Proton-proton Coupling Constants Research Articles

Influence of 2-aminoadenosine, A', on the conformational behaviour of d(T-A'-T-A'). A one-dimensional proton NMR study at 300 MHz and 500 MHz.

Proton NMR studies at 300 MHz and 500 MHz in aqueous solution were carried out on the modified self-complementary tetranucleoside trisphosphate d(T-A'-T-A'), in which d(A') represents 2-aminodeoxyadenosine. The NMR spectra were observed at two sample concentrations over the temperature range 2-70 degrees C. Assignments, based on homonuclear decoupling and nuclear Overhauser enhancement (NOE) experiments, are given. The concentration dependence of the chemical shift vs temperature profiles was used to extract information concerning duplex formation. The proton-proton and proton-phosphorus coupling constants were obtained at four temperatures and yielded accurate conformational data on the sugar ring and on the back-bone angles beta, gamma and delta. From the observed line broadening, shift profiles, NOEs, and from the observation of imino proton resonances, it is concluded that the compound exists as a miniduplex at low temperature. Comparison of these observations with similar observations on the parent compound d(T-A-T-A) indicate that substitution of dA by dA' increases the tendency towards duplex formation. At low temperature the compound adopts a stacked B-DNA type structure: destacking occurs on raising the temperature. The sequence-dependent sugar ring geometry [Mellema, J.-R., Pieters, J. M. L., van der Marel, G. A., van Boom, J. H., Haasnoot, C. A. G. & Altona, C. (1984) Eur. J. Biochem. 143, 285-301] is present in this molecule. The conformational parameters of d(T-A'-T-A') and d(T-A-T-A) are quite similar, thus substitution of dA by dA' has no measurable influence on the geometry of the sugar ring or on the backbone angles beta, gamma and delta.

Trimethylsilylation - Aid in NMR Analysis of Oligosaccharides. Assigment of29Si and13C NMR Spectra of Trimethylsilylated Methyl β-D-Xylobiosides by 2D NMR

Abstract The 1H, 13C and 29Si NMR spectra of methyl β-D-xylopyranoside and three methyl β-D-xylopyranosyl-β-D-xylopyranosides have been measured and assigned by two-dimensional NMR spectroscopy. According to the determined proton-proton coupling constants, the ring conformer ratio is essential ly the same in the studied compounds. The assigned chemical shifts provide correct substituent chemical shifts for assignments in the spectra of higher trimethylsilylated xylooligosaccharides. Heteronuclear chemical shift correlated 2D NMR spectroscopy is proven to be a usable experimental method for 29Si NMR line assignment in carbohydrates. The assigned silicon shifts identify the site of glycosidation.

The detailed conformational study of a leukotriene antagonist, FPL-55712, using high-field nuclear magnetic resonance spectroscopy.

High-field proton magnetic resonance measurements at 400 MHz and 600 MHz allowed the evaluation of the preferred conformations of a leukotriene antagonist, FPL-55712. The experiments involved an analysis of proton-proton coupling constants, longitudinal relaxation time data and nuclear Overhauser effect experiments. The NMR parameters confirm the conformational features expected from X-ray and microwave data for related substances, such as rotational freedom about C14-C15 and C15-C16, synperiplanar arrangements for C7-C8-O-C14 and C16-O-C17-C18 and segmental motion in the propyl side chains.

Cis-diamminedichloroplatinum(II) induced distortion of a single and double stranded deoxydecanucleosidenonaphosphate studied by nuclear magnetic resonance.

The structural distortion of a single- and a double-stranded decadeoxynucleotide upon binding of cis-PtCl2(NH3)2 was studied by 1H-NMR. After selective platination of d(T-C-T-C-G-G-T-C-T-C) (I) at the central d(-GpG-) site (resulting in I-Pt), several non-exchangeable base protons as well as H1', H2', H2" and H3' protons could be assigned by means of conventional NMR double-resonance techniques. Addition of the complementary decamer strand to I and I-Pt yielded the double-stranded III and III-Pt, respectively. All non-exchangeable base, H1', and most of the H2' and H2" protons in the two double stranded compounds could be assigned using 2D-chemical shift correlation (COSY) and nuclear Overhauser enhancement (NOESY) techniques. The double stranded compound III appears to adopt a B-DNA like structure. Comparison of NOEs and proton-proton coupling constants in the d(-GpG-).cisPt part in I-Pt and III-Pt reveals that their structure displays large similarity. Significant chemical shift changes (i.e. larger than 0.1 ppm) between III and III-Pt are restricted to the central four base pairs. It follows that the outer three base pairs, located on either side of the central four base pairs in III-Pt are likely to adopt a regular B-DNA type helix. The observed large upfield and downfield chemical shifts in the d(-CpGpG-) part of III with respect to III-Pt can be rationalized by describing the distortion of the double helix as a kink. A discussion of the observed physical effects upon platination of a double-stranded oligonucleotide is presented.

The 1H NMR “powder pattern” of 1,3,5-trichlorobenzene in a critical mixture of two nematic liquid crystals with opposite diamagnetic anisotropies

The 1H NMR spectrum of 1,3,5-trichlorobenzene was studied in the mixture of the liquid crystals ZLI 1167 and Phase IV which possess opposite anisotropies of the diamagnetic susceptibility. It is shown that in the exact critical state, i.e. in the state where the macroscopic diamagnetic anisotropy of the mixture vanishes, the resulting spectrum is a “powder pattern”. This spectral pattern is interpreted theoretically in terms of the proton shielding anisotropy, degree of molecular order, and the direct proton-proton coupling constant.

Conformational characteristics of the hexanucleoside pentaphosphate AUAUAU: a 2D NMR study at 500 MHz.

All 36 ribose proton resonances and most of the base proton resonances of the hexanucleoside pentaphosphate AUAUAU have been assigned unequivocally using 2D J-resolved spectroscopy, spin echo correlated spectroscopy (SECSY) and 2D NOE spectroscopy (NOESY). The NMR parameters of AUAUAU are compared with those of smaller fragments that contain methylated adenine bases: m62AU, m62AUm62A, m62AUm62AU and m62AUm62AUm62A. Previous studies on this series of compounds have shown that in all these cases purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as common feature that the interior pyrimidine residues are bulged out, whereas the purine residues stack upon each other. Chemical shift data, proton-proton coupling constants, as well as the observation of imino-proton resonances for AUAUAU show unambiguously that upon lowering the temperature the high-temperature "bulged out" situation reverts to a normal A-RNA-like double helix.

NMR and rotational angles in solution conformation of polypeptides

Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin “bracelet”, gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

300 Mhz 1H NMR spectra and conformations of biotin and related hexahydrothienoimidazolone derivatives

1H NMR spectra of biotin and four related hexahydrothienoimidazolones in which the endo pentanoate side chain of biotin is replaced by another endo or exo substituent, and the urea nitrogen atoms are substituted with benzyl groups, have been obtained at 300 MHz. Vicinal coupling constants differentiate cis and trans proton pairs. The generalized Karplus equation was utilized to calculate dihedral angles from vicinal proton-proton coupling constants. The conformation of biotin in solution, calculated from coupling constants, is in good agreement with solid state X-ray crystallographic data.

Conformational equilibrium of unsulphated iduronate in heparan sulphate tetrasaccharides

Proton-proton coupling constants for terminal α-l-iduronate residues in tetrasaccharides obtained from heparan sulphates by complete nitrous acid deaminative cleavage were shown to vary with experimental conditions. It is proposed that the iduronate residue is in a conformational equilibrium between the1C4 chair and either the2So skewboat or possibly the2H3 half-chair conformers. It was not possible to discriminate between the two non-chair forms empirically. The position of the equilibrium is sensitive to temperature, pH and sulphation of neighbouring residues. The likelihood of iduronate residues within glycosaminoglycans existing in the4C1 conformer in addition to the1C4 and2So forms is discussed.

Measurement of proton-proton geminal coupling constants via two-dimensional indirect J spectroscopy with selective spin flip

Description d'une approche speciale facilitant la mesure directe des couplages gemines ( 2 J HH ), sans resoudre le modele de couplage homonucleaire complet

Hexopyranose sugars conformation revised

Literature data for the conformations of ido- and altropyranose derivatives have been reexamined in the light of the newer values recently reported (Eliel . J. Am. Chem. Soc. 104, 3635 (1982) for the conformational free energy of methyl and hydroxymethyl substituent at position 2 in tetrahydropyran. The conclusion is that these values readily explain why the D- 4C 1 (D- 1C 4) chain form is more prevalent than predicted beforehand. Cases of poor agreement between the vicinal proton-proton coupling constants and the dihedral angles in their chair form may be interpreted by mixing with the S 2° skew conformation, rather than the D- 1C 4, (L- 4C 1) chair form.

Two-Dimensional Proton Chemical Shift Correlated NMR Spectroscopy of Digitoxose1

Abstract The hydroxyl proton coupled 1H NMR spectra of solutions of β-d-digitoxopyranose and of an equilibrated mixture of the four ring forms of d-digitoxose in dimethylsulfoxide-d 6 have been assigned completely by two-dimensional, proton chemical shift correlated NMR spectroscopy and spin decoupling at 400 MHz. Analysis of resolution enhanced, one-dimensional 1H NMR spectra yielded an almost complete set of CH and OH proton-proton coupling constants for the four ring forms. The free aldehydo form of d-digitoxose in dimethylsulfoxide-d 6 solution has been detected by means of its characteristic H-l quartet at 6 9.687. Quantitative analysis of the equilibrated mixture of the five forms of d-digitoxose gave the composition:- α-pyranose, β-pyranose, α-furanose, β-furanose, aldehydo form, 11.2, 67.3, 8.4, 13.0, and 0.1%, respectively. The 4 C 1 chair conformations have been assigned to the α- and β-pyranose forms by analysis of the coupling constants and are discussed qualitatively in terms of their relative stabilities.

Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H- 1H spin-spin coupling constants in proteins

Two-dimensional correlated spectroscopy (COSY) is used for measurements of proton-proton spin-spin coupling constants in protein 1H NMR spectra. High digital resolution along the frequency axis ω 2 is achieved by placing the carrier frequency in the center of the spectrum, using quadrature detection in both dimensions and presenting the spectrum in the phase sensitive mode. Compared to other techniques for studies of spin-spin coupling constants, COSY provides greatly improved spectral resolution. This is illustrated by experiments with H 2O solutions of the small globular protein BUSI IIA (bull seminal inhibitor IIA).

13C isotope effects on the parameters of proton magnetic resonance spectra of benzene

The proton-coupled 13C NMR spectra and the 13C satellites in the 1H NMR spectra of commercial benzene containing about 6.6% of benzene- l- 13C were measured and analyzed using the iterative LACX program; 271 lines were assigned and used in the calculations (105 lines from the proton-coupled 13C NMR spectra, 118 lines from outer satellites, and 48 lines from inner satellites in the 1H NMR spectra). The exact values of the 13Cz.sbnd; 1H coupling constants were obtained with the standard deviations not exceeding 0.004 Hz. The 12C/ 13C-induced proton isotope chemical shifts were found to be 1Δ = 2.44; 2Δ = 1.34; 3Δ = 0.51; and 4Δ = 0.33 (in parts per billion). The 12C/ 13C-induced isotope effects on the proton-proton coupling constants do not exceed 0.005 Hz.

Pertrimethylsilylation as a method for improvement of chemical shift additivity through conformational homogenization. 1H and 13C NMR spectra of pertrimethylsilylated derivatives of methyl β-D-xylopyranosides

All possible mono-, di-, and tri- O-methyl, O-benzyl, O-benzoyl, and O-acetyl derivatives of methyl β-D-xylopyranoside were fully trimethylsilylated and their 1H and 13C NMR spectra measured in deuteriochloroform solutions. The spectra were analysed and the chemical shifts completely assigned on the basis of decoupling experiments. The proton-proton coupling constants vary only very little throughout the series. Conformer population analysis by the method of average coupling constants shows that trimethylsilylation increases the C1 conformer population and makes the series conformationally homogenous. Owing to this conformational homogeneity chemical shifts (both 1H and 13C) satisfy very well direct additivity rule. It is suggested that pertrimethylsilylation should be employed whenever deviations from chemical shift additivity are caused by conformational mobility of the investigated series of compounds and when bulky groups can stabilize one of the conformers.

Configurations of glycosidic phosphates of lipopolysaccharide from Salmonella minnesota R595.

The anomeric configurations of the reducing terminal glucosamine and 4-amino-4-deoxy-L-arabinose phosphates in lipopolysaccharide from Salmonella minnesota R595 have been determined by nuclear magnetic resonance. Chemical shifts for the anomeric protons were obtained by selective decoupling of the phosphorus spectrum and proton-proton coupling constants by polarization transfer from protons to phosphorus. In both cases, the phosphate is attached to the sugar in an axial orientation.

CD and 1 H‐n.m.r. studies on the side‐chain conformation of tyrosine derivatives and tyrosine residues in di‐ and tripeptides

Tyrosine, tyrosine peptides and derivatives, in total 11 species, were selected as models for the study of optical properties (1Lb band of phenolic group) and side-chain arrangement (rotamers around C alpha-C beta bond) of tyrosine as a function of chemical structure and pH effects. Circular dichroism spectra between 240 and 320 nm and n.m.r. spectra were recorded for the different ionization states. Results are discussed in terms of charge effects from N- and C-terminal groups and local conformation influence on 1Lb band of the phenolic chromophore and on distribution of rotamer populations in side-chain of tyrosine. Fractions of rotamer populations were estimated from alpha-beta proton-proton coupling constants and, in the cases of tyrosine and N-acetyl-tyrosine, from 15N-beta nitrogen-proton coupling constants, which allow the stereospecific assignment of the beta and beta' protons. The rotamer populations of tyrosine, averaged from all the data of the samples In solution, were then compared with their statistical distribution in th solid state. Interestingly, agreement is excellent when we refer to crystal of tyrosine, tyrosine derivatives or small peptides (31 samples) and poor in the case of proteins. This leads to a discussion on both the validity of using statistical distributions of rotamers in proteins as reference for rotamer preferences inside small peptides in solution and the choice of the appropriate Jg and Jt values in Pachler's approach. The possible existence of a correlation between ellipticity and rotamer populations for such samples is examined.

Conformational analysis of the adduct cis-[Pt(NH3)2 d(GpG)]+ in aqueous solution. A high field (500-300 MHz) nuclear magnetic resonance investigation.

A 500, 400 and 300 MHz proton NMR study of the reaction product of cis-Pt(NH3)2Cl2 or cis-[Pt(NH3)2 (H2O)2] (NO3)2 with the deoxydinucleotide d(GpG): cis-[Pt(NH3)2 d(GpG)] was carried out. Complete assignment of the proton resonances by decoupling experiments and computer simulation of the high field part of the spectrum yield proton-proton and proton-phosphorus coupling constants of high precision. Analysis of these coupling constants reveal a 100% N (C3'-endo) conformation for the deoxyribose ring at the 5'-terminal part of the chelated d(GpG) moiety. In contrast, the 3'-terminal -pG part of the molecule displays the normal behaviour for deoxyriboses: the sugar ring prefers to adopt an S (C2'-endo) conformation (about 70%). Extrapolating from this model compound, it is suggested that Pt chelation by a -dGpdG- sequence of DNA would require a S to N conformational change of one deoxyribose moiety as the main conformational alteration and lead to a kink in one strand of the double-helical structure of DNA.

Tritium labelling and tritium N.M.R. II. Labelled methyl (Z)-Octadec-9-enoate obtained by partial hydrogenation on Lindlar catalyst, and its reduction to(Z)-Octadec-9-en-1-ol

The selectivity of tritium labelling of double bonds by partial hydrogenation of the acetylenic analogue on Lindlar catalyst is investigated by 3H and 13C n.m.r. Examples of both the secondary isotope effect on chemical shift and the usefulness of 3H n.m.r, measurements to calculate proton-proton coupling constants are described. In the absence of proton coupling a finite difference (0.014 ppm) in the chemical shift of tritons at positions 9 and 10 of methyl (Z)-[9,10-3H]octadec-9-enoate is observed.

1H-NMR comparative studies of dinucleoside monophosphates. Influence of different factors on the conformational equilibria of nucleoside and dinucleoside monophosphates in aqueous solution

In order to obtain information about different factors which exert a great influence on the conformational equilibria of mono-, di- and oligonucleotides, the average conformation of four heterodinucleoside monophosphates, ApC, CpA, ApU and UpA, was studied by 1H-NMR at 250 MHz and compared with that of GpC, CpG, GpU, UpG and the corresponding nucleosides and nucleotides. The ratio of N S conformers and the rotamer distribution of the exocyclic group were evaluated from proton-proton coupling constants, and the orientation of the base about the glycosidic bond from proton relaxation involving selective deuteration. The influence of intra- and intermolecular interactions on proton chemical shifts and conformational equilibria has been carefully studied from temperature and concentration effects. The results show that intermolecular base-base stacking does not modify the average conformation of dinucleoside monophosphates, while the intramolecular interaction (between residues of the same molecule) favours the N conformer, the gg rotamer and the anti conformation. The large upfield shift of H 5′ (lower field resonances) compared with H 5″ (higher field resonances) and the large variation of the N proportion with increasing temperature suggest that H 3′ is statistically closer to H 5′ than H 5″. There is a correlation between temperature, the gg rotamer and the variation in the relative chemical shifts between H 5′ and H 5″. These conclusions are in agreement with those of our previous work on GMPs using pH and temperature effects. T 1 relaxation studies indicate a large predominance of the anti conformation for both residues of ApC and ApU; these two compounds also exhibit a very high degree of association. For the naturally occurring ribonucleoside derivatives in aqueous solution, the base chemical structure, the position of the phosphate group, the temperature and pH are among the most important factors which can modify the conformation equilibria of molecules: the N conformation is generally more favoured in pyrimidine than in purine derivatives. The anti proportion is higher in 5′- than in 2′- or 3′-mononucleotides. However, the influence due to the position of the phosphate group is not determined in dinucleoside monophosphates. The temperature effect is negligible on the conformation of monomers but is remarkably large for the dimers: it consists of reducing the N and gg proportions which are preponderant in the dimers at room temperature. The pH effect is particularly large for the G residue, the conformation of which changes upon pr tonation at N 7 (p K ≈ 2.3); the N conformer is favoured at acidic pH.