A force-field study of the conformational characteristics of the iduronate ring

Methods of molecular mechanics were applied to investigate the conformation of the (methyl 2-O-sulfate-4-methyl-α-L-idopyranose) uronic acid (DMIS), in order to correlate the peculiar vicinal proton coupling constants observed in polysaccharides containing the iduronate ring to the conformational characteristics of this sugar ring. We found three conformers with comparable energies, namely the two chair forms ¹C₄ and ⁴C₁ and the skew-boat form ²S₀(L); the latter is separated from each chair form by a barrier of about 9 kcal/mol. Along the pseudorotational path three additional minima (³S₁, ¹S₃, and ¹S₅) were found, yet at least 4 kcal/mol higher than ²S₀. The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS. However, the conformational properties of the idopyranosidic ring in DMIS (and in related compounds) should still be interpreted in terms of equilibrium among these three conformers only.     

Probing furanose ring conformation by gas-phase computational methods: energy profile and structural parameters in methyl beta-D-arabinofuranoside as a function of ring conformation

The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.     

Vibrational spectra and stereoisomerism of the hexopyranose ring in epoxysaccharides

Journal of Structural Chemistry - Investigation of the potential surface of methyl 2,3-anhydro-2,3,4-trideoxy-β-D-lyxohexopyranoside has shown that the molecule has seven conformers with...     

Intramolecular radical cyclization-ring-closing metathesis approach to fused polycyclic ethers. Convergent synthesis and conformational analysis of the (E)FGH ring system of ciguatoxin

A convergent synthetic route to the (E)FGH ring system 4 of ciguatoxins, the causative toxins for ciguatera fish poisoning, has been developed. The synthesis features convergent coupling to form dioxane acetal, regioselective acetal cleavage by diethylaluminum phenylthiolate or diisobutylaluminum phenylselenolate followed by intramolecular radical cyclization to construct the oxepane ring G, and a ring-closing metathesis reaction to form the hexahydrooxonine ring F. The hexahydrooxonine ring F of tetracyclic model system 4 existed as a 5:1 equilibrium mixture of two conformers (UP and DOWN conformers), with the UP one predominating. This is the first illustration that reproduces the preference for the UP conformer over the DOWN one, which preference was observed for natural ciguatoxins.     

Synthesis and characterisation of medium-sized ring systems by oxidative cleavage. Part 2: Insights from the study of ring expanded analogues

Variable temperature NMR analysis and computational methods have been used to develop a detailed understanding of the ¹H NMR spectra of a family of medium-sized ring containing compounds. The family consists of analogues containing 10-, 11- and 12-membered rings and in all cases the NMR spectra at room temperature showed a series of diastereotopic methylene signals despite the lack of a stereogenic centre in these systems. On repeating the NMR analysis at higher temperatures, all the signals coalesced for the 12-membered ring system consistent with full interconversion of ring conformers. This was not observed in the analogous 10- and 11-membered ring systems with the interchange of conformers remaining slow on the NMR timescale. However, 1D gs-NOESY/EXSY NMR experiments showed that in the smaller ring systems interconversion of diastereotopic protons did occur. Computational studies suggest that the dynamic process observed by NMR for the 10- and 11-membered rings systems is different from that observed in the 12-membered ring containing compound.     

Conformational effects in acid-mediated ring opening of epoxides: a prominent role of the oxirane Walsh orbital

A kinetic study has been made of the BF(3)-mediated ring opening of two rigid conformers (alpha and beta) of m- and p-dimethyl-substituted homobenzoquinone epoxides spiro-linked with a twist-boat dibenzocycloheptene ring as compared with the conformationally mobile epoxides bearing diphenyl groups. The rates of the regioselective ring opening were dependent on the topological alignment of the dibenzocycloheptene ring as well as the substitution pattern of the quinone dimethyl groups, indicating pi-aryl participated orbital interaction with the vacant Walsh orbital of the oxirane ring.     

Density functional calculations of vibrational wavenumbers, ring puckering, and asymmetric CHO potential functions for cyclobutanecarboxaldehyde: comparative study between theoretical and experimental spectra

The structural parameters and energies of the trans-equatorial and gauche-equatorial conformers of cyclobutanecarboxaldehyde c-C₄H₇–CHO were investigated by quantum mechanical DFT-B3LYP (Density Functional Theory-Becke 3 exchange and Lee-Yang–Parr correlation functional) calculations using 6-311G^** basis set. The potential functions for the CHO asymmetric torsion in the equatorial molecule and for the ring puckering inversion were derived. The vibrational wavenumbers were calculated and the potential energy distributions PED among the symmetry coordinates of the normal modes were computed for the two stable conformers of the molecule. The vibrational assignments on the basis of the calculated PED values were compared to the reported ones from experimental data. The vibrational infrared and Raman spectra of the mixture of the trans-equatorial and gauche-equatorial were plotted and the line intensities were compared to the corresponding experimental ones.     

Exploring the universality of unusual conformations of the 17-membered Pt(d(G*pG*)) macrochelate ring. Dependence of conformer formation on a change in bidentate carrier ligand from an sp3 to an sp2 nitrogen donor

Early studies on cis-PtA2(d(G*pG*)) (A2 = diamine or two amines, G = N7-platinated G) and cis-Pt(NH3)2(d(G*pG*)) models for the key cisplatin-DNA cross-link suggested that they exist exclusively or mainly as the HH1 conformer (HH1 = head-to-head G bases, with 1 denoting the normal direction of backbone propagation). These dynamic models are difficult to characterize. Employing carrier A2 ligands designed to slow dynamic interchange of conformers, we found two new conformers, DeltaHT (head-to-tail G* bases with a Delta chirality) and HH2 (with 2 denoting the backbone propagation direction opposite to normal). However, establishing that the non-HH1 conformations exist as an intrinsic feature of the 17-membered Pt(d(G*pG*)) ring requires exploring a range of different carrier ligands. Here we employ the planar aromatic sp(2) N-donor 5,5'-Me(2)bipy (5,5'-dimethyl-2,2'-bipyridine) ligand, having a shape very different from those of previously used nonplanar sp(3) N-donor bidentate carrier ligands, which often bear NH groups. The 5,5'-Me(2)bipy H6 and H6' protons project toward the d(G*pG*) moiety and hinder the dynamic motion of 5,5'-Me(2)bipyPt(d(G*pG*)). We again found HH1, HH2, and DeltaHT conformers with typical properties, supporting the conclusions that the new DeltaHT and HH2 conformers exist universally in dynamic cis-PtA2(d(G*pG*)) adducts, including cis-Pt(NH3)2(d(G*pG*)), and that the carrier ligand typically has little influence on the overall structure of the Pt(d(G*pG*)) macrocyclic ring of a given conformer. The sizes of the G H8 to H6/H6' NOE cross-peaks indicate little base canting in all 5,5'-Me(2)bipyPt(d(G*pG*)) conformers, suggesting that carrier-ligand NH groups favor the canting of one G base in the HH1 and HH2 conformers of typical cis-PtA2(d(G*pG*)) adducts.     

Spectra and structure of small ring compounds. LIX

The Raman (3200 to 10 cm^–1) and far infrared (380 to 60 cm^–1) spectra of gaseous fluorocyclobutane,c-C₄H₇F, have been recorded. A series of Q-branches observed in both of these spectra beginning at 166 cm^–1 with successive transitions falling to lower frequencies have been assigned to the ring puckering vibrations of both the low energy equatorial and high energy axial conformers. These data have been fit to an asymmetric potential function of the form:V (cm^–1)=(1.76±0.05)10³X+(4.88±0.28)10⁴X²+(2.12 ±0.16)10³ exp(–5.66±0.41)10X² with a reduced mass function ofg ₄₄= 0.00386–0.00295X+0.03485X²+0.1228X³ +0.3459X⁴, whereX is the ring puckering coordinate. Utilizing this potential, the difference between the puckering angles for the two conformers was calculated to be 4° with the equatorial conformer having the larger value of 28°. This potential function is consistent with an energy difference between the equatorial and axial forms of 447 cm^–1 (1.28 kcal/mol) and a barrier to ring inversion from the equatorial to the axial conformation of 713 cm^–1 (2.04 kcal/mol). Experimental values for the enthalpy difference between the two conformers have been determined for both the liquid (400±30 c^–1) and gas (413±43 cm^–1) from investigations of the Raman spectra at variable temperatures. The conformational stability, enthalpy difference, structural parameters, and fundamental vibrational frequencies, which have been determined experimentally, are compared to those obtained from ab initio Hartree-Fock calculations employing the 3-21G, 6-31 G^*, and 6-31 G^** basis sets.For part LVIII, seeStruct. Chem. 1991,2, 195.Taken in part from the thesis of M. J. Lee, which has been submitted to the Department of Chemistry in partial fulfillment of the Ph.D. degree, May 1991.     

A new procedure for exact ring closure

An algorithm is presented that very efficiently generates all feasible values for the six torsions constrained by the condition of ring closure. Furthermore, the algorithm is straightforward to implement, thus providing an alternative to the more common and less efficient conformational search technique of breaking the ring and rejecting trial conformers with an unacceptable length for the broken bond. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 870–881, 2000     

Different chemical dynamics for different conformers of biological molecules: photoionization of glycine

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.     

A novel radical induced rearrangement of the caryophyllene skeleton

The addition of an acetyl radical on caryophyllene leads to formation of the four isomeric ketones 5-8 involving a novel rearrangement of the caryophyllene skeleton.     

Conformational study of 2-phenylethylamine by molecular-beam Fourier transform microwave spectroscopy

The conformational preferences of the simplest amine neurotransmitter 2-phenylethylamine have been investigated using molecular beam Fourier transform microwave (MB-FTMW) spectroscopy. Two new conformers have been observed together with the two previously reported by Godfrey et al. [J. Am. Chem. Soc., 1995, 117, 8204]. The (14)N nuclear quadrupole hyperfine structure has been resolved for all four conformers. Comparison of the experimental rotational and quadrupole coupling constants with those calculated theoretically provides a conclusive test for the identification of all conformers. The two most stable conformers present a gauche (folded) disposition of the alkyl-amine chain and are stabilised by a weak NH...pi interaction between the amino group and the aromatic ring. The other two conformers show an anti (extended) arrangement of the alkyl-amine chain. Tunnelling splittings have been observed in the spectrum of one of the anti conformers. The post expansion relative abundances in the supersonic jet have been also investigated and related to the conformer energies.     

Chemical composition and phytotoxic effects of essential oils from four Teucrium species

The essential oils of four Teucrium species were studied and 131 components, in all, were identified. All oils were rich in sesquiterpenes (50.0-61.9%). Caryophyllene and caryophyllene oxide were the main components of Teucrium arduini; germacrene D, delta-cadinene and gamma-cadinene predominated in Teucrium maghrebinum. Carvacrol and caryophyllene predominated in Teucrium polium ssp. capitatum, while carvacrol, caryophyllene oxide and caryophyllene were the most abundant components in Teucrium montbretii ssp. heliotropiifolium. The germination of radish and garden cress was less sensitive to the four essential oils. The radicle elongation, above all, of radish was significantly inhibited by all oils, in particular by the essential oil of T. arduini, at the highest doses tested. Among the main components of the oils, monoterpenes resulted the more active compounds.     

Conformation and stereodynamics of 1,2-diaryltetrahydropyrimidine and of its five- and seven-membered ring analogs

The 1-(2-nitrophenyl)-2-(2-methylphenyl)-1,4,5,6-tetrahydropyrimidine and its five- and seven-membered ring analogs were synthesized and their conformational properties investigated by low temperature NMR spectroscopy and DFT theoretical calculations. Restricted rotation of the aryl substituents were observed in all cases and the corresponding barriers determined. In the case of the six-membered ring derivative the additional conformers resulting from a ring inversion process were also detected.     

Abinitio方法研究2，4－二甲基－1，3－戊二烯结构

用ａｂｉｎｉｔｉｏ方法研究２，４－二甲基－１，３－戊二烯各种构象异构体的结构，找到ｓ－ｔｒａｎｓ和ｓ－ｃｉｓ两种稳定构象，且ｓ－ｔｒａｎｓ更稳定．对稳定构象的几何结构、电荷分布进行了研究，讨论了不同的电子基组对优化几何的影响，并计算了稳定构象的热力学常数，与实验结果进行了比较．     

One‐Step Multigram‐Scale Biomimetic Synthesis of Psiguadial B

A gram‐scale synthesis of psiguadial B, a purported inhibitor of human hepatoma cell growth, has been achieved in one step by a biomimetic three‐component coupling of caryophyllene, benzaldehyde, and diformylphloroglucinol. This cascade reaction is catalyzed by N,N′‐dimethylethylenediamine, and proceeds at ambient temperature to generate four stereocenters, two rings, one C−O bond, and three C−C bonds. Combined computational and experimental investigations suggest the biosynthesis of the natural product is non‐enzyme mediated, and is the result of a Michael addition between caryophyllene and a reactive ortho‐quinone methide, followed by two sequential intramolecular cationic cyclization events.     

Two distinct conformers of the cyclic heptapeptide phakellistatin 2 isolated from the fijian marine sponge stylotellaaurantium

The isolation, structure determination, and solution conformation of two conformers of the cyclic heptapeptide phakellistatin 2 (cyclo-[Phe1-cis-Pro2-Ile3-Ile4-cis-Pro5-Tyr6-cis-Pro7]) isolated from the Fijian marine sponge Stylotella aurantium are reported. The conformers can be isolated separately by HPLC and are stable in methanol solution over a period of weeks as determined by NMR. Their NMR spectra and mass spectral fragmentation patterns differ significantly. Their solution conformations were determined by NOE-restrained molecular dynamics calculations and indicated that the two conformers had different folds, hydrogen bonding patterns, and solvent accessible surfaces. These factors may contribute to the independent stability of the two conformers, and may explain the variable biological activity previously reported for phakellistatin 2.     

Chirality recognition in the glycidol···propylene oxide complex: a rotational spectroscopic study

Chirality recognition in the hydrogen-bonded glycidol···propylene oxide complex has been studied by using rotational spectroscopy and ab initio calculations. An extensive conformational search has been performed for this binary adduct at the MP2/6-311++G(d,p) level of theory and a total of 28 homo- and heterochiral conformers were identified. The eight binary conformers, built of the two dominant glycidol monomeric conformers, g-G+ and g+G-, were predicted to be the most stable ones. Jet-cooled rotational spectra of six out of the eight conformers were observed and unambiguously assigned for the first time. The experimental stability ordering has been obtained and compared with the ab initio predictions. The relative stability of the two dominant glycidol monomeric conformers is reversed in some cases when binding to propylene oxide. The contributions of monomeric energy, deformation energy, and binary intermolecular interaction energy to the relative stability of the binary conformers are discussed.     

Photoelectron spectra of the gauche and trans conformers of 1,2-dibromoethane

The He I photoelectron spectra of the gauche and trans conformers of 1,2-dibromo-ethane have been obtained. Time-averaged spectra of 1,2-dibromoethane recorded at different temperatures have been analyzed by a spectrum-stripping procedure to give resulting spectra which represent each of the two stable conformers. The correlation of the ionization potentials of the two conformers is consistent with data obtained from MO calculations. In comparison with the case of 1,2-dichloroethane, 1,2-dibromoethane shows different non-bonded Br—Br interactions and generally larger resonance splittings of the ethane orbitals.