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.

Journal of Physical Chemistry B, Vol. 113, Issues 25 to 30

Glassy Dynamics in Nanoconfinement as Revealed by 31P NMR
S. Gradmann, P. Medick and E. A. Rssler
Experimentalphysik II, Universitt Bayreuth, 95440 Bayreuth, Germany
J. Phys. Chem. B, 2009, 113 (25), pp 8443–8445

Abstract: We investigated the glass former m-tricresyl-phosphate confined in different nanoporous silica matrices with defined pore radii from 2−150 nm. While applying different 31P NMR techniques, we were able to detect the extremely stretched correlation functions extending over 7−8 decades in time and reflecting strong dynamic heterogeneities. The experimental results were explained by a topological model for which the broad distribution of correlation times G(ln τ) becomes inhomogeneous in space; that is, the “local” dynamics given by a correlation time τ(r) depend on the distance from the pore center. As τ(r) changes with temperature, we were able to reintroduce the idea of a dynamic correlation length.

Hierarchical Dynamics of As2P2S8 Quasi-Molecular Units in a Supercooled Liquid in the As−P−S System: A 31P NMR Spectroscopic Study

E. L. Gjersing and S. Sen*
J. Phys. Chem. B, 2009, 113 (25), pp 8514–8519
DOI: 10.1021/jp901388j
Abstract: The dynamics of As2P2S8 quasi-molecular units caged in an As−S network in the supercooled chalcogenide liquid of composition (As2S3)90(P2S5)10 have been studied near the glass transition region (Tg = 468 ≤ T ≤ 628 K) using 31P NMR line shape analysis and spin−lattice relaxation techniques. 31P NMR line shape analysis indicates the presence of isotropic rotational reorientation of As2P2S8 quasi-molecular units at frequencies on the order of tens of kilohertz at T <>

Proton Assisted Recoupling at High Spinning Frequencies
Jzef R. Lewandowski
§, Gal De Pape, Matthew T. Eddy, Jochem Struppe, Werner Maas and Robert G. Griffin*
J. Phys. Chem. B, 2009, 113 (27), pp 9062–9069
DOI: 10.1021/jp810280t

2008 marked the Centennial of the American Chemical Society’s Division of Physical Chemistry. To celebrate and to highlight the field of physical chemistry from both historical and future perspectives, The Journal of Physical Chemistry is publishing a special series of Centennial Feature Articles. These articles are invited contributions from current and former officers and members of the Physical Chemistry Division Executive Committee and from J. Phys. Chem. Senior Editors.,

Abstract: We demonstrate the successful application of 13C−13C proton assisted recoupling (PAR) on [U−13C,15N] N-f-MLF-OH and [U−13C,15N] protein GB1 at high magic angle spinning (MAS) frequencies (ωr/2π = 65 kHz). Specifically, by combining PAR mixing with low power heteronuclear decoupling (ω1H/2π 16 kHz) and high spinning frequencies, we obtain high resolution 2D spectra displaying long-range 13C−13C contacts from which distance estimates can be extracted. These experiments therefore demonstrate the possibility of performing high resolution structural studies in the limit of high spinning frequency and low power 1H decoupling, a regime which optimizes the resolution of protein samples and preserves their integrity.

Self-Diffusion and Mutual Diffusion of Small Molecules in High-Set Curdlan Hydrogels Studied by 31P NMR
Marc-Andr Gagnon and Michel Lafleur
J. Phys. Chem. B, 2009, 113 (27), pp 9084–9091
DOI: 10.1021/jp811105p

Abstract: Self-diffusion and mutual diffusion are two different transport mechanisms experimentally characterized on different length and time scales. NMR spectroscopy is a highly suitable technique to characterize these two phenomena as both mechanisms can be studied on the same system and in the same experimental conditions. Pulsed field gradient (PFG) NMR was used to measure the self-diffusion whereas 31P NMR profiling provided an approach to determine the mutual diffusion coefficients. We have characterized the diffusion of phosphate, trimetaphosphate, alendronate, and d-glucose-6-phosphate in hydrogels prepared with 10% (w/v) curdlan, a bacterial polysaccharide built of linear (1→3)-β-d-glucose repeating units. These solutes are small compared to the average pore size of the hydrogel, as inferred from environmental scanning electron microscopy (eSEM). Our results show that the self- and mutual-diffusion coefficients of small molecules in curdlan hydrogels are similar and are reduced by 30% compared to those measured in aqueous solutions. These observations are validated for the complete series of investigated analytes. It is therefore concluded that, for this system, the analyte diffusion in the gel is essentially reduced because of interactions at the molecular level and that the open structure of this gel has a very limited influence at the mesoscopic length scale. A literature survey indicates that these conditions prevail for the large majority of the systems that have been investigated up to now.

Validating a Strategy for Molecular Dynamics Simulations of Cyclodextrin Inclusion Complexes through Single-Crystal X-ray and NMR Experimental Data: A Case Study
Giuseppina Raffaini
*, Fabio Ganazzoli, Luciana Malpezzi, Claudio Fuganti, Giovanni Fronza, Walter Panzeri and Andrea Mele*
J. Phys. Chem. B, 2009, 113 (27), pp 9110–9122
DOI: 10.1021/jp901581e

Abstract: A theoretical and experimental study about the formation and structure of the inclusion complex (−)-menthyl-O-β-D-glucopyranoside 1 with β-cyclodextrin (β-CD) 2 is presented as paradigmatic case study to test the results of molecular dynamics (MD) simulations. The customary methodological approach—the use of experimental geometrical parameters as restraints for MD runs—is logically reversed and the calculated structures are a posteriori compared with those obtained from NMR spectroscopy in D2O solution and single crystal X-ray diffraction so as to validate the simulation procedure. The guest molecule 1 allows for a broad repertoire of intermolecular interactions (dipolar, hydrophobic, hydrogen bonds) concurring to stabilize the host−guest complex, thus providing the general applicability of the simulation procedure to cyclodextrin physical chemistry. Many starting geometries of the host−guest association were chosen, not assuming any a priori inclusion. The simulation protocol, involving energy minimization and MD runs in explicit water, yielded four possible inclusion geometries, ruling out higher-energy outer adducts. By analysis of the average energy at room temperature, the most stable geometry in solution was eventually obtained, while the kinetics of formation showed that it is also kinetically favored. The reliability of such geometry was thoroughly checked against the NOE distances via the pair distribution functions, that is, the statistical distribution of intermolecular distances among selected diagnostic atoms calculated from the MD trajectories at room temperature. An analogous procedure was adopted both with implicit solvent and in vacuo. The most stable geometry matched that found with explicit solvent but major differences were observed in the relative stability of the metastable complexes as a consequence of the lack of hydration on the polar moiety of the guest. Finally, a control set of geometrical parameters of the thermodynamically favored complex matched the corresponding one obtained from the X-ray structure, while local conformational differences were indicative of packing effects.

1H Solid-State NMR Investigation of Structure and Dynamics of Anhydrous Proton Conducting Triazole-Functionalized Siloxane Polymers
mit Akbey
, Sergio Granados-Focil, E. Bryan Coughlin§, Robert Graf and Hans Wolfgang Spiess*
J. Phys. Chem. B, 2009, 113 (27), pp 9151–9160
DOI: 10.1021/jp9030909

Abstract:1H MAS solid-state NMR methods are applied to elucidate the conduction mechanism of an anhydrous proton conducting triazole-functionalized polysiloxane. At temperatures below T = 260 K, hydrogen bonding between neighboring heterocycles is observed and a dimer formation can be excluded. From the temperature dependence of 1H MAS NMR spectra, different dynamic processes of the triazole ring contributing to the proton conduction process are qualitatively and quantitatively analyzed and detailed insight into the conduction mechanism and temperature-dependent structural changes is obtained. Although the dynamics processes on the molecular level are qualitatively in good agreement with the findings from macroscopic conductivity measurements, temperature-dependent factors on mesoscopic scales beyond the local molecular mobility influence the macroscopic conductivity and hamper quantitative interpretation.

Intra- and Intermolecular Effects on 1H Chemical Shifts in a Silk Model Peptide Determined by High-Field Solid State 1H NMR and Empirical Calculations
Yu Suzuki
, Rui Takahashi, Tadashi Shimizu, Masataka Tansho, Kazuo Yamauchi, Mike P. Williamson§ and Tetsuo Asakura*
J. Phys. Chem. B, 2009, 113 (29), pp 9756–9761
DOI: 10.1021/jp903020p

Abstract: A combination of solid state 1H NMR chemical shift measurements and empirical chemical shift calculations has been used to interpret 1H solid state chemical shifts of a model peptide (Ala-Gly)15 for the crystalline domain of Bombyx mori silk fibroin in silk I and silk II structures, including a treatment of both intra- and intermolecular arrangements. Silk I and silk II are the structures of silk fibroin before and after spinning, respectively. Two peaks with equal intensity were observed for the amide protons of (AG)15 in silk I, whereas only one broad peak was observed for silk II, reflecting a difference of 1.1 ppm in Ala HN shift between silk I and silk II, but a difference of only 0.2 ppm in Gly HN shift. Chemical shift calculations predicted chemical shifts that are in good agreement with the experimental observations and showed that the origin of these chemical shift differences was predominantly the magnetic anisotropy effect from the C═O bond that hydrogen bonds with HN, which has a more favorable geometry for Ala HN in silk II than for the other HN. This result shows that we could distinguish between proton chemical shift effects arising from intermolecular interactions and those from intramolecular interactions by combining observation of the solid state 1H NMR chemical shift and empirical chemical shift calculation.

1H Photo-CIDNP Enhancements in Heteronuclear Correlation NMR Spectroscopy
Ashok Sekhar and Silvia Cavagnero
J. Phys. Chem. B, 2009, 113 (30), p 10548
DOI: 10.1021/jp905605u
Publication Date (Web): July 9, 2009
Copyright © 2009 American Chemical Society

Sunday, July 26, 2009

J. Am. Chem. Soc., 2009, 131 (29), pp 9884–9885

15N−1H Scalar Coupling Perturbation: An Additional Probe for Measuring Structural Changes Due to Ligand Binding
Junhe Ma, James M. Gruschus and Nico Tjandra*

Chemical shift perturbation mapping of backbone amides is one of the most widely employed techniques in biomolecular NMR, providing residue-by-residue information on interaction interfaces, ligand binding, and chemical modification sites, even for samples where poor solubility, short lifetime, or large size precludes more sophisticated experimental approaches. Significant changes can also occur in the amide one-bond 15N−1H scalar coupling constants for glutamine binding protein (GlnBP) due to ligand binding. Like chemical shift perturbations, large changes (>1 Hz) are seen near the site of glutamine binding, though perturbations also occur distant to the site. The coupling constant perturbations correlate with significant structural changes, especially changes in backbone hydrogen bonding. Thus, amide scalar coupling perturbation can serve as an adjunct to chemical shift perturbation, providing additional information on both short-range and longer-range, allosteric structural changes.

Thursday, July 16, 2009

Progress in NMR, up to Volume 55, Issue 2, August 2009

Progress in NMR, up to Volume 55, Issue 2, August 2009
- HRMAS NMR for biomedical studies
- natural abundance 2H NMR
- second-order cross terms interactions in MAS NMR spectra of quadrupoles


Progress in Nuclear Magnetic Resonance Spectroscopy
Volume 55, Issue 2, August 2009, Pages 79-100


High-resolution magic angle spinning NMR spectroscopy: Application to biomedical studies

John C. Lindon, Olaf P. Beckonert, Elaine Holmes and Jeremy K. Nicholson

Department of Biomolecular Medicine, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK

Keywords: Magic angle spinning; Tissue; Cells; Cancer; Pharmaceuticals; Toxins


Progress in Nuclear Magnetic Resonance Spectroscopy
Volume 55, Issue 2, August 2009, Pages 128-159


Natural abundance deuterium NMR spectroscopy: Developments and analytical applications in liquids, liquid crystals and solid phases

Philippe Lesot and Jacques Courtieu

Université de Paris Sud 11, ICMMO, UMR CNRS 8182, Laboratoire de RMN en Milieu Orienté, Bât. 410, F-91405 Orsay Cedex, France


Progress in Nuclear Magnetic Resonance Spectroscopy
Volume 55, Issue 2, August 2009, Pages 128-159


Second-order cross-term interactions in high-resolution MAS NMR of quadrupolar nuclei

Sharon E. Ashbrook, Jamie McManus, Michael J. Thrippleton and Stephen Wimperis

School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK; Winchester College, Winchester SO23 9NA, UK; Department of Chemistry and WestCHEM, University of Glasgow, Glasgow G12 8QQ, UK

Monday, July 13, 2009

Chem. Soc. Rev. How molecules stick together in organic crystals: weak intermolecular interactions

Tutorial Review

Article citation: Jack D. Dunitz, Chem. Soc. Rev., 2009, DOI: 10.1039/b822963p

How molecules stick together in organic crystals: weak intermolecular interactions

Jack D. Dunitz and Angelo Gavezzotti

This tutorial review introduces the fundamentals of intermolecular interactions in terms of the underlying physics and goes on to illustrate the most popular methods for the computer simulation of intermolecular interactions, from atom–atom potentials to ab initio methods, including intermediate, hybrid methods, with an appreciation of their relative merits and costs. Typical results are critically presented, culminating in the most difficult exercise of all, the computer prediction of crystal structures. Perspectives on our present and future ability to understand and exploit intermolecular interactions are given.

Graphical abstract image for this article  (ID: b822963p)

Chem. Mater., Article ASAP

Investigation of the Conversion Reaction Mechanisms for Binary Copper(II) Compounds by Solid-State NMR Spectroscopy and X-ray Diffraction

Naoko Yamakawa†‡, Meng Jiang† and Clare P. Grey*†

The conversion reaction mechanisms of CuS, CuF2, and CuO during the electrochemical reaction with Li are studied by solid-state 63Cu, 19F, and 7Li nuclear magnetic resonance (NMR) and X-ray diffraction (XRD). For CuS, a two-step reaction is observed that is associated with an insertion reaction involving first limited incorporation of Li into CuS and then a two-phase reaction to form a material with the approximate composition LiCuS. This is followed by a conversion reaction to form Li2S and Cu, Cu1.96S being formed as a side product of the decomposition of LiCuS. Evidence for the insertion phases is found from both NMR and XRD. A direct conversion reaction to form LiF and Cu is seen for CuF2, whereas the 7Li NMR results indicate that CuO can tolerate a small amount of Li substitution before reacting to form Li2O and Cu. Both the diffraction and NMR results indicate that the size of the Cu particles formed on discharge are much larger in the CuS system, which is thought to result from the higher Cu1+ mobilities in the intermediate intercalation compounds LixCuS. The factors that control the possible mechanisms for these conversion reactions are discussed.

J. Am. Chem. Soc., Article ASAP

Solid-State and Solution NMR Studies of the CAP-Gly Domain of Mammalian Dynactin and Its Interaction with Microtubules

Shangjin Sun†, Amanda Siglin‡, John C. Williams*‡ and Tatyana Polenova*†

Microtubules (MTs) and microtubule binding proteins (MTBPs) play fundamental physiological roles including vesicle and organelle transport, cell motility, and cell division. Despite the importance of the MT/MTBP assemblies, there remains virtually no structural or dynamic information about their interaction at the atomic level due to the inherent insolubility and lack of long-range order of MTs. In this study, we present a combined magic angle spinning solid-state and solution NMR study of the MTBP CAP-Gly domain of mammalian dynactin and its interaction with paclitaxel-stabilized microtubules. We report resonance assignments and secondary structure analysis of the free CAP-Gly in solution and in the solid state by a combination of two- and three-dimensional homo- and heteronuclear correlation spectra. In solution, binding of CAP-Gly to microtubules is accompanied by the broadening of the majority of the peaks in HSQC spectra except for the residues at the termini, precluding further structural analysis of the CAP-Gly/microtubule complexes. In the solid state, DARR spectra of free CAP-Gly and its complex with microtubules display well-resolved lines, permitting residue-specific resonance assignments. Interestingly, a number of chemical shifts in the solid-state DARR spectra of the CAP-Gly/microtubule complex are perturbed compared to those of the free CAP-Gly, suggesting that conformational changes occur in the protein upon binding to the microtubules. These results indicate that CAP-Gly/microtubule assemblies are amenable to detailed structural characterization by magic angle spinning NMR spectroscopy and that solid-state NMR is a viable technique to study MT/protein interactions in general.

J. Am. Chem. Soc., Article ASAP

Identifying the Local Structures Formed during Lithiation of the Conversion Material, Iron Fluoride, in a Li Ion Battery: A Solid-State NMR, X-ray Diffraction, and Pair Distribution Function Analysis Study

Naoko Yamakawa†‡, Meng Jiang†, Baris Key† and Clare P. Grey*†

The structural transformations that occur when FeF3 is cycled at room temperature in a Li cell were investigated using a combination of X-ray diffraction (XRD), pair distribution function (PDF) analysis, and magic-angle-spinning NMR spectroscopy. Two regions are seen on discharge. The first occurs between Li = 0 and 1.0 and involves an insertion reaction. This first region actually comprises two steps: First, a two-phase reaction between Li = 0 and 0.5 occurs, and the Li0.5FeF3 phase that is formed gives rise to a Li NMR resonance due to Li+ ions near both Fe3+ and Fe2+ ions. On the basis of the PDF data, the local structure of this phase is closer to the rutile structure than the original ReO3 structure. Second, a single-phase intercalation reaction occurs between Li = 0.5 and 1.0, for which the Li NMR data indicate a progressive increase in the concentration of Fe2+ ions. In the second region, the conversion reaction, superparamagnetic, nanosized (3 nm) Fe metal is formed, as indicated by the XRD and NMR data, along with some LiF and a third phase that is rich in Li and F. The charge process involves the formation of a series of intercalation phases with increasing Fe oxidation state, which, on the basis of the Li NMR and PDF data, have local structures that are similar to the intercalation phases seen during the first stage of the discharge process. The solid-state NMR and XRD results for the rutile phase FeF2 are presented for comparison, and the data indicate that an insertion reaction also occurs, which is accompanied by the formation of LiF. This is followed by the formation of Fe nanoparticles and LiF via a conversion reaction.

Friday, July 10, 2009

J. Am. Chem. Soc., 2009, 131 (26), pp 9239–9249

Real-Time NMR Investigations of Structural Changes in Silicon Electrodes for Lithium-Ion Batteries
Baris Key†, Rangeet Bhattacharyya†, Mathieu Morcrette‡, Vincent Seznc‡, Jean-Marie Tarascon‡ and Clare P. Grey*

Lithium-ion batteries (LIBs) containing silicon negative electrodes have been the subject of much recent investigation because of the extremely large gravimetric and volumetric capacity of silicon. The crystalline-to-amorphous phase transition that occurs on electrochemical Li insertion into crystalline Si, during the first discharge, hinders attempts to link structure in these systems with electrochemical performance. We apply a combination of static, in situ and magic angle sample spinning, ex situ 7Li nuclear magnetic resonance (NMR) studies to investigate the changes in local structure that occur in an actual working LIB. The first discharge occurs via the formation of isolated Si atoms and smaller Si−Si clusters embedded in a Li matrix; the latter are broken apart at the end of the discharge, forming isolated Si atoms. A spontaneous reaction of the lithium silicide with the electrolyte is directly observed in the in situ NMR experiments; this mechanism results in self-discharge and potential capacity loss. The rate of this self-discharge process is much slower when CMC (carboxymethylcellulose) is used as the binder.

Science vol. 324: High-Resolution NMR in Magnetic Fields with Unknown Spatiotemporal Variations

Science 26 June 2009:Vol. 324. no. 5935, pp. 1693 - 1697DOI: 10.1126/science.1175102

High-Resolution NMR in Magnetic Fields with Unknown Spatiotemporal Variations
Philippe Pelupessy,1,* Enrico Rennella,2 Geoffrey Bodenhausen1,3

Nuclear magnetic resonance (NMR) experiments are usually carried out in homogeneous magnetic fields. In many cases, however, high-resolution spectra are virtually impossible to obtain because of the inherent heterogeneity of the samples or living organisms under investigation, as well as the poor homogeneity of the magnets (particularly when bulky samples must be placed outside their bores). Unstable power supplies and vibrations arising from cooling can lead to field fluctuations in time as well as space. We show how high-resolution NMR spectra can be obtained in inhomogeneous fields with unknown spatiotemporal variations. Our method, based on coherence transfer between spins, can accommodate spatial inhomogeneities of at least 11 gauss per centimeter and temporal fluctuations slower than 2 hertz.

Friday, July 03, 2009

J. Am. Chem. Soc., 2009, 131 (25), pp 9086–9093

Diffusion-Ordered NMR Spectroscopy in the Structural Characterization of Functionalized Carbon Nanotubes
Riccardo Marega†‡, Vincent Aroulmoji‡¶, Francesca Dinon‡, Lisa Vaccari§, Silvia Giordani, Alberto Bianco, Erminio Murano‡ and Maurizio Prato†

The emerging applications of functionalized carbon nanotubes (CNTs) in various research domains necessitate the use of many different analytical techniques to confirm their structural modifications in a fast and reliable manner. Thus far, NMR spectroscopy has not been among the main tools for characterization of organically modified carbon nanostructures. 1H analysis is limited because the signals in these derivatives are typically weak and broad, resulting in uncertainties of a few parts per million, and because of the strong interference of residual solvent signals. To overcome these limitations, we investigated the applicability of proton NMR spectroscopy based on gradient-edited diffusion pulse sequences (1D diffusion-ordered spectroscopy, DOSY) in the characterization of CNT derivatives. In general, diffusion NMR experiments allow the separation of NMR signals of different species present in a mixture, according to their own diffusion coefficients, merging spectroscopy information with size analysis. In the present study, a selected set of CNT derivatives was synthesized and analyzed using 1D DOSY experiments by applying strong magnetic field gradients (up to 42.6 G cm−1). Colorimetric tests (i.e., Kaiser test) and TGA analysis support the NMR findings, which are related to isolated and/or bundled short SWNTs, on the basis of TEM and AFM characterization. The overall results show that the diffusion-based NMR spectroscopy is a fast and promising approach for the characterization of covalently modified CNT derivatives.

Thursday, July 02, 2009

Cryst. Growth Des., 2009, 9 (7), pp 3124–3128

Engineering Crystal Packing and Internal Dynamics in Molecular Gyroscopes by Refining their Components. Fast Exchange of a Phenylene Rotator by 2H NMR
Miguel A. Garcia-Garibay* and Carlos E. Godinez

Using quadrupolar echo 2H NMR, we have determined that a relatively simple change on the periphery of the triptycene stators of molecular gyroscopes may have a profound effect on the packing arrangements, packing coefficients, and rotary dynamics of the central phenylene rotators. The previously reported crystal structure of 1,4-bis-[2-(9-triptycyl)-ethynyl]benzene (1) is characterized by the inclusion of meta-xylene and a very tightly interdigitated packing arrangement that effectively prevents the rotary motion of the phenylene rotator. Structural modifications to prevent this interdigitation led to the design and synthesis of 1,4-bis[2-(2,3,6,7,12,13-hexamethyl-10-propyl-9-triptycyl)ethynyl]benzene (2), which had been shown to crystallize in the desired manner but with the inclusion of bromobenzene. Using crystals of 2 with a 2H-labeled phenylene rotator, we determined by quadrupolar echo 2H NMR line shape analysis that rotation occurs by a 180° site exchange (2-fold flip) with frequencies in the MHz regime at low temperatures (150−183 K). From the temperature dependence of the rotational exchange frequency, we determined a barrier of 4.4 kcal/mol, which is only 1.4 kcal/mol higher than the internal barrier for ethane in the gas phase. Additional spectral narrowing observed at higher temperature was analyzed in terms of a model that considers larger amplitude excursions between the 180° jumps.

Cryst. Growth Des., 2009, 9 (7), pp 3111–3118

Rheo-NMR Measurements of Cocoa Butter Crystallized Under Shear Flow
Elizabeth M. Mudge and Gianfranco Mazzanti*

Modifications of a benchtop NMR instrument were made to apply temperature control to a shearing NMR cell. This has enabled the determination in situ of the solid fat content (SFC) of cocoa butter under shearing conditions. The cocoa butter was cooled at 3 °C/min to three final temperatures of 17.5, 20.0, and 22.5 °C with applied shear rates between 45 and 720 s−1. Polymorphic transitions of the cocoa butter were determined using synchrotron X-ray diffraction with an identical shearing system constructed of Lexan. Sheared samples were shown to have accelerated phase transitions compared to static experiments. In experiments where form V was confirmed to be the dominant polymorph, the final SFC averaged around 50%. However, when other polymorphic forms were formed, a lower SFC was measured because the final temperature was within the melting range of that polymorph and only partial crystallization happened. A shear rate of 720 s−1 delayed phase transitions, likely due to viscous heating of the sample. Pulsed NMR is an invaluable tool for determining the crystalline fraction in hydrogen containing materials, yet its use for fundamental and industrial research on fat or alkanes crystallization under shear has only recently been developed.

Cryst. Growth Des., 2009, 9 (7), pp 2999–3002

Guest Molecules Confined in Amphipathic Crystals as Revealed by X-ray Diffraction and MAS NMR†
Angiolina Comotti*‡, Silvia Bracco‡, Piero Sozzani‡, Samuel M. Hawxwell#, Chunhua Hu# and Michael D. Ward*#

Multinuclear 1H−13C heterocorrelated (HETCOR) NMR spectroscopy combined with X-ray diffraction revealed the unusual dual properties of identical guest molecules confined in two crystallographically distinct host cavities within single crystals based on hexagonal frameworks comprising guanidinium ions and organomonosulfonates. The environments of the two cavities differ substantially, as one is lined by the highly polar quasihexagonal guanidinium-sulfonate network, while the other is defined by walls consisting of nonpolar aromatic groups. The effect of these different environments on the NMR properties of the guest molecules is evident from chemical shift data and two-dimensional HETCOR spectra. The large magnetic susceptibility effect due to ring currents of the aromatic hosts enables determination of the host−guest distances and suggests intermolecular CH···π interactions. The 13C relaxation times reveal the molecular dynamics of the guests in two nanoscale environments that differ with respect to shape and dimensionality.