Isomeric Change Research Articles

FRET structure with non-radiative acceptor provided by dye-linker–glass surface complex and single-molecule photodynamics by TIRFM-polarized imaging

We present our recent study of microscopic single-molecule imaging on the artificial complex of tetramethylrhodamine linked with a propyl chain onto silica glass surface, i.e. an asymmetric fluorescence resonance energy transfer (FRET) structure with non-radiative acceptor. In the synthesis of the complex, we used a mixture of two kinds of isomers to introduce rather small photodynamic difference among them. This isomeric structure change will provide more or less a distinctive photophysical change in e.g. non-radiative relaxation rate. Our recent observation at room temperatures, so far, shows that such contributions can be discriminated in the histograms of the fluorescent spot intensities; broad but distinctive multi-components appear. To identify the isomeric difference as a cause of structures, some configurational assumptions are necessary. One such basic prerequisite is that the transition dipoles of the chromophores should be oriented almost parallel to the glass surface. In order to make clear the modeling, we also provide preliminary experiments on the polarization dependence of the imaging under rotating polarization in epi-illumination.

Electrochemical Characteristics of Some Purpurins in Aqueous and Nonaqueous Solutions

The Electrochemical Impedance Technique (EIS) and the Cyclic Voltammetric method (CV) were used to investigate the behavior of purpurin (P), Anthrapurpurin (AP) and Benzopurpurin (BP) in aqueous and in N, N-dimethylformamide (DMF) media. In the CV experiments, both the radical and the dianion of these substances were assumed to form of limited stability due to chemical protonation. In case of benzopurpurin, the CV measurements in DMF revealed a cis-trans isomerization changes of the molecule. The CV study includes also simulation of some responses using appropriate theoretical fitting models to confirm proposed reaction rates. The EIS experiments were carried out using a small AC amplitude and a relatively wide frequency range. The diagrams are characterized in the complex plane by the demonization of the Warburg impedance behavior at low frequencies and the appearance of two uncompleted semicircles in the Nyquist plot of the complex plane.

A solid-state 13C NMR analysis of ambers

Colombian copalite samples (found at 73°5′W 6°19′N in the Cimitarra quadrangle), and commercial amber samples from Chiapas (Mexico), Dominican Republic and Poland (Baltic) were studied using solid-state 13C CP-MAS Nuclear Magnetic Resonance (NMR). NMR spectra for Colombian amber are shown and compared to those reported for the resin from the genus of the African species Hymenaea verrucosa and other Hymenaea trees, for which a close resemblance is observed. NMR spectral features of the other studied ambers are also discussed. A physical aging experiment was performed on a Colombian sample at 65°C. Differences in the solid-state NMR and IR spectra are explained in terms of changes in chemical cross-linking, isomerization and morphology.

Surface-induced rotational isomerism within solid 1,3-diiodopropane thin films

Two unique solid–solid phase transitions within 1,3-diiodopropane (DIP) frozen thin films grown on a Pt(111) single crystal were observed by infrared and thermal desorption spectroscopies. Three distinct structural phases were indeed identified upon annealing the DIP films from 100 to 215 K, namely, an abrupt conformational isomerization change about 180 K and a separate molecular axis reorientation around 200 K. These DIP crystal structural and orientational changes were found to be driven by a template effect induced by the metal surface.

Effect of artificial maturation on carbazole distributions, as revealed by the hydrous pyrolysis of an organic-sulphur-rich source rock (Ghareb Formation, Jordan)

Hydrous pyrolysis experiments were performed on the Ghareb Formation (Upper Cretaceous, Jordan), a carbonate- and organic-rich (TOC 19.6%) source rock, using a temperature range of 200 to 360°C (72 h). The original sediment contains only low amounts of carbazoles, (maximum 2.2 μg/g bitumen for 1-methylcarbazole). With increasing thermal maturation, intense generation begins at temperatures only in excess of 300°C, reaching a maximum at 360°C. Likewise, during natural maturation, generation occurs at later stages of maturity (e.g. for Tithonian source rocks at >0.81% R r and for Posidonia Shale at >0.88% R r). Some isomeric changes during hydrous pyrolysis do not resemble those in nature whereas others do. The relative abundances of selected C 1- and C 2-alkylcarbazoles on ternary diagrams reveal differences, whereas the benzo[ a]carbazole/benzo[ a]carbazole+benzo[ c]carbazole ratio is closely similar. The latter result supports the contention that maturation plays a key role in controlling carbazole distributions in source rocks. However, the results for alkylcarbazoles, especially the C 2-carbazoles, are not easy to interpret.

Structure and isomerization in N,N-dimethyl-l,3-propanediamine nickel(II) thiocyanate

Abstract The complex [NiL2(NCS)2] (1), L = N,N-dimethyl-l,3-propanediamine, exhibits thennochromic solid state phase transition (temperature range 383 K–397.5 K) producing a high temperature isomer [NiL2(NCS)2] (2). The crystal structure of (2) has been solved by the X-ray powder as well as single crystal data sets and the precision of the structure determined with the X-ray single crystal diffraction data is higher than that obtained from the powder diffraction data. The triclinic unit cell of (2) having a volume approximately double to that of (1) consists of two symmetrically independent octahedral [NiL2(NCS)2] complexes with the metal atoms lying at (0 0 0) and (0 1/2 1/2), respectively. The equatorial planes around the two metal centers in isomer (2) are inclined to each other by 155.8(2)°. With the decrease of the specific volume per molecule of [NiL2(NCS)2] on isomerization (1 → 2) and significant changes in the molecular packing of the two isomers (1) and (2), the possible way of phase transition (1 → 2) is through a break up of the crystal body of isomer (1) and recrystallization into isomer (2).

Peanut glutamate dehydrogenase: A target site of herbicide action

Germination of peanut seeds in 5 mM N-(phosphonomethyl) glycine isopropylamide, 1, 2-dihydro-3, 6-pyridazinedione (maleic hydrazide), glyphosate, and isopropylamine solutions induced stress response reactions and the release of 24–100 μmol NH4+ per 50 g of seed, with consequent differential suppression of the subunits of glutamate dehydrogenase (GDH). Changes in the GDH isomerization suggested an interaction of the herbicides with the enzyme with consequent increases in the Michaelis constants (Km) from 7.7 mM in the control to 45.0, 50.0 and 77.0 mM NH4+ in the glyphosate, maleic hydrazide, and glyphosate isopropylamide treatments respectively.

Momentum-space ionization spectroscopy of iso-dichloroethylene: A comparative (e,2e) study of electron momentum distributions of the frontier-orbital and innervalence many-body states in iso-dichloroethylene and its cis and trans isomers

The ionization energy spectra of iso-dichloroethylene (iso-C2H2Cl2) at electron momentum of ∼0 and 0.7 a.u. have been obtained by molecular (e,2e) spectroscopy in the symmetric noncoplanar geometry at 1200 eV impact energy. Momentum distributions (MDs) of selected ionic states, including the outervalence states X(3b1)−1 (frontier-orbital state) and G(6b2)−1, and the innervalence states H(9a1)−1, S1(8a1 )−1, S2(5b2)−1, and S3(7a1)−1 as well as an unassigned many-body feature, have also been determined and compared with ab initio calculations using self-consistent-field wave functions of 4-31G, 6-31G, and 6-31++G** basis sets. Combined with our earlier (e,2e) results on the cis- and trans-C2H2Cl2, these MD measurements can be used to investigate the effects of isomeric changes on the valence-shell electronic structure of these disubstituted ethylene derivatives. The sensitivity of the experimental MDs to chemical bonding details can be demonstrated. In addition, ‘‘new’’ many-body features at 19–22 eV and above ∼26 eV have been observed in our ionization energy spectra, which support the breakdown of Koopmans’ theorem as predicted by an earlier Green’s function calculation. Furthermore, our MD measurements can be used to attribute the new many-body features observed at 19–22 eV to (9a1)−1 satellite states and to characterize the many-body states above ∼26 eV predominantly as (7a1)−1 satellite states.

Two-dimensional Exchange Spectroscopy Using Pure NQR

Abstract Exchange between positions with different resonance frequencies can be studied by two-dimensional spectroscopy originally developed for the NMR case. Cross intensity reflects changes of the resonance frequency due to different line shifts or anisotropic interactions. We now present analogous experiments carried out with pure NQR of polycrystalline samples. The specific requirements are discussed in comparison to 2D exchange NMR spectroscopy. The method has been demonstrated with chloroform and p-chlorobenzotrichloride, where the resonances of the 35Cl nuclei were investigated. Isomeric changes taking place in these compounds reveal themselves as cross-peaks provided the right ranges of the temperature and the mixing time are chosen. The corresponding dependences were recorded and are discussed.

Linear Alkylbenzenes (LABs) in Urban Riverine and Coastal Sediments and Their Usefulness as a Molecular Indicator of Domestic Wastes

Linear alkylbenzenes (LABs) and linear alkylbenzenesulfonates (LAS) were measured in river and coastal (bay) sediments in Tokyo metropolitan area. LABs are widely distributed in the sediments with concentrations of a few µ g/g-dry sediments. LAS contents in sediments are extremely low in Tokyo Bay (~ 0.01µg/g) as compared with those in the rivers (hundreds µg/g). This fact indicates the higher persistency of LABs in the riverine and coastal sediments. The progressive relative depletion of external isomers (in which the phenyl group is attached near to the end of the alkyl chain) was observed on going from the source (i.e. LABs in commercial LAS-detergents) to Tokyo Bay sediments. An incubation experiment substantiated that the isomeric change of LABs is caused by selective microbial degradation. The I/E ratio (ratio of [6-C12 AB + 5-C12 AB] relative to [4-C12 AB + 3-C12 AB + 2-C12]; n-Cm : n indicates the position of substitution of phenyl group to alkyl chain and m indicates the number of carbons in the alkyl chain) was proposed as an index of LAB degradation. I/E ratio of LABs in Tokyo Bay sediments indicates the degree of degradation of LABs to be 50 % at most.

Simultaneous monitoring of light-induced changes in protein side-group protonation, chromophore isomerization, and backbone motion of bacteriorhodopsin by time-resolved Fourier-transform infrared spectroscopy.

Absorbance changes in the infrared and visible spectral range were measured in parallel during the photocycle of light-adapted bacteriorhodopsin, which is accompanied by a vectorial proton transfer. A global fit analysis yielded the same rate constants for the chromophore reactions, for protonation changes of protein side groups, and for the backbone motion. From this result we conclude that all reactions in various parts of the protein are synchronized to each other and that no independent cycles exist for different parts. The carbonyl vibration of Asp-85, indicating its protonation, appears with the same rate constant as the Schiff base deprotonation. The carbonyl vibration of Asp-96 disappears, indicating most likely its deprotonation, with the same rate constant as for the Schiff base reprotonation. This result supports the proposed mechanism in which the protonated Schiff base, a deprotonated aspartic acid (Asp-85) on the proton-release pathway, and a protonated aspartic acid (Asp-96) on the proton-uptake pathway act as internal catalytic proton-binding sites.

The selectivity changes in 1-hexene isomerization and its relation to acid properties of Pd/SAPO-11, SAPO-11, HZSM-5, and H-mordenite catalysts

The activity and selectivity patterns for l-hexene isomer~'zation have been compared in the temperature range of 150-450~ fo) four different kinds of acidic zeolites (H-mordenite, HZSM-5, SAPO- 11 and PdtSAPO-I 1) differing both ir acid properties and geometric structure. At lower reaction temperatures (150-175~ the predominant reaction pathway was double bond shift(DBS) and was not influenced by the type of catalyst. At higher temperatures significant shifts in selectivity were observed from DBS to cracking (C) or skeletal rearrangement (SR) depending on the type of catalyst. Temperature programmed desorption {TPD) patterns of chemisorbed NH3 were also determined. Three different peaks were found for the most of TPD patterns. The first peak might be associated with Lewis acid- site, and the other two peaks at higher temperatures might be associated with Br6nsted acid-sites. It was found that significant loss of strong Br6nsted acidity upon Pd loading on SAPO-I 1. A selectivity correlation at 350~ showed strong dependence of DBS and cracking on total acidity. The reaction seems well suited for in- vestigation of the interrelation between pore st)ucture and surface acidity in terms of these selectivity factors.

Separation of the nativelike intermediate from unfolded forms during refolding of ribonuclease A.

In an effort to determine structural properties of the nativelike intermediate (i.e., IN) which forms during the refolding of RNase A, refolding samples were subjected to rapid HPLC gel filtration which allowed us to separate IN from unfolded forms of RNase. The comparison of these samples, enriched in IN and depleted of unfolded forms, with unseparated control samples at the same stage of refolding allowed certain conclusions to be drawn concerning the properties of IN. First, the results show that the transition from IN to native RNase occurs with only small changes in fluorescence. This means that the major fluorescence changes seen during normal refolding experiments must be associated with changes in proline isomerization of unfolded species and/or with the refolding step itself but not with the IN----N step. Second, the fluorescence assay for isomerization of proline-93 shows that IN exists with proline-93 in a state of isomerization identical with or very similar to native RNase; i.e., proline-93 is cis in IN and not trans as suggested by others. All results are semiquantitatively consistent with our earlier refolding model and not nearly so consistent with alternative models which assume that most or all of the slow-refolding forms of RNase have proline-93 in the incorrect trans state.

Primary charge motions and light-energy transduction in bacteriorhodopsin

The bacteriorhodopsin protein (bR) in the cell membrane of Halobacterium halobium is a light driven proton pump. Many details are known about its structure and the molecular mechanism of proton translocation. The events may be characterized by: (1) the changes in light absorption after photon excitation (the photocycle); (2) the charge motion cycle inside the protein: the steps taken by the proton during translocation; (3) the retinal cycle. changes in isomerization and protonation; and (4) the opsin cycle: alterations of protonation of different amino acids in the apoprotein. From a review of existing data a more or less concise picture of the parallelism of the above four cycles emerges, which may be valuable as a model for understanding other types of molecular pumps.

Hypersonic absorption and molecular relaxation in some pure n-alkanes

The acoustic absorption coefficient at 25°C of n-decane, n-dodecane, n-tetradecane and n-hexadecane has been measured as a function of frequency between 10 and 3000 MHz. The spectra show Debye-type relaxation behaviour at frequencies around 1000 MHz. Evidence is found that this relaxation process reflects the kinetics of structural isomerization of the hydrocarbon chains. The relaxation times resulting from the acoustic measurements agree with reorientation times derived from depolarized Rayleigh spectra. Both times increase with chain length of the molecules. A possibly coupling existing between orientational motions and isomeric changes of the normal alkanes is discussed.

Binding of the Ile-Val and Val-Val effector dipeptides to the binary adducts of bovine trypsinogen with kunitz and kazal inhibitors as well as the acylating agent p-nitrophenyl p-guanidinobenzoate : A thermodynamic and kinetic study

Thermodynamics and kinetics of binding of the Ile-Val and Val-Val effector dipeptides to the binary adducts of bovine trypsinogen with the bovine basic pancreatic trypsin inhibitor (BPTI, Kunitz inhibitor), the porcine pancreatic secretory inhibitor (PSTI, Kazal inhibitor) and the acylating agent p-nitrophenyl p-guanidinobenzoate have been investigated at pH 7.4 and 21(±0.5) °C. The affinity of both effector dipeptides for bovine trypsinogen: BPTI and bovine trypsinogen: PSTI binary adducts is higher than that observed for the formation of the dipeptide: bovine trypsinogen: p-guanidinobenzoate ternary complexes; moreover, the affinity of Ile-Val for the zymogen binary adducts is higher than that observed for Val-Val association. Binding of Ile-Val and Val-Val to the bovine trypsinogen binary complexes conforms to the induced-fit model, which consists of a fast pre-equilibrium followed by intramolecular isomerization change(s), the latter representing the rate-limiting first-order process. For the three bovine trypsinogen systems considered, the rate of the intramolecular isomerization change(s) is essentially independent of the nature of the dipeptide and of the proenzyme binary complex.

Nitrogen bridgehead compounds. Part 29. Tautomerism and Z–E isomerism of ethyl 9-aminomethylene-4-oxo-6,7,8,9-tetrahydro-4H-pyrido[1,2-a]pyrimidine-3-carboxylates and their homologues

1 H and 13C n.m.r. studies have proved that ethyl 9-dimethylaminomethylene-4-oxo-6,7,8,9-tetrahydro-4H-pyrido[1,2-a]pyrimidine-3-carboxylates (2)–(5) and the corresponding pyrrolo homologue (6) exist in the form of E-isomers whereas the azepino[1,2-a]pyrimidine derivative (7) appears as an equilibrium mixture of Z-and E-isomers. On the basis of 15N chemical shifts an analogous tautomeric structure has been established for the 9-dimethylaminomethylene derivatives (2)–(7) and the ethyl 9-arylaminomethylene-4-oxo-6,7,8,9-tetrahydro-4H-pyrido[1,2-a]pyrimidine-3-carboxylates (8)–(12) as well. 15N Shifts were sensitively affected by the Z–E isomerism and structural changes in remote parts of the molecule, too. Protonation of compounds (2)–(12) takes place on the N(1) atom, forming a 1,6,7,8-tetrahydro structure.

Temperature-induced changes of spin-labelled radioactive lipids in isolated guinea pig liver microsomal membranes before and in mitochondrial membranes after their translocation

Lipids of isolated guinea pig liver microsomal membranes were labelled biosynthetically with isomeric doxyl stearic acid and temperature-induced changes of these membranes were studied by electron spin resonance. A noticeable discontinuity was detected at 10--12 degree C with 12- or 16-doxyl stearic acid containing membrane lipids which was attributed to the spin-labelled lipid--microsomal membrane protein interactions since no such discontinuity was detected in liposomes prepared from total lipid extracts of microsomal membranes. When microsomal membranes containing radioactive isomeric spin-labelled lipids were incubated with unlabelled mitochondria, reisolated mitochondrial membranes contained translocated radioactive isomeric spin-labelled lipids. Temperature-induced changes in these membranes showed no discontinuity with either isomeric doxyl stearic acid derivative, establishing a difference in the environment of translocated lipids in the membrane donor compared with that in the membrane acceptor. Microsomal membranes recovered from translocation experiments showed the same behaviour as the original membranes and exhibited the same discontinuity at 10--12 degree C, establishing that the translocation incubation itself did not alter the spin-labelled lipid interaction within these membranes. Studies of the loss of paramagnetism of spin-labelled lipids in microsomal membranes before and in mitochondrial membranes after their translocation showed a significant difference and suggested that both the outer and the inner mitochondrial membranes might have been involved.

Conformation of poly(dimethyl siloxane) and polystyrene in solution measured by polarized Raman scattering

AbstractDepolarization ratios ρ have been measured over ranges of temperature T and molecular weight M for polystyrene (PS) dissolved in cyclohexane (1002 cm−1 Raman band) and for poly(dimethyl siloxane) (PDMS) dissolved in benzene (2907 cm−1 Raman band). The ranges in the case of PS are 15 < T < 65°C and 2 × 103 < M < 4 × 105 and in the case of PDMS are −3 < T < 60°C and M = 104. Measurements were also made of PDMS radii of gyration using conventional light scattering. The results are interpreted in terms of a theory connecting rotational isomeric populations with polymer extension. In the case of PDMS, an experimental value of the proportionality constant for trans isomers (D2 = −3.9 ± 0.9) is deduced. This is closer to the theoretical value than previous estimates but there is still some discrepancy. In the case of PS the isomeric changes resulting from extension are independent of M for M > 104. Deviations are observed for lower M.

Catalytic isomerization of olefins on alumina: II. Catalyst deactivation and its effects on the mechanism

The deactivation of an alumina catalyst during double-bond isomerization of 2,3-dimethyl-1-butene has been studied. An “oxygen-containing” surface compound has been suggested as being responsible for the deactivation. The hydrogen transfer during the isomerization changes from predominantly intramolecular to intermolecular during the deactivation. A simple two-site model is proposed to explain the observed phenomena and a cyclic allylic carbanion-like species is suggested as an intermediate for the intermolecular double-bond isomerization at final stable activity. Kinetic isotope effects clearly show that the allylic CH (or CD) bond cleavage must be involved in the rate-determining step.