Scalar Coupling Constants Research Articles

Theoretical and experimental evaluation of broadband decoupling techniques for in vivo nuclear magnetic resonance spectroscopy

A theoretical and experimental evaluation of existing broadband decoupling methods with respect to their utility for in vivo (1)H-(13)C NMR spectroscopy is presented. Simulations are based on a modified product operator formalism, while an experimental evaluation is performed on in vitro samples and human leg and rat brain in vivo. The performance of broadband decoupling methods was evaluated with respect to the required peak and average RF powers, decoupling bandwidth, decoupling side bands, heteronuclear scalar coupling constant, and sensitivity toward B(2) inhomogeneity. In human applications only the WALTZ and MLEV decoupling methods provide adequate decoupling performance at RF power levels that satisfy the FDA guidelines on local tissue heating. For very low RF power levels (B(2max) < 300 Hz) one should verify empirically whether the experiment will benefit from broadband decoupling. At higher RF power levels acceptable for animal studies additional decoupling techniques become available and provide superior performance. Since the average RF power of adiabatic RF pulses is almost always significantly lower than the peak RF power, it can be stated that for average RF powers suitable for animal studies it is always possible to design an adiabatic decoupling scheme that outperforms all other schemes. B(2) inhomogeneity degrades the decoupling performance of all methods, but the decoupling bandwidths for WALTZ-16 and especially adiabatic methods are still satisfactory for useful in vivo decoupling with a surface coil.

Solution Structure of the C-terminal Domain of TFIIH P44 Subunit Reveals a Novel Type of C4C4 Ring Domain Involved in Protein-Protein Interactions

The human general transcription factor TFIIH is involved in both transcription and DNA nucleotide excision repair. Among the 10 subunits of the complex, p44 subunit plays a crucial role in both mechanisms. Its N-terminal domain interacts with the XPD helicase, whereas its C-terminal domain is involved specifically in the promoter escape activity. By mutating an exposed and non-conserved cysteine residue into a serine, we produced a soluble mutant of p44-(321-395) suitable for solution structure determination. The domain adopts a C4C4 RING domain structure with sequential organization of beta-strands that is related to canonical RING domains by a circular permutation of the beta-sheet elements. Analysis of the molecular surface and mutagenesis experiments suggests that the binding of p44-(321-395) to TFIIH p34 subunit is not mediated by electrostatic interactions and, thus, differs from previously reported interaction mechanisms involving RING domains.

Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides

Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between 2H3 (N-type) and 2H3 (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4–20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the 2H3 conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the 2H3 conformation when incorporated in a d(5′-GCGT*GCG-3′)/d(5′-CGCACGC-3′) duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences.

Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase.

The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3′-processing [dinucleotide released from each 3′ end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.

Multinuclear magnetic resonance studies of gaseous and liquid dimethyl ethers

Dimethyl ethers (DME): (CH 3) 2O, CH 3OCD 3, (CD 3) 2O have been studied using advanced NMR spectroscopy in liquid and gaseous states at 300 K. Extrapolation of the gas-phase results to the zero-density limit permitted the measurements of 1H, 13C and 17O nuclear magnetic shieldings of isolated DME molecules. The significance of intermolecular effects in the gaseous state as well as by coming from gas to liquid are also reported; measured gas-to-liquid shifts for 13C and 17O nuclei are negative (deshielding effects) but positive for 1H nuclei. The very weak linear dependence on density has also been observed for the carbon-proton and carbon-deuteron scalar coupling constants over one bond in the appropriate methyl group of DME. It was possible to obtain the coupling constants free from intermolecular interactions: 1 J 0(CH)=138.84 Hz in (CH 3) 2O, 1 J 0(CH)=138.81 Hz and 1 J 0(CD)=21.17 Hz in CH 3OCD 3 and 1 J 0(CD)=21.16 Hz in (CD 3) 2O. The magnitude of isotope effects on nuclear shieldings and indirect coupling constants caused by H/D substitution is also discussed. These new experimental results are suitable for a better verification of ab initio calculations of indirect coupling constants and nuclear magnetic shieldings of all nuclei in molecules under study.

Theoretical study of31P,31P coupling constants in cyclotriphosphazenes

Several scalar coupling constants (mainly 31P, 31P) were calculated for 10 cyclotriphosphazenes and compared with experimental results when available. Although the experimental values cannot be reproduced, the calculated values are proportional to the experimental values. Some difficult cases, such as 19F, 19F couplings, are discussed.

A two-stage approach to automatic determination of1H NMR coupling constants

(1)H NMR scalar coupling constants are a rich source of information on molecular structure, but their extraction from spectra can be less than straightforward. Previous approaches to J extraction include methods proposed by Hoye, Golotvin, and the 'modified J-doubling' method. Here we describe the ACCA method, currently implemented in the NMR package MestReC, which allows a high degree of automation in the extraction of coupling patterns even in the case of complex multiplets with sublinewidth splitting. The new approach is illustrated by application to strychnine, for which it has detected previously unreported couplings.

Vacuum polarization effects in relativistic nuclear pairing

In the present work we discuss the contribution of the vacuum polarization on the nuclear pairing, in the context of the relativistic Hartree-Fock-Bogoliubov (HFB) approximation. The polarization effects on the pairing, as a function of Fermi momentum, is shown with the scalar and vector meson-nucleon coupling constants scaled by a parameter x. We have obtained that the nuclear pairing is affected by the vacuum polarization.

The absolute sign of J coupling constants determined using the order matrix calculation.

A novel methodology using the order matrix calculation to determine the absolute sign of spin-spin couplings based on the structure of organic compounds is presented. The sign of the residual dipolar coupling (RDC) depends on the sign of corresponding scalar spin-spin coupling constant and the sign of the RDC has a dramatic influence on the order matrix calculation. Therefore, the sign of the spin-spin coupling constant can be obtained by an order matrix calculation through the corresponding RDC. Six types of spin-spin coupling constants, including 2J(H,H), 1J(C,F), 2J(C,F), 3J(C,F), 2J(F,H) and 3J(F,H), were obtained simultaneously. Except for 3J(C,F) where the measured RDCs have very small magnitudes, the signs were determined unambiguously.

Direct determination of tautomerism in purine derivatives by low-temperature NMR spectroscopy

An investigation of the tautomerism of the purine derivatives N, N-dimethyl- N′-(7(9)- H-purin-6-yl)-formamidine 1 , 6-chloropurine 3 and 6-methoxy purine 5 at low temperatures by NMR spectroscopy has been carried out. Knowledge of tautomeric equilibria is important for predicting N-alkylation positions, hydrogen-bonding patterns, and interactions with biological targets. In the NMR spectra of 1 and 5 at 213 K we observed two sets of signals, whereas at laboratory temperature there was only a single set of signals, reflecting the time-averaged contribution of both components. Based on characteristic values of 13C and 15N chemical shifts and of vicinal 1H– 13C scalar coupling constants, the two components of 1 were determined to be the N7–H (71%) and N9–H (29%) tautomers and those of 5 as the N7–H (18%) and N9–H (82%) tautomers. The investigation of 3 revealed a substantial predominance of the N9–H tautomer without any separation of NMR signals at 213 K.

In vivo 1H NMR spectroscopy of individual human brain metabolites at moderate field strengths.

This article reviews spectral editing techniques for in vivo 1H NMR spectroscopy of human brain tissue at moderate field strengths of 1.5-3 Tesla. Various aspects of 1H NMR spectroscopy are discussed with regard to in vivo applications. The parameter set [delta, J, n] (delta being the relative chemical shift, J the scalar coupling constant and n the number of coupled spins) is used to characterize the spin systems under investigation and to classify the editing techniques that are used in in vivo 1H NMR spectroscopy.

NMR Studies of Phosphorus Chalcogenide—Copper Iodide Coordination Compounds.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Intermolecular 2hJNN coupling in multiply hydrogen-bonded ureidopyrimidinone dimers in solution.

15N-Labeled ureido-4[1H]-pyrimidinones 4a and 5a were synthesized in order to investigate hydrogen bonding in the strongly hydrogen-bonded dimers in solution with intermolecular (2h)J(NN) coupling. Both direct-detection (15)N NMR and one-dimensional (15)N INADEQUATE (for smaller scalar coupling constants) were employed to determine the coupling constants. For dimers of 4 in CDCl(3), a temperature-dependent (2h)J(NN) was observed ranging from 2 Hz at +10 degrees C to 5.1 Hz at -20 degrees C. In dimers of more slowly exchanging bifunctional derivative 5, the coupling constants could be determined at room temperature from an inverse-gated (1)H-decoupled (15)N NMR experiment. Coupling constants in different isomers of the dimer of 5a (4.96, 5.13, 4.37, and 5.27 Hz) were used to test the relationship between (2h)J(NN) values and N-N distances as proposed by Del Bene et al. The N-N distances calculated with the aid of this relationship show excellent agreement with the distances observed in the X-ray crystal structures of 5b, particularly when the nonlinearity of the hydrogen bonds is taken into account.

Karplus-type relationships between scalar coupling constants: 3 J HH molecular versus 4h J HH supramolecular coupling constants

The 3 J HH coupling constants in six H–X–Y–H systems (ethane, methylamine, methanol, hydrazine, hydroxylamine and hydrogen peroxide) and 4h J HH coupling constants in four H–...XH...Y–H, namely [H3NHNH3]+ (two arrangements), HOHNH3 and HOHOH2 have been calculated theoretically as a function of the torsion angle φ. For covalent situations, the corresponding Karplus equations have been fitted to calculated 3 J HH=acos2 φ+bcos φ+c. The a, b and c terms have been analyzed as a function of the electronegativities of X and Y. In the case of ammonium/ammonia complexes (proton shared and not), water/ammonia, and water dimer the values are low (maximum 0.5 Hz) but follow closely a Karplus relationship. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0486-7

A high sensitivity 3D experiment for measuring C α–H α residual dipolar coupling constants

A new sensitivity improved approach is presented to measure the C α–H α scalar and dipolar coupling constants in 13C/ 15N-labeled proteins using a HA(CA)CONH scheme. The proposed experiment has significantly higher sensitivity than the previously published (HA)CA(CO)NH sequence, and provides accurate and straightforward measurements of the scalar and residual dipolar coupling constants. The sequence is easy to implement, and has been demonstrated on the C-terminal domain of the human Ku-80 protein (152 amino acid residues). On average, sensitivity is improved by 40% for both isotropic and anisotropic samples. The sensitivity enhancement is more pronounced for structured regions than unstructured regions, with an average of 50–60% enhancement being observed in the well-structured regions of the protein.

Low-temperature NMR studies of the structure and dynamics of a novel series of acid-base complexes of HF with collidine exhibiting scalar couplings across hydrogen bonds.

The low-temperature (1)H, (19)F, and (15)N NMR spectra of mixtures of collidine-(15)N (2,4,6-trimethylpyridine-(15)N, Col) with HF have been measured using CDF(3)/CDF(2)Cl as a solvent in the temperature range 94-170 K. Below 140 K, the slow proton and hydrogen bond exchange regime is reached where four hydrogen-bonded complexes between collidine and HF with the compositions 1:1, 2:3, 1:2, and 1:3 could be observed and assigned. For these complexes, chemical shifts and scalar coupling constants across the (19)F(1)H(19)F and (19)F(1)H(15)N hydrogen bridges have been measured which allowed us to determine the chemical composition of the complexes. The simplest complex, collidine hydrofluoride ColHF, is characterized at low temperatures by a structure intermediate between a molecular and a zwitterionic complex. Its NMR parameters depend strongly on temperature and the polarity of the solvent. The 2:3 complex [ColHFHCol](+)[FHF](-) is a contact ion pair. Collidinium hydrogen difluoride [ColH](+)[FHF](-) is an ionic salt exhibiting a strong hydrogen bond between collidinium and the [FHF](-) anion. In this complex, the anion [FHF](-) is subject to a fast reorientation rendering both fluorine atoms equivalent in the NMR time scale with an activation energy of about 5 kcal mol(-)(1) for the reorientation. Finally, collidinium dihydrogen trifluoride [ColH](+)[F(HF)(2)](-) is an ionic pair exhibiting one FHN and two FHF hydrogen bonds. Together with the [F(HF)(n)()](-) clusters studied previously (Shenderovich et al., Phys. Chem. Chem. Phys. 2002, 4, 5488), the new complexes represent an interesting model system where the evolution of scalar couplings between the heavy atoms and between the proton and the heavy atoms of hydrogen bonds can be studied. As in the related FHF case, we observe also for the FHN case a sign change of the coupling constant (1)J(FH) when the F.H distance is increased and the proton shifted to nitrogen. When the sign change occurs, that is, (1)J(FH) = 0, the heavy atom coupling constant (2)J(FN) remains very large, of the order of 95 Hz. Using the valence bond order model and hydrogen bond correlations, we describe the dependence of the hydrogen bond coupling constants, of hydrogen bond chemical shifts, and of some H/D isotope effects on the latter as a function of the hydrogen bond geometries.

Structure and dynamics of the lantibiotic mutacin 1140.

Mutacin 1140 is a member of a family of ribosomally synthesized peptide bacteriocins called lantibiotics (lanthionine-containing antibiotics) and is produced by the Gram-positive bacterium Streptococcus mutans. Mutacin 1140 has been shown to be effective against a broad array of Gram-positive bacteria. Chromatography and mass spectroscopy data suggested that mutacin 1140 forms a small compact structure. Nuclear magnetic resonance (NMR) data and restrained molecular dynamics simulations showed that mutacin 1140 interconverts between multiple structures. Calculations of scalar (J) coupling constants showed the best agreement with experimental values when the entire population-weighted ensemble of structures was used, providing independent support for the ensemble. Representative structures from each major group in the ensemble had a common feature in which they are all kinked around the hinge region forming a horseshoe-like shape, and the regions of flexibility of the molecule were limited and well-defined. The structures determined in this study provide a starting point for modeling the mutacin 1140-membrane interactions and pore formation.

The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze protein.

Two-dimensional nuclear magnetic resonance spectroscopy was used to investigate the flexibility of the threonine side chains in the beta-helical Tenebrio molitor antifreeze protein (TmAFP) at low temperatures. From measurement of the (3)J(alphabeta) (1)H-(1)H scalar coupling constants, the chi(1) angles and preferred rotamer populations can be calculated. It was determined that the threonines on the ice-binding face of the protein adopt a preferred rotameric conformation at near freezing temperatures, whereas the threonines not on the ice-binding face sample many rotameric states. This suggests that TmAFP maintains a preformed ice-binding conformation in solution, wherein the rigid array of threonines that form the AFP-ice interface matches the ice crystal lattice. A key factor in binding to the ice surface and inhibition of ice crystal growth appears to be the close surface-to-surface complementarity between the AFP and crystalline ice, and the lack of an entropic penalty associated with freezing out motions in a flexible ligand.

Solution-state cross-polarization for selective excitation of scalar-coupled quadrupolar nuclei S>1/2 in the presence of a residual quadrupolar splitting

We show that solution-state cross-polarization in nuclear magnetic resonance is a valuable technique for the selective observation of scalar-coupled quadrupolar nuclei in anisotropic phases. Numerical simulations show that coherence transfer remains efficient provided the quadrupolar splitting is smaller than the scalar-coupling constant. The method is applied to a mixture of beryllium fluoride complexes. Despite severe overlap in the 9Be spectrum these results clearly demonstrate a quadrupolar splitting for BeF 3 − whereas no such splitting is resolved for BeF 4 2−.

Determination of three-bond scalar coupling between [formula omitted] and [formula omitted] in proteins using an iHN(CA),CO(α/β- J-COHA) experiment

Triple-resonance NMR experiments for measuring three-bond scalar coupling constant between 13 C ′(i−1) and 1 H α (i) spins, defining the dihedral angle φ, are presented. The novel experiments enable the measurement of 3J C ′ H α from simple two (or three)-dimensional 13 C ′ , ( 15 N/ 13 C α ) , 1 H N correlation spectra with minimal resonance overlap, thanks to solely intraresidual coherence transfer pathway and spin-state-selection. The 3J C ′ H α values measured in human ubiquitin using the proposed intraresidual iHN(CA),CO(α/β- J-COHA) TROSY method were compared with those determined previously utilizing the HCAN[C ′] experiment.