Analysis Of Coupling Constants Research Articles

In-Situ 13C and 1H NMR Analysis of the Growing Species in Living Cationic Polymerization of Isobutyl Vinyl Ether by the HCl/SnCl4 Initiating System in the Presence of a nBu4NCl Salt

Model reactions of the living cationic polymerization of isobutyl vinyl ether (IBVE) with HCl-IBVE adduct [1: CH 3 CH(OiBu)Cl]/SnCl 4 initiating system were directly analyzed by 13 C and 1 H NMR spectroscopy in CD 2 Cl 2 at -78 o C to demonstrate the formation of carbocation from 1. Under the polymerization condition, the 1/SnCl 4 initiating system gave nonliving polymers, but in the presence of nBu 4 NCl, it induced living polymerization, and the spectral data were closely correlated with the salt-assisted transition from nonliving to living polymerization. For example, upon mixing SnCl 4 with 1, the α-methine and the pendant methylene absorptions of 1 shifted remarkably downfield (e.g., up to 227 ppm in 13 C NMR for the former), and the extent of the downfield shifts increased with increasing SnCl 4 concentration. On further addition of the salt, the downfield signals returned to the original upfield positions close to those for the covalent adduct 1. Thus, these changes and coupling constant ( 1 J CH ) analysis demonstrated that 1/SnCl 4 generates an sp 2 -type carbocationic species that is in a rapid and dynamic exchange equilibrium with the covalent precursor 1, and adding nBu 4 NCl suppresses the growing carbocation, thereby leading to living cationic polymerization

Complexes of tryptophan dipeptides with the R2Sn(IV)2+ ion (R=Me, Ph): Spectroscopic studies, solution properties and structural implications

AbstractTryptophan dipeptides such as L‐tryptophyl‐L‐alanine (H2TrpAla), L‐tryptophyl‐L‐tyrosine (H2TrpTyr), L‐tryptophyl‐L‐tryptophan (H2TrpTrp), along with L‐histidyl‐L‐tyrosine (H2HisTyr), were reacted with R2SnO (R = Me, Ph) yielding the corresponding complexes. The complexes have been characterized by IR and 119Sn Mössbauer spectroscopy in the solid state and by 1H and 13C NMR in CD3OD solutions.Monomeric species were detected, with the tin atom arranged in a pentacoordinated trigonal‐bipyramidal structure. The dipeptides are coordinated via the terminal amino group, deprotonated peptide nitrogen and terminal carboxylate group.No side‐chain appears to be involved in bonding. Determination of rotamer populations for selected compounds was accomplished by vicinal coupling constant analysis and side‐chain orientations are interpreted. In this connection, the potential applications of these compounds as drugs is discussed.

Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints.

The three-dimensional structure of two thiophosphate-modified DNA.RNA hybrid duplexes d(GCTATAApsTGG).r(CCAUUAUAGC), one with R-thiophosphate chirality and one with S-thiophosphate chirality, have been determined by restrained molecular dynamics simulations (rMD). As the two yielded almost identical results, a description of results can be presented in the singular. The conformational flexibility of this hybrid has been investigated by employing time-averaged constraints during the molecular dynamics simulations (MD-tar). A set of structural restraints, comprising 322 precise interproton distance constraints obtained by a complete relaxation matrix analysis of the 2D NOE intensities as well as J coupling constants obtained from quantitative simulations of DQF-COSY cross-peaks in deoxyriboses, was reported in our previous paper [González, C., Stec, W., Kobylanska, A., Hogrefe, R. I., Reynolds, M., & James, T. L. (1994) Biochemistry 33, 11062-11072]. Multiple conformations of the deoxyribose moieties were evident from the scalar coupling constant analysis. Accurate distance constraints, obtained from complete relaxation matrix analysis, yielded a time-averaged solution structure via conventional restrained molecular dynamics which is not compatible with the experimental J coupling constants (root-mean-square deviation in J value approximately 2 Hz). However, vicinal coupling constant information can be reproduced when time-averaged constraints are used during the molecular dynamics calculations instead of the conventional restraints (Jrms approximately 0.6 Hz). MD-tar simulations also improve the NMR R factors. This improvement is more evident in the DNA than in the RNA strand, where no indication of conformational flexibility had been obtained. Analysis of the MD-tar trajectories confirms that deoxyriboses undergo pucker transitions between the S and N domain, with the major conformer in the S domain. The ribose moieties in the RNA strand, however, remain in the N domain during the entire simulation. Conformations of deoxyriboses in the intermediate domain near O4'-endo are obtained when the average structure is calculated with conventional NMR restraints. Since these conformations cannot account for the experimental J coupling information, and they only appear in a very low population in the MD-tar ensemble, we conclude that intermediate E sugar puckers are artifacts produced by the attempt to fit all the structural constraints simultaneously when in reality more than one conformer is present. Most structural features of the duplex remain the same in the average structure and in the MD-tar ensemble, e.g., the minor groove width, exhibiting an intermediate value compared with those of canonical A- and B-like structures.(ABSTRACT TRUNCATED AT 250 WORDS)

13C CP MAS and high-resolution 1H, 15N NMR study of ureido sugars

Ureido sugars with eight various alkyl groups at N-3 were studied by means of 1H, 13C, and 15N NMR spectroscopy in CDCl 3 solution and a 13C CP MAS technique in the solid state. The analysis of chemical shifts and coupling constants suggests the Z, Z-anti conformation of the ureido part of molecule. Differences of δ between the liquid and solid state are observed for the C-2, C-6, and OMe carbon atoms of the d-glucopyranose moiety, as well as the splitting of the anomeric carbon C-1 and OMe signals. The possibility of various conformations in the solid state are discussed. IR spectra of solid ureido sugars indicate that both NH groups are involved in hydrogen bonding. On the other hand, dilution with CDCl 3 followed by 1H NMR showed that N-1-H forms a stronger bond than N-3-H.

Analysis of the 57Fe Hyperfine Coupling Constants and Spin States in Nitrogenase P-Clusters

Analysis of the 57Fe Hyperfine Coupling Constants and Spin States in Nitrogenase P-Clusters

Conformational analysis of a condensed macrocyclic β-lactam by NMR and molecular dynamics calculations

Abstract The conformation of the new macrocyclic β-lactam (1) was investigated by NMR and molecular dynamics (MD) calculations. Restraints obtained from NOESY and ROESY experiments were introduced into MD simulations which led to well-defined conformations. The preference for the calculated minimum energy conformation was confirmed by the analysis of vicinal coupling constants. Experimental coupling constants agreed with computed values.

Investigation of the rotational spectrum of the hydrogen-bonded dimer formed between methylenecyclopropane and HCl

The rotational spectrum of the hydrogen bonded dimer formed between methylenecyclopropane and hydrogen chloride has been obtained with pulsed-supersonic nozzle Fourier-transform microwave spectroscopy. Analysis of rotational constants and quadrupole coupling constants for three isotopic species of the dimer shows that HCl is attached to the C=C bond of methylenecyclopropane in a T-type configuration. The HCl monomer lies in or very near the plane that bisects the cyclopropyl ring, with the Cl atom lying 3.569 Å from the center of the C=C bond. The HCl axis is bent towards the three membered ring and there are experimental indications of a near 20° bend in the hydrogen bond. The observed dimer geometry is consistent with an electrostatic model which predicts the alternative configuration with HCl T bonded to the edge of the ring (as in cyclopropane–HCl) to be less stable when the base is methylenecyclopropane.

The Synthesis and Characterization of a Pyridine-Linked Cyclodextrin Dimer

A cyclodextrin dimer has been synthesized in an overall 29% yield from β-cyclodextrin. This compound contains a pyridine bridge that links the secondary faces of two cyclodextrin units. A complete 1 H and 13 C NMR analysis was performed using a combination of one- and two-dimensional NMR pulse sequences. The results are consistent with the notion that each β-cyclodextrin moiety contains seven spectrally unique sugar resi- dues. In addition, an analysis of key coupling constants suggest that the modified sugar moiety in the individual cyclodextrin units has un- dergone a chair inversion. This analysis represents the first complete NMR characterization of a cyclodextrin dimer

Structure of the product of intracomplex alkylation of target octanucleotide pd[TGTTTGGC] by means of 4-[N-methyl-N-(2-chloro-ethyl)-amino]benzyl-5′-phosphamido derivative of heptanucleotide pd[CCAAACA]: Two-dimensional1H-NMR spectroscopy and restrained molecular mechanics refinement

The spatial structure of a covalent adduct — the product of intracomplex alkylation at N-3-position of dC-8 nucleoside residue of target octanucleotide pd[TGTTTGGC] by means of 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5′-phosphamido derivative of heptanucleotide pd[CCAAACA] — has been investigated in aqueous solution by two-dimensional (2D)1H-NMR spectroscopy and restrained molecular mechanics calculations. By using COSY, COSY-DQF and NOESY experiments the assignment of oligonucleotide protons as well as protons of modifying group was carried out. The correlation times of benzylamide fragment protons and those of neighbouring nucleotide residues dC-1 and dC-8 were shown to be equal and shorter thanτ c of intraduplex nucleotides. The analysis of proton-proton coupling constants for H1′, H2′a, H2′b and H3′ protons showed all sugar residues to be in 2′-endo conformation. The distances between protons closed in the space were determined by means of a set of one-dimensional (1D) NOE experiments. The experimental distances were used as the constraints for energy minimization by molecular mechanics calculations. Eight conformations of benzylamide fragment of the covalent adduct differed with orientations of 4-N-methyl residue of the alkylating group and 1-methyleneamide linker function were constructed as starting structures in energy minimization procedure. Among of the resulting optimized structures only one S(Alk)8* was found to satisfy both experimental data and energetic criteria. The benzylamide fragment in conformation S(Alk)8* has been shown to localize in the region of lacked nucleoside residue of the duplex at the end of heptanucleotide chain less than 5 A apart from the residues dC-1 and alkylated dC-8.

Vinyllithium: dynamic behavior in tetrahydrofuran solution and comprehensive analysis of NMR spin-spin coupling constants

Vinyllithium (ViLi; isotopically labeled with 6 Li) is an 8:1 tetramer/dimer equilibrium in tetrahydrofuran-d 8 (THF-d 8 ) at -90 o C (1.6 M solution). In the presence of equilmolar amounts of TMEDA (tetramethylethylenediamine), the tretramer:dimer ratio is 1:13 in THF-d 8 at -80 o C (1.9 M solution). Dynamic NMR phenomena are observed in the ViLi tetramer: at -90 o C in THF-d 8 , a static aggregate is found, whereas at -60 o C rapid intraaggravate exchange of the four lithium sites indicates a fluxional tetramer

Radical trapping by PBN during reperfusion in rabbit gastric mucosa.

Oxygen free radicals have been considered as a cause of ischemia-reperfusion injury in several organs, but this injury in a stomach, containing acid, may progress to severe damage. Thus, we examined the effect of ischemia-reperfusion and milk-intake on rabbit gastric mucosa. The gastric mucosal blood flow was increased after milk-intake, and gastric rupture was detected. Superoxide dismutase activity measured by an improved nitroblue tetrazolium reduction method and thiobarbituric acid reactive substances in serum is increased during ischemia-reperfusion and milk-intake. By using alpha-phenyl N-tert-butyl nitrone (PBN) as a spin trap and electron paramagnetic resonance (EPR), we detected lipidic radicals from tissue samples in chloroform-methanol solvent only during reperfusion and milk-intake period; no signal was detected before. The EPR signal of spin adducts obtained in the sample after ischemia-reperfusion and milk-intake would be a mixture of peroxyl and alkoxyl radicals from the analysis of coupling constants.

How do the gauche and anomeric effects drive the pseudorotational equilibrium of the pentofuranose moiety of nucleosides?

The conformational characteristics of abasic 1-deoxy sugars 1,2, and 3 and pentofuranose moieties in 2',3'- dideoxy-(ddA (6), ddG (7), ddC (S)), 2'-deoxy-(dA (9), dG (lo), dC (ll)), and ribo-@-D-nucleosides (Ade (12), Gua (13), Cyt (14)) were established through the analysis of vicinal proton-proton coupling constants extracted from their 500-MHz lH-NMR spectra recorded at 20 K intervals in the temperature range from 278 to 358 K in D20 solution. Two novel deuterated analogues of (S)-tetrahydrofurfuryl alcohol (l), 2-(S)-(hydroxymethyl)-4-(R)-deuteriotetrahy- drofuran (4) and 2-(S)-(hydroxymethyl)-3-(S)-deuteriotetrahydrofuran (5), have enabled unequivocal assignment of the complex nine-spin system in its 'H-NMR spectrum. The van't Hoff plots of (In(&/&)) as a function of 1 / Tgave AH' and AS' values of pseudorotational equilibrium in pentofuranoses 1-3 and pentofuranose moieties in nucleosides 614. The values of AH' were dissected into various stereoelectronic effects (gauche versus anomeric effects) of exocyclic substituents on the pentofuranose moiety. Clearly, the gauche effect of the 04'-C4'-C3'-03' fragment drives the pseudorotational equilibrium to the S-type conformations, while the gauche effect of the 04'-Cl'-C2'-02' fragment pushes the pseudorotational equilibrium to the N. These gauche effects are the strongest factors responsible for driving the N e S pseudorotational equilibrium. The strength of the gauche effect of the 04'-C4'-C3'-03' fragment in abasic sugars 1-3 is further tuned by the presence of a heterocyclic base at C1' in nucleosides 6-14. The relatively weaker anomeric effect of the heterocyclic base drives the N e S equilibrium to the N. The assessment of the relative strengths of the anomeric effects in 2',3'-dideoxy, 2'-deoxy-, and ribo-@-D-nucleosides has shown that the anomeric effect of the cytosine base is stronger than the anomeric effect of the adenine or guanine base. The experimental data suggest that the anomeric effect is considerably reduced as 04' experiences the electron-withdrawing effect(s) of 2'(3')-hydroxyls. The differences in the conformational preferences found in purine and pyrimidine ribonucleosides were additionally attributed to the distinct relative strength of the gauche effect of the N-C1'-C2'-02' fragment. The preference for the gauche orientation of the N-C1'-C2'-02' fragment and therefore S-type sugar conformation is affected by the nature of the purine or pyrimidine glycosyl nitrogen atom.

Identification of the site of the globin-derived radical in leghaemoglobins

Reaction of the Fe 3+ form of the oxygen-carrying protein leghaemoglobin (MetLb), derived from the root nodules of lupins, with H 2O 2 is shown to generate, in addition to an iron (IV)-oxo (ferryl) species, a globin radical. This radical has been detected by EPR spectroscopy and is analogous to the species previously observed with the soybean protein. Analysis of the hyperfine coupling constants and g value of the EPR signal, together with computer simulations and the similarity of the observed spectra of that detected with the soybean form suggest that this species is also a tyrosine-derived phenoxyl radical; this species is believed to arise via an electron-transfer process within the protein with an electron being transferred from the tyrosine residue to an initially-generated Compound-1-type species. Comparison of the protein sequences and structures of the two proteins show that there is only one conserved tyrosine residue (at position 133 in the soybean and 138 in the lupin); this is believed to be the site of the phenoxyl radical. The lupin phenoxyl radical reacts with added water-soluble antioxidants and reducing agents which result in repair of the radical; this may be an important protective mechanism in vivo. Analysis of molecular models of the protection structures is in accord with both the assignment of the radical to this conserved tyrosine residue and the observed radical reactivity.

Viewpoint 8 — polarization propagator analysis of spin-spin coupling constants

The analysis of electronic mechanisms that define indirect NMR spin-spin coupling constants can be efficiently carried out by combining the polarization propagator formalism with the use of localized molecular orbitals. This approach is applied to study several trends of one-bond couplings along the Periodic Table when one of the coupled nuclei bears a lone pair. This analysis is preceded by a revision of the fundamentals of the method in which its approximations, shortcomings and capabilities are commented on. A brief overview of results already published in the literature is also given. The relationship between the classical approach of Pople and Santry and the polarization propagator calculation of the Fermi contact term is discussed.

The solution conformation of (D)Phe-Pro-containing peptides: implications on the activity of Ac-(D)Phe-Pro-boroArg-OH, a potent thrombin inhibitor.

Ac-(D)Phe-Pro-boroArg-OH is a potent, competitive inhibitor of thrombin (Ki = 40 pM). 1H-NMR studies have shown that the peptide portion, -(D)Phe-Pro-, has secondary structure in aqueous solutions. This structure corresponds fairly closely to the structure of H-(D)Phe-Pro-ArgCH2Cl complexed to thrombin in the protein crystal structure (Bode, W.; et al. EMBO J. 1989, 193, 3467-3475.). These results indicate that, in addition to enthalpic interactions in the active site of the enzyme, there are significant entropic advantages in binding this molecule not previously recognized. We estimate that they contribute approximately 10-fold to binding. The structure we have observed can be explained by pi-pi interactions between the phenyl side chain of (D)Phe and the (D)Phe-Pro peptide bond. Assignment of structure is based first on the 0.8-1.2 ppm difference between the two Pro C delta protons. The magnitude of these chemical shifts are consistent with aromatic ring current-induced effects expected for distances in our structure. The structure was further defined by interproton distances and correlation times calculated by backtransformation and correction of the NOESY and ROESY data to the longitudinal and transverse cross relaxation rates. Analysis of the vicinal coupling constants show that Phe chi 1 is not fixed. Correlation times for the peptide side chains and backbone indicate that the phenyl ring and boroArg side chain possess various degrees of internal motion, and that the rest of the peptide has a fairly rigid conformation.

Conformational analysis of mu-selective [D-Ala2,MePhe4]enkephalins.

The conformational space of the potent mu-selective opioids [D-Ala2,MePhe4,Gly-ol5]enkephalin (DAGO) and [D-Ala2,MePhe4,Met(O)-ol5]enkephalin (FK 33-824) has been analyzed by 1H-NMR spectroscopy and theoretical calculations involving systematic conformational searching and energy minimizations. A cis-trans equilibrium of the Gly3-MePhe4 amide bond is induced by the N-methyl group, and the more energetically favoured trans isomer is proposed as the biologically relevant form. A compact interaction between the side chains of Tyr1 and D-Ala2 was demonstrated by NOE and ROE effects in both peptides in D2O and DMSO-d6, further supported by shielding of the D-Ala2 methyl protons in both solvents. Analysis of coupling constants, NOE and ROE data indicated significant restriction of the conformational freedom of the MePhe4 side-chain for both peptides in the two solvents. The NMR results and theoretical calculations point towards folded low energy conformations characterized by a beta II-type turn around Gly3-MePhe4. For the trans isomer, a Tyr1-MePhe4 phenyl ring separation between 8.5 and 12.5 A was accompanied by proximity between the D-Ala2 side chain and the C-terminal in low energy conformations. The results are in good agreement with available data on related active enkephalins. The conformational effects induced by simultaneous incorporation of D-Ala2 and MePhe4 in enkephalins is discussed in the light of the enhanced mu-opioid receptor selectivity and activity of these peptides.

New Eudesmanolide Sesquiterpenes from a Philippines Collection of Wedelia prostata

Two known, but previously uncharacterized, ent-kaurenic acid derivatives, 1 and 2, and four new sesquiterpenes of the eudesmanolide type, 3-6, have been isolated from Wedelia prostata. The structures were eludidated by a range of 1D and 2D high field nmr techniques, and the stereochemistry of the new eudesmanolides was defined from a combination of coupling constant analyses and nuclear Overhauser difference spectra

Structure of Hen Lysozyme in Solution

The structure of the 129-residue protein hen lysozyme has been determined in solution by two-dimensional 1H nuclear magnetic resonance methods. 1158 NOE distance restraints, 68 φ and 24 χ 1 dihedral angle restraints were employed in conjunction with distance geometry and simulated annealing procedures. The overall C α root-mean-square deviation from the average for 16 calculated structures is 1·8(±0·2)Å, but excluding 14 residues in exposed disordered regions, this value reduces to 1·3(±0·2) Å. Regions of secondary structure and the four α-helices in particular, are well defined ( C α root-mean-square deviation 0·8(±0·3) Å for helices). The main-chain fold is closely similar to structures of the protein in the crystalline state. Furthermore, many of the internal side-chains are found in well-defined conformational states in the solution structures, and these correspond well with the conformational states found in the crystal. The general high level of definition of main-chain and many internal side-chains in the solution structures is reinforced by the results of an analysis of coupling constants and ring current shifts. Many side-chains on the surface, however, are highly disordered amongst the set of solution structures. In certain cases this disorder has been shown to be dynamic in origin by the examination of 3 J αβ coupling constants.

Substituted .gamma.-lactones with vicinal hydrogen atoms. Conformational study by MM2 calculations and coupling constant analysis

The conformational analysis of substituted γ-lactones with vicinal hydrogen atoms is carried out by the MM2/3JHH tandem. The agreement between experimentally avaible and calculated data is globally correct (rms=1.16 Hz). A general preference for a hydroxyl group to occupy the equatorial position if it is on C-2 or the axial position if it is on C-3 or C-4 is observed as a consequence of the presence of H bond or of the gauche effect, respectively

Verdazyls. Part 33. EPR and ENDOR studies of 6-oxo- and 6-thioxoverdazyls. X-Ray molecular structure of 1,3,5-triphenyl-6-oxoverdazyl and 3-tert-butyl-1,5-diphenyl-6-thioxoverdazyl

A range of 6-oxoverdazyls 2b–h and 6-thioxoverdazyls 3a–c and 3e–h has been directly prepared by dehydrogenation of the corresponding 1, 4, 5, 6-tetrahydro-1, 2, 4, 5-tetrazin-3(2H)-ones 5b–h and thiones 7a–c and 7e–hwith lead dioxide, potassium hexacyanoferrate (III), or bis(4-methylphenyl)-aminyl. X-Ray analyses reveal a nearly planar verdazyl framework for the oxoverdazyl 2a, whereas the thioxoverdazyl 3ftakes on a flat boat conformation. In the latter, owing to the bulky sulfur the N-phenyl groups are considerably twisted out of the plane of the verdazyl ring. Electronic absorption spectra of the deeply coloured radicals exhibit characteristic bands in the visible region with λmax, 1 ranging from 445 to 608 nm. EPR, ENDOR and 2H NMR studies have led to a complete analysis and full assignment of all hyperfine coupling constants. The π-SOMO of 6-oxo-2 and 6-thioxo-verdazyls 3, having nodes at C(3) and C(6), is mainly confined to the nitrogens of the verdazyl ring. Spin delocalization into the N-phenyl groups is reduced, particularly in the 6-thioxoverdazyls, owing to the large torsion angle about the N–C(phenyl) bond.