Monday, August 16, 2010

Inorganic Chemistry

Separation of Geometric Isomers of a Dicopper Complex by Using a 19F-Labeled Ligand: Dynamics, Structures, and DFT Calculations
Stphanie Durot, Laila H. Hossain, Sylvain Hamman, Hlne Jamet, Maylis Orio, Isabelle Gautier-Luneau, Dominique Luneau, Christian Philouze, Jean-Louis Pierre and Catherine Belle
DOI: 10.1021/ic1006567
Introducing a fluorine group on two pyridines of the HLCH3 ligand (2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-methylphenol) allows the separation of two geometric isomers after complexation by two copper(II) ions. Methods for isolating the isomers (1meso and 1rac) as a μ-phenoxo,μ-hydroxo dicopper(II) complex as a crystalline product have been developed. Both isomers (1meso and 1rac) have been characterized by X-ray crystallography and 19F NMR. The isomerism is determined by the disposition of the fluorine atoms with respect to the plane containing the Cu2O2 core. Density functional theory calculations using different functionals were performed to provide additional support for the existence of these two forms. Dissolution of 1meso in acetone or acetonitrile causes its spontaneous isomerization into the 1rac form at room temperature. Combined experimental studies (UV−vis, 19F NMR) and theoretical calculations support this process. Paramagnetic 19F NMR appears as a unique and powerful probe for distinguishing the two isomers and supplying direct evidence of this isomerization process in solution.
A Pd6 Molecular Cage via Multicomponent Self-Assembly Incorporating Both Neutral and Anionic Linkers
Arun Kumar Bar, Golam Mostafa and Partha Sarathi Mukherjee
DOI: 10.1021/ic101139s
A Pd6 molecular cage [{(tmen)Pd}6(bpy)3(tma)2](NO3)6 [1; where tmen = N,N,N′,N′-tetramethylethylene diamine, bpy = 4,4′-bipyridyl, and H3tma = trimesic acid] was prepared via the template-free three-component self-assembly of a cis-blocked palladium(II) acceptor in combination with a tricarboxylate and a dipyridyl donor. Complex 1 represents the first example of a 3D palladium(II) cage of defined shape incorporating anionic and neutral linkers. Guest-induced exclusive formation of this cage was also monitored by an NMR study.

Friday, August 13, 2010

J. Chem. Phys.

First principles nuclear magnetic resonance signatures of graphene oxide

Ning Lu, Ying Huang , Hai-bei Li Zhenyu Li, and Jinlong Yang
Nuclear magnetic resonance (NMR) has been widely used in graphene oxide (GO) structure studies. However, the detailed relationship between its spectroscopic features and the GO structural configuration remains elusive. Based on first principles 13C chemical shift calculations using the gauge including projector augmented waves method, we provide a reliable spectrum-structure connection. The 13C chemical shift in GO is found to be very sensitive to the atomic environment, even for the same type of oxidation groups. Factors determining the chemical shifts of epoxy and hydroxy groups have been discussed. GO structures previously reported in the literature have been checked from the NMR point of view. The energetically favorable hydroxy chain structure is not expected to be widely existed in real GO samples according to our NMR simulations. The epoxy pair species we proposed previously is also supported by chemical shift calculations.

Determination of the antisymmetric part of the chemical shift anisotropy tensor via spin relaxation in nuclear magnetic resonance

Raphael Paquin, Philippe Pelupessy, Luminita Duma, Christel Gervais, and Geoffrey Bodenhausen
Relaxation processes induced by the antisymmetric part of the chemical shift anisotropy tensor (henceforth called anti-CSA) are usually neglected in NMR relaxation studies. It is shown here that anti-CSA components contribute to longitudinal relaxation rates of the indole 15N nucleus in tryptophan in solution at different magnetic fields and temperatures. To determine the parameters of several models for rotational diffusion and internal dynamics, we measured the longitudinal relaxation rates R1 = 1/T1 of 15N, the 15N–1H dipole-dipole (DD) cross-relaxation rates (Overhauser effects), and the cross-correlated CSA/DD relaxation rates involving the second-rank symmetric part of the CSA tensor of 15N at four magnetic fields B0 = 9.4, 14.1, 18.8, and 22.3 T (400, 600, 800, and 950 MHz for protons) over a temperature range of 270<T<310>. A good agreement between experimental and theoretical rates can only be obtained if the CSA tensor is assumed to comprise first-rank antisymmetric (anti-CSA) components. The magnitude of the hitherto neglected antisymmetric components is of the order of 10% of the CSA.

Noninvasive bipolar double-pulsed-field-gradient NMR reveals signatures for pore size and shape in polydisperse, randomly oriented, inhomogeneous porous media

Noam Shemesh, Evren Ozarslan, Tal Adiri, Peter J. Basser, and Yoram Cohen
Noninvasive characterization of pore size and shape in opaque porous media is a formidable challenge. NMR diffusion-diffraction patterns were found to be exceptionally useful for obtaining such morphological features, but only when pores are monodisperse and coherently placed. When locally anisotropic pores are randomly oriented, conventional diffusion NMR methods fail. Here, we present a simple, direct, and general approach to obtain both compartment size and shape even in such settings and even when pores are characterized by internal field gradients. Using controlled porous media, we show that the bipolar-double-pulsed-field-gradient (bp-d-PFG) methodology yields diffusion-diffraction patterns from which pore size can be directly obtained. Moreover, we show that pore shape, which cannot be obtained by conventional methods, can be directly inferred from the modulation of the signal in angular bp-d-PFG experiments. This new methodology significantly broadens the types of porous media that can be studied using noninvasive diffusion-diffraction NMR.

Analyzing molecular static linear response properties with perturbed localized orbitals

Jochen Autschbach and Harry F. King
Perturbed localized molecular orbitals (LMOs), correct to first order in an applied static perturbation and consistent with a chosen localization functional, are calculated using analytic derivative techniques. The formalism is outlined for a general static perturbation and variational localization functionals. Iterative and (formally) single-step approaches are compared. The implementation employs an iterative sequence of 2×2 orbital rotations. The procedure is verified by calculations of molecular electric-field perturbations. Boys LMO contributions to the electronic static polarizability and the electric-field perturbation of the r2 expectation value are calculated and analyzed for ethene, ethyne, and fluoroethene (H2CCHF). For ethene, a comparison is made with results from a Pipek–Mezey localization. The calculations show that a chemically intuitive decomposition of the calculated properties is possible with the help of the LMO contributions and that the polarizability contributions in similar molecules are approximately transferable.

Trading sensitivity for information: CarrPurcellMeiboomGill acquisition in solid-state NMR

Krishna K. Dey, Jason T. Ash, Nicole M. Trease, and Philip J. Grandinetti
The Carr–Purcell–Meiboom–Gill (CPMG) experiment has gained popularity in solid-state NMR as a method for enhancing sensitivity for anisotropically broadened spectra of both spin 1/2 and half integer quadrupolar nuclei. Most commonly, the train of CPMG echoes is Fourier transformed directly, which causes the NMR powder pattern to break up into a series of sidebands, sometimes called “spikelets.” Larger sensitivity enhancements are observed as the delay between the π pulses is shortened. As the duration between the π pulses is shortened, however, the echoes become truncated and information about the nuclear spin interactions is lost. We explored the relationship between enhanced sensitivity and loss of information as a function of the product Ω 2τ, where Ω is the span of the anisotropic lineshape and 2τ is the π pulse spacing. For a lineshape dominated by the nuclear shielding anisotropy, we found that the minimum uncertainty in the tensor values is obtained using Ω 2τ values in the range Ω 2τ ≈ 12−1+6 and Ω 2τ ≈ 9−3+3 for ηs = 0 and ηs = 1, respectively. For an anisotropic second-order quadrupolar central transition lineshape under magic-angle spinning (MAS), the optimum range of Ω 2τ ≈ 9−2+3 was found. Additionally, we show how the Two-dimensional One Pulse (TOP) like processing approach can be used to eliminate the cumbersome sideband pattern lineshape and recover a more familiar lineshape that is easily analyzed with conventional lineshape simulation algorithms

Optimized basis sets for the calculation of indirect nuclear spin-spin coupling constants involving the atoms B, Al, Si, P, and Cl

Patricio F. Provasi and Stephan P. A. Sauer
The aug-cc-pVTZ-J series of basis sets for indirect nuclear spin-spin coupling constants has been extended to the atoms B, Al, Si, P, and Cl. The basis sets were obtained according to the scheme previously described by Provasi et al. [J. Chem. Phys. 115, 1324 (2001)] . First, the completely uncontracted correlation consistent aug-cc-pVTZ basis sets were extended with four tight s and three tight d functions. Second, the s and p basis functions were contracted with the molecular orbital coefficients of self-consistent-field calculations performed with the uncontracted basis sets on the simplest hydrides of each atom. As a first illustration, we have calculated the one-bond indirect spin-spin coupling constants in BH4, BF, AlH, AlF, SiH4, SiF4, PH3, PF3, H2S, SF6, HCl, and ClF at the level of density functional theory using the Becke three parameter Lee–Yang–Parr and the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes.

Recoupling of native homonuclear dipolar couplings in magic-angle-spinning solid-state NMR by the double-oscillating field technique

Lasse Arnt Straaso and Niels Chr. Nielsen
A new solid-state NMR method, the double-oscillating field technique (DUO), that under magic-angle-spinning conditions produces an effective Hamiltonian proportional to the native high-field homonuclear dipole-dipole coupling operator is presented. The method exploits one part of the radio frequency (rf) field to recouple the dipolar coupling interaction with a relatively high scaling factor and to eliminate offset effects over a reasonable bandwidth while in the recoupling frame, the other part gives rise to a sufficiently large longitudinal component of the residual rf field that averages nonsecular terms and in addition ensures stability toward rf inhomogeneity and rf miscalibration. The capability of the DUO experiment to mediate transfer of polarization is described theoretically and compared numerically and experimentally with finite pulse rf driven recoupling and experimentally with dipolar-assisted rotational resonance. Two-dimensional recoupling experiments were performed on antiparallel amyloid fibrils of the decapeptide SNNFGAILSS with the FGAIL fragment uniformly labeled with 13C and 15N.

Wednesday, August 11, 2010

J. Am. Chem. Soc., 2010, 132 (28), pp 9561–9563

Rapid Acquisition of Multidimensional Solid-State NMR Spectra of Proteins Facilitated by Covalently Bound Paramagnetic Tags
Philippe S. Nadaud, Jonathan J. Helmus, Ishita Sengupta and Christopher P. Jaroniec

We describe a condensed data collection approach that facilitates rapid acquisition of multidimensional magic-angle spinning solid-state nuclear magnetic resonance (SSNMR) spectra of proteins by combining rapid sample spinning, optimized low-power radio frequency pulse schemes and covalently attached paramagnetic tags to enhance protein 1H spin−lattice relaxation. Using EDTA-Cu2+-modified K28C and N8C mutants of the B1 immunoglobulin binding domain of protein G as models, we demonstrate that high resolution and sensitivity 2D and 3D SSNMR chemical shift correlation spectra can be recorded in as little as several minutes and several hours, respectively, for samples containing 0.1−0.2 μmol of 13C,15N- or 2H,13C,15N-labeled protein. This mode of data acquisition is naturally suited toward the structural SSNMR studies of paramagnetic proteins, for which the typical 1H longitudinal relaxation time constants are inherently a factor of at least 3−4 lower relative to their diamagnetic counterparts. To illustrate this, we demonstrate the rapid site-specific determination of backbone amide 15N longitudinal paramagnetic relaxation enhancements using a pseudo-3D SSNMR experiment based on 15N−13C correlation spectroscopy, and we show that such measurements yield valuable long-range 15N−Cu2+ distance restraints which report on the three-dimensional protein fold.

J. Am. Chem. Soc., 2010, 132 (29), pp 9952–9953
Validation of a Lanthanide Tag for the Analysis of Protein Dynamics by Paramagnetic NMR Spectroscopy

Mathias A. S. Hass, Peter H. J. Keizers, Anneloes Blok, Yoshitaka Hiruma and Marcellus Ubbink

Paramagnetic lanthanide tags potentially can enhance the effects of microsecond to millisecond dynamics in proteins on NMR signals and provide structural information on lowly populated states encoded in the pseudocontact shifts. We have investigated the microsecond to millisecond mobility of a two-point attached lanthanide tag, CLaNP-5, using paramagnetic 1H CPMG relaxation dispersion methods. CLaNP-5 loaded with Lu3+, Yb3+, or Tm3+ was attached to three sites on the surface of two proteins, pseudoazurin and cytochrome c. The paramagnetic center causes large relaxation dispersion effects for two attachment sites, suggesting that local dynamics of the protein at the attachment site causes mobility of the paramagnetic center. At one site the relaxation dispersions are small and limited to the immediate environment of the tag. It is concluded that paramagnetic relaxation dispersion could represent a sensitive method to probe protein dynamics. However, the selection of a rigid attachment site is of critical importance.

J. Am. Chem. Soc., 2010, 132 (29), pp 9956–9957
Solid-State 13C NMR Assignment of Carbon Resonances on Metallic and Semiconducting Single-Walled Carbon Nanotubes

Chaiwat Engtrakul*†, Mark F. Davis†, Kevin Mistry†, Brian A. Larsen†, Anne C. Dillon†, Michael J. Heben‡ and Jeffrey L. Blackburn*†

Solid-state 13C NMR spectroscopy was used to investigate the chemical shift of nanotube carbons on m- and s-SWNTs (metallic and semiconducting single-walled nanotubes) for samples with widely varying s-SWNT content, including samples highly enriched with nearly 100% m- and s-SWNTs. High-resolution 13C NMR was found to be a sensitive probe for m- and s-SWNTs in mixed SWNT samples with diameters of 1.3 nm. The two highly enriched m- and s-SWNT samples clearly exhibited features for m- and s-SNWT 13C nuclei (123 and 122 ppm, respectively) and were successfully fit with a single Gaussian, while five mixed samples required two Gaussians for a satisfactory fit.

J. Am. Chem. Soc., 2010, 132 (29), pp 9979–9981
Probing Slow Protein Dynamics by Adiabatic R1ρ and R2ρ NMR Experiments

Silvia Mangia, Nathaniel J. Traaseth, Gianluigi Veglia, Michael Garwood‡ and Shalom Michaeli

Slow μs/ms dynamics involved in protein folding, binding, catalysis, and allostery are currently detected using NMR dispersion experiments such as CPMG (Carr−Purcell−Meiboom−Gill) or spin-lock R1ρ. In these methods, protein dynamics are obtained by analyzing relaxation dispersion curves obtained from either changing the time spacing between 180° pulses or by changing the effective spin-locking field strength. In this Communication, we introduce a new method to induce a dispersion of relaxation rates. Our approach relies on altering the shape of the adiabatic full passage pulse and is conceptually different from existing approaches. By changing the nature of the adiabatic radiofrequency irradiation, we are able to obtain rotating frame R1ρ and R2ρ dispersion curves that are sensitive to slow μs/ms protein dynamics (demonstrated with ubiquitin). The strengths of this method are to (a) extend the dynamic range of the relaxation dispersion analysis, (b) avoid the need for multiple magnetic field strengths to extract dynamic parameters, (c) measure accurate relaxation rates that are independent of frequency offset, and (d) reduce the stress to NMR hardware (e.g., cryoprobes).