Analysis of conformational equilibria in aplidine using selective excitation 2D NMR spectroscopy and molecular mechanics/dynamics calculations

Aplidine (dehydrodidemnin B), a natural product with potent antitumor activity currently in multicenter phase II clinical trials, exists in DMSO as a mixture of four slowly interconverting conformations in a ratio of 47:33:13:7. NMR spectroscopy shows that these arise as a consequence of cis/trans isomerization about the NMe-Leu(7)-Pro(8) and Pro(8)-Pyr amide bonds of the molecule's side chain. Two major conformations account for 47% and 33% of the total population, a ratio of 60:40 between the two. They correspond to the cis- and trans-isomers, respectively, about the Pro(8)-Pyr amide bond. Two minor conformers arise as a consequence of similar isomerism about the Pro(8)-Pyr amide bond, but in structures in which the NMe-Leu(7)-Pro(8) amide bond is cis rather than trans. These account for approximately 13% and 7% of the total population, corresponding to a ratio of 65:35 cis/trans, respectively. Molecular dynamics simulations show that the three-dimensional structures of all four conformational isomers are similar in the macrocycle and that all are essentially unchanged with respect to the macrocycle of didemnin B. Significant differences in the conformation of the molecule's side chain are, however, observed between major and minor pairs. Analysis of hydrogen-bonding patterns shows that each major conformer exhibits a beta-turn like structure and is stabilized by hydrogen bonding between a different carbonyl group of the pyruvyl unit of the molecule's side chain and the NH of the Thr(6) residue. The minor isomers have a cis-amide bond between the NMe-Leu(7) and Pro(8) residues that obliges the side chain to adopt an extended disposition where hydrogen bonding to the macrocycle is absent. These results suggest that the ability of the molecule's side chain to adopt a beta-turn-like conformation may not be a prerequisite for biological activity in the didemnins and that conformations having an extended side-chain may play a role in the biological activity of aplidine.     

Conformational analysis of thia crown ether derivatives by NMR spectroscopy and molecular mechanics calculations

Summary Addition of sulfur dichloride to tetrachlorocatechol-bisallylether (1) yields the 9- and 10-ring thia crown ether derivatives2 and3, respectively, together with the dithia-18-crown-6-ether4. The 10-membered ring compound3 represents the first thia macrocycle containing bothMarkovnikov andanti-Markovnikov constitution of the -chloro-thio structural segments in the same molecule. By¹H and¹³C NMR spectroscopy, equal amounts of two preferred conformers of the only isolated diastereomer of3 were observed at temperatures below –50°C. The signals were assigned to these conformers using COSY, HETCOR, and phase sensitive NOESY spectra at low temperatures. The preferred conformations and the relative configuration were determined using the different effects of _gauche -and _anti -positions in¹³C NMR chemical shifts and analyzing vicinal³ J _H,H coupling constants. These results were confirmed by molecular mechanics calculations.Dedicated to Prof. Dr.Rolf Borsdorf on the occasion of his 65^th birthday     

Conformational analysis of oxazolidines by molecular and quantum mechanics and NMR spectroscopy

A combined experimental (¹HNMR) and theoretical (molecular mechanics and PCILO) study of (4S,5S,6R)-4-carbome-thoxyethylenyl-N-carbobenzyloxy-5-methyl-6-phenyl oxazolidine has been carried out with the purpose of contributing to a better understanding of the steric and electronic factors responsible for the observed diastereoisomeric selectivity in the dihydroxylation of oxazolidines leading to optically active α, β dialkoxyaldehydes.     

Conformational analysis of a tetrasaccharide based on NMR spectroscopy and molecular dynamics simulations

The conformational preference of the human milk oligosaccharide lacto-N-neotetraose, beta-d-Galp-(1 --> 4)-beta-d-GlcpNAc-(1 --> 3)-beta-d-Galp-(1 --> 4)-d-Glcp, has been analyzed using (1)H,(1)H T-ROESY and (1)H,(13)C trans-glycosidic J coupling experiments in isotropic solution and (1)H,(13)C residual dipolar couplings (RDCs) obtained in lyotropic liquid crystalline media. Molecular dynamics simulations of the tetrasaccharide with explicit water as the solvent revealed that two conformational states are significantly populated at the psi glycosidic torsion angle, defined by C(anomeric)-O-C-H, of the (1 --> 3)-linkage. Calculation of order parameters, related to the molecular shape, were based on the inertia tensor and fitting of experimental RDCs to different conformational states showed that psi(+) > 0 degrees is the major and psi(-) < 0 degrees is the minor conformation in solution, in complete agreement with a two-state analysis based on the T-ROESY data. Attention was also given to the effect of salt (200 mM NaCl) in the anisotropic medium, which was a ternary mixture of n-octyl-penta(ethylene glycol), n-octanol, and D(2)O.     

Conformational analysis of ochratoxin a by NMR spectroscopy and computational molecular modeling

Two-dimensional NMR spectroscopy has been used for a complete assignment of the proton and carbon-13 spectra of the metabolite from Aspergillus ochraceus, ochratoxin A. In addition, phase-sensitive nuclear Overhauser effect spectrometry experiments and computational molecular modeling (MM2 and MMFF force field programs) have been employed to examine the conformational properties of ochratoxin A in chloroform solutions. Particular attention has been given to intramolecular hydrogen-bonding formation involving the phenolic group on dihydroisocoumarin, which may be responsible for the toxic mechanism of ochratoxin A.     

Conformational analysis—CXVII : Methyl ethyl disulfide. Molecular mechanics and molecular orbital calculations

The conformation of methyl ethyl disulfide was investigated by molecular mechanics calculations using a recently developed force field for sulfur-containing alkanes. The results indicate that in the gas phase the molecule exists predominantly in two conformations, both with the CSSC dihedral angle gauche (84°), and the SSCC dihedral angle either gauche (72°) or trans (179°), and the methyl protons staggered. Ab initio molecular orbital calculations using an STO-3G basis set were employed to corroborate that these two conformations are of roughly equal stability, and that the next most stable conformation (by 0.6 kcal/mole) has the SSCC dihedral angle gauche (295°) with the terminal methyls proximal. In contrast to earlier CNDO/2 (spd) predictions, the SSCC cis conformer is the least stable, and no sizable attractive S?HC nonbonded interactions are discerned. Reasons for this are traced to a failure of the CNDO/2 method, which is especially serious when d orbitals are included in the basis set (spd) and the rigid rotor approximation is used. The present results are found to be consistent with recent electron diffraction, IR, Raman spectroscopic and X-ray diffraction data. The conformation of diethyl disulfide was also investigated by molecular mechanics calculations, and again gauche and trans SSCC arrangements are predicted to be preferred.     

Conformational analysis of colchicine and isocolchicine by molecular mechanics

The structures of isocolchicine ( ) and colchicine ( ) have been calculated using the MMX routine. The low energy conformations for isocolchicine and colchicine fit well with x-ray crystallographic data. The B ring atropisomer of isocolchicine, which can be spectroscopically observed, is calculated to be <1 kcal/mole higher in energy than . The boat-boat inversion conformer of colchicine, which has been predicted to be important in the binding of to tubulin, is also calculated. The B ring geometry of this isomer does not differ to the extent previously predicted.     

Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy

The structural transition between two alternate conformations of bistable RNAs has been characterized by time-resolved NMR spectroscopy. The mechanism, kinetics, and thermodynamics underlying the global structural transition of bistable RNAs were delineated. Both bistable RNA conformations and a partial unstructured RNA of identical sequence could be trapped using photolabile protecting groups. This trapping allowed for an investigation of the initial folding from an unfolded RNA to one of the preferred conformations of the bistable RNA and of the structural transitions involved. Folding of the secondary structure elements occurs rapidly, while the global structural transition of the bistable RNA occurs on a time scale of minutes and shows marked temperature dependence. Comparison of these results with bistable systems previously investigated leads to the prediction of activation enthalpies (DeltaH++) associated with global structural transitions in RNA.     

Conformational analysis of phorboxazole bis-oxazole oxane fragment analogs by NMR spectroscopy and molecular modeling simulations

We present a detailed conformational study of a simplified synthetic analog of the bis-oxazole oxane fragment found in the cytostatic agents phorboxazole A and B based on results from NMR spectroscopy and molecular modeling simulations. Complete 1H and 13C resonance assignments for the bis-oxazole oxane system were carried out through the use of COSY, HSQC, HMBC, TOCSY, and HSQC-TOCSY experiments, and its conformational preferences in solution were investigated by analysis of 3J(HH) coupling constants and NOE enhancements obtained from 1D and 2D NOESY experiments. In order to solve inconsistencies from our preliminary structural studies, simulated annealing studies were performed to thoroughly sample the phase space available to the molecule. Our results reveal that the six-membered oxane ring, which constitutes the most important moiety regarding the three-dimensional (3D) structure and flexibility of the analog, exists in rapid equilibrium between its two accessible chair conformers in an approximate ratio of 70:30. The information gathered from these studies will be of critical importance in our efforts to prepare novel compounds with phorboxazole-like structure and activity.     

Conformational analysis of gossypol and its derivatives by molecular mechanics

Conformations and inversion pathways leading to racemization of all the tautomers of gossypol, gossypolone, anhydrogossypol, and a diethylamine Schiff's base of gossypol were investigated with MM3(2000). All forms have hindered rotation because of clashes between the methyl carbon atom and oxygen-containing moieties ortho to the bond linking the two naphthalene rings. Inversion energies generally agree with available experimental data. Gossypol preferentially inverts in its dihemiacetal tautomeric form through the cis pathway (where similar groups clash). Gossypolone inverts more easily than gossypol, and preferentially through the trans pathway (where dissimilar groups clash) when one of its outer rings has an enol-keto group and the other has an aldehyde group. Anhydrogossypol racemizes through the cis pathway. The bridge bond and the ortho exo-cyclic bonds in all the structures bend from planarity, and the inner naphthalene rings pucker to accommodate the inversion. For gossypol, the transition is achieved through greater bending of the exo-cyclic bonds (up to 12°) and less distortion of the inner benzyl rings (q≤0.34 Å), (up to 12.7°) . For gossypolone the transition occurs with greater distortion of the inner benzyl rings (q≤0.63 Å) and less out-of-plane bending (up to 8.4°). By isolating individual clashes, their contribution to the overall barrier can be analyzed, as shown for the dialdehyde tautomer of gossypol.     

Conformational flexibility of the pentasaccharide LNF-2 deduced from NMR spectroscopy and molecular dynamics simulations

Human milk oligosaccharides (HMOs) are important as prebiotics since they stimulate the growth of beneficial bacteria in the intestine and act as receptor analogues that can inhibit the binding of pathogens. The conformation and dynamics of the HMO Lacto-N-fucopentaose 2 (LNF-2), α-L-Fucp-(1 → 4)[β-D-Galp-(1 → 3)]-β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-D-Glcp, having a Lewis A epitope, has been investigated employing NMR spectroscopy and molecular dynamics (MD) computer simulations. 1D (1)H,(1)H-NOESY experiments were used to obtain proton-proton cross-relaxation rates from which effective distances were deduced and 2D J-HMBC and 1D long-range experiments were utilized to measure trans-glycosidic (3)J(CH) coupling constants. The MD simulations using the PARM22/SU01 force field for carbohydrates were carried out for 600 ns with explicit water as solvent which resulted in excellent sampling for flexible glycosidic torsion angles. In addition, in vacuo MD simulations were performed using an MM3-2000 force field, but the agreement was less satisfactory based on an analysis of heteronuclear trans-glycosidic coupling constants. LNF-2 has a conformationally well-defined region consisting of the terminal branched part of the pentasaccharide, i.e., the Lewis A epitope, and a flexible β-D-GlcpNAc-(1 → 3)-β-D-Galp-linkage towards the lactose unit, which is situated at the reducing end. For this β-(1 → 3)-linkage a negative ψ torsion angle is favored, when experimental NMR data is combined with the MD simulation in the analysis. In addition, flexibility on a similar time scale, i.e., on the order of the global overall molecular reorientation, may also be present for the ? torsion angle of the β-D-Galp-(1 → 4)-D-Glcp-linkage as suggested by the simulation. It was further observed from a temperature variation study that some (1)H NMR chemical shifts of LNF-2 were highly sensitive and this study indicates that Δδ/ΔT may be an additional tool for revealing conformational dynamics of oligosaccharides.     

A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy.     

Conformational analysis by HRMAS NMR spectroscopy of resin-bound homo-peptides from C(alpha)-methyl-leucine

A series of [L-(alphaMe)Leu]n (n = 1-5) homo-peptides have been covalently linked to Tentagel and POEPOP resins and submitted to a conformational study using HRMAS NMR spectroscopy. Whereas the mono- and dipeptide are mainly fully-extended, stable 3(10)-helical structures are formed beginning from the trimer.     

Conformational studies of N-carbomethoxy-2-alkoxyindolenines by dynamic NMR, crystallography, and molecular mechanics

The synthesis of N-carbomethoxy-2-alkoxyindolenines and the transformation to their tautomeric indoles is reported. Variable-temperature ¹H NMR studies of these 2-alkoxyindolenines evidenced dynamic processes involving two low-energy E and Z equilibrating conformers around the N-C(O) carbamate bond, for which the barriers (ΔG^≠) between the two conformations are in the order of 12.5-13.9 kcal/mol, as deduced from computational NMR line shape simulations. The rotational barrier decreases as the bulkiness of the alkoxyl group increases, with the E conformer being always more stable. Molecular mechanics calculations evidenced a preferred quasi-axial position of the alkoxyl group in the five-membered ring as the steric effect increases, in agreement with X-ray diffraction studies.     

Conformational analysis: crystallographic,NMR, and molecular mechanics studies of flexible sulfonic esters

Two novel X-ray structures of the sulfonic ester derivatives 2-(6-iodo-1,3-benzodioxol-5-yl)ethyl 4-nitrobenzenesulfonate, 3, and 2-(6-iodo-1,3-benzodioxol-5-yl)ethyl 4-methylbenzenesulfonate, 4, have been obtained in a study aimed at analyzing the structures and conformations of sulfonic ester derivatives that are routinely used in alkaloid syntheses. The crystal structure of 4 is highly unusual, containing four independent molecules that belong to two distinct conformational types: (1) a hairpin conformation (stabilized mainly by intramolecular pi-stacking) and (2) a stepped conformation (stabilized mainly by intermolecular pi-stacking). Compound 3, on the other hand, crystallizes exclusively as the hairpin conformer. New MM+ force field parameters for sulfonic esters have been developed using the X-ray data, empirical rules, and DFT calculations to estimate the bond dipole parameters. Grid searches of conformational space for 3 and 4 using MM methods show that there are several gas-phase conformations within 5 kcal/mol of the global minimum and that the lowest energy conformations (by approximately 4.6 kcal/mol) are of the hairpin type. Analysis of the MM conformational energies suggests that the dominant intramolecular interaction stabilizing the hairpin conformations of 3 and 4 is van der Waals attraction. Moreover, the lattice energies for packing the hairpin conformations of 3 and 4 are approximately 4 kcal/mol more favorable than for the stepped conformations. Various intermolecular interactions contribute to the complexity of the observed crystal structures of 3 and 4, including electrostatic attraction between O and I atoms in neighboring molecules. Langevin dynamics (LD) simulations at several temperatures (6.0 ns, friction coefficient = 2.5 ps(-1)) indicate that the conformational exchange rates are approximately 10(10)-10(11) s(-1) over the temperature range 213-400 K, accounting for the temperature-independent (1)H NMR spectra of 3 and 4.     

Conformational preference of [4.4.2]-propella-3,8-dienes derived from single-crystal x-ray analysis and molecular mechanics calculations.

The crystal structure of [4.4.2]-propella-3,8-diene-11-one ($\text{6}$) and ?11,12-dione ($\text{7}$) coupled with molecular mechanics calculations strongly suggest that [4.4.2]-propella-3,8-diene ($\text{5}$) exists predominantly in the $\text{E}$,$\text{E}$-conformation.     

Conformational analysis of 2-halocyclopentanones by NMR and IR spectroscopies and theoretical calculations

The conformational isomerism of 2-chlorocyclopentanone and 2-bromocyclopentanone has been determined through the solvent dependence of the ¹H NMR ³J_HH coupling constants, theoretical calculations and infrared data, using the solvation theory for the treatment of NMR data. In 2-chlorocyclopentanone, the energy difference (E_Ψ-e − E_Ψ-a), in the isolated molecule at B3LYP level of theory, between the pseudo-equatorial (Ψ-e) and pseudo-axial (Ψ-a) conformers is 0.42 kcal mol⁻¹, which decreases in CCl₄ and in acetonitrile solutions, in good agreement with infrared data (ν_CO), despite the uncertainties of the latter method. The conformational equilibrium for 2-bromocyclopentanone is also between the Ψ-e and Ψ-a conformations, with an energy difference (E_Ψ-e − E_Ψ-a), in the isolated molecule at B3LYP level of theory, is 0.85 kcal mol⁻¹ which decreases in CCl₄ and in acetonitrile solutions, also in good agreement with infrared data.     

6,6-dimethyl-1-oxa-spiro[2.5]octane. Conformational equilibrium in the gas phase as studied by microwave spectroscopy and molecular mechanics calculations

The gas-phase molecular structure of 6,6-dimethyl-1-oxa-spiro[2.5]octane has been investigated by joint analysis of the microwave spectrum and molecular mechanics calculations. Both experimental and theoretical data concur showing the presence of two stable conformational isomers having a chair cyclohexane ring. A set of structural parameters which reproduce the ground state rotational constants has been derived. The influence of 1,4 disubstitution is discussed in terms of deformations of the cyclohexane ring.     

Conformational analysis of (+)-germacrene A by variable-temperature NMR and NOE spectroscopy

(+)-Germacrene A, an important intermediate in sesquiterpene biosynthesis, was isolated in pure form from a genetically engineered yeast and was characterized by chromatographic properties (TLC, GC), MS, optical rotation, UV, IR, ¹H NMR, and ¹³C NMR data. Variable-temperature 500 MHz ¹H NMR spectra in CDCl₃ showed that this flexible cyclodecadiene ring exists as three NMR-distinguishable conformational isomers in a ratio of about 5:3:2 at or below ordinary probe temperature (25 °C). The conformer structures were assigned by ¹H NMR data comparisons, NOE experiments, and vicinal couplings as follows: 1a (52%, UU), 1b (29% UD), and 1c (19%, DU).