Vicinal Coupling Research Articles

Solvent-induced ?-hairpin to helix conformational transition in a designed peptide

An octapeptide containing a central -Aib-Gly- segment capable of adopting beta-turn conformations compatible with both hairpin (beta(II') or beta(I')) and helical (beta(I)) structures has been designed. The effect of solvent on the conformation of the peptide Boc-Leu-Val-Val-Aib-Gly-Leu-Val-Val-OMe (VIII; Boc: t-butyloxycarbonyl; OMe: methyl ester) has been investigated by NMR and CD spectroscopy. Peptide VIII adopts a well-defined beta-hairpin conformation in solvents capable of hydrogen bonding like (CD(3))(2)SO and CD(3)OH. In solvents that have a lower tendency to interact with backbone peptide groups, like CDCl(3) and CD(3)CN, helical conformations predominate. Nuclear Overhauser effects between the backbone protons and solvent shielding of NH groups involved in cross-strand hydrogen bonding, backbone chemical shifts, and vicinal coupling constants provide further support for the conformational assignments in different solvents. Truncated peptides Boc-Val-Val-Aib-Gly-Leu-Val-Val-OMe (VII), Boc-Val-Val-Aib-Gly-Leu-Val-OMe (VI), and Boc-Val-Aib-Gly-Leu-OMe (IV) were studied in CDCl(3) and (CD(3))(2)SO by 500 MHz (1)H-NMR spectroscopy. Peptides IV and VI show no evidence for hairpin conformation in both the solvents. The three truncated peptides show a well-defined helical conformation in CDCl(3). In (CD(3))(2)SO, peptide VII adopts a beta-hairpin conformation. The results establish that peptides may be designed, which are poised to undergo a dramatic conformational transition.

Influence of lysine content and pH on the stability of alanine-based copolypeptides.

To account for the relative contributions of lysine and alanine residues to the stability of alpha-helices of copolymers of these two residues, conformational energy calculations were carried out for several hexadecapeptides at several pHs. All the calculations considered explicitly the coupling between the conformation of the molecule and the ionization equilibria as a function of pH. The total free energy function used in these calculations included terms that account for the solvation free energy and free energy of ionization. These terms were evaluated by means of a fast multigrid boundary element method. Reasonable agreement with experimental values was obtained for the helix contents and vicinal coupling constants ((3)J(HNalpha)). The helix contents were found to depend strongly on the lysine content, in agreement with recent experimental results of Williams et al. (Journal of the American Chemical Society, 1998, Vol. 120, pp. 11033-11043) In the lowest energy conformation computed for a hexadecapeptide containing 3 lysine residues at pH 6, the lysine side chains are preferentially hydrated; this decreases the hydration of the backbone CO and NH groups, thereby forcing the latter to form hydrogen bonds with each other in the helical conformation. The lowest energy conformation computed for a hexadecapeptide containing 6 lysine residues at pH 6 shows a close proximity between the NH3(+) groups of the lysine side chains, a feature that was previously observed in calculations of short alanine-based oligopeptides. The calculation on a blocked 16-mer of alanine shows a 7% helix content based on the Boltzmann averaged vicinal coupling constants computed from the dihedral angles phi, consistent with previous experimental evidence on triblock copolymers containing a central block of alanines, and with earlier theoretical calculations.

Structural characterization by NMR of rifabutinol, a derivative of rifabutin

Rifabutin, a naphthalenic ansamycin, is a specific inhibitor of bacterial DNA-directed RNA polymerase and inhibits in vitro the replication of HIV-1. The synthesis of rifabutinol by PtO2–NaBH4 reduction of rifabutin in ethanol is described. Full assignments in CDCl3 are presented of the 1H and 13C NMR resonance signals using two-dimensional homonuclear and heteronuclear correlation techniques and selective proton decoupling methods. The three-dimensional structure of the ansa-chain of rifabutinol was calculated from NOE contacts and vicinal coupling constants, using a simulated annealing protocol starting from random coordinates. Measurements of the 13C T1 relaxation times of rifabutin in solution are consistent with a rigid ansa-chain. Copyright © 2000 John Wiley & Sons, Ltd.

ChemInform Abstract: Structure, Conformation and Absolute Configuration of New Antifeedant Dolabellanes from Trichilia trifolia.

Abstract The structures of three new dolabellane diterpenoids, (1R,3E,7Z,11S,12S)-dolabella-3,7,18-trien-17-oic acid (1), (1R,3E,6R,7Z,11S,12S)-dolabella-3,7,18-trien-6,17-olide (2) and (1R,3S,4R,7Z,11S,12S)-3-hydroxydolabella-7,18-dien-4,17-olide (3), isolated from the wood of Trichilia trifolia, were elucidated by 1D and 2D NMR spectroscopy. The stereochemistry of 1 and 2 was confirmed by X-ray diffraction analysis, while that of 3 was ascertained from NOESY data. Comparison between experimental and calculated 1H–1H vicinal coupling constants and the analysis of molecular mechanics structures revealed that the 11-membered ring of 1 and 2 exists in a conformational equilibrium in solution, while in 3 this ring possesses a more rigid structure. The absolute configuration of 3 was established from its Cotton effects. Dolabellanes 1–3 caused significant feeding reduction by the rice weevil Sitophilus oryzae.

A comprehensive approach for accurate measurement of proton-proton coupling constants in the sugar ring of DNA.

Stereo-selectivedeuteration has been explored as an approach for improving the accuracy of NMR-derived, three-bond vicinal proton-proton coupling constants in the 12-base-pair DNA Dickerson sequence [d(CGCGAATTCGCG)(2)]. The coupling constants are useful for DNA structure determination in restrained molecular dynamics calculations. Specifically, the A5 and A6 residues were prepared with the H2" proton stereo-selectively replaced with a deuteron. Deuteration of the H2" leads to a 42-fold reduction in the transverse cross-relaxation rate of the H2' spin, effectively negating the contribution of transverse cross relaxation to the cross peak frequencies and phases. Calculated linewidth and polarization transfer functions indicated that the reduced dipolar interaction is also expected to result in a significant increase in intensity for all cross peaks involving the H1', H2', or H3' spin. The spectral complexity is also reduced by selective deuteration. Time-shared homonuclear decoupling of passive spins during acquisition was implemented, reducing the spin system, in some cases, to an effectively isolated two-spin system. This enables the use of a 90 degrees mixing pulse instead of the 35 degrees pulse commonly used in standard P.E.COSY experiments, leading to an additional 75% increase in signal intensity. Selective excitation pulses were used to reduce the number of increments required in the indirect dimension by as much as a factor of 4. The cumulative improvement in sensitivity is striking, approaching three orders of magnitude per unit time. Separate experiments, referred to as Stripe-COSY and Superstripe-COSY, were optimized for each coupling constant measured. Finally, J-doubling was used to obtain the most accurate peak separations. This comprehensive approach shows promise as an effective method for extracting highly accurate homonuclear vicinal coupling constants in DNA.

Solution Structure of a Designed Amphipathic Antimicrobial Synthetic Peptide, PGAa

A designed peptide, PGAa showed an excellent antifungal activity as well as an efficient bactericidal activity toward gram-positive, especially in the pathogenic yeast Candida albicans 28838. The solution structures of PGAa have been determined both in 40% TFE/water solution and DPC micelle by CD and NMR spectroscopy. Based on NOEs, vicinal coupling constants, backbone amide exchange rates, and chemical shift indices, PGAa formed a long amphipathic α-helical conformation in both TFE and DPC micelle environments, spanning the residues Ile2–Ala19 in TFE and Lys5–Ala19 in DPC micelle, respectively. Solution structures suggested that the hydrophobic residues would interact with the fatty acyl chains of the lipid bilayer, while the positively charged side-chains exposed to aqueous environments. Therefore, we conclude that the α-helical structure as well as the highly amphiphatic nature of PGAa peptide may play a critical role in its antimicrobial activity as well as selectivities in different species.

Molecular mechanics (MM3) study of the conformations of methyl esters and N,N-dimethylamides of diastereoisomeric 4-cyano-3,4-diphenyl-butanoic acids

Molecular mechanics (MM3 force field) was used to examine an unexpected observation by NMR for a preference of conformations with synclinal protons around the C(3)–C(4) bond in methyl esters and dimethylamides of diastereoisomeric 4-cyano-3,4-diphenyl-butanoic acids. After the reoptimization of three torsional parameters, related to structural units containing a cyano group, we obtained a good correlation between the MM3 computed populations of the conformations and the estimates from vicinal coupling constants. The electrostatic interactions have the decisive contribution for lowering the energies of the preferred conformations.

Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis.

Two analogues of Scyliorhinin I (Scyl), a tachykinin with N-MeLeu in position 8 and a 1,5-disubstituted tetrazole ring between positions 7 and 8, introduced in order to generate local conformational constraints, were synthesized using the solid-phase method. Conformational studies in water and DMSO-d6 were performed on these peptides using a combination of the two-dimensional NMR technique and theoretical conformational analysis. The algorithm of conformational search consisted of the following three stages: (i) extensive global conformational analysis in order to find all low-energy conformations; (ii) calculation of the NOE effects and vicinal coupling constants for each of the low energy conformations; (iii) determining the statistical weights of these conformations by means of a nonlinear least-squares procedure, in order to obtain the best fit of the averaged simulated spectrum to the experimental one. In both solvents the three-dimensional structure of the analogues studied can be interpreted only in terms of an ensemble of multiple conformations. For [MeLeu8]Scyl, the C-terminal 6-10 fragment adopts more rigid structure than the N-terminal one. In the case of the analogue with the tetrazole ring in DMSO-d6 the three-dimensional structure is characterized by two dominant conformers with similar geometry of their backbones. They superimpose especially well (RMSD = 0.28 A) in the 6-9 fragments. All conformers calculated in both solvents superimpose in their C-terminal fragments much better than those of the first analogue. The results obtained indicate that the introduction of the tetrazole ring into the Scyl molecule rigidifies its structure significantly more than that of MeLeu.

Hydroxy protons in conformational study of a Lewis b tetrasaccharide derivative in aqueous solution by NMR spectroscopy

The 1H NMR chemical shifts, vicinal coupling constants, temperature coefficients, and exchange rates of the hydroxy protons of a Lewis b tetrasaccharide derivative, α- l-Fuc p-(1→2)-β- d-Gal p-(1→3)[α- l-Fuc p-(1→4)]-β- d-Glc pNAc-1-O(CH 2) 2NHCOCHCH 2, have been measured in aqueous solution. The data did not show any evidence for persistent hydrogen bonds participating in the stabilization of the structure. While most of the hydroxy proton signals have chemical shifts similar to those of the corresponding methyl glycosides, four of them, O(3)H, O(4)H, and O(6)H of Gal p, and O(2)H of the Fuc p linked to Glc pNAc, exhibit large upfield shifts. This shielding effect has been attributed to the orientation of the hydroxy protons toward the amphiphilic region constituted by the hydroxy groups of the Gal p residue and mainly the ring and methyl hydrogens of the Fuc p unit attached to the Glc pNAc. The close face to face stacking interaction between the Fuc p linked to the Glc pNAc and the Gal p residues, as well as the steric interaction between the Fuc p linked to the Gal p and the Glc pNAc are confirmed by the additional inter-residue NOEs of the exchangeable protons in sugar units which are not directly connected.

Structure, Conformation and Absolute Configuration of New Antifeedant Dolabellanes from Trichilia trifolia

The structures of three new dolabellane diterpenoids, (1 R,3 E,7 Z,11 S,12 S)-dolabella-3,7,18-trien-17-oic acid ( 1), (1 R,3 E,6 R,7 Z,11 S,12 S)-dolabella-3,7,18-trien-6,17-olide ( 2) and (1 R,3 S,4 R,7 Z,11 S,12 S)-3-hydroxydolabella-7,18-dien-4,17-olide ( 3), isolated from the wood of Trichilia trifolia, were elucidated by 1D and 2D NMR spectroscopy. The stereochemistry of 1 and 2 was confirmed by X-ray diffraction analysis, while that of 3 was ascertained from NOESY data. Comparison between experimental and calculated 1H– 1H vicinal coupling constants and the analysis of molecular mechanics structures revealed that the 11-membered ring of 1 and 2 exists in a conformational equilibrium in solution, while in 3 this ring possesses a more rigid structure. The absolute configuration of 3 was established from its Cotton effects. Dolabellanes 1– 3 caused significant feeding reduction by the rice weevil Sitophilus oryzae.

CONFORMATIONS OF 4,5,6-TRIPHENYL-TETRAHYDRO-1,3-THIAZINE-2-THIONES AND THEIR N-ALKYL DERIVATIVES. UNUSUAL THIAZINETHIONE OR AZETIDINE FORMATION UPON REACTION OF 3-AMINO- AND 3-METHYLAMINO-1,2,3-TRIPHENYLPROPYL CHLORIDES WITH POTASSIUM ETHYLXANTHATE

Reaction of 3-amino- or 3-methylamino-1,2,3-triphenylpropyl chlorides (6 or 7) with potassium ethylxanthate leads to 4.5.6-triphenyl-tetrahydro-,3-thiazine-2-thione 1 or 1-methyl-2,3,4-triphenylazetidine 8 depending on the N-substitution. Conformational distribution of all possible diastereoisomeric thiazinethiones 1 and their N-alkyl derivatives 2–5 is determined by means of 1H NMR spectroscopy. Allylic strain caused by N- substituents in the trans,cis-isomers strongly shifts the equilibrium between conformations with a,a,e or e,e,a phenyl groups towards the conformer with an axial neighbouring Ph-4 group. Vicinal couplings data for the diastereoisomeric azetidine 8 show different ring geometry depending on the configuration.

The use of locally dense basis sets in the calculation of indirect nuclear spin–spin coupling constants: The vicinal coupling constants in H3C–CH2X (X=H, F, Cl, Br, I)

We have calculated the vicinal indirect nuclear spin-spin coupling constants 3J1H1H in the series of molecules H3C–CH2X with X=H, F, Cl, Br, and I at the self-consistent field level and using the second order polarization propagator approximation (SOPPA). We have studied the effect of electron correlation and of the substituents (X=F, Cl, Br, and I) on all four contributions to the coupling constants. But in particular we have investigated the possibility of using locally dense basis sets, i.e., we have carried out calculations with basis sets, where the basis functions on the hydrogen atoms were optimized for the calculation of spin–spin coupling constants whereas on the other atoms smaller, contracted sets of basis functions were used. This changes the results for the couplings by ∼0.3 Hz or 3%. However, the change is almost entirely due to the orbital paramagnetic term and is independent of electron correlation, which enables one to estimate the SOPPA results in the full basis sets. Furthermore we find that the Fermi contact term is the dominant contribution to the vicinal coupling constants, because it is about an order of magnitude larger than the other contributions and because the two orbital angular moment terms almost cancel each other completely. Also the changes in the calculated couplings due to electron correlation are solely due to the Fermi contact term. However, the shifts in the coupling constants caused by the different substituents arise in equal amounts from the Fermi contact and the orbital diamagnetic term, whereas the changes in the orbital paramagnetic term are smaller and are in the opposite direction. In comparison with the experimental data we find very good agreement for C2H6 and C2H5F. However, the agreement becomes less good with increasing nuclear charge of the substituent X.

Spectroscopic characterization and biological activity ofL-methionyl-L histidinato complexes of R2Sn(IV) ions (R?=?Me, nBu, Ph) and X-ray structure of Me2SnMetHis ? 0.5MeOH

Complexes of L-methionyl-L-histidine (H2MetHis) with R2Sn(IV) ions (R = Me, nBu, Ph) have been synthesized. The crystal and molecular structures of Me2SnMetHis·0.5MeOH have been determined by X-ray diffraction. The title compound contains two crystallographically independent molecular units possessing the same trigonal-bipyramidal geometry at tin, each dimethyltin(IV) moiety being coordinated by the terminal amino nitrogen, deprotonated peptide nitrogen and terminal carboxylate group, neither the imidazole nor thioether groups being involved in bonding. IR spectroscopy was used to probe the structure of the complexes in the solid state, and the structure in solution (CD3OD) was assessed by 1H and 13C NMR. Me2Sn(IV)dipeptide complexes appear to be undissociated and to retain a pentacoordinated structure. Rotamer population of C-terminal histidine was determined by analysis of vicinal coupling constants and side-chain orientations have been interpreted with a view to potential applications of the compounds as recognition agents. Biological activity was tested on Ascidian embryos of Ciona intestinalis at different stages of development. Copyright © 2000 John Wiley & Sons, Ltd.

Quantum Mechanical Conformational Analysis of β-Alanine Zwitterion in Aqueous Solution

The conformational behavior of β-alanine zwitterion in aqueous solution has been investigated by post-Hartree−Fock and density functional methods using the polarizable continuum model (PCM) for the description of the solvent. Our results show that the PCM is able to reproduce the delicate balance between intramolecular hydrogen bridges and preferential solvation of isolated charged groups in determining the overall conformational preferences without any need of explicit solvent molecules. From a methodological point of view, the Hartree−Fock method is not sufficiently reliable for quantitative predictions of conformer equilibria, whereas approaches including electron correlation (DFT, MP2, MP4) perform remarkably well when using medium size basis sets including diffuse functions. Vibrational averaging arising from the torsional motion around the central CC bond leads to vicinal NMR coupling constants (J) in remarkable agreement with experiments when using an extended Karplus-type equation for the torsiona...

Solution Conformational Features of the Unsymmetrical Metalla Crown Ether cis-Mo(CO)4{2-(2,2‘-O2C12H8)PO(CH2CH2O)2- 2-C20H12-2‘-OP(2,2‘-O2C12H8)} from 2D NMR Spectroscopy and Molecular Modeling

A new unsymmetrical metalla crown ether, cis-Mo(CO)4{2-(2,2‘-O2C12H8)PO(CH2CH2O)2-2-C20H12-2‘-OP(2,2‘-O2C12H8)}, has been designed for solution conformation studies. The complex was prepared by the reaction of the α,ω-bis(phosphorus donor) polyether ligand 2-(2,2‘-O2C12H8)PO(CH2CH2O)2-2-C20H12-2‘-OP(2,2‘-O2C12H8) with Mo(CO)4(nbd). Separate 1H NMR resonances were observed for six of the eight methylene protons of the metalla crown ether, indicating that the motion of the metalla crown ether ring was restricted. The 1H, 13C, and 31P NMR chemical shifts of the metalla crown ether were completely assigned using a combination of 13C DEPT, 1H−1H COSY, 13C{1H} HETCOR, 31P{1H} HETCOR, 1H{13C} HMBC, and 1H−1H NOESY NMR experiments. The solution conformation was analyzed using 1H−1H vicinal coupling constants and 1H−1H NOESY NMR experiments. The vicinal 1H−1H coupling constants for the ethylene protons indicated that both ethylenes were gauche. The 1H−1H NOESY NMR experiments showed a number of close contacts between aromatic protons. Good qualitative agreement was observed between the H−H distances obtained from molecular modeling studies and the intensities of the direct 1H−1H NOEs of the aromatic protons. The structure of the metalla crown ether from the molecular modeling studies also explained the unusual shieldings and deshieldings of certain aromatic protons in the molecule.

NMR analysis of the configuration and conformation ofN-acetylneuraminosyl-(2 ? 3)-lactose

1D and 2D 13C NMR spectra of N-acetylneuraminosyl-(2 3)-lactose were recorded and the sign and magnitude of the geminal couplings between C-2 and the H-3 protons of the N-acetylneuraminic acid residue were determined. The C-2,H-3ax coupling constant was −8.0 Hz, indicative of an α-configuration at C-2. The vicinal coupling between C-2 and H-3′ of the β-D-galactose unit was measured to be 5.2 Hz. This result gave a set of four solutions for the dihedral angle ψ at the 2 3 glycosidic linkage: ±16°; ±149°. NOE experiments established close contacts between the sialic acid and the galactose protons. Force field calculations determined up to eight conformational minima with comparable energy distributed over the whole range of ϕ angles but only within a band of ψ angles, −60° < ψ <60°. This indicated a highly flexible 2 3 glycosidic linkage. However, by considering only the two most favored conformations (ϕ, ψ = −161°, −21° and −67°,−4°), good agreement with the coupling constant and the NOE data was found. Copyright © 2000 John Wiley & Sons, Ltd.

Microstructure analysis of poly(styrene-co-vinylidene chloride) copolymers by NMR spectroscopy

Poly(styrene-co-vinylidene chloride) (S/V) copolymers were prepared by free-radical photopolymerization using uranyl nitrate as an initiator. The microstructure of the copolymer S/V was investigated by 1H- and 13C{1H}-NMR, 1H–13C-heteronuclear shift quantum correlation (HSQC) NMR, and homonuclear total correlated spectroscopy (TOCSY). The 1H-NMR spectra of the copolymers is complex due to overlapping resonance signals of the various triad configurations. Assignments were made up to the triad and tetrad levels for the methylene and methine regions using two-dimensional HSQC experiments. A 13C-distortionless enhancement by polarization transfer (DEPT) spectrum was used to differentiate between the carbon resonance signals of methine and the methylene units. The geminal couplings in the methylene protons and vicinal coupling between the methine and methylene protons were detected from the TOCSY spectra. Monte Carlo simulations were used to investigate the effect of the degree of polymerization on the triad fractions. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 79: 544–554, 2001

Effect of oxygen substituents on two- and three-bond carbon-proton spin-spin coupling constants

Carbon–proton coupling constants of 12 iridoid glucosides were determined from NMR data. Proton–proton vicinal couplings, quantitative NOE and molecular modelling were used to determine the conformational behaviour of the compounds. The aglycone moiety of all the compounds included in the study were shown to be conformationally rigid. Comparison of the experimental carbon–proton couplings with the calculated geometries resulted in the quantification of the dependence of 2,3J(13C,1H) on the orientation of oxygen substituent attached to coupling pathway (ψ). This can be extended to other electronegative substituents. The effect was studied by considering the product of Si, the substituent constant at a given position, and a cosine type function of ψ, the dihedral angle between the considered oxygen substituent and the atoms of the coupling pathway. In taking into account the influence of —OR substituents at β- and γ-carbons on vicinal coupling constants (13Cα—Cβ—Cγ—1H fragment), we found that the Sicosϕ cosψ term can be applied successfully, where ϕ is the dihedral angle between coupled atoms. Copyright © 2000 John Wiley & Sons, Ltd.

Configurational assignments of diastereomeric γ-lactones using vicinal H–H NMR coupling constants and molecular modelling †

The conformational features of four diastereomers of the γ-lactone 2-ethyl-4-methyl-5-oxotetrahydrofuran-3-carboxylic acid were investigated by calculations which included molecular mechanics (MM3), semiempirical (AM1) and ab initio molecular orbital theory (HF/6-31G), the latter including solvent emulation. Results were compared with those obtained by 1H NMR spectroscopy of natural and synthetic analogues in which a long aliphatic chain replaces the ethyl side chain. A notable agreement was found between the experimental vicinal ring coupling constants and those computed by the ab initio calculation; MM3 also gave rise to a fair agreement, while AM1 shows large failures to encounter the potential energy surface of these and other five-membered rings.

Conformational properties of diastereomeric 5'-O-DMT-2'deoxythymidine 3'-O-(S-methyl-methanephosphonothiolate)s and -(se-methyl-methanephosphonoselenolate)s in solution as studied by NMR methods

Stereochemical characterization of diastereomerically pure 5'-O-DMT-2'deoxythymidine 3'-O-(S-methyl-methanephosphonothiolate)s and -(Se-methyl-methane-phosphono-selenolate)s by NMR methods are reported. (1)H-(1)H, (1)H-(31)P, and (13)C-(31)P coupling constants and nuclear overhauser enhancement (NOE) connectivities from transverse cross-relaxation experiments in rotating frame (T-ROESY) were measured to correlate the conformational properties of the isomers with the absolute configurations at the phosphorus obtained from X-ray studies of the relatives of S(p) configured isomers. Conformational differences between the stereoisomers were found to be restricted to the different orientation of the C3'-O3'-P bond. The NMR data reflected the preferred epsilon(-) conformation for the S(p) isomers, while in the R(p) isomers the conformational equilibrium was shifted toward the epsilon(t) domain. These results also indicated that for 5'-protected mononucleotides the absolute configuration at the phosphorus atom can be inferred from the NOE experiments and the trends observed in vicinal carbon-phosphorus coupling constants. Copyright 2000 Wiley-Liss, Inc.