SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Cyclohexane conformation

166

A new antibacterial chlorinated benzophenone derivative, (±)-pestalachloride D (1), along with a related analog, (±)-pestalachloride C (2), was recently isolated from the marine-derived fungus Pestalotiopsis sp. isolated from a soft coral Sarcophyton sp. collected from Yongxing Island in the South China Sea. Both chiral HPLC analysis and single-crystal X-ray data indicated that 1 is a racemic mixture. Interestingly, 1 did not exhibit any effect in the zebrafish embryo teratogenicity assay, while 2 led to abnormal growth. The potential impact on zebrafish embryo growth is discussed based on their crystal structures. The main difference of crystal structures between 1 and 2 is that the six-member non-aromatic ring (O4, C10, C9, C8, C2', and C3') in 1 exhibits a distorted chair conformation, while 2 shows a distorted boat conformation. Moreover, compounds 1 and 2 both exhibited moderate antibacterial activity.

Concepts: Stereochemistry, Enantiomer, Solid, South China Sea, Racemic mixture, Cyclohexane conformation, East China Sea, Adderall

28

With a view to development of novel sialidase inhibitors, mimetics of the natural inhibitor Neu5Ac2en have been prepared in which a phosphonate group replaces the sialic acid glycerol side chain. Different hex-4-en derivatives adopt half-chair conformations that place the glycosyl phosphonate in an equatorial position. For the α-L-threo-hex-4-en derivative this conformation is equivalent to that of Neu5Ac2en, and opposite to that seen for alkyl O-glycosides with the same overall stereochemistry.

Concepts: Tertiary structure, Stereochemistry, Calculus, Vector space, Derivative, Conformation, Conformational isomerism, Cyclohexane conformation

28

Novel enantiopure pseudopeptide models containing a central -(beta-lactam)-(Aa)- scaffold characterized by the combined presence of an alpha-alkyl-alpha-amino-beta-lactam (i+1) residue and a alpha-substituted (i+2) amino acid have been readily synthesized from alpha-alkyl serines. The conformational analysis of such beta-lactam pseudopeptides conducted in CDCl3 and DMSOd6 solutions using 1D and 2D-NMR techniques revealed an equilibrium between beta-II turn and gamma-turn conformers, which was ultimately modulated by the relative configuration of the -(beta-lactam)-(Aa)- residues. Long range chiral effects on the alpha-lactam pseudopeptide conformers were also found when two (i) and (i+3) chiral residues were attached to the termini of a central -(beta-lactam)-(Aib)- segment. In such mimetics, heterochiral (i) and (i+3) residues reinforced a beta-II turn conformer, whereas homochiral corner residues stabilized an overlapped beta-II/ beta-I double turn motif. No beta-hairpin nucleation was observed in any instance. In good agreement with the conformers found in solution, beta-turned and open structures were also characterized by X-ray crystallography. Relative stabilities of the different conformers were estimated computationally at a B3LYP/6-31++G** calculation level and, finally, a conformation equilibrium model based on steric inter-residual interactions around the -(beta-lactam)-(i+2)- segment was proposed to account for the observed chiral effects.

Concepts: Amino acid, Stereochemistry, Steric effects, Conformational isomerism, Isomer, Folding, Cyclohexane conformation

27

The first Si-H-containing azasilaheterocycle, 1,3-dimethyl-3-silapiperidine 1, was synthesized and its molecular structure and conformational properties were studied by gas-phase electron diffraction (GED), low temperature NMR, IR and Raman spectroscopy and quantum chemical calculations. The compound exists as a mixture of two conformers possessing the chair conformation with the equatorial NMe group and differing by axial or equatorial position of the SiMe group. In the gas phase, the SiMeax conformer predominates (GED: ax/eq = 65(7):35(7) %), ΔG = 0.36(18) kcal/mol; IR: ax/eq = 62(5) : 38(5) %), ΔG = 0.16(7) kcal/mol). In solution, at 143 K the SiMeeq conformer predominates in the frozen equilibrium (NMR: ax/eq = 31.5(1.5) : 68.5(1.5) %), ΔG = -0.22(2) kcal/mol). Thermodynamic parameters of the ring inversion are determined (ΔG≠ = 8.9-9.0 kcal/mol, ΔH≠ = 9.6 kcal/mol, ΔS≠ = 2.1 eu). High-level quantum chemical calculations (MP2, G2, CCSD(T)) nicely reproduce the experimental geometry and the predominance of the axial conformer in the gas phase.

Concepts: Fundamental physics concepts, Stereochemistry, Chemistry, Chemical bond, Temperature, Chemical compound, Conformational isomerism, Cyclohexane conformation

3

Two-dimensional materials have significant potential for the development of new devices. Here we report the electronic and structural properties of β-GeSe, a new polymorph of GeSe, with a unique crystal structure that displays strong two-dimensional structural features. β-GeSe is made at high pressure and temperature and is stable under ambient conditions. We compare it to its structural and electronic relatives α-GeSe and black phosphorus. The new β form of GeSe displays a boat configuration for its Ge-Se six-ring, while the previously known α form, and black phosphorus, display the more common chair configuration for their six-rings. Electronic structure calculations indicate that β-GeSe is semiconducting, with an approximate bulk band gap of Δ ≈ 0.5 eV, and, in its monolayer form, Δ ≈ 0.9 eV. These values fall between those of α-GeSe and black phosphorus, making β-GeSe a promising candidate for future applications. The resistivity of β-GeSe measured in-plane is on the order of ρ ≈ 1 Ωcm, while being essentially temperature independent, possibly due to defect-level dominated conductivity.

Concepts: Crystal, Structure, Semiconductor, Materials science, Electrical conductivity, Conformational isomerism, Standard conditions for temperature and pressure, Cyclohexane conformation

0

In this paper, we examine the hydration structure of dibenzo-18-crown-6 (DB18C6) complexes with K+, Rb+, and Cs+ion in the gas phase. We measure well-resolved UV photodissociation (UVPD) spectra of K+•DB18C6•(H2O)n, Rb+•DB18C6•(H2O)n, and Cs+•DB18C6•(H2O)n( n = 1-8) complexes in a cold, 22-pole ion trap. We also measure IR-UV double-resonance spectra of the Rb+•DB18C6•(H2O)1-5and the Cs+•DB18C6•(H2O)3complexes. The structure of the hydrated complexes is determined or tentatively proposed on the basis of the UV and IR spectra with the aid of quantum chemical calculations. Bare complexes (K+•DB18C6, Rb+•DB18C6, and Cs+•DB18C6) have a similar boat-type conformation, but the distance between the metal ions and the DB18C6 cavity increases with increasing ion size from K+to Cs+. Though the structural difference of the bare complexes is small, it highly affects the manner in which each is hydrated. For the hydrated K+•DB18C6 complexes, water molecules bind on both sides (top and bottom) of the boat-type K+•DB18C6 conformer, while hydration occurs only on top of the Rb+•DB18C6 and Cs+•DB18C6 complexes. Based on our analysis of the hydration manner of the gas phase complexes, we propose that for Rb+•DB18C6 and Cs+•DB18C6 complexes in aqueous solution, water molecules will preferentially bind on top of the boat conformers because of the displaced position of the metal ions relative to DB18C6. In contrast, the K+•DB18C6 complex can accept H2O molecules on both sides of the boat conformation. We also propose that the characteristic solvation manner of the K+•DB18C6 complex will contribute entropically to its high stability and thus to preferential capture of K+ion by DB18C6 in solution.

Concepts: Hydrogen, Chemistry, Chemical bond, Solubility, Solid, Infrared, Conformational isomerism, Cyclohexane conformation

0

Levoglucosan is one of the main products of the thermal degradation of glucose and cellulose and is commonly used as a tracer for biomass burning. Herein we report a conformational analysis of levoglucosan under isolation conditions, by means of microwave spectroscopy coupled with ultra-fast laser vaporization in supersonic expansions. We observed three different conformations of levoglucosan in the gas phase. They all share a common heavy atom rigid bicyclic structure. The difference between the three of them lies in the network of intramolecular hydrogen bonds that arises from the OH groups at positions 2, 3 and 4. The different combinations of H-bonds give richness to the conformational landscape of levoglucosan. The gas phase conformers obtained in this work are compared to the crystal structure of levoglucosan previously reported. While the heavy atom frame remains unchanged, there are significant differences in the positions of the H-atoms. In addition, the levoglucosan structure can be compared to the related glucose, for which gas phase conformational studies exist in the literature. In this case, in going from glucose to levoglucosan, there is an inversion in the chair conformation of the pyranose ring. This forces the OH groups to adopt axial positions (instead of the more favorable equatorial positions in glucose) and completely changes the pattern of intramolecular H-bonds.

Concepts: Fundamental physics concepts, Hydrogen, Stereochemistry, Chemical bond, Hydrogen bond, Conformation, Conformational isomerism, Cyclohexane conformation

0

Glucuronic acid is an important constituting block of biologically active glycosaminoglycans where it can be present in non-sulfated, mono-sulfated and di-sulfated forms. Despite that some investigators reported previously that the exhaustively sulfated glucuronic acid moiety was characterized with unusual 1H-1H coupling constants and some times chemical shifts, these were just qualitative studies in which their authors suggested that the mentioned deviations in NMR spectra might mean complete inversion of the normal D-pyranoside chair conformation 4C1 to 1C4. Herein we outline a detailed conformational investigation showing that the distortion in the pyranoside ring of the persulfated glucuronic acid cannot be described simply with 4C1↔1C4 inversion. Instead, the experimental NOE data clearly indicate that two skew-boat conformers, OS2 and 3S1, provide significant contribution to the conformational equilibrium.

Concepts: Stereochemistry, Chemical shift, Qualitative research, The Normal, Standard deviation, Conformation, Conformational isomerism, Cyclohexane conformation

0

A new procedure for full conformational analyses comprising the statistical analysis of molecular dynamics trajectories was developed and applied. This method included a coordinate space for sampling using molecular dynamics simulations, reduction of dimensionality using tensor decomposition tools, determination of probability distributions in a reduced space, and finally the search for all of the strict extrema points of probability distributions. These extracted extrema points formed an initial guess for geometry optimization and clustering of conformers. A complete conformational space of 1-oxaspiro[2,5]octane and its cis- and trans-4-, 5- and 6-methyl substituted derivatives was also determined. In each case, eight conformers were found with two chair-like conformers predominant at room temperature. It was found that chair-like conformers with an epoxide ring oxygen atom in the pseudo-axial position had less strain, as well as all of their conformers with the methyl substituent in an equatorial position on a cyclohexane moiety.

Concepts: Scientific method, Oxygen, Chemical bond, Factor analysis, Vector space, Force, Applied mathematics, Cyclohexane conformation

0

The regioselective protection of both methyl galactopyranoside anomers at the 2 and 3-positions as the butane diacetal (BDA) is well known. Here we describe the formation of an unexpected byproduct, which mainly occurs when α-methyl galactopyranoside is reacted with 2,3-butanedione under BF3•OEt2 catalysis. The structure of the byproduct, which did not arise from anomerisation to the β-anomer or from BDA formation at the galactopyranoside 3,4-positions, was elucidated by NMR and X-ray crystallographic analysis, and proved to be the expected BDA protected galactopyranoside, but in which the stereochemistry of both its BDA acetal centres are inverted. Interestingly, the conformation of the resulting six-membered BDA ring was distorted to a skew boat conformation in order to maintain anomeric stabilisation.

Concepts: Crystallography, Stereochemistry, X-ray crystallography, Protection, Conformational isomerism, Anomer, Cyclohexane conformation, Butane