3J Coupling Constants Research Articles

A first principles theory of nuclear magnetic resonance J-coupling in solid-state systems

A method to calculate NMR J-coupling constants from first principles in extended systems is presented. It is based on density functional theory and is formulated within a planewave-pseudopotential framework. The all-electron properties are recovered using the projector augmented wave approach. The method is validated by comparison with existing quantum chemical calculations of solution-state systems and with experimental data. The approach has also been applied to the silicophosphate, Si(5)O(PO(4))(6), giving (31)P-(29)Si-couplings which are in excellent agreement with experiment.

Dynamic stereochemistry of erigeroside by measurement of 1H– 1H and 13C– 1H coupling constants

Erigeroside was extracted from Satureja khuzistanica Jamzad (Marzeh Khuzistani in Persian, family of lamiaceae), and 1H, 13C, 13C{ 1H}, 1H– 1H COSY, HMQC and J-HMBC were obtained to identify this compound and determine a complete set of J-coupling constants ( 1 J C–H, 2 J C–H, 3 J C–H and 3 J H–H) values within the exocyclic hydroxymethyl group (CH 2OH) and anomeric center. In parallel, density functional theory (DFT) using B3LYP functional and split-valance 6-311++G** basis set has been used to optimized the structures and conformers of erigeroside. In all calculations solvent effects were considered using a polarized continuum (overlapping spheres) model (PCM). The dependencies of 1 J, 2 J and 3 J involving 1H and 13C on the C 5′–C 6′ ( ω), C 6′–O 6′ ( θ) and C 1′–O 1′ ( φ) torsion angles in erigeroside were computed using DFT method. Complete hyper surfaces for 1 J C1′,H1′, 2 J C5′,H6′R, 2 J C5′,H6′S, 2 J C6′,H5′, 3 J C4′,H6′R, 3 J C4′,H6′S and 2 J H6′R–H5′S as well as 3 J H5′,H6′R were obtained and used to derive Karplus equations to correlate these couplings to ω, θ and φ. These calculated J-couplings are in agreement with experimental values. These results confirm the reliability of DFT calculated coupling constants in aqueous solution.

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation

Introducing experimental values as restraints into molecular dynamics (MD) simulation to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, dipolar couplings, 3 J-coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. Because multiple torsion angle values varphi correspond to the same 3 J-coupling constant and high-energy barriers are separating those, restraining 3 J-coupling constants remains difficult. A method to adaptively enforce restraints using a local elevation (LE) potential energy function is presented and applied to 3 J-coupling constant restraining in an MD simulation of hen egg-white lysozyme (HEWL). The method succesfully enhances sampling of the restrained torsion angles until the 37 experimental 3 J-coupling constant values are reached, thereby also improving the agreement with the 1,630 experimental NOE atom-atom distance upper bounds. Afterwards the torsional angles varphi are kept restrained by the built-up local-elevation potential energies.

Solution-State Molecular Structure of Apo and Oleate-Liganded Liver Fatty Acid-Binding Protein

Rat liver fatty acid-binding protein (LFABP) is distinctive among intracellular lipid-binding proteins (iLBPs): more than one molecule of long-chain fatty acid and a variety of diverse ligands can be bound within its large cavity, and in vitro lipid transfer to model membranes follows a mechanism that is diffusion-controlled rather than mediated by protein-membrane collisions. Because the apoprotein has proven resistant to crystallization, nuclear magnetic resonance spectroscopy offers a unique route to functionally informative comparisons of molecular structure and dynamics for LFABP in free (apo) and liganded (holo) forms. We report herein the solution-state structures determined for apo-LFABP at pH 6.0 and for holoprotein liganded to two oleates at pH 7.0, as well as the structure of the complex including locations of the ligands. 1H, 13C, and 15N resonance assignments revealed very similar types and locations of secondary structural elements for apo- and holo-LFABP as judged from chemical shift indices. The solution-state tertiary structures of the proteins were derived with the CNS/ARIA computational protocol, using distance and angular restraints based on 1H-1H nuclear Overhauser effects (NOEs), hydrogen-bonding networks, 3J(HNHA) coupling constants, intermolecular NOEs, and residual dipolar (NH) couplings. The holo-LFABP solution-state conformation is in substantial agreement with a previously reported X-ray structure [Thompson, J., Winter, N., Terwey, D., Bratt, J., and Banaszak, L. (1997) The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates, J. Biol. Chem. 272, 7140-7150], including the typical beta-barrel capped by a helix-turn-helix portal. In the solution state, the internally bound oleate has the expected U-shaped conformation and is tethered electrostatically, but the extended portal ligand can adopt a range of conformations based on the computationally refined structures, in contrast to the single conformation observed in the crystal structure. The apo-LFABP also has a well-defined beta-barrel structural motif typical of other members of the iLBP protein family, but the portal region that is thought to facilitate ligand entry and exit exhibits conformational variability and an unusual "open cap" orientation with respect to the barrel. These structural results allow us to propose a model in which ligand binding to LFABP occurs through conformational fluctuations that adjust the helix-turn-helix motif to open or close the top of the beta-barrel, and solvent accessibility to the protein cavity favors diffusion-controlled ligand transport.

Zur Bildung einer Zinn‐Zinn‐Bindung in Bis(hexamethyldisilazyl)‐Zinn(II) unter C‐H Bindungsbruch

AbstractFormation of a Tin‐Tin‐Bond from Bis(hexamethyldisilazyl)‐Tin(II) under Fission of a C‐H BondBis(hexamethyldisilazyl)tin(II) in excess reacts with the molecular alumosiloxane (Ph2SiO)8(AlO(OH))4 to yield the well known tin(II) derivative (Ph2SiO)8(AlO2)4Sn2 and the novel bicyclic [(Me3Si)2N]Sn[N(SiMe3)SiMe2CH2]2Sn[N(SiMe3)2] containing a tin‐tin bond, which is formally related to the starting molecule by a missing hydrogen atom. From X‐ray diffraction studies on single crystals it follows that the new compound has almost C2 point symmetry (the twofold axis intersecting the tin‐tin bond) and that this tin‐tin bond is the fusion edge of anellated fivefold Sn‐Sn‐N‐Si‐C rings. The bond connecting the almost tetrahedrally coordinated tin atoms (2.737(2) Å) is astonishingly very short. This feature is also reflected in the spectroscopic data (1H, 13C, 29Si, 119Sn‐NMR) of the compound with a coupling constant 1J (117Sn/119Sn) of 9529 Hz.

Estimation of $$^{3}J_{HN\hbox{-}H\alpha}$$ and $$^{3}J_{H\alpha\hbox{-}H\beta}$$ coupling constants from heteronuclear TOCSY spectra

3 J proton–proton coupling constants bear information on the intervening dihedral angles. Methods have been developed to derive this information from NMR spectra of proteins. Using series expansion of the time dependent density matrix, and exploiting the simple topology of amino acid spin-systems, formulae for estimation of $$^{3}\hbox{J}_{{\rm HN-H}\alpha}$$ and $$^{3}\hbox{J}_{{\rm H}\alpha {\rm -H}\beta}$$ from HSQC-TOCSY spectra are derived. The results obtained on a protein entailing both α-helix and β-sheet secondary structure elements agree very well with J-coupling constants computed from the X-ray structure. The method compares well with existing methods and requires only 2D spectra which would be typically otherwise recorded for structural studies.

Analyzing molecular properties calculated with two-component relativistic methods using spin-free natural bond orbitals: NMR spin-spin coupling constants

An analysis method for static linear response properties employing two-component (spin-orbit) relativistic density functional theory along with scalar relativistic "natural localized molecular orbitals" (NLMOs) and "natural bond orbitals" (NBOs) has been developed. The spin-orbit NLMO/NBO analysis has been applied to study the indirect spin-spin coupling (J-coupling) constants in Tl-I, PbH(4), and a dinuclear Pt-Tl bonded complex with a very large Pt-Tl coupling constant (expt.: 146.8 kHz). For Tl-I it is shown that the analysis scheme based on scalar relativistic NLMOs is applicable even if spin-orbit coupling is responsible for most of the coupling's magnitude. For PbH(4) it is shown that electron delocalization plays a much larger role for the Pb-H coupling than it is the case for the C-H coupling in methane. For the Pt-Tl complex the analysis clearly demonstrates the strong influence of the ligands on the Pt-Tl coupling constant and quantifies the effect of the delocalization of the Pt-Tl bond on the Pt-Tl coupling constant.

Identification of hexose hydrolysis products in metabolic flux analytes: A case study of levulinic acid in plant protein hydrolysate

Biosynthetically directed fractional 13C labeling, a popular methodology of metabolic flux analysis, involves culture on a mixture of 13C and 12C substrates and preparation a ‘metabolic flux analyte’ (typically protein hydrolysate) from the biomass. Metabolic flux analytes prepared from complex eukaryotes may contain additional compounds than those prepared from microorganisms. We report the presence of such compounds (hexose hydrolysis products) in a plant metabolic flux analyte (acid hydrolyzed protein from soybean embryos). We designed NMR experiments to systematically identify these compounds, and found that they were levulinic acid (LVA; major) and hydroxyacetone (HyA; minor). These acid hydrolysis products of hexoses (glucose and mannose) were generated during acid hydrolysis of glycosylating sugars (glucosamine and mannose) associated with soybean embryo protein. Analysis of LVA by two-dimensional [ 13C, 1H] NMR and measurement of its J-coupling constants revealed long-range coupling between atoms C3 and C5, which enables LVA to provide more isotopomer information than its precursor hexose. Furthermore, we found that LVA and HyA preserve the isotopomeric composition of the metabolic hexose from which they are derived. An important consequence of these results is that comparison of LVA and HyA isotopomers from two separate metabolic flux analytes (protein hydrolysate and starch hydrolysate) from the same plant tissue can distinguish between parallel glycolysis and pentose phosphate pathways in different subcellular compartments.

Optimization of fast spiral chemical shift imaging using least squares reconstruction: Application for hyperpolarized 13C metabolic imaging

A least-squares-based optimization and reconstruction algorithm has been developed for rapid metabolic imaging in the context of hyperpolarized (13)C. The algorithm uses a priori knowledge of resonance frequencies, J-coupling constants, and T(2)* values to enable acquisition of high-quality metabolic images with imaging times of approximately 100 ms for an 8-cm field of view (FOV) and 0.5 cm isotropic resolution. A root-mean-square error (rMSE) analysis is introduced to optimize metabolic image quality by appropriate choice of pulse sequence parameters, echo times, and signal model. By performing the reconstruction in k-space, the algorithm also allows the inclusion of the effect of chemical shift evolution during the readout period. Single-interleaf multiecho spiral chemical shift imaging (spCSI) is analyzed in detail as an illustrative example for the use of the new reconstruction and optimization algorithm. Simulation of the in vivo spectrum following the bolus injection of hyperpolarized (13)C(1) pyruvate shows that single-interleaf spiral spectroscopic imaging can achieve image quality in 100 ms, comparable to the performance of a 13-s phase-encoded chemical shift imaging (FIDCSI) experiment. Single-interleaf spCSI was also tested at a 3-T MR scanner using a phantom containing approximately 0.5-M solutions of alanine, lactate, and a pyruvate-pyruvate hydrate C(1)-C(2) ester at thermal equilibrium polarization, all enriched to 99% (13)C in the C(1) carbonyl positions. Upon reconstruction using the k-space-based least-squares technique, metabolite ratios obtained using the spCSI method were comparable to those obtained using a reference FIDCSI acquisition.

Synthesis, crystal structure and magnetism of a three-dimensional Mn(II) coordination polymers with 2,5-dimethylpyrazine-1,4-dioxide as bridging ligand

A novel three-dimensional Mn(II) coordination polymer, {[Mn(μ1,6-dmpzdo)3] · (ClO4)2} n , has been synthesized with 2,5-dimethylpyrazine-1,4-dioxide (dmpzdo) as a bridging ligand and its crystal structure determined by X-ray crystallography. The complex crystallizes in a trigonal system with a space group R-3 and a = 11.6672(14), b = 11.6672(14), c = 16.652(4) Å. In the complex each Mn(II) is coordinated by six μ1,6-dmpzdo bridging ligands and each μ1,6-dmpzdo bridging ligand coordinates two Mn(II) ions, forming a three-dimensional structure. The variable temperature (4–300 K) magnetic susceptibility data gave the magnetic coupling constant 2J = −0.30 cm−1.

Can Changes in One-bond Spin−spin Coupling Constants in Acids Be Related to Gas-Phase Proton Affinities of Bases?

Ab initio EOM-CCSD calculations have been carried out in search of acids with one-bond spin-spin coupling constants which could serve as probes of molecular basicity upon complex formation. Only 1J(F-H) and 1J(B-Li) in complexes F-H...Y and H2B-Li...Y, respectively, are able to differentiate among the protonation energies of bases containing Y. Changes in 1J(F-H) upon complex formation are related to the protonation energies of bases, but only when these energies are about 200 kcal/mol or greater. On the other hand, changes in 1J(B-Li) upon complexation are related to base protonation energies in the range between 100 and about 190 kcal/mol. Thus, these two one-bond coupling constants 1J(F-H) and 1J(B-Li) are complementary probes. For the first time, the computed NMR property of a gas-phase one-bond spin-spin coupling constant has been related to the experimental gas-phase thermodynamic property of proton affinity.

Rapid Injection NMR in Mechanistic Organocopper Chemistry. Preparation of the Elusive Copper(III) Intermediate

A “copper(III) intermediate” has been proposed to be crucially involved in many reactions of organocopper reagents, for example, with α-enones, alkyl halides, and allylic carboxylates. By using rapid injection NMR (RI-NMR), we have been able to prepare the first example of this elusive species under conditions where it is stable for extended periods of time. Extensive NMR investigations establish its structure and include two-bond 13C−13C coupling constants 2J across copper, measured on 13C-labeled material. Especially noteworthy is the extremely deshielded nature of the methyl C atoms attached to Cu, as indicated by the downfield 13C NMR shifts of 12.43 and 25.31 ppm. Large trans couplings, 2J = 38.1 Hz (upfield methyl−ring methine) and 2J = 35.4 Hz (downfield methyl−cyano), are consistent with a square planar complex.

Variation of One-bond X−Y Coupling Constants 1J(X−Y) and the Components of 1J(X−Y) with Rotation about the X−Y Bond for Molecules HmX−YHn, with X, Y = 15N, 17O, 31P, 33S: The Importance of Nonbonding Pairs of Electrons

Ab initio EOM-CCSD calculations have been performed on molecules HmX-YHn, for X, Y = 15N, 17O, 31P, and 33S, to investigate the variation of one-bond X-Y spin-spin coupling constants 1J(X-Y) and the components of J with rotation about the X-Y single bond. The reduced Fermi-contact (FC) terms for all 10 molecules are negative and decrease in absolute value as the rotational angle theta changes from 0 degrees, at which point the lone pairs of electrons are on the same side of the X-Y bond, to 180 degrees where they are trans with respect to the X-Y bond. The signs of reduced paramagnetic spin-orbit (PSO) and spin-dipole (SD) terms are opposite that of the FC term and exhibit extremum values as theta approaches 90 degrees, the gauche conformation. While the FC term tends to dominate for molecules H2X-YH2 and H2X-YH, such is not the case for HX-YH, where the PSO and SD terms assume increased importance. Curves for 1K(X-Y) as a function of rotational angle are readily grouped according to formula H2X-YH2, H2X-YH, and HX-YH, which suggests that it is the lone pairs of electrons on X and Y which are primarily responsible for the trends observed.

Asymmetric Karplus curves for the protein side-chain 3 J couplings

The standard Karplus equation for calculating 3J coupling constants from any given dihedral angle requires three empirical coefficients be determined that relate to the magnitudes of three modes of the angle dependency of 3J. Considering cosine modes only (bimodal, unimodal and baseline component), Karplus curves are generally symmetric with respect to the sign of the angle argument. Typically, their primary and secondary maxima differ in amplitude, whereas the two minima are of equal depth. However, chiral molecular topologies, such as those surrounding the main-chain and side-chain torsions in amino-acid residues, preclude, as regards substituent positioning, exact mirror-image conformations from being formed--for any given torsion-angle value. It is therefore unlikely that 3J couplings assume identical values for the corresponding positive and negative dihedral angles. This suggests that a better empirical fit of the torsion-angle dependency of 3J could be obtained when removing the constraint of symmetrically identical coupling constants. A sine term added to the Karplus equation allows independent modelling of both curve minima typically located near dihedral-angle values of +90 degrees and -90 degrees. Revisiting an extensive 3J coupling dataset previously recorded to determine the side-chain torsions chi1 in the protein flavodoxin, the asymmetric Karplus model accomplishes a more accurate fit to the experimental data. Asymmetries revealed in the angle dependencies exceed the experimental precision in determining 3J. Accounting for these effects helps improve molecular models.

Synthesis of [18,19,21,22‐13C4]‐Labeled Tautomycin as an NMR Probe of Protein Phosphatase Inhibitor

We have accomplished the synthesis of 13C-labeled tautomycin at the C18, C19, C21, and C22 positions starting from 100% [13C]triethylphosphonoacetate for the purpose of elucidating the dynamics and conformation of the C17-C26 moiety. NMR spectroscopy of 13C-labeled tautomycin revealed strong binding with protein phosphatase type 1 and new features in the 13C NMR spectrum, such as the very small three-bond coupling constants (2J).

An “S”-shaped pentanuclear CuII cluster derived from the metal-assisted hydrolysis of pyCOpyCOpy: structural, magnetic and spectroscopic studies

Reaction of [Cu2(O2CMe)4(H2O)2] with 2,6-di-(2-pyridylcarbonyl)-pyridine (pyCOpyCOpy or dpcp) in MeCN-H2O 10:1, led to the pentanuclear copper(II) complex [Cu5(O2CMe)6{pyC(O)(OH)pyC(O)(OH)py}2] () which crystallizes in the triclinic P1 space group. The copper(II) atoms are arranged in an "S"-shaped configuration, and are bridged by the doubly deprotonated bis(gem-diol) form of the ligand, pyC(O)(OH)pyC(O)(OH)py2-. Magnetic susceptibility data indicate the interplay of both ferro- and antiferromagnetic intramolecular interactions stabilizing an S=3/2 ground state. Fitting of the data according to a next-nearest-neighbour model {H=-[J1(S1S2+S1'S2')+J2(S2S3+S3'S2')+J3(S1S3+S3'S1')+J4(S2S2')]} yields exchange coupling constants J1=+39.7 cm(-1), J2=-15.9 cm(-1), J3=-8.3 cm(-1) and J4=+4.3 cm(-1), leading to an S=3/2 ground state. X-Band EPR spectroscopy indicates a zero-field splitting of the ground state with |D3/2|=0.38 cm(-1).

NMR measurements of scalar-coupling distributions in disordered solids

The measurement of scalar (J) couplings by solid-state NMR is a field of great interest, since this interaction is a rich source of local structural information, complementary to dipolar and chemical shift interactions. Here, we first demonstrate that J-coupling distributions exist and can be observed in disordered solids, as illustrated with the observation of a pair-specific distribution of (2)J((31)P-N-(31)P) couplings in a bis-phosphino amine, and we investigate the potential effects of such distributions on the measurement of average J-coupling constants. Second, we show that the measurement of two-dimensional (2D) distributions of J-couplings provides a much richer probe of local structural disorder than one-dimensional distributions, and we introduce new methods that provide different (selective or non-selective) ways of measuring 2D J distributions in a wide range of disordered systems. These methods are finally applied to a slightly disordered polymorphic sample of fully (13)C-enriched cellulose, and then to the bis-phosphino amine sample, from which 2D (2)J(PP)-coupling distributions are clearly identified and interpreted.

Accurate heteronuclear J-coupling measurements in dilute spin systems using the multiple-quantum filtered J-resolved experiment

A new solid-state MAS NMR experiment is proposed to accurately measure heteronuclear (19)F-(207)Pb J-coupling constants, even though these couplings are not visible on high speed (19)F 1D MAS spectra; in particular, we demonstrate that the J-resolved experiment combined with scalar multiple-quantum filtering considerably improves the resolution of J-multiplet patterns for dilute spin systems.

Interlayer coupling in ferromagnetic epitaxial Fe3Si∕FeSi2 superlattices

Ferromagnetic epitaxial B2-type Fe3Si∕FeSi2 superlattices were prepared on Si(111) at room temperature by facing target direct-current sputtering. The bilinear and biquadratic coupling constants J1 and J2 of the antiferromagnetically coupled superlattice were comparable to those of the similar superlattices using Fe layers although the saturation magnetization of Fe3Si is approximately half as large as that of Fe. The authors believe that this is due to the formation of a well-ordered quantum well in the spacers, which is mainly caused by the regular accumulation of highly oriented Fe3Si layers.

On using oscillating time-dependent restraints in MD simulation

The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average (3) J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating (3) J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a (3) J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling.