Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics

Molecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS‐AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009     

Conformational analysis of p-terphenyl in solution state by infrared band intensifies

Infrared absolute band intensities of the nonplanar vibrations were measured for p-terphenyl in CS₂ solution in order to determine the molecular structure in the solution state. The normal coordinate treatments were carried out for the seven representative conformations of p-terphenyl due to the torsions about the two CC bonds between phenyl rings. Considering the vibrational modes obtained, the nonplanar band intensities were calculated for both of the fundamentals and their combinations of the seven conformations. Comparison between the calculated and the observed intensities resulted in almost unequivocal assignments of the nonplanar bands and also led to some informative results for understanding the conformation in the solution state.     

Conformational analysis of a secondary hydroxamic acid in aqueous solution by NOE spectroscopy

Hydroxamic acids are metal‐binding compounds used by micro‐organisms and possess applications in medicine and industry. Hydroxamic acids favor two conformations, E and Z; metal binding is limited to the Z conformation. The Z conformation may be identifiable by NOE spectroscopy, but analysis is complicated by the potential for long‐range coupling as well as for relayed NOEs due to conformational switching. In this report, we re‐examine the reported conformational preference of N‐methyl acetohydroxamic acid (NMHA) in D₂O using NOE spectroscopy. We find that the favored conformation of NMHA in aqueous solution is the E conformation, contrary to an earlier report. NOE build‐up curves are proposed as a valuable tool to probe conformational behavior in similar systems. Copyright © 2013 John Wiley & Sons, Ltd.     

Lanthanide induced shifts of aromatic 1,2,3-trimethoxy compounds: Conformational analysis of tetrahydrofurofuran-lignans in solution

Summary The solution conformations of 1,4-diaryl-tetrahydro-1H,3H-furo[3,4-c]furans were determined by means of the LIS technique using a modified LIS-simulation program specially designed for the requirements of the aromatic 1,2,3-trimethoxy arrangement as a bidentate coordination site for the NMR shift reagent. The resulting geometries were confirmed by force field calculations (MM2-87) and compared with X-ray derived structures. Reliable data for the conformations in solution allowed a quantitative estimation of the circular dichroism based on the coupled oscillator model.

---

Lanthanideninduzierte Verschiebungen von aromatischen 1,2,3-Trimethoxy-Verbindungen: Konformationsanalyse von Tetrahydrofurofuran-Lignanen in Lösung

Zusammenfassung Es wurden mittels der LIS-Technik die Konformationen von 1,4-Diaryl-tetrahydro-1H,3H-furo[3,4-c]furanen in Lösung bestimmt. Dazu mußte ein modifiziertes LIS-Simulationsprogramm entworfen werden, das auf die besonderen Verhältnisse der aromatischen 1,2,3-Trimethoxy-Gruppierung eingeht, welche in den untersuchten Verbindungen als zweizähnige Koordinationsstelle für das NMR-Verschiebungsreagens fungiert. Die resultierenden Geometrien wurden mittels Kraftfeldrechnungen (MM2-87) überprüft und soweit vorhanden auch mit Röntgenstrukturdaten verglichen. Für die Lösungskonformationen wurde eine quantitative Abschätzung des Circulardichroismus auf der Basis des Modells für gekoppelte Oszillatoren durchgeführt.

     

Conformational preference of polyglycine in solution to elongated structure

Do polypeptide chains ever behave like a random coil? In this report we demonstrate that glycine, the residue with the fewest backbone restrictions, exhibits a strong preference for an extended conformation in solution when polymerized in short segments of polyglycine. A model peptide system comprised of two unique tripeptide units, between which 1 to 18 glycine residues are inserted, is characterized by NMR and by small-angle X-ray scattering (SAXS). The residual dipolar coupling (RDC) values of the two tripeptide units are insensitive to changes in number of intervening glycines, suggesting that extension of the linker does not alter the average angular relationship between the tripeptides. Polyglycine segments longer than nine residues form insoluble aggregates. SAXS measurements using synchrotron radiation provide direct evidence that polyglycine peptides adopt elongated conformations. In particular, the construct with a linker with six glycines showed a scattering profile indicative of a monomeric state with a radius of gyration and the maximum dimension of 9.1 A and approximately 34 A, respectively. The ensemble averaged global structure of this 12-mer peptide can best be approximated by a cylinder with a radius of 4 A and a length of approximately 33 A, making it intermediate in extension between a beta strand and an alpha helix.     

Conformational equilibria of ethanolamine and its hydrochloride in solution

The conformational preferences of ethanolamine and its hydrochloride in solution were estimated by comparing experimental NMR vicinal proton-proton coupling constants to semiemprical coupling constants for each staggered rotamer, derived by the Haasnoot-Altona method. Strong gauche preferences are observed for both ethanolamine and its hydrochloride over a wide range of solvent polarities. Concentration was not observed to significantly affect the position of the conformer equilibria.     

Conformational properties of glucosyl-thioglucosides and their S-oxides in solution

A stereochemical study of a series of alkyl glucosyl-β-(1→6)-thioglucosides and their S-oxides by means of nuclear magnetic resonance and circular dichroism revealed that the populations around the thioglucosidic bond (ring I) as well as those of the interglycosidic linkage ω depend on the aglycone, the solvent and, in the S-oxides, on the absolute configuration of the sulfur atom. The results for the thio-disaccharides showed the strong influence of the solvent polarity on the conformational preferences of the interglycosidic bond. In polar solvents, the magnitudes of the rotamer populations, P_gg and P_gt, remained practically constant through the series, while in non-polar solvents a clear predominance of gt conformation was observed as well as the influence of the aglycone on the conformational equilibrium. The results for both (S_S)- and (R_S)-alkyl thiogentiobiosyl S-oxide series showed a clear predominance of the gt rotamer, P_gt always having a higher magnitude in the latter series than in the former. Both series exhibited linear correlations between interglycosidic P_gg and P_gt and Taft’s steric parameter (E_S) for the alkyl group attached to the sulfinyl group, especially in non-polar solvents. The stereochemical study around the C1–S bond established that the flexibility around this linkage depends on aglycone size, solvent polarity, and the absolute configuration of the sulfur, derivatives of the S_S series showing higher flexibility in both polar and non-polar media. The conformational properties of these compounds in solution are explained in terms of stereoelectronic, steric, and solvent effects.     

Conformational analysis of some mannose-containing and milk oligosaccharides: Correlation of their shape with inhibitory properties in antigen/antibody interactions

Possible conformations of two mannotetraoses and several milk oligosaccharides have been studied by an energy minimization procedure using semi-empirical potential functions. Changes in the terminal residue at the reducing end (cyclic to acyclic form) of these molecules do not affect the favored conformations of the remaining oligosaccharide moiety. However, differences in the overall shape of the native and reduced forms of the mannotetraose, mannose α(1–3) mannose α(1–2) mannose α(1–2) mannose are much less marked than between the native and reduced forms of lacto-N-tetraose. These differences are related to the effectiveness of the native forms as inhibitors of antibodies produced using synthetic antigens. Changes in the linkage of the residues at the nonreducing end of these molecules affect significantly the overall shape of these molecules. These differences also are related to their effectiveness as inhibitors. In the fucose-containing milk oligosaccharides the additional fucose residues only restrict the orientation of the backbone tetrasaccharide and do not push it into a totally new conformation. The fucose residues come on a surface of the molecule which is away from the region which may be important for binding. The present studies show that it is the overall shape of the molecule which is important in determining its inhibitory properties and give information as to how best to use the immune method for identification of unknown oligosaccharide sequences by specially prepared antibodies.     

Conformational analysis of tetraarylethanes

NMR evidence establishes that both diastereomers of 1,2-diphenyl-1,2-bis(4-pyridyl)ethane (2), identified by optical resolution of the racemic form, exist predominantly in the anti conformation. Furthermore, empirical force field calculations show that the gauche conformer of 1,1,2,2-tetrakis(2,6-dimethylphenyl)ethane (3) is less stable by ca. 10 $\text{kcal}\text{mol}$ than the anti structure. It thus appears that neither polar effects nor steric congestion are effective in reversing the marked preference of 1,1,2,2-tetraphenylethane (1) and other unclamped tetraarylethanes for an anti ground state. In contrast, as predicted by empirical force field calculations and confirmed by X-ray and NMR evidence, the ground state structure of 9,9'-bifluorenyl (4) is gauche. The conformational behavior of 1–4 is discussed in terms of the intramolecular aryl ring stacking in clamped and unclamped tetraarylethanes.     

Conformational analysis of cinnamanilides

The conformational analysis of cinnamanilides has been carried out using IR spectroscopy. All the anilides studied were found to exist as equilibrium mixtures ofs-cis ands-trans forms in benzene. Thes-cis form was predominant over thes-trans in all the anilides except in thep-nitro anilide in which thes-trans form was predominant. The relative stabilities of the conformers were found to depend upon the electrostatic repulsions between the anilide nitrogen and the β-carbon atom in thes-trans form and those between the π-electrons of the C=O and C=C bonds in thes-cis form.     

Conformational analysis of dimethylmethylphosphonate

The results of a CNDO/2 conformation analysis on dimethylmethylphosphonate are reported. Six stable conformers were found; their relative stabilities can be understood in terms of steric hindrance and gauche effect. Calculated barriers to internal rotation around P—O and O—C bonds are tabulated.     

Conformational behaviour ofZ-Pro-(thr)Ox-OMe in solution

The dipeptideZ-Pro-(thr)Ox-OMe was studied with respect to its conformation in solution using NMR spectroscopic methods. It is shown that two conformers exist at room temperature which are related to each other by acis-trans—isomerization of theZ-Pro—peptide bond. The free energy of activation of the process is estimated.Dedicated to Prof. Dr.A. Neckel on the occasion of his 60th birthday.     

Conformational flexibility of the group B meningococcal polysaccharide in solution

To elucidate the role of secondary structure in the immune response against alpha(2-->8)-linked polysialic acid, the capsular polysaccharide of Group B meningococci, we have investigated its solution dynamics by using specific models of molecular motion and hydrodynamic modeling to interpret experimental NMR data. (13)C-[(1)H] NMR relaxation times and steady-state NOE enhancements were measured for two aqueous solutions of alpha(2-->8)-linked sialic acid polysaccharides. Each contained a unique distribution of polysaccharide chain lengths, with average lengths estimated at 40 or 400 residues. Models for rigid molecule tumbling, including two based on helical conformations proposed for the polysaccharide,(31) could not explain the NMR measurements. In general for these helices, the correlation times for their overall tumbling that best account for the NMR data correspond to polysaccharide chains between 9 and 18 residues in length, far short of the average lengths estimated for either solution. The effects of internal motions incorporated into these helices was modeled with an effective correlation time representing helix tumbling as well as internal motion. This modeling demonstrated that even with extreme amounts of internal motion, "flexible helices" of 25 residues or more still could not produce the NMR measurements. All data are consistent with internal and segmental motions dominating the nuclear magnetic relaxation of the polysaccharide and not molecular tumbling. Statistical distributions of correlation times have been found specifically for the pyranose rings, linkage groups, and methoxy groups that can account for the measured relaxation times and NOE enhancements. The distributions suggest that considerable flexibility attends the polysaccharide in solution, and the ranges of motional frequencies for the linkage groups and pyranose rings are comparable. We conclude that the Group B meningococcal polysaccharide is a random coil chain in solution, and therefore, does not have antigenic epitopes dependent upon a rigid, ordered conformation.     

Conformational analysis of L-prolines in water

The results of the ring conformational analysis of L-proline, N-acetyl-L-proline, and trans-4-hydroxy-L-proline by NMR combined with calculations using density functional theory (DFT) and molecular dynamics (MD) are reported. Accurate values of 1H-1H J-couplings in water and other solvents have been determined. Using a two-site equilibrium model, the Cgamma-endo conformer of L-proline in water has been identified as intermediate between gammaTdelta [twist(Cgamma-endo, Cdelta-exo)] and gammaE [envelope(Cgamma-endo)] and the Cgamma-exo conformer as betaTgamma. Both conformers were equally populated at room temperature. The N-acetyl [cis-rotamer gammaTbeta(80%)/gammaE(20%) and trans-rotamer gammaTbeta(61%)/gammaE(39%)] and 4-hydroxy (gammaEpsilon) derivatives showed significant changes in both the population and the geometries of the preferred ring conformers. The combination of NMR predicted populations with the DFT B3LYP/6-311+G(2d,p)/IEFPCM calculations proved successful, resulting in fairly accurate predictions of J-couplings. Simulations using MD were mostly in favor of the two-site equilibrium model between Cgamma-endo and Cgamma-exo conformers, similar to that used for the analysis of NMR J-couplings. Various force fields examined for MD simulations failed to reproduce the ring conformational geometries and populations of L-proline in water accurately, while significantly better agreement with NMR was found for trans-N-acetyl-L-proline using GROMOS and AMBER force fields.     

Conformational transition and aggregation of ϰ-carrageenan macromolecules in solution

Summary Consideration has been given to the processes of conformational transition and aggregation in the aqueous solutions of -carrageenan depending on its concentration, the temperature of the system as a whole and the content of the potassium ions by the methods of polarimetry and spectroturbidimetry. It has been established that one and the same degree of mutarotation can be attained on variation of the concentration of both -carrageenan and potassium ions. The aggregation of the -carrageenan macromolecules occurs under the action of the potasssium ions and is independent of temperature.With 8 figures and 1 table     

Conformational analysis. Part 20—conformational analysis of 4-deoxy-4-fluoro-D-glucose and 6-deoxy-6-fluoro-D-galactose in solution

The ¹H and ¹⁹F NMR spectra of the α- and β-pyranose anomers of 4-deoxy-4-fluoro-D -glucose (4FG) and 6-deoxy-6-fluoro-D -galactose (6FGA) in methanol-d₄, DMSO-d₆, acetone-d₆ and D₂O solution are reported. Computer analysis of the ABMX spectra of the CH CH₂F fragments gives accurate vicinal HH and HF coupling constants. An iterative computational analysis of the observed vicinal couplings in this fragment for 6FG, 6FGA and other molecules allows the determination of both the individual rotamer couplings and the rotamer populations. Consideration of the derived rotamer couplings strongly suggests that the correct assignment for the prochiral C-6 methylene protons in 6FG is that with the 6S proton having the larger coupling to H-5. This is the reverse of the assignment of these protons in D -glucose. In contrast, the assignment of these protons in 6FGA follows that given previously for D -galactose. The relative energies for the conformations about the C-5 C-6 bond for 4FG, 6FG and 6FGA are given from the derived rotamer populations. For 6FGA the rotamer in which the fluorine is antiperiplanar to C-4 is particularly favoured. For 4FG the rotamer with OH anti-periplanar to the ring O is highly unfavoured, but the other two rotamers are of almost equal energy. Consideration of the effect of replacing hydroxyl by fluorine in these molecules indicates that any hydrogen bonding involving the C-4 or C-6 hydroxyls plays little part in determining the conformer energies of glucose or galactose in polar solutions.     

Conformational analysis of kainate in aqueous solution in relation to its binding to AMPA and kainic acid receptors

Conformational analyses for kainate in aqueous solution have been performed by using the MM3*, AMBER* and MMFF94 force fields in conjunction with the Generalized Born Solvent Accessible Surface (GB/SA) hydration model. A comparison of calculated results with experimentally determined conformational data indicates that MM3*-GB/SA strongly overestimates the stability of a hydrogen bonded ion-pair in aqueous solution in comparison with the separated and solvated ions. This results in an incorrect prediction by MM3* of the most stable conformer of kainate in aqueous solution, whereas AMBER* and MMFF94 correctly predict the lowest energy conformer. Calculated conformational energy penalties for binding of kainate to the AMPA iGluR2 receptor indicate that the lower affinity of kainate for AMPA receptors compared to its affinity for kainic acid (KA) receptors is not due to a higher energy bioactive conformation of kainate at AMPA receptors. This conclusion is strongly supported by an analysis of a recently reported nonselective AMPA/KA ligand and a comparison of the conformational and structural properties of this ligand with iGluR2-bound kainate. This comparison strongly suggests that kainate binds to AMPA and KA receptors in closely the same conformation.