Can the nonadiabatic photodynamics of aminopyrimidine be a model for the ultrafast deactivation of adenine?

The reaction path for the ultrafast deactivation of 6-aminopyrimidine (6AP) has been investigated by means of ab initio surface-hopping dynamics. The electronic vertical excitation spectrum, excited-state S1 minima, and minima on the crossing seam of 6AP resemble well those found for adenine. The deactivation from the S1 to the S0 state takes place at the ultrafast time scale of 400 fs and involves the out-of-plane ring deformation of the C4 atom, a position that is sterically restricted in adenine by the imidazole ring. Mechanical restrictions have been used to simulate in a simple way the role of the imidazole group in adenine. As a result, deactivation via out-of-plane ring deformation of the C2 and N3 atoms are observed in good agreement with predictions for adenine. These dynamics results show that the previously suggested ring puckering deactivation paths really exist at a time scale, which is compatible with experimentally observed life times. The electronic structure of the crossing seam has been shown to have the same nature as those of simple biradicaloid systems, a feature which seems to be valid for any cyclic system.     

Liquid chromatographic separation of monoamino analogues of dideoxyadenosine and 9-(dideoxy-β-D-lyxo-pentofuranosyl)adenine from adenine

Summary A liquid chromatographic method that can separate each of the monoamino analogues of dideoxyadenosine and 9-(-dideoxy--D-lyxo-pentofuranosyl)adenine from their main degradation product, adenine, is described. The influence of the pH of the mobile phase, the type and concentration of the organic modifier and the concentration of the silanol masking agent and the buffer have been investigated. Several reversed phases were examined. Samples were finally analyzed on a 10 m Spherisorb ODS1 column (250 mm×4.6 mm I.D.) using acetonitrile –0.2 M potassium phosphate buffer pH 6.0–0.2 M tetramethylammonium phosphate pH 6.0-water (550.589.5, v/v) as the mobile phase. The interactions between the solute and the stationary phase are discussed in view of the basic properties of the compounds under study.     

Can we predict the spreading of a two-liquid system from the spreading of the corresponding liquid-air systems?

We present new data obtained from the spreading of a series of oil droplets, on top of a hydrophobic grafted silicon substrate, in air and immersed in water. We follow the contact angle and radius dynamics of hexane, dodecane, hexadecane, dibutyl phthalate, and squalane from the first milliseconds to approximately 1 s. Analysis of the images allows us to make several hundred contact angle and droplet radius measurements with great accuracy. The G-Dyna (Seveno et al. Langmuir 2010, 25, 13034) software is then used to fit the data with one of the wetting theories, the molecular-kinetic theory (MKT) (Blake et al. J. Colloid Interface Sci.1969, 30, 421), which takes into account the dissipation at the three-phase zone at the contact line. This theory allows us to extract the coefficient of friction of the contact line, which expresses the relationship between the driving force, that is, the unbalanced Young force, and the contact-line velocity V. It is first shown that the MKT is appropriate to describe the experimental data and then that the contact-line friction is a linear function of the viscosity as theoretically predicted. This is checked for oil-air and oil-water systems. A linear relation between the contact-line friction measured in oil-water systems and the contact-line frictions of the parent single liquid system seems plausible. To the best of our knowledge, this is the first trial to establish a link between the dynamics of wetting in liquid-liquid and in liquid-air systems.     

Computational design of a Diels–Alderase from a thermophilic esterase: the importance of dynamics

A novel computational Diels–Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement. Molecular dynamics simulations and DFT calculations were used to optimize and estimate binding affinity and activation energies. A large quantum chemical model was used to capture the salient interactions in the crucial transition state (TS). Our quantitative estimation of kinetic parameters was validated against four experimentally characterized Diels–Alderases with good results. The final designs in this work are predicted to have rate enhancements of ≈10³–10⁶ and high predicted proficiencies. This work emphasizes the importance of considering protein dynamics in the design approach, and provides a quantitative estimate of the how the TS stabilization observed in most de novo and redesigned enzymes is decreased compared to a minimal, ‘ideal’ model. The presented design is highly interesting for further optimization and applications since it is based on a thermophilic enzyme (T _opt ?=?70?°C).     

Terminalic Acid, a New Tannin from the Fruit of Terminalia chebula

AsatheraPeuticherbusedintraditionalChinesemedicine,TerminaliachebulaisconventionallygrowninGuangdong,Guangxi,andtheYunnanprovinceofChina.Itsripefruitisefficaciouslycurativewhenusedintreatingdiarrheaandhoarsenessofthethroatandcanalsobeusedasanastringenttobringabouthemostasisortoremovesomepathogenic"internalheat"ortoxicelementsfromwithinhumanphysique'.SeveralstudiesonhydroIysabletanninswithchebuloylgrouphavebeenreportedsofar2.AspartofaprogramforasystematicstudyofTchebula,wehavesuccessfullyis…     

Structure of a new sterol from the South China sponge Dysidea fragilis

A new sterol, 5a-cholesta-8(14),24(25)-diene-3/β, 6a-diol (1) and a known sterol (24Z)-24-ethyl-cholesta-7(8),24(28)-diene-3β,5a,6β-triol (2) have been isolated from the South China Seasponge Dysidea fragilis. The structure and relative stereochemistry of 1 were established by spectralanalysis, including 2D NMR experiments.     

Reconstruction of the 3D coordinates of α-carbon atoms of proteins from a pair of stereographic figures

Summary In an attempt to promptly use the experimentally determined structures of proteins in modeling studies, we have developed the program ReconstC to generate the 3D coordinates of -carbon atoms from a pair of stereographic figures. Calculations of the 3D coordinates were performed by estimating the stereo parameters systematically. Geometrical features of C traces were used to evaluate the integrity of the calculated structure. The program was applied to four kinds of protein structures to examine the performance. It was found that the root-mean-square deviation of atomic positions between constructed and reference crystal structures ranged from 0.36 to 0.78 Å. The range represents a reasonable accuracy and its automatic feature suggests that our approach would be expedient for providing initial structures for protein modeling studies.     

Synthesis of the Precursor of Tetrasaccharide from Laminin

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Separation and identification of a new saponin from the flowers of Guaiacum officinale L

A triterpenoid saponin, guaianin O (1), oleanolic acid 3-O-{α-L-rhamnopyranosyl-(1 → 2)-[β-D-glucopyranosyl-(1 → 3)]-α-L-arabinopyranoside}-28- O-[β-D-glucopyranosyl]-ester, was isolated from the n-butanol extract of flowers of Guaiacum officinale L. The structural elucidation of 1 was accomplished by extensive studies of both one and two dimensional 1H, 13C-NMR spectra, the FAB mass spectrum, and alkaline and acid hydrolyses.     

DNA damage induced via independent generation of the radical resulting from formal hydrogen atom abstraction from the C1′-position of a nucleotide

Background: Deoxyribonucleotide radicals resulting from formal C1′-hydrogen atom abstraction are important reactive intermediates in a variety of DNA-damage processes. The reactivity of these radicals can be affected by the agents that generate them and the environment in which they are produced. As an initial step in determining the factors that control the reactivity of these important radical species, we developed a mild method for their generation at a defined site within a biopolymer.Results: Irradiation of oligonucleotides containing a photolabile nucleotide produced C1'-DNA radicals. In the absence of potential reactants other than O₂, approximately 90% of the damage events involve formation of alkaline-labile lesions, with the remainder resulting in direct strand breaks. The ratio of alkaline-labile lesions to direct strand breaks (∼ 9:1) is independent of whether the radical is generated in single-stranded DNA or double-stranded DNA. Strand damage is almost completely quenched under anaerobic conditions in the presence of low thiol concentrations. Competition studies with 02 indicate that the trapping rate of C1′-DNA radicals by β-mercaptoethanol is ∼ 1.1 x 10⁷ M⁻¹s⁻¹Conclusions: The mild generation of the C1'-DNA radical in the absence of exogenous oxidants makes it possible to examine their intrinsic reactivity. In the absence of other reactants, the formation of direct strand breaks from C1′-radicals is, at most, a minor pathway. Competition studies between β-mercaptoethanol and 02 indicate that significantly higher thiol concentrations than those in vivo or some means of increasing the effective thiol concentration near DNA are needed for these reagents to prevent the formation of DNA lesions arising from the C1'-radical under aerobic conditions.     

Gnetuhainin P, a New Isorhapontigenin Dimer from the Lianas of Gnetum hainanense

Continuous investigation on oligostilbenes from the lianas of Gnetum hainanense resulted in the isolation of a new rhapontigenin dimer, Gnetuhainin P (1), in addition to the dimers of resveratrol and oxyresveratrol reported previously1. Gnetuhainin P (1) was obtained as a yellowish amorphous powder, [(]25D +6.6 (c 0.092, MeOH). The high resolution FABMS m/z 533.1866 [M+H]+ gave a molecular formula of C30H28O9 (C30H29O9 requires 533.1812), which corresponds to a isorhapontigenin dimer. …     

Structural study on a bioactive fructan from the root of Achyranthes bidentata Blume

The structure of a saccharide component (Abs),with pronounced activity of improving immunity system,isolated from the root of Achyranthes bidentata Blume,a traditional Chinese herbal medicine,was studied.Based on 13C NMR,HPLC,and methylation analyses,Abs was shown to be a mixture of short-chain fructans with an average dp of 8,containing more (2→6) than (2→1) linked β-D-fructofuranosyl residues,with branching at O-6 or O-1 of 18% of the D-fructofuranoeyl residues.     

Reaction of adenine with an α-chlorooxetane: An approach to the synthesis of oxetane nucleosides

The reaction of adenine with 3,5-anhydro-5R-chloro-1,2-O- isopropylidenexylofuranose, a stable α-chlorooxetane, gives a mixture of the two epimers of 5-[9-adenyl]-3,5-anhydro- 1,2-O-isopropylidenexylofuranose; the structure of 5R-[9- adenyl)-3,5-anhydro-1,2-O-isopropylidenexylofuranose was established by X-ray crystallography.     

Characterization of a new epoxy-hydroxycarvotanacetone derivative from the leaf essential oil of Laggera pterodonta from Côte d’Ivoire

The leaf essential oil of Laggera pterodonta (DC.) Sch. Bip. ex Oliv. (Asteraceae) collected in the Eastern Côte d’Ivoire was investigated using a combination of chromatographic (GC-RI, CC, pc-GC) and spectroscopic (GC-MS, ¹³C NMR) techniques. Eighty-three components accounting for 98.0% of the whole composition were identified with 2,5-dimethoxy-p-cymene (43.3%), sabinene (14.1%), α-humulene (9.8%), (E)-β-caryophyllene (7.2%) and germacrene D (5.2%) as major compounds. This study led to the structural elucidation of a new natural compound, (3αH,4βH,6αH,1αMe)-1,6-epoxy-3-hydroxycarvotanacetone, angelic acid ester from the leaf oil by 1D and 2D NMR spectroscopy.     

New norditerpenoids and a diterpenoid from a sponge that inhibit the lyase activity of DNA polymerase β

Using an assay to detect inhibitors of the lyase activity of DNA polymerase β, bioassay-directed fractionation of a CHCl₃ extract of an unidentified sponge of the family Demospongiae resulted in the isolation of the new diterpenoid 1, the new bis-norditerpenoids 2-3, and the two known compounds spongia-13(16),14-dien-19-oic acid (4), and methylspongia-13(16),14-dien-19-oate (5). The structures of the new compounds were established on the basis of extensive 1D and 2D NMR spectroscopic interpretation. All five compounds inhibited the lyase activity of DNA polymerase β.     

A Novel Oligosaccharide from the Mucus of the Loach

A novel oligosaccharide was isolated and purified from the mucus of the loach, Misgurnus anguillicaudatus. Its was identified by several qualitative tests and characterized by elementary analysis,UV and IR spectrum. Its average molecular weight(Mw=1539.4) was determined by gel permeation chromatography. The major structural monomers of Misgurnus anguillicaudatus oligosaccharide were identified to be D-galactose and L-fucose by paper chromatography and gas chromatography.     

Polyoxypregnanes from the stems of Marsdenia tenacissima

From the stems ofMarsdenia tenacissima two new polyoxypregnanes were isolated, their structures were elucidated by 1D, 2D-NMR as 11α,12β-di-O-tigloyl-tenacigenin B （1） and tenacigenoside E （2）.     

Can one derive the conformational preference of a beta-peptide from its CD spectrum?

CD spectroscopy is often used to elucidate the secondary structure of peptides built from non-natural amino acids such as beta-amino acids. The interpretation of such CD spectra is not always unambiguous. Here, we present a case where two beta-hexapeptides, a dimethyl-beta-hexapeptide indicated as DM-BHP (A) and its nonmethylated analogue indicated as BHP (B), exhibit similar CD spectra, whereas they are expected to differ in secondary structure. The structural properties of both peptides were studied by molecular dynamics simulation, and from the resulting trajectories, the corresponding CD spectra were calculated. Starting from a fully extended conformation, BHP is observed to form a 3(14)-helix, while DM-BHP remains unfolded. However, even though these two peptides hardly share any conformations, their calculated CD spectra are alike and show the same features as the experimentally measured ones. Our results imply that a particular CD pattern can be induced by spatially different structures, which makes it difficult to derive the conformational preference of a peptide from its CD spectrum alone. To gain more insight into the relationship between the preferred conformation of a peptide and its CD spectrum, more accurate methods to calculate the CD spectrum for a given conformation are required.     

Supramolecular assemblies in the crystals of carboxylate salts prepared from a ferrocene β-aminoalcohol

(Ferrocenylmethyl)(2-hydroxyethyl)amine (1) reacts with mono- (CH₃CO₂H and PhCO₂H) and dicarboxylic acids (HO₂C(CH₂)_nCO₂H (n = 0-2), (E)- and (Z)-HO₂CCHCHCO₂H) to give the respective carboxylates, viz [1H](RCO₂) (2, R = CH₃; 3, R = Ph), [1H]₂(O₂C(CH₂)_nCO₂) (4, n = 0; 5, n = 1; 6, n = 2), [1H]₂((E)-O₂CCHCHCO₂) (7) and [1H]₂((Z)-HO₂CCHCHCO₂) (8), as defined crystalline solids. Crystal structures of 2-8 have been determined by single-crystal X-ray diffraction analysis, revealing extensive hydrogen bonding interactions based predominantly on charge-supported N⁺-H···O⁻ and O-H···O⁻ hydrogen bonds, and on C-H···O contacts. Whereas the crystal assemblies of the monocarboxylate salts propagate preferentially in one dimension (2: cross-linked chains, 3: columnar stacks), those of the salts prepared from the dicarboxylic acids (including hydrogenmaleate 8) are best described as layered composite arrays resulting via alternation of polar, hydrogen-bonded layers and of non-polar sheets constituted by the ferrocenyl substituents.