Monday, December 14, 2009

J. Chem. Phys. 131, 224516 (2009); doi:10.1063/1.3266422

Spatial/spectral encoding of the spin interactions in ultrafast multidimensional NMR
Yoav Shrot and Lucio Frydman

Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy provides the means to extract diverse physical, chemical, and biological information at an atomic level. Conventional sampling schemes, however, may result in relatively long 2D experiments; this has stimulated the search for alternative, rapid acquisition schemes. Among the strategies that have been recently proposed for achieving this counts an “ultrafast” approach, relying on the spatial encoding of the indirect domain evolution to provide arbitrary spectra within a single scan. A common feature of all spatial encoding schemes hitherto described is their uniform encoding of a continuous bandwidth of indirect-domain frequencies, regardless of the chemical sites' spectral distribution within it. These very general conditions, however, are often associated with a number of tradeoffs and compromises in the spectral widths and resolutions that can be achieved for both the direct and indirect domains. This paper proposes a different strategy for single-scan acquisition of 2D spectra, which performs an optimal encoding by employing a priori information regarding the positions of NMR resonances along the indirect domain. We denote this as “spatial/spectral encoding”; the underlying principles of this new approach, together with experimental results based on uni- and multidimensional rf pulse schemes, are presented. ©2009
American Institute of Physics

J. Am. Chem. Soc., 2009, 131 (49), pp 17972–17979

NMR Structure in a Membrane Environment Reveals Putative Amyloidogenic Regions of the SEVI Precursor Peptide PAP248−286
Ravi P. R. Nanga†, Jeffrey R. Brender†‡, Subramanian Vivekanandan†‡, Nataliya Popovych†‡ and Ayyalusamy Ramamoorthy*†

Semen is the main vector for HIV transmission worldwide. Recently, a peptide fragment (PAP248−286) has been isolated from seminal fluid that dramatically enhances HIV infectivity by up to 4−5 orders of magnitude. PAP248−286 appears to enhance HIV infection by forming amyloid fibers known as SEVI, which are believed to enhance the attachment of the virus by bridging interactions between virion and host-cell membranes. We have solved the atomic-level resolution structure of the SEVI precursor PAP248−286 using NMR spectroscopy in SDS micelles, which serve as a model membrane system. PAP248−286, which does not disrupt membranes like most amyloid proteins, binds superficially to the surface of the micelle, in contrast to other membrane-disruptive amyloid peptides that generally penetrate into the core of the membrane. The structure of PAP248−286 is unlike most amyloid peptides in that PAP248−286 is mostly disordered when bound to the surface of the micelle, as opposed to the α-helical structures typically found of most amyloid proteins. The highly disordered nature of the SEVI peptide may explain the unique ability of SEVI amyloid fibers to enhance HIV infection as partially disordered amyloid fibers will have a greater capture radius for the virus than compact amyloid fibers. Two regions of nascent structure (an α-helix from V262−H270 and a dynamic α/310 helix from S279−L283) match the prediction of highly amyloidogenic sequences and may serve as nuclei for aggregation and amyloid fibril formation. The structure presented here can be used for the rational design of mutagenesis studies on SEVI amyloid formation and viral infection enhancement.

J. Am. Chem. Soc., 2009, 131 (49), pp 17908–17918

Quantitative Description of Backbone Conformational Sampling of Unfolded Proteins at Amino Acid Resolution from NMR Residual Dipolar Couplings
Gabrielle Nodet†, Loc Salmon†, Valry Ozenne†, Sebastian Meier‡, Malene Ringkjøbing Jensen† and Martin Blackledge*†

An atomic resolution characterization of the structural properties of unfolded proteins that explicitly invokes the highly dynamic nature of the unfolded state will be extremely important for the development of a quantitative understanding of the thermodynamic basis of protein folding and stability. Here we develop a novel approach using residual dipolar couplings (RDCs) from unfolded proteins to determine conformational behavior on an amino acid specific basis. Conformational sampling is described in terms of ensembles of structures selected from a large pool of conformers. We test this approach, using extensive simulation, to determine how well the fitting of RDCs to reduced conformational ensembles containing few copies of the molecule can correctly reproduce the backbone conformational behavior of the protein. Having established approaches that allow accurate mapping of backbone dihedral angle conformational space from RDCs, we apply these methods to obtain an amino acid specific description of ubiquitin denatured in 8 M urea at pH 2.5. Cross-validation of data not employed in the fit verifies that an ensemble size of 200 structures is appropriate to characterize the highly fluctuating backbone. This approach allows us to identify local conformational sampling properties of urea-unfolded ubiquitin, which shows that the backbone sampling of certain types of charged or polar amino acids, in particular threonine, glutamic acid, and arginine, is affected more strongly by urea binding than amino acids with hydrophobic side chains. In general, the approach presented here establishes robust procedures for the study of all denatured and intrinsically disordered states.

J. Am. Chem. Soc., 2009, 131 (49), pp 17756–17758

Widening the View on Dispersant−Pigment Interactions in Colloidal Dispersions with Saturation Transfer Difference NMR Spectroscopy
Agnieszka Szczygiel†, Leo Timmermans‡, Bernd Fritzinger† and Jos C. Martins*†

The application of Saturation Transfer Difference (STD) NMR spectroscopy for the characterization of dispersant particle interactions is introduced. STD NMR has hitherto been applied, with great success, to the characterization of ligand−protein interactions and is currently a standard tool in biomolecular NMR spectroscopy. Nevertheless, the STD NMR technique has so far not yet crossed the boundaries of the biomolecular field. Here, we demonstrate that in spite of clear differences between a protein binding site and the surface of a pigment nanoparticle, the latter can also be subjected to STD NMR analysis, allowing us to detect (screen for) binding ligands, discriminate ligand from nonligand, and obtain information on the binding epitope. The approach should be generally applicable as long as the nanoparticle is comprised of a dense network of hydrogens, implicating almost all organic molecular nanocrystals. Thus it provides a novel investigative tool for the study of dispersions that is highly complementary to existing ones.

Friday, December 11, 2009

J. Am. Chem. Soc., 2009, 131 (48), pp 17576–17582

Ternary Protein Complex of Ferredoxin, Ferredoxin:Thioredoxin Reductase, and Thioredoxin Studied by Paramagnetic NMR Spectroscopy
Xingfu Xu†, Peter Schrmann‡, Jung-Sung Chung§, Mathias A. S. Hass†, Sung-Kun Kim§, Masakazu Hirasawa§, Jatindra N. Tripathy, David B. Knaff§ and Marcellus Ubbink*†

In oxygenic photosynthetic cells, carbon metabolism is regulated by a light-dependent redox signaling pathway through which the light signal is transmitted in the form of electrons via a redox chain comprising ferredoxin (Fd), ferredoxin:thioredoxin reductase (FTR), and thioredoxin (Trx). Trx affects the activity of a variety of enzymes via dithiol oxidation and reduction reactions. FTR reduces an intramolecular disulfide bridge of Trx, and Trx reduction involves a transient cross-link with FTR. NMR spectroscopy was used to investigate the interaction of Fd, FTR, and an m-type Trx. NMR titration experiments indicate that FTR uses distinct sites to bind Fd and Trx simultaneously to form a noncovalent ternary complex. The orientation of Trx-m relative to FTR was determined from the intermolecular paramagnetic broadening caused by the [4Fe-4S] cluster of FTR. Two models of the noncovalent binary complex of FTR/Trx-m based on the paramagnetic distance restraints were obtained. The models suggest that either a modest or major rotational movement of Trx must take place when the noncovalent binary complex proceeds to the covalent complex. This study demonstrates the complementarity of paramagnetic NMR and X-ray diffraction of crystals in the elucidation of dynamics in a transient protein complex.

J. Am. Chem. Soc., 2009, 131 (47), pp 17064–17065

Time-Resolved Dehydration-Induced Structural Changes in an Intact Bovine Cortical Bone Revealed by Solid-State NMR Spectroscopy
Peizhi Zhu†, Jiadi Xu†‡, Nadder Sahar§, Michael D. Morris*†§, David H. Kohn§ and Ayyalusamy Ramamoorthy*†‡

Understanding the structure and structural changes of bone, a highly heterogeneous material with a complex hierarchical architecture, continues to be a significant challenge even for high-resolution solid-state NMR spectroscopy. While it is known that dehydration affects mechanical properties of bone by decreasing its strength and toughness, the underlying structural mechanism at the atomic level is unknown. Solid-state NMR spectroscopy, controlled dehydration, and H/D exchange were used for the first time to reveal the structural changes of an intact piece of bovine cortical bone. 1H spectra were used to monitor the dehydration of the bone inside the rotor, and high-resolution 13C chemical shift spectra obtained under magic-angle spinning were used evaluate the dehydration-induced conformational changes in the bone. The experiments revealed the slow denaturation of collagen due to dehydration while the trans-Xaa-Pro conformation in collagen remained unchanged. Our results suggest that glycosaminoglycans in the collagen fiber and mineral interface may chelate with a Ca2+ ion present on the surface of the mineral through sulfate or carboxylate groups. These results provide insights into the role of water molecules in the bone structure and shed light on the relationship between the structure and mechanics of bone.

J. Am. Chem. Soc., 2009, 131 (47), pp 17054–17055

Double-Nucleus Enhanced Recoupling for Efficient 13C MAS NMR Correlation Spectroscopy of Perdeuterated Proteins
Umit Akbey, Hartmut Oschkinat and Barth-Jan van Rossum*

The use of both proton and deuterium dipolar coupling networks to obtain efficient 13C magic-angle-spinning NMR correlation spectroscopy is introduced. This new strategy aims to improve the efficiency of 13C spin diffusion in perdeuterated proteins. The method is called double-nucleus enhanced recoupling (DONER), and it provides significantly improved transfer efficiency for carbon spin diffusion at low proton density. The Cα cross-peak intensity in the DONER experiment is 3 and 5 times stronger than those in conventional radio-frequency-assisted diffusion (RAD) and proton-driven spin diffusion (PDSD) experiments, respectively. Remarkably, the full cross-peak pattern for the aliphatic region of an extensively perdeuterated SH3 protein sample can be obtained using the DONER approach with direct 13C excitation.

Wednesday, December 09, 2009

J. Am. Chem. Soc., 2009, 131 (44), pp 16257–16265

Selective Characterization of Microsecond Motions in Proteins by NMR Relaxation
D. Flemming Hansen*†, Haniqiao Feng‡, Zheng Zhou‡, Yawen Bai‡ and Lewis E. Kay*†

The three-dimensional structures of macromolecules fluctuate over a wide range of time-scales. Separating the individual dynamic processes according to frequency is of importance in relating protein motions to biological function and stability. We present here a general NMR method for the specific characterization of microsecond motions at backbone positions in proteins even in the presence of other dynamics such as large-amplitude nanosecond motions and millisecond chemical exchange processes. The method is based on measurement of relaxation rates of four bilinear coherences and relies on the ability of strong continuous radio frequency fields to quench millisecond chemical exchange. The utility of the methodology is demonstrated and validated through two specific examples focusing on the thermo-stable proteins, ubiquitin and protein L, where it is found that small-amplitude microsecond dynamics are more pervasive than previously thought. Specifically, these motions are localized to α helices, loop regions, and regions along the rim of β sheets in both of the proteins examined. A third example focuses on a 28 kDa ternary complex of the chaperone Chz1 and the histones H2A.Z/H2B, where it is established that pervasive microsecond motions are localized to a region of the chaperone that is important for stabilizing the complex. It is further shown that these motions can be well separated from extensive millisecond dynamics that are also present and that derive from exchange of Chz1 between bound and free states. The methodology is straightforward to implement, and data recorded at only a single static magnetic field are required.

J. Am. Chem. Soc., 2009, 131 (44), pp 16014–16015

Proton NMR of 15N-Choline Metabolites Enhanced by Dynamic Nuclear Polarization
Riddhiman Sarkar†, Arnaud Comment‡§, Paul R. Vasos†, Sami Jannin, Rolf Gruetter‡§, Geoffrey Bodenhausen†, Hlne Hall, Deniz Kirik# and Vladimir P. Denisov#

Chemical shifts of protons can report on metabolic transformations such as the conversion of choline to phosphocholine. To follow such processes in vivo, magnetization can be enhanced by dynamic nuclear polarization (DNP). We have hyperpolarized in this manner nitrogen-15 spins in 15N-labeled choline up to 3.3% by irradiating the 94 GHz electron spin resonance of admixed TEMPO nitroxide radicals in a magnetic field of 3.35 T during ca. 3 h at 1.2 K. The sample was subsequently transferred to a high-resolution magnet, and the enhanced polarization was converted from 15N to methyl- and methylene protons, using the small 2,3J(1H,15N) couplings in choline. The room-temperature lifetime of nitrogen polarization in choline, T1(15N) ≈ 200 s, could be considerably increased by partial deuteration of the molecule. This procedure enables studies of choline metabolites in vitro and in vivo using DNP-enhanced proton NMR.

J. Am. Chem. Soc., 2009, 131 (44), pp 15994–15995

Deconvolution of Complex NMR Spectra in Small Molecules by Multi Frequency Homonuclear Decoupling (MDEC)
Ana Paula D. M. Espindola†, Ronald Crouch‡, John R. DeBergh†, Joseph M. Ready† and John B. MacMillan*†

A new technique to deconvolute complex 1H NMR spectra of small molecules has been developed that utilizes shape selective pulses to simultaneously decouple multiple protons. A limitation in the assignment of the relative configuration of small molecules is the ability to accurately obtain coupling constants. Other methods such as the E.COSY and the 2D J-resolved are available to obtain complicated coupling constants; the multiple homonuclear decoupling method (MDEC) described is a rapid and simple technique. Three examples of increasing spectral complexity, menthol, cholesteryl acetate and a C16 fatty acid, demonstrate the utility of the technique. Increasing the experimental utility, the single pulse MDEC experiment can be incorporated in other 1D experiments, such as a 1D-TOCSY to solve specific problems.

J. Am. Chem. Soc., 2009, 131 (44), pp 15982–15983

Monitoring of Biological One-Electron Reduction by 19F NMR Using Hypoxia Selective Activation of an 19F-Labeled Indolequinone Derivative
Kazuhito Tanabe*†, Hiroshi Harada‡§, Michiko Narazaki, Kazuo Tanaka, Kenichi Inafuku, Hirokazu Komatsu†, Takeo Ito†, Hisatsugu Yamada†§, Yoshiki Chujo, Tetsuya Matsuda, Masahiro Hiraoka‡§ and Sei-ichi Nishimoto*†

Biological reduction of fluorine-labeled indolequinone derivative (IQ-F) was characterized by 19F NMR for quantitative molecular understanding. The chemical shift change in 19F NMR allowed monitoring of the enzymatic reduction of IQ-F. Upon hypoxic treatment of IQ-F with NADPH:cytochrome P450 reductase, IQ-F was activated via catalytic one-electron reduction to release nonafluoro-tert-butyl alcohol (F-OH), while the formation of F-OH was significantly suppressed under aerobic conditions. Similar hypoxia-selective reduction of IQ-F occurred within A549 cells, which expresses NADPH:cytochrome P450 reductase. The kinetic analysis was also performed to propose a reaction mechanism. The molecular oxygen slightly prevents the binding of IQ-F to reductase, while the rate of net reaction was decreased due to oxidation of a semiquinone anion radical intermediate generated by one-electron reduction of IQ-F. The disappearance of IQ-F and appearance of F-OH were imaged by 19F fast spin echo, thus visualizing the hypoxia-selective reduction of IQ-F by means of MR imaging.

J. Am. Chem. Soc., 2009, 131 (44), pp 15970–15971

Higher Sensitivity through Selective 13C Excitation in Solid-State NMR Spectroscopy
Jakob J. Lopez*, Christoph Kaiser, Sam Asami and Clemens Glaubitz*

A notable drawback of NMR spectroscopy is its inherently low sensitivity: 95% of the measuring time consists solely of idle delays during which nuclei regain their Boltzmann equilibrium. Here, a strategy for solid-state 13C NMR experiments is presented that allows the user to acquire spectra in time periods that are notably shorter than previously necessary. Experiments that are band-selective in nature may utilize the cooling potential of unperturbed nuclei to lower the spin temperature of their excited neighbors. As we demonstrate, it becomes possible to replace the recycle delay in a series of scans by a time period during which proton-driven spin diffusion causes relaxation enhancement by a lower spin temperature of adjacent spins (RELOAD). Typically, a duration of 200 ms suffices for this step, and for 1D 13C NMR experiments, it is shown that the omission of recycle delays (typically of 2 s length) reduces the measuring time substantially. RELOAD is applied to 2D homonuclear 13C NMR experiments, and it is demonstrated that for experiments in which correlations between 13C backbone atoms are detected, the measurement time is reduced by a factor of 10 through a time-saving combination of a smaller number of increments in the indirect dimension and RELOAD.

J. Am. Chem. Soc., 2009, 131 (44), pp 15968–15969

Large Protein Complexes with Extreme Rotational Correlation Times Investigated in Solution by Magic-Angle-Spinning NMR Spectroscopy
Andi Mainz†, Stefan Jehle†, Barth J. van Rossum†, Hartmut Oschkinat† and Bernd Reif*†‡

We show that large protein complexes can be investigated in solution using magic-angle-spinning (MAS) NMR spectroscopy without the need for sample crystallization or precipitation. In order to efficiently average anisotropic interactions with MAS, the rotational diffusion of the molecule has to be suppressed. This can be readily achieved by lowering the sample temperature and by adding glycerol to the protein solution. The approach is demonstrated using the human small heat shock protein (sHSP) αB-Crystallin, which forms oligomeric assemblies of 600 kDa. We suggest this scheme as an approach for overcoming size limitations imposed by overall tumbling in solution-state NMR investigations of large protein complexes.

Wednesday, December 02, 2009

J. Am. Chem. Soc., 2009, 131 (43), pp 15761–15768

Evaluation of Parameters Critical for Observing Nucleic Acids Inside Living Xenopus laevis Oocytes by In-Cell NMR Spectroscopy
Robert Hnsel†‡, Silvie Foldynov-Trantrkov§, Frank Lhr†‡, Janina Buck‡, Eva Bongartz†, Ernst Bamberg†, Harald Schwalbe‡, Volker Dtsch*†‡ and Luk Trantrek*§#

In-cell NMR spectroscopy of proteins in different cellular environments is a well-established technique that, however, has not been applied to nucleic acids so far. Here, we show that isotopically labeled DNA and RNA can be observed inside the eukaryotic environment of Xenopus laevis oocytes by in-cell NMR spectroscopy. One limiting factor for the observation of nucleic acids in Xenopus oocytes is their reduced stability. We demonstrate that chemical modification of DNA and RNA can protect them from degradation and can significantly enhance their lifetime. Finally, we show that the imino region of the NMR spectrum is devoid of any oocyte background signals enabling the detection even of isotopically nonlabeled molecules.

J. Am. Chem. Soc., 2009, 131 (43), pp 15596–15597

Chemical Labeling Strategy with (R)- and (S)-Trifluoromethylalanine for Solid State 19F NMR Analysis of Peptaibols in Membranes
Daniel Maisch†, Parvesh Wadhwani‡, Sergii Afonin‡, Christoph Bttcher§, Beate Koksch§ and Anne S. Ulrich*†‡

Substitution of a single Aib-residue in a peptaibol with (R)- and (S)-trifluoromethylalanine yields two local orientational constraints θ by solid state 19F NMR. The structure of the membrane-perturbing antibiotic alamethicin in DMPC bilayers was analyzed in terms of two angles τ and ρ from six such constraints, showing that the N-terminus (up to a kink at Pro14) is folded as an α-helix, tilted away from the membrane normal by 8°, and assembled as an oligomer. The new 19F NMR label CF3-Ala has thus been demonstrated to be highly sensitive, virtually unperturbing, and ideally suited to characterize peptaibols in membranes.

Monday, October 26, 2009

Cryst. Growth Des., Article ASAP

Solid-State NMR, X-ray Diffraction, and Thermoanalytical Studies Towards the Identification, Isolation, and Structural Characterization of Polymorphs in Natural Bile Acids
Nonappa, Manu Lahtinen, Satu Ikonen, Erkki Kolehmainen* and Reijo Kauppinen

AbstractCombined solid-state NMR, powder, and single crystal X-ray diffraction, as well as thermoanalytical studies were performed towards the identification, isolation, and structural characterization of polymorphs present in commercial samples of six natural bile acids. The 13C{1H} cross-polarization (CP) magic angle spinning (MAS) NMR technique was used as a primary tool to identify the mixture of polymorphs present in the natural bile acids obtained from commercial sources. A detailed study including selective crystallization of each polymorphic form of the bile acids in different solvents and mixture of solvents was carried out, and their spectral patterns were compared with the mode of packing and number of molecules present in an asymmetric unit. These studies were strongly supported by other complementary techniques such as powder/single crystal X-ray diffraction and differential scanning calorimetric (DSC) experiments. While a few single crystal X-ray structures are solved in order to confirm the correct polymorphic form, most of the powder X-ray diffraction data were compared with the simulated X-ray patterns obtained from previously reported single crystal structures. Detailed analyses using multiple experimental techniques provided useful insights towards the mode of packing which is responsible for unique spectral patterns in the solid state.

Friday, October 23, 2009

J. Am. Chem. Soc., Article ASAP

Chemical Labeling Strategy with (R)- and (S)-Trifluoromethylalanine for Solid State 19F NMR Analysis of Peptaibols in Membranes
Daniel Maisch†, Parvesh Wadhwani‡, Sergii Afonin‡, Christoph Bttcher§, Beate Koksch§ and Anne S. Ulrich*†‡

Substitution of a single Aib-residue in a peptaibol with (R)- and (S)-trifluoromethylalanine yields two local orientational constraints θ by solid state 19F NMR. The structure of the membrane-perturbing antibiotic alamethicin in DMPC bilayers was analyzed in terms of two angles τ and ρ from six such constraints, showing that the N-terminus (up to a kink at Pro14) is folded as an α-helix, tilted away from the membrane normal by 8°, and assembled as an oligomer. The new 19F NMR label CF3-Ala has thus been demonstrated to be highly sensitive, virtually unperturbing, and ideally suited to characterize peptaibols in membranes.

J. Am. Chem. Soc., Article ASAP

Higher Sensitivity through Selective 13C Excitation in Solid-State NMR Spectroscopy
Jakob J. Lopez*, Christoph Kaiser, Sam Asami and Clemens Glaubitz*

A notable drawback of NMR spectroscopy is its inherently low sensitivity: 95% of the measuring time consists solely of idle delays during which nuclei regain their Boltzmann equilibrium. Here, a strategy for solid-state 13C NMR experiments is presented that allows the user to acquire spectra in time periods that are notably shorter than previously necessary. Experiments that are band-selective in nature may utilize the cooling potential of unperturbed nuclei to lower the spin temperature of their excited neighbors. As we demonstrate, it becomes possible to replace the recycle delay in a series of scans by a time period during which proton-driven spin diffusion causes relaxation enhancement by a lower spin temperature of adjacent spins (RELOAD). Typically, a duration of 200 ms suffices for this step, and for 1D 13C NMR experiments, it is shown that the omission of recycle delays (typically of 2 s length) reduces the measuring time substantially. RELOAD is applied to 2D homonuclear 13C NMR experiments, and it is demonstrated that for experiments in which correlations between 13C backbone atoms are detected, the measurement time is reduced by a factor of 10 through a time-saving combination of a smaller number of increments in the indirect dimension and RELOAD.

J. Am. Chem. Soc., Article ASAP

Deuterium Spin Probes of Backbone Order in Proteins: 2H NMR Relaxation Study of Deuterated Carbon α Sites
Devon Sheppard‡, Da-Wei Li§, Rafael Brschweiler§ and Vitali Tugarinov*‡

2H spin relaxation NMR experiments to study the dynamics of deuterated backbone α-positions, Dα, are developed. To date, solution-state 2H relaxation measurements in proteins have been confined to side-chain deuterons—primarily 13CH2D or 13CHD2 methyl groups. It is shown that quantification of 2H relaxation rates at Dα backbone positions and the derivation of associated order parameters of Cα−Dα bond vector motions in small [U-15N,13C,2H]-labeled proteins is feasible with reasonable accuracy. The utility of the developed methodology is demonstrated on a pair of proteins—ubiquitin (8.5 kDa) at 10, 27, and 40 °C, and a variant of GB1 (6.5 kDa) at 22 °C. In both proteins, the Dα-derived parameters of the global rotational diffusion tensor are in good agreement with those obtained from 15N relaxation rates. Semiquantitative solution-state NMR measurements yield an average value of the quadrupolar coupling constant, QCC, for Dα sites in proteins equal to 174 kHz. Using a uniform value of QCC for all Dα sites, we show that Cα−Dα bond vectors are motionally distinct from the backbone amide N−H bond vectors, with 2H-derived squared order parameters of Cα−Dα bond vector motions, S2CαDα, on average slightly higher than their N−H amides counterparts, S2NH. For ubiquitin, the 2H-derived backbone mobility compares well with that found in a 1-μs molecular dynamics simulation.

J. Am. Chem. Soc., 2009, 131 (42), pp 15086–15087

1H and 13C Dynamic Nuclear Polarization in Aqueous Solution with a Two-Field (0.35 T/14 T) Shuttle DNP Spectrometer
Marcel Reese†, Maria-Teresa Trke†, Igor Tkach†, Giacomo Parigi‡, Claudio Luchinat‡, Thorsten Marquardsen§, Andreas Tavernier§, Peter Hfer§, Frank Engelke§, Christian Griesinger*† and Marina Bennati*†

Dynamic nuclear polarization (DNP) permits increasing the NMR signal of nuclei by pumping the electronic spin transitions of paramagnetic centers nearby. This method is emerging as a powerful tool to increase the inherent sensitivity of NMR in structural biology aiming at detection of macromolecules. In aqueous solution, additional technical issues associated with the penetration of microwaves in water and heating effects aggravate the performance of the experiment. To examine the feasibility of low-field (9.7 GHz/0.35 T) DNP in high resolution NMR, we have constructed the prototype of a two-field shuttle DNP spectrometer that polarizes nuclei at 9.7 GHz/0.35 T and detects the NMR spectrum at 14 T. We report our first 1H and 13C DNP enhancements with this spectrometer. Effective enhancements up to 15 were observed for small molecules at 1H 600 MHz/14 T as compared to the Boltzmann signal. The results provide a proof of principle for the feasibility of a shuttle DNP experiment and open up perspectives for the application potential of this method in solution NMR.

J. Am. Chem. Soc., 2009, 131 (36), pp 12949–12959

Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine
Anna Vulpetti*§, Ulrich Hommel§, Gregory Landrum§, Richard Lewis§ and Claudio Dalvit*§#

A novel strategy for the design of a fluorinated fragment library that takes into account the local environment of fluorine is described. The procedure, based on a fluorine fingerprints descriptor, and the criteria used in the design, selection, and construction of the library are presented. The library, named LEF (Local Environment of Fluorine), combined with 19F NMR ligand-based screening experiments represents an efficient and sensitive approach for the initial fragment identification within a fragment-based drug discovery project and for probing the presence of fluorophilic protein environments. Proper setup of the method, according to described theoretical simulations, allows the detection of very weak-affinity ligands and the detection of multiple ligands present within the same tested mixture, thus capturing all the potential fragments interacting with the receptor. These NMR hits are then used in the FAXS experiments for the fragment optimization process and for the follow-up screening aimed at identifying other chemical scaffolds relevant for the binding to the receptor

Thursday, October 22, 2009

Cryst. Growth Des., 2009, 9 (10), pp 4281–4288

Effects of Crystal Growth and Polymorphism of Triacylglycerols on NMR Relaxation Parameters. 2. Study of a Tricaprin−Tristearin Mixture
Matthieu Adam-Berret†‡§, Alain Riaublanc‡ and Franois Mariette*†§

Being able to determine the physical properties of fats such as polymorphism and crystal size is very important for the food industry. After a relationship was observed between spin−lattice relaxation time and crystal size in a solid−liquid mixture of triacylglycerols, the effects of polymorphism and crystal size were investigated by low-field NMR relaxation and powder X-ray diffraction on three binary mixtures of tricaprin and tristearin in the solid state. Second moment (M2) was proven to be only sensitive to polymorphism. Its measurements permitted the quantification of polymorphic forms in a binary mixture, with a model based on M2 of the pure components. As for the spin−lattice relaxation time (T1), it was proven to be only sensitive to crystal size and not to polymorphism. Quantification was not possible with T1 measurements, but information on the pattern of the crystal thickness distribution was obtained using the maximization entropy method algorithm. The determination of polymorphism was thus possible because of the difference in size between the α and β triacylglycerol crystals. Finally, a phase diagram mainly based on NMR data was constructed for the tricaprin/tristearin system.

Cryst. Growth Des., 2009, 9 (10), pp 4273–4280

Effects of Crystal Growth and Polymorphism of Triacylglycerols on NMR Relaxation Parameters. 1. Evidence of a Relationship between Crystal Size and Spin−Lattice Relaxation Time
Matthieu Adam-Berret†‡§, Alain Riaublanc‡, Corinne Rondeau-Mouro‡ and Franois Mariette*‡§

Fat crystal networks confer their physical properties on fat-containing products. They are characterized by the solid fat content (SFC) and the design of the crystals, that is, their polymorphism and their size. Different techniques such as NMR, differential scanning calorimetry, and X-ray diffraction (XRD) are used to determine these parameters. Low-field NMR, the reference method for evaluation of SFC, has been proven to allow the determination of polymorphism through spin−lattice relaxation time (T1) and second moment (M2) measurements. However, this technique could provide more information on the system. On the basis of the effects of supercooling on the NMR parameters, the first evidence of a possible relationship between the size of the crystals and T1 was demonstrated. The effects of a liquid phase on the fat crystal network were investigated with liquid tricaprin and solid tristearin. It was demonstrated that the two triacylglycerols can cocrystallize, and that the liquid phase modified the polymorphic behavior of tristearin. The evolution of T1 over time could be related to the Ostwald ripening phenomenon. In view of this evidence, it was concluded that there was a relationship between T1 and the size of the crystals in the fat crystal network.

J. Am. Chem. Soc., 2009, 131 (39), pp 13992–13999

Low Temperature 65Cu NMR Spectroscopy of the Cu+ Site in Azurin
Andrew S. Lipton†, Robert W. Heck†, Wibe A. de Jong†, Amy R. Gao†, Xiongjian Wu‡, Adrienne Roehrich‡, Gerard S. Harbison*‡ and Paul D. Ellis*†

65Cu central-transition NMR spectroscopy of the blue copper protein azurin in the reduced Cu(I) state, conducted at 18.8 T and 10 K, gave a strongly second order quadrupole perturbed spectrum, which yielded a 65Cu quadrupole coupling constant of ±71.2 ± 1 MHz, corresponding to an electric field gradient of ±1.49 atomic units at the copper site, and an asymmetry parameter of approximately 0.2. Quantum chemical calculations employing second order Møller−Plesset perturbation theory and large basis sets successfully reproduced these experimental results. Sensitivity and relaxation times were quite favorable, suggesting that NMR may be a useful probe of the electronic state of copper sites in proteins.

J. Am. Chem. Soc., 2009, 131 (38), pp 13722–13727

Enhanced In situ Continuous-Flow MAS NMR for Reaction Kinetics in the Nanocages
Shutao Xu†‡, Weiping Zhang*†, Xianchun Liu†, Xiuwen Han† and Xinhe Bao*†

A new approach of in situ continuous-flow laser-hyperpolarized 129Xe MAS NMR together with 13C MAS NMR is designed and applied successfully to study the adsorption and reaction kinetics in the nanospace. Methanol conversion in CHA nanocages has been investigated in detail for proof of principle demonstrating the prospect of in situ NMR of reaction kinetics. Our findings well elucidates that the reaction intermediate can be identified by 13C MAS NMR spectroscopy, meanwhile the kinetic and dynamic processes of methanol adsorption and reaction in CHA nanocages can be monitored by one- and two-dimensional hyperpolarized 129Xe MAS NMR spectroscopy under the continuous-flow condition close to the real heterogeneous catalysis. The kinetic curves and apparent activation energy of the nanocages involving the active site are obtained quantitatively. The advantages of hyperpolarized 129Xe with much higher sensitivity and shorter acquisition time allow the kinetics to be probed in a confined geometry under real working conditions.

J. Am. Chem. Soc., 2009, 131 (38), pp 13703–13708

Probing Surface Accessibility of Proteins Using Paramagnetic Relaxation in Solid-State NMR Spectroscopy
Rasmus Linser†, Uwe Fink† and Bernd Reif*†‡

Paramagnetic Relaxation Enhancement (PRE) can be used to accelerate NMR data acquisition by reducing the longitudinal proton relaxation time T1 in the solid state. We show that the presence of paramagnetic compounds in the bulk solvent induces a site-specific relaxation in addition to local dynamics, which is dependent on the surface accessibility of the respective amide proton in the protein. Differentiation between paramagnetic relaxation and dynamics was achieved by a comparison of 1H T1 times obtained from microcrystalline protein samples prepared with different concentrations of the CuII(edta) chelate. We find that relaxation can in addition be mediated by hydroxyl groups, which transfer relaxation by their ability to exchange with the quickly relaxing bulk solvent. Furthermore, relaxation seems to be transferred by water molecules which diffuse into the protein structure and yield an efficient difference PRE in flexible regions of the protein. The experiments are demonstrated using a perdeuterated sample of the α-spectrin SH3 domain, which was microcrystallized from a buffer containing 90% D2O. Deuteration is a prerequisite to avoid spin diffusion which would otherwise compromise site specific resolution.

J. Am. Chem. Soc., 2009, 131 (38), pp 13690–13702

Dynamics of Reassembled Thioredoxin Studied by Magic Angle Spinning NMR: Snapshots from Different Time Scales
Jun Yang†§, Maria Luisa Tasayco‡ and Tatyana Polenova†

Solid-state NMR spectroscopy can be used to probe internal protein dynamics in the absence of the overall molecular tumbling. In this study, we report 15N backbone dynamics in differentially enriched 1−73(U-13C,15N)/74−108(U-15N) reassembled thioredoxin on multiple time scales using a series of 2D and 3D MAS NMR experiments probing the backbone amide 15N longitudinal relaxation, 1H−15N dipolar order parameters, 15N chemical shift anisotropy (CSA), and signal intensities in the temperature-dependent and 1H T2′-filtered NCA experiments. The spin-lattice relaxation rates R1 (R1 = 1/T1) were observed in the range from 0.012 to 0.64 s−1, indicating large site-to-site variations in dynamics on pico- to nanosecond time scales. The 1H−15N dipolar order parameters, S, and 15N CSA anisotropies, δσ, reveal the backbone mobilities in reassembled thioredoxin, as reflected in the average S = 0.89 ± 0.06 and δσ = 92.3 ± 5.2 ppm, respectively. From the aggregate of experimental data from different dynamics methods, some degree of correlation between the motions on the different time scales has been suggested. Analysis of the dynamics parameters derived from these solid-state NMR experiments indicates higher mobilities for the residues constituting irregular secondary structure elements than for those located in the α-helices and β-sheets, with no apparent systematic differences in dynamics between the α-helical and β-sheet residues. Remarkably, the dipolar order parameters derived from the solid-state NMR measurements and the corresponding solution NMR generalized order parameters display similar qualitative trends as a function of the residue number. The comparison of the solid-state dynamics parameters to the crystallographic B-factors has identified the contribution of static disorder to the B-factors. The combination of longitudinal relaxation, dipolar order parameter, and CSA line shape analyses employed in this study provides snapshots of dynamics and a new insight on the correlation of these motions on multiple time scales.

J. Am. Chem. Soc., 2009, 131 (38), pp 13651–13658

Probing the Dynamics of a Protein Hydrophobic Core by Deuteron Solid-State Nuclear Magnetic Resonance Spectroscopy
Liliya Vugmeyster*†, Dmitry Ostrovsky†, Joseph J. Ford‡, Sarah D. Burton‡, Andrew S. Lipton‡, Gina L. Hoatson§ and Robert L. Vold§

With the goal of investigating dynamical features of hydrophobic cores of proteins over a wide range of temperatures, the chicken villin headpiece subdomain protein (HP36) was labeled at a “single” site corresponding to any one of the two CδD3 groups of leucine-69, which is located in a key position of the core. The main techniques employed are deuteron NMR quadrupolar echo line shape analysis, and T1Z (Zeeman) and T1Q (quadrupolar order) relaxation experiments performed at 11.7 and 17.6 T over the temperature range of 112 to 298 K. The experimental data are compared with computer simulations. The deuteron line shapes give an excellent fit to a three-mode motional model that consists of (a) fast three-site rotational jumps about the pseudo C3 methyl spinning axis, (b) slower reorientation of the spinning axis, described by diffusion along a restricted arc, and (c) large angle jumps between traces of rotameric conformers. Relaxation behavior is described by a phenomenological distribution of activation energies for three-site hops at high temperatures that collapses to a single, distinctly smaller value for lower temperatures.

Chem. Mater., 2009, 21 (18), pp 4127–4134

Insights into Oxygen Exchange Between Gaseous O2 and Supported Vanadium Oxide Catalysts via 17O NMR
Christopher A. Klug*†‡, Scott Kroeker§, Pedro M. Aguiar§, Min Zhou†, Donald F. Stec† and Israel E. Wachs#

Vanadium oxide reference compounds, KVO3 and V2O5, and supported vanadium oxide catalysts (Al2O3, TiO2, and SiO2) were investigated using magic angle sample spinning 17O NMR. All samples were 17O-enriched using gas−solid exchange. Extraction of chemical shift and quadrupolar coupling information for the model compounds KVO3 and V2O5 was performed via the simulation of MAS spectra obtained in one-pulse experiments and the observations were consistent with their known bulk structures. For the supported vanadia catalysts, it was found that the oxygen exchange process is dominated by 17O signal from the catalyst oxide supports. Spectra obtained via rotor-synchronized spin echoes revealed additional wide lines for Al2O3 and TiO2 supported vanadia catalysts that arise from 17O in the surface vanadia species of the catalysts. Additional 17O−51V TRAPDOR (TRAnsfer of Populations in DOuble Resonance) experiments support this assignment. The wide lines suggest that the local environments of the 17O nuclei associated with the dehydrated surface vanadia species are extremely heterogeneous and fall in the range of oxygen in singly (V═O) and/or doubly coordinated environments (V−O−V or V−O−Support). The relatively small total amount of 17O associated with the surface vanadia species contrasts with oxygen exchange models which commonly assume only the surface vanadium oxide layer is involved. These results demonstrate that the isotopic exchange of molecular O2 with supported metal oxide catalysts, especially supported vanadia catalysts, is a much more complex process than originally perceived.

J. Am. Chem. Soc., 2009, 131 (37), pp 13508–13515

Crystal Structure of Ammonia Monohydrate Phase II
A. Dominic Fortes*†‡, Emmanuelle Suard§, Marie-Hlne Leme-Cailleau§, Christopher J. Pickard and Richard J. Needs

We have determined the crystal structure of ammonia monohydrate phase II (AMH II) employing a combination of ab initio computational structure prediction and structure solution from neutron powder diffraction data using direct space methods. Neutron powder diffraction data were collected from perdeuterated AMH II using the D2B high-resolution diffractometer at the Institut Laue-Langevin. AMH II crystallizes in space-group Pbca with 16 formula units in a unit-cell of dimensions a = 18.8285(4) Å, b = 6.9415(2) Å, c = 6.8449(2) Å, and V = 894.61(3) Å3 [ρcalcdeuterated = 1187.56(4) kg m−3] at 502 MPa, 180 K. The structure is characterized by sheets of tessellated pentagons formed by orientationally ordered O−D···O, O−D···N, and N−D···O hydrogen-bonds; these sheets are stacked along the a-axis and connected by N−D···O hydrogen bonds alone. With the exception of the simple body-centered-cubic high-pressure phases of ammonia monohydrate and ammonia dihydrate, this is the first complex molecular structure of any of the high-pressure stoichiometric ammonia hydrates to be determined. The powder structure solution is complemented by an ab initio structure prediction using density functional theory which gives an almost identical hydrogen bonding network.

J. Am. Chem. Soc., 2009, 131 (37), pp 13430–13440

Implementation of High Resolution 43Ca Solid State NMR Spectroscopy: Toward the Elucidation of Calcium Sites in Biological Materials
Danielle Laurencin*†‡, Christel Gervais§, Alan Wong†, Cristina Coelho§, Francesco Mauri, Dominique Massiot#, Mark E. Smith† and Christian Bonhomme*§

Calcium is one of the most abundant cations in living organisms. It is found in the mineral phase of bone and in proteins like calmodulin. However, its exact environment beyond the first coordination sphere is often unknown, thus hampering the understanding of many biological processes. Here, calcium benzoate trihydrate (Ca(C6H5COO)2·3H2O) was used as a model for the NMR analysis of calcium sites in biological materials, because of the similarity of its calcium coordination, to water and carboxylate ligands, to that in several calcium-proteins. First, calcium-43 magic angle spinning (MAS) and static NMR spectra of a 43Ca enriched sample were recorded at different magnetic fields, to investigate the electronic environment of calcium. Complex static lineshapes were obtained because of the presence of anisotropic NMR interactions of similar magnitude (chemical shift anisotropy and quadrupolar interaction), and the full interpretation of the spectra required simulations and gauge-including projector augmented wave (GIPAW) DFT calculations. An NMR investigation of the coordination environment of Ca2+ was carried out, using high resolution 13C−43Ca MAS NMR experiments such as TRAPDOR (transfer of population double resonance) and heteronuclear J-spin−echoes. It was shown that despite the weakness of 13C−43Ca interactions, it is possible to discriminate carbon atoms according to their calcium environment. Long-range calcium−carbon correlations were even evidenced by TRAPDOR, reaching distances >5.6 Å. This work demonstrates that by combining solid state NMR experiments, DFT calculations, and simulations, it will be possible to elucidate the electronic and coordination environment of calcium in many important and complex materials.

J. Am. Chem. Soc., 2009, 131 (37), pp 13228–13229

13C−13C Correlation Spectroscopy of Membrane-Associated Influenza Virus Fusion Peptide Strongly Supports a Helix-Turn-Helix Motif and Two Turn Conformations

Yan Sun and David P. Weliky*

The influenza virus fusion peptide (IFP) is the N-terminal domain of the viral hemagglutinin protein, binds to the endosomal membrane, and plays a critical role in fusion between the viral and endosomal membranes which is a primary step in infection. The IFP is also an important system for testing simulation methods for membrane-associated peptides. In detergent, the IFP forms helix-turn-helix and helix-turn-strand structures at pH 5.0 and 7.4, respectively, while simulations in membranes by different groups have yielded conflicting results with some reports of a continuous helix without a turn. In this study, 13C−13C NMR correlation spectra were obtained for the membrane-associated IFP and the 13C chemical shifts supported a helix-turn-helix motif at both pH 5.0 and 7.4 with an alternate turn conformation at pH 5.0 that was absent at pH 7.4. The alternate conformation was correlated with protonation of the side chain of Glu-11 in the turn and with greater fusion at pH 5.0. The structures are overall consistent with the hypothesis of “inverted V” membrane location of the IFP with insertion of the N-terminal region into the membrane and contact of the turn with the lipid/water interface. The positions of hydrophobic residues in the pH 5.0 structure may favor membrane insertion with resultant increased membrane perturbation and fusion rate. In addition to their functional relevance, these IFP structures are important reference data for simulations of the membrane-associated IFP which can in principle detect the full conformational distribution of the IFP.

Thursday, October 15, 2009

Cryst. Growth Des., 2009, 9 (2), pp 921–937

Solid-State NMR Analysis of Organic Cocrystals and Complexes
Frederick G. Vogt*†, Jacalyn S. Clawson†, Mark Strohmeier†, Andrew J. Edwards‡, Tran N. Pham‡ and Simon A. Watson‡

Solid-state NMR (SSNMR) is capable of providing detailed structural information about organic and pharmaceutical cocrystals and complexes. SSNMR nondestructively analyzes small amounts of powdered material and generally yields data with higher information content than vibrational spectroscopy and powder X-ray diffraction methods. These advantages can be utilized in the analysis of pharmaceutical cocrystals, which are often initially produced using solvent drop grinding techniques that do not lend themselves to single crystal growth for X-ray diffraction studies. In this work, several molecular complexes and cocrystals are examined to understand the capabilities of the SSNMR techniques, particularly their ability to prove or disprove molecular association and observe structural features such as hydrogen bonding. Dipolar correlation experiments between spin pairs such as 1H−1H, 1H−13C, and 19F−13C are applied to study hydrogen bonding, intermolecular contacts, and spin diffusion to link individual molecules together in a crystal structure and quickly prove molecular association. Analysis of the principal components of chemical shift tensors is also utilized where relevant, as these are more sensitive to structural effects than the isotropic chemical shift alone. In addition, 1H T1 relaxation measurements are also demonstrated as a means to prove phase separation of components. On the basis of these results, a general experimental approach to cocrystal analysis by SSNMR is suggested.

J. Am. Chem. Soc., 2009, 131 (33), pp 11939–11948

Measurement of Methyl Axis Orientations in Invisible, Excited States of Proteins by Relaxation Dispersion NMR Spectroscopy
Andrew J. Baldwin, D. Flemming Hansen, Pramodh Vallurupalli and Lewis E. Kay*

Few detailed studies of transiently populated conformations of biological molecules have emerged despite the fact that such states are often important to processes such as protein folding, enzyme catalysis, molecular recognition and binding. A major limitation has been the lack of experimental tools to study these often invisible, short-lived conformers. Recent advances in relaxation dispersion NMR spectroscopy are changing this paradigm with the potential to generate high resolution structural information which is necessary for a rigorous characterization of these states. In this study, we present an experimental method for establishing the relative orientations of methyl groups in invisible, excited states of proteins by measuring methyl 1H−13C residual dipolar couplings (RDCs). In our approach, four two-dimensional spectra are acquired at a pair of static magnetic fields. Each spectrum contains one of the four isolated multiplet components of a coupled methyl carbon, whose signal intensities, modulated by the pulsing frequency of a Carr−Purcell−Meiboom−Gill (CPMG) element, are sensitive to both chemical shift and RDC differences between exchanging states. In addition, data sets from a CPMG experiment which monitors the decay of in-phase methyl 13C magnetization are recorded, that are sensitive only to the differences in chemical shifts between the states. Using our methodology, RDC values obtained from an invisible state in an exchanging system are shown to be in good agreement with the corresponding values measured under conditions where the invisible state is stabilized to become the highly populated ground state. The approach allows the measurement of anisotropic restraints at methyl positions in excited states and complements previously developed experiments focusing on the protein backbone.

J. Am. Chem. Soc., 2009, 131 (33), pp 11861–11874

31P MAS Refocused INADEQUATE Spin−Echo (REINE) NMR Spectroscopy: Revealing J Coupling and Chemical Shift Two-Dimensional Correlations in Disordered Solids
Paul Guerry†, Mark E. Smith and Steven P. Brown*

Two-dimensional (2D) variations in 2JP1,P1, 2JP1,P2, and 2JP2,P2 are obtained—using the REINE (REfocused INADEQUATE spin−Echo) pulse sequence presented by Cadars et al. (Phys. Chem. Chem. Phys. 2007, 9, 92−103)—from pixel-by-pixel fittings of the spin−echo modulation for the 2D correlation peaks due to linked phosphate tetrahedra (P1−P1, P1−P2, P2−P1, and P2−P2) in a 31P refocused INADEQUATE solid-state MAS NMR spectrum of a cadmium phosphate glass, 0.575CdO−0.425P2O5. In particular, separate variations for each 2D 31P REINE peak are obtained which reveal correlations between the J couplings and the 31P chemical shifts of the coupled nuclei that are much clearer than those evident in previously presented 2D z-filtered 31P spin−echo spectra. Notably, such correlations between the J couplings and the 31P chemical shifts are observed even though the conditional probability distributions extracted using the protocol of Cadars et al. (J. Am. Chem. Soc. 2005, 127, 4466−4476) indicate that there is no marked correlation between the 31P chemical shifts of neighboring phosphate tetrahedra. For 2D peaks at the P2 31P chemical shift in the direct dimension, there can be contributions from chains of three units (P1−P2−P1), chains of four units (P1−P2−P2−P1), or longer chains or rings (−P2−P2−P2−): for the representative glass considered here, best fits are obtained assuming a glass comprised predominantly of chains of four units. The following variations are found: 2JP1,P1 = 13.4 ± 0.3 to 14.8 ± 0.5 Hz, 2JP1,P2 = 15.0 ± 0.3 to 18.2 ± 0.3 Hz, and 2JP2,P2 = 5.9 ± 0.6 to 9.1 ± 0.9 Hz from the fits to the P1−P1, P1−P2, and P2−P2 peaks, respectively. The correlation of a particular J coupling with the 31P chemical shifts of the considered nucleus and the coupled nucleus is quantified by the coefficients CF2 and CF1 that correspond to the average pixel-by-pixel change in the J coupling with respect to the chemical shift of the observed (F2) and neighboring (F1) 31P nuclei, respectively.

J. Am. Chem. Soc., 2009, 131 (33), pp 11855–11860

Direct Interaction between Amphotericin B and Ergosterol in Lipid Bilayers As Revealed by 2H NMR Spectroscopy
Nobuaki Matsumori, Kazuaki Tahara, Hiroko Yamamoto, Atsushi Morooka, Mototsugu Doi, Tohru Oishi and Michio Murata

Although amphotericin B (AmB) is thought to exert its antifungal activity by forming transmembrane ion-permeable self-assemblies together with ergosterol, no previous study has directly proven AmB−ergosterol interaction. To establish the interaction, we measured 2H NMR using deuterium-labeled sterols and AmB. The 2H NMR spectra of deuterated ergosterol in palmitoyloleoylphosphatidylcholine (POPC) bilayers showed that fast axial diffusion of erogosterol was almost completely inhibited by the coexistence of AmB. Conversely, cholesterol mobility in POPC membrane was essentially unchanged with or without AmB. These results unequivocally demonstrate that ergosterol has significant interaction with AmB in POPC bilayers. In addition, we examined the mobility of AmB using deuterium-labeled AmB, and found that, although AmB is almost immobilized in sterol-free and cholesterol-containing POPC membranes, a certain ratio of AmB molecules acquires mobility in the presence of ergosterol. The similar mobility of AmB and ergosterol in POPC bilayers confirmed the idea of the direct intermolecular interaction between ergosterol and AmB.

J. Am. Chem. Soc., 2009, 131 (33), pp 11801–11810

Solid-State NMR Investigations of the Immobilization of a BF4− Salt of a Palladium(II) Complex on Silica
Jerzy W. Wiench, Christophe Michon, Arkady Ellern, Paul Hazendonk, Adriana Iuga, Robert J. Angelici and Marek Pruski

The structure of the silica supported palladium(II) complex [Pd(dppp)(S2C-NEt2)]BF4 (abbreviated as [Pd(dppp)(dtc)]BF4, where dppp is Ph2P(CH2)3PPh2) and interactions between the [Pd(dppp)(dtc)]+ cation, the BF4− anion, and the silica surface are studied using solid-state NMR spectroscopy. The unsupported, crystalline form of [Pd(dppp)(dtc)]BF4 is also investigated, both by X-ray diffraction and NMR. The structures of the cation and anion are found to be essentially the same in both unsupported and supported complex. The [Pd(dppp)(dtc)]BF4 loading has been determined by quantitative measurements of 11B, 19F, and 31P intensities, whereas the arrangement of anions and cations on the surface of silica has been established by two-dimensional heteronuclear correlation experiments involving 1H, 11B, 13C, 19F, 29Si, and 31P nuclei. At low coverages, the [Pd(dppp)(dtc)]+ cations are located near the BF4− anions, which in turn are immobilized directly on the surface near the Q4 sites. At higher loadings, which in this study corresponded to 0.06−0.15 mmol/g, the complexes stack on top of each other, despite the fact that the directly adsorbed molecules take up less than 10% of the silica surface. The relevance of these findings to heterogeneous catalysis is discussed.

J. Am. Chem. Soc., 2009, 131 (33), pp 11762–11769

89Y and 13C NMR Cluster and Carbon Cage Studies of an Yttrium Metallofullerene Family, Y3N@C2n (n = 40−43)
Wujun Fu, Liaosa Xu, Hugo Azurmendi, Jiechao Ge, Tim Fuhrer, Tianming Zuo, Jonathan Reid, Chunying Shu, Kim Harich and Harry C. Dorn*

The members of a new family of yttrium trimetallic nitride-templated (TNT) endohedral metallofullerenes (EMFs), Y3N@C2n (n = 40−43), have been synthesized and purified. On the basis of experimental and computational 13C NMR studies, we propose cage structures for Y3N@Ih-C80 (IPR allowed), Y3N@D5h-C80 (IPR allowed), Y3N@Cs-C82 (non-IPR), Y3N@Cs-C84 (non-IPR), and Y3N@D3-C86 (IPR allowed). A significant result is the limited number of isomers found for each carbon cage. For example, there are 24 isolated pentagon rule (IPR) and 51568 non-IPR structures possible for the C84 cage, but only one major isomer of Y3N@Cs-C84 was found. The current study confirms the unique role of the trimetallic nitride (M3N)6+ cluster template in the Krtschmer−Huffman electric-arc process for fullerene cage size and high symmetry isomer selectivity. This study reports the first 89Y NMR results for Y3N@Ih-C80, Y3N@Cs(51365)-C84, and Y3N@D3(19)-C86, which reveal a progression from isotropic to restricted (Y3N)6+ cluster motional processes. Even more surprising is the sensitivity of the 89Y NMR chemical shift parameter to subtle changes in the electronic environment at each yttrium nuclide in the (Y3N)6+ cluster (more than 200 ppm for these EMFs). This 89Y NMR study suggests that 89Y NMR will evolve as a powerful tool for cluster motional studies of EMFs.

Tuesday, October 13, 2009

J. Am. Chem. Soc., 2009, 131 (35), pp 12745–12754

Measurement of Methyl Group Motional Parameters of Invisible, Excited Protein States by NMR Spectroscopy
D. Flemming Hansen, Pramodh Vallurupalli and Lewis E. Kay*

An understanding of many biological processes can only be achieved through studies of the structure (enthalpy) and motions (entropy) of the key molecules that are involved, including those that are formed only transiently and with low population. These transiently formed, low populated states are invisible to most biophysical techniques but in many cases they can be studied in detail using relaxation dispersion NMR spectroscopy. Relaxation dispersion methodology has recently been described for the measurement of protein backbone excited state chemical shifts as well as bond vector orientations, which form the basis for structural studies of these invisible conformers. It is of interest to extend such studies by quantifying motional parameters of the excited state, providing a more complete description of the energy landscape that drives the biochemical event in question. Herein we describe a relaxation dispersion method for measuring site-specific motional parameters of methyl containing residues in the excited state. The approach is applied to the invisible unfolded state of the G48M Fyn SH3 domain that is in exchange with the folded conformation. Not surprisingly, the degree of disorder is in general higher in the unfolded state than in the folded conformer, although there is some ordering of side-chains in the unfolded state toward the C-terminal region of the domain. The development of the present methodology provides the first step toward characterizing the motional properties of invisible conformers, complementing the structural information that is already available from relaxation dispersion studies.

Cryst. Growth Des., 2009, 9 (9), pp 4051–4059

Solid-State NMR and X-ray Diffraction Study of Structure and Dynamics of Dihydrate and Anhydrous Form of Tyr-Ala-Phe
Katarzyna Trzeciak-Karlikowska, Anna Bujacz, Agata Jeziorna, Włodzimierz Ciesielski†, Grzegorz D. Bujacz, Jarosław Gajda†, Danuta Pentak and Marek J. Potrzebowski*

Tyr-d-Ala-Phe is a “message sequence” of naturally occurring opioid peptides, deltorphin I (Tyr-d-Ala-Phe-Asp-Val-Val-Gly-NH2), deltorphin II (Tyr-d-Ala-Phe-Glu-Val-Val-Gly-NH2), and dermorphin (Tyr-d-Ala-Phe-Gly-Tyr-Pro-Ser-NH2). Analogous heptapeptides containing l-alanine instead of d-alanine are not biologically active. In a previous paper (J. Phys. Chem. B 2004, 108 (14), 4535−4545), we reported X-ray and NMR data for Tyr-d-Ala-Phe. In the current report, we present structural studies of Tyr-Ala-Phe, a “false message sequence” of opioid peptides. It has been found that Tyr-Ala-Phe crystallizes in two forms, as anhydrate (Form I) and dihydrate (Form II). Crystal and molecular structure of both forms was established by means of low-temperature X-ray measurements. Form I is orthorhombic with space group P212121, while II is hexagonal with space group P65. Solid-state NMR was employed to study the structure and molecular dynamics of I and II. Analysis of cross-polarization buildup curves and 13C chemical shift tensor (CST) parameters obtained by a two-dimensional PASS experiment have revealed a dramatic difference in the molecular motion of both modifications. 13C T1 relaxation times have provided further evidence confirming distinct molecular dynamics. The attempt to understand the role of the stereochemistry of Ala residue in opioid peptide sequences in relation to intramolecular interactions and preorganization mechanisms is presented.

Monday, September 28, 2009

Science, v325

Some nice 27Al SSNMR spectra can be seen here:

Science, v325, page 1670

Coordinatively Unsaturated Al3+ Centers as Binding Sites for Active Catalyst Phases of Platinum on -Al2O3

Ja Hun Kwak,1,* Jianzhi Hu,1 Donghai Mei,1 Cheol-Woo Yi,2 Do Heui Kim,1 Charles H. F. Peden,1,* Lawrence F. Allard,3 Janos Szanyi1,*

In many heterogeneous catalysts, the interaction of metal particles with their oxide support can alter the electronic properties of the metal and can play a critical role in determining particle morphology and maintaining dispersion. We used a combination of ultrahigh magnetic field, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy, and high-angle annular dark-field scanning transmission electron microscopy coupled with density functional theory calculations to reveal the nature of anchoring sites of a catalytically active phase of platinum on the surface of a -Al2O3 catalyst support material. The results obtained show that coordinatively unsaturated pentacoordinate Al3+ (Al3+penta) centers present on the (100) facets of the -Al2O3 surface are anchoring Pt. At low loadings, the active catalytic phase is atomically dispersed on the support surface (Pt/Al3+penta = 1), whereas two-dimensional Pt rafts form at higher coverages.
1 Institute for Interfacial Catalysis, Pacific Northwest National Laboratory, Post Office Box 999, MSIN K8-87, Richland, WA 99352, USA.2 Department of Chemistry and Institute of Basic Science, Sungshin Women’s University, Seoul 136-742, Repulic of Korea.3 Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Thursday, September 03, 2009

Single molecule, one million times smaller than a grain of sand, pictured for first time
By Claire Bates
Last updated at 11:45 AM on 31st August 2009
Comments (330) Add to My Stories It may look like a piece of honeycomb, but this lattice-shaped image is the first ever close-up view of a single molecule.
Scientists from IBM used an atomic force microscope (AFM) to reveal the chemical bonds within a molecule.
'This is the first time that all the atoms in a molecule have been imaged,' lead researcher Leo Gross said.
The delicate inner structure of a pentacene molecule has been imaged with an atomic force microscope
The researchers focused on a single molecule of pentacene, which is commonly used in solar cells. The rectangular-shaped organic molecule is made up of 22 carbon atoms and 14 hydrogen atoms.

In the image above the hexagonal shapes of the five carbon rings are clear and even the positions of the hydrogen atoms around the carbon rings can be seen.
To give some perspective, the space between the carbon rings is only 0.14 nanometers across, which is roughly one million times smaller than the diameter of a grain of sand.
Textbook model: A computer-generated image of how we're used to seeing a molecule represented with balls and sticks
'If you think about how a doctor uses an X-ray to image bones and organs inside the human body, we are using the atomic force microscope to image the atomic structures that are the backbones of individual molecules,' said IBM researcher Gerhard Meyer.
A 3D view showing how a single carbon monoxide molecule was used to create the image using a 'tuning fork' effect
The team from IBM Research Zurich said the results could have a huge impact of the field of nanotechnology, which seeks to understand and control some of the smallest objects known to mankind.
The AFM uses a sharp metal tip that acts like a tuning fork to measure the tiny forces between the tip and the molecule. This requires great precision as the tip moves within a nanometer of the sample.

'Above the skeleton of the molecular backbone (of the pentacene) you get a different detuning than above the surface the molecule is lying on,' Mr Gross said.
This detuning is then measured and converted into an image.
To stop the tip from absorbing the pentacene molecule, the researchers replaced the metal with a single molecule of carbon monoxide. This was found to be more stable and created weaker electrostatic attractions with the pentacene, creating a higher resolution image.
Enlarge IBM researchers Nikolaj Moll, Reto Schlittler, Gerhard Meyer, Fabian Mohn and Leo Gross (l-r) stand behind an atomic force microscope Photo taken by Michael Lowry Image courtesy of IBM Research - Zurich
The experiment was also performed inside a high vacuum at the extremely cold temperature of -268C to avoid stray gas molecules or atomic vibrations from affecting the measurements.
'Eventually we want to investigate using molecules for molecular electronics,' Mr Gross said.
'We want to use molecules as wires

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Tuesday, September 01, 2009

J. Am. Chem. Soc., 2009, 131 (31), pp 11062–11079

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

Fulya Dogan†, Karl D. Hammond‡, Geoffrey A. Tompsett‡, Hua Huo†, W. Curtis Conner, Jr.‡, Scott M. Auerbach‡§ and Clare P. Grey*†

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+/NH4+) 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 1H/29Si 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 °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 °C and 48 h).

J. Am. Chem. Soc., 2009, 131 (31), pp 10834–10835

Observation of NMR Signals from Proteins Introduced into Living Mammalian Cells by Reversible Membrane Permeabilization Using a Pore-Forming Toxin, Streptolysin O

Shinji Ogino†, Satoshi Kubo†, Ryo Umemoto†, Shuxian Huang†, Noritaka Nishida† and Ichio Shimada*†‡

We have developed a new in-cell NMR method that is applicable to any type of cell and does not require target protein modification or specialized equipment. The stable-isotope-labeled target protein, thymosin β4 (Tβ4), was delivered to 293F cells, which were permeabilized by a pore-forming toxin, streptolysin O, and resealed by Ca2+ after Tβ4 uptake. As a result, we successfully observed 1H−15N HSQC signals originating from the Tβ4, including those from the N-terminal acetylation, which had occurred inside the cell as a post-translational modification.

J. Am. Chem. Soc., 2009, 131 (31), pp 10832–10833

Measuring the Signs of 1Hα Chemical Shift Differences Between Ground and Excited Protein States by Off-Resonance Spin-Lock R1ρ NMR Spectroscopy

Renate Auer†‡, Philipp Neudecker‡, D. Ranjith Muhandiram‡, Patrik Lundstrm‡§, D. Flemming Hansen‡, Robert Konrat† and Lewis E. Kay*‡

Analysis of Carr−Purcell−Meiboom−Gill (CPMG) relaxation dispersion NMR profiles provides the kinetics and thermodynamics of millisecond-time-scale exchange processes involving the interconversion of populated ground and invisible excited states. In addition, the absolute values of chemical shift differences between NMR probes in the exchanging states, |Δ|, are also extracted. Herein, we present a simple experiment for obtaining the sign of 1Hα Δ values by measuring off-resonance 1Hα decay rates, R1ρ, using weak proton spin-lock fields. A pair of R1ρ values is measured with a spin-lock field applied |Δω| downfield and upfield of the major-state peak. In many cases, these two relaxation rates differ substantially, with the larger one corresponding to the case where the spin-lock field coincides with the resonance frequency of the probe in the minor state. The utility of the methodology is demonstrated first on a system involving protein ligand exchange and subsequently on an SH3 domain exchanging between a folded state and its on-pathway folding intermediate. With this experiment, it thus becomes possible to determine 1Hα chemical shifts of the invisible excited state, which can be used as powerful restraints in defining the structural properties of these elusive conformers.

J. Am. Chem. Soc., 2009, 131 (31), pp 10830–10831

High Resolution Heteronuclear Correlation NMR Spectroscopy of an Antimicrobial Peptide in Aligned Lipid Bilayers: Peptide−Water Interactions at the Water−Bilayer Interface

Riqiang Fu*†, Eric D. Gordon‡, Daniel J. Hibbard‡ and Myriam Cotten*§

High-resolution two-dimensional (2D) 1H−15N heteronuclear correlation (HETCOR) spectroscopy has been used to characterize the structure and dynamics of 15N-backbone labeled antimicrobial piscidin 1 (p1) oriented in “native-like” hydrated lipid bilayers. Piscidin belongs to a family of amphipatic cationic antimicrobial peptides, which are membrane-active and have broad spectrum antimicrobial activity on bacteria. When the 1H chemical shifts are encoded by the 1H−15N dipolar couplings, 2D dipolar-encoded HETCOR (i.e., de-HETCOR) solid-state NMR spectra yield high resolution 1H and 15N chemical shifts as well as 1H−15N heteronuclear dipolar couplings. Several advantages of HETCOR and de-HETCOR techniques that emerge from our investigations could facilitate the atomic-level investigations of structure−function relationships in membrane-active peptides and membrane-bound species. First, the de-HETCOR NMR spectrum of a ten-site 15N-labeled sample of p1 aligned in hydrated lipid bilayers can resolve resonances that are overlapped in the standard HETCOR spectrum. Second, the resolution in de-HETCOR spectra of p1 improves significantly at higher magnetic field due to an enhanced alignment that improves spectrum definition uniformly. Third, the HETCOR spectrum of 15N−K14 p1 oriented in hydrated lipid bilayers displays not only the expected crosscorrelation between the chemical shifts of bonded amide1H and 15N spins but also a cross peak between the 1H chemical shift from bulk water and the 15N chemical shift from the labeled amide nitrogen. This information provides new insights into the intermolecular interactions of an amphipathic antimicrobial peptide optimized to partition at the water-bilayer interface and may have implications at the biological level.

J. Am. Chem. Soc., 2009, 131 (31), pp 10816–10817

Transverse-Dephasing Optimized Homonuclear J-Decoupling in Solid-State NMR Spectroscopy of Uniformly 13C-Labeled Proteins

Sgolne Laage†, Anne Lesage†, Lyndon Emsley†, Ivano Bertini‡, Isabella C. Felli‡, Roberta Pierattelli‡ and Guido Pintacuda*†

A transverse-dephasing optimized S3E (spin-state selective excitation) method is implemented in solid-state NMR experiments of uniformly labeled protein samples, and it is shown to provide a simultaneous significant gain in both resolution (up to a factor of 2.2) and sensitivity (up to a factor of 1.4). This is illustrated with high-resolution NCO and NCA correlations of a microcrystalline sample of the oxidized form of the 153 residue human Cu(II)Zn(II) superoxide dismutase (SOD), a dimeric paramagnetic enzyme of 32 kDa. This method allows the resolution of 145 signals in the highly crowded carbonyl region in the NCO correlation spectrum.

Friday, August 14, 2009

PCCP: Solid-State NMR themed issue

A great collection of papers, plus two "recent advances" articles on spin-1/2 and quadrupolar nuclei.
Guest Editors: Paul Hodgkinson, Durham, UK, and Stephen Wimperis, Glasgow, UK

Solid-State NMR Spectroscopy
Phys. Chem. Chem. Phys., 2009, DOI: 10.1039/b914008p

Recent advances in solid-state NMR spectroscopy of spin
I = 1/2 nuclei
Anne Lesage, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b907733m

Recent advances in solid-state NMR spectroscopy of
quadrupolar nuclei
Sharon E. Ashbrook, Phys. Chem. Chem. Phys., 2009,
DOI: 10.1039/b907183k

Solid-state 17O NMR as a sensitive probe of keto and gemdiol
forms of -keto acid derivatives
Jianfeng Zhu, Amanda J. Geris and Gang Wu, Phys. Chem.
Chem. Phys., 2009, DOI: 10.1039/b906438a

Anomalous resonances in 29Si and 27Al NMR spectra of
pyrope ([Mg,Fe]3Al2Si3O12) garnets: effects of paramagnetic
Jonathan F. Stebbins and Kimberly E. Kelsey, Phys. Chem.
Chem. Phys., 2009, DOI: 10.1039/b904731j

New opportunities in acquisition and analysis of natural
abundance complex solid-state 33S MAS NMR spectra:
Hans J. Jakobsen, Henrik Bildsøe, Jørgen Skibsted, Michael
Brorson, Bikshandarkoil R. Srinivasan, Christian Näther and
Wolfgang Bensch, Phys. Chem. Chem. Phys., 2009,
DOI: 10.1039/b904841n

An analytic expression for the double quantum 1H nuclear
magnetic resonance build-up and decay from a Gaussian
polymer chain with dynamics governed by a single
relaxation time
Michael E. Ries and Michael G. Brereton, Phys. Chem. Chem.
Phys., 2009, DOI: 10.1039/b905350f

Static solid-state 14N NMR and computational studies of
nitrogen EFG tensors in some crystalline amino acids
Luke A. O Dell and Robert W. Schurko, Phys. Chem. Chem.
Phys., 2009, DOI: 10.1039/b906114b

Solid state deuteron relaxation time anisotropy measured
with multiple echo acquisition
Robert L. Vold, Gina L. Hoatson, Liliya Vugmeyster, Dmitry
Ostrovsky and Peter J. De Castro, Phys. Chem. Chem. Phys.,
2009, DOI: 10.1039/b907343d

Application of multinuclear magnetic resonance and gaugeincluding
projector-augmented-wave calculations to the
study of solid group 13 chlorides
Rebecca P. Chapman and David L. Bryce, Phys. Chem. Chem.
Phys., 2009, DOI: 10.1039/b906627f

High-resolution 17O double-rotation NMR characterization of
ring and non-ring oxygen in vitreous B2O3
Alan Wong, Andy P. Howes, Ben Parkinson, Tiit Anupõld, Ago
Samoson, Diane Holland and Ray Dupree, Phys. Chem. Chem.
Phys., 2009, DOI: 10.1039/b906501f

Probing chemical disorder in glasses using silicon-29 NMR
spectral editing
Julien Hiet, Michaël Deschamps, Nadia Pellerin, Franck Fayon and
Dominique Massiot, Phys. Chem. Chem. Phys., 2009,
DOI: 10.1039/b906399d

GIPAW (gauge including projected augmented wave) and local
dynamics in 13C and 29Si solid state NMR: the study case of
silsesquioxanes (RSiO1.5)8
Christel Gervais, Laure Bonhomme-Coury, Francesco Mauri,
Florence Babonneau and Christian Bonhomme, Phys. Chem.
Chem. Phys., 2009
DOI: 10.1039/b907450c

Determining relative proton–proton proximities from the buildup
of two-dimensional correlation peaks in 1H double-quantum
MAS NMR: insight from multi-spin density-matrix simulations
Jonathan P. Bradley, Carmen Tripon, Claudiu Filip and Steven P.
Brown, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b906400a

Manifestation of Landau level effects in optically-pumped NMR
of semi-insulating GaAs
Stacy Mui, Kannan Ramaswamy, Christopher J. Stanton, Scott A.
Crooker and Sophia E. Hayes, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b907588g

Motional heterogeneity in single-site silica-supported species
revealed by deuteron NMR
Julia Gath, Gina L. Hoaston, Robert L. Vold, Romain Berthoud,
Christophe Copéret, Mary Grellier, Sylviane Sabo-Etienne, Anne
Lesage and Lyndon Emsley, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b907665d

Magnesium silicate dissolution investigated by 29Si MAS, 1H–
29Si CPMAS, 25Mg QCPMG, and 1H–25Mg CP QCPMG NMR
Michael C. Davis, William J. Brouwer, David J. Wesolowski,
Lawrence M. Anovitz, Andrew S. Lipton and Karl T. Mueller, Phys.
Chem. Chem. Phys., 2009
DOI: 10.1039/b907494e

Intermediate motions and dipolar couplings as studied by Lee–
Goldburg cross-polarization NMR: Hartmann–Hahn matching
Marcio Fernando Cobo, Kate ina Mali áková, Detlef Reichert, Kay
Saalwächter and Eduardo Ribeiro deAzevedo, Phys. Chem.
Chem. Phys., 2009
DOI: 10.1039/b907674c

Measurements of relative chemical shift tensor orientations in
solid-state NMR: new slow magic angle spinning dipolar
recoupling experiments
Andrew P. S. Jurd and Jeremy J. Titman, Phys. Chem. Chem.
Phys., 2009
DOI: 10.1039/b906814g

Signal loss in 1D magic-angle spinning exchange NMR
(CODEX): radio-frequency limitations and intermediate
Christiane Hackel, Cornelius Franz, Anja Achilles, Kay Saalwächter
and Detlef Reichert, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b906527j

Calculation of fluorine chemical shift tensors for the
interpretation of oriented 19F-NMR spectra of gramicidin A in
Ulrich Sternberg, Marco Klipfel, Stephan L. Grage, Raiker Witter
and Anne S. Ulrich, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b908236k

J-Based 3D sidechain correlation in solid-state proteins
Ye Tian, Lingling Chen, Dimitri Niks, J. Michael Kaiser, Jinfeng
Lai, Chad M. Rienstra, Michael F. Dunn and Leonard J. Mueller,
Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b911570f

Natural abundance 13C and 15N solid-state NMR analysis of
paramagnetic transition-metal cyanide coordination polymers
Pedro M. Aguiar, Michael J. Katz, Daniel B. Leznoff and Scott
Kroeker, Phys. Chem. Chem. Phys., 2009
DOI: 10.1039/b907747b

Monday, July 27, 2009

Al's Literature Update

Symmetry-based dipolar recoupling by optimal control: Band-selective experiments for assignment of solid-state NMR spectra of proteins
J. Chem. Phys. 131, 025101 (2009); DOI:10.1063/1.3157737
Anders Bodholt Nielsen, Morten Bjerring, Jakob Toudahl Nielsen, and Niels Chr. Nielsen

We present design of novel low-power homonuclear dipolar recoupling experiments for magic-angle-spinning solid-state NMR studies of proteins. The pulse sequences are developed by combining principles of symmetry-based dipolar recoupling and optimal control-based pulse sequence design. The scaffold of the pulse sequences is formed by known CN-type recoupling sequences, while the intrinsic sequence elements are designed using optimal control. This procedure allows for the development of high-performance pulse sequences demanding significantly weaker rf fields than previous symmetry-based pulse sequences while compensating for rf inhomogeneity and providing excitation over relevant ranges of chemical shifts for biological applications. The new recoupling experiments, referred to as optimal control CN (OCCN), are demonstrated numerically and experimentally by two-dimensional (2D) 13C–13C and three-dimensional (3D) 15N–13C–13C chemical shift correlation experiments on uniformly 13C, 15N-labeled ubiquitin. Exploiting the double-quantum, band-selective dipolar recoupling properties of the OCCN experiments, we demonstrate significant sensitivity enhancement for 2D and 3D correlation spectra showing exclusively one- or two-bond correlations.

Effect of glass-forming biopreservatives on head group rotational dynamics in freeze-dried phospholipid bilayers: A 31P NMR study
J. Chem. Phys. 131, 025102 (2009); DOI:10.1063/1.3170927
P. Jain, S. Sen, and S. H. Risbud

31P NMR spectroscopy has been used to elucidate the role of glass-forming sugars in the preservation of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers. 31P wideline NMR spectra of freeze-dried pure DPPC, DPPC/trehalose, DPPC/glucose, and DPPC/hydroxyethyl starch (HES) mixtures collected in the temperature range of 25–80 °C have been simulated to obtain quantitative information about rotational dynamics and orientation of the lipid head groups in these media. In the case of pure DPPC, DPPC/glucose, and DPPC/HES, the gel-to-liquid crystalline phase transition of DPPC bilayer is characterized by a sudden increase in the rate of rotational diffusion of the PO4 head groups near 40 °C. The corresponding rotational jump frequency increases from a few kilohertz in the gel phase to at least several megahertz in the liquid crystalline phase. On the other hand, in the case of DPPC/trehalose mixture the temperature of this onset of rapid head group dynamics is increased by ~10 °C. Trehalose reduces the lipid head group motions most effectively in the temperature range of T50 °C relevant for biopreservation. Additionally, and possibly more importantly, trehalose is found to strongly restrict any change in the orientation of the diffusion axis of the PO4 head groups during the phase transformation. This unique ability of trehalose to maintain the dynamical and orientational rigidity of lipid head groups is likely to be responsible for its superior ability in biopreservation.

Structural and Dynamic Properties of BaInGeH: A Rare Solid-State Indium Hydride
Inorg. Chem., 2009, 48 (13), pp 5602–5604

Michael J. Evans, Verina F. Kranak, Francisco J. Garcia-Garcia, Gregory P. Holland, Luke L. Daemen, Thomas Proffen, Myeong H. Lee, Otto F. Sankey and Ulrich Hussermann

BaInGeH was synthesized by hydrogenating the intermetallic compound BaInGe. The crystal structure determination from the powder neutron diffraction data of BaInGeD [P3m1, Z = 1, a = 4.5354(3) Å, c = 5.2795(6) Å] reveals the presence of hydrogen in tetrahedral voids defined by three Ba atoms and one In atom.

Sodium Ion Mobility in NaxCoO2 (0.6 < x < 0.75) Cobaltites Studied by 23Na MAS NMR

Inorg. Chem., 2009, 48 (15), pp 7018–7025
Dany Carlier, Maxime Blangero, Michel Mntrier, Michal Pollet, Jean-Pierre Doumerc and Claude Delmas

Various P2 and P′3-NaxCoO2 phases, with x ranging approximately from 0.6 to 0.75, have been studied by variable-temperature 23Na magic angle spinning (MAS) NMR. Signal modification versus temperature plots clearly show that Na+ ions are not totally mobile at room temperature on the NMR time scale. As the temperature increases, the line shape change of the 23Na MAS NMR signal differs for the P2 and P′3 stackings and is interpreted by the differences of Na+ ion sites and of sodium diffusion pathways in the two structures.

Reactivity of NH4H2PO4 toward LaCl3 in LiCl-KCl Melt Flux. Step by Step Formation of Monazite-Like LaPO4.
Inorg. Chem., 2009, 48 (15), pp 7141–7150
Damien Hudry, Aydar Rakhmatullin, Catherine Bessada, Isabelle Bardez, Florence Bart, Stphane Jobic and Philippe Deniard
The synthesis of lanthanum phosphates in molten LiCl-KCL eutectic was chosen to address the preliminary treatment of chlorinated wastes containing fission products that are already present in a Li/Cl eutectic. The obtained monazite compound shows interesting properties to be considered as a good candidate to trap lanthanum for a long-time. The synthesis route based on LaCl3 reaction with NH4H2PO4 in a stoichiometric amount is a key point to obtain monazite as a pure phase. Hence, the salt composition is not modified during the synthesis reaction. The chemical reactivity of ammonium dihydrogenphosphate (NH4H2PO4, hereafter abbreviated ADP) toward lanthanum chloride (LaCl3) in molten LiCl-KCl eutectic is probed by NMR spectroscopy to follow the formation of LaPO4. Formally, a direct transformation of the two aforementioned precursors into LaPO4, NH4Cl and HCl can be discarded on the basis of the low thermal stability of ADP. To shed some light on the formation of LaPO4, in situ and ex situ NMR experiments were carried out on LiCl-KCl/LaCl3/ADP, as well as LiCl-KCl/ADP, KCl/ADP, and LiCl/ADP mixtures. First, the reactivity of the precursors in contact with the eutectic was studied from room temperature to 600 °C by means of 31P, 35Cl, and 139La high temperature NMR. Second, ex situ room temperature magic angle spinning (MAS) and RadioFrequency driven recoupling (RFDR) 31P solid-state NMR experiments were carried out on solid samples prepared in different conditions (i.e., temperature and atmosphere) and quenched at room temperature to identify frozen intermediate species in their metastable state. On the basis of this approach, we propose a model for the LaPO4 formation based on a multistep mechanism which highlights the strong reactivity of ADP toward the alkaline salts but without final change in the composition of the solvent.

Journal of Physical Chemistry C, vol. 113, Issues 25-30

29Si NMR Relaxation of Silicated Nanoparticles in Tetraethoxysilane−Tetrapropylammonium Hydroxide−Water System (TEOS−TPAOH−H2O)
Mohamed Haouas
*, David P. Petry, Michael W. Anderson and Francis Taulelle
Institut Lavoisier de Versailles, Universit de Versailles-St. Quentin en Yvelines, Versailles, J. Phys. Chem. C, 2009, 113 (25), pp 10838–10841
DOI: 10.1021/jp903454f

Abstract: Silicon-29 longitudinal (T1) and transverse (T2) NMR relaxation times have been measured in the clear solution precursor of silicalite-1 of composition 25 TEOS−5 TPAOH−400 H2O. The nanoparticles as well as the silicate oligomers are giving rise to observable resonances. An unusually long T1 relaxation time of 126 s is observed for Q4 in nanoparticles. Proper care for acquisition is therefore required for quantifying the distribution of Qn of the nanoparticles, an essential measurement to follow the nanoparticles connectivity evolution.

Clathrate Hydrate Formation: Dependence on Aqueous Hydration Number
Steven F. Dec
J. Phys. Chem. C, 2009, 113 (28), pp 12355–12361
DOI: 10.1021/jp9009977
Abstract: The formation of methane−ethane (C1−C2) clathrate hydrate was studied with high-resolution, solid-state 13C NMR and density functional theory techniques. The 13C NMR experiments yield a number of significant findings: (1) the hydration number of C2(aq) is 26, (2) the initial quantity of C2−51262 sI hydrate cages outnumber C1−512 cages at 274 K, (3) C1−C2 sII hydrate forms at a C1−C2 gas phase composition where only sI hydrate is thermodynamically stable, (4) the initial composition of C1−C2 sII hydrate at 268 K contains less than the original amount of C1, (5) a quasi-liquid water layer solvating both C1 and C2 exists at 268 K, (6) any C1(qll) and C2(qll) present at 253 K is too small to be detected, (7) the initial amounts of C1−C2 sI and sII hydrates formed at 253 K are much smaller than those formed at 268 and 274 K, and (8) C1(aq), C2(aq) and C1(qll), C2(qll) facilitate the formation of C1−C2 sI and sII clathrate hydrate at 268 and 274 K, respectively. On the basis of these experimental observations, a model is developed that states that the aqueous hydration number of the most water-soluble clathrate hydrate former controls the structure of the clathrate hydrate that forms during the initial stages of the clathrate hydrate formation reaction. For methane−ethane clathrate hydrate, this means that ethane in a water liquid phase or quasi-liquid layer eliminates or adds two water molecules to its hydration shell to form the ethane-filled 51262 or 51264 cage building blocks of structure I or structure II clathrate hydrate, respectively. Density functional theory computations on methane-filled 512, 51262, and 51264 and ethane-filled 51262, 51263, and 51264 clathrate hydrate cages yield the stabilization energy of the gas-filled cages and provide theoretical evidence consistent with the experimentally based clathrate hydrate formation model. The proposed model is found to explain the results of other clathrate hydrate formation reactions.

Hierarchical Meso-/Macroporous Aluminum Phosphonate Hybrid Materials as Multifunctional Adsorbents
Tian-Yi Ma, Xue-Jun Zhang and Zhong-Yong Yuan*
J. Phys. Chem. C, 2009, 113 (29), pp 12854–12862
DOI: 10.1021/jp903412m
Abstract: Inorganic−organic hybrid aluminum phosphonate (AlPPh) materials with hierarchical meso-/macroporous structure were synthesized by using two different kinds of organophosphonic acids: amino tri(methylene phosphonic acid) and bis(hexamethylenetriamine)-penta(methylenephosphonic acid). The preparation was accomplished both with and without the assistance of surfactant F127. All the samples possess a uniform macroporous (500−2000 nm) structure of mesoporous (4−5 nm) framework, which were characterized by SEM, TEM, N2 sorption, XRD, TGA-DSC, elemental analysis, MAS NMR, and FT-IR spectroscopy techniques. The as-prepared AlPPh materials were used as multifunctional adsorbents for the efficient removal of heavy metal ions (e.g., Cu2+) and the adsorption of proteins (e.g., lysozyme). The heavy metal ion adsorption results show that the AlPPh materials have a large adsorption capacity, comparable to those of previous reported Cu(II)-adsorbents made up of functionalized mesoporous silica. The isotherms for lysozyme adsorption are of type L (Langmuir isotherm), and different monolayer capacities were calculated using Langmuir equation. The differences between the metal ion and the lysozyme adsorption were mainly caused by the nature of inorganic ions and proteins and the interactions between the adsorbents and adsorbates. The synthesized AlPPh hybrid materials were confirmed to be useful multifunctional adsorbents for both metal ions and proteins.

Observation of Distinct Surface AlIV Sites and Phosphonate Binding Modes in γ-Alumina and Concrete by High-Field 27Al and 31P MAS NMR
George W. Wagner
* and Roderick A. Fry§
J. Phys. Chem. C, 2009, 113 (30), pp 13352–13357
DOI: 10.1021/jp902474z
Publication Date (Web): July 1, 2009
Abstract: High loadings of nerve agent-related phosphonic acids adsorbed on γ-Al2O3 and concrete examined by 31P MAS NMR and high-field 27Al MAS NMR reveal the presence of several phosphonate−surface binding modes and greatly improved resolution of multiple AlIV sites. Some of the resolved AlIV sites are sensitive to surface hydroxylation/dehydroxylation are attributed to surface AlIV−OH groups (apparently having been observed for the first time). Although the number of surface AlIV sites detected by high-field 27Al MAS NMR (three) is in agreement with current surface models, their dehydroxylation behavior does not entirely concur with proposed dehydroxylation mechanisms. The various phosphonate−alumina surface species detected by 31P MAS NMR are consistent with those previously observed by IR techniques. In concrete, the formation of an aluminophosphonate species is directly observed, consistent with the recalcitrant extraction behavior exhibited by adsorbed phosphonates in environmental matrices.