Three-bond Coupling Constants Research Articles

Investigation of two‐ and three‐bond carbon–hydrogen coupling constants in cinnamic acid based compounds

Two- and three-bond coupling constants (2 JHC and 3 JHC ) were determined for a series of 12 substituted cinnamic acids using a selective 2D inphase/antiphase (IPAP)-single quantum multiple bond correlation (HSQMBC) and 1D proton coupled 13 C NMR experiments. The coupling constants from two methods were compared and found to give very similar values. The results showed coupling constant values ranging from 1.7 to 9.7 Hz and 1.0 to 9.6 Hz for the IPAP-HSQMBC and the direct 13 C NMR experiments, respectively. The experimental values of the coupling constants were compared with discrete density functional theory (DFT) calculated values and were found to be in good agreement for the 3 JHC . However, the DFT method under estimated the 2 JHC coupling constants. Knowing the limitations of the measurement and calculation of these multibond coupling constants will add confidence to the assignment of conformation or stereochemical aspects of complex molecules like natural products. Copyright © 2016 John Wiley & Sons, Ltd.

1H NMR spectra of butane‐1,4‐diol and other 1,4‐diols: DFT calculation of shifts and coupling constants

The proton nuclear magnetic resonance (NMR) spectra of butane-1,4-diol, pentane-1,4-diol, (S,S)-hexane-2,5-diol, 2,5-dimethylhexane-2,5-diol and cyclohexane-1,4-diols (cis and trans) in benzene and some other solvents have been analysed. The conformer distribution and the NMR shifts of these diols in benzene have been computed on the basis of the density functional theory, the solvent being included by means of the integral-equation-formalism polarizable continuum model implemented in Gaussian 09. Relative Gibbs energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311+G(d,p) level and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311+G(d,p) geometry and the cc-pVTZ basis set. Vicinal three-bond coupling constants for the acyclic diols are calculated from the relative conformer populations, the geometries and generalized Karplus equations developed by Altona's group; these correlate well with the experimental values. The solvent dependence of coupling constants for butane-1,4-diol is attributed to conformational change. Coupling constants for the rigid cyclohexane-1,4-diols do not change with solvent and are readily explained in terms of their geometries. The NMR shifts of hydrogen-bonded protons in individual conformers of alkane-1,n-diols show a very rough correlation with the OH · · · OH distances. The computed overall NMR shifts for CH protons in 1,2-diols, 1,3-diols and 1,4-diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01; those for OH protons correlate less well.

Pople Style Basis Sets for the Calculation of NMR Spin-Spin Coupling Constants: the 6-31G-J and 6-311G-J Basis Sets.

We present a modification of the small and popular Pople basis sets, 6-31G and 6-311G, for density functional theory calculations of Fermi contact dominated NMR indirect nuclear spin-spin coupling constants. These new basis sets, 6-31G-J and 6-311G-J, contain twice the number of contracted s-type functions but the same number of contracted p-type functions as the original Pople basis set. For our test set of 12 one-, two- and three-bond coupling constants, the new basis sets augmented with the standard diffuse and polarization functions, i.e., the 6-31+G*-J and 6-311++G**-J basis sets, lead to a maximum deviation of 5 and 2 Hz, respectively, compared to results obtained with the 6 or more times larger aug-pcJ-4 basis set. In correlated wave function calculations using the second-order polarization propagator approximation, the deviations with respect to the aug-ccJ-pVQZ basis set are 8 and 3 Hz and thus slightly larger.

Structural Studies of the Capsular Polysaccharide Produced by Leuconostoc mesenteroides ssp. cremoris PIA2

The structure of the capsular polysaccharide (CPS) produced by Leuconostoc mesenteroides ssp. cremoris PIA2 has been determined using component analysis and NMR spectroscopy. (1)H and (13)C resonances were assigned using 2D NMR experiments, and sequential information was obtained by (1)H,(1)H-NOESY and (1)H,(13)C-HMBC experiments. The CPS consists of linear pentasaccharide repeating units with the following structure: →3)-β-D-Galf-(1→6)-β-D-Galf-(1→2)-β-D-Galf-(1→6)-β-D-Galf-(1→3)-β-D-Galp-(1→, in which four out of the five sugar residues have the furanoid ring form, a structural entity found in bacteria but not in mammals. The analysis of the magnitude of the homonuclear three-bond coupling constants of the anomeric protons for the five-membered sugar rings indicates that the sugar residues substituted at a primary carbon atom show one kind of conformational preferences, whereas those substituted at a secondary carbon atom show another kind of conformational preferences.

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).

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

The experimental determination of scalar three-bond coupling constants represents a powerful method to probe both the structure and dynamics of proteins. The detailed structural interpretation of such coupling constants is usually based on Karplus relationships, which allow the measured couplings to be related to the torsion angles of the molecules. As the measured couplings are sensitive to thermal fluctuations, the parameters in the Karplus relationships are better derived from ensembles representing the distributions of dihedral angles present in solution, rather than from single conformations. We present a method to derive such parameters that uses ensembles of conformations determined through dynamic-ensemble refinement--a method that provides structural ensembles that simultaneously represent both the structure and the associated dynamics of a protein.

Spin Coupling through the N→Si Dative Bond in Penta- and Hexacoordinate Hydrido- and Fluorosilicon Complexes; Coupling through a Rapidly Dissociating−Recombining N→Si Bond

Penta- and hexacoordinate silicon complexes with spin ½ nuclei ( 1 H and 1 9 F) directly attached to silicon have been prepared and used to study NMR spin-spin interactions across the N→Si dative bond. In both hydrido and fluoro complexes, two-bond coupling constants were found to drop sharply as the geminal bond angle deviated from 90°. Three-bond coupling constants showed a Karplus-type dependence upon the corresponding dihedral angles for both 1 H and 1 9 F complexes. Four-bond coupling constants 4 J( 1 9 F-Si-N-C- 1 H) across the dative bond were observed. The correlations can be used as tools for the interpolation of bond and dihedral angles from NMR data, in cases where crystal structures are unavailable. They also demonstrate that the N→Si dative bond in hypercoordinate silicon complexes behaves essentially in the manner expected from normal covalent bonds. Rapid dissociation and recombination of the N-Si dative bond was established in several pentacoordinate complexes; however, one-, two-, and three-bond coupling constants could nevertheless be measured across this rapidly dissociating bond.

(3h)J((15)N-(31)P) spin-spin coupling constants across N[bond]H....O[bond]P hydrogen bonds.

Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been performed to evaluate three-bond (15)N-(31)P coupling constants ((3h)J(N[bond]P)) across N[bond]H....O[bond]P hydrogen bonds in model cationic and anionic complexes including NH(4)(+):OPH, NH(4)(+):OPH(3), NH(3):(-)O(2)PH(2), NFH(2):(-)O(2)PH(2), and NF(2)H:(-)O(2)PH(2). Three-bond coupling constants can be appreciable when the phosphorus is P(V), but are negligible with P(III). (3h)J(N[bond]P) values in complexes with cyclic or open structures are less than 1 Hz, a consequence of the nonlinear arrangement of N, H, O, and P atoms. For complexes with these structures, (3h)J(N[bond]P) may not be experimentally measurable. In contrast, complexes in which the N, H, O, and P atoms are collinear or nearly collinear have larger values of (3h)J(N[bond]P), even though the N[bond]P distances are longer than N[bond]P distances in cyclic and open structures. In linear complexes, (3h)J(N[bond]P) is dominated by the Fermi-contact term, which is distance dependent. Therefore, N[bond]P (and hydrogen-bonding N[bond]O) distances in these complexes can be determined from experimentally measured (15)N-(31)P coupling constants.

Conformational studies on a unique bis-sulfated glycolipid using NMR spectroscopy and molecular dynamics simulations.

The time-averaged solution conformation of a unique bis-sulfated glycolipid (HSO3)2-2,6Manalpha-2Glcalpha-1-sn-2,3-O-alkylglycerol , was studied in terms of the torsional angles of two glycosidic linkages, phi (H1-C1-O-Cx) and psi (C1-O-Cx-Hx), derived from heteronuclear three-bond coupling constants (3JC,H), and inter-residual proton-proton distances from J-HMBC 2D and ROESY experiments, respectively. The dihedral angles of Glcalpha1Gro in glycolipids were determined for the first time. The C1-C4 diagonal line of the alpha-glucose ring makes an angle of approximately 120 degrees with the glycerol backbone, suggesting that the alpha-glucose ring is almost parallel to the membrane surface in contrast with the perpendicular orientation of the beta-isomer. Furthermore, minimum-energy states around the conformation were estimated by Monte Carlo/stochastic dynamics (MCSD) mixed-mode simulations and the energy minimization with assisted model building and energy refinement (AMBER) force field. The Glcalpha1Gro linkage has a single minimum-energy structure. On the other hand, three conformers were observed for the Manalpha2Glc linkage. The flexibility of Manalpha2Glc was further confirmed by the absence of inter-residual hydrogen bonds which were judged from the temperature coefficients of the chemical shifts, ddelta/dT (-10-3 p.p.m. degrees C-1), of hydroxy protons. The conformational flexibility may facilitate interaction of extracellular substances with both sulfate groups.

The Structure of Methylcob(III)alamin in Aqueous Solution - A Water Molecule as Structuring Element of the Nucleotide Loop

The solution structure of methylcob(III)alamin (MeCbl; 3), a natural organometallic corrinoid-B12 cofactor whose crystal structure was published in 1985, was established by NMR-spectroscopic analyses of 3 in aqueous solution. The full set of unambiguously assigned 1H, 13C, and amide 15N signals was consistent with identical constitutional and configurational properties of 3 in solution and in the crystal. Specifically investigated were the conformational characteristics of 3 in solution, in particular of its unique Co-coordinating nucleotide moiety. An extensive set of NOE-derived distance constraints was acquired for this purpose, and of angle constraints, based on three-bond coupling constants. These data were used to calculate the solution structure of 3. Our data revealed that the conformation of the nucleotide loop of 3 differs significantly in aqueous solution and in the crystalline state and indicated the presence of a specific H2O molecule `bound' via cooperative H-bonds to three H-bonding functionalities of the nucleotide loop. The observed conformational differences are attributed to structuring contributors to the nucleotide conformation that differ in solution and in the crystal. Most of these can be assigned to H2O molecules, whose position in the crystal is controlled, in part, by the specific crystal packing.

Distinguishing diastereomeric organic compounds based on the concerted use of3J(C,H) and3J(N,H) values

The relative stereochemistry of the two acyclic carbons separated by a single bond was determined from three-bond homo- and heteronuclear coupling constants. The analysis of data was based on a purely qualitative interpretation of the Karplus relationships. The methodology presented could resolve acyclic diastereoisomers if adequate sets of three-bond coupling constants can be measured. Copyright © 1999 John Wiley & Sons, Ltd.

Probing the Coordination Chemistry of [Zr6BCl12]+: A Cluster Especially Amenable to NMR Study

NMR spectroscopy is demonstrated to be a powerful analytical tool for the study of solvolysis and ligand-exchange chemistry of the [Zr6BCl12]+ cluster in acetonitrile, methanol, and pyridine. 11B NMR spectra for [(Zr6BCl12)Cl6-xLx]x-5 (L = CH3CN, CH3OH, and pyridine; x = 1−6) are reported. Exceedingly narrow 11B lines are generally observed for these clusters. Two-bond (2JP-Zr-B = 8.8 Hz) and three-bond coupling constants (3JP-O-Zr-B = 1.9 Hz) are observed for the cluster complexes [(Zr6BCl12)(PR3)6]+ and [(Zr6BCl12)(OPR3)xL6-x]+ (L = CH3CN and PR3), respectively, in both 11B and 31P NMR spectra. Spin−lattice relaxation times (T1's) for 11B were measured for several cluster complexes. Homoleptic species, [(Zr6BCl12)L6]+ (L = CH3CN, CH3OH, pyridine), exhibit very long times and that for [(Zr6BCl12)(NCCH3)6]+ is the longest ever measured (T1 = 108 s) for the 11B nucleus. A thermodynamic analysis of spectra for the [(Zr6BCl12)(CH3OH)6-x(py)x]+ (x = 0−5) system reveals that [Zr6BCl12]+ binds pyridine more str...

New methods of structure refinement for macromolecular structure determination by NMR.

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.

Rapid measurement of scalar three-bond 1HN-1H alpha spin coupling constants in 15N-labelled proteins.

Two new 2D NMR experiments, CT-HMQC-HA and CT-HMQC-HN, are proposed for the rapid measurement of homonuclear 3JHNH alpha coupling constants of uniformly 15N-enriched proteins in solution. The experiments are based on the comparison of the signal intensities in a pair of constant-time [15N,1H]-HMQC spectra recorded with and without decoupling of the amide proton-alpha proton coupling. Experimental data recorded with the 78-residue N-terminal domain of the E. coli arginine repressor (ArgR-N) and with oxidized E. coli flavodoxin (176 residues) showed good agreement with 3JHNH alpha coupling constants obtained by fitting of the multiplet fine structure of the amide proton resonances or from a 3D HNHA-J experiment, respectively. Quantitative estimates for the effects from different relaxation rates of in-phase and antiphase magnetization are given.

Conformational Equilibria in Polypeptides. I. Determination of Accurate3JHCCoupling Constants in Antamanide by 2D NMR Multiplet Simulation

High-precision heteronuclear three-bond coupling constants including3J(HN, C′),3J(HN, Cβ),3J(Hα,Cγ), and3J(Hβ, C′) are determined for the nonproline residues in uniformly13C-enrichedantamanide,cyclo-(-Val1-Pro2-Pro3-Ala4-Phe5-Phe6-Pro7-Pro8-Phe9- Phe10-), using quantitative numerical 2D NMR spectrum evaluation based on the product-operator formalism. The experimental basis comprises two-dimensional1H,13C-heteronuclear relayed E.COSY spectra [J. M. Schmidt, R.R. Ernst, S. Aimoto, and M. Kainosho,J. Biomol. NMR6,95 (1995)], the multiplet patterns of which are subjected to iterative least-squares 2D multiplet-simulation procedures. Accuracy and precision of the spectrum fit are assessed byFstatistics and analysis of variances (ANOVA) leading to confidence intervals for the optimized spin-system parameters. The long-range J coupling constants obtained and their standard deviations provide the experimental foundation for a later detailed analysis of φ and χ1dihedral-angle equilibrium conformations contributing to the flexible peptide structure.

Conformational Equilibria in Polypeptides. II. Dihedral-Angle Distribution in Antamanide Based on Three-Bond Coupling Information

The use of3Jcoupling information in deriving dihedral-angle restraints for polypeptide-structure determination in the presence of conformational equilibria is illustrated withantamanide,cyclo(–Val1–Pro2– Pro3– Ala4– Phe5– Phe6– Pro7– Pro8– Phe9– Phe10–). The experimental basis comprises accurate three-bond coupling constants as obtained from both homonuclear [C. Griesinger, O.W. Sørensen, and R.R. Ernst,J. Magn. Reson.75,474 (1987)] and heteronuclear [J. M. Schmidt,J. Magn. Reson.124,298 (1997)] exclusive correlation spectroscopy (E.COSY). For the backbone and side-chain dihedral angles in the nonproline residues, φ and χ1, respectively, probability-distribution functions are derived and evaluated on the basis of χ2statistics and significance estimates. Various motional models are considered in the quantitative compilation of molecular-geometry parameters from spin-system parameters. From the3Jcoupling analysis, antamanide is found to possess a very flexible structure which is consistent with the results previously obtained in homonuclear NOE and13C–T1relaxation studies. To fully agree with experiment, rotamer equilibria must be assumed for almost all of the torsions investigated in the peptide.

31P-13C, 31P-1H SPIN-SPIN COUPLING AND STRUCTURAL ASSIGNMENT AND CONFORMATIONAL ANALYSIS OF EPIMERIC THYMIDINE-3′-YL BENZOIN PHOSPHATES

Abstract A pair of epimeric thymidine-3′-yl benzoin phosphates 3 were produced from the ester exchange reaction of oxyphosphorane 1 with thymidine 2. Their structures were identified by using the 1H, 13C and 31P NMR spectra. The chemical bonds between the ribose 3′-C and a-C atoms to the phosphoryl group were confirmed by 31P-′13C and 31P-1H spin-spin coupling. The stereosensitive three-bond coupling constants 3JP-c and 3JP-H in each diastereomer of 3 have been measured, and used for an estimation of trans and gauche conformational analysis. The relative estimated dihedral angle of P-O-C-H was discussed.

Measurement of three-bond coupling constants in the osmoregulated periplasmic glucan of Burkholderia solanacearum.

The cyclic osmoregulated periplasmic glucan produced by Burkholderia solanacearum contains 13 glucose units, all beta-(1-2) linked except for one alpha-(1-6) linkage. We report here the measurement of the 3J(C1-H2') and 3J(H1-C2') coupling constants, characterizing the glycosidic linkages, through the use of a 13C/12C double half-filtered NOESY experiments. The values obtained give information about the (phi, psi) angles of the different linkages. The results presented from an important step towards a detailed experimental model of the cyclic glucan, which might allow us to clarify its biological role and establish whether the cavity of these molecules is compatible with the capability of complexing host molecular signals.

Heteronuclear relayed E.COSY applied to the determination of accurate 3J(HN,C') and 3J(H beta,C') coupling constants in desulfovibrio vulgaris flavodoxin.

A simple constant-time 3D heteronuclear NMR pulse sequence has been developed to quantitatively determine the heteronuclear three-bond couplings 3J(HN,C') and 3J(H beta,C') in uniformly 13C-enriched proteins. The protocols for measuring accurate coupling constants are based on 1H,13C-heteronuclear relayed E.COSY [Schmidt, J.M., Ernst, R.R., Aimoto, S. and Kainosho, M. (1995) J. Biomol. NMR, 6, 95-105] in combination with numerical least-squares spectrum evaluation. Accurate coupling constants are extracted from 2D spectrum projections using 2D multiplet simulation. Confidence intervals for the obtained three-bond coupling constants are calculated from F-statistics. The three-bond couplings are relevant to the determination of phi and chi 1 dihedral-angle conformations in the amino acid backbone and side chain. The methods are demonstrated on the recombinant 13C,15N-doubly enriched 147-amino acid protein Desulfovibrio vulgaris flavodoxin with bound flavin mononucleotide in its oxidized form. In total, 109 3J(HN,C') coupling constants from a single spectrum.

Determination of heteronuclear three-bond J-coupling constants in peptides by a simple heteronuclear relayed E.COSY experiment

A simple heteronuclear relayed E.COSY pulse sequence with a minimum number of pulses is proposed for the quantitative determination of heteronuclear three-bond J-coupling constants in uniformly 13C-enriched polypeptide samples. Numerous heteronuclear three-bond coupling constants, including 3JHNC, 3JHNC beta, 3JH beta C, and 3JH alpha C gamma, can be determined for each residue from a single heteronuclear relayed E.COSY spectrum. Couplings relevant for stereospecific assignments as well as for the determination of dihedral angles in the amino acid backbone and in side chains are obtained. The method is demonstrated on the uniformly 13C-enriched decapeptide antamanide (-Val1-Pro2-Pro3-Ala4-Phe5-Phe6-Pro7-Pro8-Phe9-Phe1 0-).