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PubMed1991

Determination of site-specific carbon isotope ratios at natural abundance by carbon-13 nuclear magnetic resonance spectroscopy.

Site-specific natural isotope fractionation of hydrogen studied by deuterium NMR (SNIF-NMR) spectroscopy is a powerful source of information on hydrogen pathways occurring in biosyntheses in natural conditions. The potential of the carbon counterpart of this method has been investigated and compared. Three typical molecular species, ethanol, acetic acid, and vanillin, have been considered. Taking into account the requirements of quantitative 13C NMR, appropriate experimental procedures have been defined and the repeatability and reproducibility of the isotope ratio determinations have been checked in different conditions. It is shown that the carbon version of the SNIF-NMR method is capable of detecting small differences in the carbon-13 content of the ethyl fragment of ethanols from different botanical or synthetic origins. These results are in agreement with mass spectrometry determinations of the overall carbon isotope ratios. Deviations with respect to a statistical distribution of 13C have been detected in the case of acetic acid and vanillin. However, since the method is very sensitive to several kinds of systematic error, only a relative significance can be attached at present to the internal parameters directly accessible. Isotope dilution experiments have also been carried out in order to check the consistency of the results. In the present state of experimental accuracy, the 13C NMR method is of more limited potential than 2H SNIF-NMR spectroscopy. However it may provide complementary information. Moreover it is particularly efficient for detecting and quantifying adulterations that aim to mimic the overall carbon-13 content of a natural compound by adding a selectivity enriched species to a less expensive substrate from a different origin.

Acetates↗
PubMed2002

Monte Carlo model of nonlinear chromatography: correspondence between the microscopic stochastic model and the macroscopic Thomas kinetic model.

The Monte Carlo model of chromatography is a description of the chromatographic process from a molecular (microscopic) point of view and it is intrinsically based on the stochastic theory of chromatography originally proposed by Giddings and Eyring. The program was previously validated at infinite dilution (i.e., in linear conditions) by some of the authors of the present paper. In this work, it has been further validated under nonlinear conditions. The correspondence between the Monte Carlo model and the well-known Thomas kinetic model (macroscopic model), for which closed-form solutions are available, is demonstrated by comparing Monte Carlo simulations, performed at different loading factors, with the numerical solutions of the Thomas model calculated under the same conditions. In all the cases investigated, the agreement between Monte Carlo simulations and Thomas model results is very satisfactory. Additionally, the exact correspondence between the Thomas kinetic model and Giddings model, when near-infinite dilution conditions are approached, has been demonstrated by calculating the limit of the Thomas model when the loading factor goes to zero. The model was also validated under limit conditions, corresponding to cases of very slow adsorption-desorption kinetics or very short columns. Different hypotheses about the statistical distributions of the random variables "residence time spent by the molecule in mobile and stationary phase' are investigated with the aim to explain their effect on the peak shape and on the efficiency of the separation.

Journal Article↗
PubMed1989

Citrate synthase stabilizes the enethiolate of acetyldithio coenzyme A.

Citrate synthase catalyzes the slow condensation of acetyldithio-CoA [Ac(= S)CoA] with oxalacetate to form thiocitrate [Wlassics, I.D., Stille, C., & Anderson, V.E. (1988) Biochim. Biophys. Acta 952, 269]. During the transient approach to steady state an observable amount of the dithioester absorbance disappears. The amplitude of the decrease in absorbance corresponds to 0.32, 0.03, and 0.02 enzyme equiv at pH 8.3, 7.5, and 6.6, respectively. The difference spectra from before and after the transient exhibit the dithioester lambda max at 306 nm. Acid quenching of a stiochiometric reaction between Ac(= S)CoA and citrate synthase following the transient quantitatively regenerates Ac(= S)CoA, indicating carbon-carbon bond formation had not yet occurred. The apparent first-order rate constant of the transient is independent of Ac(= S)CoA concentration and increases with decreasing pH, being 0.007, 0.016, and 0.04 s-1 at pH 8.3, 7.5, and 6.6, respectively. 2-Fluoroacetyldithio-CoA is a better inhibitor of citrate synthase, Ki = 300 nM, and substrate, Vmax = 2 X 10(-3) s-1, than Ac(= S)CoA. 1H NMR experiments indicate that citrate synthase catalyzes the exchange of the alpha-hydrogens of Ac(= S)CoA with turnover numbers of 0.13 and 0.54 s-1 at pD 7.9 and 7.2, respectively. Analysis of the proton and deuterium decoupled 13C NMR spectra of [2-13C]Ac(= S)CoA that has exchanged 37% of the alpha-hydrogens in the presence of citrate synthase indicates that the relative proportions of CH3, CH2D, CHD2, and CD3 were 0.29, 0.39, 0.25, and 0.07, respectively. This statistical distribution indicates each exchange event is independent. The data indicate that citrate synthase stabilizes the ionized form of Ac(= S)CoA by 5 kcal/mol relative to the un-ionized form, that the ionized dithioester is on the reaction pathway, and that below pH 8.3 the slow carbon-carbon bond forming reaction is responsible for the 10(6) decrease in Vmax caused by substituting sulfur for oxygen in the thioester carbonyl.

Acyl Coenzyme A↗
PubMed1977

Interaction of DNA with poly(L-Lys-L-Ala-Gly) and poly(L-Lys-L-Ala-L-Pro). Circular dichroism and thermal denaturation studies.

Complexes of DNA with polypeptides composed of Lys, Ala, and Gly in both a sequential order, poly(L-lysine-L-alanine-glycine), and a statistical distribution, poly(L-lysine36-L-alanine28-glycine), were prepared using gradient dialysis. These polypeptide-DNA complexes were studied using ultraviolet absorption (UV) and circular dichroism (CD) to probe the conformation, binding, and melting behavior of DNA in the complex. Complexes with the sequential polypeptide showed no structural change in the DNA; however, the complexes with the random polypeptide yield CD spectra similar to phi DNA [Maniatis, T., Venable, Jr., J.S., and Lerman, L.S. (1974), J. Mol. Biol. 84, 37]. A second sequential polypeptide, poly(L-Lys-L-Ala-L-Pro)n, -DNA complex was also studied. It was found to exhibit pronounced structural changes as a function of ionic strength and poly-peptide-DNA ratio, more similar to the random sequence that the ordered sequence of the Lys, Ala, Gly polymer. Thus the importance of the composition and amino acid sequence in polypeptides which bind to DNA, even in such simple systems, is demonstrated. Evidence from thermal denaturation, employing simultaneous monitoring of CD and UV changes, supports a model in which specific polypeptides cause condensation of the DNA in the complex into an asymmetric tertiary structure. The relevance of these model systems to chromatin is discussed.

Alanine↗
PubMed1975

Modification of pig heart lipoamide dehydrogenase by cupric ions.

The insertion of a second disulfide bridge into native pig heart lipoamide dehydrogenase, requires two Cu-2+ ions for each catalytic center inactivated under anaerobic conditions. During inactivation, both metal atoms become reducible by their juxtaposition to the two participating cysteine residues and may be removed as the Cu+-chelates of neocuproine and bathocuproinesulfonate, leaving an additional disulfide bridge on the protein. Inactivation does not require the presence of oxygen, but when substoichiometric levels of copper are used under aerobic conditions the slow regeneration of Cu-2+ becomes rate-limiting. The course of aerobic inactivation is markedly biphasic at 0 degrees using 2 Cu-2+/FAD, with 30% of the total change completed rapidly, followed by a much slower phase. Both the extent of the fast phase and the rate of the second phase are enhanced by increasing levels of Cu-2+, but are relatively unaffected when the Cu-2+/FAD ratio is maintained at 2 and the protein concentration is varied. The enzyme affords several binding sites for Cu-2+ at pH 7.8, and it is suggested that competition between these sites during the initial statistical distribution of metal ions may explain this biphasic behavior.

Anaerobiosis↗
PubMed2001

Strong cooperativeness in the mononuclear iron(II) derivative exhibiting an abrupt spin transition above 400 K.

The spin crossover system, [Fe(bzimpy)(2)](ClO(4))(2).0.25H(2)O, was reinvestigated above room temperature (bzimpy = 2,6-bis(benzimidazol-2-yl)pyridine). The system exhibits an abrupt low-spin to high-spin transition at T(c) = 403 K. Liberation of a fractional amount of water does not affect the spin crossover: the system is perfectly reversible with a hysteresis width of DeltaT = 12 K. The existence of the hysteresis at such high temperature determines that the lowest limit of the solid-state cooperativity parameter is J/k > 403 K despite long iron(II) separations (10 A). The high cooperativeness has been assigned to a perfect pi-stacking of the benzimidazole rings in the crystal lattice at a distance as short as 3.6 A. Variable-temperature IR data and the heat capacity measurements match well the magnetic data. The thermodynamic properties are DeltaH = 17 kJ mol(-)(1), DeltaS = 43 J K(-)(1) mol(-)(1), so that the entropy of the spin transition shows a considerable contribution from the molecular vibrations. A theoretical model has been applied in fitting the magnetic data along the whole hysteresis path. A statistical distribution of the cooperativity parameter led to the feature that angled walls of the hysteresis loop are well reproduced.

Journal Article↗
PubMed2005

Hydrothermal single-crystal growth in the systems Ag/Hg/X/O (X = VV, AsV): crystal structures of (Ag3Hg)VO4, (Ag2Hg2)3(VO4)4, and (Ag2Hg2)2(HgO2)(AsO4)2 with the unusual tetrahedral cluster cations (Ag3Hg)3+ and (Ag2Hg2)4+ and crystal structure of AgHgVO4.

Single crystals of (Ag3Hg)VO4 (I), (Ag2Hg2)3(VO4)4 (II), AgHgVO4 (III), and (Ag2Hg2)2(HgO2)(AsO4)2 (IV) were grown under hydrothermal conditions (250 degrees C, 5 d) from starting mixtures of elementary mercury, silver nitrate, ammonium vanadate, and disodium hydrogenarsenate, respectively. All crystal structures were determined from X-ray diffraction data, and their chemical compositions were confirmed by electron microprobe analysis. I crystallizes in the tillmannsite structure, whereas II-IV adopt new structure types: (I) I4, Z = 2, a = 7.7095(2) A, c = 4.6714(2) A, 730 structure factors, 24 parameters, R[F2 > 2sigma(F2)] = 0.0365; (II) I42d, Z = 4, a = 12.6295(13) A, c = 12.566(3) A, 1524 structure factors, 55 parameters, R[F2 > 2sigma(F2)] = 0.0508; (III) C2, Z = 4, a = 9.9407(18) A, b = 5.5730(8) A, c = 7.1210(19) A, beta = 94.561(10) degrees , 1129 structure factors, 48 parameters, R[F2 > 2sigma(F2)] = 0.0358; (IV) P31c, Z = 2, a = 6.0261(9) A, c = 21.577(4) A, 1362 structure factors, 52 parameters, R[F2 > 2sigma(F2)] = 0.0477. The most striking structural features of I, II, and IV are the formation of tetrahedral cluster cations (Ag3Hg)3+ and (Ag2Hg2)4+, respectively, built of statistically distributed Ag and Hg atoms with a metal-metal distance of about 2.72 A. The electronic structure of these clusters can formally be considered as two-electron-four-center bonding. The crystal structure of III differs from the protrusive structure types insofar as silver and mercury are located on distinct crystallographic sites without a notable metal-metal interaction >3.55 A. All crystal structures are completed by tetrahedral oxo anions XO4(3-) (X = VV, AsV) and for IV additionally by a mercurate group, HgO2(2-).

Journal Article↗
PubMed2005

Immobilization of rhodium complexes at thiolate monolayers on gold surfaces: catalytic and structural studies.

Chiral rhodium-diphosphine complexes have been incorporated into self-assembled thiolate monolayers (SAMs) on gold colloids. Catalysts of this type are of interest because they combine properties of homogeneous and heterogeneous systems. In addition, it should be possible to influence the catalytic properties of the metal center by the neighboring thiolate molecules. Colloids with a diameter of ca. 3 nm, coated with a mixed monolayer of n-octanethiolates and thiolates with chiral rhodium-PYRPHOS end groups, were studied as hydrogenation catalysts. With methyl alpha-acetamido-cinnamate as substrate, virtually the same enantioselectivities (up to 93% ee) and full conversion were obtained as with the corresponding homogeneous [Rh(COD)(PYRPHOS)]BAr(F) catalyst. The colloids were easily recovered by filtration and reused as catalysts three times without loss of enantioselectivity. STM studies of analogous SAMs on Au(111) gave a detailed picture of the structure and dynamics of mixed monolayers of this type. The STM images showed that the catalyst-bearing thiolates are distributed statistically on the surface and that the ordered structure of the n-octanethiolate SAM can be retained during incorporation of the catalyst-bearing thiols using the place-exchange methodology.

Journal Article↗
PubMed2005

Insulator-metal transition of intrinsic diamond.

Insulator-metal transitions are translations characterized by a sudden change in electron transport properties from localized to itinerant behavior of electrons. In most cases, it is detected in strongly disordered semiconductors as a function of temperature with statistically distributed donors and/or acceptors. Here, we show that reversible insulator-metal transitions take place in H-terminated intrinsic (undoped) single crystalline diamond, if immersed into redox-electrolyte solutions at room temperature. The change is generated by valence-band electrons of diamond, which tunnel into the redox-electrolyte, where they occupy empty electronic sites. We applied cyclic voltammetry experiments to characterize the insulator-metal transition in combination with different redox couples. The experiments show that transfer doping accounts for the experimentally detected phenomena, and that intrinsic diamond is a promising candidate for chemical sensing in a variety of applications.

Journal Article↗
PubMed2006

Molecular complexity analysis of de novo designed ligands.

The de novo approach to structure-based rational drug design can provide a powerful tool for suggestion of entirely novel potential leads. However, programs for structure generation typically generate large numbers of putative ligands; therefore, various heuristics (such as estimation of binding affinity and synthetic accessibility) have to be adopted to evaluate and prune large answer sets with the goal of suggesting ligands with high binding affinity but low structural complexity. A novel method for complexity analysis is described. This method provides a rapid and effective ranking technique for elimination of structures with complicated molecular motifs. This complexity analysis technique, implemented within the SPROUT de novo design system, is based on the statistical distribution of various cyclic and acyclic topologies and atom substitution patterns in existing drugs or commercially available starting materials. A novel feature of the technique that distinguishes it from other published methods is that the matching takes place at various levels of abstraction, so that it can evaluate complexity scores, even for structures which contain atoms with unspecified atom type, which is sometimes the case with the initial output of de novo structure generation systems.

Binding Sites↗
PubMed2001

Structure and reactivity of mixed alkali metal alkoxide/aryloxide catalysts.

The average solution aggregation state of the ester interchange catalyst 1, obtained by mixing 1 equiv of NaOt-Bu and 3 equiv of NaOC(6)H(4)-4-t-Bu, was determined to be 4.0 by vapor pressure osmometry (VPO) in THF. Low-temperature (1)H NMR spectra of 1 indicated that the THF solution contained a mixture of tetrameric clusters. On the basis of symmetry arguments and the sensitivity of the different species to the alkoxide/aryloxide ratio, the compounds were determined to be mixed clusters with 0:4, 1:3, 2:2, and 3:1 mixtures of the NaOt-Bu and NaOC(6)H(4)-4-t-Bu components. On a per -Ot-Bu basis, each cluster has a similar absolute activity, though the aryloxide-rich catalysts are significantly longer-lived. Unlike 1, catalysts containing ortho-substituted aryloxides, 2, do not give a strictly statistical distribution of clusters, and the activities of these catalysts depend on steric and electronic factors, though the absolute rate differences are not large.

Journal Article↗
PubMed2003

Conformational studies by dynamic NMR. 95. Rotation around the adamantyl-alkyl bond. Remote substituent effect on conformational equilibrium.

Restricted rotation has been observed by NMR spectroscopy at very low temperature in isopropyladamantane, 1-tert-butyl-3-isopropyladamantane, and 1,3-diisopropyladamantane. The barriers for the corresponding dynamic processes were also determined. In the case of the disubstituted adamantane derivatives, two and four conformers, respectively, were observed and they were assigned on the basis of the symmetry properties. The relative populations deviate from the statistical distribution.

Journal Article↗
PubMed2006

Molecular dynamics simulations of electron-alkali cation pairs in bulk water.

The structural, dynamic, and thermodynamic properties of an excess electron interacting with an alkali cation (Na+, K+, Li+) in bulk water were investigated by means of a mixed quantum-classical molecular dynamics simulation technique. This study includes a reparametrization of the electron-cation pseudopotentials. The free energy calculations for all three systems show that a contact electron-cation pair can be observed, which is either as stable as the dissociated pair (Li+) or more stable by only a few kT (Na+, K+). Given that the dissociation barrier is also quite small, we suggest that the average cation-electron distance in the experiments at room temperature will not depend on this free energy profile but rather on the minimization of the Coulombic repulsive interaction between like charges in the solvent medium. This enables us to compare the present molecular dynamics simulations with the spectroscopic data obtained for different ionic strengths. The overall trend of the UV-vis hydrated absorption spectra, namely, the shift toward shorter wavelengths at high ionic strengths, is fairly well reproduced. This confirms our hypothesis of statistical distribution of the cations and solvated electrons.

Cations↗
PubMed2005

Stochastic kinetic models of chiral autocatalysis: a general tool for the quantitative interpretation of total asymmetric synthesis.

A continuous time discrete state stochastic kinetic approach is used to study various chiral autocatalytic models in which the possibility of total asymmetric synthesis arises. It is shown that this approach is superior to the deterministic approaches used earlier and is able to interpret many aspects of chiral autocatalysis. First-order autocatalysis, independently of further kinetic details of the system, leads to a unique final statistical distribution of enantiomers. Higher order autocatalysis, on the other hand, leads to a final state where one of the enantiomers is in overwhelming excess over the other. Criteria are postulated to differentiate between inherently stochastic phenomena in chiral autocatalytic reactions and irreproducibility because of insufficient control of external factors.

Journal Article↗
PubMed2006

Exciton migration by ultrafast Förster transfer in highly doped matrixes.

The energy transfer between dye molecules and the mobility of the corresponding excitons are investigated in polymethyl methacrylate films highly doped with perylene bisimide dyes. The dynamics is measured by group delay corrected, femtosecond broad-band spectroscopy revealing the transfer route via absorption changes that are specific for the participating species. In films doped with 0.14 M perylene orange an ultrafast homotransfer between the dye molecules is found by analyzing the loss of the excitation-induced anisotropy. The process exhibits a stretched exponential time dependence which is characteristic for Förster energy transfer between immobilized molecules. The transfer time is 1.5 ps for an average transfer distance of 2.3 nm and results in a high mobility of the optically generated excitons. In addition, we find that the excitons move to perylene orange dimers, which have formed in low concentration during the sample preparation. The observed energy transfer time is slightly shorter than expected for a direct Förster transfer and indicates that exciton migration by multistep transfer between the monomers speeds up the transport to the dimers. In samples doped with perylene orange and perylene red heterotransfer to perylene red takes place with transfer times down to 600 fs. The mechanism is Förster transfer as demonstrated by the agreement with calculations assuming electric dipole interaction between immobilized and statistically distributed donor and acceptor units. The model predicts the correct time dependence and concentration scaling for highly doped as well as diluted samples. The results show that ultrafast exciton migration between dye molecules in highly doped matrixes is an attractive and efficient mechanism to transport and collect energy in molecular systems and organic electronic devices. Further optimization should lead to a loss-free transport over distances typical for the thickness of active layers in these systems.

Coloring Agents↗
PubMed2006

Stochastic model of photodynamics in multichromophoric conjugated polymers.

A stochastic model of triplet exciton dynamics in multichromophoric conjugated polymers is presented and analyzed in detail, with a focus on the single molecule spectroscopy observables. The model deals with the evolution of a discrete statistical distribution of triplets in isolated polymer molecules. This approach should provide more accurate quantitative information on the dynamic processes involved, as compared to the previously used two-state model which assumes that a conjugated polymer cannot contain more than one triplet. In particular, it allows for determination of the triplet-triplet annihilation rate.

Journal Article↗
PubMedDate not supplied

The cellulose microfibril as an imperfect array of elementary fibrils.

Cellulose microfibrils are viewed as imperfect array of elementary fibrils. We have investigated the possible defects in Valonia cellulose microfibrils, which are such that the microfibrils can be broken into elementary fibrils by deformation, but are not sufficient to allow for a small angle maximum corresponding to the elementary fibril dimension. The microfibril has been constructed by convolution of th elementary fibril with a two dimensional point lattice. Defects have been incorporated in the microfibril, first by introduction of gaps between the elementary fibrils. These regular gaps were then replaced by a statistical distribution of the elementary fibrils about the lattice points, modeled by Hosemann distortions of the first type. The cylindrically averaged transforms of such structures show that significant distortions can be incorporated within the microfibril without producing large scale changes in the equatorial intensity distribution. Larger distortions are necessary before a small angle maximum corresponding to the 35 A elementary fibril is predicted, by which stage the wide angle x-ray pattern is unacceptable.

Cell Wall↗
PubMed2000

Enantioselective photoreduction of arylalkyl ketones via restricting the reaction to chirally modified zeolite cages

Obtaining a high enantiomeric excess during a photoreaction within a zeolite is hampered by the statistical distribution of reactant and chiral inductor molecules within the cages of a zeolite. By restricting the photoreactions to only those cages that contain both the reactant and a chiral inductor, one should be able to avoid reactions that yield racemic products. This approach is illustrated with the photoreduction of an arylalkyl ketone by a chiral inductor with an amino group.

Journal Article↗