Glycosidic linkage conformation of methyl-alpha-mannopyranoside

We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-alpha-mannopyranoside is preferred over its gauche anticlockwise (g-) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution.     

A spherulitic growth mechanism in amylose acetate

A typical growth mechanism of spherulite, with clearly defined bands formed by fibrillar aggregation, has been observed by the Film Formation Method of crystal growth for amylose acetate and amylose propionate. It is observed that the type of the spherulite and the extent of aggregation of fibrils are very much dependent on the solvent and concentration of polymer used for crystallization. At lower concentrations, there is development of isolated fibrils while various growth stages can be obtained by increasing concentration of polymer solution. The dense growth feature is found to open up with increasing crystallization temperature clearly revealing the presence of the fibrillar entity.     

In situ bubble‐stretching dispersion mechanism for additives in polymers

An in situ bubble‐stretching (ISBS) model has been proposed on the basis of an analysis of the dispersion process of inorganic additives in polymers. The ISBS model is applicable to a dispersion of solid granular aggregates in polymer melts because the dispersed phase itself serves as a nucleation agent, giving rise to bubbles that expand at the surface of the microgranules and their aggregates. In terms of bidirectional stretching, the ISBS process can increase the degrees of freedom of granule dispersion, which favors more homogeneous dispersion. According to theoretical predictions and indirect experimental estimations of the dispersion of nanoscale CaCO₃ and nanoscale hydrotalcite in high‐density polyethylene (HDPE), when the bubble expands, the stretching rate of the polymer melt on the bubble wall can reach 10⁵–10⁶ s^?1. The field emission scanning electron microscopic images indicated that the granular size of dispersed CaCO₃ and hydrotalcite in HDPE with the ISBS method is about 60–80 nm, two orders of magnitude smaller than that attained with a shearing rate of 10³ s^?1 in a capillary rheometer. It is also predicted that elastic bubble oscillations may be generated through suitable control of process parameters and that their oscillatory frequency can be in the ultrasound range. This type of bubble oscillation can also promote dispersion. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1051–1058, 2003     

High-resolution infrared spectrum of jet-cooled methyl acetate in the C=O stretching region: internal rotations of two inequivalent methyl tops

The jet-cooled high resolution infrared (IR) spectrum of methyl acetate (MA), CH(3)-C(=O)-O-CH(3), in the C=O fundamental band region was recorded by using a rapid scan IR laser spectrometer equipped with an astigmatic multipass cell. No high resolution IR analyses of the ro-vibrational transitions between the ground and non-torsionally excited vibrational states have hitherto been reported for molecules with two inequivalent methyl rotors. Because of the two chemically different methyl tops in MA, i.e., the acetyl -CH(3) and methoxy -CH(3), each rotational energy level is split into more than two torsional sublevels by internal rotations of these methyl groups. We were able to assign ro-vibrational transitions of four torsional species by using the ground state combination differences calculated from the molecular constants of the vibrational ground state recently determined by a global fit of the microwave and millimeter wave lines [M. Tudorie, I. Kleiner, J. T. Hougen, S. Melandri, L. W. Sutikdja, and W. Stahl, J. Mol. Spectrosc. 269, 211 (2011)]. The assigned lines were successfully fitted using the BELGI-Cs-IR program to an overall standard deviation which is comparable to the measurement accuracy. This study is also of interest in understanding the role of methyl rotors in the intramolecular vibrational-energy redistribution processes in mid-size organic molecules.     

On the antioxidant mechanism of curcumin: classical methods are needed to determine antioxidant mechanism and activity

[reaction: see structure] The antioxidant activity of curcumin (1, 7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione) was determined by inhibition of controlled initiation of styrene oxidation. Synthetic nonphenolic curcuminoids exhibited no antioxidant activity; therefore, curcumin is a classical phenolic chain-breaking antioxidant, donating H atoms from the phenolic groups not the CH(2) group as has been suggested (Jovanovic et al. J. Am. Chem. Soc. 1999, 121, 9677). The antioxidant activities of o-methoxyphenols are decreased in hydrogen bond accepting media.     

A band dispersion mechanism for Pt alloy compositional tuning of linear bound CO stretching frequencies

The C-O stretching frequency (nu(CO)) of atop CO/Pt in PtRu alloys is compositionally tuned in proportion to the Pt mole percent. The application of a Blyholder-Bagus type mechanism (i.e., increased back-donation from the metal d-band to the hybridized 2pi CO molecular orbitals (MOs)) to compositional tuning has been paradoxical because (1) a Pt-C bond contraction, expected with increased back-donation as the Pt mole percent is reduced, is not observed (i.e., calculated Pt-C bond is either elongated or insensitive to alloying and the binding energies of CO/Pt decrease with alloying) and (2) the lowering d-band center and increased d-band vacancies upon alloying (suggesting less back-donation to the higher energy metal hybridized 2pi CO MOs) must be reconciled with the alloy-induced red shift of the nu(CO). A library of spin-optimized Pt and Pt alloy clusters was the basis of density functional theory (DFT) calculations of CO binding energies, nu(CO) values, shifts, and broadening of 5sigma/2pi CO MO upon hybridization with the alloy orbitals and a DFT derived Mulliken electron population analysis. The DFT results, combined with FEFF8 local density of states (LDOS) calculations, validate a 5sigma donation-2pi back-donation mechanism, reconciling the direction of alloy compositional tuning with the lowering of the d-band center and increased vacancies. Although the d-band center decreases in energy with alloying, an asymmetric increase in the dispersion of the d-band is accompanied by an upshift of the metal cluster HOMO level. Concomitantly, the hybridization and renormalization of the CO 5sigma/2pi states results in a broadening of the 5sigma/2pi manifold with additional lower energy states closer to the upshifted (with respect to the pure Pt cluster) HOMO of the alloy cluster. The dispersion toward higher energies of the alloy d-density of states results in more 5sigma/2pi CO filled states (i.e., enhanced 2pi-back-donation). Finally, Mulliken and FEFF8 electron population analysis shows that the increase of the average d-band vacancies upon alloying and additional 2pi back-donation are not mutually exclusive. The d-electron density of the CO-adsorbed Pt atom increases with alloying while the average d-electron density throughout the cluster is reduced. The localized electron density is manifested as an electrostatic wall effect, preventing the Pt-C bond contractions expected with increased back-donation to the 2pi CO MOs.     

NH2 stretching vibration absorption and association mechanism of methylamine in n-hexane and carbon tetrachloride

Hydrogen bonding of methylamine in n-hexane is studied by recording the NH₂ stretching vibration absorption as a function of temperature and concentration and comparing it to the absorption in carbon tetrachloride. A continuous or quasi-continuous shift of the symmetric NH₂ stretching vibration on association in hexane and a discontinuous shift by about the same total amount together with an intensity change between a monomeric and an associated band in carbon tetrachloride suggest different association mechanisms in the two solvents. These are related to the enhancement of the proton donor or acceptor ability of the amine resulting from complexation with the solvent in carbon tetrachloride and to a similar influence of the added amine molecules, corresponding to the concept of hydrogen bond cooperativity, in hexane. Differences of 3–5 kJ mol⁻¹ between the mean association energy of methylamine in hexane and of methylamine or its homologues in carbon tetrachloride can be attributed to the energy needed for disruption of the complexes with the chlorine solvent and therefore support the assumption of the complex formation. Further results concern the chain-length dependence of the amine association, the association degrees in the two solvents and the intensity behaviour of the symmetric vibration of the neat compound in i.r. and Raman spectra.     

A test to determine the nature and presence of the memory effect columns packed with the amylose tris(3,5-dimethylphenylcarbamate) stationary phase

Acid/base mobile phase modifiers affect enantioseparations in ways that are not fully understood yet, for the lack of systematic studies. This makes chiral analysis of some pharmaceuticals difficult to reproduce. Once a column has been exposed to a modifier, the selectivity of certain pairs of enantiomers may change, for the better or the worse. We study the behavior of five enantiomeric pairs, three which are highly sensitive to the addition of certain modifiers and two that have little sensitivity to these modifiers. Their use permits the determination of the extent of the memory effect response on individual columns. The selectivity of 4-chlorophenylalanine methyl and ethyl ester, and of ketoprofen improve as a solution of ethanesulfonic acid is percolated through the column. As a result, these pairs are most useful for the determination of the extent of acid memory effect on a column. The selectivity of propranolol HCl and, to a lesser degree, Tröger's base increases as a solution of diisopropylethylamine is percolated through the column. The separation of each one of these five pairs is inversely affected by the percolation of the opposite acid/base solution. We used trans-stilbene oxide (TSO) as a ‘standard’ to determine the column stability because no memory effect is observed for it (its retention, enantioselectivity, and resolution remain constant). Understanding whether a column is under the influence of the memory effect is critical to both the analysis of pharmaceutical ingredients and to the development of preparative purification techniques for racemic mixtures. Thus, columns that were unreliable for method development and method transfer, due to the memory effect and a lack of proper solvent exposure records, can now be used.     

Structural analysis of amylose tris(3,5-dimethylphenylcarbamate) by NMR relevant to its chiral recognition mechanism in HPLC

The structural analysis of amylose tris(3,5-dimethylphenylcarbamate) (ADMPC) was performed by NMR spectroscopy using a sample with a lower degree of polymerization in order to understand the chiral recognition mechanism when it was used as a chiral stationary phase (CSP) in high-performance liquid chromatography (HPLC). ADMPC exhibited chiral discrimination for many enantiomers, including 1-(9-anthryl)-2,2,2-trifluoroethanol (1) and 1,1'-bi-2-naphthol (2) in both NMR and HPLC. A good agreement was observed between the HPLC and NMR results when chloroform was employed as the common solvent. The structure of ADMPC in solution was investigated by NMR using the 2D NOESY technique coupled with computer modeling, and a left-handed 4/3 helical structure was obtained as the most probable one. The binding geometry between ADMPC and the enantiomers of 1 was also investigated by (1)H NMR titration. On the basis of these results combined with molecular modeling, a rational model to explain the chiral discrimination mechanism of 1 on ADMPC was proposed.     

Photoconversion bonding mechanism in ruthenium sulfur dioxide linkage photoisomers revealed by in situ diffraction

Three new ruthenium-sulfur dioxide linkage photoisomeric complexes in the [Ru(NH(3))(4)(SO(2))X]Cl(2)·H(2)O family (X = pyridine (1); 3-chloropyridine (2); 4-chloropyridine (3)) have been developed in order to examine the effects of the trans-ligand on the nature of the photo-induced SO(2) coordination to the ruthenium ion. Solid-state metastable η(1)-O-bound (MS1) and η(2)-side S,O-bound (MS2) photoisomers are crystallographically resolved by probing a light-induced crystal with in situ diffraction. This so-called photocrystallography reveals the highest known photoconversion fraction of 58(3)% (in 1) for any solid-state SO(2) linkage photoisomer. The decay of this MS1 into the MS2 state was modeled via first-order kinetics with a non-zero asymptote. Furthermore, the MS2 decay kinetics of the three compounds were examined according to their systematically varying trans-ligand X; this offers the first experimental evidence that the MS2 state is primarily stabilized by donation from the S-O(bound) electrons into the Ru dσ-orbital rather than π-backbonding as previously envisaged. This has important consequences for the optoelectronic application of these materials since this establishes, for the first time, a design protocol that will enable one to control their photoconversion levels.     

New methodology to determine the rate-limiting adsorption kinetics mechanism from experimental dynamic surface tension data

We present a new methodology to determine the rate-limiting adsorption kinetics mechanism (diffusion-controlled vs mixed diffusion-barrier controlled), including deducing the kinetics parameters (the diffusion coefficient, D, and the energy-barrier parameter, beta), from the experimental short-time dynamic surface tension (DST) data. The new methodology has the following advantages over the existing procedure used to analyze the experimental DST data: (a) it does not require using a model for the equilibrium adsorption isotherm, and (b) it only requires using the experimental short-time DST data measured at two initial surfactant bulk solution concentrations. We apply the new methodology to analyze the experimental short-time DST data of the following alkyl poly(ethylene oxide), CiEj, nonionic surfactants: C12E4, C12E6, C12E8, and C10E8 measured using the pendant-bubble apparatus. We find that for C12E4 and C12E6, the effect of the energy barrier on the overall rate of surfactant adsorption can be neglected for surfactant bulk solution concentrations below their respective critical micelle concentrations (CMCs), and therefore, that the rate-limiting adsorption kinetics mechanism for C12E4 and C12E6 is diffusion-controlled at any of their premicellar surfactant bulk solution concentrations. On the other hand, for C12E8 and C10E8, we find that their respective CMC values are large enough to observe a significant effect of the energy barrier on the overall rate of surfactant adsorption. In other words, for C12E8 and C10E8, the rate-limiting adsorption kinetics mechanism shifts from diffusion-controlled to mixed diffusion-barrier controlled as their premicellar surfactant bulk solution concentrations increase. We test the new methodology by predicting the short-time DST profiles at other initial surfactant bulk solution concentrations, and then comparing the predicted DST profiles with those measured experimentally. Very good agreement is obtained for the four CiEj nonionic surfactants considered. We also compare the results of implementing the new methodology with those of implementing the existing procedure, and conclude that using a model for the equilibrium adsorption isotherm can lead not only to different values of D and beta, but it can also lead to a completely different determination of the rate-limiting adsorption kinetics mechanism. Since the new methodology proposed here does not require using a model for the equilibrium adsorption isotherm, we conclude that it should provide a more reliable determination of the rate-limiting adsorption kinetics mechanism, including the deduced kinetics parameters, D and beta.     

Studies on the biaxial stretching of polypropylene film. V. Orientation mechanism of the one-step biaxially stretched film

The molecular orientation behavior during one-step biaxial stretching in air of a quenched, low crystalline film differs from that of a slightly crystallized, highly crystalline film. In the case of a quenched film a plot of ?Δn_ss versus \documentclass{article}\pagestyle{empty}\begin{document}$ 1/\sqrt {va} $\end{document} is composed of three intersecting straight lines with different slopes, ?Δn_ss and v_A being the birefringence with respect to the normal to the film surface and the degree of stretching in area, respectively. On the other hand, ?Δn_ss of crystalline film changes somewhat differently. It does not increase up to fairly high stretching ratio. When a film with surface layers of different crystallinity was stretched biaxially, the relations between ?Δn_ss and \documentclass{article}\pagestyle{empty}\begin{document}$ 1/\sqrt {va} $\end{document} for the two surface layers differ, that is, a surface layer of low crystallinity shows a change of ?Δn_ss for the two surface layers differ, that is, a surface layer of low crystallinity shows a change of ?Δn_ss like that of a quenched film type and the surface layer of higher crystallinity, follows the behavior typical of highly crystalline film. However, a commercial film having different crystallinites on the two surface layers exhibits another type of ?Δn_ss change, which may be ascribed to the stress remaining frozen in the film in the manufacturing process. In addition, it is found that an Abbé refractometer can give the refractive indices of both the upper and lower surface layers of a film when the film structure is not the same on both surface layers.     

Changes in light scattering from poly(ethylene terephthalate) and nylon 6 films upon stretching in relation to the deformation mechanism

Unoriented T-die flat films of nylon 6 and PET films annealed at 90°C were stretched in water at 80°C. Amorphous PET films were stretched in water at 65–75°C. Changes in the light scattering patterns from these samples upon stretching were investigated. One of the observed LS patterns from the stretched samples is the H_v eight-leaf pattern consisting of four lobes and streaks. In the nylon 6 and heat-treated PET showing this pattern, spherulitic patterns can be seen in polarization microscopy. The microscopic spherulitic superstructure may possibly be the factor responsible for producing the lobe-and-streak pattern. On the other hand, many microscopic eight-leaf patterns can be observed in amorphous unannealed PET showing the lobe-and-streak pattern. These microscopic patterns are due to retardation at stress concentrations around impurities and nuclei. The superstructure giving these microscopic patterns must be the origin of the lobe-and-streak pattern from unannealed PET. Another scattering pattern, the V_v cruciform pattern, was observed in both stretched nylon 6 and unannealed PET. This pattern is due to an orientation change across the slip lines observed under a polarizing microscope. It is noted (1) that the appearance of the slip lines in PET coincides with the occurrence of oriented crystallization on stretching, (2) that the lobe-and-streak pattern from PET in which orientation crystallization has taken place is fairly stable to heat treatment and does not disappear until just before melting, and (3) that the superstructures produced at low stretching seem to be deformed on further stretching, in accordance with affine deformation theory.     

Use of photoaffinity nucleotide analogs to determine the mechanism of ATP regulation of a membrane-bound, cAMP-activated protein kinase.

Using a radioactively tagged, photoaffinity analog of cAMP, 8-azidoadenosine-3',5'-cyclic monophosphate (8-N3 cAMP) and [gamma32P]ATP, the membrane-binding properties of both the regulatory and catalytic subunits of the cAMP-activated protein kinase of human erythrocyte membranes were investigated. [32P]8-N3 cAMP was used to locate and quantify regulatory subunits. Increased phosphorylation of specific membrane proteins by [gamma32P]ATP was used to determine the presence of the catalytic subunit. The data support a mechanism which operates through a tight membrane-bound regulatory subunit and a catalytic subunit that is released from the membrane when cAMP is present and the Mg.ATP concentration is below approximately 10 micrometer. The catalytic subunit is not required for the Mg.ATP inhibition of 8-N3 cAMP binding. Experiments with a photoaffinity analog of ATP, 8-azidoadenosine triphosphate (8-N3ATP), support the hypothesis that ATP hydrolysis and phosphorylation are not involved in the regulation. The data indicate that the regulatory subunit contains an ATP regulatory site which inhibits 8-N3 cAMP binding and the release of the catalytic subunit. These results indicate that the membrane-bound type I enzyme (type IM) differs significantly from the soluble (type IS) enzyme studied on other tissues. These enzymes are compartmentalized by being in different cellular locations and are regulated differently by Mg.ATP.     

Crystal orientation in a semicrystalline polymer in relation to deformation of polymer spherulites. IV. Crystal orientation mechanism of nylon-6 under uniaxial stretching

A model relating crystal orientation to the deformation of nylon-6 spherulites under uniaxial stretching is discussed in terms of the orientation distribution functions of reciprocal lattice vectors of crystal planes, such as the (002) and (200) planes. The distribution functions calculated from the model are compared with those obtained from x-ray diffraction experiments. It is found that the crystal a axis and, consequently, the direction of hydrogen bonds within the crystal (α modification) orient parallel to the lamellar axis in the undeformed state, and that the crystal orientation behavior of nylon-6 is much different from that of low-density polyethylene, being characterized by much smaller values of the reorientation parameters of crystallites within orienting lamellae. Moreover, small-angle light scattering for H_v and V_v polarization is also calculated on the basis of the spherulite deformation model by taking the nylon-6 crystal as having orthogonal–biaxial symmetry in optical anisotropy. It is concluded that the H_v scattering can be realized in terms of the proposed model for spherulite deformation by taking into account a considerable contribution of hydrogen bonds to the molecular polarizability, so as to make the polarizability along the crystal a axis larger than that along the b axis. In other words, this conclusion suggests positively birefringent spherulites in the nylon-6 samples studied.     

Reaction of phenols with the 2,2-diphenyl-1-picrylhydrazyl radical. Kinetics and DFT calculations applied to determine ArO-H bond dissociation enthalpies and reaction mechanism

The formal H-atom abstraction by the 2,2-diphenyl-1-picrylhydrazyl (dpph(*)) radical from 27 phenols and two unsaturated hydrocarbons has been investigated by a combination of kinetic measurements in apolar solvents and density functional theory (DFT). The computed minimum energy structure of dpph(*) shows that the access to its divalent N is strongly hindered by an ortho H atom on each of the phenyl rings and by the o-NO(2) groups of the picryl ring. Remarkably small Arrhenius pre-exponential factors for the phenols [range (1.3-19) x 10(5) M(-1) s(-1)] are attributed to steric effects. Indeed, the entropy barrier accounts for up to ca. 70% of the free-energy barrier to reaction. Nevertheless, rate differences for different phenols are largely due to differences in the activation energy, E(a,1) (range 2 to 10 kcal/mol). In phenols, electronic effects of the substituents and intramolecular H-bonds have a large influence on the activation energies and on the ArO-H BDEs. There is a linear Evans-Polanyi relationship between E(a,1) and the ArO-H BDEs: E(a,1)/kcal x mol(-1) = 0.918 BDE(ArO-H)/kcal x mol(-1) - 70.273. The proportionality constant, 0.918, is large and implies a "late" or "product-like" transition state (TS), a conclusion that is congruent with the small deuterium kinetic isotope effects (range 1.3-3.3). This Evans-Polanyi relationship, though questionable on theoretical grounds, has profitably been used to estimate several ArO-H BDEs. Experimental ArO-H BDEs are generally in good agreement with the DFT calculations. Significant deviations between experimental and DFT calculated ArO-H BDEs were found, however, when an intramolecular H-bond to the O(*) center was present in the phenoxyl radical, e.g., in ortho semiquinone radicals. In these cases, the coupled cluster with single and double excitations correlated wave function technique with complete basis set extrapolation gave excellent results. The TSs for the reactions of dpph(*) with phenol, 3- and 4-methoxyphenol, and 1,4-cyclohexadiene were also computed. Surprisingly, these TS structures for the phenols show that the reactions cannot be described as occurring exclusively by either a HAT or a PCET mechanism, while with 1,4-cyclohexadiene the PCET character in the reaction coordinate is much better defined and shows a strong pi-pi stacking interaction between the incipient cyclohexadienyl radical and a phenyl ring of the dpph(*) radical.     

On the use of “fast kinetics” to determine the mechanism of ligand substitution at a solvated transition‐metal intermediate

Substitution of the weakly‐coordinated solvent molecule at a solvated transition‐metal intermediate is frequently investigated by “fast kinetic” methods. In typical experiments, the kinetics of the reaction are determined by following the time dependence of the changes in the reaction mixture's UV‐visible or infrared spectrum following photolytic creation of the intermediate. We consider the two limiting mechanisms (associative and dissociative), as well as the case of competition between them, and show that under typical “fast kinetics” experimental conditions, the different mechanisms are kinetically indistinguishable. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 427–433, 2004     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.