J. Am. Chem. Soc., 2010, 132 (16), pp 5538–5539
Breaking the T1 Constraint for Quantitative Measurement in Magic Angle Spinning Solid-State NMR Spectroscopy
Guangjin Hou, Shangwu Ding, Limin Zhang and Feng Deng
Quantitative solid-state NMR experimental schemes that break the conventional T1 constraint are described. The combination of broad-band homonuclear recoupling techniques and the conventional single pulse or cross-polarization (CP) schemes (referred as QUSP or QUCP) render the long T1 of low-? spins no longer a constraint for obtaining quantitative NMR spectra. During the mixing time when dipolar recoupling occurs, the nonuniformly CP enhanced or recovered spin magnetization is redistributed under the reintroduced homonuclear dipole-dipole interactions so that uniformly enhanced or recovered magnetization is achieved when the system reaches the quasi-equilibrium state. It is shown that quantitative NMR spectra can be obtained for the recycle delays substantially shorter than the conventionally required 5T1. In addition, the high efficiency gain can be achieved in QUSP and QUCP experiments with a relatively short recycle delay.
J. Am. Chem. Soc., 2010, 132 (16), pp 5546–5547
Detection of Transient Interchain Interactions in the Intrinsically Disordered Protein a-Synuclein by NMR Paramagnetic Relaxation Enhancement
Kuen-Phon Wu and Jean Baum
NMR paramagnetic relaxation enhancement experiments were applied to the intrinsically disordered protein a-synuclein, the primary protein in Parkinson's disease, to directly characterize transient intermolecular complexes at neutral and low pH. At neutral pH, we observed weak N- to C-terminal interchain contacts driven by electrostatic interactions, while at low pH, the C- to C-terminal interchain interactions are significantly stronger and driven by hydrophobic contacts. Characterization of these first interchain interactions will provide fundamental insight into the mechanism of amyloid formation.
J. Am. Chem. Soc., 2010, 132 (16), pp 5556–5557
Fibrillar vs Crystalline Full-Length ß-2-Microglobulin Studied by High-Resolution Solid-State NMR Spectroscopy
Emeline Barbet-Massin†, Stefano Ricagno‡§, Józef R. Lewandowski†, Sofia Giorgetti§, Vittorio Bellotti‡§, Martino Bolognesi, Lyndon Emsley† and Guido Pintacuda*†
Elucidating the fine structure of amyloid fibrils as well as understanding their processes of nucleation and growth remains a difficult yet essential challenge, directly linked to our current poor insight into protein misfolding and aggregation diseases. Here we consider ß-2-microglobulin (ß2m), the MHC-1 light chain component responsible for dialysis-related amyloidosis, which can give rise to amyloid fibrils in vitro under various experimental conditions, including low and neutral pH. We have used solid-state NMR to probe the structural features of fibrils formed by full-length ß2m (99 residues) at pH 2.5 and pH 7.4. A close comparison of 2D 13C-13C and 15N-13C correlation experiments performed on ß2m, in both the crystalline and fibrillar states, suggests that, in spite of structural changes affecting the protein loops linking the protein ß-strands, the protein chain retains a substantial share of its native secondary structure in the fibril assembly. Moreover, variations in the chemical shifts of the key Pro32 residue suggest the involvement of a cis-trans isomerization in the process of ß2m fibril formation. Lastly, the analogy of the spectra recorded on ß2m fibrils grown at different pH values hints at a conserved architecture of the amyloid species thus obtained.
J. Am. Chem. Soc., 2010, 132 (16), pp 5558–5559
Ultrafast MAS Solid-State NMR Permits Extensive 13C and 1H Detection in Paramagnetic Metalloproteins
Ivano Bertini, Lyndon Emsley§, Moreno Lelli, Claudio Luchinat, Jiafei Mao and Guido Pintacuda
We show here that by combining tailored approaches based on ultrafast (60 kHz) MAS on the CoII-replaced catalytic domain of matrix metalloproteinase 12 (CoMMP-12) we can observe and assign, in a highly paramagnetic protein in the solid state, 13C and even 1H resonances from the residues coordinating the metal center. In addition, by exploiting the enhanced relaxation caused by the paramagnetic center, and the low power irradiation enabled by the fast MAS, this can be achieved in remarkably short times and at very high field (21.2 T), with only less than 1 mg of sample. Furthermore, using the known crystal structure of the compound, we are able to distinguish and measure pseudocontact (PCS) contributions to the shifts up to the coordinating ligands and to unveil structural information.
J. Am. Chem. Soc., 2010, 132 (16), pp 5672–5676
NMR-Based Structural Modeling of Graphite Oxide Using Multidimensional 13C Solid-State NMR and ab Initio Chemical Shift Calculations
Leah B. Casabianca†, Medhat A. Shaibat†, Weiwei W. Cai‡, Sungjin Park‡, Richard Piner‡, Rodney S. Ruoff‡ and Yoshitaka Ishii†
Chemically modified graphenes and other graphite-based materials have attracted growing interest for their unique potential as lightweight electronic and structural nanomaterials. It is an important challenge to construct structural models of noncrystalline graphite-based materials on the basis of NMR or other spectroscopic data. To address this challenge, a solid-state NMR (SSNMR)-based structural modeling approach is presented on graphite oxide (GO), which is a prominent precursor and interesting benchmark system of modified graphene. An experimental 2D 13C double-quantum/single-quantum correlation SSNMR spectrum of 13C-labeled GO was compared with spectra simulated for different structural models using ab initio geometry optimization and chemical shift calculations. The results show that the spectral features of the GO sample are best reproduced by a geometry-optimized structural model that is based on the Lerf-Klinowski model (Lerf, A. et al. Phys. Chem. B 1998, 102, 4477); this model is composed of interconnected sp2, 1,2-epoxide, and COH carbons. This study also convincingly excludes the possibility of other previously proposed models, including the highly oxidized structures involving 1,3-epoxide carbons (Szabo, I. et al. Chem. Mater. 2006, 18, 2740). 13C chemical shift anisotropy (CSA) patterns measured by a 2D 13C CSA/isotropic shift correlation SSNMR were well reproduced by the chemical shift tensor obtained by the ab initio calculation for the former model. The approach presented here is likely to be applicable to other chemically modified graphenes and graphite-based systems.
J. Am. Chem. Soc., 2010, 132 (16), pp 5779–5788
Proton-Evolved Local-Field Solid-State NMR Studies of Cytochrome b5 Embedded in Bicelles, Revealing both Structural and Dynamical Information
Ronald Soong†, Pieter E. S. Smith†, Jiadi Xu†, Kazutoshi Yamamoto†, Sang-Choul Im‡, Lucy Waskell‡ and Ayyalusamy Ramamoorthy*†
Structural biology of membrane proteins has rapidly evolved into a new frontier of science. Although solving the structure of a membrane protein with atomic-level resolution is still a major challenge, separated local field (SLF) NMR spectroscopy has become an invaluable tool in obtaining structural images of membrane proteins under physiological conditions. Recent studies have demonstrated the use of rotating-frame SLF techniques to accurately measure strong heteronuclear dipolar couplings between directly bonded nuclei. However, in these experiments, all weak dipolar couplings are suppressed. On the other hand, weak heteronuclear dipolar couplings can be measured using laboratory-frame SLF experiments, but only at the expense of spectral resolution for strongly dipolar coupled spins. In the present study, we implemented two-dimensional proton-evolved local-field (2D PELF) pulse sequences using either composite zero cross-polarization (COMPOZER-CP) or windowless isotropic mixing (WIM) for magnetization transfer. These PELF sequences can be used for the measurement of a broad range of heteronuclear dipolar couplings, allowing for a complete mapping of protein dynamics in a lipid bilayer environment. Experimental results from magnetically aligned bicelles containing uniformly 15N-labeled cytochrome b5 are presented and theoretical analyses of the new PELF sequences are reported. Our results suggest that the PELF-based experimental approaches will have a profound impact on solid-state NMR spectroscopy of membrane proteins and other membrane-associated molecules in magnetically aligned bicelles.
J. Am. Chem. Soc., 2010, 132 (16), pp 5803–5811
Changes in Transmembrane Helix Alignment by Arginine Residues Revealed by Solid-State NMR Experiments and Coarse-Grained MD Simulations
Vitaly V. Vostrikov‡†, Benjamin A. Hall§†, Denise V. Greathouse‡, Roger E. Koeppe, II*‡ and Mark S. P. Sansom*§
Independent experimental and computational approaches show agreement concerning arginine/membrane interactions when a single arginine is introduced at selected positions within the membrane-spanning region of acetyl-GGALW5LALALAL12AL14ALALW19LAGA-ethanolamide, designated GWALP23. Peptide sequence isomers having Arg in position 12 or position 14 display markedly different behaviors, as deduced by both solid-state NMR experiments and coarse-grained molecular dynamics (CG-MD) simulations. With respect to the membrane normal of DOPC or DPPC lipid bilayer membranes, GWALP23-R14 shows one major state whose apparent average tilt is 10° greater than that of GWALP23. The presence of R14 furthermore induces bilayer thinning and peptide displacement to "lift" the charged guanidinium toward the bilayer surface. By contrast, GWALP23-R12 exhibits multiple states that are in slow exchange on the NMR time scale, with CG-MD simulations indicating two distinct positions with different screw rotation angles in the membrane, along with an increased tendency to exit the lipid bilayer.
Friday, June 25, 2010
Wednesday, June 23, 2010
Hiyam's Journal Update
J. Am. Chem. Soc., 2010, 132 (21), pp 7321–7337
Molecular Silicate and Aluminate Species in Anhydrous and Hydrated Cements
Aditya Rawal, Benjamin J. Smith†, George L. Athens, Christopher L. Edwards, Lawrence Roberts, Vijay Gupta and Bradley F. Chmelka
The compositions and molecular structures of anhydrous and hydrated cements are established by using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy methods to distinguish among different molecular species and changes that occur as a result of cement hydration and setting. One- and two-dimensional (2D) solid-state 29Si and 27Al magic-angle spinning NMR methodologies, including T1-relaxation-time- and chemical-shift-anisotropy-filtered measurements and the use of very high magnetic fields (19 T), allow resonances from different silicate and aluminate moieties to be resolved and assigned in complicated spectra. Single-pulse 29Si and 27Al NMR spectra are correlated with X-ray fluorescence results to quantify the different crystalline and disordered silicate and aluminate species in anhydrous and hydrated cements. 2D 29Si{1H} and 27Al{1H}heteronuclear correlation NMR spectra of hydrated cements establish interactions between water and hydroxyl moieties with distinct 27Al and 29Si species. The use of a 29Si T1-filter allows anhydrous and hydrated silicate species associated with iron-containing components in the cements to be distinguished, showing that they segregate from calcium silicate and aluminate components during hydration. The different compositions of white Portland and gray oilwell cements are shown to have distinct molecular characteristics that are correlated with their hydration behaviors.
A Resonance Assignment Method for Oriented-Sample Solid-State NMR of Proteins
Robert W. Knox†, George J. Lu‡, Stanley J. Opella‡ and Alexander A. Nevzorov
J. Am. Chem. Soc., 2010, 132 (24), pp 8255–8257
A general sequential assignment strategy for uniformly 15N-labeled uniaxially aligned membrane proteins is proposed. Mismatched Hartmann−Hahn magnetization transfer is employed to establish proton-mediated correlations among the neighboring 15N backbone spins. Magnetically aligned Pf1 phage coat protein was used to illustrate the method. Exchanged and nonexchanged separated local field spectra were acquired and overlaid to distinguish the cross-peaks from the main peaks. Most of the original assignments from the literature were confirmed without selectively labeled samples. This method is applicable to proteins with arbitrary topology and will find use in assigning solid-state NMR spectra of oriented membrane proteins for their subsequent structure determination.
The Polar Phase of NaNbO3: A Combined Study by Powder Diffraction, Solid-State NMR, and First-Principles Calculations
Karen E. Johnston†, Chiu C. Tang‡, Julia E. Parker‡, Kevin S. Knight§, Philip Lightfoot*† and Sharon E. Ashbrook*†
J. Am. Chem. Soc., 2010, 132 (25), pp 8732–8746
A polar phase of NaNbO3 has been successfully synthesized using sol-gel techniques. Detailed characterization of this phase has been undertaken using high-resolution powder diffraction (X-ray and neutron) and 23Na multiple-quantum (MQ) MAS NMR, supported by second harmonic generation measurements and density functional theory calculations. Samples of NaNbO3 were also synthesized using conventional solid-state methods and were observed to routinely comprise of a mixture of two different polymorphs of NaNbO3, namely, the well-known orthorhombic phase (space group Pbcm) and the current polar phase, the relative quantities of which vary considerably depending upon precise reaction conditions. Our studies show that each of these two polymorphs of NaNbO3 contains two crystallographically distinct Na sites. This is consistent with assignment of the polar phase to the orthorhombic space group P21ma, although peak broadenings in the diffraction data suggest a subtle monoclinic distortion. Using carefully monitored molten salt techniques, it was possible to eradicate the polar polymorph and synthesize the pure Pbcm phase.
NMR Methods for Characterizing the Pore Structures and Hydrogen Storage Properties of Microporous Carbons
Robert J. Anderson†, Thomas P. McNicholas‡, Alfred Kleinhammes*†, Anmiao Wang‡, Jie Liu‡ and Yue Wu†
J. Am. Chem. Soc., 2010, 132 (25), pp 8618–8626
1H NMR spectroscopy is used to investigate a series of microporous activated carbons derived from a poly(ether ether ketone) (PEEK) precursor with varying amounts of burnoff (BO). In particular, properties relevant to hydrogen storage are evaluated such as pore structure, average pore size, uptake, and binding energy. High-pressure NMR with in situ H2 loading is employed with H2 pressure ranging from 100 Pa to 10 MPa. An N2-cooled cryostat allows for NMR isotherm measurements at both room temperature (290 K) and 100 K. Two distinct 1H NMR peaks appear in the spectra which represent the gaseous H2 in intergranular pores and the H2 residing in micropores. The chemical shift of the micropore peak is observed to evolve with changing pressure, the magnitude of this effect being correlated to the amount of BO and therefore the structure. This is attributed to the different pressure dependence of the amount of adsorbed and non-adsorbed molecules within micropores, which experience significantly different chemical shifts due to the strong distance dependence of the ring current effect. In pores with a critical diameter of 1.2 nm or less, no pressure dependence is observed because they are not wide enough to host
non-adsorbed molecules; this is the case for samples with less than 35% BO. The largest estimated pore size that can contribute to the micropore peak is estimated to be around 2.4 nm. The total H2 uptake associated with pores of this size or smaller is evaluated via a calibration of the isotherms, with the highest amount being observed at 59% BO. Two binding energies are present in the micropores, with the lower, more dominant one being on the order of 5 kJ mol−1 and the higher one ranging from 7 to 9 kJ mol−1.
Characterization of RNA Invasion by 19F NMR Spectroscopy
Anu Kiviniemi and Pasi Virta*
J. Am. Chem. Soc., 2010, 132 (25), pp 8560–8562
19F NMR spectroscopy offers an efficient tool for monitoring RNA invasion. The invasion of 2′-O-methyl oligoribonucleotides into a 19F-labeled HIV-1 TAR RNA model and the temperature-dependent behavior of the complexes obtained have been examined.
Molecular Silicate and Aluminate Species in Anhydrous and Hydrated Cements
Aditya Rawal, Benjamin J. Smith†, George L. Athens, Christopher L. Edwards, Lawrence Roberts, Vijay Gupta and Bradley F. Chmelka
The compositions and molecular structures of anhydrous and hydrated cements are established by using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy methods to distinguish among different molecular species and changes that occur as a result of cement hydration and setting. One- and two-dimensional (2D) solid-state 29Si and 27Al magic-angle spinning NMR methodologies, including T1-relaxation-time- and chemical-shift-anisotropy-filtered measurements and the use of very high magnetic fields (19 T), allow resonances from different silicate and aluminate moieties to be resolved and assigned in complicated spectra. Single-pulse 29Si and 27Al NMR spectra are correlated with X-ray fluorescence results to quantify the different crystalline and disordered silicate and aluminate species in anhydrous and hydrated cements. 2D 29Si{1H} and 27Al{1H}heteronuclear correlation NMR spectra of hydrated cements establish interactions between water and hydroxyl moieties with distinct 27Al and 29Si species. The use of a 29Si T1-filter allows anhydrous and hydrated silicate species associated with iron-containing components in the cements to be distinguished, showing that they segregate from calcium silicate and aluminate components during hydration. The different compositions of white Portland and gray oilwell cements are shown to have distinct molecular characteristics that are correlated with their hydration behaviors.
A Resonance Assignment Method for Oriented-Sample Solid-State NMR of Proteins
Robert W. Knox†, George J. Lu‡, Stanley J. Opella‡ and Alexander A. Nevzorov
J. Am. Chem. Soc., 2010, 132 (24), pp 8255–8257
A general sequential assignment strategy for uniformly 15N-labeled uniaxially aligned membrane proteins is proposed. Mismatched Hartmann−Hahn magnetization transfer is employed to establish proton-mediated correlations among the neighboring 15N backbone spins. Magnetically aligned Pf1 phage coat protein was used to illustrate the method. Exchanged and nonexchanged separated local field spectra were acquired and overlaid to distinguish the cross-peaks from the main peaks. Most of the original assignments from the literature were confirmed without selectively labeled samples. This method is applicable to proteins with arbitrary topology and will find use in assigning solid-state NMR spectra of oriented membrane proteins for their subsequent structure determination.
The Polar Phase of NaNbO3: A Combined Study by Powder Diffraction, Solid-State NMR, and First-Principles Calculations
Karen E. Johnston†, Chiu C. Tang‡, Julia E. Parker‡, Kevin S. Knight§, Philip Lightfoot*† and Sharon E. Ashbrook*†
J. Am. Chem. Soc., 2010, 132 (25), pp 8732–8746
A polar phase of NaNbO3 has been successfully synthesized using sol-gel techniques. Detailed characterization of this phase has been undertaken using high-resolution powder diffraction (X-ray and neutron) and 23Na multiple-quantum (MQ) MAS NMR, supported by second harmonic generation measurements and density functional theory calculations. Samples of NaNbO3 were also synthesized using conventional solid-state methods and were observed to routinely comprise of a mixture of two different polymorphs of NaNbO3, namely, the well-known orthorhombic phase (space group Pbcm) and the current polar phase, the relative quantities of which vary considerably depending upon precise reaction conditions. Our studies show that each of these two polymorphs of NaNbO3 contains two crystallographically distinct Na sites. This is consistent with assignment of the polar phase to the orthorhombic space group P21ma, although peak broadenings in the diffraction data suggest a subtle monoclinic distortion. Using carefully monitored molten salt techniques, it was possible to eradicate the polar polymorph and synthesize the pure Pbcm phase.
NMR Methods for Characterizing the Pore Structures and Hydrogen Storage Properties of Microporous Carbons
Robert J. Anderson†, Thomas P. McNicholas‡, Alfred Kleinhammes*†, Anmiao Wang‡, Jie Liu‡ and Yue Wu†
J. Am. Chem. Soc., 2010, 132 (25), pp 8618–8626
1H NMR spectroscopy is used to investigate a series of microporous activated carbons derived from a poly(ether ether ketone) (PEEK) precursor with varying amounts of burnoff (BO). In particular, properties relevant to hydrogen storage are evaluated such as pore structure, average pore size, uptake, and binding energy. High-pressure NMR with in situ H2 loading is employed with H2 pressure ranging from 100 Pa to 10 MPa. An N2-cooled cryostat allows for NMR isotherm measurements at both room temperature (290 K) and 100 K. Two distinct 1H NMR peaks appear in the spectra which represent the gaseous H2 in intergranular pores and the H2 residing in micropores. The chemical shift of the micropore peak is observed to evolve with changing pressure, the magnitude of this effect being correlated to the amount of BO and therefore the structure. This is attributed to the different pressure dependence of the amount of adsorbed and non-adsorbed molecules within micropores, which experience significantly different chemical shifts due to the strong distance dependence of the ring current effect. In pores with a critical diameter of 1.2 nm or less, no pressure dependence is observed because they are not wide enough to host
non-adsorbed molecules; this is the case for samples with less than 35% BO. The largest estimated pore size that can contribute to the micropore peak is estimated to be around 2.4 nm. The total H2 uptake associated with pores of this size or smaller is evaluated via a calibration of the isotherms, with the highest amount being observed at 59% BO. Two binding energies are present in the micropores, with the lower, more dominant one being on the order of 5 kJ mol−1 and the higher one ranging from 7 to 9 kJ mol−1.
Characterization of RNA Invasion by 19F NMR Spectroscopy
Anu Kiviniemi and Pasi Virta*
J. Am. Chem. Soc., 2010, 132 (25), pp 8560–8562
19F NMR spectroscopy offers an efficient tool for monitoring RNA invasion. The invasion of 2′-O-methyl oligoribonucleotides into a 19F-labeled HIV-1 TAR RNA model and the temperature-dependent behavior of the complexes obtained have been examined.
Monday, June 21, 2010
J. Phys. Chem. A
Solid-State NMR Spectra and Long, Intra-Dimer Bonding in the π-[TTF]22+ (TTF = Tetrathiafulvalene) Dication
Merrill D. Halling, Joshua D. Bell, Ronald J. Pugmire, David M. Grant* and Joel S. Miller
J. Phys. Chem. A, 2010, 114 (24), pp 6622–6629
DOI: 10.1021/jp910509f
Publication Date (Web): June 2, 2010
The 13C chemical-shift tensor principal values for TTF and π-[TTF]22+ (TTF = tetrathiafulvalene) dimer dications have been measured in order to better understand the electronic structure and long intradimer bonding of these TTF-based dimer structures. The structure of π-[TTF]22+ is abnormal due to its two C−C and four S−S ca. 3.4 Å intradimer separations, which is less than the sum of the sulfur van der Waals radii, and has a singlet 1A1g electronic ground state. This study of TTF and [TTF]22+ was conducted to determine how the NMR chemical-shift tensor principal values change as a function of electronic structure. This study also establishes a better understanding of the interactions that lead to spin-pairing of the monomeric radical units. The density functional theory (DFT) calculated nuclear shielding tensors are correlated with the experimentally determined principal chemical-shift values. The embedded ion method (EIM) was used to investigate the electrostatic lattice potential in [TTF]22+. These theoretical methods provide information on the tensor magnitudes and orientations of their tensor principal values with respect to the molecular frame. The experimental chemical-shift principal values agree with the calculated quantum mechanical chemical-shielding principal values, within typical errors commonly seen for this class of molecular system. Relatively weak Wiberg bond orders between the two [TTF]+ components of the dimer dication correlate with the long bonds linking the two [TTF]+ monomers and substantiate the claim that there is weak multicenter bonding present.
_________________________________________
Interpretation of Indirect Nuclear Spin−Spin Couplings in Isomers of Adenine: Novel Approach to Analyze Coupling Electron Deformation Density Using Localized Molecular Orbitals
Radek Marek*, Aneka Kstkov, Kateina Malikov, Jaromr Touek, Jaromr Marek, Michal Hocek, Olga L. Malkina* and Vladimir G. Malkin
J. Phys. Chem. A, 2010, 114 (24), pp 6689–6700
DOI: 10.1021/jp102186r
Publication Date (Web): June 2, 2010
Adenine, an essential building block of nucleic acids present in all living systems, can occur in several tautomeric forms. The phenomenon of tautomerism can be investigated by several experimental methods, including nuclear magnetic resonance. In this study, long-range 1H−13C and 1H−15N coupling constants for N-alkyl derivatives related to four tautomers of adenine are investigated in DMSO and DMF solutions. To investigate the structural dependence of the coupling constants and to understand how polarization propagates in the system, Fermi contact (FC) terms were calculated for the individual isomers and analyzed by using density functional theory (DFT), and the coupling pathways were visualized using real-space functions. The coupling electron deformation densities (CDD) of several 1H−X (X = 13C, 15N) pairs are evaluated and compared. In order to analyze the CDD in more detail, a new approach to break down the CDD into contributions from Boys or Pipek−Mezey localized molecular orbitals (LMOs) has been developed. A similar approach has been applied to split the value of the FC contribution to the J coupling into the LMO contributions. On the basis of chemical concepts, the contributions of σ-bonds, π-electrons, and lone pairs of electrons are discussed. The lone pair of electrons at the nitrogen atom contributes significantly to the 1H−C═15N coupling, whereas the 1H−C═N−13C coupling is affected in a somewhat different way. Surprisingly, the contribution of the intervening C═N bond to the FC term for 1H−C═15N coupling originates exclusively in σ-electrons, with a vanishingly small contribution calculated for the π-electrons of this fragment. This behavior is rationalized by introducing the concept of “hard and soft J elements” derived from the polarizability of the individual components.
________________________________________
NMR Spectroscopic Parameters of Molecular Systems with Strong Hydrogen Bonds
Natalia Zarycz and Gustavo A. Aucar*
J. Phys. Chem. A, Article ASAP
DOI: 10.1021/jp1019334
Publication Date (Web): June 16, 2010
A series of closed H-bonded molecules that have (or not) delocalized bonds were studied. The dependence of both NMR spectroscopic parameters σ and J-couplings, and also the energy stability of such molecules with H-bond strength, were analyzed. The selected basic geometrical structure was that of malonaldehyde. From its full optimized geometry, the corresponding geometry of 3-OH propanal was obtained, fixing either the d(O−O) distance or a more extended local geometry and then optimizing the other part of the whole structure. Nitromalonaldehyde and nitromalonamide were also studied because they should have stronger H-bonds and their basic structure is also malonaldehyde. The last one also has electronic effects that may be varied by rotating the amino groups. By doing this it is possible to show that the effects on acidity of donors are more important than the equivalent effects on the basicity of acceptors. It is also shown that J-couplings that involve atoms close to the H-bond have important noncontact contributions that must be included in order to reproduce total J values. Noncontact contributions are more important than the Fermi contact (FC) one for J(O−O) in malonaldehyde. In nitromalonamide all three terms, FC, paramagnetic spin-orbital, and spin-dipolar are of the same order of magnitude when both amino groups are rotated. This does not happen for its planar configuration. Nuclear magnetic shielding of the hydrogen belonging to the H-bond is quite sensitive to it. The magnetic behavior of such hydrogen atom is modified when it is part of a closed H-bonded molecule. Then a relationship between the H-bond strength with the paramagnetic contributions of the shieldings of both atoms, C and O of the donor substructure, was obtained. We have found a cubic correlation between σp (C) of the C−O donor bond with σ (H) of the H-bonded hydrogen. It is observed that both the noncontact J-coupling contributions and shieldings on atoms belonging to the donor substructure, give a clear evidence about the presence of the resonance phenomenon in the model compounds that have been studied, malonaldehyde, nitromalonaldehyde, and nitromalonamide.
_________________________________
Spin-State-Corrected Gaussian-Type Orbital Basis Sets
Marcel Swart*, Mireia Gell, Josep M. Luis and Miquel Sola
J. Phys. Chem. A, Article ASAP
DOI: 10.1021/jp102712z
Publication Date (Web): June 16, 2010
Recently, we reported that the basis set has a profound influence on the computed values for spin-state splittings [ J. Phys. Chem. A 2008, 112, 6384]. In particular, small Gaussian-type orbital (GTO) basis sets were shown to be unreliable for the prediction of them. Here, we report simple modifications of the small Pople-type Gaussian-type orbital basis sets (3-21G, 3-21G*, 6-31G, 6-31G*), which correct their faulty behavior for the spin-state energies. We have investigated the basis sets for a set of 13 first-row transition-metal complexes for which reliable reference data have been obtained at the OPBE/TZ2P(STO) level. For several systems, we have used single and double spin-contamination corrections to avoid ambiguity of the results because of spin contamination, that is, the energies and geometries were obtained for the pure spin states. The spin ground states as predicted by the spin-state-corrected GTO basis sets (s6-31G, s6-31G*) are in complete agreement with the reference Slater-type orbital (STO) data, while those of the original basis sets and a recent modification by Baker and Pulay (m6-31G*) are not for all cases. The spin-state-corrected GTO basis sets also improve upon the original and modified basis sets for the accuracy of geometry optimization, while the accuracy of the vibrational frequencies is as good or better. At a limited additional cost, one therefore obtains very reliable results for these important spin-state energies.
Merrill D. Halling, Joshua D. Bell, Ronald J. Pugmire, David M. Grant* and Joel S. Miller
J. Phys. Chem. A, 2010, 114 (24), pp 6622–6629
DOI: 10.1021/jp910509f
Publication Date (Web): June 2, 2010
The 13C chemical-shift tensor principal values for TTF and π-[TTF]22+ (TTF = tetrathiafulvalene) dimer dications have been measured in order to better understand the electronic structure and long intradimer bonding of these TTF-based dimer structures. The structure of π-[TTF]22+ is abnormal due to its two C−C and four S−S ca. 3.4 Å intradimer separations, which is less than the sum of the sulfur van der Waals radii, and has a singlet 1A1g electronic ground state. This study of TTF and [TTF]22+ was conducted to determine how the NMR chemical-shift tensor principal values change as a function of electronic structure. This study also establishes a better understanding of the interactions that lead to spin-pairing of the monomeric radical units. The density functional theory (DFT) calculated nuclear shielding tensors are correlated with the experimentally determined principal chemical-shift values. The embedded ion method (EIM) was used to investigate the electrostatic lattice potential in [TTF]22+. These theoretical methods provide information on the tensor magnitudes and orientations of their tensor principal values with respect to the molecular frame. The experimental chemical-shift principal values agree with the calculated quantum mechanical chemical-shielding principal values, within typical errors commonly seen for this class of molecular system. Relatively weak Wiberg bond orders between the two [TTF]+ components of the dimer dication correlate with the long bonds linking the two [TTF]+ monomers and substantiate the claim that there is weak multicenter bonding present.
_________________________________________
Interpretation of Indirect Nuclear Spin−Spin Couplings in Isomers of Adenine: Novel Approach to Analyze Coupling Electron Deformation Density Using Localized Molecular Orbitals
Radek Marek*, Aneka Kstkov, Kateina Malikov, Jaromr Touek, Jaromr Marek, Michal Hocek, Olga L. Malkina* and Vladimir G. Malkin
J. Phys. Chem. A, 2010, 114 (24), pp 6689–6700
DOI: 10.1021/jp102186r
Publication Date (Web): June 2, 2010
Adenine, an essential building block of nucleic acids present in all living systems, can occur in several tautomeric forms. The phenomenon of tautomerism can be investigated by several experimental methods, including nuclear magnetic resonance. In this study, long-range 1H−13C and 1H−15N coupling constants for N-alkyl derivatives related to four tautomers of adenine are investigated in DMSO and DMF solutions. To investigate the structural dependence of the coupling constants and to understand how polarization propagates in the system, Fermi contact (FC) terms were calculated for the individual isomers and analyzed by using density functional theory (DFT), and the coupling pathways were visualized using real-space functions. The coupling electron deformation densities (CDD) of several 1H−X (X = 13C, 15N) pairs are evaluated and compared. In order to analyze the CDD in more detail, a new approach to break down the CDD into contributions from Boys or Pipek−Mezey localized molecular orbitals (LMOs) has been developed. A similar approach has been applied to split the value of the FC contribution to the J coupling into the LMO contributions. On the basis of chemical concepts, the contributions of σ-bonds, π-electrons, and lone pairs of electrons are discussed. The lone pair of electrons at the nitrogen atom contributes significantly to the 1H−C═15N coupling, whereas the 1H−C═N−13C coupling is affected in a somewhat different way. Surprisingly, the contribution of the intervening C═N bond to the FC term for 1H−C═15N coupling originates exclusively in σ-electrons, with a vanishingly small contribution calculated for the π-electrons of this fragment. This behavior is rationalized by introducing the concept of “hard and soft J elements” derived from the polarizability of the individual components.
________________________________________
NMR Spectroscopic Parameters of Molecular Systems with Strong Hydrogen Bonds
Natalia Zarycz and Gustavo A. Aucar*
J. Phys. Chem. A, Article ASAP
DOI: 10.1021/jp1019334
Publication Date (Web): June 16, 2010
A series of closed H-bonded molecules that have (or not) delocalized bonds were studied. The dependence of both NMR spectroscopic parameters σ and J-couplings, and also the energy stability of such molecules with H-bond strength, were analyzed. The selected basic geometrical structure was that of malonaldehyde. From its full optimized geometry, the corresponding geometry of 3-OH propanal was obtained, fixing either the d(O−O) distance or a more extended local geometry and then optimizing the other part of the whole structure. Nitromalonaldehyde and nitromalonamide were also studied because they should have stronger H-bonds and their basic structure is also malonaldehyde. The last one also has electronic effects that may be varied by rotating the amino groups. By doing this it is possible to show that the effects on acidity of donors are more important than the equivalent effects on the basicity of acceptors. It is also shown that J-couplings that involve atoms close to the H-bond have important noncontact contributions that must be included in order to reproduce total J values. Noncontact contributions are more important than the Fermi contact (FC) one for J(O−O) in malonaldehyde. In nitromalonamide all three terms, FC, paramagnetic spin-orbital, and spin-dipolar are of the same order of magnitude when both amino groups are rotated. This does not happen for its planar configuration. Nuclear magnetic shielding of the hydrogen belonging to the H-bond is quite sensitive to it. The magnetic behavior of such hydrogen atom is modified when it is part of a closed H-bonded molecule. Then a relationship between the H-bond strength with the paramagnetic contributions of the shieldings of both atoms, C and O of the donor substructure, was obtained. We have found a cubic correlation between σp (C) of the C−O donor bond with σ (H) of the H-bonded hydrogen. It is observed that both the noncontact J-coupling contributions and shieldings on atoms belonging to the donor substructure, give a clear evidence about the presence of the resonance phenomenon in the model compounds that have been studied, malonaldehyde, nitromalonaldehyde, and nitromalonamide.
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Spin-State-Corrected Gaussian-Type Orbital Basis Sets
Marcel Swart*, Mireia Gell, Josep M. Luis and Miquel Sola
J. Phys. Chem. A, Article ASAP
DOI: 10.1021/jp102712z
Publication Date (Web): June 16, 2010
Recently, we reported that the basis set has a profound influence on the computed values for spin-state splittings [ J. Phys. Chem. A 2008, 112, 6384]. In particular, small Gaussian-type orbital (GTO) basis sets were shown to be unreliable for the prediction of them. Here, we report simple modifications of the small Pople-type Gaussian-type orbital basis sets (3-21G, 3-21G*, 6-31G, 6-31G*), which correct their faulty behavior for the spin-state energies. We have investigated the basis sets for a set of 13 first-row transition-metal complexes for which reliable reference data have been obtained at the OPBE/TZ2P(STO) level. For several systems, we have used single and double spin-contamination corrections to avoid ambiguity of the results because of spin contamination, that is, the energies and geometries were obtained for the pure spin states. The spin ground states as predicted by the spin-state-corrected GTO basis sets (s6-31G, s6-31G*) are in complete agreement with the reference Slater-type orbital (STO) data, while those of the original basis sets and a recent modification by Baker and Pulay (m6-31G*) are not for all cases. The spin-state-corrected GTO basis sets also improve upon the original and modified basis sets for the accuracy of geometry optimization, while the accuracy of the vibrational frequencies is as good or better. At a limited additional cost, one therefore obtains very reliable results for these important spin-state energies.
Tuesday, June 15, 2010
Journal of Materials Chemistry
Probing the local structures and protonic conduction pathways in scandium substituted BaZrO3 by multinuclear solid-state NMR spectroscopy
Lucienne Buannic a, Frédéric Blanc a, Ivan Hung b, Zhehong Gan b and Clare P. Grey *acA comprehensive multinuclear solid-state NMR study of scandium-substituted BaZrO3 is reported. Static low field and MQMAS very high field 45Sc NMR data revealed the presence of both 5- and 6-coordinated scandium atoms, 5-coordinated scandium arising from Sc nearby an oxygen vacancy. 17O NMR spectra showed the presence of up to three different chemical oxygen environments assigned to Zr–O–Zr, Zr–O–Sc and Sc–O–Sc. From the ratios of these different oxygen sites, the distribution of the scandium cations was close to random but indicated that the maximum scandium incorporation was lower than expected, consistent with the observation of Sc2O3 impurities at substitution levels of 30% Sc for Zr. 1H and 45Sc NMR data on the hydrated materials revealed the presence of scandium next to protonic defects. Finally, variable temperature 1H NMR showed the presence of at least two different proton environments in between which proton transfer occurs at ambient temperatures (300 K).
http://www.rsc.org/delivery/_ArticleLinking/ArticleLinking.cfm?JournalCode=JM&Year=2010&ManuscriptID=c0jm00155d&Iss=Advance_Article
DOI: 10.1039/c0jm00155d
Thursday, June 10, 2010
Journal of Physical Chemistry B and C, v114, Issues 23
Crystalline Aluminum Hydroxide Fluorides AlFx(OH)3−x·H2O: Structural Insights from 1H and 2H Solid State NMR and Vibrational Spectroscopy
G. Scholz*, S. Brehme, R. Knig, D. Heidemann and E. Kemnitz*
J. Phys. Chem. C, 2010, 114 (23), pp 10535–10543
DOI: 10.1021/jp1023857
AbstractFor the first time, 1H/2H MAS NMR signals of crystalline hydroxide fluorides AlFx(OH)3−x·H2O, as well as of the dehydrated samples, both with pyrochlore structure, were resolved, identified, and assigned in direct correlation with vibrational bands of respective FT IR spectra. The use of magnetically diluted samples in combination with 1H spin−echo experiments, 2H MAS, and 19F−2H CP and 1H−2H CP MAS NMR experiments gave information on different 2H (1H) sites in relation to present structural motifs known from the crystal structure.
G. Scholz*, S. Brehme, R. Knig, D. Heidemann and E. Kemnitz*
J. Phys. Chem. C, 2010, 114 (23), pp 10535–10543
DOI: 10.1021/jp1023857
AbstractFor the first time, 1H/2H MAS NMR signals of crystalline hydroxide fluorides AlFx(OH)3−x·H2O, as well as of the dehydrated samples, both with pyrochlore structure, were resolved, identified, and assigned in direct correlation with vibrational bands of respective FT IR spectra. The use of magnetically diluted samples in combination with 1H spin−echo experiments, 2H MAS, and 19F−2H CP and 1H−2H CP MAS NMR experiments gave information on different 2H (1H) sites in relation to present structural motifs known from the crystal structure.
Angewandte Chemie International Edition
Angewandte Chemie International Edition
Early View (Articles online in advance of print)
Published Online: 8 Jun 2010
High-Resolution Studies of Uniformly 13C,15H-Labeled RNA by Solid-State NMR Spectroscopy
Alexey V. Cherepanov, Dr., Clemens Glaubitz, Prof. Dr., Harald Schwalbe, Prof. Dr.
Keywords: conformational analysis • freeze-quenching • NMR spectroscopy • RNA • solid-state structures
Abstract: Chilling out: Solid-state 13C NMR correlation spectroscopy was used to assign the signals of a uniformly labeled RNA hairpin infrozen aqueous solution. Conformational analysis shows that solutions of biologically relevant RNAs can freeze withoutsignificant changes in RNA structure and without critical loss of resolution and sensitivity in NMR experiments.
10.1002/anie.200906885
Angewandte Chemie International Edition
Early View (Articles online in advance of print)
Published Online: 8 Jun 2010
The Elusive Enamine Intermediate in Proline-Catalyzed Aldol Reactions: NMR Detection, Formation Pathway, and Stabilization Trends
Markus B. Schmid, Kirsten Zeitler, Dr., Ruth M. Gschwind, Prof. Dr.
Keywords: aldol reaction • enamines • NMR spectroscopy • organocatalysis • proline catalysis
Abstract: The missing link: The elusive enamine intermediate of nucleophilic proline catalysis was detected and stereochemicallycharacterized by NMR analysis of the aldehyde self-aldolization reaction in dipolar aprotic solvents. NMR exchange spectroscopy(EXSY) was used to observe direct enamine formation from oxazolidinones. Additionally, the stabilization of the intermediate bythe appropriate choice of solvent and substitution pattern on the aldehyde is presented.
10.1002/anie.200906629
Early View (Articles online in advance of print)
Published Online: 8 Jun 2010
High-Resolution Studies of Uniformly 13C,15H-Labeled RNA by Solid-State NMR Spectroscopy
Alexey V. Cherepanov, Dr., Clemens Glaubitz, Prof. Dr., Harald Schwalbe, Prof. Dr.
Keywords: conformational analysis • freeze-quenching • NMR spectroscopy • RNA • solid-state structures
Abstract: Chilling out: Solid-state 13C NMR correlation spectroscopy was used to assign the signals of a uniformly labeled RNA hairpin infrozen aqueous solution. Conformational analysis shows that solutions of biologically relevant RNAs can freeze withoutsignificant changes in RNA structure and without critical loss of resolution and sensitivity in NMR experiments.
10.1002/anie.200906885
Angewandte Chemie International Edition
Early View (Articles online in advance of print)
Published Online: 8 Jun 2010
The Elusive Enamine Intermediate in Proline-Catalyzed Aldol Reactions: NMR Detection, Formation Pathway, and Stabilization Trends
Markus B. Schmid, Kirsten Zeitler, Dr., Ruth M. Gschwind, Prof. Dr.
Keywords: aldol reaction • enamines • NMR spectroscopy • organocatalysis • proline catalysis
Abstract: The missing link: The elusive enamine intermediate of nucleophilic proline catalysis was detected and stereochemicallycharacterized by NMR analysis of the aldehyde self-aldolization reaction in dipolar aprotic solvents. NMR exchange spectroscopy(EXSY) was used to observe direct enamine formation from oxazolidinones. Additionally, the stabilization of the intermediate bythe appropriate choice of solvent and substitution pattern on the aldehyde is presented.
10.1002/anie.200906629
Tuesday, June 08, 2010
Phys. Chem. Chem. Phys. 2010 Vol. 12 Issue 22
An entire issue dedicated to dynamic nuclear polarization NMR (cross polarization from an added paramagnetic agent to the nucleus of interest). Requires additional hardware but it is an interesting concept. The following is a good introductory journal:
Solid-state dynamic nuclear polarization at 263 GHz: spectrometer design and experimental results
Melanie Rosay, Leo Tometich, Shane Pawsey, Reto Bader, Robert Schauwecker, Monica Blank, Philipp M. Borchard, Stephen R. Cauffman, Kevin L. Felch, Ralph T. Weber, Richard J. Temkin, Robert G. Griffin and Werner E. Maas
Dynamic Nuclear Polarization (DNP) experiments transfer polarization from electron spins to nuclear spins with microwave irradiation of the electron spins for enhanced sensitivity in nuclear magnetic resonance (NMR) spectroscopy. Design and testing of a spectrometer for magic angle spinning (MAS) DNP experiments at 263 GHz microwave frequency, 400 MHz 1H frequency is described. Microwaves are generated by a novel continuous-wave gyrotron, transmitted to the NMR probe via a transmission line, and irradiated on a 3.2 mm rotor for MAS DNP experiments. DNP signal enhancements of up to 80 have been measured at 95 K on urea and proline in water–glycerol with the biradical polarizing agent TOTAPOL. We characterize the experimental parameters affecting the DNP efficiency: the magnetic field dependence, temperature dependence and polarization build-up times, microwave power dependence, sample heating effects, and spinning frequency dependence of the DNP signal enhancement. Stable system operation, including DNP performance, is also demonstrated over a 36 h period.
http://www.rsc.org/ej/CP/2010/c003685b.pdf
Solid-state dynamic nuclear polarization at 263 GHz: spectrometer design and experimental results
Melanie Rosay, Leo Tometich, Shane Pawsey, Reto Bader, Robert Schauwecker, Monica Blank, Philipp M. Borchard, Stephen R. Cauffman, Kevin L. Felch, Ralph T. Weber, Richard J. Temkin, Robert G. Griffin and Werner E. Maas
________________________________________
Dynamic Nuclear Polarization (DNP) experiments transfer polarization from electron spins to nuclear spins with microwave irradiation of the electron spins for enhanced sensitivity in nuclear magnetic resonance (NMR) spectroscopy. Design and testing of a spectrometer for magic angle spinning (MAS) DNP experiments at 263 GHz microwave frequency, 400 MHz 1H frequency is described. Microwaves are generated by a novel continuous-wave gyrotron, transmitted to the NMR probe via a transmission line, and irradiated on a 3.2 mm rotor for MAS DNP experiments. DNP signal enhancements of up to 80 have been measured at 95 K on urea and proline in water–glycerol with the biradical polarizing agent TOTAPOL. We characterize the experimental parameters affecting the DNP efficiency: the magnetic field dependence, temperature dependence and polarization build-up times, microwave power dependence, sample heating effects, and spinning frequency dependence of the DNP signal enhancement. Stable system operation, including DNP performance, is also demonstrated over a 36 h period.
http://www.rsc.org/ej/CP/2010/c003685b.pdf
Thursday, June 03, 2010
J. Phys. Chem B and C., vol. 114, Issues 22
Multireference Ab Initio Calculations of g tensors for Trinuclear Copper Clusters in Multicopper Oxidases
Steven Vancoillie‡, Jakub Chalupsk§, Ulf Ryde, Edward I. Solomon, Kristine Pierloot‡, Frank Neese¶* and Lubomr Rulek§*
J. Phys. Chem. B, 2010, 114 (22), pp 7692–7702
DOI: 10.1021/jp103098r
Abstract: EPR spectroscopy has proven to be an indispensable tool in elucidating the structure of metal sites in proteins. In recent years, experimental EPR data have been complemented by theoretical calculations, which have become a standard tool of many quantum chemical packages. However, there have only been a few attempts to calculate EPR g tensors for exchange-coupled systems with more than two spins. In this work, we present a quantum chemical study of structural, electronic, and magnetic properties of intermediates in the reaction cycle of multicopper oxidases and of their inorganic models. All these systems contain three copper(II) ions bridged by hydroxide or O2− anions and their ground states are antiferromagnetically coupled doublets. We demonstrate that only multireference methods, such as CASSCF/CASPT2 or MRCI can yield qualitatively correct results (compared to the experimental values) and consider the accuracy of the calculated EPR g tensors as the current benchmark of quantum chemical methods. By decomposing the calculated g tensors into terms arising from interactions of the ground state with the various excited states, the origin of the zero-field splitting is explained. The results of the study demonstrate that a truly quantitative prediction of the g tensors of exchange-coupled systems is a great challenge to contemporary theory. The predictions strongly depend on small energy differences that are difficult to predict with sufficient accuracy by any quantum chemical method that is applicable to systems of the size of our target systems.
Steven Vancoillie‡, Jakub Chalupsk§, Ulf Ryde, Edward I. Solomon, Kristine Pierloot‡, Frank Neese¶* and Lubomr Rulek§*
J. Phys. Chem. B, 2010, 114 (22), pp 7692–7702
DOI: 10.1021/jp103098r
Abstract: EPR spectroscopy has proven to be an indispensable tool in elucidating the structure of metal sites in proteins. In recent years, experimental EPR data have been complemented by theoretical calculations, which have become a standard tool of many quantum chemical packages. However, there have only been a few attempts to calculate EPR g tensors for exchange-coupled systems with more than two spins. In this work, we present a quantum chemical study of structural, electronic, and magnetic properties of intermediates in the reaction cycle of multicopper oxidases and of their inorganic models. All these systems contain three copper(II) ions bridged by hydroxide or O2− anions and their ground states are antiferromagnetically coupled doublets. We demonstrate that only multireference methods, such as CASSCF/CASPT2 or MRCI can yield qualitatively correct results (compared to the experimental values) and consider the accuracy of the calculated EPR g tensors as the current benchmark of quantum chemical methods. By decomposing the calculated g tensors into terms arising from interactions of the ground state with the various excited states, the origin of the zero-field splitting is explained. The results of the study demonstrate that a truly quantitative prediction of the g tensors of exchange-coupled systems is a great challenge to contemporary theory. The predictions strongly depend on small energy differences that are difficult to predict with sufficient accuracy by any quantum chemical method that is applicable to systems of the size of our target systems.
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