Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed
Vipin Agarwal†, Yi Xue‡, Bernd Reif*† and Nikolai R. Skrynnikov*‡
Abstract
In this paper, we seek to compare the internal dynamics of a small globular protein, SH3 domain from α-spectrin, in solution and in a crystalline state. The comparison involves side-chain methyl 13C R1 relaxation rates that are highly sensitive to local dynamics in the vicinity of the methyl site. To conduct the relaxation measurements, protein samples have been prepared using specially labeled α-ketoisovalerate precursors, resulting in selective incorporation of the 1H−13C spin pair in one or both methyl groups of the valine and leucine side chains. The sparse labeling pattern in an otherwise deuterated sample makes it possible to record high-resolution 13C, 1H solid-state spectra using magic angle spinning experiment with a MAS frequency of 22 kHz. Furthermore, this labeling scheme avoids proton-driven 13C−13C spin-diffusion effects, thus allowing for accurate measurements of 13C R1 relaxation in the individual methyl groups. While the relaxation response from a polycrystalline sample is generally expected to be multiexponential, we demonstrate both theoretically and experimentally that in this particular case the relaxation profiles are, in excellent approximation, monoexponential. In fact, solid-state relaxation data can be interpreted in a model-free fashion, similar to solution data. Direct comparison between the experimentally measured solid and solution rates reveals a strong correlation, r = 0.94. Furthermore, when solution rates are corrected for the effect of the overall molecular tumbling (quantified on the basis of the solution 15N relaxation data), the results are in one-to-one agreement with the solid-state rates. This finding indicates that methyl dynamics in the solution and solid samples are quantitatively similar. More broadly, it suggests that the entire dynamic network, including motions of side chains in the protein hydrophobic core and backbone motions, is similar. This result opens interesting possibilities for combined interpretation of solid- and solution-state relaxation data, potentially leading to a detailed characterization of internal protein dynamics on a wide range of time scales.
Friday, December 05, 2008
J. Am. Chem. Soc., 2008, 130 (49), pp 16518–16520
NMR Determination of Amide N−H Equilibrium Bond Length from Concerted Dipolar Coupling Measurements
Lishan Yao, Beat Vögeli, Jinfa Ying and Ad Bax
Abstract
The N−H bond length in backbone peptide groups of the protein GB3 has been studied by liquid-crystal NMR, using five structurally conserved mutants of this protein. In the absence of additional information, the impact of dynamic fluctuations of the N−H vector orientation on the 15N−1H dipolar interaction cannot be separated from a change in N−H bond length. However, a change in N−H bond length directly impacts the orientation of C′−H vectors in the peptide group, and simultaneous analysis of 13C′−HN and 15N−HN residual dipolar couplings, measured under five different alignment orientations, permits modelfree determination of the average equilibrium N−H bond length in GB3, yielding rNHeq = 1.008 ± 0.006 Å. Anharmonicity of the bond stretching results in a slightly longer time-averaged bond length = 1.015 ± 0.006 Å, and an effective bond length reff = −1/3 = 1.023 ± 0.006 Å pertinent for NMR relaxation analysis, not including the impact of zero-point or other angular fluctuations in N−H orientation. Using a reference frame defined by the backbone Cα−C′ vectors of the protein, angular fluctuations for N−H vectors in elements of secondary structure are approximately 1.5-fold larger for out-of-plane fluctuations than motions within the peptide plane and not much larger than anticipated on the basis of quantum mechanical analysis of their zero-point librations.
Lishan Yao, Beat Vögeli, Jinfa Ying and Ad Bax
Abstract
The N−H bond length in backbone peptide groups of the protein GB3 has been studied by liquid-crystal NMR, using five structurally conserved mutants of this protein. In the absence of additional information, the impact of dynamic fluctuations of the N−H vector orientation on the 15N−1H dipolar interaction cannot be separated from a change in N−H bond length. However, a change in N−H bond length directly impacts the orientation of C′−H vectors in the peptide group, and simultaneous analysis of 13C′−HN and 15N−HN residual dipolar couplings, measured under five different alignment orientations, permits modelfree determination of the average equilibrium N−H bond length in GB3, yielding rNHeq = 1.008 ± 0.006 Å. Anharmonicity of the bond stretching results in a slightly longer time-averaged bond length
J. Am. Chem. Soc., 2008, 130 (49), pp 16515–16517
Using a Sterically Restrictive Amino Acid as a 19F NMR label To Monitor and To Control Peptide Aggregation in Membranes
Parvesh Wadhwani†, Jochen Bürck†, Erik Strandberg†, Christian Mink†, Sergii Afonin† and Anne S. Ulrich*†‡
Abstract
Aggregation of peptides into amyloid fibrils or other β-sheet structures is usually related to malfunction. This process is often induced by lipid bilayers but is difficult to monitor in the membrane-bound state. Here, we show how aggregation is readily detected by solid state 19F NMR using a fluorine-labeled amino acid and how the same sterically rigid side chain can be also be employed to prevent aggregation. Selective CF3-phenylglycine labels were incorporated either as the L- or D-enantiomer into the membrane-active model amphiphilic peptide (MAP). Oriented circular dichroism showed that the D-epimeric peptides maintained an α-helical conformation in DMPC at all peptide-to-lipid ratios, while the L-epimers turned into β-sheet structures above 1:200, just like the wild-type. Aggregation was clearly revealed by the appearance of powder lineshapes in the 19F NMR spectra of oriented samples. The 19F NMR dipolar couplings from four D-epimers were analyzed as orientational constraints, showing that the helix of MAP undergoes a concentration-dependent realignment in DMPC from a surface-bound to a tilted state.
Parvesh Wadhwani†, Jochen Bürck†, Erik Strandberg†, Christian Mink†, Sergii Afonin† and Anne S. Ulrich*†‡
Abstract
Aggregation of peptides into amyloid fibrils or other β-sheet structures is usually related to malfunction. This process is often induced by lipid bilayers but is difficult to monitor in the membrane-bound state. Here, we show how aggregation is readily detected by solid state 19F NMR using a fluorine-labeled amino acid and how the same sterically rigid side chain can be also be employed to prevent aggregation. Selective CF3-phenylglycine labels were incorporated either as the L- or D-enantiomer into the membrane-active model amphiphilic peptide (MAP). Oriented circular dichroism showed that the D-epimeric peptides maintained an α-helical conformation in DMPC at all peptide-to-lipid ratios, while the L-epimers turned into β-sheet structures above 1:200, just like the wild-type. Aggregation was clearly revealed by the appearance of powder lineshapes in the 19F NMR spectra of oriented samples. The 19F NMR dipolar couplings from four D-epimers were analyzed as orientational constraints, showing that the helix of MAP undergoes a concentration-dependent realignment in DMPC from a surface-bound to a tilted state.
J. Am. Chem. Soc., 2008, 130 (49), pp 16512–16514
Temperature-Dependent Transmembrane Insertion of the Amphiphilic Peptide PGLa in Lipid Bilayers Observed by Solid State 19F NMR Spectroscopy
Sergii Afonin†, Stephan L. Grage†, Marco Ieronimo‡, Parvesh Wadhwani† and Anne S. Ulrich*†‡
Abstract
The alignment of the antimicrobial peptide PGLa in a lipid bilayer was characterized by solid state 19F NMR on selectively CF3-labeled peptides in oriented samples. Previous studies in liquid crystalline model membranes had shown that the amphiphilic α-helix of PGLa adopts a surface-aligned S-state or a tilted T-state, depending on the peptide/lipid ratio. Only in the presence of the synergistic partner peptide magainin 2 had PGLa been found insert into the bilayer in a transmembrane I-state orientation. Here, we have characterized the peptide alignment but as a function of temperature and lipid phase state. At temperatures below the lipid chain melting transition, PGLa is now seen to be able to insert on its own, with its helical axis nearly parallel to the bilayer normal (tilt angle of ∼170°), forming the I-state. Above the lipid phase transition, PGLa is aligned in the known T-state (tilt angle of ∼130°), but it is found flip into the S-state at more elevated temperatures (tilt angle of ∼96°). This way, three distinct alignment states were found, which also differ in their mobility. The complete membrane insertion of PGLa in the I-state, which could be trapped here in a gel phase bilayer, supports mechanistic models that explain antimicrobial activity as a result of pore formation by some of the molecules.
Sergii Afonin†, Stephan L. Grage†, Marco Ieronimo‡, Parvesh Wadhwani† and Anne S. Ulrich*†‡
Abstract
The alignment of the antimicrobial peptide PGLa in a lipid bilayer was characterized by solid state 19F NMR on selectively CF3-labeled peptides in oriented samples. Previous studies in liquid crystalline model membranes had shown that the amphiphilic α-helix of PGLa adopts a surface-aligned S-state or a tilted T-state, depending on the peptide/lipid ratio. Only in the presence of the synergistic partner peptide magainin 2 had PGLa been found insert into the bilayer in a transmembrane I-state orientation. Here, we have characterized the peptide alignment but as a function of temperature and lipid phase state. At temperatures below the lipid chain melting transition, PGLa is now seen to be able to insert on its own, with its helical axis nearly parallel to the bilayer normal (tilt angle of ∼170°), forming the I-state. Above the lipid phase transition, PGLa is aligned in the known T-state (tilt angle of ∼130°), but it is found flip into the S-state at more elevated temperatures (tilt angle of ∼96°). This way, three distinct alignment states were found, which also differ in their mobility. The complete membrane insertion of PGLa in the I-state, which could be trapped here in a gel phase bilayer, supports mechanistic models that explain antimicrobial activity as a result of pore formation by some of the molecules.
J. Am. Chem. Soc., 2008, 130 (48), pp 16168–16169
Ligand-Induced Conformational Heterogeneity of Cytochrome P450 CYP119 Identified by 2D NMR Spectroscopy with the Unnatural Amino Acid 13C-p-Methoxyphenylalanine
Jed N. Lampe, Stephen N. Floor, John D. Gross, Clinton R. Nishida, Yongying Jiang, Michael J. Trnka and Paul R. Ortiz de Montellano*
Abstract
Conformational dynamics are thought to play an important role in ligand binding and catalysis by cytochrome P450 enzymes, but few techniques exist to examine them in molecular detail. Using a unique isotopic labeling strategy, we have site specifically inserted a 13C-labeled unnatural amino acid residue, 13C-p-methoxyphenylalanine (MeOF), into two different locations in the substrate binding region of the thermophilic cytochrome P450 enzyme CYP119. Surprisingly, in both cases the resonance signal from the ligand-free protein is represented by a doublet in the 1H,13C-HSQC spectrum. Upon binding of 4-phenylimidazole, the signals from the initial resonances are reduced in favor of a single new resonance, in the case of the F162MeOF mutant, or two new resonances, in the case of the F153MeOF mutant. This represents the first direct physical evidence for the ligand-dependent existence of multiple P450 conformers simultaneously in solution. This general approach may be used to further illuminate the role that conformational dynamics plays in the complex enzymatic phenomena exhibited by P450 enzymes.
Jed N. Lampe, Stephen N. Floor, John D. Gross, Clinton R. Nishida, Yongying Jiang, Michael J. Trnka and Paul R. Ortiz de Montellano*
Abstract
Conformational dynamics are thought to play an important role in ligand binding and catalysis by cytochrome P450 enzymes, but few techniques exist to examine them in molecular detail. Using a unique isotopic labeling strategy, we have site specifically inserted a 13C-labeled unnatural amino acid residue, 13C-p-methoxyphenylalanine (MeOF), into two different locations in the substrate binding region of the thermophilic cytochrome P450 enzyme CYP119. Surprisingly, in both cases the resonance signal from the ligand-free protein is represented by a doublet in the 1H,13C-HSQC spectrum. Upon binding of 4-phenylimidazole, the signals from the initial resonances are reduced in favor of a single new resonance, in the case of the F162MeOF mutant, or two new resonances, in the case of the F153MeOF mutant. This represents the first direct physical evidence for the ligand-dependent existence of multiple P450 conformers simultaneously in solution. This general approach may be used to further illuminate the role that conformational dynamics plays in the complex enzymatic phenomena exhibited by P450 enzymes.
J. Am. Chem. Soc., 2008, 130 (48), pp 16148–16149
Weak Alignment of Biomacromolecules in Collagen Gels: An Alternative Way to Yield Residual Dipolar Couplings for NMR Measurements
Junhe Ma†, Gregory I. Goldberg‡ and Nico Tjandra
Abstract
Collagen, consisting of glycine, proline, and hydroxyproline, is a fibrous protein that can form a rope-like left-hand triple helix structure. It is demonstrated here that the collagen gels prepared from polymerization in the magnetic field can provide weak alignment for protein. The alignment order induced by collagen gels is quite small when compared to other alignment media, but the magnitude of the dipolar couplings can be easily scaled up by increasing the initial concentration of collagen. The collagen gels showed good pH and detergent tolerance. These advantages of collagen gels make it a promising candidate for the alignment of large biomolecules or membrane protein−detergent complexes in the magnetic field.
Junhe Ma†, Gregory I. Goldberg‡ and Nico Tjandra
Abstract
Collagen, consisting of glycine, proline, and hydroxyproline, is a fibrous protein that can form a rope-like left-hand triple helix structure. It is demonstrated here that the collagen gels prepared from polymerization in the magnetic field can provide weak alignment for protein. The alignment order induced by collagen gels is quite small when compared to other alignment media, but the magnitude of the dipolar couplings can be easily scaled up by increasing the initial concentration of collagen. The collagen gels showed good pH and detergent tolerance. These advantages of collagen gels make it a promising candidate for the alignment of large biomolecules or membrane protein−detergent complexes in the magnetic field.
Friday, November 28, 2008
J. Am. Chem. Soc., 2008, 130 (47), pp 15990–15996
Structure Determination of Protein−Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin−Immunity Protein Complex
Rinaldo W. Montalvao†‡, Andrea Cavalli†, Xavier Salvatella†, Tom L. Blundell‡ and Michele Vendruscolo*†
Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein−protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein−protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.
Rinaldo W. Montalvao†‡, Andrea Cavalli†, Xavier Salvatella†, Tom L. Blundell‡ and Michele Vendruscolo*†
Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein−protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein−protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.
J. Am. Chem. Soc., 2008, 130 (47), pp 15927–15937
16-Fold Degeneracy of Peptide Plane Orientations from Residual Dipolar Couplings: Analytical Treatment and Implications for Protein Structure Determination
Jean-Christophe Hus#†‡, Loïc Salmon‡, Guillaume Bouvignies‡, Johannes Lotze‡, Martin Blackledge*‡ and Rafael Brüschweiler*§
Abstract
Residual dipolar couplings (RDCs) measured for internally rigid molecular fragments provide important information about the relative orientations of these fragments. Dependent on the symmetry of the alignment tensor and the symmetry of the molecular fragment, however, there generally exist more than one solution for the fragment orientation consistent with the measured RDCs. Analytical solutions are presented that describe the complete set of orientations of internally rigid fragments that are consistent with multiple dipolar couplings measured in a single alignment medium that is rhombic. For the first time, it is shown that, for a planar fragment such as the peptide plane, there generally exist 16 different solutions with their analytical expressions presented explicitly. The presence of these solutions is shown to be highly relevant for standard structure determination protocols using RDCs to refine molecular structures. In particular, when using standard protein structure refinement with RDCs that were measured in a single alignment medium as constraints, it is found that often more than one of the peptide plane solutions is physically viable; i.e., despite being consistent with measured RDCs, the local backbone structure can be incorrect. On the basis of experimental and simulated examples, it is rationalized why protein structures that are refined against RDCs measured in a single medium can have lower resolution (precision) than one would expect on the basis of the experimental accuracy of the RDCs. Conditions are discussed under which the correct solution can be identified.
Jean-Christophe Hus#†‡, Loïc Salmon‡, Guillaume Bouvignies‡, Johannes Lotze‡, Martin Blackledge*‡ and Rafael Brüschweiler*§
Abstract
Residual dipolar couplings (RDCs) measured for internally rigid molecular fragments provide important information about the relative orientations of these fragments. Dependent on the symmetry of the alignment tensor and the symmetry of the molecular fragment, however, there generally exist more than one solution for the fragment orientation consistent with the measured RDCs. Analytical solutions are presented that describe the complete set of orientations of internally rigid fragments that are consistent with multiple dipolar couplings measured in a single alignment medium that is rhombic. For the first time, it is shown that, for a planar fragment such as the peptide plane, there generally exist 16 different solutions with their analytical expressions presented explicitly. The presence of these solutions is shown to be highly relevant for standard structure determination protocols using RDCs to refine molecular structures. In particular, when using standard protein structure refinement with RDCs that were measured in a single alignment medium as constraints, it is found that often more than one of the peptide plane solutions is physically viable; i.e., despite being consistent with measured RDCs, the local backbone structure can be incorrect. On the basis of experimental and simulated examples, it is rationalized why protein structures that are refined against RDCs measured in a single medium can have lower resolution (precision) than one would expect on the basis of the experimental accuracy of the RDCs. Conditions are discussed under which the correct solution can be identified.
Thursday, November 20, 2008
J. Am. Chem. Soc., 2008, 130 (46), pp 15726–15731
17O and 15N Solid State NMR Studies on Ligand-Assisted Templating and Oxygen Coordination in the Walls of Mesoporous Nb, Ta and Ti Oxides
Yuxiang Rao†, Tom F. Kemp‡, Michel Trudeau§, Mark E. Smith*‡ and Dave M. Antonelli*†
Abstract
A multinuclear solid state NMR approach is applied to four templated mesoporous oxides (silica, titania, niobia and tantala) to include 15N and 17O magic angle spinning (MAS) NMR and double resonance 15N−93Nb, 17O Rotational-Echo Adiabatic Passage Double Resonance (REAPDOR). The templated samples were ramped in steps of 20 °C for 2 days up to typically 110 °C where the samples were left for 2−4 days. 15N MAS NMR shows that amines are the only species present in the TiO2, Nb2O5, and Ta2O5. In SiO2, amines are only present as a minor coordination (10 ± 2%), but there are several strong ammonium 15N resonances. The REAPDOR experiments show that the nitrogen interacts with niobium, confirming a ligand interaction between the Nb and N, as previously believed. In the case of silica, the amine is quaternized and there is apparently no interaction with the Si, suggesting a RNH3+ −O−Si- hydrogen-bonding interaction with the walls. 17O MAS NMR provides the clearest indication of the local wall structure. In the aged, templated samples in all cases only OM2 coordinations are present which is very different from the pure bulk oxides (apart from SiO2) and must be due to the effects of amine coordination at the metal centers. On removal of the template, these oxides behave differently, with Ta2O5 showing a mixture of OTa2 (85 ± 5%) and OTa3 (15 ± 5%) which is similar to the types of coordination found in the bulk oxide. The previously reported 17O MAS NMR data from heat-treated mesoporous niobia shows only ONb2, which is very highly ordered. In contrast for titania, the OTi2 coordination is immediately lost on removal of the template to be replaced by a mixture of OTi3 (60 ± 5%) and OTi4 (40 ± 5%), with the OTi4 becoming dominant above 250 °C, very different behavior from the corresponding bulk oxide. In summary, this NMR study shows that the local oxygen coordination in amine-templated mesoporous transition metal oxides is present as OM2 which is relatively rare in bulk oxides. The data indicates that the template interaction is largely controlled by the N−M dative bond to the wall, suppressing higher oxygen coordination numbers. Qualitatively it appears that the strength of this interaction varies greatly in the different mesoporous oxides.
Yuxiang Rao†, Tom F. Kemp‡, Michel Trudeau§, Mark E. Smith*‡ and Dave M. Antonelli*†
Abstract
A multinuclear solid state NMR approach is applied to four templated mesoporous oxides (silica, titania, niobia and tantala) to include 15N and 17O magic angle spinning (MAS) NMR and double resonance 15N−93Nb, 17O Rotational-Echo Adiabatic Passage Double Resonance (REAPDOR). The templated samples were ramped in steps of 20 °C for 2 days up to typically 110 °C where the samples were left for 2−4 days. 15N MAS NMR shows that amines are the only species present in the TiO2, Nb2O5, and Ta2O5. In SiO2, amines are only present as a minor coordination (10 ± 2%), but there are several strong ammonium 15N resonances. The REAPDOR experiments show that the nitrogen interacts with niobium, confirming a ligand interaction between the Nb and N, as previously believed. In the case of silica, the amine is quaternized and there is apparently no interaction with the Si, suggesting a RNH3+ −O−Si- hydrogen-bonding interaction with the walls. 17O MAS NMR provides the clearest indication of the local wall structure. In the aged, templated samples in all cases only OM2 coordinations are present which is very different from the pure bulk oxides (apart from SiO2) and must be due to the effects of amine coordination at the metal centers. On removal of the template, these oxides behave differently, with Ta2O5 showing a mixture of OTa2 (85 ± 5%) and OTa3 (15 ± 5%) which is similar to the types of coordination found in the bulk oxide. The previously reported 17O MAS NMR data from heat-treated mesoporous niobia shows only ONb2, which is very highly ordered. In contrast for titania, the OTi2 coordination is immediately lost on removal of the template to be replaced by a mixture of OTi3 (60 ± 5%) and OTi4 (40 ± 5%), with the OTi4 becoming dominant above 250 °C, very different behavior from the corresponding bulk oxide. In summary, this NMR study shows that the local oxygen coordination in amine-templated mesoporous transition metal oxides is present as OM2 which is relatively rare in bulk oxides. The data indicates that the template interaction is largely controlled by the N−M dative bond to the wall, suppressing higher oxygen coordination numbers. Qualitatively it appears that the strength of this interaction varies greatly in the different mesoporous oxides.
J. Phys. Chem. B, 2008, 112 (45), pp 14312–14318
Anesthetic Modulation of Protein Dynamics: Insight from an NMR Study
Christian G. Canlas†, Tanxing Cui†, Ling Li†, Yan Xu†‡ and Pei Tang
Abstract
Mistic (membrane integrating sequence for translation of integral membrane protein constructs) comprises the four-α-helix bundle scaffold found in the transmembrane domains of the Cys-loop receptors that are plausible targets for general anesthetics. Nuclear magnetic resonance (NMR) studies of anesthetic halothane interaction with Mistic in dodecyl phosphocholine (DPC) micelles provide an experimental basis for understanding molecular mechanisms of general anesthesia. Halothane was found to interact directly with Mistic, mostly in the interfacial loop regions. Although the presence of halothane had little effect on Mistic structure, 15N NMR relaxation dispersion measurements revealed that halothane affected Mistic’s motion on the microsecond−millisecond time scale. Halothane shifted the equilibrium of chemical exchange in some residues and made the exchange faster or slower in comparison to the original state in the absence of halothane. The motion on the microsecond−millisecond time scale in several residues disappeared in response to the addition of halothane. Most of the residues experiencing halothane-induced dynamics changes also exhibited profound halothane-induced changes in chemical shift, suggesting that dynamics modification of these residues might result from their direct interaction with halothane molecules. Allosteric modulation by halothane also contributed to dynamics changes, as reflected in residues I52 and Y82 where halothane introduction brought about dynamics changes but not chemical shift changes. The study suggests that inhaled general anesthetics could act on proteins via altering protein motion on the microsecond−millisecond time scale, especially motion in the flexible loops that link different alpha helices. The validation of anesthetic effect on protein dynamics that are potentially correlated with protein functions is a critical step in unraveling the mechanisms of anesthetic action on proteins.
Christian G. Canlas†, Tanxing Cui†, Ling Li†, Yan Xu†‡ and Pei Tang
Abstract
Mistic (membrane integrating sequence for translation of integral membrane protein constructs) comprises the four-α-helix bundle scaffold found in the transmembrane domains of the Cys-loop receptors that are plausible targets for general anesthetics. Nuclear magnetic resonance (NMR) studies of anesthetic halothane interaction with Mistic in dodecyl phosphocholine (DPC) micelles provide an experimental basis for understanding molecular mechanisms of general anesthesia. Halothane was found to interact directly with Mistic, mostly in the interfacial loop regions. Although the presence of halothane had little effect on Mistic structure, 15N NMR relaxation dispersion measurements revealed that halothane affected Mistic’s motion on the microsecond−millisecond time scale. Halothane shifted the equilibrium of chemical exchange in some residues and made the exchange faster or slower in comparison to the original state in the absence of halothane. The motion on the microsecond−millisecond time scale in several residues disappeared in response to the addition of halothane. Most of the residues experiencing halothane-induced dynamics changes also exhibited profound halothane-induced changes in chemical shift, suggesting that dynamics modification of these residues might result from their direct interaction with halothane molecules. Allosteric modulation by halothane also contributed to dynamics changes, as reflected in residues I52 and Y82 where halothane introduction brought about dynamics changes but not chemical shift changes. The study suggests that inhaled general anesthetics could act on proteins via altering protein motion on the microsecond−millisecond time scale, especially motion in the flexible loops that link different alpha helices. The validation of anesthetic effect on protein dynamics that are potentially correlated with protein functions is a critical step in unraveling the mechanisms of anesthetic action on proteins.
J. Am. Chem. Soc., 2008, 130 (45), pp 14990–15001
Structural Insights into the Polymorphism of Amyloid-Like Fibrils Formed by Region 20−29 of Amylin Revealed by Solid-State NMR and X-ray Fiber Diffraction
Jillian Madine†, Edward Jack‡, Peter G. Stockley§, Sheena E. Radford§, Louise C. Serpell∥ and David A. Middleton*†
Abstract
Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-β motif of repeat arrays of β-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP20−29, corresponding to the region S20NNFGAILSS29 of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of 13C dipolar couplings between backbone F23 and I26 of hIAPP20−29 fibrils are consistent with form (1) having parallel β-strands and form (2) having antiparallel strands within the β-sheet layers of the protofilament units. Seeding hIAPP20−29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP8−37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-β spine comprising two β-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel β-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.
Jillian Madine†, Edward Jack‡, Peter G. Stockley§, Sheena E. Radford§, Louise C. Serpell∥ and David A. Middleton*†
Abstract
Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-β motif of repeat arrays of β-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP20−29, corresponding to the region S20NNFGAILSS29 of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of 13C dipolar couplings between backbone F23 and I26 of hIAPP20−29 fibrils are consistent with form (1) having parallel β-strands and form (2) having antiparallel strands within the β-sheet layers of the protofilament units. Seeding hIAPP20−29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP8−37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-β spine comprising two β-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel β-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.
Cryst. Growth Des., 2008, 8 (11), pp 3941–3950
1H, 13C, and 15N Solid-State NMR Studies of Imidazole- and Morpholine-Based Model Compounds Possessing Halogen and Hydrogen Bonding Capabilities
Karim Bouchmella†, Sylvain G. Dutremez*†, Bruno Alonso‡, Francesco Mauri§ and Christel Gervais*#
Abstract
The halogen and hydrogen bonding interactions present in solid 1-(2,3,3-triiodoallyl)imidazole (1), morpholinium iodide (2), the 1:1 cocrystal 1-(2,3,3-triiodoallyl)imidazole·morpholinium iodide (3), morpholine (4), imidazole (5), and 1-(3-iodopropargyl)imidazole (6) have been investigated by solid-state 1H, 13C, and 15N NMR spectroscopies. Comparison of the 15N CP MAS NMR spectrum of 3 with that of 2 indicates that protonated morpholine is present in solid 3, but this conclusion must be taken with caution as GIPAW calculations predict a 15N chemical shift for morpholine similar to that of the morpholinium cation. Conclusive evidence for the presence of a morpholinium cation in crystalline 3 was obtained by recording the static 15N NMR spectrum of this host−guest complex and comparing the morpholinium/morpholine part of the spectrum with the static spectra of 3 and 4 as obtained from ab initio calculations of NMR parameters based on the X-ray structures of these compounds. Concerning the imidazolyl group, 15N NMR spectroscopy has proven quite valuable to identify changes in the bonding situation of the C−NC nitrogen on passing from 1 to 3. In addition, slight differences are observed between the 15N chemical shifts of 1 and 6 that are ascribed to differences in halogen bond strengths between the two compounds. Attempts have also been made to study halogen bonding by 13C NMR spectroscopy, but this method did not provide exploitable results as signals corresponding to the sp and sp2 carbon atoms bonded to iodine could not be observed experimentally. 1H NMR spectroscopy is a powerful tool to study hydrogen bonding interactions of moderate energies such as +NH2···X (X = N, O, I). Indeed, we have found that the chemical shifts of the NH hydrogens were quite sensitive to the nature of X and to the N−H···X distance. This is demonstrated by the fact that the chemical shifts of the +NH2 protons of the morpholinium cation in 2 and 3 are noticeably different.
Karim Bouchmella†, Sylvain G. Dutremez*†, Bruno Alonso‡, Francesco Mauri§ and Christel Gervais*#
Abstract
The halogen and hydrogen bonding interactions present in solid 1-(2,3,3-triiodoallyl)imidazole (1), morpholinium iodide (2), the 1:1 cocrystal 1-(2,3,3-triiodoallyl)imidazole·morpholinium iodide (3), morpholine (4), imidazole (5), and 1-(3-iodopropargyl)imidazole (6) have been investigated by solid-state 1H, 13C, and 15N NMR spectroscopies. Comparison of the 15N CP MAS NMR spectrum of 3 with that of 2 indicates that protonated morpholine is present in solid 3, but this conclusion must be taken with caution as GIPAW calculations predict a 15N chemical shift for morpholine similar to that of the morpholinium cation. Conclusive evidence for the presence of a morpholinium cation in crystalline 3 was obtained by recording the static 15N NMR spectrum of this host−guest complex and comparing the morpholinium/morpholine part of the spectrum with the static spectra of 3 and 4 as obtained from ab initio calculations of NMR parameters based on the X-ray structures of these compounds. Concerning the imidazolyl group, 15N NMR spectroscopy has proven quite valuable to identify changes in the bonding situation of the C−NC nitrogen on passing from 1 to 3. In addition, slight differences are observed between the 15N chemical shifts of 1 and 6 that are ascribed to differences in halogen bond strengths between the two compounds. Attempts have also been made to study halogen bonding by 13C NMR spectroscopy, but this method did not provide exploitable results as signals corresponding to the sp and sp2 carbon atoms bonded to iodine could not be observed experimentally. 1H NMR spectroscopy is a powerful tool to study hydrogen bonding interactions of moderate energies such as +NH2···X (X = N, O, I). Indeed, we have found that the chemical shifts of the NH hydrogens were quite sensitive to the nature of X and to the N−H···X distance. This is demonstrated by the fact that the chemical shifts of the +NH2 protons of the morpholinium cation in 2 and 3 are noticeably different.
J. Med. Chem., 2008, 51 (22), pp 7205–7215
Discovery of Ligands for a Novel Target, the Human Telomerase RNA, Based on Flexible-Target Virtual Screening and NMR
Irene Gómez Pinto†‡, Christophe Guilbert†, Nikolai B. Ulyanov†, Jay Stearns§ and Thomas L. James*†
Abstract
The human ribonucleoprotein telomerase is a validated anticancer drug target, and hTR-P2b is a part of the human telomerase RNA (hTR) essential for its activity. Interesting ligands that bind hTR-P2b were identified by iteratively using a tandem structure-based approach: docking of potential ligands from small databases to hTR-P2b via the program MORDOR, which permits flexibility in both ligand and target, with subsequent NMR screening of high-ranking compounds. A high percentage of the compounds tested experimentally were found via NMR to bind to the U-rich region of hTR-P2b; most have MW < 500 Da and are from different compound classes, and several possess a charge of 0 or +1. Of the 48 ligands identified, 24 exhibit a decided preference to bind hTR-P2b RNA rather than A-site rRNA and 10 do not bind A-site rRNA at all. Binding affinity was measured by monitoring RNA imino proton resonances for some of the compounds that showed hTR binding preference.
Irene Gómez Pinto†‡, Christophe Guilbert†, Nikolai B. Ulyanov†, Jay Stearns§ and Thomas L. James*†
Abstract
The human ribonucleoprotein telomerase is a validated anticancer drug target, and hTR-P2b is a part of the human telomerase RNA (hTR) essential for its activity. Interesting ligands that bind hTR-P2b were identified by iteratively using a tandem structure-based approach: docking of potential ligands from small databases to hTR-P2b via the program MORDOR, which permits flexibility in both ligand and target, with subsequent NMR screening of high-ranking compounds. A high percentage of the compounds tested experimentally were found via NMR to bind to the U-rich region of hTR-P2b; most have MW < 500 Da and are from different compound classes, and several possess a charge of 0 or +1. Of the 48 ligands identified, 24 exhibit a decided preference to bind hTR-P2b RNA rather than A-site rRNA and 10 do not bind A-site rRNA at all. Binding affinity was measured by monitoring RNA imino proton resonances for some of the compounds that showed hTR binding preference.
J. Am. Chem. Soc., Article ASAP
Combined NMR and DFT Studies for the Absolute Configuration Elucidation of the Spore Photoproduct, a UV-Induced DNA Lesion
Claire Mantel§, Alexia Chandor†‡, Didier Gasparutto†, Thierry Douki†, Mohamed Atta‡, Marc Fontecave‡, Pierre-Alain Bayle§, Jean-Marie Mouesca*§ and Michel Bardet*§
Abstract
By irradiation of bacterial spores under UV radiation, a photoproduct (SP) bearing a covalent methylene link between two adjacent thymines is formed in DNA. Because of the presence of an asymmetric carbon on the aglycone and of two possible orientations for the formation of the cross-link, four isomers could in principle be obtained. Currently, no conclusive structural information of this photoproduct is available. The structure of the isolated SPTpT dinucleotide was revisited in order to determine the type of cross-link and the absolute configuration of the C5a carbon. For this purpose, a study combining NMR spectroscopy and DFT calculations was pursued on the spore photoproduct of the dinucleoside TpT since its structure was previously shown to be identical to the one produced in DNA. A full characterization of SPTpT by NMR analyses was performed in D2O and DMSO. 2D NMR measurements (1H−13C, 1H−31P, COSY, NOESY, and ROESY) and DFT calculations (geometries optimization of R and S isomers and theoretical chemical shifts) lead us to conclude without ambiguity that the absolute configuration of the C5a carbon is R and that the methylene bridge of the photoproduct corresponds to the methyl group of the thymine located on the 3′-end of the dinucleoside monophosphate.
Claire Mantel§, Alexia Chandor†‡, Didier Gasparutto†, Thierry Douki†, Mohamed Atta‡, Marc Fontecave‡, Pierre-Alain Bayle§, Jean-Marie Mouesca*§ and Michel Bardet*§
Abstract
By irradiation of bacterial spores under UV radiation, a photoproduct (SP) bearing a covalent methylene link between two adjacent thymines is formed in DNA. Because of the presence of an asymmetric carbon on the aglycone and of two possible orientations for the formation of the cross-link, four isomers could in principle be obtained. Currently, no conclusive structural information of this photoproduct is available. The structure of the isolated SPTpT dinucleotide was revisited in order to determine the type of cross-link and the absolute configuration of the C5a carbon. For this purpose, a study combining NMR spectroscopy and DFT calculations was pursued on the spore photoproduct of the dinucleoside TpT since its structure was previously shown to be identical to the one produced in DNA. A full characterization of SPTpT by NMR analyses was performed in D2O and DMSO. 2D NMR measurements (1H−13C, 1H−31P, COSY, NOESY, and ROESY) and DFT calculations (geometries optimization of R and S isomers and theoretical chemical shifts) lead us to conclude without ambiguity that the absolute configuration of the C5a carbon is R and that the methylene bridge of the photoproduct corresponds to the methyl group of the thymine located on the 3′-end of the dinucleoside monophosphate.
Tuesday, November 18, 2008
Al's Update
Consolidated silica glass from nanoparticles
Journal of Solid State Chemistry 181 (2008) 2442– 2447
Thomas G. Mayerhöfer, Zhijian Shen, Ekaterina Leonova, Mattias Edén, Antje Kriltz, Jürgen Popp
Abstract:
A dense silica glass was prepared by consolidating a highly dispersed silicic acid powder (particle size less than 10 nm) with the Spark Plasma Sintering (SPS) technique. The glass was characterized by ellipsometry, transmission electron microscopy (TEM), infrared reflectance and transmittance spectroscopy, as well as by Raman, UV–Vis–NIR and solid-state nuclear magnetic resonance (NMR) spectroscopy. The prototypic sample showed a transmittance of about 63% compared to silica glass in the UV–Vis spectral range. Based on the results of infrared transmittance spectroscopy this lower transparency is due to the comparably high water content, which is about 40 times higher than that in silica glass. 1H magic-angle spinning (MAS) NMR confirmed an increase in hydroxyl groups in the sample prepared by SPS relative to that of the conventional SiO2 reference glass. Aside from the comparably high water content, we conclude from the similarity of the IR-reflectance and the 29Si MAS NMR spectra of the SPS sample and the corresponding spectra of the conventionally prepared silica glass, that the short- and medium-range order is virtually the same in both materials. Raman spectroscopy, however, suggests that the number of three- and four-membered rings is significantly smaller in the SPS sample compared to the conventionally prepared sample. Based on these results we conclude that it is possible to prepare glasses by compacting amorphous powders by the SPS process. The SPS process may therefore enable the preparation of glasses with compositions inaccessible by conventional methods.
The mechanism of paramagnetic NMR relaxation produced by Mn(II): Role of orthorhombic and fourth-order zero field splitting terms
J. Chem. Phys. 129, 144307 (2008)
Robert Sharp
Abstract:
Mn(II) is a spin-5/2 paramagnetic ion that mediates a characteristically large NMR paramagnetic relaxation enhancement (NMR-PRE) of nuclear spins in solution. In the range of high magnetic field strengths (above about 0.3 T), where the electronic Zeeman interaction provides the largest term of the electron spin Hamiltonian, NMR relaxation mechanism is well understood. In the lower field range, the physical picture is more complex because of the presence in the spin Hamiltonian of zero field splitting (ZFS) terms that are comparable to or greater than the Zeeman term. This work describes a systematic study of the relaxation mechanism in the low field range, particularly aspects involving the dependence of NMR-PRE on the orthorhombic (E) and fourth-order (a q(4)">, q=0,2,4) ZFS tensor components. It is shown that the fourfold (a4(4)"> ) and twofold (a2(4)"> ) fourth-order components exert large orientation-dependent influences on the NMR-PRE. Thus, fourth-order terms with magnitudes equal to only a few percent of the quadratic ZFS terms (D,E) produce large changes in the shape of the magnetic field profile of the PRE. Effects arising from the orthorhombic quadratic ZFS term (E) are much smaller than those of the fourth-order terms and can in most cases be neglected. However, effects due to a4(4)"> and a2(4)"> need to be included in simulations of low field data.
A magic-angle-spinning NMR method for 1H–1H distance measurement using coherent polarization transfer in 13C-labeled organic solids
J. Chem. Phys. 129, 154504 (2008)
Hiroki Takahashi, Hideo Akutsu, and Toshimichi Fujiwara
Abstract:
We have developed a theory for 1H–1H distance measurements from the direct polarization transfer in 13C-labeled solids under magic-angle spinning. The polarization transfer caused by the 1H–1H dipolar interactions was analyzed with zeroth-order average Hamiltonian for a 1H–13C–13C–1H spin system in the frame modulated by 13C–1H dipolar interactions and chemical shifts. Strong 13C–1H dipolar couplings primarily determine the recovery of the 1H–1H coupling as a function of sample spinning frequency. The effect of additional 1H spins on the polarization transfer was also taken into account. We have applied this method to the distance measurements for uniformly 13C-, 15N-labeled L-valine and adenosine. Experimental 1H polarization transfer was monitored through high-resolution 13C-NMR. The theoretical analysis provided the distances up to about 3 Å with an accuracy of about 0.2 Å and those of about 4 Å with 1 Å even from the transfer amplitudes at a few mixing times. The longer distances are partly affected by the relayed polarization transfer which makes apparent 1H–1H distances shorter. Our theory based on the coherent polarization transfer in the initial build-up regime was compared to the description by the rate equations with spin diffusion time constants.
Symmetry-based recoupling in double-rotation NMR spectroscopy
J. Chem. Phys. 129, 174507 (2008)
Andreas Brinkmann, Arno P. M. Kentgens, Tiit Anupõld, and Ago Samoson
Abstract:
In this contribution, we extend the theory of symmetry-based pulse sequences of types CN νn and RN νn in magic-angle-spinning nuclear resonance spectroscopy [M. H. Levitt, in Encyclopedia of Nuclear Magnetic Resonance, edited by D. M. Grant and R. K. Harris (Wiley, Chichester, 2002), Vol. 9]. to the case of rotating the sample simultaneously around two different angles with respect to the external magnetic field (double-rotation). We consider the case of spin-1/2 nuclei in general and the case of half-integer quadrupolar nuclei that are subjected to weak radio frequency pulses operating selectively on the central-transition polarizations. The transformation properties of the homonuclear dipolar interactions and J-couplings under central-transition-selective spin rotations are presented. We show that the pulse sequence R221R22-1 originally developed for homonuclear dipolar recoupling of half-integer quadrupolar nuclei under magic-angle-spinning conditions [M. Edén, D. Zhou, and J. Yu, Chem. Phys. Lett. 431, 397 (2006)] may be used for the same purpose in the case of double rotation, if the radio frequency pulses are synchronized with the outer rotation of the sample. We apply this sequence, sandwiched by central-transition selective 90° pulses, to excite double-quantum coherences in homonuclear spin systems consisting of 23Na and 27Al nuclei.
Three Polymorphic Forms of the Co-Crystal 4,4-Bipyridine/Pimelic Acid and their Structural, Thermal, and Spectroscopic Characterization
Chem. Eur. J., Volume 14 Issue 32, Pages 10149 - 10159
Dario Braga, Prof., Giuseppe Palladino, Dr., Marco Polito, Dr., Katia Rubini, Dr., Fabrizia Grepioni, Prof., Michele R. Chierotti, Dr., Roberto Gobetto, Prof.
Abstract:
Three crystal forms of the co-crystal 4,4-bipy/pimelic acid (bipy: bipyridine), [NH4C5-C5H4N][HOOC(CH2)5COOH], have been prepared and their relationship investigated by single-crystal X-ray diffraction, variable-temperature X-ray powder diffraction, differential scanning calorimetry and solid-state NMR spectroscopy. Both X-ray and NMR spectroscopic results indicate that no proton transfer takes place, that is, the three crystal forms are true co-crystals of neutral molecules. Forms I and II both convert into Form III at high temperature, Forms II and III being the thermodynamically stable forms at room and high temperature, respectively.
Journal of Solid State Chemistry 181 (2008) 2442– 2447
Thomas G. Mayerhöfer, Zhijian Shen, Ekaterina Leonova, Mattias Edén, Antje Kriltz, Jürgen Popp
Abstract:
A dense silica glass was prepared by consolidating a highly dispersed silicic acid powder (particle size less than 10 nm) with the Spark Plasma Sintering (SPS) technique. The glass was characterized by ellipsometry, transmission electron microscopy (TEM), infrared reflectance and transmittance spectroscopy, as well as by Raman, UV–Vis–NIR and solid-state nuclear magnetic resonance (NMR) spectroscopy. The prototypic sample showed a transmittance of about 63% compared to silica glass in the UV–Vis spectral range. Based on the results of infrared transmittance spectroscopy this lower transparency is due to the comparably high water content, which is about 40 times higher than that in silica glass. 1H magic-angle spinning (MAS) NMR confirmed an increase in hydroxyl groups in the sample prepared by SPS relative to that of the conventional SiO2 reference glass. Aside from the comparably high water content, we conclude from the similarity of the IR-reflectance and the 29Si MAS NMR spectra of the SPS sample and the corresponding spectra of the conventionally prepared silica glass, that the short- and medium-range order is virtually the same in both materials. Raman spectroscopy, however, suggests that the number of three- and four-membered rings is significantly smaller in the SPS sample compared to the conventionally prepared sample. Based on these results we conclude that it is possible to prepare glasses by compacting amorphous powders by the SPS process. The SPS process may therefore enable the preparation of glasses with compositions inaccessible by conventional methods.
The mechanism of paramagnetic NMR relaxation produced by Mn(II): Role of orthorhombic and fourth-order zero field splitting terms
J. Chem. Phys. 129, 144307 (2008)
Robert Sharp
Abstract:
Mn(II) is a spin-5/2 paramagnetic ion that mediates a characteristically large NMR paramagnetic relaxation enhancement (NMR-PRE) of nuclear spins in solution. In the range of high magnetic field strengths (above about 0.3 T), where the electronic Zeeman interaction provides the largest term of the electron spin Hamiltonian, NMR relaxation mechanism is well understood. In the lower field range, the physical picture is more complex because of the presence in the spin Hamiltonian of zero field splitting (ZFS) terms that are comparable to or greater than the Zeeman term. This work describes a systematic study of the relaxation mechanism in the low field range, particularly aspects involving the dependence of NMR-PRE on the orthorhombic (E) and fourth-order (a q(4)">, q=0,2,4) ZFS tensor components. It is shown that the fourfold (a4(4)"> ) and twofold (a2(4)"> ) fourth-order components exert large orientation-dependent influences on the NMR-PRE. Thus, fourth-order terms with magnitudes equal to only a few percent of the quadratic ZFS terms (D,E) produce large changes in the shape of the magnetic field profile of the PRE. Effects arising from the orthorhombic quadratic ZFS term (E) are much smaller than those of the fourth-order terms and can in most cases be neglected. However, effects due to a4(4)"> and a2(4)"> need to be included in simulations of low field data.
A magic-angle-spinning NMR method for 1H–1H distance measurement using coherent polarization transfer in 13C-labeled organic solids
J. Chem. Phys. 129, 154504 (2008)
Hiroki Takahashi, Hideo Akutsu, and Toshimichi Fujiwara
Abstract:
We have developed a theory for 1H–1H distance measurements from the direct polarization transfer in 13C-labeled solids under magic-angle spinning. The polarization transfer caused by the 1H–1H dipolar interactions was analyzed with zeroth-order average Hamiltonian for a 1H–13C–13C–1H spin system in the frame modulated by 13C–1H dipolar interactions and chemical shifts. Strong 13C–1H dipolar couplings primarily determine the recovery of the 1H–1H coupling as a function of sample spinning frequency. The effect of additional 1H spins on the polarization transfer was also taken into account. We have applied this method to the distance measurements for uniformly 13C-, 15N-labeled L-valine and adenosine. Experimental 1H polarization transfer was monitored through high-resolution 13C-NMR. The theoretical analysis provided the distances up to about 3 Å with an accuracy of about 0.2 Å and those of about 4 Å with 1 Å even from the transfer amplitudes at a few mixing times. The longer distances are partly affected by the relayed polarization transfer which makes apparent 1H–1H distances shorter. Our theory based on the coherent polarization transfer in the initial build-up regime was compared to the description by the rate equations with spin diffusion time constants.
Symmetry-based recoupling in double-rotation NMR spectroscopy
J. Chem. Phys. 129, 174507 (2008)
Andreas Brinkmann, Arno P. M. Kentgens, Tiit Anupõld, and Ago Samoson
Abstract:
In this contribution, we extend the theory of symmetry-based pulse sequences of types CN νn and RN νn in magic-angle-spinning nuclear resonance spectroscopy [M. H. Levitt, in Encyclopedia of Nuclear Magnetic Resonance, edited by D. M. Grant and R. K. Harris (Wiley, Chichester, 2002), Vol. 9]. to the case of rotating the sample simultaneously around two different angles with respect to the external magnetic field (double-rotation). We consider the case of spin-1/2 nuclei in general and the case of half-integer quadrupolar nuclei that are subjected to weak radio frequency pulses operating selectively on the central-transition polarizations. The transformation properties of the homonuclear dipolar interactions and J-couplings under central-transition-selective spin rotations are presented. We show that the pulse sequence R221R22-1 originally developed for homonuclear dipolar recoupling of half-integer quadrupolar nuclei under magic-angle-spinning conditions [M. Edén, D. Zhou, and J. Yu, Chem. Phys. Lett. 431, 397 (2006)] may be used for the same purpose in the case of double rotation, if the radio frequency pulses are synchronized with the outer rotation of the sample. We apply this sequence, sandwiched by central-transition selective 90° pulses, to excite double-quantum coherences in homonuclear spin systems consisting of 23Na and 27Al nuclei.
Three Polymorphic Forms of the Co-Crystal 4,4-Bipyridine/Pimelic Acid and their Structural, Thermal, and Spectroscopic Characterization
Chem. Eur. J., Volume 14 Issue 32, Pages 10149 - 10159
Dario Braga, Prof., Giuseppe Palladino, Dr., Marco Polito, Dr., Katia Rubini, Dr., Fabrizia Grepioni, Prof., Michele R. Chierotti, Dr., Roberto Gobetto, Prof.
Abstract:
Three crystal forms of the co-crystal 4,4-bipy/pimelic acid (bipy: bipyridine), [NH4C5-C5H4N][HOOC(CH2)5COOH], have been prepared and their relationship investigated by single-crystal X-ray diffraction, variable-temperature X-ray powder diffraction, differential scanning calorimetry and solid-state NMR spectroscopy. Both X-ray and NMR spectroscopic results indicate that no proton transfer takes place, that is, the three crystal forms are true co-crystals of neutral molecules. Forms I and II both convert into Form III at high temperature, Forms II and III being the thermodynamically stable forms at room and high temperature, respectively.
Monday, November 10, 2008
Journal of Magnetic Resonance - Vol 195 Issue 2
Band selective small flip angle COSY: A simple experiment for the analyses of 1H NMR spectra of small chiral molecules
Uday Ramesh Prabhu and N. Suryaprakash
The NMR spectroscopic discrimination of enantiomers in the chiral liquid crystalline solvent is more often carried out using 2H detection in its natural abundance. The employment of 1H detection for such a purpose is severely hampered due to significant loss of resolution in addition to indistinguishable overlap of the spectra from the two enantiomers. This study demonstrates that the band selected small flip angle homonuclear correlation experiment is a simple and robust technique that provides unambiguous discrimination, very high spectral resolution, reduced multiplicity of transitions, relative signs of the couplings and enormous saving of instrument time.
Biomolecular solid state NMR with magic-angle spinning at 25 K
Kent R. Thurber and Robert Tycko
A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25 K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (±5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature 13C NMR data for two biomolecular samples, namely the peptide Aβ14–23 in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin–lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and 13C MAS NMR linewidths are discussed.
Single-scan 2D DOSY NMR spectroscopy
Yoav Shrot, and Lucio Frydman
Spatial encoding is a particular kind of spin manipulation that enables the acquisition of multidimensional NMR spectra within a single scan. This encoding has been shown to possess a general applicability and to enable the completion of arbitrary nD NMR acquisitions within a single transient. The present study explores its potential towards the acquisition of 2D DOSY spectra, where the indirect dimension is meant to encode molecular displacements rather than a coherent spin evolution. We find that in its simplest form this extension shows similarities with methods that have been recently discussed for the single-scan acquisition of this kind of traces; still, a number of advantageous features are also evidenced by the “ultrafast” modality hereby introduced. The principles underlying the operation of this new single-scan 2D DOSY approach are discussed, its use is illustrated with a variety of sequences and of samples, the limitations of this new experiment are noted, and potential extensions of the methodology are mentioned.
Uday Ramesh Prabhu and N. Suryaprakash
The NMR spectroscopic discrimination of enantiomers in the chiral liquid crystalline solvent is more often carried out using 2H detection in its natural abundance. The employment of 1H detection for such a purpose is severely hampered due to significant loss of resolution in addition to indistinguishable overlap of the spectra from the two enantiomers. This study demonstrates that the band selected small flip angle homonuclear correlation experiment is a simple and robust technique that provides unambiguous discrimination, very high spectral resolution, reduced multiplicity of transitions, relative signs of the couplings and enormous saving of instrument time.
Biomolecular solid state NMR with magic-angle spinning at 25 K
Kent R. Thurber and Robert Tycko
A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25 K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (±5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature 13C NMR data for two biomolecular samples, namely the peptide Aβ14–23 in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin–lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and 13C MAS NMR linewidths are discussed.
Single-scan 2D DOSY NMR spectroscopy
Yoav Shrot, and Lucio Frydman
Spatial encoding is a particular kind of spin manipulation that enables the acquisition of multidimensional NMR spectra within a single scan. This encoding has been shown to possess a general applicability and to enable the completion of arbitrary nD NMR acquisitions within a single transient. The present study explores its potential towards the acquisition of 2D DOSY spectra, where the indirect dimension is meant to encode molecular displacements rather than a coherent spin evolution. We find that in its simplest form this extension shows similarities with methods that have been recently discussed for the single-scan acquisition of this kind of traces; still, a number of advantageous features are also evidenced by the “ultrafast” modality hereby introduced. The principles underlying the operation of this new single-scan 2D DOSY approach are discussed, its use is illustrated with a variety of sequences and of samples, the limitations of this new experiment are noted, and potential extensions of the methodology are mentioned.
Friday, November 07, 2008
J. Am. Chem. Soc., 130 (44), 14521–14532, 2008.
Raftlike Mixtures of Sphingomyelin and Cholesterol Investigated by Solid-State 2H NMR Spectroscopy
Tim Bartels, Ravi S. Lankalapalli, Robert Bittman, Klaus Beyer, and Michael F. Brown
Abstract:
Sphingomyelin is a lipid that is abundant in the nervous systems of mammals, where it is associated with putative microdomains in cellular membranes and undergoes alterations due to aging or neurodegeneration. We investigated the effect of varying the concentration of cholesterol in binary and ternary mixtures with N-palmitoylsphingomyelin (PSM) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) using deuterium nuclear magnetic resonance (2H NMR) spectroscopy in both macroscopically aligned and unoriented multilamellar dispersions. In our experiments, we used PSM and POPC perdeuterated on the N-acyl and sn-1 acyl chains, respectively. By measuring solid-state 2H NMR spectra of the two lipids separately in mixtures with the same compositions as a function of cholesterol mole fraction and temperature, we obtained clear evidence for the coexistence of two liquid-crystalline domains in distinct regions of the phase diagram. According to our analysis of the first moments M1 and the observed 2H NMR spectra, one of the domains appears to be a liquid-ordered phase. We applied a mean-torque potential model as an additional tool to calculate the average hydrocarbon thickness, the area per lipid, and structural parameters such as chain extension and thermal expansion coefficient in order to further define the two coexisting phases. Our data imply that phase separation takes place in raftlike ternary PSM/POPC/cholesterol mixtures over a broad temperature range but vanishes at cholesterol concentrations equal to or greater than a mole fraction of 0.33. Cholesterol interacts preferentially with sphingomyelin only at smaller mole fractions, above which a homogeneous liquid-ordered phase is present. The reasons for these phase separation phenomena seem to be differences in the effects of cholesterol on the configurational order of the palmitoyl chains in PSM-d31 and POPC-d31 and a difference in the affinity of cholesterol for sphingomyelin observed at low temperatures. Hydrophobic matching explains the occurrence of raftlike domains in cellular membranes at intermediate cholesterol concentrations but not saturating amounts of cholesterol.
Tim Bartels, Ravi S. Lankalapalli, Robert Bittman, Klaus Beyer, and Michael F. Brown
Abstract:
Sphingomyelin is a lipid that is abundant in the nervous systems of mammals, where it is associated with putative microdomains in cellular membranes and undergoes alterations due to aging or neurodegeneration. We investigated the effect of varying the concentration of cholesterol in binary and ternary mixtures with N-palmitoylsphingomyelin (PSM) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) using deuterium nuclear magnetic resonance (2H NMR) spectroscopy in both macroscopically aligned and unoriented multilamellar dispersions. In our experiments, we used PSM and POPC perdeuterated on the N-acyl and sn-1 acyl chains, respectively. By measuring solid-state 2H NMR spectra of the two lipids separately in mixtures with the same compositions as a function of cholesterol mole fraction and temperature, we obtained clear evidence for the coexistence of two liquid-crystalline domains in distinct regions of the phase diagram. According to our analysis of the first moments M1 and the observed 2H NMR spectra, one of the domains appears to be a liquid-ordered phase. We applied a mean-torque potential model as an additional tool to calculate the average hydrocarbon thickness, the area per lipid, and structural parameters such as chain extension and thermal expansion coefficient in order to further define the two coexisting phases. Our data imply that phase separation takes place in raftlike ternary PSM/POPC/cholesterol mixtures over a broad temperature range but vanishes at cholesterol concentrations equal to or greater than a mole fraction of 0.33. Cholesterol interacts preferentially with sphingomyelin only at smaller mole fractions, above which a homogeneous liquid-ordered phase is present. The reasons for these phase separation phenomena seem to be differences in the effects of cholesterol on the configurational order of the palmitoyl chains in PSM-d31 and POPC-d31 and a difference in the affinity of cholesterol for sphingomyelin observed at low temperatures. Hydrophobic matching explains the occurrence of raftlike domains in cellular membranes at intermediate cholesterol concentrations but not saturating amounts of cholesterol.
Thursday, November 06, 2008
J. Am. Chem. Soc., 130 (43), 14280–14286, 2008.
NMR-Based Mapping of Disulfide Bridges in Cysteine-Rich Peptides: Application to the μ-Conotoxin SxIIIA
Aleksandra Walewska,†‡ Jack J. Skalicky,§ Darrell R. Davis,∥ Min-Min Zhang,† Estuardo Lopez-Vera,†⊥ Maren Watkins,# Tiffany S. Han,† Doju Yoshikami,† Baldomero M. Olivera,† and Grzegorz Bulaj*∥
Abstract:
Disulfide-rich peptides represent a megadiverse group of natural products with very promising therapeutic potential. To accelerate their functional characterization, high-throughput chemical synthesis and folding methods are required, including efficient mapping of multiple disulfide bridges. Here, we describe a novel approach for such mapping and apply it to a three-disulfide-bridged conotoxin, μ-SxIIIA (from the venom of Conus striolatus), whose discovery is also reported here for the first time. μ-SxIIIA was chemically synthesized with three cysteine residues labeled 100% with 15N/13C, while the remaining three cysteine residues were incorporated using a mixture of 70%/30% unlabeled/labeled Fmoc-protected residues. After oxidative folding, the major product was analyzed by NMR spectroscopy. Sequence-specific resonance assignments for the isotope-enriched Cys residues were determined with 2D versions of standard triple-resonance (1H, 13C, 15N) NMR experiments and 2D [13C, 1H] HSQC. Disulfide patterns were directly determined with cross-disulfide NOEs confirming that the oxidation product had the disulfide connectivities characteristic of μ-conotoxins. μ-SxIIIA was found to be a potent blocker of the sodium channel subtype NaV1.4 (IC50 = 7 nM). These results suggest that differential incorporation of isotope-labeled cysteine residues is an efficient strategy to map disulfides and should facilitate the discovery and structure−function studies of many bioactive peptides.
Aleksandra Walewska,†‡ Jack J. Skalicky,§ Darrell R. Davis,∥ Min-Min Zhang,† Estuardo Lopez-Vera,†⊥ Maren Watkins,# Tiffany S. Han,† Doju Yoshikami,† Baldomero M. Olivera,† and Grzegorz Bulaj*∥
Abstract:
Disulfide-rich peptides represent a megadiverse group of natural products with very promising therapeutic potential. To accelerate their functional characterization, high-throughput chemical synthesis and folding methods are required, including efficient mapping of multiple disulfide bridges. Here, we describe a novel approach for such mapping and apply it to a three-disulfide-bridged conotoxin, μ-SxIIIA (from the venom of Conus striolatus), whose discovery is also reported here for the first time. μ-SxIIIA was chemically synthesized with three cysteine residues labeled 100% with 15N/13C, while the remaining three cysteine residues were incorporated using a mixture of 70%/30% unlabeled/labeled Fmoc-protected residues. After oxidative folding, the major product was analyzed by NMR spectroscopy. Sequence-specific resonance assignments for the isotope-enriched Cys residues were determined with 2D versions of standard triple-resonance (1H, 13C, 15N) NMR experiments and 2D [13C, 1H] HSQC. Disulfide patterns were directly determined with cross-disulfide NOEs confirming that the oxidation product had the disulfide connectivities characteristic of μ-conotoxins. μ-SxIIIA was found to be a potent blocker of the sodium channel subtype NaV1.4 (IC50 = 7 nM). These results suggest that differential incorporation of isotope-labeled cysteine residues is an efficient strategy to map disulfides and should facilitate the discovery and structure−function studies of many bioactive peptides.
J. Am. Chem. Soc., 130 (43), 14179–14188, 2008.
Microsolvation and 13C−Li NMR Coupling
Rudolf Knorr,* Thomas Menke, Kathrin Ferchland, Johann Mehlstäubl, and David S. Stephenson
Abstract:
The empirical expression 1JCLi = L[n(a + d)]−1 is proposed; it claims a reciprocal dependence of the NMR coupling constant 1J(13C, Li) in a C−Li compound on two factors: (i) the number n of lithium nuclei in bonding contact with the observed carbanion center and (ii) the sum (a + d) of the numbers a of anions and d of donor ligands coordinated at the Li nucleus that generates the observed 1JCLi value. The expression was derived from integrations of separate NMR resonances of coordinated and free monodentate donor ligands (t-BuOMe, Et2O, or THF) in toluene solutions of dimeric and monomeric 2-(α-aryl-α-lithiomethylidene)-1,1,3,3-tetramethylindan at moderately low temperatures. This unusually slow ligand interchange is ascribed to steric congestion in these compounds, which is further characterized by measurements of nuclear Overhauser correlations and by solid-state structures of the dimers bearing only one donor per lithium atom (d = 1). Increasing microsolvation numbers d are also accompanied by typical changes of the NMR chemical shifts δ (positive for the carbanionic 13Cα, negative for Cpara and p-H). The aforementioned empirical expression for 1JCLi appears to be applicable to other cases of solvated monomeric, dimeric, or tetrameric C−Li compounds (alkyl, alkenyl, alkynyl, and aryl) and even to unsolvated (d ≈ 0) trimeric, tetrameric, or hexameric organolithium aggregates, indicating that 1JCLi might serve as a tool for assessing unknown microsolvation numbers. The importance of obtaining evidence about the 13C NMR C−Li multiplet splitting of both the nonfluxional and fluxional aggregates is emphasized.
Rudolf Knorr,* Thomas Menke, Kathrin Ferchland, Johann Mehlstäubl, and David S. Stephenson
Abstract:
The empirical expression 1JCLi = L[n(a + d)]−1 is proposed; it claims a reciprocal dependence of the NMR coupling constant 1J(13C, Li) in a C−Li compound on two factors: (i) the number n of lithium nuclei in bonding contact with the observed carbanion center and (ii) the sum (a + d) of the numbers a of anions and d of donor ligands coordinated at the Li nucleus that generates the observed 1JCLi value. The expression was derived from integrations of separate NMR resonances of coordinated and free monodentate donor ligands (t-BuOMe, Et2O, or THF) in toluene solutions of dimeric and monomeric 2-(α-aryl-α-lithiomethylidene)-1,1,3,3-tetramethylindan at moderately low temperatures. This unusually slow ligand interchange is ascribed to steric congestion in these compounds, which is further characterized by measurements of nuclear Overhauser correlations and by solid-state structures of the dimers bearing only one donor per lithium atom (d = 1). Increasing microsolvation numbers d are also accompanied by typical changes of the NMR chemical shifts δ (positive for the carbanionic 13Cα, negative for Cpara and p-H). The aforementioned empirical expression for 1JCLi appears to be applicable to other cases of solvated monomeric, dimeric, or tetrameric C−Li compounds (alkyl, alkenyl, alkynyl, and aryl) and even to unsolvated (d ≈ 0) trimeric, tetrameric, or hexameric organolithium aggregates, indicating that 1JCLi might serve as a tool for assessing unknown microsolvation numbers. The importance of obtaining evidence about the 13C NMR C−Li multiplet splitting of both the nonfluxional and fluxional aggregates is emphasized.
Monday, October 27, 2008
Chemical and Engineering News : Cover Story on DNP
A nice article about dynamic nuclear polarization courtesy of Chemical and Engineering News.
http://pubs.acs.org/cen/coverstory/86/8643cover.html
http://pubs.acs.org/cen/coverstory/86/8643cover.html
Friday, October 24, 2008
J. Am. Chem. Soc., 130 (43), 14060–14061, 2008.
Dynamics of Ligand Binding from 13C NMR Relaxation Dispersion at Natural Abundance
John S. Zintsmaster, Brian D. Wilson, and Jeffrey W. Peng*
Abstract:
We show that Carr−Purcell−Meiboom−Gill (CPMG) 13Cα NMR relaxation dispersion measurements are a viable means for profiling μs−ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Cα nuclei that experience μs−ms modulation of their chemical shifts due to binding. 13Cα shifts are dominated by local torsion angles φ, ψ, χ1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The μs−ms dynamic information gained helps establish flexibility−activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.
John S. Zintsmaster, Brian D. Wilson, and Jeffrey W. Peng*
Abstract:
We show that Carr−Purcell−Meiboom−Gill (CPMG) 13Cα NMR relaxation dispersion measurements are a viable means for profiling μs−ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Cα nuclei that experience μs−ms modulation of their chemical shifts due to binding. 13Cα shifts are dominated by local torsion angles φ, ψ, χ1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The μs−ms dynamic information gained helps establish flexibility−activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.
Tuesday, October 21, 2008
Physical Review Letters - Up to Vol 101 No 16
93Nb NMR Spin Echo Spectroscopy in Single Crystal NbSe3
S. Suh, W. G. Clark, P. Monceau, R. E. Thorne, and S. E. Brown
Phys. Rev. Lett. 101, 136407 (2008)
We report electric field induced phase displacements of the charge density wave (CDW) in a single crystal of NbSe3 using 93Nb NMR spin-echo spectroscopy. CDW polarizations in the pinned state induced by unipolar and bipolar pulses are linear and reversible up to at least E=(0.96)ET. The polarizations have a broad distribution extending up to phase angles of order 60° for electric fields close to threshold. No evidence for polarizations in excess of a CDW wavelength or for a divergence in polarization near ET are observed. The results are consistent with elastic depinning models, provided that the critical regime expected in large systems is not observable.
Boroxol Rings in Liquid and Vitreous B2O3 from First Principles
Guillaume Ferlat, Thibault Charpentier, Ari Paavo Seitsonen, Akira Takada, Michele Lazzeri, Laurent Cormier, Georges Calas, and Francesco Mauri
Phys. Rev. Lett. 101, 065504 (2008)
We investigate the structural and vibrational properties of glassy B2O3 using first-principles molecular dynamics simulations. In particular, we determine the boroxol rings fraction f for which there is still no consensus in the literature. Two numerical models containing either a low or a high level of boroxol rings are tested against a gamut of experimental probes (static structure factor, Raman, 11B and 17O NMR data). We show that only the boroxol-rich model (f=75%) can reproduce the full set of observables. Total-energy calculations show that at the glass density, boroxol-rich structures are favored by about 6 kcal/(mol boroxol). Finally, the liquid state is explored in the 2000–4000 K range and a reduction of f to 10%–20% is obtained.
S. Suh, W. G. Clark, P. Monceau, R. E. Thorne, and S. E. Brown
Phys. Rev. Lett. 101, 136407 (2008)
We report electric field induced phase displacements of the charge density wave (CDW) in a single crystal of NbSe3 using 93Nb NMR spin-echo spectroscopy. CDW polarizations in the pinned state induced by unipolar and bipolar pulses are linear and reversible up to at least E=(0.96)ET. The polarizations have a broad distribution extending up to phase angles of order 60° for electric fields close to threshold. No evidence for polarizations in excess of a CDW wavelength or for a divergence in polarization near ET are observed. The results are consistent with elastic depinning models, provided that the critical regime expected in large systems is not observable.
Boroxol Rings in Liquid and Vitreous B2O3 from First Principles
Guillaume Ferlat, Thibault Charpentier, Ari Paavo Seitsonen, Akira Takada, Michele Lazzeri, Laurent Cormier, Georges Calas, and Francesco Mauri
Phys. Rev. Lett. 101, 065504 (2008)
We investigate the structural and vibrational properties of glassy B2O3 using first-principles molecular dynamics simulations. In particular, we determine the boroxol rings fraction f for which there is still no consensus in the literature. Two numerical models containing either a low or a high level of boroxol rings are tested against a gamut of experimental probes (static structure factor, Raman, 11B and 17O NMR data). We show that only the boroxol-rich model (f=75%) can reproduce the full set of observables. Total-energy calculations show that at the glass density, boroxol-rich structures are favored by about 6 kcal/(mol boroxol). Finally, the liquid state is explored in the 2000–4000 K range and a reduction of f to 10%–20% is obtained.
Physical Review B - Up to Vol 78 No 12
Nuclear magnetic resonance linewidth and spin diffusion in 29Si isotopically controlled silicon
Hiroshi Hayashi, Kohei M. Itoh and Leonid S. Vlasenko
Phys. Rev. B 78, 153201 (2008)
A nuclear magnetic resonance (NMR) study was performed with n-type silicon single crystals containing 29Si isotope abundance f ranges from 1.2% to 99.2%. The nuclear spin diffusion coefficient D has been determined from the linewidth of significantly enhanced 29Si NMR signals utilizing a developed dynamic nuclear polarization (DNP) method. The 29Si NMR linewidth depends linearly on f, at least when f<10%, and approaches f1/2 dependence when f>50%. The estimated 29Si nuclear spin diffusion time Tsd between phosphorus atoms used for DNP is more than ten times shorter than the nuclear polarization time T of 29Si nuclei around phosphorus. Therefore, the regime of “rapid spin diffusion” is realized in the DNP experiments.
Magnetization and Cu nuclear magnetic resonance study of Sr0.9La0.1Cu1−xNixO2
G. V. M. Williams, S. Richter, J. Haase, C. U. Jung, Hye-Gyong Lee, and Sung-Ik Lee
Phys. Rev. B 78, 104522 (2008)
We report the results from a Cu nuclear magnetic resonance (NMR) and magnetization study of the electron-doped high-temperature superconducting cuprate (HTSC) Sr0.9La0.1Cu1−xNixO2. This compound shows a large suppression of superconductivity by Ni [Tc/x=18 K/%(Ni)] that is comparable to that observed in underdoped and hole-doped HTSCs. We find small effective moments of 0.06µB/Cu for the pure sample and 0.76µB/Ni for the 1% Ni sample in the paramagnetic regime. The partial substitution of Ni for Cu causes the Cu NMR linewidth to increase and there is a further reduction in the Cu NMR intensity with decreasing temperature over and above that observed in the pure compound. This can be interpreted in terms of Ni inducing additional spin disorder and wipeout of the Cu NMR intensity for Cu sites near the Ni impurities.
19F NMR investigation of the iron pnictide superconductor LaFeAsO0.89F0.11
K. Ahilan, F. L. Ning, T. Imai, A. S. Sefat, R. Jin, M. A. McGuire, B. C. Sales, and D. Mandrus
Phys. Rev. B 78, 100501(R) (2008)
We report on 19F nuclear magnetic resonance (NMR) investigation of the high-temperature superconductor LaFeAsO0.89F0.11 (Tc~28 K). We demonstrate that low-frequency spin fluctuations exhibit pseudogap behavior above Tc. We also deduce the London penetration depth from NMR line broadening below Tc.
Atomic-scale measurement of ultraslow Li motions in glassy LiAlSi2O6 by two-time 6Li spin-alignment echo NMR correlation spectroscopy
M. Wilkening, A. Kuhn, and P. Heitjans
Phys. Rev. B 78, 054303 (2008)
6Li spin-alignment echo (SAE) nuclear-magnetic-resonance (NMR) spectroscopy is used to monitor single-particle two-time correlation functions in LiAlSi2O6 glass. The method, here applied in the temperature range from 300 to 400 K, is sensitive to ultraslow Li hopping processes with rates (1/SAE) down to 10 jumps/s. The use of a sample with natural 6Li abundance allowed the measurement of pure NMR spin-alignment echoes which are damped with increasing mixing time exclusively by slow Li jumps, i.e., free of influences arising from, e.g., interfering spin-diffusion effects. The considerably stretched correlation functions reveal the presence of a broad distribution of jump rates. The results are comprehensively compared with those recently obtained from both 7Li SAE and 7Li spin-lattice relaxation NMR as well as from dc conductivity measurements. Interestingly, the activation energy of the latter, which are sensitive to long-range Li transport parameters, is in good agreement with that microscopically probed by 6Li SAE NMR, here.
Hiroshi Hayashi, Kohei M. Itoh and Leonid S. Vlasenko
Phys. Rev. B 78, 153201 (2008)
A nuclear magnetic resonance (NMR) study was performed with n-type silicon single crystals containing 29Si isotope abundance f ranges from 1.2% to 99.2%. The nuclear spin diffusion coefficient D has been determined from the linewidth of significantly enhanced 29Si NMR signals utilizing a developed dynamic nuclear polarization (DNP) method. The 29Si NMR linewidth depends linearly on f, at least when f<10%, and approaches f1/2 dependence when f>50%. The estimated 29Si nuclear spin diffusion time Tsd between phosphorus atoms used for DNP is more than ten times shorter than the nuclear polarization time T of 29Si nuclei around phosphorus. Therefore, the regime of “rapid spin diffusion” is realized in the DNP experiments.
Magnetization and Cu nuclear magnetic resonance study of Sr0.9La0.1Cu1−xNixO2
G. V. M. Williams, S. Richter, J. Haase, C. U. Jung, Hye-Gyong Lee, and Sung-Ik Lee
Phys. Rev. B 78, 104522 (2008)
We report the results from a Cu nuclear magnetic resonance (NMR) and magnetization study of the electron-doped high-temperature superconducting cuprate (HTSC) Sr0.9La0.1Cu1−xNixO2. This compound shows a large suppression of superconductivity by Ni [Tc/x=18 K/%(Ni)] that is comparable to that observed in underdoped and hole-doped HTSCs. We find small effective moments of 0.06µB/Cu for the pure sample and 0.76µB/Ni for the 1% Ni sample in the paramagnetic regime. The partial substitution of Ni for Cu causes the Cu NMR linewidth to increase and there is a further reduction in the Cu NMR intensity with decreasing temperature over and above that observed in the pure compound. This can be interpreted in terms of Ni inducing additional spin disorder and wipeout of the Cu NMR intensity for Cu sites near the Ni impurities.
19F NMR investigation of the iron pnictide superconductor LaFeAsO0.89F0.11
K. Ahilan, F. L. Ning, T. Imai, A. S. Sefat, R. Jin, M. A. McGuire, B. C. Sales, and D. Mandrus
Phys. Rev. B 78, 100501(R) (2008)
We report on 19F nuclear magnetic resonance (NMR) investigation of the high-temperature superconductor LaFeAsO0.89F0.11 (Tc~28 K). We demonstrate that low-frequency spin fluctuations exhibit pseudogap behavior above Tc. We also deduce the London penetration depth from NMR line broadening below Tc.
Atomic-scale measurement of ultraslow Li motions in glassy LiAlSi2O6 by two-time 6Li spin-alignment echo NMR correlation spectroscopy
M. Wilkening, A. Kuhn, and P. Heitjans
Phys. Rev. B 78, 054303 (2008)
6Li spin-alignment echo (SAE) nuclear-magnetic-resonance (NMR) spectroscopy is used to monitor single-particle two-time correlation functions in LiAlSi2O6 glass. The method, here applied in the temperature range from 300 to 400 K, is sensitive to ultraslow Li hopping processes with rates (1/SAE) down to 10 jumps/s. The use of a sample with natural 6Li abundance allowed the measurement of pure NMR spin-alignment echoes which are damped with increasing mixing time exclusively by slow Li jumps, i.e., free of influences arising from, e.g., interfering spin-diffusion effects. The considerably stretched correlation functions reveal the presence of a broad distribution of jump rates. The results are comprehensively compared with those recently obtained from both 7Li SAE and 7Li spin-lattice relaxation NMR as well as from dc conductivity measurements. Interestingly, the activation energy of the latter, which are sensitive to long-range Li transport parameters, is in good agreement with that microscopically probed by 6Li SAE NMR, here.
Journal of Magnetic Resonance - Vol 195 Issue 1
Solid state water motions revealed by deuterium relaxation in 2H2O-synthesized kanemite and 2H2O-hydrated Na+-Zeolite A
Bernie O’Hare, Michael W. Grutzeck, Seong H. Kim, David B. Asay and Alan J. Benesi
Deuterium NMR relaxation experiments, low temperature deuterium NMR lineshape analysis, and FTIR spectra are consistent with a new model for solid state jump dynamics of water in 2H2O-synthesized kanemite and 2H2O-hydrated Na+-Zeolite A. Exchange occurs between two populations of water: one in which water molecules are directly coordinated to sodium ions and experience C2 symmetry jumps of their OH bonds, and a population of interstitial water molecules outside the sodium ion coordination sphere that experience tetrahedral jumps of their OH bonds. For both samples the C2 jump rate is much faster than the tetrahedral jump rate. 2H NMR relaxation experiments match well with the fast exchange regime of the model over a wide range of temperatures, including room temperature and above.
Coherence selection in double CP MAS NMR spectroscopy
Jen-Hsien Yang, Fang-Chieh Chou and Der-Lii M. Tzou
Applications of double cross-polarization (CP) magic-angle spinning (MAS) NMR spectroscopy, via 1H/15N and then 15N/13C coherence transfers, for 13C coherence selection are demonstrated on a 15N/13C-labeled N-acetyl-glucosamine (GlcNAc) compound. The 15N/13C coherence transfer is very sensitive to the settings of the experimental parameters. To resolve explicitly these parameter dependences, we have systematically monitored the 13C{15N/1H} signal as a function of the rf field strength and the MAS frequency. The data reveal that the zero-quantum coherence transfer, with which the 13C effective rf field is larger than that of the 15N by the spinning frequency, would give better signal sensitivity. We demonstrate in one- and two-dimensional double CP experiments that spectral editing can be achieved by tailoring the experimental parameters, such as the rf field strengths and/or the MAS frequency.
Bernie O’Hare, Michael W. Grutzeck, Seong H. Kim, David B. Asay and Alan J. Benesi
Deuterium NMR relaxation experiments, low temperature deuterium NMR lineshape analysis, and FTIR spectra are consistent with a new model for solid state jump dynamics of water in 2H2O-synthesized kanemite and 2H2O-hydrated Na+-Zeolite A. Exchange occurs between two populations of water: one in which water molecules are directly coordinated to sodium ions and experience C2 symmetry jumps of their OH bonds, and a population of interstitial water molecules outside the sodium ion coordination sphere that experience tetrahedral jumps of their OH bonds. For both samples the C2 jump rate is much faster than the tetrahedral jump rate. 2H NMR relaxation experiments match well with the fast exchange regime of the model over a wide range of temperatures, including room temperature and above.
Coherence selection in double CP MAS NMR spectroscopy
Jen-Hsien Yang, Fang-Chieh Chou and Der-Lii M. Tzou
Applications of double cross-polarization (CP) magic-angle spinning (MAS) NMR spectroscopy, via 1H/15N and then 15N/13C coherence transfers, for 13C coherence selection are demonstrated on a 15N/13C-labeled N-acetyl-glucosamine (GlcNAc) compound. The 15N/13C coherence transfer is very sensitive to the settings of the experimental parameters. To resolve explicitly these parameter dependences, we have systematically monitored the 13C{15N/1H} signal as a function of the rf field strength and the MAS frequency. The data reveal that the zero-quantum coherence transfer, with which the 13C effective rf field is larger than that of the 15N by the spinning frequency, would give better signal sensitivity. We demonstrate in one- and two-dimensional double CP experiments that spectral editing can be achieved by tailoring the experimental parameters, such as the rf field strengths and/or the MAS frequency.
Journal of Magnetic Resonance - Vol 194 Issue 2
The utility of phase alternated pulses for the measurement of dipolar couplings in 2D-SLF experiments
Bibhuti B. Das, N. Sinha and K.V. Ramanathan
The measurement of hetero-nuclear dipolar coupling using two-dimensional separated local field (SLF-2D) NMR experiments is a powerful technique for the determination of the structure and dynamics of molecules in the solid state and in liquid crystals. However, the experiment is sensitive to a number of factors such as the Hartmann–Hahn match condition, proton frequency off-set and rf heating. It is shown here that by the use of phase alternated pulses during spin-exchange the effect of rf mismatch on the dipolar coupling measurement can be compensated over a wide range of off-sets. Phase alternation together with time and amplitude modulation has also been considered and incorporated into a pulse scheme that combines spin exchange with homonuclear spin decoupling based on magic sandwich sequence and named as SAMPI4. Such time and amplitude averaged nutation experiments use relatively low rf power and generate less sample heating. One of these schemes has been applied on liquid crystal samples and is observed to perform well and yield spectra with high resolution.
Practical aspects of Lee–Goldburg based CRAMPS techniques for high-resolution 1H NMR spectroscopy in solids: Implementation and applications
Cristina Coelho, João Rocha, P.K. Madhu and Luís Mafra
Elucidating the local environment of the hydrogen atoms is an important problem in materials science. Because 1H spectra in solid-state nuclear magnetic resonance (NMR) suffer from low resolution due to homogeneous broadening, even under magic-angle spinning (MAS), information of chemical interest may only be obtained using certain high-resolution 1H MAS techniques. 1H Lee–Goldburg (LG) CRAMPS (Combined Rotation And Multiple-Pulse Spectroscopy) methods are particularly well suited for studying inorganic–organic hybrid materials, rich in 1H nuclei. However, setting up CRAMPS experiments is time-consuming and not entirely trivial, facts that have discouraged their widespread use by materials scientists. To change this status quo, here we describe and discuss some important aspects of the experimental implementation of CRAMPS techniques based on LG decoupling schemes, such as FSLG (Frequency Switched), and windowed and windowless PMLG (Phase Modulated). In particular, we discuss the influence on the quality of the 1H NMR spectra of the different parameters at play, for example LG (Lee–Goldburg) pulses, radio-frequency (rf) phase, frequency switching, and pulse imperfections, using glycine and adamantane as model compounds. The efficiency and robustness of the different LG-decoupling schemes is then illustrated on the following materials: organo-phosphorus ligand, N-(phosphonomethyl)iminodiacetic acid [H4pmida] [I], and inorganic–organic hybrid materials (C4H12N2)[Ge2(pmida)2OH2]·4H2O [II] and (C2H5NH3)[Ti(H1.5PO4)(PO4)]2·H2O [III].
Double-acquisition: Utilization of discarded coherences in a 2D separation experiment using the States method
Masashi Fukuchia, Munehiro Inukai, Kazuyuki Takeda and K. Takegoshi
We propose a new data-acquisition scheme for 2D separation experiments to save the spectrometer time by 1/2. This scheme, referred to as a double-acquisition scheme, is applicable to most of separation experiments with the hypercomplex time-domain data-acquisition scheme (the States method) for data collection.
Bibhuti B. Das, N. Sinha and K.V. Ramanathan
The measurement of hetero-nuclear dipolar coupling using two-dimensional separated local field (SLF-2D) NMR experiments is a powerful technique for the determination of the structure and dynamics of molecules in the solid state and in liquid crystals. However, the experiment is sensitive to a number of factors such as the Hartmann–Hahn match condition, proton frequency off-set and rf heating. It is shown here that by the use of phase alternated pulses during spin-exchange the effect of rf mismatch on the dipolar coupling measurement can be compensated over a wide range of off-sets. Phase alternation together with time and amplitude modulation has also been considered and incorporated into a pulse scheme that combines spin exchange with homonuclear spin decoupling based on magic sandwich sequence and named as SAMPI4. Such time and amplitude averaged nutation experiments use relatively low rf power and generate less sample heating. One of these schemes has been applied on liquid crystal samples and is observed to perform well and yield spectra with high resolution.
Practical aspects of Lee–Goldburg based CRAMPS techniques for high-resolution 1H NMR spectroscopy in solids: Implementation and applications
Cristina Coelho, João Rocha, P.K. Madhu and Luís Mafra
Elucidating the local environment of the hydrogen atoms is an important problem in materials science. Because 1H spectra in solid-state nuclear magnetic resonance (NMR) suffer from low resolution due to homogeneous broadening, even under magic-angle spinning (MAS), information of chemical interest may only be obtained using certain high-resolution 1H MAS techniques. 1H Lee–Goldburg (LG) CRAMPS (Combined Rotation And Multiple-Pulse Spectroscopy) methods are particularly well suited for studying inorganic–organic hybrid materials, rich in 1H nuclei. However, setting up CRAMPS experiments is time-consuming and not entirely trivial, facts that have discouraged their widespread use by materials scientists. To change this status quo, here we describe and discuss some important aspects of the experimental implementation of CRAMPS techniques based on LG decoupling schemes, such as FSLG (Frequency Switched), and windowed and windowless PMLG (Phase Modulated). In particular, we discuss the influence on the quality of the 1H NMR spectra of the different parameters at play, for example LG (Lee–Goldburg) pulses, radio-frequency (rf) phase, frequency switching, and pulse imperfections, using glycine and adamantane as model compounds. The efficiency and robustness of the different LG-decoupling schemes is then illustrated on the following materials: organo-phosphorus ligand, N-(phosphonomethyl)iminodiacetic acid [H4pmida] [I], and inorganic–organic hybrid materials (C4H12N2)[Ge2(pmida)2OH2]·4H2O [II] and (C2H5NH3)[Ti(H1.5PO4)(PO4)]2·H2O [III].
Double-acquisition: Utilization of discarded coherences in a 2D separation experiment using the States method
Masashi Fukuchia, Munehiro Inukai, Kazuyuki Takeda and K. Takegoshi
We propose a new data-acquisition scheme for 2D separation experiments to save the spectrometer time by 1/2. This scheme, referred to as a double-acquisition scheme, is applicable to most of separation experiments with the hypercomplex time-domain data-acquisition scheme (the States method) for data collection.
Friday, October 10, 2008
ASAP J. Am. Chem. Soc., ASAP Article, 10.1021/ja801789t
Raftlike Mixtures of Sphingomyelin and Cholesterol Investigated by Solid-State 2H NMR Spectroscopy
Tim Bartels, Ravi S. Lankalapalli, Robert Bittman, Klaus Beyer, and Michael F. Brown*
Abstract:
Sphingomyelin is a lipid that is abundant in the nervous systems of mammals, where it is associated with putative microdomains in cellular membranes and undergoes alterations due to aging or neurodegeneration. We investigated the effect of varying the concentration of cholesterol in binary and ternary mixtures with N-palmitoylsphingomyelin (PSM) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) using deuterium nuclear magnetic resonance (2H NMR) spectroscopy in both macroscopically aligned and unoriented multilamellar dispersions. In our experiments, we used PSM and POPC perdeuterated on the N-acyl and sn-1 acyl chains, respectively. By measuring solid-state 2H NMR spectra of the two lipids separately in mixtures with the same compositions as a function of cholesterol mole fraction and temperature, we obtained clear evidence for the coexistence of two liquid-crystalline domains in distinct regions of the phase diagram. According to our analysis of the first moments M1 and the observed 2H NMR spectra, one of the domains appears to be a liquid-ordered phase. We applied a mean-torque potential model as an additional tool to calculate the average hydrocarbon thickness, the area per lipid, and structural parameters such as chain extension and thermal expansion coefficient in order to further define the two coexisting phases. Our data imply that phase separation takes place in raftlike ternary PSM/POPC/cholesterol mixtures over a broad temperature range but vanishes at cholesterol concentrations equal to or greater than a mole fraction of 0.33. Cholesterol interacts preferentially with sphingomyelin only at smaller mole fractions, above which a homogeneous liquid-ordered phase is present. The reasons for these phase separation phenomena seem to be differences in the effects of cholesterol on the configurational order of the palmitoyl chains in PSM-d31 and POPC-d31 and a difference in the affinity of cholesterol for sphingomyelin observed at low temperatures. Hydrophobic matching explains the occurrence of raftlike domains in cellular membranes at intermediate cholesterol concentrations but not saturating amounts of cholesterol.
Tim Bartels, Ravi S. Lankalapalli, Robert Bittman, Klaus Beyer, and Michael F. Brown*
Abstract:
Sphingomyelin is a lipid that is abundant in the nervous systems of mammals, where it is associated with putative microdomains in cellular membranes and undergoes alterations due to aging or neurodegeneration. We investigated the effect of varying the concentration of cholesterol in binary and ternary mixtures with N-palmitoylsphingomyelin (PSM) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) using deuterium nuclear magnetic resonance (2H NMR) spectroscopy in both macroscopically aligned and unoriented multilamellar dispersions. In our experiments, we used PSM and POPC perdeuterated on the N-acyl and sn-1 acyl chains, respectively. By measuring solid-state 2H NMR spectra of the two lipids separately in mixtures with the same compositions as a function of cholesterol mole fraction and temperature, we obtained clear evidence for the coexistence of two liquid-crystalline domains in distinct regions of the phase diagram. According to our analysis of the first moments M1 and the observed 2H NMR spectra, one of the domains appears to be a liquid-ordered phase. We applied a mean-torque potential model as an additional tool to calculate the average hydrocarbon thickness, the area per lipid, and structural parameters such as chain extension and thermal expansion coefficient in order to further define the two coexisting phases. Our data imply that phase separation takes place in raftlike ternary PSM/POPC/cholesterol mixtures over a broad temperature range but vanishes at cholesterol concentrations equal to or greater than a mole fraction of 0.33. Cholesterol interacts preferentially with sphingomyelin only at smaller mole fractions, above which a homogeneous liquid-ordered phase is present. The reasons for these phase separation phenomena seem to be differences in the effects of cholesterol on the configurational order of the palmitoyl chains in PSM-d31 and POPC-d31 and a difference in the affinity of cholesterol for sphingomyelin observed at low temperatures. Hydrophobic matching explains the occurrence of raftlike domains in cellular membranes at intermediate cholesterol concentrations but not saturating amounts of cholesterol.
ASAP J. Am. Chem. Soc., ASAP Article, 10.1021/ja805839y
Dynamics of Ligand Binding from 13C NMR Relaxation Dispersion at Natural Abundance
John S. Zintsmaster, Brian D. Wilson, and Jeffrey W. Peng*
Abstract:
We show that Carr−Purcell−Meiboom−Gill (CPMG) 13Cα NMR relaxation dispersion measurements are a viable means for profiling μs−ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Cα nuclei that experience μs−ms modulation of their chemical shifts due to binding. 13Cα shifts are dominated by local torsion angles φ, ψ, χ1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The μs−ms dynamic information gained helps establish flexibility−activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.
John S. Zintsmaster, Brian D. Wilson, and Jeffrey W. Peng*
Abstract:
We show that Carr−Purcell−Meiboom−Gill (CPMG) 13Cα NMR relaxation dispersion measurements are a viable means for profiling μs−ms ligand dynamics involved in receptor binding. Critically, the dispersion is at natural 13C abundance; this matches typical pharmaceutical research settings in which ligand isotope-labeling is often impractical. The dispersion reveals ligand 13Cα nuclei that experience μs−ms modulation of their chemical shifts due to binding. 13Cα shifts are dominated by local torsion angles φ, ψ, χ1; hence, these experiments identify flexible torsion angles that may assist complex formation. Since the experiments detect the ligand, they are viable even in the absence of a receptor structure. The μs−ms dynamic information gained helps establish flexibility−activity relationships. We apply these experiments to study the binding of a phospho-peptide substrate ligand to the peptidyl-prolyl isomerase Pin1.
Wednesday, October 08, 2008
J. Am. Chem. Soc., 130 (41), 13664–13672, 2008.
Nanochannels of Two Distinct Cross-Sections in a Porous Al-Based Coordination Polymer
Angiolina Comotti, Silvia Bracco, Piero Sozzani, Satoshi Horike, Ryotaro Matsuda, Jinxi Chen, Masaki Takata, Yoshiki Kubota, and Susumu Kitagawa
Abstract:
A new aluminum naphthalenedicarboxylate Al(OH)(1,4-NDC)·2H2O compound has been synthesized. The crystal structure exhibits a three-dimensional framework composed of infinite chains of corner-sharing octahedral Al(OH)2O4 with 1,4-naphthanedicarboxylate ligands forming two types of channels with squared-shape cross-section. The large channels present a cross-section of 7.7 × 7.7 Å2, while the small channels are about 3.0 × 3.0 Å2. When water molecules are removed, no structural transformation occurs, generating a robust structure with permanent porosity and remarkable thermal stability. 2D 1H−13C heteronuclear correlation NMR measurements, together with the application of Lee-Goldburg homonuclear decoupling, were applied, for the first time, to porous coordination polymers revealing the spatial relationships between the 1H and 13C spin-active nuclei of the framework. To demonstrate the open pore structure and the easy accessibility of the nanochannels to the gas phase, highly sensitive hyperpolarized (HP) xenon NMR, under extreme xenon dilution, has been applied. Xenon can diffuse selectively into the large nanochannels, while the small ones show no substantial uptake of xenon due to severe restrictions along the channels that prevent the diffusion. Two-dimensional exchange experiments showed the exchange time to be as short as 15 ms. Through variable-temperature HP 129Xe NMR experiments we were able to achieve an unprecedented description of the large nanochannel space and surface, a physisorption energy of 10 kJ mol−1, and the chemical shift value of xenon probing the internal surfaces. The large pore channels are straight, parallel, and independent, allowing one-dimensional anisotropic diffusion of gases and vapors. Their walls are composed of the naphthalene moieties that create an unique environment for selective sorption. These results prompted us to measure the storage capacity toward methanol, acetone, benzene, and carbon dioxide. The selective adsorption of methanol and acetone vs that of water, together with the permanent porosity and high thermal stability, makes this compound a suitable matrix for separation and purification.
Angiolina Comotti, Silvia Bracco, Piero Sozzani, Satoshi Horike, Ryotaro Matsuda, Jinxi Chen, Masaki Takata, Yoshiki Kubota, and Susumu Kitagawa
Abstract:
A new aluminum naphthalenedicarboxylate Al(OH)(1,4-NDC)·2H2O compound has been synthesized. The crystal structure exhibits a three-dimensional framework composed of infinite chains of corner-sharing octahedral Al(OH)2O4 with 1,4-naphthanedicarboxylate ligands forming two types of channels with squared-shape cross-section. The large channels present a cross-section of 7.7 × 7.7 Å2, while the small channels are about 3.0 × 3.0 Å2. When water molecules are removed, no structural transformation occurs, generating a robust structure with permanent porosity and remarkable thermal stability. 2D 1H−13C heteronuclear correlation NMR measurements, together with the application of Lee-Goldburg homonuclear decoupling, were applied, for the first time, to porous coordination polymers revealing the spatial relationships between the 1H and 13C spin-active nuclei of the framework. To demonstrate the open pore structure and the easy accessibility of the nanochannels to the gas phase, highly sensitive hyperpolarized (HP) xenon NMR, under extreme xenon dilution, has been applied. Xenon can diffuse selectively into the large nanochannels, while the small ones show no substantial uptake of xenon due to severe restrictions along the channels that prevent the diffusion. Two-dimensional exchange experiments showed the exchange time to be as short as 15 ms. Through variable-temperature HP 129Xe NMR experiments we were able to achieve an unprecedented description of the large nanochannel space and surface, a physisorption energy of 10 kJ mol−1, and the chemical shift value of xenon probing the internal surfaces. The large pore channels are straight, parallel, and independent, allowing one-dimensional anisotropic diffusion of gases and vapors. Their walls are composed of the naphthalene moieties that create an unique environment for selective sorption. These results prompted us to measure the storage capacity toward methanol, acetone, benzene, and carbon dioxide. The selective adsorption of methanol and acetone vs that of water, together with the permanent porosity and high thermal stability, makes this compound a suitable matrix for separation and purification.
Friday, October 03, 2008
ASAP Cryst. Growth Des., ASAP Article, 10.
1H, 13C, and 15N Solid-State NMR Studies of Imidazole- and Morpholine-Based Model Compounds Possessing Halogen and Hydrogen Bonding Capabilities
Karim Bouchmella,† Sylvain G. Dutremez,*† Bruno Alonso,‡ Francesco Mauri,§ and Christel Gervais*#
Abstract:
The halogen and hydrogen bonding interactions present in solid 1-(2,3,3-triiodoallyl)imidazole (1), morpholinium iodide (2), the 1:1 cocrystal 1-(2,3,3-triiodoallyl)imidazole·morpholinium iodide (3), morpholine (4), imidazole (5), and 1-(3-iodopropargyl)imidazole (6) have been investigated by solid-state 1H, 13C, and 15N NMR spectroscopies. Comparison of the 15N CP MAS NMR spectrum of 3 with that of 2 indicates that protonated morpholine is present in solid 3, but this conclusion must be taken with caution as GIPAW calculations predict a 15N chemical shift for morpholine similar to that of the morpholinium cation. Conclusive evidence for the presence of a morpholinium cation in crystalline 3 was obtained by recording the static 15N NMR spectrum of this host−guest complex and comparing the morpholinium/morpholine part of the spectrum with the static spectra of 3 and 4 as obtained from ab initio calculations of NMR parameters based on the X-ray structures of these compounds. Concerning the imidazolyl group, 15N NMR spectroscopy has proven quite valuable to identify changes in the bonding situation of the C−NC nitrogen on passing from 1 to 3. In addition, slight differences are observed between the 15N chemical shifts of 1 and 6 that are ascribed to differences in halogen bond strengths between the two compounds. Attempts have also been made to study halogen bonding by 13C NMR spectroscopy, but this method did not provide exploitable results as signals corresponding to the sp and sp2 carbon atoms bonded to iodine could not be observed experimentally. 1H NMR spectroscopy is a powerful tool to study hydrogen bonding interactions of moderate energies such as +NH2···X (X = N, O, I). Indeed, we have found that the chemical shifts of the NH hydrogens were quite sensitive to the nature of X and to the N−H···X distance. This is demonstrated by the fact that the chemical shifts of the +NH2 protons of the morpholinium cation in 2 and 3 are noticeably different.
Karim Bouchmella,† Sylvain G. Dutremez,*† Bruno Alonso,‡ Francesco Mauri,§ and Christel Gervais*#
Abstract:
The halogen and hydrogen bonding interactions present in solid 1-(2,3,3-triiodoallyl)imidazole (1), morpholinium iodide (2), the 1:1 cocrystal 1-(2,3,3-triiodoallyl)imidazole·morpholinium iodide (3), morpholine (4), imidazole (5), and 1-(3-iodopropargyl)imidazole (6) have been investigated by solid-state 1H, 13C, and 15N NMR spectroscopies. Comparison of the 15N CP MAS NMR spectrum of 3 with that of 2 indicates that protonated morpholine is present in solid 3, but this conclusion must be taken with caution as GIPAW calculations predict a 15N chemical shift for morpholine similar to that of the morpholinium cation. Conclusive evidence for the presence of a morpholinium cation in crystalline 3 was obtained by recording the static 15N NMR spectrum of this host−guest complex and comparing the morpholinium/morpholine part of the spectrum with the static spectra of 3 and 4 as obtained from ab initio calculations of NMR parameters based on the X-ray structures of these compounds. Concerning the imidazolyl group, 15N NMR spectroscopy has proven quite valuable to identify changes in the bonding situation of the C−NC nitrogen on passing from 1 to 3. In addition, slight differences are observed between the 15N chemical shifts of 1 and 6 that are ascribed to differences in halogen bond strengths between the two compounds. Attempts have also been made to study halogen bonding by 13C NMR spectroscopy, but this method did not provide exploitable results as signals corresponding to the sp and sp2 carbon atoms bonded to iodine could not be observed experimentally. 1H NMR spectroscopy is a powerful tool to study hydrogen bonding interactions of moderate energies such as +NH2···X (X = N, O, I). Indeed, we have found that the chemical shifts of the NH hydrogens were quite sensitive to the nature of X and to the N−H···X distance. This is demonstrated by the fact that the chemical shifts of the +NH2 protons of the morpholinium cation in 2 and 3 are noticeably different.
Wednesday, October 01, 2008
J. Am. Chem. Soc., 130 (40), 13425–13432, 2008.
In Situ Observation of the Internal Structure and Composition of Biomineralized Emiliania huxleyi Calcite by Solid-State NMR Spectroscopy
Ronen Gertman, Ira Ben Shir, Shifi Kababya, and Asher Schmidt*
Abstract:
Biomineralization, particularly the formation of calcium carbonate structures by organisms under ambient conditions, is of vast fundamental and applied interest. Organisms finely control all aspects of the formation of the biomaterials: composition, polymorph, morphology, and macroscopic properties. While in situ molecular-level characterization of the resulting biominerals is a formidable task, solid-state magic angle spinning NMR is one of the most powerful analytical techniques for this purpose. It is employed in this study to elucidate the structure and composition of biogenic calcite formed by Emiliania huxleyi, a unicellular alga distinguished by its exquisitely sculptured calcite cell coverings known as coccoliths. Strain 371 (CCMP) was grown and harvested from 15N- and 13C-enriched growth medium, with biosynthetic labeling to enhance the sensitivity of the NMR measurements. Crystalline and interfacial calcite environments were selectively probed using direct and indirect (cross-polarized) 13C excitation, respectively. Different crystalline environments, in particular structural defect sites at concentrations of up to 1.4% with P and N moieties incorporated, were identified using 13C rotational-echo double-resonance (REDOR) NMR. REDOR-derived geometrical constraints show that the P and N atoms at the defect sites are 3.2 and 2.3 (0.2) Å apart from a crystalline carbon carbonate. The phosphorus and nitrogen moieties within the biogenic calcite are identified as small, non-protonated moieties, attributed to inorganic ions such as PO43− and NO3−. The carbonates adjacent to these defects are chemically indistinguishable from bulk crystalline carbonates, yet their immediate environments experience reduced rigidity, as reflected by substantial T1(13CO32−) shortening. Interfacial carbonates, on the other hand, reside in structurally/chemically perturbed environments, as reflected by heterogeneous line broadening. This study is the first to directly unravel evidence on the incorporation of P/N moieties as structural defects within E. huxleyi biogenic calcite, and on the state of the adjacent crystalline carbonates.
Ronen Gertman, Ira Ben Shir, Shifi Kababya, and Asher Schmidt*
Abstract:
Biomineralization, particularly the formation of calcium carbonate structures by organisms under ambient conditions, is of vast fundamental and applied interest. Organisms finely control all aspects of the formation of the biomaterials: composition, polymorph, morphology, and macroscopic properties. While in situ molecular-level characterization of the resulting biominerals is a formidable task, solid-state magic angle spinning NMR is one of the most powerful analytical techniques for this purpose. It is employed in this study to elucidate the structure and composition of biogenic calcite formed by Emiliania huxleyi, a unicellular alga distinguished by its exquisitely sculptured calcite cell coverings known as coccoliths. Strain 371 (CCMP) was grown and harvested from 15N- and 13C-enriched growth medium, with biosynthetic labeling to enhance the sensitivity of the NMR measurements. Crystalline and interfacial calcite environments were selectively probed using direct and indirect (cross-polarized) 13C excitation, respectively. Different crystalline environments, in particular structural defect sites at concentrations of up to 1.4% with P and N moieties incorporated, were identified using 13C rotational-echo double-resonance (REDOR) NMR. REDOR-derived geometrical constraints show that the P and N atoms at the defect sites are 3.2 and 2.3 (0.2) Å apart from a crystalline carbon carbonate. The phosphorus and nitrogen moieties within the biogenic calcite are identified as small, non-protonated moieties, attributed to inorganic ions such as PO43− and NO3−. The carbonates adjacent to these defects are chemically indistinguishable from bulk crystalline carbonates, yet their immediate environments experience reduced rigidity, as reflected by substantial T1(13CO32−) shortening. Interfacial carbonates, on the other hand, reside in structurally/chemically perturbed environments, as reflected by heterogeneous line broadening. This study is the first to directly unravel evidence on the incorporation of P/N moieties as structural defects within E. huxleyi biogenic calcite, and on the state of the adjacent crystalline carbonates.
Friday, September 26, 2008
ASAP J. Am. Chem. Soc., ASAP Article, 10.1021/ja802903a
Vicinal Deuterium Perturbations on Hydrogen NMR Chemical Shifts in CyclohexanesDaniel J. O’Leary,† Damian G. Allis,‡ Bruce S. Hudson,‡ Shelly James,‡ Katherine B. Morgera,‡ and John E. Baldwin*‡
Abstract:
The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at −80 °C or lower, all four possible perturbations of H by D as H−C−C−H is changed to D−C−C−H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Δδ perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal JH−H coupling constants as a function of dihedral angles.
Abstract:
The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at −80 °C or lower, all four possible perturbations of H by D as H−C−C−H is changed to D−C−C−H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Δδ perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal JH−H coupling constants as a function of dihedral angles.
ASAP J. Am. Chem. Soc., ASAP Article, 10.1021/ja8041614
Synthesis and X-ray or NMR/DFT Structure Elucidation of Twenty-One New Trifluoromethyl Derivatives of Soluble Cage Isomers of C76, C78, C84, and C90
Ivan E. Kareev,*†§ Alexey A. Popov,*‡ Igor V. Kuvychko,¶ Natalia B. Shustova,¶ Sergey F. Lebedkin,§ Vyachevslav P. Bubnov,† Oren P. Anderson,¶ Konrad Seppelt,# Steven H. Strauss,*¶ and Olga V. Boltalina*¶
Abstract:
Adding 1% of the metallic elements cerium, lanthanum, and yttrium to graphite rod electrodes resulted in different amounts of the hollow higher fullerenes (HHFs) C76-D2(1), C78-C2v(2), and C78-C2v(3) in carbon-arc fullerene-containing soots. The reaction of trifluoroiodomethane with these and other soluble HHFs at 520−550 °C produced 21 new C76,78,84,90(CF3)n derivatives (n = 6, 8, 10, 12, 14). The reaction with C76-D2(1) produced an abundant isomer of C2-(C76-D2(1))(CF3)10 plus smaller amounts of an isomer of C1-(C76-D2(1))(CF3)6, two isomers of C1-(C76-D2(1))(CF3)8, four isomers of C1-(C76-D2(1))(CF3)10, and one isomer of C2-(C76-D2(1))(CF3)12. The reaction with a mixture of C78-D3(1), C78-C2v(2), and C78-C2v(3) produced the previously reported isomer C1-(C78-C2v(3))(CF3)12 (characterized by X-ray crystallography in this work) and the following new compounds: C2-(C78-C2v(3))(CF3)8; C2-(C78-D3(1))(CF3)10 and Cs-(C78-C2v(2))(CF3)10 (both characterized by X-ray crystallography in this work); C2-(C78-C2v(2))(CF3)10; and C1-C78(CF3)14 (cage isomer unknown). The reaction of a mixture of soluble higher fullerenes including C84 and C90 produced the new compounds C1-C84(CF3)10 (cage isomer unknown), C1-(C84-C2(11))(CF3)12 (X-ray structure reported recently), D2-(C84-D2(22))(CF3)12, C2-(C84-D2(22))(CF3)12, C1-C84(CF3)14 (cage isomer unknown), C1-(C90-C1(32))(CF3)12, and another isomer of C1-C90(CF3)12 (cage isomer unknown). All compounds were studied by mass spectrometry, 19F NMR spectroscopy, and DFT calculations. An analysis of the addition patterns of these compounds and three other HHF(X)n compounds with bulky X groups has led to the discovery of the following addition-pattern principle for HHFs: In general, the most pyramidal cage C(sp2) atoms in the parent HHF, which form the most electron-rich and therefore the most reactive cage C−C bonds as far as 1,2-additions are concerned, are not the cage C atoms to which bulky substituents are added. Instead, ribbons of edge-sharing p-C6(X)2 hexagons, with X groups on less pyramidal cage C atoms, are formed, and the otherwise “most reactive” fullerene double bonds remain intact.
Ivan E. Kareev,*†§ Alexey A. Popov,*‡ Igor V. Kuvychko,¶ Natalia B. Shustova,¶ Sergey F. Lebedkin,§ Vyachevslav P. Bubnov,† Oren P. Anderson,¶ Konrad Seppelt,# Steven H. Strauss,*¶ and Olga V. Boltalina*¶
Abstract:
Adding 1% of the metallic elements cerium, lanthanum, and yttrium to graphite rod electrodes resulted in different amounts of the hollow higher fullerenes (HHFs) C76-D2(1), C78-C2v(2), and C78-C2v(3) in carbon-arc fullerene-containing soots. The reaction of trifluoroiodomethane with these and other soluble HHFs at 520−550 °C produced 21 new C76,78,84,90(CF3)n derivatives (n = 6, 8, 10, 12, 14). The reaction with C76-D2(1) produced an abundant isomer of C2-(C76-D2(1))(CF3)10 plus smaller amounts of an isomer of C1-(C76-D2(1))(CF3)6, two isomers of C1-(C76-D2(1))(CF3)8, four isomers of C1-(C76-D2(1))(CF3)10, and one isomer of C2-(C76-D2(1))(CF3)12. The reaction with a mixture of C78-D3(1), C78-C2v(2), and C78-C2v(3) produced the previously reported isomer C1-(C78-C2v(3))(CF3)12 (characterized by X-ray crystallography in this work) and the following new compounds: C2-(C78-C2v(3))(CF3)8; C2-(C78-D3(1))(CF3)10 and Cs-(C78-C2v(2))(CF3)10 (both characterized by X-ray crystallography in this work); C2-(C78-C2v(2))(CF3)10; and C1-C78(CF3)14 (cage isomer unknown). The reaction of a mixture of soluble higher fullerenes including C84 and C90 produced the new compounds C1-C84(CF3)10 (cage isomer unknown), C1-(C84-C2(11))(CF3)12 (X-ray structure reported recently), D2-(C84-D2(22))(CF3)12, C2-(C84-D2(22))(CF3)12, C1-C84(CF3)14 (cage isomer unknown), C1-(C90-C1(32))(CF3)12, and another isomer of C1-C90(CF3)12 (cage isomer unknown). All compounds were studied by mass spectrometry, 19F NMR spectroscopy, and DFT calculations. An analysis of the addition patterns of these compounds and three other HHF(X)n compounds with bulky X groups has led to the discovery of the following addition-pattern principle for HHFs: In general, the most pyramidal cage C(sp2) atoms in the parent HHF, which form the most electron-rich and therefore the most reactive cage C−C bonds as far as 1,2-additions are concerned, are not the cage C atoms to which bulky substituents are added. Instead, ribbons of edge-sharing p-C6(X)2 hexagons, with X groups on less pyramidal cage C atoms, are formed, and the otherwise “most reactive” fullerene double bonds remain intact.
Thursday, September 25, 2008
ASAP J. Am. Chem. Soc., ASAP Article, 10.1021/ja802578z
Residual Dipolar Coupling Measurements of Transmembrane Proteins Using Aligned Low-q Bicelles and High-Resolution Magic Angle Spinning NMR Spectroscopy
Christian G. Canlas, Dejian Ma, Pei Tang, and Yan Xu*
Abstract:
Bicelles are a major medium form to produce weak alignment of soluble proteins for residual dipolar coupling (RDC) measurements. The obstacle to using the same type of bicelles for transmembrane proteins with solution-state NMR spectroscopy is the loss of signals due to the adhesion or penetration of the proteins into large bicelles, resulting in slow protein tumbling. In this study, weak alignment of the second and third transmembrane domains (TM23) of the human glycine receptor (GlyR) was achieved in low-q bicelles (q = DMPC/DHPC). Although protein-free bicelles with such low q would likely show isotropic properties, the insertion of TM23 induced weakly preferred orientations so that the RDC of the embedded protein can be measured. The extent of the alignment increased but the TM23 signal intensity decreased when q was varied from 0.19 to 0.60. A q of 0.50 was found to be an optimal compromise between alignment and the signal-to-noise ratio. In each pair of NMR experiments for RDC measurements, the same sample and pulse sequence were used, with one being performed at high-resolution magic-angle spinning to obtain pure J-couplings without RDC. A meaningful structure refinement in bicelles was possible by iteratively fitting the experimental RDCs to the back-calculated RDCs using the high-resolution NMR structure of GlyR TM23 in trifluoroethanol as the starting template. Combination of this method with the conventional high-resolution NMR in membrane mimicking mixtures of water and organic solvents offers an attractive way to derive structural information for membrane proteins in their native environment.
Christian G. Canlas, Dejian Ma, Pei Tang, and Yan Xu*
Abstract:
Bicelles are a major medium form to produce weak alignment of soluble proteins for residual dipolar coupling (RDC) measurements. The obstacle to using the same type of bicelles for transmembrane proteins with solution-state NMR spectroscopy is the loss of signals due to the adhesion or penetration of the proteins into large bicelles, resulting in slow protein tumbling. In this study, weak alignment of the second and third transmembrane domains (TM23) of the human glycine receptor (GlyR) was achieved in low-q bicelles (q = DMPC/DHPC). Although protein-free bicelles with such low q would likely show isotropic properties, the insertion of TM23 induced weakly preferred orientations so that the RDC of the embedded protein can be measured. The extent of the alignment increased but the TM23 signal intensity decreased when q was varied from 0.19 to 0.60. A q of 0.50 was found to be an optimal compromise between alignment and the signal-to-noise ratio. In each pair of NMR experiments for RDC measurements, the same sample and pulse sequence were used, with one being performed at high-resolution magic-angle spinning to obtain pure J-couplings without RDC. A meaningful structure refinement in bicelles was possible by iteratively fitting the experimental RDCs to the back-calculated RDCs using the high-resolution NMR structure of GlyR TM23 in trifluoroethanol as the starting template. Combination of this method with the conventional high-resolution NMR in membrane mimicking mixtures of water and organic solvents offers an attractive way to derive structural information for membrane proteins in their native environment.
Wednesday, September 24, 2008
J. Am. Chem. Soc., 130 (38), 12663–12670, 2008.
Density Functional Theory Calculations of Hydrogen-Bond-Mediated NMR J Coupling in the Solid State
Siân A. Joyce,† Jonathan R. Yates,*‡ Chris J. Pickard,§ and Steven P. Brown∥
Abstract:
A recently developed method for calculating NMR J coupling in solid-state systems is applied to calculate hydrogen-bond-mediated 2hJNN couplings across intra- or intermolecular N−H···N hydrogen bonds in two 6-aminofulvene-1-aldimine derivatives and the ribbon structure formed by a deoxyguanosine derivative. Excellent quantitative agreement is observed between the calculated solid-state J couplings and those previously determined experimentally in two recent spin-echo magic-angle-spinning NMR studies (Brown, S. P.; et al. Chem. Commun.2002, 1852−1853 and Pham, T. N.; et al. Phys. Chem. Chem. Phys. 2007, 9, 3416−3423). For the 6-aminofulvene-1-aldimines, the differences in 2hJNN couplings in pyrrole and triazole derivatives are reproduced, while for the guanosine ribbons, an increase in 2hJNN is correlated with a decrease in the N−H···N hydrogen-bond distance. J couplings are additionally calculated for isolated molecules of the 6-aminofulevene-1-aldimines extracted from the crystal with and without further geometry optimization. Importantly, it is shown that experimentally observed differences between J couplings determined by solution- and solid-state NMR are not solely due to differences in geometry; long-range electrostatic effects of the crystal lattice are shown to be significant also. J couplings that are yet to be experimentally measured are calculated. Notably, 2hJNO couplings across N−H···O hydrogen bonds are found to be of a similar magnitude to 2hJNN couplings, suggesting that their utilization and quantitative determination should be experimentally feasible.
Siân A. Joyce,† Jonathan R. Yates,*‡ Chris J. Pickard,§ and Steven P. Brown∥
Abstract:
A recently developed method for calculating NMR J coupling in solid-state systems is applied to calculate hydrogen-bond-mediated 2hJNN couplings across intra- or intermolecular N−H···N hydrogen bonds in two 6-aminofulvene-1-aldimine derivatives and the ribbon structure formed by a deoxyguanosine derivative. Excellent quantitative agreement is observed between the calculated solid-state J couplings and those previously determined experimentally in two recent spin-echo magic-angle-spinning NMR studies (Brown, S. P.; et al. Chem. Commun.2002, 1852−1853 and Pham, T. N.; et al. Phys. Chem. Chem. Phys. 2007, 9, 3416−3423). For the 6-aminofulvene-1-aldimines, the differences in 2hJNN couplings in pyrrole and triazole derivatives are reproduced, while for the guanosine ribbons, an increase in 2hJNN is correlated with a decrease in the N−H···N hydrogen-bond distance. J couplings are additionally calculated for isolated molecules of the 6-aminofulevene-1-aldimines extracted from the crystal with and without further geometry optimization. Importantly, it is shown that experimentally observed differences between J couplings determined by solution- and solid-state NMR are not solely due to differences in geometry; long-range electrostatic effects of the crystal lattice are shown to be significant also. J couplings that are yet to be experimentally measured are calculated. Notably, 2hJNO couplings across N−H···O hydrogen bonds are found to be of a similar magnitude to 2hJNN couplings, suggesting that their utilization and quantitative determination should be experimentally feasible.
J. Am. Chem. Soc., 130 (38), 12568–12569, 2008.
Native Conformation at Specific Residues in Recombinant Inclusion Body Protein in Whole Cells Determined with Solid-State NMR Spectroscopy
Jaime Curtis-Fisk, Ryan M. Spencer, and David P. Weliky*
Abstract:
Inclusion bodies are insoluble aggregates that are formed by bacteria to store excess recombinant protein produced during expression. The structure of the protein in inclusion bodies is poorly understood but it has been hypothesized that the protein may form misfolded β sheet aggregates. This paper presents an isotopic labeling and solid-state nuclear magnetic resonance approach to determine the secondary structure of individual residues within a recombinant influenza virus “FHA2” protein in inclusion bodies. The inclusion bodies were studied either in the context of the unlysed hydrated E. coli cells or in the hydrated pellet formed from centrifugation of the material insoluble in the cell lysate. The native structure of FHA2 is predominantly helical and native helical structure was also observed for several specific residues in the inclusion body FHA2. This approach will be applicable to structural analysis of many inclusion body proteins and should provide useful information for optimizing solubilization and purification protocols of these proteins.
Jaime Curtis-Fisk, Ryan M. Spencer, and David P. Weliky*
Abstract:
Inclusion bodies are insoluble aggregates that are formed by bacteria to store excess recombinant protein produced during expression. The structure of the protein in inclusion bodies is poorly understood but it has been hypothesized that the protein may form misfolded β sheet aggregates. This paper presents an isotopic labeling and solid-state nuclear magnetic resonance approach to determine the secondary structure of individual residues within a recombinant influenza virus “FHA2” protein in inclusion bodies. The inclusion bodies were studied either in the context of the unlysed hydrated E. coli cells or in the hydrated pellet formed from centrifugation of the material insoluble in the cell lysate. The native structure of FHA2 is predominantly helical and native helical structure was also observed for several specific residues in the inclusion body FHA2. This approach will be applicable to structural analysis of many inclusion body proteins and should provide useful information for optimizing solubilization and purification protocols of these proteins.
Friday, September 19, 2008
Chem. Mater., 20 (18), 5787–5795, 2008.
Characterization of Noncrystalline Nanomaterials: NMR of Zinc Phosphate as a Case Study
Marcus Roming,† Claus Feldmann,*† Yamini S. Avadhut,‡ and Jörn Schmedt auf der Günne*‡
Abstract:
Zinc phosphate nanoparticles are prepared via a polyol-mediated synthesis. The nanomaterial turns out to be nonagglomerated and very uniform in size and shape, in particular 20 nm in diameter. X-ray powder diffraction analysis and high-resolution transmission electron microscopy indicate as-prepared nanoparticles to be noncrystalline. To investigate the chemical composition (stoichiometry, material homogeneity, amount of ortho-/metaphosphate, water content, type of surface-allocated adsorbents, differentiation of surface/inner core), X-ray diffraction, NMR-spectroscopy, energy-dispersive X-ray analysis, infrared spectroscopy, and thermal analysis are performed. To validate the local structure and composition, we performed 1H, 13C, and 31P magic angle spinning nuclear magnetic resonance spectroscopy and multidimensional homo- and heteronuclear multiple-pulse solid-state NMR experiments. Moreover, 31P{1H} rotational echo double-resonance experiments for various spin topologies are analyzed analytically and numerically, in order to differentiate between homogeneous nanoparticles and core−shell nanoparticles. The analysis gives a length scale to homogeneity and for bulk materials allows us to differentiate between mono- and dihydrogen phosphates, and phosphate hydrates.
Marcus Roming,† Claus Feldmann,*† Yamini S. Avadhut,‡ and Jörn Schmedt auf der Günne*‡
Abstract:
Zinc phosphate nanoparticles are prepared via a polyol-mediated synthesis. The nanomaterial turns out to be nonagglomerated and very uniform in size and shape, in particular 20 nm in diameter. X-ray powder diffraction analysis and high-resolution transmission electron microscopy indicate as-prepared nanoparticles to be noncrystalline. To investigate the chemical composition (stoichiometry, material homogeneity, amount of ortho-/metaphosphate, water content, type of surface-allocated adsorbents, differentiation of surface/inner core), X-ray diffraction, NMR-spectroscopy, energy-dispersive X-ray analysis, infrared spectroscopy, and thermal analysis are performed. To validate the local structure and composition, we performed 1H, 13C, and 31P magic angle spinning nuclear magnetic resonance spectroscopy and multidimensional homo- and heteronuclear multiple-pulse solid-state NMR experiments. Moreover, 31P{1H} rotational echo double-resonance experiments for various spin topologies are analyzed analytically and numerically, in order to differentiate between homogeneous nanoparticles and core−shell nanoparticles. The analysis gives a length scale to homogeneity and for bulk materials allows us to differentiate between mono- and dihydrogen phosphates, and phosphate hydrates.
J. Am. Chem. Soc., 130 (38), 12712–12724, 2008.
Resolving the Structure of Ligands Bound to the Surface of Superparamagnetic Iron Oxide Nanoparticles by High-Resolution Magic-Angle Spinning NMR
Spectroscopy
Laura Polito, Miriam Colombo, Diego Monti, Sergio Melato, Enrico Caneva,* and Davide Prosperi*
Abstract:
A major challenge in magnetic nanoparticle synthesis and (bio)functionalization concerns the precise characterization of the nanoparticle surface ligands. We report the first analytical NMR investigation of organic ligands stably anchored on the surface of superparamagnetic nanoparticles (MNPs) through the development of a new experimental application of high-resolution magic-angle spinning (HRMAS). The conceptual advance here is that the HRMAS technique, already being used for MAS NMR analysis of gels and semisolid matrixes, enables the fine-structure-resolved characterization of even complex organic molecules bound to paramagnetic nanocrystals, such as nanosized iron oxides, by strongly decreasing the effects of paramagnetic disturbances. This method led to detail-rich, well-resolved 1H NMR spectra, often with highly structured first-order couplings, essential in the interpretation of the data. This HRMAS application was first evaluated and optimized using simple ligands widely used as surfactants in MNP synthesis and conjugation. Next, the methodology was assessed through the structure determination of complex molecular architectures, such as those involved in MNP3 and MNP4. The comparison with conventional probes evidences that HRMAS makes it possible to work with considerably higher concentrations, thus avoiding the loss of structural information. Consistent 2D homonuclear 1H−1H and 1H−13C heteronuclear single-quantum coherence correlation spectra were also obtained, providing reliable elements on proton signal assignments and carbon characterization and opening the way to 13C NMR determination. Notably, combining the experimental evidence from HRMAS 1H NMR and diffusion-ordered spectroscopy performed on the hybrid nanoparticle dispersion confirmed that the ligands were tightly bound to the particle surface when they were dispersed in a ligand-free solvent, while they rapidly exchanged when an excess of free ligand was present in solution. In addition to HRMAS NMR, matrix-assisted laser desorption ionization time-of-flight MS analysis of modified MNPs proved very valuable in ligand mass identification, thus giving a sound support to NMR characterization achievements.
Spectroscopy
Laura Polito, Miriam Colombo, Diego Monti, Sergio Melato, Enrico Caneva,* and Davide Prosperi*
Abstract:
A major challenge in magnetic nanoparticle synthesis and (bio)functionalization concerns the precise characterization of the nanoparticle surface ligands. We report the first analytical NMR investigation of organic ligands stably anchored on the surface of superparamagnetic nanoparticles (MNPs) through the development of a new experimental application of high-resolution magic-angle spinning (HRMAS). The conceptual advance here is that the HRMAS technique, already being used for MAS NMR analysis of gels and semisolid matrixes, enables the fine-structure-resolved characterization of even complex organic molecules bound to paramagnetic nanocrystals, such as nanosized iron oxides, by strongly decreasing the effects of paramagnetic disturbances. This method led to detail-rich, well-resolved 1H NMR spectra, often with highly structured first-order couplings, essential in the interpretation of the data. This HRMAS application was first evaluated and optimized using simple ligands widely used as surfactants in MNP synthesis and conjugation. Next, the methodology was assessed through the structure determination of complex molecular architectures, such as those involved in MNP3 and MNP4. The comparison with conventional probes evidences that HRMAS makes it possible to work with considerably higher concentrations, thus avoiding the loss of structural information. Consistent 2D homonuclear 1H−1H and 1H−13C heteronuclear single-quantum coherence correlation spectra were also obtained, providing reliable elements on proton signal assignments and carbon characterization and opening the way to 13C NMR determination. Notably, combining the experimental evidence from HRMAS 1H NMR and diffusion-ordered spectroscopy performed on the hybrid nanoparticle dispersion confirmed that the ligands were tightly bound to the particle surface when they were dispersed in a ligand-free solvent, while they rapidly exchanged when an excess of free ligand was present in solution. In addition to HRMAS NMR, matrix-assisted laser desorption ionization time-of-flight MS analysis of modified MNPs proved very valuable in ligand mass identification, thus giving a sound support to NMR characterization achievements.
J. Am. Chem. Soc., 130 (38), 12671–12679, 2008.
Residue Ionization in LpxC Directly Observed by 67Zn NMR Spectroscopy
Andrew S. Lipton,† Robert W. Heck,† Marcy Hernick,‡§ Carol A. Fierke,*‡ and Paul D. Ellis*†
Abstract:
The pH dependence of the solid-state 67Zn NMR lineshapes has been measured for both the wild type (WT) and the H265A mutant of Aquifex aeolicus LpxC, each in the absence of substrate (resting state). The 67Zn NMR spectrum of WT LpxC at pH 6 (prepared at 0 °C) contains two overlapping quadrupole lineshapes with Cq values of 10 and 12.9 MHz, while the spectrum measured for the sample prepared at a pH near 9 (at 0 °C) is dominated by the appearance of a third species with a Cq of 14.3 MHz. These findings are consistent with the two pKa values previously observed by the bell-shaped dependence of the LpxC-catalyzed reaction. On the basis of comparison of the experimental results with predictions from quantum mechanical/molecular mechanical (QM/MM) modeling, we suggest that pKa1 (low pH) represents the ionization of Glu78 and pKa2 (high pH) reflects the ionization of another active site residue located near the zinc ion, such as His265. These results are also consistent with water being bound to the Zn2+ ion throughout this pH range. The 67Zn NMR spectra of the H265A mutant appear to be pH independent, with a Cq of 9.55 MHz being sufficient to describe both low- and high-pH data. The QM/MM models of the H265A mutant suggest that over this pH range water is bound to the zinc ion while Glu78 is protonated.
Andrew S. Lipton,† Robert W. Heck,† Marcy Hernick,‡§ Carol A. Fierke,*‡ and Paul D. Ellis*†
Abstract:
The pH dependence of the solid-state 67Zn NMR lineshapes has been measured for both the wild type (WT) and the H265A mutant of Aquifex aeolicus LpxC, each in the absence of substrate (resting state). The 67Zn NMR spectrum of WT LpxC at pH 6 (prepared at 0 °C) contains two overlapping quadrupole lineshapes with Cq values of 10 and 12.9 MHz, while the spectrum measured for the sample prepared at a pH near 9 (at 0 °C) is dominated by the appearance of a third species with a Cq of 14.3 MHz. These findings are consistent with the two pKa values previously observed by the bell-shaped dependence of the LpxC-catalyzed reaction. On the basis of comparison of the experimental results with predictions from quantum mechanical/molecular mechanical (QM/MM) modeling, we suggest that pKa1 (low pH) represents the ionization of Glu78 and pKa2 (high pH) reflects the ionization of another active site residue located near the zinc ion, such as His265. These results are also consistent with water being bound to the Zn2+ ion throughout this pH range. The 67Zn NMR spectra of the H265A mutant appear to be pH independent, with a Cq of 9.55 MHz being sufficient to describe both low- and high-pH data. The QM/MM models of the H265A mutant suggest that over this pH range water is bound to the zinc ion while Glu78 is protonated.
Thursday, September 18, 2008
Solid-State NMR - Volume 34 Issues 1-2
Combined NMR and computational study for azide binding to human manganese superoxide dismutase
Th. Emmler, I. Ayala, D. Silverman, S. Hafner, A.S. Galstyan, E.W. Knapp and G. Buntkowsky
Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the 15N-labeled inhibitor azide ([15N3−]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy (19F-MAS and 15N-CPMAS). Employing 19F-15N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three 15N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R1=4.85 Å between the 19F-label of Tyf34 and the nearest 15N of the azide and an azide–fluorotyrosine Tyf34 angle of 90° were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide–Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-19F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.
A new application for an old concept: Constant time (CT)-REDOR for an accurate determination of second moments in multiple spin systems with strong heteronuclear dipolar couplings
Thomas Echelmeyer, Leo van Wüllen, and Sebastian Wegner
In this contribution we present a constant time version of the well known REDOR pulse sequence which enables us to determine the second moments in multiple spin systems with strong dipolar couplings. From the resulting dipolar evolution curves, accurate values for the second moments can be obtained without the need to incorporate the full information about the detailed spin geometry of the multiple spin systems into the simulation protocol.
Characterization of local environments in crystalline borophosphates using single and double resonance NMR
Devidas B. Raskar, Hellmut Eckert, Bastian Ewald and Rüdiger Kniep
11B and 31P magic-angle spinning as well as 11B{31P} and 31P{11B} rotational echo double resonance (REDOR) NMR have been applied to characterize the local environments in the crystalline borophosphates K3[BP3O9(OH)3], NH4[ZnBP2O8] and Rb3[B2P3O11(OH)2]. Dipolar second moment values extracted from the REDOR curves at short evolution times (ΔS/S00.2) are in reasonable agreement with those calculated from the internuclear distances in the corresponding crystal structures. In particular, the method is found to be useful for distinguishing between boron and phosphorus local environments with different numbers of B–O–P connectivities, making REDOR a well-suited tool for medium-range order investigations in glasses.
Lithium ionic jump motion in the fast solid ion conductor Li5La3Nb2O12
Barbara Koch and Michael Vogel
Using 7Li NMR line-shape analysis, spin–lattice relaxation measurements and stimulated-echo spectroscopy, we investigate the lithium ionic jump motion in the garnet Li5La3Nb2O12. Results for two samples are compared, which were annealed at (GR-850) and at (GR-900), respectively. All 7Li NMR data consistently show that two lithium species with distinguishable dynamical behaviors coexist in each of the samples. While the less mobile species is the majority component in GR-850, the more mobile species is the majority component in GR-900. 7Li NMR stimulated-echo spectroscopy provides straightforward access to the correlation functions describing the jumps of the respective majority component in both samples. From the temperature-dependent correlation times, we obtain activation energies of 56 and for GR-850 and GR-900, respectively. For both samples, the correlation functions substantially deviate from simple exponential behavior, indicating a high complexity of the lithium ionic motion in Li5La3Nb2O12.
13C CPMAS NMR and DFT calculations of anthocyanidins
M. Wolniak and I. Wawer
Anthocyanidins, red dyes from flower petals and fruits, are beneficial to human health. They attract considerable attention owing to their strong antioxidant and radical scavenging properties, however they are unstable in solution and available in small amounts only. 13C CP MAS NMR spectra were recorded to characterize solid-state conformation of nine anthocyanidins: apigenidin, pelargonidin, cyanidin, delphinidin, peonidin, malvidin robinetidin, luteolinidin and diosmetinidin chlorides. For some carbons, the solid-state chemical shifts were different from those obtained for solutions, indicating differences in conformation and intermolecular interactions. The principal elements of the 13C chemical shift tensor were measured for pelargonidin, cyanidin, delphinidin and malvidin chlorides using PASS-2D NMR technique. DFT GIAO calculations of shielding constants were performed for apigenidin and several geometric isomers of pelargonidin. Comparison of experimental 13C δii with the theoretical shielding parameters was helpful in predicting the most reliable geometry in the solid state. The cross-polarization parameters were obtained from variable-contact time experiments; TCH are longer and the values of T1ρH are shorter in the order: pelargonidin cyanidin delphinidin. It is probable that solid anthocyanidins become less ordered as the number of OH groups increases.
51V solid-state NMR investigations and DFT studies of model compounds for vanadium haloperoxidases
Annika Schweitzer, Torsten Gutmann, Maria Wächtler, Hergen Breitzke, Axel Buchholz, Winfried Plass and Gerd Buntkowsky
Three cis-dioxovanadium(V) complexes with similar N-salicylidenehydrazide ligands modeling hydrogen bonding interactions of vanadate relevant for vanadium haloperoxidases are studied by 51V solid-state NMR spectroscopy. Their parameters describing the quadrupolar and chemical shift anisotropy interactions (quadrupolar coupling constant CQ, asymmetry of the quadrupolar tensor ηQ, isotropic chemical shift δiso, chemical shift anisotropy δσ, asymmetry of the chemical shift tensor ησ and the Euler angles α, β and γ) are determined both experimentally and theoretically using DFT methods. A comparative study of different methods to determine the NMR parameters by numerical simulation of the spectra is presented. Detailed theoretical investigations on the DFT level using various basis sets and structural models show that by useful choice of the methodology, the calculated parameters agree to the experimental ones in a very good manner.
Spin-diffusion NMR at low field for the study of multiphase solids
M. Mauri, Y. Thomann, H. Schneider and K. Saalwächter
The use of spin-diffusion NMR for the measurement of domain sizes in multiphase materials is becoming increasingly popular, in particular for the study of heterogeneous polymers. Under conditions where T1 relaxation can be neglected, which is mostly the case at high field, analytical and approximate solutions to the evolution of spin diffusion are available. In order to extend the technique to more general conditions, we performed a comprehensive study of the diffusion of magnetization in a model copolymer at low field, where T1 tends to be of the same order of magnitude as the typical spin-diffusion time. In order to study the effects of T1 and to delineate the optimal T1 values for back correction prior to applying the initial-rate approximation, we developed a numerical simulation based on the diffusion equation and including longitudinal relaxation. We present and discuss the limits of simple correction strategies for initial-slope analysis based on apparent relaxation times from saturation-recovery experiments or the spin-diffusion experiments themselves. Our best strategy faithfully reproduces domain sizes obtained by both TEM investigations and full simultaneous fitting of spin-diffusion and saturation-recovery curves. Full fitting of such independent data sets not only yields correct domain sizes, but also the true longitudinal relaxation times, as well as spin-diffusion coefficients. Effects of interphases with distinct mobility on spin-diffusion curves, as well as practical hints concerning the reliable component decomposition of the detected low-resolution FID signal by help of different magnetization filters are also discussed in detail.
Th. Emmler, I. Ayala, D. Silverman, S. Hafner, A.S. Galstyan, E.W. Knapp and G. Buntkowsky
Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the 15N-labeled inhibitor azide ([15N3−]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy (19F-MAS and 15N-CPMAS). Employing 19F-15N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three 15N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R1=4.85 Å between the 19F-label of Tyf34 and the nearest 15N of the azide and an azide–fluorotyrosine Tyf34 angle of 90° were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide–Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-19F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.
A new application for an old concept: Constant time (CT)-REDOR for an accurate determination of second moments in multiple spin systems with strong heteronuclear dipolar couplings
Thomas Echelmeyer, Leo van Wüllen, and Sebastian Wegner
In this contribution we present a constant time version of the well known REDOR pulse sequence which enables us to determine the second moments in multiple spin systems with strong dipolar couplings. From the resulting dipolar evolution curves, accurate values for the second moments can be obtained without the need to incorporate the full information about the detailed spin geometry of the multiple spin systems into the simulation protocol.
Characterization of local environments in crystalline borophosphates using single and double resonance NMR
Devidas B. Raskar, Hellmut Eckert, Bastian Ewald and Rüdiger Kniep
11B and 31P magic-angle spinning as well as 11B{31P} and 31P{11B} rotational echo double resonance (REDOR) NMR have been applied to characterize the local environments in the crystalline borophosphates K3[BP3O9(OH)3], NH4[ZnBP2O8] and Rb3[B2P3O11(OH)2]. Dipolar second moment values extracted from the REDOR curves at short evolution times (ΔS/S00.2) are in reasonable agreement with those calculated from the internuclear distances in the corresponding crystal structures. In particular, the method is found to be useful for distinguishing between boron and phosphorus local environments with different numbers of B–O–P connectivities, making REDOR a well-suited tool for medium-range order investigations in glasses.
Lithium ionic jump motion in the fast solid ion conductor Li5La3Nb2O12
Barbara Koch and Michael Vogel
Using 7Li NMR line-shape analysis, spin–lattice relaxation measurements and stimulated-echo spectroscopy, we investigate the lithium ionic jump motion in the garnet Li5La3Nb2O12. Results for two samples are compared, which were annealed at (GR-850) and at (GR-900), respectively. All 7Li NMR data consistently show that two lithium species with distinguishable dynamical behaviors coexist in each of the samples. While the less mobile species is the majority component in GR-850, the more mobile species is the majority component in GR-900. 7Li NMR stimulated-echo spectroscopy provides straightforward access to the correlation functions describing the jumps of the respective majority component in both samples. From the temperature-dependent correlation times, we obtain activation energies of 56 and for GR-850 and GR-900, respectively. For both samples, the correlation functions substantially deviate from simple exponential behavior, indicating a high complexity of the lithium ionic motion in Li5La3Nb2O12.
13C CPMAS NMR and DFT calculations of anthocyanidins
M. Wolniak and I. Wawer
Anthocyanidins, red dyes from flower petals and fruits, are beneficial to human health. They attract considerable attention owing to their strong antioxidant and radical scavenging properties, however they are unstable in solution and available in small amounts only. 13C CP MAS NMR spectra were recorded to characterize solid-state conformation of nine anthocyanidins: apigenidin, pelargonidin, cyanidin, delphinidin, peonidin, malvidin robinetidin, luteolinidin and diosmetinidin chlorides. For some carbons, the solid-state chemical shifts were different from those obtained for solutions, indicating differences in conformation and intermolecular interactions. The principal elements of the 13C chemical shift tensor were measured for pelargonidin, cyanidin, delphinidin and malvidin chlorides using PASS-2D NMR technique. DFT GIAO calculations of shielding constants were performed for apigenidin and several geometric isomers of pelargonidin. Comparison of experimental 13C δii with the theoretical shielding parameters was helpful in predicting the most reliable geometry in the solid state. The cross-polarization parameters were obtained from variable-contact time experiments; TCH are longer and the values of T1ρH are shorter in the order: pelargonidin cyanidin delphinidin. It is probable that solid anthocyanidins become less ordered as the number of OH groups increases.
51V solid-state NMR investigations and DFT studies of model compounds for vanadium haloperoxidases
Annika Schweitzer, Torsten Gutmann, Maria Wächtler, Hergen Breitzke, Axel Buchholz, Winfried Plass and Gerd Buntkowsky
Three cis-dioxovanadium(V) complexes with similar N-salicylidenehydrazide ligands modeling hydrogen bonding interactions of vanadate relevant for vanadium haloperoxidases are studied by 51V solid-state NMR spectroscopy. Their parameters describing the quadrupolar and chemical shift anisotropy interactions (quadrupolar coupling constant CQ, asymmetry of the quadrupolar tensor ηQ, isotropic chemical shift δiso, chemical shift anisotropy δσ, asymmetry of the chemical shift tensor ησ and the Euler angles α, β and γ) are determined both experimentally and theoretically using DFT methods. A comparative study of different methods to determine the NMR parameters by numerical simulation of the spectra is presented. Detailed theoretical investigations on the DFT level using various basis sets and structural models show that by useful choice of the methodology, the calculated parameters agree to the experimental ones in a very good manner.
Spin-diffusion NMR at low field for the study of multiphase solids
M. Mauri, Y. Thomann, H. Schneider and K. Saalwächter
The use of spin-diffusion NMR for the measurement of domain sizes in multiphase materials is becoming increasingly popular, in particular for the study of heterogeneous polymers. Under conditions where T1 relaxation can be neglected, which is mostly the case at high field, analytical and approximate solutions to the evolution of spin diffusion are available. In order to extend the technique to more general conditions, we performed a comprehensive study of the diffusion of magnetization in a model copolymer at low field, where T1 tends to be of the same order of magnitude as the typical spin-diffusion time. In order to study the effects of T1 and to delineate the optimal T1 values for back correction prior to applying the initial-rate approximation, we developed a numerical simulation based on the diffusion equation and including longitudinal relaxation. We present and discuss the limits of simple correction strategies for initial-slope analysis based on apparent relaxation times from saturation-recovery experiments or the spin-diffusion experiments themselves. Our best strategy faithfully reproduces domain sizes obtained by both TEM investigations and full simultaneous fitting of spin-diffusion and saturation-recovery curves. Full fitting of such independent data sets not only yields correct domain sizes, but also the true longitudinal relaxation times, as well as spin-diffusion coefficients. Effects of interphases with distinct mobility on spin-diffusion curves, as well as practical hints concerning the reliable component decomposition of the detected low-resolution FID signal by help of different magnetization filters are also discussed in detail.
Thursday, September 11, 2008
J. Am. Chem. Soc., 130 (36), 12007–12020, 2008.
Changes in Dynamics of SRE-RNA on Binding to the VTS1p-SAM Domain Studied by 13C NMR Relaxation
Florian C. Oberstrass, Frédéric H.-T. Allain, and Sapna Ravindranathan
Abstract:
RNA recognition by proteins is often accompanied by significant changes in RNA dynamics in addition to conformational changes. However, there are very few studies which characterize the changes in molecular motions in RNA on protein binding. We present a quantitative 13C NMR relaxation study of the changes in RNA dynamics in the pico−nanosecond time scale and micro−millisecond time scale resulting from interaction of the stem−loop SRE-RNA with the VTS1p-SAM domain. 13C relaxation rates of the protonated carbons of the nucleotide base and anomeric carbons have been analyzed by employing the model-free formalism, for a fully 13C/15N-labeled sample of the SRE-RNA in the free and protein-bound forms. In the free RNA, the nature of molecular motions are found to be distinctly different in the stem and the loop region. On binding to the protein, the nature of motions becomes more homogeneous throughout the RNA, with many residues showing increased flexibility at the aromatic carbon sites, while the anomeric carbon sites become more rigid. Surprisingly, we also observe indications of a slow collective motion of the RNA in the binding pocket of the protein. The observation of increased motions on binding is interesting in the context of growing evidence that binding does not always lead to motional restrictions and the resulting entropy gain could favor the free energy of association.
Florian C. Oberstrass, Frédéric H.-T. Allain, and Sapna Ravindranathan
Abstract:
RNA recognition by proteins is often accompanied by significant changes in RNA dynamics in addition to conformational changes. However, there are very few studies which characterize the changes in molecular motions in RNA on protein binding. We present a quantitative 13C NMR relaxation study of the changes in RNA dynamics in the pico−nanosecond time scale and micro−millisecond time scale resulting from interaction of the stem−loop SRE-RNA with the VTS1p-SAM domain. 13C relaxation rates of the protonated carbons of the nucleotide base and anomeric carbons have been analyzed by employing the model-free formalism, for a fully 13C/15N-labeled sample of the SRE-RNA in the free and protein-bound forms. In the free RNA, the nature of molecular motions are found to be distinctly different in the stem and the loop region. On binding to the protein, the nature of motions becomes more homogeneous throughout the RNA, with many residues showing increased flexibility at the aromatic carbon sites, while the anomeric carbon sites become more rigid. Surprisingly, we also observe indications of a slow collective motion of the RNA in the binding pocket of the protein. The observation of increased motions on binding is interesting in the context of growing evidence that binding does not always lead to motional restrictions and the resulting entropy gain could favor the free energy of association.
J. Am. Chem. Soc., 130 (36), 11892–11900, 2008.
13C-Labeled N-Acetyl-neuraminic Acid in Aqueous Solution: Detection and Quantification of Acyclic Keto, Keto Hydrate, and Enol Forms by 13C NMR Spectroscopy
Thomas Klepach, Ian Carmichael, and Anthony S. Serianni
Abstract:
Aqueous solutions of N-acetyl-neuraminic acid (Neu5Ac, 1) labeled with 13C at C1, C2, and/or C3 were analyzed by 13C NMR spectroscopy to detect and quantitfy the acyclic forms (keto, keto hydrate, enol) present at varying pHs. In addition to pyranoses, solutions contained the keto form, based on the detection of C2 signals at ~198 ppm (~0.7% at pH 2). Spectra of [2-13C] and [3-13C] isotopomers contained signals arising from labeled carbons at ~143 and ~120 ppm, respectively, which were attributed to enol forms. Solution studies of [1,2,3-13C3]1 substantiated the presence of enol (~0.5% at pH 2). Enol was not detected at pH > 6.0. A C2 signal observed at ~94 ppm was identified as C2 of the keto hydrate (~1.9% at pH 2), based partly on its abundance as a function of solution pH. Density functional theory (DFT) calculations were used to study the effect of enol and hydrate structure on JCH and JCC values involving C2 and C3 of these forms. Solvated DFT calculations showed that 2JC2,H3 in cis and trans enols have similar magnitudes but opposite signs, making this J-coupling potentially useful to distinguish enol configurations. Solvent deuterium exchange studies of 1 showed rapid incorporation of 2H from 2H2O at H3axial in the pyranoses at p2H 8.0, followed by slower exchange at H3equatorial. The acyclic keto form, which presumably participates in this reaction, must assume a pseudo-cyclic conformation in solution in order to account for the exchange selectivity. Weak 13C signals arising from labeled species were also observed consistently and reproducibly in aqueous solutions of 13C-labeled 1, possibly arising from products of lactonization or intermolecular esterification.
Thomas Klepach, Ian Carmichael, and Anthony S. Serianni
Abstract:
Aqueous solutions of N-acetyl-neuraminic acid (Neu5Ac, 1) labeled with 13C at C1, C2, and/or C3 were analyzed by 13C NMR spectroscopy to detect and quantitfy the acyclic forms (keto, keto hydrate, enol) present at varying pHs. In addition to pyranoses, solutions contained the keto form, based on the detection of C2 signals at ~198 ppm (~0.7% at pH 2). Spectra of [2-13C] and [3-13C] isotopomers contained signals arising from labeled carbons at ~143 and ~120 ppm, respectively, which were attributed to enol forms. Solution studies of [1,2,3-13C3]1 substantiated the presence of enol (~0.5% at pH 2). Enol was not detected at pH > 6.0. A C2 signal observed at ~94 ppm was identified as C2 of the keto hydrate (~1.9% at pH 2), based partly on its abundance as a function of solution pH. Density functional theory (DFT) calculations were used to study the effect of enol and hydrate structure on JCH and JCC values involving C2 and C3 of these forms. Solvated DFT calculations showed that 2JC2,H3 in cis and trans enols have similar magnitudes but opposite signs, making this J-coupling potentially useful to distinguish enol configurations. Solvent deuterium exchange studies of 1 showed rapid incorporation of 2H from 2H2O at H3axial in the pyranoses at p2H 8.0, followed by slower exchange at H3equatorial. The acyclic keto form, which presumably participates in this reaction, must assume a pseudo-cyclic conformation in solution in order to account for the exchange selectivity. Weak 13C signals arising from labeled species were also observed consistently and reproducibly in aqueous solutions of 13C-labeled 1, possibly arising from products of lactonization or intermolecular esterification.
Tuesday, September 09, 2008
Journal of Magnetic Resonance - Vol 194 Issue 1
Exploring the limits of broadband excitation and inversion: II. Rf-power optimized pulses
Kyryl Kobzar, Thomas E. Skinner, Navin Khaneja, Steffen J. Glaser and Burkhard Luy
In [K. Kobzar, T.E. Skinner, N. Khaneja, S.J. Glaser, B. Luy, Exploring the limits of broadband excitation and inversion, J. Magn. Reson. 170 (2004) 236–243], optimal control theory was employed in a systematic study to establish physical limits for the minimum rf-amplitudes required in broadband excitation and inversion pulses. In a number of cases, however, experimental schemes are not limited by rf-amplitudes, but by the overall rf-power applied to a sample. We therefore conducted a second systematic study of excitation and inversion pulses of varying pulse durations with respect to bandwidth and rf-tolerances, but this time using a modified algorithm involving restricted rf-power. The resulting pulses display a variety of pulse shapes with highly modulated rf-amplitudes and generally show better performance than corresponding pulses with identical pulse length and rf-power, but limited rf-amplitude. A detailed description of pulse shapes and their performance is given for the so-called power-BEBOP and power-BIBOP pulses.
Improved J-compensated sequences based on short composite pulses
A.M. Torres, W.A. Bubb, D.J. Philp and P.W. Kuchel
Efficient J-compensated sequences that are shorter in duration and use less RF pulses have been created from short but very efficient composite 90° RF pulses. The improved J-compensation transforms in-phase into antiphase magnetization and can be incorporated in any pulse sequence that involves evolution of heteronuclear J-couplings. The compensated sequences were tested and incorporated into an HMBC sequence. J-compensated experiments referred to as HMBC-J45 + 90A and HMBC-J45 + 90B, were found to be effective over a wide range of J values.
Clean HMBC: Suppression of strong-coupling induced artifacts in HMBC spectra
Peter Würtz, Perttu Permi, Niels Chr. Nielsen and Ole W. Sørensen
A new experiment, clean HMBC, is introduced for suppression of strong-coupling induced artifacts in HMBC spectra. The culprits of these artifacts are an inherent shortcoming of low-pass J filters in the presence of strong coupling and the 1H π pulse in the middle of the evolution period aimed at suppressing evolution under heteronuclear J couplings and 1H chemical shifts. A π pulse causes coherence transfer in strongly coupled spin systems and, as is well known in e.g., homonuclear J spectra, this leads to peaks that would not be there in the absence of strong coupling. Similar artifacts occur in HMBC spectra, but they have apparently been overlooked, presumably because they have been assigned to inefficiency of low-pass J filters or not noticed because of a coarse digital resolution in the spectra. Clean HMBC is the HMBC technique of choice for molecules notorious for strong coupling among protons, such as carbohydrates, and the new technique is demonstrated on D-mannose. Finally, a fundamental difference between HMBC and H2BC explains why strong-coupling artifacts are much less of a problem in the latter type of spectra.
A structure refinement strategy for NMR crystallography: An improved crystal structure of silica-ZSM-12 zeolite from 29Si chemical shift tensors
Darren H. Brouwer
A strategy for performing crystal structure refinements with NMR chemical shift tensors is described in detail and implemented for the zeolite silica-ZSM-12 (framework type code MTW). The 29Si chemical shift tensors were determined from a slow magic-angle spinning spectrum obtained at an ultrahigh magnetic field of 21.1 T. The Si and O atomic coordinate parameters were optimized to give the best agreement between experimentally measured and ab initio calculated principal components of the 29Si chemical shift tensors, with the closest Si–O, O–O, and Si–Si distances restrained to correspond with the distributions of the distances found in a set of single-crystal X-ray diffraction (XRD) structures of high-silica zeolites. An improved structure for the silica-ZSM-12 zeolite, compared to a prior structure derived from powder XRD data, is obtained in which the agreement between the experimental and calculated 29Si chemical shift tensors is dramatically improved, the Si–O, O–O, and Si–Si distances correspond to the expected distributions, while the calculated powder XRD pattern remains in good agreement with the experimental powder XRD data. It is anticipated that this “NMR crystallography” structure refinement strategy will be an important tool for the accurate structure determination of materials that are difficult to fully characterize by traditional diffraction methods.
Kyryl Kobzar, Thomas E. Skinner, Navin Khaneja, Steffen J. Glaser and Burkhard Luy
In [K. Kobzar, T.E. Skinner, N. Khaneja, S.J. Glaser, B. Luy, Exploring the limits of broadband excitation and inversion, J. Magn. Reson. 170 (2004) 236–243], optimal control theory was employed in a systematic study to establish physical limits for the minimum rf-amplitudes required in broadband excitation and inversion pulses. In a number of cases, however, experimental schemes are not limited by rf-amplitudes, but by the overall rf-power applied to a sample. We therefore conducted a second systematic study of excitation and inversion pulses of varying pulse durations with respect to bandwidth and rf-tolerances, but this time using a modified algorithm involving restricted rf-power. The resulting pulses display a variety of pulse shapes with highly modulated rf-amplitudes and generally show better performance than corresponding pulses with identical pulse length and rf-power, but limited rf-amplitude. A detailed description of pulse shapes and their performance is given for the so-called power-BEBOP and power-BIBOP pulses.
Improved J-compensated sequences based on short composite pulses
A.M. Torres, W.A. Bubb, D.J. Philp and P.W. Kuchel
Efficient J-compensated sequences that are shorter in duration and use less RF pulses have been created from short but very efficient composite 90° RF pulses. The improved J-compensation transforms in-phase into antiphase magnetization and can be incorporated in any pulse sequence that involves evolution of heteronuclear J-couplings. The compensated sequences were tested and incorporated into an HMBC sequence. J-compensated experiments referred to as HMBC-J45 + 90A and HMBC-J45 + 90B, were found to be effective over a wide range of J values.
Clean HMBC: Suppression of strong-coupling induced artifacts in HMBC spectra
Peter Würtz, Perttu Permi, Niels Chr. Nielsen and Ole W. Sørensen
A new experiment, clean HMBC, is introduced for suppression of strong-coupling induced artifacts in HMBC spectra. The culprits of these artifacts are an inherent shortcoming of low-pass J filters in the presence of strong coupling and the 1H π pulse in the middle of the evolution period aimed at suppressing evolution under heteronuclear J couplings and 1H chemical shifts. A π pulse causes coherence transfer in strongly coupled spin systems and, as is well known in e.g., homonuclear J spectra, this leads to peaks that would not be there in the absence of strong coupling. Similar artifacts occur in HMBC spectra, but they have apparently been overlooked, presumably because they have been assigned to inefficiency of low-pass J filters or not noticed because of a coarse digital resolution in the spectra. Clean HMBC is the HMBC technique of choice for molecules notorious for strong coupling among protons, such as carbohydrates, and the new technique is demonstrated on D-mannose. Finally, a fundamental difference between HMBC and H2BC explains why strong-coupling artifacts are much less of a problem in the latter type of spectra.
A structure refinement strategy for NMR crystallography: An improved crystal structure of silica-ZSM-12 zeolite from 29Si chemical shift tensors
Darren H. Brouwer
A strategy for performing crystal structure refinements with NMR chemical shift tensors is described in detail and implemented for the zeolite silica-ZSM-12 (framework type code MTW). The 29Si chemical shift tensors were determined from a slow magic-angle spinning spectrum obtained at an ultrahigh magnetic field of 21.1 T. The Si and O atomic coordinate parameters were optimized to give the best agreement between experimentally measured and ab initio calculated principal components of the 29Si chemical shift tensors, with the closest Si–O, O–O, and Si–Si distances restrained to correspond with the distributions of the distances found in a set of single-crystal X-ray diffraction (XRD) structures of high-silica zeolites. An improved structure for the silica-ZSM-12 zeolite, compared to a prior structure derived from powder XRD data, is obtained in which the agreement between the experimental and calculated 29Si chemical shift tensors is dramatically improved, the Si–O, O–O, and Si–Si distances correspond to the expected distributions, while the calculated powder XRD pattern remains in good agreement with the experimental powder XRD data. It is anticipated that this “NMR crystallography” structure refinement strategy will be an important tool for the accurate structure determination of materials that are difficult to fully characterize by traditional diffraction methods.
Monday, September 08, 2008
ASAP J. Am. Chem. Soc., ASAP Article, 10.1021/ja8047317
Temperature-Dependent Interconversion of Phosphoramidite−Cu Complexes Detected by Combined Diffusion Studies, 31P NMR, and Low-Temperature NMR Spectroscopy
Katrin Schober, Hongxia Zhang, and Ruth M. Gschwind
Abstract:
For copper-catalyzed enantioselective conjugate additions, knowledge about the precatalytic and catalytic complexes has not yet been sufficiently developed to understand the strong influence of different temperatures on these famous reactions. Therefore, NMR experiments with four Cu(I) salts and two phosphoramidite ligands have been performed to elucidate the temperature dependence and the low-temperature structures of these copper complexes. The existence of the precatalytic binuclear complex with a mixed trigonal/tetrahedral coordination on copper is for the first time proven with direct NMR spectroscopic methods. Below 200 K, intermolecular interactions between free ligands and [Cu2X2L3] complexes induce binuclear [Cu2X2L4] complexes similar to the crystal structures. By combining diffusion experiments and 31P integrals at different temperatures, it is for the first time possible to follow the formation of stoichiometrically different complexes, even under experimental conditions in which the 31P signals of the complexes are spectroscopically not resolved due to exchange processes. This allows a first correlation between the complex species observed and the synthetic conditions reported. Furthermore, different preferences to build homo- or heterochiral complexes are detected for binaphthol and biphenol phosphoramidite complexes.
Katrin Schober, Hongxia Zhang, and Ruth M. Gschwind
Abstract:
For copper-catalyzed enantioselective conjugate additions, knowledge about the precatalytic and catalytic complexes has not yet been sufficiently developed to understand the strong influence of different temperatures on these famous reactions. Therefore, NMR experiments with four Cu(I) salts and two phosphoramidite ligands have been performed to elucidate the temperature dependence and the low-temperature structures of these copper complexes. The existence of the precatalytic binuclear complex with a mixed trigonal/tetrahedral coordination on copper is for the first time proven with direct NMR spectroscopic methods. Below 200 K, intermolecular interactions between free ligands and [Cu2X2L3] complexes induce binuclear [Cu2X2L4] complexes similar to the crystal structures. By combining diffusion experiments and 31P integrals at different temperatures, it is for the first time possible to follow the formation of stoichiometrically different complexes, even under experimental conditions in which the 31P signals of the complexes are spectroscopically not resolved due to exchange processes. This allows a first correlation between the complex species observed and the synthetic conditions reported. Furthermore, different preferences to build homo- or heterochiral complexes are detected for binaphthol and biphenol phosphoramidite complexes.
Friday, September 05, 2008
J. Am. Chem. Soc., 130 (34), 11266–11267, 2008.
On the Origin of NMR Dipolar Waves in Transient Helical Elements of Partially Folded Proteins
Malene Ringkjøbing Jensen and Martin Blackledge
Abstract:
The presence of dipolar coupling waves within helical elements of proteins implies an effective tilt of the main axis of the helical element relative to the magnetic field. Here, we investigate the origin of dipolar waves observed in helical elements of partially folded proteins. We find that the dipolar waves result from an effective tilt of the helix relative to the alignment axis that is determined by the directionality of the unfolded chains projected from the helix caps. The amplitude and phase of the dipolar wave depend in a predictable way on helix length, providing direct insight into helix stability, nucleation, and fraying in partially folded proteins.
Malene Ringkjøbing Jensen and Martin Blackledge
Abstract:
The presence of dipolar coupling waves within helical elements of proteins implies an effective tilt of the main axis of the helical element relative to the magnetic field. Here, we investigate the origin of dipolar waves observed in helical elements of partially folded proteins. We find that the dipolar waves result from an effective tilt of the helix relative to the alignment axis that is determined by the directionality of the unfolded chains projected from the helix caps. The amplitude and phase of the dipolar wave depend in a predictable way on helix length, providing direct insight into helix stability, nucleation, and fraying in partially folded proteins.
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