-66.

Mesoporous hybrid silica-organic materials containing homogeneously distributed stable mono- or dinitroxide radicals covalently bound to the silica surface were developed as polarization matrixes for solid-state dynamic nuclear polarization (DNP) NMR experiments. For TEMPO-containing materials impregnated with water or 1,1,2,2-tetrachloroethane, enhancement factors of up to 36 were obtained at approximately 100 K and 9.4 T without the need for a glass-forming additive. We show that the homogeneous radical distribution and the subtle balance between the concentration of radical in the material and the fraction of radicals at a sufficient inter-radical distance to promote the cross-effect are the main determinants for the DNP enhancements we obtain. The material, as well as an analogue containing the poorly soluble biradical bTUrea, is used as a polarizing matrix for DNP NMR experiments of solutions containing alanine and pyruvic acid. The analyte is separated from the polarization matrix by simple filtration.