A poisson equation for vibrational potentials of diatomic molecules

A Poisson equation for nuclear motions in diatomic molecules is derived. The working formula is whereV _α ² is the Laplacian operator for the position of nucleusα, W is the Born-Oppenheimer molecular energy, is the atomic number ofα, and ? _β (α) is the electronic charge density evaluated atα due to orbitals centered onβ. Harmonic, anharmonic and quartic equilibrium force constants are calculated using Hartree-Fock molecular and atomic electronic charge densities, for a number of first and second row diatomic molecules. A charge-model field gradient formula for harmonic force constants $$k_e = {3 \mathord{\left/ {\vphantom {3 {R_e^3 ,}}} \right. \kern-\nulldelimiterspace} {R_e^3 ,}}$$ wherek _e is the force constant andR _e the equilibrium internuclear distance, which offers general improvement over a similar formula due to Bratoz, is presented.     

Enzymatic Oxidation and Separation of Various Saccharides with Immobilized Glucose Oxidase

Glucose oxidase from Aspergillus niger, the specific enzyme for β-d-glucose oxidation, can also oxidize other related saccharides at very slow or negligible rates. The present study aimed to compare the kinetics of d-glucose oxidation using immobilized glucose oxidase on bead cellulose for the oxidation of related saccharides using the same biocatalyst. The significant differences were observed between the reaction rates for d-glucose and other saccharides examined. As a result, k _cat/K _M ratio for d-glucose was determined to be 42 times higher than d-mannose, 61.6 times higher than d-galactose, 279 times higher than d-xylose, and 254 times higher than for d-fructose and d-cellobiose. On the basis of these differences, the ability of immobilized glucose oxidase to remove d-glucose from d-cellobiose, d-glucose from d-xylose, and d-xylose from d-lyxose was examined. Immobilized catalase on Eupergit and mixed with immobilized glucose oxidase on bead cellulose or co-immobilized with glucose oxidase on bead cellulose was used for elimination of hydrogen peroxide from the reaction mixture. The accelerated elimination of d-glucose and d-xylose in the presence of co-immobilized catalase was observed. The co-immobilized glucose oxidase and catalase were able to decrease d-glucose or d-xylose content to 0–0.005% of their initial concentrations, while a minimum decrease of low oxidized saccharides d-xylose, d-cellobiose, and d-lyxose, respectively, was observed.     

Tensile strength of Iβ crystalline cellulose predicted by molecular dynamics simulation

The mechanical properties of Iβ crystalline cellulose are studied using molecular dynamics simulation. A model Iβ crystal is deformed in the three orthogonal directions at three different strain rates. The stress–strain behaviors for each case are analyzed and then used to calculate mechanical properties. The results show that the elastic modulus, Poisson’s ratio, yield stress and strain, and ultimate stress and strain are highly anisotropic. In addition, while the properties that describe the elastic behavior of the material are independent of strain rate, the yield and ultimate properties increase with increasing strain rate. The deformation and failure modes associated with these properties and the relationships between the material’s response to tension and the evolution of the crystal structure are analyzed.     

Effect of hydrogen bonds on the axial stiffnes of crystalline native cellulose

Previous theoretical calculations of elastic constants for cellulose based on force constants for bond stretching and bending of valence angles have yielded axial stiffness values admittedly too low. The present analysis accounts for a hitherto unexamined geometrical effect associated with deformation of interchain hydrogen bonds. To do this, most primary bond deformations are neglected so the resulting calculation gives an upper bound for the axial stiffness. By using two different sets of hydrogen bond force constants, values of 24.6 and 31.9 × 10¹¹ dyne/cm² were obtained for Young's modulus in the chain direction. These values are very much larger than earlier calculations and experimental determinations from cellulosic fibers, indicating both the importance of the effect considered here and the likelihood of an exact analysis yielding an acceptable result.     

Constraints on {\rm I}\beta cellulose twist from DFT calculations of ^{13}\hbox {C} NMR chemical shifts

We investigate theoretically the NMR response of twisted configurations of \({\rm I}\beta\) cellulose in the tg conformation. These finite helical angle structures were constructed by a mathematical deformation of zero-angle configurations obtained via the periodic density functional energy minimizations with dispersion corrections (DFT-D2). Subsequent calculations of the \({^{13}\hbox {C}}\) nuclear magnetic resonance chemical shifts \(({\delta}^{13} \hbox {C})\) were compared with experimental findings by Erata et al. (Cellul Commun 4:128–131, 1997) and Kono et al. (Macromolecules 36:5131–5138, 2003). We determine the sensitivity of the NMR chemical shifts to helical deformation of the microfibril and find that a substantial range of helical angle, ±2 degrees/nm, is consistent with current experimental observations, with a most probable angle of ～0.2 degree/nm. Through exhaustive combinatorial provisional assignments, we also demonstrate that there are different choices of the chemical shift \(({\delta}^{13} \hbox {C})\) assignments which are consistent with the experiments, including ones with lower deviations than existing identifications.     

Enantioselective extraction of fenvaleric acid enantiomers by two-phase (W/O) recognition chiral extraction

To establish an extraction method for fenvaleric acid (FA) enantiomers using l-iso-butyl-l-tartaric esters and hydroxypropyl-β-cyclodextrin (HP-β-CD) as chiral selector, the distribution of FA enantiomers was examined in methanol aqueous solution containing HP-β-CD and 1,2-dichloroethane organic solution containing l-iso-butyl-l-tartaric esters. The influences of the concentration of l-iso-butyl-l-tartaric esters and HP-β-CD, organic diluent, pH, extraction temperature and the concentration of methanol aqueous solution on the partition coefficient (k) and separation factor (α) of FA were investigated. The experiment results showed that the complex formed by l-iso-butyl-l-tartaric esters with S-enantiomer is stabler than that with R-enantiomer. With the increase of the concentration of l-iso-butyl-l-tartaric ester, k and α increased; With the increase of the concentration of HP-β-CD, k increased firstly, and then decreased, but α increased all the while, k was the highest when the concentration of HP-β-CD was 4 mmol L^?1. 1,2-dichloroethane organic diluent was better than the others. With the increase of pH, k and α decreased; with further increasing concentration of methanol aqueous solution, k and α decreased, k and α were the highest when the concentration of methanol aqueous solution was 10%. The extraction temperature had a great influence on k and α, too.     

β-d-Xylosidase from Selenomonas ruminantium: Role of Glutamate 186 in Catalysis Revealed by Site-Directed Mutagenesis, Alternate Substrates, and Active-Site Inhibitor

β-d-Xylosidase/α-l-arabinofuranosidase from Selenomonas ruminantium is the most active enzyme known for catalyzing hydrolysis of 1,4-β-d-xylooligosaccharides to d-xylose. Catalysis and inhibitor binding by the GH43 β-xylosidase are governed by the protonation states of catalytic base (D14, pK _a 5.0) and catalytic acid (E186, pK _a 7.2). Biphasic inhibition by triethanolamine of E186A preparations reveals minor contamination by wild-type-like enzyme, the contaminant likely originating from translational misreading. Titration of E186A preparations with triethanolamine allows resolution of binding and kinetic parameters of the E186A mutant from those of the contaminant. The E186A mutation abolishes the pK _a assigned to E186; mutant enzyme binds only the neutral aminoalcohol $ \left( {{\text{pH}} - {\text{independent}}\;K_{\text{i}}^{\text{triethanolamine}} = 19\,{\text{mM}}} \right) $ , whereas wild-type enzyme binds only the cationic aminoalcohol $ \left( {{\text{pH}} - {\text{independent}}\;K_{\text{i}}^{\text{triethanolamine}} = 0.065\,{\text{mM}}} \right) $ . At pH 7.0 and 25°C, relative kinetic parameter, $ k_{\text{cat}}^{\text{4NPX}}/k_{\text{cat}}^{\text{4NPA}} $ , for substrates 4-nitrophenyl-β-d-xylopyranoside (4NPX) and 4-nitrophenyl-α-l-arabinofuranoside (4NPA) of E186A is 100-fold that of wild-type enzyme, consistent with the view that, on the enzyme, protonation is of greater importance to the transition state of 4NPA whereas ring deformation dominates the transition state of 4NPX.     

Molecular dynamics simulation study of xyloglucan adsorption on cellulose surfaces: effects of surface hydrophobicity and side-chain variation

The effect of surface hydrophobicity and side-chain variation on xyloglucan adsorption onto cellulose microfibrils (CMF) is investigated via molecular dynamics simulations. A molecular model of CMF with (100), (010), (1–10), (110) and (200) crystal faces was built. We considered xylogluco-oligosaccharides (XGO) with three repeating units, namely (XXXG)_3, (XXLG)₃, and (XXFG)₃ (where each (1,4)-β-d-glucosyl residue in the backbone is given a one-letter code according to its substituents: G = β-d-Glc; X = α-d-Xyl-(1,6)-β-d-Glc; L = β-d-Gal-(1,2)-α-d-Xyl-(1,6)-β-d-Glc; F = α-l-Fuc-(1,2)-β-d-Gal-(1,2)-α-d-Xyl-(1,6)-β-d-Glc). Our work shows that (XXXG)₃ binds more favorably to the CMF (100) and (200) hydrophobic surfaces than to the (110), (010) and (1–10) hydrophilic surfaces. The origin of this behavior is attributed to the topography of hydrophobic CMF surface, which stabilizes (XXXG)₃ in flat conformation. In contrast, on the rough hydrophilic CMF surface (XXXG)₃ adopts a less favorable random-coil conformation to facilitate more hydrogen bonds with the surface. Extending the xyloglucan side chains from (XXXG)₃ to (XXLG)₃ hinders their stacking on the CMF hydrophobic surface. For (XXFG)₃, the interaction with the hydrophobic surface is as strong as (XXXG)₃. All three XGOs have similar binding to the hydrophilic surface. Steered molecular dynamics simulation was performed on an adhesive model where (XXXG)₃ was sandwiched between two CMF hydrophobic surfaces. Our analysis suggests that this sandwich structure might help provide mechanical strength for plant cell walls. Our study relates to a recently revised model of primary cell walls in which extensibility is largely determined by xyloglucan located in limited regions of tight contact between CMFs.     

Asteropsiside A and other asterosaponins from the starfish Asteropsis carinifera

Three asterosaponins were isolated from the tropical starfish Asteropsis carinifera: a new one, asteropsiside A, and two known ones, regularoside A and thornasteroside A. The structure of the new compound was established using 2D NMR spectroscopy and ESI mass spectrometry as the sodium salt of 3-O-sulfonato-(20E)-6-O-{β-d-fucopyranosyl-(1→2)-β-d-galactopyranosyl-(1→4)-[β-d-quinovopyranosyl-(1→2)]-β-d-xylopyranosyl-(1→3)-β-d-quinovopyranosyl}-3β,6α-dihydroxy-5α-cholesta-9(11),20(22)-dien-23-one. Regularoside A and thornasteroside A were shown to display the ability to inhibit the growth of the T-47D and RPMI-7951 tumor cell colonies in vitro.     

Carbohydrate recognition of symmetrical tripodal receptor type tris(2-aminoethyl)amine derivatives

Carbohydrate recognition of some bioactive symmetrical tripodal receptor type tris(2-aminoethyl)amine (TAEA) derivatives was investigated. In calorimetric experiments, the highest binding constant (Ka) of compound C (C₃₅H₄₉N₅O₄S) with methyl α-d-mannopyranoside was Ka = 858 M^?1 with 1:1 stoichiometry. Formation of hydrogen bonds in binding between symmetrical tripodal receptor type compound C and sugars was suggested by the large negative values of ?H° (=?34 to ?511 kJ mol^?1). In a comparison of each set of α- and β-anomers of some monosaccharides (methyl α/β-d-galactopyranoside, methyl α/β-d-glucopyranoside, and methyl α/β-l-fucopyranoside), compound C showed that the binding constant of β-anomer was larger than that of the corresponding α-anomer, indicating higher β-anomer selectivity. The calculated energy-minimized structure of the complex of compound C with guest methyl α-d-mannopyranoside is also presented. The experimental results obtained from this work indicated that symmetrical tripodal receptor type TAEA derivative C has a lectin-like carbohydrate recognition property.     

Synthesis of N-glycyl-β-glycopyranosyl amines,derivatives of natural oligosaccharides — glucose analogs of Lex antigen

Treatment of the natural tri-, tetra-, and pentasaccharides, β-d-Galp-(1→4)-[α-l-Fucp-(1→3)]-d-Glcp, α-l-Fucp-(1→2)-β-d-Galp-(1→4)-[α-l-Fucp-(1→3)]-d-Glcp, and α-l-Fucp-(1→2)-[α-d-GalNAcp-(1→3)]-β-d-Galp-(1→4)-[α-l-Fucp-(1→3)]-d-Glcp, which are glucose analogs of Le^x, with ammonium carbamate in aqueous methanol gave the corresponding β-glycopyranosyl amines. After their N-acylation with N-Z-glycine N-hydroxysuccinimidyl ester (Z is benzyloxycarbonyl) with subsequent hydrogenolytic removal of Z-group, corresponding N-glycyl-β-glycopyranosyl amines were obtained in yields up to 70%.     

New polymorphic types of diamond

The results of calculations by PM3 and LDA-DFT methods of the structure and properties of six new polymorphic types of diamond, in which all atomic sites are crystallographically equivalent, are presented. The structures of LA5 (Cmca), LA7 (Cmcm), and LA8 (I4₁/amd) phases are obtained as a result of stitching graphene layers and of CA9 \((Fd\bar 3m)\) , CA10 \((R\bar 3m)\) , and CA11 (P6₃/mmc) phases by stitching fullerenelike clusters. For these phases the geometrically optimized structures are calculated and the structural parameters, density, sublimation energy, bulk modulus, electron density of states, and X-ray diffraction pattern are measured. It is found that the properties of polymorphic types of diamond depend on the degree of their structure deformation in comparison with the cubic diamond structure.     

Preparative Isolation and Purification of Flavonoids and Protocatechuic Acid from Sea Buckthorn Juice Concentrate (Hippophaë rhamnoides L. ssp. rhamnoides) by High-Speed Counter-Current Chromatography

High-speed counter-current chromatography (HSCCC)—a support free all liquid–liquid chromatography technique—has been successfully used for the preparative isolation of isorhamnetin 3-O-β-d-glucoside, isorhamnetin 3-O-β-rutinoside, quercetin 3-O-β-d-glucoside, syringetin 3-O-β-d-glucoside and protocatechuic acid from sea buckthorn juice concentrate (Hippophaë rhamnoides L. ssp. rhamnoides, Elaeagnaceae). The preparative HSCCC instrument was a multilayer coil planet centrifuge equipped with three preparative coils. Separation was performed with a two phase solvent system (n-hexane–n-butanol–water, 1:1:2 v/v/v) in ‘head-to-tail’ mode. Each injection of 4.1 g crude ethyl acetate extract yielded isorhamnetin 3-O-β-d-glucoside (95 mg), isorhamnetin 3-O-β-rutinoside (10 mg), quercetin 3-O-β-d-glucoside (5 mg), and protocatechuic acid (34 mg) with purities >98%. The flavonoid syringetin 3-O-β-d-glucoside (2 mg) was a novel compound for H. rhamnoides. Chemical structures of all compounds were determined by HPLC–ESI–MS–MS, 1D-NMR (¹H, ¹³C, DEPT 135) spectroscopy and for elucidation of glycosidic linkages 2D-NMR (HMBC) spectroscopy was used.     

Anisotropy of the elastic properties of crystalline cellulose Iβ from first principles density functional theory with Van der Waals interactions

In spite of the significant potential of cellulose nanocrystals as functional nanoparticles for numerous applications, a fundamental understanding of the mechanical properties of defect-free, crystalline cellulose is still lacking. In this paper, the elasticity matrix for cellulose I_β with hydrogen bonding network A was calculated using ab initio density functional theory with a semi-empirical correction for van der Waals interactions. The computed Young’s modulus is found to be 206 GPa along [001] (c-axis), 98 GPa along [010] (b-axis), and 19 GPa along [100] (a-axis). Full compliance matrices are reported for 1.0, 1.5 and 2.0 % applied strains Color contour surfaces that show variations of the Young’s modulus and average Poisson’s ratio with crystallographic direction revealed the extreme anisotropies of these important mechanical properties. The sensitivity of the elastic parameters to misalignments in the crystal were examined with 2D polar plots within selected planes containing specific bonding characteristics; these are used to explain the substantial variability in the reported experimental Young’s moduli values. Results for the lattice directions [001], [010] and [100] are within the range of reported experimental and other numerical values.     

Biospecificity chromatography the investigation of the active site ofN-acetyl-β-d-hexosaminidase with affinity chromatography

Affinity chromatography of different natural biopolymers, including enzymes, is perhaps the most widely used modern technique for isolation and purification of these molecules. We have synthesized three biospecific sorbents with weak ion exchange properties by coupling ligands to carriers through hydrazide groups. These sorbents have no ion exchange or hydrophobic groups, thereby minimizing the influence of nonspecific binding on the process of affinity chromatography. These biospecific sorbents have been used for purification ofN-acetyl-β-d-hexosaminidase (EC 3.2.1.52), and for study of its active site and of its sorption and elution mechanisms in affinity chromatography. Biospecificity of sorbents was suggested by adsorption ofN-acetyl-β-d-hexosaminidase at optimum catalytic pH and by elution of the enzyme with minimal variation of pH. By comparing the known data for mapping the active site ofN-acetyl-β-d-hexosaminidase and energetic contributions of functional groups of inhibitor molecules with the obtained results, one can infer that sorption of the enzyme on biospecific sorbents is realized only by hydrogen bonds between the ligand used and ionizable groups ofN-acetyl-β-d-hexosaminidase (pK 5.5).     

Quantitative Analysis of Caffeoylquinic Acids and Styrylpyrones in Sweetia panamensis Bark by UPLC

Six secondary metabolites from the methanolic extract of Sweetia panamensis (Fabaceae) bark were isolated and characterised. Along with the pyrones desmethylangonine β-d-O-glucopyranoside and desmethylangonine β-d-O-glucopyranosyl-(1→6)-O-β-d-glucopyranoside, already reported in this species, 5-O-caffeoylquinic acid (chlorogenic acid), 4-O-caffeoylquinic acid, 3-O-caffeoylquinic acid and the isoflavonoid 5-O-methylgenistein 7-O-β-d-glucopyranoside were isolated for the first time from S. panamensis. Additionally, an LC-ESI-MS qualitative analysis was performed and an ultra performance liquid chromatography (UPLC) method was developed and validated for the determination of these compounds. The UPLC method was applied to the quantitative analysis of plant samples. Pyrones and caffeoylquinic acids resulted to be the main compounds in the extract; in particular desmethylangonine β-d-O-glucopyranosyl-(1→6)-O-β-d-glucopyranoside was the most abundant compound.     

Mechanism of structure formation of microbial cellulose during nascent stage

The structure of microbial cellulose (MC) produced by Acetobacter xylinum was studied in presence of Fluorescent Brightener, Direct Blue 1, 14, 15, 53, Direct Red 28, 75 and 79, as probe. X-ray diffraction pattern of the product showed that it was a crystalline complex of dye and cellulose. The product has the structure in which the monomolecular layer of the dye molecule is included between the cellulose sheets corresponding to the ( $ 1\bar{1}0 $ ) planes of microbial cellulose. As a result of dye inclusion, d-spacing of lower angle plane (100) of products becomes 8.0–8.8 Å instead of 6.1 Å of MC. The d-spacing for the higher angle plane must be (010) plane due to stronger van der Waals forces between the pyranose rings which reduced 5.3 Å space of (110) plane of MC to 3.9–4.5 Å in the product. However, cellulose regenerated from FB, DR28 products was cellulose I and IV, respectively, and that from each DB1, 14, 15, 53, DR75 and 79 products was cellulose II. Solid state ¹³C NMR and deuteration-IR showed the product was non-crystalline which was contrasted to X-ray results. The regenerated celluloses were cellulose I_β, IV_I and II, respectively. Thus the structure of the product depends on the characteristics of dye which affects the conformation of cellulose at the nascent stage by the direct interaction with cellulose chains. The different regenerated celluloses as well as different fine structure in the same cellulose allomorph were produced depending mainly on number and position of the sulfonate groups in the dye.     

Mathematical modelling of steady-state concentration in immobilized glucose isomerase of packed-bed reactors

The theoretical model of the steady-state immobilized enzyme electrodes is discussed. This model is based on diffusion equation containing a non-linear term related to Michaelis–Menten kinetics of the enzymatic reaction. Homotopy perturbation method (HPM) is employed to solve the non-linear diffusion equation for the steady-state condition. Simple and approximate polynomial expression of concentration and flux are derived for all small values of parameters ${\phi_p}$ (Theiele modulus) and β (kinetic parameter). Furthermore, in this work the numerical solution of the problem is also reported using SCILAB/MATLAB program. The analytical results are compared with the numerical results and found to be in good agreement.     

Continuous stiffness mode nanoindentation response of poly(methyl methacrylate) surfaces

Indentation is a comparatively simple and virtually nondestructive method of determining mechanical properties of material surfaces by means of an indenter inducing a localized deformation. The paper present experimental results of the load-displacement curves, the hardness and the elastic modulus data, and associated analysis for poly(methyl methacrylate) (PMMA) surfaces as a function of contact displacement. The experimental results include continuous stiffness indentations performed using constant loading rate and constant displacement rate experiments. The continuous stiffness indentation involves continuous calculation of a material stiffness, and hence hardness and elastic modulus of surfaces, during discrete loading-unloading cycles, as in a conventional indentation routine, and in a comparatively smaller time constant. The dependence of the compliance curves, the hardness, the elastic modulus and the plasticity index upon the imposed penetration depth, the applied normal load and the deformation rate are described. Tip area and load frame calibrations for the continuous stiffness indentation are also reported. The paper includes practical considerations encountered during indentation of polymers specifically at low penetration depths. The experimental results show a peculiarly harder response of PMMA surfaces at the submicron (near to surface) layers.     

Study of compatibility in polymeric system cellulose nitrate-cellulose acetate by reversed-phase gas chromatography

Therm odynamic compatibility in the polymeric system cellulose nitrate-cellulose acetate is studied by reversed-phase gas chromatography. The excess enthalpy ΔH _ji ^E , entropy ΔS _ji ^E , and Gibbs energy ΔG _ji ^E of mixing of the components, and also the Flory-Huggins interaction parameter χ_ji are estimated.